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  • 1
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    Forging future organizational leaders for sustainability science (2019)
    Springer Nature
    Details
    Publication Date: 2019
    Electronic ISSN: 2398-9629
    Topics: Biology
    Published by Springer Nature
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  • 2
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    Tectono‐thermal evolution of the Broadly Rifted Zone, Ethiopian Rift (2019)
    Wiley
    In: Tectonics
    Details
    Publication Date: 2019
    Description: Abstract The Broadly Rifted Zone (BRZ) of southern Ethiopia is a long‐lived and structurally complex segment of the East African Rift System (EARS). However, due to poor surface exposure of early syn‐rift strata and a dearth of subsurface data, the evolution of the BRZ remains poorly understood. We present new apatite (U‐Th‐Sm)/He and augmented apatite fission track low‐temperature thermochronology data from the Beto and Galana basin boundary fault systems to constrain the tectono‐thermal evolution of the western and eastern BRZ, respectively. Time‐temperature reconstructions suggest that EARS‐related extension began concurrently across the BRZ in the early Miocene (20‐17 Ma), at least 6 Myr prior to faulting in the Main Ethiopian Rift further north. Increased time‐temperature resolution provided by multi‐thermochronometer analyses reveals contrasting along‐strike spatiotemporal variations in Beto and Galana margin cooling histories, which appear to mirror the disparate structural geometries of their basin‐bounding normal fault arrays. Longitudinal contrasts in basin architecture and rift‐related cooling histories across the BRZ may reflect the region's heterogeneous distribution of pre‐existing basement fabrics, namely the presence of a previously reported N‐NNE trending Neoproterozoic suture zone beneath the eastern BRZ. Its influence may explain both the development of long, curvilinear faults and the gradual basin‐wards migration of strain exhibited by the easternmost BRZ, absent further west. The anomalous evolution of the BRZ compared to the greater Ethiopian Rift, both in its earlier onset and its wider deformation zone, likely results from its inheritance of pre‐attenuated lithosphere, thermo‐mechanically modified by earlier Cretaceous‐Paleogene Anza‐South Sudan rifting and/or Eocene plume impingement.
    Print ISSN: 0278-7407
    Electronic ISSN: 1944-9194
    Topics: Geosciences
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 3
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    A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-12-18
    Description: Peptide recognition modules mediate many protein-protein interactions critical for the assembly of macromolecular complexes. Complete genome sequences have revealed thousands of these domains, requiring improved methods for identifying their physiologically relevant binding partners. We have developed a strategy combining computational prediction of interactions from phage-display ligand consensus sequences with large-scale two-hybrid physical interaction tests. Application to yeast SH3 domains generated a phage-display network containing 394 interactions among 206 proteins and a two-hybrid network containing 233 interactions among 145 proteins. Graph theoretic analysis identified 59 highly likely interactions common to both networks. Las17 (Bee1), a member of the Wiskott-Aldrich Syndrome protein (WASP) family of actin-assembly proteins, showed multiple SH3 interactions, many of which were confirmed in vivo by coimmunoprecipitation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tong, Amy Hin Yan -- Drees, Becky -- Nardelli, Giuliano -- Bader, Gary D -- Brannetti, Barbara -- Castagnoli, Luisa -- Evangelista, Marie -- Ferracuti, Silvia -- Nelson, Bryce -- Paoluzi, Serena -- Quondam, Michele -- Zucconi, Adriana -- Hogue, Christopher W V -- Fields, Stanley -- Boone, Charles -- Cesareni, Gianni -- P41 RR11823/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2002 Jan 11;295(5553):321-4. Epub 2001 Dec 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Banting and Best Department of Medical Research and Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada M5G 1L6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11743162" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; *Computational Biology ; Consensus Sequence ; *Cytoskeletal Proteins ; Databases, Genetic ; Databases, Protein ; Fungal Proteins/chemistry/metabolism ; Ligands ; Molecular Sequence Data ; Peptide Library ; Peptides/chemistry/metabolism ; Protein Binding ; Protein Structure, Tertiary ; Proteins/*chemistry/*metabolism ; *Proteome ; Saccharomyces cerevisiae/chemistry/genetics ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism ; Software ; Two-Hybrid System Techniques ; Wiskott-Aldrich Syndrome Protein ; src Homology Domains
    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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  • 4
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    Role of formins in actin assembly: nucleation and barbed-end association (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-06-08
    Description: Nucleation of branched actin filaments by the Arp2/3 complex is a conserved process in eukaryotic cells, yet the source of unbranched actin filaments has remained obscure. In yeast, formins stimulate assembly of actin cables independently of Arp2/3. Here, the conserved core of formin homology domains 1 and 2 of Bni1p (Bni1pFH1FH2) was found to nucleate unbranched actin filaments in vitro. Bni1pFH2 provided the minimal region sufficient for nucleation. Unique among actin nucleators, Bni1pFH1FH2 remained associated with the growing barbed ends of filaments. This combination of properties suggests a direct role for formins in regulating nucleation and polarization of unbranched filamentous actin structures.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pruyne, David -- Evangelista, Marie -- Yang, Changsong -- Bi, Erfei -- Zigmond, Sally -- Bretscher, Anthony -- Boone, Charles -- AI19883/AI/NIAID NIH HHS/ -- GH39066/GH/CGH CDC HHS/ -- GM59216/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2002 Jul 26;297(5581):612-5. Epub 2002 Jun 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12052901" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/*metabolism/ultrastructure ; Actins/*metabolism ; Cytochalasin B/pharmacology ; Fungal Proteins/*chemistry/*metabolism ; *Microfilament Proteins ; Microscopy, Electron ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism ; Saccharomyces cerevisiae/*metabolism/ultrastructure ; Saccharomyces cerevisiae Proteins/chemistry/metabolism
    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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  • 5
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    Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-02-05
    Description: Genome-wide transcript profiling was used to monitor signal transduction during yeast pheromone response. Genetic manipulations allowed analysis of changes in gene expression underlying pheromone signaling, cell cycle control, and polarized morphogenesis. A two-dimensional hierarchical clustered matrix, covering 383 of the most highly regulated genes, was constructed from 46 diverse experimental conditions. Diagnostic subsets of coexpressed genes reflected signaling activity, cross talk, and overlap of multiple mitogen-activated protein kinase (MAPK) pathways. Analysis of the profiles specified by two different MAPKs-Fus3p and Kss1p-revealed functional overlap of the filamentous growth and mating responses. Global transcript analysis reflects biological responses associated with the activation and perturbation of signal transduction pathways.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roberts, C J -- Nelson, B -- Marton, M J -- Stoughton, R -- Meyer, M R -- Bennett, H A -- He, Y D -- Dai, H -- Walker, W L -- Hughes, T R -- Tyers, M -- Boone, C -- Friend, S H -- New York, N.Y. -- Science. 2000 Feb 4;287(5454):873-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Rosetta Inpharmatics, 12040 115th Avenue Northeast, Kirkland, WA 98034, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10657304" target="_blank"〉PubMed〈/a〉
    Keywords: *Cell Cycle Proteins ; Cyclin-Dependent Kinase Inhibitor Proteins ; Fungal Proteins/genetics/metabolism/physiology ; G1 Phase ; *Gene Expression Profiling ; *Gene Expression Regulation, Fungal ; Genome, Fungal ; Lipoproteins/pharmacology/physiology ; *MAP Kinase Signaling System ; Mitogen-Activated Protein Kinases/metabolism ; Multigene Family ; Oligonucleotide Array Sequence Analysis ; Peptides/pharmacology/physiology ; Pheromones ; Protein Kinase C/metabolism ; *Repressor Proteins ; Saccharomyces cerevisiae/cytology/*genetics/growth & development/physiology ; *Saccharomyces cerevisiae Proteins ; Transcription Factors/metabolism ; Transcriptional Activation
    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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  • 6
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    Systematic genetic analysis with ordered arrays of yeast deletion mutants (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-12-18
    Description: In Saccharomyces cerevisiae, more than 80% of the approximately 6200 predicted genes are nonessential, implying that the genome is buffered from the phenotypic consequences of genetic perturbation. To evaluate function, we developed a method for systematic construction of double mutants, termed synthetic genetic array (SGA) analysis, in which a query mutation is crossed to an array of approximately 4700 deletion mutants. Inviable double-mutant meiotic progeny identify functional relationships between genes. SGA analysis of genes with roles in cytoskeletal organization (BNI1, ARP2, ARC40, BIM1), DNA synthesis and repair (SGS1, RAD27), or uncharacterized functions (BBC1, NBP2) generated a network of 291 interactions among 204 genes. Systematic application of this approach should produce a global map of gene function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tong, A H -- Evangelista, M -- Parsons, A B -- Xu, H -- Bader, G D -- Page, N -- Robinson, M -- Raghibizadeh, S -- Hogue, C W -- Bussey, H -- Andrews, B -- Tyers, M -- Boone, C -- New York, N.Y. -- Science. 2001 Dec 14;294(5550):2364-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Banting and Best Department of Medical Research, University of Toronto, Toronto ON, Canada M5G 1L6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11743205" target="_blank"〉PubMed〈/a〉
    Keywords: Carrier Proteins/genetics/physiology ; Cell Cycle Proteins/genetics/physiology ; Cell Polarity ; Computational Biology ; Crosses, Genetic ; *Cytoskeletal Proteins ; Cytoskeleton/physiology ; DNA Helicases/genetics/physiology ; DNA Repair ; DNA, Fungal/biosynthesis ; Databases, Genetic ; Endodeoxyribonucleases/genetics/physiology ; Flap Endonucleases ; Fungal Proteins/genetics/physiology ; *Gene Deletion ; Genes, Essential ; Genes, Fungal/*physiology ; Genetic Markers ; *Genetic Techniques ; Genome, Fungal ; *Microfilament Proteins ; Microtubule Proteins/genetics/physiology ; Mitosis ; RecQ Helicases ; Recombination, Genetic ; Robotics ; Saccharomyces cerevisiae/*genetics/growth & development/*physiology ; Saccharomyces cerevisiae Proteins/genetics/physiology
    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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  • 7
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    Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-01-16
    Description: Ubiquitin-like proteins (UBLs) can change protein function, localization or turnover by covalent attachment to lysine residues. Although UBLs achieve this conjugation through an intricate enzymatic cascade, their bacterial counterparts MoaD and ThiS function as sulphur carrier proteins. Here we show that Urm1p, the most ancient UBL, acts as a sulphur carrier in the process of eukaryotic transfer RNA (tRNA) modification, providing a possible evolutionary link between UBL and sulphur transfer. Moreover, we identify Uba4p, Ncs2p, Ncs6p and Yor251cp as components of this conserved pathway. Using in vitro assays, we show that Ncs6p binds to tRNA, whereas Uba4p first adenylates and then directly transfers sulphur onto Urm1p. Finally, functional analysis reveals that the thiolation function of Urm1p is critical to regulate cellular responses to nutrient starvation and oxidative stress conditions, most likely by increasing translation fidelity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Leidel, Sebastian -- Pedrioli, Patrick G A -- Bucher, Tamara -- Brost, Renee -- Costanzo, Michael -- Schmidt, Alexander -- Aebersold, Ruedi -- Boone, Charles -- Hofmann, Kay -- Peter, Matthias -- England -- Nature. 2009 Mar 12;458(7235):228-32. doi: 10.1038/nature07643. Epub 2009 Jan 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Biochemistry, ETH Zurich, Schafmattstrasse 18, CH-8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19145231" target="_blank"〉PubMed〈/a〉
    Keywords: Eukaryotic Cells/*metabolism ; RNA, Transfer/*metabolism ; Saccharomyces cerevisiae/metabolism/*physiology ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Sulfur/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 8
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    The genetic landscape of a cell (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-01-23
    Description: A genome-scale genetic interaction map was constructed by examining 5.4 million gene-gene pairs for synthetic genetic interactions, generating quantitative genetic interaction profiles for approximately 75% of all genes in the budding yeast, Saccharomyces cerevisiae. A network based on genetic interaction profiles reveals a functional map of the cell in which genes of similar biological processes cluster together in coherent subsets, and highly correlated profiles delineate specific pathways to define gene function. The global network identifies functional cross-connections between all bioprocesses, mapping a cellular wiring diagram of pleiotropy. Genetic interaction degree correlated with a number of different gene attributes, which may be informative about genetic network hubs in other organisms. We also demonstrate that extensive and unbiased mapping of the genetic landscape provides a key for interpretation of chemical-genetic interactions and drug target identification.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Costanzo, Michael -- Baryshnikova, Anastasia -- Bellay, Jeremy -- Kim, Yungil -- Spear, Eric D -- Sevier, Carolyn S -- Ding, Huiming -- Koh, Judice L Y -- Toufighi, Kiana -- Mostafavi, Sara -- Prinz, Jeany -- St Onge, Robert P -- VanderSluis, Benjamin -- Makhnevych, Taras -- Vizeacoumar, Franco J -- Alizadeh, Solmaz -- Bahr, Sondra -- Brost, Renee L -- Chen, Yiqun -- Cokol, Murat -- Deshpande, Raamesh -- Li, Zhijian -- Lin, Zhen-Yuan -- Liang, Wendy -- Marback, Michaela -- Paw, Jadine -- San Luis, Bryan-Joseph -- Shuteriqi, Ermira -- Tong, Amy Hin Yan -- van Dyk, Nydia -- Wallace, Iain M -- Whitney, Joseph A -- Weirauch, Matthew T -- Zhong, Guoqing -- Zhu, Hongwei -- Houry, Walid A -- Brudno, Michael -- Ragibizadeh, Sasan -- Papp, Balazs -- Pal, Csaba -- Roth, Frederick P -- Giaever, Guri -- Nislow, Corey -- Troyanskaya, Olga G -- Bussey, Howard -- Bader, Gary D -- Gingras, Anne-Claude -- Morris, Quaid D -- Kim, Philip M -- Kaiser, Chris A -- Myers, Chad L -- Andrews, Brenda J -- Boone, Charles -- 084314/Wellcome Trust/United Kingdom -- GSP-41567/Canadian Institutes of Health Research/Canada -- R01 HG003224/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2010 Jan 22;327(5964):425-31. doi: 10.1126/science.1180823.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20093466" target="_blank"〉PubMed〈/a〉
    Keywords: Computational Biology ; Gene Duplication ; Gene Expression Regulation, Fungal ; *Gene Regulatory Networks ; Genes, Fungal ; Genetic Fitness ; *Genome, Fungal ; Metabolic Networks and Pathways ; Mutation ; Protein Interaction Mapping ; Saccharomyces cerevisiae/*genetics/*metabolism/physiology ; Saccharomyces cerevisiae Proteins/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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  • 9
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    Genotype to phenotype: a complex problem (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-04-24
    Description: We generated a high-resolution whole-genome sequence and individually deleted 5100 genes in Sigma1278b, a Saccharomyces cerevisiae strain closely related to reference strain S288c. Similar to the variation between human individuals, Sigma1278b and S288c average 3.2 single-nucleotide polymorphisms per kilobase. A genome-wide comparison of deletion mutant phenotypes identified a subset of genes that were conditionally essential by strain, including 44 essential genes unique to Sigma1278b and 13 unique to S288c. Genetic analysis indicates the conditional phenotype was most often governed by complex genetic interactions, depending on multiple background-specific modifiers. Our comprehensive analysis suggests that the presence of a complex set of modifiers will often underlie the phenotypic differences between individuals.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4412269/" 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/PMC4412269/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dowell, Robin D -- Ryan, Owen -- Jansen, An -- Cheung, Doris -- Agarwala, Sudeep -- Danford, Timothy -- Bernstein, Douglas A -- Rolfe, P Alexander -- Heisler, Lawrence E -- Chin, Brian -- Nislow, Corey -- Giaever, Guri -- Phillips, Patrick C -- Fink, Gerald R -- Gifford, David K -- Boone, Charles -- DK076284/DK/NIDDK NIH HHS/ -- GM035010/GM/NIGMS NIH HHS/ -- GM069676/GM/NIGMS NIH HHS/ -- P01 NS055923/NS/NINDS NIH HHS/ -- R01 GM035010/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Apr 23;328(5977):469. doi: 10.1126/science.1189015.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Computer Science and Artificial Intelligence Laboratory, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20413493" target="_blank"〉PubMed〈/a〉
    Keywords: Crosses, Genetic ; Gene Deletion ; *Gene Expression Regulation, Fungal ; Gene Regulatory Networks ; *Genes, Essential ; *Genes, Fungal ; Genetic Variation ; Genome, Fungal ; Genotype ; Mutation ; Phenotype ; Saccharomyces cerevisiae/*genetics ; Sequence Analysis, DNA
    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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  • 10
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    Asian monsoon transport of pollution to the stratosphere (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-03-27
    Description: Transport of air from the troposphere to the stratosphere occurs primarily in the tropics, associated with the ascending branch of the Brewer-Dobson circulation. Here, we identify the transport of air masses from the surface, through the Asian monsoon, and deep into the stratosphere, using satellite observations of hydrogen cyanide (HCN), a tropospheric pollutant produced in biomass burning. A key factor in this identification is that HCN has a strong sink from contact with the ocean; much of the air in the tropical upper troposphere is relatively depleted in HCN, and hence, broad tropical upwelling cannot be the main source for the stratosphere. The monsoon circulation provides an effective pathway for pollution from Asia, India, and Indonesia to enter the global stratosphere.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Randel, William J -- Park, Mijeong -- Emmons, Louisa -- Kinnison, Doug -- Bernath, Peter -- Walker, Kaley A -- Boone, Chris -- Pumphrey, Hugh -- New York, N.Y. -- Science. 2010 Apr 30;328(5978):611-3. doi: 10.1126/science.1182274. Epub 2010 Mar 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Center for Atmospheric Research, Boulder, CO, USA. randel@ucar.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20339030" 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
    Published by American Association for the Advancement of Science (AAAS)
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