ALBERT

Description: Using data for 25,780 species categorized on the International Union for Conservation of Nature Red List, we present an assessment of the status of the world's vertebrates. One-fifth of species are classified as Threatened, and we show that this figure is increasing: On average, 52 species of mammals, birds, and amphibians move one category closer to extinction each year. However, this overall pattern conceals the impact of conservation successes, and we show that the rate of deterioration would have been at least one-fifth again as much in the absence of these. Nonetheless, current conservation efforts remain insufficient to offset the main drivers of biodiversity loss in these groups: agricultural expansion, logging, overexploitation, and invasive alien species.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hoffmann, Michael -- Hilton-Taylor, Craig -- Angulo, Ariadne -- Bohm, Monika -- Brooks, Thomas M -- Butchart, Stuart H M -- Carpenter, Kent E -- Chanson, Janice -- Collen, Ben -- Cox, Neil A -- Darwall, William R T -- Dulvy, Nicholas K -- Harrison, Lucy R -- Katariya, Vineet -- Pollock, Caroline M -- Quader, Suhel -- Richman, Nadia I -- Rodrigues, Ana S L -- Tognelli, Marcelo F -- Vie, Jean-Christophe -- Aguiar, John M -- Allen, David J -- Allen, Gerald R -- Amori, Giovanni -- Ananjeva, Natalia B -- Andreone, Franco -- Andrew, Paul -- Aquino Ortiz, Aida Luz -- Baillie, Jonathan E M -- Baldi, Ricardo -- Bell, Ben D -- Biju, S D -- Bird, Jeremy P -- Black-Decima, Patricia -- Blanc, J Julian -- Bolanos, Federico -- Bolivar-G, Wilmar -- Burfield, Ian J -- Burton, James A -- Capper, David R -- Castro, Fernando -- Catullo, Gianluca -- Cavanagh, Rachel D -- Channing, Alan -- Chao, Ning Labbish -- Chenery, Anna M -- Chiozza, Federica -- Clausnitzer, Viola -- Collar, Nigel J -- Collett, Leah C -- Collette, Bruce B -- Cortez Fernandez, Claudia F -- Craig, Matthew T -- Crosby, Michael J -- Cumberlidge, Neil -- Cuttelod, Annabelle -- Derocher, Andrew E -- Diesmos, Arvin C -- Donaldson, John S -- Duckworth, J W -- Dutson, Guy -- Dutta, S K -- Emslie, Richard H -- Farjon, Aljos -- Fowler, Sarah -- Freyhof, Jorg -- Garshelis, David L -- Gerlach, Justin -- Gower, David J -- Grant, Tandora D -- Hammerson, Geoffrey A -- Harris, Richard B -- Heaney, Lawrence R -- Hedges, S Blair -- Hero, Jean-Marc -- Hughes, Baz -- Hussain, Syed Ainul -- Icochea M, Javier -- Inger, Robert F -- Ishii, Nobuo -- Iskandar, Djoko T -- Jenkins, Richard K B -- Kaneko, Yoshio -- Kottelat, Maurice -- Kovacs, Kit M -- Kuzmin, Sergius L -- La Marca, Enrique -- Lamoreux, John F -- Lau, Michael W N -- Lavilla, Esteban O -- Leus, Kristin -- Lewison, Rebecca L -- Lichtenstein, Gabriela -- Livingstone, Suzanne R -- Lukoschek, Vimoksalehi -- Mallon, David P -- McGowan, Philip J K -- McIvor, Anna -- Moehlman, Patricia D -- Molur, Sanjay -- Munoz Alonso, Antonio -- Musick, John A -- Nowell, Kristin -- Nussbaum, Ronald A -- Olech, Wanda -- Orlov, Nikolay L -- Papenfuss, Theodore J -- Parra-Olea, Gabriela -- Perrin, William F -- Polidoro, Beth A -- Pourkazemi, Mohammad -- Racey, Paul A -- Ragle, James S -- Ram, Mala -- Rathbun, Galen -- Reynolds, Robert P -- Rhodin, Anders G J -- Richards, Stephen J -- Rodriguez, Lily O -- Ron, Santiago R -- Rondinini, Carlo -- Rylands, Anthony B -- Sadovy de Mitcheson, Yvonne -- Sanciangco, Jonnell C -- Sanders, Kate L -- Santos-Barrera, Georgina -- Schipper, Jan -- Self-Sullivan, Caryn -- Shi, Yichuan -- Shoemaker, Alan -- Short, Frederick T -- Sillero-Zubiri, Claudio -- Silvano, Debora L -- Smith, Kevin G -- Smith, Andrew T -- Snoeks, Jos -- Stattersfield, Alison J -- Symes, Andrew J -- Taber, Andrew B -- Talukdar, Bibhab K -- Temple, Helen J -- Timmins, Rob -- Tobias, Joseph A -- Tsytsulina, Katerina -- Tweddle, Denis -- Ubeda, Carmen -- Valenti, Sarah V -- van Dijk, Peter Paul -- Veiga, Liza M -- Veloso, Alberto -- Wege, David C -- Wilkinson, Mark -- Williamson, Elizabeth A -- Xie, Feng -- Young, Bruce E -- Akcakaya, H Resit -- Bennun, Leon -- Blackburn, Tim M -- Boitani, Luigi -- Dublin, Holly T -- da Fonseca, Gustavo A B -- Gascon, Claude -- Lacher, Thomas E Jr -- Mace, Georgina M -- Mainka, Susan A -- McNeely, Jeffery A -- Mittermeier, Russell A -- Reid, Gordon McGregor -- Rodriguez, Jon Paul -- Rosenberg, Andrew A -- Samways, Michael J -- Smart, Jane -- Stein, Bruce A -- Stuart, Simon N -- New York, N.Y. -- Science. 2010 Dec 10;330(6010):1503-9. doi: 10.1126/science.1194442. Epub 2010 Oct 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉IUCN SSC Species Survival Commission, c/o United Nations Environment Programme World Conservation Monitoring Centre, 219 Huntingdon Road, Cambridge CB3 0DL, UK. mike.hoffmann@iucn.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20978281" target="_blank"〉PubMed〈/a〉

Description: A challenge for HIV-1 immunogen design is the difficulty of inducing neutralizing antibodies (NAbs) against neutralization-resistant (tier 2) viruses that dominate human transmissions. We show that a soluble recombinant HIV-1 envelope glycoprotein trimer that adopts a native conformation, BG505 SOSIP.664, induced NAbs potently against the sequence-matched tier 2 virus in rabbits and similar but weaker responses in macaques. The trimer also consistently induced cross-reactive NAbs against more sensitive (tier 1) viruses. Tier 2 NAbs recognized conformational epitopes that differed between animals and in some cases overlapped with those recognized by broadly neutralizing antibodies (bNAbs), whereas tier 1 responses targeted linear V3 epitopes. A second trimer, B41 SOSIP.664, also induced a strong autologous tier 2 NAb response in rabbits. Thus, native-like trimers represent a promising starting point for the development of HIV-1 vaccines aimed at inducing bNAbs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4498988/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4498988/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sanders, Rogier W -- van Gils, Marit J -- Derking, Ronald -- Sok, Devin -- Ketas, Thomas J -- Burger, Judith A -- Ozorowski, Gabriel -- Cupo, Albert -- Simonich, Cassandra -- Goo, Leslie -- Arendt, Heather -- Kim, Helen J -- Lee, Jeong Hyun -- Pugach, Pavel -- Williams, Melissa -- Debnath, Gargi -- Moldt, Brian -- van Breemen, Marielle J -- Isik, Gozde -- Medina-Ramirez, Max -- Back, Jaap Willem -- Koff, Wayne C -- Julien, Jean-Philippe -- Rakasz, Eva G -- Seaman, Michael S -- Guttman, Miklos -- Lee, Kelly K -- Klasse, Per Johan -- LaBranche, Celia -- Schief, William R -- Wilson, Ian A -- Overbaugh, Julie -- Burton, Dennis R -- Ward, Andrew B -- Montefiori, David C -- Dean, Hansi -- Moore, John P -- 280829/European Research Council/International -- HHSN27201100016C/PHS HHS/ -- P01 AI082362/AI/NIAID NIH HHS/ -- P51 OD011106/OD/NIH HHS/ -- P51OD011106/OD/NIH HHS/ -- R01 AI076105/AI/NIAID NIH HHS/ -- R01 AI084817/AI/NIAID NIH HHS/ -- R37 AI036082/AI/NIAID NIH HHS/ -- R56 AI084817/AI/NIAID NIH HHS/ -- T32 GM007266/GM/NIGMS NIH HHS/ -- UM1 AI100663/AI/NIAID NIH HHS/ -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2015 Jul 10;349(6244):aac4223. doi: 10.1126/science.aac4223. Epub 2015 Jun 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA. Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, Netherlands. jpm2003@med.cornell.edu rws2002@med.cornell.edu. ; Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, Netherlands. ; Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative, Neutralizing Antibody Center, and Collaboration for AIDS Vaccine Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. ; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA. ; International AIDS Vaccine Initiative, Neutralizing Antibody Center, and Collaboration for AIDS Vaccine Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA. ; Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. ; International AIDS Vaccine Initiative, New York, NY 10004, USA. ; Pepscan Therapeutics, 8243RC Lelystad, Netherlands. ; Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA. ; Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA. Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Boston, MA 02114, USA. ; Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA. ; Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA. ; Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative, Neutralizing Antibody Center, and Collaboration for AIDS Vaccine Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative, New York, NY 10004, USA. Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Boston, MA 02114, USA. ; International AIDS Vaccine Initiative, Neutralizing Antibody Center, and Collaboration for AIDS Vaccine Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA. Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, CA 92037, USA. ; Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative, Neutralizing Antibody Center, and Collaboration for AIDS Vaccine Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Boston, MA 02114, USA. ; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA. jpm2003@med.cornell.edu rws2002@med.cornell.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26089353" target="_blank"〉PubMed〈/a〉

Description: The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155737/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155737/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gerstein, Mark B -- Rozowsky, Joel -- Yan, Koon-Kiu -- Wang, Daifeng -- Cheng, Chao -- Brown, James B -- Davis, Carrie A -- Hillier, LaDeana -- Sisu, Cristina -- Li, Jingyi Jessica -- Pei, Baikang -- Harmanci, Arif O -- Duff, Michael O -- Djebali, Sarah -- Alexander, Roger P -- Alver, Burak H -- Auerbach, Raymond -- Bell, Kimberly -- Bickel, Peter J -- Boeck, Max E -- Boley, Nathan P -- Booth, Benjamin W -- Cherbas, Lucy -- Cherbas, Peter -- Di, Chao -- Dobin, Alex -- Drenkow, Jorg -- Ewing, Brent -- Fang, Gang -- Fastuca, Megan -- Feingold, Elise A -- Frankish, Adam -- Gao, Guanjun -- Good, Peter J -- Guigo, Roderic -- Hammonds, Ann -- Harrow, Jen -- Hoskins, Roger A -- Howald, Cedric -- Hu, Long -- Huang, Haiyan -- Hubbard, Tim J P -- Huynh, Chau -- Jha, Sonali -- Kasper, Dionna -- Kato, Masaomi -- Kaufman, Thomas C -- Kitchen, Robert R -- Ladewig, Erik -- Lagarde, Julien -- Lai, Eric -- Leng, Jing -- Lu, Zhi -- MacCoss, Michael -- May, Gemma -- McWhirter, Rebecca -- Merrihew, Gennifer -- Miller, David M -- Mortazavi, Ali -- Murad, Rabi -- Oliver, Brian -- Olson, Sara -- Park, Peter J -- Pazin, Michael J -- Perrimon, Norbert -- Pervouchine, Dmitri -- Reinke, Valerie -- Reymond, Alexandre -- Robinson, Garrett -- Samsonova, Anastasia -- Saunders, Gary I -- Schlesinger, Felix -- Sethi, Anurag -- Slack, Frank J -- Spencer, William C -- Stoiber, Marcus H -- Strasbourger, Pnina -- Tanzer, Andrea -- Thompson, Owen A -- Wan, Kenneth H -- Wang, Guilin -- Wang, Huaien -- Watkins, Kathie L -- Wen, Jiayu -- Wen, Kejia -- Xue, Chenghai -- Yang, Li -- Yip, Kevin -- Zaleski, Chris -- Zhang, Yan -- Zheng, Henry -- Brenner, Steven E -- Graveley, Brenton R -- Celniker, Susan E -- Gingeras, Thomas R -- Waterston, Robert -- 1U01HG007031-01/HG/NHGRI NIH HHS/ -- 5U01HG004695-04/HG/NHGRI NIH HHS/ -- 5U54HG004555/HG/NHGRI NIH HHS/ -- HG007000/HG/NHGRI NIH HHS/ -- HG007355/HG/NHGRI NIH HHS/ -- K99 HG006698/HG/NHGRI NIH HHS/ -- P30 CA045508/CA/NCI NIH HHS/ -- R01 GM076655/GM/NIGMS NIH HHS/ -- RC2-HG005639/HG/NHGRI NIH HHS/ -- T15 LM007056/LM/NLM NIH HHS/ -- T32 HD060555/HD/NICHD NIH HHS/ -- U01 HG 004263/HG/NHGRI NIH HHS/ -- U01 HG004261/HG/NHGRI NIH HHS/ -- U01 HG004271/HG/NHGRI NIH HHS/ -- U01 HG007031/HG/NHGRI NIH HHS/ -- U01-HG004261/HG/NHGRI NIH HHS/ -- U01HG004258/HG/NHGRI NIH HHS/ -- U41 HG007000/HG/NHGRI NIH HHS/ -- U41 HG007234/HG/NHGRI NIH HHS/ -- U41 HG007355/HG/NHGRI NIH HHS/ -- U54 HG004555/HG/NHGRI NIH HHS/ -- U54 HG006944/HG/NHGRI NIH HHS/ -- U54 HG006994/HG/NHGRI NIH HHS/ -- U54 HG007004/HG/NHGRI NIH HHS/ -- U54 HG007005/HG/NHGRI NIH HHS/ -- U54HG007005/HG/NHGRI NIH HHS/ -- WT098051/Wellcome Trust/United Kingdom -- ZIA DK015600-18/Intramural NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2014 Aug 28;512(7515):445-8. doi: 10.1038/nature13424.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [3] Department of Computer Science, Yale University, 51 Prospect Street, New Haven, Connecticut 06511, USA [4] [5]. ; 1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [3]. ; 1] Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA [2] Institute for Quantitative Biomedical Sciences, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03766, USA [3]. ; 1] Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA [2] Department of Statistics, University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA [3]. ; 1] Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA [2]. ; 1] Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA [2]. ; 1] Department of Statistics, University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA [2] Department of Statistics, University of California, Los Angeles, California 90095-1554, USA [3] Department of Human Genetics, University of California, Los Angeles, California 90095-7088, USA [4]. ; 1] Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA [2]. ; 1] Centre for Genomic Regulation, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain [2] Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain [3]. ; 1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA. ; Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, Massachusetts 02115, USA. ; Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA. ; Department of Statistics, University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA. ; Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA. ; 1] Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA [2] Department of Biostatistics, University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA. ; Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA. ; 1] Department of Biology, Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405-7005, USA [2] Center for Genomics and Bioinformatics, Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405-7005, USA. ; MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China. ; National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA. ; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. ; 1] Centre for Genomic Regulation, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain [2] Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain. ; 1] Center for Integrative Genomics, University of Lausanne, Genopode building, Lausanne 1015, Switzerland [2] Swiss Institute of Bioinformatics, Genopode building, Lausanne 1015, Switzerland. ; 1] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK [2] Medical and Molecular Genetics, King's College London, London WC2R 2LS, UK. ; Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520-8005, USA. ; Department of Molecular, Cellular and Developmental Biology, PO Box 208103, Yale University, New Haven, Connecticut 06520, USA. ; Department of Biology, Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405-7005, USA. ; Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, New York 10065, USA. ; 1] Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA [2] Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 USA. ; Department of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue South, Nashville, Tennessee 37232-8240, USA. ; 1] Developmental and Cell Biology, University of California, Irvine, California 92697, USA [2] Center for Complex Biological Systems, University of California, Irvine, California 92697, USA. ; Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA. ; Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA. ; 1] Department of Genetics and Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA [2] Howard Hughes Medical Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA. ; Center for Integrative Genomics, University of Lausanne, Genopode building, Lausanne 1015, Switzerland. ; 1] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK [2] European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK. ; 1] Bioinformatics and Genomics Programme, Center for Genomic Regulation, Universitat Pompeu Fabra (CRG-UPF), 08003 Barcelona, Catalonia, Spain [2] Institute for Theoretical Chemistry, Theoretical Biochemistry Group (TBI), University of Vienna, Wahringerstrasse 17/3/303, A-1090 Vienna, Austria. ; 1] Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA [2] Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China. ; 1] Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong [2] 5 CUHK-BGI Innovation Institute of Trans-omics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong. ; 1] Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA [2] Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA [3]. ; 1] Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA [2].〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25164755" target="_blank"〉PubMed〈/a〉

Description: Development of the body plan is controlled by large networks of regulatory genes. A gene regulatory network that controls the specification of endoderm and mesoderm in the sea urchin embryo is summarized here. The network was derived from large-scale perturbation analyses, in combination with computational methodologies, genomic data, cis-regulatory analysis, and molecular embryology. The network contains over 40 genes at present, and each node can be directly verified at the DNA sequence level by cis-regulatory analysis. Its architecture reveals specific and general aspects of development, such as how given cells generate their ordained fates in the embryo and why the process moves inexorably forward in developmental time.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Davidson, Eric H -- Rast, Jonathan P -- Oliveri, Paola -- Ransick, Andrew -- Calestani, Cristina -- Yuh, Chiou-Hwa -- Minokawa, Takuya -- Amore, Gabriele -- Hinman, Veronica -- Arenas-Mena, Cesar -- Otim, Ochan -- Brown, C Titus -- Livi, Carolina B -- Lee, Pei Yun -- Revilla, Roger -- Rust, Alistair G -- Pan, Zheng jun -- Schilstra, Maria J -- Clarke, Peter J C -- Arnone, Maria I -- Rowen, Lee -- Cameron, R Andrew -- McClay, David R -- Hood, Leroy -- Bolouri, Hamid -- GM-61005/GM/NIGMS NIH HHS/ -- HD-37105/HD/NICHD NIH HHS/ -- RR-06591/RR/NCRR NIH HHS/ -- RR-15044/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2002 Mar 1;295(5560):1669-78.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA. davidson@caltech.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11872831" target="_blank"〉PubMed〈/a〉

Description: CpG islands (CGIs) are prominent in the mammalian genome owing to their GC-rich base composition and high density of CpG dinucleotides. Most human gene promoters are embedded within CGIs that lack DNA methylation and coincide with sites of histone H3 lysine 4 trimethylation (H3K4me3), irrespective of transcriptional activity. In spite of these intriguing correlations, the functional significance of non-methylated CGI sequences with respect to chromatin structure and transcription is unknown. By performing a search for proteins that are common to all CGIs, here we show high enrichment for Cfp1, which selectively binds to non-methylated CpGs in vitro. Chromatin immunoprecipitation of a mono-allelically methylated CGI confirmed that Cfp1 specifically associates with non-methylated CpG sites in vivo. High throughput sequencing of Cfp1-bound chromatin identified a notable concordance with non-methylated CGIs and sites of H3K4me3 in the mouse brain. Levels of H3K4me3 at CGIs were markedly reduced in Cfp1-depleted cells, consistent with the finding that Cfp1 associates with the H3K4 methyltransferase Setd1 (refs 7, 8). To test whether non-methylated CpG-dense sequences are sufficient to establish domains of H3K4me3, we analysed artificial CpG clusters that were integrated into the mouse genome. Despite the absence of promoters, the insertions recruited Cfp1 and created new peaks of H3K4me3. The data indicate that a primary function of non-methylated CGIs is to genetically influence the local chromatin modification state by interaction with Cfp1 and perhaps other CpG-binding proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3730110/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3730110/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thomson, John P -- Skene, Peter J -- Selfridge, Jim -- Clouaire, Thomas -- Guy, Jacky -- Webb, Shaun -- Kerr, Alastair R W -- Deaton, Aimee -- Andrews, Rob -- James, Keith D -- Turner, Daniel J -- Illingworth, Robert -- Bird, Adrian -- 079643/Wellcome Trust/United Kingdom -- 091580/Wellcome Trust/United Kingdom -- 098051/Wellcome Trust/United Kingdom -- G0800026/Medical Research Council/United Kingdom -- Cancer Research UK/United Kingdom -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2010 Apr 15;464(7291):1082-6. doi: 10.1038/nature08924.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Centre for Cell Biology, Michael Swann Building, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20393567" target="_blank"〉PubMed〈/a〉

Description: The extent to which low-frequency (minor allele frequency (MAF) between 1-5%) and rare (MAF 〈/= 1%) variants contribute to complex traits and disease in the general population is mainly unknown. Bone mineral density (BMD) is highly heritable, a major predictor of osteoporotic fractures, and has been previously associated with common genetic variants, as well as rare, population-specific, coding variants. Here we identify novel non-coding genetic variants with large effects on BMD (ntotal = 53,236) and fracture (ntotal = 508,253) in individuals of European ancestry from the general population. Associations for BMD were derived from whole-genome sequencing (n = 2,882 from UK10K (ref. 10); a population-based genome sequencing consortium), whole-exome sequencing (n = 3,549), deep imputation of genotyped samples using a combined UK10K/1000 Genomes reference panel (n = 26,534), and de novo replication genotyping (n = 20,271). We identified a low-frequency non-coding variant near a novel locus, EN1, with an effect size fourfold larger than the mean of previously reported common variants for lumbar spine BMD (rs11692564(T), MAF = 1.6%, replication effect size = +0.20 s.d., Pmeta = 2 x 10(-14)), which was also associated with a decreased risk of fracture (odds ratio = 0.85; P = 2 x 10(-11); ncases = 98,742 and ncontrols = 409,511). Using an En1(cre/flox) mouse model, we observed that conditional loss of En1 results in low bone mass, probably as a consequence of high bone turnover. We also identified a novel low-frequency non-coding variant with large effects on BMD near WNT16 (rs148771817(T), MAF = 1.2%, replication effect size = +0.41 s.d., Pmeta = 1 x 10(-11)). In general, there was an excess of association signals arising from deleterious coding and conserved non-coding variants. These findings provide evidence that low-frequency non-coding variants have large effects on BMD and fracture, thereby providing rationale for whole-genome sequencing and improved imputation reference panels to study the genetic architecture of complex traits and disease in the general population.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755714/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755714/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zheng, Hou-Feng -- Forgetta, Vincenzo -- Hsu, Yi-Hsiang -- Estrada, Karol -- Rosello-Diez, Alberto -- Leo, Paul J -- Dahia, Chitra L -- Park-Min, Kyung Hyun -- Tobias, Jonathan H -- Kooperberg, Charles -- Kleinman, Aaron -- Styrkarsdottir, Unnur -- Liu, Ching-Ti -- Uggla, Charlotta -- Evans, Daniel S -- Nielson, Carrie M -- Walter, Klaudia -- Pettersson-Kymmer, Ulrika -- McCarthy, Shane -- Eriksson, Joel -- Kwan, Tony -- Jhamai, Mila -- Trajanoska, Katerina -- Memari, Yasin -- Min, Josine -- Huang, Jie -- Danecek, Petr -- Wilmot, Beth -- Li, Rui -- Chou, Wen-Chi -- Mokry, Lauren E -- Moayyeri, Alireza -- Claussnitzer, Melina -- Cheng, Chia-Ho -- Cheung, Warren -- Medina-Gomez, Carolina -- Ge, Bing -- Chen, Shu-Huang -- Choi, Kwangbom -- Oei, Ling -- Fraser, James -- Kraaij, Robert -- Hibbs, Matthew A -- Gregson, Celia L -- Paquette, Denis -- Hofman, Albert -- Wibom, Carl -- Tranah, Gregory J -- Marshall, Mhairi -- Gardiner, Brooke B -- Cremin, Katie -- Auer, Paul -- Hsu, Li -- Ring, Sue -- Tung, Joyce Y -- Thorleifsson, Gudmar -- Enneman, Anke W -- van Schoor, Natasja M -- de Groot, Lisette C P G M -- van der Velde, Nathalie -- Melin, Beatrice -- Kemp, John P -- Christiansen, Claus -- Sayers, Adrian -- Zhou, Yanhua -- Calderari, Sophie -- van Rooij, Jeroen -- Carlson, Chris -- Peters, Ulrike -- Berlivet, Soizik -- Dostie, Josee -- Uitterlinden, Andre G -- Williams, Stephen R -- Farber, Charles -- Grinberg, Daniel -- LaCroix, Andrea Z -- Haessler, Jeff -- Chasman, Daniel I -- Giulianini, Franco -- Rose, Lynda M -- Ridker, Paul M -- Eisman, John A -- Nguyen, Tuan V -- Center, Jacqueline R -- Nogues, Xavier -- Garcia-Giralt, Natalia -- Launer, Lenore L -- Gudnason, Vilmunder -- Mellstrom, Dan -- Vandenput, Liesbeth -- Amin, Najaf -- van Duijn, Cornelia M -- Karlsson, Magnus K -- Ljunggren, Osten -- Svensson, Olle -- Hallmans, Goran -- Rousseau, Francois -- Giroux, Sylvie -- Bussiere, Johanne -- Arp, Pascal P -- Koromani, Fjorda -- Prince, Richard L -- Lewis, Joshua R -- Langdahl, Bente L -- Hermann, A Pernille -- Jensen, Jens-Erik B -- Kaptoge, Stephen -- Khaw, Kay-Tee -- Reeve, Jonathan -- Formosa, Melissa M -- Xuereb-Anastasi, Angela -- Akesson, Kristina -- McGuigan, Fiona E -- Garg, Gaurav -- Olmos, Jose M -- Zarrabeitia, Maria T -- Riancho, Jose A -- Ralston, Stuart H -- Alonso, Nerea -- Jiang, Xi -- Goltzman, David -- Pastinen, Tomi -- Grundberg, Elin -- Gauguier, Dominique -- Orwoll, Eric S -- Karasik, David -- Davey-Smith, George -- AOGC Consortium -- Smith, Albert V -- Siggeirsdottir, Kristin -- Harris, Tamara B -- Zillikens, M Carola -- van Meurs, Joyce B J -- Thorsteinsdottir, Unnur -- Maurano, Matthew T -- Timpson, Nicholas J -- Soranzo, Nicole -- Durbin, Richard -- Wilson, Scott G -- Ntzani, Evangelia E -- Brown, Matthew A -- Stefansson, Kari -- Hinds, David A -- Spector, Tim -- Cupples, L Adrienne -- Ohlsson, Claes -- Greenwood, Celia M T -- UK10K Consortium -- Jackson, Rebecca D -- Rowe, David W -- Loomis, Cynthia A -- Evans, David M -- Ackert-Bicknell, Cheryl L -- Joyner, Alexandra L -- Duncan, Emma L -- Kiel, Douglas P -- Rivadeneira, Fernando -- Richards, J Brent -- G1000143/Medical Research Council/United Kingdom -- K01 AR062655/AR/NIAMS NIH HHS/ -- MC_UU_12013/3/Medical Research Council/United Kingdom -- R01 AG005394/AG/NIA NIH HHS/ -- R01 AG005407/AG/NIA NIH HHS/ -- R01 AG027574/AG/NIA NIH HHS/ -- R01 AG027576/AG/NIA NIH HHS/ -- R01 AR035582/AR/NIAMS NIH HHS/ -- R01 AR035583/AR/NIAMS NIH HHS/ -- RC2 AR058973/AR/NIAMS NIH HHS/ -- U01 AG018197/AG/NIA NIH HHS/ -- U01 AG042140/AG/NIA NIH HHS/ -- U01 AG042143/AG/NIA NIH HHS/ -- U01 AR045580/AR/NIAMS NIH HHS/ -- U01 AR045583/AR/NIAMS NIH HHS/ -- U01 AR045614/AR/NIAMS NIH HHS/ -- U01 AR045632/AR/NIAMS NIH HHS/ -- U01 AR045647/AR/NIAMS NIH HHS/ -- U01 AR045654/AR/NIAMS NIH HHS/ -- U01 AR066160/AR/NIAMS NIH HHS/ -- England -- Nature. 2015 Oct 1;526(7571):112-7. doi: 10.1038/nature14878. Epub 2015 Sep 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Medicine, Human Genetics, Epidemiology and Biostatistics, McGill University, Montreal H3A 1A2, Canada. ; Department of Medicine, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal H3T 1E2, Canada. ; Institute for Aging Research, Hebrew SeniorLife, Boston, Massachusetts 02131, USA. ; Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA. ; Broad Institute of MIT and Harvard, Boston, Massachusetts 02115, USA. ; Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands. ; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA. ; Developmental Biology Program, Sloan Kettering Institute, New York, New York 10065, USA. ; The University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Brisbane 4102, Australia. ; Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, New York 10065, USA. ; Tissue Engineering, Regeneration and Repair Program, Hospital for Special Surgery, New York 10021, USA. ; Rheumatology Divison, Hospital for Special Surgery New York, New York 10021, USA. ; School of Clinical Science, University of Bristol, Bristol BS10 5NB, UK. ; MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK. ; Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA. ; Department of Research, 23andMe, Mountain View, California 94041, USA. ; Department of Population Genomics, deCODE Genetics, Reykjavik IS-101, Iceland. ; Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts 02118, USA. ; Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg S-413 45, Sweden. ; California Pacific Medical Center Research Institute, San Francisco, California 94158, USA. ; Department of Public Health and Preventive Medicine, Oregon Health &Science University, Portland, Oregon 97239, USA. ; Bone &Mineral Unit, Oregon Health &Science University, Portland, Oregon 97239, USA. ; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK. ; Departments of Pharmacology and Clinical Neurosciences, Umea University, Umea S-901 87, Sweden. ; Department of Public Health and Clinical Medicine, Umea University, Umea SE-901 87, Sweden. ; Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg S-413 45, Sweden. ; McGill University and Genome Quebec Innovation Centre, Montreal H3A 0G1, Canada. ; Department of Epidemiology, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands. ; Oregon Clinical and Translational Research Institute, Oregon Health &Science University, Portland, Oregon 97239, USA. ; Department of Medical and Clinical Informatics, Oregon Health &Science University, Portland, Oregon 97239, USA. ; Farr Institute of Health Informatics Research, University College London, London NW1 2DA, UK. ; Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK. ; Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA. ; Department of Human Genetics, McGill University, Montreal H3A 1B1, Canada. ; Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden 2300RC, The Netherlands. ; Center for Musculoskeletal Research, University of Rochester, Rochester, New York 14642, USA. ; Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal H3G 1Y6, Canada. ; Department of Computer Science, Trinity University, San Antonio, Texas 78212, USA. ; Musculoskeletal Research Unit, University of Bristol, Bristol BS10 5NB, UK. ; Department of Radiation Sciences, Umea University, Umea S-901 87, Sweden. ; School of Public Health, University of Wisconsin, Milwaukee, Wisconsin 53726, USA. ; School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK. ; Department of Statistics, deCODE Genetics, Reykjavik IS-101, Iceland. ; Department of Epidemiology and Biostatistics and the EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam 1007 MB, The Netherlands. ; Department of Human Nutrition, Wageningen University, Wageningen 6700 EV, The Netherlands. ; Department of Internal Medicine, Section Geriatrics, Academic Medical Center, Amsterdam 1105, The Netherlands. ; Nordic Bioscience, Herlev 2730, Denmark. ; Cordeliers Research Centre, INSERM UMRS 1138, Paris 75006, France. ; Institute of Cardiometabolism and Nutrition, University Pierre &Marie Curie, Paris 75013, France. ; Departments of Medicine (Cardiovascular Medicine), Centre for Public Health Genomics, University of Virginia, Charlottesville, Virginia 22908, USA. ; Department of Genetics, University of Barcelona, Barcelona 08028, Spain. ; U-720, Centre for Biomedical Network Research on Rare Diseases (CIBERER), Barcelona 28029, Spain. ; Department of Human Molecular Genetics, The Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona 08028, Spain. ; Women's Health Center of Excellence Family Medicine and Public Health, University of California - San Diego, San Diego, California 92093, USA. ; Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02215, USA. ; Osteoporosis &Bone Biology Program, Garvan Institute of Medical Research, Sydney 2010, Australia. ; School of Medicine Sydney, University of Notre Dame Australia, Sydney 6959, Australia. ; St. Vincent's Hospital &Clinical School, NSW University, Sydney 2010, Australia. ; Musculoskeletal Research Group, Institut Hospital del Mar d'Investigacions Mediques, Barcelona 08003, Spain. ; Cooperative Research Network on Aging and Fragility (RETICEF), Institute of Health Carlos III, 28029, Spain. ; Department of Internal Medicine, Hospital del Mar, Universitat Autonoma de Barcelona, Barcelona 08193, Spain. ; Neuroepidemiology Section, National Institute on Aging, National Institutes of Health, Bethesda, Maryland 20892, USA. ; Icelandic Heart Association, Kopavogur IS-201, Iceland. ; Faculty of Medicine, University of Iceland, Reykjavik IS-101, Iceland. ; Genetic epidemiology unit, Department of Epidemiology, Erasmus MC, Rotterdam 3000CA, The Netherlands. ; Department of Orthopaedics, Skane University Hospital Malmo 205 02, Sweden. ; Department of Medical Sciences, University of Uppsala, Uppsala 751 85, Sweden. ; Department of Surgical and Perioperative Sciences, Umea Unviersity, Umea 901 85, Sweden. ; Department of Molecular Biology, Medical Biochemistry and Pathology, Universite Laval, Quebec City G1V 0A6, Canada. ; Axe Sante des Populations et Pratiques Optimales en Sante, Centre de recherche du CHU de Quebec, Quebec City G1V 4G2, Canada. ; Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands 6009, Australia. ; Department of Medicine, University of Western Australia, Perth 6009, Australia. ; Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus C 8000, Denmark. ; Department of Endocrinology, Odense University Hospital, Odense C 5000, Denmark. ; Department of Endocrinology, Hvidovre University Hospital, Hvidovre 2650, Denmark. ; Clinical Gerontology Unit, University of Cambridge, Cambridge CB2 2QQ, UK. ; Medicine and Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK. ; Institute of Musculoskeletal Sciences, The Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK. ; Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida MSD 2080, Malta. ; Clinical and Molecular Osteoporosis Research Unit, Department of Clinical Sciences Malmo, Lund University, 205 02, Sweden. ; Department of Medicine and Psychiatry, University of Cantabria, Santander 39011, Spain. ; Department of Internal Medicine, Hospital U.M. Valdecilla- IDIVAL, Santander 39008, Spain. ; Department of Legal Medicine, University of Cantabria, Santander 39011, Spain. ; Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK. ; Department of Reconstructive Sciences, College of Dental Medicine, University of Connecticut Health Center, Farmington, Connecticut 06030, USA. ; Department of Medicine and Physiology, McGill University, Montreal H4A 3J1, Canada. ; Department of Medicine, Oregon Health &Science University, Portland, Oregon 97239, USA. ; Faculty of Medicine in the Galilee, Bar-Ilan University, Safed 13010, Israel. ; Laboratory of Epidemiology, National Institute on Aging, National Institutes of Health, Bethesda, Maryland 20892, USA. ; Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA. ; School of Medicine and Pharmacology, University of Western Australia, Crawley 6009, Australia. ; Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina 45110, Greece. ; Department of Health Services, Policy and Practice, Brown University School of Public Health, Providence, Rhode Island 02903, USA. ; deCODE Genetics, Reykjavik IS-101, Iceland. ; Framingham Heart Study, Framingham, Massachusetts 01702, USA. ; Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal H3A 1A2, Canada. ; Department of Oncology, Gerald Bronfman Centre, McGill University, Montreal H2W 1S6, Canada. ; Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, The Ohio State University, Columbus, Ohio 43210, USA. ; The Ronald O. Perelman Department of Dermatology and Department of Cell Biology, New York University School of Medicine, New York, New York 10016, USA. ; Department of Diabetes and Endocrinology, Royal Brisbane and Women's Hospital, Brisbane 4029, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26367794" target="_blank"〉PubMed〈/a〉

Description: Dopamine neurons play a key role in reward-related behaviors. Reward coding theories predict that dopamine neurons will be inhibited by or will not respond to aversive stimuli. Paradoxically, between 3 and 49% of presumed dopamine neurons are excited by aversive stimuli. We found that, in the ventral tegmental area of anesthetized rats, the population of presumed dopamine neurons that are excited by aversive stimuli is actually not dopaminergic. The identified dopamine neurons were inhibited by the aversive stimulus. These findings suggest that dopamine neurons are specifically excited by reward and that a population of nondopamine neurons is excited by aversive stimuli.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ungless, Mark A -- Magill, Peter J -- Bolam, J Paul -- New York, N.Y. -- Science. 2004 Mar 26;303(5666):2040-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Anatomical Neuropharmacology Unit, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3TH, UK. mark.ungless@zoo.ox.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15044807" target="_blank"〉PubMed〈/a〉

Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Balmford, Andrew -- Bennun, Leon -- Brink, Ben Ten -- Cooper, David -- Cote, Isabelle M -- Crane, Peter -- Dobson, Andrew -- Dudley, Nigel -- Dutton, Ian -- Green, Rhys E -- Gregory, Richard D -- Harrison, Jeremy -- Kennedy, Elizabeth T -- Kremen, Claire -- Leader-Williams, Nigel -- Lovejoy, Thomas E -- Mace, Georgina -- May, Robert -- Mayaux, Phillipe -- Morling, Paul -- Phillips, Joanna -- Redford, Kent -- Ricketts, Taylor H -- Rodriguez, Jon Paul -- Sanjayan, M -- Schei, Peter J -- van Jaarsveld, Albert S -- Walther, Bruno A -- New York, N.Y. -- Science. 2005 Jan 14;307(5707):212-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cambridge University and University of Cape Town.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15653489" target="_blank"〉PubMed〈/a〉

Description: The renowned soft-bodied faunas of the Cambrian period, which include the Burgess Shale, disappear from the fossil record in the late Middle Cambrian, after which the Palaeozoic fauna dominates. The disappearance of faunas of Burgess Shale type curtails the stratigraphic record of a number of iconic Cambrian taxa. One possible explanation for this loss is a major extinction, but more probably it reflects the absence of preservation of similar soft-bodied faunas in later periods. Here we report the discovery of numerous diverse soft-bodied assemblages in the Lower and Upper Fezouata Formations (Lower Ordovician) of Morocco, which include a range of remarkable stem-group morphologies normally considered characteristic of the Cambrian. It is clear that biotas of Burgess Shale type persisted after the Cambrian and are preserved where suitable facies occur. The Fezouata biota provides a link between the Burgess Shale communities and the early stages of the Great Ordovician Biodiversification Event.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Van Roy, Peter -- Orr, Patrick J -- Botting, Joseph P -- Muir, Lucy A -- Vinther, Jakob -- Lefebvre, Bertrand -- el Hariri, Khadija -- Briggs, Derek E G -- England -- Nature. 2010 May 13;465(7295):215-8. doi: 10.1038/nature09038.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geology and Geophysics, Yale University, PO Box 208109, New Haven, Connecticut 06520, USA. peter.vanroy@yale.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20463737" target="_blank"〉PubMed〈/a〉

Description: The Acheulian is one of the first defined prehistoric techno-complexes and is characterized by shaped bifacial stone tools. It probably originated in Africa, spreading to Europe and Asia perhaps as early as approximately 1 million years (Myr) ago. The origin of the Acheulian is thought to have closely coincided with major changes in human brain evolution, allowing for further technological developments. Nonetheless, the emergence of the Acheulian remains unclear because well-dated sites older than 1.4 Myr ago are scarce. Here we report on the lithic assemblage and geological context for the Kokiselei 4 archaeological site from the Nachukui formation (West Turkana, Kenya) that bears characteristic early Acheulian tools and pushes the first appearance datum for this stone-age technology back to 1.76 Myr ago. Moreover, co-occurrence of Oldowan and Acheulian artefacts at the Kokiselei site complex indicates that the two technologies are not mutually exclusive time-successive components of an evolving cultural lineage, and suggests that the Acheulian was either imported from another location yet to be identified or originated from Oldowan hominins at this vicinity. In either case, the Acheulian did not accompany the first human dispersal from Africa despite being available at the time. This may indicate that multiple groups of hominins distinguished by separate stone-tool-making behaviours and dispersal strategies coexisted in Africa at 1.76 Myr ago.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lepre, Christopher J -- Roche, Helene -- Kent, Dennis V -- Harmand, Sonia -- Quinn, Rhonda L -- Brugal, Jean-Philippe -- Texier, Pierre-Jean -- Lenoble, Arnaud -- Feibel, Craig S -- England -- Nature. 2011 Aug 31;477(7362):82-5. doi: 10.1038/nature10372.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Lamont-Doherty Earth Observatory, Palisades, New York 10964, USA. lepre@ldeo.columbia.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21886161" target="_blank"〉PubMed〈/a〉