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  • 1
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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
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    The genome of the model beetle and pest Tribolium castaneum (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-03-26
    Description: Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tribolium Genome Sequencing Consortium -- Richards, Stephen -- Gibbs, Richard A -- Weinstock, George M -- Brown, Susan J -- Denell, Robin -- Beeman, Richard W -- Gibbs, Richard -- Bucher, Gregor -- Friedrich, Markus -- Grimmelikhuijzen, Cornelis J P -- Klingler, Martin -- Lorenzen, Marce -- Roth, Siegfried -- Schroder, Reinhard -- Tautz, Diethard -- Zdobnov, Evgeny M -- Muzny, Donna -- Attaway, Tony -- Bell, Stephanie -- Buhay, Christian J -- Chandrabose, Mimi N -- Chavez, Dean -- Clerk-Blankenburg, Kerstin P -- Cree, Andrew -- Dao, Marvin -- Davis, Clay -- Chacko, Joseph -- Dinh, Huyen -- Dugan-Rocha, Shannon -- Fowler, Gerald -- Garner, Toni T -- Garnes, Jeffrey -- Gnirke, Andreas -- Hawes, Alica -- Hernandez, Judith -- Hines, Sandra -- Holder, Michael -- Hume, Jennifer -- Jhangiani, Shalini N -- Joshi, Vandita -- Khan, Ziad Mohid -- Jackson, LaRonda -- Kovar, Christie -- Kowis, Andrea -- Lee, Sandra -- Lewis, Lora R -- Margolis, Jon -- Morgan, Margaret -- Nazareth, Lynne V -- Nguyen, Ngoc -- Okwuonu, Geoffrey -- Parker, David -- Ruiz, San-Juana -- Santibanez, Jireh -- Savard, Joel -- Scherer, Steven E -- Schneider, Brian -- Sodergren, Erica -- Vattahil, Selina -- Villasana, Donna -- White, Courtney S -- Wright, Rita -- Park, Yoonseong -- Lord, Jeff -- Oppert, Brenda -- Brown, Susan -- Wang, Liangjiang -- Weinstock, George -- Liu, Yue -- Worley, Kim -- Elsik, Christine G -- Reese, Justin T -- Elhaik, Eran -- Landan, Giddy -- Graur, Dan -- Arensburger, Peter -- Atkinson, Peter -- Beidler, Jim -- Demuth, Jeffery P -- Drury, Douglas W -- Du, Yu-Zhou -- Fujiwara, Haruhiko -- Maselli, Vincenza -- Osanai, Mizuko -- Robertson, Hugh M -- Tu, Zhijian -- Wang, Jian-jun -- Wang, Suzhi -- Song, Henry -- Zhang, Lan -- Werner, Doreen -- Stanke, Mario -- Morgenstern, Burkhard -- Solovyev, Victor -- Kosarev, Peter -- Brown, Garth -- Chen, Hsiu-Chuan -- Ermolaeva, Olga -- Hlavina, Wratko -- Kapustin, Yuri -- Kiryutin, Boris -- Kitts, Paul -- Maglott, Donna -- Pruitt, Kim -- Sapojnikov, Victor -- Souvorov, Alexandre -- Mackey, Aaron J -- Waterhouse, Robert M -- Wyder, Stefan -- Kriventseva, Evgenia V -- Kadowaki, Tatsuhiko -- Bork, Peer -- Aranda, Manuel -- Bao, Riyue -- Beermann, Anke -- Berns, Nicola -- Bolognesi, Renata -- Bonneton, Francois -- Bopp, Daniel -- Butts, Thomas -- Chaumot, Arnaud -- Denell, Robin E -- Ferrier, David E K -- Gordon, Cassondra M -- Jindra, Marek -- Lan, Que -- Lattorff, H Michael G -- Laudet, Vincent -- von Levetsow, Cornelia -- Liu, Zhenyi -- Lutz, Rebekka -- Lynch, Jeremy A -- da Fonseca, Rodrigo Nunes -- Posnien, Nico -- Reuter, Rolf -- Schinko, Johannes B -- Schmitt, Christian -- Schoppmeier, Michael -- Shippy, Teresa D -- Simonnet, Franck -- Marques-Souza, Henrique -- Tomoyasu, Yoshinori -- Trauner, Jochen -- Van der Zee, Maurijn -- Vervoort, Michel -- Wittkopp, Nadine -- Wimmer, Ernst A -- Yang, Xiaoyun -- Jones, Andrew K -- Sattelle, David B -- Ebert, Paul R -- Nelson, David -- Scott, Jeffrey G -- Muthukrishnan, Subbaratnam -- Kramer, Karl J -- Arakane, Yasuyuki -- Zhu, Qingsong -- Hogenkamp, David -- Dixit, Radhika -- Jiang, Haobo -- Zou, Zhen -- Marshall, Jeremy -- Elpidina, Elena -- Vinokurov, Konstantin -- Oppert, Cris -- Evans, Jay -- Lu, Zhiqiang -- Zhao, Picheng -- Sumathipala, Niranji -- Altincicek, Boran -- Vilcinskas, Andreas -- Williams, Michael -- Hultmark, Dan -- Hetru, Charles -- Hauser, Frank -- Cazzamali, Giuseppe -- Williamson, Michael -- Li, Bin -- Tanaka, Yoshiaki -- Predel, Reinhard -- Neupert, Susanne -- Schachtner, Joachim -- Verleyen, Peter -- Raible, Florian -- Walden, Kimberly K O -- Angeli, Sergio -- Foret, Sylvain -- Schuetz, Stefan -- Maleszka, Ryszard -- Miller, Sherry C -- Grossmann, Daniela -- BBS/B/12067/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBS/B/12067/2/Biotechnology and Biological Sciences Research Council/United Kingdom -- R01 GM058634/GM/NIGMS NIH HHS/ -- R01 HD029594/HD/NICHD NIH HHS/ -- R01 HD029594-16/HD/NICHD NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- Intramural NIH HHS/ -- England -- Nature. 2008 Apr 24;452(7190):949-55. doi: 10.1038/nature06784. Epub 2008 Mar 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA. stephenr@bcm.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18362917" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Composition ; Body Patterning/genetics ; Cytochrome P-450 Enzyme System/genetics ; DNA Transposable Elements/genetics ; Genes, Insect/*genetics ; Genome, Insect/*genetics ; Growth and Development/genetics ; Humans ; Insecticides/pharmacology ; Neurotransmitter Agents/genetics ; Oogenesis/genetics ; Phylogeny ; Proteome/genetics ; RNA Interference ; Receptors, G-Protein-Coupled/genetics ; Receptors, Odorant/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Taste/genetics ; Telomere/genetics ; Tribolium/classification/embryology/*genetics/physiology ; Vision, Ocular/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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  • 3
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    The genome of black cottonwood, Populus trichocarpa (Torr. & Gray) (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-09-16
    Description: We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tuskan, G A -- Difazio, S -- Jansson, S -- Bohlmann, J -- Grigoriev, I -- Hellsten, U -- Putnam, N -- Ralph, S -- Rombauts, S -- Salamov, A -- Schein, J -- Sterck, L -- Aerts, A -- Bhalerao, R R -- Bhalerao, R P -- Blaudez, D -- Boerjan, W -- Brun, A -- Brunner, A -- Busov, V -- Campbell, M -- Carlson, J -- Chalot, M -- Chapman, J -- Chen, G-L -- Cooper, D -- Coutinho, P M -- Couturier, J -- Covert, S -- Cronk, Q -- Cunningham, R -- Davis, J -- Degroeve, S -- Dejardin, A -- Depamphilis, C -- Detter, J -- Dirks, B -- Dubchak, I -- Duplessis, S -- Ehlting, J -- Ellis, B -- Gendler, K -- Goodstein, D -- Gribskov, M -- Grimwood, J -- Groover, A -- Gunter, L -- Hamberger, B -- Heinze, B -- Helariutta, Y -- Henrissat, B -- Holligan, D -- Holt, R -- Huang, W -- Islam-Faridi, N -- Jones, S -- Jones-Rhoades, M -- Jorgensen, R -- Joshi, C -- Kangasjarvi, J -- Karlsson, J -- Kelleher, C -- Kirkpatrick, R -- Kirst, M -- Kohler, A -- Kalluri, U -- Larimer, F -- Leebens-Mack, J -- Leple, J-C -- Locascio, P -- Lou, Y -- Lucas, S -- Martin, F -- Montanini, B -- Napoli, C -- Nelson, D R -- Nelson, C -- Nieminen, K -- Nilsson, O -- Pereda, V -- Peter, G -- Philippe, R -- Pilate, G -- Poliakov, A -- Razumovskaya, J -- Richardson, P -- Rinaldi, C -- Ritland, K -- Rouze, P -- Ryaboy, D -- Schmutz, J -- Schrader, J -- Segerman, B -- Shin, H -- Siddiqui, A -- Sterky, F -- Terry, A -- Tsai, C-J -- Uberbacher, E -- Unneberg, P -- Vahala, J -- Wall, K -- Wessler, S -- Yang, G -- Yin, T -- Douglas, C -- Marra, M -- Sandberg, G -- Van de Peer, Y -- Rokhsar, D -- New York, N.Y. -- Science. 2006 Sep 15;313(5793):1596-604.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. gtk@ornl.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16973872" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/genetics ; Chromosome Mapping ; Computational Biology ; Evolution, Molecular ; Expressed Sequence Tags ; *Gene Duplication ; Gene Expression ; Genes, Plant ; *Genome, Plant ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Plant Proteins/chemistry/genetics ; Polymorphism, Single Nucleotide ; Populus/*genetics/growth & development/metabolism ; Protein Structure, Tertiary ; RNA, Plant/analysis ; RNA, Untranslated/analysis ; *Sequence Analysis, DNA
    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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  • 4
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    Founder effects in the assessment of HIV polymorphisms and HLA allele associations (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-03-17
    Description: Escape from T cell-mediated immune responses affects the ongoing evolution of rapidly evolving viruses such as HIV. By applying statistical approaches that account for phylogenetic relationships among viral sequences, we show that viral lineage effects rather than immune escape often explain apparent human leukocyte antigen (HLA)-mediated immune-escape mutations defined by older analysis methods. Phylogenetically informed methods identified immune-susceptible locations with greatly improved accuracy, and the associations we identified with these methods were experimentally validated. This approach has practical implications for understanding the impact of host immunity on pathogen evolution and for defining relevant variants for inclusion in vaccine antigens.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bhattacharya, Tanmoy -- Daniels, Marcus -- Heckerman, David -- Foley, Brian -- Frahm, Nicole -- Kadie, Carl -- Carlson, Jonathan -- Yusim, Karina -- McMahon, Ben -- Gaschen, Brian -- Mallal, Simon -- Mullins, James I -- Nickle, David C -- Herbeck, Joshua -- Rousseau, Christine -- Learn, Gerald H -- Miura, Toshiyuki -- Brander, Christian -- Walker, Bruce -- Korber, Bette -- AI27757/AI/NIAID NIH HHS/ -- AI57005/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2007 Mar 16;315(5818):1583-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Los Alamos National Laboratory, Los Alamos, NM 87545, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17363674" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Antigen Presentation ; Epitopes ; Evolution, Molecular ; *Founder Effect ; Genes, MHC Class I ; Genes, Viral ; HIV Infections/immunology/*virology ; HIV-1/classification/*genetics/*immunology ; HLA Antigens/*genetics/immunology ; HLA-C Antigens/genetics ; Humans ; Immune Tolerance ; Likelihood Functions ; Mutation ; Phenotype ; Phylogeny ; *Polymorphism, Genetic ; T-Lymphocytes, Cytotoxic/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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  • 5
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    The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007
    Description: We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rensing, Stefan A -- Lang, Daniel -- Zimmer, Andreas D -- Terry, Astrid -- Salamov, Asaf -- Shapiro, Harris -- Nishiyama, Tomoaki -- Perroud, Pierre-Francois -- Lindquist, Erika A -- Kamisugi, Yasuko -- Tanahashi, Takako -- Sakakibara, Keiko -- Fujita, Tomomichi -- Oishi, Kazuko -- Shin-I, Tadasu -- Kuroki, Yoko -- Toyoda, Atsushi -- Suzuki, Yutaka -- Hashimoto, Shin-Ichi -- Yamaguchi, Kazuo -- Sugano, Sumio -- Kohara, Yuji -- Fujiyama, Asao -- Anterola, Aldwin -- Aoki, Setsuyuki -- Ashton, Neil -- Barbazuk, W Brad -- Barker, Elizabeth -- Bennetzen, Jeffrey L -- Blankenship, Robert -- Cho, Sung Hyun -- Dutcher, Susan K -- Estelle, Mark -- Fawcett, Jeffrey A -- Gundlach, Heidrun -- Hanada, Kousuke -- Heyl, Alexander -- Hicks, Karen A -- Hughes, Jon -- Lohr, Martin -- Mayer, Klaus -- Melkozernov, Alexander -- Murata, Takashi -- Nelson, David R -- Pils, Birgit -- Prigge, Michael -- Reiss, Bernd -- Renner, Tanya -- Rombauts, Stephane -- Rushton, Paul J -- Sanderfoot, Anton -- Schween, Gabriele -- Shiu, Shin-Han -- Stueber, Kurt -- Theodoulou, Frederica L -- Tu, Hank -- Van de Peer, Yves -- Verrier, Paul J -- Waters, Elizabeth -- Wood, Andrew -- Yang, Lixing -- Cove, David -- Cuming, Andrew C -- Hasebe, Mitsuyasu -- Lucas, Susan -- Mishler, Brent D -- Reski, Ralf -- Grigoriev, Igor V -- Quatrano, Ralph S -- Boore, Jeffrey L -- BBS/E/C/00004948/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2008 Jan 4;319(5859):64-9. Epub 2007 Dec 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, D-79104 Freiburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18079367" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Angiosperms/genetics/physiology ; Animals ; Arabidopsis/genetics/physiology ; *Biological Evolution ; Bryopsida/*genetics/physiology ; Chlamydomonas reinhardtii/genetics/physiology ; Computational Biology ; DNA Repair ; Dehydration ; Gene Duplication ; Genes, Plant ; *Genome, Plant ; Metabolic Networks and Pathways/genetics ; Multigene Family ; Oryza/genetics/physiology ; Phylogeny ; Plant Proteins/genetics/physiology ; Repetitive Sequences, Nucleic Acid ; Retroelements ; Sequence Analysis, DNA ; Signal Transduction/genetics
    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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    Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-05-26
    Description: Since its identification in April 2009, an A(H1N1) virus containing a unique combination of gene segments from both North American and Eurasian swine lineages has continued to circulate in humans. The lack of similarity between the 2009 A(H1N1) virus and its nearest relatives indicates that its gene segments have been circulating undetected for an extended period. Its low genetic diversity suggests that the introduction into humans was a single event or multiple events of similar viruses. Molecular markers predictive of adaptation to humans are not currently present in 2009 A(H1N1) viruses, suggesting that previously unrecognized molecular determinants could be responsible for the transmission among humans. Antigenically the viruses are homogeneous and similar to North American swine A(H1N1) viruses but distinct from seasonal human A(H1N1).〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3250984/" 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/PMC3250984/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garten, Rebecca J -- Davis, C Todd -- Russell, Colin A -- Shu, Bo -- Lindstrom, Stephen -- Balish, Amanda -- Sessions, Wendy M -- Xu, Xiyan -- Skepner, Eugene -- Deyde, Varough -- Okomo-Adhiambo, Margaret -- Gubareva, Larisa -- Barnes, John -- Smith, Catherine B -- Emery, Shannon L -- Hillman, Michael J -- Rivailler, Pierre -- Smagala, James -- de Graaf, Miranda -- Burke, David F -- Fouchier, Ron A M -- Pappas, Claudia -- Alpuche-Aranda, Celia M -- Lopez-Gatell, Hugo -- Olivera, Hiram -- Lopez, Irma -- Myers, Christopher A -- Faix, Dennis -- Blair, Patrick J -- Yu, Cindy -- Keene, Kimberly M -- Dotson, P David Jr -- Boxrud, David -- Sambol, Anthony R -- Abid, Syed H -- St George, Kirsten -- Bannerman, Tammy -- Moore, Amanda L -- Stringer, David J -- Blevins, Patricia -- Demmler-Harrison, Gail J -- Ginsberg, Michele -- Kriner, Paula -- Waterman, Steve -- Smole, Sandra -- Guevara, Hugo F -- Belongia, Edward A -- Clark, Patricia A -- Beatrice, Sara T -- Donis, Ruben -- Katz, Jacqueline -- Finelli, Lyn -- Bridges, Carolyn B -- Shaw, Michael -- Jernigan, Daniel B -- Uyeki, Timothy M -- Smith, Derek J -- Klimov, Alexander I -- Cox, Nancy J -- DP1 OD000490-01/OD/NIH HHS/ -- DP1-OD000490-01/OD/NIH HHS/ -- HHSN266200700010C/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2009 Jul 10;325(5937):197-201. doi: 10.1126/science.1176225. Epub 2009 May 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉WHO Collaborating Center for Influenza, Centers for Disease Control and Prevention (CDC), Atlanta, GA 30333, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19465683" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies, Viral/immunology ; Antigens, Viral/genetics/*immunology ; Disease Outbreaks ; Evolution, Molecular ; Genes, Viral ; Genetic Variation ; Genome, Viral ; Hemagglutination Inhibition Tests ; Hemagglutinin Glycoproteins, Influenza Virus/chemistry/genetics/immunology ; Humans ; Influenza A Virus, H1N1 Subtype/classification/*genetics/*immunology/isolation & ; purification ; Influenza A Virus, H3N2 Subtype/genetics ; Influenza A virus/genetics ; Influenza, Human/epidemiology/immunology/*virology ; Mutation ; Neuraminidase/genetics ; Orthomyxoviridae Infections/veterinary/virology ; Phylogeny ; Reassortant Viruses/genetics ; Swine ; Swine Diseases/virology ; Viral Matrix Proteins/genetics ; Viral Nonstructural Proteins/genetics
    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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    Mapping human genetic diversity in Asia (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-12-17
    Description: Asia harbors substantial cultural and linguistic diversity, but the geographic structure of genetic variation across the continent remains enigmatic. Here we report a large-scale survey of autosomal variation from a broad geographic sample of Asian human populations. Our results show that genetic ancestry is strongly correlated with linguistic affiliations as well as geography. Most populations show relatedness within ethnic/linguistic groups, despite prevalent gene flow among populations. More than 90% of East Asian (EA) haplotypes could be found in either Southeast Asian (SEA) or Central-South Asian (CSA) populations and show clinal structure with haplotype diversity decreasing from south to north. Furthermore, 50% of EA haplotypes were found in SEA only and 5% were found in CSA only, indicating that SEA was a major geographic source of EA populations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉HUGO Pan-Asian SNP Consortium -- Abdulla, Mahmood Ameen -- Ahmed, Ikhlak -- Assawamakin, Anunchai -- Bhak, Jong -- Brahmachari, Samir K -- Calacal, Gayvelline C -- Chaurasia, Amit -- Chen, Chien-Hsiun -- Chen, Jieming -- Chen, Yuan-Tsong -- Chu, Jiayou -- Cutiongco-de la Paz, Eva Maria C -- De Ungria, Maria Corazon A -- Delfin, Frederick C -- Edo, Juli -- Fuchareon, Suthat -- Ghang, Ho -- Gojobori, Takashi -- Han, Junsong -- Ho, Sheng-Feng -- Hoh, Boon Peng -- Huang, Wei -- Inoko, Hidetoshi -- Jha, Pankaj -- Jinam, Timothy A -- Jin, Li -- Jung, Jongsun -- Kangwanpong, Daoroong -- Kampuansai, Jatupol -- Kennedy, Giulia C -- Khurana, Preeti -- Kim, Hyung-Lae -- Kim, Kwangjoong -- Kim, Sangsoo -- Kim, Woo-Yeon -- Kimm, Kuchan -- Kimura, Ryosuke -- Koike, Tomohiro -- Kulawonganunchai, Supasak -- Kumar, Vikrant -- Lai, Poh San -- Lee, Jong-Young -- Lee, Sunghoon -- Liu, Edison T -- Majumder, Partha P -- Mandapati, Kiran Kumar -- Marzuki, Sangkot -- Mitchell, Wayne -- Mukerji, Mitali -- Naritomi, Kenji -- Ngamphiw, Chumpol -- Niikawa, Norio -- Nishida, Nao -- Oh, Bermseok -- Oh, Sangho -- Ohashi, Jun -- Oka, Akira -- Ong, Rick -- Padilla, Carmencita D -- Palittapongarnpim, Prasit -- Perdigon, Henry B -- Phipps, Maude Elvira -- Png, Eileen -- Sakaki, Yoshiyuki -- Salvador, Jazelyn M -- Sandraling, Yuliana -- Scaria, Vinod -- Seielstad, Mark -- Sidek, Mohd Ros -- Sinha, Amit -- Srikummool, Metawee -- Sudoyo, Herawati -- Sugano, Sumio -- Suryadi, Helena -- Suzuki, Yoshiyuki -- Tabbada, Kristina A -- Tan, Adrian -- Tokunaga, Katsushi -- Tongsima, Sissades -- Villamor, Lilian P -- Wang, Eric -- Wang, Ying -- Wang, Haifeng -- Wu, Jer-Yuarn -- Xiao, Huasheng -- Xu, Shuhua -- Yang, Jin Ok -- Shugart, Yin Yao -- Yoo, Hyang-Sook -- Yuan, Wentao -- Zhao, Guoping -- Zilfalil, Bin Alwi -- Indian Genome Variation Consortium -- New York, N.Y. -- Science. 2009 Dec 11;326(5959):1541-5. doi: 10.1126/science.1177074.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20007900" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Asia ; Asian Continental Ancestry Group/*genetics/history ; Bayes Theorem ; Cluster Analysis ; *Emigration and Immigration/history ; Ethnic Groups/*genetics/history ; Gene Flow ; Genotype ; Geography ; *Haplotypes ; History, Ancient ; Humans ; Language ; Linguistics ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; *Polymorphism, Single Nucleotide ; Principal Component Analysis
    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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    Genome analysis of the platypus reveals unique signatures of evolution (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-05-10
    Description: We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803040/" 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/PMC2803040/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Warren, Wesley C -- Hillier, LaDeana W -- Marshall Graves, Jennifer A -- Birney, Ewan -- Ponting, Chris P -- Grutzner, Frank -- Belov, Katherine -- Miller, Webb -- Clarke, Laura -- Chinwalla, Asif T -- Yang, Shiaw-Pyng -- Heger, Andreas -- Locke, Devin P -- Miethke, Pat -- Waters, Paul D -- Veyrunes, Frederic -- Fulton, Lucinda -- Fulton, Bob -- Graves, Tina -- Wallis, John -- Puente, Xose S -- Lopez-Otin, Carlos -- Ordonez, Gonzalo R -- Eichler, Evan E -- Chen, Lin -- Cheng, Ze -- Deakin, Janine E -- Alsop, Amber -- Thompson, Katherine -- Kirby, Patrick -- Papenfuss, Anthony T -- Wakefield, Matthew J -- Olender, Tsviya -- Lancet, Doron -- Huttley, Gavin A -- Smit, Arian F A -- Pask, Andrew -- Temple-Smith, Peter -- Batzer, Mark A -- Walker, Jerilyn A -- Konkel, Miriam K -- Harris, Robert S -- Whittington, Camilla M -- Wong, Emily S W -- Gemmell, Neil J -- Buschiazzo, Emmanuel -- Vargas Jentzsch, Iris M -- Merkel, Angelika -- Schmitz, Juergen -- Zemann, Anja -- Churakov, Gennady -- Kriegs, Jan Ole -- Brosius, Juergen -- Murchison, Elizabeth P -- Sachidanandam, Ravi -- Smith, Carly -- Hannon, Gregory J -- Tsend-Ayush, Enkhjargal -- McMillan, Daniel -- Attenborough, Rosalind -- Rens, Willem -- Ferguson-Smith, Malcolm -- Lefevre, Christophe M -- Sharp, Julie A -- Nicholas, Kevin R -- Ray, David A -- Kube, Michael -- Reinhardt, Richard -- Pringle, Thomas H -- Taylor, James -- Jones, Russell C -- Nixon, Brett -- Dacheux, Jean-Louis -- Niwa, Hitoshi -- Sekita, Yoko -- Huang, Xiaoqiu -- Stark, Alexander -- Kheradpour, Pouya -- Kellis, Manolis -- Flicek, Paul -- Chen, Yuan -- Webber, Caleb -- Hardison, Ross -- Nelson, Joanne -- Hallsworth-Pepin, Kym -- Delehaunty, Kim -- Markovic, Chris -- Minx, Pat -- Feng, Yucheng -- Kremitzki, Colin -- Mitreva, Makedonka -- Glasscock, Jarret -- Wylie, Todd -- Wohldmann, Patricia -- Thiru, Prathapan -- Nhan, Michael N -- Pohl, Craig S -- Smith, Scott M -- Hou, Shunfeng -- Nefedov, Mikhail -- de Jong, Pieter J -- Renfree, Marilyn B -- Mardis, Elaine R -- Wilson, Richard K -- 062023/Wellcome Trust/United Kingdom -- HG002238/HG/NHGRI NIH HHS/ -- MC_U137761446/Medical Research Council/United Kingdom -- P01 CA013106/CA/NCI NIH HHS/ -- P01 CA013106-37/CA/NCI NIH HHS/ -- R01 GM59290/GM/NIGMS NIH HHS/ -- R01 HG002939/HG/NHGRI NIH HHS/ -- R01 HG004037/HG/NHGRI NIH HHS/ -- R01 HG004037-02/HG/NHGRI NIH HHS/ -- R01HG02385/HG/NHGRI NIH HHS/ -- Medical Research Council/United Kingdom -- England -- Nature. 2008 May 8;453(7192):175-83. doi: 10.1038/nature06936.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA. wwarren@wustl.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18464734" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Composition ; Dentition ; *Evolution, Molecular ; Female ; Genome/*genetics ; Genomic Imprinting/genetics ; Humans ; Immunity/genetics ; Male ; Mammals/genetics ; MicroRNAs/genetics ; Milk Proteins/genetics ; Phylogeny ; Platypus/*genetics/immunology/physiology ; Receptors, Odorant/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Reptiles/genetics ; Sequence Analysis, DNA ; Spermatozoa/metabolism ; Venoms/genetics ; Zona Pellucida/metabolism
    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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  • 9
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    Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-10-03
    Description: In bilaterian animals, such as humans, flies and worms, hundreds of microRNAs (miRNAs), some conserved throughout bilaterian evolution, collectively regulate a substantial fraction of the transcriptome. In addition to miRNAs, other bilaterian small RNAs, known as Piwi-interacting RNAs (piRNAs), protect the genome from transposons. Here we identify small RNAs from animal phyla that diverged before the emergence of the Bilateria. The cnidarian Nematostella vectensis (starlet sea anemone), a close relative to the Bilateria, possesses an extensive repertoire of miRNA genes, two classes of piRNAs and a complement of proteins specific to small-RNA biology comparable to that of humans. The poriferan Amphimedon queenslandica (sponge), one of the simplest animals and a distant relative of the Bilateria, also possesses miRNAs, both classes of piRNAs and a full complement of the small-RNA machinery. Animal miRNA evolution seems to have been relatively dynamic, with precursor sizes and mature miRNA sequences differing greatly between poriferans, cnidarians and bilaterians. Nonetheless, miRNAs and piRNAs have been available as classes of riboregulators to shape gene expression throughout the evolution and radiation of animal phyla.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3837422/" 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/PMC3837422/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grimson, Andrew -- Srivastava, Mansi -- Fahey, Bryony -- Woodcroft, Ben J -- Chiang, H Rosaria -- King, Nicole -- Degnan, Bernard M -- Rokhsar, Daniel S -- Bartel, David P -- R01 GM067031/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 Oct 30;455(7217):1193-7. doi: 10.1038/nature07415. Epub 2008 Oct 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18830242" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Eukaryotic Cells/metabolism ; *Evolution, Molecular ; Gene Expression Regulation ; Humans ; MicroRNAs/*genetics ; Phylogeny ; RNA, Small Interfering/*genetics ; Sea Anemones/*genetics ; Sequence Analysis
    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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  • 10
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    Biodiversity and biogeography of phages in modern stromatolites and thrombolites (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-03-04
    Description: Viruses, and more particularly phages (viruses that infect bacteria), represent one of the most abundant living entities in aquatic and terrestrial environments. The biogeography of phages has only recently been investigated and so far reveals a cosmopolitan distribution of phage genetic material (or genotypes). Here we address this cosmopolitan distribution through the analysis of phage communities in modern microbialites, the living representatives of one of the most ancient life forms on Earth. On the basis of a comparative metagenomic analysis of viral communities associated with marine (Highborne Cay, Bahamas) and freshwater (Pozas Azules II and Rio Mesquites, Mexico) microbialites, we show that some phage genotypes are geographically restricted. The high percentage of unknown sequences recovered from the three metagenomes (〉97%), the low percentage similarities with sequences from other environmental viral (n = 42) and microbial (n = 36) metagenomes, and the absence of viral genotypes shared among microbialites indicate that viruses are genetically unique in these environments. Identifiable sequences in the Highborne Cay metagenome were dominated by single-stranded DNA microphages that were not detected in any other samples examined, including sea water, fresh water, sediment, terrestrial, extreme, metazoan-associated and marine microbial mats. Finally, a marine signature was present in the phage community of the Pozas Azules II microbialites, even though this environment has not been in contact with the ocean for tens of millions of years. Taken together, these results prove that viruses in modern microbialites display biogeographical variability and suggest that they may be derived from an ancient community.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Desnues, Christelle -- Rodriguez-Brito, Beltran -- Rayhawk, Steve -- Kelley, Scott -- Tran, Tuong -- Haynes, Matthew -- Liu, Hong -- Furlan, Mike -- Wegley, Linda -- Chau, Betty -- Ruan, Yijun -- Hall, Dana -- Angly, Florent E -- Edwards, Robert A -- Li, Linlin -- Thurber, Rebecca Vega -- Reid, R Pamela -- Siefert, Janet -- Souza, Valeria -- Valentine, David L -- Swan, Brandon K -- Breitbart, Mya -- Rohwer, Forest -- England -- Nature. 2008 Mar 20;452(7185):340-3. doi: 10.1038/nature06735. Epub 2008 Mar 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, San Diego State University, San Diego, California 92182, USA. cdesnues@yahoo.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18311127" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophages/classification/genetics/*isolation & purification/*physiology ; Bahamas ; *Biodiversity ; Capsid/chemistry ; Computational Biology ; DNA, Viral/analysis/genetics ; *Ecosystem ; Fresh Water/microbiology/virology ; Genome, Viral/genetics ; Genomics ; *Geography ; Geologic Sediments/microbiology/virology ; Mexico ; Molecular Sequence Data ; Phylogeny ; Proteome/metabolism ; Seawater/microbiology/virology ; *Water Microbiology
    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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