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  • Chemistry and Materials (General)  (6)
  • Animals  (3)
  • Meteorology and Climatology  (3)
  • 2000-2004  (12)
  • 1
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    Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-11-09
    Description: Electron tomography of vitrified cells is a noninvasive three-dimensional imaging technique that opens up new vistas for exploring the supramolecular organization of the cytoplasm. We applied this technique to Dictyostelium cells, focusing on the actin cytoskeleton. In actin networks reconstructed without prior removal of membranes or extraction of soluble proteins, the cross-linking of individual microfilaments, their branching angles, and membrane attachment sites can be analyzed. At a resolution of 5 to 6 nanometers, single macromolecules with distinct shapes, such as the 26S proteasome, can be identified in an unperturbed cellular environment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Medalia, Ohad -- Weber, Igor -- Frangakis, Achilleas S -- Nicastro, Daniela -- Gerisch, Gunther -- Baumeister, Wolfgang -- New York, N.Y. -- Science. 2002 Nov 8;298(5596):1209-13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Biochemistry, D-82152 Martinsried, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12424373" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/chemistry/metabolism/*ultrastructure ; Actins/ultrastructure ; Animals ; Binding Sites ; Cell Membrane/metabolism/ultrastructure ; Cell Movement ; Dictyostelium/chemistry/physiology/*ultrastructure ; Endoplasmic Reticulum, Rough/ultrastructure ; Freezing ; *Image Processing, Computer-Assisted ; Macromolecular Substances ; Microfilament Proteins/*ultrastructure ; Organelles/*ultrastructure ; Peptide Hydrolases/ultrastructure ; *Proteasome Endopeptidase Complex ; Proteome ; Protozoan Proteins/ultrastructure ; Ribosomes/ultrastructure ; Tomography/*methods
    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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  • 2
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    Eta-1 (osteopontin): an early component of type-1 (cell-mediated) immunity (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-02-05
    Description: Cell-mediated (type-1) immunity is necessary for immune protection against most intracellular pathogens and, when excessive, can mediate organ-specific autoimmune destruction. Mice deficient in Eta-1 (also called osteopontin) gene expression have severely impaired type-1 immunity to viral infection [herpes simplex virus-type 1 (KOS strain)] and bacterial infection (Listeria monocytogenes) and do not develop sarcoid-type granulomas. Interleukin-12 (IL-12) and interferon-gamma production is diminished, and IL-10 production is increased. A phosphorylation-dependent interaction between the amino-terminal portion of Eta-1 and its integrin receptor stimulated IL-12 expression, whereas a phosphorylation-independent interaction with CD44 inhibited IL-10 expression. These findings identify Eta-1 as a key cytokine that sets the stage for efficient type-1 immune responses through differential regulation of macrophage IL-12 and IL-10 cytokine expression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ashkar, S -- Weber, G F -- Panoutsakopoulou, V -- Sanchirico, M E -- Jansson, M -- Zawaideh, S -- Rittling, S R -- Denhardt, D T -- Glimcher, M J -- Cantor, H -- AI12184/AI/NIAID NIH HHS/ -- AI37833/AI/NIAID NIH HHS/ -- CA76176/CA/NCI NIH HHS/ -- etc. -- New York, N.Y. -- Science. 2000 Feb 4;287(5454):860-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory for Skeletal Disorders and Rehabilitation, Department of Orthopedic Surgery, Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10657301" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, CD44/metabolism ; Granuloma/immunology ; Herpes Simplex/immunology ; Herpesvirus 1, Human/immunology ; Hypersensitivity, Delayed ; Interferon-gamma/biosynthesis ; Interleukin-10/*biosynthesis ; Interleukin-12/*biosynthesis ; Keratitis, Herpetic/immunology ; Listeriosis/immunology ; Lymphocyte Activation ; Macrophages/*immunology ; Mice ; Mice, Inbred C3H ; Mice, Inbred C57BL ; Mice, Nude ; Osteopontin ; Phosphorylation ; Receptors, Vitronectin/metabolism ; Sialoglycoproteins/*immunology/metabolism/pharmacology ; T-Lymphocytes/*immunology/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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  • 3
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    Reconstitution of Ca2+-regulated membrane fusion by synaptotagmin and SNAREs (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-03-27
    Description: We investigated the effect of synaptotagmin I on membrane fusion mediated by neuronal SNARE proteins, SNAP-25, syntaxin, and synaptobrevin, which were reconstituted into vesicles. In the presence of Ca2+, the cytoplasmic domain of synaptotagmin I (syt) strongly stimulated membrane fusion when synaptobrevin densities were similar to those found in native synaptic vesicles. The Ca2+ dependence of syt-stimulated fusion was modulated by changes in lipid composition of the vesicles and by a truncation that mimics cleavage of SNAP-25 by botulinum neurotoxin A. Stimulation of fusion was abolished by disrupting the Ca2+-binding activity, or by severing the tandem C2 domains, of syt. Thus, syt and SNAREs are likely to represent the minimal protein complement for Ca2+-triggered exocytosis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tucker, Ward C -- Weber, Thomas -- Chapman, Edwin R -- GM 56827/GM/NIGMS NIH HHS/ -- GM 66313/GM/NIGMS NIH HHS/ -- MH 61876/MH/NIMH NIH HHS/ -- New York, N.Y. -- Science. 2004 Apr 16;304(5669):435-8. Epub 2004 Mar 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, University of Wisconsin, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15044754" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Calcium/*metabolism ; *Calcium-Binding Proteins ; Exocytosis ; Fluorescence Resonance Energy Transfer ; Lipid Bilayers ; Lipids/analysis ; Liposomes/chemistry/metabolism ; *Membrane Fusion ; Membrane Glycoproteins/chemistry/*metabolism ; Membrane Proteins/chemistry/*metabolism ; Mice ; Mutation ; Nerve Tissue Proteins/chemistry/*metabolism ; Protein Structure, Tertiary ; Qa-SNARE Proteins ; R-SNARE Proteins ; Rats ; Synaptic Vesicles/chemistry/metabolism ; Synaptosomal-Associated Protein 25 ; Synaptotagmin I ; Synaptotagmins
    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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    Chemical Constraints Governing the Origin of Metabolism: The Thermodynamic Landscape of Carbon Group Transformations (2001)
    In:  Other Sources
    Details
    Publication Date: 2019-07-18
    Description: The thermodynamics of organic chemistry under mild aqueous conditions was examined in order to begin to understand its influence on the structure and operation of metabolism and its antecedents. Free energies were estimated for four types reactions of biochemical importance carbon-carbon bond cleavage and synthesis, hydrogen transfer between carbon groups, dehydration of alcohol groups, and aldo-keto isomerization. The energies were calculated for mainly aliphatic groups composed of carbon, hydrogen, and oxygen. The energy values showed that (1) when carbon-carbon bond cleavage involves two different types of functional groups, transfer of the shared electron-pair to the more reduced carbon group is energetically favored over transfer to the more oxidized carbon group, and (2) the energy of carbon-carbon bond transformation is strongly dependent on the type of functional group that donates the shared electron-pair during cleavage, and the group that accepts the shared electron-pair during synthesis, and (3) the energetics of C-C bond transformation is determined primarily by the half-reaction energies of the couples: carbonyl/carboxylic acid, carboxylic acid/carbon dioxide, alcohol/carbonyl, and hydrocarbon/alcohol. The energy of hydrogen-transfer between carbon groups was found to depend on the functional group class of both the hydrogen-donor and hydrogen-acceptor. From these and other observations we concluded that the chemistry of the origin of metabolism (and to a lesser degree modem metabolism) is strongly constrained by the (1) limited disproportionation energy of organic substrates that can be dissipated in a few irreversible reactions, (2) the energy-dominance of few half-reaction couples in carbon-carbon bond transformation that establishes whether a chemical reaction is energetically irreversible, reversible or unfeasible, and (3) the dependence of the transformation-energy on the oxidation state of carbon groups (functional group type) which is contingent on prior reactions in the synthetic pathway.
    Keywords: Chemistry and Materials (General)
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  • 5
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    Can One Satellite Data Set Validation Another? Validation of Envisat SCIAMACHY Data by Comparisons with NOAA-16 SBUV/2 and ERS-2 GOME (2004)
    In:  Other Sources
    Details
    Publication Date: 2019-07-18
    Description: Validation of satellite data remains a high priority for the construction of climate data sets. Traditionally ground based measurements have provided the primary comparison data for validation. For some atmospheric parameters such as ozone, a thoroughly validated satellite data record can be used to validate a new instrument s data product in addition to using ground based data. Comparing validated data with new satellite data has several advantages; availability of much more data, which will improve precision, larger geographical coverage, and the footprints are closer in size, which removes uncertainty due to different observed atmospheric volumes. To demonstrate the applicability and some limitations of this technique, observations from the newly launched SCIAMACHY instrument were compared with the NOM-16 SBW/2 and ERS-2 GOME instruments. The SBW/2 data had all ready undergone validation by comparing to the total ozone ground network. Overall the SCIAMACHY data were found to low by 3% with respect to satellite data and 1% low with respect to ground station data. There appears to be seasonal and or solar zenith angle dependences in the comparisons with SBW/2 where differences increase with higher solar zenith angles. It is known that accuracies in both satellite and ground based total ozone algorithms decrease at high solar zenith angles. There is a strong need for more accurate measurement from and the ground under these conditions. At the present time SCIAMACHY data are limited and longer data set with more coverage in both hemispheres is needed to unravel the cause of these differences.
    Keywords: Meteorology and Climatology
    Type: 2004 Fall AGU Meeting; Dec 13, 2004 - Dec 17, 2004; San Francisco, CA; United States
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  • 6
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    The Sugar Model: Catalytic Flow Reactor Dynamics of Pyruvaldehyde Synthesis from Triose Catalyzed by Poly-L-Lysine Contained in a Dialyzer (2000)
    In:  Other Sources
    Details
    Publication Date: 2019-07-17
    Description: The formation of pyruvaldehyde from triose sugars was catalyzed by poly-L-lysine contained in a small dialyzer (100 MWCO) suspended in a much larger triose substrate reservoir. The polylysine confined in the dialyzer functioned as a catalytic flow reactor that constantly brought in triose from the substrate reservoir by diffusion to offset the drop in triose concentration within the reactor caused by its conversion to pyruvaldehyde. A 400 mM solution of poly-L-lysine contained in a 0.35 ml dialyzer placed in a 120 ml solution of triose substrate (pH 5.5, 40 C) generated pyruvaldehyde 11 -times faster than an a control reaction without the catalytic dialyzer. However, since the catalytic dialyzer's volume was 343-times smaller than the control reaction, the synthetic intensity (rate/volume) of pyruvaldehyde synthesis within the catalytic dialyzer was 3400-times greater than that of the control reaction and substrate solution. A similar result was obtained using a dialyzer with a 500 MWCO value. Acting as a catalytic flow reactor the polylysine catalytic dialyzer synthesized about 3.5 molecules of pyruvaldehyde per lysine residue in 7 days -- an amount of triose equal to twice the weight of the catalyst. At 7 days the catalytic activity of polylysine was 16% of its initial value, a result indicating catalyst-poisoning caused by reaction of pyruvaldehyde with the e-amino groups of polylysine. The dialyzer method of catalyst containment was selected it provides a simple, flexible, and easily manipulated experimental system for studying the dynamics and evolutionary development of confined autocatalytic processes related to the origin of life under anaerobic conditions.
    Keywords: Chemistry and Materials (General)
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  • 7
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    New Particle Formation in Anthropogenic Plumes Advecting from Asia Observed During TRACE-P (2003)
    In:  Other Sources
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    Publication Date: 2019-07-13
    Description: The characteristics and sources of what are believed to be newly formed 3 to 4 nm particles in anthropogenic plumes advecting from Asian are reported. Airborne measurements were made from March to April 2001 as part of the NASA TRACE-P experiment at latitudes ranging from North of the Philippines to Northern Japan (20 to 45 deg. N). In the more polluted plumes, high concentrations of 3 to 4 nm diameter particles (less than 100/qu cm) were observed both within and along the upper outer edges of plumes that were identified by enhanced carbon monoxide and fine particulate sulfate concentrations. The results from two research flights are investigated in detail. Three to four-nm particle concentrations are generally correlated with gas phase sulfuric acid and found in regions of low surface areas relative to the immediate surroundings or where there are steep transitions to lower surface areas. Sulfuric acid and surface area concentrations in the most polluted plume reached 6 x l0(exp 7) and 750 micro sq m/qu cm, respectively, in regions of particle formation. In contrast to these anthropogenic plumes, few 3 to 4 nm particles were observed in the clean background and few were detected within a volcanic plume where the studies highest H2SO4 concentrations (less than lO(exp 8)/qu cm) were recorded. Enhanced SO2 concentrations in the range of approximately 2 to 7 ppb, in conjunction with other unidentified, possibly coemitted species, appear to be the driving factor for nucleation. (0345, 4801); 0322 Atmospheric Composition and Structure: Constituent sources and sinks; 0345 Atmospheric Composition and Structure: Pollution-urban and regional (0305); 4801 Oceanography: Biological and Chemical: Aerosols (0305).
    Keywords: Meteorology and Climatology
    Type: Journal of Geophysical Research (ISSN 0148-0227); 108; D21; 35-1 - 35-13
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  • 8
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    Protein Kinase Classification with 2866 Hidden Markov Models and One Support Vector Machine (2002)
    In:  Other Sources
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    Publication Date: 2019-07-18
    Description: The main application considered in this paper is predicting true kinases from randomly permuted kinases that share the same length and amino acid distributions as the true kinases. Numerous methods already exist for this classification task, such as HMMs, motif-matchers, and sequence comparison algorithms. We build on some of these efforts by creating a vector from the output of thousands of structurally based HMMs, created offline with Pfam-A seed alignments using SAM-T99, which then must be combined into an overall classification for the protein. Then we use a Support Vector Machine for classifying this large ensemble Pfam-Vector, with a polynomial and chisquared kernel. In particular, the chi-squared kernel SVM performs better than the HMMs and better than the BLAST pairwise comparisons, when predicting true from false kinases in some respects, but no one algorithm is best for all purposes or in all instances so we consider the particular strengths and weaknesses of each.
    Keywords: Chemistry and Materials (General)
    Type: RECOMB 2002: 6th Annual International Conference on Research in Computational Molecular Biology; Apr 18, 2002 - Apr 21, 2002; Washington, DC; United States
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  • 9
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    Intercomparisons of Airborne Measurements of Aerosol Ionic Chemical Composition during TRACE-P and ACE-Asia (2003)
    In:  CASI
    Details
    Publication Date: 2019-07-10
    Description: As part of the two field studies, Transport and Chemical Evolution over the Pacific (TRACE-P), and the Asian Aerosol Characterization Experiment (ACEAsia), the inorganic chemical composition of tropospheric aerosols was measured over the western Pacific from three separate aircraft using various methods. Comparisons are made between the rapid online techniques of the Particle Into Liquid Sampler (PILS) for measurement of a suite of fine particle ionic compounds and a mist chamber (MC/IC) measurement of fine sulfate, and the longer time-integrated filter and multi-orifice impactor (MOI) measurements. Comparisons between identical PILS on two separate aircraft flying in formation showed that they were highly correlated (e.g., sulfate r(sup 2) of 0.95), but were systematically different by 10 +/- 5% (linear regression slope and 95% confidence bounds), and had generally higher concentrations on the aircraft with a low turbulence inlet and shorter inlet-to-instrument transmission tubing. Comparisons of PILS and mist chamber measurements of fine sulfate on two different aircraft during formation flying had an 3 of 0.78 and a relative difference of 39% +/- 5%. MOI ionic data integrated to the PILS upper measurement size of 1.3 pm sampling from separate inlets on the same aircraft showed that for sulfate, PILS and MOI were within 14% +/- 6% and correlated with an r(sup 2) of 0.87. Most ionic compounds were within f 30%, which is in the range of differences reported between PILS and integrated samplers from ground-based comparisons. In many cases, direct intercomparison between the various instruments is difficult due to differences in upper-size detection limits. However, for this study, the results suggest that the fine particle mass composition measured from aircraft agree to within 30-40%.
    Keywords: Chemistry and Materials (General)
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  • 10
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    A Global Aerosol Model Forecast for the ACE-Asia Field Experiment (2003)
    In:  CASI
    Details
    Publication Date: 2019-07-10
    Description: We present the results of aerosol forecast during the Aerosol Characterization Experiment (ACE-Asia) field experiment in spring 2001, using the Georgia Tech/Goddard Global Ozone Chemistry Aerosol Radiation and Transport (GOCART) model and the meteorological forecast fields from the Goddard Earth Observing System Data Assimilation System (GEOS DAS). The aerosol model forecast provides direct information on aerosol optical thickness and concentrations, enabling effective flight planning, while feedbacks from measurements constantly evaluate the model, making successful model improvements. We verify the model forecast skill by comparing model predicted total aerosol extinction, dust, sulfate, and SO2 concentrations with those quantities measured by the C-130 aircraft during the ACE-Asia intensive operation period. The GEOS DAS meteorological forecast system shows excellent skills in predicting winds, relative humidity, and temperature for the ACE-Asia experiment area as well as for each individual flight, with skill scores usually above 0.7. The model is also skillful in forecast of pollution aerosols, with most scores above 0.5. The model correctly predicted the dust outbreak events and their trans-Pacific transport, but it constantly missed the high dust concentrations observed in the boundary layer. We attribute this missing dust source to the desertification regions in the Inner Mongolia Province in China, which have developed in recent years but were not included in the model during forecasting. After incorporating the desertification sources, the model is able to reproduce the observed high dust concentrations at low altitudes over the Yellow Sea. Two key elements for a successful aerosol model forecast are correct source locations that determine where the emissions take place, and realistic forecast winds and convection that determine where the aerosols are transported. We demonstrate that our global model can not only account for the large-scale intercontinental transport, but also produce the small-scale spatial and temporal variations that are adequate for aircraft measurements planning.
    Keywords: Meteorology and Climatology
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