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  • Reproducibility of Results  (484)
  • Nature Publishing Group (NPG)  (484)
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  • 1
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    IPCC flooded by criticism (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-02-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schiermeier, Quirin -- England -- Nature. 2010 Feb 4;463(7281):596-7. doi: 10.1038/463596a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20130621" target="_blank"〉PubMed〈/a〉
    Keywords: *Conflict of Interest ; Ecology/ethics/organization & administration/*standards ; Ethics, Professional ; *Global Warming/statistics & numerical data ; Ice Cover ; Reproducibility of Results ; Research Design ; Risk Assessment ; United Nations/ethics/*organization & administration/standards
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
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    Organic-walled microfossils in 3.2-billion-year-old shallow-marine siliciclastic deposits (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-02-09
    Description: Although the notion of an early origin and diversification of life on Earth during the Archaean eon has received increasing support in geochemical, sedimentological and palaeontological evidence, ambiguities and controversies persist regarding the biogenicity and syngeneity of the record older than Late Archaean. Non-biological processes are known to produce morphologies similar to some microfossils, and hydrothermal fluids have the potential to produce abiotic organic compounds with depleted carbon isotope values, making it difficult to establish unambiguous traces of life. Here we report the discovery of a population of large (up to about 300 mum in diameter) carbonaceous spheroidal microstructures in Mesoarchaean shales and siltstones of the Moodies Group, South Africa, the Earth's oldest siliciclastic alluvial to tidal-estuarine deposits. These microstructures are interpreted as organic-walled microfossils on the basis of petrographic and geochemical evidence for their endogenicity and syngeneity, their carbonaceous composition, cellular morphology and ultrastructure, occurrence in populations, taphonomic features of soft wall deformation, and the geological context plausible for life, as well as a lack of abiotic explanation falsifying a biological origin. These are the oldest and largest Archaean organic-walled spheroidal microfossils reported so far. Our observations suggest that relatively large microorganisms cohabited with earlier reported benthic microbial mats in the photic zone of marginal marine siliciclastic environments 3.2 billion years ago.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Javaux, Emmanuelle J -- Marshall, Craig P -- Bekker, Andrey -- England -- Nature. 2010 Feb 18;463(7283):934-8. doi: 10.1038/nature08793. Epub 2010 Feb 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geology, University of Liege, 17 allee du 6 Aout B18, Liege 4000, Belgium. ej.javaux@ulg.ac.be〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20139963" target="_blank"〉PubMed〈/a〉
    Keywords: Acids ; Bacteria/chemistry/cytology/isolation & purification/metabolism ; Carbon/analysis/chemistry ; Carbon Isotopes ; *Ecosystem ; Eukaryotic Cells/chemistry/cytology ; *Fossils ; Geologic Sediments/*microbiology ; History, Ancient ; Oceans and Seas ; Organic Chemicals/*analysis/chemistry ; *Phylogeny ; Reproducibility of Results ; Seawater/*microbiology ; South Africa ; Spectrum Analysis, Raman ; Sunlight
    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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    Which way for genetic-test regulation? Assign regulation appropriate to the level of risk (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-08-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Javitt, Gail -- England -- Nature. 2010 Aug 12;466(7308):817-8. doi: 10.1038/466817a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Berman Institute of Bioethics, Johns Hopkins University, USA. gjavitt1@jhu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20703288" target="_blank"〉PubMed〈/a〉
    Keywords: *Consumer Advocacy ; Genetic Counseling/*legislation & jurisprudence/standards ; Genetic Predisposition to Disease/*genetics ; Genetic Testing/*legislation & jurisprudence/*standards ; *Government Regulation ; Humans ; Marketing ; Reproducibility of Results ; United States ; United States Food and Drug Administration/legislation & jurisprudence
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
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    The killing fields (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-09-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Sep 23;467(7314):368. doi: 10.1038/467368a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20864950" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/*methods ; Animals ; Cattle ; Disease Reservoirs/microbiology/*statistics & numerical data/*veterinary ; *Federal Government ; Great Britain/epidemiology ; *Mustelidae/microbiology ; Reproducibility of Results ; Tuberculosis Vaccines ; Tuberculosis, Bovine/epidemiology/*prevention & control/transmission ; Vaccination/veterinary
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
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    Safeguarding the integrity of protein archive (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-01-30
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4456675/" 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/PMC4456675/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berman, Helen M -- Kleywegt, Gerard J -- Nakamura, Haruki -- Markley, John L -- Burley, Stephen K -- P41 LM005799/LM/NLM NIH HHS/ -- England -- Nature. 2010 Jan 28;463(7280):425. doi: 10.1038/463425c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20110969" target="_blank"〉PubMed〈/a〉
    Keywords: Databases, Protein/*ethics/*standards ; Ethics, Research ; Reproducibility of Results ; Scientific Misconduct
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
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    Questioning the timeline of H1N1 flu vaccination contracts (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-07-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cohen, Deborah -- Carter, Philip -- England -- Nature. 2010 Jul 15;466(7304):315. doi: 10.1038/466315a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20631779" target="_blank"〉PubMed〈/a〉
    Keywords: *Conflict of Interest ; *Drug Industry ; Humans ; *Influenza A Virus, H1N1 Subtype ; Influenza Vaccines/*supply & distribution ; Influenza, Human/*epidemiology/prevention & control/virology ; Reproducibility of Results ; Time Factors ; *Vaccination ; *World Health Organization
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
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    Microbe gets toxic response (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-12-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Katsnelson, Alla -- England -- Nature. 2010 Dec 9;468(7325):741. doi: 10.1038/468741a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21150963" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Arsenic/*metabolism ; Bacteria/cytology/growth & development/*metabolism ; California ; DNA, Bacterial/chemistry/metabolism ; Exobiology ; Life ; Phosphates/metabolism ; Phosphorus/metabolism ; RNA, Bacterial/chemistry/metabolism ; Reproducibility of Results
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
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    Science in court (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-03-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Mar 18;464(7287):325. doi: 10.1038/464325a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20237517" target="_blank"〉PubMed〈/a〉
    Keywords: Education, Graduate/trends ; Forensic Sciences/economics/education/organization & administration/*trends ; Reproducibility of Results ; Research/economics/organization & administration/trends ; United States ; United States Government Agencies/economics/organization & administration/trends
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 9
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    Origins and functional impact of copy number variation in the human genome (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-10-09
    Description: Structural variations of DNA greater than 1 kilobase in size account for most bases that vary among human genomes, but are still relatively under-ascertained. Here we use tiling oligonucleotide microarrays, comprising 42 million probes, to generate a comprehensive map of 11,700 copy number variations (CNVs) greater than 443 base pairs, of which most (8,599) have been validated independently. For 4,978 of these CNVs, we generated reference genotypes from 450 individuals of European, African or East Asian ancestry. The predominant mutational mechanisms differ among CNV size classes. Retrotransposition has duplicated and inserted some coding and non-coding DNA segments randomly around the genome. Furthermore, by correlation with known trait-associated single nucleotide polymorphisms (SNPs), we identified 30 loci with CNVs that are candidates for influencing disease susceptibility. Despite this, having assessed the completeness of our map and the patterns of linkage disequilibrium between CNVs and SNPs, we conclude that, for complex traits, the heritability void left by genome-wide association studies will not be accounted for by common CNVs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3330748/" 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/PMC3330748/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Conrad, Donald F -- Pinto, Dalila -- Redon, Richard -- Feuk, Lars -- Gokcumen, Omer -- Zhang, Yujun -- Aerts, Jan -- Andrews, T Daniel -- Barnes, Chris -- Campbell, Peter -- Fitzgerald, Tomas -- Hu, Min -- Ihm, Chun Hwa -- Kristiansson, Kati -- Macarthur, Daniel G -- Macdonald, Jeffrey R -- Onyiah, Ifejinelo -- Pang, Andy Wing Chun -- Robson, Sam -- Stirrups, Kathy -- Valsesia, Armand -- Walter, Klaudia -- Wei, John -- Wellcome Trust Case Control Consortium -- Tyler-Smith, Chris -- Carter, Nigel P -- Lee, Charles -- Scherer, Stephen W -- Hurles, Matthew E -- 077006/Z/05/Z/Wellcome Trust/United Kingdom -- 077008/Wellcome Trust/United Kingdom -- 077009/Wellcome Trust/United Kingdom -- 077014/Wellcome Trust/United Kingdom -- 088340/Wellcome Trust/United Kingdom -- GM081533/GM/NIGMS NIH HHS/ -- HG004221/HG/NHGRI NIH HHS/ -- Canadian Institutes of Health Research/Canada -- England -- Nature. 2010 Apr 1;464(7289):704-12. doi: 10.1038/nature08516. Epub 2009 Oct 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19812545" target="_blank"〉PubMed〈/a〉
    Keywords: Continental Population Groups/genetics ; DNA Copy Number Variations/*genetics ; Gene Duplication ; Genetic Predisposition to Disease/*genetics ; Genome, Human/*genetics ; Genome-Wide Association Study ; Genotype ; Haplotypes/genetics ; Humans ; Mutagenesis/*genetics ; Oligonucleotide Array Sequence Analysis ; Polymorphism, Single Nucleotide/genetics ; Reproducibility of Results
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 10
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    Genomics: The tough new variants (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-10-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Oct 28;467(7319):1136. doi: 10.1038/4671136a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20981104" target="_blank"〉PubMed〈/a〉
    Keywords: DNA Copy Number Variations/*genetics ; Genome, Human/*genetics ; Genomics/*methods ; Humans ; Oligonucleotide Array Sequence Analysis ; Polymorphism, Single Nucleotide/genetics ; Reproducibility of Results
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 11
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    Biologists tackle cells' identity crisis (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-06-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Katsnelson, Alla -- England -- Nature. 2010 Jun 3;465(7298):537. doi: 10.1038/465537a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20520682" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Culture Techniques/*methods/*standards ; Cell Line/*classification ; Cell Lineage ; *DNA Fingerprinting/methods/standards ; HeLa Cells ; Humans ; Organ Specificity ; Reproducibility of Results
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 12
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    Upbeat oil report questioned (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-08-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schrope, Mark -- England -- Nature. 2010 Aug 12;466(7308):802. doi: 10.1038/466802a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20703275" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Disasters/*statistics & numerical data ; Ecology ; *Ecosystem ; Marine Biology ; Oceanography ; Oceans and Seas ; Petroleum/adverse effects/*analysis ; Reproducibility of Results ; Seawater/*chemistry ; *Uncertainty ; Volatilization
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 13
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    Standard issue (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-08-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Aug 12;466(7308):797. doi: 10.1038/466797a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20703263" target="_blank"〉PubMed〈/a〉
    Keywords: *Consumer Advocacy ; Genetic Testing/*legislation & jurisprudence/*standards ; Government Regulation ; Humans ; Marketing/standards ; Oligonucleotide Array Sequence Analysis ; Reproducibility of Results ; United States ; United States Food and Drug Administration/legislation & jurisprudence
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 14
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    How accurate are cancer cell lines? (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-02-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Borrell, Brendan -- England -- Nature. 2010 Feb 18;463(7283):858. doi: 10.1038/463858a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20164888" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line, Tumor/*metabolism ; Genetics, Medical/*methods/*trends ; Genomics/*methods/*trends ; Humans ; Neoplasms/*genetics/*pathology ; Reproducibility of Results ; Sequence Analysis, DNA/trends
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 15
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    The weight of evidence (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-04-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Apr 22;464(7292):1103-4. doi: 10.1038/4641103b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20414265" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Benzhydryl Compounds ; Chemical Industry/*legislation & jurisprudence/*standards ; *Evaluation Studies as Topic ; *Federal Government ; Guidelines as Topic ; Humans ; Phenols/adverse effects/toxicity ; Reproducibility of Results ; Safety/*legislation & jurisprudence/*standards ; *Toxicity Tests/methods/standards ; United States
    Print ISSN: 0028-0836
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  • 16
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    Climate e-mails: man's mark is clear in thermometer record (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-01-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉von Storch, Hans -- Allen, Myles -- England -- Nature. 2010 Jan 7;463(7277):25. doi: 10.1038/463025a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20054378" target="_blank"〉PubMed〈/a〉
    Keywords: *Electronic Mail ; *Global Warming/statistics & numerical data ; Great Britain ; *Human Activities/statistics & numerical data ; Reproducibility of Results ; Research Personnel/ethics ; *Temperature
    Print ISSN: 0028-0836
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  • 17
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    Science in court: head case (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-03-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hughes, Virginia -- England -- Nature. 2010 Mar 18;464(7287):340-2. doi: 10.1038/464340a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20237536" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Antisocial Personality Disorder/physiopathology/psychology ; Child ; Female ; Forensic Sciences/ethics/*methods/trends ; Homicide/*legislation & jurisprudence/*psychology ; Humans ; Insanity Defense ; Magnetic Resonance Imaging/standards/*utilization ; Male ; *Neurosciences ; Positron-Emission Tomography/utilization ; Rape/legislation & jurisprudence/psychology ; Reproducibility of Results
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  • 18
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    Network organization of the human autophagy system (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-06-22
    Description: Autophagy, the process by which proteins and organelles are sequestered in autophagosomal vesicles and delivered to the lysosome/vacuole for degradation, provides a primary route for turnover of stable and defective cellular proteins. Defects in this system are linked with numerous human diseases. Although conserved protein kinase, lipid kinase and ubiquitin-like protein conjugation subnetworks controlling autophagosome formation and cargo recruitment have been defined, our understanding of the global organization of this system is limited. Here we report a proteomic analysis of the autophagy interaction network in human cells under conditions of ongoing (basal) autophagy, revealing a network of 751 interactions among 409 candidate interacting proteins with extensive connectivity among subnetworks. Many new autophagy interaction network components have roles in vesicle trafficking, protein or lipid phosphorylation and protein ubiquitination, and affect autophagosome number or flux when depleted by RNA interference. The six ATG8 orthologues in humans (MAP1LC3/GABARAP proteins) interact with a cohort of 67 proteins, with extensive binding partner overlap between family members, and frequent involvement of a conserved surface on ATG8 proteins known to interact with LC3-interacting regions in partner proteins. These studies provide a global view of the mammalian autophagy interaction landscape and a resource for mechanistic analysis of this critical protein homeostasis pathway.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2901998/" 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/PMC2901998/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Behrends, Christian -- Sowa, Mathew E -- Gygi, Steven P -- Harper, J Wade -- R01 AG011085/AG/NIA NIH HHS/ -- R01 AG011085-18/AG/NIA NIH HHS/ -- R01 GM054137/GM/NIGMS NIH HHS/ -- R01 GM054137-14/GM/NIGMS NIH HHS/ -- R01 GM054137-14S1/GM/NIGMS NIH HHS/ -- R01 GM054137-15/GM/NIGMS NIH HHS/ -- R01 GM070565/GM/NIGMS NIH HHS/ -- R01 GM070565-05S1/GM/NIGMS NIH HHS/ -- R01 GM095567/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Jul 1;466(7302):68-76. doi: 10.1038/nature09204. Epub 2010 Jun 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20562859" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/genetics/metabolism ; Autophagy/genetics/*physiology ; Homeostasis ; Humans ; Microfilament Proteins/genetics/metabolism ; Phagosomes ; Phosphorylation ; Protein Binding ; *Protein Interaction Mapping ; Proteomics ; RNA Interference ; Reproducibility of Results ; Ubiquitination
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    A painful remedy (2010)
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    Publication Date: 2010-11-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Nov 4;468(7320):6. doi: 10.1038/468006b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21048718" target="_blank"〉PubMed〈/a〉
    Keywords: Periodicals as Topic/*standards/statistics & numerical data ; Reproducibility of Results ; Research Personnel/ethics/statistics & numerical data ; *Retraction of Publication as Topic ; Scientific Misconduct/statistics & numerical data
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    The prion protein as a receptor for amyloid-beta (2010)
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    Publication Date: 2010-08-13
    Description: Increased levels of brain amyloid-beta, a secreted peptide cleavage product of amyloid precursor protein (APP), is believed to be critical in the aetiology of Alzheimer's disease. Increased amyloid-beta can cause synaptic depression, reduce the number of spine protrusions (that is, sites of synaptic contacts) and block long-term synaptic potentiation (LTP), a form of synaptic plasticity; however, the receptor through which amyloid-beta produces these synaptic perturbations has remained elusive. Lauren et al. suggested that binding between oligomeric amyloid-beta (a form of amyloid-beta thought to be most active) and the cellular prion protein (PrP(C)) is necessary for synaptic perturbations. Here we show that PrP(C) is not required for amyloid-beta-induced synaptic depression, reduction in spine density, or blockade of LTP; our results indicate that amyloid-beta-mediated synaptic defects do not require PrP(c).〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057871/" 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/PMC3057871/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kessels, Helmut W -- Nguyen, Louis N -- Nabavi, Sadegh -- Malinow, Roberto -- R01 AG032132/AG/NIA NIH HHS/ -- R01 AG032132-14/AG/NIA NIH HHS/ -- R01 AG032132-15/AG/NIA NIH HHS/ -- R01 AG032132-17/AG/NIA NIH HHS/ -- R01 AG032132-18/AG/NIA NIH HHS/ -- R01 MH049159/MH/NIMH NIH HHS/ -- R01 MH049159-09/MH/NIMH NIH HHS/ -- R01 MH049159-21/MH/NIMH NIH HHS/ -- R01 MH049159-22/MH/NIMH NIH HHS/ -- England -- Nature. 2010 Aug 12;466(7308):E3-4; discussion E4-5. doi: 10.1038/nature09217.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Neural Circuits and Behavior, 9500 Gilman Drive 0634, University of California at San Diego, La Jolla, California 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20703260" target="_blank"〉PubMed〈/a〉
    Keywords: Alzheimer Disease/metabolism/pathology ; Amyloid beta-Peptides/chemistry/genetics/*metabolism ; Animals ; Learning/physiology ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; PrPC Proteins/deficiency/genetics/*metabolism ; Reproducibility of Results ; Serotonin/metabolism ; Synapses/*metabolism/*pathology ; Synaptic Transmission
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    Inferring echolocation in ancient bats (2010)
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    Publication Date: 2010-08-21
    Description: Laryngeal echolocation, used by most living bats to form images of their surroundings and to detect and capture flying prey, is considered to be a key innovation for the evolutionary success of bats, and palaeontologists have long sought osteological correlates of echolocation that can be used to infer the behaviour of fossil bats. Veselka et al. argued that the most reliable trait indicating echolocation capabilities in bats is an articulation between the stylohyal bone (part of the hyoid apparatus that supports the throat and larynx) and the tympanic bone, which forms the floor of the middle ear. They examined the oldest and most primitive known bat, Onychonycteris finneyi (early Eocene, USA), and argued that it showed evidence of this stylohyal-tympanic articulation, from which they concluded that O. finneyi may have been capable of echolocation. We disagree with their interpretation of key fossil data and instead argue that O. finneyi was probably not an echolocating bat.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Simmons, Nancy B -- Seymour, Kevin L -- Habersetzer, Jorg -- Gunnell, Gregg F -- England -- Nature. 2010 Aug 19;466(7309):E8; discussion E9. doi: 10.1038/nature09219.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024, USA. simmons@amnh.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20724993" target="_blank"〉PubMed〈/a〉
    Keywords: Animal Structures/physiology ; Animals ; Bone and Bones/physiology ; Chiroptera/anatomy & histology/*physiology ; Echolocation/*physiology ; *Fossils ; Models, Biological ; Reproducibility of Results
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    Palaeogenetics: Icy resolve (2010)
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    Publication Date: 2010-02-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dalton, Rex -- England -- Nature. 2010 Feb 11;463(7282):724-5. doi: 10.1038/463724a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20148008" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arctic Regions ; Cryopreservation ; DNA/genetics/isolation & purification ; DNA, Mitochondrial/analysis/genetics ; Denmark ; Emigration and Immigration/*history ; Feces ; Fossils ; Genetics, Medical/history ; Genome, Human/*genetics ; Greenland/ethnology ; History, 20th Century ; History, 21st Century ; History, Ancient ; Humans ; Inuits/*ethnology/*history ; Male ; Paleontology/*history ; Phylogeny ; Reproducibility of Results ; Sequence Analysis, DNA ; Siberia/ethnology
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    Still looking for that woodpecker (2010)
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    Publication Date: 2010-02-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dalton, Rex -- England -- Nature. 2010 Feb 11;463(7282):718-9. doi: 10.1038/463718a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20148004" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Birds ; Conservation of Natural Resources/economics/*trends ; *Extinction, Biological ; Reproducibility of Results
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    History of science: quinine steps back in time (2008)
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    Publication Date: 2008-02-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ball, Philip -- England -- Nature. 2008 Feb 28;451(7182):1065-6. doi: 10.1038/4511065a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18305535" target="_blank"〉PubMed〈/a〉
    Keywords: History, 20th Century ; Quinine/*chemical synthesis/chemistry/*history ; Reproducibility of Results
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    Complex speciation of humans and chimpanzees (2008)
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    Publication Date: 2008-03-14
    Description: Genetic data from two or more species provide information about the process of speciation. In their analysis of DNA from humans, chimpanzees, gorillas, orangutans and macaques (HCGOM), Patterson et al. suggest that the apparently short divergence time between humans and chimpanzees on the X chromosome is explained by a massive interspecific hybridization event in the ancestry of these two species. However, Patterson et al. do not statistically test their own null model of simple speciation before concluding that speciation was complex, and--even if the null model could be rejected--they do not consider other explanations of a short divergence time on the X chromosome. These include natural selection on the X chromosome in the common ancestor of humans and chimpanzees, changes in the ratio of male-to-female mutation rates over time, and less extreme versions of divergence with gene flow (see ref. 2, for example). I therefore believe that their claim of hybridization is unwarranted.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wakeley, John -- England -- Nature. 2008 Mar 13;452(7184):E3-4; discussion E4. doi: 10.1038/nature06805.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA. wakeley@fas.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18337768" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chromosomes, Mammalian/genetics ; Female ; *Genetic Speciation ; Humans ; Male ; *Models, Genetic ; Mutagenesis/genetics ; Pan troglodytes/*genetics ; Phylogeny ; Reproducibility of Results ; Selection, Genetic ; Sex Characteristics ; Time Factors ; X Chromosome/genetics
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    Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning (2008)
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    Publication Date: 2008-02-19
    Description: Cytosine DNA methylation is important in regulating gene expression and in silencing transposons and other repetitive sequences. Recent genomic studies in Arabidopsis thaliana have revealed that many endogenous genes are methylated either within their promoters or within their transcribed regions, and that gene methylation is highly correlated with transcription levels. However, plants have different types of methylation controlled by different genetic pathways, and detailed information on the methylation status of each cytosine in any given genome is lacking. To this end, we generated a map at single-base-pair resolution of methylated cytosines for Arabidopsis, by combining bisulphite treatment of genomic DNA with ultra-high-throughput sequencing using the Illumina 1G Genome Analyser and Solexa sequencing technology. This approach, termed BS-Seq, unlike previous microarray-based methods, allows one to sensitively measure cytosine methylation on a genome-wide scale within specific sequence contexts. Here we describe methylation on previously inaccessible components of the genome and analyse the DNA methylation sequence composition and distribution. We also describe the effect of various DNA methylation mutants on genome-wide methylation patterns, and demonstrate that our newly developed library construction and computational methods can be applied to large genomes such as that of mouse.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2377394/" 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/PMC2377394/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cokus, Shawn J -- Feng, Suhua -- Zhang, Xiaoyu -- Chen, Zugen -- Merriman, Barry -- Haudenschild, Christian D -- Pradhan, Sriharsa -- Nelson, Stanley F -- Pellegrini, Matteo -- Jacobsen, Steven E -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 Mar 13;452(7184):215-9. doi: 10.1038/nature06745. Epub 2008 Feb 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18278030" target="_blank"〉PubMed〈/a〉
    Keywords: 5-Methylcytosine/metabolism ; Animals ; Arabidopsis/*genetics ; Base Sequence ; Computational Biology ; Cytosine/metabolism ; *DNA Methylation ; Gene Expression Regulation, Plant/genetics ; Gene Library ; Genome, Plant/*genetics ; Mice ; Mutation/genetics ; Promoter Regions, Genetic/genetics ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; Sulfites/*metabolism ; Uracil/metabolism
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    The science of doping (2008)
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    Publication Date: 2008-08-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berry, Donald A -- England -- Nature. 2008 Aug 7;454(7205):692-3. doi: 10.1038/454692a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Quantitative Sciences, Department of Biostatistics, MD Anderson Cancer Center, University of Texas, 1400 Pressler Street, Houston, Texas 77030-1402, USA. dberry@mdanderson.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18685682" target="_blank"〉PubMed〈/a〉
    Keywords: Doping in Sports/*prevention & control ; False Positive Reactions ; Female ; Humans ; Male ; Probability ; Reproducibility of Results ; Sample Size ; Sensitivity and Specificity ; *Sports/ethics/standards ; Substance Abuse Detection/methods/*standards
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    Eyewitness identification: line-ups on trial (2008)
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    Publication Date: 2008-05-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Spinney, Laura -- England -- Nature. 2008 May 22;453(7194):442-4. doi: 10.1038/453442a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18497791" target="_blank"〉PubMed〈/a〉
    Keywords: Crime/*legislation & jurisprudence ; Criminal Law/*methods/standards ; DNA Fingerprinting ; Evaluation Studies as Topic ; Great Britain ; Humans ; Police ; Reproducibility of Results ; *Research ; United States
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    The complete genome of an individual by massively parallel DNA sequencing (2008)
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    Publication Date: 2008-04-19
    Description: The association of genetic variation with disease and drug response, and improvements in nucleic acid technologies, have given great optimism for the impact of 'genomic medicine'. However, the formidable size of the diploid human genome, approximately 6 gigabases, has prevented the routine application of sequencing methods to deciphering complete individual human genomes. To realize the full potential of genomics for human health, this limitation must be overcome. Here we report the DNA sequence of a diploid genome of a single individual, James D. Watson, sequenced to 7.4-fold redundancy in two months using massively parallel sequencing in picolitre-size reaction vessels. This sequence was completed in two months at approximately one-hundredth of the cost of traditional capillary electrophoresis methods. Comparison of the sequence to the reference genome led to the identification of 3.3 million single nucleotide polymorphisms, of which 10,654 cause amino-acid substitution within the coding sequence. In addition, we accurately identified small-scale (2-40,000 base pair (bp)) insertion and deletion polymorphism as well as copy number variation resulting in the large-scale gain and loss of chromosomal segments ranging from 26,000 to 1.5 million base pairs. Overall, these results agree well with recent results of sequencing of a single individual by traditional methods. However, in addition to being faster and significantly less expensive, this sequencing technology avoids the arbitrary loss of genomic sequences inherent in random shotgun sequencing by bacterial cloning because it amplifies DNA in a cell-free system. As a result, we further demonstrate the acquisition of novel human sequence, including novel genes not previously identified by traditional genomic sequencing. This is the first genome sequenced by next-generation technologies. Therefore it is a pilot for the future challenges of 'personalized genome sequencing'.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wheeler, David A -- Srinivasan, Maithreyan -- Egholm, Michael -- Shen, Yufeng -- Chen, Lei -- McGuire, Amy -- He, Wen -- Chen, Yi-Ju -- Makhijani, Vinod -- Roth, G Thomas -- Gomes, Xavier -- Tartaro, Karrie -- Niazi, Faheem -- Turcotte, Cynthia L -- Irzyk, Gerard P -- Lupski, James R -- Chinault, Craig -- Song, Xing-zhi -- Liu, Yue -- Yuan, Ye -- Nazareth, Lynne -- Qin, Xiang -- Muzny, Donna M -- Margulies, Marcel -- Weinstock, George M -- Gibbs, Richard A -- Rothberg, Jonathan M -- U54 HG003273/HG/NHGRI NIH HHS/ -- England -- Nature. 2008 Apr 17;452(7189):872-6. doi: 10.1038/nature06884.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18421352" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Computational Biology ; Genetic Predisposition to Disease/genetics ; Genetic Variation/*genetics ; Genome, Human/*genetics ; Genomics/economics/*methods/trends ; Genotype ; Humans ; Individuality ; Male ; Oligonucleotide Array Sequence Analysis ; Polymorphism, Single Nucleotide/genetics ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Alignment ; Sequence Analysis, DNA/economics/*methods ; Software
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    Do abnormal responses show utilitarian bias? (2008)
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    Publication Date: 2008-03-21
    Description: Neuroscience has recently turned to the study of utilitarian and non-utilitarian moral judgement. Koenigs et al. examine the responses of normal subjects and those with ventromedial-prefrontal-cortex (VMPC) damage to moral scenarios drawn from functional magnetic resonance imaging studies by Greene et al., and claim that patients with VMPC damage have an abnormally "utilitarian" pattern of moral judgement. It is crucial to the claims of Koenigs et al. that the scenarios of Greene et al. pose a conflict between utilitarian consequence and duty: however, many of them do not meet this condition. Because of this methodological problem, it is too early to claim that VMPC patients have a utilitarian bias.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2922719/" 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/PMC2922719/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kahane, Guy -- Shackel, Nicholas -- P01 NS019632/NS/NINDS NIH HHS/ -- P01 NS019632-230003/NS/NINDS NIH HHS/ -- England -- Nature. 2008 Mar 20;452(7185):E5; author reply E5-6. doi: 10.1038/nature06785.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Oxford Uehiro Centre for Practical Ethics, University of Oxford, Oxford OX1 1PT, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18354427" target="_blank"〉PubMed〈/a〉
    Keywords: Brain Injuries/*physiopathology ; Choice Behavior/*physiology ; Cognition/physiology ; *Conflict (Psychology) ; Emotions/*physiology ; Humans ; Judgment/*physiology ; Magnetic Resonance Imaging ; *Morals ; Reproducibility of Results ; Social Behavior
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    Stem-cell claim gets cold reception (2008)
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    Publication Date: 2008-03-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cyranoski, David -- Baker, Monya -- England -- Nature. 2008 Mar 13;452(7184):132. doi: 10.1038/452132a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18337778" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Adult Stem Cells/*cytology ; Embryonic Stem Cells/*cytology ; Endocytosis ; Genetic Vectors ; Humans ; Male ; *Nanotubes, Carbon/adverse effects ; Peer Review, Research/standards ; Pluripotent Stem Cells/*cytology ; Reproducibility of Results ; Spermatozoa/cytology ; Time Factors ; Transfection/instrumentation/*methods ; Uncertainty
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    Fresh doubts over T. rex chicken link (2008)
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    Publication Date: 2008-08-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dalton, Rex -- England -- Nature. 2008 Aug 28;454(7208):1035. doi: 10.1038/4541035a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18756217" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chickens/*metabolism ; Collagen/analysis/chemistry ; Dinosaurs/*metabolism ; Mass Spectrometry ; *Models, Biological ; Reproducibility of Results
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    Mapping and sequencing of structural variation from eight human genomes (2008)
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    Publication Date: 2008-05-03
    Description: Genetic variation among individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single nucleotide changes. Here we explore variation on an intermediate scale--particularly insertions, deletions and inversions affecting from a few thousand to a few million base pairs. We employed a clone-based method to interrogate this intermediate structural variation in eight individuals of diverse geographic ancestry. Our analysis provides a comprehensive overview of the normal pattern of structural variation present in these genomes, refining the location of 1,695 structural variants. We find that 50% were seen in more than one individual and that nearly half lay outside regions of the genome previously described as structurally variant. We discover 525 new insertion sequences that are not present in the human reference genome and show that many of these are variable in copy number between individuals. Complete sequencing of 261 structural variants reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome. These data provide the first high-resolution sequence map of human structural variation--a standard for genotyping platforms and a prelude to future individual genome sequencing projects.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2424287/" 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/PMC2424287/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kidd, Jeffrey M -- Cooper, Gregory M -- Donahue, William F -- Hayden, Hillary S -- Sampas, Nick -- Graves, Tina -- Hansen, Nancy -- Teague, Brian -- Alkan, Can -- Antonacci, Francesca -- Haugen, Eric -- Zerr, Troy -- Yamada, N Alice -- Tsang, Peter -- Newman, Tera L -- Tuzun, Eray -- Cheng, Ze -- Ebling, Heather M -- Tusneem, Nadeem -- David, Robert -- Gillett, Will -- Phelps, Karen A -- Weaver, Molly -- Saranga, David -- Brand, Adrianne -- Tao, Wei -- Gustafson, Erik -- McKernan, Kevin -- Chen, Lin -- Malig, Maika -- Smith, Joshua D -- Korn, Joshua M -- McCarroll, Steven A -- Altshuler, David A -- Peiffer, Daniel A -- Dorschner, Michael -- Stamatoyannopoulos, John -- Schwartz, David -- Nickerson, Deborah A -- Mullikin, James C -- Wilson, Richard K -- Bruhn, Laurakay -- Olson, Maynard V -- Kaul, Rajinder -- Smith, Douglas R -- Eichler, Evan E -- 3 U54 HG002043/HG/NHGRI NIH HHS/ -- HG004120/HG/NHGRI NIH HHS/ -- P01 HG004120/HG/NHGRI NIH HHS/ -- P01 HG004120-01/HG/NHGRI NIH HHS/ -- U54 HG002043-07S1/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 May 1;453(7191):56-64. doi: 10.1038/nature06862.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18451855" target="_blank"〉PubMed〈/a〉
    Keywords: Chromosome Inversion/genetics ; Continental Population Groups/genetics ; Euchromatin/genetics ; Gene Deletion ; Genetic Variation/*genetics ; Genome, Human/*genetics ; Geography ; Haplotypes ; Humans ; Mutagenesis, Insertional/genetics ; *Physical Chromosome Mapping ; Polymorphism, Single Nucleotide/genetics ; Reproducibility of Results ; *Sequence Analysis, DNA
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    Pacific "dwarf" bones cause controversy (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-03-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dalton, Rex -- England -- Nature. 2008 Mar 13;452(7184):133. doi: 10.1038/452133a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18337779" target="_blank"〉PubMed〈/a〉
    Keywords: *Aging ; Animals ; Biological Evolution ; Bone and Bones/*anatomy & histology ; Burial ; Child ; *Dwarfism ; *Fossils ; Geography ; Hominidae/*anatomy & histology/classification ; Humans ; *Models, Biological ; Motion Pictures as Topic ; Palau/ethnology ; Reproducibility of Results ; Time Factors
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Negative results (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-05-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2008 May 15;453(7193):258. doi: 10.1038/453258b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18480760" target="_blank"〉PubMed〈/a〉
    Keywords: Drug Design ; Enzymes/metabolism ; Reproducibility of Results ; Research Personnel/*ethics ; *Retraction of Publication as Topic ; Scientific Misconduct/legislation & jurisprudence
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    Duplication: most cases on database are innocent (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-03-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brennan, Paul -- England -- Nature. 2008 Mar 6;452(7183):29. doi: 10.1038/452029d.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18322506" target="_blank"〉PubMed〈/a〉
    Keywords: Databases, Factual/*standards ; *Duplicate Publication as Topic ; Reproducibility of Results ; Research Design/statistics & numerical data
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    Ready or not (2008)
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    Publication Date: 2008-04-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2008 Apr 10;452(7188):666. doi: 10.1038/452666a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18401360" target="_blank"〉PubMed〈/a〉
    Keywords: Genetic Predisposition to Disease/*genetics ; Genetic Testing/economics/standards/*trends ; Humans ; Internationality ; Registries ; Reproducibility of Results ; Sensitivity and Specificity ; United States ; United States Food and Drug Administration/legislation & jurisprudence
    Print ISSN: 0028-0836
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    Mismanaged measures (2008)
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    Publication Date: 2008-04-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2008 Apr 3;452(7187):504. doi: 10.1038/452504a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18385690" target="_blank"〉PubMed〈/a〉
    Keywords: Atherosclerosis/blood/epidemiology ; Azetidines/adverse effects/pharmacology ; Biomarkers/*analysis ; Cholesterol/blood ; Clinical Trials as Topic/adverse effects/*methods/*mortality/standards ; Diabetes Mellitus/metabolism/mortality ; Ezetimibe ; Humans ; Reproducibility of Results ; Treatment Outcome
    Print ISSN: 0028-0836
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    Hype around nanotubes creates unrealistic hopes (2008)
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    Publication Date: 2008-05-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kostarelos, Kostas -- Bianco, Alberto -- Prato, Maurizio -- England -- Nature. 2008 May 15;453(7193):280. doi: 10.1038/453280c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18480788" target="_blank"〉PubMed〈/a〉
    Keywords: Adult Stem Cells/*cytology ; Humans ; Nanomedicine/standards/trends ; *Nanotubes, Carbon ; Reproducibility of Results
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Repairing research integrity (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-06-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Titus, Sandra L -- Wells, James A -- Rhoades, Lawrence J -- England -- Nature. 2008 Jun 19;453(7198):980-2. doi: 10.1038/453980a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Office of Research Integrity, 1101 Wootton Parkway, Suite 750, Rockville, Maryland 20852, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18563131" target="_blank"〉PubMed〈/a〉
    Keywords: Ethics, Research/*education ; Guidelines as Topic ; Mentors/education ; Reproducibility of Results ; Research Personnel/education/*ethics/psychology/standards ; Scientific Misconduct/legislation & jurisprudence/psychology/*statistics & ; numerical data ; Surveys and Questionnaires ; Whistleblowing/legislation & jurisprudence/psychology
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    Web data predict flu (2008)
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    Publication Date: 2008-11-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Butler, Declan -- England -- Nature. 2008 Nov 20;456(7220):287-8. doi: 10.1038/456287a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19020578" target="_blank"〉PubMed〈/a〉
    Keywords: *Databases, Factual ; Humans ; Influenza, Human/*epidemiology ; *Information Storage and Retrieval ; *Internet ; Population Surveillance/*methods ; Public Health Informatics/methods ; Reproducibility of Results
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    Spread the word (2008)
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    Publication Date: 2008-01-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2008 Jan 10;451(7175):108. doi: 10.1038/451108b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18185543" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Biology/*education ; Fossils ; Religion and Science ; Reproducibility of Results ; Selection, Genetic
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    Broad phylogenomic sampling improves resolution of the animal tree of life (2008)
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    Publication Date: 2008-03-07
    Description: Long-held ideas regarding the evolutionary relationships among animals have recently been upended by sometimes controversial hypotheses based largely on insights from molecular data. These new hypotheses include a clade of moulting animals (Ecdysozoa) and the close relationship of the lophophorates to molluscs and annelids (Lophotrochozoa). Many relationships remain disputed, including those that are required to polarize key features of character evolution, and support for deep nodes is often low. Phylogenomic approaches, which use data from many genes, have shown promise for resolving deep animal relationships, but are hindered by a lack of data from many important groups. Here we report a total of 39.9 Mb of expressed sequence tags from 29 animals belonging to 21 phyla, including 11 phyla previously lacking genomic or expressed-sequence-tag data. Analysed in combination with existing sequences, our data reinforce several previously identified clades that split deeply in the animal tree (including Protostomia, Ecdysozoa and Lophotrochozoa), unambiguously resolve multiple long-standing issues for which there was strong conflicting support in earlier studies with less data (such as velvet worms rather than tardigrades as the sister group of arthropods), and provide molecular support for the monophyly of molluscs, a group long recognized by morphologists. In addition, we find strong support for several new hypotheses. These include a clade that unites annelids (including sipunculans and echiurans) with nemerteans, phoronids and brachiopods, molluscs as sister to that assemblage, and the placement of ctenophores as the earliest diverging extant multicellular animals. A single origin of spiral cleavage (with subsequent losses) is inferred from well-supported nodes. Many relationships between a stable subset of taxa find strong support, and a diminishing number of lineages remain recalcitrant to placement on the tree.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dunn, Casey W -- Hejnol, Andreas -- Matus, David Q -- Pang, Kevin -- Browne, William E -- Smith, Stephen A -- Seaver, Elaine -- Rouse, Greg W -- Obst, Matthias -- Edgecombe, Gregory D -- Sorensen, Martin V -- Haddock, Steven H D -- Schmidt-Rhaesa, Andreas -- Okusu, Akiko -- Kristensen, Reinhardt Mobjerg -- Wheeler, Ward C -- Martindale, Mark Q -- Giribet, Gonzalo -- England -- Nature. 2008 Apr 10;452(7188):745-9. doi: 10.1038/nature06614. Epub 2008 Mar 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Kewalo Marine Laboratory, PBRC, University of Hawaii, 41 Ahui Street, Honolulu, Hawaii 96813, USA. casey_dunn@brown.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18322464" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bayes Theorem ; Classification/*methods ; Computational Biology ; Databases, Genetic ; Evolution, Molecular ; Expressed Sequence Tags ; Gene Library ; Humans ; Markov Chains ; *Phylogeny ; Reproducibility of Results ; Sample Size ; Sensitivity and Specificity
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    Doctors accused of doing illegal stem-cell trials (2008)
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    Publication Date: 2008-05-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abbott, Alison -- England -- Nature. 2008 May 1;453(7191):6-7. doi: 10.1038/453006a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18461707" target="_blank"〉PubMed〈/a〉
    Keywords: Aged ; Animals ; Austria ; Cell- and Tissue-Based Therapy/ethics ; Clinical Trials as Topic/*ethics ; Ethics Committees ; Humans ; Male ; Malpractice ; Physicians/*ethics ; Reproducibility of Results ; *Stem Cells ; Urinary Incontinence/*therapy
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    Frequency-modulated nuclear localization bursts coordinate gene regulation (2008)
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    Publication Date: 2008-09-27
    Description: In yeast, the transcription factor Crz1 is dephosphorylated and translocates into the nucleus in response to extracellular calcium. Here we show, using time-lapse microscopy, that Crz1 exhibits short bursts of nuclear localization (typically lasting 2 min) that occur stochastically in individual cells and propagate to the expression of downstream genes. Strikingly, calcium concentration controls the frequency, but not the duration, of localization bursts. Using an analytic model, we also show that this frequency modulation of bursts ensures proportional expression of multiple target genes across a wide dynamic range of expression levels, independent of promoter characteristics. We experimentally confirm this theory with natural and synthetic Crz1 target promoters. Another stress-response transcription factor, Msn2, exhibits similar, but largely uncorrelated, localization bursts under calcium stress suggesting that frequency-modulation regulation of localization bursts may be a general control strategy used by the cell to coordinate multi-gene responses to external signals.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2695983/" 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/PMC2695983/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cai, Long -- Dalal, Chiraj K -- Elowitz, Michael B -- P50 GM068763/GM/NIGMS NIH HHS/ -- P50 GM068763-050005/GM/NIGMS NIH HHS/ -- R01 GM079771/GM/NIGMS NIH HHS/ -- R01 GM079771-02/GM/NIGMS NIH HHS/ -- R01GM079771/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 Sep 25;455(7212):485-90. doi: 10.1038/nature07292.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Division of Biology and Department of Applied Physics, California Institute of Technology, M/C 114-96, Pasadena, California 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18818649" target="_blank"〉PubMed〈/a〉
    Keywords: Active Transport, Cell Nucleus/drug effects ; Calcium/metabolism/pharmacology ; Cell Nucleus/drug effects/*metabolism ; DNA-Binding Proteins/metabolism ; *Gene Expression Regulation, Fungal/drug effects ; Models, Genetic ; Phosphorylation/drug effects ; Promoter Regions, Genetic/genetics ; Reproducibility of Results ; Saccharomyces cerevisiae/*cytology/drug effects/*genetics ; Saccharomyces cerevisiae Proteins/*metabolism ; Stochastic Processes ; Time Factors ; Trans-Activators/*metabolism ; Transcription Factors/metabolism
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    Drug markers questioned (2008)
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    Publication Date: 2008-04-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ledford, Heidi -- England -- Nature. 2008 Apr 3;452(7187):510-1. doi: 10.1038/452510a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18385695" target="_blank"〉PubMed〈/a〉
    Keywords: Biomarkers/*analysis ; Blood Pressure/drug effects ; Clinical Trials as Topic/*methods/*mortality/standards ; *Drug Approval ; Humans ; Hypertension/drug therapy/physiopathology ; Myocardial Infarction/drug therapy/mortality/physiopathology ; Reproducibility of Results ; *Treatment Outcome ; United States/epidemiology ; United States Food and Drug Administration
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    Nobel prizewinner's paper retracted (2008)
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    Publication Date: 2008-03-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ledford, Heidi -- England -- Nature. 2008 Mar 6;452(7183):13. doi: 10.1038/452013a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18322489" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Mice ; Neural Pathways/*physiology ; *Nobel Prize ; Receptors, Odorant/*metabolism ; Reproducibility of Results ; *Research Personnel ; *Retraction of Publication as Topic ; Smell/physiology
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    Botanical identities (2008)
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    Publication Date: 2008-02-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ledford, Heidi -- England -- Nature. 2008 Feb 7;451(7179):616. doi: 10.1038/451616b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18256630" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Automatic Data Processing/methods/*trends ; Biodiversity ; Genes, Plant/*genetics ; Phylogeny ; Plants/*classification/*genetics ; Reproducibility of Results ; Species Specificity
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    Restricted access to fossils hinders claim confirmation (2008)
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    Publication Date: 2008-01-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Heesy, Christopher P -- England -- Nature. 2008 Jan 17;451(7176):244. doi: 10.1038/451244d.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18202620" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Anthropology ; *Confidentiality ; *Fossils ; Reproducibility of Results
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    Do female hyaenas choose mates based on tenure? (2008)
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    Details
    Publication Date: 2008-07-11
    Description: In their investigation into whether female mate-choice drives male dispersal, Honer et al. argue that female spotted hyaenas (Crocuta crocuta) prefer mates whose tenure in the social group is less than the females' age, to avoid paternal incest, and suggest that male dispersal reflects this preference. However, we are not persuaded that females choose mates on the basis of tenure because Honer et al. overlook the alternative hypothesis that dispersal status itself is important in female mate-choice, such that females prefer immigrants over natal males. Like mate-choice based on tenure, choice based on dispersal status reduces the risk of incest.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Van Horn, Russell C -- Watts, Heather E -- Holekamp, Kay E -- England -- Nature. 2008 Jul 10;454(7201):E1; discussion E2. doi: 10.1038/nature07122.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Zoological Society of San Diego, Conservation and Research for Endangered Species, P.O. Box 120551, San Diego, California 92112-0551, USA. rvanhorn@sandiegozoo.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18615020" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Female ; Hyaenidae/*physiology ; Inbreeding ; Male ; Mating Preference, Animal/*physiology ; Reproducibility of Results ; Social Behavior ; Time Factors
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    Why does work on same mouse models give different results? (2008)
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    Publication Date: 2008-08-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fallon, Padraic G -- England -- Nature. 2008 Aug 7;454(7205):691. doi: 10.1038/454691c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18685681" target="_blank"〉PubMed〈/a〉
    Keywords: Animal Feed ; Animals ; Artifacts ; *Disease Models, Animal ; Hypersensitivity/*immunology ; Mice ; Mice, Inbred Strains ; Reproducibility of Results ; Sterilization/methods
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    Neuroscience: Standard model (2008)
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    Publication Date: 2008-08-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schnabel, Jim -- England -- Nature. 2008 Aug 7;454(7205):682-5. doi: 10.1038/454682a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18685674" target="_blank"〉PubMed〈/a〉
    Keywords: *Amyotrophic Lateral Sclerosis/drug therapy/genetics ; Animals ; Clinical Trials as Topic ; *Disease Models, Animal ; Drug Evaluation, Preclinical/*methods/*standards ; Humans ; Meta-Analysis as Topic ; Mice ; Reproducibility of Results ; Superoxide Dismutase/genetics ; Treatment Failure
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    Schizophrenia is a disease, so electrons aren't at risk (2008)
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    Publication Date: 2008-01-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chase, Ronald -- England -- Nature. 2008 Jan 10;451(7175):127. doi: 10.1038/451127d.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18185564" target="_blank"〉PubMed〈/a〉
    Keywords: *Electrons ; Humans ; *Metaphor ; Reproducibility of Results ; Schizophrenia/*physiopathology ; Terminology as Topic
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    Does Rft1 flip an N-glycan lipid precursor? (2008)
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    Publication Date: 2008-08-01
    Description: Protein N-glycosylation requires flipping of the glycolipid Man(5)GlcNAc(2)-diphosphate dolichol (Man(5)GlcNAc(2)-PP-Dol) across the endoplasmic reticulum (ER). Helenius et al. report genetic evidence suggesting that Rft1, an essential ER membrane protein in yeast, is required directly to translocate Man(5)GlcNAc(2)-PP-Dol. We now show that a specific ER protein(s), but not Rft1, is required to flip Man(5)GlcNAc(2)-PP-Dol in reconstituted vesicles. Rft1 may have a critical accessory role in translocating Man(5)GlcNAc(2)-PP-Dol in vivo, but the Man(5)GlcNAc(2)-PP-Dol flippase itself remains to be identified.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Frank, Christian G -- Sanyal, Sumana -- Rush, Jeffrey S -- Waechter, Charles J -- Menon, Anant K -- R01 GM036065/GM/NIGMS NIH HHS/ -- R01 GM071041/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Jul 31;454(7204):E3-4; discussion E4-5. doi: 10.1038/nature07165.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Weill Cornell Medical College, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18668045" target="_blank"〉PubMed〈/a〉
    Keywords: Dolichol/*analogs & derivatives/metabolism ; Mannans/*metabolism ; Membrane Glycoproteins/*metabolism ; Membrane Transport Proteins ; Phospholipid Transfer Proteins/*metabolism ; Reproducibility of Results ; Saccharomyces cerevisiae/cytology/*metabolism ; Saccharomyces cerevisiae Proteins/*metabolism
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    Variations in DNA elucidate molecular networks that cause disease (2008)
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    Publication Date: 2008-03-18
    Description: Identifying variations in DNA that increase susceptibility to disease is one of the primary aims of genetic studies using a forward genetics approach. However, identification of disease-susceptibility genes by means of such studies provides limited functional information on how genes lead to disease. In fact, in most cases there is an absence of functional information altogether, preventing a definitive identification of the susceptibility gene or genes. Here we develop an alternative to the classic forward genetics approach for dissecting complex disease traits where, instead of identifying susceptibility genes directly affected by variations in DNA, we identify gene networks that are perturbed by susceptibility loci and that in turn lead to disease. Application of this method to liver and adipose gene expression data generated from a segregating mouse population results in the identification of a macrophage-enriched network supported as having a causal relationship with disease traits associated with metabolic syndrome. Three genes in this network, lipoprotein lipase (Lpl), lactamase beta (Lactb) and protein phosphatase 1-like (Ppm1l), are validated as previously unknown obesity genes, strengthening the association between this network and metabolic disease traits. Our analysis provides direct experimental support that complex traits such as obesity are emergent properties of molecular networks that are modulated by complex genetic loci and environmental factors.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2841398/" 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/PMC2841398/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Yanqing -- Zhu, Jun -- Lum, Pek Yee -- Yang, Xia -- Pinto, Shirly -- MacNeil, Douglas J -- Zhang, Chunsheng -- Lamb, John -- Edwards, Stephen -- Sieberts, Solveig K -- Leonardson, Amy -- Castellini, Lawrence W -- Wang, Susanna -- Champy, Marie-France -- Zhang, Bin -- Emilsson, Valur -- Doss, Sudheer -- Ghazalpour, Anatole -- Horvath, Steve -- Drake, Thomas A -- Lusis, Aldons J -- Schadt, Eric E -- P01 HL028481/HL/NHLBI NIH HHS/ -- P01 HL028481-24/HL/NHLBI NIH HHS/ -- P01 HL028481-240010/HL/NHLBI NIH HHS/ -- P01 HL030568/HL/NHLBI NIH HHS/ -- P01 HL030568-250011/HL/NHLBI NIH HHS/ -- R01 DK071673/DK/NIDDK NIH HHS/ -- R01 DK071673-03/DK/NIDDK NIH HHS/ -- England -- Nature. 2008 Mar 27;452(7186):429-35. doi: 10.1038/nature06757. Epub 2008 Mar 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Rosetta Inpharmatics, LLC, Merck & Co., Inc., 401 Terry Avenue North, Seattle, Washington 98109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18344982" target="_blank"〉PubMed〈/a〉
    Keywords: Adipose Tissue/metabolism ; Animals ; Apolipoprotein A-II/genetics ; Chromosomes, Mammalian/genetics ; Female ; Gene Regulatory Networks/*genetics ; Genetic Predisposition to Disease/*genetics ; Genetic Variation/*genetics ; Linkage Disequilibrium ; Lipoprotein Lipase/genetics ; Liver/metabolism ; Lod Score ; Macrophages/metabolism ; Male ; Membrane Proteins/genetics ; Metabolic Syndrome X/enzymology/*genetics/metabolism ; Mice ; Obesity/enzymology/*genetics/metabolism ; Phenotype ; Phosphoprotein Phosphatases/deficiency/genetics/metabolism ; Quantitative Trait Loci ; Reproducibility of Results ; Ribosomal Proteins/genetics
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    Predicting expression patterns from regulatory sequence in Drosophila segmentation (2008)
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    Publication Date: 2008-01-04
    Description: The establishment of complex expression patterns at precise times and locations is key to metazoan development, yet a mechanistic understanding of the underlying transcription control networks is still missing. Here we describe a novel thermodynamic model that computes expression patterns as a function of cis-regulatory sequence and of the binding-site preferences and expression of participating transcription factors. We apply this model to the segmentation gene network of Drosophila melanogaster and find that it predicts expression patterns of cis-regulatory modules with remarkable accuracy, demonstrating that positional information is encoded in the regulatory sequence and input factor distribution. Our analysis reveals that both strong and weaker binding sites contribute, leading to high occupancy of the module DNA, and conferring robustness against mutation; short-range homotypic clustering of weaker sites facilitates cooperative binding, which is necessary to sharpen the patterns. Our computational framework is generally applicable to most protein-DNA interaction systems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Segal, Eran -- Raveh-Sadka, Tali -- Schroeder, Mark -- Unnerstall, Ulrich -- Gaul, Ulrike -- England -- Nature. 2008 Jan 31;451(7178):535-40. doi: 10.1038/nature06496. Epub 2008 Jan 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel. eran@weizmann.ac.il〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18172436" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Site ; Animals ; Base Sequence ; Body Patterning/genetics ; Computational Biology ; DNA/genetics/metabolism ; Drosophila melanogaster/*embryology/*genetics ; Gene Expression Regulation, Developmental/*genetics ; *Models, Genetic ; Reproducibility of Results ; Response Elements/*genetics ; Thermodynamics ; Transcription Factors/metabolism
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    Doping: world agency sets standards to promote fair play (2008)
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    Publication Date: 2008-10-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ljungqvist, Arne -- Horta, Luis -- Wadler, Gary -- England -- Nature. 2008 Oct 30;455(7217):1176. doi: 10.1038/4551176a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18971999" target="_blank"〉PubMed〈/a〉
    Keywords: Doping in Sports/*prevention & control ; France ; Humans ; Male ; Quality Control ; Reference Values ; Reproducibility of Results ; Substance Abuse Detection/*methods/*standards
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    Design of protein-interaction specificity gives selective bZIP-binding peptides (2009)
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    Publication Date: 2009-04-17
    Description: Interaction specificity is a required feature of biological networks and a necessary characteristic of protein or small-molecule reagents and therapeutics. The ability to alter or inhibit protein interactions selectively would advance basic and applied molecular science. Assessing or modelling interaction specificity requires treating multiple competing complexes, which presents computational and experimental challenges. Here we present a computational framework for designing protein-interaction specificity and use it to identify specific peptide partners for human basic-region leucine zipper (bZIP) transcription factors. Protein microarrays were used to characterize designed, synthetic ligands for all but one of 20 bZIP families. The bZIP proteins share strong sequence and structural similarities and thus are challenging targets to bind specifically. Nevertheless, many of the designs, including examples that bind the oncoproteins c-Jun, c-Fos and c-Maf (also called JUN, FOS and MAF, respectively), were selective for their targets over all 19 other families. Collectively, the designs exhibit a wide range of interaction profiles and demonstrate that human bZIPs have only sparsely sampled the possible interaction space accessible to them. Our computational method provides a way to systematically analyse trade-offs between stability and specificity and is suitable for use with many types of structure-scoring functions; thus, it may prove broadly useful as a tool for protein design.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748673/" 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/PMC2748673/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grigoryan, Gevorg -- Reinke, Aaron W -- Keating, Amy E -- GM67681/GM/NIGMS NIH HHS/ -- R01 GM067681/GM/NIGMS NIH HHS/ -- R01 GM067681-04/GM/NIGMS NIH HHS/ -- R01 GM067681-05/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Apr 16;458(7240):859-64. doi: 10.1038/nature07885.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MIT Department of Biology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19370028" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Basic-Leucine Zipper Transcription Factors/*chemistry/classification/*metabolism ; Computational Biology/*methods ; Drug Design ; Humans ; Leucine Zippers ; Protein Array Analysis ; Protein Binding ; Protein Engineering/*methods ; Reproducibility of Results ; Substrate Specificity
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    Is REST a regulator of pluripotency? (2009)
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    Publication Date: 2009-02-27
    Description: Establishment and maintenance of the pluripotent state of ESCs is a key issue in stem cell biology and regenerative medicine, and consequently identification of transcription factors that regulate ESC pluripotency is an important goal. Singh et al. claim that the transcriptional repressor REST is such a regulator and that a 50% reduction of REST in ESCs leads to activation of a specific microRNA, miR-21, and that this subsequently results in loss of pluripotency markers and a reciprocal gain in some lineage-specific differentiation markers. In contrast, we show that, in haplodeficient Rest(+/-) ESCs, we detected no change in pluripotency markers, no precocious expression of differentiated neuronal markers and no interaction of REST with miR-21. It is vital that identification of factors that regulate pluripotency is based on robust, consistent data, and the contrast in data reported here undermines the claim by Singh et al. that REST is such a regulator.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Buckley, Noel J -- Johnson, Rory -- Sun, Yuh-Man -- Stanton, Lawrence W -- England -- Nature. 2009 Feb 26;457(7233):E5-6; discussion E7. doi: 10.1038/nature07784.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉King's College London, Institute of Psychiatry, Centre for the Cellular Basis of Behaviour, James Black Centre, 125 Coldharbour Lane, London SE5 9NU, UK. noel.buckley@iop.kcl.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19242418" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Embryonic Stem Cells/*cytology/*metabolism ; Gene Knockdown Techniques ; Mice ; MicroRNAs/genetics/metabolism ; Pluripotent Stem Cells/*cytology/*metabolism ; Polymerase Chain Reaction ; Repressor Proteins/genetics/*metabolism ; Reproducibility of Results
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    Research into group differences isn't wrong, just pointless (2009)
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    Publication Date: 2009-11-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rose, Steven -- England -- Nature. 2009 Nov 5;462(7269):35. doi: 10.1038/462035c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19890309" target="_blank"〉PubMed〈/a〉
    Keywords: Continental Population Groups/*genetics ; *Ethics, Research ; Female ; Humans ; Intelligence/*genetics ; Male ; Reproducibility of Results ; *Sex Characteristics
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    Identity crisis (2009)
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    Publication Date: 2009-02-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2009 Feb 19;457(7232):935-6. doi: 10.1038/457935b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19225471" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Specimen Banks/economics/*standards ; *Cell Line ; DNA Fingerprinting/economics ; Humans ; Quality Control ; Reproducibility of Results ; *Research Design
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    Were crocodiles responsible for the stones we call tools? (2009)
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    Publication Date: 2009-09-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dempsey, Patrick -- England -- Nature. 2009 Sep 17;461(7262):341. doi: 10.1038/461341a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19759599" target="_blank"〉PubMed〈/a〉
    Keywords: Africa, Eastern ; Alligators and Crocodiles/*physiology ; Animals ; Archaeology/methods ; *Hominidae ; Humans ; Paleontology/*methods ; Reproducibility of Results ; Stomach/*physiology ; *Technology
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    Jury still out on HIV vaccine results (2009)
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    Publication Date: 2009-10-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Butler, Declan -- England -- Nature. 2009 Oct 29;461(7268):1187. doi: 10.1038/4611187a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19865138" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines/*immunology ; *Clinical Trials, Phase III as Topic ; HIV Infections/*prevention & control ; Humans ; Reproducibility of Results ; Thailand ; Viral Load
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    A tunable synthetic mammalian oscillator (2009)
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    Publication Date: 2009-01-17
    Description: Autonomous and self-sustained oscillator circuits mediating the periodic induction of specific target genes are minimal genetic time-keeping devices found in the central and peripheral circadian clocks. They have attracted significant attention because of their intriguing dynamics and their importance in controlling critical repair, metabolic and signalling pathways. The precise molecular mechanism and expression dynamics of this mammalian circadian clock are still not fully understood. Here we describe a synthetic mammalian oscillator based on an auto-regulated sense-antisense transcription control circuit encoding a positive and a time-delayed negative feedback loop, enabling autonomous, self-sustained and tunable oscillatory gene expression. After detailed systems design with experimental analyses and mathematical modelling, we monitored oscillating concentrations of green fluorescent protein with tunable frequency and amplitude by time-lapse microscopy in real time in individual Chinese hamster ovary cells. The synthetic mammalian clock may provide an insight into the dynamics of natural periodic processes and foster advances in the design of prosthetic networks in future gene and cell therapies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tigges, Marcel -- Marquez-Lago, Tatiana T -- Stelling, Jorg -- Fussenegger, Martin -- England -- Nature. 2009 Jan 15;457(7227):309-12. doi: 10.1038/nature07616.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19148099" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Clocks/*physiology ; CHO Cells ; Circadian Rhythm/*physiology ; Cricetinae ; Cricetulus ; Feedback, Physiological ; Fluorescence ; Gene Expression Regulation/*genetics ; Genes, Synthetic/*genetics ; *Genetic Engineering ; Green Fluorescent Proteins/analysis/genetics/metabolism ; Models, Biological ; Reproducibility of Results ; Time Factors ; Transcription, Genetic
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    Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals (2009)
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    Publication Date: 2009-02-03
    Description: There is growing recognition that mammalian cells produce many thousands of large intergenic transcripts. However, the functional significance of these transcripts has been particularly controversial. Although there are some well-characterized examples, most (〉95%) show little evidence of evolutionary conservation and have been suggested to represent transcriptional noise. Here we report a new approach to identifying large non-coding RNAs using chromatin-state maps to discover discrete transcriptional units intervening known protein-coding loci. Our approach identified approximately 1,600 large multi-exonic RNAs across four mouse cell types. In sharp contrast to previous collections, these large intervening non-coding RNAs (lincRNAs) show strong purifying selection in their genomic loci, exonic sequences and promoter regions, with greater than 95% showing clear evolutionary conservation. We also developed a functional genomics approach that assigns putative functions to each lincRNA, demonstrating a diverse range of roles for lincRNAs in processes from embryonic stem cell pluripotency to cell proliferation. We obtained independent functional validation for the predictions for over 100 lincRNAs, using cell-based assays. In particular, we demonstrate that specific lincRNAs are transcriptionally regulated by key transcription factors in these processes such as p53, NFkappaB, Sox2, Oct4 (also known as Pou5f1) and Nanog. Together, these results define a unique collection of functional lincRNAs that are highly conserved and implicated in diverse biological processes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2754849/" 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/PMC2754849/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Guttman, Mitchell -- Amit, Ido -- Garber, Manuel -- French, Courtney -- Lin, Michael F -- Feldser, David -- Huarte, Maite -- Zuk, Or -- Carey, Bryce W -- Cassady, John P -- Cabili, Moran N -- Jaenisch, Rudolf -- Mikkelsen, Tarjei S -- Jacks, Tyler -- Hacohen, Nir -- Bernstein, Bradley E -- Kellis, Manolis -- Regev, Aviv -- Rinn, John L -- Lander, Eric S -- DP1 OD003958/OD/NIH HHS/ -- R01 HG004037/HG/NHGRI NIH HHS/ -- R01 HG004037-02/HG/NHGRI NIH HHS/ -- U54 HG003067/HG/NHGRI NIH HHS/ -- U54 HG003067-05/HG/NHGRI NIH HHS/ -- England -- Nature. 2009 Mar 12;458(7235):223-7. doi: 10.1038/nature07672. Epub 2009 Feb 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19182780" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Cells, Cultured ; Chromatin/*genetics ; *Conserved Sequence/genetics ; DNA, Intergenic ; Exons/genetics ; Mammals/*genetics ; Mice ; Promoter Regions, Genetic/genetics ; RNA/*genetics ; Reproducibility of Results ; Transcription Factors/metabolism
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Copy number variation at 1q21.1 associated with neuroblastoma (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-06-19
    Description: Common copy number variations (CNVs) represent a significant source of genetic diversity, yet their influence on phenotypic variability, including disease susceptibility, remains poorly understood. To address this problem in human cancer, we performed a genome-wide association study of CNVs in the childhood cancer neuroblastoma, a disease in which single nucleotide polymorphism variations are known to influence susceptibility. We first genotyped 846 Caucasian neuroblastoma patients and 803 healthy Caucasian controls at approximately 550,000 single nucleotide polymorphisms, and performed a CNV-based test for association. We then replicated significant observations in two independent sample sets comprised of a total of 595 cases and 3,357 controls. Here we describe the identification of a common CNV at chromosome 1q21.1 associated with neuroblastoma in the discovery set, which was confirmed in both replication sets. This CNV was validated by quantitative polymerase chain reaction, fluorescent in situ hybridization and analysis of matched tumour specimens, and was shown to be heritable in an independent set of 713 cancer-free parent-offspring trios. We identified a previously unknown transcript within the CNV that showed high sequence similarity to several neuroblastoma breakpoint family (NBPF) genes and represents a new member of this gene family (NBPF23). This transcript was preferentially expressed in fetal brain and fetal sympathetic nervous tissues, and the expression level was strictly correlated with CNV state in neuroblastoma cells. These data demonstrate that inherited copy number variation at 1q21.1 is associated with neuroblastoma and implicate a previously unknown neuroblastoma breakpoint family gene in early tumorigenesis of this childhood cancer.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755253/" 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/PMC2755253/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Diskin, Sharon J -- Hou, Cuiping -- Glessner, Joseph T -- Attiyeh, Edward F -- Laudenslager, Marci -- Bosse, Kristopher -- Cole, Kristina -- Mosse, Yael P -- Wood, Andrew -- Lynch, Jill E -- Pecor, Katlyn -- Diamond, Maura -- Winter, Cynthia -- Wang, Kai -- Kim, Cecilia -- Geiger, Elizabeth A -- McGrady, Patrick W -- Blakemore, Alexandra I F -- London, Wendy B -- Shaikh, Tamim H -- Bradfield, Jonathan -- Grant, Struan F A -- Li, Hongzhe -- Devoto, Marcella -- Rappaport, Eric R -- Hakonarson, Hakon -- Maris, John M -- GM081519/GM/NIGMS NIH HHS/ -- R00 CA151869/CA/NCI NIH HHS/ -- R01 CA087847/CA/NCI NIH HHS/ -- R01 CA087847-05/CA/NCI NIH HHS/ -- R01 CA124709/CA/NCI NIH HHS/ -- R01 CA124709-02/CA/NCI NIH HHS/ -- R01-CA124709/CA/NCI NIH HHS/ -- R01-CA87847/CA/NCI NIH HHS/ -- T32-HG000046/HG/NHGRI NIH HHS/ -- U10 CA098543/CA/NCI NIH HHS/ -- U10 CA098543-07/CA/NCI NIH HHS/ -- U10-CA98543/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Jun 18;459(7249):987-91. doi: 10.1038/nature08035.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19536264" target="_blank"〉PubMed〈/a〉
    Keywords: Child ; Chromosome Breakage ; Chromosomes, Human, Pair 1/*genetics ; European Continental Ancestry Group/genetics ; Fetus/metabolism ; Gene Dosage/*genetics ; Genetic Predisposition to Disease/genetics ; Genetic Variation/*genetics ; Genome-Wide Association Study ; Genotype ; Humans ; In Situ Hybridization, Fluorescence ; Neuroblastoma/*genetics ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide/genetics ; RNA, Messenger/genetics ; Reproducibility of Results
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    Drug discovery: Not as fab as we thought (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-03-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zlitni, Soumaya -- Brown, Eric D -- England -- Nature. 2009 Mar 5;458(7234):39-40. doi: 10.1038/458039a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19262660" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anti-Bacterial Agents/*pharmacology ; Drug Evaluation, Preclinical ; *Drug Resistance, Bacterial ; Fatty Acids/analysis/*biosynthesis/chemistry/pharmacology ; Gram-Positive Bacteria/*drug effects/enzymology/genetics/pathogenicity ; Humans ; Reproducibility of Results ; Serum/chemistry/microbiology ; Substrate Specificity
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Human genomics: The genome finishers (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-12-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dolgin, Elie -- England -- Nature. 2009 Dec 17;462(7275):843-5. doi: 10.1038/462843a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20016572" target="_blank"〉PubMed〈/a〉
    Keywords: Female ; Genome, Human/*genetics ; History, 20th Century ; History, 21st Century ; *Human Genome Project/history ; Humans ; Male ; Reproducibility of Results ; Research Design ; *Research Personnel ; Research Subjects
    Print ISSN: 0028-0836
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    Forensic labs warn of deuterated drug threat (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-04-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sanderson, Katharine -- England -- Nature. 2009 Apr 16;458(7240):817. doi: 10.1038/458817a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19369996" target="_blank"〉PubMed〈/a〉
    Keywords: Deuterium/*analysis/*chemistry ; Forensic Toxicology/*methods/standards/trends ; Humans ; Patents as Topic/legislation & jurisprudence ; Pharmaceutical Preparations/*chemistry ; Reference Standards ; Reproducibility of Results ; United States ; United States Food and Drug Administration
    Print ISSN: 0028-0836
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    Brain imaging studies under fire (2009)
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    Publication Date: 2009-01-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abbott, Alison -- England -- Nature. 2009 Jan 15;457(7227):245. doi: 10.1038/457245a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19148065" target="_blank"〉PubMed〈/a〉
    Keywords: Bias (Epidemiology) ; *Brain Mapping ; Emotions/*physiology ; Humans ; Magnetic Resonance Imaging ; Neurosciences/*standards ; Reproducibility of Results ; Research Design ; Research Personnel ; Social Sciences/*standards ; Statistics as Topic/*standards
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    Caution with claims that a species has been rediscovered (2009)
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    Publication Date: 2009-10-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ladle, Richard J -- Jepson, Paul -- Jennings, Steve -- Malhado, Ana C M -- England -- Nature. 2009 Oct 8;461(7265):723. doi: 10.1038/461723c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19812650" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Birds/*classification ; Conservation of Natural Resources/*methods/trends ; *Extinction, Biological ; Reproducibility of Results ; Species Specificity ; Time Factors
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Toxicology for the twenty-first century (2009)
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    Publication Date: 2009-07-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hartung, Thomas -- England -- Nature. 2009 Jul 9;460(7252):208-12. doi: 10.1038/460208a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Environmental Health Sciences at the Johns Hopkins University Bloomberg School of Public Health, USA. thartung@jhsph.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19587762" target="_blank"〉PubMed〈/a〉
    Keywords: Adverse Drug Reaction Reporting Systems ; Animals ; False Positive Reactions ; History, 20th Century ; Humans ; Models, Animal ; Rats ; Reproducibility of Results ; Research Design ; Toxicity Tests ; Toxicology/history/*methods/*trends
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    An agenda for personalized medicine (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-10-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ng, Pauline C -- Murray, Sarah S -- Levy, Samuel -- Venter, J Craig -- England -- Nature. 2009 Oct 8;461(7265):724-6. doi: 10.1038/461724a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉J. Craig Venter Institute, Science Center Drive, San Diego, California 92121, USA. png@jcvi.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19812653" target="_blank"〉PubMed〈/a〉
    Keywords: Ethnic Groups/genetics ; False Negative Reactions ; Female ; Gene Frequency/genetics ; Genetic Counseling/methods/*standards ; Genetic Markers/genetics ; Genetic Predisposition to Disease/*genetics ; Genetic Testing/methods/*standards ; Genetics, Medical/methods/*standards ; Genome, Human/*genetics ; Genome-Wide Association Study ; Genotype ; Health Behavior ; Humans ; Male ; Odds Ratio ; Pharmacogenetics ; *Practice Guidelines as Topic ; Prospective Studies ; Reproducibility of Results ; Sequence Analysis, DNA/standards
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    Key protein-design papers challenged (2009)
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    Publication Date: 2009-10-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hayden, Erika Check -- England -- Nature. 2009 Oct 15;461(7266):859. doi: 10.1038/461859a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19829341" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Computational Biology/*standards ; *Computer Simulation ; Drug Design ; Ligands ; Protein Binding ; *Protein Stability ; Reproducibility of Results ; Research Personnel/ethics/standards ; *Retraction of Publication as Topic ; Scientific Misconduct ; *Substrate Specificity
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    'Killer application' for protein synthesis is retracted (2009)
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    Publication Date: 2009-12-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Check Hayden, Erika -- England -- Nature. 2009 Dec 10;462(7274):707. doi: 10.1038/462707a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20010658" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/chemistry/metabolism ; Escherichia coli/*metabolism ; Glycoproteins/*biosynthesis/chemistry ; Glycosylation ; *Protein Biosynthesis ; Reproducibility of Results ; *Retraction of Publication as Topic
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    Ocean fertilization: dead in the water? (2009)
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    Publication Date: 2009-01-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schiermeier, Quirin -- England -- Nature. 2009 Jan 29;457(7229):520-1. doi: 10.1038/457520b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19177092" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/chemistry ; Carbon Dioxide/*chemistry/*isolation & purification ; *Ecosystem ; Germany ; Human Activities ; Iron/*chemistry ; Oceans and Seas ; Reproducibility of Results ; Research/*trends ; Seawater/*chemistry
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    Genome sequencing: the third generation (2009)
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    Publication Date: 2009-02-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Check Hayden, Erika -- England -- Nature. 2009 Feb 12;457(7231):768-9. doi: 10.1038/news.2009.86.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19212365" target="_blank"〉PubMed〈/a〉
    Keywords: Computational Biology/instrumentation/*methods ; *Genome ; Humans ; Reproducibility of Results ; Sequence Analysis, DNA/economics/instrumentation/*methods
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    Alzheimer's theory makes a splash (2009)
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    Publication Date: 2009-05-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schnabel, Jim -- England -- Nature. 2009 May 21;459(7245):310. doi: 10.1038/459310a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19458681" target="_blank"〉PubMed〈/a〉
    Keywords: Alzheimer Disease/blood/*metabolism/*pathology/urine ; Amyloid beta-Peptides/blood/genetics/*metabolism/urine ; Animals ; Disease Models, Animal ; Humans ; Mice ; Mice, Transgenic ; *Models, Neurological ; Peptide Fragments/blood/*metabolism/urine ; Reproducibility of Results
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    Genome-wide silencing in Drosophila captures conserved apoptotic effectors (2009)
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    Publication Date: 2009-06-02
    Description: Apoptosis is a conserved form of programmed cell death firmly established in the aetiology, pathogenesis and treatment of many human diseases. Central to the core machinery of apoptosis are the caspases and their proximal regulators. Current models for caspase control involve a balance of opposing elements, with variable contributions from positive and negative regulators among different cell types and species. To advance a comprehensive view of components that support caspase-dependent cell death, we conducted a genome-wide silencing screen in the Drosophila model. Our strategy used a library of double-stranded RNAs together with a chemical antagonist of Inhibitor of apoptosis proteins (IAPs) that simulates the action of native regulators in the Reaper and Smac (also known as Diablo) families. Here we present a highly validated set of targets that is necessary for death provoked by several stimuli. Among these, Tango7 is identified as a new effector. Cells depleted for this gene resisted apoptosis at a step before the induction of effector caspase activity, and the directed silencing of Tango7 in Drosophila prevented caspase-dependent programmed cell death. Unlike known apoptosis regulators in this model system, Tango7 activity did not influence stimulus-dependent loss of Drosophila DIAP1 (also known as th and IAP1), but instead regulated levels of the apical caspase Dronc (Nc). Similarly, the human Tango7 counterpart, PCID1 (also known as EIF3M), impinged on caspase 9, revealing a new regulatory axis affecting the apoptosome.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2777527/" 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/PMC2777527/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chew, Su Kit -- Chen, Po -- Link, Nichole -- Galindo, Kathleen A -- Pogue, Kristi -- Abrams, John M -- R01 AA017328/AA/NIAAA NIH HHS/ -- R01 AA017328-01/AA/NIAAA NIH HHS/ -- R01 AA017328-02/AA/NIAAA NIH HHS/ -- R01 GM072124/GM/NIGMS NIH HHS/ -- R01 GM072124-10/GM/NIGMS NIH HHS/ -- R01 GM072124-11/GM/NIGMS NIH HHS/ -- R01 GM072124-12/GM/NIGMS NIH HHS/ -- R01 GM072124-13/GM/NIGMS NIH HHS/ -- R01 GM072124-14A1/GM/NIGMS NIH HHS/ -- R56 GM072124/GM/NIGMS NIH HHS/ -- R56 GM072124-14/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Jul 2;460(7251):123-7. doi: 10.1038/nature08087. Epub 2009 May 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19483676" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis/*genetics/*physiology ; Apoptosomes/metabolism ; Aryl Hydrocarbon Receptor Nuclear Translocator/genetics/*metabolism ; Caspase 9/metabolism ; Caspases/metabolism ; Conserved Sequence ; Drosophila Proteins/deficiency/genetics/*metabolism ; Drosophila melanogaster/*genetics ; Eukaryotic Initiation Factor-3 ; Eukaryotic Initiation Factors/*metabolism ; *Gene Silencing ; Genes, Insect/genetics ; Genome, Insect/*genetics ; Humans ; Inhibitor of Apoptosis Proteins/antagonists & inhibitors/genetics/metabolism ; Mitochondrial Proteins ; Molecular Mimicry ; RNA Interference ; RNA, Double-Stranded/genetics ; Reproducibility of Results ; Xenopus Proteins
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    Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps (2009)
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    Details
    Publication Date: 2009-06-19
    Description: MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; however, as miRNA activity requires base pairing with only 6-8 nucleotides of messenger RNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native argonaute (Ago, also called Eif2c) protein-RNA complexes in mouse brain. This produced two simultaneous data sets-Ago-miRNA and Ago-mRNA binding sites-that were combined with bioinformatic analysis to identify interaction sites between miRNA and target mRNA. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2733940/" 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/PMC2733940/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chi, Sung Wook -- Zang, Julie B -- Mele, Aldo -- Darnell, Robert B -- R01 NS034389/NS/NINDS NIH HHS/ -- R01 NS034389-14/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Jul 23;460(7254):479-86. doi: 10.1038/nature08170. Epub 2009 Jun 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19536157" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cross-Linking Reagents/chemistry/metabolism ; *Gene Expression Regulation ; HeLa Cells ; Humans ; Immunoprecipitation/*methods ; Mice ; MicroRNAs/*metabolism ; Protein Interaction Mapping ; Reproducibility of Results
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Tbx18 and the fate of epicardial progenitors (2009)
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    Publication Date: 2009-04-17
    Description: Uncovering the origins of myocardial cells is important for understanding and treating heart diseases. Cai et al. suggest that Tbx18-expressing epicardium provides a substantial contribution to myocytes in the ventricular septum and the atrial and ventricular walls. Here we show that the T-box transcription factor gene 18 (Tbx18) itself is expressed in the myocardium, showing that their genetic lineage tracing system does not allow conclusions of an epicardial origin of cardiomyocytes in vivo to be drawn.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Christoffels, Vincent M -- Grieskamp, Thomas -- Norden, Julia -- Mommersteeg, Mathilda T M -- Rudat, Carsten -- Kispert, Andreas -- England -- Nature. 2009 Apr 16;458(7240):E8-9; discussion E9-10. doi: 10.1038/nature07916.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Anatomy & Embryology, Heart Failure Research Center, Academic Medical Center, University of Amsterdam, Meibergdreef 15 L2-108, 1105 AZ Amsterdam, The Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19369973" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Differentiation ; *Cell Lineage ; Fluorescent Dyes ; Gene Expression Regulation, Developmental ; Gene Knock-In Techniques ; Heart Ventricles/cytology/embryology/metabolism ; In Situ Hybridization ; Integrases/genetics/metabolism ; Mice ; Myocardium/*cytology ; Myocytes, Cardiac/cytology/metabolism ; Pericardium/*cytology/embryology ; RNA/analysis/genetics ; Reproducibility of Results ; Stem Cells/*cytology/*metabolism ; T-Box Domain Proteins/genetics/*metabolism
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Neuroscience: Pre-emptive blood flow (2009)
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    Publication Date: 2009-01-23
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715363/" 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/PMC2715363/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Leopold, David A -- Z01 MH002838-04/Intramural NIH HHS/ -- Z01 MH002896-01/Intramural NIH HHS/ -- Z01 MH002899-01/Intramural NIH HHS/ -- England -- Nature. 2009 Jan 22;457(7228):387-8. doi: 10.1038/457387a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19158777" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Brain Mapping ; *Cerebrovascular Circulation ; Humans ; Macaca mulatta/*physiology ; Magnetic Resonance Imaging ; Neurons/physiology ; Reproducibility of Results ; Time Factors ; Visual Cortex/*blood supply/cytology/*physiology
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    Problems with anti-plagiarism database (2009)
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    Publication Date: 2009-01-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vihinen, Mauno -- England -- Nature. 2009 Jan 1;457(7225):26. doi: 10.1038/457026b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19122620" target="_blank"〉PubMed〈/a〉
    Keywords: *Databases, Factual ; Periodicals as Topic/standards ; *Plagiarism ; Reproducibility of Results ; Software
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    The mystery ape of Pleistocene Asia (2009)
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    Publication Date: 2009-06-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ciochon, Russell L -- England -- Nature. 2009 Jun 18;459(7249):910-1. doi: 10.1038/459910a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Iowa, Iowa City, Iowa 52242, USA. russell-ciochon@uiowa.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19536242" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Asia, Southeastern ; China ; *Fossils ; *Hominidae/anatomy & histology/classification ; Humans ; Reproducibility of Results ; Tooth/anatomy & histology
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    Much ado about cognitive enhancement (2009)
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    Publication Date: 2009-01-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oliveira, Joao Ricardo -- England -- Nature. 2009 Jan 29;457(7229):532. doi: 10.1038/457532b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19177105" target="_blank"〉PubMed〈/a〉
    Keywords: Biomedical Enhancement/*ethics ; *Cognition ; Health ; Humans ; Reproducibility of Results
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Protecting the Hawaiian akepa population (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-02-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scott, J Michael -- Horne, Jon S -- Garton, Edward O -- England -- Nature. 2009 Feb 19;457(7232):956. doi: 10.1038/457956b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19225496" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Conservation of Natural Resources/*trends ; Data Collection ; Ecosystem ; Extinction, Biological ; Hawaii ; Passeriformes/*physiology ; Population Density ; Reproducibility of Results ; Time Factors
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    Gene data for endangered species have limitations (2009)
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    Publication Date: 2009-06-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hofreiter, Michael -- England -- Nature. 2009 Jun 11;459(7248):774. doi: 10.1038/459774a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19516319" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Conservation of Natural Resources/*methods ; Ecology/*methods ; *Extinction, Biological ; *Genomics ; Reproducibility of Results
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Evidence for escape from adaptive conflict? (2009)
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    Publication Date: 2009-12-17
    Description: Gene duplication is the primary source of new genes, but the molecular evolutionary mechanisms underlying functional divergence of duplicate genes are not well understood. Des Marais and Rausher argued that data from plant dihydroflavonol-4-reductase (DFR) genes support the model that gene duplication allows the escape from adaptive conflict (EAC) among several functions of a single-copy progenitor gene. As the authors indicated, the key predictions of EAC, in comparison to other models, are that (i) adaptive changes occur in both daughter genes after duplication, and (ii) these adaptive changes must improve ancestral functions. Furthermore, EAC indicates that (iii) the improvement of several ancestral functions is constrained before duplication, although this last point was not explicitly stated. Here we show that contrary to the predictions of EAC, only one of the duplicated DFR lineages exhibited adaptive sequence changes. Owing to the lack of information on enzyme concentrations we question the accuracy of enzyme activity comparisons, and it is thus not clear that any ancestral function has been improved in either lineage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barkman, Todd -- Zhang, Jianzhi -- England -- Nature. 2009 Dec 10;462(7274):E1; discussion E2-3. doi: 10.1038/nature08663.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20010636" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/*genetics ; Alcohol Oxidoreductases/*genetics/*metabolism ; Evolution, Molecular ; Gene Duplication ; Genes, Duplicate/*genetics ; Genes, Plant/*genetics ; *Models, Biological ; Reproducibility of Results ; Selection, Genetic
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    Do nations go to war over water? (2009)
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    Publication Date: 2009-03-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barnaby, Wendy -- England -- Nature. 2009 Mar 19;458(7236):282-3. doi: 10.1038/458282a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉w.barnaby@btinternet.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19295588" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/economics/methods ; Commerce/statistics & numerical data ; Conflict (Psychology) ; Food Supply/economics/statistics & numerical data ; Humans ; Reproducibility of Results ; *Warfare ; Water Supply/economics/*statistics & numerical data
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Drug discovery: Predicting promiscuity (2009)
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    Publication Date: 2009-11-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hopkins, Andrew L -- England -- Nature. 2009 Nov 12;462(7270):167-8. doi: 10.1038/462167a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19907483" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Artificial Intelligence ; *Computational Biology ; Drug Discovery/*methods ; Drug-Related Side Effects and Adverse Reactions ; Humans ; Ligands ; Off-Label Use ; Pharmaceutical Preparations/*metabolism ; Reproducibility of Results ; *Substrate Specificity
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    Gal4 turnover and transcription activation (2009)
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    Publication Date: 2009-10-09
    Description: Growing evidence supports the notion that proteasome-mediated destruction of transcriptional activators can be intimately coupled to their function. Recently, Nalley et al. challenged this view by reporting that the prototypical yeast activator Gal4 does not dynamically associate with chromatin, but rather 'locks in' to stable promoter complexes that are resistant to competition. Here we present evidence that the assay used to reach this conclusion is unsuitable, and that promoter-bound, active Gal4 is indeed susceptible to competition in vivo. Our data challenge the key evidence that Nalley et al. used to reach their conclusion, and indicate that Gal4 functions in vivo within the context of dynamic promoter complexes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072683/" 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/PMC3072683/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Collins, Galen A -- Lipford, J Russell -- Deshaies, Raymond J -- Tansey, William P -- P01 CA013106/CA/NCI NIH HHS/ -- P01 CA013106-310027/CA/NCI NIH HHS/ -- England -- Nature. 2009 Oct 8;461(7265):E7; discussion E8. doi: 10.1038/nature08406.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19812621" target="_blank"〉PubMed〈/a〉
    Keywords: Binding, Competitive/drug effects ; Chromatin Immunoprecipitation ; DNA-Binding Proteins/*metabolism ; Estradiol/pharmacology ; Galactokinase/genetics ; Promoter Regions, Genetic/genetics ; Protein Binding/drug effects ; Receptors, Estrogen/agonists/chemistry/metabolism ; Reproducibility of Results ; Research Design ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Tamoxifen/analogs & derivatives/pharmacology ; Trans-Activators/genetics ; Transcription Factors/*metabolism ; *Transcription, Genetic ; *Transcriptional Activation
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    An oestrogen-receptor-alpha-bound human chromatin interactome (2009)
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    Publication Date: 2009-11-06
    Description: Genomes are organized into high-level three-dimensional structures, and DNA elements separated by long genomic distances can in principle interact functionally. Many transcription factors bind to regulatory DNA elements distant from gene promoters. Although distal binding sites have been shown to regulate transcription by long-range chromatin interactions at a few loci, chromatin interactions and their impact on transcription regulation have not been investigated in a genome-wide manner. Here we describe the development of a new strategy, chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) for the de novo detection of global chromatin interactions, with which we have comprehensively mapped the chromatin interaction network bound by oestrogen receptor alpha (ER-alpha) in the human genome. We found that most high-confidence remote ER-alpha-binding sites are anchored at gene promoters through long-range chromatin interactions, suggesting that ER-alpha functions by extensive chromatin looping to bring genes together for coordinated transcriptional regulation. We propose that chromatin interactions constitute a primary mechanism for regulating transcription in mammalian genomes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774924/" 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/PMC2774924/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fullwood, Melissa J -- Liu, Mei Hui -- Pan, You Fu -- Liu, Jun -- Xu, Han -- Mohamed, Yusoff Bin -- Orlov, Yuriy L -- Velkov, Stoyan -- Ho, Andrea -- Mei, Poh Huay -- Chew, Elaine G Y -- Huang, Phillips Yao Hui -- Welboren, Willem-Jan -- Han, Yuyuan -- Ooi, Hong Sain -- Ariyaratne, Pramila N -- Vega, Vinsensius B -- Luo, Yanquan -- Tan, Peck Yean -- Choy, Pei Ye -- Wansa, K D Senali Abayratna -- Zhao, Bing -- Lim, Kar Sian -- Leow, Shi Chi -- Yow, Jit Sin -- Joseph, Roy -- Li, Haixia -- Desai, Kartiki V -- Thomsen, Jane S -- Lee, Yew Kok -- Karuturi, R Krishna Murthy -- Herve, Thoreau -- Bourque, Guillaume -- Stunnenberg, Hendrik G -- Ruan, Xiaoan -- Cacheux-Rataboul, Valere -- Sung, Wing-Kin -- Liu, Edison T -- Wei, Chia-Lin -- Cheung, Edwin -- Ruan, Yijun -- 1U54HG004557-01/HG/NHGRI NIH HHS/ -- R01 HG004456/HG/NHGRI NIH HHS/ -- R01 HG004456-01/HG/NHGRI NIH HHS/ -- R01 HG004456-02/HG/NHGRI NIH HHS/ -- R01 HG004456-03/HG/NHGRI NIH HHS/ -- R01HG003521-01/HG/NHGRI NIH HHS/ -- R01HG004456-01/HG/NHGRI NIH HHS/ -- U54 HG004557/HG/NHGRI NIH HHS/ -- U54 HG004557-01/HG/NHGRI NIH HHS/ -- U54 HG004557-02/HG/NHGRI NIH HHS/ -- U54 HG004557-03/HG/NHGRI NIH HHS/ -- U54 HG004557-04/HG/NHGRI NIH HHS/ -- England -- Nature. 2009 Nov 5;462(7269):58-64. doi: 10.1038/nature08497.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19890323" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cell Line ; Chromatin/*genetics/*metabolism ; Chromatin Immunoprecipitation ; Cross-Linking Reagents ; Estrogen Receptor alpha/*metabolism ; Formaldehyde ; Genome, Human/*genetics ; Humans ; Promoter Regions, Genetic/genetics ; Protein Binding ; Reproducibility of Results ; Sequence Analysis, DNA ; Transcription, Genetic ; Transcriptional Activation
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    A reevaluation of X-irradiation-induced phocomelia and proximodistal limb patterning (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-06-26
    Description: Phocomelia is a devastating, rare congenital limb malformation in which the long bones are shorter than normal, with the upper portion of the limb being most severely affected. In extreme cases, the hands or fingers are attached directly to the shoulder and the most proximal elements (those closest to the shoulder) are entirely missing. This disorder, previously known in both autosomal recessive and sporadic forms, showed a marked increase in incidence in the early 1960s due to the tragic toxicological effects of the drug thalidomide, which had been prescribed as a mild sedative. This human birth defect is mimicked in developing chick limb buds exposed to X-irradiation. Both X-irradiation and thalidomide-induced phocomelia have been interpreted as patterning defects in the context of the progress zone model, which states that a cell's proximodistal identity is determined by the length of time spent in a distal limb region termed the 'progress zone'. Indeed, studies of X-irradiation-induced phocomelia have served as one of the two major experimental lines of evidence supporting the validity of the progress zone model. Here, using a combination of molecular analysis and lineage tracing in chick, we show that X-irradiation-induced phocomelia is fundamentally not a patterning defect, but rather results from a time-dependent loss of skeletal progenitors. Because skeletal condensation proceeds from the shoulder to fingers (in a proximal to distal direction), the proximal elements are differentially affected in limb buds exposed to radiation at early stages. This conclusion changes the framework for considering the effect of thalidomide and other forms of phocomelia, suggesting the possibility that the aetiology lies not in a defect in the patterning process, but rather in progenitor cell survival and differentiation. Moreover, molecular evidence that proximodistal patterning is unaffected after X-irradiation does not support the predictions of the progress zone model.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2711994/" 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/PMC2711994/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Galloway, Jenna L -- Delgado, Irene -- Ros, Maria A -- Tabin, Clifford J -- F32 HD057701/HD/NICHD NIH HHS/ -- F32 HD057701-01/HD/NICHD NIH HHS/ -- F32 HD057701-02/HD/NICHD NIH HHS/ -- F32HD057701/HD/NICHD NIH HHS/ -- L40 HD057084/HD/NICHD NIH HHS/ -- L40 HD057084-01/HD/NICHD NIH HHS/ -- R37 HD032443/HD/NICHD NIH HHS/ -- England -- Nature. 2009 Jul 16;460(7253):400-4. doi: 10.1038/nature08117. Epub 2009 Jun 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19553938" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Body Patterning/*radiation effects ; Bone and Bones/cytology/radiation effects ; Cell Death/radiation effects ; Cell Differentiation/radiation effects ; Cell Lineage/radiation effects ; Cell Proliferation/radiation effects ; Chick Embryo ; Chondrogenesis/radiation effects ; Ectromelia/*etiology/genetics/*pathology ; Gene Expression Regulation, Developmental/radiation effects ; Limb Buds/abnormalities/*pathology/*radiation effects/transplantation ; Reproducibility of Results ; Stem Cells/cytology/radiation effects ; Thalidomide/adverse effects ; Time Factors ; X-Rays/adverse effects
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    Common genetic variants on 5p14.1 associate with autism spectrum disorders (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-05-01
    Description: Autism spectrum disorders (ASDs) represent a group of childhood neurodevelopmental and neuropsychiatric disorders characterized by deficits in verbal communication, impairment of social interaction, and restricted and repetitive patterns of interests and behaviour. To identify common genetic risk factors underlying ASDs, here we present the results of genome-wide association studies on a cohort of 780 families (3,101 subjects) with affected children, and a second cohort of 1,204 affected subjects and 6,491 control subjects, all of whom were of European ancestry. Six single nucleotide polymorphisms between cadherin 10 (CDH10) and cadherin 9 (CDH9)-two genes encoding neuronal cell-adhesion molecules-revealed strong association signals, with the most significant SNP being rs4307059 (P = 3.4 x 10(-8), odds ratio = 1.19). These signals were replicated in two independent cohorts, with combined P values ranging from 7.4 x 10(-8) to 2.1 x 10(-10). Our results implicate neuronal cell-adhesion molecules in the pathogenesis of ASDs, and represent, to our knowledge, the first demonstration of genome-wide significant association of common variants with susceptibility to ASDs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943511/" 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/PMC2943511/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Kai -- Zhang, Haitao -- Ma, Deqiong -- Bucan, Maja -- Glessner, Joseph T -- Abrahams, Brett S -- Salyakina, Daria -- Imielinski, Marcin -- Bradfield, Jonathan P -- Sleiman, Patrick M A -- Kim, Cecilia E -- Hou, Cuiping -- Frackelton, Edward -- Chiavacci, Rosetta -- Takahashi, Nagahide -- Sakurai, Takeshi -- Rappaport, Eric -- Lajonchere, Clara M -- Munson, Jeffrey -- Estes, Annette -- Korvatska, Olena -- Piven, Joseph -- Sonnenblick, Lisa I -- Alvarez Retuerto, Ana I -- Herman, Edward I -- Dong, Hongmei -- Hutman, Ted -- Sigman, Marian -- Ozonoff, Sally -- Klin, Ami -- Owley, Thomas -- Sweeney, John A -- Brune, Camille W -- Cantor, Rita M -- Bernier, Raphael -- Gilbert, John R -- Cuccaro, Michael L -- McMahon, William M -- Miller, Judith -- State, Matthew W -- Wassink, Thomas H -- Coon, Hilary -- Levy, Susan E -- Schultz, Robert T -- Nurnberger, John I -- Haines, Jonathan L -- Sutcliffe, James S -- Cook, Edwin H -- Minshew, Nancy J -- Buxbaum, Joseph D -- Dawson, Geraldine -- Grant, Struan F A -- Geschwind, Daniel H -- Pericak-Vance, Margaret A -- Schellenberg, Gerard D -- Hakonarson, Hakon -- 1U24MH081810/MH/NIMH NIH HHS/ -- HD055751/HD/NICHD NIH HHS/ -- HD055782-01/HD/NICHD NIH HHS/ -- HD055784/HD/NICHD NIH HHS/ -- M01-RR00064/RR/NCRR NIH HHS/ -- MH061009/MH/NIMH NIH HHS/ -- MH0666730/MH/NIMH NIH HHS/ -- MH080647/MH/NIMH NIH HHS/ -- MH081754/MH/NIMH NIH HHS/ -- MH64547/MH/NIMH NIH HHS/ -- MH69359/MH/NIMH NIH HHS/ -- N01-HD-4-3368/HD/NICHD NIH HHS/ -- N01-HD-4-3383/HD/NICHD NIH HHS/ -- NS049261/NS/NINDS NIH HHS/ -- NS26630/NS/NINDS NIH HHS/ -- NS36768/NS/NINDS NIH HHS/ -- P01 NS026630/NS/NINDS NIH HHS/ -- P01 NS026630-109001/NS/NINDS NIH HHS/ -- P50 HD055748/HD/NICHD NIH HHS/ -- P50 HD055751/HD/NICHD NIH HHS/ -- P50 HD055751-01/HD/NICHD NIH HHS/ -- P50 HD055782-01/HD/NICHD NIH HHS/ -- P50 HD055784/HD/NICHD NIH HHS/ -- P50 HD055784-01/HD/NICHD NIH HHS/ -- P50 HD055784-010002/HD/NICHD NIH HHS/ -- P50 HD055784-020002/HD/NICHD NIH HHS/ -- P50 HD055784-030002/HD/NICHD NIH HHS/ -- R01 MH061009/MH/NIMH NIH HHS/ -- R01 MH061009-01A1/MH/NIMH NIH HHS/ -- R01 MH064547/MH/NIMH NIH HHS/ -- R01 MH064547-01/MH/NIMH NIH HHS/ -- R01 MH064547-01S1/MH/NIMH NIH HHS/ -- R01 MH064547-02/MH/NIMH NIH HHS/ -- R01 MH064547-02S1/MH/NIMH NIH HHS/ -- R01 MH064547-03/MH/NIMH NIH HHS/ -- R01 MH064547-04/MH/NIMH NIH HHS/ -- R01 MH064547-05/MH/NIMH NIH HHS/ -- R01 MH069359/MH/NIMH NIH HHS/ -- R01 MH069359-01A2/MH/NIMH NIH HHS/ -- R01 MH080647/MH/NIMH NIH HHS/ -- R01 MH080647-11/MH/NIMH NIH HHS/ -- R01 MH081754/MH/NIMH NIH HHS/ -- R01 MH081754-01/MH/NIMH NIH HHS/ -- R01 MH081754-02/MH/NIMH NIH HHS/ -- R01 NS036768/NS/NINDS NIH HHS/ -- R01 NS036768-06/NS/NINDS NIH HHS/ -- R01 NS049261/NS/NINDS NIH HHS/ -- R01 NS049261-01A2/NS/NINDS NIH HHS/ -- U54 MH066673/MH/NIMH NIH HHS/ -- U54 MH066673-01A10001/MH/NIMH NIH HHS/ -- UL1 RR024134/RR/NCRR NIH HHS/ -- UL1 RR024134-01/RR/NCRR NIH HHS/ -- UL1-RR024134-03/RR/NCRR NIH HHS/ -- Medical Research Council/United Kingdom -- England -- Nature. 2009 May 28;459(7246):528-33. doi: 10.1038/nature07999. Epub 2009 Apr 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Applied Genomics, Children's Hospital of Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19404256" target="_blank"〉PubMed〈/a〉
    Keywords: Autistic Disorder/*genetics ; Brain/metabolism ; Cadherins/genetics ; Case-Control Studies ; Cell Adhesion/genetics ; Cell Adhesion Molecules, Neuronal/genetics ; Chromosomes, Human, Pair 5/*genetics ; Cohort Studies ; Genetic Markers/genetics ; Genetic Predisposition to Disease/*genetics ; Genetic Variation/*genetics ; Genome-Wide Association Study ; Genotype ; Humans ; Polymorphism, Single Nucleotide/genetics ; Reproducibility of Results
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Mind the spin (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-10-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2009 Oct 29;461(7268):1174. doi: 10.1038/4611174a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19865118" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines/*immunology ; *Clinical Trials, Phase III as Topic ; HIV Infections/prevention & control ; Humans ; Peer Review, Research/*standards ; Reproducibility of Results ; Research Personnel/*standards ; Thailand
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Precise genome modification in the crop species Zea mays using zinc-finger nucleases (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-05-01
    Description: Agricultural biotechnology is limited by the inefficiencies of conventional random mutagenesis and transgenesis. Because targeted genome modification in plants has been intractable, plant trait engineering remains a laborious, time-consuming and unpredictable undertaking. Here we report a broadly applicable, versatile solution to this problem: the use of designed zinc-finger nucleases (ZFNs) that induce a double-stranded break at their target locus. We describe the use of ZFNs to modify endogenous loci in plants of the crop species Zea mays. We show that simultaneous expression of ZFNs and delivery of a simple heterologous donor molecule leads to precise targeted addition of an herbicide-tolerance gene at the intended locus in a significant number of isolated events. ZFN-modified maize plants faithfully transmit these genetic changes to the next generation. Insertional disruption of one target locus, IPK1, results in both herbicide tolerance and the expected alteration of the inositol phosphate profile in developing seeds. ZFNs can be used in any plant species amenable to DNA delivery; our results therefore establish a new strategy for plant genetic manipulation in basic science and agricultural applications.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shukla, Vipula K -- Doyon, Yannick -- Miller, Jeffrey C -- DeKelver, Russell C -- Moehle, Erica A -- Worden, Sarah E -- Mitchell, Jon C -- Arnold, Nicole L -- Gopalan, Sunita -- Meng, Xiangdong -- Choi, Vivian M -- Rock, Jeremy M -- Wu, Ying-Ying -- Katibah, George E -- Zhifang, Gao -- McCaskill, David -- Simpson, Matthew A -- Blakeslee, Beth -- Greenwalt, Scott A -- Butler, Holly J -- Hinkley, Sarah J -- Zhang, Lei -- Rebar, Edward J -- Gregory, Philip D -- Urnov, Fyodor D -- England -- Nature. 2009 May 21;459(7245):437-41. doi: 10.1038/nature07992. Epub 2009 Apr 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Dow AgroSciences, 9330 Zionsville Road, Indianapolis, Indiana 46268, USA. vkshukla@dow.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19404259" target="_blank"〉PubMed〈/a〉
    Keywords: Biotechnology/*methods ; Deoxyribonucleases/*chemistry/genetics/*metabolism ; Food, Genetically Modified ; Gene Targeting/*methods ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Herbicide Resistance/genetics ; Herbicides/pharmacology ; Heredity ; Inositol Phosphates/metabolism ; Mutagenesis, Site-Directed/methods ; Plants, Genetically Modified ; Recombination, Genetic/genetics ; Reproducibility of Results ; Zea mays/*genetics ; *Zinc Fingers
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Is there an association between NPY and neuroticism? (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-04-03
    Description: Psychiatric genetics has been hampered by the fact that initially exciting findings from underpowered studies are so often not replicated in larger, more powerful, data sets. Here we show that the claims of Zhou et al. that neuropeptide Y (NPY) diplotype-predicted expression is correlated with trait anxiety (neuroticism) is not replicated in a data set consisting of phenotypically extreme individuals drawn from a large (n = 88,142) non-clinical population. We found no association between NPY diplotype or diplotype-predicted expression and neuroticism. Our reply to Zhou and colleagues forms part of a larger debate (see, for example, http://www.nature.com/news/2008/080709/full/454154a.html) about the efficacy and replicability of candidate driven versus genome wide approaches to psychiatric genetics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cotton, Colleen H -- Flint, Jonathan -- Campbell, Thomas G -- England -- Nature. 2009 Apr 2;458(7238):E6; discussion E7. doi: 10.1038/nature07927.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19340021" target="_blank"〉PubMed〈/a〉
    Keywords: Genotype ; Humans ; Neuropeptide Y/*genetics ; Neurotic Disorders/*genetics ; Polymorphism, Single Nucleotide/genetics ; Reproducibility of Results
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    Hippopotamus and whale phylogeny (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-03-20
    Description: Thewissen et al. describe new fossils from India that apparently support a phylogeny that places Cetacea (that is, whales, dolphins, porpoises) as the sister group to the extinct family Raoellidae, and Hippopotamidae as more closely related to pigs and peccaries (that is, Suina) than to cetaceans. However, our reanalysis of a modified version of the data set they used differs in retaining molecular characters and demonstrates that Hippopotamidae is the closest extant family to Cetacea and that raoellids are the closest extinct group, consistent with previous phylogenetic studies. This topology supports the view that the aquatic adaptations in hippopotamids and cetaceans are inherited from their common ancestor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Geisler, Jonathan H -- Theodor, Jessica M -- England -- Nature. 2009 Mar 19;458(7236):E1-4; discussion E5. doi: 10.1038/nature07776.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geology and Geography and Georgia Southern Museum, Georgia Southern University, Statesboro, Georgia 30460-8149, USA. geislerj@georgiasouthern.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19295550" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Artiodactyla/*classification ; Cetacea/*classification ; Extinction, Biological ; *Phylogeny ; Reproducibility of Results ; Whales/*classification
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Silk production from tarantula feet questioned (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-10-23
    Description: As with all spiders, tarantulas spin silk from specialized structures in the abdomen called spinnerets, which are key features unique to the group. Recently Gorb et al. reported that the zebra tarantula Aphonopelma seemanni also secretes silk from its feet, which might improve its ability to climb on vertical surfaces. Here we show that when the spinnerets are experimentally sealed, the zebra tarantula cannot secrete silk or similar threads, disagreeing with previous reports by Gorb et al.. Additional evidence also disagrees with leg secretion of silk.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Perez-Miles, Fernando -- Panzera, Alejandra -- Ortiz-Villatoro, David -- Perdomo, Cintya -- England -- Nature. 2009 Oct 22;461(7267):E9; discussion E9-10. doi: 10.1038/nature08404.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Seccion Entomologia, Facultad de Ciencias, Igua 4225, 11400 Montevideo, Uruguay.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19847209" target="_blank"〉PubMed〈/a〉
    Keywords: Abdomen/anatomy & histology/physiology ; Animals ; Extremities/anatomy & histology/*physiology ; Hair ; Reproducibility of Results ; Silk/*biosynthesis/*secretion ; Spiders/*anatomy & histology/*physiology
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Genetics without borders (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-10-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2009 Oct 8;461(7265):697. doi: 10.1038/461697a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19812627" target="_blank"〉PubMed〈/a〉
    Keywords: Emigration and Immigration/legislation & jurisprudence ; Genetic Testing/*ethics ; Genetics, Population/*ethics/*methods/standards ; Genome, Human/*genetics ; Geography ; Great Britain ; Humans ; *Internationality ; Male ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Refugees/*legislation & jurisprudence ; Reproducibility of Results ; Research Personnel ; Somalia
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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