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  • *Ecosystem  (129)
  • *Climate Change  (84)
  • Protein Structure, Tertiary  (71)
  • American Association for the Advancement of Science (AAAS)  (273)
  • Copernicus
  • Hindawi
  • 2010-2014  (273)
  • 1980-1984
  • 2013  (106)
  • 2012  (167)
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  • 2010-2014  (273)
  • 1980-1984
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  • 1
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-11-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Qiu, Jane -- New York, N.Y. -- Science. 2012 Nov 16;338(6109):881. doi: 10.1126/science.338.6109.881.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23161971" target="_blank"〉PubMed〈/a〉
    Keywords: Antarctic Regions ; *Climate Change ; *Ice Cover ; *Islands
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2012-06-23
    Description: Policies to reduce emissions from deforestation would benefit from clearly derived, spatially explicit, statistically bounded estimates of carbon emissions. Existing efforts derive carbon impacts of land-use change using broad assumptions, unreliable data, or both. We improve on this approach using satellite observations of gross forest cover loss and a map of forest carbon stocks to estimate gross carbon emissions across tropical regions between 2000 and 2005 as 0.81 petagram of carbon per year, with a 90% prediction interval of 0.57 to 1.22 petagrams of carbon per year. This estimate is 25 to 50% of recently published estimates. By systematically matching areas of forest loss with their carbon stocks before clearing, these results serve as a more accurate benchmark for monitoring global progress on reducing emissions from deforestation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harris, Nancy L -- Brown, Sandra -- Hagen, Stephen C -- Saatchi, Sassan S -- Petrova, Silvia -- Salas, William -- Hansen, Matthew C -- Potapov, Peter V -- Lotsch, Alexander -- New York, N.Y. -- Science. 2012 Jun 22;336(6088):1573-6. doi: 10.1126/science.1217962.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ecosystem Services Unit, Winrock International, Arlington, VA 22202, USA. nharris@winrock.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22723420" target="_blank"〉PubMed〈/a〉
    Keywords: Africa South of the Sahara ; Asia ; Biomass ; *Carbon ; *Conservation of Natural Resources ; Developing Countries ; *Ecosystem ; Latin America ; Monte Carlo Method ; Remote Sensing Technology ; Soil ; *Trees ; *Tropical Climate
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-05-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hartmann, Aaron C -- Levin, Lisa A -- New York, N.Y. -- Science. 2012 May 11;336(6082):668-9. doi: 10.1126/science.336.6082.668-a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22582242" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Aquatic Organisms ; *Ecosystem ; *Seawater
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-11-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Qiu, Jane -- New York, N.Y. -- Science. 2012 Nov 16;338(6109):879-81. doi: 10.1126/science.338.6109.879.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23161970" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antarctic Regions ; *Climate Change ; Global Warming ; *Ice Cover ; Spheniscidae/*physiology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-01-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Midgley, Guy F -- New York, N.Y. -- Science. 2012 Jan 13;335(6065):174-5. doi: 10.1126/science.1217245.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Climate Change and Bioadaptation, South African National Biodiversity Institute, Rhodes Drive, Cape Town 7735, South Africa. g.midgley@sanbi.org.za〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22246761" target="_blank"〉PubMed〈/a〉
    Keywords: *Biodiversity ; *Climate ; *Ecosystem ; *Plants
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2012-05-05
    Description: Hirota et al. (Reports, 14 October 2011, p. 232) used spatial data to show that grasslands, savannas, and forests represent opposing stable states. Reanalyzing their data and drawing from temporal studies, we argue that spatial analyses underestimate the bistability of grasslands and savannas due to limitations of substituting space for time. We propose that temporal and spatial data are needed to predict critical transitions between grasslands and savannas.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ratajczak, Zak -- Nippert, Jesse B -- New York, N.Y. -- Science. 2012 May 4;336(6081):541; author reply 541. doi: 10.1126/science.1219346.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506, USA. zarata@ksu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22556235" target="_blank"〉PubMed〈/a〉
    Keywords: *Ecosystem ; *Trees ; *Tropical Climate
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2012-04-21
    Description: Prion conversion from a soluble protein to an aggregated state may be involved in the cellular adaptation of yeast to the environment. However, it remains unclear whether and how cells actively use prion conversion to acquire a fitness advantage in response to environmental stress. We identified Mod5, a yeast transfer RNA isopentenyltransferase lacking glutamine/asparagine-rich domains, as a yeast prion protein and found that its prion conversion in yeast regulated the sterol biosynthetic pathway for acquired cellular resistance against antifungal agents. Furthermore, selective pressure by antifungal drugs on yeast facilitated the de novo appearance of Mod5 prion states for cell survival. Thus, phenotypic changes caused by active prion conversion under environmental selection may contribute to cellular adaptation in living organisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Suzuki, Genjiro -- Shimazu, Naoyuki -- Tanaka, Motomasa -- New York, N.Y. -- Science. 2012 Apr 20;336(6079):355-9. doi: 10.1126/science.1219491.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory for Protein Conformation Diseases, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22517861" target="_blank"〉PubMed〈/a〉
    Keywords: Alkyl and Aryl Transferases/*chemistry/genetics/*metabolism ; Antifungal Agents/*pharmacology ; Biosynthetic Pathways ; Crosses, Genetic ; Drug Resistance, Fungal ; Ergosterol/biosynthesis ; Fluorouracil/pharmacology ; Microbial Viability ; Prions/*chemistry/genetics/metabolism ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Fungal/metabolism ; RNA, Transfer/metabolism ; Recombinant Fusion Proteins/chemistry/metabolism ; Saccharomyces cerevisiae/chemistry/*drug effects/genetics/*physiology ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism ; Selection, Genetic ; Solubility ; *Stress, Physiological
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  • 8
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-11-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haward, Marcus -- Jabour, Julia -- Press, A J -- New York, N.Y. -- Science. 2012 Nov 2;338(6107):603. doi: 10.1126/science.338.6107.603.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23118165" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Conservation of Natural Resources ; *Ecosystem ; Humans
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-05-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Strain, Daniel -- New York, N.Y. -- Science. 2012 May 11;336(6082):664-5. doi: 10.1126/science.336.6082.664.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22582239" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Ecosystem ; *Introduced Species ; *Lakes ; *Seawater ; *Ships ; United States
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
    Publication Date: 2012-11-01
    Description: Johnson and colleagues (Reports, 18 May 2012, p. 904) claim that conspecific negative density dependence is a pervasive mechanism driving forest diversity, especially for rare tree species. We show that their results are due to a statistical bias in their analysis caused by the exclusion of joint absences.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dickie, Ian A -- Hurst, Jennifer M -- Bellingham, Peter J -- New York, N.Y. -- Science. 2012 Oct 26;338(6106):469; author reply 469. doi: 10.1126/science.1225520.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Landcare Research, Lincoln, 7640 New Zealand. dickiei@landcareresearch.co.nz〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23112313" target="_blank"〉PubMed〈/a〉
    Keywords: *Biodiversity ; *Ecosystem ; *Trees
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  • 11
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-07-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rangel, Thiago F -- New York, N.Y. -- Science. 2012 Jul 13;337(6091):162-3. doi: 10.1126/science.1224819.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology, Federal University of Goias, CxP. 131, Goiania, Goias, Brazil 74970-001. thiagorangel@icb.ufg.br〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22798589" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Conservation of Natural Resources ; *Ecosystem ; *Extinction, Biological ; *Trees ; *Vertebrates
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  • 12
    Publication Date: 2012-03-24
    Description: Development of fertilization-competent oocytes depends on integrated processes controlling meiosis, cytoplasmic development, and maintenance of genomic integrity. We show that meiosis arrest female 1 (MARF1) is required for these processes in mammalian oocytes. Mutations of Marf1 cause female infertility characterized by up-regulation of a cohort of transcripts, increased retrotransposon expression, defective cytoplasmic maturation, and meiotic arrest. Up-regulation of protein phosphatase 2 catalytic subunit (PPP2CB) is key to the meiotic arrest phenotype. Moreover, Iap and Line1 retrotransposon messenger RNAs are also up-regulated, and, concomitantly, DNA double-strand breaks are elevated in mutant oocytes. Therefore MARF1, by suppressing levels of specific transcripts, is an essential regulator of important oogenic processes leading to female fertility and the development of healthy offspring.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3612990/" 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/PMC3612990/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Su, You-Qiang -- Sugiura, Koji -- Sun, Fengyun -- Pendola, Janice K -- Cox, Gregory A -- Handel, Mary Ann -- Schimenti, John C -- Eppig, John J -- CA34196/CA/NCI NIH HHS/ -- HD42137/HD/NICHD NIH HHS/ -- P01 HD042137/HD/NICHD NIH HHS/ -- P30 CA034196/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2012 Mar 23;335(6075):1496-9. doi: 10.1126/science.1214680.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Jackson Laboratory, Bar Harbor, ME 04609, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22442484" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Cell Cycle Proteins/chemistry/genetics/*metabolism ; DNA Breaks, Double-Stranded ; Embryonic Development ; Female ; *Fertility ; Meiosis ; Mice ; Molecular Sequence Data ; Mutation ; Oocytes/*physiology ; *Oogenesis ; Phenotype ; Protein Phosphatase 2/genetics/metabolism ; Protein Structure, Tertiary ; RNA, Messenger/genetics/metabolism ; Retroelements ; Transcription, Genetic ; Transcriptome ; Up-Regulation
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  • 13
    Publication Date: 2012-09-22
    Description: Identifying causal networks is important for effective policy and management recommendations on climate, epidemiology, financial regulation, and much else. We introduce a method, based on nonlinear state space reconstruction, that can distinguish causality from correlation. It extends to nonseparable weakly connected dynamic systems (cases not covered by the current Granger causality paradigm). The approach is illustrated both by simple models (where, in contrast to the real world, we know the underlying equations/relations and so can check the validity of our method) and by application to real ecological systems, including the controversial sardine-anchovy-temperature problem.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sugihara, George -- May, Robert -- Ye, Hao -- Hsieh, Chih-hao -- Deyle, Ethan -- Fogarty, Michael -- Munch, Stephan -- New York, N.Y. -- Science. 2012 Oct 26;338(6106):496-500. doi: 10.1126/science.1227079. Epub 2012 Sep 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. gsugihara@ucsd.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22997134" target="_blank"〉PubMed〈/a〉
    Keywords: *Causality ; Ciliophora ; *Ecosystem ; *Models, Statistical ; Nonlinear Dynamics ; Paramecium
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  • 14
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-03-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brook, Edward -- New York, N.Y. -- Science. 2012 May 11;336(6082):682-3. doi: 10.1126/science.1219710. Epub 2012 Mar 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR 97331, USA. brooke@oregonstate.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22461499" target="_blank"〉PubMed〈/a〉
    Keywords: *Atmosphere ; *Carbon Cycle ; *Carbon Isotopes ; *Climate Change ; *Ice Cover ; *Seawater
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 15
    Publication Date: 2012-09-22
    Description: Cytoplasmic dynein is a microtubule-based motor required for intracellular transport and cell division. Its movement involves coupling cycles of track binding and release with cycles of force-generating nucleotide hydrolysis. How this is accomplished given the ~25 nanometers separating dynein's track- and nucleotide-binding sites is not understood. Here, we present a subnanometer-resolution structure of dynein's microtubule-binding domain bound to microtubules by cryo-electron microscopy that was used to generate a pseudo-atomic model of the complex with molecular dynamics. We identified large rearrangements triggered by track binding and specific interactions, confirmed by mutagenesis and single-molecule motility assays, which tune dynein's affinity for microtubules. Our results provide a molecular model for how dynein's binding to microtubules is communicated to the rest of the motor.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3919166/" 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/PMC3919166/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Redwine, William B -- Hernandez-Lopez, Rogelio -- Zou, Sirui -- Huang, Julie -- Reck-Peterson, Samara L -- Leschziner, Andres E -- 1 DP2 OD004268-1/OD/NIH HHS/ -- DP2 OD004268/OD/NIH HHS/ -- New York, N.Y. -- Science. 2012 Sep 21;337(6101):1532-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22997337" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Binding Sites ; Cryoelectron Microscopy ; Cytoplasmic Dyneins/*chemistry/metabolism ; Hydrogen Bonding ; Microtubules/*metabolism ; Models, Molecular ; Molecular Dynamics Simulation ; Mutagenesis ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Saccharomyces cerevisiae Proteins/chemistry/genetics/metabolism
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  • 16
    Publication Date: 2012-05-05
    Description: Plant diversity generally promotes biomass production, but how the shape of the response curve changes with time remains unclear. This is a critical knowledge gap because the shape of this relationship indicates the extent to which loss of the first few species will influence biomass production. Using two long-term (〉/=13 years) biodiversity experiments, we show that the effects of diversity on biomass productivity increased and became less saturating over time. Our analyses suggest that effects of diversity-dependent ecosystem feedbacks and interspecific complementarity accumulate over time, causing high-diversity species combinations that appeared functionally redundant during early years to become more functionally unique through time. Consequently, simplification of diverse ecosystems will likely have greater negative impacts on ecosystem functioning than has been suggested by short-term experiments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reich, Peter B -- Tilman, David -- Isbell, Forest -- Mueller, Kevin -- Hobbie, Sarah E -- Flynn, Dan F B -- Eisenhauer, Nico -- New York, N.Y. -- Science. 2012 May 4;336(6081):589-92. doi: 10.1126/science.1217909.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Forest Resources, University of Minnesota, St. Paul, MN 55108, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22556253" target="_blank"〉PubMed〈/a〉
    Keywords: *Biodiversity ; Biomass ; *Ecosystem ; Fabaceae/growth & development ; Minnesota ; Nitrogen ; Nitrogen Cycle ; Plant Development ; *Plants ; *Poaceae/growth & development ; Soil/chemistry ; Time Factors
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  • 17
    Publication Date: 2012-05-15
    Description: Poly(ADP-ribose) polymerase-1 (PARP-1) (ADP, adenosine diphosphate) has a modular domain architecture that couples DNA damage detection to poly(ADP-ribosyl)ation activity through a poorly understood mechanism. Here, we report the crystal structure of a DNA double-strand break in complex with human PARP-1 domains essential for activation (Zn1, Zn3, WGR-CAT). PARP-1 engages DNA as a monomer, and the interaction with DNA damage organizes PARP-1 domains into a collapsed conformation that can explain the strong preference for automodification. The Zn1, Zn3, and WGR domains collectively bind to DNA, forming a network of interdomain contacts that links the DNA damage interface to the catalytic domain (CAT). The DNA damage-induced conformation of PARP-1 results in structural distortions that destabilize the CAT. Our results suggest that an increase in CAT protein dynamics underlies the DNA-dependent activation mechanism of PARP-1.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3532513/" 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/PMC3532513/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Langelier, Marie-France -- Planck, Jamie L -- Roy, Swati -- Pascal, John M -- P30 EB009998/EB/NIBIB NIH HHS/ -- P30CA56036/CA/NCI NIH HHS/ -- R01 GM087282/GM/NIGMS NIH HHS/ -- R01087282/PHS HHS/ -- New York, N.Y. -- Science. 2012 May 11;336(6082):728-32. doi: 10.1126/science.1216338.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, The Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22582261" target="_blank"〉PubMed〈/a〉
    Keywords: Catalytic Domain ; Crystallography, X-Ray ; DNA/*chemistry/*metabolism ; *DNA Breaks, Double-Stranded ; Enzyme Stability ; Humans ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Nucleic Acid Conformation ; Poly Adenosine Diphosphate Ribose/*metabolism ; Poly(ADP-ribose) Polymerases/*chemistry/*metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary
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  • 18
    Publication Date: 2012-12-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reis, S -- Grennfelt, P -- Klimont, Z -- Amann, M -- ApSimon, H -- Hettelingh, J-P -- Holland, M -- LeGall, A-C -- Maas, R -- Posch, M -- Spranger, T -- Sutton, M A -- Williams, M -- New York, N.Y. -- Science. 2012 Nov 30;338(6111):1153-4. doi: 10.1126/science.1226514.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Ecology & Hydrology, Penicuik EH26 0QB, UK. srei@ceh.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23197517" target="_blank"〉PubMed〈/a〉
    Keywords: Acid Rain/*prevention & control ; *Air Pollutants ; Air Pollution/*prevention & control ; Canada ; *Climate Change ; Environmental Policy/*trends ; Europe ; *Guidelines as Topic ; *United Nations ; United States ; Vehicle Emissions/prevention & control
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  • 19
    Publication Date: 2012-01-28
    Description: Patterns of species richness and relative abundance at some scales cannot be distinguished from predictions of null models, including zero-sum neutral models of population change and random speciation-extinction models of evolutionary diversification. Both models predict that species richness or population abundance produced by independent iterations of the same processes in different regions should be uncorrelated. We find instead that the number of species and individuals in families of trees in forest plots are strongly correlated across Southeast Asia, Africa, and tropical America. These correlations imply that deterministic processes influenced by evolutionarily conservative family-level traits constrain the number of confamilial tree species and individuals that can be supported in regional species pools and local assemblages in humid tropical forests.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ricklefs, Robert E -- Renner, Susanne S -- New York, N.Y. -- Science. 2012 Jan 27;335(6067):464-7. doi: 10.1126/science.1215182.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Missouri-St. Louis, MO 63121-4499, USA. ricklefs@umsl.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22282811" target="_blank"〉PubMed〈/a〉
    Keywords: Africa, Western ; Asia, Southeastern ; *Biodiversity ; *Biological Evolution ; *Ecosystem ; Extinction, Biological ; Genetic Speciation ; Geography ; South America ; *Trees ; Tropical Climate
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  • 20
    Publication Date: 2012-05-05
    Description: Phytoplankton blooms characterize temperate ocean margin zones in spring. We investigated the bacterioplankton response to a diatom bloom in the North Sea and observed a dynamic succession of populations at genus-level resolution. Taxonomically distinct expressions of carbohydrate-active enzymes (transporters; in particular, TonB-dependent transporters) and phosphate acquisition strategies were found, indicating that distinct populations of Bacteroidetes, Gammaproteobacteria, and Alphaproteobacteria are specialized for successive decomposition of algal-derived organic matter. Our results suggest that algal substrate availability provided a series of ecological niches in which specialized populations could bloom. This reveals how planktonic species, despite their seemingly homogeneous habitat, can evade extinction by direct competition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Teeling, Hanno -- Fuchs, Bernhard M -- Becher, Dorte -- Klockow, Christine -- Gardebrecht, Antje -- Bennke, Christin M -- Kassabgy, Mariette -- Huang, Sixing -- Mann, Alexander J -- Waldmann, Jost -- Weber, Marc -- Klindworth, Anna -- Otto, Andreas -- Lange, Jana -- Bernhardt, Jorg -- Reinsch, Christine -- Hecker, Michael -- Peplies, Jorg -- Bockelmann, Frank D -- Callies, Ulrich -- Gerdts, Gunnar -- Wichels, Antje -- Wiltshire, Karen H -- Glockner, Frank Oliver -- Schweder, Thomas -- Amann, Rudolf -- New York, N.Y. -- Science. 2012 May 4;336(6081):608-11. doi: 10.1126/science.1218344.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22556258" target="_blank"〉PubMed〈/a〉
    Keywords: Alphaproteobacteria/enzymology/genetics/*growth & development/metabolism ; Bacterial Proteins/genetics/metabolism ; Bacteroidetes/enzymology/genetics/*growth & development/metabolism ; Diatoms/*growth & development/metabolism ; *Ecosystem ; *Eutrophication ; Gammaproteobacteria/enzymology/genetics/*growth & development/metabolism ; Glycoside Hydrolases/genetics/metabolism ; Membrane Proteins/genetics/metabolism ; Membrane Transport Proteins/genetics/metabolism ; Metagenome ; Microbial Interactions ; North Sea ; Phosphates/metabolism ; Phytoplankton/*growth & development/metabolism ; Seawater/*microbiology ; Sulfatases/genetics/metabolism
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  • 21
    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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  • 22
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-03-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cao, Shixiong -- Feng, Qi -- New York, N.Y. -- Science. 2012 Mar 9;335(6073):1168-9. doi: 10.1126/science.335.6073.1168-b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22403370" target="_blank"〉PubMed〈/a〉
    Keywords: China ; *Conservation of Natural Resources ; *Drugs, Chinese Herbal ; *Ecosystem ; Environment ; *Plants, Medicinal
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 23
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-05-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉New York, N.Y. -- Science. 2012 Apr 27;336(6080):432.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22548215" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Ecosystem ; Endangered Species ; Humans ; Introduced Species ; *Juniperus ; Midwestern United States
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 24
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-05-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cardinale, Bradley -- New York, N.Y. -- Science. 2012 May 4;336(6081):552-3. doi: 10.1126/science.1222102.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Natural Resources and Environment, University of Michigan, 440 Church Street, Ann Arbor, MI 48109, USA. bradcard@umich.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22556243" target="_blank"〉PubMed〈/a〉
    Keywords: *Biodiversity ; *Ecosystem ; *Plants ; *Poaceae
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  • 25
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-03-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dupont, Lydie -- New York, N.Y. -- Science. 2012 Mar 9;335(6073):1180-1. doi: 10.1126/science.1219903.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MARUM-Center for Marine Environmental Sciences, University of Bremen, P.O. Box 330440, 28334 Bremen, Germany. dupont@uni-bremen.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22403379" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/*history ; *Climate Change ; *Conservation of Natural Resources ; Geologic Sediments/*chemistry ; Humans ; *Trees
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  • 26
    Publication Date: 2012-03-03
    Description: Ocean acidification may have severe consequences for marine ecosystems; however, assessing its future impact is difficult because laboratory experiments and field observations are limited by their reduced ecologic complexity and sample period, respectively. In contrast, the geological record contains long-term evidence for a variety of global environmental perturbations, including ocean acidification plus their associated biotic responses. We review events exhibiting evidence for elevated atmospheric CO(2), global warming, and ocean acidification over the past ~300 million years of Earth's history, some with contemporaneous extinction or evolutionary turnover among marine calcifiers. Although similarities exist, no past event perfectly parallels future projections in terms of disrupting the balance of ocean carbonate chemistry-a consequence of the unprecedented rapidity of CO(2) release currently taking place.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Honisch, Barbel -- Ridgwell, Andy -- Schmidt, Daniela N -- Thomas, Ellen -- Gibbs, Samantha J -- Sluijs, Appy -- Zeebe, Richard -- Kump, Lee -- Martindale, Rowan C -- Greene, Sarah E -- Kiessling, Wolfgang -- Ries, Justin -- Zachos, James C -- Royer, Dana L -- Barker, Stephen -- Marchitto, Thomas M Jr -- Moyer, Ryan -- Pelejero, Carles -- Ziveri, Patrizia -- Foster, Gavin L -- Williams, Branwen -- New York, N.Y. -- Science. 2012 Mar 2;335(6072):1058-63. doi: 10.1126/science.1208277.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Lamont-Doherty Earth Observatory of Columbia University, Palisades, NY 10964, USA. hoenisch@ldeo.columbia.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22383840" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological ; Animals ; *Aquatic Organisms ; Atmosphere ; Carbon Dioxide ; Carbonates/analysis ; *Ecosystem ; Extinction, Biological ; Forecasting ; Fossils ; *Geological Phenomena ; Hydrogen-Ion Concentration ; Oceans and Seas ; Seawater/*chemistry
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 27
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-11-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vineis, Paolo -- Khan, Aneire -- New York, N.Y. -- Science. 2012 Nov 23;338(6110):1028-9. doi: 10.1126/science.338.6110.1028-b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23180844" target="_blank"〉PubMed〈/a〉
    Keywords: *Climate Change ; Drinking Water/*chemistry ; Heart Diseases/epidemiology ; Humans ; Hypertension/epidemiology ; Male ; *Public Health ; *Salinity ; Soil/*chemistry
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  • 28
    Publication Date: 2012-11-28
    Description: The plasma membrane protein Orai forms the pore of the calcium release-activated calcium (CRAC) channel and generates sustained cytosolic calcium signals when triggered by depletion of calcium from the endoplasmic reticulum. The crystal structure of Orai from Drosophila melanogaster, determined at 3.35 angstrom resolution, reveals that the calcium channel is composed of a hexameric assembly of Orai subunits arranged around a central ion pore. The pore traverses the membrane and extends into the cytosol. A ring of glutamate residues on its extracellular side forms the selectivity filter. A basic region near the intracellular side can bind anions that may stabilize the closed state. The architecture of the channel differs markedly from other ion channels and gives insight into the principles of selective calcium permeation and gating.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3695727/" 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/PMC3695727/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hou, Xiaowei -- Pedi, Leanne -- Diver, Melinda M -- Long, Stephen B -- GM094273/GM/NIGMS NIH HHS/ -- P30 CA008748/CA/NCI NIH HHS/ -- R01 GM094273/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Dec 7;338(6112):1308-13. doi: 10.1126/science.1228757. Epub 2012 Nov 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23180775" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Calcium/*chemistry ; Calcium Channels/*chemistry ; Crystallography, X-Ray ; Drosophila Proteins/agonists/*chemistry ; Glutamic Acid/chemistry ; Membrane Proteins/agonists/*chemistry ; Porosity ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 29
    Publication Date: 2012-02-04
    Description: Ecosystems are shaped by complex communities of mostly unculturable microbes. Metagenomes provide a fragmented view of such communities, but the ecosystem functions of major groups of organisms remain mysterious. To better characterize members of these communities, we developed methods to reconstruct genomes directly from mate-paired short-read metagenomes. We closed a genome representing the as-yet uncultured marine group II Euryarchaeota, assembled de novo from 1.7% of a metagenome sequenced from surface seawater. The genome describes a motile, photo-heterotrophic cell focused on degradation of protein and lipids and clarifies the origin of proteorhodopsin. It also demonstrates that high-coverage mate-paired sequence can overcome assembly difficulties caused by interstrain variation in complex microbial communities, enabling inference of ecosystem functions for uncultured members.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Iverson, Vaughn -- Morris, Robert M -- Frazar, Christian D -- Berthiaume, Chris T -- Morales, Rhonda L -- Armbrust, E Virginia -- New York, N.Y. -- Science. 2012 Feb 3;335(6068):587-90. doi: 10.1126/science.1212665.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Oceanography, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22301318" target="_blank"〉PubMed〈/a〉
    Keywords: Archaeal Proteins/*genetics/metabolism ; Biota ; *Ecosystem ; Enzymes/genetics/metabolism ; Euryarchaeota/classification/*genetics/metabolism/*physiology ; Genes, Archaeal ; *Genome, Archaeal ; Genome, Bacterial ; Heterotrophic Processes ; Lipid Metabolism/genetics ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Microbial Consortia ; Molecular Sequence Data ; Pacific Ocean ; Peptide Hydrolases/genetics/metabolism ; Phylogeny ; Proteins/metabolism ; Rhodopsin/genetics ; Rhodopsins, Microbial ; Seawater/*microbiology ; Sequence Alignment ; Sequence Analysis, DNA
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  • 30
    Publication Date: 2012-09-01
    Description: Bayon et al. (Reports, 9 March 2012, p. 1219) interpreted unusually high aluminum-potassium ratio values in an Atlantic sediment core as indicating anthropogenic deforestation around 2500 years before the present (B.P.). We argue that there is no terrestrial evidence for forest destruction by humans and that the third millennium B.P. rainforest crisis can be clearly attributed mostly to climatic change.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3556809/" 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/PMC3556809/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Neumann, K -- Eggert, M K H -- Oslisly, R -- Clist, B -- Denham, T -- de Maret, P -- Ozainne, S -- Hildebrand, E -- Bostoen, K -- Salzmann, U -- Schwartz, D -- Eichhorn, B -- Tchiengue, B -- Hohn, A -- 284126/European Research Council/International -- New York, N.Y. -- Science. 2012 Aug 31;337(6098):1040; author reply 1040. doi: 10.1126/science.1221747.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Goethe University, Institute of Archaeological Sciences, Frankfurt, Germany. k.neumann@em.uni-frankfurt.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22936758" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/*history ; *Climate Change ; *Conservation of Natural Resources ; Geologic Sediments/*chemistry ; Humans ; *Trees
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  • 31
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-03-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jacob, Nitya P -- New York, N.Y. -- Science. 2012 Mar 30;335(6076):1588-9. doi: 10.1126/science.1213692.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Oxford College of Emory University, Oxford, GA 30054, USA. njacob@emory.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22461602" target="_blank"〉PubMed〈/a〉
    Keywords: Awards and Prizes ; *Bacteria/classification/genetics/isolation & purification ; Bacteriological Techniques ; Biodiversity ; Biology/*education ; DNA, Bacterial/genetics/isolation & purification ; *Ecosystem ; *Geological Phenomena ; Georgia ; Research/*education ; Sequence Analysis, DNA ; Silicon Dioxide ; *Soil Microbiology ; Universities
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  • 32
    Publication Date: 2012-04-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lindgren, Elisabet -- Andersson, Yvonne -- Suk, Jonathan E -- Sudre, Bertrand -- Semenza, Jan C -- New York, N.Y. -- Science. 2012 Apr 27;336(6080):418-9. doi: 10.1126/science.1215735.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22539705" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Climate Change ; Communicable Diseases, Emerging/*epidemiology/veterinary ; Disease Vectors ; Europe/epidemiology ; *European Union ; Humans ; Internationality ; Mandatory Reporting ; *Population Surveillance ; Risk Assessment
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  • 33
    Publication Date: 2012-06-30
    Description: Ricklefs and Renner (Reports, 27 January 2012, p. 464) suggested that strong correlations in the diversity of shared families between isolated tree assemblages reject neutrality. Simulations of a neutral model indicate, however, that isolated assemblages under various configurations of random speciation and extinction do sustain strong correlations in the diversity of shared families. Thus, reported correlations support rather than reject neutral theory.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mora, Camilo -- New York, N.Y. -- Science. 2012 Jun 29;336(6089):1639; author reply 1639. doi: 10.1126/science.1220980.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geography, University of Hawaii, Honolulu, HI 96822, USA. cmora@hawaii.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22745402" target="_blank"〉PubMed〈/a〉
    Keywords: *Biodiversity ; *Biological Evolution ; *Ecosystem ; *Trees
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  • 34
    Publication Date: 2012-06-02
    Description: The circadian clock in mammals is driven by an autoregulatory transcriptional feedback mechanism that takes approximately 24 hours to complete. A key component of this mechanism is a heterodimeric transcriptional activator consisting of two basic helix-loop-helix PER-ARNT-SIM (bHLH-PAS) domain protein subunits, CLOCK and BMAL1. Here, we report the crystal structure of a complex containing the mouse CLOCK:BMAL1 bHLH-PAS domains at 2.3 A resolution. The structure reveals an unusual asymmetric heterodimer with the three domains in each of the two subunits--bHLH, PAS-A, and PAS-B--tightly intertwined and involved in dimerization interactions, resulting in three distinct protein interfaces. Mutations that perturb the observed heterodimer interfaces affect the stability and activity of the CLOCK:BMAL1 complex as well as the periodicity of the circadian oscillator. The structure of the CLOCK:BMAL1 complex is a starting point for understanding at an atomic level the mechanism driving the mammalian circadian clock.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694778/" 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/PMC3694778/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Nian -- Chelliah, Yogarany -- Shan, Yongli -- Taylor, Clinton A -- Yoo, Seung-Hee -- Partch, Carrie -- Green, Carla B -- Zhang, Hong -- Takahashi, Joseph S -- R01 GM081875/GM/NIGMS NIH HHS/ -- R01 GM090247/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Jul 13;337(6091):189-94. doi: 10.1126/science.1222804. Epub 2012 May 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22653727" target="_blank"〉PubMed〈/a〉
    Keywords: ARNTL Transcription Factors/*chemistry/genetics/metabolism ; Amino Acid Sequence ; Animals ; CLOCK Proteins/*chemistry/genetics/metabolism ; Cells, Cultured ; *Circadian Rhythm ; Crystallography, X-Ray ; DNA/metabolism ; HEK293 Cells ; Helix-Loop-Helix Motifs ; Humans ; Mice ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Static Electricity ; *Transcriptional Activation
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  • 35
    Publication Date: 2012-01-17
    Description: Exocytosis is essential to the lytic cycle of apicomplexan parasites and required for the pathogenesis of toxoplasmosis and malaria. DOC2 proteins recruit the membrane fusion machinery required for exocytosis in a Ca(2+)-dependent fashion. Here, the phenotype of a Toxoplasma gondii conditional mutant impaired in host cell invasion and egress was pinpointed to a defect in secretion of the micronemes, an apicomplexan-specific organelle that contains adhesion proteins. Whole-genome sequencing identified the etiological point mutation in TgDOC2.1. A conditional allele of the orthologous gene engineered into Plasmodium falciparum was also defective in microneme secretion. However, the major effect was on invasion, suggesting that microneme secretion is dispensable for Plasmodium egress.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3354045/" 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/PMC3354045/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Farrell, Andrew -- Thirugnanam, Sivasakthivel -- Lorestani, Alexander -- Dvorin, Jeffrey D -- Eidell, Keith P -- Ferguson, David J P -- Anderson-White, Brooke R -- Duraisingh, Manoj T -- Marth, Gabor T -- Gubbels, Marc-Jan -- AI057919/AI/NIAID NIH HHS/ -- AI081220/AI/NIAID NIH HHS/ -- AI087874/AI/NIAID NIH HHS/ -- AI088314/AI/NIAID NIH HHS/ -- HG004719/HG/NHGRI NIH HHS/ -- K08 AI087874/AI/NIAID NIH HHS/ -- K08 AI087874-02/AI/NIAID NIH HHS/ -- R01 AI057919/AI/NIAID NIH HHS/ -- R01 HG004719/HG/NHGRI NIH HHS/ -- R21 AI081220/AI/NIAID NIH HHS/ -- R21 AI088314/AI/NIAID NIH HHS/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2012 Jan 13;335(6065):218-21. doi: 10.1126/science.1210829.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Boston College, Chestnut Hill, MA 02467, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22246776" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Calcium/*metabolism ; Calcium-Binding Proteins/chemistry/genetics/*metabolism ; Cell Line ; *Exocytosis ; Genes, Protozoan ; Genetic Complementation Test ; Genome, Protozoan ; Humans ; Models, Molecular ; Molecular Sequence Data ; Movement ; Mutagenesis ; Organelles/*metabolism ; Plasmodium falciparum/genetics/growth & development/physiology ; Point Mutation ; Protein Structure, Tertiary ; Protozoan Proteins/chemistry/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism ; Toxoplasma/genetics/growth & development/*physiology/ultrastructure
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  • 36
    Publication Date: 2012-05-19
    Description: Current debates over the relation between climate change and conflict originate in a lack of data, as well as the complexity of pathways connecting the two phenomena.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scheffran, Jurgen -- Brzoska, Michael -- Kominek, Jasmin -- Link, P Michael -- Schilling, Janpeter -- New York, N.Y. -- Science. 2012 May 18;336(6083):869-71. doi: 10.1126/science.1221339.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Research Group Climate Change and Security, Institute of Geography and KlimaCampus, University of Hamburg, Grindelberg 5, D-20144 Hamburg, Germany. juergen.scheffran@zmaw.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22605765" target="_blank"〉PubMed〈/a〉
    Keywords: Aggression ; *Climate Change ; *Conflict (Psychology) ; Conservation of Natural Resources ; Data Collection ; Databases, Factual ; Humans ; Politics ; Socioeconomic Factors ; *Violence
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  • 37
    Publication Date: 2012-04-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Jane J -- New York, N.Y. -- Science. 2012 Apr 13;336(6078):141-3. doi: 10.1126/science.336.6078.141.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22499911" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Aquatic Organisms/physiology ; *Ecosystem ; Marine Biology/instrumentation/methods ; Pacific Ocean ; Pressure ; *Seawater
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  • 38
    Publication Date: 2012-05-19
    Description: Microbial communities can subsist at depth in marine sediments without fresh supply of organic matter for millions of years. At threshold sedimentation rates of 1 millimeter per 1000 years, the low rates of microbial community metabolism in the North Pacific Gyre allow sediments to remain oxygenated tens of meters below the sea floor. We found that the oxygen respiration rates dropped from 10 micromoles of O(2) liter(-1) year(-1) near the sediment-water interface to 0.001 micromoles of O(2) liter(-1) year(-1) at 30-meter depth within 86 million-year-old sediment. The cell-specific respiration rate decreased with depth but stabilized at around 10(-3) femtomoles of O(2) cell(-1) day(-1) 10 meters below the seafloor. This result indicated that the community size is controlled by the rate of carbon oxidation and thereby by the low available energy flux.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roy, Hans -- Kallmeyer, Jens -- Adhikari, Rishi Ram -- Pockalny, Robert -- Jorgensen, Bo Barker -- D'Hondt, Steven -- New York, N.Y. -- Science. 2012 May 18;336(6083):922-5. doi: 10.1126/science.1219424.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 116, 8000 Aarhus C, Denmark. hans.roy@biology.au.dk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22605778" target="_blank"〉PubMed〈/a〉
    Keywords: Aerobiosis ; Aluminum Silicates ; Bacteria/*metabolism ; Bacterial Load ; Bacterial Physiological Phenomena ; Carbon/analysis/metabolism ; Computer Simulation ; *Ecosystem ; Energy Metabolism ; Geologic Sediments/*chemistry/*microbiology ; Oxidation-Reduction ; Oxygen/*analysis ; *Oxygen Consumption ; Pacific Ocean ; Prokaryotic Cells/*metabolism/physiology ; Seawater/chemistry/microbiology ; Time ; Water Movements
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  • 39
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-09-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Morlon, Helene -- New York, N.Y. -- Science. 2012 Sep 7;337(6099):1184-5. doi: 10.1126/science.1227512.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Applied Mathematics, UMR 7641 CNRS, Ecole Polytechnique, Route de Saclay Palaiseau, 91128 France. helene.morlon@cmap.polytechnique.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22955826" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/*biosynthesis ; *Antibiosis ; *Drug Resistance, Bacterial ; *Ecosystem ; *Microbial Interactions ; Seawater/*microbiology ; Vibrio/*drug effects/*physiology
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  • 40
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-09-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Running, Steven W -- New York, N.Y. -- Science. 2012 Sep 21;337(6101):1458-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Numerical Terradynamic Simulation Group, University of Montana, Missoula, MT 59812, USA. swr@ntsg.umt.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22997311" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture ; Biodiversity ; Carbon Cycle ; Conservation of Natural Resources ; Crops, Agricultural/growth & development/metabolism ; *Ecosystem ; Food Chain ; Human Activities ; Humans ; *Photosynthesis ; *Plant Development ; Plants/*metabolism ; Population Growth
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  • 41
    Publication Date: 2012-03-24
    Description: Giant vertebrates dominated many Pleistocene ecosystems. Many were herbivores, and their sudden extinction in prehistory could have had large ecological impacts. We used a high-resolution 130,000-year environmental record to help resolve the cause and reconstruct the ecological consequences of extinction of Australia's megafauna. Our results suggest that human arrival rather than climate caused megafaunal extinction, which then triggered replacement of mixed rainforest by sclerophyll vegetation through a combination of direct effects on vegetation of relaxed herbivore pressure and increased fire in the landscape. This ecosystem shift was as large as any effect of climate change over the last glacial cycle, and indicates the magnitude of changes that may have followed megafaunal extinction elsewhere in the world.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rule, Susan -- Brook, Barry W -- Haberle, Simon G -- Turney, Chris S M -- Kershaw, A Peter -- Johnson, Christopher N -- New York, N.Y. -- Science. 2012 Mar 23;335(6075):1483-6. doi: 10.1126/science.1214261.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Culture, History and Language, The Australian National University, Canberra, ACT, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22442481" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Ascomycota ; Biomass ; Charcoal ; Climate Change ; *Ecosystem ; *Extinction, Biological ; Fires ; Fossils ; Herbivory ; Humans ; Plants ; Population Dynamics ; Queensland ; Time ; Trees ; *Vertebrates
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  • 42
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-02-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hulme, Philip E -- New York, N.Y. -- Science. 2012 Feb 3;335(6068):537-8; author reply 538-9. doi: 10.1126/science.335.6068.537-b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22301301" target="_blank"〉PubMed〈/a〉
    Keywords: *Climate Change ; *Ecosystem
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  • 43
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-06-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hulme, Philip E -- Pysek, Petr -- Winter, Marten -- New York, N.Y. -- Science. 2012 Jun 1;336(6085):1102, 1104. doi: 10.1126/science.336.6085.1102-b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22654041" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antarctic Regions ; *Ecosystem ; Environment ; International Cooperation ; *Introduced Species/legislation & jurisprudence ; Plants ; Travel
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  • 44
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-02-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Humphries, Courtney -- New York, N.Y. -- Science. 2012 Feb 10;335(6069):648-50. doi: 10.1126/science.335.6069.648.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22323793" target="_blank"〉PubMed〈/a〉
    Keywords: Air Microbiology ; Animals ; Bacteria/*isolation & purification ; Biodiversity ; Biota ; Databases, Genetic ; *Ecosystem ; *Environmental Microbiology ; Foundations ; Hospitals ; Housing ; Humans ; Metagenome ; Research Support as Topic ; Toilet Facilities ; Workplace
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  • 45
    Publication Date: 2012-03-01
    Description: de Jager et al. (Reports, 24 June 2011, p. 1551) concluded that mussels Levy walk. We confronted a larger model set with these data and found that mussels do not Levy walk: Their movement is best described by a composite Brownian walk. This shows how model selection based on an impoverished set of candidate models can lead to incorrect inferences.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jansen, Vincent A A -- Mashanova, Alla -- Petrovskii, Sergei -- BB/G007934/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2012 Feb 24;335(6071):918; author reply 918. doi: 10.1126/science.1215747.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biological Sciences, Royal Holloway, University of London, Surrey TW20 0EX, UK. vincent.jansen@rhul.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22362991" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Ecosystem ; Mytilus edulis/*physiology
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  • 46
    Publication Date: 2012-08-21
    Description: Stu2p/XMAP215/Dis1 family proteins are evolutionarily conserved regulatory factors that use alphabeta-tubulin-interacting tumor overexpressed gene (TOG) domains to catalyze fast microtubule growth. Catalysis requires that these polymerases discriminate between unpolymerized and polymerized forms of alphabeta-tubulin, but the mechanism by which they do so has remained unclear. Here, we report the structure of the TOG1 domain from Stu2p bound to yeast alphabeta-tubulin. TOG1 binds alphabeta-tubulin in a way that excludes equivalent binding of a second TOG domain. Furthermore, TOG1 preferentially binds a curved conformation of alphabeta-tubulin that cannot be incorporated into microtubules, contacting alpha- and beta-tubulin surfaces that do not participate in microtubule assembly. Conformation-selective interactions with alphabeta-tubulin explain how TOG-containing polymerases discriminate between unpolymerized and polymerized forms of alphabeta-tubulin and how they selectively recognize the growing end of the microtubule.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734851/" 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/PMC3734851/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ayaz, Pelin -- Ye, Xuecheng -- Huddleston, Patrick -- Brautigam, Chad A -- Rice, Luke M -- GM-098543/GM/NIGMS NIH HHS/ -- R01 GM098543/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Aug 17;337(6096):857-60. doi: 10.1126/science.1221698.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22904013" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Gene Expression Regulation, Neoplastic ; Genes, Neoplasm ; Microtubule-Associated Proteins/*chemistry/genetics ; Microtubules/*enzymology ; Polymerization ; Protein Conformation ; Protein Structure, Tertiary ; Saccharomyces cerevisiae Proteins/*chemistry/genetics ; Tubulin/*chemistry
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  • 47
    Publication Date: 2012-01-28
    Description: Current paradigms generally assume that increased plant nitrogen (N) should enhance herbivore performance by relieving protein limitation, increasing herbivorous insect populations. We show, in contrast to this scenario, that host plant N enrichment and high-protein artificial diets decreased the size and viability of Oedaleus asiaticus, a dominant locust of north Asian grasslands. This locust preferred plants with low N content and artificial diets with low protein and high carbohydrate content. Plant N content was lowest and locust abundance highest in heavily livestock-grazed fields where soils were N-depleted, likely due to enhanced erosion. These results suggest that heavy livestock grazing and consequent steppe degradation in the Eurasian grassland promote outbreaks of this locust by reducing plant protein content.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cease, Arianne J -- Elser, James J -- Ford, Colleen F -- Hao, Shuguang -- Kang, Le -- Harrison, Jon F -- New York, N.Y. -- Science. 2012 Jan 27;335(6067):467-9. doi: 10.1126/science.1214433.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA. arianne.cease@asu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22282812" target="_blank"〉PubMed〈/a〉
    Keywords: Animal Husbandry ; Animals ; Biomass ; Diet ; Dietary Proteins/administration & dosage ; *Ecosystem ; Feeding Behavior ; Fertilizers ; Food Preferences ; Grasshoppers/growth & development/*physiology ; Herbivory/physiology ; *Livestock ; Nitrogen/*analysis ; Plant Proteins/*analysis ; Plants/*chemistry ; Poaceae/chemistry/growth & development ; Population Dynamics ; Sheep
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  • 48
    Publication Date: 2012-03-31
    Description: Kraft et al. (Report, 23 September 2011, p. 1755) argued that the latitudinal trend in beta diversity is spurious and just reflects a trend in gamma diversity. Their results depend on the idiosyncrasies of their data, especially the latitudinally varying degree of undersampling and a local sampling setup that is not suitable for analyzing drivers of beta diversity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tuomisto, Hanna -- Ruokolainen, Kalle -- New York, N.Y. -- Science. 2012 Mar 30;335(6076):1573; author reply 1573. doi: 10.1126/science.1216393.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Turku, Turku, Finland. hanna.tuomisto@utu.fi〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22461591" target="_blank"〉PubMed〈/a〉
    Keywords: *Altitude ; *Biodiversity ; *Ecosystem ; *Environment ; *Plants ; *Trees
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  • 49
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-01-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lei, Fu-Min -- New York, N.Y. -- Science. 2012 Jan 20;335(6066):284-5; author reply 285-6. doi: 10.1126/science.335.6066.284-b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22267791" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; *Climate Change
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  • 50
    Publication Date: 2012-09-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Babu, M Madan -- Kriwacki, Richard W -- Pappu, Rohit V -- MC_U105185859/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2012 Sep 21;337(6101):1460-1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK. madanm@mrc-lmb.cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22997313" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Computer Simulation ; Evolution, Molecular ; Mutation ; Protein Binding ; Protein Folding ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Proteins/*chemistry/genetics/*metabolism
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  • 51
    Publication Date: 2012-05-26
    Description: Crystal structure analyses for biological macromolecules without known structural relatives entail solving the crystallographic phase problem. Typical de novo phase evaluations depend on incorporating heavier atoms than those found natively; most commonly, multi- or single-wavelength anomalous diffraction (MAD or SAD) experiments exploit selenomethionyl proteins. Here, we realize routine structure determination using intrinsic anomalous scattering from native macromolecules. We devised robust procedures for enhancing the signal-to-noise ratio in the slight anomalous scattering from generic native structures by combining data measured from multiple crystals at lower-than-usual x-ray energy. Using this multicrystal SAD method (5 to 13 equivalent crystals), we determined structures at modest resolution (2.8 to 2.3 angstroms) for native proteins varying in size (127 to 1148 unique residues) and number of sulfur sites (3 to 28). With no requirement for heavy-atom incorporation, such experiments provide an attractive alternative to selenomethionyl SAD experiments.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3769101/" 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/PMC3769101/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Qun -- Dahmane, Tassadite -- Zhang, Zhen -- Assur, Zahra -- Brasch, Julia -- Shapiro, Lawrence -- Mancia, Filippo -- Hendrickson, Wayne A -- GM034102/GM/NIGMS NIH HHS/ -- GM062270/GM/NIGMS NIH HHS/ -- GM095315/GM/NIGMS NIH HHS/ -- R01 GM034102/GM/NIGMS NIH HHS/ -- R01 GM062270/GM/NIGMS NIH HHS/ -- U54 GM075026/GM/NIGMS NIH HHS/ -- U54 GM095315/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 May 25;336(6084):1033-7. doi: 10.1126/science.1218753.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉New York Structural Biology Center, National Synchrotron Light Source (NSLS) X4, Brookhaven National Laboratory, Upton, NY 11973, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22628655" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry ; Crystallography, X-Ray/*methods ; Data Interpretation, Statistical ; GPI-Linked Proteins/chemistry ; Models, Molecular ; Nerve Tissue Proteins/chemistry ; *Protein Conformation ; Protein Kinases/chemistry ; Protein Structure, Tertiary ; Proteins/*chemistry ; Selenomethionine/chemistry ; Signal-To-Noise Ratio ; Sulfur/chemistry ; X-Ray Diffraction
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  • 52
    Publication Date: 2012-06-02
    Description: Pattern recognition receptors confer plant resistance to pathogen infection by recognizing the conserved pathogen-associated molecular patterns. The cell surface receptor chitin elicitor receptor kinase 1 of Arabidopsis (AtCERK1) directly binds chitin through its lysine motif (LysM)-containing ectodomain (AtCERK1-ECD) to activate immune responses. The crystal structure that we solved of an AtCERK1-ECD complexed with a chitin pentamer reveals that their interaction is primarily mediated by a LysM and three chitin residues. By acting as a bivalent ligand, a chitin octamer induces AtCERK1-ECD dimerization that is inhibited by shorter chitin oligomers. A mutation attenuating chitin-induced AtCERK1-ECD dimerization or formation of nonproductive AtCERK1 dimer by overexpression of AtCERK1-ECD compromises AtCERK1-mediated signaling in plant cells. Together, our data support the notion that chitin-induced AtCERK1 dimerization is critical for its activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Tingting -- Liu, Zixu -- Song, Chuanjun -- Hu, Yunfei -- Han, Zhifu -- She, Ji -- Fan, Fangfang -- Wang, Jiawei -- Jin, Changwen -- Chang, Junbiao -- Zhou, Jian-Min -- Chai, Jijie -- New York, N.Y. -- Science. 2012 Jun 1;336(6085):1160-4. doi: 10.1126/science.1218867.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate Program in Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22654057" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylglucosamine/chemistry/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Arabidopsis/immunology/*metabolism ; Arabidopsis Proteins/*chemistry/genetics/*metabolism ; Binding Sites ; Chitin/chemistry/*metabolism ; Crystallography, X-Ray ; Hydrogen Bonding ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Phosphorylation ; Plants, Genetically Modified ; Protein Multimerization ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/*chemistry/genetics/*metabolism ; Receptors, Pattern Recognition/*chemistry/genetics/*metabolism ; Signal Transduction
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  • 53
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-07-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hvistendahl, Mara -- New York, N.Y. -- Science. 2012 Jul 6;337(6090):26-7. doi: 10.1126/science.337.6090.26.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22767908" target="_blank"〉PubMed〈/a〉
    Keywords: China ; *Conservation of Natural Resources ; Economic Development ; *Ecosystem ; *Forestry ; Local Government ; *Trees
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 54
    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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  • 55
    Publication Date: 2012-09-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aldy, Joseph E -- Stavins, Robert N -- New York, N.Y. -- Science. 2012 Aug 31;337(6098):1043-4. doi: 10.1126/science.1223836.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉John F. Kennedy School of Government, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22936761" target="_blank"〉PubMed〈/a〉
    Keywords: Air Pollutants/analysis ; Air Pollution/*prevention & control ; *Climate Change ; *Environmental Policy ; *International Cooperation
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  • 56
    Publication Date: 2012-06-30
    Description: Ricklefs and Renner (Reports, 27 January 2012, p. 464) found significant correlations for abundances and species diversities of families and orders of trees on different continents, which they suggested falsifies the neutral theory of biodiversity (NTB). We argue that the correlations among families and orders and the lack of correlations among genera can be explained by the NTB.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Anping -- Wang, Shaopeng -- Pacala, Stephen W -- New York, N.Y. -- Science. 2012 Jun 29;336(6089):1639; author reply 1639. doi: 10.1126/science.1222534.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA. anpingc@princeton.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22745403" target="_blank"〉PubMed〈/a〉
    Keywords: *Biodiversity ; *Biological Evolution ; *Ecosystem ; *Trees
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  • 57
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-05-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hvistendahl, Mara -- New York, N.Y. -- Science. 2012 May 11;336(6082):662-3. doi: 10.1126/science.336.6082.662.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22582238" target="_blank"〉PubMed〈/a〉
    Keywords: China ; Climate Change ; Coal Mining ; *Ecosystem ; Extinction, Biological ; Ferns ; *Fossils ; *Plants ; *Trees ; Volcanic Eruptions
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  • 58
    Publication Date: 2012-07-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chown, S L -- Lee, J E -- Hughes, K A -- Barnes, J -- Barrett, P J -- Bergstrom, D M -- Convey, P -- Cowan, D A -- Crosbie, K -- Dyer, G -- Frenot, Y -- Grant, S M -- Herr, D -- Kennicutt, M C 2nd -- Lamers, M -- Murray, A -- Possingham, H P -- Reid, K -- Riddle, M J -- Ryan, P G -- Sanson, L -- Shaw, J D -- Sparrow, M D -- Summerhayes, C -- Terauds, A -- Wall, D H -- New York, N.Y. -- Science. 2012 Jul 13;337(6091):158-9. doi: 10.1126/science.1222821.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Invasion Biology, Stellenbosch University, Matieland, South Africa. steven.chown@monash.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22798586" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antarctic Regions ; Climate Change ; *Conservation of Natural Resources/trends ; *Ecosystem ; Forecasting ; Human Activities ; Humans ; Public Policy ; Travel
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  • 59
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-02-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Joppa, Lucas N -- New York, N.Y. -- Science. 2012 Feb 10;335(6069):656; author reply 656-7. doi: 10.1126/science.335.6069.656-a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22323798" target="_blank"〉PubMed〈/a〉
    Keywords: Ecology/*economics ; *Ecosystem
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  • 60
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-08-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bakker, Karen -- New York, N.Y. -- Science. 2012 Aug 24;337(6097):914-5. doi: 10.1126/science.1226337.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program on Water Governance, Department of Geography and Institute for Resources, Environment, and Sustainability, University of British Columbia, Vancouver, BC V6T 1Z2, Canada. karen.bakker@ubc.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22923564" target="_blank"〉PubMed〈/a〉
    Keywords: Climatic Processes ; *Conservation of Natural Resources ; *Ecosystem ; Environment ; Humans ; *Public Policy ; Research ; *Water ; Water Cycle ; *Water Supply
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  • 61
    Publication Date: 2012-03-01
    Description: The transition path is the tiny fraction of an equilibrium molecular trajectory when a transition occurs as the free-energy barrier between two states is crossed. It is a single-molecule property that contains all the mechanistic information on how a process occurs. As a step toward observing transition paths in protein folding, we determined the average transition-path time for a fast- and a slow-folding protein from a photon-by-photon analysis of fluorescence trajectories in single-molecule Forster resonance energy transfer experiments. Whereas the folding rate coefficients differ by a factor of 10,000, the transition-path times differ by a factor of less than 5, which shows that a fast- and a slow-folding protein take almost the same time to fold when folding actually happens. A very simple model based on energy landscape theory can explain this result.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3878298/" 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/PMC3878298/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chung, Hoi Sung -- McHale, Kevin -- Louis, John M -- Eaton, William A -- Z99 DK999999/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2012 Feb 24;335(6071):981-4. doi: 10.1126/science.1215768.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (NIH), Bethesda, MD 20892-0520, USA. chunghoi@niddk.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22363011" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry ; Carrier Proteins/*chemistry ; Fluorescence Resonance Energy Transfer ; Kinetics ; Likelihood Functions ; Models, Molecular ; Molecular Sequence Data ; Photons ; Protein Conformation ; *Protein Folding ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Thermodynamics
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  • 62
    Publication Date: 2012-09-29
    Description: The water cycle in the western United States changed dramatically over glacial cycles. In the past 20,000 years, higher precipitation caused desert lakes to form which have since dried out. Higher glacial precipitation has been hypothesized to result from a southward shift of Pacific winter storm tracks. We compared Pacific Ocean data to lake levels from the interior west and found that Great Basin lake high stands are older than coastal wet periods at the same latitude. Westerly storms were not the source of high precipitation. Instead, air masses from the tropical Pacific were transported northward, bringing more precipitation into the Great Basin when coastal California was still dry. The changing climate during the deglaciation altered precipitation source regions and strongly affected the regional water cycle.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lyle, Mitchell -- Heusser, Linda -- Ravelo, Christina -- Yamamoto, Masanobu -- Barron, John -- Diffenbaugh, Noah S -- Herbert, Timothy -- Andreasen, Dyke -- New York, N.Y. -- Science. 2012 Sep 28;337(6102):1629-33.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Oceanography, Texas A&M University, College Station, TX 77843, USA. mlyle@ocean.tamu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23019644" target="_blank"〉PubMed〈/a〉
    Keywords: *Climate ; *Climate Change ; *Ice Cover ; *Lakes ; Rain ; United States
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  • 63
    Publication Date: 2012-06-02
    Description: C99 is the transmembrane carboxyl-terminal domain of the amyloid precursor protein that is cleaved by gamma-secretase to release the amyloid-beta polypeptides, which are associated with Alzheimer's disease. Nuclear magnetic resonance and electron paramagnetic resonance spectroscopy show that the extracellular amino terminus of C99 includes a surface-embedded "N-helix" followed by a short "N-loop" connecting to the transmembrane domain (TMD). The TMD is a flexibly curved alpha helix, making it well suited for processive cleavage by gamma-secretase. Titration of C99 reveals a binding site for cholesterol, providing mechanistic insight into how cholesterol promotes amyloidogenesis. Membrane-buried GXXXG motifs (G, Gly; X, any amino acid), which have an established role in oligomerization, were also shown to play a key role in cholesterol binding. The structure and cholesterol binding properties of C99 may aid in the design of Alzheimer's therapeutics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3528355/" 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/PMC3528355/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barrett, Paul J -- Song, Yuanli -- Van Horn, Wade D -- Hustedt, Eric J -- Schafer, Johanna M -- Hadziselimovic, Arina -- Beel, Andrew J -- Sanders, Charles R -- F31 NS077681/NS/NINDS NIH HHS/ -- P01 GM080513/GM/NIGMS NIH HHS/ -- T32 GM008320/GM/NIGMS NIH HHS/ -- T32 GM08320/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Jun 1;336(6085):1168-71. doi: 10.1126/science.1219988.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Center for Structural Biology and Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, TN 37232 USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22654059" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Amyloid beta-Protein Precursor/*chemistry/genetics/*metabolism ; Binding Sites ; Cholesterol/*metabolism ; Electron Spin Resonance Spectroscopy ; Humans ; Micelles ; Molecular Sequence Data ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; Peptide Fragments/*chemistry/genetics/*metabolism ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 64
    Publication Date: 2012-03-17
    Description: In bacteria, the hybrid transfer-messenger RNA (tmRNA) rescues ribosomes stalled on defective messenger RNAs (mRNAs). However, certain gram-negative bacteria have evolved proteins that are capable of rescuing stalled ribosomes in a tmRNA-independent manner. Here, we report a 3.2 angstrom-resolution crystal structure of the rescue factor YaeJ bound to the Thermus thermophilus 70S ribosome in complex with the initiator tRNA(i)(fMet) and a short mRNA. The structure reveals that the C-terminal tail of YaeJ functions as a sensor to discriminate between stalled and actively translating ribosomes by binding in the mRNA entry channel downstream of the A site between the head and shoulder of the 30S subunit. This allows the N-terminal globular domain to sample different conformations, so that its conserved GGQ motif is optimally positioned to catalyze the hydrolysis of peptidyl-tRNA. This structure gives insights into the mechanism of YaeJ function and provides a basis for understanding how it rescues stalled ribosomes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3377438/" 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/PMC3377438/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gagnon, Matthieu G -- Seetharaman, Sai V -- Bulkley, David -- Steitz, Thomas A -- GM022778/GM/NIGMS NIH HHS/ -- P01 GM022778/GM/NIGMS NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Mar 16;335(6074):1370-2. doi: 10.1126/science.1217443.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22422986" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Carboxylic Ester Hydrolases/*chemistry/*metabolism ; Crystallography, X-Ray ; Escherichia coli/*chemistry ; Escherichia coli Proteins/*chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Biosynthesis ; Protein Structure, Tertiary ; RNA, Bacterial/chemistry/metabolism ; RNA, Messenger/chemistry/metabolism ; RNA, Ribosomal/chemistry/metabolism ; RNA, Transfer, Amino Acyl/chemistry/metabolism ; RNA, Transfer, Met/chemistry/metabolism ; Ribosome Subunits, Large, Bacterial/chemistry/metabolism ; Ribosome Subunits, Small, Bacterial/chemistry/metabolism ; Ribosomes/*chemistry/metabolism ; Thermus thermophilus/*chemistry/metabolism/ultrastructure
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  • 65
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-06-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Palmer, Margaret A -- Febria, Catherine M -- New York, N.Y. -- Science. 2012 Jun 15;336(6087):1393-4. doi: 10.1126/science.1223250.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science, Solomons, MD 20688, USA. mpalmer@sesync.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22700910" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Ecosystem ; Invertebrates/*metabolism ; *Plant Leaves ; *Rivers ; *Water Pollution, Chemical
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  • 66
    Publication Date: 2012-03-24
    Description: Adler et al. (Reports, 23 September 2011, p. 1750) analyzed the standardized sampling data from 48 herbaceous-dominated plant communities and concluded that "Productivity is a poor predictor of plant species richness" at fine-scale. However, their method was biased toward site-number-dominated plant communities. They also failed to provide enough data for regional analysis and detailed information for within-site analysis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pan, Xubin -- Liu, Fengqiao -- Zhang, Mi -- New York, N.Y. -- Science. 2012 Mar 23;335(6075):1441; author reply 1441. doi: 10.1126/science.1214786.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Environmental Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363, USA. xubin.hu.pan@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22442463" target="_blank"〉PubMed〈/a〉
    Keywords: *Biodiversity ; *Biomass ; *Ecosystem ; *Plants
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  • 67
    Publication Date: 2012-05-26
    Description: Acyl acid amido synthetases of the GH3 family act as critical prereceptor modulators of plant hormone action; however, the molecular basis for their hormone selectivity is unclear. Here, we report the crystal structures of benzoate-specific Arabidopsis thaliana AtGH3.12/PBS3 and jasmonic acid-specific AtGH3.11/JAR1. These structures, combined with biochemical analysis, define features for the conjugation of amino acids to diverse acyl acid substrates and highlight the importance of conformational changes in the carboxyl-terminal domain for catalysis. We also identify residues forming the acyl acid binding site across the GH3 family and residues critical for amino acid recognition. Our results demonstrate how a highly adaptable three-dimensional scaffold is used for the evolution of promiscuous activity across an enzyme family for modulation of plant signaling molecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Westfall, Corey S -- Zubieta, Chloe -- Herrmann, Jonathan -- Kapp, Ulrike -- Nanao, Max H -- Jez, Joseph M -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Jun 29;336(6089):1708-11. doi: 10.1126/science.1221863. Epub 2012 May 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Washington University, St. Louis, MO 63130, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22628555" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acids/chemistry/metabolism ; Arabidopsis ; Arabidopsis Proteins/*chemistry/metabolism ; Benzoates/chemistry ; Binding Sites ; Crystallography, X-Ray ; Cyclopentanes/chemistry ; Indoleacetic Acids/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nucleotidyltransferases/*chemistry/metabolism ; Oxylipins/chemistry ; Plant Growth Regulators/chemistry/metabolism ; Protein Structure, Tertiary ; Structure-Activity Relationship ; Substrate Specificity
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  • 68
    Publication Date: 2012-04-12
    Description: Genetic exchange is common among bacteria, but its effect on population diversity during ecological differentiation remains controversial. A fundamental question is whether advantageous mutations lead to selection of clonal genomes or, as in sexual eukaryotes, sweep through populations on their own. Here, we show that in two recently diverged populations of ocean bacteria, ecological differentiation has occurred akin to a sexual mechanism: A few genome regions have swept through subpopulations in a habitat-specific manner, accompanied by gradual separation of gene pools as evidenced by increased habitat specificity of the most recent recombinations. These findings reconcile previous, seemingly contradictory empirical observations of the genetic structure of bacterial populations and point to a more unified process of differentiation in bacteria and sexual eukaryotes than previously thought.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337212/" 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/PMC3337212/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shapiro, B Jesse -- Friedman, Jonathan -- Cordero, Otto X -- Preheim, Sarah P -- Timberlake, Sonia C -- Szabo, Gitta -- Polz, Martin F -- Alm, Eric J -- U54 GM088558/GM/NIGMS NIH HHS/ -- U54 GM088558-02/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Apr 6;336(6077):48-51. doi: 10.1126/science.1218198.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22491847" target="_blank"〉PubMed〈/a〉
    Keywords: Chromosomes, Bacterial/genetics ; *Ecosystem ; *Evolution, Molecular ; Gene Flow ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; *Genome, Bacterial ; Models, Genetic ; Molecular Sequence Data ; Mutation ; Oceans and Seas ; Phylogeny ; Polymorphism, Single Nucleotide ; *Recombination, Genetic ; Seawater/*microbiology ; *Selection, Genetic ; Vibrio/classification/*genetics
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  • 69
    Publication Date: 2012-03-03
    Description: It is commonly believed that trees were absent in Scandinavia during the last glaciation and first recolonized the Scandinavian Peninsula with the retreat of its ice sheet some 9000 years ago. Here, we show the presence of a rare mitochondrial DNA haplotype of spruce that appears unique to Scandinavia and with its highest frequency to the west-an area believed to sustain ice-free refugia during most of the last ice age. We further show the survival of DNA from this haplotype in lake sediments and pollen of Trondelag in central Norway dating back ~10,300 years and chloroplast DNA of pine and spruce in lake sediments adjacent to the ice-free Andoya refugium in northwestern Norway as early as ~22,000 and 17,700 years ago, respectively. Our findings imply that conifer trees survived in ice-free refugia of Scandinavia during the last glaciation, challenging current views on survival and spread of trees as a response to climate changes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Parducci, Laura -- Jorgensen, Tina -- Tollefsrud, Mari Mette -- Elverland, Ellen -- Alm, Torbjorn -- Fontana, Sonia L -- Bennett, K D -- Haile, James -- Matetovici, Irina -- Suyama, Yoshihisa -- Edwards, Mary E -- Andersen, Kenneth -- Rasmussen, Morten -- Boessenkool, Sanne -- Coissac, Eric -- Brochmann, Christian -- Taberlet, Pierre -- Houmark-Nielsen, Michael -- Larsen, Nicolaj Krog -- Orlando, Ludovic -- Gilbert, M Thomas P -- Kjaer, Kurt H -- Alsos, Inger Greve -- Willerslev, Eske -- New York, N.Y. -- Science. 2012 Mar 2;335(6072):1083-6. doi: 10.1126/science.1216043.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22383845" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/genetics ; *Ecosystem ; Europe ; *Fossils ; Geologic Sediments ; Haplotypes ; *Ice Cover ; Molecular Sequence Data ; Mutation ; Norway ; *Picea/genetics ; *Pinus/genetics ; Scandinavian and Nordic Countries ; Time
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 70
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-07-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Service, Robert F -- New York, N.Y. -- Science. 2012 Jul 13;337(6091):146-8. doi: 10.1126/science.337.6091.146.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22798578" target="_blank"〉PubMed〈/a〉
    Keywords: Calcium Carbonate/*analysis ; *Ecosystem ; Seawater/*chemistry
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  • 71
    Publication Date: 2012-12-01
    Description: We combined an ensemble of satellite altimetry, interferometry, and gravimetry data sets using common geographical regions, time intervals, and models of surface mass balance and glacial isostatic adjustment to estimate the mass balance of Earth's polar ice sheets. We find that there is good agreement between different satellite methods--especially in Greenland and West Antarctica--and that combining satellite data sets leads to greater certainty. Between 1992 and 2011, the ice sheets of Greenland, East Antarctica, West Antarctica, and the Antarctic Peninsula changed in mass by -142 +/- 49, +14 +/- 43, -65 +/- 26, and -20 +/- 14 gigatonnes year(-1), respectively. Since 1992, the polar ice sheets have contributed, on average, 0.59 +/- 0.20 millimeter year(-1) to the rate of global sea-level rise.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shepherd, Andrew -- Ivins, Erik R -- A, Geruo -- Barletta, Valentina R -- Bentley, Mike J -- Bettadpur, Srinivas -- Briggs, Kate H -- Bromwich, David H -- Forsberg, Rene -- Galin, Natalia -- Horwath, Martin -- Jacobs, Stan -- Joughin, Ian -- King, Matt A -- Lenaerts, Jan T M -- Li, Jilu -- Ligtenberg, Stefan R M -- Luckman, Adrian -- Luthcke, Scott B -- McMillan, Malcolm -- Meister, Rakia -- Milne, Glenn -- Mouginot, Jeremie -- Muir, Alan -- Nicolas, Julien P -- Paden, John -- Payne, Antony J -- Pritchard, Hamish -- Rignot, Eric -- Rott, Helmut -- Sorensen, Louise Sandberg -- Scambos, Ted A -- Scheuchl, Bernd -- Schrama, Ernst J O -- Smith, Ben -- Sundal, Aud V -- van Angelen, Jan H -- van de Berg, Willem J -- van den Broeke, Michiel R -- Vaughan, David G -- Velicogna, Isabella -- Wahr, John -- Whitehouse, Pippa L -- Wingham, Duncan J -- Yi, Donghui -- Young, Duncan -- Zwally, H Jay -- New York, N.Y. -- Science. 2012 Nov 30;338(6111):1183-9. doi: 10.1126/science.1228102.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK. ashepherd@leeds.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23197528" target="_blank"〉PubMed〈/a〉
    Keywords: Antarctic Regions ; *Climate Change ; Geographic Information Systems ; Greenland ; *Ice Cover
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  • 72
    Publication Date: 2012-12-01
    Description: Placental development and genomic imprinting coevolved with parental conflict over resource distribution to mammalian offspring. The imprinted genes IGF2 and IGF2R code for the growth promoter insulin-like growth factor 2 (IGF2) and its inhibitor, mannose 6-phosphate (M6P)/IGF2 receptor (IGF2R), respectively. M6P/IGF2R of birds and fish do not recognize IGF2. In monotremes, which lack imprinting, IGF2 specifically bound M6P/IGF2R via a hydrophobic CD loop. We show that the DNA coding the CD loop in monotremes functions as an exon splice enhancer (ESE) and that structural evolution of binding site loops (AB, HI, FG) improved therian IGF2 affinity. We propose that ESE evolution led to the fortuitous acquisition of IGF2 binding by M6P/IGF2R that drew IGF2R into parental conflict; subsequent imprinting may then have accelerated affinity maturation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4658703/" 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/PMC4658703/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Williams, Christopher -- Hoppe, Hans-Jurgen -- Rezgui, Dellel -- Strickland, Madeleine -- Forbes, Briony E -- Grutzner, Frank -- Frago, Susana -- Ellis, Rosamund Z -- Wattana-Amorn, Pakorn -- Prince, Stuart N -- Zaccheo, Oliver J -- Nolan, Catherine M -- Mungall, Andrew J -- Jones, E Yvonne -- Crump, Matthew P -- Hassan, A Bassim -- 082352/Wellcome Trust/United Kingdom -- 090532/Wellcome Trust/United Kingdom -- 9891/Cancer Research UK/United Kingdom -- A13295/Cancer Research UK/United Kingdom -- A9891/Cancer Research UK/United Kingdom -- C375/Cancer Research UK/United Kingdom -- C429/Cancer Research UK/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2012 Nov 30;338(6111):1209-13. doi: 10.1126/science.1228633.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Organic and Biological Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23197533" target="_blank"〉PubMed〈/a〉
    Keywords: *Alternative Splicing ; Amino Acid Sequence ; Animals ; Binding Sites/genetics ; Conserved Sequence ; Enhancer Elements, Genetic/*genetics ; *Evolution, Molecular ; *Exons ; Genomic Imprinting ; Humans ; Insulin-Like Growth Factor II/*chemistry/classification/genetics ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Receptor, IGF Type 2/*chemistry/classification/genetics ; Species Specificity
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  • 73
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-07-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Malakoff, David -- New York, N.Y. -- Science. 2012 Jul 6;337(6090):22. doi: 10.1126/science.337.6090.22.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22767905" target="_blank"〉PubMed〈/a〉
    Keywords: *Ecosystem ; Gulf of Mexico ; Industry/*economics/legislation & jurisprudence ; *Petroleum ; *Petroleum Pollution/economics/legislation & jurisprudence ; United States ; *Water Pollution, Chemical/economics/legislation & jurisprudence ; *Wetlands
    Print ISSN: 0036-8075
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  • 74
    Publication Date: 2012-01-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Beddington, J R -- Asaduzzaman, M -- Clark, M E -- Fernandez Bremauntz, A -- Guillou, M D -- Howlett, D J B -- Jahn, M M -- Lin, E -- Mamo, T -- Negra, C -- Nobre, C A -- Scholes, R J -- Van Bo, N -- Wakhungu, J -- New York, N.Y. -- Science. 2012 Jan 20;335(6066):289-90. doi: 10.1126/science.1217941.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Government Office of Science, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22267797" target="_blank"〉PubMed〈/a〉
    Keywords: *Agriculture/methods/trends ; *Climate Change ; Conservation of Natural Resources ; Food Supply ; Forestry ; *Policy Making ; United Nations
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  • 75
    Publication Date: 2012-03-17
    Description: Neurotransmitters are released through nascent fusion pores, which ordinarily dilate after bilayer fusion, preventing consistent biochemical studies. We used lipid bilayer nanodiscs as fusion partners; their rigid protein framework prevents dilation and reveals properties of the fusion pore induced by SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor). We found that although only one SNARE per nanodisc is required for maximum rates of bilayer fusion, efficient release of content on the physiologically relevant time scale of synaptic transmission apparently requires three or more SNARE complexes (SNAREpins) and the native transmembrane domain of vesicle-associated membrane protein 2 (VAMP2). We suggest that several SNAREpins simultaneously zippering their SNARE transmembrane helices within the freshly fused bilayers provide a radial force that prevents the nascent pore from resealing during synchronous neurotransmitter release.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3736847/" 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/PMC3736847/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shi, Lei -- Shen, Qing-Tao -- Kiel, Alexander -- Wang, Jing -- Wang, Hong-Wei -- Melia, Thomas J -- Rothman, James E -- Pincet, Frederic -- R01 DK027044/DK/NIDDK NIH HHS/ -- R37 DK027044/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2012 Mar 16;335(6074):1355-9. doi: 10.1126/science.1214984.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22422984" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcium/metabolism ; Diffusion ; *Lipid Bilayers ; Liposomes ; *Membrane Fusion ; Membrane Proteins/chemistry/metabolism ; Mice ; Neurotransmitter Agents/metabolism ; Protein Structure, Tertiary ; Proteolipids/chemistry ; Rats ; Recombinant Fusion Proteins/chemistry/metabolism ; SNARE Proteins/*chemistry/*metabolism ; Synaptic Transmission ; Synaptic Vesicles/*chemistry/metabolism ; Synaptosomal-Associated Protein 25/chemistry/metabolism ; Syntaxin 1/chemistry/metabolism ; Vesicle-Associated Membrane Protein 2/*chemistry/*metabolism
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  • 76
    Publication Date: 2012-01-17
    Description: Tropospheric ozone and black carbon (BC) contribute to both degraded air quality and global warming. We considered ~400 emission control measures to reduce these pollutants by using current technology and experience. We identified 14 measures targeting methane and BC emissions that reduce projected global mean warming ~0.5 degrees C by 2050. This strategy avoids 0.7 to 4.7 million annual premature deaths from outdoor air pollution and increases annual crop yields by 30 to 135 million metric tons due to ozone reductions in 2030 and beyond. Benefits of methane emissions reductions are valued at $700 to $5000 per metric ton, which is well above typical marginal abatement costs (less than $250). The selected controls target different sources and influence climate on shorter time scales than those of carbon dioxide-reduction measures. Implementing both substantially reduces the risks of crossing the 2 degrees C threshold.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shindell, Drew -- Kuylenstierna, Johan C I -- Vignati, Elisabetta -- van Dingenen, Rita -- Amann, Markus -- Klimont, Zbigniew -- Anenberg, Susan C -- Muller, Nicholas -- Janssens-Maenhout, Greet -- Raes, Frank -- Schwartz, Joel -- Faluvegi, Greg -- Pozzoli, Luca -- Kupiainen, Kaarle -- Hoglund-Isaksson, Lena -- Emberson, Lisa -- Streets, David -- Ramanathan, V -- Hicks, Kevin -- Oanh, N T Kim -- Milly, George -- Williams, Martin -- Demkine, Volodymyr -- Fowler, David -- New York, N.Y. -- Science. 2012 Jan 13;335(6065):183-9. doi: 10.1126/science.1210026.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉NASA Goddard Institute for Space Studies and Columbia Earth Institute, Columbia University, New York, NY 10025, USA. drew.t.shindell@nasa.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22246768" target="_blank"〉PubMed〈/a〉
    Keywords: Aerosols ; *Air Pollutants/analysis ; Air Pollution/*prevention & control ; *Climate Change ; Computer Simulation ; Cost-Benefit Analysis ; *Food Supply ; *Health ; Humans ; *Methane/analysis ; Mortality, Premature ; *Ozone/analysis ; *Soot/analysis
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  • 77
    Publication Date: 2012-09-01
    Description: Bayon et al. (Reports, 9 March 2012, p. 1219) claim that the "rainforest crisis" in Central Africa centered around 2500 years before the present "was not triggered by natural climatic factors" and that it was caused by widespread deforestation resulting from the arrival of the Bantu colonists. However, there is a consensus among palaeoecologists that this landscape change and the related physical erosion it caused was due mainly to a shift to more seasonal rainfall regime.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maley, Jean -- Giresse, Pierre -- Doumenge, Charles -- Favier, Charly -- New York, N.Y. -- Science. 2012 Aug 31;337(6098):1040; author reply 1040. doi: 10.1126/science.1221820.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departement Paleoenvironnements et Paleoclimatologie, Institut des Sciences de l'Evolution de Montpellier, CNRS/UMR 5554, Universite de Montpellier-2, Montpellier, France. jean.maley@univ-montp2.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22936759" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/*history ; *Climate Change ; *Conservation of Natural Resources ; Geologic Sediments/*chemistry ; Humans ; *Trees
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  • 78
    Publication Date: 2012-02-04
    Description: Resistance of nematodes to anthelmintics such as avermectins has emerged as a major global health and agricultural problem, but genes conferring natural resistance to avermectins are unknown. We show that a naturally occurring four-amino-acid deletion in the ligand-binding domain of GLC-1, the alpha-subunit of a glutamate-gated chloride channel, confers resistance to avermectins in the model nematode Caenorhabditis elegans. We also find that the same variant confers resistance to the avermectin-producing bacterium Streptomyces avermitilis. Population-genetic analyses identified two highly divergent haplotypes at the glc-1 locus that have been maintained at intermediate frequencies by long-term balancing selection. These results implicate variation in glutamate-gated chloride channels in avermectin resistance and provide a mechanism by which such resistance can be maintained.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3273849/" 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/PMC3273849/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ghosh, Rajarshi -- Andersen, Erik C -- Shapiro, Joshua A -- Gerke, Justin P -- Kruglyak, Leonid -- P50-GM071508/GM/NIGMS NIH HHS/ -- R01 HG004321/HG/NHGRI NIH HHS/ -- R01 HG004321-03/HG/NHGRI NIH HHS/ -- R01-HG004321/HG/NHGRI NIH HHS/ -- R37- MH59520/MH/NIMH NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Feb 3;335(6068):574-8. doi: 10.1126/science.1214318.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Lewis-Sigler Institute for Integrative Genomics, Department of Ecology and Evolutionary Biology, and Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22301316" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Animals, Genetically Modified ; Antinematodal Agents/*pharmacology ; Caenorhabditis elegans/*drug effects/*genetics/physiology ; Caenorhabditis elegans Proteins/chemistry/*genetics/metabolism ; Chloride Channels/chemistry/*genetics/metabolism ; Crosses, Genetic ; Drug Resistance/genetics ; Genes, Helminth ; Genome-Wide Association Study ; Ivermectin/*analogs & derivatives/*pharmacology ; Ligands ; Molecular Sequence Data ; Mutation ; Polymorphism, Single Nucleotide ; Protein Structure, Tertiary ; Quantitative Trait Loci ; Selection, Genetic ; Streptomyces/physiology
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  • 79
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-08-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2012 Aug 24;337(6097):906-7. doi: 10.1126/science.337.6097.906.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22923558" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Atlantic Ocean ; *Biological Evolution ; *Daphnia/genetics/physiology ; *Ecosystem ; *Fishes/anatomy & histology/genetics/physiology ; *Food Chain ; Lakes ; Phytoplankton ; Rivers ; Zooplankton
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 80
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-08-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2012 Aug 24;337(6097):904-8. doi: 10.1126/science.337.6097.904.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22923557" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Ecosystem ; *Environment ; Female ; Invertebrates ; Male ; *Poecilia/anatomy & histology/genetics/physiology ; Population Dynamics ; Population Growth ; Predatory Behavior ; Reproduction ; *Rivers ; Selection, Genetic ; Trinidad and Tobago
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 81
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-03-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McGlone, Matt -- New York, N.Y. -- Science. 2012 Mar 23;335(6075):1452-3. doi: 10.1126/science.1220176.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Landcare Research, Lincoln, 7640 New Zealand. mcglonem@landcareresearch.co.nz〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22442471" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Ecosystem ; *Extinction, Biological ; Humans ; *Vertebrates
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  • 82
    Publication Date: 2012-01-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Margalida, Antoni -- Carrete, Martina -- Sanchez-Zapata, Jose A -- Donazar, Jose A -- New York, N.Y. -- Science. 2012 Jan 20;335(6066):284. doi: 10.1126/science.335.6066.284-a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22267790" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Conservation of Natural Resources/*legislation & jurisprudence ; *Ecosystem ; *Falconiformes ; Spain
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  • 83
    Publication Date: 2012-07-28
    Description: The brain tumor glioblastoma multiforme (GBM) is among the most lethal forms of human cancer. Here, we report that a small subset of GBMs (3.1%; 3 of 97 tumors examined) harbors oncogenic chromosomal translocations that fuse in-frame the tyrosine kinase coding domains of fibroblast growth factor receptor (FGFR) genes (FGFR1 or FGFR3) to the transforming acidic coiled-coil (TACC) coding domains of TACC1 or TACC3, respectively. The FGFR-TACC fusion protein displays oncogenic activity when introduced into astrocytes or stereotactically transduced in the mouse brain. The fusion protein, which localizes to mitotic spindle poles, has constitutive kinase activity and induces mitotic and chromosomal segregation defects and triggers aneuploidy. Inhibition of FGFR kinase corrects the aneuploidy, and oral administration of an FGFR inhibitor prolongs survival of mice harboring intracranial FGFR3-TACC3-initiated glioma. FGFR-TACC fusions could potentially identify a subset of GBM patients who would benefit from targeted FGFR kinase inhibition.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3677224/" 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/PMC3677224/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Singh, Devendra -- Chan, Joseph Minhow -- Zoppoli, Pietro -- Niola, Francesco -- Sullivan, Ryan -- Castano, Angelica -- Liu, Eric Minwei -- Reichel, Jonathan -- Porrati, Paola -- Pellegatta, Serena -- Qiu, Kunlong -- Gao, Zhibo -- Ceccarelli, Michele -- Riccardi, Riccardo -- Brat, Daniel J -- Guha, Abhijit -- Aldape, Ken -- Golfinos, John G -- Zagzag, David -- Mikkelsen, Tom -- Finocchiaro, Gaetano -- Lasorella, Anna -- Rabadan, Raul -- Iavarone, Antonio -- 1R01LM010140-01/LM/NLM NIH HHS/ -- R01 CA085628/CA/NCI NIH HHS/ -- R01 CA101644/CA/NCI NIH HHS/ -- R01 CA127643/CA/NCI NIH HHS/ -- R01 CA131126/CA/NCI NIH HHS/ -- R01 LM010140/LM/NLM NIH HHS/ -- R01 NS061776/NS/NINDS NIH HHS/ -- R01CA085628/CA/NCI NIH HHS/ -- R01CA101644/CA/NCI NIH HHS/ -- R01CA127643/CA/NCI NIH HHS/ -- R01CA131126/CA/NCI NIH HHS/ -- R01NS061776/NS/NINDS NIH HHS/ -- U54 CA121852/CA/NCI NIH HHS/ -- U54 CA121852-05/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2012 Sep 7;337(6099):1231-5. doi: 10.1126/science.1220834. Epub 2012 Jul 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22837387" target="_blank"〉PubMed〈/a〉
    Keywords: Aneuploidy ; Animals ; Antineoplastic Agents/pharmacology ; Benzamides/pharmacology ; Brain Neoplasms/genetics/metabolism ; *Cell Transformation, Neoplastic ; Chromosomal Instability ; Enzyme Inhibitors/pharmacology ; Fetal Proteins/chemistry/*genetics/metabolism ; Glioblastoma/*genetics/metabolism ; Humans ; Mice ; Microtubule-Associated Proteins/chemistry/*genetics/metabolism ; Mitosis ; Neoplasm Transplantation ; Nuclear Proteins/chemistry/*genetics/metabolism ; Oncogene Fusion ; Oncogene Proteins, Fusion/chemistry/genetics/*metabolism ; Piperazines/pharmacology ; Protein Structure, Tertiary ; Pyrazoles/pharmacology ; Pyrimidines/pharmacology ; Receptor, Fibroblast Growth Factor, Type 1/antagonists & ; inhibitors/chemistry/*genetics/metabolism ; Receptor, Fibroblast Growth Factor, Type 3/antagonists & ; inhibitors/chemistry/*genetics/metabolism ; Spindle Apparatus/metabolism ; Translocation, Genetic ; Xenograft Model Antitumor Assays
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  • 84
    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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  • 85
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-12-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kerr, Richard A -- New York, N.Y. -- Science. 2012 Nov 30;338(6111):1138. doi: 10.1126/science.338.6111.1138.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23197507" target="_blank"〉PubMed〈/a〉
    Keywords: *Climate Change ; *Ice Cover
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  • 86
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-02-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Corbera, Esteve -- Pascual, Unai -- New York, N.Y. -- Science. 2012 Feb 10;335(6069):655-6; author reply 656-7. doi: 10.1126/science.335.6069.655-c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22323797" target="_blank"〉PubMed〈/a〉
    Keywords: Ecology/*economics ; *Ecosystem
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  • 87
    Publication Date: 2012-09-08
    Description: In animals and plants, social structure can reduce conflict within populations and bias aggression toward competing populations; however, for bacteria in the wild it remains unknown whether such population-level organization exists. Here, we show that environmental bacteria are organized into socially cohesive units in which antagonism occurs between rather than within ecologically defined populations. By screening approximately 35,000 possible mutual interactions among Vibrionaceae isolates from the ocean, we show that genotypic clusters known to have cohesive habitat association also act as units in terms of antibiotic production and resistance. Genetic analyses show that within populations, broad-range antibiotics are produced by few genotypes, whereas all others are resistant, suggesting cooperation between conspecifics. Natural antibiotics may thus mediate competition between populations rather than solely increase the success of individuals.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cordero, Otto X -- Wildschutte, Hans -- Kirkup, Benjamin -- Proehl, Sarah -- Ngo, Lynn -- Hussain, Fatima -- Le Roux, Frederique -- Mincer, Tracy -- Polz, Martin F -- New York, N.Y. -- Science. 2012 Sep 7;337(6099):1228-31. doi: 10.1126/science.1219385.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22955834" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/*biosynthesis ; *Antibiosis ; DNA Transposable Elements ; *Drug Resistance, Bacterial ; *Ecosystem ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Genotype ; *Microbial Interactions ; Molecular Sequence Data ; Oceans and Seas ; Polyketide Synthases/genetics ; Seawater/*microbiology ; Vibrio/*drug effects/genetics/metabolism/*physiology
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  • 88
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-06-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2012 Jun 15;336(6087):1368-9. doi: 10.1126/science.336.6087.1368.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22700897" target="_blank"〉PubMed〈/a〉
    Keywords: Angiosperms/*physiology ; Animals ; Bacteria/*metabolism ; Bivalvia/*physiology ; *Ecosystem ; *Seawater ; *Symbiosis ; Zosteraceae/*physiology
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  • 89
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-09-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kerr, Richard A -- New York, N.Y. -- Science. 2012 Sep 28;337(6102):1591.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23019619" target="_blank"〉PubMed〈/a〉
    Keywords: Arctic Regions ; *Climate Change ; *Computer Simulation ; *Ice Cover ; *Seawater
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  • 90
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    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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  • 91
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-04-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2012 Apr 13;336(6078):172-4. doi: 10.1126/science.336.6078.172.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22499936" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Animals ; *Behavior, Animal ; *Body Temperature ; Body Temperature Regulation ; Climate Change ; *Computer Simulation ; *Ecosystem ; Energy Transfer ; Environment ; Lizards/anatomy & histology/physiology ; Microclimate ; *Models, Biological ; *Physiological Processes ; Software ; Temperature
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 92
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-03-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smith, Felisa A -- New York, N.Y. -- Science. 2012 Feb 24;335(6071):924-5. doi: 10.1126/science.1219233.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA. fasmith@unm.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22362994" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Climate Change ; Equidae/*anatomy & histology ; *Fossils ; Horses/*anatomy & histology
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  • 93
    Publication Date: 2012-12-15
    Description: Epigenetic regulators represent a promising new class of therapeutic targets for cancer. Enhancer of zeste homolog 2 (EZH2), a subunit of Polycomb repressive complex 2 (PRC2), silences gene expression via its histone methyltransferase activity. We found that the oncogenic function of EZH2 in cells of castration-resistant prostate cancer is independent of its role as a transcriptional repressor. Instead, it involves the ability of EZH2 to act as a coactivator for critical transcription factors including the androgen receptor. This functional switch is dependent on phosphorylation of EZH2 and requires an intact methyltransferase domain. Hence, targeting the non-PRC2 function of EZH2 may have therapeutic efficacy for treating metastatic, hormone-refractory prostate cancer.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3625962/" 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/PMC3625962/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Kexin -- Wu, Zhenhua Jeremy -- Groner, Anna C -- He, Housheng Hansen -- Cai, Changmeng -- Lis, Rosina T -- Wu, Xiaoqiu -- Stack, Edward C -- Loda, Massimo -- Liu, Tao -- Xu, Han -- Cato, Laura -- Thornton, James E -- Gregory, Richard I -- Morrissey, Colm -- Vessella, Robert L -- Montironi, Rodolfo -- Magi-Galluzzi, Cristina -- Kantoff, Philip W -- Balk, Steven P -- Liu, X Shirley -- Brown, Myles -- CA090381/CA/NCI NIH HHS/ -- CA097186/CA/NCI NIH HHS/ -- CA111803/CA/NCI NIH HHS/ -- CA131945/CA/NCI NIH HHS/ -- CA166507/CA/NCI NIH HHS/ -- CA85859/CA/NCI NIH HHS/ -- CA89021/CA/NCI NIH HHS/ -- CA90381/CA/NCI NIH HHS/ -- GM99409/GM/NIGMS NIH HHS/ -- K99 CA166507/CA/NCI NIH HHS/ -- P50 CA090381/CA/NCI NIH HHS/ -- R01 GM099409/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Dec 14;338(6113):1465-9. doi: 10.1126/science.1227604.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Functional Cancer Epigenetics, 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/23239736" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Castration ; Cell Line, Tumor ; Cohort Studies ; Gene Expression Regulation, Neoplastic ; Gene Silencing ; Humans ; Jumonji Domain-Containing Histone Demethylases/metabolism ; Male ; Methyltransferases/chemistry/genetics/metabolism ; Mice ; Mice, Inbred ICR ; Mice, SCID ; Oncogene Proteins/genetics/*metabolism ; Polycomb Repressive Complex 2/genetics/*metabolism ; Prostatic Neoplasms/genetics/*metabolism/mortality ; Protein Structure, Tertiary ; Receptors, Androgen/metabolism ; Xenograft Model Antitumor Assays
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  • 94
    Publication Date: 2012-04-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maxwell, Sara M -- Hazen, Elliott L -- Morgan, Lance E -- Bailey, Helen -- Lewison, Rebecca -- New York, N.Y. -- Science. 2012 Apr 27;336(6080):413. doi: 10.1126/science.336.6080.413-a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22539701" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Conservation of Natural Resources ; *Ecosystem ; *Fisheries ; *Fishes
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  • 95
    Publication Date: 2012-02-11
    Description: DNMT1, the major maintenance DNA methyltransferase in animals, helps to regulate gene expression, genome imprinting, and X-chromosome inactivation. We report on the crystal structure of a productive covalent mouse DNMT1(731-1602)-DNA complex containing a central hemimethylated CpG site. The methyl group of methylcytosine is positioned within a shallow hydrophobic concave surface, whereas the cytosine on the target strand is looped out and covalently anchored within the catalytic pocket. The DNA is distorted at the hemimethylated CpG step, with side chains from catalytic and recognition loops inserting through both grooves to fill an intercalation-type cavity associated with a dual base flip-out on partner strands. Structural and biochemical data establish how a combination of active and autoinhibitory mechanisms ensures the high fidelity of DNMT1-mediated maintenance DNA methylation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4693633/" 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/PMC4693633/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Song, Jikui -- Teplova, Marianna -- Ishibe-Murakami, Satoko -- Patel, Dinshaw J -- P30 CA008748/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2012 Feb 10;335(6069):709-12. doi: 10.1126/science.1214453.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22323818" target="_blank"〉PubMed〈/a〉
    Keywords: 5-Methylcytosine/chemistry/metabolism ; Animals ; Base Pairing ; Catalytic Domain ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; DNA (Cytosine-5-)-Methyltransferase/*chemistry/genetics/*metabolism ; *DNA Methylation ; Dinucleoside Phosphates/chemistry ; Hydrophobic and Hydrophilic Interactions ; Mice ; Models, Molecular ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Substrate Specificity
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 96
    Publication Date: 2012-03-17
    Description: The assumption that climatic niche requirements of invasive species are conserved between their native and invaded ranges is key to predicting the risk of invasion. However, this assumption has been challenged recently by evidence of niche shifts in some species. Here, we report the first large-scale test of niche conservatism for 50 terrestrial plant invaders between Eurasia, North America, and Australia. We show that when analog climates are compared between regions, fewer than 15% of species have more than 10% of their invaded distribution outside their native climatic niche. These findings reveal that substantial niche shifts are rare in terrestrial plant invaders, providing support for an appropriate use of ecological niche models for the prediction of both biological invasions and responses to climate change.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Petitpierre, Blaise -- Kueffer, Christoph -- Broennimann, Olivier -- Randin, Christophe -- Daehler, Curtis -- Guisan, Antoine -- New York, N.Y. -- Science. 2012 Mar 16;335(6074):1344-8. doi: 10.1126/science.1215933.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22422981" target="_blank"〉PubMed〈/a〉
    Keywords: Angiosperms/*growth & development ; Asia ; Australia ; Biodiversity ; *Climate ; Climate Change ; *Ecosystem ; Europe ; *Introduced Species ; North America ; Phylogeography
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 97
    Publication Date: 2013-02-09
    Description: HSP-100 protein machines, such as ClpB, play an essential role in reactivating protein aggregates that can otherwise be lethal to cells. Although the players involved are known, including the DnaK/DnaJ/GrpE chaperone system in bacteria, details of the molecular interactions are not well understood. Using methyl-transverse relaxation-optimized nuclear magnetic resonance spectroscopy, we present an atomic-resolution model for the ClpB-DnaK complex, which we verified by mutagenesis and functional assays. ClpB and GrpE compete for binding to the DnaK nucleotide binding domain, with GrpE binding inhibiting disaggregation. DnaK, in turn, plays a dual role in both disaggregation and subsequent refolding of polypeptide chains as they emerge from the aggregate. On the basis of a combined structural-biochemical analysis, we propose a model for the mechanism of protein aggregate reactivation by ClpB.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rosenzweig, Rina -- Moradi, Shoeib -- Zarrine-Afsar, Arash -- Glover, John R -- Kay, Lewis E -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2013 Mar 1;339(6123):1080-3. doi: 10.1126/science.1233066. Epub 2013 Feb 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada. rina.rosenzweig@utoronto.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23393091" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/*chemistry/genetics ; Adenosine Triphosphate/chemistry/metabolism ; Bacterial Proteins/chemistry ; Heat-Shock Proteins/*chemistry/genetics ; Hydrolysis ; *Models, Chemical ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; Protein Interaction Domains and Motifs ; Protein Interaction Maps ; Protein Multimerization ; *Protein Refolding ; Protein Structure, Tertiary ; Protein Transport ; Thermus thermophilus
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 98
    Publication Date: 2013-04-06
    Description: The 21st amino acid, selenocysteine (Sec), is synthesized on its cognate transfer RNA (tRNA(Sec)). In bacteria, SelA synthesizes Sec from Ser-tRNA(Sec), whereas in archaea and eukaryotes SepSecS forms Sec from phosphoserine (Sep) acylated to tRNA(Sec). We determined the crystal structures of Aquifex aeolicus SelA complexes, which revealed a ring-shaped homodecamer that binds 10 tRNA(Sec) molecules, each interacting with four SelA subunits. The SelA N-terminal domain binds the tRNA(Sec)-specific D-arm structure, thereby discriminating Ser-tRNA(Sec) from Ser-tRNA(Ser). A large cleft is created between two subunits and accommodates the 3'-terminal region of Ser-tRNA(Sec). The SelA structures together with in vivo and in vitro enzyme assays show decamerization to be essential for SelA function. SelA catalyzes pyridoxal 5'-phosphate-dependent Sec formation involving Arg residues nonhomologous to those in SepSecS. Different protein architecture and substrate coordination of the bacterial enzyme provide structural evidence for independent evolution of the two Sec synthesis systems present in nature.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3976565/" 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/PMC3976565/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Itoh, Yuzuru -- Brocker, Markus J -- Sekine, Shun-ichi -- Hammond, Gifty -- Suetsugu, Shiro -- Soll, Dieter -- Yokoyama, Shigeyuki -- GM22854/GM/NIGMS NIH HHS/ -- R01 GM022854/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Apr 5;340(6128):75-8. doi: 10.1126/science.1229521.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama 230-0045, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23559248" target="_blank"〉PubMed〈/a〉
    Keywords: Arginine/chemistry ; Bacteria/*enzymology ; Bacterial Proteins/*chemistry ; Catalysis ; Catalytic Domain ; Crystallography, X-Ray ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Pyridoxal Phosphate/chemistry ; RNA, Transfer, Amino Acyl/*chemistry ; Selenocysteine/*biosynthesis ; Transferases/*chemistry
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 99
    Publication Date: 2013-10-26
    Description: Painful venoms are used to deter predators. Pain itself, however, can signal damage and thus serves an important adaptive function. Evolution to reduce general pain responses, although valuable for preying on venomous species, is rare, likely because it comes with the risk of reduced response to tissue damage. Bark scorpions capitalize on the protective pain pathway of predators by inflicting intensely painful stings. However, grasshopper mice regularly attack and consume bark scorpions, grooming only briefly when stung. Bark scorpion venom induces pain in many mammals (house mice, rats, humans) by activating the voltage-gated Na(+) channel Nav1.7, but has no effect on Nav1.8. Grasshopper mice Nav1.8 has amino acid variants that bind bark scorpion toxins and inhibit Na(+) currents, blocking action potential propagation and inducing analgesia. Thus, grasshopper mice have solved the predator-pain problem by using a toxin bound to a nontarget channel to block transmission of the pain signals the venom itself is initiating.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4172297/" 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/PMC4172297/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rowe, Ashlee H -- Xiao, Yucheng -- Rowe, Matthew P -- Cummins, Theodore R -- Zakon, Harold H -- NS 053422/NS/NINDS NIH HHS/ -- R01 NS053422/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2013 Oct 25;342(6157):441-6. doi: 10.1126/science.1236451.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Neurobiology, The University of Texas at Austin, Austin, TX 78712, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24159039" target="_blank"〉PubMed〈/a〉
    Keywords: Action Potentials/drug effects/physiology ; Amino Acid Sequence ; Animals ; Arvicolinae/*metabolism ; *Food Chain ; Formaldehyde/pharmacology ; Mice ; Molecular Sequence Data ; NAV1.7 Voltage-Gated Sodium Channel/chemistry/genetics/*metabolism ; NAV1.8 Voltage-Gated Sodium Channel/chemistry/genetics/*metabolism ; Pain/chemically induced/*metabolism ; *Predatory Behavior ; Protein Structure, Tertiary ; Scorpion Venoms
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 100
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-11-03
    Description: Marine bacteria influence Earth's environmental dynamics in fundamental ways by controlling the biogeochemistry and productivity of the oceans. These large-scale consequences result from the combined effect of countless interactions occurring at the level of the individual cells. At these small scales, the ocean is surprisingly heterogeneous, and microbes experience an environment of pervasive and dynamic chemical and physical gradients. Many species actively exploit this heterogeneity, while others rely on gradient-independent adaptations. This is an exciting time to explore this frontier of oceanography, but understanding microbial behavior and competition in the context of the water column's microarchitecture calls for new ecological frameworks, such as a microbial optimal foraging theory, to determine the relevant trade-offs and global consequences of microbial life in a sea of gradients.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stocker, Roman -- 1R01GM100473/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Nov 2;338(6107):628-33. doi: 10.1126/science.1208929.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ralph M. Parsons Laboratory, Department of Civil and Environmental Engineering, 49-213, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA. romans@mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23118182" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Aquatic Organisms/*physiology ; Bacteria/genetics/growth & development ; *Bacterial Physiological Phenomena ; Biodiversity ; Biological Evolution ; *Chemotaxis ; *Ecosystem ; Environment ; Oceans and Seas ; Seawater/*chemistry/*microbiology ; Water Microbiology
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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