ALBERT

Description: Many bacterial pathogens encode a multisubunit toxin, termed cytolethal distending toxin (CDT), that induces cell cycle arrest, cytoplasm distention, and, eventually, chromatin fragmentation and cell death. In one such pathogen, Campylobacter jejuni, one of the subunits of this toxin, CdtB, was shown to exhibit features of type I deoxyribonucleases. Transient expression of this subunit in cultured cells caused marked chromatin disruption. Microinjection of low amounts of CdtB induced cytoplasmic distention and cell cycle arrest. CdtB mutants with substitutions in residues equivalent to those required for catalysis or magnesium binding in type I deoxyribonucleases did not cause chromatin disruption. CDT holotoxin containing these mutant forms of CdtB did not induce morphological changes or cell cycle arrest.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lara-Tejero, M -- Galan, J E -- New York, N.Y. -- Science. 2000 Oct 13;290(5490):354-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Microbial Pathogenesis, Boyer Center for Molecular Medicine, Yale School of Medicine, New Haven, CT 06536, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11030657" target="_blank"〉PubMed〈/a〉

Description: 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 approximately 4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for approximately 60% 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.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207357/" 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/PMC3207357/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lindblad-Toh, Kerstin -- Garber, Manuel -- Zuk, Or -- Lin, Michael F -- Parker, Brian J -- Washietl, Stefan -- Kheradpour, Pouya -- Ernst, Jason -- Jordan, Gregory -- Mauceli, Evan -- Ward, Lucas D -- Lowe, Craig B -- Holloway, Alisha K -- Clamp, Michele -- Gnerre, Sante -- Alfoldi, Jessica -- Beal, Kathryn -- Chang, Jean -- Clawson, Hiram -- Cuff, James -- Di Palma, Federica -- Fitzgerald, Stephen -- Flicek, Paul -- Guttman, Mitchell -- Hubisz, Melissa J -- Jaffe, David B -- Jungreis, Irwin -- Kent, W James -- Kostka, Dennis -- Lara, Marcia -- Martins, Andre L -- Massingham, Tim -- Moltke, Ida -- Raney, Brian J -- Rasmussen, Matthew D -- Robinson, Jim -- Stark, Alexander -- Vilella, Albert J -- Wen, Jiayu -- Xie, Xiaohui -- Zody, Michael C -- Broad Institute Sequencing Platform and Whole Genome Assembly Team -- Baldwin, Jen -- Bloom, Toby -- Chin, Chee Whye -- Heiman, Dave -- Nicol, Robert -- Nusbaum, Chad -- Young, Sarah -- Wilkinson, Jane -- Worley, Kim C -- Kovar, Christie L -- Muzny, Donna M -- Gibbs, Richard A -- Baylor College of Medicine Human Genome Sequencing Center Sequencing Team -- Cree, Andrew -- Dihn, Huyen H -- Fowler, Gerald -- Jhangiani, Shalili -- Joshi, Vandita -- Lee, Sandra -- Lewis, Lora R -- Nazareth, Lynne V -- Okwuonu, Geoffrey -- Santibanez, Jireh -- Warren, Wesley C -- Mardis, Elaine R -- Weinstock, George M -- Wilson, Richard K -- Genome Institute at Washington University -- Delehaunty, Kim -- Dooling, David -- Fronik, Catrina -- Fulton, Lucinda -- Fulton, Bob -- Graves, Tina -- Minx, Patrick -- Sodergren, Erica -- Birney, Ewan -- Margulies, Elliott H -- Herrero, Javier -- Green, Eric D -- Haussler, David -- Siepel, Adam -- Goldman, Nick -- Pollard, Katherine S -- Pedersen, Jakob S -- Lander, Eric S -- Kellis, Manolis -- 095908/Wellcome Trust/United Kingdom -- GM82901/GM/NIGMS NIH HHS/ -- R01 HG003474/HG/NHGRI NIH HHS/ -- R01 HG004037/HG/NHGRI NIH HHS/ -- U54 HG003067/HG/NHGRI NIH HHS/ -- U54 HG003067-09/HG/NHGRI NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 Oct 12;478(7370):476-82. doi: 10.1038/nature10530.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA. kersli@broadinstitute.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21993624" target="_blank"〉PubMed〈/a〉

Description: Somatic cells can be inefficiently and stochastically reprogrammed into induced pluripotent stem (iPS) cells by exogenous expression of Oct4 (also called Pou5f1), Sox2, Klf4 and Myc (hereafter referred to as OSKM). The nature of the predominant rate-limiting barrier(s) preventing the majority of cells to successfully and synchronously reprogram remains to be defined. Here we show that depleting Mbd3, a core member of the Mbd3/NuRD (nucleosome remodelling and deacetylation) repressor complex, together with OSKM transduction and reprogramming in naive pluripotency promoting conditions, result in deterministic and synchronized iPS cell reprogramming (near 100% efficiency within seven days from mouse and human cells). Our findings uncover a dichotomous molecular function for the reprogramming factors, serving to reactivate endogenous pluripotency networks while simultaneously directly recruiting the Mbd3/NuRD repressor complex that potently restrains the reactivation of OSKM downstream target genes. Subsequently, the latter interactions, which are largely depleted during early pre-implantation development in vivo, lead to a stochastic and protracted reprogramming trajectory towards pluripotency in vitro. The deterministic reprogramming approach devised here offers a novel platform for the dissection of molecular dynamics leading to establishing pluripotency at unprecedented flexibility and resolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rais, Yoach -- Zviran, Asaf -- Geula, Shay -- Gafni, Ohad -- Chomsky, Elad -- Viukov, Sergey -- Mansour, Abed AlFatah -- Caspi, Inbal -- Krupalnik, Vladislav -- Zerbib, Mirie -- Maza, Itay -- Mor, Nofar -- Baran, Dror -- Weinberger, Leehee -- Jaitin, Diego A -- Lara-Astiaso, David -- Blecher-Gonen, Ronnie -- Shipony, Zohar -- Mukamel, Zohar -- Hagai, Tzachi -- Gilad, Shlomit -- Amann-Zalcenstein, Daniela -- Tanay, Amos -- Amit, Ido -- Novershtern, Noa -- Hanna, Jacob H -- England -- Nature. 2013 Oct 3;502(7469):65-70. doi: 10.1038/nature12587. Epub 2013 Sep 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24048479" target="_blank"〉PubMed〈/a〉

Description: The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features. Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633110/" 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/PMC3633110/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Amemiya, Chris T -- Alfoldi, Jessica -- Lee, Alison P -- Fan, Shaohua -- Philippe, Herve -- Maccallum, Iain -- Braasch, Ingo -- Manousaki, Tereza -- Schneider, Igor -- Rohner, Nicolas -- Organ, Chris -- Chalopin, Domitille -- Smith, Jeramiah J -- Robinson, Mark -- Dorrington, Rosemary A -- Gerdol, Marco -- Aken, Bronwen -- Biscotti, Maria Assunta -- Barucca, Marco -- Baurain, Denis -- Berlin, Aaron M -- Blatch, Gregory L -- Buonocore, Francesco -- Burmester, Thorsten -- Campbell, Michael S -- Canapa, Adriana -- Cannon, John P -- Christoffels, Alan -- De Moro, Gianluca -- Edkins, Adrienne L -- Fan, Lin -- Fausto, Anna Maria -- Feiner, Nathalie -- Forconi, Mariko -- Gamieldien, Junaid -- Gnerre, Sante -- Gnirke, Andreas -- Goldstone, Jared V -- Haerty, Wilfried -- Hahn, Mark E -- Hesse, Uljana -- Hoffmann, Steve -- Johnson, Jeremy -- Karchner, Sibel I -- Kuraku, Shigehiro -- Lara, Marcia -- Levin, Joshua Z -- Litman, Gary W -- Mauceli, Evan -- Miyake, Tsutomu -- Mueller, M Gail -- Nelson, David R -- Nitsche, Anne -- Olmo, Ettore -- Ota, Tatsuya -- Pallavicini, Alberto -- Panji, Sumir -- Picone, Barbara -- Ponting, Chris P -- Prohaska, Sonja J -- Przybylski, Dariusz -- Saha, Nil Ratan -- Ravi, Vydianathan -- Ribeiro, Filipe J -- Sauka-Spengler, Tatjana -- Scapigliati, Giuseppe -- Searle, Stephen M J -- Sharpe, Ted -- Simakov, Oleg -- Stadler, Peter F -- Stegeman, John J -- Sumiyama, Kenta -- Tabbaa, Diana -- Tafer, Hakim -- Turner-Maier, Jason -- van Heusden, Peter -- White, Simon -- Williams, Louise -- Yandell, Mark -- Brinkmann, Henner -- Volff, Jean-Nicolas -- Tabin, Clifford J -- Shubin, Neil -- Schartl, Manfred -- Jaffe, David B -- Postlethwait, John H -- Venkatesh, Byrappa -- Di Palma, Federica -- Lander, Eric S -- Meyer, Axel -- Lindblad-Toh, Kerstin -- 095908/Wellcome Trust/United Kingdom -- MC_U137761446/Medical Research Council/United Kingdom -- P42 ES007381/ES/NIEHS NIH HHS/ -- R01 ES006272/ES/NIEHS NIH HHS/ -- R01 HG003474/HG/NHGRI NIH HHS/ -- R01 OD011116/OD/NIH HHS/ -- R24 OD011199/OD/NIH HHS/ -- R24 RR032670/RR/NCRR NIH HHS/ -- R37 HD032443/HD/NICHD NIH HHS/ -- U54 HG003067/HG/NHGRI NIH HHS/ -- England -- Nature. 2013 Apr 18;496(7445):311-6. doi: 10.1038/nature12027.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Genetics Program, Benaroya Research Institute, Seattle, Washington 98101, USA. camemiya@benaroyaresearch.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23598338" target="_blank"〉PubMed〈/a〉

Description: Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4353498/" 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/PMC4353498/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brawand, David -- Wagner, Catherine E -- Li, Yang I -- Malinsky, Milan -- Keller, Irene -- Fan, Shaohua -- Simakov, Oleg -- Ng, Alvin Y -- Lim, Zhi Wei -- Bezault, Etienne -- Turner-Maier, Jason -- Johnson, Jeremy -- Alcazar, Rosa -- Noh, Hyun Ji -- Russell, Pamela -- Aken, Bronwen -- Alfoldi, Jessica -- Amemiya, Chris -- Azzouzi, Naoual -- Baroiller, Jean-Francois -- Barloy-Hubler, Frederique -- Berlin, Aaron -- Bloomquist, Ryan -- Carleton, Karen L -- Conte, Matthew A -- D'Cotta, Helena -- Eshel, Orly -- Gaffney, Leslie -- Galibert, Francis -- Gante, Hugo F -- Gnerre, Sante -- Greuter, Lucie -- Guyon, Richard -- Haddad, Natalie S -- Haerty, Wilfried -- Harris, Rayna M -- Hofmann, Hans A -- Hourlier, Thibaut -- Hulata, Gideon -- Jaffe, David B -- Lara, Marcia -- Lee, Alison P -- MacCallum, Iain -- Mwaiko, Salome -- Nikaido, Masato -- Nishihara, Hidenori -- Ozouf-Costaz, Catherine -- Penman, David J -- Przybylski, Dariusz -- Rakotomanga, Michaelle -- Renn, Suzy C P -- Ribeiro, Filipe J -- Ron, Micha -- Salzburger, Walter -- Sanchez-Pulido, Luis -- Santos, M Emilia -- Searle, Steve -- Sharpe, Ted -- Swofford, Ross -- Tan, Frederick J -- Williams, Louise -- Young, Sarah -- Yin, Shuangye -- Okada, Norihiro -- Kocher, Thomas D -- Miska, Eric A -- Lander, Eric S -- Venkatesh, Byrappa -- Fernald, Russell D -- Meyer, Axel -- Ponting, Chris P -- Streelman, J Todd -- Lindblad-Toh, Kerstin -- Seehausen, Ole -- Di Palma, Federica -- 2R01DE019637-04/DE/NIDCR NIH HHS/ -- F30 DE023013/DE/NIDCR NIH HHS/ -- MC_U137761446/Medical Research Council/United Kingdom -- R01 DE019637/DE/NIDCR NIH HHS/ -- R01 NS034950/NS/NINDS NIH HHS/ -- U54 HG002045/HG/NHGRI NIH HHS/ -- Wellcome Trust/United Kingdom -- England -- Nature. 2014 Sep 18;513(7518):375-81. doi: 10.1038/nature13726. Epub 2014 Sep 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK [3]. ; 1] Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution &Biogeochemistry, CH-6047 Kastanienbaum, Switzerland [2] Division of Aquatic Ecology, Institute of Ecology &Evolution, University of Bern, CH-3012 Bern, Switzerland [3]. ; 1] MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK [2]. ; 1] Gurdon Institute, Cambridge CB2 1QN, UK [2] Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK. ; Division of Aquatic Ecology, Institute of Ecology &Evolution, University of Bern, CH-3012 Bern, Switzerland. ; Department of Biology, University of Konstanz, D-78457 Konstanz, Germany. ; 1] Department of Biology, University of Konstanz, D-78457 Konstanz, Germany [2] European Molecular Biology Laboratory, 69117 Heidelberg, Germany. ; Institute of Molecular and Cell Biology, A*STAR, 138673 Singapore. ; Department of Biology, Reed College, Portland, Oregon 97202, USA. ; Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. ; Biology Department, Stanford University, Stanford, California 94305-5020, USA. ; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA. ; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK. ; Benaroya Research Institute at Virginia Mason, Seattle, Washington 98101, USA. ; Institut Genetique et Developpement, CNRS/University of Rennes, 35043 Rennes, France. ; CIRAD, Campus International de Baillarguet, TA B-110/A, 34398 Montpellier cedex 5, France. ; School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0230, USA. ; Department of Biology, University of Maryland, College Park, Maryland 20742, USA. ; Animal Genetics, Institute of Animal Science, ARO, The Volcani Center, Bet-Dagan, 50250 Israel. ; Zoological Institute, University of Basel, CH-4051 Basel, Switzerland. ; 1] Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution &Biogeochemistry, CH-6047 Kastanienbaum, Switzerland [2] Division of Aquatic Ecology, Institute of Ecology &Evolution, University of Bern, CH-3012 Bern, Switzerland. ; MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK. ; Department of Integrative Biology, Center for Computational Biology and Bioinformatics; The University of Texas at Austin, Austin, Texas 78712, USA. ; Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution &Biogeochemistry, CH-6047 Kastanienbaum, Switzerland. ; Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 226-8501 Yokohama, Japan. ; Systematique, Adaptation, Evolution, National Museum of Natural History, 75005 Paris, France. ; Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK. ; Carnegie Institution of Washington, Department of Embryology, 3520 San Martin Drive Baltimore, Maryland 21218, USA. ; 1] Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 226-8501 Yokohama, Japan [2] National Cheng Kung University, Tainan City, 704 Taiwan. ; Gurdon Institute, Cambridge CB2 1QN, UK. ; 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden. ; 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Vertebrate and Health Genomics, The Genome Analysis Centre, Norwich NR18 7UH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25186727" target="_blank"〉PubMed〈/a〉

Description: The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments. Among amniotes, genome sequences are available for mammals and birds, but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes. Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds. We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3184186/" 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/PMC3184186/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alfoldi, Jessica -- Di Palma, Federica -- Grabherr, Manfred -- Williams, Christina -- Kong, Lesheng -- Mauceli, Evan -- Russell, Pamela -- Lowe, Craig B -- Glor, Richard E -- Jaffe, Jacob D -- Ray, David A -- Boissinot, Stephane -- Shedlock, Andrew M -- Botka, Christopher -- Castoe, Todd A -- Colbourne, John K -- Fujita, Matthew K -- Moreno, Ricardo Godinez -- ten Hallers, Boudewijn F -- Haussler, David -- Heger, Andreas -- Heiman, David -- Janes, Daniel E -- Johnson, Jeremy -- de Jong, Pieter J -- Koriabine, Maxim Y -- Lara, Marcia -- Novick, Peter A -- Organ, Chris L -- Peach, Sally E -- Poe, Steven -- Pollock, David D -- de Queiroz, Kevin -- Sanger, Thomas -- Searle, Steve -- Smith, Jeremy D -- Smith, Zachary -- Swofford, Ross -- Turner-Maier, Jason -- Wade, Juli -- Young, Sarah -- Zadissa, Amonida -- Edwards, Scott V -- Glenn, Travis C -- Schneider, Christopher J -- Losos, Jonathan B -- Lander, Eric S -- Breen, Matthew -- Ponting, Chris P -- Lindblad-Toh, Kerstin -- BB/F007590/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- MC_U137761446/Medical Research Council/United Kingdom -- U54 HG003067/HG/NHGRI NIH HHS/ -- U54 HG003067-08/HG/NHGRI NIH HHS/ -- England -- Nature. 2011 Aug 31;477(7366):587-91. doi: 10.1038/nature10390.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. jalfoldi@broadinstitute.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21881562" target="_blank"〉PubMed〈/a〉

Description: A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. Previous efforts to dissect the genotype-phenotype map were based on incomplete genotypic information. Here, we describe the Drosophila melanogaster Genetic Reference Panel (DGRP), a community resource for analysis of population genomics and quantitative traits. The DGRP consists of fully sequenced inbred lines derived from a natural population. Population genomic analyses reveal reduced polymorphism in centromeric autosomal regions and the X chromosome, evidence for positive and negative selection, and rapid evolution of the X chromosome. Many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. The DGRP facilitates genotype-phenotype mapping using the power of Drosophila genetics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3683990/" 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/PMC3683990/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mackay, Trudy F C -- Richards, Stephen -- Stone, Eric A -- Barbadilla, Antonio -- Ayroles, Julien F -- Zhu, Dianhui -- Casillas, Sonia -- Han, Yi -- Magwire, Michael M -- Cridland, Julie M -- Richardson, Mark F -- Anholt, Robert R H -- Barron, Maite -- Bess, Crystal -- Blankenburg, Kerstin Petra -- Carbone, Mary Anna -- Castellano, David -- Chaboub, Lesley -- Duncan, Laura -- Harris, Zeke -- Javaid, Mehwish -- Jayaseelan, Joy Christina -- Jhangiani, Shalini N -- Jordan, Katherine W -- Lara, Fremiet -- Lawrence, Faye -- Lee, Sandra L -- Librado, Pablo -- Linheiro, Raquel S -- Lyman, Richard F -- Mackey, Aaron J -- Munidasa, Mala -- Muzny, Donna Marie -- Nazareth, Lynne -- Newsham, Irene -- Perales, Lora -- Pu, Ling-Ling -- Qu, Carson -- Ramia, Miquel -- Reid, Jeffrey G -- Rollmann, Stephanie M -- Rozas, Julio -- Saada, Nehad -- Turlapati, Lavanya -- Worley, Kim C -- Wu, Yuan-Qing -- Yamamoto, Akihiko -- Zhu, Yiming -- Bergman, Casey M -- Thornton, Kevin R -- Mittelman, David -- Gibbs, Richard A -- GM 45146/GM/NIGMS NIH HHS/ -- R01 GM 059469/GM/NIGMS NIH HHS/ -- R01 GM 085183/GM/NIGMS NIH HHS/ -- R01 GM045146/GM/NIGMS NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- England -- Nature. 2012 Feb 8;482(7384):173-8. doi: 10.1038/nature10811.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA. trudy_mackay@ncsu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22318601" target="_blank"〉PubMed〈/a〉

Description: It is predicted that climate change will cause species extinctions and distributional shifts in coming decades, but data to validate these predictions are relatively scarce. Here, we compare recent and historical surveys for 48 Mexican lizard species at 200 sites. Since 1975, 12% of local populations have gone extinct. We verified physiological models of extinction risk with observed local extinctions and extended projections worldwide. Since 1975, we estimate that 4% of local populations have gone extinct worldwide, but by 2080 local extinctions are projected to reach 39% worldwide, and species extinctions may reach 20%. Global extinction projections were validated with local extinctions observed from 1975 to 2009 for regional biotas on four other continents, suggesting that lizards have already crossed a threshold for extinctions caused by climate change.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sinervo, Barry -- Mendez-de-la-Cruz, Fausto -- Miles, Donald B -- Heulin, Benoit -- Bastiaans, Elizabeth -- Villagran-Santa Cruz, Maricela -- Lara-Resendiz, Rafael -- Martinez-Mendez, Norberto -- Calderon-Espinosa, Martha Lucia -- Meza-Lazaro, Rubi Nelsi -- Gadsden, Hector -- Avila, Luciano Javier -- Morando, Mariana -- De la Riva, Ignacio J -- Victoriano Sepulveda, Pedro -- Rocha, Carlos Frederico Duarte -- Ibarguengoytia, Nora -- Aguilar Puntriano, Cesar -- Massot, Manuel -- Lepetz, Virginie -- Oksanen, Tuula A -- Chapple, David G -- Bauer, Aaron M -- Branch, William R -- Clobert, Jean -- Sites, Jack W Jr -- New York, N.Y. -- Science. 2010 May 14;328(5980):894-9. doi: 10.1126/science.1184695.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA. lizardrps@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20466932" target="_blank"〉PubMed〈/a〉

Description: Chromatin modifications are crucial for development, yet little is known about their dynamics during differentiation. Hematopoiesis provides a well-defined model to study chromatin state dynamics; however, technical limitations impede profiling of homogeneous differentiation intermediates. We developed a high-sensitivity indexing-first chromatin immunoprecipitation approach to profile the dynamics of four chromatin modifications across 16 stages of hematopoietic differentiation. We identify 48,415 enhancer regions and characterize their dynamics. We find that lineage commitment involves de novo establishment of 17,035 lineage-specific enhancers. These enhancer repertoire expansions foreshadow transcriptional programs in differentiated cells. Combining our enhancer catalog with gene expression profiles, we elucidate the transcription factor network controlling chromatin dynamics and lineage specification in hematopoiesis. Together, our results provide a comprehensive model of chromatin dynamics during development.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4412442/" 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/PMC4412442/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lara-Astiaso, David -- Weiner, Assaf -- Lorenzo-Vivas, Erika -- Zaretsky, Irina -- Jaitin, Diego Adhemar -- David, Eyal -- Keren-Shaul, Hadas -- Mildner, Alexander -- Winter, Deborah -- Jung, Steffen -- Friedman, Nir -- Amit, Ido -- 1P50HG006193/HG/NHGRI NIH HHS/ -- P50 HG006193/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2014 Aug 22;345(6199):943-9. doi: 10.1126/science.1256271. Epub 2014 Aug 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology, Weizmann Institute of Science, Rehovot, Israel. ; Institute of Life Sciences, The Hebrew University, Jerusalem, Israel. School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel. ; Institute of Life Sciences, The Hebrew University, Jerusalem, Israel. School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel. nir@cs.huji.ac.il ido.amit@weizmann.ac.il. ; Department of Immunology, Weizmann Institute of Science, Rehovot, Israel. nir@cs.huji.ac.il ido.amit@weizmann.ac.il.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25103404" target="_blank"〉PubMed〈/a〉

Description: Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, 〉0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at ~150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups. Diversity emerged at all taxonomic levels, both within the groups comprising the ~11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies. Most eukaryotic plankton biodiversity belonged to heterotrophic protistan groups, particularly those known to be parasites or symbiotic hosts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉de Vargas, Colomban -- Audic, Stephane -- Henry, Nicolas -- Decelle, Johan -- Mahe, Frederic -- Logares, Ramiro -- Lara, Enrique -- Berney, Cedric -- Le Bescot, Noan -- Probert, Ian -- Carmichael, Margaux -- Poulain, Julie -- Romac, Sarah -- Colin, Sebastien -- Aury, Jean-Marc -- Bittner, Lucie -- Chaffron, Samuel -- Dunthorn, Micah -- Engelen, Stefan -- Flegontova, Olga -- Guidi, Lionel -- Horak, Ales -- Jaillon, Olivier -- Lima-Mendez, Gipsi -- Lukes, Julius -- Malviya, Shruti -- Morard, Raphael -- Mulot, Matthieu -- Scalco, Eleonora -- Siano, Raffaele -- Vincent, Flora -- Zingone, Adriana -- Dimier, Celine -- Picheral, Marc -- Searson, Sarah -- Kandels-Lewis, Stefanie -- Tara Oceans Coordinators -- Acinas, Silvia G -- Bork, Peer -- Bowler, Chris -- Gorsky, Gabriel -- Grimsley, Nigel -- Hingamp, Pascal -- Iudicone, Daniele -- Not, Fabrice -- Ogata, Hiroyuki -- Pesant, Stephane -- Raes, Jeroen -- Sieracki, Michael E -- Speich, Sabrina -- Stemmann, Lars -- Sunagawa, Shinichi -- Weissenbach, Jean -- Wincker, Patrick -- Karsenti, Eric -- New York, N.Y. -- Science. 2015 May 22;348(6237):1261605. doi: 10.1126/science.1261605.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universites, Universite Pierre et Marie Curie (UPMC) Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. vargas@sb-roscoff.fr pwincker@genoscope.cns.fr karsenti@embl.de. ; CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universites, Universite Pierre et Marie Curie (UPMC) Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. ; Department of Ecology, University of Kaiserslautern, Erwin-Schroedinger Street, 67663 Kaiserslautern, Germany. CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universites, Universite Pierre et Marie Curie (UPMC) Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. ; Department of Marine Biology and Oceanography, Institute of Marine Science (ICM)-Consejo Superior de Investigaciones Cientificas (CSIC), Passeig Maritim de la Barceloneta 37-49, Barcelona E08003, Spain. ; Laboratory of Soil Biology, University of Neuchatel, Rue Emile-Argand 11, 2000 Neuchatel, Switzerland. ; CNRS, FR2424, Roscoff Culture Collection, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universites, UPMC Paris 06, FR 2424, Roscoff Culture Collection, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. ; CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universites, Universite Pierre et Marie Curie (UPMC) Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Ecole Normale Superieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, Paris, F-75005 France. ; Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Genomique, GENOSCOPE, 2 rue Gaston Cremieux, 91000 Evry, France. ; CNRS FR3631, Institut de Biologie Paris-Seine, F-75005, Paris, France. Sorbonne Universites, UPMC Paris 06, Institut de Biologie Paris-Seine, F-75005, Paris, France. Ecole Normale Superieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, Paris, F-75005 France. CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universites, Universite Pierre et Marie Curie (UPMC) Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. ; Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium. ; Department of Ecology, University of Kaiserslautern, Erwin-Schroedinger Street, 67663 Kaiserslautern, Germany. ; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branisovska 31, 37005 Ceske Budejovice, Czech Republic. Faculty of Science, University of South Bohemia, Branisovska 31, 37005 Ceske Budejovice, Czech Republic. ; CNRS, UMR 7093, Laboratoire d'Oceanographie de Villefranche-sur-Mer (LOV), Observatoire Oceanologique, F-06230, Villefranche-sur-Mer, France. Sorbonne Universites, UPMC Paris 06, UMR 7093, LOV, Observatoire Oceanologique, F-06230, Villefranche-sur-Mer, France. ; Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Genomique, GENOSCOPE, 2 rue Gaston Cremieux, 91000 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Universite d'Evry, UMR 8030, CP5706, Evry, France. ; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branisovska 31, 37005 Ceske Budejovice, Czech Republic. Faculty of Science, University of South Bohemia, Branisovska 31, 37005 Ceske Budejovice, Czech Republic. Canadian Institute for Advanced Research, 180 Dundas Street West, Suite 1400, Toronto, Ontario M5G 1Z8, Canada. ; Ecole Normale Superieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, Paris, F-75005 France. ; MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany. CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universites, Universite Pierre et Marie Curie (UPMC) Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. ; Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy. ; Ifremer, Centre de Brest, DYNECO/Pelagos CS 10070, 29280 Plouzane, France. ; Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Ecole Normale Superieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, Paris, F-75005 France. ; Structural and Computational Biology, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany. Directors' Research, EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany. ; Structural and Computational Biology, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany. Max-Delbruck-Centre for Molecular Medicine, 13092 Berlin, Germany. ; CNRS UMR 7232, Biologie Integrative des Organismes Marins (BIOM), Avenue du Fontaule, 66650 Banyuls-sur-Mer, France. Sorbonne Universites Paris 06, Observatoire Oceanologique de Banyuls (OOB) UPMC, Avenue du Fontaule, 66650 Banyuls-sur-Mer, France. ; Aix Marseille Universite, CNRS IGS UMR 7256, 13288 Marseille, France. ; Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan. ; PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany. MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany. ; Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, USA. National Science Foundation, Arlington, VA 22230, USA. ; Department of Geosciences, Laboratoire de Meteorologie Dynamique (LMD), Ecole Normale Superieure, 24 rue Lhomond, 75231 Paris Cedex 05, France. Laboratoire de Physique des Oceans, Universite de Bretagne Occidentale (UBO)-Institut Universitaire Europeen de la Mer (IUEM), Place Copernic, 29820 Plouzane, France. ; Structural and Computational Biology, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany. ; Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Genomique, GENOSCOPE, 2 rue Gaston Cremieux, 91000 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Universite d'Evry, UMR 8030, CP5706, Evry, France. vargas@sb-roscoff.fr pwincker@genoscope.cns.fr karsenti@embl.de. ; Directors' Research, EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Ecole Normale Superieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, Paris, F-75005 France. vargas@sb-roscoff.fr pwincker@genoscope.cns.fr karsenti@embl.de.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25999516" target="_blank"〉PubMed〈/a〉