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  • Reproducibility of Results  (303)
  • Nature Publishing Group (NPG)  (303)
  • American Institute of Physics (AIP)
  • 2010-2014  (303)
  • 1990-1994
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  • 1
    Publication Date: 2014-12-24
    Description: Models derived from human pluripotent stem cells that accurately recapitulate neural development in vitro and allow for the generation of specific neuronal subtypes are of major interest to the stem cell and biomedical community. Notch signalling, particularly through the Notch effector HES5, is a major pathway critical for the onset and maintenance of neural progenitor cells in the embryonic and adult nervous system. Here we report the transcriptional and epigenomic analysis of six consecutive neural progenitor cell stages derived from a HES5::eGFP reporter human embryonic stem cell line. Using this system, we aimed to model cell-fate decisions including specification, expansion and patterning during the ontogeny of cortical neural stem and progenitor cells. In order to dissect regulatory mechanisms that orchestrate the stage-specific differentiation process, we developed a computational framework to infer key regulators of each cell-state transition based on the progressive remodelling of the epigenetic landscape and then validated these through a pooled short hairpin RNA screen. We were also able to refine our previous observations on epigenetic priming at transcription factor binding sites and suggest here that they are mediated by combinations of core and stage-specific factors. Taken together, we demonstrate the utility of our system and outline a general framework, not limited to the context of the neural lineage, to dissect regulatory circuits of differentiation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4336237/" 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/PMC4336237/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ziller, Michael J -- Edri, Reuven -- Yaffe, Yakey -- Donaghey, Julie -- Pop, Ramona -- Mallard, William -- Issner, Robbyn -- Gifford, Casey A -- Goren, Alon -- Xing, Jeffrey -- Gu, Hongcang -- Cacchiarelli, Davide -- Tsankov, Alexander M -- Epstein, Charles -- Rinn, John L -- Mikkelsen, Tarjei S -- Kohlbacher, Oliver -- Gnirke, Andreas -- Bernstein, Bradley E -- Elkabetz, Yechiel -- Meissner, Alexander -- F32 DK095537/DK/NIDDK NIH HHS/ -- HG006911/HG/NHGRI NIH HHS/ -- P01 GM099117/GM/NIGMS NIH HHS/ -- P01GM099117/GM/NIGMS NIH HHS/ -- U01 ES017155/ES/NIEHS NIH HHS/ -- U01ES017155/ES/NIEHS NIH HHS/ -- U54 HG006991/HG/NHGRI NIH HHS/ -- England -- Nature. 2015 Feb 19;518(7539):355-9. doi: 10.1038/nature13990. Epub 2014 Dec 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA [3] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA. ; Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Ramat Aviv 6997801, Israel. ; 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA. ; Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. ; 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA [3] Center for Systems Biology and Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA. ; Applied Bioinformatics, Center for Bioinformatics and Quantitative Biology Center, University of Tubingen, Tubingen 72076, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25533951" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cell Differentiation/*genetics ; Cell Lineage/genetics ; Embryonic Stem Cells/*cytology/metabolism ; Epigenesis, Genetic/*genetics ; Epigenomics/*methods ; Humans ; Neural Stem Cells/*cytology/*metabolism ; RNA, Small Interfering/analysis/genetics ; Reproducibility of Results ; Transcription Factors/metabolism ; Transcription, Genetic/genetics
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  • 2
    Publication Date: 2014-12-11
    Description: Systematic interrogation of gene function requires the ability to perturb gene expression in a robust and generalizable manner. Here we describe structure-guided engineering of a CRISPR-Cas9 complex to mediate efficient transcriptional activation at endogenous genomic loci. We used these engineered Cas9 activation complexes to investigate single-guide RNA (sgRNA) targeting rules for effective transcriptional activation, to demonstrate multiplexed activation of ten genes simultaneously, and to upregulate long intergenic non-coding RNA (lincRNA) transcripts. We also synthesized a library consisting of 70,290 guides targeting all human RefSeq coding isoforms to screen for genes that, upon activation, confer resistance to a BRAF inhibitor. The top hits included genes previously shown to be able to confer resistance, and novel candidates were validated using individual sgRNA and complementary DNA overexpression. A gene expression signature based on the top screening hits correlated with markers of BRAF inhibitor resistance in cell lines and patient-derived samples. These results collectively demonstrate the potential of Cas9-based activators as a powerful genetic perturbation technology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4420636/" 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/PMC4420636/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Konermann, Silvana -- Brigham, Mark D -- Trevino, Alexandro E -- Joung, Julia -- Abudayyeh, Omar O -- Barcena, Clea -- Hsu, Patrick D -- Habib, Naomi -- Gootenberg, Jonathan S -- Nishimasu, Hiroshi -- Nureki, Osamu -- Zhang, Feng -- DP1 MH100706/MH/NIMH NIH HHS/ -- DP1-MH100706/DP/NCCDPHP CDC HHS/ -- R01 NS062849/NS/NINDS NIH HHS/ -- R01 NS073124/NS/NINDS NIH HHS/ -- R01-NS07312401/NS/NINDS NIH HHS/ -- England -- Nature. 2015 Jan 29;517(7536):583-8. doi: 10.1038/nature14136. Epub 2014 Dec 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, Massachusetts 02142, USA [2] McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [3] Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [4] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. ; 1] Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, Massachusetts 02142, USA [2] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. ; Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, Massachusetts 02142, USA. ; 1] Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, Massachusetts 02142, USA [2] McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [3] Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [4] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [5] Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA. ; 1] Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi Bunkyo, Tokyo 113-0032, Japan [2] JST, PRESTO 2-11-16 Yayoi Bunkyo, Tokyo 113-0032, Japan. ; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi Bunkyo, Tokyo 113-0032, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25494202" target="_blank"〉PubMed〈/a〉
    Keywords: CRISPR-Associated Proteins/genetics/metabolism ; CRISPR-Cas Systems/*genetics ; Cell Line, Tumor ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; DNA, Complementary/biosynthesis/genetics ; Drug Resistance, Neoplasm/drug effects/genetics ; Gene Expression Regulation, Neoplastic/genetics ; Gene Library ; Genetic Engineering/*methods ; Genetic Loci/genetics ; Genetic Testing ; Genome, Human/*genetics ; Humans ; Indoles/pharmacology ; Melanoma/drug therapy/*genetics ; Proto-Oncogene Proteins B-raf/antagonists & inhibitors ; RNA, Untranslated/biosynthesis/genetics/metabolism ; Reproducibility of Results ; Sulfonamides/pharmacology ; Transcriptional Activation/*genetics ; Up-Regulation/genetics
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  • 3
    Publication Date: 2014-10-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉See, Linda -- Fritz, Steffen -- McCallum, Ian -- England -- Nature. 2014 Oct 9;514(7521):168. doi: 10.1038/514168a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉International Institute for Applied Systems Analysis, Laxenburg, Austria.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25297427" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Biodiversity ; Calibration ; Environmental Monitoring ; *Information Dissemination ; Reproducibility of Results ; *Satellite Imagery ; Trees
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  • 4
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    Nature Publishing Group (NPG)
    Publication Date: 2014-03-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Perrin, Steve -- England -- Nature. 2014 Mar 27;507(7493):423-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24678540" target="_blank"〉PubMed〈/a〉
    Keywords: Amyotrophic Lateral Sclerosis/genetics/pathology/therapy ; Animals ; Cause of Death ; Clinical Trials as Topic/economics/standards ; *Disease Models, Animal ; Disease Progression ; Dose-Response Relationship, Drug ; Drug Evaluation, Preclinical/economics/*methods/*standards ; False Positive Reactions ; Guidelines as Topic ; Half-Life ; Humans ; Mice ; Organ Specificity ; Reproducibility of Results ; *Research Design ; Superoxide Dismutase/deficiency/genetics/metabolism ; Survival Analysis ; Translational Medical Research/economics/*methods/*standards ; Treatment Failure
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  • 5
    Publication Date: 2014-06-05
    Description: Transcriptional enhancers are crucial regulators of gene expression and animal development and the characterization of their genomic organization, spatiotemporal activities and sequence properties is a key goal in modern biology. Here we characterize the in vivo activity of 7,705 Drosophila melanogaster enhancer candidates covering 13.5% of the non-coding non-repetitive genome throughout embryogenesis. 3,557 (46%) candidates are active, suggesting a high density with 50,000 to 100,000 developmental enhancers genome-wide. The vast majority of enhancers display specific spatial patterns that are highly dynamic during development. Most appear to regulate their neighbouring genes, suggesting that the cis-regulatory genome is organized locally into domains, which are supported by chromosomal domains, insulator binding and genome evolution. However, 12 to 21 per cent of enhancers appear to skip non-expressed neighbours and regulate a more distal gene. Finally, we computationally identify cis-regulatory motifs that are predictive and required for enhancer activity, as we validate experimentally. This work provides global insights into the organization of an animal regulatory genome and the make-up of enhancer sequences and confirms and generalizes principles from previous studies. All enhancer patterns are annotated manually with a controlled vocabulary and all results are available through a web interface (http://enhancers.starklab.org), including the raw images of all microscopy slides for manual inspection at arbitrary zoom levels.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kvon, Evgeny Z -- Kazmar, Tomas -- Stampfel, Gerald -- Yanez-Cuna, J Omar -- Pagani, Michaela -- Schernhuber, Katharina -- Dickson, Barry J -- Stark, Alexander -- England -- Nature. 2014 Aug 7;512(7512):91-5. doi: 10.1038/nature13395. Epub 2014 Jun 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Research Institute of Molecular Pathology (IMP), Vienna Biocenter VBC, Dr Bohr-Gasse 7, 1030 Vienna, Austria [2] Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia 20147, USA (B.J.D.); Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA (E.Z.K.). ; Research Institute of Molecular Pathology (IMP), Vienna Biocenter VBC, Dr Bohr-Gasse 7, 1030 Vienna, Austria. ; 1] Research Institute of Molecular Pathology (IMP), Vienna Biocenter VBC, Dr Bohr-Gasse 7, 1030 Vienna, Austria [2].〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24896182" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Drosophila melanogaster/*embryology/*genetics ; Embryonic Development/*genetics ; Enhancer Elements, Genetic/*genetics ; Gene Expression Regulation, Developmental/*genetics ; Genome, Insect/*genetics ; Internet ; Nucleotide Motifs/genetics ; Organ Specificity/genetics ; Regulatory Sequences, Nucleic Acid/genetics ; Reproducibility of Results ; User-Computer Interface
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  • 6
    Publication Date: 2014-02-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lewis, Simon L -- England -- Nature. 2014 Feb 27;506(7489):409. doi: 10.1038/506409a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24572388" target="_blank"〉PubMed〈/a〉
    Keywords: *Climate Change ; *Dissent and Disputes ; Floods/statistics & numerical data ; Great Britain ; Journalism/standards ; Mass Media/standards ; *Public Opinion ; Rain ; Reproducibility of Results ; Uncertainty
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  • 7
    Publication Date: 2014-08-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hanage, William P -- England -- Nature. 2014 Aug 21;512(7514):247-8. doi: 10.1038/512247a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Harvard School of Public Health in Boston, Massachusetts, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25143098" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Humans ; *Microbiota/genetics/physiology ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Science/*standards ; *Uncertainty
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  • 8
    Publication Date: 2014-04-18
    Description: Ice volume (and hence sea level) and deep-sea temperature are key measures of global climate change. Sea level has been documented using several independent methods over the past 0.5 million years (Myr). Older periods, however, lack such independent validation; all existing records are related to deep-sea oxygen isotope (delta(18)O) data that are influenced by processes unrelated to sea level. For deep-sea temperature, only one continuous high-resolution (Mg/Ca-based) record exists, with related sea-level estimates, spanning the past 1.5 Myr. Here we present a novel sea-level reconstruction, with associated estimates of deep-sea temperature, which independently validates the previous 0-1.5 Myr reconstruction and extends it back to 5.3 Myr ago. We find that deep-sea temperature and sea level generally decreased through time, but distinctly out of synchrony, which is remarkable given the importance of ice-albedo feedbacks on the radiative forcing of climate. In particular, we observe a large temporal offset during the onset of Plio-Pleistocene ice ages, between a marked cooling step at 2.73 Myr ago and the first major glaciation at 2.15 Myr ago. Last, we tentatively infer that ice sheets may have grown largest during glacials with more modest reductions in deep-sea temperature.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rohling, E J -- Foster, G L -- Grant, K M -- Marino, G -- Roberts, A P -- Tamisiea, M E -- Williams, F -- England -- Nature. 2014 Apr 24;508(7497):477-82. doi: 10.1038/nature13230. Epub 2014 Apr 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Research School of Earth Sciences, The Australian National University, Canberra 0200, Australia [2] Ocean and Earth Science, University of Southampton, National Oceanography Centre, Southampton SO14 3ZH, UK. ; Ocean and Earth Science, University of Southampton, National Oceanography Centre, Southampton SO14 3ZH, UK. ; Research School of Earth Sciences, The Australian National University, Canberra 0200, Australia. ; National Oceanography Centre, Joseph Proudman Building, Liverpool L3 5DA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24739960" target="_blank"〉PubMed〈/a〉
    Keywords: Foraminifera ; History, Ancient ; Ice Cover ; Mediterranean Sea ; Oxygen Isotopes ; Reproducibility of Results ; Seawater/*analysis ; *Temperature ; Time Factors
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  • 9
    Publication Date: 2014-05-09
    Description: Electromagnetic noise is emitted everywhere humans use electronic devices. For decades, it has been hotly debated whether man-made electric and magnetic fields affect biological processes, including human health. So far, no putative effect of anthropogenic electromagnetic noise at intensities below the guidelines adopted by the World Health Organization has withstood the test of independent replication under truly blinded experimental conditions. No effect has therefore been widely accepted as scientifically proven. Here we show that migratory birds are unable to use their magnetic compass in the presence of urban electromagnetic noise. When European robins, Erithacus rubecula, were exposed to the background electromagnetic noise present in unscreened wooden huts at the University of Oldenburg campus, they could not orient using their magnetic compass. Their magnetic orientation capabilities reappeared in electrically grounded, aluminium-screened huts, which attenuated electromagnetic noise in the frequency range from 50 kHz to 5 MHz by approximately two orders of magnitude. When the grounding was removed or when broadband electromagnetic noise was deliberately generated inside the screened and grounded huts, the birds again lost their magnetic orientation capabilities. The disruptive effect of radiofrequency electromagnetic fields is not confined to a narrow frequency band and birds tested far from sources of electromagnetic noise required no screening to orient with their magnetic compass. These fully double-blinded tests document a reproducible effect of anthropogenic electromagnetic noise on the behaviour of an intact vertebrate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Engels, Svenja -- Schneider, Nils-Lasse -- Lefeldt, Nele -- Hein, Christine Maira -- Zapka, Manuela -- Michalik, Andreas -- Elbers, Dana -- Kittel, Achim -- Hore, P J -- Mouritsen, Henrik -- England -- Nature. 2014 May 15;509(7500):353-6. doi: 10.1038/nature13290. Epub 2014 May 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Institut fur Biologie und Umweltwissenschaften, Universitat Oldenburg, D-26111 Oldenburg, Germany [2] Research Centre for Neurosensory Sciences, University of Oldenburg, D-26111 Oldenburg, Germany [3]. ; 1] Institut fur Biologie und Umweltwissenschaften, Universitat Oldenburg, D-26111 Oldenburg, Germany [2] Research Centre for Neurosensory Sciences, University of Oldenburg, D-26111 Oldenburg, Germany. ; Institute of Physics, University of Oldenburg, D-26111 Oldenburg, Germany. ; Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, Oxford OX1 3QZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24805233" target="_blank"〉PubMed〈/a〉
    Keywords: Aluminum ; Animal Migration/*physiology ; Animals ; Cities ; Conservation of Natural Resources ; Double-Blind Method ; Electricity/adverse effects ; Electromagnetic Fields/*adverse effects ; Electronics/instrumentation ; Germany ; Housing ; *Magnetic Fields ; Orientation/*physiology ; Radio Waves/adverse effects ; Reproducibility of Results ; Seasons ; Songbirds/*physiology ; Universities
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  • 10
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    Nature Publishing Group (NPG)
    Publication Date: 2014-01-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abbott, Alison -- England -- Nature. 2014 Jan 9;505(7482):139-40. doi: 10.1038/505139a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24402259" target="_blank"〉PubMed〈/a〉
    Keywords: Child ; Clinical Trials as Topic/adverse effects/*ethics/legislation & ; jurisprudence/standards ; Confidentiality/legislation & jurisprudence ; Foundations ; Humans ; Italy ; Mesenchymal Stromal Cells/cytology ; Neural Stem Cells/cytology/transplantation ; Reproducibility of Results ; Stem Cell Transplantation/*adverse effects/*ethics/legislation & ; jurisprudence/standards ; Uncertainty
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  • 11
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    Nature Publishing Group (NPG)
    Publication Date: 2014-02-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nuzzo, Regina -- England -- Nature. 2014 Feb 13;506(7487):150-2. doi: 10.1038/506150a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Gallaudet University in Washington DC.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24522584" target="_blank"〉PubMed〈/a〉
    Keywords: *Data Interpretation, Statistical ; Data Mining ; Reproducibility of Results ; Research Design/*standards
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  • 12
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    Nature Publishing Group (NPG)
    Publication Date: 2014-04-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cyranoski, David -- England -- Nature. 2014 Apr 17;508(7496):299. doi: 10.1038/508299a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24740046" target="_blank"〉PubMed〈/a〉
    Keywords: Acids/pharmacology ; Cell Dedifferentiation/drug effects ; Induced Pluripotent Stem Cells/cytology/drug effects ; Japan ; Lymphocytes/cytology/drug effects ; Pressure ; Reproducibility of Results ; Research Personnel/*ethics/*psychology/standards ; *Scientific Misconduct ; Stem Cell Research/*ethics ; Uncertainty
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  • 13
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    Nature Publishing Group (NPG)
    Publication Date: 2014-02-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bohle, Shannon -- England -- Nature. 2014 Feb 13;506(7487):159. doi: 10.1038/506159e.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24522589" target="_blank"〉PubMed〈/a〉
    Keywords: *Access to Information ; *Internet/economics ; *Laboratories ; Patents as Topic ; *Records as Topic/economics ; Reproducibility of Results ; United States
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  • 14
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    Nature Publishing Group (NPG)
    Publication Date: 2014-02-01
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058759/" 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/PMC4058759/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Collins, Francis S -- Tabak, Lawrence A -- Z99 OD999999/Intramural NIH HHS/ -- England -- Nature. 2014 Jan 30;505(7485):612-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24482835" target="_blank"〉PubMed〈/a〉
    Keywords: Access to Information ; Animals ; Biomedical Research/*standards ; Disclosure/standards ; Female ; Humans ; Male ; *National Institutes of Health (U.S.) ; Pilot Projects ; Reproducibility of Results ; Research Design/*standards ; Scientific Misconduct/statistics & numerical data ; Sex Characteristics ; United States
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  • 15
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    Nature Publishing Group (NPG)
    Publication Date: 2014-05-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, Vivien -- England -- Nature. 2014 May 29;509(7502):645-9. doi: 10.1038/509645a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Nature and Nature Methods.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24870547" target="_blank"〉PubMed〈/a〉
    Keywords: Anatomy, Artistic ; Antibodies/analysis/immunology ; Antibody Specificity ; Atlases as Topic ; Automation ; *Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; Humans ; Immunohistochemistry ; Organ Specificity ; Protein Transport ; Proteome/analysis/genetics/*metabolism/secretion ; Reproducibility of Results ; Staining and Labeling ; Tissue Array Analysis
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 16
    Publication Date: 2014-11-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barbier, Edward B -- England -- Nature. 2014 Nov 6;515(7525):32-3. doi: 10.1038/515032a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Wyoming, Laramie, Wyoming, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25373661" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Conservation of Natural Resources/*economics/*statistics & numerical data ; *Ecosystem ; *Models, Economic ; Pilot Projects ; Reproducibility of Results ; Rhizophoraceae ; Thailand ; Wood
    Print ISSN: 0028-0836
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  • 17
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    Nature Publishing Group (NPG)
    Publication Date: 2014-04-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Katsnelson, Alla -- England -- Nature. 2014 Apr 3;508(7494):S8-9. doi: 10.1038/508S8a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24695336" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antipsychotic Agents/therapeutic use ; Cognition/physiology ; Cognition Disorders/drug therapy/pathology/physiopathology ; *Disease Models, Animal ; Drug Discovery/*methods/standards ; Humans ; Mice ; Mice, Transgenic ; Multifactorial Inheritance/genetics ; Rats ; Reproducibility of Results ; *Schizophrenia/chemically induced/drug therapy/etiology/physiopathology
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 18
    Publication Date: 2014-04-04
    Description: Cancers have dysfunctional redox regulation resulting in reactive oxygen species production, damaging both DNA and free dNTPs. The MTH1 protein sanitizes oxidized dNTP pools to prevent incorporation of damaged bases during DNA replication. Although MTH1 is non-essential in normal cells, we show that cancer cells require MTH1 activity to avoid incorporation of oxidized dNTPs, resulting in DNA damage and cell death. We validate MTH1 as an anticancer target in vivo and describe small molecules TH287 and TH588 as first-in-class nudix hydrolase family inhibitors that potently and selectively engage and inhibit the MTH1 protein in cells. Protein co-crystal structures demonstrate that the inhibitors bind in the active site of MTH1. The inhibitors cause incorporation of oxidized dNTPs in cancer cells, leading to DNA damage, cytotoxicity and therapeutic responses in patient-derived mouse xenografts. This study exemplifies the non-oncogene addiction concept for anticancer treatment and validates MTH1 as being cancer phenotypic lethal.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gad, Helge -- Koolmeister, Tobias -- Jemth, Ann-Sofie -- Eshtad, Saeed -- Jacques, Sylvain A -- Strom, Cecilia E -- Svensson, Linda M -- Schultz, Niklas -- Lundback, Thomas -- Einarsdottir, Berglind Osk -- Saleh, Aljona -- Gokturk, Camilla -- Baranczewski, Pawel -- Svensson, Richard -- Berntsson, Ronnie P-A -- Gustafsson, Robert -- Stromberg, Kia -- Sanjiv, Kumar -- Jacques-Cordonnier, Marie-Caroline -- Desroses, Matthieu -- Gustavsson, Anna-Lena -- Olofsson, Roger -- Johansson, Fredrik -- Homan, Evert J -- Loseva, Olga -- Brautigam, Lars -- Johansson, Lars -- Hoglund, Andreas -- Hagenkort, Anna -- Pham, Therese -- Altun, Mikael -- Gaugaz, Fabienne Z -- Vikingsson, Svante -- Evers, Bastiaan -- Henriksson, Martin -- Vallin, Karl S A -- Wallner, Olov A -- Hammarstrom, Lars G J -- Wiita, Elisee -- Almlof, Ingrid -- Kalderen, Christina -- Axelsson, Hanna -- Djureinovic, Tatjana -- Puigvert, Jordi Carreras -- Haggblad, Maria -- Jeppsson, Fredrik -- Martens, Ulf -- Lundin, Cecilia -- Lundgren, Bo -- Granelli, Ingrid -- Jensen, Annika Jenmalm -- Artursson, Per -- Nilsson, Jonas A -- Stenmark, Pal -- Scobie, Martin -- Berglund, Ulrika Warpman -- Helleday, Thomas -- England -- Nature. 2014 Apr 10;508(7495):215-21. doi: 10.1038/nature13181. Epub 2014 Apr 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden [2]. ; Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden. ; Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden. ; 1] Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden [2] Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden. ; Sahlgrenska Translational Melanoma Group, Sahlgrenska Cancer Center, Department of Surgery, University of Gothenburg and Sahlgrenska University Hospital, S-405 30 Gothenburg, Sweden. ; Department of Analytical Chemistry, Stockholm University, S-106 91 Stockholm, Sweden. ; 1] Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden [2] Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Department of Pharmacy, Uppsala University, S-751 23 Uppsala, Sweden. ; 1] Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden [2] Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Department of Pharmacy, Uppsala University, S-751 23 Uppsala, Sweden. ; Department of Genetics, Microbiology and Toxicology, Stockholm University, S-106 91 Stockholm, Sweden. ; 1] Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden [2] Clinical Pharmacology, Department of Medical and Health Sciences, Linkoping University, S-58185 Linkoping, Sweden. ; 1] Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden [2] Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1006 Amsterdam, The Netherlands (B.E.); Department of Immunology, Genetics, and Pathology, Uppsala University, S-751 23 Uppsala, Sweden (T.D.). ; 1] Department of Genetics, Microbiology and Toxicology, Stockholm University, S-106 91 Stockholm, Sweden [2] Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1006 Amsterdam, The Netherlands (B.E.); Department of Immunology, Genetics, and Pathology, Uppsala University, S-751 23 Uppsala, Sweden (T.D.). ; Science for Life Laboratory, RNAi Cell Screening Facility, Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24695224" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Catalytic Domain ; Cell Death/drug effects ; Cell Survival/drug effects ; Crystallization ; DNA Damage ; DNA Repair Enzymes/*antagonists & inhibitors/chemistry/metabolism ; Deoxyguanine Nucleotides/metabolism ; Enzyme Inhibitors/chemistry/pharmacokinetics/pharmacology/therapeutic use ; Female ; Humans ; Male ; Mice ; Models, Molecular ; Molecular Conformation ; Molecular Targeted Therapy ; Neoplasms/*drug therapy/*metabolism/pathology ; Nucleotides/*metabolism ; Oxidation-Reduction/drug effects ; Phosphoric Monoester Hydrolases/*antagonists & inhibitors/chemistry/metabolism ; Pyrimidines/chemistry/pharmacokinetics/pharmacology/therapeutic use ; Pyrophosphatases/antagonists & inhibitors ; Reproducibility of Results ; Xenograft Model Antitumor Assays
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  • 19
    Publication Date: 2014-04-25
    Description: The discovery of rare genetic variants is accelerating, and clear guidelines for distinguishing disease-causing sequence variants from the many potentially functional variants present in any human genome are urgently needed. Without rigorous standards we risk an acceleration of false-positive reports of causality, which would impede the translation of genomic research findings into the clinical diagnostic setting and hinder biological understanding of disease. Here we discuss the key challenges of assessing sequence variants in human disease, integrating both gene-level and variant-level support for causality. We propose guidelines for summarizing confidence in variant pathogenicity and highlight several areas that require further resource development.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4180223/" 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/PMC4180223/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉MacArthur, D G -- Manolio, T A -- Dimmock, D P -- Rehm, H L -- Shendure, J -- Abecasis, G R -- Adams, D R -- Altman, R B -- Antonarakis, S E -- Ashley, E A -- Barrett, J C -- Biesecker, L G -- Conrad, D F -- Cooper, G M -- Cox, N J -- Daly, M J -- Gerstein, M B -- Goldstein, D B -- Hirschhorn, J N -- Leal, S M -- Pennacchio, L A -- Stamatoyannopoulos, J A -- Sunyaev, S R -- Valle, D -- Voight, B F -- Winckler, W -- Gunter, C -- P30 DK020595/DK/NIDDK NIH HHS/ -- P30 DK042086/DK/NIDDK NIH HHS/ -- R01 HG007022/HG/NHGRI NIH HHS/ -- R01 HL117626/HL/NHLBI NIH HHS/ -- R01 MH101810/MH/NIMH NIH HHS/ -- U54 HG006997/HG/NHGRI NIH HHS/ -- England -- Nature. 2014 Apr 24;508(7497):469-76. doi: 10.1038/nature13127.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA [2] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA. ; Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, Maryland 20892, USA. ; Division of Genetics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA. ; 1] Laboratory for Molecular Medicine, Partners Healthcare Center for Personalized Genetic Medicine, Cambridge, Massachusetts 02139, USA [2] Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA. ; Department of Genome Sciences, University of Washington, Seattle, Washington 98115, USA. ; Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA. ; 1] NIH Undiagnosed Diseases Program, National Institutes of Health Office of Rare Diseases Research and National Human Genome Research Institute, Bethesda, Maryland 20892, USA [2] Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA. ; Departments of Bioengineering & Genetics, Stanford University, Stanford, California 94305, USA. ; 1] Department of Genetic Medicine, University of Geneva Medical School, 1211 Geneva, Switzerland [2] iGE3 Institute of Genetics and Genomics of Geneva, 1211 Geneva, Switzerland. ; Center for Inherited Cardiovascular Disease, Stanford University School of Medicine, Stanford, California 94305, USA. ; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK. ; Genetic Disease Research Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland 20892, USA. ; Departments of Genetics, Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA. ; HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, Alabama 35806, USA. ; Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA. ; 1] Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA [2] Departments of Computer Science, Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA. ; Center for Human Genome Variation, Duke University School of Medicine, Durham, North Carolina 27708, USA. ; 1] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA [2] Divisions of Genetics and Endocrinology, Children's Hospital, Boston, Massachusetts 02115, USA. ; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA. ; 1] Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA [2] US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA. ; Department of Genome Sciences, University of Washington, 1705 Northeast Pacific Street, Seattle, Washington 98195, USA. ; 1] Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA [2] Harvard Medical School, Boston, Massachusetts 02115, USA. ; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA. ; Department of Pharmacology and Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA. ; 1] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA [2] Next Generation Diagnostics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA (W.W.); Marcus Autism Center, Children's Healthcare of Atlanta, Atlanta, Georgia 30329, USA (C.G.). ; 1] HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, Alabama 35806, USA [2] Next Generation Diagnostics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA (W.W.); Marcus Autism Center, Children's Healthcare of Atlanta, Atlanta, Georgia 30329, USA (C.G.).〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24759409" target="_blank"〉PubMed〈/a〉
    Keywords: *Disease ; False Positive Reactions ; Genes/genetics ; Genetic Predisposition to Disease/*genetics ; Genetic Variation/*genetics ; *Guidelines as Topic ; Humans ; Information Dissemination ; Publishing ; Reproducibility of Results ; Research Design ; Translational Medical Research/standards
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  • 20
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2014-11-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2014 Nov 6;515(7525):7. doi: 10.1038/515007a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25373636" target="_blank"〉PubMed〈/a〉
    Keywords: Biomedical Research/*standards ; *Guidelines as Topic ; Periodicals as Topic/*standards ; Quality Control ; Reproducibility of Results ; Research Report/*standards
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  • 21
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    Nature Publishing Group (NPG)
    Publication Date: 2014-10-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2014 Oct 30;514(7524):536. doi: 10.1038/514536a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25355323" target="_blank"〉PubMed〈/a〉
    Keywords: Information Dissemination/*methods ; *Periodicals as Topic/standards ; Reproducibility of Results ; *Research ; *Software
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  • 22
    Publication Date: 2014-06-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pagan-Jimenez, Jaime R -- Rodriguez-Ramos, Reniel -- Oliver, Jose R -- England -- Nature. 2014 Jun 26;510(7506):473. doi: 10.1038/510473b.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Leiden University, the Netherlands. ; University of Puerto Rico, Utuado, Puerto Rico. ; University College London, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24965639" target="_blank"〉PubMed〈/a〉
    Keywords: Archaeology ; Bolivia/ethnology ; Crops, Agricultural/genetics/*history ; Culture ; DNA, Plant/analysis ; Feces/chemistry ; History, Ancient ; Humans ; Phylogeography ; Puerto Rico ; Reproducibility of Results ; *Zea mays/genetics
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 23
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2014-11-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Butler, Declan -- England -- Nature. 2014 Nov 6;515(7525):18. doi: 10.1038/515018a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25373654" target="_blank"〉PubMed〈/a〉
    Keywords: Disaster Planning/methods ; Disease Outbreaks/*statistics & numerical data ; Hemorrhagic Fever, Ebola/*epidemiology/*transmission ; Humans ; Liberia/epidemiology ; *Models, Biological ; Reproducibility of Results ; Uncertainty
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 24
    Publication Date: 2014-07-22
    Description: A comprehensive account of the causes of alcohol misuse must accommodate individual differences in biology, psychology and environment, and must disentangle cause and effect. Animal models can demonstrate the effects of neurotoxic substances; however, they provide limited insight into the psycho-social and higher cognitive factors involved in the initiation of substance use and progression to misuse. One can search for pre-existing risk factors by testing for endophenotypic biomarkers in non-using relatives; however, these relatives may have personality or neural resilience factors that protect them from developing dependence. A longitudinal study has potential to identify predictors of adolescent substance misuse, particularly if it can incorporate a wide range of potential causal factors, both proximal and distal, and their influence on numerous social, psychological and biological mechanisms. Here we apply machine learning to a wide range of data from a large sample of adolescents (n = 692) to generate models of current and future adolescent alcohol misuse that incorporate brain structure and function, individual personality and cognitive differences, environmental factors (including gestational cigarette and alcohol exposure), life experiences, and candidate genes. These models were accurate and generalized to novel data, and point to life experiences, neurobiological differences and personality as important antecedents of binge drinking. By identifying the vulnerability factors underlying individual differences in alcohol misuse, these models shed light on the aetiology of alcohol misuse and suggest targets for prevention.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4486207/" 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/PMC4486207/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Whelan, Robert -- Watts, Richard -- Orr, Catherine A -- Althoff, Robert R -- Artiges, Eric -- Banaschewski, Tobias -- Barker, Gareth J -- Bokde, Arun L W -- Buchel, Christian -- Carvalho, Fabiana M -- Conrod, Patricia J -- Flor, Herta -- Fauth-Buhler, Mira -- Frouin, Vincent -- Gallinat, Juergen -- Gan, Gabriela -- Gowland, Penny -- Heinz, Andreas -- Ittermann, Bernd -- Lawrence, Claire -- Mann, Karl -- Martinot, Jean-Luc -- Nees, Frauke -- Ortiz, Nick -- Paillere-Martinot, Marie-Laure -- Paus, Tomas -- Pausova, Zdenka -- Rietschel, Marcella -- Robbins, Trevor W -- Smolka, Michael N -- Strohle, Andreas -- Schumann, Gunter -- Garavan, Hugh -- IMAGEN Consortium -- MH082116/MH/NIMH NIH HHS/ -- P20 GM103644/GM/NIGMS NIH HHS/ -- P20GM103644/GM/NIGMS NIH HHS/ -- P50 DA036114/DA/NIDA NIH HHS/ -- P50DA036114/DA/NIDA NIH HHS/ -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2014 Aug 14;512(7513):185-9. doi: 10.1038/nature13402. Epub 2014 Jul 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Psychiatry, University of Vermont, Burlington, Vermont 05401, USA [2] Department of Psychology, University College Dublin, Dublin 4, Ireland. ; Department of Radiology, University of Vermont, Burlington, Vermont 05401, USA. ; Vermont Center for Children, Youth, and Families, University of Vermont, Burlington, Vermont 05401, USA. ; 1] Department of Pediatrics, University of Vermont, Burlington, Vermont 05401, USA [2] Department of Psychology, University of Vermont, Burlington, Vermont 05401, USA. ; 1] Institut National de la Sante et de la Recherche Medicale, INSERM CEA Unit 1000 "Imaging &Psychiatry", University Paris Sud, 91400 Orsay, France [2] Department of Psychiatry, Orsay Hospital, 4 place du General Leclerc, 91400 Orsay, France. ; Department of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159 Mannheim, Germany. ; Institute of Psychiatry, King's College London, London SE5 8AF, UK. ; Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland. ; 1] Department of Systems Neuroscience, Universitatsklinikum Hamburg Eppendorf, 20246 Hamburg, Germany [2] Department of Psychology, Stanford University, Stanford, California 94305, USA. ; 1] Institute of Psychiatry, King's College London, London SE5 8AF, UK [2] Department of Psychiatry, Universite de Montreal, CHU Ste Justine Hospital, Montreal H3T 1C5, Canada. ; 1] Department of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159 Mannheim, Germany [2] Department of Addictive Behaviour and Addiction Medicine, Heidelberg University, 68159 Mannheim, Germany. ; 14 CEA, DSV, I2BM, Neurospin bat 145, 91191 Gif-Sur-Yvette, France. ; 1] Department of Systems Neuroscience, Universitatsklinikum Hamburg Eppendorf, 20246 Hamburg, Germany [2] Department of Psychiatry and Psychotherapy, Campus Charite Mitte, Charite-Universitatsmedizin Berlin 10117, Germany. ; Department of Psychiatry and Neuroimaging Center, Technische Universitat Dresden, 01062 Dresden, Germany. ; School of Physics and Astronomy, University of Nottingham, Nottingham NG7 2RD, UK. ; Department of Psychiatry and Psychotherapy, Campus Charite Mitte, Charite-Universitatsmedizin Berlin 10117, Germany. ; Physikalisch-Technische Bundesanstalt (PTB), 10587 Berlin, Germany. ; School of Psychology, University of Nottingham, Nottingham NG7 2RD, UK. ; 1] Institut National de la Sante et de la Recherche Medicale, INSERM CEA Unit 1000 "Imaging &Psychiatry", University Paris Sud, 91400 Orsay, France [2] AP-HP Department of Adolescent Psychopathology and Medicine, Maison de Solenn, University Paris Descartes, 75006 Paris, France. ; 1] Department of Psychiatry, University of Vermont, Burlington, Vermont 05401, USA [2] Neuroscience Graduate Program, University of Vermont, Burlington, Vermont 05401, USA. ; 1] Department of Psychiatry and Psychotherapy, Campus Charite Mitte, Charite-Universitatsmedizin Berlin 10117, Germany [2] AP-HP Department of Adolescent Psychopathology and Medicine, Maison de Solenn, University Paris Descartes, 75006 Paris, France. ; 1] Rotman Research Institute, University of Toronto, Toronto, Ontario M5R 0A3, Canada [2] Montreal Neurological Institute, McGill University, H3A 2B4, Canada. ; The Hospital for Sick Children, University of Toronto, Toronto, Ontario M5G 0A4, Canada. ; Behavioural and Clinical Neuroscience Institute and Department of Psychology, University of Cambridge, Cambridge CB2 1TN, UK. ; 1] Institute of Psychiatry, King's College London, London SE5 8AF, UK [2] MRC Social, Genetic and Developmental Psychiatry (SGDP) Centre, London, London WC2R 2LS, UK. ; 1] Department of Psychiatry, University of Vermont, Burlington, Vermont 05401, USA [2] Department of Psychology, University of Vermont, Burlington, Vermont 05401, USA [3] Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25043041" target="_blank"〉PubMed〈/a〉
    Keywords: Adolescent ; Alcohol Drinking/*psychology ; Alcoholism/genetics/prevention & control/*psychology ; Artificial Intelligence ; Brain/physiology ; Cognition/physiology ; Environment ; Humans ; Life Change Events ; Longitudinal Studies ; *Models, Theoretical ; Personality/physiology ; Polymorphism, Single Nucleotide ; Psychology ; Reproducibility of Results ; Risk Factors
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  • 25
    Publication Date: 2014-05-30
    Description: The availability of human genome sequence has transformed biomedical research over the past decade. However, an equivalent map for the human proteome with direct measurements of proteins and peptides does not exist yet. Here we present a draft map of the human proteome using high-resolution Fourier-transform mass spectrometry. In-depth proteomic profiling of 30 histologically normal human samples, including 17 adult tissues, 7 fetal tissues and 6 purified primary haematopoietic cells, resulted in identification of proteins encoded by 17,294 genes accounting for approximately 84% of the total annotated protein-coding genes in humans. A unique and comprehensive strategy for proteogenomic analysis enabled us to discover a number of novel protein-coding regions, which includes translated pseudogenes, non-coding RNAs and upstream open reading frames. This large human proteome catalogue (available as an interactive web-based resource at http://www.humanproteomemap.org) will complement available human genome and transcriptome data to accelerate biomedical research in health and disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4403737/" 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/PMC4403737/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Min-Sik -- Pinto, Sneha M -- Getnet, Derese -- Nirujogi, Raja Sekhar -- Manda, Srikanth S -- Chaerkady, Raghothama -- Madugundu, Anil K -- Kelkar, Dhanashree S -- Isserlin, Ruth -- Jain, Shobhit -- Thomas, Joji K -- Muthusamy, Babylakshmi -- Leal-Rojas, Pamela -- Kumar, Praveen -- Sahasrabuddhe, Nandini A -- Balakrishnan, Lavanya -- Advani, Jayshree -- George, Bijesh -- Renuse, Santosh -- Selvan, Lakshmi Dhevi N -- Patil, Arun H -- Nanjappa, Vishalakshi -- Radhakrishnan, Aneesha -- Prasad, Samarjeet -- Subbannayya, Tejaswini -- Raju, Rajesh -- Kumar, Manish -- Sreenivasamurthy, Sreelakshmi K -- Marimuthu, Arivusudar -- Sathe, Gajanan J -- Chavan, Sandip -- Datta, Keshava K -- Subbannayya, Yashwanth -- Sahu, Apeksha -- Yelamanchi, Soujanya D -- Jayaram, Savita -- Rajagopalan, Pavithra -- Sharma, Jyoti -- Murthy, Krishna R -- Syed, Nazia -- Goel, Renu -- Khan, Aafaque A -- Ahmad, Sartaj -- Dey, Gourav -- Mudgal, Keshav -- Chatterjee, Aditi -- Huang, Tai-Chung -- Zhong, Jun -- Wu, Xinyan -- Shaw, Patrick G -- Freed, Donald -- Zahari, Muhammad S -- Mukherjee, Kanchan K -- Shankar, Subramanian -- Mahadevan, Anita -- Lam, Henry -- Mitchell, Christopher J -- Shankar, Susarla Krishna -- Satishchandra, Parthasarathy -- Schroeder, John T -- Sirdeshmukh, Ravi -- Maitra, Anirban -- Leach, Steven D -- Drake, Charles G -- Halushka, Marc K -- Prasad, T S Keshava -- Hruban, Ralph H -- Kerr, Candace L -- Bader, Gary D -- Iacobuzio-Donahue, Christine A -- Gowda, Harsha -- Pandey, Akhilesh -- HHSN268201000032C/HL/NHLBI NIH HHS/ -- HHSN268201000032C/PHS HHS/ -- P41 GM103504/GM/NIGMS NIH HHS/ -- P41GM103504/GM/NIGMS NIH HHS/ -- T32 GM007814/GM/NIGMS NIH HHS/ -- U24 CA160036/CA/NCI NIH HHS/ -- U24CA160036/CA/NCI NIH HHS/ -- U54 GM103520/GM/NIGMS NIH HHS/ -- U54GM103520/GM/NIGMS NIH HHS/ -- England -- Nature. 2014 May 29;509(7502):575-81. doi: 10.1038/nature13302.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA [2] Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA. ; Institute of Bioinformatics, International Tech Park, Bangalore 560066, India. ; 1] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA [2] Adrienne Helis Malvin Medical Research Foundation, New Orleans, Louisiana 70130, USA. ; The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada. ; 1] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA [2] Department of Pathology, Universidad de La Frontera, Center of Genetic and Immunological Studies-Scientific and Technological Bioresource Nucleus, Temuco 4811230, Chile. ; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA. ; School of Medicine, Imperial College London, South Kensington Campus, London SW7 2AZ, UK. ; Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA. ; Department of Neurosurgery, Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India. ; Department of Internal Medicine Armed Forces Medical College, Pune 411040, India. ; 1] Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India [2] Human Brain Tissue Repository, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore 560029, India. ; Department of Chemical and Biomolecular Engineering and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong. ; Department of Neurology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India. ; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21224, USA. ; 1] The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA [2] Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA. ; 1] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA [2] Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA. ; 1] Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA [2] Departments of Immunology and Urology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA. ; The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA. ; 1] Department of Obstetrics and Gynecology, Johns Hopkins University School of Medicine Baltimore, Maryland 21205, USA [2] Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA. ; 1] The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA [2] Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA [3] Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA. ; 1] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA [2] Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA [3] Institute of Bioinformatics, International Tech Park, Bangalore 560066, India [4] Adrienne Helis Malvin Medical Research Foundation, New Orleans, Louisiana 70130, USA [5] The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA [6] Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA [7] Diana Helis Henry Medical Research Foundation, New Orleans, Louisiana 70130, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24870542" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Cells, Cultured ; Databases, Protein ; Fetus/metabolism ; Fourier Analysis ; Gene Expression Profiling ; Genome, Human/genetics ; Hematopoietic Stem Cells/cytology/metabolism ; Humans ; Internet ; Mass Spectrometry ; Molecular Sequence Annotation ; Open Reading Frames/genetics ; Organ Specificity ; Protein Biosynthesis ; Protein Isoforms/analysis/genetics/metabolism ; Protein Sorting Signals ; Protein Transport ; Proteome/analysis/chemistry/genetics/*metabolism ; *Proteomics ; Pseudogenes/genetics ; RNA, Untranslated/genetics ; Reproducibility of Results ; Untranslated Regions/genetics
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  • 26
    Publication Date: 2014-11-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yarborough, Mark -- England -- Nature. 2014 Nov 20;515(7527):313. doi: 10.1038/515313a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25409791" target="_blank"〉PubMed〈/a〉
    Keywords: Access to Information ; Bias (Epidemiology) ; *Communication ; Conflict of Interest ; *Public Opinion ; Quality Control ; Reproducibility of Results ; Research Design ; *Research Personnel/ethics/standards ; Science/*standards ; *Trust
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  • 27
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    Nature Publishing Group (NPG)
    Publication Date: 2014-04-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Callaway, Ewen -- England -- Nature. 2014 Apr 3;508(7494):22. doi: 10.1038/508022a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24695296" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Aging/blood/genetics ; Basic Helix-Loop-Helix Transcription Factors/genetics ; Body Mass Index ; Case-Control Studies ; DNA Methylation ; *Epigenomics/standards/trends ; Gene-Environment Interaction ; Genome-Wide Association Study/standards ; Humans ; Infant, Newborn ; Obesity/genetics ; Repressor Proteins/genetics ; Reproducibility of Results
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 28
    Publication Date: 2014-04-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hsu, Angel -- Malik, Omar -- Johnson, Laura -- Esty, Daniel C -- England -- Nature. 2014 Apr 3;508(7494):33-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24707525" target="_blank"〉PubMed〈/a〉
    Keywords: Bias (Epidemiology) ; Conservation of Natural Resources/*methods/*statistics & numerical data ; Crowdsourcing ; Ecology/*manpower/*methods ; Environmental Monitoring/standards ; Environmental Policy/legislation & jurisprudence ; Federal Government ; *Goals ; Politics ; *Program Evaluation/standards ; Reproducibility of Results ; United Nations/legislation & jurisprudence
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  • 29
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    Nature Publishing Group (NPG)
    Publication Date: 2014-05-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abbott, Alison -- England -- Nature. 2014 May 1;509(7498):15-6. doi: 10.1038/509015a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24784193" target="_blank"〉PubMed〈/a〉
    Keywords: Adult Stem Cells/transplantation ; Clinical Trials, Phase III as Topic/economics/trends ; Heart Diseases/*therapy ; Heart Failure/therapy ; Humans ; Mesenchymal Stem Cell Transplantation ; Myocardial Infarction/therapy ; Randomized Controlled Trials as Topic/standards/*statistics & numerical data ; Reproducibility of Results ; *Stem Cell Transplantation
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  • 30
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    Nature Publishing Group (NPG)
    Publication Date: 2014-03-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marris, Emma -- England -- Nature. 2014 Mar 13;507(7491):158-60. doi: 10.1038/507158a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24622187" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Food Chain ; *Models, Biological ; Predatory Behavior/*physiology ; Reproducibility of Results ; Wolves/*physiology
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  • 31
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    Nature Publishing Group (NPG)
    Publication Date: 2014-10-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marshall, Barry -- Azad, Meghan -- England -- Nature. 2014 Oct 16;514(7522):S6-7. doi: 10.1038/514S6a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25317594" target="_blank"〉PubMed〈/a〉
    Keywords: Helicobacter pylori/genetics/isolation & purification/*pathogenicity ; History, 20th Century ; History, 21st Century ; Human Migration ; Humans ; Hygiene Hypothesis ; Job Satisfaction ; Male ; Nobel Prize ; Reproducibility of Results ; Stomach Ulcer/*etiology/history/*microbiology ; Stress, Psychological ; Vaccines, Edible
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  • 32
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    Nature Publishing Group (NPG)
    Publication Date: 2014-08-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2014 Aug 28;512(7515):347. doi: 10.1038/512347b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25164715" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Psychological ; *Attitude ; *Behavior ; Global Warming/prevention & control/*statistics & numerical data ; Human Activities ; Humans ; *Models, Psychological ; Reproducibility of Results
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  • 33
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    Nature Publishing Group (NPG)
    Publication Date: 2014-03-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cyranoski, David -- England -- Nature. 2014 Mar 20;507(7492):283. doi: 10.1038/507283a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24646974" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Cellular Reprogramming ; Dissertations, Academic as Topic/standards ; Embryonic Stem Cells/cytology ; Induced Pluripotent Stem Cells/*cytology ; Japan ; Mice ; Reproducibility of Results ; Research Personnel/*ethics ; Retraction of Publication as Topic ; Scientific Misconduct/*legislation & jurisprudence ; Stem Cell Transplantation
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  • 34
    Publication Date: 2014-01-31
    Description: Recent clinical trials showed that targeting of inhibitory receptors on T cells induces durable responses in a subset of cancer patients, despite advanced disease. However, the regulatory switches controlling T-cell function in immunosuppressive tumours are not well understood. Here we show that such inhibitory mechanisms can be systematically discovered in the tumour microenvironment. We devised an in vivo pooled short hairpin RNA (shRNA) screen in which shRNAs targeting negative regulators became highly enriched in murine tumours by releasing a block on T-cell proliferation upon tumour antigen recognition. Such shRNAs were identified by deep sequencing of the shRNA cassette from T cells infiltrating tumour or control tissues. One of the target genes was Ppp2r2d, a regulatory subunit of the PP2A phosphatase family. In tumours, Ppp2r2d knockdown inhibited T-cell apoptosis and enhanced T-cell proliferation as well as cytokine production. Key regulators of immune function can therefore be discovered in relevant tissue microenvironments.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4052214/" 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/PMC4052214/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Penghui -- Shaffer, Donald R -- Alvarez Arias, Diana A -- Nakazaki, Yukoh -- Pos, Wouter -- Torres, Alexis J -- Cremasco, Viviana -- Dougan, Stephanie K -- Cowley, Glenn S -- Elpek, Kutlu -- Brogdon, Jennifer -- Lamb, John -- Turley, Shannon J -- Ploegh, Hidde L -- Root, David E -- Love, J Christopher -- Dranoff, Glenn -- Hacohen, Nir -- Cantor, Harvey -- Wucherpfennig, Kai W -- 1R01CA173750/CA/NCI NIH HHS/ -- DP3 DK097681/DK/NIDDK NIH HHS/ -- P01 AI045757/AI/NIAID NIH HHS/ -- P30 CA014051/CA/NCI NIH HHS/ -- P30-CA14051/CA/NCI NIH HHS/ -- R01 CA173750/CA/NCI NIH HHS/ -- T32 AI007386/AI/NIAID NIH HHS/ -- T32 AI07386/AI/NIAID NIH HHS/ -- England -- Nature. 2014 Feb 6;506(7486):52-7. doi: 10.1038/nature12988. Epub 2014 Jan 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA [2]. ; 1] Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA [2] [3] Jounce Therapeutics, Cambridge, Massachusetts 02138, USA. ; Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA. ; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA. ; Whitehead Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA. ; Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. ; 1] Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA [2] Jounce Therapeutics, Cambridge, Massachusetts 02138, USA. ; Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA. ; Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24476824" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, Neoplasm/immunology ; Apoptosis/immunology ; CD4-Positive T-Lymphocytes/immunology ; CD8-Positive T-Lymphocytes/cytology/immunology/secretion ; Cell Proliferation ; Cytokines/immunology/secretion ; Female ; Gene Knockdown Techniques ; High-Throughput Nucleotide Sequencing ; *Immunotherapy/methods ; Lymphocytes, Tumor-Infiltrating/cytology/immunology/metabolism/secretion ; Melanoma, Experimental/immunology ; Mice ; Mice, Inbred C57BL ; *Molecular Targeted Therapy ; Protein Phosphatase 2/deficiency/genetics/*metabolism ; RNA, Small Interfering/genetics ; Reproducibility of Results ; Tumor Microenvironment/*immunology
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  • 35
    Publication Date: 2014-04-11
    Description: Targeted genome editing technologies are powerful tools for studying biology and disease, and have a broad range of research applications. In contrast to the rapid development of toolkits to manipulate individual genes, large-scale screening methods based on the complete loss of gene expression are only now beginning to be developed. Here we report the development of a focused CRISPR/Cas-based (clustered regularly interspaced short palindromic repeats/CRISPR-associated) lentiviral library in human cells and a method of gene identification based on functional screening and high-throughput sequencing analysis. Using knockout library screens, we successfully identified the host genes essential for the intoxication of cells by anthrax and diphtheria toxins, which were confirmed by functional validation. The broad application of this powerful genetic screening strategy will not only facilitate the rapid identification of genes important for bacterial toxicity but will also enable the discovery of genes that participate in other biological processes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Yuexin -- Zhu, Shiyou -- Cai, Changzu -- Yuan, Pengfei -- Li, Chunmei -- Huang, Yanyi -- Wei, Wensheng -- England -- Nature. 2014 May 22;509(7501):487-91. doi: 10.1038/nature13166. Epub 2014 Apr 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China [2]. ; State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China. ; Biodynamic Optical Imaging Centre (BIOPIC), College of Engineering, Peking University, Beijing 100871, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24717434" target="_blank"〉PubMed〈/a〉
    Keywords: Antigens, Bacterial/pharmacology ; Bacterial Toxins/pharmacology ; CRISPR-Associated Proteins/*genetics ; Cell Line ; Cells/drug effects/*metabolism ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; Diphtheria Toxin/pharmacology ; *Gene Library ; Genomics/*methods ; High-Throughput Screening Assays/*methods ; Humans ; INDEL Mutation/genetics ; Lentivirus/genetics ; Organic Cation Transporter 1/genetics ; RNA, Guide/genetics ; Reproducibility of Results
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  • 36
    Publication Date: 2014-11-05
    Description: Whole exome sequencing has proven to be a powerful tool for understanding the genetic architecture of human disease. Here we apply it to more than 2,500 simplex families, each having a child with an autistic spectrum disorder. By comparing affected to unaffected siblings, we show that 13% of de novo missense mutations and 43% of de novo likely gene-disrupting (LGD) mutations contribute to 12% and 9% of diagnoses, respectively. Including copy number variants, coding de novo mutations contribute to about 30% of all simplex and 45% of female diagnoses. Almost all LGD mutations occur opposite wild-type alleles. LGD targets in affected females significantly overlap the targets in males of lower intelligence quotient (IQ), but neither overlaps significantly with targets in males of higher IQ. We estimate that LGD mutation in about 400 genes can contribute to the joint class of affected females and males of lower IQ, with an overlapping and similar number of genes vulnerable to contributory missense mutation. LGD targets in the joint class overlap with published targets for intellectual disability and schizophrenia, and are enriched for chromatin modifiers, FMRP-associated genes and embryonically expressed genes. Most of the significance for the latter comes from affected females.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313871/" 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/PMC4313871/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Iossifov, Ivan -- O'Roak, Brian J -- Sanders, Stephan J -- Ronemus, Michael -- Krumm, Niklas -- Levy, Dan -- Stessman, Holly A -- Witherspoon, Kali T -- Vives, Laura -- Patterson, Karynne E -- Smith, Joshua D -- Paeper, Bryan -- Nickerson, Deborah A -- Dea, Jeanselle -- Dong, Shan -- Gonzalez, Luis E -- Mandell, Jeffrey D -- Mane, Shrikant M -- Murtha, Michael T -- Sullivan, Catherine A -- Walker, Michael F -- Waqar, Zainulabedin -- Wei, Liping -- Willsey, A Jeremy -- Yamrom, Boris -- Lee, Yoon-ha -- Grabowska, Ewa -- Dalkic, Ertugrul -- Wang, Zihua -- Marks, Steven -- Andrews, Peter -- Leotta, Anthony -- Kendall, Jude -- Hakker, Inessa -- Rosenbaum, Julie -- Ma, Beicong -- Rodgers, Linda -- Troge, Jennifer -- Narzisi, Giuseppe -- Yoon, Seungtai -- Schatz, Michael C -- Ye, Kenny -- McCombie, W Richard -- Shendure, Jay -- Eichler, Evan E -- State, Matthew W -- Wigler, Michael -- P30 CA016359/CA/NCI NIH HHS/ -- T32 GM007266/GM/NIGMS NIH HHS/ -- U54 HD083091/HD/NICHD NIH HHS/ -- UL1 TR000142/TR/NCATS NIH HHS/ -- Canadian Institutes of Health Research/Canada -- Howard Hughes Medical Institute/ -- England -- Nature. 2014 Nov 13;515(7526):216-21. doi: 10.1038/nature13908. Epub 2014 Oct 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA. ; 1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA [2] Molecular &Medical Genetics, Oregon Health &Science University, Portland, Oregon 97208, USA. ; 1] Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, USA [2] Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA. ; Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA. ; Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, USA. ; 1] Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA [2] Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China. ; Child Study Center, Yale University School of Medicine, New Haven, Connecticut 06520, USA. ; Yale Center for Genomic Analysis, Yale University School of Medicine, New Haven, Connecticut 06520, USA. ; 1] Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China [2] National Institute of Biological Sciences, Beijing 102206, China. ; 1] Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA [2] New York Genome Center, New York, New York 10013, USA. ; 1] Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA [2] Department of Medical Biology, Bulent Ecevit University School of Medicine, 67600 Zonguldak, Turkey. ; Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York 10461, USA. ; 1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA [2] Howard Hughes Medical Institute, Seattle, Washington 98195, USA. ; 1] Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, USA [2] Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA [3] Child Study Center, Yale University School of Medicine, New Haven, Connecticut 06520, USA [4] Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25363768" target="_blank"〉PubMed〈/a〉
    Keywords: Child ; Child Development Disorders, Pervasive/*genetics ; Cluster Analysis ; Exome/genetics ; Female ; Genes ; Genetic Predisposition to Disease/*genetics ; Humans ; Intelligence Tests ; Male ; Mutation/*genetics ; Open Reading Frames/*genetics ; Reproducibility of Results
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  • 37
    Publication Date: 2014-04-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McCullough, Michael E -- Kelly, David L -- England -- Nature. 2014 Apr 17;508(7496):319. doi: 10.1038/508319c.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Miami, Coral Gables, Florida, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24740058" target="_blank"〉PubMed〈/a〉
    Keywords: Publishing/standards ; Reproducibility of Results ; Research/economics/*standards ; *Research Design ; Research Personnel/standards
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  • 38
    facet.materialart.
    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2014-05-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2014 May 22;509(7501):399.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24860878" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Specimen Banks ; Disease ; Disease Models, Animal ; Drug Discovery/methods ; Genome/*genetics ; Mice/*genetics ; Mice, Knockout/*genetics ; Mice, Mutant Strains ; *Phenotype ; Reproducibility of Results
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  • 39
    Publication Date: 2014-08-01
    Description: Liver cirrhosis occurs as a consequence of many chronic liver diseases that are prevalent worldwide. Here we characterize the gut microbiome in liver cirrhosis by comparing 98 patients and 83 healthy control individuals. We build a reference gene set for the cohort containing 2.69 million genes, 36.1% of which are novel. Quantitative metagenomics reveals 75,245 genes that differ in abundance between the patients and healthy individuals (false discovery rate 〈 0.0001) and can be grouped into 66 clusters representing cognate bacterial species; 28 are enriched in patients and 38 in control individuals. Most (54%) of the patient-enriched, taxonomically assigned species are of buccal origin, suggesting an invasion of the gut from the mouth in liver cirrhosis. Biomarkers specific to liver cirrhosis at gene and function levels are revealed by a comparison with those for type 2 diabetes and inflammatory bowel disease. On the basis of only 15 biomarkers, a highly accurate patient discrimination index is created and validated on an independent cohort. Thus microbiota-targeted biomarkers may be a powerful tool for diagnosis of different diseases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Qin, Nan -- Yang, Fengling -- Li, Ang -- Prifti, Edi -- Chen, Yanfei -- Shao, Li -- Guo, Jing -- Le Chatelier, Emmanuelle -- Yao, Jian -- Wu, Lingjiao -- Zhou, Jiawei -- Ni, Shujun -- Liu, Lin -- Pons, Nicolas -- Batto, Jean Michel -- Kennedy, Sean P -- Leonard, Pierre -- Yuan, Chunhui -- Ding, Wenchao -- Chen, Yuanting -- Hu, Xinjun -- Zheng, Beiwen -- Qian, Guirong -- Xu, Wei -- Ehrlich, S Dusko -- Zheng, Shusen -- Li, Lanjuan -- England -- Nature. 2014 Sep 4;513(7516):59-64. doi: 10.1038/nature13568. Epub 2014 Jul 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China [3]. ; 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2]. ; 1] Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France [2]. ; State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China. ; Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France. ; 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China. ; 1] Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France [2] King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London Bridge, London SE1 9RT, UK. ; 1] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China [2] Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University, 310003 Hangzhou, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25079328" target="_blank"〉PubMed〈/a〉
    Keywords: Case-Control Studies ; Chronic Disease ; Diabetes Mellitus, Type 2/microbiology ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Genetic Markers/genetics ; Health ; Humans ; Inflammatory Bowel Diseases/microbiology ; Liver Cirrhosis/*diagnosis/*microbiology ; *Metagenomics ; Microbiota/*genetics/*physiology ; Mouth/microbiology ; Phylogeny ; Reproducibility of Results
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  • 40
    Publication Date: 2014-05-09
    Description: The motor cortex is capable of reliably driving complex movements yet exhibits considerable plasticity during motor learning. These observations suggest that the fundamental relationship between motor cortex activity and movement may not be fixed but is instead shaped by learning; however, to what extent and how motor learning shapes this relationship are not fully understood. Here we addressed this issue by using in vivo two-photon calcium imaging to monitor the activity of the same population of hundreds of layer 2/3 neurons while mice learned a forelimb lever-press task over two weeks. Excitatory and inhibitory neurons were identified by transgenic labelling. Inhibitory neuron activity was relatively stable and balanced local excitatory neuron activity on a movement-by-movement basis, whereas excitatory neuron activity showed higher dynamism during the initial phase of learning. The dynamics of excitatory neurons during the initial phase involved the expansion of the movement-related population which explored various activity patterns even during similar movements. This was followed by a refinement into a smaller population exhibiting reproducible spatiotemporal sequences of activity. This pattern of activity associated with the learned movement was unique to expert animals and not observed during similar movements made during the naive phase, and the relationship between neuronal activity and individual movements became more consistent with learning. These changes in population activity coincided with a transient increase in dendritic spine turnover in these neurons. Our results indicate that a novel and reproducible activity-movement relationship develops as a result of motor learning, and we speculate that synaptic plasticity within the motor cortex underlies the emergence of reproducible spatiotemporal activity patterns for learned movements. These results underscore the profound influence of learning on the way that the cortex produces movements.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Peters, Andrew J -- Chen, Simon X -- Komiyama, Takaki -- AG000216/AG/NIA NIH HHS/ -- England -- Nature. 2014 Jun 12;510(7504):263-7. doi: 10.1038/nature13235. Epub 2014 May 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Neurobiology Section, Center for Neural Circuits and Behavior, and Department of Neurosciences, University of California, San Diego, La Jolla, California 92093, USA. ; 1] Neurobiology Section, Center for Neural Circuits and Behavior, and Department of Neurosciences, University of California, San Diego, La Jolla, California 92093, USA [2] JST, PRESTO, University of California, San Diego, La Jolla, California 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24805237" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcium/metabolism ; Dendritic Spines/physiology ; Female ; Forelimb/physiology ; Learning/*physiology ; Male ; Mice ; Models, Neurological ; Motor Cortex/*physiology ; Motor Skills/*physiology ; Neural Inhibition ; Neuronal Plasticity/physiology ; Reproducibility of Results ; *Spatio-Temporal Analysis
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  • 41
    Publication Date: 2014-06-05
    Description: Intracranial germ cell tumours (IGCTs) are a group of rare heterogeneous brain tumours that are clinically and histologically similar to the more common gonadal GCTs. IGCTs show great variation in their geographical and gender distribution, histological composition and treatment outcomes. The incidence of IGCTs is historically five- to eightfold greater in Japan and other East Asian countries than in Western countries, with peak incidence near the time of puberty. About half of the tumours are located in the pineal region. The male-to-female incidence ratio is approximately 3-4:1 overall, but is even higher for tumours located in the pineal region. Owing to the scarcity of tumour specimens available for research, little is currently known about this rare disease. Here we report the analysis of 62 cases by next-generation sequencing, single nucleotide polymorphism array and expression array. We find the KIT/RAS signalling pathway frequently mutated in more than 50% of IGCTs, including novel recurrent somatic mutations in KIT, its downstream mediators KRAS and NRAS, and its negative regulator CBL. Novel somatic alterations in the AKT/mTOR pathway included copy number gains of the AKT1 locus at 14q32.33 in 19% of patients, with corresponding upregulation of AKT1 expression. We identified loss-of-function mutations in BCORL1, a transcriptional co-repressor and tumour suppressor. We report significant enrichment of novel and rare germline variants in JMJD1C, which codes for a histone demethylase and is a coactivator of the androgen receptor, among Japanese IGCT patients. This study establishes a molecular foundation for understanding the biology of IGCTs and suggests potentially promising therapeutic strategies focusing on the inhibition of KIT/RAS activation and the AKT1/mTOR pathway.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532372/" 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/PMC4532372/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Linghua -- Yamaguchi, Shigeru -- Burstein, Matthew D -- Terashima, Keita -- Chang, Kyle -- Ng, Ho-Keung -- Nakamura, Hideo -- He, Zongxiao -- Doddapaneni, Harshavardhan -- Lewis, Lora -- Wang, Mark -- Suzuki, Tomonari -- Nishikawa, Ryo -- Natsume, Atsushi -- Terasaka, Shunsuke -- Dauser, Robert -- Whitehead, William -- Adekunle, Adesina -- Sun, Jiayi -- Qiao, Yi -- Marth, Gabor -- Muzny, Donna M -- Gibbs, Richard A -- Leal, Suzanne M -- Wheeler, David A -- Lau, Ching C -- 5T15 LM07093-18/LM/NLM NIH HHS/ -- 5T15 LM07093-19/LM/NLM NIH HHS/ -- 5U54HG003273/HG/NHGRI NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- England -- Nature. 2014 Jul 10;511(7508):241-5. doi: 10.1038/nature13296. Epub 2014 Jun 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA. ; Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston, Texas 77030, USA. ; 1] Structural and Computational Biology and Molecular Biophysics Program, Baylor College of Medicine, Houston, Texas 77030, USA [2] Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA. ; 1] Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston, Texas 77030, USA [2] National Center for Child Health and Development, Tokyo, 157-8535, Japan. ; Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong. ; Department of Neurosurgery, Kumamoto University, Kumamoto, 860-0862, Japan. ; Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA. ; Department of Neurosurgery, Saitama Medical University, Saitama, 350-0495, Japan. ; Department of Neurosurgery, Nagoya University, Nagoya, 466-8550, Japan. ; Department of Neurosurgery, Hokkaido University, Hokkaido Prefecture, 060-0808, Japan. ; Department of Neurosurgery, Baylor College of Medicine, Houston, Texas 77030, USA. ; Department of Pathology, Baylor College of Medicine, Houston, Texas 77030, USA. ; Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA. ; Department of Biology, Boston College, Chestnut Hill, Maryland 02467, USA. ; 1] Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston, Texas 77030, USA [2] Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA [3] Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24896186" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Brain Neoplasms/*genetics/pathology ; Child ; Female ; Germ-Line Mutation/*genetics ; Humans ; Japan ; Male ; Mutation/*genetics ; Neoplasms, Germ Cell and Embryonal/*genetics/pathology ; Oncogene Protein v-akt/genetics ; Proto-Oncogene Proteins c-kit/genetics ; Reproducibility of Results ; Signal Transduction/genetics ; TOR Serine-Threonine Kinases/genetics ; Young Adult ; ras Proteins/genetics
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  • 42
    facet.materialart.
    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2014-06-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2014 Jun 5;510(7503):8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24910867" target="_blank"〉PubMed〈/a〉
    Keywords: *Awards and Prizes ; China ; Diffusion of Innovation ; Ireland ; *Mentors ; *Periodicals as Topic ; Reproducibility of Results ; Research/*standards ; Research Personnel/*ethics/*standards ; Truth Disclosure/ethics
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  • 43
    Publication Date: 2014-02-28
    Description: Epistasis is the phenomenon whereby one polymorphism's effect on a trait depends on other polymorphisms present in the genome. The extent to which epistasis influences complex traits and contributes to their variation is a fundamental question in evolution and human genetics. Although often demonstrated in artificial gene manipulation studies in model organisms, and some examples have been reported in other species, few examples exist for epistasis among natural polymorphisms in human traits. Its absence from empirical findings may simply be due to low incidence in the genetic control of complex traits, but an alternative view is that it has previously been too technically challenging to detect owing to statistical and computational issues. Here we show, using advanced computation and a gene expression study design, that many instances of epistasis are found between common single nucleotide polymorphisms (SNPs). In a cohort of 846 individuals with 7,339 gene expression levels measured in peripheral blood, we found 501 significant pairwise interactions between common SNPs influencing the expression of 238 genes (P 〈 2.91 x 10(-16)). Replication of these interactions in two independent data sets showed both concordance of direction of epistatic effects (P = 5.56 x 10(-31)) and enrichment of interaction P values, with 30 being significant at a conservative threshold of P 〈 9.98 x 10(-5). Forty-four of the genetic interactions are located within 5 megabases of regions of known physical chromosome interactions (P = 1.8 x 10(-10)). Epistatic networks of three SNPs or more influence the expression levels of 129 genes, whereby one cis-acting SNP is modulated by several trans-acting SNPs. For example, MBNL1 is influenced by an additive effect at rs13069559, which itself is masked by trans-SNPs on 14 different chromosomes, with nearly identical genotype-phenotype maps for each cis-trans interaction. This study presents the first evidence, to our knowledge, for many instances of segregating common polymorphisms interacting to influence human traits.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3984375/" 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/PMC3984375/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hemani, Gibran -- Shakhbazov, Konstantin -- Westra, Harm-Jan -- Esko, Tonu -- Henders, Anjali K -- McRae, Allan F -- Yang, Jian -- Gibson, Greg -- Martin, Nicholas G -- Metspalu, Andres -- Franke, Lude -- Montgomery, Grant W -- Visscher, Peter M -- Powell, Joseph E -- AA014041/AA/NIAAA NIH HHS/ -- AA07535/AA/NIAAA NIH HHS/ -- AA10248/AA/NIAAA NIH HHS/ -- AA13320/AA/NIAAA NIH HHS/ -- AA13321/AA/NIAAA NIH HHS/ -- AA13326/AA/NIAAA NIH HHS/ -- DA12854/DA/NIDA NIH HHS/ -- GM057091/GM/NIGMS NIH HHS/ -- GM099568/GM/NIGMS NIH HHS/ -- P01 GM099568/GM/NIGMS NIH HHS/ -- R01 GM075091/GM/NIGMS NIH HHS/ -- England -- Nature. 2014 Apr 10;508(7495):249-53. doi: 10.1038/nature13005. Epub 2014 Feb 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia [2] University of Queensland Diamantina Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4072, Australia. ; Department of Genetics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9700 RB Groningen, The Netherlands. ; 1] Estonian Genome Center, University of Tartu, Tartu 51010, Estonia [2] Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts 02142, USA [3] Divisions of Endocrinology, Children's Hospital, Boston, Massachusetts 02115, USA. ; Queensland Institute of Medical Research, Brisbane, Queensland 4006, Australia. ; Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia. ; School of Biology and Centre for Integrative Genomics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA. ; Estonian Genome Center, University of Tartu, Tartu 51010, Estonia. ; 1] Queensland Institute of Medical Research, Brisbane, Queensland 4006, Australia [2]. ; 1] Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia [2] University of Queensland Diamantina Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4072, Australia [3].〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24572353" target="_blank"〉PubMed〈/a〉
    Keywords: Cohort Studies ; Epistasis, Genetic/*genetics ; Europe/ethnology ; Female ; Gene Expression Profiling ; Gene Expression Regulation/*genetics ; Genetic Association Studies ; Humans ; Linkage Disequilibrium ; Male ; Pedigree ; Polymorphism, Single Nucleotide/genetics ; Quantitative Trait Loci ; Reproducibility of Results ; Transcription, Genetic/*genetics
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  • 44
    Publication Date: 2014-10-14
    Description: Alzheimer's disease is the most common form of dementia, characterized by two pathological hallmarks: amyloid-beta plaques and neurofibrillary tangles. The amyloid hypothesis of Alzheimer's disease posits that the excessive accumulation of amyloid-beta peptide leads to neurofibrillary tangles composed of aggregated hyperphosphorylated tau. However, to date, no single disease model has serially linked these two pathological events using human neuronal cells. Mouse models with familial Alzheimer's disease (FAD) mutations exhibit amyloid-beta-induced synaptic and memory deficits but they do not fully recapitulate other key pathological events of Alzheimer's disease, including distinct neurofibrillary tangle pathology. Human neurons derived from Alzheimer's disease patients have shown elevated levels of toxic amyloid-beta species and phosphorylated tau but did not demonstrate amyloid-beta plaques or neurofibrillary tangles. Here we report that FAD mutations in beta-amyloid precursor protein and presenilin 1 are able to induce robust extracellular deposition of amyloid-beta, including amyloid-beta plaques, in a human neural stem-cell-derived three-dimensional (3D) culture system. More importantly, the 3D-differentiated neuronal cells expressing FAD mutations exhibited high levels of detergent-resistant, silver-positive aggregates of phosphorylated tau in the soma and neurites, as well as filamentous tau, as detected by immunoelectron microscopy. Inhibition of amyloid-beta generation with beta- or gamma-secretase inhibitors not only decreased amyloid-beta pathology, but also attenuated tauopathy. We also found that glycogen synthase kinase 3 (GSK3) regulated amyloid-beta-mediated tau phosphorylation. We have successfully recapitulated amyloid-beta and tau pathology in a single 3D human neural cell culture system. Our unique strategy for recapitulating Alzheimer's disease pathology in a 3D neural cell culture model should also serve to facilitate the development of more precise human neural cell models of other neurodegenerative disorders.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4366007/" 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/PMC4366007/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Choi, Se Hoon -- Kim, Young Hye -- Hebisch, Matthias -- Sliwinski, Christopher -- Lee, Seungkyu -- D'Avanzo, Carla -- Chen, Hechao -- Hooli, Basavaraj -- Asselin, Caroline -- Muffat, Julien -- Klee, Justin B -- Zhang, Can -- Wainger, Brian J -- Peitz, Michael -- Kovacs, Dora M -- Woolf, Clifford J -- Wagner, Steven L -- Tanzi, Rudolph E -- Kim, Doo Yeon -- 5P01AG15379/AG/NIA NIH HHS/ -- 5R37MH060009/MH/NIMH NIH HHS/ -- P01 AG004953/AG/NIA NIH HHS/ -- P01 AG015379/AG/NIA NIH HHS/ -- P30 HD018655/HD/NICHD NIH HHS/ -- P30 NS045776/NS/NINDS NIH HHS/ -- P50 AG005134/AG/NIA NIH HHS/ -- R01 AG014713/AG/NIA NIH HHS/ -- R01 NS045860/NS/NINDS NIH HHS/ -- R21 AG031483/AG/NIA NIH HHS/ -- RF1 AG048080/AG/NIA NIH HHS/ -- England -- Nature. 2014 Nov 13;515(7526):274-8. doi: 10.1038/nature13800. Epub 2014 Oct 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA [2]. ; 1] Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA [2] Division of Mass Spectrometry Research, Korea Basic Science Institute, Cheongju-si, Chungbuk 363-883, South Korea [3]. ; 1] Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA [2] Institute of Reconstructive Neurobiology, Life and Brain Center, University of Bonn and Hertie Foundation, 53127 Bonn, Germany. ; Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA. ; FM Kirby Neurobiology Center, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, Massachusetts 02115, USA. ; The Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA. ; Institute of Reconstructive Neurobiology, Life and Brain Center, University of Bonn and Hertie Foundation, 53127 Bonn, Germany. ; Department of Neurosciences, University of California, San Diego, La Jolla, California 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25307057" target="_blank"〉PubMed〈/a〉
    Keywords: Alzheimer Disease/genetics/*metabolism/*pathology ; Amyloid beta-Peptides/chemistry/genetics/metabolism ; Cell Culture Techniques/*methods ; Cell Differentiation ; Drug Evaluation, Preclinical/methods ; Extracellular Space/metabolism ; Glycogen Synthase Kinase 3/metabolism ; Humans ; Microtubule-Associated Proteins/metabolism ; *Models, Biological ; Neural Stem Cells/*metabolism/pathology ; Neurites/metabolism ; Phosphorylation ; Presenilin-1/metabolism ; Protein Aggregation, Pathological ; Reproducibility of Results ; tau Proteins/chemistry/metabolism
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  • 45
    Publication Date: 2014-10-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Laland, Kevin -- Uller, Tobias -- Feldman, Marc -- Sterelny, Kim -- Muller, Gerd B -- Moczek, Armin -- Jablonka, Eva -- Odling-Smee, John -- Wray, Gregory A -- Hoekstra, Hopi E -- Futuyma, Douglas J -- Lenski, Richard E -- Mackay, Trudy F C -- Schluter, Dolph -- Strassmann, Joan E -- England -- Nature. 2014 Oct 9;514(7521):161-4. doi: 10.1038/514161a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25297418" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/genetics ; Animals ; *Biological Evolution ; *Developmental Biology/trends ; Ecosystem ; Epigenesis, Genetic ; *Gene-Environment Interaction ; Genetic Speciation ; *Models, Biological ; Models, Genetic ; Phenotype ; Reproducibility of Results ; Selection, Genetic
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  • 46
    Publication Date: 2014-09-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baell, Jonathan -- Walters, Michael A -- England -- Nature. 2014 Sep 25;513(7519):481-3. doi: 10.1038/513481a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25254460" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Artifacts ; Binding Sites ; Drug Discovery/methods/*standards ; Humans ; Pharmacology/methods/*standards ; Protein Binding ; Reproducibility of Results ; Research Personnel/standards
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  • 47
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    Nature Publishing Group (NPG)
    Publication Date: 2014-11-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2014 Nov 20;515(7527):312. doi: 10.1038/515312a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25409790" target="_blank"〉PubMed〈/a〉
    Keywords: Datasets as Topic/*utilization ; *Editorial Policies ; Information Dissemination/*methods ; *Periodicals as Topic ; Reproducibility of Results
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  • 48
    Publication Date: 2014-08-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barrett, Paul M -- Munt, Martin C -- England -- Nature. 2014 Aug 7;512(7512):28. doi: 10.1038/512028a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Natural History Museum, London, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25100472" target="_blank"〉PubMed〈/a〉
    Keywords: *Access to Information ; Animals ; *Birds ; Germany ; *Paleontology ; *Private Sector ; Reproducibility of Results
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  • 49
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    Nature Publishing Group (NPG)
    Publication Date: 2014-05-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schiermeier, Quirin -- England -- Nature. 2014 May 15;509(7500):270-1. doi: 10.1038/509270a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24828170" target="_blank"〉PubMed〈/a〉
    Keywords: Atlantic Ocean ; Climate Change/statistics & numerical data ; Ecosystem ; Environmental Monitoring ; Human Activities ; Reproducibility of Results ; *Seawater/analysis ; *Temperature ; *Water Movements
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  • 50
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    Nature Publishing Group (NPG)
    Publication Date: 2014-04-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bernstein, Rachel -- England -- Nature. 2014 Apr 3;508(7494):139-40.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24712027" target="_blank"〉PubMed〈/a〉
    Keywords: Allergy and Immunology/education/manpower ; Humans ; Immunotherapy/economics/*trends ; Leukemia, B-Cell/immunology/therapy ; Lymphoma, B-Cell/immunology/therapy ; Neoplasms/drug therapy/genetics/*immunology/*therapy ; Precision Medicine/methods/trends ; Reproducibility of Results ; T-Lymphocytes/immunology ; *Translational Medical Research/manpower/trends
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  • 51
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    Nature Publishing Group (NPG)
    Publication Date: 2014-10-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2014 Oct 9;514(7521):139-40. doi: 10.1038/514139b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25297397" target="_blank"〉PubMed〈/a〉
    Keywords: Aluminum Oxide/standards ; Biological Science Disciplines ; *Information Dissemination ; *Knowledge ; Reproducibility of Results
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  • 52
    Publication Date: 2014-11-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schooler, Jonathan W -- England -- Nature. 2014 Nov 6;515(7525):9. doi: 10.1038/515009a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25373639" target="_blank"〉PubMed〈/a〉
    Keywords: Psychology/standards ; Publishing/standards ; Reproducibility of Results ; Research/*standards ; *Research Design ; Research Report/*standards
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  • 53
    Publication Date: 2014-12-24
    Description: The plant cell wall is an important factor for determining cell shape, function and response to the environment. Secondary cell walls, such as those found in xylem, are composed of cellulose, hemicelluloses and lignin and account for the bulk of plant biomass. The coordination between transcriptional regulation of synthesis for each polymer is complex and vital to cell function. A regulatory hierarchy of developmental switches has been proposed, although the full complement of regulators remains unknown. Here we present a protein-DNA network between Arabidopsis thaliana transcription factors and secondary cell wall metabolic genes with gene expression regulated by a series of feed-forward loops. This model allowed us to develop and validate new hypotheses about secondary wall gene regulation under abiotic stress. Distinct stresses are able to perturb targeted genes to potentially promote functional adaptation. These interactions will serve as a foundation for understanding the regulation of a complex, integral plant component.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333722/" 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/PMC4333722/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Taylor-Teeples, M -- Lin, L -- de Lucas, M -- Turco, G -- Toal, T W -- Gaudinier, A -- Young, N F -- Trabucco, G M -- Veling, M T -- Lamothe, R -- Handakumbura, P P -- Xiong, G -- Wang, C -- Corwin, J -- Tsoukalas, A -- Zhang, L -- Ware, D -- Pauly, M -- Kliebenstein, D J -- Dehesh, K -- Tagkopoulos, I -- Breton, G -- Pruneda-Paz, J L -- Ahnert, S E -- Kay, S A -- Hazen, S P -- Brady, S M -- R01 GM056006/GM/NIGMS NIH HHS/ -- R01 GM107311/GM/NIGMS NIH HHS/ -- R01GM056006/GM/NIGMS NIH HHS/ -- R01GM107311/GM/NIGMS NIH HHS/ -- R25 GM056765/GM/NIGMS NIH HHS/ -- RC2 GM092412/GM/NIGMS NIH HHS/ -- RC2GM092412/GM/NIGMS NIH HHS/ -- England -- Nature. 2015 Jan 29;517(7536):571-5. doi: 10.1038/nature14099. Epub 2014 Dec 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, California 95616, USA [2] Genome Center, University of California Davis, One Shields Avenue, Davis, California 95616, USA. ; Biology Department, University of Massachusetts, Amherst, Massachusetts 01003, USA. ; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720, USA. ; Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, California 95616, USA. ; Department of Plant Sciences, University of California Davis, One Shields Avenue, Davis, California 95616, USA. ; 1] Genome Center, University of California Davis, One Shields Avenue, Davis, California 95616, USA [2] Department of Computer Science, University of California Davis, One Shields Avenue, Davis, California 95616, USA. ; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA. ; 1] Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA [2] US Department of Agriculture, Agricultural Research Service, Ithaca, New York 14853, USA. ; Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA. ; Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25533953" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/*genetics/growth & development/*metabolism ; Arabidopsis Proteins/genetics/metabolism ; Cell Wall/*metabolism ; DNA, Plant/genetics/metabolism ; E2F Transcription Factors/metabolism ; Feedback ; Gene Expression Regulation, Developmental/genetics ; Gene Expression Regulation, Plant/*genetics ; Gene Regulatory Networks/*genetics ; Iron/deficiency ; Organ Specificity ; Promoter Regions, Genetic/genetics ; Reproducibility of Results ; Salinity ; Time Factors ; Transcription Factors/*metabolism ; Xylem/genetics/growth & development/metabolism
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  • 54
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    Nature Publishing Group (NPG)
    Publication Date: 2013-01-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2012 Dec 20;492(7429):311.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23281497" target="_blank"〉PubMed〈/a〉
    Keywords: 2-Pyridinylmethylsulfinylbenzimidazoles ; Clinical Trials as Topic/statistics & numerical data ; Drug Approval/legislation & jurisprudence ; Drug Industry/economics/ethics/*legislation & jurisprudence ; Drug Prescriptions/standards ; *Freedom ; Humans ; Marketing/*ethics/*legislation & jurisprudence ; Off-Label Use/*ethics/*legislation & jurisprudence ; Patient Advocacy/legislation & jurisprudence ; Reproducibility of Results ; Sodium Oxybate ; United States ; United States Food and Drug Administration/legislation & jurisprudence
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  • 55
    Publication Date: 2013-01-22
    Description: Interferon-induced proteins with tetratricopeptide repeats (IFITs) are innate immune effector molecules that are thought to confer antiviral defence through disruption of protein-protein interactions in the host translation-initiation machinery. However, it was recently discovered that IFITs can directly recognize viral RNA bearing a 5'-triphosphate group (PPP-RNA), which is a molecular signature that distinguishes it from host RNA. Here we report crystal structures of human IFIT5, its complex with PPP-RNAs, and an amino-terminal fragment of IFIT1. The structures reveal a new helical domain that houses a positively charged cavity designed to specifically engage only single-stranded PPP-RNA, thus distinguishing it from the canonical cytosolic sensor of double-stranded viral PPP-RNA, retinoic acid-inducible gene I (RIG-I, also known as DDX58). Mutational analysis, proteolysis and gel-shift assays reveal that PPP-RNA is bound in a non-sequence-specific manner and requires a 5'-overhang of approximately three nucleotides. Abrogation of PPP-RNA binding in IFIT1 and IFIT5 was found to cause a defect in the antiviral response by human embryonic kidney cells. These results demonstrate the mechanism by which IFIT proteins selectively recognize viral RNA, and lend insight into their downstream effector function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abbas, Yazan M -- Pichlmair, Andreas -- Gorna, Maria W -- Superti-Furga, Giulio -- Nagar, Bhushan -- MOP-82929/Canadian Institutes of Health Research/Canada -- England -- Nature. 2013 Feb 7;494(7435):60-4. doi: 10.1038/nature11783. Epub 2013 Jan 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Groupe de Recherche Axe sur la Structure des Proteines, McGill University, Montreal, Quebec H3G 0B1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23334420" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Binding Sites ; Carrier Proteins/*chemistry/*metabolism ; Humans ; Immunity, Innate/immunology ; Models, Molecular ; Neoplasm Proteins/*chemistry/*metabolism ; Phosphorylation ; Protein Conformation ; RNA, Viral/*chemistry/genetics/*metabolism ; Reproducibility of Results ; Substrate Specificity
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  • 56
    Publication Date: 2013-06-19
    Description: Major international projects are underway that are aimed at creating a comprehensive catalogue of all the genes responsible for the initiation and progression of cancer. These studies involve the sequencing of matched tumour-normal samples followed by mathematical analysis to identify those genes in which mutations occur more frequently than expected by random chance. Here we describe a fundamental problem with cancer genome studies: as the sample size increases, the list of putatively significant genes produced by current analytical methods burgeons into the hundreds. The list includes many implausible genes (such as those encoding olfactory receptors and the muscle protein titin), suggesting extensive false-positive findings that overshadow true driver events. We show that this problem stems largely from mutational heterogeneity and provide a novel analytical methodology, MutSigCV, for resolving the problem. We apply MutSigCV to exome sequences from 3,083 tumour-normal pairs and discover extraordinary variation in mutation frequency and spectrum within cancer types, which sheds light on mutational processes and disease aetiology, and in mutation frequency across the genome, which is strongly correlated with DNA replication timing and also with transcriptional activity. By incorporating mutational heterogeneity into the analyses, MutSigCV is able to eliminate most of the apparent artefactual findings and enable the identification of genes truly associated with cancer.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3919509/" 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/PMC3919509/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lawrence, Michael S -- Stojanov, Petar -- Polak, Paz -- Kryukov, Gregory V -- Cibulskis, Kristian -- Sivachenko, Andrey -- Carter, Scott L -- Stewart, Chip -- Mermel, Craig H -- Roberts, Steven A -- Kiezun, Adam -- Hammerman, Peter S -- McKenna, Aaron -- Drier, Yotam -- Zou, Lihua -- Ramos, Alex H -- Pugh, Trevor J -- Stransky, Nicolas -- Helman, Elena -- Kim, Jaegil -- Sougnez, Carrie -- Ambrogio, Lauren -- Nickerson, Elizabeth -- Shefler, Erica -- Cortes, Maria L -- Auclair, Daniel -- Saksena, Gordon -- Voet, Douglas -- Noble, Michael -- DiCara, Daniel -- Lin, Pei -- Lichtenstein, Lee -- Heiman, David I -- Fennell, Timothy -- Imielinski, Marcin -- Hernandez, Bryan -- Hodis, Eran -- Baca, Sylvan -- Dulak, Austin M -- Lohr, Jens -- Landau, Dan-Avi -- Wu, Catherine J -- Melendez-Zajgla, Jorge -- Hidalgo-Miranda, Alfredo -- Koren, Amnon -- McCarroll, Steven A -- Mora, Jaume -- Lee, Ryan S -- Crompton, Brian -- Onofrio, Robert -- Parkin, Melissa -- Winckler, Wendy -- Ardlie, Kristin -- Gabriel, Stacey B -- Roberts, Charles W M -- Biegel, Jaclyn A -- Stegmaier, Kimberly -- Bass, Adam J -- Garraway, Levi A -- Meyerson, Matthew -- Golub, Todd R -- Gordenin, Dmitry A -- Sunyaev, Shamil -- Lander, Eric S -- Getz, Gad -- ES065073/ES/NIEHS NIH HHS/ -- T32 CA009172/CA/NCI NIH HHS/ -- T32 CA009216/CA/NCI NIH HHS/ -- T32 GM007753/GM/NIGMS NIH HHS/ -- U24 CA143845/CA/NCI NIH HHS/ -- U54 HG003067/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- Intramural NIH HHS/ -- England -- Nature. 2013 Jul 11;499(7457):214-8. doi: 10.1038/nature12213. Epub 2013 Jun 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23770567" target="_blank"〉PubMed〈/a〉
    Keywords: Artifacts ; DNA Replication Timing ; Exome/genetics ; False Positive Reactions ; Gene Expression ; *Genetic Heterogeneity ; Genome, Human/genetics ; Humans ; Lung Neoplasms/genetics ; Mutation/*genetics ; Mutation Rate ; Neoplasms/classification/*genetics/pathology ; Neoplasms, Squamous Cell/genetics ; Oncogenes/*genetics ; Reproducibility of Results ; Sample Size
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  • 57
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    Nature Publishing Group (NPG)
    Publication Date: 2013-07-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abbott, Alison -- England -- Nature. 2013 Jul 25;499(7459):390. doi: 10.1038/499390a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23887410" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Separation ; *Cell Size ; Embryo, Mammalian/cytology ; Humans ; Mice ; Reproducibility of Results ; Stem Cell Transplantation ; Stem Cells/*cytology ; *Uncertainty
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  • 58
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    Nature Publishing Group (NPG)
    Publication Date: 2013-11-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Callaway, Ewen -- England -- Nature. 2013 Nov 7;503(7474):18-9. doi: 10.1038/503018a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24201261" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Archaeology/methods ; Collagen/analysis/genetics ; Elephants/*classification/metabolism ; Evolution, Molecular ; Fossils ; Humans ; Mass Spectrometry ; Phylogeny ; Proteomics/*methods ; Reproducibility of Results ; Sequence Analysis, DNA
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  • 59
    Publication Date: 2013-05-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abbott, Alison -- England -- Nature. 2013 May 2;497(7447):16. doi: 10.1038/497016a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23636371" target="_blank"〉PubMed〈/a〉
    Keywords: *Cues ; Humans ; *Intelligence Tests ; Psychology/standards ; Reproducibility of Results ; Scientific Misconduct ; Sociology/standards ; *Unconscious (Psychology)
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  • 60
    Publication Date: 2013-10-15
    Description: The mechanisms by which genetic variation affects transcription regulation and phenotypes at the nucleotide level are incompletely understood. Here we use natural genetic variation as an in vivo mutagenesis screen to assess the genome-wide effects of sequence variation on lineage-determining and signal-specific transcription factor binding, epigenomics and transcriptional outcomes in primary macrophages from different mouse strains. We find substantial genetic evidence to support the concept that lineage-determining transcription factors define epigenetic and transcriptomic states by selecting enhancer-like regions in the genome in a collaborative fashion and facilitating binding of signal-dependent factors. This hierarchical model of transcription factor function suggests that limited sets of genomic data for lineage-determining transcription factors and informative histone modifications can be used for the prioritization of disease-associated regulatory variants.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3994126/" 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/PMC3994126/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Heinz, S -- Romanoski, C E -- Benner, C -- Allison, K A -- Kaikkonen, M U -- Orozco, L D -- Glass, C K -- 5T32DK007494/DK/NIDDK NIH HHS/ -- CA17390/CA/NCI NIH HHS/ -- DK063491/DK/NIDDK NIH HHS/ -- DK091183/DK/NIDDK NIH HHS/ -- P01 DK074868/DK/NIDDK NIH HHS/ -- P30 CA023100/CA/NCI NIH HHS/ -- P30 DK063491/DK/NIDDK NIH HHS/ -- R01 CA173903/CA/NCI NIH HHS/ -- R01 DK091183/DK/NIDDK NIH HHS/ -- T32 AR059033/AR/NIAMS NIH HHS/ -- England -- Nature. 2013 Nov 28;503(7477):487-92. doi: 10.1038/nature12615. Epub 2013 Oct 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, Mail Code 0651, La Jolla, California 92093, USA [2].〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24121437" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs/genetics ; Animals ; Base Sequence ; Cell Lineage/genetics ; DNA-Binding Proteins/metabolism ; Enhancer Elements, Genetic/*genetics ; Gene Expression Regulation/*genetics ; Genetic Variation/*genetics ; Histones/chemistry/metabolism ; Macrophages/metabolism ; Male ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Models, Biological ; Mutation/genetics ; NF-kappa B/metabolism ; Protein Binding ; Reproducibility of Results ; Selection, Genetic/*genetics ; Transcription Factor RelA/metabolism ; Transcription Factors/*metabolism
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  • 61
    Publication Date: 2013-10-15
    Description: The design of G-protein-coupled receptor (GPCR) allosteric modulators, an active area of modern pharmaceutical research, has proved challenging because neither the binding modes nor the molecular mechanisms of such drugs are known. Here we determine binding sites, bound conformations and specific drug-receptor interactions for several allosteric modulators of the M2 muscarinic acetylcholine receptor (M2 receptor), a prototypical family A GPCR, using atomic-level simulations in which the modulators spontaneously associate with the receptor. Despite substantial structural diversity, all modulators form cation-pi interactions with clusters of aromatic residues in the receptor extracellular vestibule, approximately 15 A from the classical, 'orthosteric' ligand-binding site. We validate the observed modulator binding modes through radioligand binding experiments on receptor mutants designed, on the basis of our simulations, either to increase or to decrease modulator affinity. Simulations also revealed mechanisms that contribute to positive and negative allosteric modulation of classical ligand binding, including coupled conformational changes of the two binding sites and electrostatic interactions between ligands in these sites. These observations enabled the design of chemical modifications that substantially alter a modulator's allosteric effects. Our findings thus provide a structural basis for the rational design of allosteric modulators targeting muscarinic and possibly other GPCRs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dror, Ron O -- Green, Hillary F -- Valant, Celine -- Borhani, David W -- Valcourt, James R -- Pan, Albert C -- Arlow, Daniel H -- Canals, Meritxell -- Lane, J Robert -- Rahmani, Raphael -- Baell, Jonathan B -- Sexton, Patrick M -- Christopoulos, Arthur -- Shaw, David E -- England -- Nature. 2013 Nov 14;503(7475):295-9. doi: 10.1038/nature12595. Epub 2013 Oct 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] D. E. Shaw Research, 120 West 45th Street, 39th Floor, New York, New York 10036, USA [2].〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24121438" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation/physiology ; Animals ; Binding Sites ; CHO Cells ; Cricetulus ; *Drug Design ; Humans ; Models, Chemical ; Molecular Conformation ; Molecular Dynamics Simulation ; Mutation ; Protein Binding ; Receptors, G-Protein-Coupled/*antagonists & inhibitors/*chemistry/genetics ; Reproducibility of Results
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  • 62
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    Nature Publishing Group (NPG)
    Publication Date: 2013-02-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Butler, Declan -- England -- Nature. 2013 Feb 14;494(7436):155-6. doi: 10.1038/494155a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23407515" target="_blank"〉PubMed〈/a〉
    Keywords: Crowdsourcing ; Data Mining/*methods ; *Epidemiological Monitoring ; Humans ; Influenza A Virus, H3N2 Subtype/isolation & purification/pathogenicity ; Influenza, Human/*epidemiology/mortality/virology ; *Internet ; Reproducibility of Results ; Social Media ; United States/epidemiology
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  • 63
    Publication Date: 2013-11-12
    Description: Myocardial infarction, a leading cause of death in the Western world, usually occurs when the fibrous cap overlying an atherosclerotic plaque in a coronary artery ruptures. The resulting exposure of blood to the atherosclerotic material then triggers thrombus formation, which occludes the artery. The importance of genetic predisposition to coronary artery disease and myocardial infarction is best documented by the predictive value of a positive family history. Next-generation sequencing in families with several affected individuals has revolutionized mutation identification. Here we report the segregation of two private, heterozygous mutations in two functionally related genes, GUCY1A3 (p.Leu163Phefs*24) and CCT7 (p.Ser525Leu), in an extended myocardial infarction family. GUCY1A3 encodes the alpha1 subunit of soluble guanylyl cyclase (alpha1-sGC), and CCT7 encodes CCTeta, a member of the tailless complex polypeptide 1 ring complex, which, among other functions, stabilizes soluble guanylyl cyclase. After stimulation with nitric oxide, soluble guanylyl cyclase generates cGMP, which induces vasodilation and inhibits platelet activation. We demonstrate in vitro that mutations in both GUCY1A3 and CCT7 severely reduce alpha1-sGC as well as beta1-sGC protein content, and impair soluble guanylyl cyclase activity. Moreover, platelets from digenic mutation carriers contained less soluble guanylyl cyclase protein and consequently displayed reduced nitric-oxide-induced cGMP formation. Mice deficient in alpha1-sGC protein displayed accelerated thrombus formation in the microcirculation after local trauma. Starting with a severely affected family, we have identified a link between impaired soluble-guanylyl-cyclase-dependent nitric oxide signalling and myocardial infarction risk, possibly through accelerated thrombus formation. Reversing this defect may provide a new therapeutic target for reducing the risk of myocardial infarction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Erdmann, Jeanette -- Stark, Klaus -- Esslinger, Ulrike B -- Rumpf, Philipp Moritz -- Koesling, Doris -- de Wit, Cor -- Kaiser, Frank J -- Braunholz, Diana -- Medack, Anja -- Fischer, Marcus -- Zimmermann, Martina E -- Tennstedt, Stephanie -- Graf, Elisabeth -- Eck, Sebastian -- Aherrahrou, Zouhair -- Nahrstaedt, Janja -- Willenborg, Christina -- Bruse, Petra -- Braenne, Ingrid -- Nothen, Markus M -- Hofmann, Per -- Braund, Peter S -- Mergia, Evanthia -- Reinhard, Wibke -- Burgdorf, Christof -- Schreiber, Stefan -- Balmforth, Anthony J -- Hall, Alistair S -- Bertram, Lars -- Steinhagen-Thiessen, Elisabeth -- Li, Shu-Chen -- Marz, Winfried -- Reilly, Muredach -- Kathiresan, Sekar -- McPherson, Ruth -- Walter, Ulrich -- CARDIoGRAM -- Ott, Jurg -- Samani, Nilesh J -- Strom, Tim M -- Meitinger, Thomas -- Hengstenberg, Christian -- Schunkert, Heribert -- British Heart Foundation/United Kingdom -- England -- Nature. 2013 Dec 19;504(7480):432-6. doi: 10.1038/nature12722. Epub 2013 Nov 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Institut fur Integrative und Experimentelle Genomik, Universitat zu Lubeck, 23562 Lubeck, Germany [2] German Centre for Cardiovascular Research (DZHK), partner site Hamburg/Lubeck/Kiel, 23562 Lubeck, Germany [3]. ; 1] Klinik und Poliklinik fur Innere Medizin II, Universitatsklinikum Regensburg, 93053 Regensburg, Germany [2] Department of Genetic Epidemiology, University of Regensburg, 93053 Regensburg, Germany [3]. ; 1] Klinik und Poliklinik fur Innere Medizin II, Universitatsklinikum Regensburg, 93053 Regensburg, Germany [2] Institut National de la Sante et de la Recherche Medicale (INSERM), UMR-S937 Paris, France [3]. ; 1] Deutsches Herzzentrum Munchen and 1. Medizinische Klinik, Klinikum rechts der Isar, Technische Universitat Munchen, 80636 Munchen, Germany [2] German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80636 Munich, Germany [3]. ; Department of Pharmacology and Toxicology, Ruhr-University Bochum, 44801 Bochum, Germany. ; 1] German Centre for Cardiovascular Research (DZHK), partner site Hamburg/Lubeck/Kiel, 23562 Lubeck, Germany [2] Institut fur Physiologie, Universitat zu Lubeck, 23562 Lubeck, Germany. ; 1] German Centre for Cardiovascular Research (DZHK), partner site Hamburg/Lubeck/Kiel, 23562 Lubeck, Germany [2] Institut fur Humangenetik, Universitat zu Lubeck, 23562 Lubeck, Germany. ; Institut fur Humangenetik, Universitat zu Lubeck, 23562 Lubeck, Germany. ; Institut fur Integrative und Experimentelle Genomik, Universitat zu Lubeck, 23562 Lubeck, Germany. ; Klinik und Poliklinik fur Innere Medizin II, Universitatsklinikum Regensburg, 93053 Regensburg, Germany. ; 1] Institute of Human Genetics, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, 85764 Neuherberg, Germany [2] Institute of Human Genetics, Technische Universitat Munchen, 81675 Munchen, Germany. ; 1] Institut fur Integrative und Experimentelle Genomik, Universitat zu Lubeck, 23562 Lubeck, Germany [2] German Centre for Cardiovascular Research (DZHK), partner site Hamburg/Lubeck/Kiel, 23562 Lubeck, Germany. ; 1] Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany [2] Department of Genomics, Research Center Life & Brain, University of Bonn, 53127 Bonn, Germany. ; 1] Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany [2] Division of Medical Genetics, University Hospital Basel and Department of Biomedicine, University of Basel, 4003 Basel, Switzerland. ; 1] Department of Cardiovascular Sciences, University of Leicester, Leicester LE1 7RH, UK [2] Leicester National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester LE1 7RH, UK. ; 1] Deutsches Herzzentrum Munchen and 1. Medizinische Klinik, Klinikum rechts der Isar, Technische Universitat Munchen, 80636 Munchen, Germany [2] German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80636 Munich, Germany. ; Deutsches Herzzentrum Munchen and 1. Medizinische Klinik, Klinikum rechts der Isar, Technische Universitat Munchen, 80636 Munchen, Germany. ; Institute of Clinical Molecular Biology, Christian-Albrecht-Universitat, 24105 Kiel, Germany. ; Division of Cardiovascular and Diabetes Research, Multidisciplinary Cardiovascular Research Centre, Leeds Institute of Genetics, Health and Therapeutics, University of Leeds, Leeds LS2 9JT, UK. ; Division of Cardiovascular and Neuronal Remodelling, Multidisciplinary Cardiovascular Research Centre, Leeds Institute of Genetics, Health and Therapeutics, University of Leeds, Leeds LS2 9JT, UK. ; Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany. ; Charite Research Group on Geriatrics, Charite-Universitatsmedizin, 10117 Berlin, Germany. ; 1] Center for Lifespan Psychology, Max Planck Institute for Human Development, 14195 Berlin, Germany [2] Department of Psychology, TU Dresden, 01062 Dresden, Germany. ; 1] Synlab Academy and Business Development, synlab Services GmbH, 68165 Mannheim, Germany [2] Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, 8036 Graz, Austria [3] Medical Clinic V, Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany. ; The Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA. ; 1] Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital, Boston, Massachusetts 02215, USA [2] Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02215, USA [3] Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02215, USA. ; University of Ottawa, Heart Institute, Ottawa, Ontario K1Y 4W7, Canada. ; 1] Centrum fur Thrombose und Hamostase (CTH), Universitatsmedizin Mainz, 55131 Mainz, Germany [2] German Centre for Cardiovascular Research (DZHK), partner site RheinMain, 55131 Mainz, Germany. ; 1] Institute of Psychology, Chinese Academy of Sciences, Beijing 100864, China [2] Laboratory of Statistical Genetics, Rockefeller University, New York 10065, USA. ; 1] Deutsches Herzzentrum Munchen and 1. Medizinische Klinik, Klinikum rechts der Isar, Technische Universitat Munchen, 80636 Munchen, Germany [2] Institute of Human Genetics, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, 85764 Neuherberg, Germany [3] Institute of Human Genetics, Technische Universitat Munchen, 81675 Munchen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24213632" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chaperonin Containing TCP-1/genetics/metabolism ; Cyclic GMP/metabolism ; Disease Susceptibility/*metabolism ; Exome/genetics ; Female ; Genetic Predisposition to Disease ; Guanylate Cyclase/deficiency/genetics/metabolism ; HEK293 Cells ; Humans ; Male ; Mice ; Mutation/genetics ; Myocardial Infarction/genetics/*metabolism/physiopathology ; Nitric Oxide/*metabolism ; Pedigree ; Platelet Activation ; Receptors, Cytoplasmic and Nuclear/deficiency/genetics/metabolism ; Reproducibility of Results ; *Signal Transduction ; Solubility ; Thrombosis/metabolism ; Vasodilation
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  • 64
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    Nature Publishing Group (NPG)
    Publication Date: 2013-12-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2013 Dec 19;504(7480):331.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24358504" target="_blank"〉PubMed〈/a〉
    Keywords: Access to Information ; Bias (Epidemiology) ; Clinical Trials as Topic/adverse effects/*ethics/*legislation & jurisprudence ; Expert Testimony ; *Federal Government ; Humans ; Italy ; *Patient Advocacy ; Reproducibility of Results ; Stem Cell Transplantation/adverse effects/*ethics/*legislation & jurisprudence
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  • 65
    Publication Date: 2013-04-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Russell, Jonathan F -- England -- Nature. 2013 Apr 4;496(7443):7. doi: 10.1038/496007a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉jonathan.russell@ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23552910" target="_blank"〉PubMed〈/a〉
    Keywords: Biomedical Research/economics/manpower/*methods/*standards ; Publishing/economics/trends ; Reproducibility of Results ; Research Design/*standards ; Research Personnel/psychology ; Scientific Misconduct/ethics/statistics & numerical data ; Validation Studies as Topic
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  • 66
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    Nature Publishing Group (NPG)
    Publication Date: 2013-05-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yong, Ed -- England -- Nature. 2013 May 16;497(7449):297-9. doi: 10.1038/497297a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23676731" target="_blank"〉PubMed〈/a〉
    Keywords: Adolescent ; Child ; China ; Eugenics ; Genome, Human/genetics ; Genomics ; Great Britain ; Humans ; Intelligence/*genetics ; Intelligence Tests ; Learning Disorders/genetics ; Male ; Polymorphism, Single Nucleotide/genetics ; Reproducibility of Results ; Sample Size ; Sequence Analysis, DNA ; Uncertainty ; United States
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  • 67
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    Nature Publishing Group (NPG)
    Publication Date: 2013-07-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Van Noorden, Richard -- England -- Nature. 2013 Jul 4;499(7456):13-4. doi: 10.1038/499013a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23823771" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/statistics & numerical data ; *Biofuels/supply & distribution/utilization ; Environmental Policy/economics/*legislation & jurisprudence ; *European Union/economics ; *Policy Making ; Renewable Energy/*statistics & numerical data ; Reproducibility of Results
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  • 68
    Publication Date: 2013-03-15
    Description: Magnetic resonance is an exceptionally powerful and versatile measurement technique. The basic structure of a magnetic resonance experiment has remained largely unchanged for almost 50 years, being mainly restricted to the qualitative probing of only a limited set of the properties that can in principle be accessed by this technique. Here we introduce an approach to data acquisition, post-processing and visualization--which we term 'magnetic resonance fingerprinting' (MRF)--that permits the simultaneous non-invasive quantification of multiple important properties of a material or tissue. MRF thus provides an alternative way to quantitatively detect and analyse complex changes that can represent physical alterations of a substance or early indicators of disease. MRF can also be used to identify the presence of a specific target material or tissue, which will increase the sensitivity, specificity and speed of a magnetic resonance study, and potentially lead to new diagnostic testing methodologies. When paired with an appropriate pattern-recognition algorithm, MRF inherently suppresses measurement errors and can thus improve measurement accuracy.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3602925/" 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/PMC3602925/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ma, Dan -- Gulani, Vikas -- Seiberlich, Nicole -- Liu, Kecheng -- Sunshine, Jeffrey L -- Duerk, Jeffrey L -- Griswold, Mark A -- KL2 TR000440/TR/NCATS NIH HHS/ -- R01 HL094557/HL/NHLBI NIH HHS/ -- R01HL094557/HL/NHLBI NIH HHS/ -- England -- Nature. 2013 Mar 14;495(7440):187-92. doi: 10.1038/nature11971.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biomedical Engineering, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23486058" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Diagnostic Tests, Routine/*methods ; Humans ; Magnetic Resonance Spectroscopy/*methods ; Motion ; Pattern Recognition, Automated ; Phantoms, Imaging ; Reproducibility of Results ; Research Design ; Sensitivity and Specificity
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  • 69
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    Nature Publishing Group (NPG)
    Publication Date: 2013-05-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hughes, Virginia -- England -- Nature. 2013 May 23;497(7450):428-30. doi: 10.1038/497428a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23698426" target="_blank"〉PubMed〈/a〉
    Keywords: Age Factors ; Body Mass Index ; Cause of Death ; Confounding Factors (Epidemiology) ; Humans ; *Life Expectancy ; Longevity/physiology ; Meta-Analysis as Topic ; Overweight/*mortality ; Public Health/*statistics & numerical data ; Reproducibility of Results ; Sex Factors ; Smoking/epidemiology
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  • 70
    Publication Date: 2013-07-05
    Description: We have taken the first steps towards a complete reconstruction of the Mycobacterium tuberculosis regulatory network based on ChIP-Seq and combined this reconstruction with system-wide profiling of messenger RNAs, proteins, metabolites and lipids during hypoxia and re-aeration. Adaptations to hypoxia are thought to have a prominent role in M. tuberculosis pathogenesis. Using ChIP-Seq combined with expression data from the induction of the same factors, we have reconstructed a draft regulatory network based on 50 transcription factors. This network model revealed a direct interconnection between the hypoxic response, lipid catabolism, lipid anabolism and the production of cell wall lipids. As a validation of this model, in response to oxygen availability we observe substantial alterations in lipid content and changes in gene expression and metabolites in corresponding metabolic pathways. The regulatory network reveals transcription factors underlying these changes, allows us to computationally predict expression changes, and indicates that Rv0081 is a regulatory hub.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4087036/" 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/PMC4087036/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Galagan, James E -- Minch, Kyle -- Peterson, Matthew -- Lyubetskaya, Anna -- Azizi, Elham -- Sweet, Linsday -- Gomes, Antonio -- Rustad, Tige -- Dolganov, Gregory -- Glotova, Irina -- Abeel, Thomas -- Mahwinney, Chris -- Kennedy, Adam D -- Allard, Rene -- Brabant, William -- Krueger, Andrew -- Jaini, Suma -- Honda, Brent -- Yu, Wen-Han -- Hickey, Mark J -- Zucker, Jeremy -- Garay, Christopher -- Weiner, Brian -- Sisk, Peter -- Stolte, Christian -- Winkler, Jessica K -- Van de Peer, Yves -- Iazzetti, Paul -- Camacho, Diogo -- Dreyfuss, Jonathan -- Liu, Yang -- Dorhoi, Anca -- Mollenkopf, Hans-Joachim -- Drogaris, Paul -- Lamontagne, Julie -- Zhou, Yiyong -- Piquenot, Julie -- Park, Sang Tae -- Raman, Sahadevan -- Kaufmann, Stefan H E -- Mohney, Robert P -- Chelsky, Daniel -- Moody, D Branch -- Sherman, David R -- Schoolnik, Gary K -- HHSN272200800059C/AI/NIAID NIH HHS/ -- HHSN272200800059C/PHS HHS/ -- R01 AI 071155/AI/NIAID NIH HHS/ -- R01 AI071155/AI/NIAID NIH HHS/ -- U19 AI 076217/AI/NIAID NIH HHS/ -- U19 AI076217/AI/NIAID NIH HHS/ -- England -- Nature. 2013 Jul 11;499(7457):178-83. doi: 10.1038/nature12337. Epub 2013 Jul 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA. jgalag@bu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23823726" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Anoxia/*genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Binding Sites ; Chromatin Immunoprecipitation ; Gene Expression Profiling ; *Gene Regulatory Networks/genetics ; Genomics ; Lipid Metabolism/genetics ; Metabolic Networks and Pathways/*genetics ; Models, Biological ; Mycobacterium tuberculosis/drug effects/*genetics/*metabolism/physiology ; Oxygen/pharmacology ; Proteolysis ; RNA, Messenger/genetics/metabolism ; Reproducibility of Results ; Sequence Analysis, DNA ; Transcription Factors/genetics/metabolism ; Tuberculosis/metabolism/microbiology
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  • 71
    Publication Date: 2013-10-15
    Description: The biogenic amine transporters (BATs) regulate endogenous neurotransmitter concentrations and are targets for a broad range of therapeutic agents including selective serotonin reuptake inhibitors (SSRIs), serotonin-noradrenaline reuptake inhibitors (SNRIs) and tricyclic antidepressants (TCAs). Because eukaryotic BATs are recalcitrant to crystallographic analysis, our understanding of the mechanism of these inhibitors and antidepressants is limited. LeuT is a bacterial homologue of BATs and has proven to be a valuable paradigm for understanding relationships between their structure and function. However, because only approximately 25% of the amino acid sequence of LeuT is in common with that of BATs, and as LeuT is a promiscuous amino acid transporter, it does not recapitulate the pharmacological properties of BATs. Indeed, SSRIs and TCAs bind in the extracellular vestibule of LeuT and act as non-competitive inhibitors of transport. By contrast, multiple studies demonstrate that both TCAs and SSRIs are competitive inhibitors for eukaryotic BATs and bind to the primary binding pocket. Here we engineered LeuT to harbour human BAT-like pharmacology by mutating key residues around the primary binding pocket. The final LeuBAT mutant binds the SSRI sertraline with a binding constant of 18 nM and displays high-affinity binding to a range of SSRIs, SNRIs and a TCA. We determined 12 crystal structures of LeuBAT in complex with four classes of antidepressants. The chemically diverse inhibitors have a remarkably similar mode of binding in which they straddle transmembrane helix (TM) 3, wedge between TM3/TM8 and TM1/TM6, and lock the transporter in a sodium- and chloride-bound outward-facing open conformation. Together, these studies define common and simple principles for the action of SSRIs, SNRIs and TCAs on BATs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3904662/" 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/PMC3904662/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Hui -- Goehring, April -- Wang, Kevin H -- Penmatsa, Aravind -- Ressler, Ryan -- Gouaux, Eric -- R37 MH070039/MH/NIMH NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2013 Nov 7;503(7474):141-5. doi: 10.1038/nature12648. Epub 2013 Oct 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vollum Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24121440" target="_blank"〉PubMed〈/a〉
    Keywords: Antidepressive Agents, Second-Generation/metabolism/*pharmacology ; Antidepressive Agents, Tricyclic/metabolism/*pharmacology ; Bacterial Proteins/antagonists & inhibitors/chemistry/genetics/metabolism ; Binding, Competitive/drug effects ; Biogenic Amines/*metabolism ; Chlorides/metabolism ; Crystallography, X-Ray ; Humans ; Mazindol/metabolism/pharmacology ; Models, Molecular ; Mutation ; Norepinephrine/metabolism ; *Plasma Membrane Neurotransmitter Transport Proteins/antagonists & ; inhibitors/chemistry/genetics/metabolism ; Protein Conformation/drug effects ; Recombinant Fusion Proteins/*chemistry/genetics/metabolism ; Reproducibility of Results ; Serotonin Plasma Membrane Transport Proteins/*chemistry/genetics/*metabolism ; Serotonin Uptake Inhibitors/metabolism/*pharmacology ; Sertraline/metabolism/pharmacology ; Sodium/metabolism ; Structure-Activity Relationship
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  • 72
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    Nature Publishing Group (NPG)
    Publication Date: 2013-04-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, Vivien -- England -- Nature. 2013 Apr 11;496(7444):253-8. doi: 10.1038/496253a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23579682" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Aggregation/drug effects ; Cell Culture Techniques/instrumentation/*methods ; Cell Division/drug effects ; Cell Transdifferentiation/drug effects ; Coculture Techniques ; Collagen/chemistry ; Cryopreservation ; Culture Media/*chemistry/*pharmacology ; Drug Combinations ; Drug Evaluation, Preclinical/instrumentation/methods ; Embryoid Bodies/cytology/drug effects ; Humans ; Induced Pluripotent Stem Cells/cytology/drug effects ; Laminin/chemistry ; Magnetic Fields ; Neurons/cytology/drug effects ; Proteoglycans/chemistry ; Reproducibility of Results ; Serum/chemistry
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  • 73
    facet.materialart.
    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2013-07-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2013 Jul 11;499(7457):125-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23858536" target="_blank"〉PubMed〈/a〉
    Keywords: Germany ; *Guidelines as Topic ; Plagiarism ; Punishment ; Reproducibility of Results ; Research Support as Topic/*organization & administration ; *Scientific Misconduct/legislation & jurisprudence ; Universities ; *Whistleblowing/legislation & jurisprudence
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  • 74
    facet.materialart.
    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2013-11-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Watson, Traci -- England -- Nature. 2013 Nov 21;503(7476):322-3. doi: 10.1038/503322a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24256786" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Conservation of Natural Resources/*methods ; Dissent and Disputes ; Ecosystem ; *Lions/physiology ; Nigeria ; Population Density ; Reproducibility of Results
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  • 75
    Publication Date: 2013-11-29
    Description: Two large-scale pharmacogenomic studies were published recently in this journal. Genomic data are well correlated between studies; however, the measured drug response data are highly discordant. Although the source of inconsistencies remains uncertain, it has potential implications for using these outcome measures to assess gene-drug associations or select potential anticancer drugs on the basis of their reported results.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4237165/" 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/PMC4237165/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haibe-Kains, Benjamin -- El-Hachem, Nehme -- Birkbak, Nicolai Juul -- Jin, Andrew C -- Beck, Andrew H -- Aerts, Hugo J W L -- Quackenbush, John -- CA087969/CA/NCI NIH HHS/ -- P01 CA087969/CA/NCI NIH HHS/ -- U19 CA148065/CA/NCI NIH HHS/ -- U19 CA148065-01/CA/NCI NIH HHS/ -- England -- Nature. 2013 Dec 19;504(7480):389-93. doi: 10.1038/nature12831. Epub 2013 Nov 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Institut de Recherches Cliniques de Montreal, University of Montreal, Montreal, Quebec, Canada [2] Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada. ; Institut de Recherches Cliniques de Montreal, University of Montreal, Montreal, Quebec, Canada. ; Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark. ; Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02215, USA. ; 1] Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02215, USA [2]. ; 1] Department of Biostatistics and Computational Biology and Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Radiation Oncology & Radiology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA [3] Department of Radiation Oncology, Maastricht University, Maastricht 6200 MD, The Netherlands [4]. ; 1] Department of Biostatistics and Computational Biology and Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [3].〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24284626" target="_blank"〉PubMed〈/a〉
    Keywords: Antineoplastic Agents/*pharmacology ; Area Under Curve ; Cell Line ; Drug Resistance, Neoplasm/drug effects/genetics ; Gene Expression Profiling ; Genome, Human/genetics ; Humans ; Inhibitory Concentration 50 ; Neoplasms/drug therapy/genetics/pathology ; *Pharmacogenetics ; Reproducibility of Results
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  • 76
    Publication Date: 2013-11-29
    Description: Achieving the goal of malaria elimination will depend on targeting Plasmodium pathways essential across all life stages. Here we identify a lipid kinase, phosphatidylinositol-4-OH kinase (PI(4)K), as the target of imidazopyrazines, a new antimalarial compound class that inhibits the intracellular development of multiple Plasmodium species at each stage of infection in the vertebrate host. Imidazopyrazines demonstrate potent preventive, therapeutic, and transmission-blocking activity in rodent malaria models, are active against blood-stage field isolates of the major human pathogens P. falciparum and P. vivax, and inhibit liver-stage hypnozoites in the simian parasite P. cynomolgi. We show that imidazopyrazines exert their effect through inhibitory interaction with the ATP-binding pocket of PI(4)K, altering the intracellular distribution of phosphatidylinositol-4-phosphate. Collectively, our data define PI(4)K as a key Plasmodium vulnerability, opening up new avenues of target-based discovery to identify drugs with an ideal activity profile for the prevention, treatment and elimination of malaria.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3940870/" 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/PMC3940870/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McNamara, Case W -- Lee, Marcus C S -- Lim, Chek Shik -- Lim, Siau Hoi -- Roland, Jason -- Nagle, Advait -- Simon, Oliver -- Yeung, Bryan K S -- Chatterjee, Arnab K -- McCormack, Susan L -- Manary, Micah J -- Zeeman, Anne-Marie -- Dechering, Koen J -- Kumar, T R Santha -- Henrich, Philipp P -- Gagaring, Kerstin -- Ibanez, Maureen -- Kato, Nobutaka -- Kuhen, Kelli L -- Fischli, Christoph -- Rottmann, Matthias -- Plouffe, David M -- Bursulaya, Badry -- Meister, Stephan -- Rameh, Lucia -- Trappe, Joerg -- Haasen, Dorothea -- Timmerman, Martijn -- Sauerwein, Robert W -- Suwanarusk, Rossarin -- Russell, Bruce -- Renia, Laurent -- Nosten, Francois -- Tully, David C -- Kocken, Clemens H M -- Glynne, Richard J -- Bodenreider, Christophe -- Fidock, David A -- Diagana, Thierry T -- Winzeler, Elizabeth A -- 078285/Wellcome Trust/United Kingdom -- 089275/Wellcome Trust/United Kingdom -- 090534/Wellcome Trust/United Kingdom -- 096157/Wellcome Trust/United Kingdom -- R01 AI079709/AI/NIAID NIH HHS/ -- R01 AI085584/AI/NIAID NIH HHS/ -- R01 AI090141/AI/NIAID NIH HHS/ -- R01 AI103058/AI/NIAID NIH HHS/ -- R01079709/PHS HHS/ -- R01085584/PHS HHS/ -- R01AI090141/AI/NIAID NIH HHS/ -- WT078285/Wellcome Trust/United Kingdom -- WT096157/Wellcome Trust/United Kingdom -- England -- Nature. 2013 Dec 12;504(7479):248-53. doi: 10.1038/nature12782. Epub 2013 Nov 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA [2]. ; 1] Department of Microbiology & Immunology, Columbia University Medical Center, New York, New York 10032, USA [2]. ; Novartis Institutes for Tropical Disease, 138670 Singapore. ; Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA. ; Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA. ; Department of Parasitology, Biomedical Primate Research Centre, PO Box 3306, 2280 GH Rijswijk, The Netherlands. ; TropIQ Health Sciences, 6525 GA Nijmegen, The Netherlands. ; Department of Microbiology & Immunology, Columbia University Medical Center, New York, New York 10032, USA. ; Swiss Tropical and Public Health Institute, CH-4002 Basel, Switzerland. ; 1] Swiss Tropical and Public Health Institute, CH-4002 Basel, Switzerland [2] University of Basel, CH-4003 Basel, Switzerland. ; Department of Medicine, School of Medicine, Boston University, Boston, Massachusetts 02118, USA. ; Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland. ; 1] TropIQ Health Sciences, 6525 GA Nijmegen, The Netherlands [2] Department of Medical Microbiology, Radboud University, Nijmegen Medical CentrePO Box 9101, 6500 HB Nijmegen, The Netherlands. ; Laboratory of Malaria Immunobiology, Singapore Immunology Network, Agency for Science Technology and Research (A*STAR), Biopolis, 138648 Singapore. ; 1] Laboratory of Malaria Immunobiology, Singapore Immunology Network, Agency for Science Technology and Research (A*STAR), Biopolis, 138648 Singapore [2] Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, 117545 Singapore. ; 1] Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK [2] Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot 63110, Thailand. ; 1] Department of Microbiology & Immunology, Columbia University Medical Center, New York, New York 10032, USA [2] Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, New York 10032, USA. ; 1] Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA [2] Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24284631" target="_blank"〉PubMed〈/a〉
    Keywords: 1-Phosphatidylinositol 4-Kinase/*antagonists & ; inhibitors/chemistry/genetics/metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Binding Sites ; Cytokinesis/drug effects ; Drug Resistance/drug effects/genetics ; Fatty Acids/metabolism ; Female ; Hepatocytes/parasitology ; Humans ; Imidazoles/metabolism/pharmacology ; Life Cycle Stages/drug effects ; Macaca mulatta ; Malaria/*drug therapy/*parasitology ; Male ; Models, Biological ; Models, Molecular ; Phosphatidylinositol Phosphates/metabolism ; Plasmodium/classification/*drug effects/*enzymology/growth & development ; Pyrazoles/metabolism/pharmacology ; Quinoxalines/metabolism/pharmacology ; Reproducibility of Results ; Schizonts/cytology/drug effects ; rab GTP-Binding Proteins/genetics/metabolism
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  • 77
    Publication Date: 2013-12-18
    Description: The protozoan parasites Trypanosoma brucei spp. cause important human and livestock diseases in sub-Saharan Africa. In mammalian blood, two developmental forms of the parasite exist: proliferative 'slender' forms and arrested 'stumpy' forms that are responsible for transmission to tsetse flies. The slender to stumpy differentiation is a density-dependent response that resembles quorum sensing in microbial systems and is crucial for the parasite life cycle, ensuring both infection chronicity and disease transmission. This response is triggered by an elusive 'stumpy induction factor' (SIF) whose intracellular signalling pathway is also uncharacterized. Laboratory-adapted (monomorphic) trypanosome strains respond inefficiently to SIF but can generate forms with stumpy characteristics when exposed to cell-permeable cAMP and AMP analogues. Exploiting this, we have used a genome-wide RNA interference library screen to identify the signalling components driving stumpy formation. In separate screens, monomorphic parasites were exposed to 8-(4-chlorophenylthio)-cAMP (pCPT-cAMP) or 8-pCPT-2'-O-methyl-5'-AMP to select cells that were unresponsive to these signals and hence remained proliferative. Genome-wide Ion Torrent based RNAi target sequencing identified cohorts of genes implicated in each step of the signalling pathway, from purine metabolism, through signal transducers (kinases, phosphatases) to gene expression regulators. Genes at each step were independently validated in cells naturally capable of stumpy formation, confirming their role in density sensing in vivo. The putative RNA-binding protein, RBP7, was required for normal quorum sensing and promoted cell-cycle arrest and transmission competence when overexpressed. This study reveals that quorum sensing signalling in trypanosomes shares similarities to fundamental quiescence pathways in eukaryotic cells, its components providing targets for quorum-sensing interference-based therapeutics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3908871/" 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/PMC3908871/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mony, Binny M -- MacGregor, Paula -- Ivens, Alasdair -- Rojas, Federico -- Cowton, Andrew -- Young, Julie -- Horn, David -- Matthews, Keith -- 088293/Wellcome Trust/United Kingdom -- 088293MA/Wellcome Trust/United Kingdom -- 095831/Wellcome Trust/United Kingdom -- 095831MA/Wellcome Trust/United Kingdom -- 100320/Wellcome Trust/United Kingdom -- 100320/Z/12/Z/Wellcome Trust/United Kingdom -- BB/I004602/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- England -- Nature. 2014 Jan 30;505(7485):681-5. doi: 10.1038/nature12864. Epub 2013 Dec 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK [2]. ; Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK. ; Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24336212" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Differentiation ; Cyclic AMP/metabolism ; G1 Phase ; G1 Phase Cell Cycle Checkpoints ; Gene Expression Regulation ; Genome/*genetics ; Protein Kinases/genetics ; Quorum Sensing/*genetics ; RNA Interference ; RNA-Binding Proteins/genetics/metabolism ; Reproducibility of Results ; Signal Transduction/*genetics ; Trypanosoma brucei brucei/enzymology/*genetics/growth & development/*metabolism
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  • 78
    Publication Date: 2013-12-03
    Description: The increasing demands placed on natural resources for fuel and food production require that we explore the use of efficient, sustainable feedstocks such as brown macroalgae. The full potential of brown macroalgae as feedstocks for commercial-scale fuel ethanol production, however, requires extensive re-engineering of the alginate and mannitol catabolic pathways in the standard industrial microbe Saccharomyces cerevisiae. Here we present the discovery of an alginate monomer (4-deoxy-L-erythro-5-hexoseulose uronate, or DEHU) transporter from the alginolytic eukaryote Asteromyces cruciatus. The genomic integration and overexpression of the gene encoding this transporter, together with the necessary bacterial alginate and deregulated native mannitol catabolism genes, conferred the ability of an S. cerevisiae strain to efficiently metabolize DEHU and mannitol. When this platform was further adapted to grow on mannitol and DEHU under anaerobic conditions, it was capable of ethanol fermentation from mannitol and DEHU, achieving titres of 4.6% (v/v) (36.2 g l(-1)) and yields up to 83% of the maximum theoretical yield from consumed sugars. These results show that all major sugars in brown macroalgae can be used as feedstocks for biofuels and value-added renewable chemicals in a manner that is comparable to traditional arable-land-based feedstocks.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Enquist-Newman, Maria -- Faust, Ann Marie E -- Bravo, Daniel D -- Santos, Christine Nicole S -- Raisner, Ryan M -- Hanel, Arthur -- Sarvabhowman, Preethi -- Le, Chi -- Regitsky, Drew D -- Cooper, Susan R -- Peereboom, Lars -- Clark, Alana -- Martinez, Yessica -- Goldsmith, Joshua -- Cho, Min Y -- Donohoue, Paul D -- Luo, Lily -- Lamberson, Brigit -- Tamrakar, Pramila -- Kim, Edward J -- Villari, Jeffrey L -- Gill, Avinash -- Tripathi, Shital A -- Karamchedu, Padma -- Paredes, Carlos J -- Rajgarhia, Vineet -- Kotlar, Hans Kristian -- Bailey, Richard B -- Miller, Dennis J -- Ohler, Nicholas L -- Swimmer, Candace -- Yoshikuni, Yasuo -- England -- Nature. 2014 Jan 9;505(7482):239-43. doi: 10.1038/nature12771. Epub 2013 Dec 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA [2]. ; 1] Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA [2] Manus Biosynthesis Inc., 790 Memorial Drive, Suite 102, Cambridge, Massachusetts 02139 (C.N.S.S.); Calysta Energy, 1140 O'Brien Drive, Menlo Park, California 94025 (D.D.R.); Sutro Biopharma lnc., 310 Utah Avenue, Suite 150, South San Francisco, California 94080, USA (A.G.); Total New Energies USA, 5858 Horton Street, Emeryville, California 94560 (S.A.T.; V.R.). ; Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA. ; Department of Chemical Engineering and Materials Science, Michigan State University, 2527 Engineering Building, East Lansing, Michigan 48824-1226, USA. ; Statoil ASA, Statoil Research Centre, Arkitekt Ebbells vei 10, Rotvoll, 7005 Trondheim, Norway. ; 1] Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA [2] BALChile S.A., Badajoz 100, Oficina 1404, Las Condes, Santiago 7550000, Chile [3] BAL Biofuels S.A., Badajoz 100, Oficina 1404, Las Condes, Santiago 7550000, Chile.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24291791" target="_blank"〉PubMed〈/a〉
    Keywords: Alginates/metabolism ; Anaerobiosis ; Ascomycota/genetics/metabolism ; Biofuels/*supply & distribution ; Biotechnology ; *Carbohydrate Metabolism ; Carrier Proteins/genetics/metabolism ; Ethanol/*metabolism ; Evolution, Molecular ; Fermentation ; Genetic Complementation Test ; *Genetic Engineering ; Glucuronic Acid/metabolism ; Hexuronic Acids/metabolism ; Mannitol/metabolism ; Phaeophyta/genetics/*metabolism ; Quinic Acid/metabolism ; Reproducibility of Results ; Saccharomyces cerevisiae/genetics/*metabolism ; Seaweed/genetics/metabolism ; Uronic Acids/metabolism
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  • 79
    Publication Date: 2013-12-10
    Description: Bile acids are synthesized from cholesterol in hepatocytes and secreted through the biliary tract into the small intestine, where they aid in absorption of lipids and fat-soluble vitamins. Through a process known as enterohepatic recirculation, more than 90% of secreted bile acids are then retrieved from the intestine and returned to the liver for resecretion. In humans, there are two Na(+)-dependent bile acid transporters involved in enterohepatic recirculation, the Na(+)-taurocholate co-transporting polypeptide (NTCP; also known as SLC10A1) expressed in hepatocytes, and the apical sodium-dependent bile acid transporter (ASBT; also known as SLC10A2) expressed on enterocytes in the terminal ileum. In recent years, ASBT has attracted much interest as a potential drug target for treatment of hypercholesterolaemia, because inhibition of ASBT reduces reabsorption of bile acids, thus increasing bile acid synthesis and consequently cholesterol consumption. However, a lack of three-dimensional structures of bile acid transporters hampers our ability to understand the molecular mechanisms of substrate selectivity and transport, and to interpret the wealth of existing functional data. The crystal structure of an ASBT homologue from Neisseria meningitidis (ASBT(NM)) in detergent was reported recently, showing the protein in an inward-open conformation bound to two Na(+) and a taurocholic acid. However, the structural changes that bring bile acid and Na(+) across the membrane are difficult to infer from a single structure. To understand the structural changes associated with the coupled transport of Na(+) and bile acids, here we solved two structures of an ASBT homologue from Yersinia frederiksenii (ASBTYf) in a lipid environment, which reveal that a large rigid-body rotation of a substrate-binding domain gives the conserved 'crossover' region, where two discontinuous helices cross each other, alternating accessibility from either side of the cell membrane. This result has implications for the location and orientation of the bile acid during transport, as well as for the translocation pathway for Na(+).〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4142352/" 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/PMC4142352/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Xiaoming -- Levin, Elena J -- Pan, Yaping -- McCoy, Jason G -- Sharma, Ruchika -- Kloss, Brian -- Bruni, Renato -- Quick, Matthias -- Zhou, Ming -- R01 DK088057/DK/NIDDK NIH HHS/ -- R01 GM098878/GM/NIGMS NIH HHS/ -- R01DK088057/DK/NIDDK NIH HHS/ -- R01GM098878/GM/NIGMS NIH HHS/ -- U54 GM075026/GM/NIGMS NIH HHS/ -- U54 GM087519/GM/NIGMS NIH HHS/ -- U54 GM095315/GM/NIGMS NIH HHS/ -- U54GM087519/GM/NIGMS NIH HHS/ -- U54GM095315/GM/NIGMS NIH HHS/ -- England -- Nature. 2014 Jan 23;505(7484):569-73. doi: 10.1038/nature12811. Epub 2013 Dec 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA [2] Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA [3]. ; 1] Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA [2]. ; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA. ; Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA. ; New York Consortium on Membrane Protein Structure, New York, New York 10027, USA. ; 1] Department of Psychiatry and Center for Molecular Recognition, Columbia University, New York, New York 10032, USA [2] New York State Psychiatric Institute, Division of Molecular Therapeutics, New York, New York 10032, USA. ; 1] Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA [2] Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA [3] Ion Channel Research and Drug Development Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24317697" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/*metabolism ; Bile Acids and Salts/metabolism ; Biological Transport ; Carrier Proteins/*chemistry/*metabolism ; Cell Membrane/metabolism ; Crystallography, X-Ray ; Membrane Glycoproteins/*chemistry/*metabolism ; Models, Molecular ; Protein Conformation ; Reproducibility of Results ; Rotation ; Sodium/metabolism ; Structure-Activity Relationship ; Yersinia/*chemistry
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  • 80
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    Nature Publishing Group (NPG)
    Publication Date: 2013-03-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2013 Mar 14;495(7440):141-2.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23495393" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Dissent and Disputes ; Genome, Human/*genetics ; Genomics ; Humans ; *Models, Genetic ; Molecular Sequence Annotation/*standards ; Reproducibility of Results ; Semantics ; *Terminology as Topic
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  • 81
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    Nature Publishing Group (NPG)
    Publication Date: 2013-04-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2013 Apr 18;496(7445):269.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23607131" target="_blank"〉PubMed〈/a〉
    Keywords: *Budgets ; Decision Making ; Evidence-Based Medicine ; *Federal Government ; *Policy Making ; Reproducibility of Results ; United States
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  • 82
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    Nature Publishing Group (NPG)
    Publication Date: 2013-04-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2013 Apr 11;496(7444):137.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23586093" target="_blank"〉PubMed〈/a〉
    Keywords: Chromosomes, Human, Y/genetics ; DNA, Mitochondrial/genetics ; Female ; *Freedom ; Genetics, Medical ; Great Britain ; Humans ; Male ; Phylogeny ; Reproducibility of Results ; *Speech
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  • 83
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    Nature Publishing Group (NPG)
    Publication Date: 2013-01-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2013 Jan 10;493(7431):133-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23310980" target="_blank"〉PubMed〈/a〉
    Keywords: Europe ; Food Labeling/*legislation & jurisprudence/*standards ; Humans ; Nutritional Sciences ; Probiotics/pharmacology ; Reproducibility of Results
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  • 84
    Publication Date: 2013-04-12
    Description: Inhibition of kynurenine 3-monooxygenase (KMO), an enzyme in the eukaryotic tryptophan catabolic pathway (that is, kynurenine pathway), leads to amelioration of Huntington's-disease-relevant phenotypes in yeast, fruitfly and mouse models, as well as in a mouse model of Alzheimer's disease. KMO is a flavin adenine dinucleotide (FAD)-dependent monooxygenase and is located in the outer mitochondrial membrane where it converts l-kynurenine to 3-hydroxykynurenine. Perturbations in the levels of kynurenine pathway metabolites have been linked to the pathogenesis of a spectrum of brain disorders, as well as cancer and several peripheral inflammatory conditions. Despite the importance of KMO as a target for neurodegenerative disease, the molecular basis of KMO inhibition by available lead compounds has remained unknown. Here we report the first crystal structure of Saccharomyces cerevisiae KMO, in the free form and in complex with the tight-binding inhibitor UPF 648. UPF 648 binds close to the FAD cofactor and perturbs the local active-site structure, preventing productive binding of the substrate l-kynurenine. Functional assays and targeted mutagenesis reveal that the active-site architecture and UPF 648 binding are essentially identical in human KMO, validating the yeast KMO-UPF 648 structure as a template for structure-based drug design. This will inform the search for new KMO inhibitors that are able to cross the blood-brain barrier in targeted therapies against neurodegenerative diseases such as Huntington's, Alzheimer's and Parkinson's diseases.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3736096/" 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/PMC3736096/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Amaral, Marta -- Levy, Colin -- Heyes, Derren J -- Lafite, Pierre -- Outeiro, Tiago F -- Giorgini, Flaviano -- Leys, David -- Scrutton, Nigel S -- BB/D01963X/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- England -- Nature. 2013 Apr 18;496(7445):382-5. doi: 10.1038/nature12039. Epub 2013 Apr 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23575632" target="_blank"〉PubMed〈/a〉
    Keywords: Arginine/metabolism ; Blood-Brain Barrier/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Cyclopropanes/*chemistry/*pharmacology ; Drug Design ; Enzyme Inhibitors/*chemistry/*pharmacology ; Humans ; Huntington Disease/drug therapy/enzymology ; Kynurenine/metabolism ; Kynurenine 3-Monooxygenase/*antagonists & inhibitors/*chemistry/metabolism ; Models, Molecular ; Molecular Targeted Therapy ; Protein Conformation ; Reproducibility of Results ; Saccharomyces cerevisiae/*enzymology ; Structure-Activity Relationship
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  • 85
    Publication Date: 2013-05-24
    Description: Longevity is regulated by a network of closely linked metabolic systems. We used a combination of mouse population genetics and RNA interference in Caenorhabditis elegans to identify mitochondrial ribosomal protein S5 (Mrps5) and other mitochondrial ribosomal proteins as metabolic and longevity regulators. MRP knockdown triggers mitonuclear protein imbalance, reducing mitochondrial respiration and activating the mitochondrial unfolded protein response. Specific antibiotics targeting mitochondrial translation and ethidium bromide (which impairs mitochondrial DNA transcription) pharmacologically mimic mrp knockdown and extend worm lifespan by inducing mitonuclear protein imbalance, a stoichiometric imbalance between nuclear and mitochondrially encoded proteins. This mechanism was also conserved in mammalian cells. In addition, resveratrol and rapamycin, longevity compounds acting on different molecular targets, similarly induced mitonuclear protein imbalance, the mitochondrial unfolded protein response and lifespan extension in C. elegans. Collectively these data demonstrate that MRPs represent an evolutionarily conserved protein family that ties the mitochondrial ribosome and mitonuclear protein imbalance to the mitochondrial unfolded protein response, an overarching longevity pathway across many species.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3663447/" 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/PMC3663447/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Houtkooper, Riekelt H -- Mouchiroud, Laurent -- Ryu, Dongryeol -- Moullan, Norman -- Katsyuba, Elena -- Knott, Graham -- Williams, Robert W -- Auwerx, Johan -- 231138/European Research Council/International -- P20 DA021131/DA/NIDA NIH HHS/ -- P20-DA 21131/DA/NIDA NIH HHS/ -- R01AG043930/AG/NIA NIH HHS/ -- U01 AA013499/AA/NIAAA NIH HHS/ -- U01AA14425/AA/NIAAA NIH HHS/ -- UO1AA13499/AA/NIAAA NIH HHS/ -- England -- Nature. 2013 May 23;497(7450):451-7. doi: 10.1038/nature12188.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory for Integrative and Systems Physiology, Ecole Polytechnique Federale de Lausanne, CH-1015 Lausanne, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23698443" target="_blank"〉PubMed〈/a〉
    Keywords: Aging/genetics/metabolism ; Animals ; Anti-Bacterial Agents/pharmacology ; Caenorhabditis elegans/drug effects/genetics/*physiology ; Caenorhabditis elegans Proteins/genetics/metabolism ; Doxycycline/pharmacology ; Evolution, Molecular ; Female ; Longevity/drug effects/genetics/*physiology ; Male ; Mice ; Mice, Inbred Strains ; Mitochondria/drug effects/genetics/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Quantitative Trait Loci ; RNA Interference ; Reproducibility of Results ; Ribosomal Proteins/genetics/*metabolism ; Sirolimus/pharmacology ; Unfolded Protein Response/genetics/physiology
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  • 86
    Publication Date: 2013-05-24
    Description: Early-life dietary transitions reflect fundamental aspects of primate evolution and are important determinants of health in contemporary human populations. Weaning is critical to developmental and reproductive rates; early weaning can have detrimental health effects but enables shorter inter-birth intervals, which influences population growth. Uncovering early-life dietary history in fossils is hampered by the absence of prospectively validated biomarkers that are not modified during fossilization. Here we show that large dietary shifts in early life manifest as compositional variations in dental tissues. Teeth from human children and captive macaques, with prospectively recorded diet histories, demonstrate that barium (Ba) distributions accurately reflect dietary transitions from the introduction of mother's milk through the weaning process. We also document dietary transitions in a Middle Palaeolithic juvenile Neanderthal, which shows a pattern of exclusive breastfeeding for seven months, followed by seven months of supplementation. After this point, Ba levels in enamel returned to baseline prenatal levels, indicating an abrupt cessation of breastfeeding at 1.2 years of age. Integration of Ba spatial distributions and histological mapping of tooth formation enables novel studies of the evolution of human life history, dietary ontogeny in wild primates, and human health investigations through accurate reconstructions of breastfeeding history.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3725337/" 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/PMC3725337/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Austin, Christine -- Smith, Tanya M -- Bradman, Asa -- Hinde, Katie -- Joannes-Boyau, Renaud -- Bishop, David -- Hare, Dominic J -- Doble, Philip -- Eskenazi, Brenda -- Arora, Manish -- 4R00ES019597-03/ES/NIEHS NIH HHS/ -- P01 ES009605/ES/NIEHS NIH HHS/ -- R00 ES019597/ES/NIEHS NIH HHS/ -- England -- Nature. 2013 Jun 13;498(7453):216-9. doi: 10.1038/nature12169. Epub 2013 May 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23698370" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Animals ; Barium/*analysis ; Breast Feeding/history ; Calcium/analysis ; Child, Preschool ; *Diet/veterinary ; Female ; *Fossils ; History, Ancient ; Humans ; Infant ; Macaca/*physiology ; Neanderthals/*physiology ; Reproducibility of Results ; Tooth/*chemistry ; *Weaning
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  • 87
    Publication Date: 2013-09-06
    Description: The ability to design proteins with high affinity and selectivity for any given small molecule is a rigorous test of our understanding of the physiochemical principles that govern molecular recognition. Attempts to rationally design ligand-binding proteins have met with little success, however, and the computational design of protein-small-molecule interfaces remains an unsolved problem. Current approaches for designing ligand-binding proteins for medical and biotechnological uses rely on raising antibodies against a target antigen in immunized animals and/or performing laboratory-directed evolution of proteins with an existing low affinity for the desired ligand, neither of which allows complete control over the interactions involved in binding. Here we describe a general computational method for designing pre-organized and shape complementary small-molecule-binding sites, and use it to generate protein binders to the steroid digoxigenin (DIG). Of seventeen experimentally characterized designs, two bind DIG; the model of the higher affinity binder has the most energetically favourable and pre-organized interface in the design set. A comprehensive binding-fitness landscape of this design, generated by library selections and deep sequencing, was used to optimize its binding affinity to a picomolar level, and X-ray co-crystal structures of two variants show atomic-level agreement with the corresponding computational models. The optimized binder is selective for DIG over the related steroids digitoxigenin, progesterone and beta-oestradiol, and this steroid binding preference can be reprogrammed by manipulation of explicitly designed hydrogen-bonding interactions. The computational design method presented here should enable the development of a new generation of biosensors, therapeutics and diagnostics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3898436/" 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/PMC3898436/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tinberg, Christine E -- Khare, Sagar D -- Dou, Jiayi -- Doyle, Lindsey -- Nelson, Jorgen W -- Schena, Alberto -- Jankowski, Wojciech -- Kalodimos, Charalampos G -- Johnsson, Kai -- Stoddard, Barry L -- Baker, David -- P41 GM103533/GM/NIGMS NIH HHS/ -- R01 GM049857/GM/NIGMS NIH HHS/ -- T32 HG000035/HG/NHGRI NIH HHS/ -- T32 HG00035/HG/NHGRI NIH HHS/ -- England -- Nature. 2013 Sep 12;501(7466):212-6. doi: 10.1038/nature12443. Epub 2013 Sep 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24005320" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Biotechnology ; *Computer Simulation ; Crystallography, X-Ray ; Digoxigenin/chemistry/*metabolism ; *Drug Design ; Estradiol/chemistry/metabolism ; Ligands ; Models, Molecular ; Progesterone/chemistry/metabolism ; Protein Binding ; Proteins/*chemistry/*metabolism ; Reproducibility of Results ; Substrate Specificity
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  • 88
    Publication Date: 2013-11-01
    Description: Mouse embryonic stem (ES) cells are isolated from the inner cell mass of blastocysts, and can be preserved in vitro in a naive inner-cell-mass-like configuration by providing exogenous stimulation with leukaemia inhibitory factor (LIF) and small molecule inhibition of ERK1/ERK2 and GSK3beta signalling (termed 2i/LIF conditions). Hallmarks of naive pluripotency include driving Oct4 (also known as Pou5f1) transcription by its distal enhancer, retaining a pre-inactivation X chromosome state, and global reduction in DNA methylation and in H3K27me3 repressive chromatin mark deposition on developmental regulatory gene promoters. Upon withdrawal of 2i/LIF, naive mouse ES cells can drift towards a primed pluripotent state resembling that of the post-implantation epiblast. Although human ES cells share several molecular features with naive mouse ES cells, they also share a variety of epigenetic properties with primed murine epiblast stem cells (EpiSCs). These include predominant use of the proximal enhancer element to maintain OCT4 expression, pronounced tendency for X chromosome inactivation in most female human ES cells, increase in DNA methylation and prominent deposition of H3K27me3 and bivalent domain acquisition on lineage regulatory genes. The feasibility of establishing human ground state naive pluripotency in vitro with equivalent molecular and functional features to those characterized in mouse ES cells remains to be defined. Here we establish defined conditions that facilitate the derivation of genetically unmodified human naive pluripotent stem cells from already established primed human ES cells, from somatic cells through induced pluripotent stem (iPS) cell reprogramming or directly from blastocysts. The novel naive pluripotent cells validated herein retain molecular characteristics and functional properties that are highly similar to mouse naive ES cells, and distinct from conventional primed human pluripotent cells. This includes competence in the generation of cross-species chimaeric mouse embryos that underwent organogenesis following microinjection of human naive iPS cells into mouse morulas. Collectively, our findings establish new avenues for regenerative medicine, patient-specific iPS cell disease modelling and the study of early human development in vitro and in vivo.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gafni, Ohad -- Weinberger, Leehee -- Mansour, Abed AlFatah -- Manor, Yair S -- Chomsky, Elad -- Ben-Yosef, Dalit -- Kalma, Yael -- Viukov, Sergey -- Maza, Itay -- Zviran, Asaf -- Rais, Yoach -- Shipony, Zohar -- Mukamel, Zohar -- Krupalnik, Vladislav -- Zerbib, Mirie -- Geula, Shay -- Caspi, Inbal -- Schneir, Dan -- Shwartz, Tamar -- Gilad, Shlomit -- Amann-Zalcenstein, Daniela -- Benjamin, Sima -- Amit, Ido -- Tanay, Amos -- Massarwa, Rada -- Novershtern, Noa -- Hanna, Jacob H -- England -- Nature. 2013 Dec 12;504(7479):282-6. doi: 10.1038/nature12745. Epub 2013 Oct 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel [2]. ; 1] The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel [2] The Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel [3] The Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel [4]. ; 1] Wolfe PGD Stem Cell Lab, Racine IVF Unit, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, Tel-Aviv, Israel [2] The Department of Cell and Developmental Biology, Sackler Medical School, Tel-Aviv University, Israel. ; Wolfe PGD Stem Cell Lab, Racine IVF Unit, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, Tel-Aviv, Israel. ; The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel. ; 1] The Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel [2] The Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel. ; The Israel National Center for Personalized Medicine (INCPM), Weizmann Institute of Science, Rehovot 76100, Israel. ; The Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24172903" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Blastocyst/cytology ; Cellular Reprogramming ; Chimera/embryology ; Chromatin/metabolism ; DNA Methylation ; Embryo, Mammalian/cytology/embryology ; Embryonic Stem Cells/cytology/metabolism ; Epigenesis, Genetic ; Female ; Germ Layers/cytology ; Histones/metabolism ; Humans ; Induced Pluripotent Stem Cells/*cytology/metabolism/transplantation ; Male ; Mice ; Morula/cytology ; Organogenesis ; Promoter Regions, Genetic/genetics ; Regenerative Medicine ; Reproducibility of Results ; Signal Transduction ; X Chromosome Inactivation
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  • 89
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    Nature Publishing Group (NPG)
    Publication Date: 2013-03-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cressey, Daniel -- England -- Nature. 2013 Mar 14;495(7440):155. doi: 10.1038/495155a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23486037" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Australia ; Bias (Epidemiology) ; *Biodiversity ; Conservation of Natural Resources/economics/*methods ; Coral Reefs ; Ecology/economics/*methods ; Fossil Fuels/economics/supply & distribution ; Marine Biology/economics/*methods ; *Oceans and Seas ; Reproducibility of Results ; *Wilderness
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  • 90
    Publication Date: 2013-01-11
    Description: Insulin receptor signalling has a central role in mammalian biology, regulating cellular metabolism, growth, division, differentiation and survival. Insulin resistance contributes to the pathogenesis of type 2 diabetes mellitus and the onset of Alzheimer's disease; aberrant signalling occurs in diverse cancers, exacerbated by cross-talk with the homologous type 1 insulin-like growth factor receptor (IGF1R). Despite more than three decades of investigation, the three-dimensional structure of the insulin-insulin receptor complex has proved elusive, confounded by the complexity of producing the receptor protein. Here we present the first view, to our knowledge, of the interaction of insulin with its primary binding site on the insulin receptor, on the basis of four crystal structures of insulin bound to truncated insulin receptor constructs. The direct interaction of insulin with the first leucine-rich-repeat domain (L1) of insulin receptor is seen to be sparse, the hormone instead engaging the insulin receptor carboxy-terminal alpha-chain (alphaCT) segment, which is itself remodelled on the face of L1 upon insulin binding. Contact between insulin and L1 is restricted to insulin B-chain residues. The alphaCT segment displaces the B-chain C-terminal beta-strand away from the hormone core, revealing the mechanism of a long-proposed conformational switch in insulin upon receptor engagement. This mode of hormone-receptor recognition is novel within the broader family of receptor tyrosine kinases. We support these findings by photo-crosslinking data that place the suggested interactions into the context of the holoreceptor and by isothermal titration calorimetry data that dissect the hormone-insulin receptor interface. Together, our findings provide an explanation for a wealth of biochemical data from the insulin receptor and IGF1R systems relevant to the design of therapeutic insulin analogues.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3793637/" 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/PMC3793637/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Menting, John G -- Whittaker, Jonathan -- Margetts, Mai B -- Whittaker, Linda J -- Kong, Geoffrey K-W -- Smith, Brian J -- Watson, Christopher J -- Zakova, Lenka -- Kletvikova, Emilia -- Jiracek, Jiri -- Chan, Shu Jin -- Steiner, Donald F -- Dodson, Guy G -- Brzozowski, Andrzej M -- Weiss, Michael A -- Ward, Colin W -- Lawrence, Michael C -- DK13914/DK/NIDDK NIH HHS/ -- DK20595/DK/NIDDK NIH HHS/ -- DK40949/DK/NIDDK NIH HHS/ -- R01 DK040949/DK/NIDDK NIH HHS/ -- UL1 TR000439/TR/NCATS NIH HHS/ -- Biotechnology and Biological Sciences Research Council/United Kingdom -- England -- Nature. 2013 Jan 10;493(7431):241-5. doi: 10.1038/nature11781.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23302862" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Calorimetry ; Cattle ; Cell Line ; Crystallography, X-Ray ; Humans ; Insulin/*chemistry/*metabolism ; Leucine/metabolism ; Ligands ; Models, Molecular ; Protein Binding ; Protein Structure, Secondary ; Receptor, Insulin/*chemistry/*metabolism ; Reproducibility of Results
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  • 91
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    Nature Publishing Group (NPG)
    Publication Date: 2013-06-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cyranoski, David -- England -- Nature. 2013 Jun 20;498(7454):283-4. doi: 10.1038/498283a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23783608" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; China ; Disease Models, Animal ; Drug Industry/ethics/*organization & administration/standards ; Health ; Humans ; London ; Mice ; Models, Immunological ; *Multiple Sclerosis/drug therapy/immunology/pathology ; Receptors, Interleukin-7/antagonists & inhibitors/immunology/metabolism ; Reproducibility of Results ; *Research Personnel/ethics/standards ; *Retraction of Publication as Topic ; Th17 Cells/immunology/pathology ; *Unemployment
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  • 92
    Publication Date: 2013-05-21
    Description: Recent molecular studies have shown that, even when derived from a seemingly homogenous population, individual cells can exhibit substantial differences in gene expression, protein levels and phenotypic output, with important functional consequences. Existing studies of cellular heterogeneity, however, have typically measured only a few pre-selected RNAs or proteins simultaneously, because genomic profiling methods could not be applied to single cells until very recently. Here we use single-cell RNA sequencing to investigate heterogeneity in the response of mouse bone-marrow-derived dendritic cells (BMDCs) to lipopolysaccharide. We find extensive, and previously unobserved, bimodal variation in messenger RNA abundance and splicing patterns, which we validate by RNA-fluorescence in situ hybridization for select transcripts. In particular, hundreds of key immune genes are bimodally expressed across cells, surprisingly even for genes that are very highly expressed at the population average. Moreover, splicing patterns demonstrate previously unobserved levels of heterogeneity between cells. Some of the observed bimodality can be attributed to closely related, yet distinct, known maturity states of BMDCs; other portions reflect differences in the usage of key regulatory circuits. For example, we identify a module of 137 highly variable, yet co-regulated, antiviral response genes. Using cells from knockout mice, we show that variability in this module may be propagated through an interferon feedback circuit, involving the transcriptional regulators Stat2 and Irf7. Our study demonstrates the power and promise of single-cell genomics in uncovering functional diversity between cells and in deciphering cell states and circuits.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3683364/" 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/PMC3683364/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shalek, Alex K -- Satija, Rahul -- Adiconis, Xian -- Gertner, Rona S -- Gaublomme, Jellert T -- Raychowdhury, Raktima -- Schwartz, Schraga -- Yosef, Nir -- Malboeuf, Christine -- Lu, Diana -- Trombetta, John J -- Gennert, Dave -- Gnirke, Andreas -- Goren, Alon -- Hacohen, Nir -- Levin, Joshua Z -- Park, Hongkun -- Regev, Aviv -- 1F32HD075541-01/HD/NICHD NIH HHS/ -- 1P50HG006193-01/HG/NHGRI NIH HHS/ -- 5DP1OD003893-03/OD/NIH HHS/ -- DP1 CA174427/CA/NCI NIH HHS/ -- DP1 DA035083/DA/NIDA NIH HHS/ -- DP1 OD003958/OD/NIH HHS/ -- DP1OD003958-01/OD/NIH HHS/ -- DP2 OD002230/OD/NIH HHS/ -- F32 HD075541/HD/NICHD NIH HHS/ -- P50 HG006193/HG/NHGRI NIH HHS/ -- U54 AI057159/AI/NIAID NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2013 Jun 13;498(7453):236-40. doi: 10.1038/nature12172. Epub 2013 May 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23685454" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bone Marrow Cells/cytology/immunology ; Dendritic Cells/cytology/immunology/*metabolism ; *Gene Expression Profiling ; Gene Expression Regulation/*immunology ; In Situ Hybridization, Fluorescence ; Interferon Regulatory Factor-7 ; Interferons/immunology ; Lipopolysaccharides/immunology ; Mice ; Mice, Knockout ; Protein Isoforms/genetics ; RNA Splicing/*immunology ; RNA, Messenger/analysis/genetics ; Reproducibility of Results ; STAT2 Transcription Factor ; Sequence Analysis, RNA ; *Single-Cell Analysis ; Transcriptome/*genetics ; Viruses/immunology
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  • 93
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    Nature Publishing Group (NPG)
    Publication Date: 2013-05-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cyranoski, David -- England -- Nature. 2013 May 30;497(7451):543-4. doi: 10.1038/497543a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23719438" target="_blank"〉PubMed〈/a〉
    Keywords: Cellular Reprogramming ; Humans ; Peer Review, Research/*standards ; Periodicals as Topic/*standards ; Quality Control ; Reproducibility of Results ; Research Design ; Scientific Misconduct ; *Stem Cell Research ; Stem Cells/cytology ; Time Factors
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  • 94
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    Nature Publishing Group (NPG)
    Publication Date: 2013-07-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2013 Jul 11;499(7457):125.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23858535" target="_blank"〉PubMed〈/a〉
    Keywords: Clinical Trials as Topic/economics/*ethics/standards ; Compassionate Use Trials/economics/ethics/standards ; Federal Government ; Humans ; Italy ; Patients/psychology ; Reproducibility of Results ; Stem Cell Transplantation/*ethics/standards ; *Uncertainty
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  • 95
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    Nature Publishing Group (NPG)
    Publication Date: 2013-08-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wadman, Meredith -- England -- Nature. 2013 Aug 1;500(7460):14-6. doi: 10.1038/500014a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23903729" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biomedical Research/economics/*standards ; Clinical Trials as Topic/standards ; Contract Services ; Drug Industry/standards ; Humans ; *National Institutes of Health (U.S.)/economics ; Peer Review, Research/methods/standards ; Reproducibility of Results ; United States ; *Validation Studies as Topic
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  • 96
    Publication Date: 2013-04-27
    Description: Modern small-angle scattering (SAS) experiments with X-rays or neutrons provide a comprehensive, resolution-limited observation of the thermodynamic state. However, methods for evaluating mass and validating SAS-based models and resolution have been inadequate. Here we define the volume of correlation, Vc, a SAS invariant derived from the scattered intensities that is specific to the structural state of the particle, but independent of concentration and the requirements of a compact, folded particle. We show that Vc defines a ratio, QR, that determines the molecular mass of proteins or RNA ranging from 10 to 1,000 kilodaltons. Furthermore, we propose a statistically robust method for assessing model-data agreements (chi(2)free) akin to cross-validation. Our approach prevents over-fitting of the SAS data and can be used with a newly defined metric, RSAS, for quantitative evaluation of resolution. Together, these metrics (Vc, QR, chi(2)free and RSAS) provide analytical tools for unbiased and accurate macromolecular structural characterizations in solution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3714217/" 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/PMC3714217/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rambo, Robert P -- Tainer, John A -- R01 GM105404/GM/NIGMS NIH HHS/ -- R01GM105404/GM/NIGMS NIH HHS/ -- England -- Nature. 2013 Apr 25;496(7446):477-81. doi: 10.1038/nature12070.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Life Sciences Division, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA. rprambo@lbl.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23619693" target="_blank"〉PubMed〈/a〉
    Keywords: Aldose-Ketose Isomerases/chemistry ; DNA-Binding Proteins/chemistry ; Models, Chemical ; *Models, Molecular ; Molecular Conformation ; Molecular Weight ; Pliability ; RNA, Viral/chemistry ; Reproducibility of Results ; Riboswitch/genetics ; *Scattering, Small Angle ; Solutions
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  • 97
    Publication Date: 2013-11-26
    Description: An increasing body of evidence points to mitochondrial dysfunction as a contributor to the molecular pathogenesis of neurodegenerative diseases such as Parkinson's disease. Recent studies of the Parkinson's disease associated genes PINK1 (ref. 2) and parkin (PARK2, ref. 3) indicate that they may act in a quality control pathway preventing the accumulation of dysfunctional mitochondria. Here we elucidate regulators that have an impact on parkin translocation to damaged mitochondria with genome-wide small interfering RNA (siRNA) screens coupled to high-content microscopy. Screening yielded gene candidates involved in diverse cellular processes that were subsequently validated in low-throughput assays. This led to characterization of TOMM7 as essential for stabilizing PINK1 on the outer mitochondrial membrane following mitochondrial damage. We also discovered that HSPA1L (HSP70 family member) and BAG4 have mutually opposing roles in the regulation of parkin translocation. The screens revealed that SIAH3, found to localize to mitochondria, inhibits PINK1 accumulation after mitochondrial insult, reducing parkin translocation. Overall, our screens provide a rich resource to understand mitochondrial quality control.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hasson, Samuel A -- Kane, Lesley A -- Yamano, Koji -- Huang, Chiu-Hui -- Sliter, Danielle A -- Buehler, Eugen -- Wang, Chunxin -- Heman-Ackah, Sabrina M -- Hessa, Tara -- Guha, Rajarshi -- Martin, Scott E -- Youle, Richard J -- Intramural NIH HHS/ -- England -- Nature. 2013 Dec 12;504(7479):291-5. doi: 10.1038/nature12748. Epub 2013 Nov 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA [2] Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, USA [3]. ; 1] Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA [2]. ; Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA. ; Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, USA. ; NIH Center for Regenerative Medicine, Bethesda, Maryland 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24270810" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/metabolism ; Genome, Human/*genetics ; HCT116 Cells ; HEK293 Cells ; HSP70 Heat-Shock Proteins/metabolism ; HeLa Cells ; Humans ; Membrane Proteins/metabolism ; Mitochondria/metabolism/pathology ; *Mitochondrial Degradation ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/metabolism ; Multigene Family/genetics ; Parkinson Disease/metabolism/pathology ; Protein Kinases/metabolism ; Protein Transport ; *RNA Interference ; RNA, Small Interfering/analysis/genetics ; Reproducibility of Results ; Ubiquitin-Protein Ligases/*metabolism
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  • 98
    Publication Date: 2013-12-18
    Description: The increase in solar luminosity over geological timescales should warm the Earth's climate, increasing water evaporation, which will in turn enhance the atmospheric greenhouse effect. Above a certain critical insolation, this destabilizing greenhouse feedback can 'run away' until the oceans have completely evaporated. Through increases in stratospheric humidity, warming may also cause evaporative loss of the oceans to space before the runaway greenhouse state occurs. The critical insolation thresholds for these processes, however, remain uncertain because they have so far been evaluated using one-dimensional models that cannot account for the dynamical and cloud feedback effects that are key stabilizing features of the Earth's climate. Here we use a three-dimensional global climate model to show that the insolation threshold for the runaway greenhouse state to occur is about 375 W m(-2), which is significantly higher than previously thought. Our model is specifically developed to quantify the climate response of Earth-like planets to increased insolation in hot and extremely moist atmospheres. In contrast with previous studies, we find that clouds have a destabilizing feedback effect on the long-term warming. However, subsident, unsaturated regions created by the Hadley circulation have a stabilizing effect that is strong enough to shift the runaway greenhouse limit to higher values of insolation than are inferred from one-dimensional models. Furthermore, because of wavelength-dependent radiative effects, the stratosphere remains sufficiently cold and dry to hamper the escape of atmospheric water, even at large fluxes. This has strong implications for the possibility of liquid water existing on Venus early in its history, and extends the size of the habitable zone around other stars.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Leconte, Jeremy -- Forget, Francois -- Charnay, Benjamin -- Wordsworth, Robin -- Pottier, Alizee -- England -- Nature. 2013 Dec 12;504(7479):268-71. doi: 10.1038/nature12827.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratoire de Meteorologie Dynamique, Institut Pierre Simon Laplace, 4 Place Jussieu, BP 99, 75252 Paris, France. ; Department of Geological Sciences, University of Chicago, Chicago, Illinois 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24336285" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/analysis/chemistry ; *Earth (Planet) ; Exobiology ; *Greenhouse Effect ; Humidity ; Models, Theoretical ; *Planets ; Reproducibility of Results ; *Solar Activity ; *Stars, Celestial ; Temperature ; Venus ; Water/analysis ; Water Cycle ; Wind
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  • 99
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    Nature Publishing Group (NPG)
    Publication Date: 2013-06-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Callaway, Ewen -- England -- Nature. 2013 Jun 20;498(7454):282-3. doi: 10.1038/498282a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23783607" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Domestic/classification/*genetics/physiology ; Animals, Wild/classification/*genetics/physiology ; China ; Dogs/classification/*genetics/physiology ; Extinction, Biological ; Fossils ; *Phylogeny ; Reproducibility of Results ; Time Factors ; Uncertainty ; Wolves/classification/*genetics/physiology
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  • 100
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    Nature Publishing Group (NPG)
    Publication Date: 2013-05-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reich, Eugenie Samuel -- England -- Nature. 2013 May 9;497(7448):170-1. doi: 10.1038/497170a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23657329" target="_blank"〉PubMed〈/a〉
    Keywords: Adolescent ; Altruism ; Anatomy ; Animals ; Dancing/*physiology ; Female ; Humans ; Jamaica ; Male ; Mating Preference, Animal ; Physical Fitness ; Reproducibility of Results ; Retraction of Publication as Topic ; *Scientific Misconduct
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