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  • Nature Publishing Group (NPG)  (11)
  • 1
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    Lunar apatite with terrestrial volatile abundances (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-07-24
    Description: The Moon is thought to be depleted relative to the Earth in volatile elements such as H, Cl and the alkalis. Nevertheless, evidence for lunar explosive volcanism has been used to infer that some lunar magmas exsolved a CO-rich and CO(2)-rich vapour phase before or during eruption. Although there is also evidence for other volatile species on glass spherules, until recently there had been no unambiguous reports of indigenous H in lunar rocks. Here we report quantitative ion microprobe measurements of late-stage apatite from lunar basalt 14053 that document concentrations of H, Cl and S that are indistinguishable from apatites in common terrestrial igneous rocks. These volatile contents could reflect post-magmatic metamorphic volatile addition or growth from a late-stage, interstitial, sulphide-saturated melt that contained approximately 1,600 parts per million H(2)O and approximately 3,500 parts per million Cl. Both metamorphic and igneous models of apatite formation suggest a volatile inventory for at least some lunar materials that is similar to comparable terrestrial materials. One possible implication is that portions of the lunar mantle or crust are more volatile-rich than previously thought.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boyce, Jeremy W -- Liu, Yang -- Rossman, George R -- Guan, Yunbin -- Eiler, John M -- Stolper, Edward M -- Taylor, Lawrence A -- England -- Nature. 2010 Jul 22;466(7305):466-9. doi: 10.1038/nature09274.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California 91125-2500, USA. jwboyce@alum.mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20651686" target="_blank"〉PubMed〈/a〉
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    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
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    Injury-induced mechanical hypersensitivity requires C-low threshold mechanoreceptors (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-11-17
    Description: Mechanical pain contributes to the morbidity associated with inflammation and trauma, but primary sensory neurons that convey the sensation of acute and persistent mechanical pain have not been identified. Dorsal root ganglion (DRG) neurons transmit sensory information to the spinal cord using the excitatory transmitter glutamate, a process that depends on glutamate transport into synaptic vesicles for regulated exocytotic release. Here we report that a small subset of cells in the DRG expresses the low abundance vesicular glutamate transporter VGLUT3 (also known as SLC17A8). In the dorsal horn of the spinal cord, these afferents project to lamina I and the innermost layer of lamina II, which has previously been implicated in persistent pain caused by injury. Because the different VGLUT isoforms generally have a non-redundant pattern of expression, we used Vglut3 knockout mice to assess the role of VGLUT3(+) primary afferents in the behavioural response to somatosensory input. The loss of VGLUT3 specifically impairs mechanical pain sensation, and in particular the mechanical hypersensitivity to normally innocuous stimuli that accompanies inflammation, nerve injury and trauma. Direct recording from VGLUT3(+) neurons in the DRG further identifies them as a poorly understood population of unmyelinated, low threshold mechanoreceptors (C-LTMRs). The analysis of Vglut3(-/-) mice now indicates a critical role for C-LTMRs in the mechanical hypersensitivity caused by injury.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2810205/" 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/PMC2810205/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Seal, Rebecca P -- Wang, Xidao -- Guan, Yun -- Raja, Srinivasa N -- Woodbury, C Jeffery -- Basbaum, Allan I -- Edwards, Robert H -- F32 MH068085/MH/NIMH NIH HHS/ -- F32 MH068085-02/MH/NIMH NIH HHS/ -- R01 MH050712/MH/NIMH NIH HHS/ -- R01 MH050712-17/MH/NIMH NIH HHS/ -- R01 NS044094/NS/NINDS NIH HHS/ -- R01 NS044094-06/NS/NINDS NIH HHS/ -- England -- Nature. 2009 Dec 3;462(7273):651-5. doi: 10.1038/nature08505. Epub 2009 Nov 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, University of California, San Francisco School of Medicine, California 94143, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19915548" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Transport Systems, Acidic/genetics/*metabolism ; Animals ; Behavior, Animal/physiology ; Female ; Ganglia, Spinal/*metabolism ; Gene Expression Regulation ; Hypersensitivity/*genetics/*physiopathology ; Mechanoreceptors/*physiology ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Pain/*genetics ; Wounds and Injuries/*physiopathology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
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    Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-06-12
    Description: In March and early April 2009, a new swine-origin influenza A (H1N1) virus (S-OIV) emerged in Mexico and the United States. During the first few weeks of surveillance, the virus spread worldwide to 30 countries (as of May 11) by human-to-human transmission, causing the World Health Organization to raise its pandemic alert to level 5 of 6. This virus has the potential to develop into the first influenza pandemic of the twenty-first century. Here we use evolutionary analysis to estimate the timescale of the origins and the early development of the S-OIV epidemic. We show that it was derived from several viruses circulating in swine, and that the initial transmission to humans occurred several months before recognition of the outbreak. A phylogenetic estimate of the gaps in genetic surveillance indicates a long period of unsampled ancestry before the S-OIV outbreak, suggesting that the reassortment of swine lineages may have occurred years before emergence in humans, and that the multiple genetic ancestry of S-OIV is not indicative of an artificial origin. Furthermore, the unsampled history of the epidemic means that the nature and location of the genetically closest swine viruses reveal little about the immediate origin of the epidemic, despite the fact that we included a panel of closely related and previously unpublished swine influenza isolates. Our results highlight the need for systematic surveillance of influenza in swine, and provide evidence that the mixing of new genetic elements in swine can result in the emergence of viruses with pandemic potential in humans.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smith, Gavin J D -- Vijaykrishna, Dhanasekaran -- Bahl, Justin -- Lycett, Samantha J -- Worobey, Michael -- Pybus, Oliver G -- Ma, Siu Kit -- Cheung, Chung Lam -- Raghwani, Jayna -- Bhatt, Samir -- Peiris, J S Malik -- Guan, Yi -- Rambaut, Andrew -- BB/E009670/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- HHSN266200700005C/PHS HHS/ -- Biotechnology and Biological Sciences Research Council/United Kingdom -- England -- Nature. 2009 Jun 25;459(7250):1122-5. doi: 10.1038/nature08182.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉State Key Laboratory of Emerging Infectious Diseases & Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19516283" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Disease Outbreaks ; *Evolution, Molecular ; Genome, Viral/*genetics ; Humans ; Influenza A Virus, H1N1 Subtype/classification/*genetics ; *Influenza, Human/epidemiology/virology ; Molecular Sequence Data ; Orthomyxoviridae Infections/epidemiology/veterinary/virology ; Phylogeny ; Reassortant Viruses/classification/*genetics ; Swine ; Swine Diseases/*virology ; Time Factors
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
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    The mutation spectrum revealed by paired genome sequences from a lung cancer patient (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-05-28
    Description: Lung cancer is the leading cause of cancer-related mortality worldwide, with non-small-cell lung carcinomas in smokers being the predominant form of the disease. Although previous studies have identified important common somatic mutations in lung cancers, they have primarily focused on a limited set of genes and have thus provided a constrained view of the mutational spectrum. Recent cancer sequencing efforts have used next-generation sequencing technologies to provide a genome-wide view of mutations in leukaemia, breast cancer and cancer cell lines. Here we present the complete sequences of a primary lung tumour (60x coverage) and adjacent normal tissue (46x). Comparing the two genomes, we identify a wide variety of somatic variations, including 〉50,000 high-confidence single nucleotide variants. We validated 530 somatic single nucleotide variants in this tumour, including one in the KRAS proto-oncogene and 391 others in coding regions, as well as 43 large-scale structural variations. These constitute a large set of new somatic mutations and yield an estimated 17.7 per megabase genome-wide somatic mutation rate. Notably, we observe a distinct pattern of selection against mutations within expressed genes compared to non-expressed genes and in promoter regions up to 5 kilobases upstream of all protein-coding genes. Furthermore, we observe a higher rate of amino acid-changing mutations in kinase genes. We present a comprehensive view of somatic alterations in a single lung tumour, and provide the first evidence, to our knowledge, of distinct selective pressures present within the tumour environment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, William -- Jiang, Zhaoshi -- Liu, Jinfeng -- Haverty, Peter M -- Guan, Yinghui -- Stinson, Jeremy -- Yue, Peng -- Zhang, Yan -- Pant, Krishna P -- Bhatt, Deepali -- Ha, Connie -- Johnson, Stephanie -- Kennemer, Michael I -- Mohan, Sankar -- Nazarenko, Igor -- Watanabe, Colin -- Sparks, Andrew B -- Shames, David S -- Gentleman, Robert -- de Sauvage, Frederic J -- Stern, Howard -- Pandita, Ajay -- Ballinger, Dennis G -- Drmanac, Radoje -- Modrusan, Zora -- Seshagiri, Somasekar -- Zhang, Zemin -- England -- Nature. 2010 May 27;465(7297):473-7. doi: 10.1038/nature09004.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California 94080, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20505728" target="_blank"〉PubMed〈/a〉
    Keywords: Carcinoma, Non-Small-Cell Lung/*genetics ; DNA Mutational Analysis ; Genome, Human/*genetics ; Humans ; Lung Neoplasms/*genetics ; Male ; Middle Aged ; Models, Biological ; Point Mutation/*genetics ; Selection, Genetic/genetics
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  • 5
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    Long-term evolution and transmission dynamics of swine influenza A virus (2011)
    Nature Publishing Group (NPG)
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    Publication Date: 2011-05-27
    Description: Swine influenza A viruses (SwIV) cause significant economic losses in animal husbandry as well as instances of human disease and occasionally give rise to human pandemics, including that caused by the H1N1/2009 virus. The lack of systematic and longitudinal influenza surveillance in pigs has hampered attempts to reconstruct the origins of this pandemic. Most existing swine data were derived from opportunistic samples collected from diseased pigs in disparate geographical regions, not from prospective studies in defined locations, hence the evolutionary and transmission dynamics of SwIV are poorly understood. Here we quantify the epidemiological, genetic and antigenic dynamics of SwIV in Hong Kong using a data set of more than 650 SwIV isolates and more than 800 swine sera from 12 years of systematic surveillance in this region, supplemented with data stretching back 34 years. Intercontinental virus movement has led to reassortment and lineage replacement, creating an antigenically and genetically diverse virus population whose dynamics are quantitatively different from those previously observed for human influenza viruses. Our findings indicate that increased antigenic drift is associated with reassortment events and offer insights into the emergence of influenza viruses with epidemic potential in swine and humans.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vijaykrishna, Dhanasekaran -- Smith, Gavin J D -- Pybus, Oliver G -- Zhu, Huachen -- Bhatt, Samir -- Poon, Leo L M -- Riley, Steven -- Bahl, Justin -- Ma, Siu K -- Cheung, Chung L -- Perera, Ranawaka A P M -- Chen, Honglin -- Shortridge, Kennedy F -- Webby, Richard J -- Webster, Robert G -- Guan, Yi -- Peiris, J S Malik -- HHSN26600700005C/PHS HHS/ -- MC_G0902096/Medical Research Council/United Kingdom -- England -- Nature. 2011 May 26;473(7348):519-22. doi: 10.1038/nature10004.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉State Key Laboratory of Emerging Infectious Diseases & Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21614079" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Birds/virology ; *Evolution, Molecular ; Female ; Hong Kong/epidemiology ; Humans ; Influenza A Virus, H1N1 Subtype/classification/genetics/isolation & ; purification/*physiology ; Influenza in Birds/transmission/virology ; Influenza, Human/epidemiology/transmission/virology ; Male ; Molecular Epidemiology ; Molecular Sequence Data ; Orthomyxoviridae Infections/epidemiology/transmission/*veterinary/virology ; Phylogeny ; Population Surveillance ; Reassortant Viruses/genetics/immunology/isolation & purification/physiology ; Swine/blood/*virology ; Swine Diseases/blood/epidemiology/*transmission/*virology ; Zoonoses/epidemiology/transmission/*virology
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  • 6
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    The genesis and source of the H7N9 influenza viruses causing human infections in China (2013)
    Nature Publishing Group (NPG)
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    Publication Date: 2013-08-24
    Description: A novel H7N9 influenza A virus first detected in March 2013 has since caused more than 130 human infections in China, resulting in 40 deaths. Preliminary analyses suggest that the virus is a reassortant of H7, N9 and H9N2 avian influenza viruses, and carries some amino acids associated with mammalian receptor binding, raising concerns of a new pandemic. However, neither the source populations of the H7N9 outbreak lineage nor the conditions for its genesis are fully known. Using a combination of active surveillance, screening of virus archives, and evolutionary analyses, here we show that H7 viruses probably transferred from domestic duck to chicken populations in China on at least two independent occasions. We show that the H7 viruses subsequently reassorted with enzootic H9N2 viruses to generate the H7N9 outbreak lineage, and a related previously unrecognized H7N7 lineage. The H7N9 outbreak lineage has spread over a large geographic region and is prevalent in chickens at live poultry markets, which are thought to be the immediate source of human infections. Whether the H7N9 outbreak lineage has, or will, become enzootic in China and neighbouring regions requires further investigation. The discovery here of a related H7N7 influenza virus in chickens that has the ability to infect mammals experimentally, suggests that H7 viruses may pose threats beyond the current outbreak. The continuing prevalence of H7 viruses in poultry could lead to the generation of highly pathogenic variants and further sporadic human infections, with a continued risk of the virus acquiring human-to-human transmissibility.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3801098/" 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/PMC3801098/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lam, Tommy Tsan-Yuk -- Wang, Jia -- Shen, Yongyi -- Zhou, Boping -- Duan, Lian -- Cheung, Chung-Lam -- Ma, Chi -- Lycett, Samantha J -- Leung, Connie Yin-Hung -- Chen, Xinchun -- Li, Lifeng -- Hong, Wenshan -- Chai, Yujuan -- Zhou, Linlin -- Liang, Huyi -- Ou, Zhihua -- Liu, Yongmei -- Farooqui, Amber -- Kelvin, David J -- Poon, Leo L M -- Smith, David K -- Pybus, Oliver G -- Leung, Gabriel M -- Shu, Yuelong -- Webster, Robert G -- Webby, Richard J -- Peiris, Joseph S M -- Rambaut, Andrew -- Zhu, Huachen -- Guan, Yi -- 092807/Wellcome Trust/United Kingdom -- 095831/Wellcome Trust/United Kingdom -- 260864/European Research Council/International -- BB/E009670/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- HHSN266200700005C/AI/NIAID NIH HHS/ -- HSN266200700005C/PHS HHS/ -- England -- Nature. 2013 Oct 10;502(7470):241-4. doi: 10.1038/nature12515. Epub 2013 Aug 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou 515041, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23965623" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chickens ; China ; Ducks ; Genes, Viral/genetics ; Humans ; Influenza A Virus, H7N7 Subtype/classification/genetics ; Influenza A Virus, H9N2 Subtype/classification/genetics ; Influenza A virus/*classification/*genetics ; Influenza in Birds/transmission/virology ; Influenza, Human/transmission/*virology ; Molecular Sequence Data ; *Phylogeny ; Reassortant Viruses/classification/genetics
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  • 7
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    A metagenome-wide association study of gut microbiota in type 2 diabetes (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-10-02
    Description: Assessment and characterization of gut microbiota has become a major research area in human disease, including type 2 diabetes, the most prevalent endocrine disease worldwide. To carry out analysis on gut microbial content in patients with type 2 diabetes, we developed a protocol for a metagenome-wide association study (MGWAS) and undertook a two-stage MGWAS based on deep shotgun sequencing of the gut microbial DNA from 345 Chinese individuals. We identified and validated approximately 60,000 type-2-diabetes-associated markers and established the concept of a metagenomic linkage group, enabling taxonomic species-level analyses. MGWAS analysis showed that patients with type 2 diabetes were characterized by a moderate degree of gut microbial dysbiosis, a decrease in the abundance of some universal butyrate-producing bacteria and an increase in various opportunistic pathogens, as well as an enrichment of other microbial functions conferring sulphate reduction and oxidative stress resistance. An analysis of 23 additional individuals demonstrated that these gut microbial markers might be useful for classifying type 2 diabetes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Qin, Junjie -- Li, Yingrui -- Cai, Zhiming -- Li, Shenghui -- Zhu, Jianfeng -- Zhang, Fan -- Liang, Suisha -- Zhang, Wenwei -- Guan, Yuanlin -- Shen, Dongqian -- Peng, Yangqing -- Zhang, Dongya -- Jie, Zhuye -- Wu, Wenxian -- Qin, Youwen -- Xue, Wenbin -- Li, Junhua -- Han, Lingchuan -- Lu, Donghui -- Wu, Peixian -- Dai, Yali -- Sun, Xiaojuan -- Li, Zesong -- Tang, Aifa -- Zhong, Shilong -- Li, Xiaoping -- Chen, Weineng -- Xu, Ran -- Wang, Mingbang -- Feng, Qiang -- Gong, Meihua -- Yu, Jing -- Zhang, Yanyan -- Zhang, Ming -- Hansen, Torben -- Sanchez, Gaston -- Raes, Jeroen -- Falony, Gwen -- Okuda, Shujiro -- Almeida, Mathieu -- LeChatelier, Emmanuelle -- Renault, Pierre -- Pons, Nicolas -- Batto, Jean-Michel -- Zhang, Zhaoxi -- Chen, Hua -- Yang, Ruifu -- Zheng, Weimou -- Li, Songgang -- Yang, Huanming -- Wang, Jian -- Ehrlich, S Dusko -- Nielsen, Rasmus -- Pedersen, Oluf -- Kristiansen, Karsten -- Wang, Jun -- England -- Nature. 2012 Oct 4;490(7418):55-60. doi: 10.1038/nature11450. Epub 2012 Sep 26.〈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/23023125" target="_blank"〉PubMed〈/a〉
    Keywords: Asian Continental Ancestry Group ; Butyrates/metabolism ; China/ethnology ; Cohort Studies ; Diabetes Mellitus, Type ; 2/classification/complications/*microbiology/physiopathology ; Feces/microbiology ; Genetic Linkage/genetics ; Genetic Markers ; Genome-Wide Association Study/*methods ; High-Throughput Nucleotide Sequencing ; Humans ; Intestines/*microbiology ; Metabolic Networks and Pathways/genetics ; Metagenome/*genetics ; Metagenomics/*methods ; Opportunistic Infections/complications/microbiology ; Reference Standards ; Sulfates/metabolism
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  • 8
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    Avian flu: Gain-of-function experiments on H7N9 (2013)
    Nature Publishing Group (NPG)
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    Publication Date: 2013-08-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fouchier, Ron A M -- Kawaoka, Yoshihiro -- Cardona, Carol -- Compans, Richard W -- Garcia-Sastre, Adolfo -- Govorkova, Elena A -- Guan, Yi -- Herfst, Sander -- Orenstein, Walter A -- Peiris, J S Malik -- Perez, Daniel R -- Richt, Juergen A -- Russell, Charles -- Schultz-Cherry, Stacey L -- Smith, Derek J -- Steel, John -- Tompkins, S Mark -- Topham, David J -- Treanor, John J -- Tripp, Ralph A -- Webby, Richard J -- Webster, Robert G -- England -- Nature. 2013 Aug 8;500(7461):150-1. doi: 10.1038/500150a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23925229" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Birds ; Drug Resistance, Viral ; Humans ; Influenza A virus/*genetics/pathogenicity ; Influenza in Birds/transmission/*virology ; Orthomyxoviridae Infections/transmission/*virology ; Pandemics/prevention & control ; Research/standards ; Viral Proteins/genetics/metabolism ; Viral Vaccines
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  • 9
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    Recurrent R-spondin fusions in colon cancer (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-08-17
    Description: Identifying and understanding changes in cancer genomes is essential for the development of targeted therapeutics. Here we analyse systematically more than 70 pairs of primary human colon tumours by applying next-generation sequencing to characterize their exomes, transcriptomes and copy-number alterations. We have identified 36,303 protein-altering somatic changes that include several new recurrent mutations in the Wnt pathway gene TCF7L2, chromatin-remodelling genes such as TET2 and TET3 and receptor tyrosine kinases including ERBB3. Our analysis for significantly mutated cancer genes identified 23 candidates, including the cell cycle checkpoint kinase ATM. Copy-number and RNA-seq data analysis identified amplifications and corresponding overexpression of IGF2 in a subset of colon tumours. Furthermore, using RNA-seq data we identified multiple fusion transcripts including recurrent gene fusions involving R-spondin family members RSPO2 and RSPO3 that together occur in 10% of colon tumours. The RSPO fusions were mutually exclusive with APC mutations, indicating that they probably have a role in the activation of Wnt signalling and tumorigenesis. Consistent with this we show that the RSPO fusion proteins were capable of potentiating Wnt signalling. The R-spondin gene fusions and several other gene mutations identified in this study provide new potential opportunities for therapeutic intervention in colon cancer.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3690621/" 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/PMC3690621/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Seshagiri, Somasekar -- Stawiski, Eric W -- Durinck, Steffen -- Modrusan, Zora -- Storm, Elaine E -- Conboy, Caitlin B -- Chaudhuri, Subhra -- Guan, Yinghui -- Janakiraman, Vasantharajan -- Jaiswal, Bijay S -- Guillory, Joseph -- Ha, Connie -- Dijkgraaf, Gerrit J P -- Stinson, Jeremy -- Gnad, Florian -- Huntley, Melanie A -- Degenhardt, Jeremiah D -- Haverty, Peter M -- Bourgon, Richard -- Wang, Weiru -- Koeppen, Hartmut -- Gentleman, Robert -- Starr, Timothy K -- Zhang, Zemin -- Largaespada, David A -- Wu, Thomas D -- de Sauvage, Frederic J -- R00 CA151672/CA/NCI NIH HHS/ -- R01 CA134759/CA/NCI NIH HHS/ -- R01-CA134759/CA/NCI NIH HHS/ -- T32 CA009138/CA/NCI NIH HHS/ -- England -- Nature. 2012 Aug 30;488(7413):660-4. doi: 10.1038/nature11282.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, USA. sekar@gene.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22895193" target="_blank"〉PubMed〈/a〉
    Keywords: Ataxia Telangiectasia Mutated Proteins ; Base Sequence ; Cell Cycle Proteins/genetics ; Colonic Neoplasms/*genetics/metabolism/pathology ; DNA Copy Number Variations/genetics ; DNA-Binding Proteins/genetics ; Dioxygenases/genetics ; Exome/genetics ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic/genetics ; Gene Fusion/*genetics ; Genes, APC ; Genes, Neoplasm/*genetics ; Humans ; Insulin-Like Growth Factor II/genetics ; Intercellular Signaling Peptides and Proteins/*genetics ; Molecular Sequence Data ; Mutation/genetics ; Polymorphism, Single Nucleotide/genetics ; Protein-Serine-Threonine Kinases/genetics ; Proto-Oncogene Proteins/genetics ; Receptor, ErbB-3/genetics ; Sequence Analysis, RNA ; Signal Transduction/genetics ; Thrombospondins/*genetics ; Transcription Factor 7-Like 2 Protein/genetics ; Tumor Suppressor Proteins/genetics ; Wnt Proteins/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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    H5N1: How to track a flu virus (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-03-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Guan, Yi -- Webby, Richard -- Capua, Ilaria -- Waldenstrom, Jonas -- England -- Nature. 2012 Mar 28;483(7391):535-6. doi: 10.1038/483535a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22460882" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Domestic/virology ; Animals, Wild/virology ; Asia/epidemiology ; Birds/*virology ; Disease Outbreaks/veterinary ; Ducks/*virology ; Egypt/epidemiology ; Humans ; Influenza A Virus, H5N1 Subtype/genetics/*isolation & purification/pathogenicity ; Influenza in Birds/epidemiology/transmission/virology ; Influenza, Human/epidemiology/transmission/virology ; Middle East/epidemiology ; Orthomyxoviridae Infections/epidemiology/transmission/*veterinary/virology ; Population Surveillance ; Swine/*virology ; United States/epidemiology ; Zoonoses/epidemiology/transmission/virology
    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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