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  • Phylogeny  (8)
  • Mutation  (7)
  • Multigene Family  (6)
  • American Association for the Advancement of Science (AAAS)  (18)
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  • 1
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    Comparative genomics of the eukaryotes (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-03-24
    Description: A comparative analysis of the genomes of Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae-and the proteins they are predicted to encode-was undertaken in the context of cellular, developmental, and evolutionary processes. The nonredundant protein sets of flies and worms are similar in size and are only twice that of yeast, but different gene families are expanded in each genome, and the multidomain proteins and signaling pathways of the fly and worm are far more complex than those of yeast. The fly has orthologs to 177 of the 289 human disease genes examined and provides the foundation for rapid analysis of some of the basic processes involved in human disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2754258/" 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/PMC2754258/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rubin, G M -- Yandell, M D -- Wortman, J R -- Gabor Miklos, G L -- Nelson, C R -- Hariharan, I K -- Fortini, M E -- Li, P W -- Apweiler, R -- Fleischmann, W -- Cherry, J M -- Henikoff, S -- Skupski, M P -- Misra, S -- Ashburner, M -- Birney, E -- Boguski, M S -- Brody, T -- Brokstein, P -- Celniker, S E -- Chervitz, S A -- Coates, D -- Cravchik, A -- Gabrielian, A -- Galle, R F -- Gelbart, W M -- George, R A -- Goldstein, L S -- Gong, F -- Guan, P -- Harris, N L -- Hay, B A -- Hoskins, R A -- Li, J -- Li, Z -- Hynes, R O -- Jones, S J -- Kuehl, P M -- Lemaitre, B -- Littleton, J T -- Morrison, D K -- Mungall, C -- O'Farrell, P H -- Pickeral, O K -- Shue, C -- Vosshall, L B -- Zhang, J -- Zhao, Q -- Zheng, X H -- Lewis, S -- P4IHG00739/HG/NHGRI NIH HHS/ -- P50HG00750/HG/NHGRI NIH HHS/ -- R01 GM037193/GM/NIGMS NIH HHS/ -- R01 GM037193-14/GM/NIGMS NIH HHS/ -- R01 GM037193-15/GM/NIGMS NIH HHS/ -- R01 GM060988/GM/NIGMS NIH HHS/ -- R01 GM060988-01/GM/NIGMS NIH HHS/ -- R01 NS040296/NS/NINDS NIH HHS/ -- R01 NS040296-01/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2000 Mar 24;287(5461):2204-15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Molecular and Cell Biology, Berkeley Drosophila Genome Project, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10731134" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis/genetics ; Biological Evolution ; Caenorhabditis elegans/chemistry/*genetics/physiology ; Cell Adhesion/genetics ; Cell Cycle/genetics ; Drosophila melanogaster/chemistry/*genetics/physiology ; Fungal Proteins/chemistry/genetics ; Genes, Duplicate ; Genetic Diseases, Inborn/genetics ; Genetics, Medical ; *Genome ; Helminth Proteins/chemistry/genetics ; Humans ; Immunity/genetics ; Insect Proteins/chemistry/genetics ; Multigene Family ; Neoplasms/genetics ; Protein Structure, Tertiary ; *Proteome ; Saccharomyces cerevisiae/chemistry/*genetics/physiology ; Signal Transduction/genetics
    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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  • 2
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    BLM heterozygosity and the risk of colorectal cancer (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-09-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gruber, Stephen B -- Ellis, Nathan A -- Scott, Karen K -- Almog, Ronit -- Kolachana, Prema -- Bonner, Joseph D -- Kirchhoff, Tomas -- Tomsho, Lynn P -- Nafa, Khedoudja -- Pierce, Heather -- Low, Marcelo -- Satagopan, Jaya -- Rennert, Hedy -- Huang, Helen -- Greenson, Joel K -- Groden, Joanna -- Rapaport, Beth -- Shia, Jinru -- Johnson, Stephen -- Gregersen, Peter K -- Harris, Curtis C -- Boyd, Jeff -- Rennert, Gad -- Offit, Kenneth -- R01CA81488/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2002 Sep 20;297(5589):2013.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Internal Medicine and Epidemiology, University of Michigan, Ann Arbor, MI 48109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12242432" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/*genetics ; Alleles ; Animals ; Bloom Syndrome/genetics ; Case-Control Studies ; Colorectal Neoplasms/*genetics ; DNA Helicases/*genetics ; Female ; Genes, APC ; *Genetic Predisposition to Disease ; *Heterozygote ; Humans ; Israel ; Jews/genetics ; Male ; Mice ; Mutation ; New York ; RecQ Helicases ; Risk 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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  • 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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    Evolutionary and biomedical insights from the rhesus macaque genome (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-04-14
    Description: The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rhesus Macaque Genome Sequencing and Analysis Consortium -- Gibbs, Richard A -- Rogers, Jeffrey -- Katze, Michael G -- Bumgarner, Roger -- Weinstock, George M -- Mardis, Elaine R -- Remington, Karin A -- Strausberg, Robert L -- Venter, J Craig -- Wilson, Richard K -- Batzer, Mark A -- Bustamante, Carlos D -- Eichler, Evan E -- Hahn, Matthew W -- Hardison, Ross C -- Makova, Kateryna D -- Miller, Webb -- Milosavljevic, Aleksandar -- Palermo, Robert E -- Siepel, Adam -- Sikela, James M -- Attaway, Tony -- Bell, Stephanie -- Bernard, Kelly E -- Buhay, Christian J -- Chandrabose, Mimi N -- Dao, Marvin -- Davis, Clay -- Delehaunty, Kimberly D -- Ding, Yan -- Dinh, Huyen H -- Dugan-Rocha, Shannon -- Fulton, Lucinda A -- Gabisi, Ramatu Ayiesha -- Garner, Toni T -- Godfrey, Jennifer -- Hawes, Alicia C -- Hernandez, Judith -- Hines, Sandra -- Holder, Michael -- Hume, Jennifer -- Jhangiani, Shalini N -- Joshi, Vandita -- Khan, Ziad Mohid -- Kirkness, Ewen F -- Cree, Andrew -- Fowler, R Gerald -- Lee, Sandra -- Lewis, Lora R -- Li, Zhangwan -- Liu, Yih-Shin -- Moore, Stephanie M -- Muzny, Donna -- Nazareth, Lynne V -- Ngo, Dinh Ngoc -- Okwuonu, Geoffrey O -- Pai, Grace -- Parker, David -- Paul, Heidie A -- Pfannkoch, Cynthia -- Pohl, Craig S -- Rogers, Yu-Hui -- Ruiz, San Juana -- Sabo, Aniko -- Santibanez, Jireh -- Schneider, Brian W -- Smith, Scott M -- Sodergren, Erica -- Svatek, Amanda F -- Utterback, Teresa R -- Vattathil, Selina -- Warren, Wesley -- White, Courtney Sherell -- Chinwalla, Asif T -- Feng, Yucheng -- Halpern, Aaron L -- Hillier, Ladeana W -- Huang, Xiaoqiu -- Minx, Pat -- Nelson, Joanne O -- Pepin, Kymberlie H -- Qin, Xiang -- Sutton, Granger G -- Venter, Eli -- Walenz, Brian P -- Wallis, John W -- Worley, Kim C -- Yang, Shiaw-Pyng -- Jones, Steven M -- Marra, Marco A -- Rocchi, Mariano -- Schein, Jacqueline E -- Baertsch, Robert -- Clarke, Laura -- Csuros, Miklos -- Glasscock, Jarret -- Harris, R Alan -- Havlak, Paul -- Jackson, Andrew R -- Jiang, Huaiyang -- Liu, Yue -- Messina, David N -- Shen, Yufeng -- Song, Henry Xing-Zhi -- Wylie, Todd -- Zhang, Lan -- Birney, Ewan -- Han, Kyudong -- Konkel, Miriam K -- Lee, Jungnam -- Smit, Arian F A -- Ullmer, Brygg -- Wang, Hui -- Xing, Jinchuan -- Burhans, Richard -- Cheng, Ze -- Karro, John E -- Ma, Jian -- Raney, Brian -- She, Xinwei -- Cox, Michael J -- Demuth, Jeffery P -- Dumas, Laura J -- Han, Sang-Gook -- Hopkins, Janet -- Karimpour-Fard, Anis -- Kim, Young H -- Pollack, Jonathan R -- Vinar, Tomas -- Addo-Quaye, Charles -- Degenhardt, Jeremiah -- Denby, Alexandra -- Hubisz, Melissa J -- Indap, Amit -- Kosiol, Carolin -- Lahn, Bruce T -- Lawson, Heather A -- Marklein, Alison -- Nielsen, Rasmus -- Vallender, Eric J -- Clark, Andrew G -- Ferguson, Betsy -- Hernandez, Ryan D -- Hirani, Kashif -- Kehrer-Sawatzki, Hildegard -- Kolb, Jessica -- Patil, Shobha -- Pu, Ling-Ling -- Ren, Yanru -- Smith, David Glenn -- Wheeler, David A -- Schenck, Ian -- Ball, Edward V -- Chen, Rui -- Cooper, David N -- Giardine, Belinda -- Hsu, Fan -- Kent, W James -- Lesk, Arthur -- Nelson, David L -- O'brien, William E -- Prufer, Kay -- Stenson, Peter D -- Wallace, James C -- Ke, Hui -- Liu, Xiao-Ming -- Wang, Peng -- Xiang, Andy Peng -- Yang, Fan -- Barber, Galt P -- Haussler, David -- Karolchik, Donna -- Kern, Andy D -- Kuhn, Robert M -- Smith, Kayla E -- Zwieg, Ann S -- 062023/Wellcome Trust/United Kingdom -- R01 HG002939/HG/NHGRI NIH HHS/ -- U54 HG003068/HG/NHGRI NIH HHS/ -- U54 HG003079/HG/NHGRI NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2007 Apr 13;316(5822):222-34.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA. agibbs@bcm.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17431167" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biomedical Research ; *Evolution, Molecular ; Female ; Gene Duplication ; Gene Rearrangement ; Genetic Diseases, Inborn ; Genetic Variation ; *Genome ; Humans ; Macaca mulatta/*genetics ; Male ; Multigene Family ; Mutation ; Pan troglodytes/genetics ; Sequence Analysis, DNA ; Species Specificity
    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 status of the world's land and marine mammals: diversity, threat, and knowledge (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-10-11
    Description: Knowledge of mammalian diversity is still surprisingly disparate, both regionally and taxonomically. Here, we present a comprehensive assessment of the conservation status and distribution of the world's mammals. Data, compiled by 1700+ experts, cover all 5487 species, including marine mammals. Global macroecological patterns are very different for land and marine species but suggest common mechanisms driving diversity and endemism across systems. Compared with land species, threat levels are higher among marine mammals, driven by different processes (accidental mortality and pollution, rather than habitat loss), and are spatially distinct (peaking in northern oceans, rather than in Southeast Asia). Marine mammals are also disproportionately poorly known. These data are made freely available to support further scientific developments and conservation action.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schipper, Jan -- Chanson, Janice S -- Chiozza, Federica -- Cox, Neil A -- Hoffmann, Michael -- Katariya, Vineet -- Lamoreux, John -- Rodrigues, Ana S L -- Stuart, Simon N -- Temple, Helen J -- Baillie, Jonathan -- Boitani, Luigi -- Lacher, Thomas E Jr -- Mittermeier, Russell A -- Smith, Andrew T -- Absolon, Daniel -- Aguiar, John M -- Amori, Giovanni -- Bakkour, Noura -- Baldi, Ricardo -- Berridge, Richard J -- Bielby, Jon -- Black, Patricia Ann -- Blanc, J Julian -- Brooks, Thomas M -- Burton, James A -- Butynski, Thomas M -- Catullo, Gianluca -- Chapman, Roselle -- Cokeliss, Zoe -- Collen, Ben -- Conroy, Jim -- Cooke, Justin G -- da Fonseca, Gustavo A B -- Derocher, Andrew E -- Dublin, Holly T -- Duckworth, J W -- Emmons, Louise -- Emslie, Richard H -- Festa-Bianchet, Marco -- Foster, Matt -- Foster, Sabrina -- Garshelis, David L -- Gates, Cormack -- Gimenez-Dixon, Mariano -- Gonzalez, Susana -- Gonzalez-Maya, Jose Fernando -- Good, Tatjana C -- Hammerson, Geoffrey -- Hammond, Philip S -- Happold, David -- Happold, Meredith -- Hare, John -- Harris, Richard B -- Hawkins, Clare E -- Haywood, Mandy -- Heaney, Lawrence R -- Hedges, Simon -- Helgen, Kristofer M -- Hilton-Taylor, Craig -- Hussain, Syed Ainul -- Ishii, Nobuo -- Jefferson, Thomas A -- Jenkins, Richard K B -- Johnston, Charlotte H -- Keith, Mark -- Kingdon, Jonathan -- Knox, David H -- Kovacs, Kit M -- Langhammer, Penny -- Leus, Kristin -- Lewison, Rebecca -- Lichtenstein, Gabriela -- Lowry, Lloyd F -- Macavoy, Zoe -- Mace, Georgina M -- Mallon, David P -- Masi, Monica -- McKnight, Meghan W -- Medellin, Rodrigo A -- Medici, Patricia -- Mills, Gus -- Moehlman, Patricia D -- Molur, Sanjay -- Mora, Arturo -- Nowell, Kristin -- Oates, John F -- Olech, Wanda -- Oliver, William R L -- Oprea, Monik -- Patterson, Bruce D -- Perrin, William F -- Polidoro, Beth A -- Pollock, Caroline -- Powel, Abigail -- Protas, Yelizaveta -- Racey, Paul -- Ragle, Jim -- Ramani, Pavithra -- Rathbun, Galen -- Reeves, Randall R -- Reilly, Stephen B -- Reynolds, John E 3rd -- Rondinini, Carlo -- Rosell-Ambal, Ruth Grace -- Rulli, Monica -- Rylands, Anthony B -- Savini, Simona -- Schank, Cody J -- Sechrest, Wes -- Self-Sullivan, Caryn -- Shoemaker, Alan -- Sillero-Zubiri, Claudio -- De Silva, Naamal -- Smith, David E -- Srinivasulu, Chelmala -- Stephenson, Peter J -- van Strien, Nico -- Talukdar, Bibhab Kumar -- Taylor, Barbara L -- Timmins, Rob -- Tirira, Diego G -- Tognelli, Marcelo F -- Tsytsulina, Katerina -- Veiga, Liza M -- Vie, Jean-Christophe -- Williamson, Elizabeth A -- Wyatt, Sarah A -- Xie, Yan -- Young, Bruce E -- New York, N.Y. -- Science. 2008 Oct 10;322(5899):225-30. doi: 10.1126/science.1165115.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉International Union for Conservation of Nature (IUCN) Species Programme, IUCN, 28 Rue Mauverney, 1196 Gland, Switzerland. jan.schipper@iucn.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18845749" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; Body Size ; Conservation of Natural Resources ; Databases, Factual ; Ecosystem ; *Extinction, Biological ; *Mammals/anatomy & histology/classification/physiology ; Marine Biology ; Phylogeny ; Population Dynamics ; Seawater
    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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    Evolution of MRSA during hospital transmission and intercontinental spread (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-01-23
    Description: Current methods for differentiating isolates of predominant lineages of pathogenic bacteria often do not provide sufficient resolution to define precise relationships. Here, we describe a high-throughput genomics approach that provides a high-resolution view of the epidemiology and microevolution of a dominant strain of methicillin-resistant Staphylococcus aureus (MRSA). This approach reveals the global geographic structure within the lineage, its intercontinental transmission through four decades, and the potential to trace person-to-person transmission within a hospital environment. The ability to interrogate and resolve bacterial populations is applicable to a range of infectious diseases, as well as microbial ecology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2821690/" 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/PMC2821690/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harris, Simon R -- Feil, Edward J -- Holden, Matthew T G -- Quail, Michael A -- Nickerson, Emma K -- Chantratita, Narisara -- Gardete, Susana -- Tavares, Ana -- Day, Nick -- Lindsay, Jodi A -- Edgeworth, Jonathan D -- de Lencastre, Herminia -- Parkhill, Julian -- Peacock, Sharon J -- Bentley, Stephen D -- 076964/Wellcome Trust/United Kingdom -- Department of Health/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2010 Jan 22;327(5964):469-74. doi: 10.1126/science.1182395.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 15A, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20093474" target="_blank"〉PubMed〈/a〉
    Keywords: Asia/epidemiology ; Bacterial Typing Techniques ; Cross Infection/epidemiology/*microbiology/transmission ; Europe/epidemiology ; Evolution, Molecular ; *Genome, Bacterial ; Genomics/methods ; Humans ; Likelihood Functions ; Methicillin-Resistant Staphylococcus aureus/*classification/*genetics/isolation & ; purification ; Molecular Epidemiology ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; South America/epidemiology ; Staphylococcal Infections/epidemiology/*microbiology/transmission ; Time Factors ; United States/epidemiology
    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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    Rapid pneumococcal evolution in response to clinical interventions (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-01-29
    Description: Epidemiological studies of the naturally transformable bacterial pathogen Streptococcus pneumoniae have previously been confounded by high rates of recombination. Sequencing 240 isolates of the PMEN1 (Spain(23F)-1) multidrug-resistant lineage enabled base substitutions to be distinguished from polymorphisms arising through horizontal sequence transfer. More than 700 recombinations were detected, with genes encoding major antigens frequently affected. Among these were 10 capsule-switching events, one of which accompanied a population shift as vaccine-escape serotype 19A isolates emerged in the USA after the introduction of the conjugate polysaccharide vaccine. The evolution of resistance to fluoroquinolones, rifampicin, and macrolides was observed to occur on multiple occasions. This study details how genomic plasticity within lineages of recombinogenic bacteria can permit adaptation to clinical interventions over remarkably short time scales.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3648787/" 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/PMC3648787/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Croucher, Nicholas J -- Harris, Simon R -- Fraser, Christophe -- Quail, Michael A -- Burton, John -- van der Linden, Mark -- McGee, Lesley -- von Gottberg, Anne -- Song, Jae Hoon -- Ko, Kwan Soo -- Pichon, Bruno -- Baker, Stephen -- Parry, Christopher M -- Lambertsen, Lotte M -- Shahinas, Dea -- Pillai, Dylan R -- Mitchell, Timothy J -- Dougan, Gordon -- Tomasz, Alexander -- Klugman, Keith P -- Parkhill, Julian -- Hanage, William P -- Bentley, Stephen D -- 076962/Wellcome Trust/United Kingdom -- 076964/Wellcome Trust/United Kingdom -- G0800596/Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2011 Jan 28;331(6016):430-4. doi: 10.1126/science.1198545.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21273480" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Anti-Bacterial Agents/pharmacology ; Antigenic Variation ; DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial ; *Evolution, Molecular ; Genome, Bacterial ; Humans ; Molecular Epidemiology ; Phylogeny ; Phylogeography ; Pneumococcal Infections/drug therapy/*microbiology ; Pneumococcal Vaccines/immunology ; Polymorphism, Single Nucleotide ; Prophages/genetics ; *Recombination, Genetic ; Selection, Genetic ; Serotyping ; Streptococcus Phages/genetics ; Streptococcus pneumoniae/classification/drug effects/*genetics/immunology
    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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  • 8
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    Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-09-14
    Description: The global epidemic of multidrug-resistant Salmonella Typhimurium DT104 provides an important example, both in terms of the agent and its resistance, of a widely disseminated zoonotic pathogen. Here, with an unprecedented national collection of isolates collected contemporaneously from humans and animals and including a sample of internationally derived isolates, we have used whole-genome sequencing to dissect the phylogenetic associations of the bacterium and its antimicrobial resistance genes through the course of an epidemic. Contrary to current tenets supporting a single homogeneous epidemic, we demonstrate that the bacterium and its resistance genes were largely maintained within animal and human populations separately and that there was limited transmission, in either direction. We also show considerable variation in the resistance profiles, in contrast to the largely stable bacterial core genome, which emphasizes the critical importance of integrated genotypic data sets in understanding the ecology of bacterial zoonoses and antimicrobial resistance.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4012302/" 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/PMC4012302/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mather, A E -- Reid, S W J -- Maskell, D J -- Parkhill, J -- Fookes, M C -- Harris, S R -- Brown, D J -- Coia, J E -- Mulvey, M R -- Gilmour, M W -- Petrovska, L -- de Pinna, E -- Kuroda, M -- Akiba, M -- Izumiya, H -- Connor, T R -- Suchard, M A -- Lemey, P -- Mellor, D J -- Haydon, D T -- Thomson, N R -- 098051/Wellcome Trust/United Kingdom -- 260864/European Research Council/International -- AI107034/AI/NIAID NIH HHS/ -- HG006139/HG/NHGRI NIH HHS/ -- R01 AI107034/AI/NIAID NIH HHS/ -- R01 GM086887/GM/NIGMS NIH HHS/ -- R01 HG006139/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2013 Sep 27;341(6153):1514-7. doi: 10.1126/science.1240578. Epub 2013 Sep 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉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/24030491" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Drug Resistance, Multiple, Bacterial/*genetics ; Epidemics ; Genome, Bacterial ; *Host-Pathogen Interactions ; Humans ; Molecular Sequence Data ; Phylogeny ; Salmonella Infections/epidemiology/*microbiology ; Salmonella Infections, Animal/epidemiology/*microbiology ; Salmonella typhimurium/*classification/drug effects/genetics ; Zoonoses/*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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  • 9
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    The genome of the kinetoplastid parasite, Leishmania major (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-07-16
    Description: Leishmania species cause a spectrum of human diseases in tropical and subtropical regions of the world. We have sequenced the 36 chromosomes of the 32.8-megabase haploid genome of Leishmania major (Friedlin strain) and predict 911 RNA genes, 39 pseudogenes, and 8272 protein-coding genes, of which 36% can be ascribed a putative function. These include genes involved in host-pathogen interactions, such as proteolytic enzymes, and extensive machinery for synthesis of complex surface glycoconjugates. The organization of protein-coding genes into long, strand-specific, polycistronic clusters and lack of general transcription factors in the L. major, Trypanosoma brucei, and Trypanosoma cruzi (Tritryp) genomes suggest that the mechanisms regulating RNA polymerase II-directed transcription are distinct from those operating in other eukaryotes, although the trypanosomatids appear capable of chromatin remodeling. Abundant RNA-binding proteins are encoded in the Tritryp genomes, consistent with active posttranscriptional regulation of gene expression.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1470643/" 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/PMC1470643/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ivens, Alasdair C -- Peacock, Christopher S -- Worthey, Elizabeth A -- Murphy, Lee -- Aggarwal, Gautam -- Berriman, Matthew -- Sisk, Ellen -- Rajandream, Marie-Adele -- Adlem, Ellen -- Aert, Rita -- Anupama, Atashi -- Apostolou, Zina -- Attipoe, Philip -- Bason, Nathalie -- Bauser, Christopher -- Beck, Alfred -- Beverley, Stephen M -- Bianchettin, Gabriella -- Borzym, Katja -- Bothe, Gordana -- Bruschi, Carlo V -- Collins, Matt -- Cadag, Eithon -- Ciarloni, Laura -- Clayton, Christine -- Coulson, Richard M R -- Cronin, Ann -- Cruz, Angela K -- Davies, Robert M -- De Gaudenzi, Javier -- Dobson, Deborah E -- Duesterhoeft, Andreas -- Fazelina, Gholam -- Fosker, Nigel -- Frasch, Alberto Carlos -- Fraser, Audrey -- Fuchs, Monika -- Gabel, Claudia -- Goble, Arlette -- Goffeau, Andre -- Harris, David -- Hertz-Fowler, Christiane -- Hilbert, Helmut -- Horn, David -- Huang, Yiting -- Klages, Sven -- Knights, Andrew -- Kube, Michael -- Larke, Natasha -- Litvin, Lyudmila -- Lord, Angela -- Louie, Tin -- Marra, Marco -- Masuy, David -- Matthews, Keith -- Michaeli, Shulamit -- Mottram, Jeremy C -- Muller-Auer, Silke -- Munden, Heather -- Nelson, Siri -- Norbertczak, Halina -- Oliver, Karen -- O'neil, Susan -- Pentony, Martin -- Pohl, Thomas M -- Price, Claire -- Purnelle, Benedicte -- Quail, Michael A -- Rabbinowitsch, Ester -- Reinhardt, Richard -- Rieger, Michael -- Rinta, Joel -- Robben, Johan -- Robertson, Laura -- Ruiz, Jeronimo C -- Rutter, Simon -- Saunders, David -- Schafer, Melanie -- Schein, Jacquie -- Schwartz, David C -- Seeger, Kathy -- Seyler, Amber -- Sharp, Sarah -- Shin, Heesun -- Sivam, Dhileep -- Squares, Rob -- Squares, Steve -- Tosato, Valentina -- Vogt, Christy -- Volckaert, Guido -- Wambutt, Rolf -- Warren, Tim -- Wedler, Holger -- Woodward, John -- Zhou, Shiguo -- Zimmermann, Wolfgang -- Smith, Deborah F -- Blackwell, Jenefer M -- Stuart, Kenneth D -- Barrell, Bart -- Myler, Peter J -- R01 AI040599/AI/NIAID NIH HHS/ -- R01 AI053667/AI/NIAID NIH HHS/ -- U01 AI040599/AI/NIAID NIH HHS/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2005 Jul 15;309(5733):436-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK. alicat@sanger.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16020728" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chromatin/genetics/metabolism ; Gene Expression Regulation ; Genes, Protozoan ; Genes, rRNA ; *Genome, Protozoan ; Glycoconjugates/biosynthesis/metabolism ; Leishmania major/chemistry/*genetics/metabolism ; Leishmaniasis, Cutaneous/parasitology ; Lipid Metabolism ; Membrane Proteins/biosynthesis/chemistry/genetics/metabolism ; Molecular Sequence Data ; Multigene Family ; Protein Biosynthesis ; Protein Processing, Post-Translational ; Protozoan Proteins/biosynthesis/chemistry/genetics/metabolism ; RNA Processing, Post-Transcriptional ; RNA Splicing ; RNA, Protozoan/genetics/metabolism ; *Sequence Analysis, DNA ; Transcription, Genetic
    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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  • 10
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    Genome of the host-cell transforming parasite Theileria annulata compared with T. parva (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-07-05
    Description: Theileria annulata and T. parva are closely related protozoan parasites that cause lymphoproliferative diseases of cattle. We sequenced the genome of T. annulata and compared it with that of T. parva to understand the mechanisms underlying transformation and tropism. Despite high conservation of gene sequences and synteny, the analysis reveals unequally expanded gene families and species-specific genes. We also identify divergent families of putative secreted polypeptides that may reduce immune recognition, candidate regulators of host-cell transformation, and a Theileria-specific protein domain [frequently associated in Theileria (FAINT)] present in a large number of secreted proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pain, Arnab -- Renauld, Hubert -- Berriman, Matthew -- Murphy, Lee -- Yeats, Corin A -- Weir, William -- Kerhornou, Arnaud -- Aslett, Martin -- Bishop, Richard -- Bouchier, Christiane -- Cochet, Madeleine -- Coulson, Richard M R -- Cronin, Ann -- de Villiers, Etienne P -- Fraser, Audrey -- Fosker, Nigel -- Gardner, Malcolm -- Goble, Arlette -- Griffiths-Jones, Sam -- Harris, David E -- Katzer, Frank -- Larke, Natasha -- Lord, Angela -- Maser, Pascal -- McKellar, Sue -- Mooney, Paul -- Morton, Fraser -- Nene, Vishvanath -- O'Neil, Susan -- Price, Claire -- Quail, Michael A -- Rabbinowitsch, Ester -- Rawlings, Neil D -- Rutter, Simon -- Saunders, David -- Seeger, Kathy -- Shah, Trushar -- Squares, Robert -- Squares, Steven -- Tivey, Adrian -- Walker, Alan R -- Woodward, John -- Dobbelaere, Dirk A E -- Langsley, Gordon -- Rajandream, Marie-Adele -- McKeever, Declan -- Shiels, Brian -- Tait, Andrew -- Barrell, Bart -- Hall, Neil -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2005 Jul 1;309(5731):131-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. ap2@sanger.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15994557" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Cattle ; Cell Proliferation ; Chromosome Mapping ; Chromosomes/genetics ; Conserved Sequence ; Genes, Protozoan ; *Genome, Protozoan ; Life Cycle Stages ; Lipid Metabolism ; Lymphocytes/cytology/parasitology ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Protein Sorting Signals/genetics ; Protein Structure, Tertiary ; Proteome ; Protozoan Proteins/chemistry/*genetics/physiology ; Sequence Analysis, DNA ; Species Specificity ; Synteny ; Telomere/genetics ; Theileria annulata/*genetics/growth & development/immunology/pathogenicity ; Theileria parva/*genetics/growth & development/immunology/pathogenicity
    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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