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  • 1
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    Sequencing of 50 human exomes reveals adaptation to high altitude (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-07-03
    Description: Residents of the Tibetan Plateau show heritable adaptations to extreme altitude. We sequenced 50 exomes of ethnic Tibetans, encompassing coding sequences of 92% of human genes, with an average coverage of 18x per individual. Genes showing population-specific allele frequency changes, which represent strong candidates for altitude adaptation, were identified. The strongest signal of natural selection came from endothelial Per-Arnt-Sim (PAS) domain protein 1 (EPAS1), a transcription factor involved in response to hypoxia. One single-nucleotide polymorphism (SNP) at EPAS1 shows a 78% frequency difference between Tibetan and Han samples, representing the fastest allele frequency change observed at any human gene to date. This SNP's association with erythrocyte abundance supports the role of EPAS1 in adaptation to hypoxia. Thus, a population genomic survey has revealed a functionally important locus in genetic adaptation to high altitude.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3711608/" 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/PMC3711608/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yi, Xin -- Liang, Yu -- Huerta-Sanchez, Emilia -- Jin, Xin -- Cuo, Zha Xi Ping -- Pool, John E -- Xu, Xun -- Jiang, Hui -- Vinckenbosch, Nicolas -- Korneliussen, Thorfinn Sand -- Zheng, Hancheng -- Liu, Tao -- He, Weiming -- Li, Kui -- Luo, Ruibang -- Nie, Xifang -- Wu, Honglong -- Zhao, Meiru -- Cao, Hongzhi -- Zou, Jing -- Shan, Ying -- Li, Shuzheng -- Yang, Qi -- Asan -- Ni, Peixiang -- Tian, Geng -- Xu, Junming -- Liu, Xiao -- Jiang, Tao -- Wu, Renhua -- Zhou, Guangyu -- Tang, Meifang -- Qin, Junjie -- Wang, Tong -- Feng, Shuijian -- Li, Guohong -- Huasang -- Luosang, Jiangbai -- Wang, Wei -- Chen, Fang -- Wang, Yading -- Zheng, Xiaoguang -- Li, Zhuo -- Bianba, Zhuoma -- Yang, Ge -- Wang, Xinping -- Tang, Shuhui -- Gao, Guoyi -- Chen, Yong -- Luo, Zhen -- Gusang, Lamu -- Cao, Zheng -- Zhang, Qinghui -- Ouyang, Weihan -- Ren, Xiaoli -- Liang, Huiqing -- Zheng, Huisong -- Huang, Yebo -- Li, Jingxiang -- Bolund, Lars -- Kristiansen, Karsten -- Li, Yingrui -- Zhang, Yong -- Zhang, Xiuqing -- Li, Ruiqiang -- Li, Songgang -- Yang, Huanming -- Nielsen, Rasmus -- Wang, Jun -- Wang, Jian -- R01 HG003229/HG/NHGRI NIH HHS/ -- R01 MH084695/MH/NIMH NIH HHS/ -- R01HG003229/HG/NHGRI NIH HHS/ -- R01MHG084695/PHS HHS/ -- New York, N.Y. -- Science. 2010 Jul 2;329(5987):75-8. doi: 10.1126/science.1190371.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉BGI-Shenzhen, Shenzhen 518083, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20595611" target="_blank"〉PubMed〈/a〉
    Keywords: Acclimatization/*genetics ; *Altitude ; Asian Continental Ancestry Group/genetics ; Basic Helix-Loop-Helix Transcription Factors/*genetics/physiology ; Bayes Theorem ; China ; Erythrocyte Count ; Ethnic Groups/genetics ; *Exons ; Female ; Gene Frequency ; Genetic Association Studies ; *Genome, Human ; Hemoglobins/analysis ; Humans ; Male ; Oxygen/blood ; Polymorphism, Single Nucleotide ; *Selection, Genetic ; Sequence Analysis, DNA ; Tibet
    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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    Ascaris suum draft genome (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-10-28
    Description: Parasitic diseases have a devastating, long-term impact on human health, welfare and food production worldwide. More than two billion people are infected with geohelminths, including the roundworms Ascaris (common roundworm), Necator and Ancylostoma (hookworms), and Trichuris (whipworm), mainly in developing or impoverished nations of Asia, Africa and Latin America. In humans, the diseases caused by these parasites result in about 135,000 deaths annually, with a global burden comparable with that of malaria or tuberculosis in disability-adjusted life years. Ascaris alone infects around 1.2 billion people and, in children, causes nutritional deficiency, impaired physical and cognitive development and, in severe cases, death. Ascaris also causes major production losses in pigs owing to reduced growth, failure to thrive and mortality. The Ascaris-swine model makes it possible to study the parasite, its relationship with the host, and ascariasis at the molecular level. To enable such molecular studies, we report the 273 megabase draft genome of Ascaris suum and compare it with other nematode genomes. This genome has low repeat content (4.4%) and encodes about 18,500 protein-coding genes. Notably, the A. suum secretome (about 750 molecules) is rich in peptidases linked to the penetration and degradation of host tissues, and an assemblage of molecules likely to modulate or evade host immune responses. This genome provides a comprehensive resource to the scientific community and underpins the development of new and urgently needed interventions (drugs, vaccines and diagnostic tests) against ascariasis and other nematodiases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jex, Aaron R -- Liu, Shiping -- Li, Bo -- Young, Neil D -- Hall, Ross S -- Li, Yingrui -- Yang, Linfeng -- Zeng, Na -- Xu, Xun -- Xiong, Zijun -- Chen, Fangyuan -- Wu, Xuan -- Zhang, Guojie -- Fang, Xiaodong -- Kang, Yi -- Anderson, Garry A -- Harris, Todd W -- Campbell, Bronwyn E -- Vlaminck, Johnny -- Wang, Tao -- Cantacessi, Cinzia -- Schwarz, Erich M -- Ranganathan, Shoba -- Geldhof, Peter -- Nejsum, Peter -- Sternberg, Paul W -- Yang, Huanming -- Wang, Jun -- Wang, Jian -- Gasser, Robin B -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 Oct 26;479(7374):529-33. doi: 10.1038/nature10553.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria 3010, Australia. ajex@unimelb.edu.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22031327" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antinematodal Agents ; Ascariasis/drug therapy/parasitology ; Ascaris suum/drug effects/*genetics ; Drug Design ; Genes, Helminth/genetics ; Genome, Helminth/*genetics ; Genomics ; Molecular Sequence Annotation ; Molecular Targeted Therapy
    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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    China's grain relies on foreign fertilizer (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-08-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Fang -- Wan, Kai-yuan -- Liu, Yi -- Tao, Yong -- England -- Nature. 2011 Aug 3;476(7358):33. doi: 10.1038/476033d.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21814266" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/*statistics & numerical data/trends ; China ; Edible Grain/*growth & development ; Fertilizers/*utilization ; Food Supply/*statistics & numerical data ; *Internationality ; Potassium
    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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  • 4
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    Metagenomic discovery of biomass-degrading genes and genomes from cow rumen (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-01-29
    Description: The paucity of enzymes that efficiently deconstruct plant polysaccharides represents a major bottleneck for industrial-scale conversion of cellulosic biomass into biofuels. Cow rumen microbes specialize in degradation of cellulosic plant material, but most members of this complex community resist cultivation. To characterize biomass-degrading genes and genomes, we sequenced and analyzed 268 gigabases of metagenomic DNA from microbes adherent to plant fiber incubated in cow rumen. From these data, we identified 27,755 putative carbohydrate-active genes and expressed 90 candidate proteins, of which 57% were enzymatically active against cellulosic substrates. We also assembled 15 uncultured microbial genomes, which were validated by complementary methods including single-cell genome sequencing. These data sets provide a substantially expanded catalog of genes and genomes participating in the deconstruction of cellulosic biomass.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hess, Matthias -- Sczyrba, Alexander -- Egan, Rob -- Kim, Tae-Wan -- Chokhawala, Harshal -- Schroth, Gary -- Luo, Shujun -- Clark, Douglas S -- Chen, Feng -- Zhang, Tao -- Mackie, Roderick I -- Pennacchio, Len A -- Tringe, Susannah G -- Visel, Axel -- Woyke, Tanja -- Wang, Zhong -- Rubin, Edward M -- New York, N.Y. -- Science. 2011 Jan 28;331(6016):463-7. doi: 10.1126/science.1200387.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21273488" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Bacteria/enzymology/*genetics/isolation & purification/metabolism ; Bacterial Proteins/chemistry/genetics/metabolism ; *Biomass ; Carbohydrate Metabolism ; Cattle/*microbiology ; Cellulase/genetics/metabolism ; Cellulases/chemistry/*genetics/metabolism ; Cellulose/*metabolism ; Cellulose 1,4-beta-Cellobiosidase/genetics/metabolism ; Genes, Bacterial ; Genome, Bacterial ; *Metagenome ; Metagenomics/methods ; Molecular Sequence Annotation ; Molecular Sequence Data ; Poaceae/microbiology ; Rumen/metabolism/*microbiology ; 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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