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  • Kinetics  (129)
  • American Association for the Advancement of Science (AAAS)  (129)
  • Institute of Physics
  • 2005-2009  (26)
  • 1985-1989  (55)
  • 1980-1984  (48)
  • 1965-1969
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  • 1
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    Real-time DNA sequencing from single polymerase molecules (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-11-22
    Description: We present single-molecule, real-time sequencing data obtained from a DNA polymerase performing uninterrupted template-directed synthesis using four distinguishable fluorescently labeled deoxyribonucleoside triphosphates (dNTPs). We detected the temporal order of their enzymatic incorporation into a growing DNA strand with zero-mode waveguide nanostructure arrays, which provide optical observation volume confinement and enable parallel, simultaneous detection of thousands of single-molecule sequencing reactions. Conjugation of fluorophores to the terminal phosphate moiety of the dNTPs allows continuous observation of DNA synthesis over thousands of bases without steric hindrance. The data report directly on polymerase dynamics, revealing distinct polymerization states and pause sites corresponding to DNA secondary structure. Sequence data were aligned with the known reference sequence to assay biophysical parameters of polymerization for each template position. Consensus sequences were generated from the single-molecule reads at 15-fold coverage, showing a median accuracy of 99.3%, with no systematic error beyond fluorophore-dependent error rates.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eid, John -- Fehr, Adrian -- Gray, Jeremy -- Luong, Khai -- Lyle, John -- Otto, Geoff -- Peluso, Paul -- Rank, David -- Baybayan, Primo -- Bettman, Brad -- Bibillo, Arkadiusz -- Bjornson, Keith -- Chaudhuri, Bidhan -- Christians, Frederick -- Cicero, Ronald -- Clark, Sonya -- Dalal, Ravindra -- Dewinter, Alex -- Dixon, John -- Foquet, Mathieu -- Gaertner, Alfred -- Hardenbol, Paul -- Heiner, Cheryl -- Hester, Kevin -- Holden, David -- Kearns, Gregory -- Kong, Xiangxu -- Kuse, Ronald -- Lacroix, Yves -- Lin, Steven -- Lundquist, Paul -- Ma, Congcong -- Marks, Patrick -- Maxham, Mark -- Murphy, Devon -- Park, Insil -- Pham, Thang -- Phillips, Michael -- Roy, Joy -- Sebra, Robert -- Shen, Gene -- Sorenson, Jon -- Tomaney, Austin -- Travers, Kevin -- Trulson, Mark -- Vieceli, John -- Wegener, Jeffrey -- Wu, Dawn -- Yang, Alicia -- Zaccarin, Denis -- Zhao, Peter -- Zhong, Frank -- Korlach, Jonas -- Turner, Stephen -- R01HG003710/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2009 Jan 2;323(5910):133-8. doi: 10.1126/science.1162986. Epub 2008 Nov 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Pacific Biosciences, 1505 Adams Drive, Menlo Park, CA 94025, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19023044" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Consensus Sequence ; DNA/biosynthesis ; DNA, Circular/chemistry ; DNA, Single-Stranded/chemistry ; DNA-Directed DNA Polymerase/*metabolism ; Deoxyribonucleotides/metabolism ; Enzymes, Immobilized ; Fluorescent Dyes ; Kinetics ; Nanostructures ; Sequence Analysis, DNA/*methods ; Spectrometry, Fluorescence
    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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  • 2
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    Regulation of leucine metabolism in man: a stable isotope study (1981)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1981-12-04
    Description: Leucine catabolism is regulated by either of the first two degradative steps: (reversible) transamination to the keto acid or subsequent decarboxylation. A method is described to measure rates of leucine transamination, reamination, and keto acid oxidation. The method is applied directly to humans by infusing the nonradioactive tracer, L-[15N,1-13C]leucine. Leucine transamination was found to be operating several times faster than the keto acid decarboxylation and to be of equal magnitude in adult human males under two different dietary conditions, postabsorptive and fed. These results indicate that decarboxylation, not transamination, is the rate-limiting step in normal human leucine metabolism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Matthews, D E -- Bier, D M -- Rennie, M J -- Edwards, R H -- Halliday, D -- Millward, D J -- Clugston, G A -- AM-25994/AM/NIADDK NIH HHS/ -- HD-10667/HD/NICHD NIH HHS/ -- RR-00954/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1981 Dec 4;214(4525):1129-31.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7302583" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Carbon Isotopes ; Humans ; Kinetics ; Leucine/*metabolism ; Male ; Models, Biological ; Nitrogen Isotopes ; Oxidation-Reduction
    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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    De novo computational design of retro-aldol enzymes (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-03-08
    Description: The creation of enzymes capable of catalyzing any desired chemical reaction is a grand challenge for computational protein design. Using new algorithms that rely on hashing techniques to construct active sites for multistep reactions, we designed retro-aldolases that use four different catalytic motifs to catalyze the breaking of a carbon-carbon bond in a nonnatural substrate. Of the 72 designs that were experimentally characterized, 32, spanning a range of protein folds, had detectable retro-aldolase activity. Designs that used an explicit water molecule to mediate proton shuffling were significantly more successful, with rate accelerations of up to four orders of magnitude and multiple turnovers, than those involving charged side-chain networks. The atomic accuracy of the design process was confirmed by the x-ray crystal structure of active designs embedded in two protein scaffolds, both of which were nearly superimposable on the design model.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431203/" 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/PMC3431203/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jiang, Lin -- Althoff, Eric A -- Clemente, Fernando R -- Doyle, Lindsey -- Rothlisberger, Daniela -- Zanghellini, Alexandre -- Gallaher, Jasmine L -- Betker, Jamie L -- Tanaka, Fujie -- Barbas, Carlos F 3rd -- Hilvert, Donald -- Houk, Kendall N -- Stoddard, Barry L -- Baker, David -- R01 CA097328/CA/NCI NIH HHS/ -- R01 GM049857/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Mar 7;319(5868):1387-91. doi: 10.1126/science.1152692.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18323453" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde-Lyases/*chemistry/metabolism ; *Algorithms ; Binding Sites ; Catalysis ; Catalytic Domain ; Computer Simulation ; Crystallography, X-Ray ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Models, Molecular ; Protein Conformation ; Protein Engineering
    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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    The dynamic energy landscape of dihydrofolate reductase catalysis (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-09-16
    Description: We used nuclear magnetic resonance relaxation dispersion to characterize higher energy conformational substates of Escherichia coli dihydrofolate reductase. Each intermediate in the catalytic cycle samples low-lying excited states whose conformations resemble the ground-state structures of preceding and following intermediates. Substrate and cofactor exchange occurs through these excited substates. The maximum hydride transfer and steady-state turnover rates are governed by the dynamics of transitions between ground and excited states of the intermediates. Thus, the modulation of the energy landscape by the bound ligands funnels the enzyme through its reaction cycle along a preferred kinetic path.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boehr, David D -- McElheny, Dan -- Dyson, H Jane -- Wright, Peter E -- GM56879/GM/NIGMS NIH HHS/ -- GM75995/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Sep 15;313(5793):1638-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Skaggs Institute for Chemical Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16973882" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Escherichia coli/*enzymology ; Kinetics ; Ligands ; Models, Molecular ; NADP/metabolism ; Nuclear Magnetic Resonance, Biomolecular ; Protein Binding ; *Protein Conformation ; Tetrahydrofolate Dehydrogenase/*chemistry/*metabolism ; Tetrahydrofolates/metabolism ; Thermodynamics
    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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  • 5
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    Free-solution, label-free molecular interactions studied by back-scattering interferometry (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-22
    Description: Free-solution, label-free molecular interactions were investigated with back-scattering interferometry in a simple optical train composed of a helium-neon laser, a microfluidic channel, and a position sensor. Molecular binding interactions between proteins, ions and protein, and small molecules and protein, were determined with high dynamic range dissociation constants (Kd spanning six decades) and unmatched sensitivity (picomolar Kd's and detection limits of 10,000s of molecules). With this technique, equilibrium dissociation constants were quantified for protein A and immunoglobulin G, interleukin-2 with its monoclonal antibody, and calmodulin with calcium ion Ca2+, a small molecule inhibitor, the protein calcineurin, and the M13 peptide. The high sensitivity of back-scattering interferometry and small volumes of microfluidics allowed the entire calmodulin assay to be performed with 200 picomoles of solute.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bornhop, Darryl J -- Latham, Joey C -- Kussrow, Amanda -- Markov, Dmitry A -- Jones, Richard D -- Sorensen, Henrik S -- R-01 EB0003537-01A2/EB/NIBIB NIH HHS/ -- T32 GM065086/GM/NIGMS NIH HHS/ -- T32-EY07135/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 21;317(5845):1732-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt University, VU Station B 351822, Nashville, TN 37235-1822, USA. darryl.bornhop@vanderbilt.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17885132" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Calcineurin/chemistry ; Calcium/chemistry ; Calmodulin/chemistry ; Dimethylpolysiloxanes ; Humans ; Immunoglobulin G/chemistry ; Interferometry/*methods ; Kinetics ; Molecular Sequence Data ; Myosin-Light-Chain Kinase/chemistry ; Peptide Fragments/chemistry ; *Protein Binding ; Rabbits ; Refractometry ; Silicones ; Solutions
    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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  • 6
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    The thymus-adrenal connection: thymosin has corticotropin-releasing activity in primates (1983)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1983-12-23
    Description: Endotoxin-free thymosin fraction 5 elevated corticotropin, beta-endorphin, and cortisol in a dose- and time-dependent fashion when administered intravenously to prepubertal cynomolgus monkeys. Two synthetic component peptides of thymosin fraction 5 had no acute effects on pituitary function, suggesting that some other peptides in thymosin fraction 5 were responsible for its corticotropin-releasing activity. In agreement with these observations, total thymectomy of juvenile macaques was associated with decreases in plasma cortisol, corticotropin, and beta-endorphin. These findings indicate that the prepubertal primate thymus contains corticotropin-releasing activity that may contribute to a physiological immunoregulatory circuit between the developing immunological and pituitary-adrenal systems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Healy, D L -- Hodgen, G D -- Schulte, H M -- Chrousos, G P -- Loriaux, D L -- Hall, N R -- Goldstein, A L -- CA 24974/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1983 Dec 23;222(4630):1353-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6318312" target="_blank"〉PubMed〈/a〉
    Keywords: Adrenocorticotropic Hormone/*blood ; Animals ; Dose-Response Relationship, Drug ; Endorphins/blood ; Female ; Hydrocortisone/blood ; Kinetics ; Macaca fascicularis ; Thymectomy ; Thymosin/analogs & derivatives/*pharmacology ; Thymus Gland/*physiology ; beta-Endorphin
    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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  • 7
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    Matrix-driven translocation of cells and nonliving particles (1985)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1985-05-17
    Description: Cells of metazoan organisms produce and react to complex macromolecular microenvironments known as extracellular matrices. Assembly in vitro of native, compositionally nonuniform collagen-fibronectin matrices caused translocation of certain types of cells or polystyrene-latex beads from regions lacking fibronectin into regions containing it. The translocation process was not due to diffusion, convection, or electrostatic distribution effects, but may depend on nonequilibrium phenomena at the interface of contiguous collagen matrices formed in the presence and absence of fibronectin or particles. Extracellular matrix formation alone was sufficient to drive translocation by a biophysical process that may play a role in cellular migration during embryogenesis, as well as in other types of tissue reorganization such as inflammation, wound healing, and tumor invasion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Newman, S A -- Frenz, D A -- Tomasek, J J -- Rabuzzi, D D -- HD18148/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 1985 May 17;228(4701):885-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/4001925" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cartilage/cytology/embryology ; *Cell Movement/drug effects ; Chick Embryo ; Collagen/*pharmacology ; Diffusion ; Extracellular Matrix/*physiology ; Fibroblasts/cytology ; Fibronectins/*pharmacology ; Humans ; In Vitro Techniques ; Kinetics ; Microspheres ; Movement
    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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  • 8
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    Potassium channels in cardiac cells activated by arachidonic acid and phospholipids (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-06-09
    Description: Two types of potassium-selective channels activated by intracellular arachidonic acid or phosphatidylcholine have been found in neonatal rat atrial cells. In inside-out patches, arachidonic acid and phosphatidylcholine each opened outwardly rectifying potassium-selective channels with conductances of 160 picosiemens (IK.AA) and 68 picosiemens (IK.PC), respectively. These potassium channels were not sensitive to internally applied adenosine triphosphate (ATP), magnesium, or calcium. Lowering the intracellular pH from 7.2 to 6.8 or 6.4 reversibly increased IK.AA channel activity three- or tenfold, respectively. A number of fatty acid derivatives were tested for their ability to activate IK.AA. These potassium-selective channels may help explain the increase in potassium conductance observed in ischemic cells and raise the possibility that fatty acid derivatives act as second messengers.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, D -- Clapham, D E -- HL 34873/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1989 Jun 9;244(4909):1174-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, Mayo Foundation, Rochester, MN 55905.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2727703" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Newborn ; Arachidonic Acids/*pharmacology ; Atrial Function ; Heart/*physiology ; Hydrogen-Ion Concentration ; In Vitro Techniques ; Kinetics ; Membrane Potentials ; Phosphatidylcholines/*pharmacology ; Potassium Channels/drug effects/*physiology ; Rats
    Print ISSN: 0036-8075
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  • 9
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    Catalytic hydrolysis of vasoactive intestinal peptide by human autoantibody (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-06-09
    Description: Vasoactive intestinal peptide (VIP) labeled with 125I, [Tyr10-125I]VIP, can be hydrolyzed by immunoglobulin G (IgG) purified from a human subject, as judged by trichloroacetic acid precipitation and reversed-phase high-performance liquid chromatography (HPLC). The hydrolytic activity was precipitated by antibody to human IgG, it was bound by immobilized protein G and showed a molecular mass close to 150 kilodaltons by gel filtration chromatography, properties similar to those of authentic IgG. The Fab fragment, prepared from IgG by papain treatment, retained the VIP hydrolytic activity of the IgG. Peptide fragments produced by treatment of VIP with the antibody fraction were purified by reversed-phase HPLC and identified by fast atom bombardment-mass spectrometry and peptide sequencing. The scissile bond in VIP deduced from these experiments was Gln16-Met17. The antibody concentration (73.4 fmol per milligram of IgG) and the Kd (0.4 nM) were computed from analysis of VIP binding under conditions that did not result in peptide hydrolysis. Analysis of the antibody-mediated VIP hydrolysis at varying concentrations of substrate suggested conformity with Michaelis-Menton kinetics (Km). The values for Km (37.9 X 10(-9) M) and the turnover number kcat (15.6 min-1) suggested relatively tight VIP binding and a moderate catalytic efficiency of the antibody.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Paul, S -- Volle, D J -- Beach, C M -- Johnson, D R -- Powell, M J -- Massey, R J -- HL 35506/HL/NHLBI NIH HHS/ -- HL 40348/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1989 Jun 9;244(4909):1158-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of Nebraska Medical Center, Omaha 68105.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2727702" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Autoantibodies ; Catalysis ; Chromatography, High Pressure Liquid ; Humans ; Hydrolysis ; Immunoglobulin Fab Fragments ; *Immunoglobulin G ; Kinetics ; Molecular Sequence Data ; Peptide Fragments/isolation & purification ; Vasoactive Intestinal Peptide/*immunology
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  • 10
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    Physical model for the decay and preservation of marine organic carbon (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-06-02
    Description: Degradation of marine organic carbon provides a major source of atmospheric carbon dioxide, whereas preservation in sediments results in accumulation of oxygen. These processes involve the slow decay of chemically recalcitrant compounds and physical protection. To assess the importance of physical protection, we constructed a reaction-diffusion model in which organic matter differs only in its accessibility to microbial degradation but not its intrinsic reactivity. The model predicts that organic matter decays logarithmically with time t and that decay rates decrease approximately as 0.2 x t(-1) until burial. Analyses of sediment-core data are consistent with these predictions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rothman, Daniel H -- Forney, David C -- New York, N.Y. -- Science. 2007 Jun 1;316(5829):1325-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. dhr@mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17540901" target="_blank"〉PubMed〈/a〉
    Keywords: Aluminum Silicates ; Bacteria/*metabolism ; *Biodegradation, Environmental ; *Carbon/metabolism ; Databases, Factual ; Diffusion ; Enzymes/metabolism ; *Geologic Sediments/chemistry/microbiology ; Hydrolysis ; Kinetics ; Mathematics ; *Models, Theoretical ; Oceans and Seas ; *Organic Chemicals/chemistry/metabolism ; Oxygen/analysis ; *Seawater
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