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  • Lunar and Planetary Science and Exploration  (66)
  • Phylogeny  (37)
  • Life and Medical Sciences
  • ASTROPHYSICS
  • 2010-2014  (103)
  • 2010  (103)
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  • 2010-2014  (103)
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  • 1
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    Deep-sea oil plume enriches indigenous oil-degrading bacteria (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-08-26
    Description: The biological effects and expected fate of the vast amount of oil in the Gulf of Mexico from the Deepwater Horizon blowout are unknown owing to the depth and magnitude of this event. Here, we report that the dispersed hydrocarbon plume stimulated deep-sea indigenous gamma-Proteobacteria that are closely related to known petroleum degraders. Hydrocarbon-degrading genes coincided with the concentration of various oil contaminants. Changes in hydrocarbon composition with distance from the source and incubation experiments with environmental isolates demonstrated faster-than-expected hydrocarbon biodegradation rates at 5 degrees C. Based on these results, the potential exists for intrinsic bioremediation of the oil plume in the deep-water column without substantial oxygen drawdown.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hazen, Terry C -- Dubinsky, Eric A -- DeSantis, Todd Z -- Andersen, Gary L -- Piceno, Yvette M -- Singh, Navjeet -- Jansson, Janet K -- Probst, Alexander -- Borglin, Sharon E -- Fortney, Julian L -- Stringfellow, William T -- Bill, Markus -- Conrad, Mark E -- Tom, Lauren M -- Chavarria, Krystle L -- Alusi, Thana R -- Lamendella, Regina -- Joyner, Dominique C -- Spier, Chelsea -- Baelum, Jacob -- Auer, Manfred -- Zemla, Marcin L -- Chakraborty, Romy -- Sonnenthal, Eric L -- D'haeseleer, Patrik -- Holman, Hoi-Ying N -- Osman, Shariff -- Lu, Zhenmei -- Van Nostrand, Joy D -- Deng, Ye -- Zhou, Jizhong -- Mason, Olivia U -- New York, N.Y. -- Science. 2010 Oct 8;330(6001):204-8. doi: 10.1126/science.1195979. Epub 2010 Aug 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MS 70A-3317, One Cyclotron Road, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. tchazen@lbl.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20736401" target="_blank"〉PubMed〈/a〉
    Keywords: *Biodegradation, Environmental ; Biomass ; Colony Count, Microbial ; *Environmental Pollution ; Fatty Acids/analysis ; Gammaproteobacteria/classification/growth & development/isolation & ; purification/*metabolism ; Genes, Bacterial ; Genes, rRNA ; Hydrocarbons/*metabolism ; Molecular Sequence Data ; Oceanospirillaceae/classification/genetics/isolation & purification/*metabolism ; Petroleum/*metabolism ; Phospholipids/analysis ; Phylogeny ; Seawater/*microbiology
    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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    A catalog of reference genomes from the human microbiome (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-05-22
    Description: The human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body. The National Institutes of Health launched an initiative that focuses on describing the diversity of microbial species that are associated with health and disease. The first phase of this initiative includes the sequencing of hundreds of microbial reference genomes, coupled to metagenomic sequencing from multiple body sites. Here we present results from an initial reference genome sequencing of 178 microbial genomes. From 547,968 predicted polypeptides that correspond to the gene complement of these strains, previously unidentified ("novel") polypeptides that had both unmasked sequence length greater than 100 amino acids and no BLASTP match to any nonreference entry in the nonredundant subset were defined. This analysis resulted in a set of 30,867 polypeptides, of which 29,987 (approximately 97%) were unique. In addition, this set of microbial genomes allows for approximately 40% of random sequences from the microbiome of the gastrointestinal tract to be associated with organisms based on the match criteria used. Insights into pan-genome analysis suggest that we are still far from saturating microbial species genetic data sets. In addition, the associated metrics and standards used by our group for quality assurance are presented.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940224/" 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/PMC2940224/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Human Microbiome Jumpstart Reference Strains Consortium -- Nelson, Karen E -- Weinstock, George M -- Highlander, Sarah K -- Worley, Kim C -- Creasy, Heather Huot -- Wortman, Jennifer Russo -- Rusch, Douglas B -- Mitreva, Makedonka -- Sodergren, Erica -- Chinwalla, Asif T -- Feldgarden, Michael -- Gevers, Dirk -- Haas, Brian J -- Madupu, Ramana -- Ward, Doyle V -- Birren, Bruce W -- Gibbs, Richard A -- Methe, Barbara -- Petrosino, Joseph F -- Strausberg, Robert L -- Sutton, Granger G -- White, Owen R -- Wilson, Richard K -- Durkin, Scott -- Giglio, Michelle Gwinn -- Gujja, Sharvari -- Howarth, Clint -- Kodira, Chinnappa D -- Kyrpides, Nikos -- Mehta, Teena -- Muzny, Donna M -- Pearson, Matthew -- Pepin, Kymberlie -- Pati, Amrita -- Qin, Xiang -- Yandava, Chandri -- Zeng, Qiandong -- Zhang, Lan -- Berlin, Aaron M -- Chen, Lei -- Hepburn, Theresa A -- Johnson, Justin -- McCorrison, Jamison -- Miller, Jason -- Minx, Pat -- Nusbaum, Chad -- Russ, Carsten -- Sykes, Sean M -- Tomlinson, Chad M -- Young, Sarah -- Warren, Wesley C -- Badger, Jonathan -- Crabtree, Jonathan -- Markowitz, Victor M -- Orvis, Joshua -- Cree, Andrew -- Ferriera, Steve -- Fulton, Lucinda L -- Fulton, Robert S -- Gillis, Marcus -- Hemphill, Lisa D -- Joshi, Vandita -- Kovar, Christie -- Torralba, Manolito -- Wetterstrand, Kris A -- Abouellleil, Amr -- Wollam, Aye M -- Buhay, Christian J -- Ding, Yan -- Dugan, Shannon -- FitzGerald, Michael G -- Holder, Mike -- Hostetler, Jessica -- Clifton, Sandra W -- Allen-Vercoe, Emma -- Earl, Ashlee M -- Farmer, Candace N -- Liolios, Konstantinos -- Surette, Michael G -- Xu, Qiang -- Pohl, Craig -- Wilczek-Boney, Katarzyna -- Zhu, Dianhui -- HHSN272200900017C/PHS HHS/ -- N01 AI30071/AI/NIAID NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- U54 HG003273-04/HG/NHGRI NIH HHS/ -- U54 HG003273-04S1/HG/NHGRI NIH HHS/ -- U54 HG003273-05/HG/NHGRI NIH HHS/ -- U54 HG003273-05S1/HG/NHGRI NIH HHS/ -- U54 HG003273-05S2/HG/NHGRI NIH HHS/ -- U54 HG003273-06/HG/NHGRI NIH HHS/ -- U54 HG003273-06S1/HG/NHGRI NIH HHS/ -- U54 HG003273-06S2/HG/NHGRI NIH HHS/ -- U54 HG003273-07/HG/NHGRI NIH HHS/ -- U54 HG003273-08/HG/NHGRI NIH HHS/ -- U54 HG004973/HG/NHGRI NIH HHS/ -- U54 HG004973-01/HG/NHGRI NIH HHS/ -- U54 HG004973-02/HG/NHGRI NIH HHS/ -- U54-AI084844/AI/NIAID NIH HHS/ -- U54-HG003079/HG/NHGRI NIH HHS/ -- U54-HG003273/HG/NHGRI NIH HHS/ -- U54-HG004968/HG/NHGRI NIH HHS/ -- U54-HG004969/HG/NHGRI NIH HHS/ -- U54-HG004973/HG/NHGRI NIH HHS/ -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2010 May 21;328(5981):994-9. doi: 10.1126/science.1183605.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20489017" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/classification/genetics ; Bacterial Proteins/chemistry/genetics ; Biodiversity ; Computational Biology ; Databases, Genetic ; Gastrointestinal Tract/microbiology ; Genes, Bacterial ; Genetic Variation ; Genome, Archaeal ; *Genome, Bacterial ; Humans ; Metagenome/*genetics ; Metagenomics/methods/standards ; Mouth/microbiology ; Peptides/chemistry/genetics ; Phylogeny ; Respiratory System/microbiology ; *Sequence Analysis, DNA/standards ; Skin/microbiology ; Urogenital System/microbiology
    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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    Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-10-12
    Description: Culex quinquefasciatus (the southern house mosquito) is an important mosquito vector of viruses such as West Nile virus and St. Louis encephalitis virus, as well as of nematodes that cause lymphatic filariasis. C. quinquefasciatus is one species within the Culex pipiens species complex and can be found throughout tropical and temperate climates of the world. The ability of C. quinquefasciatus to take blood meals from birds, livestock, and humans contributes to its ability to vector pathogens between species. Here, we describe the genomic sequence of C. quinquefasciatus: Its repertoire of 18,883 protein-coding genes is 22% larger than that of Aedes aegypti and 52% larger than that of Anopheles gambiae with multiple gene-family expansions, including olfactory and gustatory receptors, salivary gland genes, and genes associated with xenobiotic detoxification.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3740384/" 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/PMC3740384/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Arensburger, Peter -- Megy, Karine -- Waterhouse, Robert M -- Abrudan, Jenica -- Amedeo, Paolo -- Antelo, Beatriz -- Bartholomay, Lyric -- Bidwell, Shelby -- Caler, Elisabet -- Camara, Francisco -- Campbell, Corey L -- Campbell, Kathryn S -- Casola, Claudio -- Castro, Marta T -- Chandramouliswaran, Ishwar -- Chapman, Sinead B -- Christley, Scott -- Costas, Javier -- Eisenstadt, Eric -- Feschotte, Cedric -- Fraser-Liggett, Claire -- Guigo, Roderic -- Haas, Brian -- Hammond, Martin -- Hansson, Bill S -- Hemingway, Janet -- Hill, Sharon R -- Howarth, Clint -- Ignell, Rickard -- Kennedy, Ryan C -- Kodira, Chinnappa D -- Lobo, Neil F -- Mao, Chunhong -- Mayhew, George -- Michel, Kristin -- Mori, Akio -- Liu, Nannan -- Naveira, Horacio -- Nene, Vishvanath -- Nguyen, Nam -- Pearson, Matthew D -- Pritham, Ellen J -- Puiu, Daniela -- Qi, Yumin -- Ranson, Hilary -- Ribeiro, Jose M C -- Roberston, Hugh M -- Severson, David W -- Shumway, Martin -- Stanke, Mario -- Strausberg, Robert L -- Sun, Cheng -- Sutton, Granger -- Tu, Zhijian Jake -- Tubio, Jose Manuel C -- Unger, Maria F -- Vanlandingham, Dana L -- Vilella, Albert J -- White, Owen -- White, Jared R -- Wondji, Charles S -- Wortman, Jennifer -- Zdobnov, Evgeny M -- Birren, Bruce -- Christensen, Bruce M -- Collins, Frank H -- Cornel, Anthony -- Dimopoulos, George -- Hannick, Linda I -- Higgs, Stephen -- Lanzaro, Gregory C -- Lawson, Daniel -- Lee, Norman H -- Muskavitch, Marc A T -- Raikhel, Alexander S -- Atkinson, Peter W -- HHSN266200400001C/PHS HHS/ -- HHSN266200400039C/AI/NIAID NIH HHS/ -- HHSN266200400039C/PHS HHS/ -- N01-AI-30071/AI/NIAID NIH HHS/ -- N01AI30071/AI/NIAID NIH HHS/ -- ZIA AI000810-13/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Oct 1;330(6000):86-8. doi: 10.1126/science.1191864.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Disease Vector Research, University of California Riverside, Riverside, CA 92521, USA. arensburger@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20929810" target="_blank"〉PubMed〈/a〉
    Keywords: Aedes/genetics ; Animals ; Anopheles gambiae/genetics ; Chromosome Mapping ; Chromosomes/*genetics ; Culex/classification/*genetics/physiology ; DNA Transposable Elements ; *Genes, Insect ; *Genome ; Insect Proteins/genetics/physiology ; Insect Vectors/genetics ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Receptors, Odorant/genetics ; Retroelements ; *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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    Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-03-20
    Description: Fusarium species are among the most important phytopathogenic and toxigenic fungi. To understand the molecular underpinnings of pathogenicity in the genus Fusarium, we compared the genomes of three phenotypically diverse species: Fusarium graminearum, Fusarium verticillioides and Fusarium oxysporum f. sp. lycopersici. Our analysis revealed lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity, indicative of horizontal acquisition. Experimentally, we demonstrate the transfer of two LS chromosomes between strains of F. oxysporum, converting a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in F. oxysporum. These findings put the evolution of fungal pathogenicity into a new perspective.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048781/" 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/PMC3048781/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ma, Li-Jun -- van der Does, H Charlotte -- Borkovich, Katherine A -- Coleman, Jeffrey J -- Daboussi, Marie-Josee -- Di Pietro, Antonio -- Dufresne, Marie -- Freitag, Michael -- Grabherr, Manfred -- Henrissat, Bernard -- Houterman, Petra M -- Kang, Seogchan -- Shim, Won-Bo -- Woloshuk, Charles -- Xie, Xiaohui -- Xu, Jin-Rong -- Antoniw, John -- Baker, Scott E -- Bluhm, Burton H -- Breakspear, Andrew -- Brown, Daren W -- Butchko, Robert A E -- Chapman, Sinead -- Coulson, Richard -- Coutinho, Pedro M -- Danchin, Etienne G J -- Diener, Andrew -- Gale, Liane R -- Gardiner, Donald M -- Goff, Stephen -- Hammond-Kosack, Kim E -- Hilburn, Karen -- Hua-Van, Aurelie -- Jonkers, Wilfried -- Kazan, Kemal -- Kodira, Chinnappa D -- Koehrsen, Michael -- Kumar, Lokesh -- Lee, Yong-Hwan -- Li, Liande -- Manners, John M -- Miranda-Saavedra, Diego -- Mukherjee, Mala -- Park, Gyungsoon -- Park, Jongsun -- Park, Sook-Young -- Proctor, Robert H -- Regev, Aviv -- Ruiz-Roldan, M Carmen -- Sain, Divya -- Sakthikumar, Sharadha -- Sykes, Sean -- Schwartz, David C -- Turgeon, B Gillian -- Wapinski, Ilan -- Yoder, Olen -- Young, Sarah -- Zeng, Qiandong -- Zhou, Shiguo -- Galagan, James -- Cuomo, Christina A -- Kistler, H Corby -- Rep, Martijn -- BBS/E/C/00004973/Biotechnology and Biological Sciences Research Council/United Kingdom -- DP1 OD003958/OD/NIH HHS/ -- R01 GM086565/GM/NIGMS NIH HHS/ -- R01 GM086565-03/GM/NIGMS NIH HHS/ -- R01 HG000225/HG/NHGRI NIH HHS/ -- England -- Nature. 2010 Mar 18;464(7287):367-73. doi: 10.1038/nature08850.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Broad Institute, Cambridge, Massachusetts 02141, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20237561" target="_blank"〉PubMed〈/a〉
    Keywords: Chromosomes, Fungal/*genetics ; Evolution, Molecular ; Fusarium/classification/*genetics/*pathogenicity ; Genome, Fungal/*genetics ; *Genomics ; Host-Parasite Interactions/genetics ; Multigene Family/genetics ; Phenotype ; Phylogeny ; Proteome/genetics ; Sequence Analysis, DNA ; Synteny/genetics ; Virulence/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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  • 5
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    Pathogenomics of Culex quinquefasciatus and meta-analysis of infection responses to diverse pathogens (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-10-12
    Description: The mosquito Culex quinquefasciatus poses a substantial threat to human and veterinary health as a primary vector of West Nile virus (WNV), the filarial worm Wuchereria bancrofti, and an avian malaria parasite. Comparative phylogenomics revealed an expanded canonical C. quinquefasciatus immune gene repertoire compared with those of Aedes aegypti and Anopheles gambiae. Transcriptomic analysis of C. quinquefasciatus genes responsive to WNV, W. bancrofti, and non-native bacteria facilitated an unprecedented meta-analysis of 25 vector-pathogen interactions involving arboviruses, filarial worms, bacteria, and malaria parasites, revealing common and distinct responses to these pathogen types in three mosquito genera. Our findings provide support for the hypothesis that mosquito-borne pathogens have evolved to evade innate immune responses in three vector mosquito species of major medical importance.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3104938/" 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/PMC3104938/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bartholomay, Lyric C -- Waterhouse, Robert M -- Mayhew, George F -- Campbell, Corey L -- Michel, Kristin -- Zou, Zhen -- Ramirez, Jose L -- Das, Suchismita -- Alvarez, Kanwal -- Arensburger, Peter -- Bryant, Bart -- Chapman, Sinead B -- Dong, Yuemei -- Erickson, Sara M -- Karunaratne, S H P Parakrama -- Kokoza, Vladimir -- Kodira, Chinnappa D -- Pignatelli, Patricia -- Shin, Sang Woon -- Vanlandingham, Dana L -- Atkinson, Peter W -- Birren, Bruce -- Christophides, George K -- Clem, Rollie J -- Hemingway, Janet -- Higgs, Stephen -- Megy, Karine -- Ranson, Hilary -- Zdobnov, Evgeny M -- Raikhel, Alexander S -- Christensen, Bruce M -- Dimopoulos, George -- Muskavitch, Marc A T -- F31 AI080161/AI/NIAID NIH HHS/ -- F31 AI080161-01A1/AI/NIAID NIH HHS/ -- HHSN266200400001C/AO/NIAID NIH HHS/ -- HHSN266200400001C/PHS HHS/ -- HHSN266200400039C/AI/NIAID NIH HHS/ -- HHSN266200400039C/PHS HHS/ -- P20 RR017686/RR/NCRR NIH HHS/ -- P20 RR017686-01/RR/NCRR NIH HHS/ -- R01 AI019769/AI/NIAID NIH HHS/ -- R01 AI019769-26/AI/NIAID NIH HHS/ -- R01 AI059492/AI/NIAID NIH HHS/ -- R01 AI059492-05/AI/NIAID NIH HHS/ -- R01 AI061576/AI/NIAID NIH HHS/ -- R01 AI061576-08/AI/NIAID NIH HHS/ -- R01 AI067698/AI/NIAID NIH HHS/ -- R01 AI067698-05/AI/NIAID NIH HHS/ -- R01 AI078997/AI/NIAID NIH HHS/ -- R01 AI078997-02/AI/NIAID NIH HHS/ -- R01 AI095842/AI/NIAID NIH HHS/ -- R01 AI19769/AI/NIAID NIH HHS/ -- R01 AI59492/AI/NIAID NIH HHS/ -- R01 AI67698/AI/NIAID NIH HHS/ -- R21 AI067642/AI/NIAID NIH HHS/ -- R21 AI067642-01/AI/NIAID NIH HHS/ -- T01CCT622892/PHS HHS/ -- T32 A107536/PHS HHS/ -- T32 AI007414/AI/NIAID NIH HHS/ -- T32 AI007417/AI/NIAID NIH HHS/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2010 Oct 1;330(6000):88-90. doi: 10.1126/science.1193162.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Entomology, Iowa State University, Ames, IA 50011, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20929811" target="_blank"〉PubMed〈/a〉
    Keywords: Aedes/genetics/immunology/microbiology/parasitology ; Animals ; Anopheles gambiae/genetics/metabolism/microbiology/parasitology ; Arboviruses/immunology/pathogenicity/physiology ; Bacteria/immunology/pathogenicity ; Biological Evolution ; Culex/*genetics/*immunology/microbiology/parasitology ; Ecosystem ; Filarioidea/immunology/pathogenicity/physiology ; Gene Expression Profiling ; Gene Expression Regulation ; *Genes, Insect ; *Host-Pathogen Interactions ; Immunity, Innate/*genetics ; Insect Vectors/*genetics/*immunology/microbiology/parasitology ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; RNA Interference ; Transcription, Genetic ; West Nile virus/immunology/pathogenicity/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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  • 6
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    Thousands of chemical starting points for antimalarial lead identification (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-05-21
    Description: Malaria is a devastating infection caused by protozoa of the genus Plasmodium. Drug resistance is widespread, no new chemical class of antimalarials has been introduced into clinical practice since 1996 and there is a recent rise of parasite strains with reduced sensitivity to the newest drugs. We screened nearly 2 million compounds in GlaxoSmithKline's chemical library for inhibitors of P. falciparum, of which 13,533 were confirmed to inhibit parasite growth by at least 80% at 2 microM concentration. More than 8,000 also showed potent activity against the multidrug resistant strain Dd2. Most (82%) compounds originate from internal company projects and are new to the malaria community. Analyses using historic assay data suggest several novel mechanisms of antimalarial action, such as inhibition of protein kinases and host-pathogen interaction related targets. Chemical structures and associated data are hereby made public to encourage additional drug lead identification efforts and further research into this disease.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gamo, Francisco-Javier -- Sanz, Laura M -- Vidal, Jaume -- de Cozar, Cristina -- Alvarez, Emilio -- Lavandera, Jose-Luis -- Vanderwall, Dana E -- Green, Darren V S -- Kumar, Vinod -- Hasan, Samiul -- Brown, James R -- Peishoff, Catherine E -- Cardon, Lon R -- Garcia-Bustos, Jose F -- England -- Nature. 2010 May 20;465(7296):305-10. doi: 10.1038/nature09107.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20485427" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antimalarials/*analysis/chemistry/*pharmacology/toxicity ; Cell Line, Tumor ; *Drug Discovery ; Drug Resistance, Multiple/drug effects ; Humans ; Malaria, Falciparum/*drug therapy/parasitology ; Models, Biological ; Phylogeny ; Plasmodium falciparum/*drug effects/enzymology/genetics/growth & development ; Small Molecule Libraries/*analysis/chemistry/*pharmacology/toxicity
    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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  • 7
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    Complete Khoisan and Bantu genomes from southern Africa (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-02-19
    Description: The genetic structure of the indigenous hunter-gatherer peoples of southern Africa, the oldest known lineage of modern human, is important for understanding human diversity. Studies based on mitochondrial and small sets of nuclear markers have shown that these hunter-gatherers, known as Khoisan, San, or Bushmen, are genetically divergent from other humans. However, until now, fully sequenced human genomes have been limited to recently diverged populations. Here we present the complete genome sequences of an indigenous hunter-gatherer from the Kalahari Desert and a Bantu from southern Africa, as well as protein-coding regions from an additional three hunter-gatherers from disparate regions of the Kalahari. We characterize the extent of whole-genome and exome diversity among the five men, reporting 1.3 million novel DNA differences genome-wide, including 13,146 novel amino acid variants. In terms of nucleotide substitutions, the Bushmen seem to be, on average, more different from each other than, for example, a European and an Asian. Observed genomic differences between the hunter-gatherers and others may help to pinpoint genetic adaptations to an agricultural lifestyle. Adding the described variants to current databases will facilitate inclusion of southern Africans in medical research efforts, particularly when family and medical histories can be correlated with genome-wide data.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890430/" 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/PMC3890430/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schuster, Stephan C -- Miller, Webb -- Ratan, Aakrosh -- Tomsho, Lynn P -- Giardine, Belinda -- Kasson, Lindsay R -- Harris, Robert S -- Petersen, Desiree C -- Zhao, Fangqing -- Qi, Ji -- Alkan, Can -- Kidd, Jeffrey M -- Sun, Yazhou -- Drautz, Daniela I -- Bouffard, Pascal -- Muzny, Donna M -- Reid, Jeffrey G -- Nazareth, Lynne V -- Wang, Qingyu -- Burhans, Richard -- Riemer, Cathy -- Wittekindt, Nicola E -- Moorjani, Priya -- Tindall, Elizabeth A -- Danko, Charles G -- Teo, Wee Siang -- Buboltz, Anne M -- Zhang, Zhenhai -- Ma, Qianyi -- Oosthuysen, Arno -- Steenkamp, Abraham W -- Oostuisen, Hermann -- Venter, Philippus -- Gajewski, John -- Zhang, Yu -- Pugh, B Franklin -- Makova, Kateryna D -- Nekrutenko, Anton -- Mardis, Elaine R -- Patterson, Nick -- Pringle, Tom H -- Chiaromonte, Francesca -- Mullikin, James C -- Eichler, Evan E -- Hardison, Ross C -- Gibbs, Richard A -- Harkins, Timothy T -- Hayes, Vanessa M -- R01 GM087472/GM/NIGMS NIH HHS/ -- R01 HG004909/HG/NHGRI NIH HHS/ -- R01GM087472/GM/NIGMS NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- Intramural NIH HHS/ -- England -- Nature. 2010 Feb 18;463(7283):943-7. doi: 10.1038/nature08795.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Lab, University Park, Pennsylvania 16802, USA. scs@bx.psu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20164927" target="_blank"〉PubMed〈/a〉
    Keywords: African Continental Ancestry Group/*genetics ; Asian Continental Ancestry Group/genetics ; Ethnic Groups/*genetics ; European Continental Ancestry Group/genetics ; Exons/genetics ; Genetics, Medical ; Genome, Human/*genetics ; Humans ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; South Africa/ethnology
    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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  • 8
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    Reassortment of pandemic H1N1/2009 influenza A virus in swine (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-06-19
    Description: The emergence of pandemic H1N1/2009 influenza demonstrated that pandemic viruses could be generated in swine. Subsequent reintroduction of H1N1/2009 to swine has occurred in multiple countries. Through systematic surveillance of influenza viruses in swine from a Hong Kong abattoir, we characterize a reassortant progeny of H1N1/2009 with swine viruses. Swine experimentally infected with this reassortant developed mild illness and transmitted infection to contact animals. Continued reassortment of H1N1/2009 with swine influenza viruses could produce variants with transmissibility and altered virulence for humans. Global systematic surveillance of influenza viruses in swine is warranted.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3569847/" 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/PMC3569847/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vijaykrishna, D -- Poon, L L M -- Zhu, H C -- Ma, S K -- Li, O T W -- Cheung, C L -- Smith, G J D -- Peiris, J S M -- Guan, Y -- HHSN266200700005C/AI/NIAID NIH HHS/ -- HHSN266200700005C/PHS HHS/ -- New York, N.Y. -- Science. 2010 Jun 18;328(5985):1529. doi: 10.1126/science.1189132.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉State Key Laboratory of Emerging Infectious Diseases and Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20558710" target="_blank"〉PubMed〈/a〉
    Keywords: Abattoirs ; Animals ; Disease Outbreaks ; Genes, Viral ; Genotype ; Hemagglutinin Glycoproteins, Influenza Virus/genetics ; Hong Kong ; Humans ; Influenza A Virus, H1N1 Subtype/classification/*genetics/isolation & ; purification/pathogenicity ; Influenza A Virus, H1N2 Subtype/classification/genetics/isolation & purification ; Influenza, Human/epidemiology/virology ; Molecular Sequence Data ; Neuraminidase/genetics ; Orthomyxoviridae Infections/epidemiology/transmission/*veterinary/virology ; Phylogeny ; Population Surveillance ; Reassortant Viruses/classification/*genetics/isolation & purification ; Swine/*virology ; Swine Diseases/epidemiology/transmission/*virology
    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 Western clawed frog Xenopus tropicalis (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-05-01
    Description: The western clawed frog Xenopus tropicalis is an important model for vertebrate development that combines experimental advantages of the African clawed frog Xenopus laevis with more tractable genetics. Here we present a draft genome sequence assembly of X. tropicalis. This genome encodes more than 20,000 protein-coding genes, including orthologs of at least 1700 human disease genes. Over 1 million expressed sequence tags validated the annotation. More than one-third of the genome consists of transposable elements, with unusually prevalent DNA transposons. Like that of other tetrapods, the genome of X. tropicalis contains gene deserts enriched for conserved noncoding elements. The genome exhibits substantial shared synteny with human and chicken over major parts of large chromosomes, broken by lineage-specific chromosome fusions and fissions, mainly in the mammalian lineage.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2994648/" 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/PMC2994648/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hellsten, Uffe -- Harland, Richard M -- Gilchrist, Michael J -- Hendrix, David -- Jurka, Jerzy -- Kapitonov, Vladimir -- Ovcharenko, Ivan -- Putnam, Nicholas H -- Shu, Shengqiang -- Taher, Leila -- Blitz, Ira L -- Blumberg, Bruce -- Dichmann, Darwin S -- Dubchak, Inna -- Amaya, Enrique -- Detter, John C -- Fletcher, Russell -- Gerhard, Daniela S -- Goodstein, David -- Graves, Tina -- Grigoriev, Igor V -- Grimwood, Jane -- Kawashima, Takeshi -- Lindquist, Erika -- Lucas, Susan M -- Mead, Paul E -- Mitros, Therese -- Ogino, Hajime -- Ohta, Yuko -- Poliakov, Alexander V -- Pollet, Nicolas -- Robert, Jacques -- Salamov, Asaf -- Sater, Amy K -- Schmutz, Jeremy -- Terry, Astrid -- Vize, Peter D -- Warren, Wesley C -- Wells, Dan -- Wills, Andrea -- Wilson, Richard K -- Zimmerman, Lyle B -- Zorn, Aaron M -- Grainger, Robert -- Grammer, Timothy -- Khokha, Mustafa K -- Richardson, Paul M -- Rokhsar, Daniel S -- HHSN261200800001E/CA/NCI NIH HHS/ -- MC_U117560482/Medical Research Council/United Kingdom -- P41 HD064556/HD/NICHD NIH HHS/ -- P41 HD064556-01/HD/NICHD NIH HHS/ -- P41 HD064556-02/HD/NICHD NIH HHS/ -- R01 AI027877/AI/NIAID NIH HHS/ -- R01 AI027877-20/AI/NIAID NIH HHS/ -- R01 DK070858/DK/NIDDK NIH HHS/ -- R01 DK070858-05/DK/NIDDK NIH HHS/ -- R01 EY018000/EY/NEI NIH HHS/ -- R01 EY018000-03/EY/NEI NIH HHS/ -- R01 GM060572/GM/NIGMS NIH HHS/ -- R01 GM060572-05/GM/NIGMS NIH HHS/ -- R01 GM086321/GM/NIGMS NIH HHS/ -- R01 GM086321-03/GM/NIGMS NIH HHS/ -- R01 HD042294/HD/NICHD NIH HHS/ -- R01 HD042294-05/HD/NICHD NIH HHS/ -- R01 HD045776/HD/NICHD NIH HHS/ -- R01 HD045776-05/HD/NICHD NIH HHS/ -- R01 HD046661-03/HD/NICHD NIH HHS/ -- R01 MH079381/MH/NIMH NIH HHS/ -- R01 MH079381-02/MH/NIMH NIH HHS/ -- R21 HD065713/HD/NICHD NIH HHS/ -- R24 AI059830/AI/NIAID NIH HHS/ -- R24 AI059830-08/AI/NIAID NIH HHS/ -- R24 RR015088/RR/NCRR NIH HHS/ -- R24 RR015088-03/RR/NCRR NIH HHS/ -- U01 HG002155-05/HG/NHGRI NIH HHS/ -- U01 HG02155/HG/NHGRI NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Apr 30;328(5978):633-6. doi: 10.1126/science.1183670.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA. uhellsten@lbl.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20431018" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chickens/genetics ; Chromosome Mapping ; Chromosomes/genetics ; Computational Biology ; Conserved Sequence ; DNA Transposable Elements ; DNA, Complementary ; Embryo, Nonmammalian/metabolism ; Evolution, Molecular ; Expressed Sequence Tags ; Gene Duplication ; Genes ; *Genome ; Humans ; Phylogeny ; *Sequence Analysis, DNA ; Synteny ; Vertebrates/genetics ; Xenopus/embryology/*genetics ; Xenopus Proteins/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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    Ancient human genome sequence of an extinct Palaeo-Eskimo (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-02-12
    Description: We report here the genome sequence of an ancient human. Obtained from approximately 4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20x, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies. We identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), of which 6.8% have not been reported previously. We estimate raw read contamination to be no higher than 0.8%. We use functional SNP assessment to assign possible phenotypic characteristics of the individual that belonged to a culture whose location has yielded only trace human remains. We compare the high-confidence SNPs to those of contemporary populations to find the populations most closely related to the individual. This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951495/" 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/PMC3951495/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rasmussen, Morten -- Li, Yingrui -- Lindgreen, Stinus -- Pedersen, Jakob Skou -- Albrechtsen, Anders -- Moltke, Ida -- Metspalu, Mait -- Metspalu, Ene -- Kivisild, Toomas -- Gupta, Ramneek -- Bertalan, Marcelo -- Nielsen, Kasper -- Gilbert, M Thomas P -- Wang, Yong -- Raghavan, Maanasa -- Campos, Paula F -- Kamp, Hanne Munkholm -- Wilson, Andrew S -- Gledhill, Andrew -- Tridico, Silvana -- Bunce, Michael -- Lorenzen, Eline D -- Binladen, Jonas -- Guo, Xiaosen -- Zhao, Jing -- Zhang, Xiuqing -- Zhang, Hao -- Li, Zhuo -- Chen, Minfeng -- Orlando, Ludovic -- Kristiansen, Karsten -- Bak, Mads -- Tommerup, Niels -- Bendixen, Christian -- Pierre, Tracey L -- Gronnow, Bjarne -- Meldgaard, Morten -- Andreasen, Claus -- Fedorova, Sardana A -- Osipova, Ludmila P -- Higham, Thomas F G -- Ramsey, Christopher Bronk -- Hansen, Thomas V O -- Nielsen, Finn C -- Crawford, Michael H -- Brunak, Soren -- Sicheritz-Ponten, Thomas -- Villems, Richard -- Nielsen, Rasmus -- Krogh, Anders -- Wang, Jun -- Willerslev, Eske -- R01 HG003229/HG/NHGRI NIH HHS/ -- R01 HG003229-05/HG/NHGRI NIH HHS/ -- England -- Nature. 2010 Feb 11;463(7282):757-62. doi: 10.1038/nature08835.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for GeoGenetics, Natural History Museum of Denmark and Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20148029" target="_blank"〉PubMed〈/a〉
    Keywords: *Cryopreservation ; Emigration and Immigration/history ; *Extinction, Biological ; Genetics, Population ; Genome, Human/*genetics ; Genomics ; Genotype ; Greenland ; Hair ; History, Ancient ; Humans ; Inuits/*genetics ; Male ; Phenotype ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA ; Siberia/ethnology
    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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