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  • 1
    Publication Date: 2012-11-16
    Description: For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars approximately 1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566564/" 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/PMC3566564/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Groenen, Martien A M -- Archibald, Alan L -- Uenishi, Hirohide -- Tuggle, Christopher K -- Takeuchi, Yasuhiro -- Rothschild, Max F -- Rogel-Gaillard, Claire -- Park, Chankyu -- Milan, Denis -- Megens, Hendrik-Jan -- Li, Shengting -- Larkin, Denis M -- Kim, Heebal -- Frantz, Laurent A F -- Caccamo, Mario -- Ahn, Hyeonju -- Aken, Bronwen L -- Anselmo, Anna -- Anthon, Christian -- Auvil, Loretta -- Badaoui, Bouabid -- Beattie, Craig W -- Bendixen, Christian -- Berman, Daniel -- Blecha, Frank -- Blomberg, Jonas -- Bolund, Lars -- Bosse, Mirte -- Botti, Sara -- Bujie, Zhan -- Bystrom, Megan -- Capitanu, Boris -- Carvalho-Silva, Denise -- Chardon, Patrick -- Chen, Celine -- Cheng, Ryan -- Choi, Sang-Haeng -- Chow, William -- Clark, Richard C -- Clee, Christopher -- Crooijmans, Richard P M A -- Dawson, Harry D -- Dehais, Patrice -- De Sapio, Fioravante -- Dibbits, Bert -- Drou, Nizar -- Du, Zhi-Qiang -- Eversole, Kellye -- Fadista, Joao -- Fairley, Susan -- Faraut, Thomas -- Faulkner, Geoffrey J -- Fowler, Katie E -- Fredholm, Merete -- Fritz, Eric -- Gilbert, James G R -- Giuffra, Elisabetta -- Gorodkin, Jan -- Griffin, Darren K -- Harrow, Jennifer L -- Hayward, Alexander -- Howe, Kerstin -- Hu, Zhi-Liang -- Humphray, Sean J -- Hunt, Toby -- Hornshoj, Henrik -- Jeon, Jin-Tae -- Jern, Patric -- Jones, Matthew -- Jurka, Jerzy -- Kanamori, Hiroyuki -- Kapetanovic, Ronan -- Kim, Jaebum -- Kim, Jae-Hwan -- Kim, Kyu-Won -- Kim, Tae-Hun -- Larson, Greger -- Lee, Kyooyeol -- Lee, Kyung-Tai -- Leggett, Richard -- Lewin, Harris A -- Li, Yingrui -- Liu, Wansheng -- Loveland, Jane E -- Lu, Yao -- Lunney, Joan K -- Ma, Jian -- Madsen, Ole -- Mann, Katherine -- Matthews, Lucy -- McLaren, Stuart -- Morozumi, Takeya -- Murtaugh, Michael P -- Narayan, Jitendra -- Nguyen, Dinh Truong -- Ni, Peixiang -- Oh, Song-Jung -- Onteru, Suneel -- Panitz, Frank -- Park, Eung-Woo -- Park, Hong-Seog -- Pascal, Geraldine -- Paudel, Yogesh -- Perez-Enciso, Miguel -- Ramirez-Gonzalez, Ricardo -- Reecy, James M -- Rodriguez-Zas, Sandra -- Rohrer, Gary A -- Rund, Lauretta -- Sang, Yongming -- Schachtschneider, Kyle -- Schraiber, Joshua G -- Schwartz, John -- Scobie, Linda -- Scott, Carol -- Searle, Stephen -- Servin, Bertrand -- Southey, Bruce R -- Sperber, Goran -- Stadler, Peter -- Sweedler, Jonathan V -- Tafer, Hakim -- Thomsen, Bo -- Wali, Rashmi -- Wang, Jian -- Wang, Jun -- White, Simon -- Xu, Xun -- Yerle, Martine -- Zhang, Guojie -- Zhang, Jianguo -- Zhang, Jie -- Zhao, Shuhong -- Rogers, Jane -- Churcher, Carol -- Schook, Lawrence B -- 095908/Wellcome Trust/United Kingdom -- 249894/European Research Council/International -- 5 P41 LM006252/LM/NLM NIH HHS/ -- 5 P41LM006252/LM/NLM NIH HHS/ -- BB/E010520/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E010520/2/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E010768/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E011640/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G004013/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/H005935/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/I025328/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- G0900950/Medical Research Council/United Kingdom -- P20-RR017686/RR/NCRR NIH HHS/ -- P30 DA018310/DA/NIDA NIH HHS/ -- R13 RR020283A/RR/NCRR NIH HHS/ -- R13 RR032267A/RR/NCRR NIH HHS/ -- R21 DA027548/DA/NIDA NIH HHS/ -- R21 HG006464/HG/NHGRI NIH HHS/ -- T32 AI083196/AI/NIAID NIH HHS/ -- England -- Nature. 2012 Nov 15;491(7424):393-8. doi: 10.1038/nature11622.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands. martien.groenen@wur.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23151582" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Demography ; Genome/*genetics ; Models, Animal ; Molecular Sequence Data ; *Phylogeny ; Population Dynamics ; Sus scrofa/*classification/*genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2012-10-30
    Description: Pancreatic cancer is a highly lethal malignancy with few effective therapies. We performed exome sequencing and copy number analysis to define genomic aberrations in a prospectively accrued clinical cohort (n = 142) of early (stage I and II) sporadic pancreatic ductal adenocarcinoma. Detailed analysis of 99 informative tumours identified substantial heterogeneity with 2,016 non-silent mutations and 1,628 copy-number variations. We define 16 significantly mutated genes, reaffirming known mutations (KRAS, TP53, CDKN2A, SMAD4, MLL3, TGFBR2, ARID1A and SF3B1), and uncover novel mutated genes including additional genes involved in chromatin modification (EPC1 and ARID2), DNA damage repair (ATM) and other mechanisms (ZIM2, MAP2K4, NALCN, SLC16A4 and MAGEA6). Integrative analysis with in vitro functional data and animal models provided supportive evidence for potential roles for these genetic aberrations in carcinogenesis. Pathway-based analysis of recurrently mutated genes recapitulated clustering in core signalling pathways in pancreatic ductal adenocarcinoma, and identified new mutated genes in each pathway. We also identified frequent and diverse somatic aberrations in genes described traditionally as embryonic regulators of axon guidance, particularly SLIT/ROBO signalling, which was also evident in murine Sleeping Beauty transposon-mediated somatic mutagenesis models of pancreatic cancer, providing further supportive evidence for the potential involvement of axon guidance genes in pancreatic carcinogenesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530898/" 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/PMC3530898/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Biankin, Andrew V -- Waddell, Nicola -- Kassahn, Karin S -- Gingras, Marie-Claude -- Muthuswamy, Lakshmi B -- Johns, Amber L -- Miller, David K -- Wilson, Peter J -- Patch, Ann-Marie -- Wu, Jianmin -- Chang, David K -- Cowley, Mark J -- Gardiner, Brooke B -- Song, Sarah -- Harliwong, Ivon -- Idrisoglu, Senel -- Nourse, Craig -- Nourbakhsh, Ehsan -- Manning, Suzanne -- Wani, Shivangi -- Gongora, Milena -- Pajic, Marina -- Scarlett, Christopher J -- Gill, Anthony J -- Pinho, Andreia V -- Rooman, Ilse -- Anderson, Matthew -- Holmes, Oliver -- Leonard, Conrad -- Taylor, Darrin -- Wood, Scott -- Xu, Qinying -- Nones, Katia -- Fink, J Lynn -- Christ, Angelika -- Bruxner, Tim -- Cloonan, Nicole -- Kolle, Gabriel -- Newell, Felicity -- Pinese, Mark -- Mead, R Scott -- Humphris, Jeremy L -- Kaplan, Warren -- Jones, Marc D -- Colvin, Emily K -- Nagrial, Adnan M -- Humphrey, Emily S -- Chou, Angela -- Chin, Venessa T -- Chantrill, Lorraine A -- Mawson, Amanda -- Samra, Jaswinder S -- Kench, James G -- Lovell, Jessica A -- Daly, Roger J -- Merrett, Neil D -- Toon, Christopher -- Epari, Krishna -- Nguyen, Nam Q -- Barbour, Andrew -- Zeps, Nikolajs -- Australian Pancreatic Cancer Genome Initiative -- Kakkar, Nipun -- Zhao, Fengmei -- Wu, Yuan Qing -- Wang, Min -- Muzny, Donna M -- Fisher, William E -- Brunicardi, F Charles -- Hodges, Sally E -- Reid, Jeffrey G -- Drummond, Jennifer -- Chang, Kyle -- Han, Yi -- Lewis, Lora R -- Dinh, Huyen -- Buhay, Christian J -- Beck, Timothy -- Timms, Lee -- Sam, Michelle -- Begley, Kimberly -- Brown, Andrew -- Pai, Deepa -- Panchal, Ami -- Buchner, Nicholas -- De Borja, Richard -- Denroche, Robert E -- Yung, Christina K -- Serra, Stefano -- Onetto, Nicole -- Mukhopadhyay, Debabrata -- Tsao, Ming-Sound -- Shaw, Patricia A -- Petersen, Gloria M -- Gallinger, Steven -- Hruban, Ralph H -- Maitra, Anirban -- Iacobuzio-Donahue, Christine A -- Schulick, Richard D -- Wolfgang, Christopher L -- Morgan, Richard A -- Lawlor, Rita T -- Capelli, Paola -- Corbo, Vincenzo -- Scardoni, Maria -- Tortora, Giampaolo -- Tempero, Margaret A -- Mann, Karen M -- Jenkins, Nancy A -- Perez-Mancera, Pedro A -- Adams, David J -- Largaespada, David A -- Wessels, Lodewyk F A -- Rust, Alistair G -- Stein, Lincoln D -- Tuveson, David A -- Copeland, Neal G -- Musgrove, Elizabeth A -- Scarpa, Aldo -- Eshleman, James R -- Hudson, Thomas J -- Sutherland, Robert L -- Wheeler, David A -- Pearson, John V -- McPherson, John D -- Gibbs, Richard A -- Grimmond, Sean M -- 13031/Cancer Research UK/United Kingdom -- 2P50CA101955/CA/NCI NIH HHS/ -- P01CA134292/CA/NCI NIH HHS/ -- P50 CA101955/CA/NCI NIH HHS/ -- P50 CA102701/CA/NCI NIH HHS/ -- P50CA062924/CA/NCI NIH HHS/ -- R01 CA097075/CA/NCI NIH HHS/ -- R01 CA97075/CA/NCI NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- Cancer Research UK/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2012 Nov 15;491(7424):399-405. doi: 10.1038/nature11547. Epub 2012 Oct 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst, Sydney, New South Wales 2010, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23103869" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Axons/*metabolism ; Carcinoma, Pancreatic Ductal/*genetics/*pathology ; Gene Dosage ; Gene Expression Regulation, Neoplastic ; Genome/*genetics ; Humans ; Kaplan-Meier Estimate ; Mice ; Mutation ; Pancreatic Neoplasms/*genetics/*pathology ; Proteins/genetics ; Signal Transduction
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2012-12-12
    Description: 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 〈 10(-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.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3623669/" 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/PMC3623669/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉van der Harst, Pim -- Zhang, Weihua -- Mateo Leach, Irene -- Rendon, Augusto -- Verweij, Niek -- Sehmi, Joban -- Paul, Dirk S -- Elling, Ulrich -- Allayee, Hooman -- Li, Xinzhong -- Radhakrishnan, Aparna -- Tan, Sian-Tsung -- Voss, Katrin -- Weichenberger, Christian X -- Albers, Cornelis A -- Al-Hussani, Abtehale -- Asselbergs, Folkert W -- Ciullo, Marina -- Danjou, Fabrice -- Dina, Christian -- Esko, Tonu -- Evans, David M -- Franke, Lude -- Gogele, Martin -- Hartiala, Jaana -- Hersch, Micha -- Holm, Hilma -- Hottenga, Jouke-Jan -- Kanoni, Stavroula -- Kleber, Marcus E -- Lagou, Vasiliki -- Langenberg, Claudia -- Lopez, Lorna M -- Lyytikainen, Leo-Pekka -- Melander, Olle -- Murgia, Federico -- Nolte, Ilja M -- O'Reilly, Paul F -- Padmanabhan, Sandosh -- Parsa, Afshin -- Pirastu, Nicola -- Porcu, Eleonora -- Portas, Laura -- Prokopenko, Inga -- Ried, Janina S -- Shin, So-Youn -- Tang, Clara S -- Teumer, Alexander -- Traglia, Michela -- Ulivi, Sheila -- Westra, Harm-Jan -- Yang, Jian -- Zhao, Jing Hua -- Anni, Franco -- Abdellaoui, Abdel -- Attwood, Antony -- Balkau, Beverley -- Bandinelli, Stefania -- Bastardot, Francois -- Benyamin, Beben -- Boehm, Bernhard O -- Cookson, William O -- Das, Debashish -- de Bakker, Paul I W -- de Boer, Rudolf A -- de Geus, Eco J C -- de Moor, Marleen H -- Dimitriou, Maria -- Domingues, Francisco S -- Doring, Angela -- Engstrom, Gunnar -- Eyjolfsson, Gudmundur Ingi -- Ferrucci, Luigi -- Fischer, Krista -- Galanello, Renzo -- Garner, Stephen F -- Genser, Bernd -- Gibson, Quince D -- Girotto, Giorgia -- Gudbjartsson, Daniel Fannar -- Harris, Sarah E -- Hartikainen, Anna-Liisa -- Hastie, Claire E -- Hedblad, Bo -- Illig, Thomas -- Jolley, Jennifer -- Kahonen, Mika -- Kema, Ido P -- Kemp, John P -- Liang, Liming -- Lloyd-Jones, Heather -- Loos, Ruth J F -- Meacham, Stuart -- Medland, Sarah E -- Meisinger, Christa -- Memari, Yasin -- Mihailov, Evelin -- Miller, Kathy -- Moffatt, Miriam F -- Nauck, Matthias -- Novatchkova, Maria -- Nutile, Teresa -- Olafsson, Isleifur -- Onundarson, Pall T -- Parracciani, Debora -- Penninx, Brenda W -- Perseu, Lucia -- Piga, Antonio -- Pistis, Giorgio -- Pouta, Anneli -- Puc, Ursula -- Raitakari, Olli -- Ring, Susan M -- Robino, Antonietta -- Ruggiero, Daniela -- Ruokonen, Aimo -- Saint-Pierre, Aude -- Sala, Cinzia -- Salumets, Andres -- Sambrook, Jennifer -- Schepers, Hein -- Schmidt, Carsten Oliver -- Sillje, Herman H W -- Sladek, Rob -- Smit, Johannes H -- Starr, John M -- Stephens, Jonathan -- Sulem, Patrick -- Tanaka, Toshiko -- Thorsteinsdottir, Unnur -- Tragante, Vinicius -- van Gilst, Wiek H -- van Pelt, L Joost -- van Veldhuisen, Dirk J -- Volker, Uwe -- Whitfield, John B -- Willemsen, Gonneke -- Winkelmann, Bernhard R -- Wirnsberger, Gerald -- Algra, Ale -- Cucca, Francesco -- d'Adamo, Adamo Pio -- Danesh, John -- Deary, Ian J -- Dominiczak, Anna F -- Elliott, Paul -- Fortina, Paolo -- Froguel, Philippe -- Gasparini, Paolo -- Greinacher, Andreas -- Hazen, Stanley L -- Jarvelin, Marjo-Riitta -- Khaw, Kay Tee -- Lehtimaki, Terho -- Maerz, Winfried -- Martin, Nicholas G -- Metspalu, Andres -- Mitchell, Braxton D -- Montgomery, Grant W -- Moore, Carmel -- Navis, Gerjan -- Pirastu, Mario -- Pramstaller, Peter P -- Ramirez-Solis, Ramiro -- Schadt, Eric -- Scott, James -- Shuldiner, Alan R -- Smith, George Davey -- Smith, J Gustav -- Snieder, Harold -- Sorice, Rossella -- Spector, Tim D -- Stefansson, Kari -- Stumvoll, Michael -- Tang, W H Wilson -- Toniolo, Daniela -- Tonjes, Anke -- Visscher, Peter M -- Vollenweider, Peter -- Wareham, Nicholas J -- Wolffenbuttel, Bruce H R -- Boomsma, Dorret I -- Beckmann, Jacques S -- Dedoussis, George V -- Deloukas, Panos -- Ferreira, Manuel A -- Sanna, Serena -- Uda, Manuela -- Hicks, Andrew A -- Penninger, Josef Martin -- Gieger, Christian -- Kooner, Jaspal S -- Ouwehand, Willem H -- Soranzo, Nicole -- Chambers, John C -- 092731/Wellcome Trust/United Kingdom -- 097117/Wellcome Trust/United Kingdom -- 14136/Cancer Research UK/United Kingdom -- CZB/4/505/Chief Scientist Office/United Kingdom -- ETM/55/Chief Scientist Office/United Kingdom -- G0600705/Medical Research Council/United Kingdom -- G0700704/Medical Research Council/United Kingdom -- G0801056/Medical Research Council/United Kingdom -- G1000143/Medical Research Council/United Kingdom -- G1002084/Medical Research Council/United Kingdom -- G9815508/Medical Research Council/United Kingdom -- HHSN268201100005C/HL/NHLBI NIH HHS/ -- HHSN268201100006C/HL/NHLBI NIH HHS/ -- HHSN268201100007C/HL/NHLBI NIH HHS/ -- HHSN268201100008C/HL/NHLBI NIH HHS/ -- HHSN268201100009C/HL/NHLBI NIH HHS/ -- HHSN268201100010C/HL/NHLBI NIH HHS/ -- HHSN268201100011C/HL/NHLBI NIH HHS/ -- HHSN268201100012C/HL/NHLBI NIH HHS/ -- HHSN271201100005C/DA/NIDA NIH HHS/ -- K12 RR023250/RR/NCRR NIH HHS/ -- MC_U106179471/Medical Research Council/United Kingdom -- MC_U106188470/Medical Research Council/United Kingdom -- N01AG12109/AG/NIA NIH HHS/ -- P01 HL076491/HL/NHLBI NIH HHS/ -- P01 HL098055/HL/NHLBI NIH HHS/ -- P20 HL113452/HL/NHLBI NIH HHS/ -- P30 DK072488/DK/NIDDK NIH HHS/ -- R01 AG018728/AG/NIA NIH HHS/ -- R01 CA165001/CA/NCI NIH HHS/ -- R01 GM053275/GM/NIGMS NIH HHS/ -- R01 HD042157/HD/NICHD NIH HHS/ -- R01 HL059367/HL/NHLBI NIH HHS/ -- R01 HL086694/HL/NHLBI NIH HHS/ -- R01 HL087641/HL/NHLBI NIH HHS/ -- R01 HL087679/HL/NHLBI NIH HHS/ -- R01 HL088119/HL/NHLBI NIH HHS/ -- R01 HL103866/HL/NHLBI NIH HHS/ -- R01 HL103931/HL/NHLBI NIH HHS/ -- R01 LM010098/LM/NLM NIH HHS/ -- R01 MH081802/MH/NIMH NIH HHS/ -- RG/09/012/28096/British Heart Foundation/United Kingdom -- RL1 MH083268/MH/NIMH NIH HHS/ -- U01 GM074518/GM/NIGMS NIH HHS/ -- U01 HG004402/HG/NHGRI NIH HHS/ -- U01 HL072515/HL/NHLBI NIH HHS/ -- U01 HL084756/HL/NHLBI NIH HHS/ -- U24 MH068457/MH/NIMH NIH HHS/ -- U54 RR020278/RR/NCRR NIH HHS/ -- UL1 RR025005/RR/NCRR NIH HHS/ -- UL1 TR000439/TR/NCATS NIH HHS/ -- England -- Nature. 2012 Dec 20;492(7429):369-75. doi: 10.1038/nature11677. Epub 2012 Dec 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cardiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands. p.van.der.harst@umcg.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23222517" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Cycle/genetics ; Cytokines/metabolism ; Drosophila melanogaster/genetics ; Erythrocytes/cytology/*metabolism ; Female ; Gene Expression Regulation/genetics ; *Genetic Loci ; *Genome-Wide Association Study ; Hematopoiesis/genetics ; Hemoglobins/genetics ; Humans ; Male ; Mice ; Organ Specificity ; *Phenotype ; Polymorphism, Single Nucleotide/genetics ; RNA Interference ; Signal Transduction/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2012-07-27
    Description: The rapid disruption of tropical forests probably imperils global biodiversity more than any other contemporary phenomenon. With deforestation advancing quickly, protected areas are increasingly becoming final refuges for threatened species and natural ecosystem processes. However, many protected areas in the tropics are themselves vulnerable to human encroachment and other environmental stresses. As pressures mount, it is vital to know whether existing reserves can sustain their biodiversity. A critical constraint in addressing this question has been that data describing a broad array of biodiversity groups have been unavailable for a sufficiently large and representative sample of reserves. Here we present a uniquely comprehensive data set on changes over the past 20 to 30 years in 31 functional groups of species and 21 potential drivers of environmental change, for 60 protected areas stratified across the world's major tropical regions. Our analysis reveals great variation in reserve 'health': about half of all reserves have been effective or performed passably, but the rest are experiencing an erosion of biodiversity that is often alarmingly widespread taxonomically and functionally. Habitat disruption, hunting and forest-product exploitation were the strongest predictors of declining reserve health. Crucially, environmental changes immediately outside reserves seemed nearly as important as those inside in determining their ecological fate, with changes inside reserves strongly mirroring those occurring around them. These findings suggest that tropical protected areas are often intimately linked ecologically to their surrounding habitats, and that a failure to stem broad-scale loss and degradation of such habitats could sharply increase the likelihood of serious biodiversity declines.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Laurance, William F -- Useche, D Carolina -- Rendeiro, Julio -- Kalka, Margareta -- Bradshaw, Corey J A -- Sloan, Sean P -- Laurance, Susan G -- Campbell, Mason -- Abernethy, Kate -- Alvarez, Patricia -- Arroyo-Rodriguez, Victor -- Ashton, Peter -- Benitez-Malvido, Julieta -- Blom, Allard -- Bobo, Kadiri S -- Cannon, Charles H -- Cao, Min -- Carroll, Richard -- Chapman, Colin -- Coates, Rosamond -- Cords, Marina -- Danielsen, Finn -- De Dijn, Bart -- Dinerstein, Eric -- Donnelly, Maureen A -- Edwards, David -- Edwards, Felicity -- Farwig, Nina -- Fashing, Peter -- Forget, Pierre-Michel -- Foster, Mercedes -- Gale, George -- Harris, David -- Harrison, Rhett -- Hart, John -- Karpanty, Sarah -- Kress, W John -- Krishnaswamy, Jagdish -- Logsdon, Willis -- Lovett, Jon -- Magnusson, William -- Maisels, Fiona -- Marshall, Andrew R -- McClearn, Deedra -- Mudappa, Divya -- Nielsen, Martin R -- Pearson, Richard -- Pitman, Nigel -- van der Ploeg, Jan -- Plumptre, Andrew -- Poulsen, John -- Quesada, Mauricio -- Rainey, Hugo -- Robinson, Douglas -- Roetgers, Christiane -- Rovero, Francesco -- Scatena, Frederick -- Schulze, Christian -- Sheil, Douglas -- Struhsaker, Thomas -- Terborgh, John -- Thomas, Duncan -- Timm, Robert -- Urbina-Cardona, J Nicolas -- Vasudevan, Karthikeyan -- Wright, S Joseph -- Arias-G, Juan Carlos -- Arroyo, Luzmila -- Ashton, Mark -- Auzel, Philippe -- Babaasa, Dennis -- Babweteera, Fred -- Baker, Patrick -- Banki, Olaf -- Bass, Margot -- Bila-Isia, Inogwabini -- Blake, Stephen -- Brockelman, Warren -- Brokaw, Nicholas -- Bruhl, Carsten A -- Bunyavejchewin, Sarayudh -- Chao, Jung-Tai -- Chave, Jerome -- Chellam, Ravi -- Clark, Connie J -- Clavijo, Jose -- Congdon, Robert -- Corlett, Richard -- Dattaraja, H S -- Dave, Chittaranjan -- Davies, Glyn -- Beisiegel, Beatriz de Mello -- da Silva, Rosa de Nazare Paes -- Di Fiore, Anthony -- Diesmos, Arvin -- Dirzo, Rodolfo -- Doran-Sheehy, Diane -- Eaton, Mitchell -- Emmons, Louise -- Estrada, Alejandro -- Ewango, Corneille -- Fedigan, Linda -- Feer, Francois -- Fruth, Barbara -- Willis, Jacalyn Giacalone -- Goodale, Uromi -- Goodman, Steven -- Guix, Juan C -- Guthiga, Paul -- Haber, William -- Hamer, Keith -- Herbinger, Ilka -- Hill, Jane -- Huang, Zhongliang -- Sun, I Fang -- Ickes, Kalan -- Itoh, Akira -- Ivanauskas, Natalia -- Jackes, Betsy -- Janovec, John -- Janzen, Daniel -- Jiangming, Mo -- Jin, Chen -- Jones, Trevor -- Justiniano, Hermes -- Kalko, Elisabeth -- Kasangaki, Aventino -- Killeen, Timothy -- King, Hen-biau -- Klop, Erik -- Knott, Cheryl -- Kone, Inza -- Kudavidanage, Enoka -- Ribeiro, Jose Lahoz da Silva -- Lattke, John -- Laval, Richard -- Lawton, Robert -- Leal, Miguel -- Leighton, Mark -- Lentino, Miguel -- Leonel, Cristiane -- Lindsell, Jeremy -- Ling-Ling, Lee -- Linsenmair, K Eduard -- Losos, Elizabeth -- Lugo, Ariel -- Lwanga, Jeremiah -- Mack, Andrew L -- Martins, Marlucia -- McGraw, W Scott -- McNab, Roan -- Montag, Luciano -- Thompson, Jo Myers -- Nabe-Nielsen, Jacob -- Nakagawa, Michiko -- Nepal, Sanjay -- Norconk, Marilyn -- Novotny, Vojtech -- O'Donnell, Sean -- Opiang, Muse -- Ouboter, Paul -- Parker, Kenneth -- Parthasarathy, N -- Pisciotta, Katia -- Prawiradilaga, Dewi -- Pringle, Catherine -- Rajathurai, Subaraj -- Reichard, Ulrich -- Reinartz, Gay -- Renton, Katherine -- Reynolds, Glen -- Reynolds, Vernon -- Riley, Erin -- Rodel, Mark-Oliver -- Rothman, Jessica -- Round, Philip -- Sakai, Shoko -- Sanaiotti, Tania -- Savini, Tommaso -- Schaab, Gertrud -- Seidensticker, John -- Siaka, Alhaji -- Silman, Miles R -- Smith, Thomas B -- de Almeida, Samuel Soares -- Sodhi, Navjot -- Stanford, Craig -- Stewart, Kristine -- Stokes, Emma -- Stoner, Kathryn E -- Sukumar, Raman -- Surbeck, Martin -- Tobler, Mathias -- Tscharntke, Teja -- Turkalo, Andrea -- Umapathy, Govindaswamy -- van Weerd, Merlijn -- Rivera, Jorge Vega -- Venkataraman, Meena -- Venn, Linda -- Verea, Carlos -- de Castilho, Carolina Volkmer -- Waltert, Matthias -- Wang, Benjamin -- Watts, David -- Weber, William -- West, Paige -- Whitacre, David -- Whitney, Ken -- Wilkie, David -- Williams, Stephen -- Wright, Debra D -- Wright, Patricia -- Xiankai, Lu -- Yonzon, Pralad -- Zamzani, Franky -- England -- Nature. 2012 Sep 13;489(7415):290-4. doi: 10.1038/nature11318.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Tropical Environmental and Sustainability Science and School of Marine and Tropical Biology, James Cook University, Cairns, Queensland 4878, Australia. bill.laurance@jcu.edu.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22832582" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/statistics & numerical data ; Animals ; *Biodiversity ; Conservation of Natural Resources/*statistics & numerical data ; Data Collection ; Ecology/statistics & numerical data ; Endangered Species/*statistics & numerical data ; Environmental Pollution/adverse effects/statistics & numerical data ; Fires/statistics & numerical data ; Forestry/statistics & numerical data ; Interviews as Topic ; Mining/statistics & numerical data ; Population Growth ; Rain ; Reproducibility of Results ; Research Personnel ; Surveys and Questionnaires ; Temperature ; Trees/*physiology ; *Tropical Climate
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2012-02-10
    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〉
    Keywords: Alleles ; Animals ; Centromere/genetics ; Chromosomes, Insect/genetics ; Drosophila melanogaster/*genetics ; *Genome-Wide Association Study ; *Genomics ; Genotype ; Phenotype ; Polymorphism, Single Nucleotide/genetics ; Quantitative Trait Loci/*genetics ; Selection, Genetic/genetics ; Starvation/genetics ; Telomere/genetics ; X Chromosome/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2012-09-21
    Description: The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Guofan -- Fang, Xiaodong -- Guo, Ximing -- Li, Li -- Luo, Ruibang -- Xu, Fei -- Yang, Pengcheng -- Zhang, Linlin -- Wang, Xiaotong -- Qi, Haigang -- Xiong, Zhiqiang -- Que, Huayong -- Xie, Yinlong -- Holland, Peter W H -- Paps, Jordi -- Zhu, Yabing -- Wu, Fucun -- Chen, Yuanxin -- Wang, Jiafeng -- Peng, Chunfang -- Meng, Jie -- Yang, Lan -- Liu, Jun -- Wen, Bo -- Zhang, Na -- Huang, Zhiyong -- Zhu, Qihui -- Feng, Yue -- Mount, Andrew -- Hedgecock, Dennis -- Xu, Zhe -- Liu, Yunjie -- Domazet-Loso, Tomislav -- Du, Yishuai -- Sun, Xiaoqing -- Zhang, Shoudu -- Liu, Binghang -- Cheng, Peizhou -- Jiang, Xuanting -- Li, Juan -- Fan, Dingding -- Wang, Wei -- Fu, Wenjing -- Wang, Tong -- Wang, Bo -- Zhang, Jibiao -- Peng, Zhiyu -- Li, Yingxiang -- Li, Na -- Wang, Jinpeng -- Chen, Maoshan -- He, Yan -- Tan, Fengji -- Song, Xiaorui -- Zheng, Qiumei -- Huang, Ronglian -- Yang, Hailong -- Du, Xuedi -- Chen, Li -- Yang, Mei -- Gaffney, Patrick M -- Wang, Shan -- Luo, Longhai -- She, Zhicai -- Ming, Yao -- Huang, Wen -- Zhang, Shu -- Huang, Baoyu -- Zhang, Yong -- Qu, Tao -- Ni, Peixiang -- Miao, Guoying -- Wang, Junyi -- Wang, Qiang -- Steinberg, Christian E W -- Wang, Haiyan -- Li, Ning -- Qian, Lumin -- Zhang, Guojie -- Li, Yingrui -- Yang, Huanming -- Liu, Xiao -- Wang, Jian -- Yin, Ye -- Wang, Jun -- 268513/European Research Council/International -- England -- Nature. 2012 Oct 4;490(7418):49-54. doi: 10.1038/nature11413. Epub 2012 Sep 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22992520" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/*genetics ; Animal Shells/chemistry/*growth & development ; Animals ; Apoptosis Regulatory Proteins/genetics ; Crassostrea/*genetics ; DNA Transposable Elements/genetics ; Evolution, Molecular ; Female ; Gene Expression Regulation, Developmental/genetics ; Genes, Homeobox/genetics ; Genome/*genetics ; Genomics ; HSP70 Heat-Shock Proteins/genetics ; Humans ; Larva/genetics/growth & development ; Mass Spectrometry ; Molecular Sequence Annotation ; Molecular Sequence Data ; Polymorphism, Genetic/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Sequence Analysis, DNA ; Stress, Physiological/genetics/*physiology ; Transcriptome/genetics
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2012-07-17
    Description: The Paisley Caves in Oregon record the oldest directly dated human remains (DNA) in the Western Hemisphere. More than 100 high-precision radiocarbon dates show that deposits containing artifacts and coprolites ranging in age from 12,450 to 2295 (14)C years ago are well stratified. Western Stemmed projectile points were recovered in deposits dated to 11,070 to 11,340 (14)C years ago, a time contemporaneous with or preceding the Clovis technology. There is no evidence of diagnostic Clovis technology at the site. These two distinct technologies were parallel developments, not the product of a unilinear technological evolution. "Blind testing" analysis of coprolites by an independent laboratory confirms the presence of human DNA in specimens of pre-Clovis age. The colonization of the Americas involved multiple technologically divergent, and possibly genetically divergent, founding groups.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jenkins, Dennis L -- Davis, Loren G -- Stafford, Thomas W Jr -- Campos, Paula F -- Hockett, Bryan -- Jones, George T -- Cummings, Linda Scott -- Yost, Chad -- Connolly, Thomas J -- Yohe, Robert M 2nd -- Gibbons, Summer C -- Raghavan, Maanasa -- Rasmussen, Morten -- Paijmans, Johanna L A -- Hofreiter, Michael -- Kemp, Brian M -- Barta, Jodi Lynn -- Monroe, Cara -- Gilbert, M Thomas P -- Willerslev, Eske -- New York, N.Y. -- Science. 2012 Jul 13;337(6091):223-8. doi: 10.1126/science.1218443.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Museum of Natural and Cultural History, University of Oregon, Eugene, OR 97403, USA. djenkins@uoregon.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22798611" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Archaeology ; *Caves ; DNA/analysis ; Emigration and Immigration/history ; Feces ; *Fossils ; History, Ancient ; Humans ; Molecular Sequence Data ; North America ; Oregon ; Population Dynamics ; Radiometric Dating ; Rodentia ; Technology/history ; Time
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2012-12-15
    Description: Most eukaryotic organisms are arthropods. Yet, their diversity in rich terrestrial ecosystems is still unknown. Here we produce tangible estimates of the total species richness of arthropods in a tropical rainforest. Using a comprehensive range of structured protocols, we sampled the phylogenetic breadth of arthropod taxa from the soil to the forest canopy in the San Lorenzo forest, Panama. We collected 6144 arthropod species from 0.48 hectare and extrapolated total species richness to larger areas on the basis of competing models. The whole 6000-hectare forest reserve most likely sustains 25,000 arthropod species. Notably, just 1 hectare of rainforest yields 〉60% of the arthropod biodiversity held in the wider landscape. Models based on plant diversity fitted the accumulated species richness of both herbivore and nonherbivore taxa exceptionally well. This lends credence to global estimates of arthropod biodiversity developed from plant models.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Basset, Yves -- Cizek, Lukas -- Cuenoud, Philippe -- Didham, Raphael K -- Guilhaumon, Francois -- Missa, Olivier -- Novotny, Vojtech -- Odegaard, Frode -- Roslin, Tomas -- Schmidl, Jurgen -- Tishechkin, Alexey K -- Winchester, Neville N -- Roubik, David W -- Aberlenc, Henri-Pierre -- Bail, Johannes -- Barrios, Hector -- Bridle, Jon R -- Castano-Meneses, Gabriela -- Corbara, Bruno -- Curletti, Gianfranco -- Duarte da Rocha, Wesley -- De Bakker, Domir -- Delabie, Jacques H C -- Dejean, Alain -- Fagan, Laura L -- Floren, Andreas -- Kitching, Roger L -- Medianero, Enrique -- Miller, Scott E -- Gama de Oliveira, Evandro -- Orivel, Jerome -- Pollet, Marc -- Rapp, Mathieu -- Ribeiro, Servio P -- Roisin, Yves -- Schmidt, Jesper B -- Sorensen, Line -- Leponce, Maurice -- New York, N.Y. -- Science. 2012 Dec 14;338(6113):1481-4. doi: 10.1126/science.1226727.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Smithsonian Tropical Research Institute, Panama City, Republic of Panama. bassety@si.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23239740" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arthropods/*anatomy & histology/*classification ; *Biodiversity ; Herbivory ; Rain ; Trees ; Tropical Climate
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2012-09-22
    Description: Neuroanatomically precise, genome-wide maps of transcript distributions are critical resources to complement genomic sequence data and to correlate functional and genetic brain architecture. Here we describe the generation and analysis of a transcriptional atlas of the adult human brain, comprising extensive histological analysis and comprehensive microarray profiling of approximately 900 neuroanatomically precise subdivisions in two individuals. Transcriptional regulation varies enormously by anatomical location, with different regions and their constituent cell types displaying robust molecular signatures that are highly conserved between individuals. Analysis of differential gene expression and gene co-expression relationships demonstrates that brain-wide variation strongly reflects the distributions of major cell classes such as neurons, oligodendrocytes, astrocytes and microglia. Local neighbourhood relationships between fine anatomical subdivisions are associated with discrete neuronal subtypes and genes involved with synaptic transmission. The neocortex displays a relatively homogeneous transcriptional pattern, but with distinct features associated selectively with primary sensorimotor cortices and with enriched frontal lobe expression. Notably, the spatial topography of the neocortex is strongly reflected in its molecular topography-the closer two cortical regions, the more similar their transcriptomes. This freely accessible online data resource forms a high-resolution transcriptional baseline for neurogenetic studies of normal and abnormal human brain function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4243026/" 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/PMC4243026/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hawrylycz, Michael J -- Lein, Ed S -- Guillozet-Bongaarts, Angela L -- Shen, Elaine H -- Ng, Lydia -- Miller, Jeremy A -- van de Lagemaat, Louie N -- Smith, Kimberly A -- Ebbert, Amanda -- Riley, Zackery L -- Abajian, Chris -- Beckmann, Christian F -- Bernard, Amy -- Bertagnolli, Darren -- Boe, Andrew F -- Cartagena, Preston M -- Chakravarty, M Mallar -- Chapin, Mike -- Chong, Jimmy -- Dalley, Rachel A -- Daly, Barry David -- Dang, Chinh -- Datta, Suvro -- Dee, Nick -- Dolbeare, Tim A -- Faber, Vance -- Feng, David -- Fowler, David R -- Goldy, Jeff -- Gregor, Benjamin W -- Haradon, Zeb -- Haynor, David R -- Hohmann, John G -- Horvath, Steve -- Howard, Robert E -- Jeromin, Andreas -- Jochim, Jayson M -- Kinnunen, Marty -- Lau, Christopher -- Lazarz, Evan T -- Lee, Changkyu -- Lemon, Tracy A -- Li, Ling -- Li, Yang -- Morris, John A -- Overly, Caroline C -- Parker, Patrick D -- Parry, Sheana E -- Reding, Melissa -- Royall, Joshua J -- Schulkin, Jay -- Sequeira, Pedro Adolfo -- Slaughterbeck, Clifford R -- Smith, Simon C -- Sodt, Andy J -- Sunkin, Susan M -- Swanson, Beryl E -- Vawter, Marquis P -- Williams, Derric -- Wohnoutka, Paul -- Zielke, H Ronald -- Geschwind, Daniel H -- Hof, Patrick R -- Smith, Stephen M -- Koch, Christof -- Grant, Seth G N -- Jones, Allan R -- 066717/Wellcome Trust/United Kingdom -- 077155/Wellcome Trust/United Kingdom -- 1C76HF15069-01-00/PHS HHS/ -- 1C76HF19619-01-00/PHS HHS/ -- G0700399/Medical Research Council/United Kingdom -- G0802238/Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2012 Sep 20;489(7416):391-9. doi: 10.1038/nature11405.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Allen Institute for Brain Science, Seattle, Washington 98103, USA. mikeh@alleninstitute.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22996553" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; *Anatomy, Artistic ; Animals ; *Atlases as Topic ; Brain/*anatomy & histology/cytology/*metabolism ; Calbindins ; Databases, Genetic ; Dopamine/metabolism ; *Gene Expression Profiling ; Health ; Hippocampus/cytology/metabolism ; Humans ; In Situ Hybridization ; Internet ; Macaca mulatta/anatomy & histology/genetics ; Male ; Mice ; Neocortex/anatomy & histology/cytology/metabolism ; Oligonucleotide Array Sequence Analysis ; Post-Synaptic Density/genetics ; RNA, Messenger/analysis/genetics ; S100 Calcium Binding Protein G/genetics ; Species Specificity ; Transcriptome/*genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 10
    Publication Date: 2012-08-31
    Description: Locomotion in mammals relies on a central pattern-generating circuitry of spinal interneurons established during development that coordinates limb movement. These networks produce left-right alternation of limbs as well as coordinated activation of flexor and extensor muscles. Here we show that a premature stop codon in the DMRT3 gene has a major effect on the pattern of locomotion in horses. The mutation is permissive for the ability to perform alternate gaits and has a favourable effect on harness racing performance. Examination of wild-type and Dmrt3-null mice demonstrates that Dmrt3 is expressed in the dI6 subdivision of spinal cord neurons, takes part in neuronal specification within this subdivision, and is critical for the normal development of a coordinated locomotor network controlling limb movements. Our discovery positions Dmrt3 in a pivotal role for configuring the spinal circuits controlling stride in vertebrates. The DMRT3 mutation has had a major effect on the diversification of the domestic horse, as the altered gait characteristics of a number of breeds apparently require this mutation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3523687/" 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/PMC3523687/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Andersson, Lisa S -- Larhammar, Martin -- Memic, Fatima -- Wootz, Hanna -- Schwochow, Doreen -- Rubin, Carl-Johan -- Patra, Kalicharan -- Arnason, Thorvaldur -- Wellbring, Lisbeth -- Hjalm, Goran -- Imsland, Freyja -- Petersen, Jessica L -- McCue, Molly E -- Mickelson, James R -- Cothran, Gus -- Ahituv, Nadav -- Roepstorff, Lars -- Mikko, Sofia -- Vallstedt, Anna -- Lindgren, Gabriella -- Andersson, Leif -- Kullander, Klas -- R01 HD059862/HD/NICHD NIH HHS/ -- R01HD059862/HD/NICHD NIH HHS/ -- England -- Nature. 2012 Aug 30;488(7413):642-6. doi: 10.1038/nature11399.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75124 Uppsala, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22932389" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Codon, Nonsense/genetics ; Gait/*genetics/physiology ; Gene Expression Profiling ; Gene Frequency ; Horses/classification/*genetics/*physiology ; Iceland ; Mice ; Molecular Sequence Data ; Mutation/*genetics ; Neural Pathways/physiology ; Psychomotor Performance/physiology ; Spinal Cord/cytology/*physiology ; Transcription Factors/deficiency/*genetics/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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