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  • Carbon Dioxide  (4)
  • Protein Folding  (4)
  • American Association for the Advancement of Science (AAAS)  (8)
  • American Association of Petroleum Geologists (AAPG)
  • Cambridge University Press
  • Springer Nature
  • 2005-2009  (6)
  • 2000-2004  (2)
  • 1965-1969
Collection
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (8)
  • American Association of Petroleum Geologists (AAPG)
  • Cambridge University Press
  • Springer Nature
Years
  • 2005-2009  (6)
  • 2000-2004  (2)
  • 1965-1969
  • 2010-2014  (1)
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  • 1
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    Consistent land- and atmosphere-based U.S. carbon sink estimates (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-06-26
    Description: For the period 1980-89, we estimate a carbon sink in the coterminous United States between 0.30 and 0.58 petagrams of carbon per year (petagrams of carbon = 10(15) grams of carbon). The net carbon flux from the atmosphere to the land was higher, 0.37 to 0.71 petagrams of carbon per year, because a net flux of 0.07 to 0.13 petagrams of carbon per year was exported by rivers and commerce and returned to the atmosphere elsewhere. These land-based estimates are larger than those from previous studies (0.08 to 0.35 petagrams of carbon per year) because of the inclusion of additional processes and revised estimates of some component fluxes. Although component estimates are uncertain, about one-half of the total is outside the forest sector. We also estimated the sink using atmospheric models and the atmospheric concentration of carbon dioxide (the tracer-transport inversion method). The range of results from the atmosphere-based inversions contains the land-based estimates. Atmosphere- and land-based estimates are thus consistent, within the large ranges of uncertainty for both methods. Atmosphere-based results for 1980-89 are similar to those for 1985-89 and 1990-94, indicating a relatively stable U.S. sink throughout the period.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pacala, S W -- Hurtt, G C -- Baker, D -- Peylin, P -- Houghton, R A -- Birdsey, R A -- Heath, L -- Sundquist, E T -- Stallard, R F -- Ciais, P -- Moorcroft, P -- Caspersen, J P -- Shevliakova, E -- Moore, B -- Kohlmaier, G -- Holland, E -- Gloor, M -- Harmon, M E -- Fan, S M -- Sarmiento, J L -- Goodale, C L -- Schimel, D -- Field, C B -- New York, N.Y. -- Science. 2001 Jun 22;292(5525):2316-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, Atmospheric and Oceanic Sciences Program, Princeton University, Princeton, NJ 08544, USA. Pacala@princeton.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11423659" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture ; *Atmosphere ; *Carbon/metabolism ; Carbon Dioxide ; Conservation of Natural Resources ; Ecosystem ; Fires ; Forestry ; Soil ; Time Factors ; *Trees/metabolism ; United States ; Wood
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Protein structure prediction and structural genomics (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-10-06
    Description: Genome sequencing projects are producing linear amino acid sequences, but full understanding of the biological role of these proteins will require knowledge of their structure and function. Although experimental structure determination methods are providing high-resolution structure information about a subset of the proteins, computational structure prediction methods will provide valuable information for the large fraction of sequences whose structures will not be determined experimentally. The first class of protein structure prediction methods, including threading and comparative modeling, rely on detectable similarity spanning most of the modeled sequence and at least one known structure. The second class of methods, de novo or ab initio methods, predict the structure from sequence alone, without relying on similarity at the fold level between the modeled sequence and any of the known structures. In this Viewpoint, we begin by describing the essential features of the methods, the accuracy of the models, and their application to the prediction and understanding of protein function, both for single proteins and on the scale of whole genomes. We then discuss the important role that protein structure prediction methods play in the growing worldwide effort in structural genomics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, D -- Sali, A -- GM 54762/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Oct 5;294(5540):93-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA. dabaker@u.washington.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11588250" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; *Computational Biology ; Computer Simulation ; Databases, Factual ; *Genomics ; Humans ; Internet ; *Models, Molecular ; *Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Proteins/*chemistry/genetics/physiology ; Sequence Alignment ; Software ; Templates, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    Drought sensitivity of the Amazon rainforest (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-03-07
    Description: Amazon forests are a key but poorly understood component of the global carbon cycle. If, as anticipated, they dry this century, they might accelerate climate change through carbon losses and changed surface energy balances. We used records from multiple long-term monitoring plots across Amazonia to assess forest responses to the intense 2005 drought, a possible analog of future events. Affected forest lost biomass, reversing a large long-term carbon sink, with the greatest impacts observed where the dry season was unusually intense. Relative to pre-2005 conditions, forest subjected to a 100-millimeter increase in water deficit lost 5.3 megagrams of aboveground biomass of carbon per hectare. The drought had a total biomass carbon impact of 1.2 to 1.6 petagrams (1.2 x 10(15) to 1.6 x 10(15) grams). Amazon forests therefore appear vulnerable to increasing moisture stress, with the potential for large carbon losses to exert feedback on climate change.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Phillips, Oliver L -- Aragao, Luiz E O C -- Lewis, Simon L -- Fisher, Joshua B -- Lloyd, Jon -- Lopez-Gonzalez, Gabriela -- Malhi, Yadvinder -- Monteagudo, Abel -- Peacock, Julie -- Quesada, Carlos A -- van der Heijden, Geertje -- Almeida, Samuel -- Amaral, Ieda -- Arroyo, Luzmila -- Aymard, Gerardo -- Baker, Tim R -- Banki, Olaf -- Blanc, Lilian -- Bonal, Damien -- Brando, Paulo -- Chave, Jerome -- de Oliveira, Atila Cristina Alves -- Cardozo, Nallaret Davila -- Czimczik, Claudia I -- Feldpausch, Ted R -- Freitas, Maria Aparecida -- Gloor, Emanuel -- Higuchi, Niro -- Jimenez, Eliana -- Lloyd, Gareth -- Meir, Patrick -- Mendoza, Casimiro -- Morel, Alexandra -- Neill, David A -- Nepstad, Daniel -- Patino, Sandra -- Penuela, Maria Cristina -- Prieto, Adriana -- Ramirez, Fredy -- Schwarz, Michael -- Silva, Javier -- Silveira, Marcos -- Thomas, Anne Sota -- Steege, Hans Ter -- Stropp, Juliana -- Vasquez, Rodolfo -- Zelazowski, Przemyslaw -- Alvarez Davila, Esteban -- Andelman, Sandy -- Andrade, Ana -- Chao, Kuo-Jung -- Erwin, Terry -- Di Fiore, Anthony -- Honorio C, Euridice -- Keeling, Helen -- Killeen, Tim J -- Laurance, William F -- Pena Cruz, Antonio -- Pitman, Nigel C A -- Nunez Vargas, Percy -- Ramirez-Angulo, Hirma -- Rudas, Agustin -- Salamao, Rafael -- Silva, Natalino -- Terborgh, John -- Torres-Lezama, Armando -- New York, N.Y. -- Science. 2009 Mar 6;323(5919):1344-7. doi: 10.1126/science.1164033.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ecology and Global Change, School of Geography, University of Leeds, Leeds LS2 9JT, UK. o.phillips@leeds.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19265020" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere ; *Biomass ; Brazil ; Carbon ; Carbon Dioxide ; Climate ; *Droughts ; *Ecosystem ; South America ; *Trees/growth & development ; Tropical Climate
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Toward high-resolution de novo structure prediction for small proteins (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-09-17
    Description: The prediction of protein structure from amino acid sequence is a grand challenge of computational molecular biology. By using a combination of improved low- and high-resolution conformational sampling methods, improved atomically detailed potential functions that capture the jigsaw puzzle-like packing of protein cores, and high-performance computing, high-resolution structure prediction (〈1.5 angstroms) can be achieved for small protein domains (〈85 residues). The primary bottleneck to consistent high-resolution prediction appears to be conformational sampling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bradley, Philip -- Misura, Kira M S -- Baker, David -- New York, N.Y. -- Science. 2005 Sep 16;309(5742):1868-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Washington, Department of Biochemistry, and Howard Hughes Medical Institute, Box 357350, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16166519" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Chemistry, Physical ; *Computational Biology ; Computer Simulation ; Hydrogen Bonding ; Models, Molecular ; Monte Carlo Method ; Physicochemical Phenomena ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/*chemistry ; Sequence Alignment ; Thermodynamics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    Computational thermostabilization of an enzyme (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-05-10
    Description: Thermostabilizing an enzyme while maintaining its activity for industrial or biomedical applications can be difficult with traditional selection methods. We describe a rapid computational approach that identified three mutations within a model enzyme that produced a 10 degrees C increase in apparent melting temperature T(m) and a 30-fold increase in half-life at 50 degrees C, with no reduction in catalytic efficiency. The effects of the mutations were synergistic, giving an increase in excess of the sum of their individual effects. The redesigned enzyme induced an increased, temperature-dependent bacterial growth rate under conditions that required its activity, thereby coupling molecular and metabolic engineering.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3412875/" 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/PMC3412875/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Korkegian, Aaron -- Black, Margaret E -- Baker, David -- Stoddard, Barry L -- CA85939/CA/NCI NIH HHS/ -- CA97328/CA/NCI NIH HHS/ -- GM49857/GM/NIGMS NIH HHS/ -- GM59224/GM/NIGMS NIH HHS/ -- R01 CA097328/CA/NCI NIH HHS/ -- R01 GM049857/GM/NIGMS NIH HHS/ -- T32-GM08268/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 May 6;308(5723):857-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Basic Sciences, Fred Hutchinson Cancer Research Center (FHCRC), 1100 Fairview Avenue North, Seattle, WA 98109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15879217" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Catalysis ; Circular Dichroism ; *Computer Simulation ; Crystallography, X-Ray ; Cytosine Deaminase/*chemistry/*metabolism ; Enzyme Stability ; Escherichia coli/genetics/metabolism ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Monte Carlo Method ; Mutagenesis, Site-Directed ; Point Mutation ; Protein Conformation ; Protein Denaturation ; *Protein Engineering ; Protein Folding ; Protein Structure, Secondary ; Software ; Temperature ; Thermodynamics ; Transformation, Genetic ; Yeasts/enzymology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    Global iron connections between desert dust, ocean biogeochemistry, and climate (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-04-02
    Description: The environmental conditions of Earth, including the climate, are determined by physical, chemical, biological, and human interactions that transform and transport materials and energy. This is the "Earth system": a highly complex entity characterized by multiple nonlinear responses and thresholds, with linkages between disparate components. One important part of this system is the iron cycle, in which iron-containing soil dust is transported from land through the atmosphere to the oceans, affecting ocean biogeochemistry and hence having feedback effects on climate and dust production. Here we review the key components of this cycle, identifying critical uncertainties and priorities for future research.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jickells, T D -- An, Z S -- Andersen, K K -- Baker, A R -- Bergametti, G -- Brooks, N -- Cao, J J -- Boyd, P W -- Duce, R A -- Hunter, K A -- Kawahata, H -- Kubilay, N -- laRoche, J -- Liss, P S -- Mahowald, N -- Prospero, J M -- Ridgwell, A J -- Tegen, I -- Torres, R -- New York, N.Y. -- Science. 2005 Apr 1;308(5718):67-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Environmental Sciences, University of East Anglia, Norwich NR47TJ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15802595" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere ; Carbon Dioxide ; *Climate ; Desert Climate ; *Dust ; *Iron/metabolism ; Oceans and Seas ; Phytoplankton/physiology ; *Seawater ; Soil
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Community proteomics of a natural microbial biofilm (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-05-10
    Description: Using genomic and mass spectrometry-based proteomic methods, we evaluated gene expression, identified key activities, and examined partitioning of metabolic functions in a natural acid mine drainage (AMD) microbial biofilm community. We detected 2033 proteins from the five most abundant species in the biofilm, including 48% of the predicted proteins from the dominant biofilm organism, Leptospirillum group II. Proteins involved in protein refolding and response to oxidative stress appeared to be highly expressed, which suggests that damage to biomolecules is a key challenge for survival. We validated and estimated the relative abundance and cellular localization of 357 unique and 215 conserved novel proteins and determined that one abundant novel protein is a cytochrome central to iron oxidation and AMD formation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ram, Rachna J -- Verberkmoes, Nathan C -- Thelen, Michael P -- Tyson, Gene W -- Baker, Brett J -- Blake, Robert C 2nd -- Shah, Manesh -- Hettich, Robert L -- Banfield, Jillian F -- New York, N.Y. -- Science. 2005 Jun 24;308(5730):1915-20. Epub 2005 May 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15879173" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/metabolism ; Archaeal Proteins/*analysis/chemistry ; Bacteria/chemistry/genetics/*metabolism ; Bacterial Proteins/*analysis/chemistry/genetics/physiology ; *Biofilms/growth & development ; Cytochromes/analysis/chemistry ; *Ecosystem ; Gene Expression ; Genes, Archaeal ; Genes, Bacterial ; Genome, Archaeal ; Genome, Bacterial ; Genomics ; Hydrogen-Ion Concentration ; Iron/metabolism ; Isoelectric Point ; Mass Spectrometry ; *Mining ; Molecular Sequence Data ; Oxidation-Reduction ; Protein Biosynthesis ; Protein Folding ; Proteome ; *Proteomics ; Thermoplasmales/chemistry/genetics/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    Hurricane Katrina's carbon footprint on U.S. Gulf Coast forests (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-11-17
    Description: Hurricane Katrina's impact on U.S. Gulf Coast forests was quantified by linking ecological field studies, Landsat and Moderate Resolution Imaging Spectroradiometer (MODIS) image analyses, and empirically based models. Within areas affected by relatively constant wind speed, tree mortality and damage exhibited strong species-controlled gradients. Spatially explicit forest disturbance maps coupled with extrapolation models predicted mortality and severe structural damage to approximately 320 million large trees totaling 105 teragrams of carbon, representing 50 to 140% of the net annual U.S. forest tree carbon sink. Changes in disturbance regimes from increased storm activity expected under a warming climate will reduce forest biomass stocks, increase ecosystem respiration, and may represent an important positive feedback mechanism to elevated atmospheric carbon dioxide.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chambers, Jeffrey Q -- Fisher, Jeremy I -- Zeng, Hongcheng -- Chapman, Elise L -- Baker, David B -- Hurtt, George C -- New York, N.Y. -- Science. 2007 Nov 16;318(5853):1107.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ecology and Evolutionary Biology, Tulane University, 400 Lindy Boggs, New Orleans, LA 70118, USA. chambers@tulane.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18006740" target="_blank"〉PubMed〈/a〉
    Keywords: Biomass ; *Carbon ; Carbon Dioxide ; *Disasters ; Ecosystem ; Southeastern United States ; *Trees
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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