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  • Meteorology and Climatology  (55)
  • Signal Transduction  (25)
  • 2005-2009  (80)
  • 2007  (80)
  • 1
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    Legumes symbioses: absence of Nod genes in photosynthetic bradyrhizobia (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-06-02
    Description: Leguminous plants (such as peas and soybeans) and rhizobial soil bacteria are symbiotic partners that communicate through molecular signaling pathways, resulting in the formation of nodules on legume roots and occasionally stems that house nitrogen-fixing bacteria. Nodule formation has been assumed to be exclusively initiated by the binding of bacterial, host-specific lipochito-oligosaccharidic Nod factors, encoded by the nodABC genes, to kinase-like receptors of the plant. Here we show by complete genome sequencing of two symbiotic, photosynthetic, Bradyrhizobium strains, BTAi1 and ORS278, that canonical nodABC genes and typical lipochito-oligosaccharidic Nod factors are not required for symbiosis in some legumes. Mutational analyses indicated that these unique rhizobia use an alternative pathway to initiate symbioses, where a purine derivative may play a key role in triggering nodule formation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Giraud, Eric -- Moulin, Lionel -- Vallenet, David -- Barbe, Valerie -- Cytryn, Eddie -- Avarre, Jean-Christophe -- Jaubert, Marianne -- Simon, Damien -- Cartieaux, Fabienne -- Prin, Yves -- Bena, Gilles -- Hannibal, Laure -- Fardoux, Joel -- Kojadinovic, Mila -- Vuillet, Laurie -- Lajus, Aurelie -- Cruveiller, Stephane -- Rouy, Zoe -- Mangenot, Sophie -- Segurens, Beatrice -- Dossat, Carole -- Franck, William L -- Chang, Woo-Suk -- Saunders, Elizabeth -- Bruce, David -- Richardson, Paul -- Normand, Philippe -- Dreyfus, Bernard -- Pignol, David -- Stacey, Gary -- Emerich, David -- Vermeglio, Andre -- Medigue, Claudine -- Sadowsky, Michael -- New York, N.Y. -- Science. 2007 Jun 1;316(5829):1307-12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut de Recherche pour le Developpement, Centre de Cooperation International en Recherche Agronomique pour le Developpement, Institut National de la Recherche Agronomique, Universite Montpellier 2, France. giraud@mpl.ird.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17540897" target="_blank"〉PubMed〈/a〉
    Keywords: Acyltransferases/genetics/metabolism ; Amidohydrolases/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Bradyrhizobium/*genetics/growth & development/*physiology ; Cytokinins/metabolism ; Fabaceae/*microbiology ; Genes, Bacterial ; Genome, Bacterial ; Genomics ; Lipopolysaccharides/metabolism ; Molecular Sequence Data ; Mutation ; N-Acetylglucosaminyltransferases/genetics/metabolism ; Photosynthesis ; Plant Roots/microbiology ; Plant Stems/*microbiology ; Purines/biosynthesis ; Root Nodules, Plant/microbiology/*physiology ; Signal Transduction ; *Symbiosis
    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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    Validation of the Aura Microwave Limb Sounder Temperature and Geopotential Height Measurements (2007)
    In:  CASI
    Details
    Publication Date: 2018-06-06
    Description: This paper describes the retrievals algorithm used to determine temperature and height from radiance measurements by the Microwave Limb Sounder on EOS Aura. MLS is a "limbscanning" instrument, meaning that it views the atmosphere along paths that do not intersect the surface - it actually looks forwards from the Aura satellite. This means that the temperature retrievals are for a "profile" of the atmosphere somewhat ahead of the satellite. Because of the need to view a finite sample of the atmosphere, the sample spans a box about 1.5km deep and several tens of kilometers in width; the optical characteristics of the atmosphere mean that the sample is representative of a tube about 200-300km long in the direction of view. The retrievals use temperature analyses from NASA's Goddard Earth Observing System, Version 5 (GEOS-5) data assimilation system as a priori states. The temperature retrievals are somewhat deperrde~zt on these a priori states, especially in the lower stratosphere. An important part of the validation of any new dataset involves comparison with other, independent datasets. A large part of this study is concerned with such comparisons, using a number of independent space-based measurements obtained using different techniques, and with meteorological analyses. The MLS temperature data are shown to have biases that vary with height, but also depend on the validation dataset. MLS data are apparently biased slightly cold relative to correlative data in the upper troposphere and slightly warm in the middle stratosphere. A warm MLS bias in the upper stratosphere may be due to a cold bias in GEOS-5 temperatures.
    Keywords: Meteorology and Climatology
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  • 3
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    Evolutionary dynamics of immune-related genes and pathways in disease-vector mosquitoes (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-06-26
    Description: Mosquitoes are vectors of parasitic and viral diseases of immense importance for public health. The acquisition of the genome sequence of the yellow fever and Dengue vector, Aedes aegypti (Aa), has enabled a comparative phylogenomic analysis of the insect immune repertoire: in Aa, the malaria vector Anopheles gambiae (Ag), and the fruit fly Drosophila melanogaster (Dm). Analysis of immune signaling pathways and response modules reveals both conservative and rapidly evolving features associated with different functional gene categories and particular aspects of immune reactions. These dynamics reflect in part continuous readjustment between accommodation and rejection of pathogens and suggest how innate immunity may have evolved.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2042107/" 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/PMC2042107/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Waterhouse, Robert M -- Kriventseva, Evgenia V -- Meister, Stephan -- Xi, Zhiyong -- Alvarez, Kanwal S -- Bartholomay, Lyric C -- Barillas-Mury, Carolina -- Bian, Guowu -- Blandin, Stephanie -- Christensen, Bruce M -- Dong, Yuemei -- Jiang, Haobo -- Kanost, Michael R -- Koutsos, Anastasios C -- Levashina, Elena A -- Li, Jianyong -- Ligoxygakis, Petros -- Maccallum, Robert M -- Mayhew, George F -- Mendes, Antonio -- Michel, Kristin -- Osta, Mike A -- Paskewitz, Susan -- Shin, Sang Woon -- Vlachou, Dina -- Wang, Lihui -- Wei, Weiqi -- Zheng, Liangbiao -- Zou, Zhen -- Severson, David W -- Raikhel, Alexander S -- Kafatos, Fotis C -- Dimopoulos, George -- Zdobnov, Evgeny M -- Christophides, George K -- 1 R01 AI059492-01A1/AI/NIAID NIH HHS/ -- 5 R01 AI61576-2/AI/NIAID NIH HHS/ -- G0300170/Medical Research Council/United Kingdom -- GM41247/GM/NIGMS NIH HHS/ -- GR077229MA/Wellcome Trust/United Kingdom -- P01 AI044220-06A1/AI/NIAID NIH HHS/ -- R01 AI037083/AI/NIAID NIH HHS/ -- R01 GM058634/GM/NIGMS NIH HHS/ -- R01 GM058634-09/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Jun 22;316(5832):1738-43.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Cell and Molecular Biology, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17588928" target="_blank"〉PubMed〈/a〉
    Keywords: Aedes/*genetics/immunology ; Animals ; Anopheles/*genetics/immunology ; Antimicrobial Cationic Peptides/physiology ; Carrier Proteins/genetics/physiology ; Drosophila melanogaster/genetics/immunology ; *Evolution, Molecular ; Genes, Insect ; Immunity, Innate/*genetics ; Insect Proteins/genetics/physiology ; Insect Vectors/*genetics/immunology ; Malaria/transmission ; Melanins/metabolism ; Multigene Family ; Signal Transduction ; Species Specificity
    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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    Reactive Nitrogen Distribution and Partitioning in the North American Troposphere and Lowermost Stratosphere (2007)
    In:  CASI
    Details
    Publication Date: 2019-07-12
    Description: A comprehensive group of reactive nitrogen species (NO, NO2, HNO3, HO2NO2, PANs, alkyl nitrates, and aerosol-NO3) were measured in the troposphere and lowermost stratosphere over North America and the Atlantic during July/August 2004 (INTEX-A) from the NASA DC-8 platform (0.1-12 km). Less reactive nitrogen species (HCN and CH3CN), that are also unique tracers of biomass combustion, were also measured along with a host of other gaseous (CO, VOC, OVOC, halocarbon) and aerosol tracers. Clean background air as well as air with influences from biogenic emissions, anthropogenic pollution, biomass combustion, and stratosphere was sampled both over continental U. S., Atlantic and Pacific. The North American upper troposphere was found to be greatly influenced by both lightning NO(x) and surface pollution lofted via convection and contained elevated concentrations of PAN, ozone, hydrocarbons, and NO(x). Under polluted conditions PAN was a dominant carrier of reactive nitrogen in the upper troposphere while nitric acid dominated in the lower troposphere. Peroxynitric acid (HO2NO2) was present in sizable concentrations always peaking at around 8 km. Aerosol nitrate appeared to be mostly contained in large soil based particles in the lower troposphere. Plumes from Alaskan fires contained large amounts of PAN and very little enhancement in ozone. Observational data suggest that lightning was a far greater contributor to NO(x) in the upper troposphere than previously believed. NO(x) and NO(y) reservoir appeared to be in steady state only in the middle troposphere where NO(x)/NO(y) was independent of air mass age. A first comparison of observed data with simulations from four 3-D models shows significant differences between observations and models as well as among models. These uncertainties likely propagate themselves in satellites derived NOx data. Observed data are interpreted to suggest that soil sinks of HCN/CH3CN are at best very small. We investigate the partitioning and interplay of the reactive nitrogen species within characteristic air masses and further examine their role in ozone formation.
    Keywords: Meteorology and Climatology
    Type: Submitted to the Journal of Geophysical Research to be published in volume 112, pp. 1-15, April 2007
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  • 5
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    Evaluating Model Performance of an Ensemble-based Chemical Data Assimilation System During INTEX-B Field Mission (2007)
    In:  Other Sources
    Details
    Publication Date: 2019-07-13
    Description: We present a global chemical data assimilation system using a global atmosphere model, the Community Atmosphere Model (CAM3) with simplified chemistry and the Data Assimilation Research Testbed (DART) assimilation package. DART is a community software facility for assimilation studies using the ensemble Kalman filter approach. Here, we apply the assimilation system to constrain global tropospheric carbon monoxide (CO) by assimilating meteorological observations of temperature and horizontal wind velocity and satellite CO retrievals from the Measurement of Pollution in the Troposphere (MOPITT) satellite instrument. We verify the system performance using independent CO observations taken on board the NSFINCAR C-130 and NASA DC-8 aircrafts during the April 2006 part of the Intercontinental Chemical Transport Experiment (INTEX-B). Our evaluations show that MOPITT data assimilation provides significant improvements in terms of capturing the observed CO variability relative to no MOPITT assimilation (i.e. the correlation improves from 0.62 to 0.71, significant at 99% confidence). The assimilation provides evidence of median CO loading of about 150 ppbv at 700 hPa over the NE Pacific during April 2006. This is marginally higher than the modeled CO with no MOPITT assimilation (-140 ppbv). Our ensemble-based estimates of model uncertainty also show model overprediction over the source region (i.e. China) and underprediction over the NE Pacific, suggesting model errors that cannot be readily explained by emissions alone. These results have important implications for improving regional chemical forecasts and for inverse modeling of CO sources and further demonstrate the utility of the assimilation system in comparing non-coincident measurements, e.g. comparing satellite retrievals of CO with in-situ aircraft measurements. The work described above also brought to light several short-comings of the data assimilation approach for CO profiles. Because of the limited vertical resolution of the measurement, the retrievals at different altitudes are correlated which can lead to problems with numerical error and overall efficiency. This has resulted in a manuscript that is about to be submitted to JGR:
    Keywords: Meteorology and Climatology
    Type: Journal of Atmospheric Chemistry and Physics; 7; 5695-5710
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  • 6
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    Coactivation of receptor tyrosine kinases affects the response of tumor cells to targeted therapies (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-18
    Description: Targeted therapies that inhibit receptor tyrosine kinases (RTKs) and the downstream phosphatidylinositol 3-kinase (PI3K) signaling pathway have shown promising anticancer activity, but their efficacy in the brain tumor glioblastoma multiforme (GBM) and other solid tumors has been modest. We hypothesized that multiple RTKs are coactivated in these tumors and that redundant inputs drive and maintain downstream signaling, thereby limiting the efficacy of therapies targeting single RTKs. Tumor cell lines, xenotransplants, and primary tumors indeed show multiple concomitantly activated RTKs. Combinations of RTK inhibitors and/or RNA interference, but not single agents, decreased signaling, cell survival, and anchorage-independent growth even in glioma cells deficient in PTEN, a frequently inactivated inhibitor of PI3K. Thus, effective GBM therapy may require combined regimens targeting multiple RTKs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stommel, Jayne M -- Kimmelman, Alec C -- Ying, Haoqiang -- Nabioullin, Roustem -- Ponugoti, Aditya H -- Wiedemeyer, Ruprecht -- Stegh, Alexander H -- Bradner, James E -- Ligon, Keith L -- Brennan, Cameron -- Chin, Lynda -- DePinho, Ronald A -- 5P01CA95616/CA/NCI NIH HHS/ -- R01CA99041/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2007 Oct 12;318(5848):287-90. Epub 2007 Sep 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17872411" target="_blank"〉PubMed〈/a〉
    Keywords: Antineoplastic Agents/*pharmacology ; Antineoplastic Combined Chemotherapy Protocols/pharmacology/therapeutic use ; Brain Neoplasms/drug therapy/*enzymology ; Cell Line, Tumor ; Cell Survival ; Enzyme Activation ; Erlotinib Hydrochloride ; Glioblastoma/drug therapy/*enzymology ; Humans ; Indoles/pharmacology ; PTEN Phosphohydrolase/genetics/metabolism ; Phosphatidylinositol 3-Kinases/metabolism ; Phosphorylation ; Piperazines/pharmacology ; Protein Kinase Inhibitors/*pharmacology ; Proto-Oncogene Proteins/metabolism ; Proto-Oncogene Proteins c-met ; Quinazolines/pharmacology ; Receptor Protein-Tyrosine Kinases/antagonists & inhibitors/*metabolism ; Receptor, Epidermal Growth Factor/antagonists & inhibitors/metabolism ; Receptors, Growth Factor/metabolism ; Signal Transduction ; Sulfonamides/pharmacology
    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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    Promotion of tissue inflammation by the immune receptor Tim-3 expressed on innate immune cells (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-11-17
    Description: CD4+ T helper 1 (TH1) cells are important mediators of inflammation and are regulated by numerous pathways, including the negative immune receptor Tim-3. We found that Tim-3 is constitutively expressed on cells of the innate immune system in both mice and humans, and that it can synergize with Toll-like receptors. Moreover, an antibody agonist of Tim-3 acted as an adjuvant during induced immune responses, and Tim-3 ligation induced distinct signaling events in T cells and dendritic cells; the latter finding could explain the apparent divergent functions of Tim-3 in these cell types. Thus, by virtue of differential expression on innate versus adaptive immune cells, Tim-3 can either promote or terminate TH1 immunity and may be able to influence a range of inflammatory conditions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Anderson, Ana C -- Anderson, David E -- Bregoli, Lisa -- Hastings, William D -- Kassam, Nasim -- Lei, Charles -- Chandwaskar, Rucha -- Karman, Jozsef -- Su, Ee W -- Hirashima, Mitsuomi -- Bruce, Jeffrey N -- Kane, Lawrence P -- Kuchroo, Vijay K -- Hafler, David A -- R01 AI067544/AI/NIAID NIH HHS/ -- R01 AI067544-01A2/AI/NIAID NIH HHS/ -- R56 AI067544/AI/NIAID NIH HHS/ -- R56 AI067544-01A1/AI/NIAID NIH HHS/ -- R56 AI067544-02/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2007 Nov 16;318(5853):1141-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Molecular Immunology, Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18006747" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, CD11b/immunology ; Astrocytes/immunology ; Central Nervous System Neoplasms/immunology ; Dendritic Cells/immunology ; Encephalomyelitis, Autoimmune, Experimental/immunology ; Galectins/immunology ; Glioblastoma/immunology ; Humans ; Immunity, Innate ; Inflammation Mediators/*immunology ; Lipopolysaccharides/immunology ; Macrophages/immunology ; Membrane Proteins/biosynthesis/*immunology ; Mice ; Microglia/immunology ; Multiple Sclerosis/immunology ; Rats ; Receptors, Immunologic/biosynthesis/*immunology ; Receptors, Virus/biosynthesis/*immunology ; Signal Transduction ; T-Lymphocytes/immunology ; Th1 Cells/*immunology ; Toll-Like Receptors
    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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    Observed and Modeled HOCl Profiles in the Midlatitude Stratosphere: Implication for Ozone Loss (2007)
    In:  Other Sources
    Details
    Publication Date: 2018-06-11
    Description: Vertical profiles of stratospheric HOCl calculated with a diurnal steady-state photochemical model that uses currently recommended reaction rates and photolysis cross sections underestimate observed profiles of HOCl obtained by two balloon-borne instruments, FIRS-2 (a far-infrared emission spectrometer) and MkIV (a mid-infrared, solar absorption spectrometer). Considerable uncertainty (a factor of two) persists in laboratory measurements of the rate constant (k(sub 1)) for the reaction ClO + HO2 yields HOCl + O2. Agreement between modeled and measured HOCl can be attained using a value of k(sub 1) from Stimpfle et al. (1979) that is about a factor-of-two faster than the currently recommended rate constant. Comparison of modeled and measured HOCl suggests that models using the currently recommended value for k(sub 1) may underestimate the role of the HOCl catalytic cycle for ozone depletion, important in the midlatitude lower stratosphere.
    Keywords: Meteorology and Climatology
    Type: Geophysical Research Letters (ISSN 0094-8276); Volume 34
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  • 9
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    Solar Occultation Satellite Data and Derived Meteorological Products: Sampling Issues and Comparisons with Aura MLS (2007)
    In:  CASI
    Details
    Publication Date: 2018-06-06
    Description: Derived Meteorological Products (DMPs, including potential temperature (theta), potential vorticity, equivalent latitude (EqL), horizontal winds and tropopause locations) have been produced for the locations and times of measurements by several solar occultation (SO) instruments and the Aura Microwave Limb Sounder (MLS). DMPs are calculated from several meteorological analyses for the Atmospheric Chemistry Experiment-Fourier Transform Spectrometer, Stratospheric Aerosol and Gas Experiment II and III, Halogen Occultation Experiment, and Polar Ozone and Aerosol Measurement II and III SO instruments and MLS. Time-series comparisons of MLS version 1.5 and SO data using DMPs show good qualitative agreement in time evolution of O3, N2O, H20, CO, HNO3, HCl and temperature; quantitative agreement is good in most cases. EqL-coordinate comparisons of MLS version 2.2 and SO data show good quantitative agreement throughout the stratosphere for most of these species, with significant biases for a few species in localized regions. Comparisons in EqL coordinates of MLS and SO data, and of SO data with geographically coincident MLS data provide insight into where and how sampling effects are important in interpretation of the sparse SO data, thus assisting in fully utilizing the SO data in scientific studies and comparisons with other sparse datasets. The DMPs are valuable for scientific studies and to facilitate validation of non-coincident measurements.
    Keywords: Meteorology and Climatology
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  • 10
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    Condensed-Phase Nitric Acid in a Tropical Subvisible Cirrus Cloud (2007)
    In:  Other Sources
    Details
    Publication Date: 2019-07-13
    Description: In situ observations in a tropical subvisible cirrus cloud during the Costa Rica Aura Validation Experiment on 2 February 2006 show the presence of condensed-phase nitric acid. The cloud was observed near the tropopause at altitudes of 16.3-17.7 km in an extremely cold (183-191 K) and dry 5 ppm H2O) air mass. Relative humidities with respect to ice ranged from 150-250% throughout most of the cloud. Optical particle measurements indicate the presence of ice crystals as large as 90 microns in diameter. Condensed RN031H20 molar ratios observed in the cloud particles were 1-2 orders of magnitude greater than ratios observed previously in cirrus clouds at similar RN03 partial pressures. Nitric acid trihydrate saturation ratios were 10 or greater during much of the cloud encounter, indicating that RN03 may be present in the cloud particles as a stable condensate and not simply physically adsorbed on or trapped in the particles.
    Keywords: Meteorology and Climatology
    Type: Geophysical Research Letters (ISSN 0094-8276); 34
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