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  • 1
    Publication Date: 2011-06-01
    Description: Young poorly crystalline graphite in the 〉3.8-Gyr-old Nuvvuagittuq banded iron formation Nature Geoscience 4, 376 (2011). doi:10.1038/ngeo1155 Authors: D. Papineau, B. T. De Gregorio, G. D. Cody, J. O’Neil, A. Steele, R. M. Stroud & M. L. Fogel Carbonaceous material present in ancient rocks can be used as an indicator of life during the time the rocks were formed. In particular, evidence for the existence of life more than 3,800 million years ago might come from mineral associations between apatite and graphite in rocks from southern West Greenland. However, this interpretation is partly based on the assumption that the graphite was formed at the same time as the host rocks, an assumption that has been difficult to prove. Here we investigate the origins of poorly crystalline graphite associated with apatite in metamorphosed banded iron formations from northern Canada that are 3,750 to 4,280 million years old. We measured average δ13Cgraphite values of −22.8±1.9‰ (1σ), similar to values from West Greenland sedimentary rocks of comparable age, and that point to a biological source for this carbon. Our microscopic and spectroscopic analyses suggest, however, that the graphite experienced much lower temperatures than the host rocks during metamorphism. We conclude that the poorly crystalline graphite in these rocks was deposited by fluids after peak metamorphism of the banded iron formations. We suggest that the occurrence of carbonaceous material with low δ13C values in Eoarchaean rocks cannot be used to indicate the presence of a microbial biosphere on the earliest Earth unless the syngeneity of the carbonaceous material in the host rock can be confirmed.
    Print ISSN: 1752-0894
    Electronic ISSN: 1752-0908
    Topics: Geosciences
    Published by Springer Nature
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  • 2
    Publication Date: 1999-04-24
    Description: Low-density nanoscale mesoporous composites may be readily synthesized by adding a colloidal or dispersed solid to an about-to-gel silica sol. The silica sol can "glue" a range of chemically and physically diverse particles into the three-dimensional silica network formed upon gelation. If the composite gel is supercritically dried so as to maintain the high porosity of the wet gel, a composite aerogel is formed in which the nanoscopic surface and bulk properties of each component are retained in the solid composite. The volume fraction of the second solid can be varied above or below a percolation threshold to tune the transport properties of the composite aerogel and thereby design nanoscale materials for chemical, electronic, and optical applications.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Morris -- Anderson -- Stroud -- Merzbacher -- Rolison -- New York, N.Y. -- Science. 1999 Apr 23;284(5414):622-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Surface Chemistry (Code 6170), Surface Modification (Code 6370), and Optical Techniques (Code 5670) Branches, Naval Research Laboratory (NRL), Washington, DC 20375, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10213681" target="_blank"〉PubMed〈/a〉
    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
    Publication Date: 2000-10-20
    Description: Membrane channel proteins of the aquaporin family are highly selective for permeation of specific small molecules, with absolute exclusion of ions and charged solutes and without dissipation of the electrochemical potential across the cell membrane. We report the crystal structure of the Escherichia coli glycerol facilitator (GlpF) with its primary permeant substrate glycerol at 2.2 angstrom resolution. Glycerol molecules line up in an amphipathic channel in single file. In the narrow selectivity filter of the channel the glycerol alkyl backbone is wedged against a hydrophobic corner, and successive hydroxyl groups form hydrogen bonds with a pair of acceptor, and donor atoms. Two conserved aspartic acid-proline-alanine motifs form a key interface between two gene-duplicated segments that each encode three-and-one-half membrane-spanning helices around the channel. This structure elucidates the mechanism of selective permeability for linear carbohydrates and suggests how ions and water are excluded.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fu, D -- Libson, A -- Miercke, L J -- Weitzman, C -- Nollert, P -- Krucinski, J -- Stroud, R M -- GM24485/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Oct 20;290(5491):481-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, School of Medicine, University of California, San Francisco, CA 94143-0448, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11039922" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Aquaporins/chemistry/metabolism ; *Bacterial Outer Membrane Proteins/*chemistry/metabolism ; Cell Membrane Permeability ; Conserved Sequence ; Crystallography, X-Ray ; Escherichia coli/*chemistry ; *Escherichia coli Proteins ; Glycerol/chemistry/*metabolism ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Proteolipids/metabolism ; Stereoisomerism ; Sugar Alcohols/metabolism ; Water/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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  • 4
    Publication Date: 2002-04-20
    Description: Aquaporins are transmembrane channels found in cell membranes of all life forms. We examine their apparently paradoxical property, facilitation of efficient permeation of water while excluding protons, which is of critical importance to preserving the electrochemical potential across the cell membrane. We have determined the structure of the Escherichia coli aquaglyceroporin GlpF with bound water, in native (2.7 angstroms) and in W48F/F200T mutant (2.1 angstroms) forms, and carried out 12-nanosecond molecular dynamics simulations that define the spatial and temporal probability distribution and orientation of a single file of seven to nine water molecules inside the channel. Two conserved asparagines force a central water molecule to serve strictly as a hydrogen bond donor to its neighboring water molecules. Assisted by the electrostatic potential generated by two half-membrane spanning loops, this dictates opposite orientations of water molecules in the two halves of the channel, and thus prevents the formation of a "proton wire," while permitting rapid water diffusion. Both simulations and observations revealed a more regular distribution of channel water and an increased water permeability for the W48F/F200T mutant.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tajkhorshid, Emad -- Nollert, Peter -- Jensen, Morten O -- Miercke, Larry J W -- O'Connell, Joseph -- Stroud, Robert M -- Schulten, Klaus -- New York, N.Y. -- Science. 2002 Apr 19;296(5567):525-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Theoretical Biophysics Group, Beckman Institute, University of Illinois at Urbana-Champaign, 405 North Mathews, Urbana, IL 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11964478" target="_blank"〉PubMed〈/a〉
    Keywords: Aquaporins/*chemistry/genetics/metabolism ; Asparagine/chemistry ; Chemistry, Physical ; Computer Simulation ; Crystallography, X-Ray ; Diffusion ; Electrochemistry ; Escherichia coli ; Escherichia coli Proteins/*chemistry/genetics/metabolism ; Glycerol/metabolism ; Hydrogen Bonding ; Models, Molecular ; Mutation ; Physicochemical Phenomena ; Protein Conformation ; Protein Structure, Secondary ; Protons ; Static Electricity ; Water/chemistry/*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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  • 5
    Publication Date: 2008-12-17
    Description: Aberrant folding of proteins in the endoplasmic reticulum activates the bifunctional transmembrane kinase/endoribonuclease Ire1. Ire1 excises an intron from HAC1 messenger RNA in yeasts and Xbp1 messenger RNA in metozoans encoding homologous transcription factors. This non-conventional mRNA splicing event initiates the unfolded protein response, a transcriptional program that relieves the endoplasmic reticulum stress. Here we show that oligomerization is central to Ire1 function and is an intrinsic attribute of its cytosolic domains. We obtained the 3.2-A crystal structure of the oligomer of the Ire1 cytosolic domains in complex with a kinase inhibitor that acts as a potent activator of the Ire1 RNase. The structure reveals a rod-shaped assembly that has no known precedence among kinases. This assembly positions the kinase domain for trans-autophosphorylation, orders the RNase domain, and creates an interaction surface for binding of the mRNA substrate. Activation of Ire1 through oligomerization expands the mechanistic repertoire of kinase-based signalling receptors.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2846394/" 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/PMC2846394/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Korennykh, Alexei V -- Egea, Pascal F -- Korostelev, Andrei A -- Finer-Moore, Janet -- Zhang, Chao -- Shokat, Kevan M -- Stroud, Robert M -- Walter, Peter -- R01 GM060641/GM/NIGMS NIH HHS/ -- R01 GM060641-01/GM/NIGMS NIH HHS/ -- R01 GM60641/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Feb 5;457(7230):687-93. doi: 10.1038/nature07661. Epub 2008 Dec 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA. alexei.korennykh@ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19079236" target="_blank"〉PubMed〈/a〉
    Keywords: Basic-Leucine Zipper Transcription Factors/genetics ; Binding Sites ; Crystallography, X-Ray ; Cytosol/metabolism ; Enzyme Activation/drug effects ; Introns/genetics ; Membrane Glycoproteins/antagonists & inhibitors/*chemistry/*metabolism ; Models, Molecular ; Phosphorylation/drug effects ; Protein Binding/drug effects ; Protein Denaturation ; *Protein Folding ; Protein Kinase Inhibitors/chemistry/metabolism/pharmacology ; Protein Multimerization ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/antagonists & inhibitors/*chemistry/*metabolism ; Repressor Proteins/genetics ; Ribonucleases/chemistry/metabolism ; Saccharomyces cerevisiae/*chemistry/*enzymology ; Saccharomyces cerevisiae Proteins/antagonists & ; inhibitors/*chemistry/genetics/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2014-11-05
    Description: ATP-binding cassette (ABC) transporters translocate substrates across cell membranes, using energy harnessed from ATP binding and hydrolysis at their nucleotide-binding domains. ABC exporters are present both in prokaryotes and eukaryotes, with examples implicated in multidrug resistance of pathogens and cancer cells, as well as in many human diseases. TmrAB is a heterodimeric ABC exporter from the thermophilic Gram-negative eubacterium Thermus thermophilus; it is homologous to various multidrug transporters and contains one degenerate site with a non-catalytic residue next to the Walker B motif. Here we report a subnanometre-resolution structure of detergent-solubilized TmrAB in a nucleotide-free, inward-facing conformation by single-particle electron cryomicroscopy. The reconstructions clearly resolve characteristic features of ABC transporters, including helices in the transmembrane domain and nucleotide-binding domains. A cavity in the transmembrane domain is accessible laterally from the cytoplasmic side of the membrane as well as from the cytoplasm, indicating that the transporter lies in an inward-facing open conformation. The two nucleotide-binding domains remain in contact via their carboxy-terminal helices. Furthermore, comparison between our structure and the crystal structures of other ABC transporters suggests a possible trajectory of conformational changes that involves a sliding and rotating motion between the two nucleotide-binding domains during the transition from the inward-facing to outward-facing conformations.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4372080/" 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/PMC4372080/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, JungMin -- Wu, Shenping -- Tomasiak, Thomas M -- Mergel, Claudia -- Winter, Michael B -- Stiller, Sebastian B -- Robles-Colmanares, Yaneth -- Stroud, Robert M -- Tampe, Robert -- Craik, Charles S -- Cheng, Yifan -- 1P41CA196276-01/CA/NCI NIH HHS/ -- P41 CA196276/CA/NCI NIH HHS/ -- P50 GM073210/GM/NIGMS NIH HHS/ -- P50 GM082250/GM/NIGMS NIH HHS/ -- P50GM073210/GM/NIGMS NIH HHS/ -- P50GM082250/GM/NIGMS NIH HHS/ -- R01 GM024485/GM/NIGMS NIH HHS/ -- R01 GM098672/GM/NIGMS NIH HHS/ -- R01GM098672/GM/NIGMS NIH HHS/ -- R37 GM024485/GM/NIGMS NIH HHS/ -- R37GM024485/GM/NIGMS NIH HHS/ -- S10 RR026814/RR/NCRR NIH HHS/ -- S10RR026814/RR/NCRR NIH HHS/ -- England -- Nature. 2015 Jan 15;517(7534):396-400. doi: 10.1038/nature13872. Epub 2014 Nov 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, San Francisco, California 94158, USA. ; Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, California 94158, USA. ; Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany. ; 1] Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, San Francisco, California 94158, USA [2] Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, California 94158, USA. ; 1] Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany [2] Cluster of Excellence - Macromolecular Complexes, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25363761" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*chemistry/immunology/*ultrastructure ; Antigens/chemistry/immunology ; Binding Sites ; *Cryoelectron Microscopy ; Crystallography, X-Ray ; Models, Molecular ; Nucleotides/metabolism ; Protein Multimerization ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Rotation ; Thermus thermophilus/*chemistry
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 1990-08-31
    Description: The isocitrate dehydrogenase of Escherichia coli is an example of a ubiquitous class of enzymes that are regulated by covalent modification. In the three-dimensional structure of the enzyme-substrate complex, isocitrate forms a hydrogen bond with Ser113, the site of regulatory phosphorylation. The structures of Asp113 and Glu113 mutants, which mimic the inactivation of the enzyme by phosphorylation, show minimal conformational changes from wild type, as in the phosphorylated enzyme. Calculations based on observed structures suggest that the change in electrostatic potential when a negative charge is introduced either by phosporylation or site-directed mutagenesis is sufficient to inactivate the enzyme. Thus, direct interaction at a ligand binding site is an alternative mechanism to induced conformational changes from an allosteric site in the regulation of protein activity by phosphorylation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hurley, J H -- Dean, A M -- Sohl, J L -- Koshland, D E Jr -- Stroud, R M -- GM 24485/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 Aug 31;249(4972):1012-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2204109" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Escherichia coli/*enzymology/genetics ; Homeostasis ; Isocitrate Dehydrogenase/genetics/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Phosphorylation ; Protein Conformation
    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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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1991-08-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stroud, R M -- New York, N.Y. -- Science. 1991 Aug 9;253(5020):685-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17772373" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
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  • 9
    Publication Date: 2006-12-16
    Description: We measured the elemental compositions of material from 23 particles in aerogel and from residue in seven craters in aluminum foil that was collected during passage of the Stardust spacecraft through the coma of comet 81P/Wild 2. These particles are chemically heterogeneous at the largest size scale analyzed ( approximately 180 ng). The mean elemental composition of this Wild 2 material is consistent with the CI meteorite composition, which is thought to represent the bulk composition of the solar system, for the elements Mg, Si, Mn, Fe, and Ni to 35%, and for Ca and Ti to 60%. The elements Cu, Zn, and Ga appear enriched in this Wild 2 material, which suggests that the CI meteorites may not represent the solar system composition for these moderately volatile minor elements.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Flynn, George J -- Bleuet, Pierre -- Borg, Janet -- Bradley, John P -- Brenker, Frank E -- Brennan, Sean -- Bridges, John -- Brownlee, Don E -- Bullock, Emma S -- Burghammer, Manfred -- Clark, Benton C -- Dai, Zu Rong -- Daghlian, Charles P -- Djouadi, Zahia -- Fakra, Sirine -- Ferroir, Tristan -- Floss, Christine -- Franchi, Ian A -- Gainsforth, Zack -- Gallien, Jean-Paul -- Gillet, Philippe -- Grant, Patrick G -- Graham, Giles A -- Green, Simon F -- Grossemy, Faustine -- Heck, Philipp R -- Herzog, Gregory F -- Hoppe, Peter -- Horz, Friedrich -- Huth, Joachim -- Ignatyev, Konstantin -- Ishii, Hope A -- Janssens, Koen -- Joswiak, David -- Kearsley, Anton T -- Khodja, Hicham -- Lanzirotti, Antonio -- Leitner, Jan -- Lemelle, Laurence -- Leroux, Hugues -- Luening, Katharina -- Macpherson, Glenn J -- Marhas, Kuljeet K -- Marcus, Matthew A -- Matrajt, Graciela -- Nakamura, Tomoki -- Nakamura-Messenger, Keiko -- Nakano, Tsukasa -- Newville, Matthew -- Papanastassiou, Dimitri A -- Pianetta, Piero -- Rao, William -- Riekel, Christian -- Rietmeijer, Frans J M -- Rost, Detlef -- Schwandt, Craig S -- See, Thomas H -- Sheffield-Parker, Julie -- Simionovici, Alexandre -- Sitnitsky, Ilona -- Snead, Christopher J -- Stadermann, Frank J -- Stephan, Thomas -- Stroud, Rhonda M -- Susini, Jean -- Suzuki, Yoshio -- Sutton, Stephen R -- Taylor, Susan -- Teslich, Nick -- Troadec, D -- Tsou, Peter -- Tsuchiyama, Akira -- Uesugi, Kentaro -- Vekemans, Bart -- Vicenzi, Edward P -- Vincze, Laszlo -- Westphal, Andrew J -- Wozniakiewicz, Penelope -- Zinner, Ernst -- Zolensky, Michael E -- New York, N.Y. -- Science. 2006 Dec 15;314(5806):1731-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, State University of New York at Plattsburgh, 101 Broad Street, Plattsburgh, NY 12901, USA. george.flynn@plattsburgh.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17170294" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
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  • 10
    Publication Date: 2011-06-11
    Description: The complex suite of organic materials in carbonaceous chondrite meteorites probably originally formed in the interstellar medium and/or the solar protoplanetary disk, but was subsequently modified in the meteorites' asteroidal parent bodies. The mechanisms of formation and modification are still very poorly understood. We carried out a systematic study of variations in the mineralogy, petrology, and soluble and insoluble organic matter in distinct fragments of the Tagish Lake meteorite. The variations correlate with indicators of parent body aqueous alteration. At least some molecules of prebiotic importance formed during the alteration.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Herd, Christopher D K -- Blinova, Alexandra -- Simkus, Danielle N -- Huang, Yongsong -- Tarozo, Rafael -- Alexander, Conel M O'D -- Gyngard, Frank -- Nittler, Larry R -- Cody, George D -- Fogel, Marilyn L -- Kebukawa, Yoko -- Kilcoyne, A L David -- Hilts, Robert W -- Slater, Greg F -- Glavin, Daniel P -- Dworkin, Jason P -- Callahan, Michael P -- Elsila, Jamie E -- De Gregorio, Bradley T -- Stroud, Rhonda M -- New York, N.Y. -- Science. 2011 Jun 10;332(6035):1304-7. doi: 10.1126/science.1203290.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta T6G 2E3, Canada. herd@ualberta.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21659601" target="_blank"〉PubMed〈/a〉
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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