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  • 1
    Publication Date: 2016-01-07
    Description: The MetaCyc database ( MetaCyc.org ) is a freely accessible comprehensive database describing metabolic pathways and enzymes from all domains of life. The majority of MetaCyc pathways are small-molecule metabolic pathways that have been experimentally determined. MetaCyc contains more than 2400 pathways derived from 〉46 000 publications, and is the largest curated collection of metabolic pathways. BioCyc ( BioCyc.org ) is a collection of 5700 organism-specific Pathway/Genome Databases (PGDBs), each containing the full genome and predicted metabolic network of one organism, including metabolites, enzymes, reactions, metabolic pathways, predicted operons, transport systems, and pathway-hole fillers. The BioCyc website offers a variety of tools for querying and analyzing PGDBs, including Omics Viewers and tools for comparative analysis. This article provides an update of new developments in MetaCyc and BioCyc during the last two years, including addition of Gibbs free energy values for compounds and reactions; redesign of the primary gene/protein page; addition of a tool for creating diagrams containing multiple linked pathways; several new search capabilities, including searching for genes based on sequence patterns, searching for databases based on an organism's phenotypes, and a cross-organism search; and a metabolite identifier translation service.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2011-06-01
    Description: Polysaccharides are the most important components of herbal biomass with a high application potential. Their thermochemical characteristics, however, have been little studied. In the present paper, an effective thermodynamic analysis was carried out with the aim of setting a method for reasonably estimating the thermochemical properties of polysaccharides such as cellulose. The properties of formation and heat capacities were estimated by general thermodynamic methods like group contribution methods as well as methods followed from synthetic polymer studies. The results were compared with those obtained by empirical correlations derived from the data for short chain carbohydrates, the only literature data available for validation. The properties were determined depending on the degree of polymerization and temperature. Convenient thermodynamic methods for the estimation of thermochemical properties were analyzed with the objective of specifying those that could provide reasonable values for the homologous series of carbohydrates. The properties were determined as a function of temperature and carbo-hydrate chain length. These allow the prediction of formation properties of polysaccharides such as cellulose.
    Print ISSN: 0930-7516
    Electronic ISSN: 1521-4125
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Published by Wiley
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  • 3
    Publication Date: 2011-11-15
    Description: The physical as well as the chemical solubility of carbon dioxide in several ionic liquids were predicted with quantum chemical a priori methods. The physical solubility was described with the model COSMO-RS. The results were compared to experimental data. Both a qualitative and – based on the concept of relative solubility – quantitative benchmark for the solvents were possible. For the part of chemical absorption, the free reaction enthalpy, Δ R g , and reaction enthalpy, Δ R h , were determined with DFT calculations on the B3LYP/def2-TZVPP level. By combining reaction and phase equilibrium, the CO 2 loading of the reactive solvents were predicted. The results were validated with literature data. An approach was developed for a quantitative a priori description of both physical and chemical solvation of CO 2 . A new approach is presented for the a priori screening of physical and reacting absorbents for CO 2 . Predictions of physical solubility are made using COSMO-RS. For the description of the chemical reaction, the chemical and phase equilibrium are simultaneously solved by combining quantum chemical calculations on the DFT level with a model for the phase equilibrium.
    Print ISSN: 0930-7516
    Electronic ISSN: 1521-4125
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Published by Wiley
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  • 4
    Publication Date: 2012-02-24
    Description: Biomass holds great promise as a renewable source of hydrogen and thus as a zero-emission, carbon-neutral, and nearly inexhaustible energy resource. Thermodynamic analysis of biomass hydration is carried out to study the reaction properties considering a series of saccharides as a model. Equilibrium constants and composition are estimated in dependence on the saccharide chain length and temperature. The latter is also studied as a function of the reactant ratios and in the presence of nonreacting additives. Being highly endothermic, the reaction is thermodynamically favorable due to a high entropic contribution. Increase in the saccharide chain length affects the conversion only slightly, so the results for low-molecular-weight saccharides can be transferred to long-chain ones. The hydration of oligosaccharides to hydrogen is evaluated from the equilibrium thermodynamics viewpoint. The reaction is thermodynamically favorable even at mild conditions and is entropically driven. With increasing oligosaccharide chain length, the conversion remains nearly constant. Therefore, results for short chain saccharides can also be applied to long chain sugars such as cellulose.
    Print ISSN: 0930-7516
    Electronic ISSN: 1521-4125
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Published by Wiley
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  • 5
    Publication Date: 2012-04-15
    Description: Biomass holds great promise as a renewable source of hydrogen and thus as a zero-emission, carbon-neutral, and nearly inexhaustible energy resource. Thermodynamic analysis of biomass hydration is carried out to study the reaction properties considering a series of saccharides as a model. Equilibrium constants and composition are estimated in dependence on the saccharide chain length and temperature. The latter is also studied as a function of the reactant ratios and in the presence of nonreacting additives. Being highly endothermic, the reaction is thermodynamically favorable due to a high entropic contribution. Increase in the saccharide chain length affects the conversion only slightly, so the results for low-molecular-weight saccharides can be transferred to long-chain ones. The hydration of oligosaccharides to hydrogen is evaluated from the equilibrium thermodynamics viewpoint. The reaction is thermodynamically favorable even at mild conditions and is entropically driven. With increasing oligosaccharide chain length, the conversion remains nearly constant. Therefore, results for short chain saccharides can also be applied to long chain sugars such as cellulose.
    Print ISSN: 0930-7516
    Electronic ISSN: 1521-4125
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Published by Wiley
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  • 6
    Publication Date: 2012-05-03
    Description: Basal melting of ice shelves around Antarctica contributes to formation of Antarctic Bottom Water and can affect global sea level by altering the offshore flow of grounded ice streams and glaciers. Tides influence ice shelf basal melt rate (wb) by contributing to ocean mixing and mean circulation as well as thermohaline exchanges with the ice shelf. We use a three-dimensional ocean model, thermodynamically coupled to a nonevolving ice shelf, to investigate the relationship between topography, tides, and wb for Larsen C Ice Shelf (LCIS) in the northwestern Weddell Sea, Antarctica. Using our best estimates of ice shelf thickness and seabed topography, we find that the largest modeled LCIS melt rates occur in the northeast, where our model predicts strong diurnal tidal currents (∼0.4 m s−1). This distribution is significantly different from models with no tidal forcing, which predict largest melt rates along the deep grounding lines. We compare several model runs to explore melt rate sensitivity to geometry, initial ocean potential temperature (θ0), thermodynamic parameterizations of heat and freshwater ice-ocean exchange, and tidal forcing. The resulting range of LCIS-averaged wb is ∼0.11–0.44 m a−1. The spatial distribution of wb is very sensitive to model geometry and thermodynamic parameterization while the overall magnitude of wb is influenced by θ0. These sensitivities in wb predictions reinforce a need for high-resolution maps of ice draft and sub-ice-shelf seabed topography together with ocean temperature measurements at the ice shelf front to improve representation of ice shelves in coupled climate system models.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 7
    Publication Date: 2011-04-05
    Description: In situ Microscopy (ISM) is an optical analysis method that allows non-invasive monitoring of processes in real-time. In this article online monitoring of enzyme carriers and the determination of their mechanical stability are presented as new application areas for ISM. As proof of principle the fragmentation of Lewatit VP OC 1600 particles in a stirred tank reactor is tracked. The image algorithm that was used to analyze the acquired image data is described and the results of the stability study are shown. Additional application possibilities of ISM in the area of two-phase systems are demonstrated. In situ microscopy (ISM) is an optical analysis method that allows noninvasive acquisition of image information from running processes. It is demonstrated how this analysis technique can be used to determine the mechanical stability of enzyme carriers. Furthermore, application possibilities of ISM for the characterization of two-phase systems are presented.
    Print ISSN: 0930-7516
    Electronic ISSN: 1521-4125
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Published by Wiley
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  • 8
    Publication Date: 2015-01-16
    Description: The Sol Genomics Network (SGN, http://solgenomics.net ) is a web portal with genomic and phenotypic data, and analysis tools for the Solanaceae family and close relatives. SGN hosts whole genome data for an increasing number of Solanaceae family members including tomato, potato, pepper, eggplant, tobacco and Nicotiana benthamiana . The database also stores loci and phenotype data, which researchers can upload and edit with user-friendly web interfaces. Tools such as BLAST, GBrowse and JBrowse for browsing genomes, expression and map data viewers, a locus community annotation system and a QTL analysis tools are available. A new tool was recently implemented to improve Virus-Induced Gene Silencing (VIGS) constructs called the SGN VIGS tool. With the growing genomic and phenotypic data in the database, SGN is now advancing to develop new web-based breeding tools and implement the code and database structure for other species or clade-specific databases.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 9
    Publication Date: 2012-07-28
    Description: Sulfamate groups (NHSO 3 – ) are important structural elements in the glycosaminoglycans (GAGs) heparin and heparan sulfate (HS). In this work, proton nuclear magnetic resonance (NMR) line-shape analysis is used to explore the solvent exchange properties of the sulfamate NH groups within heparin-related mono-, di-, tetra- and pentasaccharides as a function of pH and temperature. The results of these experiments identified a persistent hydrogen bond within the Arixtra (fondaparinux sodium) pentasaccharide between the internal glucosamine sulfamate NH and the adjacent 3- O -sulfo group. This discovery provides new insights into the solution structure of the Arixtra pentasaccharide and suggests that 3- O -sulfation of the heparin N -sulfoglucosamine (GlcNS) residues pre-organize the secondary structure in a way that facilitates binding to antithrombin-III. NMR studies of the GlcNS NH groups can provide important information about heparin structure complementary to that available from NMR spectral analysis of the carbon-bound protons.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
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  • 10
    Publication Date: 2014-07-19
    Description: The accuracy of state-of-the-art global barotropic tide models is assessed using bottom-pressure data, coastal tide gauges, satellite altimetry, various geodetic data on Antarctic ice shelves, and independent tracked satellite orbit perturbations. Tidemodels under review include empirical, purely hydrodynamic (“forward”), and assimilative dynamical, i.e., constrained by observations. Ten dominant tidal constituents in the diurnal, semidiurnal, and quarter-diurnal bands are considered. Since the last major model-comparison project in 1997, models have improved markedly, especially in shallow-water regions but also in the deep ocean. The root-sum-square differences between tide observations and the best models for 8 major constituentsis approximately 0.9, 5.0, and 6.5 cm for pelagic, shelf, and coastal conditions, respectively. Large inter-model discrepancies occur in high latitudes, but testing in those regions is impeded by the paucity of high-quality in-situ tide records. Long-wavelength components of models tested by analyzing satellite laser ranging measurements suggest several models are comparably accurate for use in precise orbit determination, but analyses of GRACE inter-satellite ranging data show that all models are still imperfect on basin and sub-basin scales, especially near Antarctica. For the M 2 constituent, errors in purely hydrodynamic models are now almost comparable to the 1980-era Schwiderski empirical solution, indicating marked advancement in dynamical modeling. Assessing model accuracy using tidal currents remains problematic owing to uncertainties in in-situ current-meter estimates and the inability to isolate the barotropic mode. Velocity tests against both acoustic tomography and current meters do confirm that assimilative models perform better than purely hydrodynamic models.
    Print ISSN: 8755-1209
    Topics: Geosciences
    Published by Wiley on behalf of American Geophysical Union (AGU).
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