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  • Animals  (380)
  • Humans  (311)
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  • 2010-2014  (704)
  • 1995-1999
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  • 11
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    Whole-genome analysis informs breast cancer response to aromatase inhibition (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-06-23
    Description: To correlate the variable clinical features of oestrogen-receptor-positive breast cancer with somatic alterations, we studied pretreatment tumour biopsies accrued from patients in two studies of neoadjuvant aromatase inhibitor therapy by massively parallel sequencing and analysis. Eighteen significantly mutated genes were identified, including five genes (RUNX1, CBFB, MYH9, MLL3 and SF3B1) previously linked to haematopoietic disorders. Mutant MAP3K1 was associated with luminal A status, low-grade histology and low proliferation rates, whereas mutant TP53 was associated with the opposite pattern. Moreover, mutant GATA3 correlated with suppression of proliferation upon aromatase inhibitor treatment. Pathway analysis demonstrated that mutations in MAP2K4, a MAP3K1 substrate, produced similar perturbations as MAP3K1 loss. Distinct phenotypes in oestrogen-receptor-positive breast cancer are associated with specific patterns of somatic mutations that map into cellular pathways linked to tumour biology, but most recurrent mutations are relatively infrequent. Prospective clinical trials based on these findings will require comprehensive genome sequencing.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3383766/" 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/PMC3383766/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ellis, Matthew J -- Ding, Li -- Shen, Dong -- Luo, Jingqin -- Suman, Vera J -- Wallis, John W -- Van Tine, Brian A -- Hoog, Jeremy -- Goiffon, Reece J -- Goldstein, Theodore C -- Ng, Sam -- Lin, Li -- Crowder, Robert -- Snider, Jacqueline -- Ballman, Karla -- Weber, Jason -- Chen, Ken -- Koboldt, Daniel C -- Kandoth, Cyriac -- Schierding, William S -- McMichael, Joshua F -- Miller, Christopher A -- Lu, Charles -- Harris, Christopher C -- McLellan, Michael D -- Wendl, Michael C -- DeSchryver, Katherine -- Allred, D Craig -- Esserman, Laura -- Unzeitig, Gary -- Margenthaler, Julie -- Babiera, G V -- Marcom, P Kelly -- Guenther, J M -- Leitch, Marilyn -- Hunt, Kelly -- Olson, John -- Tao, Yu -- Maher, Christopher A -- Fulton, Lucinda L -- Fulton, Robert S -- Harrison, Michelle -- Oberkfell, Ben -- Du, Feiyu -- Demeter, Ryan -- Vickery, Tammi L -- Elhammali, Adnan -- Piwnica-Worms, Helen -- McDonald, Sandra -- Watson, Mark -- Dooling, David J -- Ota, David -- Chang, Li-Wei -- Bose, Ron -- Ley, Timothy J -- Piwnica-Worms, David -- Stuart, Joshua M -- Wilson, Richard K -- Mardis, Elaine R -- 3P50 CA68438/CA/NCI NIH HHS/ -- P30 CA091842/CA/NCI NIH HHS/ -- P30 CA091842-01/CA/NCI NIH HHS/ -- P50 CA068438/CA/NCI NIH HHS/ -- P50 CA068438-05/CA/NCI NIH HHS/ -- P50 CA094056/CA/NCI NIH HHS/ -- P50 CA094056-10/CA/NCI NIH HHS/ -- P50 CA94056/CA/NCI NIH HHS/ -- R01 CA095614/CA/NCI NIH HHS/ -- R01 CA095614-01A1/CA/NCI NIH HHS/ -- U01 CA114722/CA/NCI NIH HHS/ -- U01 CA114722-01/CA/NCI NIH HHS/ -- U10 CA076001/CA/NCI NIH HHS/ -- U10 CA076001-13/CA/NCI NIH HHS/ -- U54 HG003079/HG/NHGRI NIH HHS/ -- U54 HG003079-04/HG/NHGRI NIH HHS/ -- U54HG003079/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Jun 10;486(7403):353-60. doi: 10.1038/nature11143.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Internal Medicine, Division of Oncology, Washington University, St Louis, Missouri 63110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22722193" target="_blank"〉PubMed〈/a〉
    Keywords: Androstadienes/pharmacology/therapeutic use ; Antineoplastic Agents/pharmacology/therapeutic use ; Aromatase/*metabolism ; Aromatase Inhibitors/*therapeutic use ; Breast Neoplasms/*drug therapy/*genetics/metabolism/pathology ; DNA Repair ; Exome/genetics ; Exons/genetics ; Female ; Genetic Variation/genetics ; Genome, Human/*genetics ; Humans ; MAP Kinase Kinase 4/genetics ; MAP Kinase Kinase Kinase 1/genetics ; Mutation/genetics ; Nitriles/pharmacology/therapeutic use ; Receptors, Estrogen/metabolism ; Treatment Outcome ; Triazoles/pharmacology/therapeutic use
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 12
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    The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-03-31
    Description: The systematic translation of cancer genomic data into knowledge of tumour biology and therapeutic possibilities remains challenging. Such efforts should be greatly aided by robust preclinical model systems that reflect the genomic diversity of human cancers and for which detailed genetic and pharmacological annotation is available. Here we describe the Cancer Cell Line Encyclopedia (CCLE): a compilation of gene expression, chromosomal copy number and massively parallel sequencing data from 947 human cancer cell lines. When coupled with pharmacological profiles for 24 anticancer drugs across 479 of the cell lines, this collection allowed identification of genetic, lineage, and gene-expression-based predictors of drug sensitivity. In addition to known predictors, we found that plasma cell lineage correlated with sensitivity to IGF1 receptor inhibitors; AHR expression was associated with MEK inhibitor efficacy in NRAS-mutant lines; and SLFN11 expression predicted sensitivity to topoisomerase inhibitors. Together, our results indicate that large, annotated cell-line collections may help to enable preclinical stratification schemata for anticancer agents. The generation of genetic predictions of drug response in the preclinical setting and their incorporation into cancer clinical trial design could speed the emergence of 'personalized' therapeutic regimens.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3320027/" 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/PMC3320027/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barretina, Jordi -- Caponigro, Giordano -- Stransky, Nicolas -- Venkatesan, Kavitha -- Margolin, Adam A -- Kim, Sungjoon -- Wilson, Christopher J -- Lehar, Joseph -- Kryukov, Gregory V -- Sonkin, Dmitriy -- Reddy, Anupama -- Liu, Manway -- Murray, Lauren -- Berger, Michael F -- Monahan, John E -- Morais, Paula -- Meltzer, Jodi -- Korejwa, Adam -- Jane-Valbuena, Judit -- Mapa, Felipa A -- Thibault, Joseph -- Bric-Furlong, Eva -- Raman, Pichai -- Shipway, Aaron -- Engels, Ingo H -- Cheng, Jill -- Yu, Guoying K -- Yu, Jianjun -- Aspesi, Peter Jr -- de Silva, Melanie -- Jagtap, Kalpana -- Jones, Michael D -- Wang, Li -- Hatton, Charles -- Palescandolo, Emanuele -- Gupta, Supriya -- Mahan, Scott -- Sougnez, Carrie -- Onofrio, Robert C -- Liefeld, Ted -- MacConaill, Laura -- Winckler, Wendy -- Reich, Michael -- Li, Nanxin -- Mesirov, Jill P -- Gabriel, Stacey B -- Getz, Gad -- Ardlie, Kristin -- Chan, Vivien -- Myer, Vic E -- Weber, Barbara L -- Porter, Jeff -- Warmuth, Markus -- Finan, Peter -- Harris, Jennifer L -- Meyerson, Matthew -- Golub, Todd R -- Morrissey, Michael P -- Sellers, William R -- Schlegel, Robert -- Garraway, Levi A -- DP2 OD002750/OD/NIH HHS/ -- DP2 OD002750-01/OD/NIH HHS/ -- R33 CA126674/CA/NCI NIH HHS/ -- R33 CA126674-04/CA/NCI NIH HHS/ -- R33 CA155554/CA/NCI NIH HHS/ -- R33 CA155554-02/CA/NCI NIH HHS/ -- England -- Nature. 2012 Mar 28;483(7391):603-7. doi: 10.1038/nature11003.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22460905" target="_blank"〉PubMed〈/a〉
    Keywords: Antineoplastic Agents/pharmacology ; Cell Line, Tumor ; Cell Lineage ; Chromosomes, Human/genetics ; Clinical Trials as Topic/methods ; *Databases, Factual ; Drug Screening Assays, Antitumor/*methods ; *Encyclopedias as Topic ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Genes, ras/genetics ; Genome, Human/genetics ; Genomics ; Humans ; Mitogen-Activated Protein Kinase Kinases/antagonists & inhibitors/metabolism ; *Models, Biological ; Neoplasms/*drug therapy/genetics/metabolism/*pathology ; Pharmacogenetics ; Plasma Cells/cytology/drug effects/metabolism ; Precision Medicine/methods ; Receptor, IGF Type 1/antagonists & inhibitors/metabolism ; Receptors, Aryl Hydrocarbon/genetics/metabolism ; Sequence Analysis, DNA ; Topoisomerase Inhibitors/pharmacology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 13
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    Reconstructing Native American population history (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-07-18
    Description: The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved. One contentious issue is whether the settlement occurred by means of a single migration or multiple streams of migration from Siberia. The pattern of dispersals within the Americas is also poorly understood. To address these questions at a higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. Here we show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call 'First American'. However, speakers of Eskimo-Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan speakers on both sides of the Panama isthmus, who have ancestry from both North and South America.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3615710/" 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/PMC3615710/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reich, David -- Patterson, Nick -- Campbell, Desmond -- Tandon, Arti -- Mazieres, Stephane -- Ray, Nicolas -- Parra, Maria V -- Rojas, Winston -- Duque, Constanza -- Mesa, Natalia -- Garcia, Luis F -- Triana, Omar -- Blair, Silvia -- Maestre, Amanda -- Dib, Juan C -- Bravi, Claudio M -- Bailliet, Graciela -- Corach, Daniel -- Hunemeier, Tabita -- Bortolini, Maria Catira -- Salzano, Francisco M -- Petzl-Erler, Maria Luiza -- Acuna-Alonzo, Victor -- Aguilar-Salinas, Carlos -- Canizales-Quinteros, Samuel -- Tusie-Luna, Teresa -- Riba, Laura -- Rodriguez-Cruz, Maricela -- Lopez-Alarcon, Mardia -- Coral-Vazquez, Ramon -- Canto-Cetina, Thelma -- Silva-Zolezzi, Irma -- Fernandez-Lopez, Juan Carlos -- Contreras, Alejandra V -- Jimenez-Sanchez, Gerardo -- Gomez-Vazquez, Maria Jose -- Molina, Julio -- Carracedo, Angel -- Salas, Antonio -- Gallo, Carla -- Poletti, Giovanni -- Witonsky, David B -- Alkorta-Aranburu, Gorka -- Sukernik, Rem I -- Osipova, Ludmila -- Fedorova, Sardana A -- Vasquez, Rene -- Villena, Mercedes -- Moreau, Claudia -- Barrantes, Ramiro -- Pauls, David -- Excoffier, Laurent -- Bedoya, Gabriel -- Rothhammer, Francisco -- Dugoujon, Jean-Michel -- Larrouy, Georges -- Klitz, William -- Labuda, Damian -- Kidd, Judith -- Kidd, Kenneth -- Di Rienzo, Anna -- Freimer, Nelson B -- Price, Alkes L -- Ruiz-Linares, Andres -- BB/1021213/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- GM057672/GM/NIGMS NIH HHS/ -- GM079558/GM/NIGMS NIH HHS/ -- GM079558-S1/GM/NIGMS NIH HHS/ -- HG006399/HG/NHGRI NIH HHS/ -- MH075007/MH/NIMH NIH HHS/ -- NS037484/NS/NINDS NIH HHS/ -- NS043538/NS/NINDS NIH HHS/ -- R01 GM079558/GM/NIGMS NIH HHS/ -- R01 GM100233/GM/NIGMS NIH HHS/ -- R01 HG006399/HG/NHGRI NIH HHS/ -- R21 DK073818/DK/NIDDK NIH HHS/ -- Canadian Institutes of Health Research/Canada -- England -- Nature. 2012 Aug 16;488(7411):370-4. doi: 10.1038/nature11258.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. reich@genetics.med.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22801491" target="_blank"〉PubMed〈/a〉
    Keywords: Americas ; Asia ; Cluster Analysis ; Emigration and Immigration/*history/statistics & numerical data ; Gene Flow ; Genetics, Population ; History, Ancient ; Humans ; Indians, North American/*genetics/*history ; Models, Genetic ; *Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Siberia
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 14
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    The oyster genome reveals stress adaptation and complexity of shell formation (2012)
    Nature Publishing Group (NPG)
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    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
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 15
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    Clovis age Western Stemmed projectile points and human coprolites at the Paisley Caves (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    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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  • 16
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    Arthropod diversity in a tropical forest (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    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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  • 17
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    An anatomically comprehensive atlas of the adult human brain transcriptome (2012)
    Nature Publishing Group (NPG)
    Details
    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
    Published by Nature Publishing Group (NPG)
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  • 18
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    Melanoma genome sequencing reveals frequent PREX2 mutations (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-05-25
    Description: Melanoma is notable for its metastatic propensity, lethality in the advanced setting and association with ultraviolet exposure early in life. To obtain a comprehensive genomic view of melanoma in humans, we sequenced the genomes of 25 metastatic melanomas and matched germline DNA. A wide range of point mutation rates was observed: lowest in melanomas whose primaries arose on non-ultraviolet-exposed hairless skin of the extremities (3 and 14 per megabase (Mb) of genome), intermediate in those originating from hair-bearing skin of the trunk (5-55 per Mb), and highest in a patient with a documented history of chronic sun exposure (111 per Mb). Analysis of whole-genome sequence data identified PREX2 (phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2)--a PTEN-interacting protein and negative regulator of PTEN in breast cancer--as a significantly mutated gene with a mutation frequency of approximately 14% in an independent extension cohort of 107 human melanomas. PREX2 mutations are biologically relevant, as ectopic expression of mutant PREX2 accelerated tumour formation of immortalized human melanocytes in vivo. Thus, whole-genome sequencing of human melanoma tumours revealed genomic evidence of ultraviolet pathogenesis and discovered a new recurrently mutated gene in melanoma.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367798/" 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/PMC3367798/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berger, Michael F -- Hodis, Eran -- Heffernan, Timothy P -- Deribe, Yonathan Lissanu -- Lawrence, Michael S -- Protopopov, Alexei -- Ivanova, Elena -- Watson, Ian R -- Nickerson, Elizabeth -- Ghosh, Papia -- Zhang, Hailei -- Zeid, Rhamy -- Ren, Xiaojia -- Cibulskis, Kristian -- Sivachenko, Andrey Y -- Wagle, Nikhil -- Sucker, Antje -- Sougnez, Carrie -- Onofrio, Robert -- Ambrogio, Lauren -- Auclair, Daniel -- Fennell, Timothy -- Carter, Scott L -- Drier, Yotam -- Stojanov, Petar -- Singer, Meredith A -- Voet, Douglas -- Jing, Rui -- Saksena, Gordon -- Barretina, Jordi -- Ramos, Alex H -- Pugh, Trevor J -- Stransky, Nicolas -- Parkin, Melissa -- Winckler, Wendy -- Mahan, Scott -- Ardlie, Kristin -- Baldwin, Jennifer -- Wargo, Jennifer -- Schadendorf, Dirk -- Meyerson, Matthew -- Gabriel, Stacey B -- Golub, Todd R -- Wagner, Stephan N -- Lander, Eric S -- Getz, Gad -- Chin, Lynda -- Garraway, Levi A -- DP2 OD002750/OD/NIH HHS/ -- DP2 OD002750-01/OD/NIH HHS/ -- R33 CA126674/CA/NCI NIH HHS/ -- R33 CA126674-03/CA/NCI NIH HHS/ -- R33 CA126674-04/CA/NCI NIH HHS/ -- R33 CA155554/CA/NCI NIH HHS/ -- R33 CA155554-01/CA/NCI NIH HHS/ -- T32 CA009172/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 May 9;485(7399):502-6. doi: 10.1038/nature11071.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22622578" target="_blank"〉PubMed〈/a〉
    Keywords: Chromosome Breakpoints/radiation effects ; DNA Damage ; DNA Mutational Analysis ; Gene Expression Regulation, Neoplastic ; Genome, Human/*genetics ; Guanine Nucleotide Exchange Factors/*genetics/metabolism ; Humans ; Melanocytes/metabolism/pathology ; Melanoma/*genetics/pathology ; Mutagenesis/radiation effects ; Mutation/*genetics/radiation effects ; Oncogenes/genetics ; Sunlight/*adverse effects ; Ultraviolet Rays/adverse effects
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 19
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    Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice (2012)
    Nature Publishing Group (NPG)
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    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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    The landscape of cancer genes and mutational processes in breast cancer (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-06-23
    Description: All cancers carry somatic mutations in their genomes. A subset, known as driver mutations, confer clonal selective advantage on cancer cells and are causally implicated in oncogenesis, and the remainder are passenger mutations. The driver mutations and mutational processes operative in breast cancer have not yet been comprehensively explored. Here we examine the genomes of 100 tumours for somatic copy number changes and mutations in the coding exons of protein-coding genes. The number of somatic mutations varied markedly between individual tumours. We found strong correlations between mutation number, age at which cancer was diagnosed and cancer histological grade, and observed multiple mutational signatures, including one present in about ten per cent of tumours characterized by numerous mutations of cytosine at TpC dinucleotides. Driver mutations were identified in several new cancer genes including AKT2, ARID1B, CASP8, CDKN1B, MAP3K1, MAP3K13, NCOR1, SMARCD1 and TBX3. Among the 100 tumours, we found driver mutations in at least 40 cancer genes and 73 different combinations of mutated cancer genes. The results highlight the substantial genetic diversity underlying this common disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3428862/" 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/PMC3428862/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stephens, Philip J -- Tarpey, Patrick S -- Davies, Helen -- Van Loo, Peter -- Greenman, Chris -- Wedge, David C -- Nik-Zainal, Serena -- Martin, Sancha -- Varela, Ignacio -- Bignell, Graham R -- Yates, Lucy R -- Papaemmanuil, Elli -- Beare, David -- Butler, Adam -- Cheverton, Angela -- Gamble, John -- Hinton, Jonathan -- Jia, Mingming -- Jayakumar, Alagu -- Jones, David -- Latimer, Calli -- Lau, King Wai -- McLaren, Stuart -- McBride, David J -- Menzies, Andrew -- Mudie, Laura -- Raine, Keiran -- Rad, Roland -- Chapman, Michael Spencer -- Teague, Jon -- Easton, Douglas -- Langerod, Anita -- Oslo Breast Cancer Consortium (OSBREAC) -- Lee, Ming Ta Michael -- Shen, Chen-Yang -- Tee, Benita Tan Kiat -- Huimin, Bernice Wong -- Broeks, Annegien -- Vargas, Ana Cristina -- Turashvili, Gulisa -- Martens, John -- Fatima, Aquila -- Miron, Penelope -- Chin, Suet-Feung -- Thomas, Gilles -- Boyault, Sandrine -- Mariani, Odette -- Lakhani, Sunil R -- van de Vijver, Marc -- van 't Veer, Laura -- Foekens, John -- Desmedt, Christine -- Sotiriou, Christos -- Tutt, Andrew -- Caldas, Carlos -- Reis-Filho, Jorge S -- Aparicio, Samuel A J R -- Salomon, Anne Vincent -- Borresen-Dale, Anne-Lise -- Richardson, Andrea L -- Campbell, Peter J -- Futreal, P Andrew -- Stratton, Michael R -- 077012/Z/05/Z/Wellcome Trust/United Kingdom -- 088340/Wellcome Trust/United Kingdom -- 093867/Wellcome Trust/United Kingdom -- 10118/Cancer Research UK/United Kingdom -- CA089393/CA/NCI NIH HHS/ -- P30 CA016672/CA/NCI NIH HHS/ -- WT088340MA/Wellcome Trust/United Kingdom -- Cancer Research UK/United Kingdom -- Chief Scientist Office/United Kingdom -- Department of Health/United Kingdom -- England -- Nature. 2012 May 16;486(7403):400-4. doi: 10.1038/nature11017.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22722201" target="_blank"〉PubMed〈/a〉
    Keywords: Age Factors ; Breast Neoplasms/classification/*genetics/pathology ; Cell Transformation, Neoplastic/*genetics ; Cytosine/metabolism ; DNA Mutational Analysis ; Female ; Humans ; JNK Mitogen-Activated Protein Kinases/metabolism ; Mutagenesis/*genetics ; Mutation/*genetics ; Neoplasm Grading ; Oncogenes/*genetics ; Reproducibility of Results ; Signal Transduction/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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