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  • 1
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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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  • 2
    Electronic Resource
    Electronic Resource
    Interactive effects of predation pressure and insecticide (temefos) toxicity on populations of the marsh fiddler crab Uca pugnax (1976)
    Springer
    Marine biology 35 (1976), S. 119-126 
    Details
    ISSN: 1432-1793
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The interaction of predation pressure with lethal and sublethal effects of temefos (Abate®) an organophosphorous insecticide, were studied in field populations of Uca pugnax (S.I. Smith). Changes in fiddler crab population densities were followed in open-marsh temefos-treated and untreated test plots and in treated and untreated plots which were caged over to reduce predation by marsh birds. Temefos significantly reduced the population density of U. pugnax in the open test plots but not in the caged plots. These results indicate that temefos has a primarily sublethal effect on the crabs, the effect becoming lethal only after interaction with avian predation. Evidence from the presence of a time-lag effect in the population decrease, from a calculated predation index, and from laboratory studies reported elsewhere of behavioral alteration by temefos also supports the conclusion that temefos primarily impairs the escape response of U. pugnax: this leads to increased predation and subsequently to a decreased fiddler crab population. Such studies of sublethal effects of toxicants and field studies of interactions of lethal and sublethal effects of such compounds with natural population dynamics of affected species are necessary to evaluate possible effects of toxicants on populations.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00390933
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  • 3
    Electronic Resource
    Electronic Resource
    Regeneration of soybean (Glycine max L. Merr.) from cultured primary leaf tissue (1987)
    Springer
    Plant cell reports 6 (1987), S. 83-89 
    Details
    ISSN: 1432-203X
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A reproducible method for regeneration of plants from primary leaf tissue of 27 varieties of soybean (Glycine max), encompassing maturity groups 00 to VIII, has been developed. Progeny from seeds recovered from regenerated plants appear normal. Best regeneration was from leaf explants (2.1–4.0 mm) obtained from 5 day old seedlings. While 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) was demonstrated to be essential for regeneration, addition of benzyladenine (BA) was found to enhance regeneration. Of the 6 other auxins tested, only picloram induced any regenerative response. Using identical volumes of medium and other conditions, regeneration could be obtained in 95 × 25 mm glass culture tubes but not in 60 × 15 mm Petri dishes. The regeneration of soybeans from primary leaf tissue was shown to be greatly enhanced by pyroglutamic acid (5-oxoproline). Stimulatory effects were attained if pyroglutamic acid was added directly to the medium or if it was formed in situ as a result of chemical transformation of glutamine during autoclaving. The “active” component produced by autoclaving glutamine was not a conjugate of glutamine with inorganic salts or another organic component of the medium. Filter-sterilized glutamine was shown to be inhibitory to regeneration. Murashige and Skoog (MS) and Schenk and Hildebrandt (SH) basal media were compared to Gamborg B5 medium. All contained 0.1 mg/l 2,4,5-T, 40 mg/l adenine sulfate and 10 mM pyroglutamic acid. No regeneration occurred when MS medium was used. Growth and appearance of callus growing on SH and B5 media with the additives were similar. The incidence of regeneration among cultures growing on SH medium was only one third compared to cultures grown on B5 medium.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00276659
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  • 4
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    The six functions of Agrobacterium VirE2 (2001)
    National Academy of Sciences
    Details
    Publication Date: 2001-01-16
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 5
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    Peptide linkage mapping of the Agrobacterium tumefaciens vir-encoded type IV secretion system reveals protein subassemblies (2002)
    National Academy of Sciences
    Details
    Publication Date: 2002-08-12
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 6
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    Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung (2009)
    National Academy of Sciences
    Details
    Publication Date: 2009-09-04
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 7
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    Interactive effects of predation pressure and insecticide (temefos) toxicity on populations of the marsh fiddler crab Uca pugnax (1976)
    Springer
    Details
    Publication Date: 1976-01-01
    Print ISSN: 0025-3162
    Electronic ISSN: 1432-1793
    Topics: Biology
    Published by Springer
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