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  • Reproducibility of Results  (96)
  • Nature Publishing Group (NPG)  (96)
  • Springer Nature
  • Essen : Verl. Glückauf
  • Krefeld : Geologischer Dienst Nordhein-Westfalen
  • 2005-2009  (96)
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  • 1
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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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  • 2
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    Design of protein-interaction specificity gives selective bZIP-binding peptides (2009)
    Nature Publishing Group (NPG)
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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
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
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    Is REST a regulator of pluripotency? (2009)
    Nature Publishing Group (NPG)
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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
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
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    Research into group differences isn't wrong, just pointless (2009)
    Nature Publishing Group (NPG)
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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
    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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    Identity crisis (2009)
    Nature Publishing Group (NPG)
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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
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
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    Were crocodiles responsible for the stones we call tools? (2009)
    Nature Publishing Group (NPG)
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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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  • 7
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    Jury still out on HIV vaccine results (2009)
    Nature Publishing Group (NPG)
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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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  • 8
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    A tunable synthetic mammalian oscillator (2009)
    Nature Publishing Group (NPG)
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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
    Print ISSN: 0028-0836
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  • 9
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    Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals (2009)
    Nature Publishing Group (NPG)
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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
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  • 10
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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
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  • 12
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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
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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
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  • 14
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    Brain imaging studies under fire (2009)
    Nature Publishing Group (NPG)
    Details
    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)
    Nature Publishing Group (NPG)
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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
    Print ISSN: 0028-0836
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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)
    Nature Publishing Group (NPG)
    Details
    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
    Print ISSN: 0028-0836
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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
    Print ISSN: 0028-0836
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    Key protein-design papers challenged (2009)
    Nature Publishing Group (NPG)
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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
    Print ISSN: 0028-0836
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    'Killer application' for protein synthesis is retracted (2009)
    Nature Publishing Group (NPG)
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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
    Print ISSN: 0028-0836
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    Ocean fertilization: dead in the water? (2009)
    Nature Publishing Group (NPG)
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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
    Print ISSN: 0028-0836
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    Genome sequencing: the third generation (2009)
    Nature Publishing Group (NPG)
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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)
    Nature Publishing Group (NPG)
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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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    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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    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
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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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    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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    Protecting the Hawaiian akepa population (2009)
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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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    Evidence for escape from adaptive conflict? (2009)
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    Details
    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)
    Nature Publishing Group (NPG)
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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)
    Nature Publishing Group (NPG)
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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)
    Nature Publishing Group (NPG)
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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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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    An oestrogen-receptor-alpha-bound human chromatin interactome (2009)
    Nature Publishing Group (NPG)
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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)
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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)
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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
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    Mind the spin (2009)
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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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    Precise genome modification in the crop species Zea mays using zinc-finger nucleases (2009)
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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
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    Is there an association between NPY and neuroticism? (2009)
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    Details
    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)
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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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    Silk production from tarantula feet questioned (2009)
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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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    Genetics without borders (2009)
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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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    Culture clash in Chinese university: a response (2009)
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    Publication Date: 2009-01-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cui, Keming -- England -- Nature. 2009 Jan 22;457(7228):379. doi: 10.1038/457379e.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19158767" target="_blank"〉PubMed〈/a〉
    Keywords: China ; Laboratories/*organization & administration ; Reproducibility of Results ; Research Personnel/*organization & administration ; Universities/*organization & administration
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    Anticipatory haemodynamic signals in sensory cortex not predicted by local neuronal activity (2009)
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    Publication Date: 2009-01-23
    Description: Haemodynamic signals underlying functional brain imaging (for example, functional magnetic resonance imaging (fMRI)) are assumed to reflect metabolic demand generated by local neuronal activity, with equal increases in haemodynamic signal implying equal increases in the underlying neuronal activity. Few studies have compared neuronal and haemodynamic signals in alert animals to test for this assumed correspondence. Here we present evidence that brings this assumption into question. Using a dual-wavelength optical imaging technique that independently measures cerebral blood volume and oxygenation, continuously, in alert behaving monkeys, we find two distinct components to the haemodynamic signal in the alert animals' primary visual cortex (V1). One component is reliably predictable from neuronal responses generated by visual input. The other component-of almost comparable strength-is a hitherto unknown signal that entrains to task structure independently of visual input or of standard neural predictors of haemodynamics. This latter component shows predictive timing, with increases of cerebral blood volume in anticipation of trial onsets even in darkness. This trial-locked haemodynamic signal could be due to an accompanying V1 arterial pumping mechanism, closely matched in time, with peaks of arterial dilation entrained to predicted trial onsets. These findings (tested in two animals) challenge the current understanding of the link between brain haemodynamics and local neuronal activity. They also suggest the existence of a novel preparatory mechanism in the brain that brings additional arterial blood to cortex in anticipation of expected tasks.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705195/" 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/PMC2705195/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sirotin, Yevgeniy B -- Das, Aniruddha -- R01 EY013759/EY/NEI NIH HHS/ -- R01 EY013759-01A1/EY/NEI NIH HHS/ -- England -- Nature. 2009 Jan 22;457(7228):475-9. doi: 10.1038/nature07664.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neuroscience, Columbia University, New York, New York 10027, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19158795" target="_blank"〉PubMed〈/a〉
    Keywords: Acoustic Stimulation ; Animals ; Auditory Cortex/blood supply/cytology/physiology ; Brain Mapping ; *Cerebrovascular Circulation ; Darkness ; Fixation, Ocular/physiology ; *Hemodynamics ; Macaca mulatta/*physiology ; Magnetic Resonance Imaging ; Models, Neurological ; Neurons/*physiology ; Oxygen Consumption/physiology ; Photic Stimulation ; Reproducibility of Results ; Time Factors ; Visual Cortex/*blood supply/cytology/*physiology
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    Biodiversity: Rack and field (2009)
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    Publication Date: 2009-08-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gewin, Virginia -- England -- Nature. 2009 Aug 20;460(7258):944-6. doi: 10.1038/460944a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19693059" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; Conservation of Natural Resources/*methods ; Ecology/*methods ; Eukaryota/physiology ; Extinction, Biological ; *Models, Biological ; Predatory Behavior/physiology ; Reproducibility of Results ; Rivers ; Water Movements
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    Sharing: guidelines go one step forwards, two steps back (2009)
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    Publication Date: 2009-10-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wicherts, Jelte -- Bakker, Marjan -- England -- Nature. 2009 Oct 22;461(7267):1053. doi: 10.1038/4611053c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19847239" target="_blank"〉PubMed〈/a〉
    Keywords: *Access to Information/ethics ; *Guidelines as Topic ; *Information Dissemination/ethics ; Psychology/ethics/*standards ; Reproducibility of Results ; Research/*standards
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    Nanoparticle safety in doubt (2009)
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    Publication Date: 2009-08-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gilbert, Natasha -- England -- Nature. 2009 Aug 20;460(7258):937. doi: 10.1038/460937a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19693048" target="_blank"〉PubMed〈/a〉
    Keywords: Adolescent ; Adult ; Air Pollutants, Occupational/*adverse effects ; China ; Female ; Granuloma/chemically induced ; Humans ; Lung Injury/*chemically induced/pathology ; Middle Aged ; *Nanoparticles/administration & dosage/adverse effects ; Nanotechnology ; Occupational Exposure/*adverse effects ; Reproducibility of Results
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Is REST required for ESC pluripotency? (2009)
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    Publication Date: 2009-02-27
    Description: The DNA-binding protein REST (also called NRSF) is a transcriptional repressor that targets many neuronal genes and is abundant in human and mouse pluripotent embryonic stem cells (ESCs). In a recent Letter to Nature, Singh et al. suggested that REST controls the self-renewal and pluripotency of ESCs, because they found that ESCs in which a single REST allele was disrupted (Fig. 1a, beta-geo-stop insertion) had reduced alkaline phosphatase activity and expressed lower levels of several pluripotency-associated genes. Here we show that partial or complete loss of functional REST protein does not abrogate ESC potential as reflected by marker gene expression. These data are consistent with earlier reports, and argue that REST is not required for maintaining ESC pluripotency.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jorgensen, Helle F -- Chen, Zhou-Feng -- Merkenschlager, Matthias -- Fisher, Amanda G -- MC_U120027516/Medical Research Council/United Kingdom -- England -- Nature. 2009 Feb 26;457(7233):E4-5; discussion E7. doi: 10.1038/nature07783.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK. helle.jorgensen@imperial.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19242417" target="_blank"〉PubMed〈/a〉
    Keywords: Alkaline Phosphatase/metabolism ; Animals ; Embryonic Stem Cells/*cytology/*metabolism ; Gene Knockdown Techniques ; Humans ; Mice ; Pluripotent Stem Cells/*cytology/*metabolism ; Polymerase Chain Reaction ; Repressor Proteins/genetics/*metabolism ; Reproducibility of Results ; Tretinoin/pharmacology
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    A burst of segmental duplications in the genome of the African great ape ancestor (2009)
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    Publication Date: 2009-02-13
    Description: It is generally accepted that the extent of phenotypic change between human and great apes is dissonant with the rate of molecular change. Between these two groups, proteins are virtually identical, cytogenetically there are few rearrangements that distinguish ape-human chromosomes, and rates of single-base-pair change and retrotransposon activity have slowed particularly within hominid lineages when compared to rodents or monkeys. Studies of gene family evolution indicate that gene loss and gain are enriched within the primate lineage. Here, we perform a systematic analysis of duplication content of four primate genomes (macaque, orang-utan, chimpanzee and human) in an effort to understand the pattern and rates of genomic duplication during hominid evolution. We find that the ancestral branch leading to human and African great apes shows the most significant increase in duplication activity both in terms of base pairs and in terms of events. This duplication acceleration within the ancestral species is significant when compared to lineage-specific rate estimates even after accounting for copy-number polymorphism and homoplasy. We discover striking examples of recurrent and independent gene-containing duplications within the gorilla and chimpanzee that are absent in the human lineage. Our results suggest that the evolutionary properties of copy-number mutation differ significantly from other forms of genetic mutation and, in contrast to the hominid slowdown of single-base-pair mutations, there has been a genomic burst of duplication activity at this period during human evolution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2751663/" 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/PMC2751663/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marques-Bonet, Tomas -- Kidd, Jeffrey M -- Ventura, Mario -- Graves, Tina A -- Cheng, Ze -- Hillier, LaDeana W -- Jiang, Zhaoshi -- Baker, Carl -- Malfavon-Borja, Ray -- Fulton, Lucinda A -- Alkan, Can -- Aksay, Gozde -- Girirajan, Santhosh -- Siswara, Priscillia -- Chen, Lin -- Cardone, Maria Francesca -- Navarro, Arcadi -- Mardis, Elaine R -- Wilson, Richard K -- Eichler, Evan E -- HG002385/HG/NHGRI NIH HHS/ -- P51-RR013986/RR/NCRR NIH HHS/ -- R01 HG002385/HG/NHGRI NIH HHS/ -- R01 HG002385-08/HG/NHGRI NIH HHS/ -- U54 HG003079/HG/NHGRI NIH HHS/ -- U54 HG003079-06/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Feb 12;457(7231):877-81. doi: 10.1038/nature07744.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genome Sciences, University of Washington and the Howard Hughes Medical Institute, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19212409" target="_blank"〉PubMed〈/a〉
    Keywords: Africa ; Animals ; Catarrhini/classification/*genetics ; Chromosome Mapping ; *Evolution, Molecular ; *Gene Duplication ; Genome/*genetics ; Humans ; Polymorphism, Genetic ; Reproducibility of Results
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    Unjust burdens of proof (2009)
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    Publication Date: 2009-06-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2009 Jun 11;459(7248):751. doi: 10.1038/459751a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19516290" target="_blank"〉PubMed〈/a〉
    Keywords: Chiropractic/*standards ; *Freedom ; Great Britain ; Journalism/*legislation & jurisprudence/standards ; Reproducibility of Results ; Writing/standards
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    Autism genome-wide copy number variation reveals ubiquitin and neuronal genes (2009)
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    Publication Date: 2009-05-01
    Description: Autism spectrum disorders (ASDs) are childhood neurodevelopmental disorders with complex genetic origins. Previous studies focusing on candidate genes or genomic regions have identified several copy number variations (CNVs) that are associated with an increased risk of ASDs. Here we present the results from a whole-genome CNV study on a cohort of 859 ASD cases and 1,409 healthy children of European ancestry who were genotyped with approximately 550,000 single nucleotide polymorphism markers, in an attempt to comprehensively identify CNVs conferring susceptibility to ASDs. Positive findings were evaluated in an independent cohort of 1,336 ASD cases and 1,110 controls of European ancestry. Besides previously reported ASD candidate genes, such as NRXN1 (ref. 10) and CNTN4 (refs 11, 12), several new susceptibility genes encoding neuronal cell-adhesion molecules, including NLGN1 and ASTN2, were enriched with CNVs in ASD cases compared to controls (P = 9.5 x 10(-3)). Furthermore, CNVs within or surrounding genes involved in the ubiquitin pathways, including UBE3A, PARK2, RFWD2 and FBXO40, were affected by CNVs not observed in controls (P = 3.3 x 10(-3)). We also identified duplications 55 kilobases upstream of complementary DNA AK123120 (P = 3.6 x 10(-6)). Although these variants may be individually rare, they target genes involved in neuronal cell-adhesion or ubiquitin degradation, indicating that these two important gene networks expressed within the central nervous system may contribute to the genetic susceptibility of ASD.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2925224/" 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/PMC2925224/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Glessner, Joseph T -- Wang, Kai -- Cai, Guiqing -- Korvatska, Olena -- Kim, Cecilia E -- Wood, Shawn -- Zhang, Haitao -- Estes, Annette -- Brune, Camille W -- Bradfield, Jonathan P -- Imielinski, Marcin -- Frackelton, Edward C -- Reichert, Jennifer -- Crawford, Emily L -- Munson, Jeffrey -- Sleiman, Patrick M A -- Chiavacci, Rosetta -- Annaiah, Kiran -- Thomas, Kelly -- Hou, Cuiping -- Glaberson, Wendy -- Flory, James -- Otieno, Frederick -- Garris, Maria -- Soorya, Latha -- Klei, Lambertus -- Piven, Joseph -- Meyer, Kacie J -- Anagnostou, Evdokia -- Sakurai, Takeshi -- Game, Rachel M -- Rudd, Danielle S -- Zurawiecki, Danielle -- McDougle, Christopher J -- Davis, Lea K -- Miller, Judith -- Posey, David J -- Michaels, Shana -- Kolevzon, Alexander -- Silverman, Jeremy M -- Bernier, Raphael -- Levy, Susan E -- Schultz, Robert T -- Dawson, Geraldine -- Owley, Thomas -- McMahon, William M -- Wassink, Thomas H -- Sweeney, John A -- Nurnberger, John I -- Coon, Hilary -- Sutcliffe, James S -- Minshew, Nancy J -- Grant, Struan F A -- Bucan, Maja -- Cook, Edwin H -- Buxbaum, Joseph D -- Devlin, Bernie -- Schellenberg, Gerard D -- Hakonarson, Hakon -- 1U24MH081810/MH/NIMH NIH HHS/ -- HD055751/HD/NICHD NIH HHS/ -- HD055782-01/HD/NICHD NIH HHS/ -- HD35476/HD/NICHD NIH HHS/ -- M01 RR000064-340579/RR/NCRR NIH HHS/ -- M01 RR000064-350579/RR/NCRR NIH HHS/ -- M01 RR000064-35S10579/RR/NCRR NIH HHS/ -- M01 RR000064-35S10591/RR/NCRR NIH HHS/ -- M01 RR000064-35S10602/RR/NCRR NIH HHS/ -- M01 RR000064-35S20579/RR/NCRR NIH HHS/ -- M01 RR000064-35S20591/RR/NCRR NIH HHS/ -- M01 RR000064-35S20602/RR/NCRR NIH HHS/ -- M01 RR000064-360579/RR/NCRR NIH HHS/ -- M01 RR000064-360582/RR/NCRR NIH HHS/ -- M01 RR000064-360591/RR/NCRR NIH HHS/ -- M01 RR000064-36S10579/RR/NCRR NIH HHS/ -- M01 RR000064-36S10582/RR/NCRR NIH HHS/ -- M01 RR000064-36S10591/RR/NCRR NIH HHS/ -- M01 RR000064-370579/RR/NCRR NIH HHS/ -- M01 RR000064-370582/RR/NCRR NIH HHS/ -- M01 RR000064-370591/RR/NCRR NIH HHS/ -- M01 RR000064-37S10579/RR/NCRR NIH HHS/ -- M01 RR000064-37S10582/RR/NCRR NIH HHS/ -- M01 RR000064-37S10591/RR/NCRR NIH HHS/ -- M01 RR000064-380579/RR/NCRR NIH HHS/ -- M01 RR000064-380582/RR/NCRR NIH HHS/ -- M01 RR000064-380591/RR/NCRR NIH HHS/ -- M01 RR000064-390579/RR/NCRR NIH HHS/ -- M01 RR000064-390582/RR/NCRR NIH HHS/ -- M01 RR000064-390591/RR/NCRR NIH HHS/ -- M01-RR00064/RR/NCRR NIH HHS/ -- MH061009/MH/NIMH NIH HHS/ -- MH0666730/MH/NIMH NIH HHS/ -- MH64547/MH/NIMH NIH HHS/ -- MH69359/MH/NIMH NIH HHS/ -- NS049261/NS/NINDS NIH HHS/ -- P01 HD035476-03/HD/NICHD NIH HHS/ -- P01 HD035476-04/HD/NICHD NIH HHS/ -- P01 HD035476-04S1/HD/NICHD NIH HHS/ -- P01 HD035476-04S2/HD/NICHD NIH HHS/ -- P01 HD035476-05/HD/NICHD NIH HHS/ -- P50 HD055751/HD/NICHD NIH HHS/ -- P50 HD055751-01/HD/NICHD NIH HHS/ -- P50 HD055751-010002/HD/NICHD NIH HHS/ -- P50 HD055751-019003/HD/NICHD NIH HHS/ -- P50 HD055751-02/HD/NICHD NIH HHS/ -- P50 HD055751-020002/HD/NICHD NIH HHS/ -- P50 HD055751-03/HD/NICHD NIH HHS/ -- P50 HD055751-030002/HD/NICHD NIH HHS/ -- P50 HD055751-04/HD/NICHD NIH HHS/ -- P50 HD055782-01/HD/NICHD NIH HHS/ -- R01 MH057881/MH/NIMH NIH HHS/ -- R01 MH061009/MH/NIMH NIH HHS/ -- R01 MH061009-01A1/MH/NIMH NIH HHS/ -- R01 MH061009-01A1S1/MH/NIMH NIH HHS/ -- R01 MH061009-02/MH/NIMH NIH HHS/ -- R01 MH061009-03/MH/NIMH NIH HHS/ -- R01 MH061009-04A1/MH/NIMH NIH HHS/ -- R01 MH061009-05/MH/NIMH NIH HHS/ -- R01 MH061009-06/MH/NIMH NIH HHS/ -- R01 MH061009-07/MH/NIMH NIH HHS/ -- R01 MH061009-08/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 MH069359-02/MH/NIMH NIH HHS/ -- R01 MH069359-03/MH/NIMH NIH HHS/ -- R01 MH069359-04/MH/NIMH NIH HHS/ -- R01 MH069359-05/MH/NIMH NIH HHS/ -- R01 NS049261/NS/NINDS NIH HHS/ -- R01 NS049261-01A2/NS/NINDS NIH HHS/ -- R01 NS049261-02/NS/NINDS NIH HHS/ -- R01 NS049261-03/NS/NINDS NIH HHS/ -- R01 NS049261-04/NS/NINDS NIH HHS/ -- R01 NS049261-05/NS/NINDS NIH HHS/ -- U10 MH066766-02S1/MH/NIMH NIH HHS/ -- U10MH66766-02S1/MH/NIMH NIH HHS/ -- U19 HD035476-06/HD/NICHD NIH HHS/ -- U19 HD035476-07/HD/NICHD NIH HHS/ -- U19 HD035476-08/HD/NICHD NIH HHS/ -- U19 HD035476-09/HD/NICHD NIH HHS/ -- U19 HD035476-10/HD/NICHD NIH HHS/ -- U24 MH081810/MH/NIMH NIH HHS/ -- U24 MH081810-01/MH/NIMH NIH HHS/ -- U24 MH081810-02/MH/NIMH NIH HHS/ -- U24 MH081810-03/MH/NIMH NIH HHS/ -- U24 MH081810-04/MH/NIMH NIH HHS/ -- U54 MH066673/MH/NIMH NIH HHS/ -- U54 MH066673-01A10001/MH/NIMH NIH HHS/ -- U54 MH066673-020001/MH/NIMH NIH HHS/ -- U54 MH066673-030001/MH/NIMH NIH HHS/ -- U54 MH066673-040001/MH/NIMH NIH HHS/ -- U54 MH066673-05/MH/NIMH NIH HHS/ -- U54 MH066673-050001/MH/NIMH NIH HHS/ -- UL1 RR024134/RR/NCRR NIH HHS/ -- UL1 RR024134-03/RR/NCRR NIH HHS/ -- UL1-RR024134-03/RR/NCRR NIH HHS/ -- Medical Research Council/United Kingdom -- England -- Nature. 2009 May 28;459(7246):569-73. doi: 10.1038/nature07953. Epub 2009 Apr 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19404257" target="_blank"〉PubMed〈/a〉
    Keywords: Autistic Disorder/*genetics ; Case-Control Studies ; Cell Adhesion Molecules, Neuronal/genetics ; Cohort Studies ; Europe/ethnology ; Gene Dosage/*genetics ; Gene Regulatory Networks/genetics ; Genetic Predisposition to Disease/genetics ; Genetic Variation/*genetics ; Genome, Human/*genetics ; Genotype ; Humans ; Neurons/*metabolism ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide/genetics ; Reproducibility of Results ; Ubiquitin/*metabolism
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    Impact theory under fire once more (2009)
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    Publication Date: 2009-10-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dalton, Rex -- England -- Nature. 2009 Oct 15;461(7266):861. doi: 10.1038/461861a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19829343" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Charcoal/analysis/chemistry ; *Extinction, Biological ; Fires/history ; Geologic Sediments/chemistry ; History, Ancient ; Humans ; Magnetics ; *Meteoroids ; *Models, Theoretical ; Pollen ; Reproducibility of Results ; United States
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    Type II fatty acid synthesis is not a suitable antibiotic target for Gram-positive pathogens (2009)
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    Publication Date: 2009-03-06
    Description: Antimicrobial drugs targeting the reportedly essential type II fatty acid synthesis (FASII) pathway have been recently acclaimed for their efficacy against infections caused by multiresistant Gram-positive bacteria. Our findings show that the strategy for antibiotic development based on FASII pathway targets is fundamentally flawed by the fact that exogenous fatty acids fully bypass inhibition of this pathway in both in vitro and in vivo conditions. We demonstrate that major Gram-positive pathogens-such as streptococci, pneumococci, enterococci and staphylococci-overcome drug-induced FASII pathway inhibition when supplied with exogenous fatty acids, and human serum proves to be a highly effective source of fatty acids. For opportunist pathogen Streptococcus agalactiae, growth in serum leads to an overall decrease of FASII gene expression. No antibiotic inhibitor could have a stronger effect than the inactivation of the target gene, so we challenged the role of FASII using deletion mutants. Our results unequivocally show that the FASII target enzymes are dispensable in vivo during S. agalactiae infection. The results of this study largely compromise the use of FASII-based antimicrobials for treating sepsis caused by Gram-positive pathogens.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brinster, Sophie -- Lamberet, Gilles -- Staels, Bart -- Trieu-Cuot, Patrick -- Gruss, Alexandra -- Poyart, Claire -- England -- Nature. 2009 Mar 5;458(7234):83-6. doi: 10.1038/nature07772.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut Cochin, Universite Paris Descartes, CNRS (UMR 8104), Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19262672" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anti-Bacterial Agents/*pharmacology ; *Drug Resistance, Bacterial ; Fatty Acids/analysis/*biosynthesis/chemistry/pharmacology ; Gene Expression Regulation, Bacterial/drug effects ; Genes, Bacterial/genetics ; Gram-Positive Bacteria/*drug effects/genetics/metabolism/pathogenicity ; Humans ; Mice ; Mice, Inbred C57BL ; Microbial Sensitivity Tests ; Rats ; Rats, Sprague-Dawley ; Reproducibility of Results ; Sepsis/drug therapy/microbiology ; Serum/chemistry/microbiology ; Streptococcal Infections/drug therapy/microbiology ; Streptococcus agalactiae/drug effects/enzymology/genetics/metabolism ; Substrate Specificity ; Virulence/genetics
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Media frenzy (2009)
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    Publication Date: 2009-05-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2009 May 28;459(7246):484. doi: 10.1038/459484a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19478735" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Extinction, Biological ; *Fossils ; Germany ; Humans ; Literature, Modern ; Motion Pictures as Topic ; *Phylogeny ; Primates/*classification ; Reproducibility of Results ; Television ; Time Factors
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    Early man becomes early ape (2009)
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    Publication Date: 2009-06-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dalton, Rex -- England -- Nature. 2009 Jun 18;459(7249):899. doi: 10.1038/459899a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19536228" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; China ; *Fossils ; *Hominidae/anatomy & histology ; Humans ; *Mandible ; Reproducibility of Results
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Journal club. A biogeochemist sees the value of diversity in a changing ocean (2009)
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    Publication Date: 2009-08-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stoll, Heather -- England -- Nature. 2009 Aug 20;460(7258):935. doi: 10.1038/460935e.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geology, University of Oviedo, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19693042" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/genetics ; Animals ; Carbon Dioxide/analysis ; Eukaryota/classification/*genetics/*physiology ; *Genetic Variation ; Hydrogen-Ion Concentration ; Oceans and Seas ; Reproducibility of Results ; Seawater/*chemistry/*microbiology ; Selection, Genetic
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Ocean fertilization: time to move on (2009)
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    Publication Date: 2009-09-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Strong, Aaron -- Chisholm, Sallie -- Miller, Charles -- Cullen, John -- England -- Nature. 2009 Sep 17;461(7262):347-8. doi: 10.1038/461347a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Massachusetts Institute of Technology in Cambridge, Massachusetts, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19759603" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Carbon Dioxide/metabolism ; Ecology/*methods ; *Ecosystem ; *Greenhouse Effect ; Iron/*metabolism ; Oxygen/metabolism ; Phytoplankton/metabolism ; Reproducibility of Results ; Seawater/*chemistry/parasitology
    Print ISSN: 0028-0836
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    Prejudice and truth about the effect of testosterone on human bargaining behaviour (2009)
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    Publication Date: 2009-12-10
    Description: Both biosociological and psychological models, as well as animal research, suggest that testosterone has a key role in social interactions. Evidence from animal studies in rodents shows that testosterone causes aggressive behaviour towards conspecifics. Folk wisdom generalizes and adapts these findings to humans, suggesting that testosterone induces antisocial, egoistic, or even aggressive human behaviours. However, many researchers have questioned this folk hypothesis, arguing that testosterone is primarily involved in status-related behaviours in challenging social interactions, but causal evidence that discriminates between these views is sparse. Here we show that the sublingual administration of a single dose of testosterone in women causes a substantial increase in fair bargaining behaviour, thereby reducing bargaining conflicts and increasing the efficiency of social interactions. However, subjects who believed that they received testosterone-regardless of whether they actually received it or not-behaved much more unfairly than those who believed that they were treated with placebo. Thus, the folk hypothesis seems to generate a strong negative association between subjects' beliefs and the fairness of their offers, even though testosterone administration actually causes a substantial increase in the frequency of fair bargaining offers in our experiment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eisenegger, C -- Naef, M -- Snozzi, R -- Heinrichs, M -- Fehr, E -- England -- Nature. 2010 Jan 21;463(7279):356-9. doi: 10.1038/nature08711.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Empirical Research in Economics, Laboratory for Social and Neural Systems Research, University of Zurich, 8006 Zurich, Switzerland. eisenegger@iew.uzh.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19997098" target="_blank"〉PubMed〈/a〉
    Keywords: Administration, Sublingual ; Adult ; Aggression/drug effects/physiology/psychology ; Cooperative Behavior ; Double-Blind Method ; Female ; *Game Theory ; Humans ; Models, Biological ; Placebos ; *Prejudice ; Reproducibility of Results ; *Social Behavior ; Social Class ; Testosterone/administration & dosage/*pharmacology
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    The transcriptional network for mesenchymal transformation of brain tumours (2009)
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    Publication Date: 2009-12-25
    Description: The inference of transcriptional networks that regulate transitions into physiological or pathological cellular states remains a central challenge in systems biology. A mesenchymal phenotype is the hallmark of tumour aggressiveness in human malignant glioma, but the regulatory programs responsible for implementing the associated molecular signature are largely unknown. Here we show that reverse-engineering and an unbiased interrogation of a glioma-specific regulatory network reveal the transcriptional module that activates expression of mesenchymal genes in malignant glioma. Two transcription factors (C/EBPbeta and STAT3) emerge as synergistic initiators and master regulators of mesenchymal transformation. Ectopic co-expression of C/EBPbeta and STAT3 reprograms neural stem cells along the aberrant mesenchymal lineage, whereas elimination of the two factors in glioma cells leads to collapse of the mesenchymal signature and reduces tumour aggressiveness. In human glioma, expression of C/EBPbeta and STAT3 correlates with mesenchymal differentiation and predicts poor clinical outcome. These results show that the activation of a small regulatory module is necessary and sufficient to initiate and maintain an aberrant phenotypic state in cancer cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4011561/" 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/PMC4011561/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carro, Maria Stella -- Lim, Wei Keat -- Alvarez, Mariano Javier -- Bollo, Robert J -- Zhao, Xudong -- Snyder, Evan Y -- Sulman, Erik P -- Anne, Sandrine L -- Doetsch, Fiona -- Colman, Howard -- Lasorella, Anna -- Aldape, Ken -- Califano, Andrea -- Iavarone, Antonio -- 1RC2CA148308-01/CA/NCI NIH HHS/ -- P20 GM075059/GM/NIGMS NIH HHS/ -- P20GM075059/GM/NIGMS NIH HHS/ -- R01 CA085628/CA/NCI NIH HHS/ -- R01 CA101644/CA/NCI NIH HHS/ -- R01 CA109755/CA/NCI NIH HHS/ -- R01 CA127643/CA/NCI NIH HHS/ -- R01 NS061776/NS/NINDS NIH HHS/ -- R01 NS061776-01A2/NS/NINDS NIH HHS/ -- R01 NS061776-02/NS/NINDS NIH HHS/ -- R01CA085628/CA/NCI NIH HHS/ -- R01CA101644/CA/NCI NIH HHS/ -- R01CA109755/CA/NCI NIH HHS/ -- R01NS061776/NS/NINDS NIH HHS/ -- RC2 CA148308/CA/NCI NIH HHS/ -- U01 CA168426/CA/NCI NIH HHS/ -- U54 CA121852/CA/NCI NIH HHS/ -- U54CA121852/CA/NCI NIH HHS/ -- England -- Nature. 2010 Jan 21;463(7279):318-25. doi: 10.1038/nature08712. Epub 2009 Dec 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Cancer Genetics, Columbia University Medical Center, New York, New York 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20032975" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Brain Neoplasms/diagnosis/*genetics/*pathology ; CCAAT-Enhancer-Binding Protein-beta/genetics/metabolism ; Cell Differentiation/genetics ; Cell Line, Tumor ; Cell Transformation, Neoplastic/genetics/metabolism/pathology ; Cellular Reprogramming/genetics ; Computational Biology ; *Gene Expression Regulation, Neoplastic ; *Gene Regulatory Networks ; Glioma/diagnosis/genetics/pathology ; Humans ; Mesenchymal Stromal Cells/metabolism/pathology ; Mesoderm/*metabolism/*pathology ; Mice ; Mice, Inbred NOD ; Mice, SCID ; Neoplasm Invasiveness/genetics/pathology ; Neurons/metabolism/pathology ; Prognosis ; Reproducibility of Results ; STAT3 Transcription Factor/genetics/metabolism ; *Transcription, Genetic
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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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    Details
    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)
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    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
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    Negative results (2008)
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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)
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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
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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
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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
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    Repairing research integrity (2008)
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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)
    Nature Publishing Group (NPG)
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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)
    Nature Publishing Group (NPG)
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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)
    Nature Publishing Group (NPG)
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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)
    Nature Publishing Group (NPG)
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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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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Nobel prizewinner's paper retracted (2008)
    Nature Publishing Group (NPG)
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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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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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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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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Restricted access to fossils hinders claim confirmation (2008)
    Nature Publishing Group (NPG)
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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)
    Nature Publishing Group (NPG)
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    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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    Detecting influenza epidemics using search engine query data (2008)
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    Publication Date: 2008-11-21
    Description: Seasonal influenza epidemics are a major public health concern, causing tens of millions of respiratory illnesses and 250,000 to 500,000 deaths worldwide each year. In addition to seasonal influenza, a new strain of influenza virus against which no previous immunity exists and that demonstrates human-to-human transmission could result in a pandemic with millions of fatalities. Early detection of disease activity, when followed by a rapid response, can reduce the impact of both seasonal and pandemic influenza. One way to improve early detection is to monitor health-seeking behaviour in the form of queries to online search engines, which are submitted by millions of users around the world each day. Here we present a method of analysing large numbers of Google search queries to track influenza-like illness in a population. Because the relative frequency of certain queries is highly correlated with the percentage of physician visits in which a patient presents with influenza-like symptoms, we can accurately estimate the current level of weekly influenza activity in each region of the United States, with a reporting lag of about one day. This approach may make it possible to use search queries to detect influenza epidemics in areas with a large population of web search users.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ginsberg, Jeremy -- Mohebbi, Matthew H -- Patel, Rajan S -- Brammer, Lynnette -- Smolinski, Mark S -- Brilliant, Larry -- England -- Nature. 2009 Feb 19;457(7232):1012-4. doi: 10.1038/nature07634.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Google Inc., 1600 Amphitheatre Parkway, Mountain View, California 94043, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19020500" target="_blank"〉PubMed〈/a〉
    Keywords: Centers for Disease Control and Prevention (U.S.) ; Databases, Factual ; *Health Behavior ; Health Education/*statistics & numerical data ; Humans ; Influenza, Human/diagnosis/*epidemiology/transmission/virology ; Internationality ; Internet/*utilization ; Linear Models ; Office Visits/statistics & numerical data ; Population Surveillance/*methods ; Reproducibility of Results ; Seasons ; Time Factors ; United States ; *User-Computer Interface
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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