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  • 1
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    Transport and chemistry of formaldehyde by mesoscale convective systems in West Africa during AMMA 2006 (2012)
    Wiley
    Details
    Publication Date: 2012-06-16
    Description: In situ measurements of formaldehyde (CH2O) onboard four European research aircraft in August 2006 as part of the African Monsoon Multidisciplinary Analysis (AMMA) experiment in West Africa are used (1) to examine the redistribution of CH2O by mesoscale convective systems (MCS) in the tropical upper troposphere (UT), (2) to evaluate the scavenging efficiency (SE) of CH2O by MCS and (3) to quantify the impact of CH2O on UT photooxidant production downwind of MCS. The intercomparison of CH2O measurements is first tested, providing a unique and consistent 3-D-spatially resolved CH2O database in background and convective conditions. While carbon monoxide (CO) is vertically uplifted by deep convection up to 12 km, CH2O is also affected by cloud processing as seen from its ratio relative to CO with altitude. A new observation-based model is established to quantify the SE of CH2O. This model shows that convective entrainment of free tropospheric air cannot be neglected since it contributes to 40% of the convective UT air. For the 4 studied MCS, SE shows a large variability within a 4% to 39% range at a relative standard deviation of 30%, which is consistent with MCS features. A time-dependent photochemical box model is applied to convective UT air. After convection, 60% of CH2O is due to its photochemical production rather than to its direct transport. Model results indicate that CH2O directly injected by convection does not impact ozone and HOx production in the tropical UT of West Africa. NOx and anthropogenic hydrocarbon precursors dominate the secondary production of CH2O, ozone and HOx.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 2
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    The glyoxal budget and its contribution to organic aerosol for Los Angeles, California, during CalNex 2010 (2011)
    Wiley
    Details
    Publication Date: 2011-10-28
    Description: Recent laboratory and field studies have indicated that glyoxal is a potentially large contributor to secondary organic aerosol mass. We present in situ glyoxal measurements acquired with a recently developed, high sensitivity spectroscopic instrument during the CalNex 2010 field campaign in Pasadena, California. We use three methods to quantify the production and loss of glyoxal in Los Angeles and its contribution to organic aerosol. First, we calculate the difference between steady state sources and sinks of glyoxal at the Pasadena site, assuming that the remainder is available for aerosol uptake. Second, we use the Master Chemical Mechanism to construct a two-dimensional model for gas-phase glyoxal chemistry in Los Angeles, assuming that the difference between the modeled and measured glyoxal concentration is available for aerosol uptake. Third, we examine the nighttime loss of glyoxal in the absence of its photochemical sources and sinks. Using these methods we constrain the glyoxal loss to aerosol to be 0–5 × 10−5 s−1 during clear days and (1 ± 0.3) × 10−5 s−1 at night. Between 07:00–15:00 local time, the diurnally averaged secondary organic aerosol mass increases from 3.2 μg m−3 to a maximum of 8.8 μg m−3. The constraints on the glyoxal budget from this analysis indicate that it contributes 0–0.2 μg m−3 or 0–4% of the secondary organic aerosol mass.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 3
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    City lights and urban air (2011)
    Springer Nature
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    Publication Date: 2011-11-01
    Description: City lights and urban air Nature Geoscience 4, 730 (2011). doi:10.1038/ngeo1300 Authors: H. Stark, S. S. Brown, K. W. Wong, J. Stutz, C. D. Elvidge, I. B. Pollack, T. B. Ryerson, W. P. Dube, N. L. Wagner & D. D. Parrish
    Print ISSN: 1752-0894
    Electronic ISSN: 1752-0908
    Topics: Geosciences
    Published by Springer Nature
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  • 4
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    Atmospheric emissions from the Deepwater Horizon spill constrain air-water partitioning, hydrocarbon fate, and leak rate (2011)
    Wiley
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    Publication Date: 2011-04-14
    Description: The fate of deepwater releases of gas and oil mixtures is initially determined by solubility and volatility of individual hydrocarbon species; these attributes determine partitioning between air and water. Quantifying this partitioning is necessary to constrain simulations of gas and oil transport, to predict marine bioavailability of different fractions of the gas-oil mixture, and to develop a comprehensive picture of the fate of leaked hydrocarbons in the marine environment. Analysis of airborne atmospheric data shows massive amounts (∼258,000 kg/day) of hydrocarbons evaporating promptly from the Deepwater Horizon spill; these data collected during two research flights constrain air-water partitioning, thus bioavailability and fate, of the leaked fluid. This analysis quantifies the fraction of surfacing hydrocarbons that dissolves in the water column (∼33% by mass), the fraction that does not dissolve, and the fraction that evaporates promptly after surfacing (∼14% by mass). We do not quantify the leaked fraction lacking a surface expression; therefore, calculation of atmospheric mass fluxes provides a lower limit to the total hydrocarbon leak rate of 32,600 to 47,700 barrels of fluid per day, depending on reservoir fluid composition information. This study demonstrates a new approach for rapid-response airborne assessment of future oil spills.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 5
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    Gasoline emissions dominate over diesel in formation of secondary organic aerosol mass (2012)
    Wiley
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    Publication Date: 2012-03-20
    Description: Although laboratory experiments have shown that organic compounds in both gasoline fuel and diesel engine exhaust can form secondary organic aerosol (SOA), the fractional contribution from gasoline and diesel exhaust emissions to ambient SOA in urban environments is poorly known. Here we use airborne and ground-based measurements of organic aerosol (OA) in the Los Angeles (LA) Basin, California made during May and June 2010 to assess the amount of SOA formed from diesel emissions. Diesel emissions in the LA Basin vary between weekdays and weekends, with 54% lower diesel emissions on weekends. Despite this difference in source contributions, in air masses with similar degrees of photochemical processing, formation of OA is the same on weekends and weekdays, within the measurement uncertainties. This result indicates that the contribution from diesel emissions to SOA formation is zero within our uncertainties. Therefore, substantial reductions of SOA mass on local to global scales will be achieved by reducing gasoline vehicle emissions.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 6
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    Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-07-16
    Description: The translocation step of protein synthesis entails large-scale rearrangements of the ribosome-transfer RNA (tRNA) complex. Here we have followed tRNA movement through the ribosome during translocation by time-resolved single-particle electron cryomicroscopy (cryo-EM). Unbiased computational sorting of cryo-EM images yielded 50 distinct three-dimensional reconstructions, showing the tRNAs in classical, hybrid and various novel intermediate states that provide trajectories and kinetic information about tRNA movement through the ribosome. The structures indicate how tRNA movement is coupled with global and local conformational changes of the ribosome, in particular of the head and body of the small ribosomal subunit, and show that dynamic interactions between tRNAs and ribosomal residues confine the path of the tRNAs through the ribosome. The temperature dependence of ribosome dynamics reveals a surprisingly flat energy landscape of conformational variations at physiological temperature. The ribosome functions as a Brownian machine that couples spontaneous conformational changes driven by thermal energy to directed movement.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fischer, Niels -- Konevega, Andrey L -- Wintermeyer, Wolfgang -- Rodnina, Marina V -- Stark, Holger -- England -- Nature. 2010 Jul 15;466(7304):329-33. doi: 10.1038/nature09206.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉3D Electron Cryomicroscopy Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20631791" target="_blank"〉PubMed〈/a〉
    Keywords: Cryoelectron Microscopy ; Escherichia coli ; Kinetics ; Models, Molecular ; Molecular Conformation ; *Movement ; *Protein Biosynthesis ; RNA, Transfer/genetics/*metabolism ; Ribosome Subunits, Large, Bacterial/chemistry/metabolism ; Ribosome Subunits, Small, Bacterial/chemistry/metabolism ; Ribosomes/chemistry/*metabolism ; Temperature ; Thermodynamics ; Time Factors
    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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  • 7
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    Self-assembly of a nanoscale DNA box with a controllable lid (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-05-09
    Description: The unique structural motifs and self-recognition properties of DNA can be exploited to generate self-assembling DNA nanostructures of specific shapes using a 'bottom-up' approach. Several assembly strategies have been developed for building complex three-dimensional (3D) DNA nanostructures. Recently, the DNA 'origami' method was used to build two-dimensional addressable DNA structures of arbitrary shape that can be used as platforms to arrange nanomaterials with high precision and specificity. A long-term goal of this field has been to construct fully addressable 3D DNA nanostructures. Here we extend the DNA origami method into three dimensions by creating an addressable DNA box 42 x 36 x 36 nm(3) in size that can be opened in the presence of externally supplied DNA 'keys'. We thoroughly characterize the structure of this DNA box using cryogenic transmission electron microscopy, small-angle X-ray scattering and atomic force microscopy, and use fluorescence resonance energy transfer to optically monitor the opening of the lid. Controlled access to the interior compartment of this DNA nanocontainer could yield several interesting applications, for example as a logic sensor for multiple-sequence signals or for the controlled release of nanocargos.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Andersen, Ebbe S -- Dong, Mingdong -- Nielsen, Morten M -- Jahn, Kasper -- Subramani, Ramesh -- Mamdouh, Wael -- Golas, Monika M -- Sander, Bjoern -- Stark, Holger -- Oliveira, Cristiano L P -- Pedersen, Jan Skov -- Birkedal, Victoria -- Besenbacher, Flemming -- Gothelf, Kurt V -- Kjems, Jorgen -- England -- Nature. 2009 May 7;459(7243):73-6. doi: 10.1038/nature07971.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Danish National Research Foundation: Centre for DNA Nanotechnology.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19424153" target="_blank"〉PubMed〈/a〉
    Keywords: Cryoelectron Microscopy ; DNA/*chemistry ; Imaging, Three-Dimensional ; Microscopy, Atomic Force ; Nanostructures/*chemistry ; *Nucleic Acid Conformation
    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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    Structure of the anaphase-promoting complex/cyclosome interacting with a mitotic checkpoint complex (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-03-17
    Description: Once all chromosomes are connected to the mitotic spindle (bioriented), anaphase is initiated by the protein ubiquitylation activity of the anaphase-promoting complex/cyclosome (APC/C) and its coactivator Cdc20 (APC/C(Cdc20)). Before chromosome biorientation, anaphase is delayed by a mitotic checkpoint complex (MCC) that inhibits APC/C(Cdc20). We used single-particle electron microscopy to obtain three-dimensional models of human APC/C in various functional states: bound to MCC, to Cdc20, or to neither (apo-APC/C). These experiments revealed that MCC associates with the Cdc20 binding site on APC/C, locks the otherwise flexible APC/C in a "closed" state, and prevents binding and ubiquitylation of a wide range of different APC/C substrates. These observations clarify the structural basis for the inhibition of APC/C by spindle checkpoint proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2989460/" 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/PMC2989460/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Herzog, Franz -- Primorac, Ivana -- Dube, Prakash -- Lenart, Peter -- Sander, Bjorn -- Mechtler, Karl -- Stark, Holger -- Peters, Jan-Michael -- F 3407/Austrian Science Fund FWF/Austria -- New York, N.Y. -- Science. 2009 Mar 13;323(5920):1477-81. doi: 10.1126/science.1163300.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, 1030 Vienna, Austria.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19286556" target="_blank"〉PubMed〈/a〉
    Keywords: Anaphase ; Anaphase-Promoting Complex-Cyclosome ; Cdc20 Proteins ; Cell Cycle Proteins/chemistry/metabolism ; HeLa Cells ; Humans ; Image Processing, Computer-Assisted ; Imaging, Three-Dimensional ; Microscopy, Electron ; *Mitosis ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Spindle Apparatus/*metabolism ; Ubiquitin-Conjugating Enzymes/chemistry/metabolism ; Ubiquitin-Protein Ligase Complexes/*chemistry/*metabolism ; Ubiquitination
    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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  • 9
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    Systematic analysis of human protein complexes identifies chromosome segregation proteins (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-04-03
    Description: Chromosome segregation and cell division are essential, highly ordered processes that depend on numerous protein complexes. Results from recent RNA interference screens indicate that the identity and composition of these protein complexes is incompletely understood. Using gene tagging on bacterial artificial chromosomes, protein localization, and tandem-affinity purification-mass spectrometry, the MitoCheck consortium has analyzed about 100 human protein complexes, many of which had not or had only incompletely been characterized. This work has led to the discovery of previously unknown, evolutionarily conserved subunits of the anaphase-promoting complex and the gamma-tubulin ring complex--large complexes that are essential for spindle assembly and chromosome segregation. The approaches we describe here are generally applicable to high-throughput follow-up analyses of phenotypic screens in mammalian cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2989461/" 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/PMC2989461/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hutchins, James R A -- Toyoda, Yusuke -- Hegemann, Bjorn -- Poser, Ina -- Heriche, Jean-Karim -- Sykora, Martina M -- Augsburg, Martina -- Hudecz, Otto -- Buschhorn, Bettina A -- Bulkescher, Jutta -- Conrad, Christian -- Comartin, David -- Schleiffer, Alexander -- Sarov, Mihail -- Pozniakovsky, Andrei -- Slabicki, Mikolaj Michal -- Schloissnig, Siegfried -- Steinmacher, Ines -- Leuschner, Marit -- Ssykor, Andrea -- Lawo, Steffen -- Pelletier, Laurence -- Stark, Holger -- Nasmyth, Kim -- Ellenberg, Jan -- Durbin, Richard -- Buchholz, Frank -- Mechtler, Karl -- Hyman, Anthony A -- Peters, Jan-Michael -- F 3407/Austrian Science Fund FWF/Austria -- New York, N.Y. -- Science. 2010 Apr 30;328(5978):593-9. doi: 10.1126/science.1181348. Epub 2010 Apr 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20360068" target="_blank"〉PubMed〈/a〉
    Keywords: Anaphase-Promoting Complex-Cyclosome ; Centrosome/metabolism ; *Chromosome Segregation ; Chromosomes, Artificial, Bacterial ; Databases, Genetic ; Genomics ; Green Fluorescent Proteins ; HeLa Cells ; Humans ; *Mitosis ; Multiprotein Complexes/*metabolism ; Open Reading Frames ; Protein Binding ; Protein Interaction Mapping ; Protein Subunits/metabolism ; RNA Interference ; Spindle Apparatus/*metabolism ; Tubulin/*metabolism ; Ubiquitin-Protein Ligase Complexes/*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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  • 10
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    Novel Colloidal Interactions in Anisotropic Fluids (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-03-21
    Description: Small water droplets dispersed in a nematic liquid crystal exhibit a novel class of colloidal interactions, arising from the orientational elastic energy of the anisotropic host fluid. These interactions include a short-range repulsion and a long-range dipolar attraction, and they lead to the formation of anisotropic chainlike structures by the colloidal particles. The repulsive interaction can lead to novel mechanisms for colloid stabilization.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Poulin -- Stark -- Lubensky -- Weitz -- New York, N.Y. -- Science. 1997 Mar 21;275(5307):1770-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9065396" 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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