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  • 101
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2011-03-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Raiborg, Camilla -- Stenmark, Harald -- New York, N.Y. -- Science. 2011 Mar 25;331(6024):1533-4. doi: 10.1126/science.1204208.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Montebello, Oslo, Norway.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21436431" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/metabolism ; Calcium-Binding Proteins/metabolism ; Cell Cycle Proteins/metabolism ; *Cell Division ; Cell Membrane/metabolism ; Endosomal Sorting Complexes Required for Transport/*chemistry/*metabolism ; Humans ; Microscopy, Electron ; Microtubules/*metabolism/*ultrastructure ; Models, Biological ; Nuclear Proteins/metabolism ; Protein Conformation ; Protein Multimerization
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 102
    Publication Date: 2011-08-20
    Description: Immune clearance and resource limitation (via red blood cell depletion) shape the peaks and troughs of malaria parasitemia, which in turn affect disease severity and transmission. Quantitatively partitioning the relative roles of these effects through time is challenging. Using data from rodent malaria, we estimated the effective propagation number, which reflects the relative importance of contrasting within-host control mechanisms through time and is sensitive to the inoculating parasite dose. Our analysis showed that the capacity of innate responses to restrict initial parasite growth saturates with parasite dose and that experimentally enhanced innate immunity can affect parasite density indirectly via resource depletion. Such a statistical approach offers a tool to improve targeting of drugs or vaccines for human therapy by revealing the dynamics and interactions of within-host regulatory mechanisms.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3891600/" 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/PMC3891600/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Metcalf, C J E -- Graham, A L -- Huijben, S -- Barclay, V C -- Long, G H -- Grenfell, B T -- Read, A F -- Bjornstad, O N -- R01 GM089932/GM/NIGMS NIH HHS/ -- R01GM089932/GM/NIGMS NIH HHS/ -- R24 HD047879/HD/NICHD NIH HHS/ -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2011 Aug 19;333(6045):984-8. doi: 10.1126/science.1204588.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology, Oxford University, Oxford OX1 3PS, UK. charlotte.metcalf@zoo.ox.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21852493" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptive Immunity ; Animals ; Antibodies/immunology ; CD4-Positive T-Lymphocytes/immunology ; Erythrocyte Aging ; Erythrocyte Count ; Erythrocytes/*parasitology/physiology ; Host-Parasite Interactions ; Humans ; Immunity, Innate ; Interleukin-10/immunology/metabolism ; Malaria/blood/*immunology/*parasitology ; Mice ; Models, Biological ; Models, Statistical ; *Parasitemia/blood/immunology/parasitology ; Plasmodium chabaudi/immunology/*physiology ; Receptors, Interleukin-10/immunology ; Regression Analysis
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 103
    Publication Date: 2011-07-23
    Description: Low-trophic level species account for more than 30% of global fisheries production and contribute substantially to global food security. We used a range of ecosystem models to explore the effects of fishing low-trophic level species on marine ecosystems, including marine mammals and seabirds, and on other commercially important species. In five well-studied ecosystems, we found that fishing these species at conventional maximum sustainable yield (MSY) levels can have large impacts on other parts of the ecosystem, particularly when they constitute a high proportion of the biomass in the ecosystem or are highly connected in the food web. Halving exploitation rates would result in much lower impacts on marine ecosystems while still achieving 80% of MSY.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smith, Anthony D M -- Brown, Christopher J -- Bulman, Catherine M -- Fulton, Elizabeth A -- Johnson, Penny -- Kaplan, Isaac C -- Lozano-Montes, Hector -- Mackinson, Steven -- Marzloff, Martin -- Shannon, Lynne J -- Shin, Yunne-Jai -- Tam, Jorge -- New York, N.Y. -- Science. 2011 Aug 26;333(6046):1147-50. doi: 10.1126/science.1209395. Epub 2011 Jul 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Commonwealth Scientific and Industrial Research Organization, Wealth from Oceans Flagship, Hobart, TAS 7001, Australia. tony.d.smith@csiro.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21778363" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Aquatic Organisms ; Biodiversity ; Biomass ; Birds ; *Ecosystem ; *Fisheries ; *Fishes ; *Food Chain ; Mammals ; Models, Biological ; Oceans and Seas ; Population Dynamics
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  • 104
    Publication Date: 2012-06-30
    Description: Metabolic engineering of plants can reduce the cost and environmental impact of agriculture while providing for the needs of a growing population. Although our understanding of plant metabolism continues to increase at a rapid pace, relatively few plant metabolic engineering projects with commercial potential have emerged, in part because of a lack of principles for the rational manipulation of plant phenotype. One underexplored approach to identifying such design principles derives from analysis of the dominant constraints on plant fitness, and the evolutionary innovations in response to those constraints, that gave rise to the enormous diversity of natural plant metabolic pathways.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Milo, Ron -- Last, Robert L -- 260392/European Research Council/International -- New York, N.Y. -- Science. 2012 Jun 29;336(6089):1663-7. doi: 10.1126/science.1217665.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22745419" target="_blank"〉PubMed〈/a〉
    Keywords: *Biodiversity ; Evolution, Molecular ; Metabolic Engineering ; Models, Biological ; Plants/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 105
    Publication Date: 2012-03-31
    Description: The occurrence and magnitude of disease outbreaks can strongly influence host evolution. In particular, when hosts face a resistance-fecundity trade-off, they might evolve increased resistance to infection during larger epidemics but increased susceptibility during smaller ones. We tested this theoretical prediction by using a zooplankton-yeast host-parasite system in which ecological factors determine epidemic size. Lakes with high productivity and low predation pressure had large yeast epidemics; during these outbreaks, hosts became more resistant to infection. However, with low productivity and high predation, epidemics remained small and hosts evolved increased susceptibility. Thus, by modulating disease outbreaks, ecological context (productivity and predation) shaped host evolution during epidemics. Consequently, anthropogenic alteration of productivity and predation might strongly influence both ecological and evolutionary outcomes of disease.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Duffy, Meghan A -- Ochs, Jessica Housley -- Penczykowski, Rachel M -- Civitello, David J -- Klausmeier, Christopher A -- Hall, Spencer R -- New York, N.Y. -- Science. 2012 Mar 30;335(6076):1636-8. doi: 10.1126/science.1215429.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biology, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA. duffy@gatech.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22461614" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Daphnia/*microbiology/*physiology ; *Ecosystem ; Female ; Fishes ; *Host-Pathogen Interactions ; Indiana ; *Lakes ; Male ; Metschnikowia/*pathogenicity ; Models, Biological ; Population Dynamics ; Predatory Behavior ; Reproduction ; Zooplankton/microbiology/physiology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 106
    Publication Date: 2012-04-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vinson, Valda -- Purnell, Beverly A -- Zahn, Laura M -- Travis, John -- New York, N.Y. -- Science. 2012 Apr 13;336(6078):171. doi: 10.1126/science.336.6078.171.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22499935" target="_blank"〉PubMed〈/a〉
    Keywords: *Computational Biology ; Computer Simulation ; Genomics ; Models, Biological ; Morphogenesis
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  • 107
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-07-24
    Description: Ecological theory predicts that a complex community formed by a number of species is inherently unstable, guiding ecologists to identify what maintains species diversity in nature. Earlier studies often assumed a community with only one interaction type, either an antagonistic, competitive, or mutualistic interaction, leaving open the question of what the diversity of interaction types contributes to the community maintenance. We show theoretically that the multiple interaction types might hold the key to understanding community dynamics. A moderate mixture of antagonistic and mutualistic interactions can stabilize population dynamics. Furthermore, increasing complexity leads to increased stability in a "hybrid" community. We hypothesize that the diversity of species and interaction types may be the essential element of biodiversity that maintains ecological communities.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mougi, A -- Kondoh, M -- New York, N.Y. -- Science. 2012 Jul 20;337(6092):349-51. doi: 10.1126/science.1220529.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Environmental Solution Technology, Faculty of Science and Technology, Ryukoku University, 1-5 Yokoya, Seta Oe-cho, Otsu 520-2194, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22822151" target="_blank"〉PubMed〈/a〉
    Keywords: *Biodiversity ; *Biota ; Models, Biological ; Population Dynamics
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  • 108
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-09-08
    Description: Cells have developed ways to sense and control the size of their organelles. Size-sensing mechanisms range from direct measurements provided by dedicated reporters to indirect functional readouts, and they are used to modify organelle size under both normal and stress conditions. Organelle size can also be controlled in the absence of an identifiable size sensor. Studies on flagella have dissected principles of size sensing and control, and it will be exciting to see how these principles apply to other organelles.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3625396/" 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/PMC3625396/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chan, Yee-Hung M -- Marshall, Wallace F -- 1F32GM090442-01A1/GM/NIGMS NIH HHS/ -- P50 GM081879/GM/NIGMS NIH HHS/ -- P50GM081879/GM/NIGMS NIH HHS/ -- R01 GM097017/GM/NIGMS NIH HHS/ -- R01GM097017/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Sep 7;337(6099):1186-9. doi: 10.1126/science.1223539.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, UCSF Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, CA 94158, USA. yhmchan@ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22955827" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Transport ; *Cell Physiological Phenomena ; Flagella/metabolism/physiology/ultrastructure ; Humans ; Models, Biological ; *Organelle Size ; *Organelles/chemistry/metabolism/ultrastructure
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  • 109
    Publication Date: 2012-04-14
    Description: The mechanism of ion channel voltage gating-how channels open and close in response to voltage changes-has been debated since Hodgkin and Huxley's seminal discovery that the crux of nerve conduction is ion flow across cellular membranes. Using all-atom molecular dynamics simulations, we show how a voltage-gated potassium channel (KV) switches between activated and deactivated states. On deactivation, pore hydrophobic collapse rapidly halts ion flow. Subsequent voltage-sensing domain (VSD) relaxation, including inward, 15-angstrom S4-helix motion, completes the transition. On activation, outward S4 motion tightens the VSD-pore linker, perturbing linker-S6-helix packing. Fluctuations allow water, then potassium ions, to reenter the pore; linker-S6 repacking stabilizes the open pore. We propose a mechanistic model for the sodium/potassium/calcium voltage-gated ion channel superfamily that reconciles apparently conflicting experimental data.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jensen, Morten O -- Jogini, Vishwanath -- Borhani, David W -- Leffler, Abba E -- Dror, Ron O -- Shaw, David E -- New York, N.Y. -- Science. 2012 Apr 13;336(6078):229-33. doi: 10.1126/science.1216533.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉D E Shaw Research, New York, NY 10036, USA. morten.jensen@DEShawResearch.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22499946" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Hydrophobic and Hydrophilic Interactions ; *Ion Channel Gating ; Kv1.2 Potassium Channel/*chemistry/*metabolism ; Membrane Potentials ; Models, Biological ; Models, Molecular ; Molecular Dynamics Simulation ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rats ; Recombinant Fusion Proteins/chemistry/metabolism ; Shab Potassium Channels/*chemistry/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 110
    Publication Date: 2012-05-05
    Description: Although the network topology of metabolism is well known, understanding the principles that govern the distribution of fluxes through metabolism lags behind. Experimentally, these fluxes can be measured by (13)C-flux analysis, and there has been a long-standing interest in understanding this functional network operation from an evolutionary perspective. On the basis of (13)C-determined fluxes from nine bacteria and multi-objective optimization theory, we show that metabolism operates close to the Pareto-optimal surface of a three-dimensional space defined by competing objectives. Consistent with flux data from evolved Escherichia coli, we propose that flux states evolve under the trade-off between two principles: optimality under one given condition and minimal adjustment between conditions. These principles form the forces by which evolution shapes metabolic fluxes in microorganisms' environmental context.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schuetz, Robert -- Zamboni, Nicola -- Zampieri, Mattia -- Heinemann, Matthias -- Sauer, Uwe -- New York, N.Y. -- Science. 2012 May 4;336(6081):601-4. doi: 10.1126/science.1216882.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule Zurich, Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22556256" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Adenosine Triphosphate/metabolism ; Aerobiosis ; Algorithms ; Bacteria/growth & development/*metabolism ; *Biological Evolution ; Biomass ; Computer Simulation ; Escherichia coli/genetics/growth & development/*metabolism ; Glucose/metabolism ; *Metabolic Networks and Pathways ; Models, Biological
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  • 111
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-11-03
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3705936/" 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/PMC3705936/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baudisch, Annette -- Vaupel, James W -- AG-031719/AG/NIA NIH HHS/ -- P01 AG031719/AG/NIA NIH HHS/ -- New York, N.Y. -- Science. 2012 Nov 2;338(6107):618-9. doi: 10.1126/science.1226467.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Research Group for Modeling the Evolution of Aging, Rostock, Germany. baudisch@demogr.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23118175" target="_blank"〉PubMed〈/a〉
    Keywords: *Aging ; Animals ; *Biological Evolution ; Fertility ; Humans ; Models, Biological ; Mortality ; Reproduction
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  • 112
    Publication Date: 2012-03-03
    Description: Over 90 capsular serotypes of Streptococcus pneumoniae, a common nasopharyngeal colonizer and major cause of pneumonia, bacteremia, and meningitis, are known. It is unclear why some serotypes can persist at all: They are more easily cleared from carriage and compete poorly in vivo. Serotype-specific immune responses, which could promote diversity in principle, are weak enough to allow repeated colonizations by the same type. We show that weak serotype-specific immunity and an acquired response not specific to the capsule can together reproduce observed diversity. Serotype-specific immunity stabilizes competition, and acquired immunity to noncapsular antigens reduces fitness differences. Our model can be used to explain the effects of pneumococcal vaccination and indicates general factors that regulate the diversity of pathogens.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3341938/" 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/PMC3341938/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cobey, Sarah -- Lipsitch, Marc -- 1F32GM097997/GM/NIGMS NIH HHS/ -- 5R01AI048935/AI/NIAID NIH HHS/ -- F32 GM097997/GM/NIGMS NIH HHS/ -- U54 GM088558/GM/NIGMS NIH HHS/ -- U54 GM088558-02/GM/NIGMS NIH HHS/ -- U54GM088558/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Mar 16;335(6074):1376-80. doi: 10.1126/science.1215947. Epub 2012 Mar 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Communicable Disease Dynamics and Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA. scobey@hsph.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22383809" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptive Immunity ; Adult ; Antigenic Variation ; Antigens, Bacterial/*immunology ; Bacterial Capsules/immunology ; Carrier State/immunology/*microbiology ; Child ; Child, Preschool ; Computer Simulation ; Humans ; Immunity, Innate ; Infant ; Models, Biological ; Nasopharynx/*microbiology ; Pneumococcal Infections/immunology/*microbiology ; Pneumococcal Vaccines/immunology ; Serotyping ; Streptococcus pneumoniae/classification/*immunology/*physiology ; Time Factors
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  • 113
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-04-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kelly, Daniel P -- R01 DK045416/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2012 Apr 6;336(6077):42-3. doi: 10.1126/science.1221688.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Diabetes and Obesity Research Center, Sanford-Burnham Medical Research Institute, Orlando, FL 32827, USA. dkelly@sanfordburnham.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22491843" target="_blank"〉PubMed〈/a〉
    Keywords: Adipocytes, Brown/metabolism ; Adipocytes, White/*metabolism ; Animals ; Energy Metabolism ; *Exercise ; Fibronectins/genetics/*metabolism ; Gene Expression Regulation ; Hormones/*metabolism ; Humans ; Mice ; Models, Biological ; Muscle Fibers, Skeletal/metabolism ; Muscle, Skeletal/*metabolism ; Oxygen Consumption ; Physical Conditioning, Animal ; Physical Endurance ; *Physical Exertion ; Thermogenesis ; Trans-Activators/*metabolism ; Transcription Factors
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  • 114
    Publication Date: 2012-04-28
    Description: Biological systems that perform multiple tasks face a fundamental trade-off: A given phenotype cannot be optimal at all tasks. Here we ask how trade-offs affect the range of phenotypes found in nature. Using the Pareto front concept from economics and engineering, we find that best-trade-off phenotypes are weighted averages of archetypes--phenotypes specialized for single tasks. For two tasks, phenotypes fall on the line connecting the two archetypes, which could explain linear trait correlations, allometric relationships, as well as bacterial gene-expression patterns. For three tasks, phenotypes fall within a triangle in phenotype space, whose vertices are the archetypes, as evident in morphological studies, including on Darwin's finches. Tasks can be inferred from measured phenotypes based on the behavior of organisms nearest the archetypes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shoval, O -- Sheftel, H -- Shinar, G -- Hart, Y -- Ramote, O -- Mayo, A -- Dekel, E -- Kavanagh, K -- Alon, U -- New York, N.Y. -- Science. 2012 Jun 1;336(6085):1157-60. doi: 10.1126/science.1217405. Epub 2012 Apr 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22539553" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Beak/anatomy & histology ; *Biological Evolution ; Body Size ; Escherichia coli/genetics/growth & development/metabolism ; Finches/anatomy & histology ; Gene Expression ; *Genetic Fitness ; Models, Biological ; Models, Statistical ; *Phenotype ; Selection, Genetic
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  • 115
    Publication Date: 2012-02-04
    Description: Eukaryotic secretory proteins exit the endoplasmic reticulum (ER) via transport vesicles generated by the essential coat protein complex II (COPII) proteins. The outer coat complex, Sec13-Sec31, forms a scaffold that is thought to enforce curvature. By exploiting yeast bypass-of-sec-thirteen (bst) mutants, where Sec13p is dispensable, we probed the relationship between a compromised COPII coat and the cellular context in which it could still function. Genetic and biochemical analyses suggested that Sec13p was required to generate vesicles from membranes that contained asymmetrically distributed cargoes that were likely to confer opposing curvature. Thus, Sec13p may rigidify the COPII cage and increase its membrane-bending capacity; this function could be bypassed when a bst mutation renders the membrane more deformable.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3306526/" 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/PMC3306526/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Copic, Alenka -- Latham, Catherine F -- Horlbeck, Max A -- D'Arcangelo, Jennifer G -- Miller, Elizabeth A -- GM078186/GM/NIGMS NIH HHS/ -- GM085089/GM/NIGMS NIH HHS/ -- R01 GM078186/GM/NIGMS NIH HHS/ -- R01 GM078186-05/GM/NIGMS NIH HHS/ -- R01 GM085089/GM/NIGMS NIH HHS/ -- R01 GM085089-04/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Mar 16;335(6074):1359-62. doi: 10.1126/science.1215909. Epub 2012 Feb 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Columbia University, New York, NY 10027, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22300850" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; COP-Coated Vesicles/*chemistry/metabolism/ultrastructure ; Endoplasmic Reticulum/*metabolism ; Genes, Fungal ; Models, Biological ; Models, Molecular ; Mutant Proteins/chemistry/metabolism ; Mutation ; Nuclear Pore Complex Proteins/chemistry/genetics/*metabolism ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Protein Transport ; Saccharomyces cerevisiae/genetics/*metabolism/ultrastructure ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Vesicular Transport Proteins/chemistry/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 116
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-02-11
    Description: Ocean warming occurs every year in seasonal cycles that can help us to understand long-term responses of plankton to climate change. Rhythmic seasonal patterns of microbial community turnover are revealed when high-resolution measurements of microbial plankton diversity are applied to samples collected in lengthy time series. Seasonal cycles in microbial plankton are complex, but the expansion of fixed ocean stations monitoring long-term change and the development of automated instrumentation are providing the time-series data needed to understand how these cycles vary across broad geographical scales. By accumulating data and using predictive modeling, we gain insights into changes that will occur as the ocean surface continues to warm and as the extent and duration of ocean stratification increase. These developments will enable marine scientists to predict changes in geochemical cycles mediated by microbial communities and to gauge their broader impacts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Giovannoni, Stephen J -- Vergin, Kevin L -- New York, N.Y. -- Science. 2012 Feb 10;335(6069):671-6. doi: 10.1126/science.1198078.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA. steve.giovannoni@oregonstate.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22323811" target="_blank"〉PubMed〈/a〉
    Keywords: Alphaproteobacteria/physiology ; Archaea/*physiology ; *Bacterial Physiological Phenomena ; Climate Change ; *Ecosystem ; Models, Biological ; Oceans and Seas ; Phytoplankton/growth & development/*physiology ; *Seasons ; Seawater/chemistry/*microbiology ; Temperature
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 117
    facet.materialart.
    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-09-22
    Description: The blood-testis barrier includes strands of tight junctions between somatic Sertoli cells that restricts solutes from crossing the paracellular space, creating a microenvironment within seminiferous tubules and providing immune privilege to meiotic and postmeiotic cells. Large cysts of germ cells transit the Sertoli cell tight junctions (SCTJs) without compromising their integrity. We used confocal microscopy to visualize SCTJ components during germ cell cyst migration across the SCTJs. Cysts become enclosed within a network of transient compartments fully bounded by old and new tight junctions. Dissolution of the old tight junctions releases the germ cells into the adluminal compartment, thus completing transit across the blood-testis barrier. Claudin 3, a tight junction protein, is transiently incorporated into new tight junctions and then replaced by claudin 11.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694388/" 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/PMC3694388/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smith, Benjamin E -- Braun, Robert E -- CA34196/CA/NCI NIH HHS/ -- HD12629/HD/NICHD NIH HHS/ -- P30 CA034196/CA/NCI NIH HHS/ -- U54 HD012629/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2012 Nov 9;338(6108):798-802. doi: 10.1126/science.1219969. Epub 2012 Sep 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22997133" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Blood-Testis Barrier/*ultrastructure ; *Cell Movement ; Claudin-3/analysis/metabolism ; Claudins/analysis/metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Microscopy, Confocal ; Models, Biological ; Seminiferous Tubules/chemistry/ultrastructure ; Sertoli Cells/chemistry/physiology/*ultrastructure ; Spermatocytes/*physiology/ultrastructure ; Spermatogenesis ; Tight Junctions/chemistry/physiology/*ultrastructure
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 118
    Publication Date: 2012-08-11
    Description: Cells reuse signaling proteins in multiple pathways, raising the potential for improper cross talk. Scaffold proteins are thought to insulate against such miscommunication by sequestering proteins into distinct physical complexes. We show that the scaffold protein Ste5, which organizes the yeast mating mitogen-activated protein kinase (MAPK) pathway, does not use sequestration to prevent misactivation of the mating response. Instead, Ste5 appears to use a conformation mechanism: Under basal conditions, an intramolecular interaction of the pleckstrin homology (PH) domain with the von Willebrand type A (VWA) domain blocks the ability to coactivate the mating-specific MAPK Fus3. Pheromone-induced membrane binding of Ste5 triggers release of this autoinhibition. Thus, in addition to serving as a conduit guiding kinase communication, Ste5 directly receives input information to decide if and when signal can be transmitted to mating output.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631425/" 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/PMC3631425/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zalatan, Jesse G -- Coyle, Scott M -- Rajan, Saravanan -- Sidhu, Sachdev S -- Lim, Wendell A -- MOPS-93725/Canadian Institutes of Health Research/Canada -- P41 RR001614/RR/NCRR NIH HHS/ -- P50 GM081879/GM/NIGMS NIH HHS/ -- PN2 EY016546/EY/NEI NIH HHS/ -- R01 GM055040/GM/NIGMS NIH HHS/ -- R01 GM55040/GM/NIGMS NIH HHS/ -- R01 GM62583/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Sep 7;337(6099):1218-22. doi: 10.1126/science.1220683. Epub 2012 Aug 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22878499" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/antagonists & ; inhibitors/*chemistry/*metabolism ; Enzyme Activation ; MAP Kinase Kinase Kinases/metabolism ; MAP Kinase Signaling System ; Mitogen-Activated Protein Kinase Kinases/metabolism ; Mitogen-Activated Protein Kinases/*metabolism ; Models, Biological ; Phosphorylation ; Protein Conformation ; Protein Interaction Domains and Motifs ; Protein Kinases/metabolism ; Protein Precursors/metabolism ; Saccharomyces cerevisiae/*metabolism/physiology ; Saccharomyces cerevisiae Proteins/antagonists & inhibitors/*chemistry/*metabolism
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  • 119
    Publication Date: 2013-11-23
    Description: Cancer is a disease in which cells accumulate genetic aberrations that are believed to confer a clonal advantage over cells in the surrounding tissue. However, the quantitative benefit of frequently occurring mutations during tumor development remains unknown. We quantified the competitive advantage of Apc loss, Kras activation, and P53 mutations in the mouse intestine. Our findings indicate that the fate conferred by these mutations is not deterministic, and many mutated stem cells are replaced by wild-type stem cells after biased, but still stochastic events. Furthermore, P53 mutations display a condition-dependent advantage, and especially in colitis-affected intestines, clones harboring mutations in this gene are favored. Our work confirms the previously theoretical notion that the tissue architecture of the intestine suppresses the accumulation of mutated lineages.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vermeulen, Louis -- Morrissey, Edward -- van der Heijden, Maartje -- Nicholson, Anna M -- Sottoriva, Andrea -- Buczacki, Simon -- Kemp, Richard -- Tavare, Simon -- Winton, Douglas J -- Cancer Research UK/United Kingdom -- New York, N.Y. -- Science. 2013 Nov 22;342(6161):995-8. doi: 10.1126/science.1243148.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Research UK, Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24264992" target="_blank"〉PubMed〈/a〉
    Keywords: Adenomatous Polyposis Coli Protein/genetics ; Animals ; Cell Transformation, Neoplastic/*genetics/*pathology ; *Gene Expression Regulation, Neoplastic ; Intestinal Neoplasms/*genetics/*pathology ; Mice ; Mice, Mutant Strains ; Models, Biological ; Mutation ; Neoplastic Stem Cells/metabolism/*pathology ; Proto-Oncogene Proteins p21(ras)/genetics ; Transcriptional Activation ; Tumor Suppressor Protein p53/genetics
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  • 120
    Publication Date: 2013-04-27
    Description: Color patterns of bird plumage affect animal behavior and speciation. Diverse patterns are present in different species and within the individual. Here, we study the cellular and molecular basis of feather pigment pattern formation. Melanocyte progenitors are distributed as a horizontal ring in the proximal follicle, sending melanocytes vertically up into the epithelial cylinder, which gradually emerges as feathers grow. Different pigment patterns form by modulating the presence, arrangement, or differentiation of melanocytes. A layer of peripheral pulp further regulates pigmentation via patterned agouti expression. Lifetime feather cyclic regeneration resets pigment patterns for physiological needs. Thus, the evolution of stem cell niche topology allows complex pigment patterning through combinatorial co-option of simple regulatory mechanisms.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4144997/" 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/PMC4144997/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lin, S J -- Foley, J -- Jiang, T X -- Yeh, C Y -- Wu, P -- Foley, A -- Yen, C M -- Huang, Y C -- Cheng, H C -- Chen, C F -- Reeder, B -- Jee, S H -- Widelitz, R B -- Chuong, C M -- AR060306/AR/NIAMS NIH HHS/ -- AR42177/AR/NIAMS NIH HHS/ -- AR47364/AR/NIAMS NIH HHS/ -- R01 AR042177/AR/NIAMS NIH HHS/ -- R01 AR047364/AR/NIAMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Jun 21;340(6139):1442-5. doi: 10.1126/science.1230374. Epub 2013 Apr 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23618762" target="_blank"〉PubMed〈/a〉
    Keywords: Agouti Signaling Protein/metabolism ; Animals ; Birds/*anatomy & histology/physiology ; Cell Differentiation ; Cell Lineage ; Cell Proliferation ; Chickens/anatomy & histology/physiology ; Columbidae/anatomy & histology/physiology ; Feathers/*cytology/growth & development ; Female ; Galliformes/anatomy & histology/physiology ; Male ; Melanocytes/*cytology/physiology ; Models, Biological ; *Pigmentation ; Regeneration ; *Stem Cell Niche ; Stem Cells/*cytology/physiology
    Print ISSN: 0036-8075
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  • 121
    Publication Date: 2013-08-03
    Description: Insects often undergo regular outbreaks in population density but identifying the causal mechanism for such outbreaks in any particular species has proven difficult. Here, we show that outbreak cycles in the tea tortrix Adoxophyes honmai can be explained by temperature-driven changes in system stability. Wavelet analysis of a 51-year time series spanning more than 200 outbreaks reveals a threshold in outbreak amplitude each spring when temperature exceeds 15 degrees C and a secession of outbreaks each fall as temperature decreases. This is in close agreement with our independently parameterized mathematical model that predicts the system crosses a Hopf bifurcation from stability to sustained cycles as temperature increases. These results suggest that temperature can alter system stability and provide an explanation for generation cycles in multivoltine insects.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nelson, William A -- Bjornstad, Ottar N -- Yamanaka, Takehiko -- New York, N.Y. -- Science. 2013 Aug 16;341(6147):796-9. doi: 10.1126/science.1238477. Epub 2013 Aug 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Queen's University, Kingston, Ontario, Canada. nelsonw@queensu.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23907532" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Life Cycle Stages ; Models, Biological ; Moths/growth & development/*physiology ; Population Density ; Population Dynamics ; *Seasons ; *Temperature ; Wavelet Analysis
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  • 122
    Publication Date: 2012-06-16
    Description: Cells transmit information through molecular signals that often show complex dynamical patterns. The dynamic behavior of the tumor suppressor p53 varies depending on the stimulus; in response to double-strand DNA breaks, it shows a series of repeated pulses. Using a computational model, we identified a sequence of precisely timed drug additions that alter p53 pulses to instead produce a sustained p53 response. This leads to the expression of a different set of downstream genes and also alters cell fate: Cells that experience p53 pulses recover from DNA damage, whereas cells exposed to sustained p53 signaling frequently undergo senescence. Our results show that protein dynamics can be an important part of a signal, directly influencing cellular fate decisions.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4162876/" 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/PMC4162876/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Purvis, Jeremy E -- Karhohs, Kyle W -- Mock, Caroline -- Batchelor, Eric -- Loewer, Alexander -- Lahav, Galit -- F32 GM095168/GM/NIGMS NIH HHS/ -- F32GM095168/GM/NIGMS NIH HHS/ -- GM083303/GM/NIGMS NIH HHS/ -- K99 GM102372/GM/NIGMS NIH HHS/ -- R00 GM102372/GM/NIGMS NIH HHS/ -- R01 GM083303/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Jun 15;336(6087):1440-4. doi: 10.1126/science.1218351.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22700930" target="_blank"〉PubMed〈/a〉
    Keywords: Apoptosis/genetics ; Cell Aging/*genetics ; Cell Cycle Checkpoints ; Cell Line, Tumor ; Cyclin-Dependent Kinase Inhibitor p21/genetics ; *DNA Breaks, Double-Stranded ; DNA Repair ; Gamma Rays ; Humans ; Imidazoles/metabolism/pharmacology ; Models, Biological ; Nuclear Proteins/genetics ; Piperazines/metabolism/pharmacology ; *Signal Transduction ; Single-Cell Analysis ; Transcription Factors/genetics ; Transcriptional Activation ; Tumor Suppressor Protein p53/*metabolism ; Tumor Suppressor Proteins/genetics
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  • 123
    Publication Date: 2013-06-08
    Description: Genome-scale network reconstruction has enabled predictive modeling of metabolism for many systems. Traditionally, protein structural information has not been represented in such reconstructions. Expansion of a genome-scale model of Escherichia coli metabolism by including experimental and predicted protein structures enabled the analysis of protein thermostability in a network context. This analysis allowed the prediction of protein activities that limit network function at superoptimal temperatures and mechanistic interpretations of mutations found in strains adapted to heat. Predicted growth-limiting factors for thermotolerance were validated through nutrient supplementation experiments and defined metabolic sensitivities to heat stress, providing evidence that metabolic enzyme thermostability is rate-limiting at superoptimal temperatures. Inclusion of structural information expanded the content and predictive capability of genome-scale metabolic networks that enable structural systems biology of metabolism.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3777776/" 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/PMC3777776/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chang, Roger L -- Andrews, Kathleen -- Kim, Donghyuk -- Li, Zhanwen -- Godzik, Adam -- Palsson, Bernhard O -- R01 GM057089/GM/NIGMS NIH HHS/ -- R01 GM101457/GM/NIGMS NIH HHS/ -- R01GM101457/GM/NIGMS NIH HHS/ -- U54 GM094586/GM/NIGMS NIH HHS/ -- U54GM094586/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Jun 7;340(6137):1220-3. doi: 10.1126/science.1234012.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093-0412, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23744946" target="_blank"〉PubMed〈/a〉
    Keywords: Escherichia coli/*genetics/growth & development/*metabolism ; Escherichia coli Proteins/chemistry/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; *Hot Temperature ; *Metabolic Networks and Pathways ; Models, Biological ; Protein Conformation ; Systems Biology ; Transcriptional Activation
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  • 124
    Publication Date: 2013-02-09
    Description: Mutations in IDH1 and IDH2, the genes coding for isocitrate dehydrogenases 1 and 2, are common in several human cancers, including leukemias, and result in overproduction of the (R)-enantiomer of 2-hydroxyglutarate [(R)-2HG]. Elucidation of the role of IDH mutations and (R)-2HG in leukemogenesis has been hampered by a lack of appropriate cell-based models. Here, we show that a canonical IDH1 mutant, IDH1 R132H, promotes cytokine independence and blocks differentiation in hematopoietic cells. These effects can be recapitulated by (R)-2HG, but not (S)-2HG, despite the fact that (S)-2HG more potently inhibits enzymes, such as the 5'-methylcytosine hydroxylase TET2, that have previously been linked to the pathogenesis of IDH mutant tumors. We provide evidence that this paradox relates to the ability of (S)-2HG, but not (R)-2HG, to inhibit the EglN prolyl hydroxylases. Additionally, we show that transformation by (R)-2HG is reversible.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836459/" 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/PMC3836459/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Losman, Julie-Aurore -- Looper, Ryan E -- Koivunen, Peppi -- Lee, Sungwoo -- Schneider, Rebekka K -- McMahon, Christine -- Cowley, Glenn S -- Root, David E -- Ebert, Benjamin L -- Kaelin, William G Jr -- P30 DK049216/DK/NIDDK NIH HHS/ -- R01 CA068490/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2013 Mar 29;339(6127):1621-5. doi: 10.1126/science.1231677. Epub 2013 Feb 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23393090" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line, Tumor ; Cell Transformation, Neoplastic/genetics/*metabolism ; Glutarates/*metabolism ; *Hematopoiesis ; Humans ; Isocitrate Dehydrogenase/genetics/*metabolism ; Leukemia/*enzymology/genetics ; Models, Biological ; Procollagen-Proline Dioxygenase/*antagonists & inhibitors
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  • 125
    Publication Date: 2013-03-23
    Description: Biological membrane fission requires protein-driven stress. The guanosine triphosphatase (GTPase) dynamin builds up membrane stress by polymerizing into a helical collar that constricts the neck of budding vesicles. How this curvature stress mediates nonleaky membrane remodeling is actively debated. Using lipid nanotubes as substrates to directly measure geometric intermediates of the fission pathway, we found that GTP hydrolysis limits dynamin polymerization into short, metastable collars that are optimal for fission. Collars as short as two rungs translated radial constriction to reversible hemifission via membrane wedging of the pleckstrin homology domains (PHDs) of dynamin. Modeling revealed that tilting of the PHDs to conform with membrane deformations creates the low-energy pathway for hemifission. This local coordination of dynamin and lipids suggests how membranes can be remodeled in cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3980720/" 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/PMC3980720/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shnyrova, Anna V -- Bashkirov, Pavel V -- Akimov, Sergey A -- Pucadyil, Thomas J -- Zimmerberg, Joshua -- Schmid, Sandra L -- Frolov, Vadim A -- GM42455/GM/NIGMS NIH HHS/ -- R01 GM042455/GM/NIGMS NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2013 Mar 22;339(6126):1433-6. doi: 10.1126/science.1233920.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biophysics Unit (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23520112" target="_blank"〉PubMed〈/a〉
    Keywords: Biocatalysis ; Dynamin I/*chemistry/*metabolism ; Guanosine Triphosphate/metabolism ; Hydrolysis ; Lipid Bilayers/chemistry/*metabolism ; Models, Biological ; Nanotubes ; Protein Conformation ; Protein Multimerization ; Protein Structure, Tertiary ; Thermodynamics
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  • 126
    Publication Date: 2013-06-08
    Description: Colonial breeding is widespread among animals. Some, such as eusocial insects, may use agonistic behavior to partition available foraging habitat into mutually exclusive territories; others, such as breeding seabirds, do not. We found that northern gannets, satellite-tracked from 12 neighboring colonies, nonetheless forage in largely mutually exclusive areas and that these colony-specific home ranges are determined by density-dependent competition. This segregation may be enhanced by individual-level public information transfer, leading to cultural evolution and divergence among colonies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wakefield, Ewan D -- Bodey, Thomas W -- Bearhop, Stuart -- Blackburn, Jez -- Colhoun, Kendrew -- Davies, Rachel -- Dwyer, Ross G -- Green, Jonathan A -- Gremillet, David -- Jackson, Andrew L -- Jessopp, Mark J -- Kane, Adam -- Langston, Rowena H W -- Lescroel, Amelie -- Murray, Stuart -- Le Nuz, Melanie -- Patrick, Samantha C -- Peron, Clara -- Soanes, Louise M -- Wanless, Sarah -- Votier, Stephen C -- Hamer, Keith C -- New York, N.Y. -- Science. 2013 Jul 5;341(6141):68-70. doi: 10.1126/science.1236077. Epub 2013 Jun 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biology, University of Leeds, Leeds, UK. e.d.wakefield@leeds.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23744776" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Birds/*physiology ; Breeding ; *Feeding Behavior ; *Homing Behavior ; Models, Biological ; *Territoriality
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  • 127
    Publication Date: 2012-12-22
    Description: Neurotransmitter release depends critically on Munc18-1, Munc13, the Ca(2+) sensor synaptotagmin-1, and the soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptors (SNAREs) syntaxin-1, synaptobrevin, and SNAP-25. In vitro reconstitutions have shown that syntaxin-1-SNAP-25 liposomes fuse efficiently with synaptobrevin liposomes in the presence of synaptotagmin-1-Ca(2+), but neurotransmitter release also requires Munc18-1 and Munc13 in vivo. We found that Munc18-1 could displace SNAP-25 from syntaxin-1 and that fusion of syntaxin-1-Munc18-1 liposomes with synaptobrevin liposomes required Munc13, in addition to SNAP-25 and synaptotagmin-1-Ca(2+). Moreover, when starting with syntaxin-1-SNAP-25 liposomes, NSF-alpha-SNAP disassembled the syntaxin-1-SNAP-25 heterodimers and abrogated fusion, which then required Munc18-1 and Munc13. We propose that fusion does not proceed through syntaxin-1-SNAP-25 heterodimers but starts with the syntaxin-1-Munc18-1 complex; Munc18-1 and Munc13 then orchestrate membrane fusion together with the SNAREs and synaptotagmin-1-Ca(2+) in an NSF- and SNAP-resistant manner.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3733786/" 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/PMC3733786/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ma, Cong -- Su, Lijing -- Seven, Alpay B -- Xu, Yibin -- Rizo, Josep -- NS37200/NS/NINDS NIH HHS/ -- NS40944/NS/NINDS NIH HHS/ -- R01 NS037200/NS/NINDS NIH HHS/ -- R01 NS040944/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2013 Jan 25;339(6118):421-5. doi: 10.1126/science.1230473. Epub 2012 Dec 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Key Laboratory of Molecular Biophysics, Ministry of Education, and Institute of Biophysics and Biochemistry, Huazhong University of Science and Technology, Wuhan 430074, China. cong.ma7@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23258414" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcium/metabolism ; Humans ; Liposomes ; *Membrane Fusion ; Models, Biological ; Munc18 Proteins/*metabolism ; Nerve Tissue Proteins/*metabolism ; Neurotransmitter Agents/*metabolism ; Protein Binding ; Protein Multimerization ; R-SNARE Proteins/metabolism ; Rats ; Synaptic Vesicles/*metabolism ; Synaptosomal-Associated Protein 25/metabolism ; Synaptotagmin I/metabolism ; Syntaxin 1/metabolism
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  • 128
    Publication Date: 2013-01-12
    Description: The relationship between phenotype and fitness can be visualized as a rugged landscape. Multiple fitness peaks on this landscape are predicted to drive early bursts of niche diversification during adaptive radiation. We measured the adaptive landscape in a nascent adaptive radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas, and found multiple coexisting high-fitness regions driven by increased competition at high densities, supporting the early burst model. Hybrids resembling the generalist phenotype were isolated on a local fitness peak separated by a valley from a higher-fitness region corresponding to trophic specialization. This complex landscape could explain both the rarity of specialists across many similar environments due to stabilizing selection on generalists and the rapid morphological diversification rate of specialists due to their higher fitness.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Martin, Christopher H -- Wainwright, Peter C -- New York, N.Y. -- Science. 2013 Jan 11;339(6116):208-11. doi: 10.1126/science.1227710.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Evolution and Ecology and Center for Population Biology, University of California, One Shields Avenue, Davis, CA, USA. chmartin@ucdavis.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23307743" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/*genetics ; Animals ; Bahamas ; *Biological Evolution ; Crosses, Genetic ; Ecosystem ; Environment ; Female ; *Genetic Fitness ; Genetic Speciation ; Hybridization, Genetic ; Killifishes/*genetics/*physiology ; Lakes ; Male ; Models, Biological ; Phenotype ; Selection, Genetic
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  • 129
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2013-11-16
    Description: Experimental studies of evolution have increased greatly in number in recent years, stimulated by the growing power of genomic tools. However, organismal fitness remains the ultimate metric for interpreting these experiments, and the dynamics of fitness remain poorly understood over long time scales. Here, we examine fitness trajectories for 12 Escherichia coli populations during 50,000 generations. Mean fitness appears to increase without bound, consistent with a power law. We also derive this power-law relation theoretically by incorporating clonal interference and diminishing-returns epistasis into a dynamical model of changes in mean fitness over time.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wiser, Michael J -- Ribeck, Noah -- Lenski, Richard E -- New York, N.Y. -- Science. 2013 Dec 13;342(6164):1364-7. doi: 10.1126/science.1243357. Epub 2013 Nov 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24231808" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; Escherichia coli/*genetics/*physiology ; *Genetic Fitness ; Models, Biological ; *Reproduction, Asexual
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  • 130
    Publication Date: 2013-01-26
    Description: Signaling pathways can induce different dynamics of transcription factor (TF) activation. We explored how TFs process signaling inputs to generate diverse dynamic responses. The budding yeast general stress-responsive TF Msn2 acted as a tunable signal processor that could track, filter, or integrate signals in an input-dependent manner. This tunable signal processing appears to originate from dual regulation of both nuclear import and export by phosphorylation, as mutants with one form of regulation sustained only one signal-processing function. Versatile signal processing by Msn2 is crucial for generating distinct dynamic responses to different natural stresses. Our findings reveal how complex signal-processing functions are integrated into a single molecule and provide a guide for the design of TFs with "programmable" signal-processing functions.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3746486/" 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/PMC3746486/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hao, Nan -- Budnik, Bogdan A -- Gunawardena, Jeremy -- O'Shea, Erin K -- R01 GM081578/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2013 Jan 25;339(6118):460-4. doi: 10.1126/science.1227299.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Harvard University Faculty of Arts and Sciences Center for Systems Biology, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23349292" target="_blank"〉PubMed〈/a〉
    Keywords: Active Transport, Cell Nucleus ; Cell Nucleus/*metabolism ; Cyclic AMP-Dependent Protein Kinases/antagonists & inhibitors/genetics/metabolism ; Cytoplasm/metabolism ; DNA-Binding Proteins/*metabolism ; Models, Biological ; Nuclear Export Signals ; Nuclear Localization Signals ; Osmotic Pressure ; Oxidative Stress ; Phosphorylation ; Proteins/pharmacology ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/*metabolism ; *Signal Transduction ; Stress, Physiological ; Transcription Factors/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 131
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2013-07-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stone, Richard -- New York, N.Y. -- Science. 2013 Jul 19;341(6143):230-3. doi: 10.1126/science.341.6143.230.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23868998" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Armadillos ; *Extinction, Biological ; Marine Biology ; Marsupialia ; Models, Biological ; Panama ; *Phylogeography ; Porcupines
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  • 132
    Publication Date: 2013-10-19
    Description: The vast extent of the Amazon Basin has historically restricted the study of its tree communities to the local and regional scales. Here, we provide empirical data on the commonness, rarity, and richness of lowland tree species across the entire Amazon Basin and Guiana Shield (Amazonia), collected in 1170 tree plots in all major forest types. Extrapolations suggest that Amazonia harbors roughly 16,000 tree species, of which just 227 (1.4%) account for half of all trees. Most of these are habitat specialists and only dominant in one or two regions of the basin. We discuss some implications of the finding that a small group of species--less diverse than the North American tree flora--accounts for half of the world's most diverse tree community.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉ter Steege, Hans -- Pitman, Nigel C A -- Sabatier, Daniel -- Baraloto, Christopher -- Salomao, Rafael P -- Guevara, Juan Ernesto -- Phillips, Oliver L -- Castilho, Carolina V -- Magnusson, William E -- Molino, Jean-Francois -- Monteagudo, Abel -- Nunez Vargas, Percy -- Montero, Juan Carlos -- Feldpausch, Ted R -- Coronado, Euridice N Honorio -- Killeen, Tim J -- Mostacedo, Bonifacio -- Vasquez, Rodolfo -- Assis, Rafael L -- Terborgh, John -- Wittmann, Florian -- Andrade, Ana -- Laurance, William F -- Laurance, Susan G W -- Marimon, Beatriz S -- Marimon, Ben-Hur Jr -- Guimaraes Vieira, Ima Celia -- Amaral, Ieda Leao -- Brienen, Roel -- Castellanos, Hernan -- Cardenas Lopez, Dairon -- Duivenvoorden, Joost F -- Mogollon, Hugo F -- Matos, Francisca Dionizia de Almeida -- Davila, Nallarett -- Garcia-Villacorta, Roosevelt -- Stevenson Diaz, Pablo Roberto -- Costa, Flavia -- Emilio, Thaise -- Levis, Carolina -- Schietti, Juliana -- Souza, Priscila -- Alonso, Alfonso -- Dallmeier, Francisco -- Montoya, Alvaro Javier Duque -- Fernandez Piedade, Maria Teresa -- Araujo-Murakami, Alejandro -- Arroyo, Luzmila -- Gribel, Rogerio -- Fine, Paul V A -- Peres, Carlos A -- Toledo, Marisol -- Aymard C, Gerardo A -- Baker, Tim R -- Ceron, Carlos -- Engel, Julien -- Henkel, Terry W -- Maas, Paul -- Petronelli, Pascal -- Stropp, Juliana -- Zartman, Charles Eugene -- Daly, Doug -- Neill, David -- Silveira, Marcos -- Paredes, Marcos Rios -- Chave, Jerome -- Lima Filho, Diogenes de Andrade -- Jorgensen, Peter Moller -- Fuentes, Alfredo -- Schongart, Jochen -- Cornejo Valverde, Fernando -- Di Fiore, Anthony -- Jimenez, Eliana M -- Penuela Mora, Maria Cristina -- Phillips, Juan Fernando -- Rivas, Gonzalo -- van Andel, Tinde R -- von Hildebrand, Patricio -- Hoffman, Bruce -- Zent, Eglee L -- Malhi, Yadvinder -- Prieto, Adriana -- Rudas, Agustin -- Ruschell, Ademir R -- Silva, Natalino -- Vos, Vincent -- Zent, Stanford -- Oliveira, Alexandre A -- Schutz, Angela Cano -- Gonzales, Therany -- Trindade Nascimento, Marcelo -- Ramirez-Angulo, Hirma -- Sierra, Rodrigo -- Tirado, Milton -- Umana Medina, Maria Natalia -- van der Heijden, Geertje -- Vela, Cesar I A -- Vilanova Torre, Emilio -- Vriesendorp, Corine -- Wang, Ophelia -- Young, Kenneth R -- Baider, Claudia -- Balslev, Henrik -- Ferreira, Cid -- Mesones, Italo -- Torres-Lezama, Armando -- Urrego Giraldo, Ligia Estela -- Zagt, Roderick -- Alexiades, Miguel N -- Hernandez, Lionel -- Huamantupa-Chuquimaco, Isau -- Milliken, William -- Palacios Cuenca, Walter -- Pauletto, Daniela -- Valderrama Sandoval, Elvis -- Valenzuela Gamarra, Luis -- Dexter, Kyle G -- Feeley, Ken -- Lopez-Gonzalez, Gabriela -- Silman, Miles R -- New York, N.Y. -- Science. 2013 Oct 18;342(6156):1243092. doi: 10.1126/science.1243092.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Naturalis Biodiversity Center, Leiden, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24136971" target="_blank"〉PubMed〈/a〉
    Keywords: *Biodiversity ; Models, Biological ; Population ; *Rivers ; South America ; Trees/*classification/*physiology
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  • 133
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2013-05-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Min -- Schekman, Randy -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2013 May 3;340(6132):559-61. doi: 10.1126/science.1234740.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA 94720-3370, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23641104" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Autophagy ; Carrier Proteins/metabolism ; Cell Membrane/metabolism/*secretion ; Exosomes/metabolism ; Lysosomes/metabolism ; Membrane Fusion ; Membrane Proteins/metabolism ; Membrane Transport Proteins/metabolism ; Models, Biological ; Phagosomes/metabolism ; Proteins/*metabolism/*secretion ; *Secretory Pathway ; Secretory Vesicles/metabolism
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  • 134
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-01-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stokstad, Erik -- New York, N.Y. -- Science. 2014 Jan 17;343(6168):238. doi: 10.1126/science.343.6168.238.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24436398" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture ; Air Pollutants/*adverse effects/analysis ; Air Pollution/*adverse effects/prevention & control ; Ammonia/*adverse effects/analysis ; Animals ; Fertilizers/*adverse effects ; Health/*economics ; Heart Diseases/chemically induced ; Humans ; Livestock ; Models, Biological ; North Carolina ; Particulate Matter/*adverse effects/analysis ; Respiratory Tract Diseases/chemically induced ; United States ; United States Environmental Protection Agency
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  • 135
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-09-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kupferschmidt, Kai -- New York, N.Y. -- Science. 2014 Sep 5;345(6201):1108. doi: 10.1126/science.345.6201.1108.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25190771" target="_blank"〉PubMed〈/a〉
    Keywords: Africa, Western/epidemiology ; *Ebolavirus ; Epidemics ; Hemorrhagic Fever, Ebola/*epidemiology/*prevention & control ; Humans ; Models, Biological
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  • 136
    Publication Date: 2014-08-02
    Description: During limb development, digits emerge from the undifferentiated mesenchymal tissue that constitutes the limb bud. It has been proposed that this process is controlled by a self-organizing Turing mechanism, whereby diffusible molecules interact to produce a periodic pattern of digital and interdigital fates. However, the identities of the molecules remain unknown. By combining experiments and modeling, we reveal evidence that a Turing network implemented by Bmp, Sox9, and Wnt drives digit specification. We develop a realistic two-dimensional simulation of digit patterning and show that this network, when modulated by morphogen gradients, recapitulates the expression patterns of Sox9 in the wild type and in perturbation experiments. Our systems biology approach reveals how a combination of growth, morphogen gradients, and a self-organizing Turing network can achieve robust and reproducible pattern formation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Raspopovic, J -- Marcon, L -- Russo, L -- Sharpe, J -- New York, N.Y. -- Science. 2014 Aug 1;345(6196):566-70. doi: 10.1126/science.1252960.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Systems Biology Program, Centre for Genomic Regulation (CRG), and Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain. ; Systems Biology Program, Centre for Genomic Regulation (CRG), and Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain. Institucio Catalana de Recerca i Estudis Avancats (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain. james.sharpe@crg.eu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25082703" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Body Patterning/*genetics ; Bone Morphogenetic Proteins/*metabolism ; Computer Simulation ; Extremities/*embryology ; Female ; *Gene Expression Regulation, Developmental ; Gene Knockdown Techniques ; Green Fluorescent Proteins/genetics/metabolism ; Limb Buds/*embryology ; Mice ; Mice, Inbred Strains ; Models, Biological ; Oligonucleotide Array Sequence Analysis ; SOX9 Transcription Factor/genetics/*metabolism ; Wnt Proteins/*metabolism
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  • 137
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    Nature Publishing Group (NPG)
    Publication Date: 2010-01-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schrope, Mark -- England -- Nature. 2010 Jan 7;463(7277):22-3. doi: 10.1038/463022a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20054373" target="_blank"〉PubMed〈/a〉
    Keywords: Animal Identification Systems ; Animals ; *Biodiversity ; Ecology/*methods ; *Geography ; Global Warming ; Models, Biological ; Population Dynamics ; Rain ; West Indies ; *Wilderness
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 138
    Publication Date: 2010-01-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mitchison, T J -- Mitchison, H M -- England -- Nature. 2010 Jan 21;463(7279):308-9. doi: 10.1038/463308a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20090745" target="_blank"〉PubMed〈/a〉
    Keywords: Axoneme/physiology ; Cilia/pathology/*physiology ; Ciliary Motility Disorders/metabolism/pathology ; Dyneins/metabolism ; Flagella/physiology ; Humans ; Models, Biological ; Movement/*physiology ; Periodicity
    Print ISSN: 0028-0836
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  • 139
    Publication Date: 2010-06-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Blaustein, Andrew R -- Johnson, Pieter T J -- England -- Nature. 2010 Jun 17;465(7300):881-2. doi: 10.1038/465881a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20559377" target="_blank"〉PubMed〈/a〉
    Keywords: Amphibians/*microbiology ; Animals ; Chytridiomycota/*physiology ; *Conservation of Natural Resources ; Models, Biological ; Mycoses/*microbiology/mortality/transmission ; Population Density
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  • 140
    Publication Date: 2011-02-26
    Description: Mammalian prions cause fatal neurodegenerative conditions including Creutzfeldt-Jakob disease in humans and scrapie and bovine spongiform encephalopathy in animals. Prion infections are typically associated with remarkably prolonged but highly consistent incubation periods followed by a rapid clinical phase. The relationship between prion propagation, generation of neurotoxic species and clinical onset has remained obscure. Prion incubation periods in experimental animals are known to vary inversely with expression level of cellular prion protein. Here we demonstrate that prion propagation in brain proceeds via two distinct phases: a clinically silent exponential phase not rate-limited by prion protein concentration which rapidly reaches a maximal prion titre, followed by a distinct switch to a plateau phase. The latter determines time to clinical onset in a manner inversely proportional to prion protein concentration. These findings demonstrate an uncoupling of infectivity and toxicity. We suggest that prions themselves are not neurotoxic but catalyse the formation of such species from PrP(C). Production of neurotoxic species is triggered when prion propagation saturates, leading to a switch from autocatalytic production of infectivity (phase 1) to a toxic (phase 2) pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sandberg, Malin K -- Al-Doujaily, Huda -- Sharps, Bernadette -- Clarke, Anthony R -- Collinge, John -- MC_U123160656/Medical Research Council/United Kingdom -- MC_U123192748/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- England -- Nature. 2011 Feb 24;470(7335):540-2. doi: 10.1038/nature09768.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Prion Unit and Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21350487" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biocatalysis ; Biological Assay ; Disease Models, Animal ; Gene Expression ; Kinetics ; Mice ; Mice, Transgenic ; Models, Biological ; PrPC Proteins/analysis/biosynthesis/genetics/metabolism ; PrPSc Proteins/biosynthesis/*metabolism/*pathogenicity/toxicity ; Prion Diseases/*metabolism/*pathology/physiopathology/transmission ; Survival Rate ; Time Factors ; Toxicity Tests
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  • 141
    Publication Date: 2011-07-08
    Description: A central challenge for predators is achieving positive energy balance when prey are spatially and temporally heterogeneous. Ecological heterogeneity produces evolutionary trade-offs in the physiological design of predators; this is because the ability to capitalize on pulses of food abundance requires high capacity for food-processing, yet maintaining such capacity imposes energetic costs that are taxing during periods of food scarcity. Recent advances in physiology show that when variation in foraging opportunities is predictable, animals may adjust energetic trade-offs by rapidly modulating their digestive system to track variation in foraging opportunities. However, it is increasingly recognized that foraging opportunities for animals are unpredictable, which should favour animals that maintain a capacity for food-processing that exceeds average levels of consumption (loads). Despite this basic principle of quantitative evolutionary design, estimates of digestive load:capacity ratios in wild animals are virtually non-existent. Here we provide an extensive assessment of load:capacity ratios for the digestive systems of predators in the wild, compiling 639 estimates across 38 species of fish. We found that piscine predators typically maintain the physiological capacity to feed at daily rates 2-3 times higher than what they experience on average. A numerical simulation of the trade-off between food-processing capacity and metabolic cost suggests that the observed level of physiological opportunism is profitable only if predator-prey encounters, and thus predator energy budgets, are far more variable in nature than currently assumed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Armstrong, Jonathan B -- Schindler, Daniel E -- England -- Nature. 2011 Jul 6;476(7358):84-7. doi: 10.1038/nature10240.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Aquatic and Fishery Sciences, Box 355020, University of Washington, Seattle, Washington 98195, USA. Jonny99@uw.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21734659" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Evolution ; Digestion/*physiology ; Energy Metabolism/*physiology ; Feeding Behavior/*physiology ; Fishes/*physiology ; Models, Biological ; *Predatory Behavior/physiology ; Starvation/*physiopathology/*veterinary ; Time Factors ; *Uncertainty
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  • 142
    Publication Date: 2011-01-21
    Description: Many tumours are composed of genetically diverse cells; however, little is known about how diversity evolves or the impact that diversity has on functional properties. Here, using xenografting and DNA copy number alteration (CNA) profiling of human BCR-ABL1 lymphoblastic leukaemia, we demonstrate that genetic diversity occurs in functionally defined leukaemia-initiating cells and that many diagnostic patient samples contain multiple genetically distinct leukaemia-initiating cell subclones. Reconstructing the subclonal genetic ancestry of several samples by CNA profiling demonstrated a branching multi-clonal evolution model of leukaemogenesis, rather than linear succession. For some patient samples, the predominant diagnostic clone repopulated xenografts, whereas in others it was outcompeted by minor subclones. Reconstitution with the predominant diagnosis clone was associated with more aggressive growth properties in xenografts, deletion of CDKN2A and CDKN2B, and a trend towards poorer patient outcome. Our findings link clonal diversity with leukaemia-initiating-cell function and underscore the importance of developing therapies that eradicate all intratumoral subclones.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Notta, Faiyaz -- Mullighan, Charles G -- Wang, Jean C Y -- Poeppl, Armando -- Doulatov, Sergei -- Phillips, Letha A -- Ma, Jing -- Minden, Mark D -- Downing, James R -- Dick, John E -- Canadian Institutes of Health Research/Canada -- England -- Nature. 2011 Jan 20;469(7330):362-7. doi: 10.1038/nature09733.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Stem Cell and Developmental Biology, Campbell Family Institute for Cancer Research/Ontario Cancer Institute, Toronto, Ontario M5G 1L7, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21248843" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Survival ; Clone Cells/*metabolism/*pathology ; Cyclin-Dependent Kinase Inhibitor p15/deficiency/genetics ; DNA Copy Number Variations/genetics ; Disease Progression ; *Evolution, Molecular ; Fusion Proteins, bcr-abl/*genetics ; Genes, p16 ; Humans ; Mice ; Mice, Inbred NOD ; Mice, SCID ; Models, Biological ; Neoplasm Transplantation ; Oligonucleotide Array Sequence Analysis ; Philadelphia Chromosome ; Polymorphism, Single Nucleotide/genetics ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/*genetics/*pathology ; Survival Rate ; Transplantation, Heterologous
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  • 143
    Publication Date: 2011-03-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chouard, Tanguy -- England -- Nature. 2011 Mar 10;471(7337):151-3. doi: 10.1038/471151a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21390105" target="_blank"〉PubMed〈/a〉
    Keywords: CREB-Binding Protein/metabolism ; Calcineurin/chemistry/metabolism ; Cell Cycle Proteins/chemistry/metabolism ; Computational Biology ; Crystallization ; Cyclic AMP Response Element-Binding Protein/chemistry/metabolism ; Cyclin-Dependent Kinase Inhibitor Proteins/chemistry/metabolism ; F-Box Proteins/chemistry/metabolism ; Humans ; Models, Biological ; Models, Molecular ; Pliability ; Protein Conformation ; Protein Folding ; *Protein Unfolding ; Proteins/*chemistry/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism ; Structure-Activity Relationship ; Tumor Suppressor Protein p53/chemistry/metabolism ; Ubiquitin-Protein Ligases/chemistry/metabolism
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  • 144
    Publication Date: 2010-02-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abeliovich, Asa -- England -- Nature. 2010 Feb 11;463(7282):744-5. doi: 10.1038/463744a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20148026" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Autophagy ; Dopamine/metabolism ; Drosophila melanogaster/genetics/metabolism ; Environment ; Humans ; Membrane Potentials/drug effects ; Mitochondria/drug effects/*metabolism/*pathology ; Models, Biological ; Oxidative Stress ; Parkinson Disease/genetics/*metabolism/*pathology ; Protein Kinases/deficiency/genetics/*metabolism ; Ubiquitin-Protein Ligases/genetics/metabolism
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  • 145
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2011-06-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ball, Philip -- England -- Nature. 2011 Jun 15;474(7351):272-4. doi: 10.1038/474272a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21677723" target="_blank"〉PubMed〈/a〉
    Keywords: Animal Migration ; Animals ; Birds/physiology ; *Life ; Magnetics ; Models, Biological ; Nature ; Photosynthesis/physiology ; *Quantum Theory
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  • 146
    Publication Date: 2011-05-13
    Description: Protein translocation across the bacterial membrane, mediated by the secretory translocon SecYEG and the SecA ATPase, is enhanced by proton motive force and membrane-integrated SecDF, which associates with SecYEG. The role of SecDF has remained unclear, although it is proposed to function in later stages of translocation as well as in membrane protein biogenesis. Here, we determined the crystal structure of Thermus thermophilus SecDF at 3.3 A resolution, revealing a pseudo-symmetrical, 12-helix transmembrane domain belonging to the RND superfamily and two major periplasmic domains, P1 and P4. Higher-resolution analysis of the periplasmic domains suggested that P1, which binds an unfolded protein, undergoes functionally important conformational changes. In vitro analyses identified an ATP-independent step of protein translocation that requires both SecDF and proton motive force. Electrophysiological analyses revealed that SecDF conducts protons in a manner dependent on pH and the presence of an unfolded protein, with conserved Asp and Arg residues at the transmembrane interface between SecD and SecF playing essential roles in the movements of protons and preproteins. Therefore, we propose that SecDF functions as a membrane-integrated chaperone, powered by proton motive force, to achieve ATP-independent protein translocation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3697915/" 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/PMC3697915/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tsukazaki, Tomoya -- Mori, Hiroyuki -- Echizen, Yuka -- Ishitani, Ryuichiro -- Fukai, Shuya -- Tanaka, Takeshi -- Perederina, Anna -- Vassylyev, Dmitry G -- Kohno, Toshiyuki -- Maturana, Andres D -- Ito, Koreaki -- Nureki, Osamu -- R01 GM074840/GM/NIGMS NIH HHS/ -- England -- Nature. 2011 May 11;474(7350):235-8. doi: 10.1038/nature09980.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21562494" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Arginine/metabolism ; Asparagine/metabolism ; Bacterial Proteins/*chemistry/*metabolism ; Crystallography, X-Ray ; Hydrogen-Ion Concentration ; Membrane Proteins/*chemistry/*metabolism ; Membrane Transport Proteins/*chemistry/*metabolism ; Models, Biological ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Periplasm/chemistry/metabolism ; Protein Structure, Tertiary ; Protein Transport ; Protein Unfolding ; Proton-Motive Force ; Static Electricity ; Structure-Activity Relationship ; Thermus thermophilus/*chemistry/cytology
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  • 147
    Publication Date: 2011-08-09
    Description: Cytokinesis, the physical separation of daughter cells at the end of mitosis, requires precise regulation of the mechanical properties of the cell periphery. Although studies of cytokinetic mechanics mostly focus on the equatorial constriction ring, a contractile actomyosin cortex is also present at the poles of dividing cells. Whether polar forces influence cytokinetic cell shape and furrow positioning remains an open question. Here we demonstrate that the polar cortex makes cytokinesis inherently unstable. We show that limited asymmetric polar contractions occur during cytokinesis, and that perturbing the polar cortex leads to cell shape oscillations, resulting in furrow displacement and aneuploidy. A theoretical model based on a competition between cortex turnover and contraction dynamics accurately accounts for the oscillations. We further propose that membrane blebs, which commonly form at the poles of dividing cells and whose role in cytokinesis has long been enigmatic, stabilize cell shape by acting as valves releasing cortical contractility. Our findings reveal an inherent instability in the shape of the dividing cell and unveil a novel, spindle-independent mechanism ensuring the stability of cleavage furrow positioning.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sedzinski, Jakub -- Biro, Mate -- Oswald, Annelie -- Tinevez, Jean-Yves -- Salbreux, Guillaume -- Paluch, Ewa -- England -- Nature. 2011 Aug 7;476(7361):462-6. doi: 10.1038/nature10286.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21822289" target="_blank"〉PubMed〈/a〉
    Keywords: Actomyosin/*metabolism ; Amides/pharmacology ; Aneuploidy ; Cell Line ; Cell Shape/drug effects/*physiology ; Cell Size/drug effects ; Cytokinesis/drug effects/*physiology ; HeLa Cells ; Humans ; Models, Biological ; Pyridines/pharmacology
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  • 148
    Publication Date: 2011-03-23
    Description: The nucleobase/ascorbate transporter (NAT) proteins, also known as nucleobase/cation symporter 2 (NCS2) proteins, are responsible for the uptake of nucleobases in all kingdoms of life and for the transport of vitamin C in mammals. Despite functional characterization of the NAT family members in bacteria, fungi and mammals, detailed structural information remains unavailable. Here we report the crystal structure of a representative NAT protein, the Escherichia coli uracil/H(+) symporter UraA, in complex with uracil at a resolution of 2.8 A. UraA has a novel structural fold, with 14 transmembrane segments (TMs) divided into two inverted repeats. A pair of antiparallel beta-strands is located between TM3 and TM10 and has an important role in structural organization and substrate recognition. The structure is spatially arranged into a core domain and a gate domain. Uracil, located at the interface between the two domains, is coordinated mainly by residues from the core domain. Structural analysis suggests that alternating access of the substrate may be achieved through conformational changes of the gate domain.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lu, Feiran -- Li, Shuo -- Jiang, Yang -- Jiang, Jing -- Fan, He -- Lu, Guifeng -- Deng, Dong -- Dang, Shangyu -- Zhang, Xu -- Wang, Jiawei -- Yan, Nieng -- England -- Nature. 2011 Apr 14;472(7342):243-6. doi: 10.1038/nature09885. Epub 2011 Mar 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉State Key Laboratory of Bio-membrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21423164" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Transport ; Crystallography, X-Ray ; Escherichia coli/*chemistry ; Escherichia coli Proteins/*chemistry/*metabolism ; Hydrogen Bonding ; Membrane Transport Proteins/*chemistry/*metabolism ; Models, Biological ; Models, Molecular ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protons ; Structure-Activity Relationship ; Uracil/chemistry/*metabolism
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  • 149
    Publication Date: 2011-10-21
    Description: Climate change is driving latitudinal and altitudinal shifts in species distribution worldwide, leading to novel species assemblages. Lags between these biotic responses and contemporary climate changes have been reported for plants and animals. Theoretically, the magnitude of these lags should be greatest in lowland areas, where the velocity of climate change is expected to be much greater than that in highland areas. We compared temperature trends to temperatures reconstructed from plant assemblages (observed in 76,634 surveys) over a 44-year period in France (1965-2008). Here we report that forest plant communities had responded to 0.54 degrees C of the effective increase of 1.07 degrees C in highland areas (500-2,600 m above sea level), while they had responded to only 0.02 degrees C of the 1.11 degrees C warming trend in lowland areas. There was a larger temperature lag (by 3.1 times) between the climate and plant community composition in lowland forests than in highland forests. The explanation of such disparity lies in the following properties of lowland, as compared to highland, forests: the higher proportion of species with greater ability for local persistence as the climate warms, the reduced opportunity for short-distance escapes, and the greater habitat fragmentation. Although mountains are currently considered to be among the ecosystems most threatened by climate change (owing to mountaintop extinction), the current inertia of plant communities in lowland forests should also be noted, as it could lead to lowland biotic attrition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bertrand, Romain -- Lenoir, Jonathan -- Piedallu, Christian -- Riofrio-Dillon, Gabriela -- de Ruffray, Patrice -- Vidal, Claude -- Pierrat, Jean-Claude -- Gegout, Jean-Claude -- England -- Nature. 2011 Oct 19;479(7374):517-20. doi: 10.1038/nature10548.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉AgroParisTech, ENGREF, UMR1092 Laboratoire d'Etude des Ressources Foret-Bois (LERFoB), 14 rue Girardet, F-54000 Nancy, France. romain.bertrand@engref.agroparistech.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22012261" target="_blank"〉PubMed〈/a〉
    Keywords: Altitude ; *Biota ; France ; Global Warming/*statistics & numerical data ; History, 20th Century ; History, 21st Century ; Models, Biological ; *Plants ; Temperature ; Time Factors ; *Trees
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  • 150
    Publication Date: 2011-10-21
    Description: The radiation of the mammals provides a 165-million-year test case for evolutionary theories of how species occupy and then fill ecological niches. It is widely assumed that species often diverge rapidly early in their evolution, and that this is followed by a longer, drawn-out period of slower evolutionary fine-tuning as natural selection fits organisms into an increasingly occupied niche space. But recent studies have hinted that the process may not be so simple. Here we apply statistical methods that automatically detect temporal shifts in the rate of evolution through time to a comprehensive mammalian phylogeny and data set of body sizes of 3,185 extant species. Unexpectedly, the majority of mammal species, including two of the most speciose orders (Rodentia and Chiroptera), have no history of substantial and sustained increases in the rates of evolution. Instead, a subset of the mammals has experienced an explosive increase (between 10- and 52-fold) in the rate of evolution along the single branch leading to the common ancestor of their monophyletic group (for example Chiroptera), followed by a quick return to lower or background levels. The remaining species are a taxonomically diverse assemblage showing a significant, sustained increase or decrease in their rates of evolution. These results necessarily decouple morphological diversification from speciation and suggest that the processes that give rise to the morphological diversity of a class of animals are far more free to vary than previously considered. Niches do not seem to fill up, and diversity seems to arise whenever, wherever and at whatever rate it is advantageous.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Venditti, Chris -- Meade, Andrew -- Pagel, Mark -- England -- Nature. 2011 Oct 19;479(7373):393-6. doi: 10.1038/nature10516.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK. c.venditti@hull.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22012260" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; *Biological Evolution ; Body Size ; Genetic Speciation ; Mammals/anatomy & histology/classification/*physiology ; Models, Biological ; Phylogeny ; Time Factors
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  • 151
    Publication Date: 2011-10-28
    Description: Molluscs (snails, octopuses, clams and their relatives) have a great disparity of body plans and, among the animals, only arthropods surpass them in species number. This diversity has made Mollusca one of the best-studied groups of animals, yet their evolutionary relationships remain poorly resolved. Open questions have important implications for the origin of Mollusca and for morphological evolution within the group. These questions include whether the shell-less, vermiform aplacophoran molluscs diverged before the origin of the shelled molluscs (Conchifera) or lost their shells secondarily. Monoplacophorans were not included in molecular studies until recently, when it was proposed that they constitute a clade named Serialia together with Polyplacophora (chitons), reflecting the serial repetition of body organs in both groups. Attempts to understand the early evolution of molluscs become even more complex when considering the large diversity of Cambrian fossils. These can have multiple dorsal shell plates and sclerites or can be shell-less but with a typical molluscan radula and serially repeated gills. To better resolve the relationships among molluscs, we generated transcriptome data for 15 species that, in combination with existing data, represent for the first time all major molluscan groups. We analysed multiple data sets containing up to 216,402 sites and 1,185 gene regions using multiple models and methods. Our results support the clade Aculifera, containing the three molluscan groups with spicules but without true shells, and they support the monophyly of Conchifera. Monoplacophora is not the sister group to other Conchifera but to Cephalopoda. Strong support is found for a clade that comprises Scaphopoda (tusk shells), Gastropoda and Bivalvia, with most analyses placing Scaphopoda and Gastropoda as sister groups. This well-resolved tree will constitute a framework for further studies of mollusc evolution, development and anatomy.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smith, Stephen A -- Wilson, Nerida G -- Goetz, Freya E -- Feehery, Caitlin -- Andrade, Sonia C S -- Rouse, Greg W -- Giribet, Gonzalo -- Dunn, Casey W -- England -- Nature. 2011 Oct 26;480(7377):364-7. doi: 10.1038/nature10526.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22031330" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bivalvia/classification/genetics ; Cephalopoda/classification/genetics ; Gastropoda/classification/genetics ; Gene Expression Profiling ; Likelihood Functions ; Models, Biological ; Mollusca/*classification/*genetics ; *Phylogeny ; Species Specificity ; Transcriptome/*genetics
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  • 152
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2011-01-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brown, Mark J F -- England -- Nature. 2011 Jan 13;469(7329):169-70. doi: 10.1038/469169a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21228865" target="_blank"〉PubMed〈/a〉
    Keywords: Amphibians/microbiology ; Animals ; Bees/classification/genetics/*parasitology/*physiology ; Conservation of Natural Resources/trends ; *Ecosystem ; Europe ; Extinction, Biological ; Humans ; Models, Biological ; Pollination ; Population Dynamics ; Time Factors ; United States
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  • 153
    Publication Date: 2011-08-19
    Description: Latency and ongoing replication have both been proposed to explain the drug-insensitive human immunodeficiency virus (HIV) reservoir maintained during antiretroviral therapy. Here we explore a novel mechanism for ongoing HIV replication in the face of antiretroviral drugs. We propose a model whereby multiple infections per cell lead to reduced sensitivity to drugs without requiring drug-resistant mutations, and experimentally validate the model using multiple infections per cell by cell-free HIV in the presence of the drug tenofovir. We then examine the drug sensitivity of cell-to-cell spread of HIV, a mode of HIV transmission that can lead to multiple infection events per target cell. Infections originating from cell-free virus decrease strongly in the presence of antiretrovirals tenofovir and efavirenz whereas infections involving cell-to-cell spread are markedly less sensitive to the drugs. The reduction in sensitivity is sufficient to keep multiple rounds of infection from terminating in the presence of drugs. We examine replication from cell-to-cell spread in the presence of clinical drug concentrations using a stochastic infection model and find that replication is intermittent, without substantial accumulation of mutations. If cell-to-cell spread has the same properties in vivo, it may have adverse consequences for the immune system, lead to therapy failure in individuals with risk factors, and potentially contribute to viral persistence and hence be a barrier to curing HIV infection.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sigal, Alex -- Kim, Jocelyn T -- Balazs, Alejandro B -- Dekel, Erez -- Mayo, Avi -- Milo, Ron -- Baltimore, David -- HHSN266200500035C/PHS HHS/ -- T32 AI089398/AI/NIAID NIH HHS/ -- England -- Nature. 2011 Aug 17;477(7362):95-8. doi: 10.1038/nature10347.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21849975" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/analogs & derivatives/pharmacology ; Anti-Retroviral Agents/*pharmacology ; Cell Line ; Drug Resistance, Viral/physiology ; HEK293 Cells ; HIV Infections/transmission/*virology ; HIV-1/drug effects/*physiology ; Humans ; Models, Biological ; Organophosphonates/pharmacology ; Tenofovir ; Virus Replication/drug effects/*physiology
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  • 154
    Publication Date: 2011-07-22
    Description: The impressive capabilities of the mammalian brain--ranging from perception, pattern recognition and memory formation to decision making and motor activity control--have inspired their re-creation in a wide range of artificial intelligence systems for applications such as face recognition, anomaly detection, medical diagnosis and robotic vehicle control. Yet before neuron-based brains evolved, complex biomolecular circuits provided individual cells with the 'intelligent' behaviour required for survival. However, the study of how molecules can 'think' has not produced an equal variety of computational models and applications of artificial chemical systems. Although biomolecular systems have been hypothesized to carry out neural-network-like computations in vivo and the synthesis of artificial chemical analogues has been proposed theoretically, experimental work has so far fallen short of fully implementing even a single neuron. Here, building on the richness of DNA computing and strand displacement circuitry, we show how molecular systems can exhibit autonomous brain-like behaviours. Using a simple DNA gate architecture that allows experimental scale-up of multilayer digital circuits, we systematically transform arbitrary linear threshold circuits (an artificial neural network model) into DNA strand displacement cascades that function as small neural networks. Our approach even allows us to implement a Hopfield associative memory with four fully connected artificial neurons that, after training in silico, remembers four single-stranded DNA patterns and recalls the most similar one when presented with an incomplete pattern. Our results suggest that DNA strand displacement cascades could be used to endow autonomous chemical systems with the capability of recognizing patterns of molecular events, making decisions and responding to the environment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Qian, Lulu -- Winfree, Erik -- Bruck, Jehoshua -- England -- Nature. 2011 Jul 20;475(7356):368-72. doi: 10.1038/nature10262.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Bioengineering, California Institute of Technology, Pasadena, California 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21776082" target="_blank"〉PubMed〈/a〉
    Keywords: Biomimetics ; *Computers, Molecular ; DNA/analysis/*chemistry ; Decision Making ; Memory ; Models, Biological ; Nanotechnology ; *Neural Networks (Computer) ; Neurons ; Synthetic Biology
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  • 155
    Publication Date: 2011-10-07
    Description: Maize smut caused by the fungus Ustilago maydis is a widespread disease characterized by the development of large plant tumours. U. maydis is a biotrophic pathogen that requires living plant tissue for its development and establishes an intimate interaction zone between fungal hyphae and the plant plasma membrane. U. maydis actively suppresses plant defence responses by secreted protein effectors. Its effector repertoire comprises at least 386 genes mostly encoding proteins of unknown function and expressed exclusively during the biotrophic stage. The U. maydis secretome also contains about 150 proteins with probable roles in fungal nutrition, fungal cell wall modification and host penetration as well as proteins unlikely to act in the fungal-host interface like a chorismate mutase. Chorismate mutases are key enzymes of the shikimate pathway and catalyse the conversion of chorismate to prephenate, the precursor for tyrosine and phenylalanine synthesis. Root-knot nematodes inject a secreted chorismate mutase into plant cells likely to affect development. Here we show that the chorismate mutase Cmu1 secreted by U. maydis is a virulence factor. The enzyme is taken up by plant cells, can spread to neighbouring cells and changes the metabolic status of these cells through metabolic priming. Secreted chorismate mutases are found in many plant-associated microbes and might serve as general tools for host manipulation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Djamei, Armin -- Schipper, Kerstin -- Rabe, Franziska -- Ghosh, Anupama -- Vincon, Volker -- Kahnt, Jorg -- Osorio, Sonia -- Tohge, Takayuki -- Fernie, Alisdair R -- Feussner, Ivo -- Feussner, Kirstin -- Meinicke, Peter -- Stierhof, York-Dieter -- Schwarz, Heinz -- Macek, Boris -- Mann, Matthias -- Kahmann, Regine -- England -- Nature. 2011 Oct 5;478(7369):395-8. doi: 10.1038/nature10454.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21976020" target="_blank"〉PubMed〈/a〉
    Keywords: Chorismate Mutase/*metabolism ; Cytoplasm/enzymology ; Gene Expression Regulation, Plant ; Genetic Complementation Test ; Host-Pathogen Interactions ; Metabolome ; Models, Biological ; Plant Proteins/metabolism ; Plastids/enzymology ; Protein Multimerization ; Saccharomyces cerevisiae/genetics ; Salicylic Acid/metabolism ; Two-Hybrid System Techniques ; Ustilago/*enzymology/*pathogenicity ; Virulence Factors/genetics/*metabolism ; Zea mays/*metabolism/*microbiology
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  • 156
    Publication Date: 2011-07-08
    Description: Swi2/Snf2-type ATPases regulate genome-associated processes such as transcription, replication and repair by catalysing the disruption, assembly or remodelling of nucleosomes or other protein-DNA complexes. It has been suggested that ATP-driven motor activity along DNA disrupts target protein-DNA interactions in the remodelling reaction. However, the complex and highly specific remodelling reactions are poorly understood, mostly because of a lack of high-resolution structural information about how remodellers bind to their substrate proteins. Mot1 (modifier of transcription 1 in Saccharomyces cerevisiae, denoted BTAF1 in humans) is a Swi2/Snf2 enzyme that specifically displaces the TATA box binding protein (TBP) from the promoter DNA and regulates transcription globally by generating a highly dynamic TBP pool in the cell. As a Swi2/Snf2 enzyme that functions as a single polypeptide and interacts with a relatively simple substrate, Mot1 offers an ideal system from which to gain a better understanding of this important enzyme family. To reveal how Mot1 specifically disrupts TBP-DNA complexes, we combined crystal and electron microscopy structures of Mot1-TBP from Encephalitozoon cuniculi with biochemical studies. Here we show that Mot1 wraps around TBP and seems to act like a bottle opener: a spring-like array of 16 HEAT (huntingtin, elongation factor 3, protein phosphatase 2A and lipid kinase TOR) repeats grips the DNA-distal side of TBP via loop insertions, and the Swi2/Snf2 domain binds to upstream DNA, positioned to weaken the TBP-DNA interaction by DNA translocation. A 'latch' subsequently blocks the DNA-binding groove of TBP, acting as a chaperone to prevent DNA re-association and ensure efficient promoter clearance. This work shows how a remodelling enzyme can combine both motor and chaperone activities to achieve functional specificity using a conserved Swi2/Snf2 translocase.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3276066/" 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/PMC3276066/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wollmann, Petra -- Cui, Sheng -- Viswanathan, Ramya -- Berninghausen, Otto -- Wells, Melissa N -- Moldt, Manuela -- Witte, Gregor -- Butryn, Agata -- Wendler, Petra -- Beckmann, Roland -- Auble, David T -- Hopfner, Karl-Peter -- GM55763/GM/NIGMS NIH HHS/ -- R01 GM055763/GM/NIGMS NIH HHS/ -- R01 GM055763-13/GM/NIGMS NIH HHS/ -- England -- Nature. 2011 Jul 6;475(7356):403-7. doi: 10.1038/nature10215.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Ludwig-Maximilians University, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21734658" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA/chemistry/genetics/metabolism/ultrastructure ; Encephalitozoon cuniculi/*chemistry ; Fungal Proteins/*chemistry/*metabolism/ultrastructure ; Microscopy, Electron ; Models, Biological ; Models, Molecular ; Promoter Regions, Genetic/genetics ; Protein Conformation ; Protein Structure, Tertiary ; Structure-Activity Relationship ; Substrate Specificity ; TATA-Box Binding Protein/*chemistry/*metabolism/ultrastructure ; Transcription Factor TFIIB/chemistry/metabolism
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  • 157
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    Nature Publishing Group (NPG)
    Publication Date: 2011-07-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eisenstein, Michael -- England -- Nature. 2011 Jul 13;475(7355):S20-2. doi: 10.1038/475S20a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21760580" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/genetics ; Age of Onset ; Alzheimer Disease/*genetics/immunology/metabolism/pathology ; Amyloid beta-Peptides/chemistry/genetics/metabolism ; Apolipoprotein E4/*genetics/immunology/metabolism ; Biological Transport ; Cholesterol/metabolism ; Clusterin/genetics/metabolism ; DNA, Mitochondrial/genetics ; Exons/genetics ; *Genetic Predisposition to Disease ; Genome-Wide Association Study ; Humans ; LDL-Receptor Related Proteins/genetics ; Lipid Metabolism/genetics ; Membrane Transport Proteins/genetics ; Meta-Analysis as Topic ; Models, Biological ; Monomeric Clathrin Assembly Proteins/genetics/metabolism ; Polymorphism, Single Nucleotide/genetics ; Receptors, Complement/genetics/immunology
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  • 158
    Publication Date: 2011-02-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wickner, Reed B -- England -- Nature. 2011 Feb 24;470(7335):470-1. doi: 10.1038/470470a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21350474" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Assay ; Gene Expression ; Humans ; Mice ; Models, Biological ; PrPC Proteins/analysis/biosynthesis/genetics/metabolism ; PrPSc Proteins/biosynthesis/*metabolism/*pathogenicity/toxicity ; Prion Diseases/*metabolism/pathology/physiopathology/*transmission ; Survival Rate ; Time Factors ; Toxicity Tests
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  • 159
    Publication Date: 2011-01-05
    Description: During mitosis, adherent animal cells undergo a drastic shape change, from essentially flat to round. Mitotic cell rounding is thought to facilitate organization within the mitotic cell and be necessary for the geometric requirements of division. However, the forces that drive this shape change remain poorly understood in the presence of external impediments, such as a tissue environment. Here we use cantilevers to track cell rounding force and volume. We show that cells have an outward rounding force, which increases as cells enter mitosis. We find that this mitotic rounding force depends both on the actomyosin cytoskeleton and the cells' ability to regulate osmolarity. The rounding force itself is generated by an osmotic pressure. However, the actomyosin cortex is required to maintain this rounding force against external impediments. Instantaneous disruption of the actomyosin cortex leads to volume increase, and stimulation of actomyosin contraction leads to volume decrease. These results show that in cells, osmotic pressure is balanced by inwardly directed actomyosin cortex contraction. Thus, by locally modulating actomyosin-cortex-dependent surface tension and globally regulating osmotic pressure, cells can control their volume, shape and mechanical properties.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stewart, Martin P -- Helenius, Jonne -- Toyoda, Yusuke -- Ramanathan, Subramanian P -- Muller, Daniel J -- Hyman, Anthony A -- England -- Nature. 2011 Jan 13;469(7329):226-30. doi: 10.1038/nature09642. Epub 2011 Jan 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉ETH Zurich, Department of Biosystems Science and Engineering, CH-4058 Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21196934" target="_blank"〉PubMed〈/a〉
    Keywords: Actomyosin/*metabolism ; Animals ; Cell Shape/drug effects/*physiology ; Cell Size/drug effects ; Cytochalasin D/pharmacology ; Cytoskeleton/drug effects/*metabolism ; HeLa Cells ; Humans ; Hydrostatic Pressure ; Microscopy, Atomic Force ; *Mitosis ; Models, Biological ; Osmolar Concentration ; Osmotic Pressure ; Prophase
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  • 160
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    Nature Publishing Group (NPG)
    Publication Date: 2011-04-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hector, Andy -- England -- Nature. 2011 Apr 7;472(7341):45-6. doi: 10.1038/472045a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21475190" target="_blank"〉PubMed〈/a〉
    Keywords: *Biodiversity ; Biofilms/growth & development ; Biomass ; Chlorophyta/growth & development/*physiology ; Diatoms/growth & development/*physiology ; Models, Biological ; Nitrogen/analysis/metabolism ; Population Density ; Rivers/*chemistry/*microbiology
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  • 161
    Publication Date: 2011-04-02
    Description: Arising from W. Wiltschko et al. 419, 467-470 (2002); Wiltschko et al. replyThe magnetic compass of migratory birds is embedded in the visual system and it has been reported by Wiltschko et al. that European Robins, Erithacus rubecula, cannot show magnetic compass orientation using their left eye only. This has led to the notion that the magnetic compass should be located only in the right eye of birds. However, a complete right lateralization of the magnetic compass would be very surprising, and functional neuroanatomical data have questioned this notion. Here we show that the results of Wiltschko et al. could not be independently confirmed using double-blind protocols. European Robins can perform magnetic compass orientation with both eyes open, with the left eye open only, and with the right eye open only. No clear lateralization is observed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hein, Christine Maira -- Engels, Svenja -- Kishkinev, Dmitry -- Mouritsen, Henrik -- England -- Nature. 2011 Mar 31;471(7340):E11-2; discussion E12-3. doi: 10.1038/nature09875.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉AG Neurosensorik/Animal Navigation, IBU, University of Oldenburg, D-26111 Oldenburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21455128" target="_blank"〉PubMed〈/a〉
    Keywords: Animal Migration/*physiology/radiation effects ; Animals ; *Eye/radiation effects ; Functional Laterality/physiology ; *Magnetics ; Models, Biological ; *Ocular Physiological Phenomena/radiation effects ; Orientation/*physiology/radiation effects ; Photic Stimulation ; Reproducibility of Results ; Seasons ; Songbirds/anatomy & histology/*physiology
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  • 162
    Publication Date: 2011-05-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hayden, Erika Check -- England -- Nature. 2011 May 19;473(7347):272-4. doi: 10.1038/473272a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21593837" target="_blank"〉PubMed〈/a〉
    Keywords: Adult Stem Cells/cytology/metabolism ; Animals ; Cellular Reprogramming/genetics ; Epistasis, Genetic/genetics ; Humans ; Induced Pluripotent Stem Cells/*cytology/metabolism ; Insulin-Secreting Cells/cytology/transplantation ; Mice ; Models, Biological ; Mutation ; Precision Medicine/trends ; Regenerative Medicine/*trends ; *Stem Cell Research
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  • 163
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    Nature Publishing Group (NPG)
    Publication Date: 2012-02-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Butler, Declan -- England -- Nature. 2012 Feb 13;482(7385):289. doi: 10.1038/482289a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22337028" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies, Viral/analysis/immunology ; Humans ; Influenza A Virus, H5N1 Subtype/*genetics/immunology/isolation & ; purification/*pathogenicity ; Influenza, Human/epidemiology/immunology/*mortality/virology ; Models, Biological ; Poultry/virology ; Seroepidemiologic Studies ; Zoonoses/epidemiology/transmission/virology
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  • 164
    Publication Date: 2012-09-07
    Description: Animal and plant development starts with a constituting phase called embryogenesis, which evolved independently in both lineages. Comparative anatomy of vertebrate development--based on the Meckel-Serres law and von Baer's laws of embryology from the early nineteenth century--shows that embryos from various taxa appear different in early stages, converge to a similar form during mid-embryogenesis, and again diverge in later stages. This morphogenetic series is known as the embryonic 'hourglass', and its bottleneck of high conservation in mid-embryogenesis is referred to as the phylotypic stage. Recent analyses in zebrafish and Drosophila embryos provided convincing molecular support for the hourglass model, because during the phylotypic stage the transcriptome was dominated by ancient genes and global gene expression profiles were reported to be most conserved. Although extensively explored in animals, an embryonic hourglass has not been reported in plants, which represent the second major kingdom in the tree of life that evolved embryogenesis. Here we provide phylotranscriptomic evidence for a molecular embryonic hourglass in Arabidopsis thaliana, using two complementary approaches. This is particularly significant because the possible absence of an hourglass based on morphological features in plants suggests that morphological and molecular patterns might be uncoupled. Together with the reported developmental hourglass patterns in animals, these findings indicate convergent evolution of the molecular hourglass and a conserved logic of embryogenesis across kingdoms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Quint, Marcel -- Drost, Hajk-Georg -- Gabel, Alexander -- Ullrich, Kristian Karsten -- Bonn, Markus -- Grosse, Ivo -- England -- Nature. 2012 Oct 4;490(7418):98-101. doi: 10.1038/nature11394. Epub 2012 Sep 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Leibniz Institute of Plant Biochemistry, Department of Molecular Signal Processing, Weinberg 3, 06120 Halle (Saale), Germany. mquint@ipb-halle.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22951968" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arabidopsis/classification/*embryology/*genetics ; Brassicaceae/genetics ; Conserved Sequence/genetics ; Developmental Biology ; Drosophila/embryology/genetics ; Embryonic Development/genetics ; Evolution, Molecular ; Gene Expression Profiling ; Gene Expression Regulation, Plant/*genetics ; Genes, Plant/genetics ; Models, Biological ; Plant Development/*genetics ; Transcriptome/*genetics ; Zebrafish/embryology
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  • 165
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    Nature Publishing Group (NPG)
    Publication Date: 2012-02-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reinitz, John -- England -- Nature. 2012 Feb 22;482(7386):464. doi: 10.1038/482464a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Statistics, University of Chicago, Chicago, Illinois 60637, USA. reinitz@galton.uchicago.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22358813" target="_blank"〉PubMed〈/a〉
    Keywords: Computer Simulation ; Developmental Biology/*history ; Diffusion ; History, 19th Century ; History, 20th Century ; Models, Biological ; Morphogenesis/*physiology
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  • 166
    Publication Date: 2012-03-16
    Description: Derivatives of vitamin B(12) are used in methyl group transfer in biological processes as diverse as methionine synthesis in humans and CO(2) fixation in acetogenic bacteria. This seemingly straightforward reaction requires large, multimodular enzyme complexes that adopt multiple conformations to alternately activate, protect and perform catalysis on the reactive B(12) cofactor. Crystal structures determined thus far have provided structural information for only fragments of these complexes, inspiring speculation about the overall protein assembly and conformational movements inherent to activity. Here we present X-ray crystal structures of a complete 220 kDa complex that contains all enzymes responsible for B(12)-dependent methyl transfer, namely the corrinoid iron-sulphur protein and its methyltransferase from the model acetogen Moorella thermoacetica. These structures provide the first three-dimensional depiction of all protein modules required for the activation, protection and catalytic steps of B(12)-dependent methyl transfer. In addition, the structures capture B(12) at multiple locations between its 'resting' and catalytic positions, allowing visualization of the dramatic protein rearrangements that enable methyl transfer and identification of the trajectory for B(12) movement within the large enzyme scaffold. The structures are also presented alongside in crystallo spectroscopic data, which confirm enzymatic activity within crystals and demonstrate the largest known conformational movements of proteins in a crystalline state. Taken together, this work provides a model for the molecular juggling that accompanies turnover and helps explain why such an elaborate protein framework is required for such a simple, yet biologically essential reaction.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3326194/" 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/PMC3326194/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kung, Yan -- Ando, Nozomi -- Doukov, Tzanko I -- Blasiak, Leah C -- Bender, Gunes -- Seravalli, Javier -- Ragsdale, Stephen W -- Drennan, Catherine L -- GM39451/GM/NIGMS NIH HHS/ -- GM69857/GM/NIGMS NIH HHS/ -- R01 GM039451/GM/NIGMS NIH HHS/ -- R01 GM039451-25/GM/NIGMS NIH HHS/ -- R01 GM069857/GM/NIGMS NIH HHS/ -- R37 GM039451/GM/NIGMS NIH HHS/ -- RR-15301/RR/NCRR NIH HHS/ -- T32 GM008334/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Mar 14;484(7393):265-9. doi: 10.1038/nature10916.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22419154" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Biocatalysis ; Corrinoids/metabolism ; Crystallography, X-Ray ; Folic Acid/metabolism ; Iron-Sulfur Proteins/*chemistry/*metabolism ; Methylation ; Methyltransferases/*chemistry/*metabolism ; Models, Biological ; Models, Molecular ; Moorella/chemistry/*enzymology ; Protein Multimerization ; Protein Structure, Tertiary ; Vitamin B 12/*metabolism
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  • 167
    Publication Date: 2012-03-23
    Description: Spontaneous collective motion, as in some flocks of bird and schools of fish, is an example of an emergent phenomenon. Such phenomena are at present of great interest and physicists have put forward a number of theoretical results that so far lack experimental verification. In animal behaviour studies, large-scale data collection is now technologically possible, but data are still scarce and arise from observations rather than controlled experiments. Multicellular biological systems, such as bacterial colonies or tissues, allow more control, but may have many hidden variables and interactions, hindering proper tests of theoretical ideas. However, in systems on the subcellular scale such tests may be possible, particularly in in vitro experiments with only few purified components. Motility assays, in which protein filaments are driven by molecular motors grafted to a substrate in the presence of ATP, can show collective motion for high densities of motors and attached filaments. This was demonstrated recently for the actomyosin system, but a complete understanding of the mechanisms at work is still lacking. Here we report experiments in which microtubules are propelled by surface-bound dyneins. In this system it is possible to study the local interaction: we find that colliding microtubules align with each other with high probability. At high densities, this alignment results in self-organization of the microtubules, which are on average 15 microm long, into vortices with diameters of around 400 microm. Inside the vortices, the microtubules circulate both clockwise and anticlockwise. On longer timescales, the vortices form a lattice structure. The emergence of these structures, as verified by a mathematical model, is the result of the smooth, reptation-like motion of single microtubules in combination with local interactions (the nematic alignment due to collisions)--there is no need for long-range interactions. Apart from its potential relevance to cortical arrays in plant cells and other biological situations, our study provides evidence for the existence of previously unsuspected universality classes of collective motion phenomena.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sumino, Yutaka -- Nagai, Ken H -- Shitaka, Yuji -- Tanaka, Dan -- Yoshikawa, Kenichi -- Chate, Hugues -- Oiwa, Kazuhiro -- England -- Nature. 2012 Mar 21;483(7390):448-52. doi: 10.1038/nature10874.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Aichi University of Education, Aichi 448-8542, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22437613" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chlamydomonas ; Dyneins/metabolism ; Flagella ; Microtubules/*metabolism ; Models, Biological ; *Movement
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  • 168
    Publication Date: 2011-12-20
    Description: Ion-translocating rotary ATPases serve either as ATP synthases, using energy from a transmembrane ion motive force to create the cell's supply of ATP, or as transmembrane ion pumps that are powered by ATP hydrolysis. The members of this family of enzymes each contain two rotary motors: one that couples ion translocation to rotation and one that couples rotation to ATP synthesis or hydrolysis. During ATP synthesis, ion translocation through the membrane-bound region of the complex causes rotation of a central rotor that drives conformational changes and ATP synthesis in the catalytic region of the complex. There are no structural models available for the intact membrane region of any ion-translocating rotary ATPase. Here we present a 9.7 A resolution map of the H(+)-driven ATP synthase from Thermus thermophilus obtained by electron cryomicroscopy of single particles in ice. The 600-kilodalton complex has an overall subunit composition of A(3)B(3)CDE(2)FG(2)IL(12). The membrane-bound motor consists of a ring of L subunits and the carboxy-terminal region of subunit I, which are equivalent to the c and a subunits of most other rotary ATPases, respectively. The map shows that the ring contains 12 L subunits and that the I subunit has eight transmembrane helices. The L(12) ring and I subunit have a surprisingly small contact area in the middle of the membrane, with helices from the I subunit making contacts with two different L subunits. The transmembrane helices of subunit I form bundles that could serve as half-channels across the membrane, with the first half-channel conducting protons from the periplasm to the L(12) ring and the second half-channel conducting protons from the L(12) ring to the cytoplasm. This structure therefore suggests the mechanism by which a transmembrane proton motive force is converted to rotation in rotary ATPases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lau, Wilson C Y -- Rubinstein, John L -- MOP 81294/Canadian Institutes of Health Research/Canada -- England -- Nature. 2011 Dec 18;481(7380):214-8. doi: 10.1038/nature10699.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Structure and Function Program, The Hospital for Sick Children Research Institute, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22178924" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Membrane/metabolism ; *Cryoelectron Microscopy ; Ice ; Models, Biological ; Models, Molecular ; Protein Subunits/chemistry/metabolism ; Proton-Motive Force ; Proton-Translocating ATPases/*chemistry/metabolism/*ultrastructure ; *Protons ; Rotation ; Structure-Activity Relationship ; Thermus thermophilus/*enzymology
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  • 169
    Publication Date: 2012-07-06
    Description: It is possible that anthropogenic climate change will drive the Earth system into a qualitatively different state. Although different types of uncertainty limit our capacity to assess this risk, Earth system scientists are particularly concerned about tipping elements, large-scale components of the Earth system that can be switched into qualitatively different states by small perturbations. Despite growing evidence that tipping elements exist in the climate system, whether large-scale vegetation systems can tip into alternative states is poorly understood. Here we show that tropical grassland, savanna and forest ecosystems, areas large enough to have powerful impacts on the Earth system, are likely to shift to alternative states. Specifically, we show that increasing atmospheric CO2 concentration will force transitions to vegetation states characterized by higher biomass and/or woody-plant dominance. The timing of these critical transitions varies as a result of between-site variance in the rate of temperature increase, as well as a dependence on stochastic variation in fire severity and rainfall. We further show that the locations of bistable vegetation zones (zones where alternative vegetation states can exist) will shift as climate changes. We conclude that even though large-scale directional regime shifts in terrestrial ecosystems are likely, asynchrony in the timing of these shifts may serve to dampen, but not nullify, the shock that these changes may represent to the Earth system.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Higgins, Steven I -- Scheiter, Simon -- England -- Nature. 2012 Aug 9;488(7410):209-12. doi: 10.1038/nature11238.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Physische Geographie, Goethe Universitat Frankfurt am Main, 60438 Frankfurt am Main, Germany. higgins@em.uni-frankfurt.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22763447" target="_blank"〉PubMed〈/a〉
    Keywords: Africa ; Atmosphere/*chemistry ; Biomass ; Carbon/metabolism ; Carbon Dioxide/analysis/*metabolism ; Climate Change/*statistics & numerical data ; *Ecosystem ; Fires ; Geography ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Hot Temperature ; Models, Biological ; Photosynthesis/physiology ; Poaceae/growth & development/metabolism ; Probability ; Rain ; Stochastic Processes ; Time Factors ; Trees/*growth & development/metabolism ; Wood
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  • 170
    Publication Date: 2012-01-06
    Description: In 1969, a palaeontologist proposed that theropod dinosaurs used their tails as dynamic stabilizers during rapid or irregular movements, contributing to their depiction as active and agile predators. Since then the inertia of swinging appendages has been implicated in stabilizing human walking, aiding acrobatic manoeuvres by primates and rodents, and enabling cats to balance on branches. Recent studies on geckos suggest that active tail stabilization occurs during climbing, righting and gliding. By contrast, studies on the effect of lizard tail loss show evidence of a decrease, an increase or no change in performance. Application of a control-theoretic framework could advance our general understanding of inertial appendage use in locomotion. Here we report that lizards control the swing of their tails in a measured manner to redirect angular momentum from their bodies to their tails, stabilizing body attitude in the sagittal plane. We video-recorded Red-Headed Agama lizards (Agama agama) leaping towards a vertical surface by first vaulting onto an obstacle with variable traction to induce a range of perturbations in body angular momentum. To examine a known controlled tail response, we built a lizard-sized robot with an active tail that used sensory feedback to stabilize pitch as it drove off a ramp. Our dynamics model revealed that a body swinging its tail experienced less rotation than a body with a rigid tail, a passively compliant tail or no tail. To compare a range of tails, we calculated tail effectiveness as the amount of tailless body rotation a tail could stabilize. A model Velociraptor mongoliensis supported the initial tail stabilization hypothesis, showing as it did a greater tail effectiveness than the Agama lizards. Leaping lizards show that inertial control of body attitude can advance our understanding of appendage evolution and provide biological inspiration for the next generation of manoeuvrable search-and-rescue robots.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Libby, Thomas -- Moore, Talia Y -- Chang-Siu, Evan -- Li, Deborah -- Cohen, Daniel J -- Jusufi, Ardian -- Full, Robert J -- England -- Nature. 2012 Jan 4;481(7380):181-4. doi: 10.1038/nature10710.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Interdisciplinary Bio-Inspiration in Education and Research, University of California, Berkeley, California 94720-3140, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22217942" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Evolution ; Biomechanical Phenomena ; Computer Simulation ; Dinosaurs/*anatomy & histology/*physiology ; Feedback, Sensory/physiology ; Lizards/*anatomy & histology/*physiology ; Models, Biological ; Posture/physiology ; *Robotics/instrumentation ; Rotation ; Tail/*physiology
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  • 171
    Publication Date: 2012-06-09
    Description: Evidence is mounting that extinctions are altering key processes important to the productivity and sustainability of Earth's ecosystems. Further species loss will accelerate change in ecosystem processes, but it is unclear how these effects compare to the direct effects of other forms of environmental change that are both driving diversity loss and altering ecosystem function. Here we use a suite of meta-analyses of published data to show that the effects of species loss on productivity and decomposition--two processes important in all ecosystems--are of comparable magnitude to the effects of many other global environmental changes. In experiments, intermediate levels of species loss (21-40%) reduced plant production by 5-10%, comparable to previously documented effects of ultraviolet radiation and climate warming. Higher levels of extinction (41-60%) had effects rivalling those of ozone, acidification, elevated CO(2) and nutrient pollution. At intermediate levels, species loss generally had equal or greater effects on decomposition than did elevated CO(2) and nitrogen addition. The identity of species lost also had a large effect on changes in productivity and decomposition, generating a wide range of plausible outcomes for extinction. Despite the need for more studies on interactive effects of diversity loss and environmental changes, our analyses clearly show that the ecosystem consequences of local species loss are as quantitatively significant as the direct effects of several global change stressors that have mobilized major international concern and remediation efforts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hooper, David U -- Adair, E Carol -- Cardinale, Bradley J -- Byrnes, Jarrett E K -- Hungate, Bruce A -- Matulich, Kristin L -- Gonzalez, Andrew -- Duffy, J Emmett -- Gamfeldt, Lars -- O'Connor, Mary I -- England -- Nature. 2012 May 2;486(7401):105-8. doi: 10.1038/nature11118.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Western Washington University, Bellingham, Washington 98225-9160, USA. hooper@biol.wwu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22678289" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; Ecology ; *Ecosystem ; *Extinction, Biological ; Models, Biological
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  • 172
    Publication Date: 2012-02-03
    Description: Natural materials are renowned for exquisite designs that optimize function, as illustrated by the elasticity of blood vessels, the toughness of bone and the protection offered by nacre. Particularly intriguing are spider silks, with studies having explored properties ranging from their protein sequence to the geometry of a web. This material system, highly adapted to meet a spider's many needs, has superior mechanical properties. In spite of much research into the molecular design underpinning the outstanding performance of silk fibres, and into the mechanical characteristics of web-like structures, it remains unknown how the mechanical characteristics of spider silk contribute to the integrity and performance of a spider web. Here we report web deformation experiments and simulations that identify the nonlinear response of silk threads to stress--involving softening at a yield point and substantial stiffening at large strain until failure--as being crucial to localize load-induced deformation and resulting in mechanically robust spider webs. Control simulations confirmed that a nonlinear stress response results in superior resistance to structural defects in the web compared to linear elastic or elastic-plastic (softening) material behaviour. We also show that under distributed loads, such as those exerted by wind, the stiff behaviour of silk under small deformation, before the yield point, is essential in maintaining the web's structural integrity. The superior performance of silk in webs is therefore not due merely to its exceptional ultimate strength and strain, but arises from the nonlinear response of silk threads to strain and their geometrical arrangement in a web.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cranford, Steven W -- Tarakanova, Anna -- Pugno, Nicola M -- Buehler, Markus J -- England -- Nature. 2012 Feb 1;482(7383):72-6. doi: 10.1038/nature10739.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22297972" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biomechanical Phenomena ; Elasticity ; Hardness ; Models, Biological ; Silk/*chemistry ; *Spiders/physiology ; *Tensile Strength ; Wind
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  • 173
    Publication Date: 2012-10-30
    Description: Escherichia coli RecA is the defining member of a ubiquitous class of DNA strand-exchange proteins that are essential for homologous recombination, a pathway that maintains genomic integrity by repairing broken DNA. To function, filaments of RecA must nucleate and grow on single-stranded DNA (ssDNA) in direct competition with ssDNA-binding protein (SSB), which rapidly binds and continuously sequesters ssDNA, kinetically blocking RecA assembly. This dynamic self-assembly on a DNA lattice, in competition with another protein, is unique for the RecA family compared to other filament-forming proteins such as actin and tubulin. The complexity of this process has hindered our understanding of RecA filament assembly because ensemble measurements cannot reliably distinguish between the nucleation and growth phases, despite extensive and diverse attempts. Previous single-molecule assays have measured the nucleation and growth of RecA--and its eukaryotic homologue RAD51--on naked double-stranded DNA and ssDNA; however, the template for RecA self-assembly in vivo is SSB-coated ssDNA. Using single-molecule microscopy, here we directly visualize RecA filament assembly on single molecules of SSB-coated ssDNA, simultaneously measuring nucleation and growth. We establish that a dimer of RecA is required for nucleation, followed by growth of the filament through monomer addition, consistent with the finding that nucleation, but not growth, is modulated by nucleotide and magnesium ion cofactors. Filament growth is bidirectional, albeit faster in the 5'--〉3' direction. Both nucleation and growth are repressed at physiological conditions, highlighting the essential role of recombination mediators in potentiating assembly in vivo. We define a two-step kinetic mechanism in which RecA nucleates on transiently exposed ssDNA during SSB sliding and/or partial dissociation (DNA unwrapping) and then the RecA filament grows. We further demonstrate that the recombination mediator protein pair, RecOR (RecO and RecR), accelerates both RecA nucleation and filament growth, and that the introduction of RecF further stimulates RecA nucleation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4112059/" 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/PMC4112059/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bell, Jason C -- Plank, Jody L -- Dombrowski, Christopher C -- Kowalczykowski, Stephen C -- CA136103/CA/NCI NIH HHS/ -- F32 CA136103/CA/NCI NIH HHS/ -- GM62653/GM/NIGMS NIH HHS/ -- GM64745/GM/NIGMS NIH HHS/ -- R01 GM062653/GM/NIGMS NIH HHS/ -- R01 GM064745/GM/NIGMS NIH HHS/ -- T32 CA10052159/CA/NCI NIH HHS/ -- T32 CA108459/CA/NCI NIH HHS/ -- T32 GM007377/GM/NIGMS NIH HHS/ -- England -- Nature. 2012 Nov 8;491(7423):274-8. doi: 10.1038/nature11598. Epub 2012 Oct 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, University of California, Davis, California 95616, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23103864" target="_blank"〉PubMed〈/a〉
    Keywords: DNA, Single-Stranded/chemistry/*metabolism ; DNA-Binding Proteins/*metabolism ; Escherichia coli/*chemistry/enzymology ; Escherichia coli Proteins/*metabolism ; Hydrogen-Ion Concentration ; Ligands ; Microscopy, Fluorescence/*methods ; Models, Biological ; Models, Molecular ; Molecular Conformation ; Protein Multimerization ; Rec A Recombinases/*chemistry/*metabolism
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  • 174
    Publication Date: 2012-10-13
    Description: Calcium-dependent exocytosis of synaptic vesicles mediates the release of neurotransmitters. Important proteins in this process have been identified such as the SNAREs, synaptotagmins, complexins, Munc18 and Munc13. Structural and functional studies have yielded a wealth of information about the physiological role of these proteins. However, it has been surprisingly difficult to arrive at a unified picture of the molecular sequence of events from vesicle docking to calcium-triggered membrane fusion. Using mainly a biochemical and biophysical perspective, we briefly survey the molecular mechanisms in an attempt to functionally integrate the key proteins into the emerging picture of the neuronal fusion machine.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461657/" 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/PMC4461657/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jahn, Reinhard -- Fasshauer, Dirk -- 3P01GM072694-05S1/GM/NIGMS NIH HHS/ -- P01 GM072694/GM/NIGMS NIH HHS/ -- England -- Nature. 2012 Oct 11;490(7419):201-7. doi: 10.1038/nature11320.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, 37077 Gottingen, Germany. rjahn@gwdg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23060190" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcium/metabolism ; Exocytosis/*physiology ; Humans ; Lipid Metabolism ; Models, Biological ; SNARE Proteins/chemistry/metabolism ; Synaptic Vesicles/*physiology
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  • 175
    Publication Date: 2012-03-13
    Description: The hydrosulphide ion (HS(-)) and its undissociated form, hydrogen sulphide (H(2)S), which are believed to have been critical to the origin of life on Earth, remain important in physiology and cellular signalling. As a major metabolite in anaerobic bacterial growth, hydrogen sulphide is a product of both assimilatory and dissimilatory sulphate reduction. These pathways can reduce various oxidized sulphur compounds including sulphate, sulphite and thiosulphate. The dissimilatory sulphate reduction pathway uses this molecule as the terminal electron acceptor for anaerobic respiration, in which process it produces excess amounts of H(2)S (ref. 4). The reduction of sulphite is a key intermediate step in all sulphate reduction pathways. In Clostridium and Salmonella, an inducible sulphite reductase is directly linked to the regeneration of NAD(+), which has been suggested to have a role in energy production and growth, as well as in the detoxification of sulphite. Above a certain concentration threshold, both H(2)S and HS(-) inhibit cell growth by binding the metal centres of enzymes and cytochrome oxidase, necessitating a release mechanism for the export of this toxic metabolite from the cell. Here we report the identification of a hydrosulphide ion channel in the pathogen Clostridium difficile through a combination of genetic, biochemical and functional approaches. The HS(-) channel is a member of the formate/nitrite transport family, in which about 50 hydrosulphide ion channels form a third subfamily alongside those for formate (FocA) and for nitrite (NirC). The hydrosulphide ion channel is permeable to formate and nitrite as well as to HS(-) ions. Such polyspecificity can be explained by the conserved ion selectivity filter observed in the channel's crystal structure. The channel has a low open probability and is tightly regulated, to avoid decoupling of the membrane proton gradient.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3711795/" 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/PMC3711795/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Czyzewski, Bryan K -- Wang, Da-Neng -- F31 AI086072/AI/NIAID NIH HHS/ -- F31-AI086072/AI/NIAID NIH HHS/ -- R01 DK053973/DK/NIDDK NIH HHS/ -- R01 GM093825/GM/NIGMS NIH HHS/ -- R01 MH083840/MH/NIMH NIH HHS/ -- R01-DK053973-08A1S1/DK/NIDDK NIH HHS/ -- R01-DK073973/DK/NIDDK NIH HHS/ -- R01-GM093825/GM/NIGMS NIH HHS/ -- R01-MH083840/MH/NIMH NIH HHS/ -- U54 GM075026/GM/NIGMS NIH HHS/ -- U54-GM075026/GM/NIGMS NIH HHS/ -- England -- Nature. 2012 Mar 11;483(7390):494-7. doi: 10.1038/nature10881.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, New York University School of Medicine, 540 First Avenue, New York, New York 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22407320" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/genetics/isolation & purification/metabolism ; *Clostridium difficile/chemistry/drug effects/genetics ; Crystallography, X-Ray ; Formates/metabolism ; Ion Channel Gating ; Ion Channels/chemistry/genetics/*isolation & purification/*metabolism ; Ion Transport ; Models, Biological ; Models, Molecular ; Nitrites/metabolism ; Operon/genetics ; Proteolipids/metabolism ; Proton-Motive Force ; Structure-Activity Relationship ; Substrate Specificity ; Sulfides/*metabolism/toxicity
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  • 176
    Publication Date: 2012-02-18
    Description: Species diversity can be lost through two different but potentially interacting extinction processes: demographic decline and speciation reversal through introgressive hybridization. To investigate the relative contribution of these processes, we analysed historical and contemporary data of replicate whitefish radiations from 17 pre-alpine European lakes and reconstructed changes in genetic species differentiation through time using historical samples. Here we provide evidence that species diversity evolved in response to ecological opportunity, and that eutrophication, by diminishing this opportunity, has driven extinctions through speciation reversal and demographic decline. Across the radiations, the magnitude of eutrophication explains the pattern of species loss and levels of genetic and functional distinctiveness among remaining species. We argue that extinction by speciation reversal may be more widespread than currently appreciated. Preventing such extinctions will require that conservation efforts not only target existing species but identify and protect the ecological and evolutionary processes that generate and maintain species.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vonlanthen, P -- Bittner, D -- Hudson, A G -- Young, K A -- Muller, R -- Lundsgaard-Hansen, B -- Roy, D -- Di Piazza, S -- Largiader, C R -- Seehausen, O -- England -- Nature. 2012 Feb 15;482(7385):357-62. doi: 10.1038/nature10824.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012 Bern, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22337055" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; *Biological Evolution ; Europe ; Eutrophication/*physiology ; *Extinction, Biological ; *Genetic Speciation ; Lakes ; Models, Biological ; Phenotype ; Salmonidae/genetics/*physiology
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  • 177
    Publication Date: 2012-04-17
    Description: The development and maintenance of an epithelium requires finely balanced rates of growth and cell death. However, the mechanical and biochemical mechanisms that ensure proper feedback control of tissue growth, which when deregulated contribute to tumorigenesis, are poorly understood. Here we use the fly notum as a model system to identify a novel process of crowding-induced cell delamination that balances growth to ensure the development of well-ordered cell packing. In crowded regions of the tissue, a proportion of cells undergo a serial loss of cell-cell junctions and a progressive loss of apical area, before being squeezed out by their neighbours. This path of delamination is recapitulated by a simple computational model of epithelial mechanics, in which stochastic cell loss relieves overcrowding as the system tends towards equilibrium. We show that this process of delamination is mechanistically distinct from apoptosis-mediated cell extrusion and precedes the first signs of cell death. Overall, this analysis reveals a simple mechanism that buffers epithelia against variations in growth. Because live-cell delamination constitutes a mechanistic link between epithelial hyperplasia and cell invasion, this is likely to have important implications for our understanding of the early stages of cancer development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marinari, Eliana -- Mehonic, Aida -- Curran, Scott -- Gale, Jonathan -- Duke, Thomas -- Baum, Buzz -- 9786/Cancer Research UK/United Kingdom -- Cancer Research UK/United Kingdom -- England -- Nature. 2012 Apr 15;484(7395):542-5. doi: 10.1038/nature10984.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Laboratory of Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22504180" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis ; Cell Communication ; Cell Count ; Cell Death ; Cell Growth Processes ; Cell Survival ; Drosophila melanogaster/*cytology ; Epithelial Cells/*cytology ; Female ; Male ; Models, Biological ; Neoplasms/pathology ; Stochastic Processes
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  • 178
    Publication Date: 2012-06-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Polymenis, Michael -- Kennedy, Brian K -- England -- Nature. 2012 Jun 6;486(7401):37-8. doi: 10.1038/486037a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22678274" target="_blank"〉PubMed〈/a〉
    Keywords: Automation ; *Cell Aging ; Cell Biology/instrumentation ; Cell Culture Techniques/*instrumentation ; Microfluidic Analytical Techniques/*instrumentation ; Miniaturization ; Models, Biological ; Saccharomyces cerevisiae/*cytology ; Single-Cell Analysis/*instrumentation/*methods
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  • 179
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    Nature Publishing Group (NPG)
    Publication Date: 2012-09-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maxmen, Amy -- England -- Nature. 2012 Sep 20;489(7416):349-50. doi: 10.1038/489349a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22996526" target="_blank"〉PubMed〈/a〉
    Keywords: Humans ; Kidney/pathology/virology ; Kidney Diseases/*etiology/pathology/prevention & control/*virology ; Models, Biological ; RNA, Viral/urine ; Reproducibility of Results ; United States/epidemiology ; West Nile Fever/*complications/epidemiology/therapy ; West Nile virus/genetics/isolation & purification/*pathogenicity
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  • 180
    Publication Date: 2012-08-03
    Description: Recent studies using the isolation of a subpopulation of tumour cells followed by their transplantation into immunodeficient mice provide evidence that certain tumours, including squamous skin tumours, contain cells with high clonogenic potential that have been referred to as cancer stem cells (CSCs). Until now, CSC properties have only been investigated by transplantation assays, and their existence in unperturbed tumour growth is unproven. Here we make use of clonal analysis of squamous skin tumours using genetic lineage tracing to unravel the mode of tumour growth in vivo in its native environment. To this end, we used a genetic labelling strategy that allows individual tumour cells to be marked and traced over time at different stages of tumour progression. Surprisingly, we found that the majority of labelled tumour cells in benign papilloma have only limited proliferative potential, whereas a fraction has the capacity to persist long term, giving rise to progeny that occupy a significant part of the tumour. As well as confirming the presence of two distinct proliferative cell compartments within the papilloma, mirroring the composition, hierarchy and fate behaviour of normal tissue, quantitative analysis of clonal fate data indicates that the more persistent population has stem-cell-like characteristics and cycles twice per day, whereas the second represents a slower cycling transient population that gives rise to terminally differentiated tumour cells. Such behaviour is shown to be consistent with double-labelling experiments and detailed clonal fate characteristics. By contrast, measurements of clone size and proliferative potential in invasive squamous cell carcinoma show a different pattern of behaviour, consistent with geometric expansion of a single CSC population with limited potential for terminal differentiation. This study presents the first experimental evidence for the existence of CSCs during unperturbed solid tumour growth.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Driessens, Gregory -- Beck, Benjamin -- Caauwe, Amelie -- Simons, Benjamin D -- Blanpain, Cedric -- 079249/Wellcome Trust/United Kingdom -- 092096/Wellcome Trust/United Kingdom -- England -- Nature. 2012 Aug 23;488(7412):527-30. doi: 10.1038/nature11344.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Universite Libre de Bruxelles, IRIBHM, Brussels B-1070, Belgium.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22854777" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Carcinoma, Squamous Cell/genetics/pathology ; Cell Count ; Cell Differentiation ; *Cell Lineage ; Cell Proliferation ; *Cell Tracking ; Clone Cells/metabolism/pathology ; Disease Models, Animal ; Humans ; Mice ; Models, Biological ; Neoplastic Stem Cells/metabolism/pathology ; Skin Neoplasms/genetics/*pathology ; Stochastic Processes ; Tumor Microenvironment
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  • 181
    Publication Date: 2013-06-07
    Description: G-protein-gated inward rectifier K(+) (GIRK) channels allow neurotransmitters, through G-protein-coupled receptor stimulation, to control cellular electrical excitability. In cardiac and neuronal cells this control regulates heart rate and neural circuit activity, respectively. Here we present the 3.5 A resolution crystal structure of the mammalian GIRK2 channel in complex with betagamma G-protein subunits, the central signalling complex that links G-protein-coupled receptor stimulation to K(+) channel activity. Short-range atomic and long-range electrostatic interactions stabilize four betagamma G-protein subunits at the interfaces between four K(+) channel subunits, inducing a pre-open state of the channel. The pre-open state exhibits a conformation that is intermediate between the closed conformation and the open conformation of the constitutively active mutant. The resultant structural picture is compatible with 'membrane delimited' activation of GIRK channels by G proteins and the characteristic burst kinetics of channel gating. The structures also permit a conceptual understanding of how the signalling lipid phosphatidylinositol-4,5-bisphosphate (PIP2) and intracellular Na(+) ions participate in multi-ligand regulation of GIRK channels.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4654628/" 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/PMC4654628/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Whorton, Matthew R -- MacKinnon, Roderick -- 1S10RR022321-01/RR/NCRR NIH HHS/ -- 1S10RR027037-01/RR/NCRR NIH HHS/ -- S10 RR027037/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2013 Jun 13;498(7453):190-7. doi: 10.1038/nature12241. Epub 2013 Jun 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23739333" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; G Protein-Coupled Inwardly-Rectifying Potassium ; Channels/*chemistry/genetics/metabolism ; Heterotrimeric GTP-Binding Proteins/*chemistry/genetics/metabolism ; Humans ; Ion Channel Gating ; Models, Biological ; Models, Molecular ; Phosphatidylinositol 4,5-Diphosphate/metabolism ; Protein Conformation ; Protein Interaction Domains and Motifs ; Protein Subunits/chemistry/metabolism ; Sodium/metabolism ; Static Electricity
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  • 182
    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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  • 183
    Publication Date: 2013-07-23
    Description: Loss of sexual reproduction is considered an evolutionary dead end for metazoans, but bdelloid rotifers challenge this view as they appear to have persisted asexually for millions of years. Neither male sex organs nor meiosis have ever been observed in these microscopic animals: oocytes are formed through mitotic divisions, with no reduction of chromosome number and no indication of chromosome pairing. However, current evidence does not exclude that they may engage in sex on rare, cryptic occasions. Here we report the genome of a bdelloid rotifer, Adineta vaga (Davis, 1873), and show that its structure is incompatible with conventional meiosis. At gene scale, the genome of A. vaga is tetraploid and comprises both anciently duplicated segments and less divergent allelic regions. However, in contrast to sexual species, the allelic regions are rearranged and sometimes even found on the same chromosome. Such structure does not allow meiotic pairing; instead, we find abundant evidence of gene conversion, which may limit the accumulation of deleterious mutations in the absence of meiosis. Gene families involved in resistance to oxidation, carbohydrate metabolism and defence against transposons are significantly expanded, which may explain why transposable elements cover only 3% of the assembled sequence. Furthermore, 8% of the genes are likely to be of non-metazoan origin and were probably acquired horizontally. This apparent convergence between bdelloids and prokaryotes sheds new light on the evolutionary significance of sex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Flot, Jean-Francois -- Hespeels, Boris -- Li, Xiang -- Noel, Benjamin -- Arkhipova, Irina -- Danchin, Etienne G J -- Hejnol, Andreas -- Henrissat, Bernard -- Koszul, Romain -- Aury, Jean-Marc -- Barbe, Valerie -- Barthelemy, Roxane-Marie -- Bast, Jens -- Bazykin, Georgii A -- Chabrol, Olivier -- Couloux, Arnaud -- Da Rocha, Martine -- Da Silva, Corinne -- Gladyshev, Eugene -- Gouret, Philippe -- Hallatschek, Oskar -- Hecox-Lea, Bette -- Labadie, Karine -- Lejeune, Benjamin -- Piskurek, Oliver -- Poulain, Julie -- Rodriguez, Fernando -- Ryan, Joseph F -- Vakhrusheva, Olga A -- Wajnberg, Eric -- Wirth, Benedicte -- Yushenova, Irina -- Kellis, Manolis -- Kondrashov, Alexey S -- Mark Welch, David B -- Pontarotti, Pierre -- Weissenbach, Jean -- Wincker, Patrick -- Jaillon, Olivier -- Van Doninck, Karine -- England -- Nature. 2013 Aug 22;500(7463):453-7. doi: 10.1038/nature12326. Epub 2013 Jul 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Namur, Department of Biology, URBE, Laboratory of Evolutionary Genetics and Ecology, 5000 Namur, Belgium. jean-francois.flot@ds.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23873043" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Gene Conversion/*genetics ; Gene Transfer, Horizontal/genetics ; Genome/*genetics ; Genomics ; Meiosis/genetics ; Models, Biological ; Reproduction, Asexual/*genetics ; Rotifera/*genetics ; Tetraploidy
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  • 184
    Publication Date: 2013-11-08
    Description: In nuclear pre-messenger RNA splicing, introns are excised by the spliceosome, a dynamic machine composed of both proteins and small nuclear RNAs (snRNAs). Over thirty years ago, after the discovery of self-splicing group II intron RNAs, the snRNAs were proposed to catalyse splicing. However, no definitive evidence for a role of either RNA or protein in catalysis by the spliceosome has been reported so far. By using metal rescue strategies in spliceosomes from budding yeast, here we show that the U6 snRNA catalyses both of the two splicing reactions by positioning divalent metals that stabilize the leaving groups during each reaction. Notably, all of the U6 catalytic metal ligands we identified correspond to the ligands observed to position catalytic, divalent metals in crystal structures of a group II intron RNA. These findings indicate that group II introns and the spliceosome share common catalytic mechanisms and probably common evolutionary origins. Our results demonstrate that RNA mediates catalysis within the spliceosome.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666680/" 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/PMC4666680/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fica, Sebastian M -- Tuttle, Nicole -- Novak, Thaddeus -- Li, Nan-Sheng -- Lu, Jun -- Koodathingal, Prakash -- Dai, Qing -- Staley, Jonathan P -- Piccirilli, Joseph A -- 5T32GM008720/GM/NIGMS NIH HHS/ -- R01 GM088656/GM/NIGMS NIH HHS/ -- R01GM088656/GM/NIGMS NIH HHS/ -- England -- Nature. 2013 Nov 14;503(7475):229-34. doi: 10.1038/nature12734. Epub 2013 Nov 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Graduate Program in Cell and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA [2] Department of Molecular Genetics and Cell Biology, Cummings Life Sciences Center, 920 East 58th Street, The University of Chicago, Chicago, Illinois 60637, USA [3].〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24196718" target="_blank"〉PubMed〈/a〉
    Keywords: Catalysis ; Cell Nucleus/metabolism ; Introns/genetics ; Metals/metabolism ; Models, Biological ; RNA Precursors/*metabolism ; *RNA Splicing ; RNA, Fungal/metabolism ; RNA, Small Nuclear/*metabolism ; Saccharomyces cerevisiae/*genetics/*metabolism ; Spliceosomes/metabolism
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  • 185
    Publication Date: 2013-04-26
    Description: Cell-surface-receptor binding by influenza viruses is a key determinant of their transmissibility, both from avian and animal species to humans as well as from human to human. Highly pathogenic avian H5N1 viruses that are a threat to public health have been observed to acquire affinity for human receptors, and transmissible-mutant-selection experiments have identified a virus that is transmissible in ferrets, the generally accepted experimental model for influenza in humans. Here, our quantitative biophysical measurements of the receptor-binding properties of haemagglutinin (HA) from the transmissible mutant indicate a small increase in affinity for human receptor and a marked decrease in affinity for avian receptor. From analysis of virus and HA binding data we have derived an algorithm that predicts virus avidity from the affinity of individual HA-receptor interactions. It reveals that the transmissible-mutant virus has a 200-fold preference for binding human over avian receptors. The crystal structure of the transmissible-mutant HA in complex with receptor analogues shows that it has acquired the ability to bind human receptor in the same folded-back conformation as seen for HA from the 1918, 1957 (ref. 4), 1968 (ref. 5) and 2009 (ref. 6) pandemic viruses. This binding mode is substantially different from that by which non-transmissible wild-type H5 virus HA binds human receptor. The structure of the complex also explains how the change in preference from avian to human receptors arises from the Gln226Leu substitution, which facilitates binding to human receptor but restricts binding to avian receptor. Both features probably contribute to the acquisition of transmissibility by this mutant virus.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xiong, Xiaoli -- Coombs, Peter J -- Martin, Stephen R -- Liu, Junfeng -- Xiao, Haixia -- McCauley, John W -- Locher, Kathrin -- Walker, Philip A -- Collins, Patrick J -- Kawaoka, Yoshihiro -- Skehel, John J -- Gamblin, Steven J -- BB/E010806/Biotechnology and Biological Sciences Research Council/United Kingdom -- MC_U117512723/Medical Research Council/United Kingdom -- MC_U117584222/Medical Research Council/United Kingdom -- U117512723/Medical Research Council/United Kingdom -- U117570592/Medical Research Council/United Kingdom -- U117584222/Medical Research Council/United Kingdom -- England -- Nature. 2013 May 16;497(7449):392-6. doi: 10.1038/nature12144. Epub 2013 Apr 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23615615" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Birds/metabolism/virology ; Chick Embryo ; Crystallography, X-Ray ; Ferrets/*virology ; Hemagglutinin Glycoproteins, Influenza Virus/*chemistry/genetics/*metabolism ; *Host Specificity ; Humans ; Influenza A Virus, H5N1 Subtype/chemistry/*genetics/*metabolism/pathogenicity ; Models, Biological ; Models, Molecular ; Mutation ; Orthomyxoviridae Infections/*transmission/*virology ; Protein Conformation ; Receptors, Virus/*metabolism ; Species Specificity
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  • 186
    Publication Date: 2013-06-01
    Description: Cytosolic DNA arising from intracellular bacterial or viral infections is a powerful pathogen-associated molecular pattern (PAMP) that leads to innate immune host defence by the production of type I interferon and inflammatory cytokines. Recognition of cytosolic DNA by the recently discovered cyclic-GMP-AMP (cGAMP) synthase (cGAS) induces the production of cGAMP to activate the stimulator of interferon genes (STING). Here we report the crystal structure of cGAS alone and in complex with DNA, ATP and GTP along with functional studies. Our results explain the broad DNA sensing specificity of cGAS, show how cGAS catalyses dinucleotide formation and indicate activation by a DNA-induced structural switch. cGAS possesses a remarkable structural similarity to the antiviral cytosolic double-stranded RNA sensor 2'-5'oligoadenylate synthase (OAS1), but contains a unique zinc thumb that recognizes B-form double-stranded DNA. Our results mechanistically unify dsRNA and dsDNA innate immune sensing by OAS1 and cGAS nucleotidyl transferases.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3768140/" 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/PMC3768140/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Civril, Filiz -- Deimling, Tobias -- de Oliveira Mann, Carina C -- Ablasser, Andrea -- Moldt, Manuela -- Witte, Gregor -- Hornung, Veit -- Hopfner, Karl-Peter -- 243046/European Research Council/International -- U19 AI083025/AI/NIAID NIH HHS/ -- U19AI083025/AI/NIAID NIH HHS/ -- England -- Nature. 2013 Jun 20;498(7454):332-7. doi: 10.1038/nature12305. Epub 2013 May 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23722159" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/chemistry/metabolism ; Animals ; Base Sequence ; Catalytic Domain ; Crystallography, X-Ray ; *Cytosol ; DNA/chemistry/*metabolism/pharmacology ; Guanosine Triphosphate/chemistry/metabolism ; HEK293 Cells ; Humans ; Membrane Proteins/genetics/metabolism ; Mice ; Models, Biological ; Models, Molecular ; Mutation ; Nucleotidyltransferases/*chemistry/genetics/metabolism ; Protein Conformation/drug effects ; Structure-Activity Relationship ; Substrate Specificity ; Swine ; Uridine Triphosphate/chemistry/metabolism ; Zinc/chemistry/metabolism
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  • 187
    Publication Date: 2013-05-31
    Description: Human language, as well as birdsong, relies on the ability to arrange vocal elements in new sequences. However, little is known about the ontogenetic origin of this capacity. Here we track the development of vocal combinatorial capacity in three species of vocal learners, combining an experimental approach in zebra finches (Taeniopygia guttata) with an analysis of natural development of vocal transitions in Bengalese finches (Lonchura striata domestica) and pre-lingual human infants. We find a common, stepwise pattern of acquiring vocal transitions across species. In our first study, juvenile zebra finches were trained to perform one song and then the training target was altered, prompting the birds to swap syllable order, or insert a new syllable into a string. All birds solved these permutation tasks in a series of steps, gradually approximating the target sequence by acquiring new pairwise syllable transitions, sometimes too slowly to accomplish the task fully. Similarly, in the more complex songs of Bengalese finches, branching points and bidirectional transitions in song syntax were acquired in a stepwise fashion, starting from a more restrictive set of vocal transitions. The babbling of pre-lingual human infants showed a similar pattern: instead of a single developmental shift from reduplicated to variegated babbling (that is, from repetitive to diverse sequences), we observed multiple shifts, where each new syllable type slowly acquired a diversity of pairwise transitions, asynchronously over development. Collectively, these results point to a common generative process that is conserved across species, suggesting that the long-noted gap between perceptual versus motor combinatorial capabilities in human infants may arise partly from the challenges in constructing new pairwise vocal transitions.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3676428/" 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/PMC3676428/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lipkind, Dina -- Marcus, Gary F -- Bemis, Douglas K -- Sasahara, Kazutoshi -- Jacoby, Nori -- Takahasi, Miki -- Suzuki, Kenta -- Feher, Olga -- Ravbar, Primoz -- Okanoya, Kazuo -- Tchernichovski, Ofer -- R01 DC004722/DC/NIDCD NIH HHS/ -- England -- Nature. 2013 Jun 6;498(7452):104-8. doi: 10.1038/nature12173. Epub 2013 May 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Psychology, Hunter College, City University of New York, New York, NY 10065, USA. dina.lipkind@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23719373" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Evolution ; *Child Language ; Finches/*physiology ; Humans ; Infant ; Male ; Models, Biological ; Phonetics ; Speech/physiology ; Time Factors ; Vocalization, Animal/*physiology
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  • 188
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2013-11-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2013 Nov 7;503(7474):6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24218658" target="_blank"〉PubMed〈/a〉
    Keywords: Electric Stimulation ; Humans ; Hydrodynamics ; *Mass Behavior ; *Microspheres ; Models, Biological ; Plastics ; Static Electricity
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  • 189
    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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  • 190
    Publication Date: 2013-12-18
    Description: Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching. SL signalling requires the hormone-dependent interaction of DWARF 14 (D14), a probable candidate SL receptor, with DWARF 3 (D3), an F-box component of the Skp-Cullin-F-box (SCF) E3 ubiquitin ligase complex. Here we report the characterization of a dominant SL-insensitive rice (Oryza sativa) mutant dwarf 53 (d53) and the cloning of D53, which encodes a substrate of the SCF(D3) ubiquitination complex and functions as a repressor of SL signalling. Treatments with GR24, a synthetic SL analogue, cause D53 degradation via the proteasome in a manner that requires D14 and the SCF(D3) ubiquitin ligase, whereas the dominant form of D53 is resistant to SL-mediated degradation. Moreover, D53 can interact with transcriptional co-repressors known as TOPLESS-RELATED PROTEINS. Our results suggest a model of SL signalling that involves SL-dependent degradation of the D53 repressor mediated by the D14-D3 complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jiang, Liang -- Liu, Xue -- Xiong, Guosheng -- Liu, Huihui -- Chen, Fulu -- Wang, Lei -- Meng, Xiangbing -- Liu, Guifu -- Yu, Hong -- Yuan, Yundong -- Yi, Wei -- Zhao, Lihua -- Ma, Honglei -- He, Yuanzheng -- Wu, Zhongshan -- Melcher, Karsten -- Qian, Qian -- Xu, H Eric -- Wang, Yonghong -- Li, Jiayang -- England -- Nature. 2013 Dec 19;504(7480):401-5. doi: 10.1038/nature12870. Epub 2013 Dec 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China [2]. ; State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China. ; VARI-SIMM Center, Center for Structure and Function of Drug Targets, CAS-Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. ; Laboratory of Structural Sciences, Van Andel Research Institute, 333 Bostwick Avenue Northeast, Grand Rapids, Michigan 49503, USA. ; State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China. ; 1] VARI-SIMM Center, Center for Structure and Function of Drug Targets, CAS-Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China [2] Laboratory of Structural Sciences, Van Andel Research Institute, 333 Bostwick Avenue Northeast, Grand Rapids, Michigan 49503, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24336200" target="_blank"〉PubMed〈/a〉
    Keywords: Cloning, Molecular ; Gene Expression Regulation, Plant ; Lactones/*antagonists & inhibitors/*metabolism ; Models, Biological ; Multiprotein Complexes/chemistry/metabolism ; Mutation/genetics ; Oryza/genetics/*metabolism ; Plant Growth Regulators/antagonists & inhibitors/*metabolism ; Plant Proteins/chemistry/genetics/*metabolism ; Proteasome Endopeptidase Complex/metabolism ; Protein Binding ; Proteolysis ; *Signal Transduction ; Ubiquitin/metabolism
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  • 191
    Publication Date: 2013-04-09
    Description: In vertebrate development, the body plan is determined by primordial morphogen gradients that suffuse the embryo. Retinoic acid (RA) is an important morphogen involved in patterning the anterior-posterior axis of structures, including the hindbrain and paraxial mesoderm. RA diffuses over long distances, and its activity is spatially restricted by synthesizing and degrading enzymes. However, gradients of endogenous morphogens in live embryos have not been directly observed; indeed, their existence, distribution and requirement for correct patterning remain controversial. Here we report a family of genetically encoded indicators for RA that we have termed GEPRAs (genetically encoded probes for RA). Using the principle of fluorescence resonance energy transfer we engineered the ligand-binding domains of RA receptors to incorporate cyan-emitting and yellow-emitting fluorescent proteins as fluorescence resonance energy transfer donor and acceptor, respectively, for the reliable detection of ambient free RA. We created three GEPRAs with different affinities for RA, enabling the quantitative measurement of physiological RA concentrations. Live imaging of zebrafish embryos at the gastrula and somitogenesis stages revealed a linear concentration gradient of endogenous RA in a two-tailed source-sink arrangement across the embryo. Modelling of the observed linear RA gradient suggests that the rate of RA diffusion exceeds the spatiotemporal dynamics of embryogenesis, resulting in stability to perturbation. Furthermore, we used GEPRAs in combination with genetic and pharmacological perturbations to resolve competing hypotheses on the structure of the RA gradient during hindbrain formation and somitogenesis. Live imaging of endogenous concentration gradients across embryonic development will allow the precise assignment of molecular mechanisms to developmental dynamics and will accelerate the application of approaches based on morphogen gradients to tissue engineering and regenerative medicine.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shimozono, Satoshi -- Iimura, Tadahiro -- Kitaguchi, Tetsuya -- Higashijima, Shin-Ichi -- Miyawaki, Atsushi -- England -- Nature. 2013 Apr 18;496(7445):363-6. doi: 10.1038/nature12037. Epub 2013 Apr 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory for Cell Function Dynamics, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama 351-0198, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23563268" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Genetically Modified ; Body Patterning/physiology ; Embryo, Nonmammalian/embryology/metabolism ; Embryonic Development/*physiology ; Fibroblast Growth Factors/genetics/metabolism ; Fluorescence Resonance Energy Transfer ; Gastrula/embryology/metabolism ; HeLa Cells ; Humans ; Models, Biological ; Molecular Probes/analysis/genetics/metabolism ; Molecular Sequence Data ; Rhombencephalon/embryology/metabolism ; Somites/embryology/metabolism ; Substrate Specificity ; Tretinoin/analysis/*metabolism ; Zebrafish/*embryology/*metabolism ; Zebrafish Proteins/genetics/metabolism
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  • 192
    Publication Date: 2014-02-07
    Description: Alveoli are gas-exchange sacs lined by squamous alveolar type (AT) 1 cells and cuboidal, surfactant-secreting AT2 cells. Classical studies suggested that AT1 arise from AT2 cells, but recent studies propose other sources. Here we use molecular markers, lineage tracing and clonal analysis to map alveolar progenitors throughout the mouse lifespan. We show that, during development, AT1 and AT2 cells arise directly from a bipotent progenitor, whereas after birth new AT1 cells derive from rare, self-renewing, long-lived, mature AT2 cells that produce slowly expanding clonal foci of alveolar renewal. This stem-cell function is broadly activated by AT1 injury, and AT2 self-renewal is selectively induced by EGFR (epidermal growth factor receptor) ligands in vitro and oncogenic Kras(G12D) in vivo, efficiently generating multifocal, clonal adenomas. Thus, there is a switch after birth, when AT2 cells function as stem cells that contribute to alveolar renewal, repair and cancer. We propose that local signals regulate AT2 stem-cell activity: a signal transduced by EGFR-KRAS controls self-renewal and is hijacked during oncogenesis, whereas another signal controls reprogramming to AT1 fate.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4013278/" 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/PMC4013278/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Desai, Tushar J -- Brownfield, Douglas G -- Krasnow, Mark A -- P30 CA124435/CA/NCI NIH HHS/ -- U01 HL099995/HL/NHLBI NIH HHS/ -- U01 HL099999/HL/NHLBI NIH HHS/ -- England -- Nature. 2014 Mar 13;507(7491):190-4. doi: 10.1038/nature12930. Epub 2014 Feb 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305-5307, USA [2] Department of Internal Medicine, Division of Pulmonary and Critical Care, Stanford University School of Medicine, Stanford, California 94305-5307, USA. ; Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305-5307, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24499815" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Differentiation ; Cell Division ; Cell Lineage ; Cell Transformation, Neoplastic/metabolism/pathology ; Cells, Cultured ; Cellular Reprogramming ; Clone Cells/cytology ; Female ; Lung/*cytology/embryology/*growth & development/pathology ; Lung Neoplasms/metabolism/*pathology ; Male ; Mice ; Models, Biological ; Multipotent Stem Cells/*cytology/metabolism/*pathology ; Proto-Oncogene Proteins p21(ras)/genetics/metabolism ; Pulmonary Alveoli/*cytology ; Receptor, Epidermal Growth Factor/metabolism ; *Regeneration ; Signal Transduction
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  • 193
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2013-04-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boehm, Thomas -- England -- Nature. 2013 Apr 18;496(7445):304-5. doi: 10.1038/496304a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23598335" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Genetic Variation ; Genome/*genetics ; *Heredity ; Ligands ; Major Histocompatibility Complex/genetics/immunology ; Mice ; Models, Biological ; Peptides/chemistry/genetics/urine ; Proteins/analysis/chemistry/genetics ; Proteolysis ; Sensory Receptor Cells/metabolism ; Smell/*physiology
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  • 194
    Publication Date: 2014-05-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gibney, Elizabeth -- England -- Nature. 2014 May 29;509(7502):544-5. doi: 10.1038/509544a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24870523" target="_blank"〉PubMed〈/a〉
    Keywords: Academies and Institutes/*organization & administration ; Biomedical Research/*manpower/methods/*organization & administration/trends ; Interdisciplinary Communication ; Interdisciplinary Studies/*trends ; London ; Models, Biological ; Physics/methods/*organization & administration ; *Research Personnel
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  • 195
    Publication Date: 2013-10-11
    Description: Cyanobacteria are photosynthetic organisms responsible for approximately 25% of organic carbon fixation on the Earth. These bacteria began to convert solar energy and carbon dioxide into bioenergy and oxygen more than two billion years ago. Cyanophages, which infect these bacteria, have an important role in regulating the marine ecosystem by controlling cyanobacteria community organization and mediating lateral gene transfer. Here we visualize the maturation process of cyanophage Syn5 inside its host cell, Synechococcus, using Zernike phase contrast electron cryo-tomography (cryoET). This imaging modality yields dramatic enhancement of image contrast over conventional cryoET and thus facilitates the direct identification of subcellular components, including thylakoid membranes, carboxysomes and polyribosomes, as well as phages, inside the congested cytosol of the infected cell. By correlating the structural features and relative abundance of viral progeny within cells at different stages of infection, we identify distinct Syn5 assembly intermediates. Our results indicate that the procapsid releases scaffolding proteins and expands its volume at an early stage of genome packaging. Later in the assembly process, we detected full particles with a tail either with or without an additional horn. The morphogenetic pathway we describe here is highly conserved and was probably established long before that of double-stranded DNA viruses infecting more complex organisms.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3984937/" 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/PMC3984937/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dai, Wei -- Fu, Caroline -- Raytcheva, Desislava -- Flanagan, John -- Khant, Htet A -- Liu, Xiangan -- Rochat, Ryan H -- Haase-Pettingell, Cameron -- Piret, Jacqueline -- Ludtke, Steve J -- Nagayama, Kuniaki -- Schmid, Michael F -- King, Jonathan A -- Chiu, Wah -- AI0175208/AI/NIAID NIH HHS/ -- GM080139/GM/NIGMS NIH HHS/ -- P41 GM103832/GM/NIGMS NIH HHS/ -- P41GM123832/GM/NIGMS NIH HHS/ -- PN2 EY016525/EY/NEI NIH HHS/ -- PN2EY016525/EY/NEI NIH HHS/ -- R01 GM080139/GM/NIGMS NIH HHS/ -- R56 AI075208/AI/NIAID NIH HHS/ -- T15 LM007093/LM/NLM NIH HHS/ -- T15LM007093/LM/NLM NIH HHS/ -- T32GM007330/GM/NIGMS NIH HHS/ -- England -- Nature. 2013 Oct 31;502(7473):707-10. doi: 10.1038/nature12604. Epub 2013 Oct 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Center for Macromolecular Imaging, Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, 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/24107993" target="_blank"〉PubMed〈/a〉
    Keywords: Aquatic Organisms/cytology/ultrastructure/virology ; Bacteriophages/*growth & development/*ultrastructure ; Cryoelectron Microscopy/*methods ; Electron Microscope Tomography/*methods ; Models, Biological ; Synechococcus/cytology/*ultrastructure/*virology ; *Virus Assembly
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  • 196
    Publication Date: 2013-06-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pongratz, Julia -- England -- Nature. 2013 Jun 6;498(7452):47-8. doi: 10.1038/498047a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23739422" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/chemistry ; Carbon Dioxide/metabolism ; *Carbon Sequestration ; Climate Change/statistics & numerical data ; Ecology/*methods ; *Forestry/methods ; Human Activities ; Models, Biological ; Nitrogen/analysis/*metabolism ; Nitrogen Fixation ; Soil Microbiology ; Trees/growth & development/*metabolism ; Uncertainty
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  • 197
    Publication Date: 2013-05-28
    Description: Fusing left and right eye images into a single view is dependent on precise ocular alignment, which relies on coordinated eye movements. During movements of the head this alignment is maintained by numerous reflexes. Although rodents share with other mammals the key components of eye movement control, the coordination of eye movements in freely moving rodents is unknown. Here we show that movements of the two eyes in freely moving rats differ fundamentally from the precisely controlled eye movements used by other mammals to maintain continuous binocular fusion. The observed eye movements serve to keep the visual fields of the two eyes continuously overlapping above the animal during free movement, but not continuously aligned. Overhead visual stimuli presented to rats freely exploring an open arena evoke an immediate shelter-seeking behaviour, but are ineffective when presented beside the arena. We suggest that continuously overlapping visual fields overhead would be of evolutionary benefit for predator detection by minimizing blind spots.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wallace, Damian J -- Greenberg, David S -- Sawinski, Juergen -- Rulla, Stefanie -- Notaro, Giuseppe -- Kerr, Jason N D -- England -- Nature. 2013 Jun 6;498(7452):65-9. doi: 10.1038/nature12153. Epub 2013 May 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Network Imaging Group, Max Planck Institute for Biological Cybernetics, Spemannstrasse 41, 72076 Tubingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23708965" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Escape Reaction/physiology ; Exploratory Behavior/physiology ; Eye Movements/physiology ; Head/physiology ; Models, Biological ; Movement/physiology ; Optic Disk/physiology ; Predatory Behavior ; Rats ; Retina/physiology ; Vision, Binocular/*physiology ; Visual Fields/*physiology
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  • 198
    Publication Date: 2014-04-18
    Description: The equilibrium theory of island biogeography is the basis for estimating extinction rates and a pillar of conservation science. The default strategy for conserving biodiversity is the designation of nature reserves, treated as islands in an inhospitable sea of human activity. Despite the profound influence of islands on conservation theory and practice, their mainland analogues, forest fragments in human-dominated landscapes, consistently defy expected biodiversity patterns based on island biogeography theory. Countryside biogeography is an alternative framework, which recognizes that the fate of the world's wildlife will be decided largely by the hospitality of agricultural or countryside ecosystems. Here we directly test these biogeographic theories by comparing a Neotropical countryside ecosystem with a nearby island ecosystem, and show that each supports similar bat biodiversity in fundamentally different ways. The island ecosystem conforms to island biogeographic predictions of bat species loss, in which the water matrix is not habitat. In contrast, the countryside ecosystem has high species richness and evenness across forest reserves and smaller forest fragments. Relative to forest reserves and fragments, deforested countryside habitat supports a less species-rich, yet equally even, bat assemblage. Moreover, the bat assemblage associated with deforested habitat is compositionally novel because of predictable changes in abundances by many species using human-made habitat. Finally, we perform a global meta-analysis of bat biogeographic studies, spanning more than 700 species. It generalizes our findings, showing that separate biogeographic theories for countryside and island ecosystems are necessary. A theory of countryside biogeography is essential to conservation strategy in the agricultural ecosystems that comprise roughly half of the global land surface and are likely to increase even further.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mendenhall, Chase D -- Karp, Daniel S -- Meyer, Christoph F J -- Hadly, Elizabeth A -- Daily, Gretchen C -- England -- Nature. 2014 May 8;509(7499):213-7. doi: 10.1038/nature13139. Epub 2014 Apr 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Center for Conservation Biology, Stanford University, Stanford, California 94305, USA [2] Department of Biology, Stanford University, Stanford, California 94305, USA. ; 1] Center for Conservation Biology, Stanford University, Stanford, California 94305, USA [2] Department of Biology, Stanford University, Stanford, California 94305, USA [3] Department of Environmental Science, Policy & Management, University of California, Berkeley, California 94720, USA [4] The Nature Conservancy, Berkeley, California 94705, USA. ; 1] Institute of Experimental Ecology, University of Ulm, 89069 Ulm, Germany [2] Centre for Environmental Biology, University of Lisbon, 1749-016 Lisbon, Portugal. ; Department of Biology, Stanford University, Stanford, California 94305, USA. ; 1] Center for Conservation Biology, Stanford University, Stanford, California 94305, USA [2] Department of Biology, Stanford University, Stanford, California 94305, USA [3] Woods Institute for the Environment, Stanford University, Stanford, California 94305, USA [4] Global Economic Dynamics and the Biosphere, Royal Swedish Academy of Sciences, Stockholm, SE-104 05, Sweden [5] Stockholm Resilience Centre, University of Stockholm, Stockholm, SE-106 91, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24739971" target="_blank"〉PubMed〈/a〉
    Keywords: *Agriculture/methods ; Animals ; *Biodiversity ; Chiroptera/physiology ; *Conservation of Natural Resources ; Costa Rica ; Extinction, Biological ; *Geography ; Islands ; Lakes ; Models, Biological ; Population Dynamics ; Trees/*growth & development
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  • 199
    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
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 200
    Publication Date: 2014-06-06
    Description: Advances in our understanding of the mechanisms that bring about the resolution of acute inflammation have uncovered a new genus of pro-resolving lipid mediators that include the lipoxin, resolvin, protectin and maresin families, collectively called specialized pro-resolving mediators. Synthetic versions of these mediators have potent bioactions when administered in vivo. In animal experiments, the mediators evoke anti-inflammatory and novel pro-resolving mechanisms, and enhance microbial clearance. Although they have been identified in inflammation resolution, specialized pro-resolving mediators are conserved structures that also function in host defence, pain, organ protection and tissue remodelling. This Review covers the mechanisms of specialized pro-resolving mediators and omega-3 essential fatty acid pathways that could help us to understand their physiological functions.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263681/" 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/PMC4263681/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Serhan, Charles N -- P01 GM095467/GM/NIGMS NIH HHS/ -- P01GM095467/GM/NIGMS NIH HHS/ -- R01 GM038765/GM/NIGMS NIH HHS/ -- R01GM038765/GM/NIGMS NIH HHS/ -- England -- Nature. 2014 Jun 5;510(7503):92-101. doi: 10.1038/nature13479.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Harvard Institutes of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24899309" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chronic Disease ; Docosahexaenoic Acids/metabolism ; Fatty Acids, Omega-3/*metabolism ; Fatty Acids, Unsaturated/metabolism ; Humans ; Immunity ; Infection/metabolism ; Inflammation/drug therapy/*metabolism/pathology ; Inflammation Mediators/*metabolism/therapeutic use ; Models, Biological ; Pain/metabolism ; Regeneration ; Translational Medical Research ; Wound Healing
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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