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  • Sequence Analysis, DNA  (6)
  • Base Sequence  (5)
  • American Association for the Advancement of Science (AAAS)  (9)
  • Wiley
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  • American Association for the Advancement of Science (AAAS)  (9)
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  • 1
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    The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-12-14
    Description: The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains approximately 16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dehal, Paramvir -- Satou, Yutaka -- Campbell, Robert K -- Chapman, Jarrod -- Degnan, Bernard -- De Tomaso, Anthony -- Davidson, Brad -- Di Gregorio, Anna -- Gelpke, Maarten -- Goodstein, David M -- Harafuji, Naoe -- Hastings, Kenneth E M -- Ho, Isaac -- Hotta, Kohji -- Huang, Wayne -- Kawashima, Takeshi -- Lemaire, Patrick -- Martinez, Diego -- Meinertzhagen, Ian A -- Necula, Simona -- Nonaka, Masaru -- Putnam, Nik -- Rash, Sam -- Saiga, Hidetoshi -- Satake, Masanobu -- Terry, Astrid -- Yamada, Lixy -- Wang, Hong-Gang -- Awazu, Satoko -- Azumi, Kaoru -- Boore, Jeffrey -- Branno, Margherita -- Chin-Bow, Stephen -- DeSantis, Rosaria -- Doyle, Sharon -- Francino, Pilar -- Keys, David N -- Haga, Shinobu -- Hayashi, Hiroko -- Hino, Kyosuke -- Imai, Kaoru S -- Inaba, Kazuo -- Kano, Shungo -- Kobayashi, Kenji -- Kobayashi, Mari -- Lee, Byung-In -- Makabe, Kazuhiro W -- Manohar, Chitra -- Matassi, Giorgio -- Medina, Monica -- Mochizuki, Yasuaki -- Mount, Steve -- Morishita, Tomomi -- Miura, Sachiko -- Nakayama, Akie -- Nishizaka, Satoko -- Nomoto, Hisayo -- Ohta, Fumiko -- Oishi, Kazuko -- Rigoutsos, Isidore -- Sano, Masako -- Sasaki, Akane -- Sasakura, Yasunori -- Shoguchi, Eiichi -- Shin-i, Tadasu -- Spagnuolo, Antoinetta -- Stainier, Didier -- Suzuki, Miho M -- Tassy, Olivier -- Takatori, Naohito -- Tokuoka, Miki -- Yagi, Kasumi -- Yoshizaki, Fumiko -- Wada, Shuichi -- Zhang, Cindy -- Hyatt, P Douglas -- Larimer, Frank -- Detter, Chris -- Doggett, Norman -- Glavina, Tijana -- Hawkins, Trevor -- Richardson, Paul -- Lucas, Susan -- Kohara, Yuji -- Levine, Michael -- Satoh, Nori -- Rokhsar, Daniel S -- HD-37105/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2002 Dec 13;298(5601):2157-67.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12481130" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Apoptosis ; Base Sequence ; Cellulose/metabolism ; Central Nervous System/physiology ; Ciona intestinalis/anatomy & histology/classification/*genetics/physiology ; Computational Biology ; Endocrine System/physiology ; Gene Dosage ; Gene Duplication ; Genes ; Genes, Homeobox ; *Genome ; Heart/embryology/physiology ; Immunity/genetics ; Molecular Sequence Data ; Multigene Family ; Muscle Proteins/genetics ; Organizers, Embryonic/physiology ; Phylogeny ; Polymorphism, Genetic ; Proteins/genetics/physiology ; *Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Species Specificity ; Thyroid Gland/physiology ; Urochordata/genetics ; Vertebrates/anatomy & histology/classification/genetics/physiology
    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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  • 2
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    Oncostatin M as a potent mitogen for AIDS-Kaposi's sarcoma-derived cells (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-03-13
    Description: Oncostatin M, a cytokine produced by activated lymphoid cells, regulates the growth and differentiation of a number of tumor and normal cells. In contrast to its effects on normal endothelial and aortic smooth muscle cell cultures, Oncostatin M was a potent mitogen for cells derived from acquired immunodeficiency syndrome-related Kaposi's sarcoma (AIDS-KS). After exposure to Oncostatin M, AIDS-KS cells assumed a spindle morphology, had an increased ability to proliferate in soft agar, and secreted increased amounts of interleukin-6. Oncostatin M RNA and immunoreactive Oncostatin M protein were found in AIDS-KS-derived cell isolates. These results suggest that Oncostatin M may play a role in the pathogenesis of AIDS-KS.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miles, S A -- Martinez-Maza, O -- Rezai, A -- Magpantay, L -- Kishimoto, T -- Nakamura, S -- Radka, S F -- Linsley, P S -- AI27660/AI/NIAID NIH HHS/ -- CA 01588/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1992 Mar 13;255(5050):1432-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉UCLA AIDS Center 90024.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1542793" target="_blank"〉PubMed〈/a〉
    Keywords: Acquired Immunodeficiency Syndrome/*complications ; Base Sequence ; Cell Division/drug effects ; Growth Substances/biosynthesis/*physiology ; Humans ; Molecular Sequence Data ; Neoplasm Proteins/biosynthesis ; Oncostatin M ; Peptide Biosynthesis ; Peptides/*physiology ; Recombinant Proteins/pharmacology ; Sarcoma, Kaposi/etiology/metabolism/*pathology ; Tumor Cells, Cultured
    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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  • 3
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    The Chlamydomonas genome reveals the evolution of key animal and plant functions (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-10-13
    Description: Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875087/" 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/PMC2875087/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Merchant, Sabeeha S -- Prochnik, Simon E -- Vallon, Olivier -- Harris, Elizabeth H -- Karpowicz, Steven J -- Witman, George B -- Terry, Astrid -- Salamov, Asaf -- Fritz-Laylin, Lillian K -- Marechal-Drouard, Laurence -- Marshall, Wallace F -- Qu, Liang-Hu -- Nelson, David R -- Sanderfoot, Anton A -- Spalding, Martin H -- Kapitonov, Vladimir V -- Ren, Qinghu -- Ferris, Patrick -- Lindquist, Erika -- Shapiro, Harris -- Lucas, Susan M -- Grimwood, Jane -- Schmutz, Jeremy -- Cardol, Pierre -- Cerutti, Heriberto -- Chanfreau, Guillaume -- Chen, Chun-Long -- Cognat, Valerie -- Croft, Martin T -- Dent, Rachel -- Dutcher, Susan -- Fernandez, Emilio -- Fukuzawa, Hideya -- Gonzalez-Ballester, David -- Gonzalez-Halphen, Diego -- Hallmann, Armin -- Hanikenne, Marc -- Hippler, Michael -- Inwood, William -- Jabbari, Kamel -- Kalanon, Ming -- Kuras, Richard -- Lefebvre, Paul A -- Lemaire, Stephane D -- Lobanov, Alexey V -- Lohr, Martin -- Manuell, Andrea -- Meier, Iris -- Mets, Laurens -- Mittag, Maria -- Mittelmeier, Telsa -- Moroney, James V -- Moseley, Jeffrey -- Napoli, Carolyn -- Nedelcu, Aurora M -- Niyogi, Krishna -- Novoselov, Sergey V -- Paulsen, Ian T -- Pazour, Greg -- Purton, Saul -- Ral, Jean-Philippe -- Riano-Pachon, Diego Mauricio -- Riekhof, Wayne -- Rymarquis, Linda -- Schroda, Michael -- Stern, David -- Umen, James -- Willows, Robert -- Wilson, Nedra -- Zimmer, Sara Lana -- Allmer, Jens -- Balk, Janneke -- Bisova, Katerina -- Chen, Chong-Jian -- Elias, Marek -- Gendler, Karla -- Hauser, Charles -- Lamb, Mary Rose -- Ledford, Heidi -- Long, Joanne C -- Minagawa, Jun -- Page, M Dudley -- Pan, Junmin -- Pootakham, Wirulda -- Roje, Sanja -- Rose, Annkatrin -- Stahlberg, Eric -- Terauchi, Aimee M -- Yang, Pinfen -- Ball, Steven -- Bowler, Chris -- Dieckmann, Carol L -- Gladyshev, Vadim N -- Green, Pamela -- Jorgensen, Richard -- Mayfield, Stephen -- Mueller-Roeber, Bernd -- Rajamani, Sathish -- Sayre, Richard T -- Brokstein, Peter -- Dubchak, Inna -- Goodstein, David -- Hornick, Leila -- Huang, Y Wayne -- Jhaveri, Jinal -- Luo, Yigong -- Martinez, Diego -- Ngau, Wing Chi Abby -- Otillar, Bobby -- Poliakov, Alexander -- Porter, Aaron -- Szajkowski, Lukasz -- Werner, Gregory -- Zhou, Kemin -- Grigoriev, Igor V -- Rokhsar, Daniel S -- Grossman, Arthur R -- GM07185/GM/NIGMS NIH HHS/ -- GM42143/GM/NIGMS NIH HHS/ -- R01 GM032843/GM/NIGMS NIH HHS/ -- R01 GM042143/GM/NIGMS NIH HHS/ -- R01 GM042143-09/GM/NIGMS NIH HHS/ -- R01 GM060992/GM/NIGMS NIH HHS/ -- R01 GM062915-06/GM/NIGMS NIH HHS/ -- R37 GM030626/GM/NIGMS NIH HHS/ -- R37 GM042143/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Oct 12;318(5848):245-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17932292" target="_blank"〉PubMed〈/a〉
    Keywords: Algal Proteins/*genetics/*physiology ; Animals ; *Biological Evolution ; Chlamydomonas reinhardtii/*genetics/physiology ; Chloroplasts/metabolism ; Computational Biology ; DNA, Algal/genetics ; Flagella/metabolism ; Genes ; *Genome ; Genomics ; Membrane Transport Proteins/genetics/physiology ; Molecular Sequence Data ; Multigene Family ; Photosynthesis/genetics ; Phylogeny ; Plants/genetics ; Proteome ; Sequence Analysis, DNA
    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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  • 4
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    The Palomero genome suggests metal effects on domestication (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-12-08
    Description: Maize domestication (Zea mays ssp. mays L.) resulted in a wide diversity of native landraces that represent an invaluable source of genetic information for exploring natural variation and genome evolution. We sequenced de novo the approximately 2-gigabase genome of the Mexican landrace Palomero Toluqueno (Palomero) and compared its features to those of the modern inbred line B73. We revealed differences concordant with its ancient origin and identified chromosomal regions of low nucleotide variability that contain domestication genes involved in heavy-metal detoxification. Our results indicate that environmental changes were important selective forces acting on maize domestication.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vielle-Calzada, Jean-Philippe -- Martinez de la Vega, Octavio -- Hernandez-Guzman, Gustavo -- Ibarra-Laclette, Enrique -- Alvarez-Mejia, Cesar -- Vega-Arreguin, Julio C -- Jimenez-Moraila, Beatriz -- Fernandez-Cortes, Araceli -- Corona-Armenta, Guillermo -- Herrera-Estrella, Luis -- Herrera-Estrella, Alfredo -- New York, N.Y. -- Science. 2009 Nov 20;326(5956):1078. doi: 10.1126/science.1178437.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratorio Nacional de Genomica para la Biodiversidad, CINVESTAV Irapuato, Km 9.6 Libramiento Norte Carretera Irapuato-Leon, 36500 Irapuato, Mexico.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19965420" target="_blank"〉PubMed〈/a〉
    Keywords: Chromosome Mapping ; Chromosomes, Plant/genetics ; Crops, Agricultural/genetics/growth & development ; *Genes, Plant ; Genetic Variation ; *Genome, Plant ; Metals, Heavy/analysis/*metabolism/toxicity ; Molecular Sequence Data ; *Selection, Genetic ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Soil/analysis ; Zea mays/*genetics/growth & development/*metabolism
    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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  • 5
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    The protein kinase complement of the human genome (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-12-10
    Description: We have catalogued the protein kinase complement of the human genome (the "kinome") using public and proprietary genomic, complementary DNA, and expressed sequence tag (EST) sequences. This provides a starting point for comprehensive analysis of protein phosphorylation in normal and disease states, as well as a detailed view of the current state of human genome analysis through a focus on one large gene family. We identify 518 putative protein kinase genes, of which 71 have not previously been reported or described as kinases, and we extend or correct the protein sequences of 56 more kinases. New genes include members of well-studied families as well as previously unidentified families, some of which are conserved in model organisms. Classification and comparison with model organism kinomes identified orthologous groups and highlighted expansions specific to human and other lineages. We also identified 106 protein kinase pseudogenes. Chromosomal mapping revealed several small clusters of kinase genes and revealed that 244 kinases map to disease loci or cancer amplicons.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Manning, G -- Whyte, D B -- Martinez, R -- Hunter, T -- Sudarsanam, S -- New York, N.Y. -- Science. 2002 Dec 6;298(5600):1912-34.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉SUGEN Inc., 230 East Grand Avenue, South San Francisco, CA 94080, USA. gerard-manning@sugen.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12471243" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Catalysis ; Chromosome Mapping ; Computational Biology ; Databases, Genetic ; Genes ; *Genome, Human ; Humans ; Neoplasms/genetics ; Phylogeny ; Protein Kinases/chemistry/classification/*genetics/*metabolism ; Protein Structure, Tertiary ; Pseudogenes ; Sequence Analysis, DNA ; Signal Transduction
    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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  • 6
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    Community genomics among stratified microbial assemblages in the ocean's interior (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-01-28
    Description: Microbial life predominates in the ocean, yet little is known about its genomic variability, especially along the depth continuum. We report here genomic analyses of planktonic microbial communities in the North Pacific Subtropical Gyre, from the ocean's surface to near-sea floor depths. Sequence variation in microbial community genes reflected vertical zonation of taxonomic groups, functional gene repertoires, and metabolic potential. The distributional patterns of microbial genes suggested depth-variable community trends in carbon and energy metabolism, attachment and motility, gene mobility, and host-viral interactions. Comparative genomic analyses of stratified microbial communities have the potential to provide significant insight into higher-order community organization and dynamics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DeLong, Edward F -- Preston, Christina M -- Mincer, Tracy -- Rich, Virginia -- Hallam, Steven J -- Frigaard, Niels-Ulrik -- Martinez, Asuncion -- Sullivan, Matthew B -- Edwards, Robert -- Brito, Beltran Rodriguez -- Chisholm, Sallie W -- Karl, David M -- New York, N.Y. -- Science. 2006 Jan 27;311(5760):496-503.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Massachusetts Institute of Technology, Cambridge, MA 02139, USA. delong@mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16439655" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Archaea/classification/*genetics/metabolism ; Archaeal Proteins/chemistry/genetics/metabolism ; Bacteria/classification/*genetics/metabolism ; Bacterial Proteins/chemistry/genetics/metabolism ; Bacteriophages/genetics ; Base Sequence ; Cloning, Molecular ; Cluster Analysis ; Computational Biology ; Cosmids ; DNA, Viral/chemistry/genetics ; Ecosystem ; Gene Library ; *Genes, Archaeal ; *Genes, Bacterial ; Genes, rRNA ; *Genomics ; Molecular Sequence Data ; Pacific Ocean ; Seawater/*microbiology ; Sequence Analysis, DNA ; Water Microbiology
    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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  • 7
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    Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-04-10
    Description: Transcription factors (TFs) direct gene expression by binding to DNA regulatory regions. To explore the evolution of gene regulation, we used chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) to determine experimentally the genome-wide occupancy of two TFs, CCAAT/enhancer-binding protein alpha and hepatocyte nuclear factor 4 alpha, in the livers of five vertebrates. Although each TF displays highly conserved DNA binding preferences, most binding is species-specific, and aligned binding events present in all five species are rare. Regions near genes with expression levels that are dependent on a TF are often bound by the TF in multiple species yet show no enhanced DNA sequence constraint. Binding divergence between species can be largely explained by sequence changes to the bound motifs. Among the binding events lost in one lineage, only half are recovered by another binding event within 10 kilobases. Our results reveal large interspecies differences in transcriptional regulation and provide insight into regulatory evolution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008766/" 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/PMC3008766/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schmidt, Dominic -- Wilson, Michael D -- Ballester, Benoit -- Schwalie, Petra C -- Brown, Gordon D -- Marshall, Aileen -- Kutter, Claudia -- Watt, Stephen -- Martinez-Jimenez, Celia P -- Mackay, Sarah -- Talianidis, Iannis -- Flicek, Paul -- Odom, Duncan T -- 062023/Wellcome Trust/United Kingdom -- 079643/Wellcome Trust/United Kingdom -- 15603/Cancer Research UK/United Kingdom -- 202218/European Research Council/International -- A15603/Cancer Research UK/United Kingdom -- WT062023/Wellcome Trust/United Kingdom -- WT079643/Wellcome Trust/United Kingdom -- Cancer Research UK/United Kingdom -- New York, N.Y. -- Science. 2010 May 21;328(5981):1036-40. doi: 10.1126/science.1186176. Epub 2010 Apr 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20378774" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Animals ; Base Sequence ; Binding Sites ; Biological Evolution ; CCAAT-Enhancer-Binding Protein-alpha/*metabolism ; Chickens/genetics ; Chromatin Immunoprecipitation ; DNA/genetics/metabolism ; Dogs ; *Evolution, Molecular ; *Gene Expression Regulation ; *Genome ; Genome, Human ; Hepatocyte Nuclear Factor 4/*metabolism ; Humans ; Liver/*metabolism ; Mice ; Opossums/genetics ; Protein Binding ; Regulatory Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Species Specificity ; Vertebrates/*genetics/metabolism
    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
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    Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding (2015)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2015-04-11
    Description: Mountain gorillas are an endangered great ape subspecies and a prominent focus for conservation, yet we know little about their genomic diversity and evolutionary past. We sequenced whole genomes from multiple wild individuals and compared the genomes of all four Gorilla subspecies. We found that the two eastern subspecies have experienced a prolonged population decline over the past 100,000 years, resulting in very low genetic diversity and an increased overall burden of deleterious variation. A further recent decline in the mountain gorilla population has led to extensive inbreeding, such that individuals are typically homozygous at 34% of their sequence, leading to the purging of severely deleterious recessive mutations from the population. We discuss the causes of their decline and the consequences for their future survival.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4668944/" 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/PMC4668944/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xue, Yali -- Prado-Martinez, Javier -- Sudmant, Peter H -- Narasimhan, Vagheesh -- Ayub, Qasim -- Szpak, Michal -- Frandsen, Peter -- Chen, Yuan -- Yngvadottir, Bryndis -- Cooper, David N -- de Manuel, Marc -- Hernandez-Rodriguez, Jessica -- Lobon, Irene -- Siegismund, Hans R -- Pagani, Luca -- Quail, Michael A -- Hvilsom, Christina -- Mudakikwa, Antoine -- Eichler, Evan E -- Cranfield, Michael R -- Marques-Bonet, Tomas -- Tyler-Smith, Chris -- Scally, Aylwyn -- 098051/Wellcome Trust/United Kingdom -- 099769/Z/12/Z/Wellcome Trust/United Kingdom -- 260372/European Research Council/International -- HG002385/HG/NHGRI NIH HHS/ -- R01 HG002385/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2015 Apr 10;348(6231):242-5. doi: 10.1126/science.aaa3952. Epub 2015 Apr 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK. ; Institut de Biologia Evolutiva (CSIC/UPF), Parque de Investigacion Biomedica de Barcelona (PRBB), Barcelona, Catalonia 08003, Spain. ; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. ; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK. Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0WA, UK. ; Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark. ; Institute of Medical Genetics, Cardiff University, Cardiff CF14 4XN, UK. ; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK. Department of Biological, Geological and Environmental Sciences, University of Bologna, 40134 Bologna, Italy. ; Research and Conservation, Copenhagen Zoo, DK-2000 Frederiksberg, Denmark. ; Rwanda Development Board, KG 9 Avenue, Kigali, Rwanda. ; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, Seattle, WA 91895, USA. ; Gorilla Doctors, Karen C. Drayer Wildlife Health Center, University of California, Davis, CA 95616, USA. ; Institut de Biologia Evolutiva (CSIC/UPF), Parque de Investigacion Biomedica de Barcelona (PRBB), Barcelona, Catalonia 08003, Spain. Centro Nacional de Analisis Genomico (Parc Cientific de Barcelona), Baldiri Reixac 4, 08028 Barcelona, Spain. ; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK. cts@sanger.ac.uk aos21@cam.ac.uk. ; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK. cts@sanger.ac.uk aos21@cam.ac.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25859046" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Animals ; Biological Evolution ; DNA Copy Number Variations ; Democratic Republic of the Congo ; Endangered Species ; Female ; *Genetic Variation ; *Genome ; Gorilla gorilla/classification/*genetics/physiology ; Homozygote ; *Inbreeding ; Linkage Disequilibrium ; Male ; Mutation ; Population Dynamics ; Rwanda ; Selection, Genetic ; Sequence Analysis, DNA ; Species Specificity ; Time Factors
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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    Neuronal pp60c-src contains a six-amino acid insertion relative to its non-neuronal counterpart (1987)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1987-07-24
    Description: Neuronal cells express a pp60c-src variant that displays an altered electrophoretic mobility and a different V8 peptide pattern relative to pp60c-src expressed in tissues of non-neuronal origin. To determine whether the neuronal form of pp60c-src is encoded by a brain-specific messenger RNA, a mouse brain complementary DNA (cDNA) library was screened with a chicken c-src probe and a 3.8-kilobase c-src cDNA clone was isolated. This clone encodes a 60-kilodalton protein that differs from chicken or human pp60c-src primarily in having six extra amino acids (Arg-Lys-Val-Asp-Val-Arg) within the NH2-terminal 16 kilodaltons of the molecule. S1 nuclease protection analysis confirmed that brain c-src RNA contains an 18-nucleotide insertion at the position of the extra six amino acids. This insertion occurs at a position that corresponds to a splice junction in the chicken and human c-src genes. The isolated c-src cDNA clone encodes a protein that displays an identical V8 peptide pattern to that observed in pp60c-src isolated from tissues of neuronal origin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Martinez, R -- Mathey-Prevot, B -- Bernards, A -- Baltimore, D -- P0I CA38497/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1987 Jul 24;237(4813):411-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2440106" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Brain/enzymology ; Chickens ; Cloning, Molecular ; DNA/metabolism ; DNA Restriction Enzymes ; DNA Transposable Elements ; Humans ; Isoenzymes/*genetics ; Mice ; Neurons/*enzymology ; Protein Kinases/*genetics ; Proto-Oncogene Proteins/*genetics ; Proto-Oncogene Proteins pp60(c-src) ; Sequence Homology, Nucleic Acid ; Species Specificity
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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