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Sample records for central metabolic flux

  1. Transcript abundance on its own cannot be used to infer fluxes in central metabolism

    OpenAIRE

    Jörg eSchwender; Christina eKönig; Matthias eKlapperstück; Nicolas eHeinzel; Eberhard eMunz; Inga eHebbelmann; Jordan O. Hay; Peter eDenolf; Stefanie De Bodt; Henning eRedestig; Evelyne eCaestecker; Peter M. Jakob; Ljudmilla eBorisjuk; Hardy eRolletschek

    2014-01-01

    An attempt has been made to define the extent to which metabolic flux in central plant metabolism is reflected by changes in the transcriptome and metabolome, based on an analysis of in vitro cultured immature embryos of two oilseed rape (Brassica napus) accessions which contrast for seed lipid accumulation. Metabolic flux analysis was used to constrain a flux balance metabolic model which included 671 biochemical and transport reactions within the central metabolism. This highly confident fl...

  2. Transcript abundance on its own cannot be used to infer fluxes in central metabolism

    OpenAIRE

    Schwender, Jörg; König, Christina; Klapperstück, Matthias; Heinzel, Nicolas; Munz, Eberhard; Hebbelmann, Inga; Jordan O. Hay; Denolf, Peter; De Bodt, Stefanie; Redestig, Henning; Caestecker, Evelyne; Peter M. Jakob; Borisjuk, Ljudmilla; Rolletschek, Hardy

    2014-01-01

    An attempt has been made to define the extent to which metabolic flux in central plant metabolism is reflected by changes in the transcriptome and metabolome, based on an analysis of in vitro cultured immature embryos of two oilseed rape (Brassica napus) accessions which contrast for seed lipid accumulation. Metabolic flux analysis (MFA) was used to constrain a flux balance metabolic model which included 671 biochemical and transport reactions within the central metabolism. This highly confid...

  3. Metabolic Flux Analysis of Shewanella spp. Reveals Evolutionary Robustness in Central Carbon Metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Yinjie J.; Martin, Hector Garcia; Dehal, Paramvir S.; Deutschbauer, Adam; Llora, Xavier; Meadows, Adam; Arkin, Adam; Keasling, Jay D.

    2009-08-19

    Shewanella spp. are a group of facultative anaerobic bacteria widely distributed in marine and fresh-water environments. In this study, we profiled the central metabolic fluxes of eight recently sequenced Shewanella species grown under the same condition in minimal med-ium with [3-13C] lactate. Although the tested Shewanella species had slightly different growth rates (0.23-0.29 h31) and produced different amounts of acetate and pyruvate during early exponential growth (pseudo-steady state), the relative intracellular metabolic flux distributions were remarkably similar. This result indicates that Shewanella species share similar regulation in regard to central carbon metabolic fluxes under steady growth conditions: the maintenance of metabolic robustness is not only evident in a single species under genetic perturbations (Fischer and Sauer, 2005; Nat Genet 37(6):636-640), but also observed through evolutionary related microbial species. This remarkable conservation of relative flux profiles through phylogenetic differences prompts us to introduce the concept of metabotype as an alternative scheme to classify microbial fluxomics. On the other hand, Shewanella spp. display flexibility in the relative flux profiles when switching their metabolism from consuming lactate to consuming pyruvate and acetate.

  4. Investigation into the flux distribution of central carbon metabolism in Corynebacterium glutamicum using principal component analysis

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    Shang Chuanyu

    2015-01-01

    Full Text Available Central carbon metabolism is the main source of energy required by organisms and it provides precursors for other in vivo metabolic processes. The flux flowing through the pathways involved in central carbon metabolism characterizes its biological function and genetic readout between species or environments. In recent years, using a 13C tracer technique, researchers have measured the flux of central carbon metabolism in Corynebacterium glutamicum under a variety of nutritional and environmental changes or genetic modifications. However, there is no integrated and comparative analysis of these measured flux values. In this study, the flux values of central carbon metabolism in Corynebacterium glutamicum that were obtained in other recent studies were consolidated. A preliminary examination of the distribution characteristics of flux values in each metabolic pathway was conducted and the regression relationship between different fluxes was investigated. The principal components of the flux vector were further extracted and aggregated based on the components, and the general features of flux distribution of central carbon metabolism as well as the influence of environmental and genetic factors on the flux distribution were determined. This study provides a foundation for further investigation into the flux distribution and regulation characteristics of central carbon metabolism.

  5. Transcript abundance on its own cannot be used to infer fluxes in central metabolism

    Directory of Open Access Journals (Sweden)

    Jörg eSchwender

    2014-11-01

    Full Text Available An attempt has been made to define the extent to which metabolic flux in central plant metabolism is reflected by changes in the transcriptome and metabolome, based on an analysis of in vitro cultured immature embryos of two oilseed rape (Brassica napus accessions which contrast for seed lipid accumulation. Metabolic flux analysis was used to constrain a flux balance metabolic model which included 671 biochemical and transport reactions within the central metabolism. This highly confident flux information was eventually used for comparative analysis of flux versus transcript (metabolite. Metabolite profiling succeeded in identifying 79 intermediates within the central metabolism, some of which differed quantitatively between the two accessions and displayed a significant shift corresponding to flux. An RNA-Seq based transcriptome analysis revealed a large number of genes which were differentially transcribed in the two accessions, including some enzymes/proteins active in major metabolic pathways. With a few exceptions, differential activity in the major pathways (glycolysis, TCA cycle, amino acid and fatty acid synthesis was not reflected in contrasting abundances of the relevant transcripts. The conclusion was that transcript abundance on its own cannot be used to infer metabolic activity/fluxes in central plant metabolism. This limitation needs to be borne in mind in evaluating transcriptome data and designing metabolic engineering experiments.

  6. Invariability of Central Metabolic Flux Distribution in Shewanella oneidensis MR-1 Under Environmental or Genetic Perturbations

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Yinjie; Martin, Hector Garcia; Deutschbauer, Adam; Feng, Xueyang; Huang, Rick; Llora, Xavier; Arkin, Adam; Keasling, Jay D.

    2009-04-21

    An environmentally important bacterium with versatile respiration, Shewanella oneidensis MR-1, displayed significantly different growth rates under three culture conditions: minimal medium (doubling time {approx} 3 hrs), salt stressed minimal medium (doubling time {approx} 6 hrs), and minimal medium with amino acid supplementation (doubling time {approx}1.5 hrs). {sup 13}C-based metabolic flux analysis indicated that fluxes of central metabolic reactions remained relatively constant under the three growth conditions, which is in stark contrast to the reported significant changes in the transcript and metabolite profiles under various growth conditions. Furthermore, ten transposon mutants of S. oneidensis MR-1 were randomly chosen from a transposon library and their flux distributions through central metabolic pathways were revealed to be identical, even though such mutational processes altered the secondary metabolism, for example, glycine and C1 (5,10-Me-THF) metabolism.

  7. Flux analysis of central metabolic pathways in Geobactermetallireducens during reduction of solubleFe(III)-NTA

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Yinjie J.; Chakraborty, Romy; Garcia-Martin, Hector; Chu,Jeannie; Hazen, Terry C.; Keasling, Jay D.

    2007-01-01

    We analyzed the carbon fluxes in the central metabolism ofGeobacter metallireducens strain GS-15 using 13C isotopomer modeling.Acetate labeled in the 1st or 2nd position was the sole carbon source,and Fe-NTA was the sole terminal electron acceptor. The measured labeledacetate uptake rate was 21 mmol/gdw/h in the exponential growth phase.The resulting isotope labeling pattern of amino acids allowed an accuratedetermination of the in vivo global metabolic reaction rates (fluxes)through the central metabolic pathways using a computational isotopomermodel. The tracer experiments showed that G. metallireducens containedcomplete biosynthesis pathways for essential metabolism, and this strainmight also have an unusual isoleucine biosynthesis route (usingacetyl-CoA and pyruvate as the precursors). The model indicated that over90 percent of the acetate was completely oxidized to CO2 via a completetricarboxylic acid (TCA) cycle while reducing iron. Pyruvate carboxylaseand phosphoenolpyruvate carboxykinase were present under theseconditions, but enzymes in the glyoxylate shunt and malic enzyme wereabsent. Gluconeogenesis and the pentose phosphate pathway were mainlyemployed for biosynthesis and accounted for less than 3 percent of totalcarbon consumption. The model also indicated surprisingly highreversibility in the reaction between oxoglutarate and succinate. Thisstep operates close to the thermodynamic equilibrium possibly becausesuccinate is synthesized via a transferase reaction, and the conversionof oxoglutarate to succinate is a rate limiting step for carbonmetabolism. These findings enable a better understanding of therelationship between genome annotation and extant metabolic pathways inG. metallireducens.

  8. Elementary Flux Mode Analysis Revealed Cyclization Pathway as a Powerful Way for NADPH Regeneration of Central Carbon Metabolism.

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    Bin Rui

    Full Text Available NADPH regeneration capacity is attracting growing research attention due to its important role in resisting oxidative stress. Besides, NADPH availability has been regarded as a limiting factor in production of industrially valuable compounds. The central carbon metabolism carries the carbon skeleton flux supporting the operation of NADPH-regenerating enzyme and offers flexibility in coping with NADPH demand for varied intracellular environment. To acquire an insightful understanding of its NADPH regeneration capacity, the elementary mode method was employed to compute all elementary flux modes (EFMs of a network representative of central carbon metabolism. Based on the metabolic flux distributions of these modes, a cluster analysis of EFMs with high NADPH regeneration rate was conducted using the self-organizing map clustering algorithm. The clustering results were used to study the relationship between the flux of total NADPH regeneration and the flux in each NADPH producing enzyme. The results identified several reaction combinations supporting high NADPH regeneration, which are proven to be feasible in cells via thermodynamic analysis and coincident with a great deal of previous experimental report. Meanwhile, the reaction combinations showed some common characteristics: there were one or two decarboxylation oxidation reactions in the combinations that produced NADPH and the combination constitution included certain gluconeogenesis pathways. These findings suggested cyclization pathways as a powerful way for NADPH regeneration capacity of bacterial central carbon metabolism.

  9. Investigating the effects of perturbations to pgi and eno gene expression on central carbon metabolism in Escherichia coli using 13 C metabolic flux analysis

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    Usui Yuki

    2012-06-01

    Full Text Available Abstract Background It has long been recognized that analyzing the behaviour of the complex intracellular biological networks is important for breeding industrially useful microorganisms. However, because of the complexity of these biological networks, it is currently not possible to obtain all the desired microorganisms. In this study, we constructed a system for analyzing the effect of gene expression perturbations on the behavior of biological networks in Escherichia coli. Specifically, we utilized 13 C metabolic flux analysis (13 C-MFA to analyze the effect of perturbations to the expression levels of pgi and eno genes encoding phosphoglucose isomerase and enolase, respectively on metabolic fluxes. Results We constructed gene expression-controllable E. coli strains using a single-copy mini F plasmid. Using the pgi expression-controllable strain, we found that the specific growth rate correlated with the pgi expression level. 13 C-MFA of this strain revealed that the fluxes for the pentose phosphate pathway and Entner-Doudoroff pathway decreased, as the pgi expression lelvel increased. In addition, the glyoxylate shunt became active when the pgi expression level was almost zero. Moreover, the flux for the glyoxylate shunt increased when the pgi expression level decreased, but was significantly reduced in the pgi-knockout cells. Comparatively, eno expression could not be decreased compared to the parent strain, but we found that increased eno expression resulted in a decreased specific growth rate. 13 C-MFA revealed that the metabolic flux distribution was not altered by an increased eno expression level, but the overall metabolic activity of the central metabolism decreased. Furthermore, to evaluate the impact of perturbed expression of pgi and eno genes on changes in metabolic fluxes in E. coli quantitatively, metabolic sensitivity analysis was performed. As a result, the perturbed expression of pgi gene had a great impact to the

  10. Metabolic flux determination using carbon 13 NMR. Application to normal and tumoral cells from central nervous system

    International Nuclear Information System (INIS)

    Carbon 13 NMR constitutes a potent tool to study cellular metabolism by the use of 13C enriched substrates. Analyzes of 13C NMR spectra recorded from acidic cell extracts lead to the evaluation of specific enrichment of various metabolites. On the other hand, the measure of homonuclear 13C-13C spin coupling gives information on the different isotopomers for a given molecule. Mathematical models were different isotopomers for a given molecule. Mathematical models were developed to interpret the NMR data in terms of metabolic fluxes through the metabolic network of interest. Various models established in our laboratory are presented. These models were applied to metabolic studies of cultured central nervous system cells as rat cerebellar astrocytes and granule cells, and the C6 glioma cell line. (authors). 17 refs., 3 figs., 2 tabs

  11. Carbon conversion efficiency and central metabolic fluxes in developing sunflower (Helianthus annuus L.) embryos.

    Science.gov (United States)

    Alonso, Ana P; Goffman, Fernando D; Ohlrogge, John B; Shachar-Hill, Yair

    2007-10-01

    The efficiency with which developing sunflower embryos convert substrates into seed storage reserves was determined by labeling embryos with [U-(14)C6]glucose or [U-(14)C5]glutamine and measuring their conversion to CO2, oil, protein and other biomass compounds. The average carbon conversion efficiency was 50%, which contrasts with a value of over 80% previously observed in Brassica napus embryos (Goffman et al., 2005), in which light and the RuBisCO bypass pathway allow more efficient conversion of hexose to oil. Labeling levels after incubating sunflower embryos with [U-(14)C4]malate indicated that some carbon from malate enters the plastidic compartment and contributes to oil synthesis. To test this and to map the underlying pattern of metabolic fluxes, separate experiments were carried out in which embryos were labeled to isotopic steady state using [1-(13)C1]glucose, [2-(13)C1]glucose, or [U-(13)C5]glutamine. The resultant labeling in sugars, starch, fatty acids and amino acids was analyzed by NMR and GC-MS. The fluxes through intermediary metabolism were then quantified by computer-aided modeling. The resulting flux map accounted well for the labeling data, was in good agreement with the observed carbon efficiency, and was further validated by testing for agreement with gas exchange measurements. The map shows that the influx of malate into oil is low and that flux through futile cycles (wasting ATP) is low, which contrasts with the high rates previously determined for growing root tips and heterotrophic cell cultures. PMID:17683473

  12. Flux analysis of central metabolic pathways in the Fe(III)-reducing organism Geobacter metallireducens via 13C isotopiclabeling

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Yinjie J.; Chakraborty, Romy; Martin, Hector Garcia; Chu,Jeannie; Hazen, Terry C.; Keasling, Jay D.

    2007-08-13

    We analyzed the carbon fluxes in the central metabolism ofGeobacter metallireducens strain GS-15 using 13C isotopomer modeling.Acetate labeled in the 1st or 2nd position was the sole carbon source,and Fe-NTA was the sole terminal electron acceptor. The measured labeledacetate uptake rate was 21 mmol/gdw/h in the exponential growth phase.The resulting isotope labeling pattern of amino acids allowed an accuratedetermination of the in vivo global metabolic reaction rates (fluxes)through the central metabolic pathways using a computational isotopomermodel. The model indicated that over 90 percent of the acetate wascompletely oxidized to CO2 via a complete tricarboxylic acid (TCA) cyclewhile reducing iron. Pyruvate carboxylase and phosphoenolpyruvatecarboxykinase were present under these conditions, but enzymes in theglyoxylate shunt and malic enzyme were absent. Gluconeogenesis and thepentose phosphate pathway were mainly employed for biosynthesis andaccounted for less than 3 percent of total carbon consumption. The modelalso indicated surprisingly high reversibility in the reaction betweenoxoglutarate and succinate. This step operates close to the thermodynamicequilibrium possibly because succinate is synthesized via a transferasereaction, and its product, acetyl-CoA, inhibits the conversion ofoxoglutarate to succinate. These findings enable a better understandingof the relationship between genome annotation and extant metabolicpathways in G. metallireducens.

  13. Shigella reroutes host cell central metabolism to obtain high-flux nutrient supply for vigorous intracellular growth

    OpenAIRE

    Kentner, David; Martano, Giuseppe; Callon, Morgane; Chiquet, Petra; Brodmann, Maj; Burton, Olga; Wahlander, Asa; Nanni, Paolo; Delmotte, Nathanaël; Grossmann, Jonas; Limenitakis, Julien; Schlapbach, Ralph; Kiefer, Patrick; Vorholt, Julia A.; Hiller, Sebastian

    2014-01-01

    Shigella flexneri proliferate in infected human epithelial cells at exceptionally high rates. This vigorous growth has important consequences for rapid progression to life-threatening bloody diarrhea, but the underlying metabolic mechanisms remain poorly understood. Here, we used metabolomics, proteomics, and genetic experiments to determine host and Shigella metabolism during infection in a cell culture model. The data suggest that infected host cells maintain largely normal fluxes through g...

  14. Flux-P: Automating Metabolic Flux Analysis

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    Birgitta E. Ebert

    2012-11-01

    Full Text Available Quantitative knowledge of intracellular fluxes in metabolic networks is invaluable for inferring metabolic system behavior and the design principles of biological systems. However, intracellular reaction rates can not often be calculated directly but have to be estimated; for instance, via 13C-based metabolic flux analysis, a model-based interpretation of stable carbon isotope patterns in intermediates of metabolism. Existing software such as FiatFlux, OpenFLUX or 13CFLUX supports experts in this complex analysis, but requires several steps that have to be carried out manually, hence restricting the use of this software for data interpretation to a rather small number of experiments. In this paper, we present Flux-P as an approach to automate and standardize 13C-based metabolic flux analysis, using the Bio-jETI workflow framework. Exemplarily based on the FiatFlux software, it demonstrates how services can be created that carry out the different analysis steps autonomously and how these can subsequently be assembled into software workflows that perform automated, high-throughput intracellular flux analysis of high quality and reproducibility. Besides significant acceleration and standardization of the data analysis, the agile workflow-based realization supports flexible changes of the analysis workflows on the user level, making it easy to perform custom analyses.

  15. Shigella reroutes host cell central metabolism to obtain high-flux nutrient supply for vigorous intracellular growth.

    Science.gov (United States)

    Kentner, David; Martano, Giuseppe; Callon, Morgane; Chiquet, Petra; Brodmann, Maj; Burton, Olga; Wahlander, Asa; Nanni, Paolo; Delmotte, Nathanaël; Grossmann, Jonas; Limenitakis, Julien; Schlapbach, Ralph; Kiefer, Patrick; Vorholt, Julia A; Hiller, Sebastian; Bumann, Dirk

    2014-07-01

    Shigella flexneri proliferate in infected human epithelial cells at exceptionally high rates. This vigorous growth has important consequences for rapid progression to life-threatening bloody diarrhea, but the underlying metabolic mechanisms remain poorly understood. Here, we used metabolomics, proteomics, and genetic experiments to determine host and Shigella metabolism during infection in a cell culture model. The data suggest that infected host cells maintain largely normal fluxes through glycolytic pathways, but the entire output of these pathways is captured by Shigella, most likely in the form of pyruvate. This striking strategy provides Shigella with an abundant favorable energy source, while preserving host cell ATP generation, energy charge maintenance, and survival, despite ongoing vigorous exploitation. Shigella uses a simple three-step pathway to metabolize pyruvate at high rates with acetate as an excreted waste product. The crucial role of this pathway for Shigella intracellular growth suggests targets for antimicrobial chemotherapy of this devastating disease. PMID:24958876

  16. Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism.

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    Ahmad A Mannan

    Full Text Available An understanding of the dynamics of the metabolic profile of a bacterial cell is sought from a dynamical systems analysis of kinetic models. This modelling formalism relies on a deterministic mathematical description of enzyme kinetics and their metabolite regulation. However, it is severely impeded by the lack of available kinetic information, limiting the size of the system that can be modelled. Furthermore, the subsystem of the metabolic network whose dynamics can be modelled is faced with three problems: how to parameterize the model with mostly incomplete steady state data, how to close what is now an inherently open system, and how to account for the impact on growth. In this study we address these challenges of kinetic modelling by capitalizing on multi-'omics' steady state data and a genome-scale metabolic network model. We use these to generate parameters that integrate knowledge embedded in the genome-scale metabolic network model, into the most comprehensive kinetic model of the central carbon metabolism of E. coli realized to date. As an application, we performed a dynamical systems analysis of the resulting enriched model. This revealed bistability of the central carbon metabolism and thus its potential to express two distinct metabolic states. Furthermore, since our model-informing technique ensures both stable states are constrained by the same thermodynamically feasible steady state growth rate, the ensuing bistability represents a temporal coexistence of the two states, and by extension, reveals the emergence of a phenotypically heterogeneous population.

  17. Flux networks in metabolic graphs

    International Nuclear Information System (INIS)

    A metabolic model can be represented as a bipartite graph comprising linked reaction and metabolite nodes. Here it is shown how a network of conserved fluxes can be assigned to the edges of such a graph by combining the reaction fluxes with a conserved metabolite property such as molecular weight. A similar flux network can be constructed by combining the primal and dual solutions to the linear programming problem that typically arises in constraint-based modelling. Such constructions may help with the visualization of flux distributions in complex metabolic networks. The analysis also explains the strong correlation observed between metabolite shadow prices (the dual linear programming variables) and conserved metabolite properties. The methods were applied to recent metabolic models for Escherichia coli, Saccharomyces cerevisiae and Methanosarcina barkeri. Detailed results are reported for E. coli; similar results were found for other organisms

  18. Optimal flux patterns in cellular metabolic networks

    Energy Technology Data Exchange (ETDEWEB)

    Almaas, E

    2007-01-20

    The availability of whole-cell level metabolic networks of high quality has made it possible to develop a predictive understanding of bacterial metabolism. Using the optimization framework of flux balance analysis, I investigate metabolic response and activity patterns to variations in the availability of nutrient and chemical factors such as oxygen and ammonia by simulating 30,000 random cellular environments. The distribution of reaction fluxes is heavy-tailed for the bacteria H. pylori and E. coli, and the eukaryote S. cerevisiae. While the majority of flux balance investigations have relied on implementations of the simplex method, it is necessary to use interior-point optimization algorithms to adequately characterize the full range of activity patterns on metabolic networks. The interior-point activity pattern is bimodal for E. coli and S. cerevisiae, suggesting that most metabolic reaction are either in frequent use or are rarely active. The trimodal activity pattern of H. pylori indicates that a group of its metabolic reactions (20%) are active in approximately half of the simulated environments. Constructing the high-flux backbone of the network for every environment, there is a clear trend that the more frequently a reaction is active, the more likely it is a part of the backbone. Finally, I briefly discuss the predicted activity patterns of the central-carbon metabolic pathways for the sample of random environments.

  19. Flux-balance modelling of plant metabolism

    OpenAIRE

    Lee James Sweetlove; R. George eRatcliffe

    2011-01-01

    Flux-balance modelling of plant metabolic networks provides an important complement to 13C-based metabolic flux analysis. Flux-balance modelling is a constraints-based approach in which steady-state fluxes in a metabolic network are predicted by using optimisation algorithms within an experimentally bounded solution space. In the last two years several flux-balance models of plant metabolism have been published including genome-scale models of Arabidopsis metabolism. In this review we conside...

  20. Modeling the Contribution of Allosteric Regulation for Flux Control in the Central Carbon Metabolism of E. coli

    DEFF Research Database (Denmark)

    Machado, Daniel; Herrgard, Markus; Rocha, Isabel

    2015-01-01

    Modeling cellular metabolism is fundamental for many biotechnological applications, including drug discovery and rational cell factory design. Central carbon metabolism (CCM) is particularly important as it provides the energy and precursors for other biological processes. However, the complex...

  1. Pathway confirmation and flux analysis of central metabolic pathways in Desulfovibrio vulgaris Hildenborough using Gas Chromatography-Mass Spectrometry and Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry

    International Nuclear Information System (INIS)

    Flux distribution in central metabolic pathways of Desulfovibrio vulgaris Hildenborough was examined using 13C tracer experiments. Consistent with the current genome annotation and independent evidence from enzyme activity assays, the isotopomer results from both GC-MS and Fourier Transform-Ion Cyclotron Resonance mass spectrometry (FT-ICR MS) indicate the lack of oxidatively functional TCA cycle and an incomplete pentose phosphate pathway. Results from this study suggest that fluxes through both pathways are limited to biosynthesis. The data also indicate that >80 percent of the lactate was converted to acetate and the reactions involved are the primary route of energy production (NAD(P)H and ATP production). Independent of the TCA cycle, direct cleavage of acetyl-CoA to CO and 5,10-methyl-THF also leads to production of NADH and ATP. Although the genome annotation implicates a ferredoxin-dependent oxoglutarate synthase, isotopic evidence does not support flux through this reaction in either the oxidative or reductive mode; therefore, the TCA cycle is incomplete. FT-ICR MS was used to locate the labeled carbon distribution in aspartate and glutamate and confirmed the presence of an atypical enzyme for citrate formation suggested in previous reports (the citrate synthesized by this enzyme is the isotopic antipode of the citrate synthesized by the (S)-citrate synthase). These findings enable a better understanding of the relation between genome annotation and actual metabolic pathways in D. vulgaris, and also demonstrate FT-ICR MS as a powerful tool for isotopomer analysis, overcoming problems in both GC-MS and NMR spectroscopy

  2. Measuring and modeling C flux rates through the central metabolic pathways in microbial communities using position-specific 13C-labeled tracers

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    Dijkstra, P.; van Groenigen, K.; Hagerty, S.; Salpas, E.; Fairbanks, D. E.; Hungate, B. A.; KOCH, G. W.; Schwartz, E.

    2012-12-01

    The production of energy and metabolic precursors occurs in well-known processes such as glycolysis and Krebs cycle. We use position-specific 13C-labeled metabolic tracers, combined with models of microbial metabolic organization, to analyze the response of microbial community energy production, biosynthesis, and C use efficiency (CUE) in soils, decomposing litter, and aquatic communities. The method consists of adding position-specific 13C -labeled metabolic tracers to parallel soil incubations, in this case 1-13C and 2,3-13C pyruvate and 1-13C and U-13C glucose. The measurement of CO2 released from the labeled tracers is used to calculate the C flux rates through the various metabolic pathways. A simplified metabolic model consisting of 23 reactions is solved using results of the metabolic tracer experiments and assumptions of microbial precursor demand. This new method enables direct estimation of fundamental aspects of microbial energy production, CUE, and soil organic matter formation in relatively undisturbed microbial communities. We will present results showing the range of metabolic patterns observed in these communities and discuss results from testing metabolic models.

  3. Simulation of Flux Distribution in Central Metabolism of Saccharomyces cerevisiae by Hybridized Genetic Algorithm%杂合基因算法在酵母中间代谢途径代谢通量分析中的应用

    Institute of Scientific and Technical Information of China (English)

    张慧敏; 姚善泾

    2007-01-01

    A scheme of investigating the intracellular metabolic fluxes in central metabolism of Saccharomyces cerevisiae based on isotope model and tracer experiment was developed. The metabolic model applied in this study includes the Embden-Meyerhof-Parnas pathway, the pentose phosphate pathway, the tricarboxylic acid cycle, CO2 anaplerotic reactions, ethanol and acetate formation, and pathways involved in amino acid synthesis. The approach of hybridized genetic algorithm combined with the sequential simplex technique was used to optimize a quadratic error function without the requirement of the information on the partial derivatives. The impact of some key parameters on the algorithm was studied. This approach was proved to be rapid and numerically stable in the analysis of the central metabolism of S.cerevisiae.

  4. Controlling fluxes for microbial metabolic engineering

    OpenAIRE

    Sachdeva, Gairik

    2014-01-01

    This thesis presents novel synthetic biology tools and design principles usable for microbial metabolic engineering. Controlling metabolic fluxes is essential for biological manufacturing of fuels, materials, and high value chemicals. Insulating the flow of metabolites is a successful natural strategy for metabolic flux regulation. Recently, approaches using scaffolds, both in vitro and in vivo, to spatially co-localize enzymes have reported significant gains in product yields. RNA is suitabl...

  5. Metabolic flux rewiring in mammalian cell cultures.

    Science.gov (United States)

    Young, Jamey D

    2013-12-01

    Continuous cell lines (CCLs) engage in 'wasteful' glucose and glutamine metabolism that leads to accumulation of inhibitory byproducts, primarily lactate and ammonium. Advances in techniques for mapping intracellular carbon fluxes and profiling global changes in enzyme expression have led to a deeper understanding of the molecular drivers underlying these metabolic alterations. However, recent studies have revealed that CCLs are not necessarily entrenched in a glycolytic or glutaminolytic phenotype, but instead can shift their metabolism toward increased oxidative metabolism as nutrients become depleted and/or growth rate slows. Progress to understand dynamic flux regulation in CCLs has enabled the development of novel strategies to force cultures into desirable metabolic phenotypes, by combining fed-batch feeding strategies with direct metabolic engineering of host cells. PMID:23726154

  6. Comparison between elementary flux modes analysis and 13C-metabolic fluxes measured in bacterial and plant cells

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    Dieuaide-Noubhani Martine

    2011-06-01

    Full Text Available Abstract Background 13C metabolic flux analysis is one of the pertinent ways to compare two or more physiological states. From a more theoretical standpoint, the structural properties of metabolic networks can be analysed to explore feasible metabolic behaviours and to define the boundaries of steady state flux distributions. Elementary flux mode analysis is one of the most efficient methods for performing this analysis. In this context, recent approaches have tended to compare experimental flux measurements with topological network analysis. Results Metabolic networks describing the main pathways of central carbon metabolism were set up for a bacteria species (Corynebacterium glutamicum and a plant species (Brassica napus for which experimental flux maps were available. The structural properties of each network were then studied using the concept of elementary flux modes. To do this, coefficients of flux efficiency were calculated for each reaction within the networks by using selected sets of elementary flux modes. Then the relative differences - reflecting the change of substrate i.e. a sugar source for C. glutamicum and a nitrogen source for B. napus - of both flux efficiency and flux measured experimentally were compared. For both organisms, there is a clear relationship between these parameters, thus indicating that the network structure described by the elementary flux modes had captured a significant part of the metabolic activity in both biological systems. In B. napus, the extension of the elementary flux mode analysis to an enlarged metabolic network still resulted in a clear relationship between the change in the coefficients and that of the measured fluxes. Nevertheless, the limitations of the method to fit some particular fluxes are discussed. Conclusion This consistency between EFM analysis and experimental flux measurements, validated on two metabolic systems allows us to conclude that elementary flux mode analysis could be a

  7. 13C metabolic flux analysis at a genome-scale.

    Science.gov (United States)

    Gopalakrishnan, Saratram; Maranas, Costas D

    2015-11-01

    Metabolic models used in 13C metabolic flux analysis generally include a limited number of reactions primarily from central metabolism. They typically omit degradation pathways, complete cofactor balances, and atom transition contributions for reactions outside central metabolism. This study addresses the impact on prediction fidelity of scaling-up mapping models to a genome-scale. The core mapping model employed in this study accounts for (75 reactions and 65 metabolites) primarily from central metabolism. The genome-scale metabolic mapping model (GSMM) (697 reaction and 595 metabolites) is constructed using as a basis the iAF1260 model upon eliminating reactions guaranteed not to carry flux based on growth and fermentation data for a minimal glucose growth medium. Labeling data for 17 amino acid fragments obtained from cells fed with glucose labeled at the second carbon was used to obtain fluxes and ranges. Metabolic fluxes and confidence intervals are estimated, for both core and genome-scale mapping models, by minimizing the sum of square of differences between predicted and experimentally measured labeling patterns using the EMU decomposition algorithm. Overall, we find that both topology and estimated values of the metabolic fluxes remain largely consistent between core and GSM model. Stepping up to a genome-scale mapping model leads to wider flux inference ranges for 20 key reactions present in the core model. The glycolysis flux range doubles due to the possibility of active gluconeogenesis, the TCA flux range expanded by 80% due to the availability of a bypass through arginine consistent with labeling data, and the transhydrogenase reaction flux was essentially unresolved due to the presence of as many as five routes for the inter-conversion of NADPH to NADH afforded by the genome-scale model. By globally accounting for ATP demands in the GSMM model the unused ATP decreased drastically with the lower bound matching the maintenance ATP requirement. A non

  8. Metabolic flux rewiring in mammalian cell cultures

    OpenAIRE

    Young, Jamey D.

    2013-01-01

    Continuous cell lines (CCLs) engage in “wasteful” glucose and glutamine metabolism that leads to accumulation of inhibitory byproducts, primarily lactate and ammonium. Advances in techniques for mapping intracellular carbon fluxes and profiling global changes in enzyme expression have led to a deeper understanding of the molecular drivers underlying these metabolic alterations. However, recent studies have revealed that CCLs are not necessarily entrenched in a glycolytic or glutaminolytic phe...

  9. Metabolism as means for hypoxia adaptation: metabolic profiling and flux balance analysis

    Directory of Open Access Journals (Sweden)

    Paternostro Giovanni

    2009-09-01

    Full Text Available Abstract Background Cellular hypoxia is a component of many diseases, but mechanisms of global hypoxic adaptation and resistance are not completely understood. Previously, a population of Drosophila flies was experimentally selected over several generations to survive a chronically hypoxic environment. NMR-based metabolomics, combined with flux-balance simulations of genome-scale metabolic networks, can generate specific hypotheses for global reaction fluxes within the cell. We applied these techniques to compare metabolic activity during acute hypoxia in muscle tissue of adapted versus "naïve" control flies. Results Metabolic profiles were gathered for adapted and control flies after exposure to acute hypoxia using 1H NMR spectroscopy. Principal Component Analysis suggested that the adapted flies are tuned to survive a specific oxygen level. Adapted flies better tolerate acute hypoxic stress, and we explored the mechanisms of this tolerance using a flux-balance model of central metabolism. In the model, adapted flies produced more ATP per glucose and created fewer protons than control flies, had lower pyruvate carboxylase flux, and had greater usage of Complex I over Complex II. Conclusion We suggest a network-level hypothesis of metabolic regulation in hypoxia-adapted flies, in which lower baseline rates of biosynthesis in adapted flies draws less anaplerotic flux, resulting in lower rates of glycolysis, less acidosis, and more efficient use of substrate during acute hypoxic stress. In addition we suggest new specific hypothesis, which were found to be consistent with existing data.

  10. Assessing compartmentalized flux in lipid metabolism with isotopes.

    Science.gov (United States)

    Allen, Doug K

    2016-09-01

    Metabolism in plants takes place across multiple cell types and within distinct organelles. The distributions equate to spatial heterogeneity; though the limited means to experimentally assess metabolism frequently involve homogenizing tissues and mixing metabolites from different locations. Most current isotope investigations of metabolism therefore lack the ability to resolve spatially distinct events. Recognition of this limitation has resulted in inspired efforts to advance metabolic flux analysis and isotopic labeling techniques. Though a number of these efforts have been applied to studies in central metabolism; recent advances in instrumentation and techniques present an untapped opportunity to make similar progress in lipid metabolism where the use of stable isotopes has been more limited. These efforts will benefit from sophisticated radiolabeling reports that continue to enrich our knowledge on lipid biosynthetic pathways and provide some direction for stable isotope experimental design and extension of MFA. Evidence for this assertion is presented through the review of several elegant stable isotope studies and by taking stock of what has been learned from radioisotope investigations when spatial aspects of metabolism were considered. The studies emphasize that glycerolipid production occurs across several locations with assembly of lipids in the ER or plastid, fatty acid biosynthesis occurring in the plastid, and the generation of acetyl-CoA and glycerol-3-phosphate taking place at multiple sites. Considering metabolism in this context underscores the cellular and subcellular organization that is important to enhanced production of glycerolipids in plants. An attempt is made to unify salient features from a number of reports into a diagrammatic model of lipid metabolism and propose where stable isotope labeling experiments and further flux analysis may help address questions in the field. This article is part of a Special Issue entitled: Plant Lipid

  11. Evidence for Central Regulation of Glucose Metabolism*

    OpenAIRE

    Carey, Michelle; Kehlenbrink, Sylvia; Hawkins, Meredith

    2013-01-01

    Evidence for central regulation of glucose homeostasis is accumulating from both animal and human studies. Central nutrient and hormone sensing in the hypothalamus appears to coordinate regulation of whole body metabolism. Central signals activate ATP-sensitive potassium (KATP) channels, thereby down-regulating glucose production, likely through vagal efferent signals. Recent human studies are consistent with this hypothesis. The contributions of direct and central inputs to metabolic regulat...

  12. Mapping photoautotrophic metabolism with isotopically nonstationary 13C flux analysis

    OpenAIRE

    Young, Jamey D.; Shastri, Avantika A.; Stephanopoulos, Gregory; Morgan, John A.

    2011-01-01

    Understanding in vivo regulation of photoautotrophic metabolism is important for identifying strategies to improve photosynthetic efficiency or re-route carbon fluxes to desirable end products. We have developed an approach to reconstruct comprehensive flux maps of photoautotrophic metabolism by computational analysis of dynamic isotope labeling measurements and have applied it to determine metabolic pathway fluxes in the cyanobacterium Synechocystis sp. PCC6803. Comparison to a theoretically...

  13. Hybrid optimization for 13C metabolic flux analysis using systems parametrized by compactification

    Directory of Open Access Journals (Sweden)

    Frick Oliver

    2008-03-01

    Full Text Available Abstract Background The importance and power of isotope-based metabolic flux analysis and its contribution to understanding the metabolic network is increasingly recognized. Its application is, however, still limited partly due to computational inefficiency. 13C metabolic flux analysis aims to compute in vivo metabolic fluxes in terms of metabolite balancing extended by carbon isotopomer balances and involves a nonlinear least-squares problem. To solve the problem more efficiently, improved numerical optimization techniques are necessary. Results For flux computation, we developed a gradient-based hybrid optimization algorithm. Here, independent flux variables were compactified into [0, 1-ranged variables using a single transformation rule. The compactified parameters could be discriminated between non-identifiable and identifiable variables after model linearization. The developed hybrid algorithm was applied to the central metabolism of Bacillus subtilis with only succinate and glutamate as carbon sources. This creates difficulties caused by symmetry of succinate leading to limited introduction of 13C labeling information into the system. The algorithm was found to be superior to its parent algorithms and to global optimization methods both in accuracy and speed. The hybrid optimization with tolerance adjustment quickly converged to the minimum with close to zero deviation and exactly re-estimated flux variables. In the metabolic network studied, some fluxes were found to be either non-identifiable or nonlinearly correlated. The non-identifiable fluxes could correctly be predicted a priori using the model identification method applied, whereas the nonlinear flux correlation was revealed only by identification runs using different starting values a posteriori. Conclusion This fast, robust and accurate optimization method is useful for high-throughput metabolic flux analysis, a posteriori identification of possible parameter correlations, and

  14. Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production.

    Directory of Open Access Journals (Sweden)

    Caroline Colijn

    2009-08-01

    Full Text Available Metabolism is central to cell physiology, and metabolic disturbances play a role in numerous disease states. Despite its importance, the ability to study metabolism at a global scale using genomic technologies is limited. In principle, complete genome sequences describe the range of metabolic reactions that are possible for an organism, but cannot quantitatively describe the behaviour of these reactions. We present a novel method for modeling metabolic states using whole cell measurements of gene expression. Our method, which we call E-Flux (as a combination of flux and expression, extends the technique of Flux Balance Analysis by modeling maximum flux constraints as a function of measured gene expression. In contrast to previous methods for metabolically interpreting gene expression data, E-Flux utilizes a model of the underlying metabolic network to directly predict changes in metabolic flux capacity. We applied E-Flux to Mycobacterium tuberculosis, the bacterium that causes tuberculosis (TB. Key components of mycobacterial cell walls are mycolic acids which are targets for several first-line TB drugs. We used E-Flux to predict the impact of 75 different drugs, drug combinations, and nutrient conditions on mycolic acid biosynthesis capacity in M. tuberculosis, using a public compendium of over 400 expression arrays. We tested our method using a model of mycolic acid biosynthesis as well as on a genome-scale model of M. tuberculosis metabolism. Our method correctly predicts seven of the eight known fatty acid inhibitors in this compendium and makes accurate predictions regarding the specificity of these compounds for fatty acid biosynthesis. Our method also predicts a number of additional potential modulators of TB mycolic acid biosynthesis. E-Flux thus provides a promising new approach for algorithmically predicting metabolic state from gene expression data.

  15. OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis

    Directory of Open Access Journals (Sweden)

    Nielsen Lars K

    2009-05-01

    Full Text Available Abstract Background The quantitative analysis of metabolic fluxes, i.e., in vivo activities of intracellular enzymes and pathways, provides key information on biological systems in systems biology and metabolic engineering. It is based on a comprehensive approach combining (i tracer cultivation on 13C substrates, (ii 13C labelling analysis by mass spectrometry and (iii mathematical modelling for experimental design, data processing, flux calculation and statistics. Whereas the cultivation and the analytical part is fairly advanced, a lack of appropriate modelling software solutions for all modelling aspects in flux studies is limiting the application of metabolic flux analysis. Results We have developed OpenFLUX as a user friendly, yet flexible software application for small and large scale 13C metabolic flux analysis. The application is based on the new Elementary Metabolite Unit (EMU framework, significantly enhancing computation speed for flux calculation. From simple notation of metabolic reaction networks defined in a spreadsheet, the OpenFLUX parser automatically generates MATLAB-readable metabolite and isotopomer balances, thus strongly facilitating model creation. The model can be used to perform experimental design, parameter estimation and sensitivity analysis either using the built-in gradient-based search or Monte Carlo algorithms or in user-defined algorithms. Exemplified for a microbial flux study with 71 reactions, 8 free flux parameters and mass isotopomer distribution of 10 metabolites, OpenFLUX allowed to automatically compile the EMU-based model from an Excel file containing metabolic reactions and carbon transfer mechanisms, showing it's user-friendliness. It reliably reproduced the published data and optimum flux distributions for the network under study were found quickly ( Conclusion We have developed a fast, accurate application to perform steady-state 13C metabolic flux analysis. OpenFLUX will strongly facilitate and

  16. Metabolic Fluxes in Corynebacterium glutamicum during Lysine Production with Sucrose as Carbon Source

    OpenAIRE

    Wittmann, Christoph; Kiefer, Patrick; Zelder, Oskar

    2004-01-01

    Metabolic fluxes in the central metabolism were determined for lysine-producing Corynebacterium glutamicum ATCC 21526 with sucrose as a carbon source, providing an insight into molasses-based industrial production processes with this organism. For this purpose, 13C metabolic flux analysis with parallel studies on [1-13CFru]sucrose, [1-13CGlc]sucrose, and [13C6Fru]sucrose was carried out. C. glutamicum directed 27.4% of sucrose toward extracellular lysine. The strain exhibited a relatively hig...

  17. Pool size measurements facilitate the determination of fluxes at branching points in nonstationary metabolic flux analysis: The case of Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Robert eHeise

    2015-06-01

    Full Text Available Pool size measurements are important for the estimation of absolute intracellular fluxes in particular scenarios based on data from heavy carbon isotope experiments. Recently, steady-state fluxes estimates were obtained for central carbon metabolism in an intact illuminated rosette of Arabidopsis thaliana grown photoautotrophically (Szecowka et al., 2013; Heise et al., 2014. Fluxes were estimated therein by integrating mass-spectrometric data of the dynamics of the unlabeled metabolic fraction, data on metabolic pool sizes, partitioning of metabolic pools between cellular compartments and estimates of photosynthetically inactive pools, with a simplified model of plant central carbon metabolism. However, the fluxes were determined by treating the pool sizes as fixed parameters. Here we investigated whether and, if so, to what extent the treatment of pool sizes as parameters to be optimized in three scenarios may affect the flux estimates. The results are discussed in terms of benchmark values for canonical pathways and reactions, including starch and sucrose synthesis as well as the ribulose-1,5-bisphosphate carboxylation and oxygenation reactions. In addition, we discuss pathways emerging from a divergent branch point for which pool sizes are required for flux estimation, irrespective of the computational approach used for the simulation of the observable labelling pattern. Therefore, our findings indicate the necessity for development of techniques for accurate pool size measurements to improve the quality of flux estimates from nonstationary flux estimates in intact plant cells in the absence of alternative flux measurements.

  18. Metabolic syndrome and central retinal artery occlusion

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    Kosanović-Jaković Natalija

    2005-01-01

    Full Text Available Background. The accumulation of risk factors for central retinal artery occlusion can be seen in a single person and might be explained by the metabolic syndrome. Case report. We presented the case of a 52-year-old man with no light perception in his right eye. The visual loss was monocular and painless, fundoscopy showed central retinal artery occlusion and the laboratory investigation showed the raised erythrocyte sedimentation rate of 105 mm/h and the raised C-reactive protein of 22 mg/l. Specific laboratory investigations and fluorescein angiography excluded the presence of vasculitis, collagen vascular diseases, hypercoagulable state and antiphospholipid syndrome. Conclusion. The patient met all the five of the National Cholesterol Education Program (NCEP criteria for the metabolic syndrome: hypertension, abnormal lipid profile, abnormal glucose metabolism, obesity and hyperuricemia. Measurement of C-reactive protein is useful for the assessment of therapeutic systemic effect on any abnormality in the metabolic syndrome. Individual therapy for all risk factors in the metabolic syndrome is necessary to prevent complications such as cardiovascular, retinal vascular diseases and stroke.

  19. Towards dynamic metabolic flux analysis in CHO cell cultures.

    Science.gov (United States)

    Ahn, Woo Suk; Antoniewicz, Maciek R

    2012-01-01

    Chinese hamster ovary (CHO) cells are the most widely used mammalian cell line for biopharmaceutical production, with a total global market approaching $100 billion per year. In the pharmaceutical industry CHO cells are grown in fed-batch culture, where cellular metabolism is characterized by high glucose and glutamine uptake rates combined with high rates of ammonium and lactate secretion. The metabolism of CHO cells changes dramatically during a fed-batch culture as the cells adapt to a changing environment and transition from exponential growth phase to stationary phase. Thus far, it has been challenging to study metabolic flux dynamics in CHO cell cultures using conventional metabolic flux analysis techniques that were developed for systems at metabolic steady state. In this paper we review progress on flux analysis in CHO cells and techniques for dynamic metabolic flux analysis. Application of these new tools may allow identification of intracellular metabolic bottlenecks at specific stages in CHO cell cultures and eventually lead to novel strategies for improving CHO cell metabolism and optimizing biopharmaceutical process performance. PMID:22102428

  20. Metabolic regulation and maximal reaction optimization in the central metabolism of a yeast cell

    Science.gov (United States)

    Kasbawati, Gunawan, A. Y.; Hertadi, R.; Sidarto, K. A.

    2015-03-01

    Regulation of fluxes in a metabolic system aims to enhance the production rates of biotechnologically important compounds. Regulation is held via modification the cellular activities of a metabolic system. In this study, we present a metabolic analysis of ethanol fermentation process of a yeast cell in terms of continuous culture scheme. The metabolic regulation is based on the kinetic formulation in combination with metabolic control analysis to indicate the key enzymes which can be modified to enhance ethanol production. The model is used to calculate the intracellular fluxes in the central metabolism of the yeast cell. Optimal control is then applied to the kinetic model to find the optimal regulation for the fermentation system. The sensitivity results show that there are external and internal control parameters which are adjusted in enhancing ethanol production. As an external control parameter, glucose supply should be chosen in appropriate way such that the optimal ethanol production can be achieved. For the internal control parameter, we find three enzymes as regulation targets namely acetaldehyde dehydrogenase, pyruvate decarboxylase, and alcohol dehydrogenase which reside in the acetaldehyde branch. Among the three enzymes, however, only acetaldehyde dehydrogenase has a significant effect to obtain optimal ethanol production efficiently.

  1. Metabolic syndrome and central retinal artery occlusion

    OpenAIRE

    Kosanović-Jaković Natalija; Petrović Lidija; Risimić Dijana; Milenković Svetislav; Matić Danica

    2005-01-01

    Background. The accumulation of risk factors for central retinal artery occlusion can be seen in a single person and might be explained by the metabolic syndrome. Case report. We presented the case of a 52-year-old man with no light perception in his right eye. The visual loss was monocular and painless, fundoscopy showed central retinal artery occlusion and the laboratory investigation showed the raised erythrocyte sedimentation rate of 105 mm/h and the raised C-reactive protein of 22 mg/l. ...

  2. Mapping photoautotrophic metabolism with isotopically nonstationary (13)C flux analysis.

    Science.gov (United States)

    Young, Jamey D; Shastri, Avantika A; Stephanopoulos, Gregory; Morgan, John A

    2011-11-01

    Understanding in vivo regulation of photoautotrophic metabolism is important for identifying strategies to improve photosynthetic efficiency or re-route carbon fluxes to desirable end products. We have developed an approach to reconstruct comprehensive flux maps of photoautotrophic metabolism by computational analysis of dynamic isotope labeling measurements and have applied it to determine metabolic pathway fluxes in the cyanobacterium Synechocystis sp. PCC6803. Comparison to a theoretically predicted flux map revealed inefficiencies in photosynthesis due to oxidative pentose phosphate pathway and malic enzyme activity, despite negligible photorespiration. This approach has potential to fill important gaps in our understanding of how carbon and energy flows are systemically regulated in cyanobacteria, plants, and algae. PMID:21907300

  3. Metabolic carbon fluxes and biosynthesis of polyhydroxyalkanoates in Ralstonia eutropha on short chain fatty acids.

    Science.gov (United States)

    Yu, Jian; Si, Yingtao

    2004-01-01

    Short chain fatty acids such as acetic, propionic, and butyric acids can be synthesized into polyhydroxyalkanoates (PHAs) by Ralstonia eutropha. Metabolic carbon fluxes of the acids in living cells have significant effect on the yield, composition, and thermomechanical properties of PHA bioplastics. Based on the general knowledge of central metabolism pathways and the unusual metabolic pathways in R. eutropha, a metabolic network of 41 bioreactions is constructed to analyze the carbon fluxes on utilization of the short chain fatty acids. In fed-batch cultures with constant feeding of acid media, carbon metabolism and distribution in R. eutropha were measured involving CO2, PHA biopolymers, and residual cell mass. As the cells underwent unsteady state metabolism and PHA biosynthesis under nitrogen-limited conditions, accumulative carbon balance was applied for pseudo-steady-state analysis of the metabolic carbon fluxes. Cofactor NADP/NADPH balanced between PHA synthesis and the C3/C4 pathway provided an independent constraint for solution of the underdetermined metabolic network. A major portion of propionyl-CoA was directed to pyruvate via the 2-methylcitrate cycle and further decarboxylated to acetyl-CoA. Only a small amount of propionate carbon (acetic acid in the medium. Malate is the node of the C3/C4 pathway and TCA cycle and its decarboxylation to dehydrogenation ranges from 0.33 to 1.28 in response to the demands on NADPH and oxaloacetate for short chain fatty acids utilization. PMID:15296425

  4. Experimental determination of group flux control coefficients in metabolic networks

    Energy Technology Data Exchange (ETDEWEB)

    Simpson, T.W.; Shimizu, Hiroshi; Stephanopoulos, G. [Massachusetts Inst. of Tech., Cambridge, MA (United States). Dept. of Chemical Engineering

    1998-04-20

    Grouping of reactions around key metabolite branch points can facilitate the study of metabolic control of complex metabolic networks. This top-down Metabolic Control Analysis is exemplified through the introduction of group control coefficients whose magnitudes provide a measure of the relative impact of each reaction group on the overall network flux, as well as on the overall network stability, following enzymatic amplification. In this article, the authors demonstrate the application of previously developed theory to the determination of group flux control coefficients. Experimental data for the changes in metabolic fluxes obtained in response to the introduction of six different environmental perturbations are used to determine the group flux control coefficients for three reaction groups formed around the phosphoenolpyruvate/pyruvate branch point. The consistency of the obtained group flux control coefficient estimates is systematically analyzed to ensure that all necessary conditions are satisfied. The magnitudes of the determined control coefficients suggest that the control of lysine production flux in Corynebacterium glutamicum cells at a growth base state resides within the lysine biosynthetic pathway that begins with the PEP/PYR carboxylation anaplorotic pathway.

  5. Synergy between 13C-metabolic flux analysis and flux balance analysis for understanding metabolic adaption to anaerobiosis in e. coli

    Science.gov (United States)

    Genome-based Flux Balance Analysis (FBA, constraints based flux analysis) and steady state isotopic-labeling-based Metabolic Flux Analysis (MFA) are complimentary approaches to predicting and measuring the operation and regulation of metabolic networks. Here a genome-derived model of E. coli metabol...

  6. Flux balance analysis of plant metabolism: the effect of biomass composition and model structure on model predictions

    Directory of Open Access Journals (Sweden)

    Huili eYuan

    2016-04-01

    Full Text Available The biomass composition represented in constraint-based metabolic models is a key component for predicting cellular metabolism using flux balance analysis (FBA. Despite major advances in analytical technologies, it is often challenging to obtain a detailed composition of all major biomass components experimentally. Studies examining the influence of the biomass composition on the predictions of metabolic models have so far mostly been done on models of microorganisms. Little is known about the impact of varying biomass composition on flux prediction in FBA models of plants, whose metabolism is very versatile and complex because of the presence of multiple subcellular compartments. Also, the published metabolic models of plants differ in size and complexity. In this study, we examined the sensitivity of the predicted fluxes of plant metabolic models to biomass composition and model structure. These questions were addressed by evaluating the sensitivity of predictions of growth rates and central carbon metabolic fluxes to varying biomass compositions in three different genome-/large-scale metabolic models of Arabidopsis thaliana. Our results showed that fluxes through the central carbon metabolism were robust to changes in biomass composition. Nevertheless, comparisons between the predictions from three models using identical modelling constraints and objective function showed that model predictions were sensitive to the structure of the models, highlighting large discrepancies between the published models.

  7. Expanded flux variability analysis on metabolic network of Escherichia coli

    Institute of Scientific and Technical Information of China (English)

    CHEN Tong; XIE ZhengWei; OUYANG Qi

    2009-01-01

    Flux balance analysis,based on the mass conservation law in a cellular organism,has been extensively employed to study the interplay between structures and functions of cellular metabolic networks.Consequently,the phenotypes of the metabolism can be well elucidated.In this paper,we introduce the Expanded Flux Variability Analysis (EFVA) to characterize the intrinsic nature of metabolic reactions,such as flexibility,modularity and essentiality,by exploring the trend of the range,the maximum and the minimum flux of reactions.We took the metabolic network of Escherichia coli as an example and analyzed the variability of reaction fluxes under different growth rate constraints.The average variability of all reactions decreases dramatically when the growth rate increases.Consider the noise effect on the metabolic system,we thus argue that the microorganism may practically grow under a suboptimal state.Besides,under the EFVA framework,the reactions are easily to be grouped into catabolic and anabolic groups.And the anabolic groups can be further assigned to specific biomass constitute.We also discovered the growth rate dependent essentiality of reactions.

  8. Gaussian mixture models as flux prediction method for central receivers

    Science.gov (United States)

    Grobler, Annemarie; Gauché, Paul; Smit, Willie

    2016-05-01

    Flux prediction methods are crucial to the design and operation of central receiver systems. Current methods such as the circular and elliptical (bivariate) Gaussian prediction methods are often used in field layout design and aiming strategies. For experimental or small central receiver systems, the flux profile of a single heliostat often deviates significantly from the circular and elliptical Gaussian models. Therefore a novel method of flux prediction was developed by incorporating the fitting of Gaussian mixture models onto flux profiles produced by flux measurement or ray tracing. A method was also developed to predict the Gaussian mixture model parameters of a single heliostat for a given time using image processing. Recording the predicted parameters in a database ensures that more accurate predictions are made in a shorter time frame.

  9. Reconstructed Metabolic Network Models Predict Flux-Level Metabolic Reprogramming in Glioblastoma

    Science.gov (United States)

    Özcan, Emrah; Çakır, Tunahan

    2016-01-01

    Developments in genome scale metabolic modeling techniques and omics technologies have enabled the reconstruction of context-specific metabolic models. In this study, glioblastoma multiforme (GBM), one of the most common and aggressive malignant brain tumors, is investigated by mapping GBM gene expression data on the growth-implemented brain specific genome-scale metabolic network, and GBM-specific models are generated. The models are used to calculate metabolic flux distributions in the tumor cells. Metabolic phenotypes predicted by the GBM-specific metabolic models reconstructed in this work reflect the general metabolic reprogramming of GBM, reported both in in-vitro and in-vivo experiments. The computed flux profiles quantitatively predict that major sources of the acetyl-CoA and oxaloacetic acid pool used in TCA cycle are pyruvate dehydrogenase from glycolysis and anaplerotic flux from glutaminolysis, respectively. Also, our results, in accordance with recent studies, predict a contribution of oxidative phosphorylation to ATP pool via a slightly active TCA cycle in addition to the major contributor aerobic glycolysis. We verified our results by using different computational methods that incorporate transcriptome data with genome-scale models and by using different transcriptome datasets. Correct predictions of flux distributions in glycolysis, glutaminolysis, TCA cycle and lipid precursor metabolism validate the reconstructed models for further use in future to simulate more specific metabolic patterns for GBM.

  10. C-13 Tracer experiments and metabolite balancing for metabolic flux analysis

    DEFF Research Database (Denmark)

    Schmidt, Karsten; Marx, A.; de Graaf, A. A.;

    1998-01-01

    Conventional metabolic flux analysis uses the information gained from determination of measurable fluxes and a steady-state assumption for intracellular metabolites to calculate the metabolic fluxes in a given metabolic network. The determination of intracellular fluxes depends heavily on the cor...

  11. Improving metabolic flux predictions using absolute gene expression data

    Directory of Open Access Journals (Sweden)

    Lee Dave

    2012-06-01

    Full Text Available Abstract Background Constraint-based analysis of genome-scale metabolic models typically relies upon maximisation of a cellular objective function such as the rate or efficiency of biomass production. Whilst this assumption may be valid in the case of microorganisms growing under certain conditions, it is likely invalid in general, and especially for multicellular organisms, where cellular objectives differ greatly both between and within cell types. Moreover, for the purposes of biotechnological applications, it is normally the flux to a specific metabolite or product that is of interest rather than the rate of production of biomass per se. Results An alternative objective function is presented, that is based upon maximising the correlation between experimentally measured absolute gene expression data and predicted internal reaction fluxes. Using quantitative transcriptomics data acquired from Saccharomyces cerevisiae cultures under two growth conditions, the method outperforms traditional approaches for predicting experimentally measured exometabolic flux that are reliant upon maximisation of the rate of biomass production. Conclusion Due to its improved prediction of experimentally measured metabolic fluxes, and of its lack of a requirement for knowledge of the biomass composition of the organism under the conditions of interest, the approach is likely to be of rather general utility. The method has been shown to predict fluxes reliably in single cellular systems. Subsequent work will investigate the method’s ability to generate condition- and tissue-specific flux predictions in multicellular organisms.

  12. Regulatory schemes to achieve optimal flux partitioning in bacterial metabolism

    Science.gov (United States)

    Tang, Lei-Han; Yang, Zhu; Hui, Sheng; Kim, Pan-Jun; Li, Xue-Fei; Hwa, Terence

    2012-02-01

    The flux balance analysis (FBA) offers a way to compute the optimal performance of a given metabolic network when the maximum incoming flux of nutrient molecules and other essential ingredients for biosynthesis are specified. Here we report a theoretical and computational analysis of the network structure and regulatory interactions in an E. coli cell. An automated scheme is devised to simplify the network topology and to enumerate the independent flux degrees of freedom. The network organization revealed by the scheme enables a detailed interpretation of the three layers of metabolic regulation known in the literature: i) independent transcriptional regulation of biosynthesis and salvage pathways to render the network tree-like under a given nutrient condition; ii) allosteric end-product inhibition of enzyme activity at entry points of synthesis pathways for metabolic flux partitioning according to consumption; iii) homeostasis of currency and carrier compounds to maintain sufficient supply of global commodities. Using the amino-acid synthesis pathways as an example, we show that the FBA result can be reproduced with suitable implementation of the three classes of regulatory interactions with literature evidence.

  13. Exhaustive Analysis of a Genotype Space Comprising 10(15 Central Carbon Metabolisms Reveals an Organization Conducive to Metabolic Innovation.

    Directory of Open Access Journals (Sweden)

    Sayed-Rzgar Hosseini

    2015-08-01

    Full Text Available All biological evolution takes place in a space of possible genotypes and their phenotypes. The structure of this space defines the evolutionary potential and limitations of an evolving system. Metabolism is one of the most ancient and fundamental evolving systems, sustaining life by extracting energy from extracellular nutrients. Here we study metabolism's potential for innovation by analyzing an exhaustive genotype-phenotype map for a space of 10(15 metabolisms that encodes all possible subsets of 51 reactions in central carbon metabolism. Using flux balance analysis, we predict the viability of these metabolisms on 10 different carbon sources which give rise to 1024 potential metabolic phenotypes. Although viable metabolisms with any one phenotype comprise a tiny fraction of genotype space, their absolute numbers exceed 10(9 for some phenotypes. Metabolisms with any one phenotype typically form a single network of genotypes that extends far or all the way through metabolic genotype space, where any two genotypes can be reached from each other through a series of single reaction changes. The minimal distance of genotype networks associated with different phenotypes is small, such that one can reach metabolisms with novel phenotypes--viable on new carbon sources--through one or few genotypic changes. Exceptions to these principles exist for those metabolisms whose complexity (number of reactions is close to the minimum needed for viability. Increasing metabolic complexity enhances the potential for both evolutionary conservation and evolutionary innovation.

  14. Maintenance metabolism and carbon fluxes in Bacillus species

    Directory of Open Access Journals (Sweden)

    Decasper Seraina

    2008-06-01

    Full Text Available Abstract Background Selection of an appropriate host organism is crucial for the economic success of biotechnological processes. A generally important selection criterion is a low maintenance energy metabolism to reduce non-productive consumption of substrate. We here investigated, whether various bacilli that are closely related to Bacillus subtilis are potential riboflavin production hosts with low maintenance metabolism. Results While B. subtilis exhibited indeed the highest maintenance energy coefficient, B. licheniformis and B. amyloliquefaciens exhibited only statistically insignificantly reduced maintenance metabolism. Both B. pumilus and B. subtilis (natto exhibited irregular growth patterns under glucose limitation such that the maintenance metabolism could not be determined. The sole exception with significantly reduced maintenance energy requirements was the B. licheniformis strain T380B. The frequently used spo0A mutation significantly increased the maintenance metabolism of B. subtilis. At the level of 13C-detected intracellular fluxes, all investigated bacilli exhibited a significant flux through the pentose phosphate pathway, a prerequisite for efficient riboflavin production. Different from all other species, B. subtilis featured high respiratory tricarboxylic acid cycle fluxes in batch and chemostat cultures. In particular under glucose-limited conditions, this led to significant excess formation of NADPH of B. subtilis, while anabolic consumption was rather balanced with catabolic NADPH formation in the other bacilli. Conclusion Despite its successful commercial production of riboflavin, B. subtilis does not seem to be the optimal cell factory from a bioenergetic point of view. The best choice of the investigated strains is the sporulation-deficient B. licheniformis T380B strain. Beside a low maintenance energy coefficient, this strain grows robustly under different conditions and exhibits only moderate acetate overflow, hence

  15. Investigating xylose metabolism in recombinant Saccharomyces cerevisiae via 13C metabolic flux analysis

    OpenAIRE

    Feng, Xueyang; Zhao, Huimin

    2013-01-01

    Background To engineer Saccharomyces cerevisiae for efficient xylose utilization, a fungal pathway consisting of xylose reductase, xylitol dehydrogenase, and xylulose kinase is often introduced to the host strain. Despite extensive in vitro studies on the xylose pathway, the intracellular metabolism rewiring in response to the heterologous xylose pathway remains largely unknown. In this study, we applied 13C metabolic flux analysis and stoichiometric modeling to systemically investigate the f...

  16. Reconstruction and flux analysis of coupling between metabolic pathways of astrocytes and neurons: application to cerebral hypoxia

    Directory of Open Access Journals (Sweden)

    Akιn Ata

    2007-12-01

    Full Text Available Abstract Background It is a daunting task to identify all the metabolic pathways of brain energy metabolism and develop a dynamic simulation environment that will cover a time scale ranging from seconds to hours. To simplify this task and make it more practicable, we undertook stoichiometric modeling of brain energy metabolism with the major aim of including the main interacting pathways in and between astrocytes and neurons. Model The constructed model includes central metabolism (glycolysis, pentose phosphate pathway, TCA cycle, lipid metabolism, reactive oxygen species (ROS detoxification, amino acid metabolism (synthesis and catabolism, the well-known glutamate-glutamine cycle, other coupling reactions between astrocytes and neurons, and neurotransmitter metabolism. This is, to our knowledge, the most comprehensive attempt at stoichiometric modeling of brain metabolism to date in terms of its coverage of a wide range of metabolic pathways. We then attempted to model the basal physiological behaviour and hypoxic behaviour of the brain cells where astrocytes and neurons are tightly coupled. Results The reconstructed stoichiometric reaction model included 217 reactions (184 internal, 33 exchange and 216 metabolites (183 internal, 33 external distributed in and between astrocytes and neurons. Flux balance analysis (FBA techniques were applied to the reconstructed model to elucidate the underlying cellular principles of neuron-astrocyte coupling. Simulation of resting conditions under the constraints of maximization of glutamate/glutamine/GABA cycle fluxes between the two cell types with subsequent minimization of Euclidean norm of fluxes resulted in a flux distribution in accordance with literature-based findings. As a further validation of our model, the effect of oxygen deprivation (hypoxia on fluxes was simulated using an FBA-derivative approach, known as minimization of metabolic adjustment (MOMA. The results show the power of the

  17. Polyamine acetylation modulates polyamine metabolic flux, a prelude to broader metabolic consequences.

    Science.gov (United States)

    Kramer, Debora L; Diegelman, Paula; Jell, Jason; Vujcic, Slavoljub; Merali, Salim; Porter, Carl W

    2008-02-15

    Recent studies suggest that overexpression of the polyamine-acetylating enzyme spermidine/spermine N(1)-acetyltransferase (SSAT) significantly increases metabolic flux through the polyamine pathway. The concept derives from the observation that SSAT-induced acetylation of polyamines gives rise to a compensatory increase in biosynthesis and presumably to increased flow through the pathway. Despite the strength of this deduction, the existence of heightened polyamine flux has not yet been experimentally demonstrated. Here, we use the artificial polyamine precursor 4-fluoro-ornithine to measure polyamine flux by tracking fluorine unit permeation of polyamine pools in human prostate carcinoma LNCaP cells. Conditional overexpression of SSAT was accompanied by a massive increase in intracellular and extracellular acetylated spermidine and by a 6-20-fold increase in biosynthetic enzyme activities. In the presence of 300 microM 4-fluoro-ornithine, SSAT overexpression led to the sequential appearance of fluorinated putrescine, spermidine, acetylated spermidine, and spermine. As fluorinated polyamines increased, endogenous polyamines decreased, so that the total polyamine pool size remained relatively constant. At 24 h, 56% of the spermine pool in the induced SSAT cells was fluorine-labeled compared with only 12% in uninduced cells. Thus, SSAT induction increased metabolic flux by approximately 5-fold. Flux could be interrupted by inhibition of polyamine biosynthesis but not by inhibition of polyamine oxidation. Overall, the findings are consistent with a paradigm whereby flux is initiated by SSAT acetylation of spermine and particularly spermidine followed by a marked increase in key biosynthetic enzymes. The latter sustains the flux cycle by providing a constant supply of polyamines for subsequent acetylation by SSAT. The broader metabolic implications of this futile metabolic cycling are discussed in detail. PMID:18089555

  18. Helioseismic constraints to the central solar temperature and neutrino fluxes

    OpenAIRE

    Ricci, B.; Berezinsky, V.; Degl'Innocenti, S.; Dziembowski, W. A.; Fiorentini, G.

    1997-01-01

    The central solar temperature T and its uncertainties are calculated in helioseismologically-constrained solar models. From the best fit to the convective radius, density at the convective radius and seismically determined helium abundance the central temperature is found to be T=1.58x10^7 K, in excellent agreement with Standard Solar Models. Conservatively, we estimate that the accuracy of this determination is Delta T/T=1.4 %, better than that in SSM. Neutrino fluxes are calculated. The low...

  19. A scientific workflow framework for (13)C metabolic flux analysis.

    Science.gov (United States)

    Dalman, Tolga; Wiechert, Wolfgang; Nöh, Katharina

    2016-08-20

    Metabolic flux analysis (MFA) with (13)C labeling data is a high-precision technique to quantify intracellular reaction rates (fluxes). One of the major challenges of (13)C MFA is the interactivity of the computational workflow according to which the fluxes are determined from the input data (metabolic network model, labeling data, and physiological rates). Here, the workflow assembly is inevitably determined by the scientist who has to consider interacting biological, experimental, and computational aspects. Decision-making is context dependent and requires expertise, rendering an automated evaluation process hardly possible. Here, we present a scientific workflow framework (SWF) for creating, executing, and controlling on demand (13)C MFA workflows. (13)C MFA-specific tools and libraries, such as the high-performance simulation toolbox 13CFLUX2, are wrapped as web services and thereby integrated into a service-oriented architecture. Besides workflow steering, the SWF features transparent provenance collection and enables full flexibility for ad hoc scripting solutions. To handle compute-intensive tasks, cloud computing is supported. We demonstrate how the challenges posed by (13)C MFA workflows can be solved with our approach on the basis of two proof-of-concept use cases. PMID:26721184

  20. Web application for genetic modification flux with database to estimate metabolic fluxes of genetic mutants.

    Science.gov (United States)

    Mohd Ali, Noorlin; Tsuboi, Ryo; Matsumoto, Yuta; Koishi, Daisuke; Inoue, Kentaro; Maeda, Kazuhiro; Kurata, Hiroyuki

    2016-07-01

    Computational analysis of metabolic fluxes is essential in understanding the structure and function of a metabolic network and in rationally designing genetically modified mutants for an engineering purpose. We had presented the genetic modification flux (GMF) that predicts the flux distribution of a broad range of genetically modified mutants. To enhance the feasibility and usability of GMF, we have developed a web application with a metabolic network database to predict a flux distribution of genetically modified mutants. One hundred and twelve data sets of Escherichia coli, Corynebacterium glutamicum, Saccharomyces cerevisiae, and Chinese hamster ovary were registered as standard models. PMID:26777238

  1. Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions

    Directory of Open Access Journals (Sweden)

    Edwards Jeremy S

    2000-07-01

    Full Text Available Abstract Background Genome sequencing and bioinformatics are producing detailed lists of the molecular components contained in many prokaryotic organisms. From this 'parts catalogue' of a microbial cell, in silico representations of integrated metabolic functions can be constructed and analyzed using flux balance analysis (FBA. FBA is particularly well-suited to study metabolic networks based on genomic, biochemical, and strain specific information. Results Herein, we have utilized FBA to interpret and analyze the metabolic capabilities of Escherichia coli. We have computationally mapped the metabolic capabilities of E. coli using FBA and examined the optimal utilization of the E. coli metabolic pathways as a function of environmental variables. We have used an in silico analysis to identify seven gene products of central metabolism (glycolysis, pentose phosphate pathway, TCA cycle, electron transport system essential for aerobic growth of E. coli on glucose minimal media, and 15 gene products essential for anaerobic growth on glucose minimal media. The in silico tpi-, zwf, and pta- mutant strains were examined in more detail by mapping the capabilities of these in silico isogenic strains. Conclusions We found that computational models of E. coli metabolism based on physicochemical constraints can be used to interpret mutant behavior. These in silica results lead to a further understanding of the complex genotype-phenotype relation. Supplementary information: http://gcrg.ucsd.edu/supplementary_data/DeletionAnalysis/main.htm

  2. Dynamics in the Central Plant Cell Metabolism

    OpenAIRE

    Ampofo-Asiama, Jerry

    2014-01-01

    As part of their development, plants have acquired adaptive mechanisms to cope with different stress situations they encounter in their environment. These adaptive mechanisms include the ability to alter their metabolism when faced with extreme environmental conditions such as low oxygen. In higher plants, oxygen (O2) availability is important for energy production through respiratory metabolism. Under conditions where O2 becomes limiting, respiratory metabolism can be impeded leading to impa...

  3. Hybrid optimization for 13C metabolic flux analysis using systems parametrized by compactification

    OpenAIRE

    Frick Oliver; Yang Tae Hoon; Heinzle Elmar

    2008-01-01

    Abstract Background The importance and power of isotope-based metabolic flux analysis and its contribution to understanding the metabolic network is increasingly recognized. Its application is, however, still limited partly due to computational inefficiency. 13C metabolic flux analysis aims to compute in vivo metabolic fluxes in terms of metabolite balancing extended by carbon isotopomer balances and involves a nonlinear least-squares problem. To solve the problem more efficiently, improved n...

  4. Metabolic flux analysis during the exponential growth phase of Saccharomyces cerevisiae in wine fermentations.

    Directory of Open Access Journals (Sweden)

    Manuel Quirós

    Full Text Available As a consequence of the increase in global average temperature, grapes with the adequate phenolic and aromatic maturity tend to be overripe by the time of harvest, resulting in increased sugar concentrations and imbalanced C/N ratios in fermenting musts. This fact sets obvious additional hurdles in the challenge of obtaining wines with reduced alcohols levels, a new trend in consumer demands. It would therefore be interesting to understand Saccharomyces cerevisiae physiology during the fermentation of must with these altered characteristics. The present study aims to determine the distribution of metabolic fluxes during the yeast exponential growth phase, when both carbon and nitrogen sources are in excess, using continuous cultures. Two different sugar concentrations were studied under two different winemaking temperature conditions. Although consumption and production rates for key metabolites were severely affected by the different experimental conditions studied, the general distribution of fluxes in central carbon metabolism was basically conserved in all cases. It was also observed that temperature and sugar concentration exerted a higher effect on the pentose phosphate pathway and glycerol formation than on glycolysis and ethanol production. Additionally, nitrogen uptake, both quantitatively and qualitatively, was strongly influenced by environmental conditions. This work provides the most complete stoichiometric model used for Metabolic Flux Analysis of S. cerevisiae in wine fermentations employed so far, including the synthesis and release of relevant aroma compounds and could be used in the design of optimal nitrogen supplementation of wine fermentations.

  5. MID Max: LC–MS/MS Method for Measuring the Precursor and Product Mass Isotopomer Distributions of Metabolic Intermediates and Cofactors for Metabolic Flux Analysis Applications

    DEFF Research Database (Denmark)

    McCloskey, Douglas; Young, Jamey D.; Xu, Sibei;

    2016-01-01

    that takes advantage of additional scan types that maximizes the number of mass isotopomer distributions (MIDs) that can be acquired in a given experiment. The analytical method was found to measure the MIDs of 97 metabolites, corresponding to 74 unique metabolite-fragment pairs (32 precursor spectra...... and 42 product spectra) with accuracy and precision. The compounds measured included metabolic intermediates in central carbohydrate metabolism and cofactors of peripheral metabolism (e.g., ATP). Using only a subset of the acquired MIDs, the method was found to improve the precision of flux...

  6. The nutritional status of Methanosarcina acetivorans regulates glycogen metabolism and gluconeogenesis and glycolysis fluxes.

    Science.gov (United States)

    Santiago-Martínez, Michel Geovanni; Encalada, Rusely; Lira-Silva, Elizabeth; Pineda, Erika; Gallardo-Pérez, Juan Carlos; Reyes-García, Marco Antonio; Saavedra, Emma; Moreno-Sánchez, Rafael; Marín-Hernández, Alvaro; Jasso-Chávez, Ricardo

    2016-05-01

    Gluconeogenesis is an essential pathway in methanogens because they are unable to use exogenous hexoses as carbon source for cell growth. With the aim of understanding the regulatory mechanisms of central carbon metabolism in Methanosarcina acetivorans, the present study investigated gene expression, the activities and metabolic regulation of key enzymes, metabolite contents and fluxes of gluconeogenesis, as well as glycolysis and glycogen synthesis/degradation pathways. Cells were grown with methanol as a carbon source. Key enzymes were kinetically characterized at physiological pH/temperature. Active consumption of methanol during exponential cell growth correlated with significant methanogenesis, gluconeogenic flux and steady glycogen synthesis. After methanol exhaustion, cells reached the stationary growth phase, which correlated with the rise in glycogen consumption and glycolytic flux, decreased methanogenesis, negligible acetate production and an absence of gluconeogenesis. Elevated activities of carbon monoxide dehydrogenase/acetyl-CoA synthetase complex and pyruvate: ferredoxin oxidoreductase suggested the generation of acetyl-CoA and pyruvate for glycogen synthesis. In the early stationary growth phase, the transcript contents and activities of pyruvate phosphate dikinase, fructose 1,6-bisphosphatase and glycogen synthase decreased, whereas those of glycogen phosphorylase, ADP-phosphofructokinase and pyruvate kinase increased. Therefore, glycogen and gluconeogenic metabolites were synthesized when an external carbon source was provided. Once such a carbon source became depleted, glycolysis and methanogenesis fed by glycogen degradation provided the ATP supply. Weak inhibition of key enzymes by metabolites suggested that the pathways evaluated were mainly transcriptionally regulated. Because glycogen metabolism and glycolysis/gluconeogenesis are not present in all methanogens, the overall data suggest that glycogen storage might represent an environmental

  7. Quantitative Multilevel Analysis of Central Metabolism in Developing Oilseeds of Oilseed Rape During In Vitro Culture

    Energy Technology Data Exchange (ETDEWEB)

    Schwender, Jorg [Brookhaven National Lab. (BNL), Upton, NY (United States); Hebbelmann, Inga [Brookhaven National Lab. (BNL), Upton, NY (United States); Heinzel, Nicholas [Leibniz Inst. of Plant Genetics and Crop Plant Research, Gatersleben (Germany); Hildebrandt, Tatjana [Univ. of Hannover (Germany); Rogers, Alistair [Brookhaven National Lab. (BNL), Upton, NY (United States); Naik, Dhiraj [Brookhaven National Lab. (BNL), Upton, NY (United States); Indian Inst. of Advanced Research Koba, Gujarat (India); Klapperstuck, Matthias [Monash Univ., Melbourne, VIC (Australia); Braun, Hans -Peter [Univ. of Hannover (Germany); Schreiber, Falk [Monash Univ., Melbourne, VIC (Australia); Univ. Halle-Wittenberg, Melbourne (Australia); Denolf, Peter [Bayer CropScience (Belgium); Borisjuk, Ljudmilla [Leibniz Inst. of Plant Genetics and Crop Plant Research, Gatersleben (Germany); Rolletschek, Hardy [Leibniz Inst. of Plant Genetics and Crop Plant Research, Gatersleben (Germany)

    2015-07-01

    Seeds provide the basis for many food, feed, and fuel products. Continued increases in seed yield, composition, and quality require an improved understanding of how the developing seed converts carbon and nitrogen supplies into storage. Current knowledge of this process is often based on the premise that transcriptional regulation directly translates via enzyme concentration into flux. In an attempt to highlight metabolic control, we explore genotypic differences in carbon partitioning for in vitro cultured developing embryos of oilseed rape (Brassica napus). We determined biomass composition as well as 79 net fluxes, the levels of 77 metabolites, and 26 enzyme activities with specific focus on central metabolism in nine selected germplasm accessions. We observed a tradeoff between the biomass component fractions of lipid and starch. With increasing lipid content over the spectrum of genotypes, plastidic fatty acid synthesis and glycolytic flux increased concomitantly, while glycolytic intermediates decreased. The lipid/starch tradeoff was not reflected at the proteome level, pointing to the significance of (posttranslational) metabolic control. Enzyme activity/flux and metabolite/flux correlations suggest that plastidic pyruvate kinase exerts flux control and that the lipid/starch tradeoff is most likely mediated by allosteric feedback regulation of phosphofructokinase and ADP-glucose pyrophosphorylase. Also, quantitative data were used to calculate in vivo mass action ratios, reaction equilibria, and metabolite turnover times. Compounds like cyclic 3',5'-AMP and sucrose-6-phosphate were identified to potentially be involved in so far unknown mechanisms of metabolic control. This study provides a rich source of quantitative data for those studying central metabolism..

  8. Quantitative Multilevel Analysis of Central Metabolism in Developing Oilseeds of Oilseed Rape during in Vitro Culture.

    Science.gov (United States)

    Schwender, Jörg; Hebbelmann, Inga; Heinzel, Nicolas; Hildebrandt, Tatjana; Rogers, Alistair; Naik, Dhiraj; Klapperstück, Matthias; Braun, Hans-Peter; Schreiber, Falk; Denolf, Peter; Borisjuk, Ljudmilla; Rolletschek, Hardy

    2015-07-01

    Seeds provide the basis for many food, feed, and fuel products. Continued increases in seed yield, composition, and quality require an improved understanding of how the developing seed converts carbon and nitrogen supplies into storage. Current knowledge of this process is often based on the premise that transcriptional regulation directly translates via enzyme concentration into flux. In an attempt to highlight metabolic control, we explore genotypic differences in carbon partitioning for in vitro cultured developing embryos of oilseed rape (Brassica napus). We determined biomass composition as well as 79 net fluxes, the levels of 77 metabolites, and 26 enzyme activities with specific focus on central metabolism in nine selected germplasm accessions. Overall, we observed a tradeoff between the biomass component fractions of lipid and starch. With increasing lipid content over the spectrum of genotypes, plastidic fatty acid synthesis and glycolytic flux increased concomitantly, while glycolytic intermediates decreased. The lipid/starch tradeoff was not reflected at the proteome level, pointing to the significance of (posttranslational) metabolic control. Enzyme activity/flux and metabolite/flux correlations suggest that plastidic pyruvate kinase exerts flux control and that the lipid/starch tradeoff is most likely mediated by allosteric feedback regulation of phosphofructokinase and ADP-glucose pyrophosphorylase. Quantitative data were also used to calculate in vivo mass action ratios, reaction equilibria, and metabolite turnover times. Compounds like cyclic 3',5'-AMP and sucrose-6-phosphate were identified to potentially be involved in so far unknown mechanisms of metabolic control. This study provides a rich source of quantitative data for those studying central metabolism. PMID:25944824

  9. Rewriting central metabolism for carbon conservation

    OpenAIRE

    Bogorad, Igor Walter

    2015-01-01

    The efficient use of carbon sources is a core objective in metabolic engineering and biorefinery. Most approaches have focused on optimizing naturally occurring pathways to improve titer, productivity, and yield. However, certain inherent limitations cannot be surpassed if natural pathways are used. Here we designed two synthetic metabolic pathways, Non-Oxidative Glycolysis (NOG) and Methanol Condensation Cycle (MCC) for the utilization of sugar and methanol, respectively. We also created a ...

  10. Estimation of dynamic flux profiles from metabolic time series data

    Directory of Open Access Journals (Sweden)

    Chou I-Chun

    2012-07-01

    Full Text Available Abstract Background Advances in modern high-throughput techniques of molecular biology have enabled top-down approaches for the estimation of parameter values in metabolic systems, based on time series data. Special among them is the recent method of dynamic flux estimation (DFE, which uses such data not only for parameter estimation but also for the identification of functional forms of the processes governing a metabolic system. DFE furthermore provides diagnostic tools for the evaluation of model validity and of the quality of a model fit beyond residual errors. Unfortunately, DFE works only when the data are more or less complete and the system contains as many independent fluxes as metabolites. These drawbacks may be ameliorated with other types of estimation and information. However, such supplementations incur their own limitations. In particular, assumptions must be made regarding the functional forms of some processes and detailed kinetic information must be available, in addition to the time series data. Results The authors propose here a systematic approach that supplements DFE and overcomes some of its shortcomings. Like DFE, the approach is model-free and requires only minimal assumptions. If sufficient time series data are available, the approach allows the determination of a subset of fluxes that enables the subsequent applicability of DFE to the rest of the flux system. The authors demonstrate the procedure with three artificial pathway systems exhibiting distinct characteristics and with actual data of the trehalose pathway in Saccharomyces cerevisiae. Conclusions The results demonstrate that the proposed method successfully complements DFE under various situations and without a priori assumptions regarding the model representation. The proposed method also permits an examination of whether at all, to what degree, or within what range the available time series data can be validly represented in a particular functional format of

  11. Flux balance analysis of cyanobacterial metabolism: the metabolic network of Synechocystis sp. PCC 6803.

    Directory of Open Access Journals (Sweden)

    Henning Knoop

    Full Text Available Cyanobacteria are versatile unicellular phototrophic microorganisms that are highly abundant in many environments. Owing to their capability to utilize solar energy and atmospheric carbon dioxide for growth, cyanobacteria are increasingly recognized as a prolific resource for the synthesis of valuable chemicals and various biofuels. To fully harness the metabolic capabilities of cyanobacteria necessitates an in-depth understanding of the metabolic interconversions taking place during phototrophic growth, as provided by genome-scale reconstructions of microbial organisms. Here we present an extended reconstruction and analysis of the metabolic network of the unicellular cyanobacterium Synechocystis sp. PCC 6803. Building upon several recent reconstructions of cyanobacterial metabolism, unclear reaction steps are experimentally validated and the functional consequences of unknown or dissenting pathway topologies are discussed. The updated model integrates novel results with respect to the cyanobacterial TCA cycle, an alleged glyoxylate shunt, and the role of photorespiration in cellular growth. Going beyond conventional flux-balance analysis, we extend the computational analysis to diurnal light/dark cycles of cyanobacterial metabolism.

  12. From the selfish gene to selfish metabolism: revisiting the central dogma.

    Science.gov (United States)

    de Lorenzo, Víctor

    2014-03-01

    The standard representation of the Central Dogma (CD) of Molecular Biology conspicuously ignores metabolism. However, both the metabolites and the biochemical fluxes behind any biological phenomenon are encrypted in the DNA sequence. Metabolism constrains and even changes the information flow when the DNA-encoded instructions conflict with the homeostasis of the biochemical network. Inspection of adaptive virulence programs and emergence of xenobiotic-biodegradation pathways in environmental bacteria suggest that their main evolutionary drive is the expansion of their metabolic networks towards new chemical landscapes rather than perpetuation and spreading of their DNA sequences. Faulty enzymatic reactions on suboptimal substrates often produce reactive oxygen species (ROS), a process that fosters DNA diversification and ultimately couples catabolism of the new chemicals to growth. All this calls for a revision of the CD in which metabolism (rather than DNA) has the leading role. PMID:24419968

  13. Quantitative Metabolomics and Instationary 13C-Metabolic Flux Analysis Reveals Impact of Recombinant Protein Production on Trehalose and Energy Metabolism in Pichia pastoris

    OpenAIRE

    Joel Jordà; Hugo Cueto Rojas; Marc Carnicer; Aljoscha Wahl; Pau Ferrer; Joan Albiol

    2014-01-01

    Pichia pastoris has been recognized as an effective host for recombinant protein production. In this work, we combine metabolomics and instationary 13C metabolic flux analysis (INST 13C-MFA) using GC-MS and LC-MS/MS to evaluate the potential impact of the production of a Rhizopus oryzae lipase (Rol) on P. pastoris central carbon metabolism. Higher oxygen uptake and CO2 production rates and slightly reduced biomass yield suggest an increased energy demand for the producing strain. This observa...

  14. Bidirectionality and compartmentation of metabolic fluxes are revealed in the dynamics of isotopomer networks.

    Science.gov (United States)

    Schryer, David W; Peterson, Pearu; Paalme, Toomas; Vendelin, Marko

    2009-04-01

    Isotope labeling is one of the few methods of revealing the in vivo bidirectionality and compartmentalization of metabolic fluxes within metabolic networks. We argue that a shift from steady state to dynamic isotopomer analysis is required to deal with these cellular complexities and provide a review of dynamic studies of compartmentalized energy fluxes in eukaryotic cells including cardiac muscle, plants, and astrocytes. Knowledge of complex metabolic behaviour on a molecular level is prerequisite for the intelligent design of genetically modified organisms able to realize their potential of revolutionizing food, energy, and pharmaceutical production. We describe techniques to explore the bidirectionality and compartmentalization of metabolic fluxes using information contained in the isotopic transient, and discuss the integration of kinetic models with MFA. The flux parameters of an example metabolic network were optimized to examine the compartmentalization of metabolites and and the bidirectionality of fluxes in the TCA cycle of Saccharomyces uvarum for steady-state respiratory growth. PMID:19468334

  15. Bidirectionality and Compartmentation of Metabolic Fluxes Are Revealed in the Dynamics of Isotopomer Networks

    Directory of Open Access Journals (Sweden)

    Marko Vendelin

    2009-04-01

    Full Text Available Isotope labeling is one of the few methods of revealing the in vivo bidirectionality and compartmentalization of metabolic fluxes within metabolic networks. We argue that a shift from steady state to dynamic isotopomer analysis is required to deal with these cellular complexities and provide a review of dynamic studies of compartmentalized energy fluxes in eukaryotic cells including cardiac muscle, plants, and astrocytes. Knowledge of complex metabolic behaviour on a molecular level is prerequisite for the intelligent design of genetically modified organisms able to realize their potential of revolutionizing food, energy, and pharmaceutical production. We describe techniques to explore the bidirectionality and compartmentalization of metabolic fluxes using information contained in the isotopic transient, and discuss the integration of kinetic models with MFA. The flux parameters of an example metabolic network were optimized to examine the compartmentalization of metabolites and and the bidirectionality of fluxes in the TCA cycle of Saccharomyces uvarum for steady-state respiratory growth.

  16. Bidirectionality and Compartmentation of Metabolic Fluxes Are Revealed in the Dynamics of Isotopomer Networks

    OpenAIRE

    Marko Vendelin; Pearu Peterson; Toomas Paalme; Schryer, David W

    2009-01-01

    Isotope labeling is one of the few methods of revealing the in vivo bidirectionality and compartmentalization of metabolic fluxes within metabolic networks. We argue that a shift from steady state to dynamic isotopomer analysis is required to deal with these cellular complexities and provide a review of dynamic studies of compartmentalized energy fluxes in eukaryotic cells including cardiac muscle, plants, and astrocytes. Knowledge of complex metabolic behaviour on a molecular level is prereq...

  17. Analysis of Metabolic Pathways and Fluxes in a Newly Discovered Thermophilic and Ethanol-Tolerant Geobacillus Strain

    OpenAIRE

    Tang, Yinjie J.

    2009-01-01

    A recently discovered thermophilic bacterium, Geobacillus thermoglucosidasius M10EXG, ferments a range of C5 (e.g., xylose) and C6 sugars (e.g., glucose) and is tolerant to high ethanol concentrations (10percent, v/v). We have investigated the central metabolism of this bacterium using both in vitro enzyme assays and 13C-based flux analysis to provide insights into the physiological properties of this extremophile and explore its metabolism for bio-ethanol or other bioprocess applications. Ou...

  18. MicrobesFlux: a web platform for drafting metabolic models from the KEGG database

    Directory of Open Access Journals (Sweden)

    Feng Xueyang

    2012-08-01

    Full Text Available Abstract Background Concurrent with the efforts currently underway in mapping microbial genomes using high-throughput sequencing methods, systems biologists are building metabolic models to characterize and predict cell metabolisms. One of the key steps in building a metabolic model is using multiple databases to collect and assemble essential information about genome-annotations and the architecture of the metabolic network for a specific organism. To speed up metabolic model development for a large number of microorganisms, we need a user-friendly platform to construct metabolic networks and to perform constraint-based flux balance analysis based on genome databases and experimental results. Results We have developed a semi-automatic, web-based platform (MicrobesFlux for generating and reconstructing metabolic models for annotated microorganisms. MicrobesFlux is able to automatically download the metabolic network (including enzymatic reactions and metabolites of ~1,200 species from the KEGG database (Kyoto Encyclopedia of Genes and Genomes and then convert it to a metabolic model draft. The platform also provides diverse customized tools, such as gene knockouts and the introduction of heterologous pathways, for users to reconstruct the model network. The reconstructed metabolic network can be formulated to a constraint-based flux model to predict and analyze the carbon fluxes in microbial metabolisms. The simulation results can be exported in the SBML format (The Systems Biology Markup Language. Furthermore, we also demonstrated the platform functionalities by developing an FBA model (including 229 reactions for a recent annotated bioethanol producer, Thermoanaerobacter sp. strain X514, to predict its biomass growth and ethanol production. Conclusion MicrobesFlux is an installation-free and open-source platform that enables biologists without prior programming knowledge to develop metabolic models for annotated microorganisms in the KEGG

  19. Metabolic flux analysis of the hydrogen production potential in Synechocystis sp. PCC6803

    Energy Technology Data Exchange (ETDEWEB)

    Navarro, E. [Departamento de Lenguajes y Ciencias de la Computacion, Campus de Teatrinos, Universidad de Malaga, 29071 Malaga (Spain); Montagud, A.; Fernandez de Cordoba, P.; Urchueguia, J.F. [Instituto Universitario de Matematica Pura y Aplicada, Universidad Politecnica de Valencia, Camino de Vera 14, 46022 Valencia (Spain)

    2009-11-15

    Hydrogen is a promising energy vector; however, finding methods to produce it from renewable sources is essential to allow its wide-scale use. In that line, biological hydrogen production, although it is considered as a possible alternative, requires substantial improvements to overcome its present low yields. In that direction, genetic manipulation probably will play a central role and from that point of view metabolic flux analysis (MFA) constitutes an important tool to guide a priori most suitable genetic modifications oriented to a hydrogen yield increase. In this work MFA has been applied to analyze hydrogen photoproduction of Synechocystis sp. PCC6803. Flux analysis was carried out based on literature data and several basic fluxes were estimated in different growing conditions of the system. From this analysis, an upper limit for hydrogen photoproduction has been determined indicating a wide margin for improvement. MFA was also used to find a feasible operating space for hydrogen production, which avoids oxygen inhibition, one of the most important limitations to make hydrogen production cost effective. In addition, a set of biotechnological strategies are proposed that would be consistent with the performed mathematical analysis. (author)

  20. Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico

    Directory of Open Access Journals (Sweden)

    McAnulty Michael J

    2012-05-01

    Full Text Available Abstract Background Genome-scale metabolic networks and flux models are an effective platform for linking an organism genotype to its phenotype. However, few modeling approaches offer predictive capabilities to evaluate potential metabolic engineering strategies in silico. Results A new method called “flux balance analysis with flux ratios (FBrAtio” was developed in this research and applied to a new genome-scale model of Clostridium acetobutylicum ATCC 824 (iCAC490 that contains 707 metabolites and 794 reactions. FBrAtio was used to model wild-type metabolism and metabolically engineered strains of C. acetobutylicum where only flux ratio constraints and thermodynamic reversibility of reactions were required. The FBrAtio approach allowed solutions to be found through standard linear programming. Five flux ratio constraints were required to achieve a qualitative picture of wild-type metabolism for C. acetobutylicum for the production of: (i acetate, (ii lactate, (iii butyrate, (iv acetone, (v butanol, (vi ethanol, (vii CO2 and (viii H2. Results of this simulation study coincide with published experimental results and show the knockdown of the acetoacetyl-CoA transferase increases butanol to acetone selectivity, while the simultaneous over-expression of the aldehyde/alcohol dehydrogenase greatly increases ethanol production. Conclusions FBrAtio is a promising new method for constraining genome-scale models using internal flux ratios. The method was effective for modeling wild-type and engineered strains of C. acetobutylicum.

  1. The Central Carbon and Energy Metabolism of Marine Diatoms

    Directory of Open Access Journals (Sweden)

    Adriano Nunes-Nesi

    2013-05-01

    Full Text Available Diatoms are heterokont algae derived from a secondary symbiotic event in which a eukaryotic host cell acquired an eukaryotic red alga as plastid. The multiple endosymbiosis and horizontal gene transfer processes provide diatoms unusual opportunities for gene mixing to establish distinctive biosynthetic pathways and metabolic control structures. Diatoms are also known to have significant impact on global ecosystems as one of the most dominant phytoplankton species in the contemporary ocean. As such their metabolism and growth regulating factors have been of particular interest for many years. The publication of the genomic sequences of two independent species of diatoms and the advent of an enhanced experimental toolbox for molecular biological investigations have afforded far greater opportunities than were previously apparent for these species and re-invigorated studies regarding the central carbon metabolism of diatoms. In this review we discuss distinctive features of the central carbon metabolism of diatoms and its response to forthcoming environmental changes and recent advances facilitating the possibility of industrial use of diatoms for oil production. Although the operation and importance of several key pathways of diatom metabolism have already been demonstrated and determined, we will also highlight other potentially important pathways wherein this has yet to be achieved.

  2. Making metabolism accessible and meaningful: is the definition of a central metabolic dogma within reach?

    Science.gov (United States)

    LaRossa, Robert A

    2015-04-01

    Intermediary metabolism, a dominant research area before the emergence of molecular biology, is attracting renewed interest for fundamental and applied reasons as documented here. Nonetheless, the field may appear to be a thicket precluding entry to all but the most determined. Here we present a metabolic overview that makes this important and fascinating area accessible to a broad range of the molecular biological and biotechnological communities that are being attracted to biological problems crying out for metabolic solutions. This is accomplished by identifying seven key concepts, a so-called metabolic central dogma, that provide a core understanding analogous to the "Central Dogma of Molecular Biology" which focused upon maintenance and flow of genetic information. PMID:25515796

  3. Dynamic metabolic flux analysis using a convex analysis approach: Application to hybridoma cell cultures in perfusion.

    Science.gov (United States)

    Fernandes de Sousa, Sofia; Bastin, Georges; Jolicoeur, Mario; Vande Wouwer, Alain

    2016-05-01

    In recent years, dynamic metabolic flux analysis (DMFA) has been developed in order to evaluate the dynamic evolution of the metabolic fluxes. Most of the proposed approaches are dedicated to exactly determined or overdetermined systems. When an underdetermined system is considered, the literature suggests the use of dynamic flux balance analysis (DFBA). However the main challenge of this approach is to determine an appropriate objective function, which remains valid over the whole culture. In this work, we propose an alternative dynamic metabolic flux analysis based on convex analysis, DMFCA, which allows the determination of bounded intervals for the fluxes using the available knowledge of the metabolic network and information provided by the time evolution of extracellular component concentrations. Smoothing splines and mass balance differential equations are used to estimate the time evolution of the uptake and excretion rates from this experimental data. The main advantage of the proposed procedure is that it does not require additional constraints or objective functions, and provides relatively narrow intervals for the intracellular metabolic fluxes. DMFCA is applied to experimental data from hybridoma HB58 cell perfusion cultures, in order to investigate the influence of the operating mode (batch and perfusion) on the metabolic flux distribution. Biotechnol. Bioeng. 2016;113: 1102-1112. © 2015 Wiley Periodicals, Inc. PMID:26551676

  4. Central metabolic pathways of Aureobasidium pullulans CGMCC1234 for pullulan production.

    Science.gov (United States)

    Sheng, Long; Liu, Chang; Tong, Qunyi; Ma, Meihu

    2015-12-10

    With the purpose of understanding the metabolic network of Aureobasidium pullulans, the central metabolic pathways were confirmed by the activities of the key enzymes involved in different pathways. The effect of different iodoacetic acid concentrations on pullulan fermentation was also investigated in this paper. The activities of phosphofructokinases and glucose-6-phosphate dehydrogenase existed in A. pullulans CGMCC1234, whereas 2-keto-3-deoxy-6-phosphogluconate aldolase activity was not detected. We proposed that the central metabolic pathways of A. pullulans CGMCC1234 included EMP and PPP, but no ED. Pullulan production declined fast as the iodoacetic acid increased, while cell growth offered upgrade firstly than descending latter tendency. Compared to the control group, the ratio of ATP/ADP of 0.60 mM iodoacetic acid group was lower at different stages of pullulan fermentation. The findings revealed that low concentration of iodoacetic acid might impel carbon flux flow toward the PPP, but reduce the flux of the EMP. PMID:26428132

  5. Cutaneous heat flux models do not reliably predict metabolic rates of marine mammals.

    Science.gov (United States)

    Boily, P; Kvadsheim, P H; Folkow, L P

    2000-12-01

    Heat flux models have been used to predict metabolic rates of marine mammals, generally by estimating conductive heat transfer through their blubber layer. Recently, Kvadsheim et al. (1997) found that such models tend to overestimate metabolic rates, and that such errors probably result from the asymmetrical distribution of blubber. This problem may be avoided if reliable estimates of heat flux through the skin of the animals are obtained by using models that combine calculations of conductive heat flux through the skin and fur, and convective heat flux from the surface of the animal to the environment. We evaluated this approach based on simultaneous measurements of metabolic rates and of input parameters necessary for heat flux calculations, as obtained from four harp seals (Phoca groenlandica) resting in cold water. Heat flux estimates were made using two free convection models (double-flat-plate and cylindrical geometry) and one forced convection model (single-flat-plate geometry). We found that heat flux estimates generally underestimated metabolic rates, on average by 26-58%, and that small variations in input parameters caused large variations in these estimates. We conclude that cutaneous heat flux models are too inaccurate and sensitive to small errors in input parameters to provide reliable estimates of metabolic rates of marine mammals. PMID:11082302

  6. FluxSimulator: An R package to simulate isotopomer distributions in metabolic networks

    OpenAIRE

    Binsl, Thomas W; Mullen, Katharine M.; Ivo H. M. van Stokkum; Jaap Heringa; van Beek, Johannes H G M

    2007-01-01

    The representation of biochemical knowledge in terms of fluxes (transformation rates) in a metabolic network is often a crucial step in the development of new drugs and efficient bioreactors. Mass spectroscopy (MS) and nuclear magnetic resonance spectroscopy (NMRS) in combination with 13C labeled substrates are experimental techniques resulting in data that may be used to quantify fluxes in the metabolic network underlying a process. The massive amount of data generated by spectroscopic exper...

  7. Enzyme allocation problems in kinetic metabolic networks: optimal solutions are elementary flux modes.

    Science.gov (United States)

    Müller, Stefan; Regensburger, Georg; Steuer, Ralf

    2014-04-21

    The survival and proliferation of cells and organisms require a highly coordinated allocation of cellular resources to ensure the efficient synthesis of cellular components. In particular, the total enzymatic capacity for cellular metabolism is limited by finite resources that are shared between all enzymes, such as cytosolic space, energy expenditure for amino-acid synthesis, or micro-nutrients. While extensive work has been done to study constrained optimization problems based only on stoichiometric information, mathematical results that characterize the optimal flux in kinetic metabolic networks are still scarce. Here, we study constrained enzyme allocation problems with general kinetics, using the theory of oriented matroids. We give a rigorous proof for the fact that optimal solutions of the non-linear optimization problem are elementary flux modes. This finding has significant consequences for our understanding of optimality in metabolic networks as well as for the identification of metabolic switches and the computation of optimal flux distributions in kinetic metabolic networks. PMID:24295962

  8. Flux Analysis Uncovers Key Role of Functional Redundancy in Formaldehyde Metabolism

    Directory of Open Access Journals (Sweden)

    Marx Christopher J

    2005-01-01

    Full Text Available Genome-scale analysis of predicted metabolic pathways has revealed the common occurrence of apparent redundancy for specific functional units, or metabolic modules. In many cases, mutation analysis does not resolve function, and instead, direct experimental analysis of metabolic flux under changing conditions is necessary. In order to use genome sequences to build models of cellular function, it is important to define function for such apparently redundant systems. Here we describe direct flux measurements to determine the role of redundancy in three modules involved in formaldehyde assimilation and dissimilation in a bacterium growing on methanol. A combination of deuterium and 14C labeling was used to measure the flux through each of the branches of metabolism for growth on methanol during transitions into and out of methylotrophy. The cells were found to differentially partition formaldehyde among the three modules depending on the flux of methanol into the cell. A dynamic mathematical model demonstrated that the kinetic constants of the enzymes involved are sufficient to account for this phenomenon. We demonstrate the role of redundancy in formaldehyde metabolism and have uncovered a new paradigm for coping with toxic, high-flux metabolic intermediates: a dynamic, interconnected metabolic loop.

  9. Synergizing metabolic flux analysis and nucleotide sugar metabolism to understand the control of glycosylation of recombinant protein in CHO cells

    LENUS (Irish Health Repository)

    Burleigh, Susan C

    2011-10-18

    Abstract Background The glycosylation of recombinant proteins can be altered by a range of parameters including cellular metabolism, metabolic flux and the efficiency of the glycosylation process. We present an experimental set-up that allows determination of these key processes associated with the control of N-linked glycosylation of recombinant proteins. Results Chinese hamster ovary cells (CHO) were cultivated in shake flasks at 0 mM glutamine and displayed a reduced growth rate, glucose metabolism and a slower decrease in pH, when compared to other glutamine-supplemented cultures. The N-linked glycosylation of recombinant human chorionic gonadotrophin (HCG) was also altered under these conditions; the sialylation, fucosylation and antennarity decreased, while the proportion of neutral structures increased. A continuous culture set-up was subsequently used to understand the control of HCG glycosylation in the presence of varied glutamine concentrations; when glycolytic flux was reduced in the absence of glutamine, the glycosylation changes that were observed in shake flask culture were similarly detected. The intracellular content of UDP-GlcNAc was also reduced, which correlated with a decrease in sialylation and antennarity of the N-linked glycans attached to HCG. Conclusions The use of metabolic flux analysis illustrated a case of steady state multiplicity, where use of the same operating conditions at each steady state resulted in altered flux through glycolysis and the TCA cycle. This study clearly demonstrated that the control of glycoprotein microheterogeneity may be examined by use of a continuous culture system, metabolic flux analysis and assay of intracellular nucleotides. This system advances our knowledge of the relationship between metabolic flux and the glycosylation of biotherapeutics in CHO cells and will be of benefit to the bioprocessing industry.

  10. A comprehensive metabolic profile of cultured astrocytes using isotopic transient metabolic flux analysis and 13C-labeled glucose

    Directory of Open Access Journals (Sweden)

    Ursula Sonnewald

    2011-09-01

    Full Text Available Metabolic models have been used to elucidate important aspects of brain metabolism in recent years. This work applies for the first time the concept of isotopic transient 13C metabolic flux analysis (MFA to estimate intracellular fluxes of cultured astrocytes. This methodology comprehensively explores the information provided by 13C labeling time-courses of intracellular metabolites after administration of a 13C labeled substrate. Cells were incubated with medium containing [1-13C]glucose for 24 h and samples of cell supernatant and extracts collected at different time-points were then analyzed by mass spectrometry and/or HPLC. Metabolic fluxes were estimated by fitting a carbon labeling network model to isotopomer profiles experimentally determined. Both the fast isotopic equilibrium of glycolytic metabolite pools and the slow labeling dynamics of TCA cycle intermediates are described well by the model. The large pools of glutamate and aspartate which are linked to the TCA cycle via reversible aminotransferase reactions are likely to be responsible for the observed delay in equilibration of TCA cycle intermediates. Furthermore, it was estimated that 11% of the glucose taken up by astrocytes was diverted to the pentose phosphate pathway. In addition, considerable fluxes through pyruvate carboxylase (PC (PC/pyruvate dehydrogenase (PDH ratio = 0.5, malic enzyme (5% of the total pyruvate production and catabolism of branched-chained amino acids (contributing with ~40% to total acetyl-CoA produced confirmed the significance of these pathways to astrocytic metabolism. Consistent with the need of maintaining cytosolic redox potential, the fluxes through the malate-aspartate shuttle and the PDH pathway were comparable. Finally, the estimated glutamate/α-ketoglutarate exchange rate (~0.7 µmol.mg prot-1.h-1 was similar to the TCA cycle flux. In conclusion, this work demonstrates the potential of isotopic transient MFA for a comprehensive analysis of

  11. Co-regulation of metabolic genes is better explained by flux coupling than by network distance.

    Directory of Open Access Journals (Sweden)

    Richard A Notebaart

    2008-01-01

    Full Text Available To what extent can modes of gene regulation be explained by systems-level properties of metabolic networks? Prior studies on co-regulation of metabolic genes have mainly focused on graph-theoretical features of metabolic networks and demonstrated a decreasing level of co-expression with increasing network distance, a naïve, but widely used, topological index. Others have suggested that static graph representations can poorly capture dynamic functional associations, e.g., in the form of dependence of metabolic fluxes across genes in the network. Here, we systematically tested the relative importance of metabolic flux coupling and network position on gene co-regulation, using a genome-scale metabolic model of Escherichia coli. After validating the computational method with empirical data on flux correlations, we confirm that genes coupled by their enzymatic fluxes not only show similar expression patterns, but also share transcriptional regulators and frequently reside in the same operon. In contrast, we demonstrate that network distance per se has relatively minor influence on gene co-regulation. Moreover, the type of flux coupling can explain refined properties of the regulatory network that are ignored by simple graph-theoretical indices. Our results underline the importance of studying functional states of cellular networks to define physiologically relevant associations between genes and should stimulate future developments of novel functional genomic tools.

  12. Co-regulation of metabolic genes is better explained by flux coupling than by network distance.

    Science.gov (United States)

    Notebaart, Richard A; Teusink, Bas; Siezen, Roland J; Papp, Balázs

    2008-01-01

    To what extent can modes of gene regulation be explained by systems-level properties of metabolic networks? Prior studies on co-regulation of metabolic genes have mainly focused on graph-theoretical features of metabolic networks and demonstrated a decreasing level of co-expression with increasing network distance, a naïve, but widely used, topological index. Others have suggested that static graph representations can poorly capture dynamic functional associations, e.g., in the form of dependence of metabolic fluxes across genes in the network. Here, we systematically tested the relative importance of metabolic flux coupling and network position on gene co-regulation, using a genome-scale metabolic model of Escherichia coli. After validating the computational method with empirical data on flux correlations, we confirm that genes coupled by their enzymatic fluxes not only show similar expression patterns, but also share transcriptional regulators and frequently reside in the same operon. In contrast, we demonstrate that network distance per se has relatively minor influence on gene co-regulation. Moreover, the type of flux coupling can explain refined properties of the regulatory network that are ignored by simple graph-theoretical indices. Our results underline the importance of studying functional states of cellular networks to define physiologically relevant associations between genes and should stimulate future developments of novel functional genomic tools. PMID:18225949

  13. Integration of a constraint-based metabolic model of Brassica napus developing seeds with 13C-Metabolic Flux Analysis

    Directory of Open Access Journals (Sweden)

    Jordan eHay

    2014-12-01

    Full Text Available The use of large-scale or genome-scale metabolic reconstructions for modeling and simulation of plant metabolism and integration of those models with large-scale omics and experimental flux data is becoming increasingly important in plant metabolic research. Here we report an updated version of bna572, a bottom-up reconstruction of oilseed rape (Brassica napus L.; Brassicaceae developing seeds with emphasis on representation of biomass-component biosynthesis. New features include additional seed-relevant pathways for isoprenoid, sterol, phenylpropanoid, flavonoid, and choline biosynthesis. Being now based on standardized data formats and procedures for model reconstruction, bna572+ is available as a COBRA-compliant Systems Biology Markup Language (SBML model and conforms to the Minimum Information Requested in the Annotation of Biochemical Models (MIRIAM standards for annotation of external data resources. Bna572+ contains 966 genes, 671 reactions, and 666 metabolites distributed among 11 subcellular compartments. It is referenced to the Arabidopsis thaliana genome, with gene-protein-reaction associations resolving subcellular localization. Detailed mass and charge balancing and confidence scoring were applied to all reactions. Using Brassica napus seed specific transcriptome data, expression was verified for 78% of bna572+ genes and 97% of reactions. Alongside bna572+ we also present a revised carbon centric model for 13C-Metabolic Flux Analysis (13C-MFA with all its reactions being referenced to bna572+ based on linear projections. By integration of flux ratio constraints obtained from 13C-MFA and by elimination of infinite flux bounds around thermodynamically infeasible loops based on COBRA loopless methods, we demonstrate improvements in predictive power of Flux Variability Analysis (FVA. Using this combined approach we characterize the difference in metabolic flux of developing seeds of two Brassica napus genotypes contrasting in starch and

  14. Quantitative characterization of metabolism and metabolic shifts during growth of the new human cell line AGE1.HN using time resolved metabolic flux analysis.

    Science.gov (United States)

    Niklas, Jens; Schräder, Eva; Sandig, Volker; Noll, Thomas; Heinzle, Elmar

    2011-06-01

    For the improved production of vaccines and therapeutic proteins, a detailed understanding of the metabolic dynamics during batch or fed-batch production is requested. To study the new human cell line AGE1.HN, a flexible metabolic flux analysis method was developed that is considering dynamic changes in growth and metabolism during cultivation. This method comprises analysis of formation of cellular components as well as conversion of major substrates and products, spline fitting of dynamic data and flux estimation using metabolite balancing. During batch cultivation of AGE1.HN three distinct phases were observed, an initial one with consumption of pyruvate and high glycolytic activity, a second characterized by a highly efficient metabolism with very little energy spilling waste production and a third with glutamine limitation and decreasing viability. Main events triggering changes in cellular metabolism were depletion of pyruvate and glutamine. Potential targets for the improvement identified from the analysis are (i) reduction of overflow metabolism in the beginning of cultivation, e.g. accomplished by reduction of pyruvate content in the medium and (ii) prolongation of phase 2 with its highly efficient energy metabolism applying e.g. specific feeding strategies. The method presented allows fast and reliable metabolic flux analysis during the development of producer cells and production processes from microtiter plate to large scale reactors with moderate analytical and computational effort. It seems well suited to guide media optimization and genetic engineering of producing cell lines. PMID:21188421

  15. Analysis of Metabolic Pathways and Fluxes in a Newly Discovered Thermophilic and Ethanol-Tolerant Geobacillus Strain

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Yinjie J.; Sapra, Rajat; Joyner, Dominique; Hazen, Terry C.; Myers, Samuel; Reichmuth, David; Blanch, Harvey; Keasling, Jay D.

    2009-01-20

    A recently discovered thermophilic bacterium, Geobacillus thermoglucosidasius M10EXG, ferments a range of C5 (e.g., xylose) and C6 sugars (e.g., glucose) and istolerant to high ethanol concentrations (10percent, v/v). We have investigated the central metabolism of this bacterium using both in vitro enzyme assays and 13C-based flux analysis to provide insights into the physiological properties of this extremophile and explore its metabolism for bio-ethanol or other bioprocess applications. Our findings show that glucose metabolism in G. thermoglucosidasius M10EXG proceeds via glycolysis, the pentose phosphate pathway, and the TCA cycle; the Entner?Doudoroff pathway and transhydrogenase activity were not detected. Anaplerotic reactions (including the glyoxylate shunt, pyruvate carboxylase, and phosphoenolpyruvate carboxykinase) were active, but fluxes through those pathways could not be accuratelydetermined using amino acid labeling. When growth conditions were switched from aerobic to micro-aerobic conditions, fluxes (based on a normalized glucose uptake rate of 100 units (g DCW)-1 h-1) through the TCA cycle and oxidative pentose phosphate pathway were reduced from 64+-3 to 25+-2 and from 30+-2 to 19+-2, respectively. The carbon flux under micro-aerobic growth was directed formate. Under fully anerobic conditions, G. thermoglucosidasius M10EXG used a mixed acid fermentation process and exhibited a maximum ethanol yield of 0.38+-0.07 mol mol-1 glucose. In silico flux balance modeling demonstrates that lactate and acetate production from G. thermoglucosidasius M10EXG reduces the maximum ethanol yieldby approximately threefold, thus indicating that both pathways should be modified to maximize ethanol production.

  16. Retrobiosynthetic nuclear magnetic resonance analysis of amino acid biosynthesis and intermediary metabolism. Metabolic flux in developing maize kernels.

    Science.gov (United States)

    Glawischnig, E; Gierl, A; Tomas, A; Bacher, A; Eisenreich, W

    2001-03-01

    Information on metabolic networks could provide the basis for the design of targets for metabolic engineering. To study metabolic flux in cereals, developing maize (Zea mays) kernels were grown in sterile culture on medium containing [U-(13)C(6)]glucose or [1,2-(13)C(2)]acetate. After growth, amino acids, lipids, and sitosterol were isolated from kernels as well as from the cobs, and their (13)C isotopomer compositions were determined by quantitative nuclear magnetic resonance spectroscopy. The highly specific labeling patterns were used to analyze the metabolic pathways leading to amino acids and the triterpene on a quantitative basis. The data show that serine is generated from phosphoglycerate, as well as from glycine. Lysine is formed entirely via the diaminopimelate pathway and sitosterol is synthesized entirely via the mevalonate route. The labeling data of amino acids and sitosterol were used to reconstruct the labeling patterns of key metabolic intermediates (e.g. acetyl-coenzyme A, pyruvate, phosphoenolpyruvate, erythrose 4-phosphate, and Rib 5-phosphate) that revealed quantitative information about carbon flux in the intermediary metabolism of developing maize kernels. Exogenous acetate served as an efficient precursor of sitosterol, as well as of amino acids of the aspartate and glutamate family; in comparison, metabolites formed in the plastidic compartments showed low acetate incorporation. PMID:11244098

  17. Analysis and Engineering of Metabolic Pathway Fluxes in Corynebacterium glutamicum

    Science.gov (United States)

    Wittmann, Christoph

    The Gram-positive soil bacterium Corynebacterium glutamicum was discovered as a natural overproducer of glutamate about 50 years ago. Linked to the steadily increasing economical importance of this microorganism for production of glutamate and other amino acids, the quest for efficient production strains has been an intense area of research during the past few decades. Efficient production strains were created by applying classical mutagenesis and selection and especially metabolic engineering strategies with the advent of recombinant DNA technology. Hereby experimental and computational approaches have provided fascinating insights into the metabolism of this microorganism and directed strain engineering. Today, C. glutamicum is applied to the industrial production of more than 2 million tons of amino acids per year. The huge achievements in recent years, including the sequencing of the complete genome and efficient post genomic approaches, now provide the basis for a new, fascinating era of research - analysis of metabolic and regulatory properties of C. glutamicum on a global scale towards novel and superior bioprocesses.

  18. OptFlux: an open-source software platform for in silico metabolic engineering

    Directory of Open Access Journals (Sweden)

    Pinto José P

    2010-04-01

    Full Text Available Abstract Background Over the last few years a number of methods have been proposed for the phenotype simulation of microorganisms under different environmental and genetic conditions. These have been used as the basis to support the discovery of successful genetic modifications of the microbial metabolism to address industrial goals. However, the use of these methods has been restricted to bioinformaticians or other expert researchers. The main aim of this work is, therefore, to provide a user-friendly computational tool for Metabolic Engineering applications. Results OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets, using Evolutionary Algorithms/Simulated Annealing metaheuristics or the previously proposed OptKnock algorithm. It also allows the use of stoichiometric metabolic models for (i phenotype simulation of both wild-type and mutant organisms, using the methods of Flux Balance Analysis, Minimization of Metabolic Adjustment or Regulatory on/off Minimization of Metabolic flux changes, (ii Metabolic Flux Analysis, computing the admissible flux space given a set of measured fluxes, and (iii pathway analysis through the calculation of Elementary Flux Modes. OptFlux also contemplates several methods for model simplification and other pre-processing operations aimed at reducing the search space for optimization algorithms. The software supports importing/exporting to several flat file formats and it is compatible with the SBML standard. OptFlux has a visualization module that allows the analysis of the model structure that is compatible with the layout information of Cell Designer, allowing the superimposition of simulation results with the model graph. Conclusions The OptFlux software is freely available, together with documentation and other resources, thus

  19. Determination of the Neutron Flux Density Distribution Inside the Central Experimental Tube of the TRIGA Mainz

    Energy Technology Data Exchange (ETDEWEB)

    Hampel, G.; Wiehl, N. [Institute for Nuclear Chemistry, University of Mainz, Fritz Strassmann Weg 2, 55128 Mainz (Germany); Scherer, U.W.; Koenn, F. [Campus Juelich, Aachen University of Applied Sciences, Heinrich-Mussmann Strasse 1, 52428 Juelich (Germany); Boldt, F.M.; Hampel, J. [Fraunhofer Institute for Solar Energy Systems ISE, Heidenhofstrasse 2, 79110 Freiburg (Germany)

    2011-07-01

    Related to the analysis of 3d-metals in rods of directionally solidified silicon for the solar cell production, the relative neutron flux density in the vertical direction was determined for the central experimental tube of the TRIGA Mark II reactor at the Johannes Gutenberg-University in Mainz. The standard irradiation capsule was modified to achieve a fixed irradiation position. Nickel and iron were used as flux monitors. After normalisation of the activities, a profile of the neutron flux for thermal and epithermal/fast neutrons inside the central experimental tube is obtained. (author)

  20. Determination of the Neutron Flux Density Distribution Inside the Central Experimental Tube of the TRIGA Mainz

    International Nuclear Information System (INIS)

    Related to the analysis of 3d-metals in rods of directionally solidified silicon for the solar cell production, the relative neutron flux density in the vertical direction was determined for the central experimental tube of the TRIGA Mark II reactor at the Johannes Gutenberg-University in Mainz. The standard irradiation capsule was modified to achieve a fixed irradiation position. Nickel and iron were used as flux monitors. After normalisation of the activities, a profile of the neutron flux for thermal and epithermal/fast neutrons inside the central experimental tube is obtained. (author)

  1. Metabolic Flux Analysis in Isotope Labeling Experiments using the Adjoint Approach

    OpenAIRE

    Mottelet, Stéphane; Gaullier, Gil; Sadaka, Georges

    2016-01-01

    Comprehension of metabolic pathways is considerably enhanced by metabolic flux analysis (MFA-ILE) in isotope labeling experiments. The balance equations are given by hundreds of algebraic (stationary MFA) or ordinary differential equations (nonstationary MFA), and reducing the number of operations is therefore a crucial part of reducing the computation cost. The main bottleneck for deterministic algorithms is the computation of derivatives, particularly for nonstationary MFA. In this article ...

  2. Comparative Metabolic Flux Analysis of Lysine-Producing Corynebacterium glutamicum Cultured on Glucose or Fructose

    OpenAIRE

    Kiefer, Patrick; Heinzle, Elmar; Zelder, Oskar; Wittmann, Christoph

    2004-01-01

    A comprehensive approach to 13C tracer studies, labeling measurements by gas chromatography-mass spectrometry, metabolite balancing, and isotopomer modeling, was applied for comparative metabolic network analysis of lysine-producing Corynebacterium glutamicum on glucose or fructose. Significantly reduced yields of lysine and biomass and enhanced formation of dihydroxyacetone, glycerol, and lactate in comparison to those for glucose resulted on fructose. Metabolic flux analysis revealed drasti...

  3. Resource constrained flux balance analysis predicts selective pressure on the global structure of metabolic networks

    OpenAIRE

    Abedpour, Nima; Kollmann, Markus

    2015-01-01

    Background A universal feature of metabolic networks is their hourglass or bow-tie structure on cellular level. This architecture reflects the conversion of multiple input nutrients into multiple biomass components via a small set of precursor metabolites. However, it is yet unclear to what extent this structural feature is the result of natural selection. Results We extend flux balance analysis to account for limited cellular resources. Using this model, optimal structure of metabolic networ...

  4. Detection of metabolic fluxes of O and H atoms into intracellular water in mammalian cells.

    Science.gov (United States)

    Kreuzer, Helen W; Quaroni, Luca; Podlesak, David W; Zlateva, Theodora; Bollinger, Nikki; McAllister, Aaron; Lott, Michael J; Hegg, Eric L

    2012-01-01

    Metabolic processes result in the release and exchange of H and O atoms from organic material as well as some inorganic salts and gases. These fluxes of H and O atoms into intracellular water result in an isotopic gradient that can be measured experimentally. Using isotope ratio mass spectroscopy, we revealed that slightly over 50% of the H and O atoms in the intracellular water of exponentially-growing cultured Rat-1 fibroblasts were isotopically distinct from growth medium water. We then employed infrared spectromicroscopy to detect in real time the flux of H atoms in these same cells. Importantly, both of these techniques indicate that the H and O fluxes are dependent on metabolic processes; cells that are in lag phase or are quiescent exhibit a much smaller flux. In addition, water extracted from the muscle tissue of rats contained a population of H and O atoms that were isotopically distinct from body water, consistent with the results obtained using the cultured Rat-1 fibroblasts. Together these data demonstrate that metabolic processes produce fluxes of H and O atoms into intracellular water, and that these fluxes can be detected and measured in both cultured mammalian cells and in mammalian tissue. PMID:22848359

  5. FluxExplorer: A general platform for modeling and analyses of metabolic networks based on stoichiometry

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Stoichiometry-based analyses of meta- bolic networks have aroused significant interest of systems biology researchers in recent years. It is necessary to develop a more convenient modeling platform on which users can reconstruct their network models using completely graphical operations, and explore them with powerful analyzing modules to get a better understanding of the properties of metabolic systems. Herein, an in silico platform, FluxExplorer, for metabolic modeling and analyses based on stoichiometry has been developed as a publicly available tool for systems biology research. This platform integrates various analytic approaches, in- cluding flux balance analysis, minimization of meta- bolic adjustment, extreme pathways analysis, shadow prices analysis, and singular value decom- position, providing a thorough characterization of the metabolic system. Using a graphic modeling process, metabolic networks can be reconstructed and modi- fied intuitively and conveniently. The inconsistencies of a model with respect to the FBA principles can be proved automatically. In addition, this platform sup- ports systems biology markup language (SBML). FluxExplorer has been applied to rebuild a metabolic network in mammalian mitochondria, producing meaningful results. Generally, it is a powerful and very convenient tool for metabolic network modeling and analysis.

  6. In vivo dynamics of galactose metabolism in Saccharomyces cerevisiae: Metabolic fluxes and metabolite levels

    DEFF Research Database (Denmark)

    Østergaard, Simon; Olsson, Lisbeth; Nielsen, Jens

    2001-01-01

    The dynamics of galactose metabolism in Saccharomyces cerevisiae was studied by analyzing the metabolic response of the CEN.PK 113-7D wild-type strain when exposed to a galactose pulse during aerobic growth in a galactose-limited steady-state cultivation at a dilution rate of 0.097 h(-1). A fast ...

  7. Dynamic metabolic flux analysis using B-splines to study the effects of temperature shift on CHO cell metabolism

    Directory of Open Access Journals (Sweden)

    Verónica S. Martínez

    2015-12-01

    Full Text Available Metabolic flux analysis (MFA is widely used to estimate intracellular fluxes. Conventional MFA, however, is limited to continuous cultures and the mid-exponential growth phase of batch cultures. Dynamic MFA (DMFA has emerged to characterize time-resolved metabolic fluxes for the entire culture period. Here, the linear DMFA approach was extended using B-spline fitting (B-DMFA to estimate mass balanced fluxes. Smoother fits were achieved using reduced number of knots and parameters. Additionally, computation time was greatly reduced using a new heuristic algorithm for knot placement. B-DMFA revealed that Chinese hamster ovary cells shifted from 37 °C to 32 °C maintained a constant IgG volume-specific productivity, whereas the productivity for the controls peaked during mid-exponential growth phase and declined afterward. The observed 42% increase in product titer at 32 °C was explained by a prolonged cell growth with high cell viability, a larger cell volume and a more stable volume-specific productivity.

  8. ¹³C-based metabolic flux analysis in yeast: the Pichia pastoris case.

    Science.gov (United States)

    Ferrer, Pau; Albiol, Joan

    2014-01-01

    Metabolic flux analysis based on tracing patterns of stable isotopes, particularly (13)C, comprises a set of methodologies to experimentally quantify intracellular biochemical reaction rates, i.e., to measure carbon flux distributions through a metabolic network. This allows quantifying the response of a metabolic network to an environmental or genetic perturbation (i.e., the metabolic phenotype). Here, we describe a protocol based on growing yeast on a (13)C-labelled substrate and subsequent NMR detection of (13)C-patterns in proteinogenic amino acids. To calculate metabolic fluxes, we describe two complementary mathematical approaches using available software; namely, an approach based on the estimation of local ratios in network nodes, and a method based on a global iterative fitting approach. Furthermore, we consider specificities of these protocols for their application to the yeast Pichia pastoris growing on multicarbon substrates other than glucose (glycerol), as well as the case when methanol is used as co-substrate in combination with glucose or glycerol. PMID:24744036

  9. Understanding the control of acyl flux through the lipid metabolic network of plant oil biosynthesis.

    Science.gov (United States)

    Bates, Philip D

    2016-09-01

    Plant oil biosynthesis involves a complex metabolic network with multiple subcellular compartments, parallel pathways, cycles, and pathways that have a dual function to produce essential membrane lipids and triacylglycerol. Modern molecular biology techniques provide tools to alter plant oil compositions through bioengineering, however with few exceptions the final composition of triacylglycerol cannot be predicted. One reason for limited success in oilseed bioengineering is the inadequate understanding of how to control the flux of fatty acids through various fatty acid modification, and triacylglycerol assembly pathways of the lipid metabolic network. This review focuses on the mechanisms of acyl flux through the lipid metabolic network, and highlights where uncertainty resides in our understanding of seed oil biosynthesis. This article is part of a Special Issue entitled: Plant Lipid Biology edited by Kent D. Chapman and Ivo Feussner. PMID:27003249

  10. Flux Balance Analysis of Cyanobacterial Metabolism: The Metabolic Network of Synechocystis sp PCC 6803

    OpenAIRE

    Knoop, Henning; Gründel, Marianne; Zilliges, Yvonne; Lehmann, Robert; Hoffmann, Sabrina; Lockau, Wolfgang; Steuer, Ralf

    2013-01-01

    Cyanobacteria are versatile unicellular phototrophic microorganisms that are highly abundant in many environments. Owing to their capability to utilize solar energy and atmospheric carbon dioxide for growth, cyanobacteria are increasingly recognized as a prolific resource for the synthesis of valuable chemicals and various biofuels. To fully harness the metabolic capabilities of cyanobacteria necessitates an in-depth understanding of the metabolic interconversions taking place during phototro...

  11. Development of Computational Tools for Metabolic Model Curation, Flux Elucidation and Strain Design

    Energy Technology Data Exchange (ETDEWEB)

    Maranas, Costas D

    2012-05-21

    An overarching goal of the Department of Energy mission is the efficient deployment and engineering of microbial and plant systems to enable biomass conversion in pursuit of high energy density liquid biofuels. This has spurred the pace at which new organisms are sequenced and annotated. This torrent of genomic information has opened the door to understanding metabolism in not just skeletal pathways and a handful of microorganisms but for truly genome-scale reconstructions derived for hundreds of microbes and plants. Understanding and redirecting metabolism is crucial because metabolic fluxes are unique descriptors of cellular physiology that directly assess the current cellular state and quantify the effect of genetic engineering interventions. At the same time, however, trying to keep pace with the rate of genomic data generation has ushered in a number of modeling and computational challenges related to (i) the automated assembly, testing and correction of genome-scale metabolic models, (ii) metabolic flux elucidation using labeled isotopes, and (iii) comprehensive identification of engineering interventions leading to the desired metabolism redirection.

  12. Simulating the Energy and Water Fluxes from Two Alkaline Desert Ecosystems over Central Asia

    Directory of Open Access Journals (Sweden)

    Chang-Qing Jing

    2016-01-01

    Full Text Available The Central Asia region is covered by vast desert ecosystems, where the characteristic of energy and water fluxes is different from other humid ecosystems. The application of land surface models (LSMs in arid and semiarid ecosystems was largely limited. This paper presents a detailed evaluation of Common Land Model (CoLM at two eddy covariance (EC sites in alkaline desert ecosystems over Central Asia. Simulations of the net radiation (Rnet, latent heat flux (Qle, sensible heat flux (Qh, and soil temperature showed that refined estimate of roughness length (Z0m significantly improved the performance of CoLM in simulating turbulent heat fluxes. Qle was increased but Qh was decreased, which were in better agreement with the observations from EC system. The results indicated that accurate parameterization of Z0m is of crucial importance for predicting energy and water fluxes in LSM when applied in Central Asia desert ecosystems. Sensitivity analysis regarding leaf area index (LAI, Z0m, and albedo (α showed that Rnet is very sensitive to α but Qle, Qh, and soil temperature (Tsoil are sensitively varying with the estimate of Z0m at the two EC sites over Central Asia.

  13. Reference equilibrium core with central flux irradiation facility for Pakistan research reactor-1

    International Nuclear Information System (INIS)

    In order to assess various core parameters a reference equilibrium core with Low Enriched Uranium (LEU) fuel for Pakistan Research Reactor (PARR-1) was assembled. Due to increased volume of reference core, the average neutron flux reduced as compared to the first higher power operation. To get a higher neutron flux an irradiation facility was created in centre of the reference equilibrium core where the advantage of the neutron flux peaking was taken. Various low power experiments were performed in order to evaluate control rods worth and neutron flux mapping inside the core. The neutron flux inside the central irradiation facility almost doubled. With this arrangement reactor operation time was cut down from 72 hours to 48 hours for the production of the required specific radioactivity. (author)

  14. Biochemical Hypermedia: Glucose as a Central Molecule in Metabolism

    Directory of Open Access Journals (Sweden)

    J.K. Sugai

    2008-05-01

    Full Text Available The technologies of information, together with education resources, have been pointed out as a solution to the improvement of teaching approach, but they still claim for programs to fulfill the demands of didactic materials. So, a biochemical software was developed aiming to contribute for the better understanding of the glycolysis. It was prepared with the help of concept maps, ISIS Draw, ADOBE Photoshop and FLASH MX Program. The introduction screen shows a teacher in a theater presenting glucose as a central molecule in the metabolism of animals, plants and many microorganisms. She invites for a better knowledge of glucose through a view of its discovery and its metabolism. A step by step animation process shows the interaction of glucose in aerobic conditions with the enzymes of the glycolytic pathways and its products. An explanation text of each enzyme catalytic process is provided by links. A static pathway is always available through a link. The fates of pyruvate yielding lactic acid and ethanol under anaerobic conditions are shown as well. The overall reactions of gluconeogenesis and the functional significance of this pathway are presented. The experimental treatment involved the presentation of this hypermedia for Nutrition undergraduate students (UFSC as a tool for better comprehension of the theme. The students revealed that it was extremely effective in promoting the understanding of the enzymatic mechanisms involved in glycolysis. This suggests that there is a significant added value in employing the software as an instructional effort to enhance student’s abilities to understand biochemical pathways.

  15. Neural-metabolic coupling in the central visual pathway.

    Science.gov (United States)

    Freeman, Ralph D; Li, Baowang

    2016-10-01

    Studies are described which are intended to improve our understanding of the primary measurements made in non-invasive neural imaging. The blood oxygenation level-dependent signal used in functional magnetic resonance imaging (fMRI) reflects changes in deoxygenated haemoglobin. Tissue oxygen concentration, along with blood flow, changes during neural activation. Therefore, measurements of tissue oxygen together with the use of a neural sensor can provide direct estimates of neural-metabolic interactions. We have used this relationship in a series of studies in which a neural microelectrode is combined with an oxygen micro-sensor to make simultaneous co-localized measurements in the central visual pathway. Oxygen responses are typically biphasic with small initial dips followed by large secondary peaks during neural activation. By the use of established visual response characteristics, we have determined that the oxygen initial dip provides a better estimate of local neural function than the positive peak. This contrasts sharply with fMRI for which the initial dip is unreliable. To extend these studies, we have examined the relationship between the primary metabolic agents, glucose and lactate, and associated neural activity. For this work, we also use a Doppler technique to measure cerebral blood flow (CBF) together with neural activity. Results show consistent synchronously timed changes such that increases in neural activity are accompanied by decreases in glucose and simultaneous increases in lactate. Measurements of CBF show clear delays with respect to neural response. This is consistent with a slight delay in blood flow with respect to oxygen delivery during neural activation.This article is part of the themed issue 'Interpreting BOLD: a dialogue between cognitive and cellular neuroscience'. PMID:27574310

  16. Seasonal trends in concentrations and fluxes of volatile organic compounds above central London

    Directory of Open Access Journals (Sweden)

    A. C. Valach

    2015-03-01

    Full Text Available Concentrations and fluxes of seven volatile organic compounds (VOCs were measured between August and December 2012 at a roof-top site in central London as part of the ClearfLo project (Clean Air for London. VOC concentrations were quantified using a proton transfer reaction-mass spectrometer and fluxes were calculated using a virtual disjunct eddy covariance technique. The median VOC fluxes, including aromatics, oxygenated compounds and isoprene, ranged from 0.07 to 0.33 mg m−2 h−1 and mixing ratios were 7.27 ppb for methanol (m / z 33 and <1 ppb for the remaining compounds. Strong relationships were observed between most VOC fluxes and concentrations with traffic density, but also with photosynthetically active radiation (PAR and temperature for the oxygenated compounds and isoprene. An estimated 50–90 % of aromatic fluxes were attributable to traffic activity, which showed little seasonal variation, suggesting boundary layer effects or possibly advected pollution may be the primary causes of increased concentrations of aromatics in winter. PAR and temperature-dependent processes accounted for the majority of isoprene, methanol and acetaldehyde fluxes and concentrations in August and September, when fluxes and concentrations were largest. Modelled biogenic isoprene fluxes using the G95 algorithm agreed well with measured fluxes in August and September, due to urban vegetation. Comparisons of estimated annual benzene emissions from the London and National Atmospheric Emissions Inventory agreed well with measured benzene fluxes. Flux footprint analysis indicated emission sources were localized and that boundary layer dynamics and source strengths were responsible for temporal and spatial VOC flux and concentration variability during the measurement period.

  17. Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans.

    Science.gov (United States)

    Watson, Emma; Olin-Sandoval, Viridiana; Hoy, Michael J; Li, Chi-Hua; Louisse, Timo; Yao, Victoria; Mori, Akihiro; Holdorf, Amy D; Troyanskaya, Olga G; Ralser, Markus; Walhout, Albertha Jm

    2016-01-01

    Metabolic network rewiring is the rerouting of metabolism through the use of alternate enzymes to adjust pathway flux and accomplish specific anabolic or catabolic objectives. Here, we report the first characterization of two parallel pathways for the breakdown of the short chain fatty acid propionate in Caenorhabditis elegans. Using genetic interaction mapping, gene co-expression analysis, pathway intermediate quantification and carbon tracing, we uncover a vitamin B12-independent propionate breakdown shunt that is transcriptionally activated on vitamin B12 deficient diets, or under genetic conditions mimicking the human diseases propionic- and methylmalonic acidemia, in which the canonical B12-dependent propionate breakdown pathway is blocked. Our study presents the first example of transcriptional vitamin-directed metabolic network rewiring to promote survival under vitamin deficiency. The ability to reroute propionate breakdown according to B12 availability may provide C. elegans with metabolic plasticity and thus a selective advantage on different diets in the wild. PMID:27383050

  18. 3D TOCSY-HSQC NMR for Metabolic Flux Analysis using Non-Uniform Sampling

    Energy Technology Data Exchange (ETDEWEB)

    Reardon, Patrick N.; Marean-Reardon, Carrie; Bukovec, Melanie A.; Coggins, B. E.; Isern, Nancy G.

    2016-02-05

    13C-Metabolic Flux Analysis (13C-MFA) is rapidly being recognized as the authoritative method for determining fluxes through metabolic networks. Site-specific 13C enrichment information obtained using NMR spectroscopy is a valuable input for 13C-MFA experiments. Chemical shift overlaps in the 1D or 2D NMR experiments typically used for 13C-MFA frequently hinder assignment and quantitation of site-specific 13C enrichment. Here we propose the use of a 3D TOCSY-HSQC experiment for 13C-MFA. We employ Non-Uniform Sampling (NUS) to reduce the acquisition time of the experiment to a few hours, making it practical for use in 13C-MFA experiments. Our data show that the NUS experiment is linear and quantitative. Identification of metabolites in complex mixtures, such as a biomass hydrolysate, is simplified by virtue of the 13C chemical shift obtained in the experiment. In addition, the experiment reports 13C-labeling information that reveals the position specific labeling of subsets of isotopomers. The information provided by this technique will enable more accurate estimation of metabolic fluxes in larger metabolic networks.

  19. ¹³C-based metabolic flux analysis of Saccharomyces cerevisiae with a reduced Crabtree effect.

    Science.gov (United States)

    Kajihata, Shuichi; Matsuda, Fumio; Yoshimi, Mika; Hayakawa, Kenshi; Furusawa, Chikara; Kanda, Akihisa; Shimizu, Hiroshi

    2015-08-01

    Saccharomyces cerevisiae shows a Crabtree effect that produces ethanol in a high glucose concentration even under fully aerobic condition. For efficient production of cake yeast or compressed yeast for baking, ethanol by-production is not desired since glucose limited chemostat or fed-batch cultivations are performed to suppress the Crabtree effect. In this study, the (13)C-based metabolic flux analysis ((13)C-MFA) was performed for the S288C derived S. cerevisiae strain to characterize a metabolic state under the reduced Crabtree effect. S. cerevisiae cells were cultured at a low dilution rate (0.1 h(-1)) under the glucose-limited chemostat condition. The estimated metabolic flux distribution showed that the acetyl-CoA in mitochondria was mainly produced from pyruvate by pyruvate dehydrogenase (PDH) reaction and that the level of the metabolic flux through the pentose phosphate pathway was much higher than that of the Embden-Meyerhof-Parnas pathway, which contributes to high biomass yield at low dilution rate by supplying NADPH required for cell growth. PMID:25634548

  20. Measurement of the 36Cl deposition flux in central Japan: natural background levels and seasonal variability

    International Nuclear Information System (INIS)

    Essential parameters for the applications of 36Cl as a tracer in groundwater studies include the initial 36Cl/Cl ratio, at the time of recharge, and/or the natural background deposition flux of 36Cl in the recharge area. To facilitate the hydrological use of 36Cl in central Japan, this study aimed to obtain a precise estimate of the long-term average local 36Cl flux and to characterize its seasonal variability. The 36Cl in precipitation was continuously monitored in Tsukuba, central Japan over a period of >5 years. The 36Cl flux showed a clear seasonal variation with an annual peak during the spring, which was attributed to the seasonal variability of tropopause height. The long-term average 36Cl flux (32 ± 2 atoms m−2 s−1), estimated from the measured data, was consistent with the prediction from the 36Cl latitudinal fallout model scaled using the global mean production rate of 20 atoms m−2 s−1. The initial 36Cl/Cl ratio was estimated to be (41 ± 6) × 10−15, which is similar to that of pre-bomb groundwater in the Tsukuba Upland. An observation period covering an 11-year solar cycle would yield more accurate estimates of the values, given the increased 36Cl flux during the solar minimum. - Highlights: ► We monitored 36Cl in precipitation in central Japan over a period of >5 years. ► The 36Cl flux varied seasonally, with a peak in spring. ► The long-term average 36Cl flux and the initial 36Cl/Cl ratio were 32 ± 2 atoms m−2 s−1 and (41 ± 6) × 10−15, respectively. ► An observation period covering an 11-year solar cycle would yield more accurate estimates of the values, given the increased 36Cl flux during the solar minimum.

  1. Central versus peripheral cardiovascular risk in metabolic syndrome

    Directory of Open Access Journals (Sweden)

    J.KevinShoemaker

    2012-02-01

    Full Text Available Individuals with metabolic syndrome (MetS; i.e. 3 of 5 of the following risk factors (RFs: elevated blood pressure, waist circumference, triglycerides, blood glucose or reduced HDL are thought to be prone to serious cardiovascular disease and there is debate as to whether the disease begins in the peripheral vasculature or centrally. This study investigates hemodynamics, cardiac function/morphology, as well as mechanical properties of the central (heart, carotid artery and peripheral (total peripheral resistance, forearm vascular bed vasculature in individuals without (1-2 RFs; n=28, or with (≥3 RFs; n=46 MetS. After adjustments for statin and blood pressure medication use, those with MetS had lower mitral valve E/A ratios (<3 RFs: 1.24±0.07; ≥3 RFs: 1.01±0.04; P=0.025, and higher total peripheral resistance index (<3 RFs: 48±2 mmHg/L/min/m2; ≥3 RFs: 53±2 mmHg/L/min/m2; P=0.04. There were no differences in heart size, carotid artery measurements, cardiovagal baroreflex sensitivity, pulse wave velocity, stroke volume index, or cardiac output index due to MetS after adjustments for statin and blood pressure medication use. In a separate analysis, the use of statins was associated with increased inertia in the brachial vascular bed, increased HbA1c and decreased LDL cholesterol. The independent use of anti-hypertensive medication was associated with decreased predicted VO2max, triglycerides, diastolic blood pressure, interventricular septum thickness, calculated left ventricle mass, left ventricle posterior wall thickness, and left ventricle pre-ejection period, but increased carotid stiffness, HDL cholesterol, and heart rate. These data imply that both a central cardiac effect and a peripheral effect of vascular resistance are expressed in MetS. These data also indicate that variance in between-group responses due to pharmacological treatments are important factors to consider in studying cardiovascular changes in these individuals.

  2. Flux Balance Analysis of Cyanobacterial Metabolism.The Metabolic Network of Synechocystis sp. PCC 6803

    Czech Academy of Sciences Publication Activity Database

    Knoop, H.; Gründel, M.; Zilliges, Y.; Lehmann, R.; Hoffmann, S.; Lockau, W.; Steuer, Ralf

    2013-01-01

    Roč. 9, č. 6 (2013), e1003081-e1003081. ISSN 1553-7358 R&D Projects: GA MŠk(CZ) EE2.3.20.0256 Institutional support: RVO:67179843 Keywords : SP STRAIN PCC-6803 * SP ATCC 51142 * photoautotrophic metabolism * anacystis-nidulans * reconstructions * pathway * plants * models * growth Subject RIV: EI - Biotechnology ; Bionics Impact factor: 4.829, year: 2013

  3. OptFlux: an open-source software platform for in silico metabolic engineering

    DEFF Research Database (Denmark)

    Rocha, I.; Maia, P.; Evangelista, P.;

    2010-01-01

    of simulation results with the model graph. Conclusions: The OptFlux software is freely available, together with documentation and other resources, thus bridging the gap from research in strain optimization algorithms and the final users. It is a valuable platform for researchers in the field that have...... to address industrial goals. However, the use of these methods has been restricted to bioinformaticians or other expert researchers. The main aim of this work is, therefore, to provide a user-friendly computational tool for Metabolic Engineering applications. Results: OptFlux is an open-source and modular...... software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets, using Evolutionary Algorithms/Simulated Annealing metaheuristics or the previously proposed Opt...

  4. Mapping cancer cell metabolism with 13 C flux analysis: Recent progress and future challenges

    Directory of Open Access Journals (Sweden)

    Casey Scott Duckwall

    2013-01-01

    Full Text Available The reprogramming of energy metabolism is emerging as an important molecular hallmark of cancer cells. Recent discoveries linking specific metabolic alterations to cancer development have strengthened the idea that altered metabolism is more than a side effect of malignant transformation, but may in fact be a functional driver of tumor growth and progression in some cancers. As a result, dysregulated metabolic pathways have become attractive targets for cancer therapeutics. This review highlights the application of 13 C metabolic flux analysis (MFA to map the flow of carbon through intracellular biochemical pathways of cancer cells. We summarize several recent applications of MFA that have identified novel biosynthetic pathways involved in cancer cell proliferation and shed light on the role of specific oncogenes in regulating these pathways. Through such studies, it has become apparent that the metabolic phenotypes of cancer cells are not as homogeneous as once thought, but instead depend strongly on the molecular alterations and environmental factors at play in each case.

  5. Carbon Flux of Down Woody Materials in Forests of the North Central United States

    International Nuclear Information System (INIS)

    Across large scales, the carbon (C) flux of down woody material (DWM) detrital pools has largely been simulated based on forest stand attributes (e.g., stand age and forest type). The annual change in forest DWM C stocks and other attributes (e.g., size and decay class changes) was assessed using a forest inventory in the north central United States to provide an empirical assessment of strategic-scale DWM C flux. Using DWM inventory data from the USDA Forest Service's Forest Inventory and Analysis program, DWM C stocks were found to be relatively static across the study region with an annual flux rate not statistically different from zero. Mean C flux rates across the study area were -0.25, -0.12, -0.01, and -0.04 (Mg/ha/yr) for standing live trees, standing dead trees, coarse woody debris, and fine woody debris, respectively. Flux rates varied in their both magnitude and status (emission/sequestration) by forest types, latitude, and DWM component size. Given the complex dynamics of DWM C flux, early implementation of inventory re measurement, and relatively low sample size, numerous future research directions are suggested.

  6. Study on roles of anaplerotic pathways in glutamate overproduction of Corynebacterium glutamicum by metabolic flux analysis

    Directory of Open Access Journals (Sweden)

    Shioya Suteaki

    2007-06-01

    Full Text Available Abstract Background Corynebacterium glutamicum has several anaplerotic pathways (anaplerosis, which are essential for the productions of amino acids, such as lysine and glutamate. It is still not clear how flux changes in anaplerotic pathways happen when glutamate production is induced by triggers, such as biotin depletion and the addition of the detergent material, Tween 40. In this study, we quantitatively analyzed which anaplerotic pathway flux most markedly changes the glutamate overproduction induced by Tween 40 addition. Results We performed a metabolic flux analysis (MFA with [1-13C]- and [U-13C]-labeled glucose in the glutamate production phase of C. glutamicum, based on the analysis of the time courses of 13C incorporation into proteinogenic amino acids by gas chromatography-mass spectrometry (GC-MS. The flux from phosphoenolpyruvate (PEP to oxaloacetate (Oxa catalyzed by phosphoenolpyruvate carboxylase (PEPc was active in the growth phase not producing glutamate, whereas that from pyruvate to Oxa catalyzed by pyruvate carboxylase (Pc was inactive. In the glutamate overproduction phase induced by the addition of the detergent material Tween 40, the reaction catalyzed by Pc also became active in addition to the reaction catalyzed by PEPc. Conclusion It was clarified by a quantitative 13C MFA that the reaction catalyzed by Pc is most markedly increased, whereas other fluxes of PEPc and PEPck remain constant in the glutamate overproduction induced by Tween 40. This result is consistent with the previous results obtained in a comparative study on the glutamate productions of genetically recombinant Pc- and PEPc-overexpressing strains. The importance of a specific reaction in an anaplerotic pathway was elucidated at a metabolic level by MFA.

  7. Flux Balance Analysis Inspired Bioprocess Upgrading for Lycopene Production by a Metabolically Engineered Strain of Yarrowia lipolytica

    OpenAIRE

    Komi Nambou; Xingxing Jian; Xinkai Zhang; Liujing Wei; Jiajia Lou; Catherine Madzak; Qiang Hua

    2015-01-01

    Genome-scale metabolic models embody a significant advantage of systems biology since their applications as metabolic flux simulation models enable predictions for the production of industrially-interesting metabolites. The biotechnological production of lycopene from Yarrowia lipolytica is an emerging scope that has not been fully scrutinized, especially for what concerns cultivation conditions of newly generated engineered strains. In this study, by combining flux balance analysis (FBA) and...

  8. Characterization of physiological responses to 22 gene knockouts in Escherichia coli central carbon metabolism.

    Science.gov (United States)

    Long, Christopher P; Gonzalez, Jacqueline E; Sandoval, Nicholas R; Antoniewicz, Maciek R

    2016-09-01

    Understanding the impact of gene knockouts on cellular physiology, and metabolism in particular, is centrally important to quantitative systems biology and metabolic engineering. Here, we present a comprehensive physiological characterization of wild-type Escherichia coli and 22 knockouts of enzymes in the upper part of central carbon metabolism, including the PTS system, glycolysis, pentose phosphate pathway and Entner-Doudoroff pathway. Our results reveal significant metabolic changes that are affected by specific gene knockouts. Analysis of collective trends and correlations in the data using principal component analysis (PCA) provide new, and sometimes surprising, insights into E. coli physiology. Additionally, by comparing the data-to-model predictions from constraint-based approaches such as FBA, MOMA and RELATCH we demonstrate the important role of less well-understood kinetic and regulatory effects in central carbon metabolism. PMID:27212692

  9. A procedure for the estimation over time of metabolic fluxes in scenarios where measurements are uncertain and/or insufficient

    Directory of Open Access Journals (Sweden)

    Picó Jesús

    2007-10-01

    Full Text Available Abstract Background An indirect approach is usually used to estimate the metabolic fluxes of an organism: couple the available measurements with known biological constraints (e.g. stoichiometry. Typically this estimation is done under a static point of view. Therefore, the fluxes so obtained are only valid while the environmental conditions and the cell state remain stable. However, estimating the evolution over time of the metabolic fluxes is valuable to investigate the dynamic behaviour of an organism and also to monitor industrial processes. Although Metabolic Flux Analysis can be successively applied with this aim, this approach has two drawbacks: i sometimes it cannot be used because there is a lack of measurable fluxes, and ii the uncertainty of experimental measurements cannot be considered. The Flux Balance Analysis could be used instead, but the assumption of optimal behaviour of the organism brings other difficulties. Results We propose a procedure to estimate the evolution of the metabolic fluxes that is structured as follows: 1 measure the concentrations of extracellular species and biomass, 2 convert this data to measured fluxes and 3 estimate the non-measured fluxes using the Flux Spectrum Approach, a variant of Metabolic Flux Analysis that overcomes the difficulties mentioned above without assuming optimal behaviour. We apply the procedure to a real problem taken from the literature: estimate the metabolic fluxes during a cultivation of CHO cells in batch mode. We show that it provides a reliable and rich estimation of the non-measured fluxes, thanks to considering measurements uncertainty and reversibility constraints. We also demonstrate that this procedure can estimate the non-measured fluxes even when there is a lack of measurable species. In addition, it offers a new method to deal with inconsistency. Conclusion This work introduces a procedure to estimate time-varying metabolic fluxes that copes with the insufficiency of

  10. Metabolic network reconstruction and flux variability analysis of storage synthesis in developing oilseed rape (Brassica napus L.) embryos

    Energy Technology Data Exchange (ETDEWEB)

    Hay, J.; Schwender, J.

    2011-08-01

    Computational simulation of large-scale biochemical networks can be used to analyze and predict the metabolic behavior of an organism, such as a developing seed. Based on the biochemical literature, pathways databases and decision rules defining reaction directionality we reconstructed bna572, a stoichiometric metabolic network model representing Brassica napus seed storage metabolism. In the highly compartmentalized network about 25% of the 572 reactions are transport reactions interconnecting nine subcellular compartments and the environment. According to known physiological capabilities of developing B. napus embryos, four nutritional conditions were defined to simulate heterotrophy or photoheterotrophy, each in combination with the availability of inorganic nitrogen (ammonia, nitrate) or amino acids as nitrogen sources. Based on mathematical linear optimization the optimal solution space was comprehensively explored by flux variability analysis, thereby identifying for each reaction the range of flux values allowable under optimality. The range and variability of flux values was then categorized into flux variability types. Across the four nutritional conditions, approximately 13% of the reactions have variable flux values and 10-11% are substitutable (can be inactive), both indicating metabolic redundancy given, for example, by isoenzymes, subcellular compartmentalization or the presence of alternative pathways. About one-third of the reactions are never used and are associated with pathways that are suboptimal for storage synthesis. Fifty-seven reactions change flux variability type among the different nutritional conditions, indicating their function in metabolic adjustments. This predictive modeling framework allows analysis and quantitative exploration of storage metabolism of a developing B. napus oilseed.

  11. Effect of 56Fe resonance scattering in the central flux of ZPR6-7

    International Nuclear Information System (INIS)

    The result obtained in early calculations, where a depletion was observed due to the 56Fe resonance scattering (28,8 KeV), in the central flux calculated for the ZPR6-7 critical assembly, when the scheme of ETOE-MC**2-UNIMUG calculation is used, and the out of appearance of these depletion, when the scheme of NJOY-ANISIN calculation is used, is explained. (M.C.K.)

  12. Reconstruction and flux analysis of coupling between metabolic pathways of astrocytes and neurons: application to cerebral hypoxia

    OpenAIRE

    Akιn Ata; Saybaşιlι Hale; Alsan Selma; Çakιr Tunahan; Ülgen Kutlu Ö

    2007-01-01

    Abstract Background It is a daunting task to identify all the metabolic pathways of brain energy metabolism and develop a dynamic simulation environment that will cover a time scale ranging from seconds to hours. To simplify this task and make it more practicable, we undertook stoichiometric modeling of brain energy metabolism with the major aim of including the main interacting pathways in and between astrocytes and neurons. Model The constructed model includes central metabolism (glycolysis...

  13. Integrated in silico Analyses of Regulatory and Metabolic Networks of Synechococcus sp. PCC 7002 Reveal Relationships between Gene Centrality and Essentiality

    Directory of Open Access Journals (Sweden)

    Hyun-Seob Song

    2015-03-01

    Full Text Available Cyanobacteria dynamically relay environmental inputs to intracellular adaptations through a coordinated adjustment of photosynthetic efficiency and carbon processing rates. The output of such adaptations is reflected through changes in transcriptional patterns and metabolic flux distributions that ultimately define growth strategy. To address interrelationships between metabolism and regulation, we performed integrative analyses of metabolic and gene co-expression networks in a model cyanobacterium, Synechococcus sp. PCC 7002. Centrality analyses using the gene co-expression network identified a set of key genes, which were defined here as “topologically important.” Parallel in silico gene knock-out simulations, using the genome-scale metabolic network, classified what we termed as “functionally important” genes, deletion of which affected growth or metabolism. A strong positive correlation was observed between topologically and functionally important genes. Functionally important genes exhibited variable levels of topological centrality; however, the majority of topologically central genes were found to be functionally essential for growth. Subsequent functional enrichment analysis revealed that both functionally and topologically important genes in Synechococcus sp. PCC 7002 are predominantly associated with translation and energy metabolism, two cellular processes critical for growth. This research demonstrates how synergistic network-level analyses can be used for reconciliation of metabolic and gene expression data to uncover fundamental biological principles.

  14. Exploring lysine riboswitch for metabolic flux control and improvement of L-lysine synthesis in Corynebacterium glutamicum.

    Science.gov (United States)

    Zhou, Li-Bang; Zeng, An-Ping

    2015-06-19

    Riboswitch, a regulatory part of an mRNA molecule that can specifically bind a metabolite and regulate gene expression, is attractive for engineering biological systems, especially for the control of metabolic fluxes in industrial microorganisms. Here, we demonstrate the use of lysine riboswitch and intracellular l-lysine as a signal to control the competing but essential metabolic by-pathways of lysine biosynthesis. To this end, we first examined the natural lysine riboswitches of Eschericia coli (ECRS) and Bacillus subtilis (BSRS) to control the expression of citrate synthase (gltA) and thus the metabolic flux in the tricarboxylic acid (TCA) cycle in E. coli. ECRS and BSRS were then successfully used to control the gltA gene and TCA cycle activity in a lysine producing strain Corynebacterium glutamicum LP917, respectively. Compared with the strain LP917, the growth of both lysine riboswitch-gltA mutants was slower, suggesting a reduced TCA cycle activity. The lysine production was 63% higher in the mutant ECRS-gltA and 38% higher in the mutant BSRS-gltA, indicating a higher metabolic flux into the lysine synthesis pathway. This is the first report on using an amino acid riboswitch for improvement of lysine biosynthesis. The lysine riboswitches can be easily adapted to dynamically control other essential but competing metabolic pathways or even be engineered as an "on-switch" to enhance the metabolic fluxes of desired metabolic pathways. PMID:25575181

  15. iMS2Flux – a high–throughput processing tool for stable isotope labeled mass spectrometric data used for metabolic flux analysis

    Directory of Open Access Journals (Sweden)

    Poskar C Hart

    2012-11-01

    Full Text Available Abstract Background Metabolic flux analysis has become an established method in systems biology and functional genomics. The most common approach for determining intracellular metabolic fluxes is to utilize mass spectrometry in combination with stable isotope labeling experiments. However, before the mass spectrometric data can be used it has to be corrected for biases caused by naturally occurring stable isotopes, by the analytical technique(s employed, or by the biological sample itself. Finally the MS data and the labeling information it contains have to be assembled into a data format usable by flux analysis software (of which several dedicated packages exist. Currently the processing of mass spectrometric data is time-consuming and error-prone requiring peak by peak cut-and-paste analysis and manual curation. In order to facilitate high-throughput metabolic flux analysis, the automation of multiple steps in the analytical workflow is necessary. Results Here we describe iMS2Flux, software developed to automate, standardize and connect the data flow between mass spectrometric measurements and flux analysis programs. This tool streamlines the transfer of data from extraction via correction tools to 13C-Flux software by processing MS data from stable isotope labeling experiments. It allows the correction of large and heterogeneous MS datasets for the presence of naturally occurring stable isotopes, initial biomass and several mass spectrometry effects. Before and after data correction, several checks can be performed to ensure accurate data. The corrected data may be returned in a variety of formats including those used by metabolic flux analysis software such as 13CFLUX, OpenFLUX and 13CFLUX2. Conclusion iMS2Flux is a versatile, easy to use tool for the automated processing of mass spectrometric data containing isotope labeling information. It represents the core framework for a standardized workflow and data processing. Due to its flexibility

  16. Fatty Acids in Energy Metabolism of the Central Nervous System

    Directory of Open Access Journals (Sweden)

    Alexander Panov

    2014-01-01

    Full Text Available In this review, we analyze the current hypotheses regarding energy metabolism in the neurons and astroglia. Recently, it was shown that up to 20% of the total brain’s energy is provided by mitochondrial oxidation of fatty acids. However, the existing hypotheses consider glucose, or its derivative lactate, as the only main energy substrate for the brain. Astroglia metabolically supports the neurons by providing lactate as a substrate for neuronal mitochondria. In addition, a significant amount of neuromediators, glutamate and GABA, is transported into neurons and also serves as substrates for mitochondria. Thus, neuronal mitochondria may simultaneously oxidize several substrates. Astrocytes have to replenish the pool of neuromediators by synthesis de novo, which requires large amounts of energy. In this review, we made an attempt to reconcile β-oxidation of fatty acids by astrocytic mitochondria with the existing hypothesis on regulation of aerobic glycolysis. We suggest that, under condition of neuronal excitation, both metabolic pathways may exist simultaneously. We provide experimental evidence that isolated neuronal mitochondria may oxidize palmitoyl carnitine in the presence of other mitochondrial substrates. We also suggest that variations in the brain mitochondrial metabolic phenotype may be associated with different mtDNA haplogroups.

  17. Planktic foraminifer and coccolith contribution to carbonate export fluxes over the central Kerguelen Plateau

    Science.gov (United States)

    Rembauville, M.; Meilland, J.; Ziveri, P.; Schiebel, R.; Blain, S.; Salter, I.

    2016-05-01

    We report the contribution of planktic foraminifers and coccoliths to the particulate inorganic carbon (PIC) export fluxes collected over an annual cycle (October 2011/September 2012) on the central Kerguelen Plateau in the Antarctic Zone (AAZ) south of the Polar Front (PF). The seasonality of PIC flux was decoupled from surface chlorophyll a concentration and particulate organic carbon (POC) fluxes and was characterized by a late summer (February) maximum. This peak was concomitant with the highest satellite-derived sea surface PIC and corresponded to a Emiliania huxleyi coccoliths export event that accounted for 85% of the annual PIC export. The foraminifer contribution to the annual PIC flux was much lower (15%) and dominated by Turborotalita quinqueloba and Neogloboquadrina pachyderma. Foraminifer export fluxes were closely related to the surface chlorophyll a concentration, suggesting food availability as an important factor regulating the foraminifer's biomass. We compared size-normalized test weight (SNW) of the foraminifers with previously published SNW from the Crozet Islands using the same methodology and found no significant difference in SNW between sites for a given species. However, the SNW was significantly species-specific with a threefold increase from T. quinqueloba to Globigerina bulloides. The annual PIC:POC molar ratio of 0.07 was close to the mean ratio for the global ocean and lead to a low carbonate counter pump effect (~5%) compared to a previous study north of the PF (6-32%). We suggest that lowers counter pump effect south of the PF despite similar productivity levels is due to a dominance of coccoliths in the PIC fluxes and a difference in the foraminifers species assemblage with a predominance of polar species with lower SNW.

  18. Designer Micelles Accelerate Flux Through Engineered Metabolism in E. coli and Support Biocompatible Chemistry.

    Science.gov (United States)

    Wallace, Stephen; Balskus, Emily P

    2016-05-10

    Synthetic biology has enabled the production of many value-added chemicals via microbial fermentation. However, the problem of low product titers from recombinant pathways has limited the utility of this approach. Methods to increase metabolic flux are therefore critical to the success of metabolic engineering. Here we demonstrate that vitamin E-derived designer micelles, originally developed for use in synthetic chemistry, are biocompatible and accelerate flux through a styrene production pathway in Escherichia coli. We show that these micelles associate non-covalently with the bacterial outer-membrane and that this interaction increases membrane permeability. In addition, these micelles also accommodate both heterogeneous and organic-soluble transition metal catalysts and accelerate biocompatible cyclopropanation in vivo. Overall, this work demonstrates that these surfactants hold great promise for further application in the field of synthetic biotechnology, and for expanding the types of molecules that can be readily accessed from renewable resources via the combination of microbial fermentation and biocompatible chemistry. PMID:27061024

  19. Mapping regional distribution of land surface heat fluxes on the southern side of the central Himalayas using TESEBS

    Science.gov (United States)

    Amatya, Pukar Man; Ma, Yaoming; Han, Cunbo; Wang, Binbin; Devkota, Lochan Prasad

    2016-05-01

    Recent scientific studies based on large-scale climate model have highlighted the importance of the heat release from the southern side of the Himalayas for the development of South Asian Summer Monsoon. However, studies related to land surface heat fluxes are nonexistent on the southern side. In this study, we test the feasibility of deriving land surface heat fluxes on the central Himalayan region using Topographically Enhanced Surface Energy Balance System (TESEBS), which is forced by MODIS land surface products and Global Land Data Assimilation System (GLDAS) meteorological data. The model results were validated using the first eddy covariance measurement system established in the southern side of the central Himalayas. The derived land surface heat fluxes were close to the field measurements with mean bias of 15.97, -19.89, 8.79, and -20.39 W m-2 for net radiation flux, ground heat flux, sensible heat flux, and latent heat flux respectively. Land surface heat fluxes show strong contrast in pre monsoon, summer monsoon, post monsoon, and winter seasons and different land surface states among the different physiographic regions. In the central Himalayas, the latent heat flux is the dominant consumer of available energy for all physiographic regions except for the High Himalaya where the sensible heat flux is high.

  20. Immunosuppressive activity enhances central carbon metabolism and bioenergetics in myeloid-derived suppressor cells in vitro models

    Directory of Open Access Journals (Sweden)

    Hammami Ines

    2012-07-01

    Full Text Available Abstract Background The tumor microenvironment contains a vast array of pro- and anti-inflammatory cytokines that alter myelopoiesis and lead to the maturation of immunosuppressive cells known as myeloid-derived suppressor cells (MDSCs. Incubating bone marrow (BM precursors with a combination of granulocyte-macrophage colony-stimulating factor (GM-CSF and interleukin-6 (IL-6 generated a tumor-infiltrating MDSC-like population that impaired anti-tumor specific T-cell functions. This in vitro experimental approach was used to simulate MDSC maturation, and the cellular metabolic response was then monitored. A complementary experimental model that inhibited L-arginine (L-Arg metabolizing enzymes in MSC-1 cells, an immortalized cell line derived from primary MDSCs, was used to study the metabolic events related to immunosuppression. Results Exposure of BM cells to GM-CSF and IL-6 activated, within 24 h, L-Arg metabolizing enzymes which are responsible for the MDSCs immunosuppressive potential. This was accompanied by an increased uptake of L-glutamine (L-Gln and glucose, the latter being metabolized by anaerobic glycolysis. The up-regulation of nutrient uptake lead to the accumulation of TCA cycle intermediates and lactate as well as the endogenous synthesis of L-Arg and the production of energy-rich nucleotides. Moreover, inhibition of L-Arg metabolism in MSC-1 cells down-regulated central carbon metabolism activity, including glycolysis, glutaminolysis and TCA cycle activity, and led to a deterioration of cell bioenergetic status. The simultaneous increase of cell specific concentrations of ATP and a decrease in ATP-to-ADP ratio in BM-derived MDSCs suggested cells were metabolically active during maturation. Moreover, AMP-activated protein kinase (AMPK was activated during MDSC maturation in GM-CSF and IL-6–treated cultures, as revealed by the continuous increase of AMP-to-ATP ratios and the phosphorylation of AMPK. Likewise, AMPK activity was

  1. Computational analysis of storage synthesis in developing Brassica napus L. (oilseed rape) embryos: Flux variability analysis in relation to 13C-metabolic flux analysis

    Energy Technology Data Exchange (ETDEWEB)

    Hay, J.; Schwender, J.

    2011-08-01

    Plant oils are an important renewable resource, and seed oil content is a key agronomical trait that is in part controlled by the metabolic processes within developing seeds. A large-scale model of cellular metabolism in developing embryos of Brassica napus (bna572) was used to predict biomass formation and to analyze metabolic steady states by flux variability analysis under different physiological conditions. Predicted flux patterns are highly correlated with results from prior 13C metabolic flux analysis of B. napus developing embryos. Minor differences from the experimental results arose because bna572 always selected only one sugar and one nitrogen source from the available alternatives, and failed to predict the use of the oxidative pentose phosphate pathway. Flux variability, indicative of alternative optimal solutions, revealed alternative pathways that can provide pyruvate and NADPH to plastidic fatty acid synthesis. The nutritional values of different medium substrates were compared based on the overall carbon conversion efficiency (CCE) for the biosynthesis of biomass. Although bna572 has a functional nitrogen assimilation pathway via glutamate synthase, the simulations predict an unexpected role of glycine decarboxylase operating in the direction of NH4+ assimilation. Analysis of the light-dependent improvement of carbon economy predicted two metabolic phases. At very low light levels small reductions in CO2 efflux can be attributed to enzymes of the tricarboxylic acid cycle (oxoglutarate dehydrogenase, isocitrate dehydrogenase) and glycine decarboxylase. At higher light levels relevant to the 13C flux studies, ribulose-1,5-bisphosphate carboxylase activity is predicted to account fully for the light-dependent changes in carbon balance.

  2. ¹³C metabolic flux analysis identifies an unusual route for pyruvate dissimilation in mycobacteria which requires isocitrate lyase and carbon dioxide fixation.

    Directory of Open Access Journals (Sweden)

    Dany J V Beste

    2011-07-01

    Full Text Available Mycobacterium tuberculosis requires the enzyme isocitrate lyase (ICL for growth and virulence in vivo. The demonstration that M. tuberculosis also requires ICL for survival during nutrient starvation and has a role during steady state growth in a glycerol limited chemostat indicates a function for this enzyme which extends beyond fat metabolism. As isocitrate lyase is a potential drug target elucidating the role of this enzyme is of importance; however, the role of isocitrate lyase has never been investigated at the level of in vivo fluxes. Here we show that deletion of one of the two icl genes impairs the replication of Mycobacterium bovis BCG at slow growth rate in a carbon limited chemostat. In order to further understand the role of isocitrate lyase in the central metabolism of mycobacteria the effect of growth rate on the in vivo fluxes was studied for the first time using ¹³C-metabolic flux analysis (MFA. Tracer experiments were performed with steady state chemostat cultures of BCG or M. tuberculosis supplied with ¹³C labeled glycerol or sodium bicarbonate. Through measurements of the ¹³C isotopomer labeling patterns in protein-derived amino acids and enzymatic activity assays we have identified the activity of a novel pathway for pyruvate dissimilation. We named this the GAS pathway because it utilizes the Glyoxylate shunt and Anapleurotic reactions for oxidation of pyruvate, and Succinyl CoA synthetase for the generation of succinyl CoA combined with a very low flux through the succinate--oxaloacetate segment of the tricarboxylic acid cycle. We confirm that M. tuberculosis can fix carbon from CO₂ into biomass. As the human host is abundant in CO₂ this finding requires further investigation in vivo as CO₂ fixation may provide a point of vulnerability that could be targeted with novel drugs. This study also provides a platform for further studies into the metabolism of M. tuberculosis using ¹³C-MFA.

  3. Looking at the metabolic consequences of the colchicine-based in vivo autophagic flux assay.

    Science.gov (United States)

    Seiliez, Iban; Belghit, Ikram; Gao, Yujie; Skiba-Cassy, Sandrine; Dias, Karine; Cluzeaud, Marianne; Rémond, Didier; Hafnaoui, Nordine; Salin, Bénédicte; Camougrand, Nadine; Panserat, Stéphane

    2016-02-01

    Monitoring autophagic flux in vivo or in organs remains limited and the ideal methods relative to the techniques possible with cell culture may not exist. Recently, a few papers have demonstrated the feasibility of measuring autophagic flux in vivo by intraperitoneal (IP) injection of pharmacological agents (chloroquine, leupeptin, vinblastine, and colchicine). However, the metabolic consequences of the administration of these drugs remain largely unknown. Here, we report that 0.8 mg/kg/day IP colchicine increased LC3-II protein levels in the liver of fasted trout, supporting the usefulness of this drug for studying autophagic flux in vivo in our model organism. This effect was accompanied by a decrease of plasma glucose concentration associated with a fall in the mRNA levels of gluconeogenesis-related genes. Concurrently, triglycerides and lipid droplets content in the liver increased. In contrast, transcript levels of β-oxidation-related gene Cpt1a dropped significantly. Together, these results match with the reported role of autophagy in the regulation of glucose homeostasis and intracellular lipid stores, and highlight the importance of considering these effects when using colchicine as an in vivo "autophagometer." PMID:26902586

  4. BVOC and tropospheric ozone fluxes from an orange orchard in the California Central Valley

    Science.gov (United States)

    Fares, S.; Gentner, D. R.; Park, J.; Weber, R.; Karlik, J. F.; Goldstein, A. H.

    2010-12-01

    Citrus plants, especially oranges, are widely cultivated in the Central Valley of California and in many other countries experiencing Mediterranean climates. In many of these areas, orchards are often exposed to high levels of tropospheric ozone (O3) due to their location in polluted airsheds. Citrus take up O3 through their stomata and emit biogenic volatile organic compounds (BVOC), which can contribute to non-stomatal O3 removal through fast gas-phase reactions with O3. The study was performed in a navel orange orchard in Exeter, California. The CO2 & water fluxes, together with O3 uptake and BVOC emissions were measured continuously using eddy covariance techniques. Vertical concentration gradients of these compounds were also measured at 4 heights from the orchard floor to above the canopy. We observed high levels (up to 40 ppb) of volatile organic compounds including methanol, isoprene, monoterpenes, sesquiterpenes, and some additional oxygenated BVOC. Methanol dominated BVOC emissions (up to 5 nmol m-2 s-1) followed by acetone. Monoterpenes fluxes were also recorded during the all vegetative period, with the highest emissions taking place during flowering periods. The orchard represented a sink for ozone, with uptake rates on the order of 10 nmol m-2 s-1 during the central hours of the day. BVOC fluxes were highly temperature dependent, while ozone fluxes were more dependent on the physiology of the orchard, consistent with dominant removal occurring through the stomatal opening. The current research is aimed at: 1. Quantifying the uptake of O3 by citrus and partitioning it into stomatal and non-stomatal processes; 2. Quantifying the BVOC emissions and their dependence on physical and ecophysiological parameters.

  5. Nitrous oxide fluxes and nitrogen cycling along a pasture chronosequence in Central Amazonia, Brazil

    Directory of Open Access Journals (Sweden)

    B. Wick

    2005-01-01

    Full Text Available We studied nitrous oxide (N2O fluxes and soil nitrogen (N cycling following forest conversion to pasture in the central Amazon near Santarém, Pará, Brazil. Two undisturbed forest sites and 27 pasture sites of 0.5 to 60 years were sampled once each during wet and dry seasons. In addition to soil-atmosphere fluxes of N2O we measured 27 soil chemical, soil microbiological and soil physical variables. Soil N2O fluxes were higher in the wet season than in the dry season. Fluxes of N2O from forest soils always exceeded fluxes from pasture soils and showed no consistent trend with pasture age. At our forest sites, nitrate was the dominant form of inorganic N both during wet and dry season. At our pasture sites nitrate generally dominated the inorganic N pools during the wet season and ammonium dominated during the dry season. Net mineralization and nitrification rates displayed large variations. During the dry season net immobilization of N was observed in some pastures. Compared to forest sites, young pasture sites (≤2 years had low microbial biomass N and protease activities. Protease activity and microbial biomass N peaked in pastures of intermediate age (4 to 8 years followed by consistently lower values in older pasture (10 to 60 years. The C/N ratio of litter was low at the forest sites (~25 and rapidly increased with pasture age reaching values of 60-70 at pastures of 15 years and older. Nitrous oxide emissions at our sites were controlled by C and N availability and soil aeration. Fluxes of N2O were negatively correlated to leaf litter C/N ratio, NH4+-N and the ratio of NO3--N to the sum of NO3--N + NH4+-N (indicators of N availability, and methane fluxes and bulk density (indicators of soil aeration status during the wet season. During the dry season fluxes of N2O were positively correlated to microbial biomass N, β-glucosidase activity, total inorganic N stocks and NH4+-N. In our study region, pastures of all age emitted less N2O than

  6. Impact of xylose and mannose on central metabolism of yeast Saccharomyces cerevisiae

    Energy Technology Data Exchange (ETDEWEB)

    Pitkaenen, J.P.

    2005-07-01

    In this study, understanding of the central metabolism was improved by quantification of metabolite concentrations, enzyme activities, protein abundances, and gene transcript concentrations. Intracellular fluxes were estimated by applying stoichiometric models of metabolism. The methods were applied in the study of yeast Saccharomyces cerevisiae in two separate projects. A xylose project aimed at improved utilization of D- xylose as a substrate for, e.g., producing biomaterial- based fuel ethanol. A mannose project studied the production of GDP-mannose from D-mannose in a strain lacking the gene for phosphomannose isomerase (PMI40 deletion). Hexose, D-glucose is the only sugar more abundant than pentose D-xylose. D-xylose is common in hardwoods (e.g. birch) and crop residues (ca. 25% of dry weight). However, S. cerevisiae is unable to utilize D- xylose without a recombinant pathway where D-xylose is converted to Dxylulose. In this study D-xylose was converted in two steps via xylitol: by D-xylose reductase and xylitol dehydrogenase encoded by XYL1 and XYL2 from Pichia stipitis, respectively. Additionally, endogenous xylulokinase (XKS1) was overexpressed in order to increase the consumption of D-xylose by enhancing the phosphorylation of D-xylulose. Despite of the functional recombinant pathway the utilization rates of D xylose still remained low. This study proposes a set of limitations that are responsible for the low utilization rates of D-xylose under microaerobic conditions. Cells compensated for the cofactor imbalance, caused by the conversion of D-xylose to D- xylulose, by increasing the flux through the oxidative pentose phosphate pathway and by shuttling NADH redox potential to mitochondrion to be oxidized in oxidative phosphorylation. However, mitochondrial NADH inhibits citrate synthase in citric acid cycle, and consequently lower flux through citric acid cycle limits oxidative phosphorylation. Further, limitations in the uptake of D- xylose, in the

  7. Staphylococcus aureus Coordinates Leukocidin Expression and Pathogenesis by Sensing Metabolic Fluxes via RpiRc

    Science.gov (United States)

    Balasubramanian, Divya; Ohneck, Elizabeth A.; Chapman, Jessica; Weiss, Andy; Kim, Min Kyung; Reyes-Robles, Tamara; Zhong, Judy; Shaw, Lindsey N.; Lun, Desmond S.; Ueberheide, Beatrix; Shopsin, Bo

    2016-01-01

    ABSTRACT Staphylococcus aureus is a formidable human pathogen that uses secreted cytolytic factors to injure immune cells and promote infection of its host. Of these proteins, the bicomponent family of pore-forming leukocidins play critical roles in S. aureus pathogenesis. The regulatory mechanisms governing the expression of these toxins are incompletely defined. In this work, we performed a screen to identify transcriptional regulators involved in leukocidin expression in S. aureus strain USA300. We discovered that a metabolic sensor-regulator, RpiRc, is a potent and selective repressor of two leukocidins, LukED and LukSF-PV. Whole-genome transcriptomics, S. aureus exoprotein proteomics, and metabolomic analyses revealed that RpiRc influences the expression and production of disparate virulence factors. Additionally, RpiRc altered metabolic fluxes in the trichloroacetic acid cycle, glycolysis, and amino acid metabolism. Using mutational analyses, we confirmed and extended the observation that RpiRc signals through the accessory gene regulatory (Agr) quorum-sensing system in USA300. Specifically, RpiRc represses the rnaIII promoter, resulting in increased repressor of toxins (Rot) levels, which in turn negatively affect leukocidin expression. Inactivation of rpiRc phenocopied rot deletion and increased S. aureus killing of primary human polymorphonuclear leukocytes and the pathogenesis of bloodstream infection in vivo. Collectively, our results suggest that S. aureus senses metabolic shifts by RpiRc to differentially regulate the expression of leukocidins and to promote invasive disease. PMID:27329753

  8. A holistic view of dietary carbohydrate utilization in lobster: digestion, postprandial nutrient flux, and metabolism.

    Science.gov (United States)

    Rodríguez-Viera, Leandro; Perera, Erick; Casuso, Antonio; Perdomo-Morales, Rolando; Gutierrez, Odilia; Scull, Idania; Carrillo, Olimpia; Martos-Sitcha, Juan A; García-Galano, Tsai; Mancera, Juan Miguel

    2014-01-01

    Crustaceans exhibit a remarkable variation in their feeding habits and food type, but most knowledge on carbohydrate digestion and utilization in this group has come from research on few species. The aim of this study was to make an integrative analysis of dietary carbohydrate utilization in the spiny lobster Panulirus argus. We used complementary methodologies such as different assessments of digestibility, activity measurements of digestive and metabolic enzymes, and post-feeding flux of nutrients and metabolites. Several carbohydrates were well digested by the lobster, but maize starch was less digestible than all other starches studied, and its inclusion in diet affected protein digestibility. Most intense hydrolysis of carbohydrates in the gastric chamber of lobster occurred between 2-6 h after ingestion and afterwards free glucose increased in hemolymph. The inclusion of wheat in diet produced a slow clearance of glucose from the gastric fluid and a gradual increase in hemolymph glucose. More intense hydrolysis of protein in the gastric chamber occurred 6-12 h after ingestion and then amino acids tended to increase in hemolymph. Triglyceride concentration in hemolymph rose earlier in wheat-fed lobsters than in lobsters fed other carbohydrates, but it decreased the most 24 h later. Analyses of metabolite levels and activities of different metabolic enzymes revealed that intermolt lobsters had a low capacity to store and use glycogen, although it was slightly higher in wheat-fed lobsters. Lobsters fed maize and rice diets increased amino acid catabolism, while wheat-fed lobsters exhibited higher utilization of fatty acids. Multivariate analysis confirmed that the type of carbohydrate ingested had a profound effect on overall metabolism. Although we found no evidence of a protein-sparing effect of dietary carbohydrate, differences in the kinetics of their digestion and absorption impacted lobster metabolism determining the fate of other nutrients. PMID:25268641

  9. A holistic view of dietary carbohydrate utilization in lobster: digestion, postprandial nutrient flux, and metabolism.

    Directory of Open Access Journals (Sweden)

    Leandro Rodríguez-Viera

    Full Text Available Crustaceans exhibit a remarkable variation in their feeding habits and food type, but most knowledge on carbohydrate digestion and utilization in this group has come from research on few species. The aim of this study was to make an integrative analysis of dietary carbohydrate utilization in the spiny lobster Panulirus argus. We used complementary methodologies such as different assessments of digestibility, activity measurements of digestive and metabolic enzymes, and post-feeding flux of nutrients and metabolites. Several carbohydrates were well digested by the lobster, but maize starch was less digestible than all other starches studied, and its inclusion in diet affected protein digestibility. Most intense hydrolysis of carbohydrates in the gastric chamber of lobster occurred between 2-6 h after ingestion and afterwards free glucose increased in hemolymph. The inclusion of wheat in diet produced a slow clearance of glucose from the gastric fluid and a gradual increase in hemolymph glucose. More intense hydrolysis of protein in the gastric chamber occurred 6-12 h after ingestion and then amino acids tended to increase in hemolymph. Triglyceride concentration in hemolymph rose earlier in wheat-fed lobsters than in lobsters fed other carbohydrates, but it decreased the most 24 h later. Analyses of metabolite levels and activities of different metabolic enzymes revealed that intermolt lobsters had a low capacity to store and use glycogen, although it was slightly higher in wheat-fed lobsters. Lobsters fed maize and rice diets increased amino acid catabolism, while wheat-fed lobsters exhibited higher utilization of fatty acids. Multivariate analysis confirmed that the type of carbohydrate ingested had a profound effect on overall metabolism. Although we found no evidence of a protein-sparing effect of dietary carbohydrate, differences in the kinetics of their digestion and absorption impacted lobster metabolism determining the fate of other

  10. THERMAL SIGNATURES OF TETHER-CUTTING RECONNECTIONS IN PRE-ERUPTION CORONAL FLUX ROPES: HOT CENTRAL VOIDS IN CORONAL CAVITIES

    Energy Technology Data Exchange (ETDEWEB)

    Fan, Y. [High Altitude Observatory, National Center for Atmospheric Research, 3080 Center Green Drive, Boulder, CO 80301 (United States)

    2012-10-10

    Using a three-dimensional MHD simulation, we model the quasi-static evolution and the onset of eruption of a coronal flux rope. The simulation begins with a twisted flux rope emerging at the lower boundary and pushing into a pre-existing coronal potential arcade field. At a chosen time the emergence is stopped with the lower boundary taken to be rigid. Then the coronal flux rope settles into a quasi-static rise phase during which an underlying, central sigmoid-shaped current layer forms along the so-called hyperbolic flux tube (HFT), a generalization of the X-line configuration. Reconnections in the dissipating current layer effectively add twisted flux to the flux rope and thus allow it to rise quasi-statically, even though the magnetic energy is decreasing as the system relaxes. We examine the thermal features produced by the current layer formation and the associated 'tether-cutting' reconnections as a result of heating and field aligned thermal conduction. It is found that a central hot, low-density channel containing reconnected, twisted flux threading under the flux rope axis forms on top of the central current layer. When viewed in the line of sight roughly aligned with the hot channel (which is roughly along the neutral line), the central current layer appears as a high-density vertical column with upward extensions as a {sup U-}shaped dense shell enclosing a central hot, low-density void. Such thermal features have been observed within coronal prominence cavities. Our MHD simulation suggests that they are the signatures of the development of the HFT topology and the associated tether-cutting reconnections, and that the central void grows and rises with the reconnections, until the flux rope reaches the critical height for the onset of the torus instability and dynamic eruption ensues.

  11. THERMAL SIGNATURES OF TETHER-CUTTING RECONNECTIONS IN PRE-ERUPTION CORONAL FLUX ROPES: HOT CENTRAL VOIDS IN CORONAL CAVITIES

    International Nuclear Information System (INIS)

    Using a three-dimensional MHD simulation, we model the quasi-static evolution and the onset of eruption of a coronal flux rope. The simulation begins with a twisted flux rope emerging at the lower boundary and pushing into a pre-existing coronal potential arcade field. At a chosen time the emergence is stopped with the lower boundary taken to be rigid. Then the coronal flux rope settles into a quasi-static rise phase during which an underlying, central sigmoid-shaped current layer forms along the so-called hyperbolic flux tube (HFT), a generalization of the X-line configuration. Reconnections in the dissipating current layer effectively add twisted flux to the flux rope and thus allow it to rise quasi-statically, even though the magnetic energy is decreasing as the system relaxes. We examine the thermal features produced by the current layer formation and the associated 'tether-cutting' reconnections as a result of heating and field aligned thermal conduction. It is found that a central hot, low-density channel containing reconnected, twisted flux threading under the flux rope axis forms on top of the central current layer. When viewed in the line of sight roughly aligned with the hot channel (which is roughly along the neutral line), the central current layer appears as a high-density vertical column with upward extensions as a U-shaped dense shell enclosing a central hot, low-density void. Such thermal features have been observed within coronal prominence cavities. Our MHD simulation suggests that they are the signatures of the development of the HFT topology and the associated tether-cutting reconnections, and that the central void grows and rises with the reconnections, until the flux rope reaches the critical height for the onset of the torus instability and dynamic eruption ensues.

  12. Thermal Signatures of Tether-cutting Reconnections in Pre-eruption Coronal Flux Ropes: Hot Central Voids in Coronal Cavities

    Science.gov (United States)

    Fan, Y.

    2012-10-01

    Using a three-dimensional MHD simulation, we model the quasi-static evolution and the onset of eruption of a coronal flux rope. The simulation begins with a twisted flux rope emerging at the lower boundary and pushing into a pre-existing coronal potential arcade field. At a chosen time the emergence is stopped with the lower boundary taken to be rigid. Then the coronal flux rope settles into a quasi-static rise phase during which an underlying, central sigmoid-shaped current layer forms along the so-called hyperbolic flux tube (HFT), a generalization of the X-line configuration. Reconnections in the dissipating current layer effectively add twisted flux to the flux rope and thus allow it to rise quasi-statically, even though the magnetic energy is decreasing as the system relaxes. We examine the thermal features produced by the current layer formation and the associated "tether-cutting" reconnections as a result of heating and field aligned thermal conduction. It is found that a central hot, low-density channel containing reconnected, twisted flux threading under the flux rope axis forms on top of the central current layer. When viewed in the line of sight roughly aligned with the hot channel (which is roughly along the neutral line), the central current layer appears as a high-density vertical column with upward extensions as a "U"-shaped dense shell enclosing a central hot, low-density void. Such thermal features have been observed within coronal prominence cavities. Our MHD simulation suggests that they are the signatures of the development of the HFT topology and the associated tether-cutting reconnections, and that the central void grows and rises with the reconnections, until the flux rope reaches the critical height for the onset of the torus instability and dynamic eruption ensues.

  13. Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p

    DEFF Research Database (Denmark)

    Moxley, Joel F.; Jewett, Michael Christopher; Antoniewicz, Maciek R.;

    2009-01-01

    Genome sequencing dramatically increased our ability to understand cellular response to perturbation. Integrating system-wide measurements such as gene expression with networks of protein protein interactions and transcription factor binding revealed critical insights into cellular behavior. Howe...... integrated approach focusing on metabolic measurements will facilitate construction of more realistic models of cellular regulation for understanding diseases and constructing strains for industrial applications....... regulator Gcn4p. Although mRNA expression alone did not directly predict metabolic response, this correlation improved through incorporating a network-based model of amino acid biosynthesis (from r = 0.07 to 0.80 for mRNA-flux agreement). The model provides evidence of general biological principles......: rewiring of metabolic flux (i.e., use of different reaction pathways) by transcriptional regulation and metabolite interaction density (i.e., level of pairwise metabolite-protein interactions) as a key biosynthetic control determinant. Furthermore, this model predicted flux rewiring in studies of follow...

  14. Metabolic flux analysis in a nonstationary system: Fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol

    OpenAIRE

    Antoniewicz, Maciek R.; Kraynie, David F.; Laffend, Lisa A.; González-Lergier, Joanna; Kelleher, Joanne K.; Stephanopoulos, Gregory

    2007-01-01

    Metabolic fluxes estimated from stable-isotope studies provide a key to understanding cell physiology and regulation of metabolism. A limitation of the classical method for metabolic flux analysis (MFA) is the requirement for isotopic steady state. To extend the scope of flux determination from stationary to nonstationary systems, we present a novel modeling strategy that combines key ideas from isotopomer spectral analysis (ISA) and stationary MFA. Isotopic transients of the precursor pool a...

  15. Annual benthic metabolism and organic carbon fluxes in a semi-enclosed Mediterranean bay dominated by the macroalgae Caulerpa prolifera

    OpenAIRE

    Ruiz-Halpern, Sergio; Vaquer-Sunyer, Raquel; Duarte, Carlos M.

    2014-01-01

    Coastal areas play an important role on carbon cycling. Elucidating the dynamics on the production, transport, and fate of organic carbon (OC) is relevant to gain a better understanding on the role coastal areas play in the global carbon budget. Here, we assess the metabolic status and associated OC fluxes of a semi-enclosed Mediterranean bay supporting a meadow of Caulerpa prolifera. We test whether the EDOC pool is a significant component of the OC pool and associated fluxes in this ecosyst...

  16. Flux-based classification of reactions reveals a functional bow-tie organization of complex metabolic networks

    OpenAIRE

    Singh, Shalini; Samal, Areejit; Giri, Varun; Krishna, Sandeep; Raghuram, Nandula; Jain, Sanjay

    2012-01-01

    Unraveling the structure of complex biological networks and relating it to their functional role is an important task in systems biology. Here we attempt to characterize the functional organization of the large-scale metabolic networks of three microorganisms. We apply flux balance analysis to study the optimal growth states of these organisms in different environments. By investigating the differential usage of reactions across flux patterns for different environments, we observe a striking ...

  17. The brain at work: a cerebral metabolic manifestation of central fatigue?

    Science.gov (United States)

    Dalsgaard, Mads K; Secher, Niels H

    2007-11-15

    Central fatigue refers to circumstances in which strength appears to be limited by the ability of the central nervous system to recruit motoneurons. Central fatigue manifests when the effort to contract skeletal muscles is intense and, thus, is aggravated when exercise is performed under stress, whereas it becomes attenuated following training. Central fatigue has not been explained, but the cerebral metabolic response to intense exercise, as to other modalities of cerebral activation, is a reduction in its "metabolic ratio" (MR), i.e., the brain's uptake of oxygen relative to that of carbohydrate. At rest the MR is close to 6 but during intense whole-body exercise it decreases to less than 3, with the uptake of lactate becoming as important as that of glucose. It remains debated what underlies this apparent inability of the brain to oxidize the carbohydrate taken up, but it may approach approximately 10 mmol glucose equivalents. In the case of exercise, a concomitant uptake of ammonium for formation of amino acids may account for only approximately 10% of this "extra" carbohydrate taken up. Also, accumulation of intermediates in metabolic pathways and compartmentalization of metabolism between astrocytes and neurons are avenues that have to be explored. Depletion of glycogen stores and subsequent supercompensation during periods of low neuronal activity may not only play a role but also link brain metabolism to its function. PMID:17394258

  18. Measurement of NOx fluxes from a tall tower in central London, UK and comparison with emissions inventories

    OpenAIRE

    Lee, James D.; Helfter, Carole; Purvis, Ruth M.; Beevers, Sean D.; Carslaw, David C.; Alastair C. Lewis; Moller, Sarah J.; Tremper, Anja; Vaughan, Adam; Nemitz, Eiko G.

    2015-01-01

    Direct measurements of NOx concentration and flux were made from a tall tower in central London, UK as part of the Clean Air for London (ClearfLo) project. Fast time resolution (10 Hz) NO and NO2 concentrations were measured and combined with fast vertical wind measurements to provide top-down flux estimates using the eddy covariance technique. Measured NOx fluxes were usually positive and ranged from close to zero at night to 2000–8000 ng m–2 s–1 during the day. Peak fluxes were usually obse...

  19. Application of Metabolic Flux Analysis to Identify the Mechanisms of Free Fatty Acid Toxicity to Human Hepatoma Cell Line

    OpenAIRE

    Srivastava, Shireesh; Chan, Christina

    2008-01-01

    Chronic exposure to elevated levels of free fatty acids (FFAs) has been shown to cause cell death (lipotoxicity), but the underlying mechanisms of lipotoxicity in hepatocytes remain unclear. We have previously shown that the saturated FFAs cause much greater toxicity to human hepatoma cells (HepG2) than the unsaturated ones (Srivastava and Chan, 2007). In this study, metabolic flux analysis (MFA) was applied to identify the metabolic changes associated with the cytotoxicity of saturated FFA. ...

  20. The influence of management on GHG fluxes over Central European grasslands

    Science.gov (United States)

    Hoertnagl, Lukas; Bahn, Michael; Buchmann, Nina; Dias-Pinez, Eugenio; Eugster, Werner; Kiese, Ralf; Klumpp, Katja; Thomas, Ladreiter-Knauss; Lu, Haiyan; Wohlfahrt, Georg; Zeeman, Matthias; Merbold, Lutz

    2016-04-01

    Central European grasslands are characterized by a wide range of different agricultural practices along an altitudinal and management gradient, reaching from low pastures and meadows up to high alpine grasslands above the tree line. In the future, the intensification of already available agricultural land as a consequence of increased demand for feed and food will play an important role because of the scarcity of unused, productive land. The land use intensity strongly affects the exchange of trace gases between the biosphere and atmosphere. Therefore, the greenhouse gas (GHG) reduction potential for different farming strategies needs to be quantified before effective greenhouse gas mitigation strategies can be introduced. Direct measurements of long-term grassland GHG exchange at ecosystem scale along altitudinal and management gradients can help in identifying key processes that lead to GHG emissions. In this synthesis we investigated GHG fluxes with a focus on N2O and CH4 from 15 grassland sites, quantified by means of the eddy covariance or chamber technique. Grasslands were a source of N2O, with the exception of one abandoned site, while they were a source or small sink for CH4. The predictive power of soil temperature and water-filled pore space for N2O and CH4 flux patterns during snow-free time periods in-between management events was generally low but varied considerably across the year. However, setting fluxes in relation to classes of the two soil parameters revealed favorable conditions ('sweet spots') for N2O and CH4 emissions for some sites. In addition, fertilization had a clear impact on N2O and CH4 fluxes, with emission peaks on the day of fertilization or one day later. N2O-N emission factors at fertilized sites were found to be slightly higher than the IPCC Tier 1 approach, ranging between 1.31 and 1.53 %, depending on the gap-filling method to calculate yearly cumulative N2O emissions.

  1. Evidence for transketolase-like TKTL1 flux in CHO cells based on parallel labeling experiments and (13)C-metabolic flux analysis.

    Science.gov (United States)

    Ahn, Woo Suk; Crown, Scott B; Antoniewicz, Maciek R

    2016-09-01

    The pentose phosphate pathway (PPP) is a fundamental component of cellular metabolism. It provides precursors for the biosynthesis of nucleotides and contributes to the production of reducing power in the form of NADPH. It has been hypothesized that mammalian cells may contain a hidden reaction in PPP catalyzed by transketolase-like protein 1 (TKTL1) that is closely related to the classical transketolase enzyme; however, until now there has been no direct experimental evidence for this reaction. In this work, we have applied state-of-the-art techniques in (13)C metabolic flux analysis ((13)C-MFA) based on parallel labeling experiments and integrated flux fitting to estimate the TKTL1 flux in CHO cells. We identified a set of three parallel labeling experiments with [1-(13)C]glucose+[4,5,6-(13)C]glucose, [2-(13)C]glucose+[4,5,6-(13)C]glucose, and [3-(13)C]glucose+[4,5,6-(13)C]glucose and developed a new method to measure (13)C-labeling of fructose 6-phosphate by GC-MS that allows intuitive interpretation of mass isotopomer distributions to determine key fluxes in the model, including glycolysis, oxidative PPP, non-oxidative PPP, and the TKTL1 flux. Using these tracers we detected a significant TKTL1 flux in CHO cells at the stationary phase. The flux results suggest that the main function of oxidative PPP in CHO cells at the stationary phase is to fuel the TKTL1 reaction. Overall, this study demonstrates for the first time that carbon atoms can be lost in the PPP, by means other than the oxidative PPP, and that this loss of carbon atoms is consistent with the hypothesized TKTL1 reaction in mammalian cells. PMID:27174718

  2. Pyruvate modifies metabolic flux and nutrient sensing during extracorporeal membrane oxygenation in an immature swine model

    Energy Technology Data Exchange (ETDEWEB)

    Ledee, Dolena R.; Kajimoto, Masaki; O' Kelly-Priddy, Colleen M.; Olson, Aaron; Isern, Nancy G.; Robillard Frayne, Isabelle; Des Rosiers, Christine; Portman, Michael A.

    2015-07-01

    Extracorporeal membrane oxygenation (ECMO) provides mechanical circulatory support for infants and children with postoperative cardiopulmonary failure. Nutritional support is mandatory during ECMO, although specific actions for substrates on the heart have not been delineated. Prior work shows that enhancing pyruvate oxidation promotes successful weaning from ECMO. Accordingly, we closely examined the role of prolonged systemic pyruvate supplementation in modifying metabolic parameters during the unique conditions of ventricular unloading provided by ECMO. Twelve male mixed breed Yorkshire piglets (age 30-49 days) received systemic infusion of either normal saline (Group C) or pyruvate (Group P) during ECMO for 8 hours. Over the final hour piglets received [2-13C] pyruvate, and [13C6]-L-leucine, as an indicator for oxidation and protein synthesis. A significant increase in lactate and pyruvate concentrations occurred, along with an increase in the absolute concentration of all measured CAC intermediates. Group P showed greater anaplerotic flux through pyruvate carboxylation although pyruvate oxidation relative to citrate synthase flux was similar to Group C. The groups demonstrated similar leucine fractional contributions to acetyl-CoA and fractional protein synthesis rates. Pyruvate also promoted an increase in the phosphorylation state of several nutrient sensitive enzymes, such as AMPK and ACC, and promoted O-GlcNAcylation through the hexosamine biosynthetic pathway (HBP). In conclusion, prolonged pyruvate supplementation during ECMO modified anaplerotic pyruvate flux and elicited changes in important nutrient and energy sensitive pathways, while preserving protein synthesis. Therefore, the observed results support the further study of nutritional supplementation and its downstream effects on cardiac adaptation during ventricular unloading.

  3. Central Pathways Integrating Metabolism and Reproduction in Teleosts

    Directory of Open Access Journals (Sweden)

    Md eShahjahan

    2014-03-01

    Full Text Available Energy balance plays an important role in the control of reproduction. However, the cellular and molecular mechanisms connecting the two systems are not well understood especially in teleosts. The hypothalamus plays a crucial role in the regulation of both energy balance and reproduction, and contains a number of neuropeptides, including gonadotropin-releasing hormone (GnRH, orexin, neuropeptide-Y (NPY, ghrelin, pituitary adenylate cyclase-activating polypeptide (PACAP, α-melanocyte stimulating hormone (α-MSH, melanin-concentrating hormone (MCH, cholecystokinin (CCK, 26RFa, nesfatin, kisspeptin, and gonadotropin-inhibitory hormone (GnIH. These neuropeptides are involved in the control of energy balance and reproduction either directly or indirectly. On the other hand, synthesis and release of these hypothalamic neuropeptides are regulated by metabolic signals from the gut and the adipose tissue. Furthermore, neurons producing these neuropeptides interact with each other, providing neuronal basis of the link between energy balance and reproduction. This review summarizes the advances made in our understanding of the physiological roles of the hypothalamic neuropeptides in energy balance and reproduction in teleosts, and discusses how they interact with GnRH, kisspeptin, and pituitary gonadotropins to control reproduction in teleosts.

  4. Staphylococcus aureus redirects central metabolism to increase iron availability.

    Directory of Open Access Journals (Sweden)

    David B Friedman

    2006-08-01

    Full Text Available Staphylococcus aureus pathogenesis is significantly influenced by the iron status of the host. However, the regulatory impact of host iron sources on S. aureus gene expression remains unknown. In this study, we combine multivariable difference gel electrophoresis and mass spectrometry with multivariate statistical analyses to systematically cluster cellular protein response across distinct iron-exposure conditions. Quadruplicate samples were simultaneously analyzed for alterations in protein abundance and/or post-translational modification state in response to environmental (iron chelation, hemin treatment or genetic (Deltafur alterations in bacterial iron exposure. We identified 120 proteins representing several coordinated biochemical pathways that are affected by changes in iron-exposure status. Highlighted in these experiments is the identification of the heme-regulated transport system (HrtAB, a novel transport system which plays a critical role in staphylococcal heme metabolism. Further, we show that regulated overproduction of acidic end-products brought on by iron starvation decreases local pH resulting in the release of iron from the host iron-sequestering protein transferrin. These findings reveal novel strategies used by S. aureus to acquire scarce nutrients in the hostile host environment and begin to define the iron and heme-dependent regulons of S. aureus.

  5. Comparative 13C Metabolic Flux Analysis of Pyruvate Dehydrogenase Complex-Deficient, l-Valine-Producing Corynebacterium glutamicum▿†

    OpenAIRE

    Bartek, Tobias; Blombach, Bastian; Lang, Siegmund; Eikmanns, Bernhard J.; Wiechert, Wolfgang; Oldiges, Marco; Nöh, Katharina; Noack, Stephan

    2011-01-01

    l-Valine can be formed successfully using C. glutamicum strains missing an active pyruvate dehydrogenase enzyme complex (PDHC). Wild-type C. glutamicum and four PDHC-deficient strains were compared by 13C metabolic flux analysis, especially focusing on the split ratio between glycolysis and the pentose phosphate pathway (PPP). Compared to the wild type, showing a carbon flux of 69% ± 14% through the PPP, a strong increase in the PPP flux was observed in PDHC-deficient strains with a maximum o...

  6. Systems-wide analysis and engineering of metabolic pathway fluxes in bio-succinate producing Basfia succiniciproducens.

    Science.gov (United States)

    Becker, Judith; Reinefeld, Jasper; Stellmacher, René; Schäfer, Rudolf; Lange, Anna; Meyer, Hanna; Lalk, Michael; Zelder, Oskar; von Abendroth, Gregory; Schröder, Hartwig; Haefner, Stefan; Wittmann, Christoph

    2013-11-01

    Basfia succiniciproducens has been recently isolated as novel producer for succinate, an important platform chemical. In batch culture, the wild type exhibited a high natural yield of 0.75 mol succinate (mol glucose)⁻¹. Systems-wide ¹³C metabolic flux analysis identified undesired fluxes through pyruvate-formate lyase (PflD) and lactate dehydrogenase (LdhA). The double deletion strain B. succiniciproducens ΔldhA ΔpflD revealed a 45% improved product yield of 1.08 mol mol⁻¹. In addition, metabolic flux analysis unraveled the parallel in vivo activity of the oxidative and reductive branch of the TCA cycle in B. succiniciproducens, whereby the oxidative part mainly served for anabolism. The wild type re-directed surplus NADH via a cycle involving malic enzyme or via transhydrogenase, respectively, to supply NADPH for anabolism, because the fluxes through the oxidative PPP and isocitrate dehydrogenase, that also provide this cofactor, were not sufficient. This was not observed for the deletion mutants, B. succiniciproducens ΔpflD and ΔldhA ΔpflD, where PPP and isocitrate dehydrogenase flux alone matched with the reduced anabolic NADPH demand. The integration of the production performance into the theoretical flux space, computed by elementary flux mode analysis, revealed that B. succiniciproducens ΔldhA ΔpflD reached 62% of the theoretical maximum yield. PMID:23832568

  7. Metabolic pathway analysis of Scheffersomyces (Pichia) stipitis. Effect of oxygen availability on ethanol synthesis and flux distributions

    Energy Technology Data Exchange (ETDEWEB)

    Unrean, Pornkamol [King Mongkut' s Univ. of Technology Thonburi, Bangkok (Thailand). Biochemical Engineering and Pilot Plant Research and Development Unit; National Center for Genetik Engineering and Biotechnology (BIOTEC), Pathumtani (Thailand); Nguyen, Nhung H.A. [King Mongkut' s Univ. of Technology Thonburi, Bangkok (Thailand). Biochemical Engineering and Pilot Plant Research and Development Unit

    2012-06-15

    Elementary mode analysis (EMA) identifies all possible metabolic states of the cell metabolic network. Investigation of these states can provide a detailed insight into the underlying metabolism in the cell. In this study, the flux states of Scheffersomyces (Pichia) stipitis metabolism were examined. It was shown that increasing oxygen levels led to a decrease of ethanol synthesis. This trend was confirmed by experimental evaluation of S. stipitis in glucose-xylose fermentation. The oxygen transfer rate for an optimal ethanol production was 1.8 mmol/l/h, which gave the ethanol yield of 0.40 g/g and the ethanol productivity of 0.25 g/l/h. For a better understanding of the cell's regulatory mechanism in response to oxygenation levels, EMA was used to examine metabolic flux patterns under different oxygen levels. Up- and downregulation of enzymes in the network during the change of culturing condition from oxygen limitation to oxygen sufficiency were identified. The results indicated the flexibility of S. stipitis metabolism to cope with oxygen availability. In addition, relevant genetic targets towards improved ethanol-producing strains under all oxygenation levels were identified. These targeted genes limited the metabolic functionality of the cell to function according to the most efficient ethanol synthesis pathways. The presented approach is promising and can contribute to the development of culture optimization and strain engineers for improved lignocellulosic ethanol production by S. stipitis. (orig.)

  8. Central obesity measurements predict metabolic syndrome in a retrospective cohort study of postmenopausal women

    Directory of Open Access Journals (Sweden)

    Manuel Rosety-Rodríguez

    2013-12-01

    Full Text Available Introduction: The various diagnostic classifications in the literature concur as regards the important role of abdominal obesity in the onset and progression of metabolic syndrome. Accordingly, this study was aimed at clarifying whether central obesity measurements assessed by dual X-ray absorptiometry (DXA may predict metabolic syndrome in Spanish postmenopausal women. Material and methods: This historical cohort study included a total of 1326 postmenopausal women aged > 45 years old who had routinely undergone DXA to measure their bone mineral density between january 2006 and january 2011. The regions of interest (ROI envisaged in our study by using DXA were the lumbar regions L1-L4 and L4-L5. At the same time, they underwent a complete medical examination including personal medical history assessment, biochemical blood analysis, blood pressure measurement and anthropometrical evaluation. Metabolic syndrome was diagnosed attending to the criteria established by National Cholesterol Education Program Adult Treatment Panel III (NECP-ATP-III. Results: During the observation period, 537 women, representing 40.5% of the total studied, met the diagnostic criteria for metabolic syndrome. L1-L4 and L4-L5 abdominal fat mass determinations were associated with the development of metabolic syndrome in all regression models tested, showing an increasing gradient from the lowest to highest quintile. Conclusion: Central adiposity measurements assessed by DXA, especially L1-L4 region of interest, could be considered a powerful predictor of metabolic syndrome in postmenopausal women.

  9. Enzymatic passaging of human embryonic stem cells alters central carbon metabolism and glycan abundance

    Science.gov (United States)

    Badur, Mehmet G.; Zhang, Hui; Metallo, Christian M.

    2016-01-01

    To realize the potential of human embryonic stem cells (hESCs) in regenerative medicine and drug discovery applications, large numbers of cells that accurately recapitulate cell and tissue function must be robustly produced. Previous studies have suggested that genetic instability and epigenetic changes occur as a consequence of enzymatic passaging. However, the potential impacts of such passaging methods on the metabolism of hESCs have not been described. Using stable isotope tracing and mass spectrometry-based metabolomics, we have explored how different passaging reagents impact hESC metabolism. Enzymatic passaging caused significant decreases in glucose utilization throughout central carbon metabolism along with attenuated de novo lipogenesis. In addition, we developed and validated a method for rapidly quantifying glycan abundance and isotopic labeling in hydrolyzed biomass. Enzymatic passaging reagents significantly altered levels of glycans immediately after digestion but surprisingly glucose contribution to glycans was not affected. These results demonstrate that there is an immediate effect on hESC metabolism after enzymatic passaging in both central carbon metabolism and biosynthesis. HESCs subjected to enzymatic passaging are routinely placed in a state requiring re-synthesis of biomass components, subtly influencing their metabolic needs in a manner that may impact cell performance in regenerative medicine applications. PMID:26289220

  10. A central role of abscisic acid in stress-regulated carbohydrate metabolism.

    Directory of Open Access Journals (Sweden)

    Stefan Kempa

    Full Text Available BACKGROUND: Abiotic stresses adversely affect plant growth and development. The hormone abscisic acid (ABA plays a central role in the response and adaptation to environmental constraints. However, apart from the well established role of ABA in regulating gene expression programmes, little is known about its function in plant stress metabolism. PRINCIPAL FINDINGS: Using an integrative multiparallel approach of metabolome and transcriptome analyses, we studied the dynamic response of the model glyophyte Arabidopsis thaliana to ABA and high salt conditions. Our work shows that salt stress induces complex re-adjustment of carbohydrate metabolism and that ABA triggers the initial steps of carbon mobilisation. SIGNIFICANCE: These findings open new perspectives on how high salinity and ABA impact on central carbohydrate metabolism and highlight the power of iterative combinatorial approaches of non-targeted and hypothesis-driven experiments in stress biology.

  11. Semi-automated curation of metabolic models via flux balance analysis: a case study with Mycoplasma gallisepticum.

    Directory of Open Access Journals (Sweden)

    Eddy J Bautista

    Full Text Available Primarily used for metabolic engineering and synthetic biology, genome-scale metabolic modeling shows tremendous potential as a tool for fundamental research and curation of metabolism. Through a novel integration of flux balance analysis and genetic algorithms, a strategy to curate metabolic networks and facilitate identification of metabolic pathways that may not be directly inferable solely from genome annotation was developed. Specifically, metabolites involved in unknown reactions can be determined, and potentially erroneous pathways can be identified. The procedure developed allows for new fundamental insight into metabolism, as well as acting as a semi-automated curation methodology for genome-scale metabolic modeling. To validate the methodology, a genome-scale metabolic model for the bacterium Mycoplasma gallisepticum was created. Several reactions not predicted by the genome annotation were postulated and validated via the literature. The model predicted an average growth rate of 0.358±0.12[Formula: see text], closely matching the experimentally determined growth rate of M. gallisepticum of 0.244±0.03[Formula: see text]. This work presents a powerful algorithm for facilitating the identification and curation of previously known and new metabolic pathways, as well as presenting the first genome-scale reconstruction of M. gallisepticum.

  12. Thermocline mixing and vertical oxygen fluxes in the stratified central North Sea

    Science.gov (United States)

    Rovelli, Lorenzo; Dengler, Marcus; Schmidt, Mark; Sommer, Stefan; Linke, Peter; McGinnis, Daniel F.

    2016-03-01

    In recent decades, the central North Sea has been experiencing a general trend of decreasing dissolved oxygen (O2) levels during summer. To understand potential causes driving lower O2, we investigated a 3-day period of summertime turbulence and O2 dynamics in the thermocline and bottom boundary layer (BBL). The study focuses on coupling biogeochemical with physical transport processes to identify key drivers of the O2 and organic carbon turnover within the BBL. Combining our flux observations with an analytical process-oriented approach, we resolve drivers that ultimately contribute to determining the BBL O2 levels. We report substantial turbulent O2 fluxes from the thermocline into the otherwise isolated bottom water attributed to the presence of a baroclinic near-inertial wave. This contribution to the local bottom water O2 and carbon budgets has been largely overlooked and is shown to play a role in promoting high carbon turnover in the bottom water while simultaneously maintaining high O2 concentrations. This process may become suppressed with warming climate and stronger stratification, conditions which could promote migrating algal species that potentially shift the O2 production zone higher up within the thermocline.

  13. Regional CO2 fluxes inferred from mixing ratio measurements: estimates from flask air samples in central Kansas, USA

    OpenAIRE

    Lai, Chun-Ta; Schauer, Andrew J.; Owensby, Clenton; Ham, Hay M.; Helliker, Brent; Tans, Pieter P.; Ehleringer, James R

    2011-01-01

    We estimated regional fluxes of carbon dioxide (CO2) using mixing ratios measured in a tallgrass prairie in central Kansas, USA over 3 yr (2002–2004). Glass flasks were used to collect whole air samples in the midafternoon for determining CO2 mixing ratios and their carbon isotopic composition. Regional CO2 fluxes were calculated assuming atmospheric boundary layer (ABL) approaches an equilibrium state on a monthly basis. CO2 mixing ratios derived from the marine boundary layer data were used...

  14. Combining Flux Balance and Energy Balance Analysis for Large-Scale Metabolic Network: Biochemical Circuit Theory for Analysis of Large-Scale Metabolic Networks

    Science.gov (United States)

    Beard, Daniel A.; Liang, Shou-Dan; Qian, Hong; Biegel, Bryan (Technical Monitor)

    2001-01-01

    Predicting behavior of large-scale biochemical metabolic networks represents one of the greatest challenges of bioinformatics and computational biology. Approaches, such as flux balance analysis (FBA), that account for the known stoichiometry of the reaction network while avoiding implementation of detailed reaction kinetics are perhaps the most promising tools for the analysis of large complex networks. As a step towards building a complete theory of biochemical circuit analysis, we introduce energy balance analysis (EBA), which compliments the FBA approach by introducing fundamental constraints based on the first and second laws of thermodynamics. Fluxes obtained with EBA are thermodynamically feasible and provide valuable insight into the activation and suppression of biochemical pathways.

  15. Some aspects on the variations in depositional flux of excess thorium-230 in the central Indian basin during late quaternary

    International Nuclear Information System (INIS)

    Examined in this paper is the tentative history of the depositional flux of 230Thxs (the unsupported fraction of 230Th scavenged from the overlying water column), for the late quaternary period from a sediment core of the central Indian basin (CIB). The measured depositional flux of 230Thxs is found to be substantially higher than that of the possible theoretical flux from the overlying water column. The average ratio of the measured depositional flux to that of the predicted flux from the overlying water column, indicates that the core site acts as a sink for 230Thxs and based on the existence of bottom current activity; the 230Thxs could be the result of focusing of younger sediments. (author). 29 refs., 2 figs., 2 tabs

  16. Fluxes of BVOC and tropospheric ozone from a Citrus orchard in the California Central Valley

    Science.gov (United States)

    Fares, S.; Park, J.; Weber, R.; Gentner, D. R.; Karlik, J. F.; Goldstein, A. H.

    2011-12-01

    Citrus plants, especially oranges, are widely cultivated in many countries experiencing Mediterranean climates. In many of these areas, orchards are often exposed to high levels of tropospheric ozone (O3) due to their location in polluted airsheds. Citrus take up O3 through their stomata and emit biogenic volatile organic compounds (BVOC), which can contribute to non-stomatal O3 removal through fast gas-phase reactions with O3. The study was performed in a valencia orange orchard in Exeter, California. From fall 2009 to winter 2010, CO2 & water fluxes, together with O3 uptake and BVOC emissions were measured continuously in situ with specific sensors (e.g. fast ozone analyzer and Proton Transfer Reaction Mass Spectrometer) using the eddy covariance techniques. Vertical concentration gradients of these compounds were also measured at 4 heights from the orchard floor to above the canopy. We observed high levels (up to 60 ppb) of volatile organic compounds including methanol, isoprene, monoterpenes, sesquiterpenes, and some additional oxygenated BVOC. Methanol dominated BVOC emissions (up to 7 nmol m-2 s-1) followed by acetone. Monoterpenes fluxes were also recorded during the all vegetative period, with the highest emissions taking place during flowering periods, and in general highly temperature dependent. The orchard represented a sink for ozone, with uptake rates on the order of 10 nmol m-2 s-1 during the central hours of the day. We found that BVOC played a major role in removing ozone through chemical reactions in the gas-phase, while only up to 40 % of ozone was removed via stomatal uptake. The current research aimed at investigating the fate of BVOC emitted from orange trees will help understanding the role of Citrus orchards in the complex oxidation mechanisms taking place in the polluted atmosphere of the San Joaquin Valley (California).

  17. Control of Proteobacterial Central Carbon Metabolism by the HexR Transcriptional Regulator. A Case Study in Shewanella oneidensis

    Energy Technology Data Exchange (ETDEWEB)

    Leyn, Semen; Li, Xiaoqing; Zheng, Qijing; Novichkov, Pavel; Reed, Samantha B.; Romine, Margaret F.; Fredrickson, Jim K.; Yang, Chen; Osterman, Andrei L.; Rodionov, Dmitry A.

    2011-08-17

    Bacteria exploit multiple mechanisms for controlling central carbon metabolism (CCM). Thus, a bioinformatic analysis together with some experimental data implicated HexR transcriptional factor as a global CCM regulator in some lineages of Gammaproteobacteria operating as a functional replacement of Cra regulator characteristic of Enterobacteriales. In this study we combined a large-scale comparative genomic reconstruction of HexRcontrolled regulons in 87 species of Proteobacteria with the detailed experimental analysis of HexR regulatory network in Shewanella oneidensis model system. Although nearly all of the HexR-controlled genes are associated with CCM, remarkable variations were revealed in the scale (from 1-2 target operons in Enterobacteriales up to 20 operons in Aeromonadales) and gene content of HexR regulons between 11 compared lineages. A predicted 17-bp pseudo-palindrome with a consensus tTGTAATwwwATTACa, was confirmed as HexR-binding motif for 15 target operons (comprising 30 genes) by in vitro binding assays. The negative effect of the key CCM intermediate, 2-keto-3-deoxy-6- phosphogluconate, on the DNA-regulator complex formation was verified. A dual mode of HexR action on various target promoters, repression of genes involved in catabolic pathways and activation of gluconeogenic genes, was for the first time predicted by the bioinformatc analysis and experimentally verified by changed gene expression pattern in S. oneidensis AhexR mutant. Phenotypic profiling revealed the inability of this mutant to grow on lactate or pyruvate as a single carbon source. A comparative metabolic flux analysis of wild-type and mutant strains of S. oneidensis using 13Clactate labeling and GC-MS analysis confirmed the hypothesized HexR role as a master regulator of gluconeogenic flux from pyruvate via the transcriptional activation of phosphoenolpyruvate synthase (PpsA).

  18. Modelling and analysis of central metabolism operating regulatory interactions in salt stress conditions in a L-carnitine overproducing E. coli strain.

    Directory of Open Access Journals (Sweden)

    Guido Santos

    Full Text Available Based on experimental data from E. coli cultures, we have devised a mathematical model in the GMA-power law formalism that describes the central and L-carnitine metabolism in and between two steady states, non-osmotic and hyperosmotic (0.3 M NaCl. A key feature of this model is the introduction of type of kinetic order, the osmotic stress kinetic orders (g(OSn, derived from the power law general formalism, which represent the effect of osmotic stress in each metabolic process of the model.By considering the values of the g(OSn linked to each metabolic process we found that osmotic stress has a positive and determinant influence on the increase in flux in energetic metabolism (glycolysis; L-carnitine biosynthesis production; the transformation/excretion of Acetyl-CoA into acetate and ethanol; the input flux of peptone into the cell; the anabolic use of pyruvate and biomass decomposition. In contrast, we found that although the osmotic stress has an inhibitory effect on the transformation flux from the glycolytic end products (pyruvate to Acetyl-CoA, this inhibition is counteracted by other effects (the increase in pyruvate concentration to the extent that the whole flux increases. In the same vein, the down regulation exerted by osmotic stress on fumarate uptake and its oxidation and the production and export of lactate and pyruvate are reversed by other factors up to the point that the first increased and the second remained unchanged.The model analysis shows that in osmotic conditions the energy and fermentation pathways undergo substantial rearrangement. This is illustrated by the observation that the increase in the fermentation fluxes is not connected with fluxes towards the tricaboxylic acid intermediates and the synthesis of biomass. The osmotic stress associated with these fluxes reflects these changes. All these observations support that the responses to salt stress observed in E. coli might be conserved in halophiles.Flux evolution

  19. Influence of the late winter bloom on migrant zooplankton metabolism and its implications on export fluxes

    Science.gov (United States)

    Putzeys, S.; Yebra, L.; Almeida, C.; Bécognée, P.; Hernández-León, S.

    2011-12-01

    Studies on carbon active fluxes due to diel migrants are scarce and critical for carbon flux models and biogeochemical estimates. We studied the temporal variability and vertical distribution of biomass, indices of feeding and respiration of the zooplanktonic community north off the Canary Islands during the end of the late winter bloom, in order to assess vertical carbon fluxes in this area. Biomass distribution during the day presented two dense layers of organisms at 0-200 m and around 500 m, whereas at night, most of the biomass concentrated in the epipelagic layer. The gut pigment flux (0.05-0.18 mgC·m - 2 ·d - 1 ) represented 0.22% of the estimated passive export flux (POC flux) while potential ingestion represented 3.91% of the POC (1.24-3.40 mgC·m - 2 ·d - 1 ). The active respiratory flux (0.50-1.36 mgC·m - 2 ·d - 1 ) was only 1.57% of the POC flux. The total carbon flux mediated by diel migrants (respiration plus potential ingestion) ranged between 3.37 and 9.22% of the POC flux; which is three-fold higher than calculating ingestion fluxes from gut pigments. Our results suggest that the fluxes by diel migrants play a small role in the downward flux of carbon in the open ocean during the post-bloom period.

  20. Niche-specific regulation of central metabolic pathways in a fungal pathogen

    OpenAIRE

    Barelle, Caroline J; Priest, Claire L; MacCallum, Donna M.; Gow, Neil AR; Odds, Frank C; Brown, Alistair JP

    2006-01-01

    Summary To establish an infection, the pathogen Candida albicans must assimilate carbon and grow in its mammalian host. This fungus assimilates six-carbon compounds via the glycolytic pathway, and two-carbon compounds via the glyoxylate cycle and gluconeogenesis. We address a paradox regarding the roles of these central metabolic pathways in C. albicans pathogenesis: the glyoxylate cycle is apparently required for virulence although glyoxylate cycle genes are repressed by glucose at concentra...

  1. Fructan biosynthesis and degradation as part of plant metabolism controlling sugar fluxes during durum wheat kernel maturation

    OpenAIRE

    Cimini, Sara; Locato, Vittoria; Vergauwen, Rudy; Paradiso, Annalisa; Cecchini, Cristina; Vandenpoel, Liesbeth; Verspreet, Joran; Courtin, Christophe M.; D'Egidio, Maria Grazia; Van den Ende, Wim; De Gara, Laura

    2015-01-01

    Wheat kernels contain fructans, fructose based oligosaccharides with prebiotic properties, in levels between 2 and 35 weight % depending on the developmental stage of the kernel. To improve knowledge on the metabolic pathways leading to fructan storage and degradation, carbohydrate fluxes occurring during durum wheat kernel development were analyzed. Kernels were collected at various developmental stages and quali-quantitative analysis of carbohydrates (mono- and di-saccharides, fructans, sta...

  2. Split core experiments; Part I. Axial neutron flux distribution measurements in the reactor core with a central horizontal reflector

    International Nuclear Information System (INIS)

    A series of critical experiments were performed on the RB reactor in order to determine the thermal neutron flux increase in the central horizontal reflector formed by a split reactor core. The objectives of these experiments were to study the possibilities of improving the thermal neutron flux characteristics of the neutron beam in the horizontal beam tube of the RA research reactor. The construction of RA reactor enables to split the core in two, to form a central horizontal reflector in front of the beam tube. This is achieved by replacing 2% enriched uranium slugs in the fuel channel by dummy aluminium slugs. The purpose of the first series of experiments was to study the gain in thermal neutron component inside the horizontal reflector and the loss of reactivity as a function of the lattice pitch and central reflector thickness

  3. Metabolic Targeting of Malignant Tumors: Small-Molecule Inhibitors of Bioenergetic Flux

    OpenAIRE

    Mathupala, Saroj P.

    2011-01-01

    Metabolism in tumors deviates significantly from that of normal tissues. Increasingly, the underlying aberrant metabolic pathways are being considered as novel targets for cancer therapy. Denoted “metabolic targeting”, small molecule drugs are under investigation for focused inhibition of key metabolic steps that are utilized by tumors, since such inhibitors should harbor minimal toxicity towards surrounding normal tissues.This review will examine the primary biochemical pathways that tumors ...

  4. Cutting the Gordian Knot: Identifiability of anaplerotic reactions in Corynebacterium glutamicum by means of (13) C-metabolic flux analysis.

    Science.gov (United States)

    Kappelmann, Jannick; Wiechert, Wolfgang; Noack, Stephan

    2016-03-01

    Corynebacterium glutamicum is the major workhorse for the microbial production of several amino and organic acids. As long as these derive from tricarboxylic acid cycle intermediates, the activity of anaplerotic reactions is pivotal for a high biosynthetic yield. To determine single anaplerotic activities (13) C-Metabolic Flux Analysis ((13) C-MFA) has been extensively used for C. glutamicum, however with different network topologies, inconsistent or poorly determined anaplerotic reaction rates. Therefore, in this study we set out to investigate whether a focused isotopomer model of the anaplerotic node can at all admit a unique solution for all fluxes. By analyzing different scenarios of active anaplerotic reactions, we show in full generality that for C. glutamicum only certain anaplerotic deletion mutants allow to uniquely determine the anaplerotic fluxes from (13) C-isotopomer data. We stress that the result of this analysis for different assumptions on active enzymes is directly transferable to other compartment-free organisms. Our results demonstrate that there exist biologically relevant metabolic network topologies for which the flux distribution cannot be inferred by classical (13) C-MFA. PMID:26375179

  5. IsoDesign: a software for optimizing the design of 13C-metabolic flux analysis experiments.

    Science.gov (United States)

    Millard, Pierre; Sokol, Serguei; Letisse, Fabien; Portais, Jean-Charles

    2014-01-01

    The growing demand for (13) C-metabolic flux analysis ((13) C-MFA) in the field of metabolic engineering and systems biology is driving the need to rationalize expensive and time-consuming (13) C-labeling experiments. Experimental design is a key step in improving both the number of fluxes that can be calculated from a set of isotopic data and the precision of flux values. We present IsoDesign, a software that enables these parameters to be maximized by optimizing the isotopic composition of the label input. It can be applied to (13) C-MFA investigations using a broad panel of analytical tools (MS, MS/MS, (1) H NMR, (13) C NMR, etc.) individually or in combination. It includes a visualization module to intuitively select the optimal label input depending on the biological question to be addressed. Applications of IsoDesign are described, with an example of the entire (13) C-MFA workflow from the experimental design to the flux map including important practical considerations. IsoDesign makes the experimental design of (13) C-MFA experiments more accessible to a wider biological community. IsoDesign is distributed under an open source license at http://metasys.insa-toulouse.fr/software/isodes/ PMID:23893473

  6. Flux-based classification of reactions reveals a functional bow-tie organization of complex metabolic networks.

    Science.gov (United States)

    Singh, Shalini; Samal, Areejit; Giri, Varun; Krishna, Sandeep; Raghuram, Nandula; Jain, Sanjay

    2013-05-01

    Unraveling the structure of complex biological networks and relating it to their functional role is an important task in systems biology. Here we attempt to characterize the functional organization of the large-scale metabolic networks of three microorganisms. We apply flux balance analysis to study the optimal growth states of these organisms in different environments. By investigating the differential usage of reactions across flux patterns for different environments, we observe a striking bimodal distribution in the activity of reactions. Motivated by this, we propose a simple algorithm to decompose the metabolic network into three subnetworks. It turns out that our reaction classifier, which is blind to the biochemical role of pathways, leads to three functionally relevant subnetworks that correspond to input, output, and intermediate parts of the metabolic network with distinct structural characteristics. Our decomposition method unveils a functional bow-tie organization of metabolic networks that is different from the bow-tie structure determined by graph-theoretic methods that do not incorporate functionality. PMID:23767567

  7. Metabolic flux analysis in a nonstationary system: fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol.

    Science.gov (United States)

    Antoniewicz, Maciek R; Kraynie, David F; Laffend, Lisa A; González-Lergier, Joanna; Kelleher, Joanne K; Stephanopoulos, Gregory

    2007-05-01

    Metabolic fluxes estimated from stable-isotope studies provide a key to understanding cell physiology and regulation of metabolism. A limitation of the classical method for metabolic flux analysis (MFA) is the requirement for isotopic steady state. To extend the scope of flux determination from stationary to nonstationary systems, we present a novel modeling strategy that combines key ideas from isotopomer spectral analysis (ISA) and stationary MFA. Isotopic transients of the precursor pool and the sampled products are described by two parameters, D and G parameters, respectively, which are incorporated into the flux model. The G value is the fraction of labeled product in the sample, and the D value is the fractional contribution of the feed for the production of labeled products. We illustrate the novel modeling strategy with a nonstationary system that closely resembles industrial production conditions, i.e. fed-batch fermentation of Escherichia coli that produces 1,3-propanediol (PDO). Metabolic fluxes and the D and G parameters were estimated by fitting labeling distributions of biomass amino acids measured by GC/MS to a model of E. coli metabolism. We obtained highly consistent fits from the data with 82 redundant measurements. Metabolic fluxes were estimated for 20 time points during course of the fermentation. As such we established, for the first time, detailed time profiles of in vivo fluxes. We found that intracellular fluxes changed significantly during the fed-batch. The intracellular flux associated with PDO pathway increased by 10%. Concurrently, we observed a decrease in the split ratio between glycolysis and pentose phosphate pathway from 70/30 to 50/50 as a function of time. The TCA cycle flux, on the other hand, remained constant throughout the fermentation. Furthermore, our flux results provided additional insight in support of the assumed genotype of the organism. PMID:17400499

  8. Annual benthic metabolism and organic carbon fluxes in a semi-enclosed Mediterranean bay dominated by the macroalgae Caulerpa prolifera.

    Directory of Open Access Journals (Sweden)

    Sergio eRuiz-Halpern

    2014-12-01

    Full Text Available Coastal areas play an important role on carbon cycling. Elucidating the dynamics on the production, transport and fate of organic carbon is relevant to gain a better understanding of the role coastal areas play in the global carbon budget. Here, we assess the metabolic status and associated organic carbon fluxes of a semi-enclosed Mediterranean bay supporting a meadow of Caulerpa prolifera. We test whether the EDOC pool is a significant component of the organic carbon pool and associated fluxes in this ecosystem. The Bay of Portocolom was in net metabolic balance on a yearly basis, but heterotrophic during the summer months. Community respiration (CR was positively correlated to C. prolifera biomass, while net community production (NCP had a negative correlation. The benthic compartment represented, on average, 72.6 ± 5.2 % of CR and 86.8 ± 4.5 % of gross primary production (GPP. Dissolved organic carbon (DOC production peaked in summer and was always positive, with the incubations performed in the dark almost doubling the flux of those performed in the light. Exchangeable dissolved organic carbon (EDOC, however, oscillated between production and uptake, being completely recycled within the system and representing around 14% of the DOC flux. The pools of bottom and surface DOC were high for an oligotrophic environment, and were positively correlated to the pool of EDOC. Thus, despite being in metabolic balance, this ecosystem acted as a conduit for organic carbon (OC, as it is able to export OC to adjacent areas derived from allochtonous inputs during heterotrophic conditions. These inputs likely come from groundwater discharge, human activity in the watershed, delivered to the sediments through the high capacity of C. prolifera to remove particles from the water column, and from the air-water exchange of EDOC, demonstrating that these communities are a major contributor to the cycling of OC in coastal embayments.

  9. Revealing differences in metabolic flux distributions between a mutant strain and its parent strain Gluconacetobacter xylinus CGMCC 2955.

    Directory of Open Access Journals (Sweden)

    Cheng Zhong

    Full Text Available A better understanding of metabolic fluxes is important for manipulating microbial metabolism toward desired end products, or away from undesirable by-products. A mutant strain, Gluconacetobacter xylinus AX2-16, was obtained by combined chemical mutation of the parent strain (G. xylinus CGMCC 2955 using DEC (diethyl sulfate and LiCl. The highest bacterial cellulose production for this mutant was obtained at about 11.75 g/L, which was an increase of 62% compared with that by the parent strain. In contrast, gluconic acid (the main byproduct concentration was only 5.71 g/L for mutant strain, which was 55.7% lower than that of parent strain. Metabolic flux analysis indicated that 40.1% of the carbon source was transformed to bacterial cellulose in mutant strain, compared with 24.2% for parent strain. Only 32.7% and 4.0% of the carbon source were converted into gluconic acid and acetic acid in mutant strain, compared with 58.5% and 9.5% of that in parent strain. In addition, a higher flux of tricarboxylic acid (TCA cycle was obtained in mutant strain (57.0% compared with parent strain (17.0%. It was also indicated from the flux analysis that more ATP was produced in mutant strain from pentose phosphate pathway (PPP and TCA cycle. The enzymatic activity of succinate dehydrogenase (SDH, which is one of the key enzymes in TCA cycle, was 1.65-fold higher in mutant strain than that in parent strain at the end of culture. It was further validated by the measurement of ATPase that 3.53-6.41 fold higher enzymatic activity was obtained from mutant strain compared with parent strain.

  10. Control of fluxes towards antibiotics and the role of primary metabolism in production of antibiotics

    DEFF Research Database (Denmark)

    Gunnarsson, Nina; Eliasson Lantz, Anna; Nielsen, Jacob

    2004-01-01

    Yield improvements in antibiotic-producing strains have classically been obtained through random mutagenesis and screening. An attractive alternative to this strategy is the rational design of producer strains via metabolic engineering, an approach that offers the possibility to increase yields...... metabolic network. Here we describe and discuss available methods for identification of these steps, both in antibiotic biosynthesis pathways and in the primary metabolism, which serves as the supplier of precursors and cofactors for the secondary metabolism. Finally, the importance of precursor and...... cofactor supply from primary metabolism in the biosynthesis of different types of antibiotics is discussed and recent developments in metabolic engineering towards increased product yields in antibiotic producing strains are reviewed....

  11. Effects of adenosine metabolism in astrocytes on central nervous system oxygen toxicity.

    Science.gov (United States)

    Chen, Yu-liang; Zhang, Ya-nan; Wang, Zhong-zhuang; Xu, Wei-gang; Li, Run-ping; Zhang, Jun-dong

    2016-03-15

    Hyperbaric oxygen (HBO) is widely used in military operations, especially underwater missions. However, prolonged and continuous inhalation of HBO can cause central nervous system oxygen toxicity (CNS-OT), which greatly limits HBO's application. The regulation of astrocytes to the metabolism of adenosine is involved in epilepsy. In our study, we aimed to observe the effects of HBO exposure on the metabolism of adenosine in the brain. Furthermore, we aimed to confirm the possible mechanism underlying adenosine's mediation of the CNS-OT. Firstly, anesthetized rats exposed to 5 atm absolute HBO for 80 min. The concentrations of extracellular adenosine, ATP, ADP, and AMP were detected. Secondly, free-moving rats were exposed to HBO at the same pressure for 20 min, and the activities of 5'-nucleotidase and ADK in brain tissues were measured. For the mechanism studies, we observed the effects of a series of different doses of drugs related to adenosine metabolism on the latency of CNS-OT. Results showed HBO exposure could increase adenosine content by inhibiting ADK activity and improving 5'-nucleotidase activity. And adenosine metabolism during HBO exposure may be a protective response against HBO-induced CNS-OT. Moreover, the improvement of adenosine concentration, activation of adenosine A1R, or suppression of ADK and adenosine A2AR, which are involved in the prevention of HBO-induced CNS-OT. This is the first study to demonstrate HBO exposure regulated adenosine metabolism in the brain. Adenosine metabolism and adenosine receptors are related to HBO-induced CNS-OT development. These results will provide new potential targets for the termination or the attenuation of CNS-OT. PMID:26806404

  12. Role of phosphate in the central metabolism of two lactic acid bacteria-a comparative systems biology approach

    NARCIS (Netherlands)

    Levering, J.; Musters, M.W.J.M.; Bekker, M.; Bellomo, D.; Fiedler, T.; Vos, de W.M.; Hugenholtz, F.; Kreikemeyer, B.; Kummer, U.; Teusink, B.

    2012-01-01

    Lactic acid-producing bacteria survive in distinct environments, but show common metabolic characteristics. Here we studied the dynamic interactions of the central metabolism in Lactococcus lactis, extensively used as a starter culture in the dairy industry, and Streptococcus pyogenes, a human patho

  13. Role of phosphate in the central metabolism of two lactic acid bacteria - a comparative systems biology approach.

    NARCIS (Netherlands)

    J. Levering; M.W. Musters; M. Bekker; D. Bellomo; T. Fiedler; W.M. de Vos; J. Hugenholtz; B. Kreikemeyer; U. Kummer; B. Teusink

    2012-01-01

    Lactic acid-producing bacteria survive in distinct environments, but show common metabolic characteristics. Here we studied the dynamic interactions of the central metabolism in Lactococcus lactis, extensively used as a starter culture in the dairy industry, and Streptococcus pyogenes, a human patho

  14. Testicular Metabolic Reprogramming in Neonatal Streptozotocin-Induced Type 2 Diabetic Rats Impairs Glycolytic Flux and Promotes Glycogen Synthesis.

    Science.gov (United States)

    Rato, L; Alves, M G; Dias, T R; Cavaco, J E; Oliveira, Pedro F

    2015-01-01

    Defects in testicular metabolism are directly implicated with male infertility, but most of the mechanisms associated with type 2 diabetes- (T2DM) induced male infertility remain unknown. We aimed to evaluate the effects of T2DM on testicular glucose metabolism by using a neonatal-streptozotocin- (n-STZ) T2DM animal model. Plasma and testicular hormonal levels were evaluated using specific kits. mRNA and protein expression levels were assessed by real-time PCR and Western Blot, respectively. Testicular metabolic profile was assessed by (1)H-NMR spectroscopy. T2DM rats showed increased glycemic levels, impaired glucose tolerance and hyperinsulinemia. Both testicular and serum testosterone levels were decreased, whereas those of 17β-estradiol were not altered. Testicular glycolytic flux was not favored in testicles of T2DM rats, since, despite the increased expression of both glucose transporters 1 and 3 and the enzyme phosphofructokinase 1, lactate dehydrogenase activity was severely decreased contributing to lower testicular lactate content. However, T2DM enhanced testicular glycogen accumulation, by modulating the availability of the precursors for its synthesis. T2DM also affected the reproductive sperm parameters. Taken together these results indicate that T2DM is able to reprogram testicular metabolism by enhancing alternative metabolic pathways, particularly glycogen synthesis, and such alterations are associated with impaired sperm parameters. PMID:26064993

  15. Testicular Metabolic Reprogramming in Neonatal Streptozotocin-Induced Type 2 Diabetic Rats Impairs Glycolytic Flux and Promotes Glycogen Synthesis

    Directory of Open Access Journals (Sweden)

    L. Rato

    2015-01-01

    Full Text Available Defects in testicular metabolism are directly implicated with male infertility, but most of the mechanisms associated with type 2 diabetes- (T2DM induced male infertility remain unknown. We aimed to evaluate the effects of T2DM on testicular glucose metabolism by using a neonatal-streptozotocin- (n-STZ T2DM animal model. Plasma and testicular hormonal levels were evaluated using specific kits. mRNA and protein expression levels were assessed by real-time PCR and Western Blot, respectively. Testicular metabolic profile was assessed by 1H-NMR spectroscopy. T2DM rats showed increased glycemic levels, impaired glucose tolerance and hyperinsulinemia. Both testicular and serum testosterone levels were decreased, whereas those of 17β-estradiol were not altered. Testicular glycolytic flux was not favored in testicles of T2DM rats, since, despite the increased expression of both glucose transporters 1 and 3 and the enzyme phosphofructokinase 1, lactate dehydrogenase activity was severely decreased contributing to lower testicular lactate content. However, T2DM enhanced testicular glycogen accumulation, by modulating the availability of the precursors for its synthesis. T2DM also affected the reproductive sperm parameters. Taken together these results indicate that T2DM is able to reprogram testicular metabolism by enhancing alternative metabolic pathways, particularly glycogen synthesis, and such alterations are associated with impaired sperm parameters.

  16. Seasonal and annual variations of marine sinking particulate flux during 1993~1996 in the central South China Sea

    Institute of Scientific and Technical Information of China (English)

    CHEN Ronghua; WIESNER M G; ZHENG Yulong; CHENG Xinrong; JIN Haiyan; ZHAO Qingying; ZHENG Lianfu

    2007-01-01

    A total of 67 samples from the upper and lower sediment traps in the central South China Sea were analyzed, which were collected during 1993~1996. It is indicated that the distribution of stable isotope values, surface primary productivity, fluxes of total particulate matter, carbonate, biogenic opal, organic carbon, planktonic foraminiferal species and their total amount exhibit obviously seasonal and annual fluctuations. High values of the fluxes occurred in the prevailing periods of the northeastern and southwestern monsoons, and the low values occurred during the periods between the two monsoons. The fluxes of some planktonic foraminiferal species (Globigerinoides sacculifer, G. ruber, Globigerinita glutinata, Neogloboquadrina dutertrei) and their percentages also exhibit two prominent peaks during the prevailing periods of the northeastern and southwestern monsoons respectively, while those of Globigerina bulloides, Globorotalia menardii and Pulleniatina obliquiloculata only exhibit one peak in the prevailing periods of the northeastern monsoon. In addition, fluxes and percentages of Globigerinoides sacculifer and Globorotalia menardii as well as the fluxes of carbonate and total amount of planktonic foraminifera decrease gradually from 1993 to 1996, and those of Globigerina bulloides, Globigerinita glutinata and biogenic opal increase gradually from 1993 to 1996. The fluxes of carbonate and organic carbon in the upper trap are higher than those in the lower one. The study indicates that the seasonal and annual variations of the sediment fluxes and planktonic foraminiferal species are mainly controlled by the changes of surface primary productivity and hydrological conditions related to the East Asian monsoon. The lower carbonate and organic carbon fluxes in the lower trap are related to the dissolution.

  17. Central and Metabolic Effects of High Fructose Consumption: Evidence from Animal and Human Studies

    Directory of Open Access Journals (Sweden)

    Alexandra Stoianov

    2014-12-01

    Full Text Available Fructose consumption has increased dramatically in the last 40 years, and its role in the pathogenesis of the metabolic syndrome has been implicated by many studies. It is most often encountered in the diet as sucrose (glucose and fructose or high-fructose corn syrup (55% fructose. At high levels, dietary exposure to fructose triggers a series of metabolic changes originating in the liver, leading to hepatic steatosis, hypertriglyceridemia, insulin resistance, and decreased leptin sensitivity. Fructose has been identified to alter biological pathways in other tissues including the central nervous system (CNS, adipose tissue, and the gastrointestinal system. Unlike glucose, consumption of fructose produces smaller increases in the circulating satiety hormone glucagon-like peptide 1 (GLP-1, and does not attenuate levels of the appetite suppressing hormone ghrelin. In the brain, fructose contributes to increased food consumption by activating appetite and reward pathways, and stimulating hypothalamic AMPK activity, a nutrient-sensitive regulator of food intake. Recent studies investigating the neurophysiological factors linking fructose consumption and weight gain in humans have demonstrated differential activation of brain regions that govern appetite, motivation and reward processing. Compared to fructose, glucose ingestion produces a greater reduction of hypothalamic neuronal activity, and increases functional connectivity between the hypothalamus and other reward regions of the brain, indicating that these two sugars regulate feeding behavior through distinct neural circuits. This review article outlines the current findings in fructose-feeding studies in both human and animal models, and discusses the central effects on the CNS that may lead to increased appetite and food intake. Keywords: Fructose, Metabolic syndrome, Appetite, Central nervous system

  18. Flux Balance Analysis Inspired Bioprocess Upgrading for Lycopene Production by a Metabolically Engineered Strain of Yarrowia lipolytica

    Directory of Open Access Journals (Sweden)

    Komi Nambou

    2015-12-01

    Full Text Available Genome-scale metabolic models embody a significant advantage of systems biology since their applications as metabolic flux simulation models enable predictions for the production of industrially-interesting metabolites. The biotechnological production of lycopene from Yarrowia lipolytica is an emerging scope that has not been fully scrutinized, especially for what concerns cultivation conditions of newly generated engineered strains. In this study, by combining flux balance analysis (FBA and Plackett-Burman design, we screened chemicals for lycopene production from a metabolically engineered strain of Y. lipolytica. Lycopene concentrations of 126 and 242 mg/L were achieved correspondingly from the FBA-independent and the FBA-assisted designed media in fed-batch cultivation mode. Transcriptional studies revealed upregulations of heterologous genes in media designed according to FBA, thus implying the efficiency of model predictions. Our study will potentially support upgraded lycopene and other terpenoids production from existing or prospect bioengineered strains of Y. lipolytica and/or closely related yeast species.

  19. Flux Balance Analysis Inspired Bioprocess Upgrading for Lycopene Production by a Metabolically Engineered Strain of Yarrowia lipolytica.

    Science.gov (United States)

    Nambou, Komi; Jian, Xingxing; Zhang, Xinkai; Wei, Liujing; Lou, Jiajia; Madzak, Catherine; Hua, Qiang

    2015-01-01

    Genome-scale metabolic models embody a significant advantage of systems biology since their applications as metabolic flux simulation models enable predictions for the production of industrially-interesting metabolites. The biotechnological production of lycopene from Yarrowia lipolytica is an emerging scope that has not been fully scrutinized, especially for what concerns cultivation conditions of newly generated engineered strains. In this study, by combining flux balance analysis (FBA) and Plackett-Burman design, we screened chemicals for lycopene production from a metabolically engineered strain of Y. lipolytica. Lycopene concentrations of 126 and 242 mg/L were achieved correspondingly from the FBA-independent and the FBA-assisted designed media in fed-batch cultivation mode. Transcriptional studies revealed upregulations of heterologous genes in media designed according to FBA, thus implying the efficiency of model predictions. Our study will potentially support upgraded lycopene and other terpenoids production from existing or prospect bioengineered strains of Y. lipolytica and/or closely related yeast species. PMID:26703753

  20. Evaluating Contaminant Flux from the Vadose Zone to the Groundwater in the Hanford Central Plateau. SX Tank Farms Case Study

    Energy Technology Data Exchange (ETDEWEB)

    Truex, Michael J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Oostrom, Martinus [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Last, George V. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Strickland, Christopher E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Tartakovsky, Guzel D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2015-09-01

    At the DOE Hanford Site, contaminants were discharged to the subsurface through engineered waste sites in the Hanford Central Plateau. Additional waste was released through waste storage tank leaks. Much of the contaminant inventory is still present within the unsaturated vadose zone sediments. The nature and extent of future groundwater contaminant plumes and the growth or decline of current groundwater plumes beneath the Hanford Central Plateau are a function of the contaminant flux from the vadose zone to the groundwater. In general, contaminant transport is slow through the vadose zone and it is difficult to directly measure contaminant flux in the vadose zone. Predictive analysis, supported by site characterization and monitoring data, was applied using a structured, systems-based approach to estimate the future contaminant flux to groundwater in support of remediation decisions for the vadose zone and groundwater (Truex and Carroll 2013). The SX Tank Farm was used as a case study because of the existing contaminant inventory in the vadose zone, observations of elevated moisture content in portions of the vadose zone, presence of a limited-extent groundwater plume, and the relatively large amount and wide variety of data available for the site. Although the SX Tank Farm case study is most representative of conditions at tank farm sites, the study has elements that are also relevant to other types of disposal sites in the Hanford Central Plateau.

  1. Metabolic flux analysis of a phenol producing mutant of Pseudomonas putida S12: Verification and complementation of hypotheses derived from transcriptomics

    NARCIS (Netherlands)

    Wierckx, N.; Ruijssenaars, H.J.; Winde, J.H.de; Schmid, A.; Blank, L.M.

    2009-01-01

    The physiological effects of genetic and transcriptional changes observed in a phenol producing mutant of the solvent-tolerant Pseudomonas putida S12 were assessed with metabolic flux analysis. The upregulation of a malate/lactate dehydrogenase encoding gene could be connected to a flux increase fro

  2. The Metabolic Response of Arabidopsis Roots to Oxidative Stress is Distinct from that of Heterotrophic Cells in Culture and Highlights a Complex Relationship between the Levels of Transcripts,Metabolites,and Flux

    Institute of Scientific and Technical Information of China (English)

    Martin Lehmann; Markus Schwarzl(a)inder; Toshihiro Obata; Supaart Sirikantaramas; Meike Burow; Carl Erik Olsen; Takayuki Tohge; Mark D.Fricker; Birger Lindberg Mφller; Alisdair R.Fernie; Lee J.Sweetloveb; Miriam Laxa

    2009-01-01

    Metabolic adjustments are a significant,but poorly understood,part of the response of plants to oxidative stress.In a previous study (Baxter et al.,2007),the metabolic response of Arabidopsis cells in culture to induction of ox-idative stress by menadione was characterized.An emergency survival strategy was uncovered in which anabolic primary metabolism was largely down-regulated in favour of catabolic and antioxidant metabolism.The response in whole plant tissues may be different and we have therefore investigated the response of Arabidopsis roots to menadione treatment,analyzing the transcriptome,metabolome and key metabolic fluxes with focus on primary as well as secondary metab-olism.Using a redox-sensitive GFP,it was also shown that menadione causes redox perturbation,not just in the mitochon-drion,but also in the cytosol and plastids of roots.In the first 30 min of treatment,the response was similar to the cell culture:there was a decrease in metabolites of the TCA cycle and amino acid biosynthesis and the transcriptomic response was dominated by up-regulation of DNA regulatory proteins.After 2 and 6 h of treatment,the response of the roots was different to the cell culture.Metabolite levels did not remain depressed,but instead recovered and,in the case of pyruvate,some amino acids and aliphatic glucosinolates showed a steady increase above control levels.However,no major changes in fluxes of central carbon metabolism were observed and metabolic transcripts changed largely independently of the corresponding metabolites.Together,the results suggest that root tissues can recover metabolic activity after oxidative inhibition and highlight potentially important roles for glycolysis and the oxidative pentose phosphate pathway.

  3. Preferential use of central metabolism in vivo reveals a nutritional basis for polymicrobial infection.

    Directory of Open Access Journals (Sweden)

    Christopher J Alteri

    2015-01-01

    Full Text Available The human genitourinary tract is a common anatomical niche for polymicrobial infection and a leading site for the development of bacteremia and sepsis. Most uncomplicated, community-acquired urinary tract infections (UTI are caused by Escherichia coli, while another bacterium, Proteus mirabilis, is more often associated with complicated UTI. Here, we report that uropathogenic E. coli and P. mirabilis have divergent requirements for specific central pathways in vivo despite colonizing and occupying the same host environment. Using mutants of specific central metabolism enzymes, we determined glycolysis mutants lacking pgi, tpiA, pfkA, or pykA all have fitness defects in vivo for P. mirabilis but do not affect colonization of E. coli during UTI. Similarly, the oxidative pentose phosphate pathway is required only for P. mirabilis in vivo. In contrast, gluconeogenesis is required only for E. coli fitness in vivo. The remarkable difference in central pathway utilization between E. coli and P. mirabilis during experimental UTI was also observed for TCA cycle mutants in sdhB, fumC, and frdA. The distinct in vivo requirements between these pathogens suggest E. coli and P. mirabilis are not direct competitors within host urinary tract nutritional niche. In support of this, we found that co-infection with E. coli and P. mirabilis wild-type strains enhanced bacterial colonization and persistence of both pathogens during UTI. Our results reveal that complementary utilization of central carbon metabolism facilitates polymicrobial disease and suggests microbial activity in vivo alters the host urinary tract nutritional niche.

  4. A novel role for central ACBP/DBI as a regulator of long-chain fatty acid metabolism in astrocytes

    DEFF Research Database (Denmark)

    Bouyakdan, Khalil; Taïb, Bouchra; Budry, Lionel;

    2015-01-01

    Diazepam-Binding Inhibitor, a secreted peptide acting as an allosteric modulator of the GABAA receptor. However, its role in central LCFA metabolism remains unknown. In the present study, we investigated ACBP cellular expression, ACBP regulation of LCFA intracellular metabolism, FA profile, and FA......Acyl-CoA-binding protein (ACBP) is a ubiquitously expressed protein that binds intracellular acyl-CoA esters. Several studies have suggested that ACBP acts as an acyl-CoA pool former and regulates long-chain fatty acids (LCFA) metabolism in peripheral tissues. In the brain, ACBP is known as...... response to palmitate in hypothalamic astrocytes. Collectively, these findings reveal for the first time that central ACBP acts as a regulator of LCFA intracellular metabolism in astrocytes. Acyl-CoA-binding protein (ACBP) or diazepam-binding inhibitor is a secreted peptide acting centrally as a GABAA...

  5. Methane fluxes measured by eddy covariance and static chamber techniques at a temperate forest in central Ontario, Canada

    Directory of Open Access Journals (Sweden)

    J. M. Wang

    2013-06-01

    Full Text Available Methane flux measurements were carried out at a temperate forest (Haliburton Forest and Wildlife Reserve in central Ontario (45°17´11´´ N, 78°32´19´´ W from June to October 2011. Continuous measurements were made by an off-axis integrated cavity output spectrometer that measures methane (CH4 at 10 Hz sampling rates. Fluxes were calculated from the gas measurements in conjunction with wind data collected by a 3-D sonic anemometer using the eddy covariance (EC method. Observed methane fluxes showed net uptake of CH4 over the measurement period with an average uptake flux (±standard deviation of the mean of −2.7 ± 0.13 nmol m−2 s−1. Methane fluxes showed a seasonal progression with average rates of uptake increasing from June through September and remaining high in October. This pattern was consistent with a decreasing trend in soil moisture content at the monthly timescale. On the diurnal timescale, there was evidence of increased uptake during the day, when the mid-canopy wind speed was at a maximum. These patterns suggest that substrate supply of CH4 to methanotrophs, and in certain cases hypoxic soil conditions supporting methanogenesis in low-slope areas, drives the observed variability in fluxes. A network of soil static chambers used at the tower site showed reasonable agreement with the seasonal trend and overall magnitude of the eddy covariance flux measurements. This suggests that soil-level microbial processes, and not abiological leaf-level CH4 production, drive overall CH4 dynamics in temperate forest ecosystems such as Haliburton Forest.

  6. Methane fluxes measured by eddy covariance and static chamber techniques at a temperate forest in central ontario, Canada

    Directory of Open Access Journals (Sweden)

    J. M. Wang

    2012-12-01

    Full Text Available Methane flux measurements were carried out at a temperate forest (Haliburton Forest and Wildlife Reserve in central Ontario (45°17´11´´ N, 78°32´19´´ W from June–October, 2011. Continuous measurements were made by an off-axis integrated cavity output spectrometer Fast Greenhouse Gas Analyzer (FGGA from Los Gatos Research Inc. that measures methane (CH4 at 10 Hz sampling rates. Fluxes were calculated from the gas measurements in conjunction with wind data collected by a 3-D sonic anemometer using the eddy covariance (EC method. Observed methane fluxes showed net uptake of CH4 over the measurement period with an average uptake flux (± standard deviation of the mean of −2.7 ± 0.13 nmol m−2 s−1. Methane fluxes showed a seasonal progression with average rates of uptake increasing from June through September and remaining high in October. This pattern was consistent with a decreasing trend in soil moisture content at the monthly time scale. On the diurnal timescale, there was evidence of increased uptake during the day, when the mid-canopy wind speed was at a maximum. These patterns suggest that substrate supply of CH4 and oxygen to methanotrophs, and in certain cases hypoxic soil conditions supporting methanogenesis in low-slope areas, drive the observed variability in fluxes. A network of soil static chambers used at the tower site showed close agreement with the eddy covariance flux measurements. This suggests that soil-level microbial processes, and not abiological leaf-level CH4 production, drive overall CH4 dynamics in temperate forest ecosystems such as Haliburton Forest.

  7. Methane fluxes measured by eddy covariance and static chamber techniques at a temperate forest in central Ontario, Canada

    Science.gov (United States)

    Wang, J. M.; Murphy, J. G.; Geddes, J. A.; Winsborough, C. L.; Basiliko, N.; Thomas, S. C.

    2013-06-01

    Methane flux measurements were carried out at a temperate forest (Haliburton Forest and Wildlife Reserve) in central Ontario (45°17´11´´ N, 78°32´19´´ W) from June to October 2011. Continuous measurements were made by an off-axis integrated cavity output spectrometer that measures methane (CH4) at 10 Hz sampling rates. Fluxes were calculated from the gas measurements in conjunction with wind data collected by a 3-D sonic anemometer using the eddy covariance (EC) method. Observed methane fluxes showed net uptake of CH4 over the measurement period with an average uptake flux (±standard deviation of the mean) of -2.7 ± 0.13 nmol m-2 s-1. Methane fluxes showed a seasonal progression with average rates of uptake increasing from June through September and remaining high in October. This pattern was consistent with a decreasing trend in soil moisture content at the monthly timescale. On the diurnal timescale, there was evidence of increased uptake during the day, when the mid-canopy wind speed was at a maximum. These patterns suggest that substrate supply of CH4 to methanotrophs, and in certain cases hypoxic soil conditions supporting methanogenesis in low-slope areas, drives the observed variability in fluxes. A network of soil static chambers used at the tower site showed reasonable agreement with the seasonal trend and overall magnitude of the eddy covariance flux measurements. This suggests that soil-level microbial processes, and not abiological leaf-level CH4 production, drive overall CH4 dynamics in temperate forest ecosystems such as Haliburton Forest.

  8. Linking Central Metabolism with Increased Pathway Flux: l-Valine Accumulation by Corynebacterium glutamicum

    OpenAIRE

    Radmacher, Eva; Vaitsikova, Adela; Burger, Udo; Krumbach, Karin; Sahm, Hermann; Eggeling, Lothar

    2002-01-01

    Mutants of Corynebacterium glutamicum were made and enzymatically characterized to clone ilvD and ilvE, which encode dihydroxy acid dehydratase and transaminase B, respectively. These genes of the branched-chain amino acid synthesis were overexpressed together with ilvBN (which encodes acetohydroxy acid synthase) and ilvC (which encodes isomeroreductase) in the wild type, which does not excrete l-valine, to result in an accumulation of this amino acid to a concentration of 42 mM. Since l-vali...

  9. Climate determined differences in carbon dioxide fluxes dynamics between two comparable agroecosystems of Central Russia

    Science.gov (United States)

    Yaroslavtsev, Alexis; Meshalkina, Joulia; Mazirov, Ilya; Valentini, Riccardo; Vasenev, Ivan

    2015-04-01

    Creation of Russian part of Fluxnet - Rusfluxnet, aims to fill the carbon dioxide fluxes data shortage. Because the Central Russia is still one of the less GHG-investigated European areas especially in case of agroecosystem-level carbon dioxide fluxes monitoring by eddy covariance method. For the first time eddy covariance (EC) GHG study has been conducted at two representative agroecosystems of Central Russia belonging to different climate zones (climate and soils), but both with the same land use: the both fields were under barley. The study was carried out in 2013 and supported by RF Government grant No. 11.G34.31.0079. The first agricultural field located at Precision Farming Experimental Field of the Timiryazev Agricultural University situated in Moscow. It's arable Albeluvisols Umbric have around 1% of SOC, 5.4 pH(KCl) and NPK medium-enhanced contents in sandy loam topsoil. The field was used for barley planting (Hordeum vulgare L., breeding line Mihailovsky). Sowing was in early May 2013 and harvest was in August, 14. The second agricultural field near the Pristen placed at Kursk region of Russia. It's arable Chernozems have around 4% of SOC, 6.5 pH(KCl) and NPK high-enhanced contents in sandy loam topsoil. The field was used for barley planting (Hordeum vulgare L., breeding line Xanadu). Sowing was 25-27 of April and harvest was 14-19 of August. Instrumental equipments (mainly LI-COR) were the same for both stations. Both towers height was 1.4m. Footprints were considered by fields edges, and were about 55m for Moscow and about 150m for Pristen. Canopy growth and snow melting were taking into account in the model. Surface roughness was neglected. Calculations were done using EddyPro software. Since Pristen field is 600 km to the South than the Moscow one, higher PAR values were observed for Pristen field. Modal PAR values were 600 and 400 umol m-2 s-1 for Pristen and Moscow fields respectively. Nevertheless temporal pattern of PAR was similar for both

  10. Study on roles of anaplerotic pathways in glutamate overproduction of Corynebacterium glutamicum by metabolic flux analysis

    OpenAIRE

    Shioya Suteaki; Nagahisa Keisuke; Furusawa Chikara; Fujimura Koki; Shirai Tomokazu; Shimizu Hiroshi

    2007-01-01

    Abstract Background Corynebacterium glutamicum has several anaplerotic pathways (anaplerosis), which are essential for the productions of amino acids, such as lysine and glutamate. It is still not clear how flux changes in anaplerotic pathways happen when glutamate production is induced by triggers, such as biotin depletion and the addition of the detergent material, Tween 40. In this study, we quantitatively analyzed which anaplerotic pathway flux most markedly changes the glutamate overprod...

  11. Direct Heat-Flux Measurement System (MDF) for Solar central Receiver Evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Ballestrin, J.

    2001-07-01

    A direct flux measurement system, MDF, has been designed, constructed and mounted on top of the SSPS-CRS tower at the Plataforma Solar de Almeria (PSA) in addition to an indirect flux measurement system based on a CCD camera. It's one of the main future objectives to compare systematically both measurements of the concentrated solar power, increasing in this way the confidence in the estimate of this quantity. Today everything is prepared to perform the direct flux measurement on the aperture of solar receivers: calorimeter array, data acquisition system and software. the geometry of the receiver determines the operation and analysis procedures to obtain the indecent power onto the defined area. The study of previous experiences with direct flux measurement systems ha been useful to define a new simpler and more accurate system. A description of each component of the MDF system is included, focusing on the heat-flux sensors or calorimeters, which enables these measurements to be done in a few seconds without water-cooling. The incident solar power and the spatial flux distribution on the aperture of the volumetric receiver Hitrec II are supplied by the above-mentioned MDF system. The first results obtained during the evaluation of this solar receiver are presented including a sunrise-sunset test. All these measurements have been concentrated in one coefficient that describes the global behavior of the Solar Power Plant. (Author) 18 refs.

  12. Direct Heat-Flux Measurement System (MDF) for Solar Central Receiver Evaluation

    International Nuclear Information System (INIS)

    A direct flux measurement system, MDF, has been designed, constructed and mounted on top of the SSPSCRS tower at the Plataforma Solar de Almeria (PSA) in addition to an indirect flux measurement system based on a CCD camera. It's one of the main future objectives to compare systematically both measurements of the concentrated solar power, increasing in this way the confidence in the estimate of this quantity. Today everything is prepared to perform the direct flux measurement on the aperture of solar receivers: calorimeter array, data acquisition system and software. The geometry of the receiver determines the operation and analysis procedures to obtain the incident power onto the defined area. The study of previous experiences with direct flux measurement systems has been useful to define a new, simpler and more accurate system. A description of each component of the MDF system is included, focusing on the heat-flux sensors or calorimeters, which enables these measurements to be done in a few seconds without water-cooling. The incident solar power and the spatial flux distribution on the aperture of the volumetric receiver Hitrec II are supplied by the above-mentioned MDF system. The first results obtained during the evaluation of this solar receiver are presented including a sunrise-sunset test. AU these measurements have been concentrated in one coefficient that describes the global behavior of the Solar Power Plant. (Author) 18 refs

  13. CO2 flux spatial variability in a tropical reservoir in the Central Amazonia

    Science.gov (United States)

    Santana, R. A. S. D.; do Vale, R. S.; Tota, J.; Miller, S. D.; Ferreira, R. B., Jr.; Alves, E. G.; Batalha, S. S. A.; Souza, R. A. F. D.

    2014-12-01

    The carbon budget over water surfaces in the Amazon has an important role in the total budget of this greenhouse gas a regional and global scale. However, more accurate estimates of the spatial and temporal distribution of the CO2 flux over those water surfaces are still required. In this context, this study aims to understand the spatial distribution of CO2 flux in the Balbina hydroelectric reservoir, located at Presidente Figueiredo city, Amazonas, Brazil. The floating chamber method was used to measure and calculate the CO2 flux. This method coup a chamber of known volume with an infrared gas analyzer (LiCor, LI-840A). Measurements were performed at 1 Hz during 20-30 minutes at 5 different points of the reservoir, four upstream (two near the edge and two in the middle) and one downstream of the dam. At all locations the surface water was supersaturated in pCO2 and fluxes were from the water to the atmosphere. The maximum CO2 flux observed was 1.2 μmol m-2 s-1 at the center point of the reservoir upstream the dam. The minimum CO2 flux was 0.05 μmol m-2 s-1, observed near the edge on the upstream side of the dam. On average, CO2 fluxes were larger downstream of the dam, 0.7 μmol m-2 s-1, compared to upstream, 0.45 μmol m-2 s-1. This pattern is consistent with that found in previous studies at this site using other flux estimation methods, and is consistent with turbulent mixing promoted by the water turbine. However, the mean CO2 flux for all measured points using the chambers, 0.47 μmol m-2 s-1, was much lower than those previously found using other methods. The reason for the difference between methods is unclear. In situ deployment of multiple flux estimation methods would be valuable, as would longer periods of measurements.

  14. High-frequency fluxes of labile compounds in the central Ligurian Sea, northwestern Mediterranean

    Science.gov (United States)

    Goutx, M.; Momzikoff, A.; Striby, L.; Andersen, V.; Marty, J. C.; Vescovali, I.

    2000-03-01

    Sinking particles were collected every 4 h with drifting sediment traps deployed at 200 m depth in May 1995 in a 1-D vertical system during the DYNAPROC observations in the northwestern Mediterranean sea. POC, proteins, glucosamine and lipid classes were used as indicators of the intensity and quality of the particle flux. The roles of day/night cycle and wind on the particle flux were examined. The transient regime of production from late spring bloom to pre-oligotrophy determined the flux intensity and quality. POC fluxes decreased from, on average, 34 to 11 mg m -2 d -1, representing 6-14% of the primary production under late spring bloom conditions to 1-2% under pre-oligotrophic conditions. Total protein and chloroplast lipid fluxes correlated with POC and reflected the input of algal biomass into the traps. As the season proceeded, changes in the biochemical composition of the exported material were observed. The C/N ratio rose from 7.8 to 12. Increases of serine (10-28% of total proteins), total lipids (7-9 to 14-28% of POC) and reserve lipids (1-5 to 5-22% of total lipids) were noticeable, whereas total protein content in POC decreased (20-27 to 18-7%). N-acetyl glucosamine, a tracer of fecal pellet flux, showed that zooplankton grazing was a major vector of downward export during the decaying bloom. Against this background pattern, episodic events specifically increased the flux, modifying the quality and the settling velocity of particles. Day/night signals in biotracers (POC, N-acetyl glucosamine, protein and chloroplast lipids) showed that zooplankton migrations were responsible for sedimentation of fresh material through fast sinking particles ( V=170-180 m d -1) at night. Periodic signatures of re-processed material (high lipolysis and bacterial biomass indices) suggested that other zooplankton fecal pellets or small aggregates, probably of lower settling velocities ( V<170 m d -1), contributed to the flux during calm periods. At the beginning of the

  15. Evidence for a link between tail biting and central monoamine metabolism in pigs (Sus scrofa domestica).

    Science.gov (United States)

    Valros, Anna; Palander, Pälvi; Heinonen, Mari; Munsterhjelm, Camilla; Brunberg, Emma; Keeling, Linda; Piepponen, Petteri

    2015-05-01

    Tail biting in pigs is a major welfare problem within the swine industry. Even though there is plenty of information on housing and management-related risk factors, the biological bases of this behavioral problem are poorly understood. The aim of this study was to investigate a possible link between tail biting, based on behavioral recordings of pigs during an ongoing outbreak, and certain neurotransmitters in different brain regions of these pigs. We used a total of 33 pigs at a farm with a long-standing problem of tail biting. Three equally big behavioral phenotypic groups, balanced for gender and age were selected, the data thus consisting of 11 trios of pigs. Two of the pigs in each trio originated from the same pen: one tail biter (TB) and one tail biting victim (V). A control (C) pig was selected from a pen without significant tail biting in the same farm room. We found an effect of tail biting behavioral phenotype on the metabolism of serotonin and dopamine, with a tendency for a higher 5-HIAA level in the prefrontal cortex (PFC) of TB compared to the other groups, while V pigs showed changes in both serotonin and dopamine metabolism in the striatum (ST) and limbic cortex (LC). Trp:BCAA and Trp:LNAA correlated positively with serotonin and 5-HIAA in the PFC, but only in TB pigs. Furthermore, in both ST and LC, several of the neurotransmitters and their metabolites correlated positively with the frequency of bites received by the pig. This is the first study indicating a link between brain neurotransmission and tail biting behavior in pigs with TB pigs showing a tendency for increased PFC serotonin metabolism and V pigs showing several changes in central dopamine and serotonin metabolism in their ST and LC, possibly due to the acute stress caused by being bitten. PMID:25728243

  16. Regional CO{sub 2} fluxes inferred from mixing ratio measurements: estimates from flask air samples in central Kansas, USA

    Energy Technology Data Exchange (ETDEWEB)

    Lai, Chun-Ta; Schauer, Andrew J.; Ehleringer, James R. [Univ. of Utah, Salt Lake City, UT (United States). Dept. of Biology; Owensby, Clenton; Ham, Jay M. [Kansas State Univ., Manhattan, KS (United States). Dept. of Agronomy; Helliker, Brent [Univ. of Pennsylvania, Philadelphia, PA (United States). Dept. of Biology; Tans, Pieter P. [National Oceanic and Atmospheric Administration, Boulder, CO (United States). Climate Monitoring and Diagnostics Laboratory

    2006-11-15

    We estimated regional fluxes of carbon dioxide (CO{sub 2}) using mixing ratios measured in a tallgrass prairie in central Kansas, USA over 3 yr (2002-2004). Glass flasks were used to collect whole air samples in the mid afternoon for determining CO{sub 2} mixing ratios and their carbon isotopic composition. Regional CO{sub 2} fluxes were calculated assuming atmospheric boundary layer (ABL) approaches an equilibrium state on a monthly basis. CO{sub 2} mixing ratios derived from the marine boundary layer data were used as a proxy to represent those in the free troposphere, which allowed for determining a boundary layer CO{sub 2} gradient primarily resulting from surface exchange. We estimated temporal changes in the ABL height for this region on a monthly basis (600-1700 m asl for a 5-yr average between 1997 and 2001) from European Center for Medium-Range Weather Forecasts (ECMWF) model data. Accordingly, we estimated the rate of entrainment (flux density) by interpolating NCAR/NCEP reanalysis data to the estimated ABL height. Our study differentiates from previous studies in several aspects: (1) we used flask-based mixing ratio measurements; (2) only discrete midday CO{sub 2} mixing ratio data were used to construct weekly CO{sub 2} gradients between free troposphere and the ABL and (3) we propose a new means for estimating monthly values of vertical transport. Modelled regional CO{sub 2} fluxes were compared to net ecosystem exchange (NEE) of CO{sub 2} fluxes measured by eddy covariance method. Assuming negligible vertical CO{sub 2} gradients between mid-ABL and the surface layer and with no correction applied, calculated NEE showed a general agreement with measured NEE fluxes throughout the growing season. Using CO mixing ratio data, we show that fossil fuel burning contributed negligible CO{sub 2} fluxes in summer but partially explained the discrepancy between modelled regional CO{sub 2} fluxes and measured NEE in winter. This wintertime fossil fuel input was

  17. Regional CO{sub 2} fluxes inferred from mixing ratio measurements: estimates from flask air samples in central Kansas, USA.

    Energy Technology Data Exchange (ETDEWEB)

    Lai, Chun-Ta; Schauer, Andrew J.; Ehleringer, James R. [Univ. of Utah, Salt Lake City, UT (United States). Dept. of Biology; Owensby, Clenton; Ham, Jay M. [Kansas State Univ., Manhattan, KS (United States). Dept. of Agronomy; Helliker, Brent [Univ. of Pennsylvania, Philadelphia, PA (United States). Dept. of Biology; Tans, Pieter P. [National Oceanic and Atmospheric Administration, Boulder, CO (United States). Climate Monitoring and Diagnostics Laboratory

    2006-11-15

    We estimated regional fluxes of carbon dioxide (CO{sub 2}) using mixing ratios measured in a tallgrass prairie in central Kansas, USA over 3 yr (2002-2004). Glass flasks were used to collect whole air samples in the mid afternoon for determining CO{sub 2} mixing ratios and their carbon isotopic composition. Regional CO{sub 2} fluxes were calculated assuming atmospheric boundary layer (ABL) approaches an equilibrium state on a monthly basis. CO{sub 2} mixing ratios derived from the marine boundary layer data were used as a proxy to represent those in the free troposphere, which allowed for determining a boundary layer CO{sub 2} gradient primarily resulting from surface exchange. We estimated temporal changes in the ABL height for this region on a monthly basis (600-1700 m asl for a 5-yr average between 1997 and 2001) from European Center for Medium-Range Weather Forecasts (ECMWF) model data. Accordingly, we estimated the rate of entrainment (flux density) by interpolating NCAR/NCEP reanalysis data to the estimated ABL height. Our study differentiates from previous studies in several aspects: (1) we used flask-based mixing ratio measurements; (2) only discrete midday CO{sub 2} mixing ratio data were used to construct weekly CO{sub 2} gradients between free troposphere and the ABL and (3) we propose a new means for estimating monthly values of vertical transport. Modelled regional CO{sub 2} fluxes were compared to net ecosystem exchange (NEE) of CO{sub 2} fluxes measured by eddy covariance method. Assuming negligible vertical CO{sub 2} gradients between mid-ABL and the surface layer and with no correction applied, calculated NEE showed a general agreement with measured NEE fluxes throughout the growing season. Using CO mixing ratio data, we show that fossil fuel burning contributed negligible CO{sub 2} fluxes in summer but partially explained the discrepancy between modelled regional CO{sub 2} fluxes and measured NEE in winter. This wintertime fossil fuel input was

  18. Whole-system metabolism and CO2 fluxes in a Mediterranean Bay dominated by seagrass beds (Palma Bay, NW Mediterranean

    Directory of Open Access Journals (Sweden)

    A. V. Borges

    2004-10-01

    Full Text Available The relationship between whole-system metabolism estimates based on planktonic and benthic incubations (bare sediments and seagrass, Posidonia oceanica meadows, and CO2 fluxes across the air-sea interface were examined in the Bay of Palma (Mallorca, Spain during two cruises in March and June 2002. Moreover, planktonic and benthic incubations were performed at monthly intervals from March 2001 to October 2002 in a seagrass vegetated area of the bay. From the annual study, results showed a contrast between the planktonic compartment, which was heterotrophic during most of the year, except for occasional bloom episodes, and the benthic compartment, which was slightly autotrophic. Whereas the seagrass community was autotrophic, the excess organic carbon production therein could only balance the excess respiration of the planktonic compartment in shallow waters (2 fields and fluxes across the bay observed during the two extensive cruises in 2002. Finally, dissolved inorganic carbon and oxygen budgets provided NEP estimates in fair agreement with those derived from direct metabolic estimates based on incubated samples over the Posidonia oceanica meadow.

  19. Fluxes of nitrous oxide and carbon dioxide over four potential biofuel crops in Central Illinois

    Science.gov (United States)

    Zeri, M.; Hickman, G. C.; Bernacchi, C.

    2009-12-01

    Nitrous oxide (N2O) and carbon dioxide (CO2) are important greenhouse gases that contribute to global climate change. Agriculture is a significant source of N2O to the atmosphere due to the use of nitrogen-based fertilizers. Fluxes of N2O and CO2 are measured using the flux-gradient technique over four different crops at the Energy Farm, a University of Illinois research facility in Urbana, Illinois. Measurements started in June of 2009 and are part of a project that aims to assess the impacts of potential biofuel crops on the carbon, water and nitrogen cycles. The species chosen are Maize (Zea mays), Miscanthus (Miscanthus x giganteus), Switchgrass (Panicum virgatum) and Prairie (a mix of several native species). The choice of species was based on their potential for the production of second-generation biofuels, i.e., fuels derived from the decomposition of the cellulosic material in the plant biomass. The use of corn residue for cellulosic biofuels might impact the carbon cycle through the reduction of soil organic content. Miscanthus is a perennial grass with great potential for biomass production. However, the total water used during the growing season and its water use efficiency might impose limits on the regions where this biofuel crop can be sustainably planted on a large scale. Switchgrass and the prairie species are less productive but might be suited for being well adapted and easy to establish. This study is the first side-by-side comparison of fluxes of N2O for these agro-ecosystems. The measurements are performed at micrometeorological towers placed at the center of 4 ha plots. The air is sampled at two heights over the vegetation and is analyzed in a tunable diode laser (TDL) installed nearby. A valve system cycles the TDL measurements trough all the intakes in the plots. The fluxes are calculated using the flux-gradient method, which requires the knowledge of the scalar vertical gradient as well as of the friction velocity (u*) and the Monin

  20. Neutron flux measurement in the central channel (XC1) of TRIGA 14 MW LEU core

    International Nuclear Information System (INIS)

    The full conversion of the 14 MW TRIGA Research Reactor was completed in May 2006 and each step of the conversion was achieved by removal of HEU fuel and replaced by LEU fuel. The operation was accompanied by a large set of theoretical evaluations and physical measurements intended to confirm the performances of gradual conversion. After the core full conversion, a program of measurements and comparisons with previous results of core physics and measurements is underway, allowing data acquisition for normal operation, demonstration of safety and economics of the converted core. Neutron flux spectrum measurements in the XC-1 water-filled channel were performed using multi-foil activation techniques. The neutron spectra and flux are obtained by unfolding from measured reaction rates using SAND II computer code. The integral flux measured value for LEU core and 14 MW reactor power is 4.66x1014 n/cm2s. For standard core the integral neutron flux for 14 MW reactor power was 4.27x1014 n/cm2s. (authors)

  1. Enzyme allocation problems in kinetic metabolic networks: Optimal solutions are elementary flux modes

    Czech Academy of Sciences Publication Activity Database

    Müller, Stefan; Regensburger, G.; Steuer, Ralf

    2014-01-01

    Roč. 347, APR 2014 (2014), s. 182-190. ISSN 0022-5193 R&D Projects: GA MŠk(CZ) EE2.3.20.0256 Institutional support: RVO:67179843 Keywords : metabolic optimization * enzyme kinetics * oriented matroid * elementary vector * conformal sum Subject RIV: EI - Biotechnology ; Bionics Impact factor: 2.116, year: 2014

  2. Metabolic flux analysis model for optimizing xylose conversion into ethanol by the natural C5-fermenting yeast Candida shehatae.

    Science.gov (United States)

    Bideaux, Carine; Montheard, Julie; Cameleyre, Xavier; Molina-Jouve, Carole; Alfenore, Sandrine

    2016-02-01

    A metabolic flux analysis (MFA) model was developed to optimize the xylose conversion into ethanol using Candida shehatae strain. This metabolic model was compartmented and constructed with xylose as carbon substrate integrating the enzymatic duality of the first step of xylose degradation via an algebraic coefficient. The model included the pentose phosphate pathway, glycolysis, synthesis of major metabolites like ethanol, acetic acid and glycerol, the tricarboxylic acid cycle as well as the respiratory chain, the cofactor balance, and the maintenance. The biomass composition and thus production were integrated considering the major biochemical synthesis reactions from monomers to each constitutive macromolecule (i.e., proteins, lipids, polysaccharides, nucleic acids). The construction of the model resulted into a 122-linear equation system to be resolved. A first experiment allowed was to verify the accuracy of the model by comparing calculated and experimental data. The metabolic model was utilized to determine the theoretical yield taking into account oxido-reductive balance and to optimize ethanol production. The maximal theoretical yield was calculated at 0.62 Cmolethanol/Cmolxylose for an oxygen requirement of 0.33 moloxygen/molxylose linked to the cofactors of the xylose reductase. Cultivations in chemostat mode allowed the fine tuning of both xylose and oxygen uptakes and showed that lower was the oxygen/xylose ratio, higher was the ethanol production yield. The best experimental ethanol production yield (0.51 Cmolethanol/Cmolxylose) was obtained for an oxygen supply of 0.47 moloxygen/molxylose. PMID:26536879

  3. Maximal sum of metabolic exchange fluxes outperforms biomass yield as a predictor of growth rate of microorganisms.

    Science.gov (United States)

    Zarecki, Raphy; Oberhardt, Matthew A; Yizhak, Keren; Wagner, Allon; Shtifman Segal, Ella; Freilich, Shiri; Henry, Christopher S; Gophna, Uri; Ruppin, Eytan

    2014-01-01

    Growth rate has long been considered one of the most valuable phenotypes that can be measured in cells. Aside from being highly accessible and informative in laboratory cultures, maximal growth rate is often a prime determinant of cellular fitness, and predicting phenotypes that underlie fitness is key to both understanding and manipulating life. Despite this, current methods for predicting microbial fitness typically focus on yields [e.g., predictions of biomass yield using GEnome-scale metabolic Models (GEMs)] or notably require many empirical kinetic constants or substrate uptake rates, which render these methods ineffective in cases where fitness derives most directly from growth rate. Here we present a new method for predicting cellular growth rate, termed SUMEX, which does not require any empirical variables apart from a metabolic network (i.e., a GEM) and the growth medium. SUMEX is calculated by maximizing the SUM of molar EXchange fluxes (hence SUMEX) in a genome-scale metabolic model. SUMEX successfully predicts relative microbial growth rates across species, environments, and genetic conditions, outperforming traditional cellular objectives (most notably, the convention assuming biomass maximization). The success of SUMEX suggests that the ability of a cell to catabolize substrates and produce a strong proton gradient enables fast cell growth. Easily applicable heuristics for predicting growth rate, such as what we demonstrate with SUMEX, may contribute to numerous medical and biotechnological goals, ranging from the engineering of faster-growing industrial strains, modeling of mixed ecological communities, and the inhibition of cancer growth. PMID:24866123

  4. Maximal sum of metabolic exchange fluxes outperforms biomass yield as a predictor of growth rate of microorganisms.

    Directory of Open Access Journals (Sweden)

    Raphy Zarecki

    Full Text Available Growth rate has long been considered one of the most valuable phenotypes that can be measured in cells. Aside from being highly accessible and informative in laboratory cultures, maximal growth rate is often a prime determinant of cellular fitness, and predicting phenotypes that underlie fitness is key to both understanding and manipulating life. Despite this, current methods for predicting microbial fitness typically focus on yields [e.g., predictions of biomass yield using GEnome-scale metabolic Models (GEMs] or notably require many empirical kinetic constants or substrate uptake rates, which render these methods ineffective in cases where fitness derives most directly from growth rate. Here we present a new method for predicting cellular growth rate, termed SUMEX, which does not require any empirical variables apart from a metabolic network (i.e., a GEM and the growth medium. SUMEX is calculated by maximizing the SUM of molar EXchange fluxes (hence SUMEX in a genome-scale metabolic model. SUMEX successfully predicts relative microbial growth rates across species, environments, and genetic conditions, outperforming traditional cellular objectives (most notably, the convention assuming biomass maximization. The success of SUMEX suggests that the ability of a cell to catabolize substrates and produce a strong proton gradient enables fast cell growth. Easily applicable heuristics for predicting growth rate, such as what we demonstrate with SUMEX, may contribute to numerous medical and biotechnological goals, ranging from the engineering of faster-growing industrial strains, modeling of mixed ecological communities, and the inhibition of cancer growth.

  5. Central leptin insufficiency syndrome: an interactive etiology for obesity, metabolic and neural diseases and for designing new therapeutic interventions

    OpenAIRE

    Kalra, Satya P.

    2007-01-01

    This review critically reappraises recent scientific evidence concerning central leptin insufficiency versus leptin resistance formulations to explain metabolic and neural disorders resulting from subnormal or defective leptin signaling in various sites in the brain. Research at various fronts to unravel the complexities of the neurobiology of leptin is surveyed to provide a comprehensive account of the neural and metabolic effects of environmentally-imposed fluctuations in leptin availabilit...

  6. Exhaustive analysis of a genotype space comprising 1015 central carbon metabolisms reveals an organization conducive to metabolic innovation

    OpenAIRE

    Hosseini, Sayed-Rzgar; Barve, Aditya; Wagner, Andreas

    2015-01-01

    All biological evolution takes place in a space of possible genotypes and their phenotypes. The structure of this space defines the evolutionary potential and limitations of an evolving system. Metabolism is one of the most ancient and fundamental evolving systems, sustaining life by extracting energy from extracellular nutrients. Here we study metabolism's potential for innovation by analyzing an exhaustive genotype-phenotype map for a space of 10(15) metabolisms that encodes all possible su...

  7. Exhaustive Analysis of a Genotype Space Comprising 10(15 )Central Carbon Metabolisms Reveals an Organization Conducive to Metabolic Innovation.

    OpenAIRE

    Sayed-Rzgar Hosseini; Aditya Barve; Andreas Wagner

    2015-01-01

    All biological evolution takes place in a space of possible genotypes and their phenotypes. The structure of this space defines the evolutionary potential and limitations of an evolving system. Metabolism is one of the most ancient and fundamental evolving systems, sustaining life by extracting energy from extracellular nutrients. Here we study metabolism's potential for innovation by analyzing an exhaustive genotype-phenotype map for a space of 10(15) metabolisms that encodes all possible su...

  8. Investigation of thermal energy transport from an anisotropic central heating element to the adjacent channels: A multipoint flux approximation

    International Nuclear Information System (INIS)

    Highlights: • The multipoint flux method is used to solve the problem of heat transfer in anisotropic medium. • The anisotropy results in skewness of the temperature field. • This makes the heat flux to the two channels asymmetric. • The temperature profiles of the coolant in the two channels becomes also different. - Abstract: The problem of heat transfer from a central heating element pressed between two clad plates to cooling channels adjacent and outboard of the plates is investigated numerically. The aim of this work is to highlight the role of thermal conductivity anisotropy of the heating element and/or the encompassing plates on thermal energy transport to the fluid passing through the two channels. When the medium is anisotropic with respect to thermal conductivity; energy transport to the neighboring channels is no longer symmetric. This asymmetry in energy fluxes influence heat transfer to the coolant resulting in different patterns of temperature fields. In particular, it is found that the temperature fields are skewed towards the principal direction of anisotropy. In addition, the heat flux distributions along the edges of the heating element are also different as a manifestation of thermal conductivity anisotropy. Furthermore, the peak temperature at the channel walls change location and magnitude depending on the principal direction of anisotropy. Based on scaling arguments, it is found that, the ratio of width to the height of the heating system is a key parameter which can suggest when one may ignore the effect of the cross-diagonal terms of the full conductivity tensor. To account for anisotropy in thermal conductivity, the method of multipoint flux approximation (MPFA) is employed. Using this technique, it is possible to find a finite difference stencil which can handle full thermal conductivity tensor and in the same time enjoys the simplicity of finite difference approximation. Although the finite difference stencil based on MPFA is

  9. Neutron flux measurement in the central channel (XC-1) of TRIGA 14 MW LEU core

    International Nuclear Information System (INIS)

    The TRIGA 14 MW reactor, operated by Institute for Nuclear Research Pitesti, Romania, is a pool type reactor, and has a rectangular shape which holds fuel bundles and is surrounded with beryllium reflectors. Each fuel bundle is composed of 25 nuclear fuel rods. The TRIGA 14 MW reactor was commissioned 28 years ago with HEU fuel rods. The conversion was gradually achieved, starting in February 1992 and completed in March 2006. The full conversion of the 14 MW TRIGA Research Reactor was completed in May 2006 and each step of the conversion was achieved by removal of HEU fuel, replaced by LEU fuel, accompanied by a large set of theoretical evaluation and physical measurements intended to confirm the performances of gradual conversion. After the core full conversion, a program of measurements and comparisons with previous results of core physics and measurements is underway, allowing data acquisition for normal operation, demonstration of safety and economics of the converted core. Neutron flux spectrum measurements in the XC in the XC-1 water 1 water-filled channel were performed using multi multi-foil activation techniques. The neutron spectra and flux are obtained by unfolding from measured reaction rates using SAND II computer code. The integral neutron flux value for LEU core is greater of 13% than for the standard HEU core. Also thermal neutron flux value for converted LEU core is smaller by 0.38% than for the standard HEU core. These differences appear because the foil activation detectors have been irradiated using a pneumatic rabbit having a diameter of 32 mm, whereas foil irradiations in standard HEU core has been performed with a pneumatic rabbit having a diameter of 14 mm, and therefore the neutron spectra in LEU core is less thermalized and the weight of fast neutron is greater

  10. Neutron flux measurement in the central channel (XC-1) of TRIGA 14 MW LEU core

    Energy Technology Data Exchange (ETDEWEB)

    BARBOS, D.; BUSUIOC, P.; ROTH, Cs.; PAUNOIU, C. [Institute for Nuclear Research - ICN Pitesti (Romania)

    2008-10-29

    The TRIGA 14 MW reactor, operated by Institute for Nuclear Research Pitesti, Romania, is a pool type reactor, and has a rectangular shape which holds fuel bundles and is surrounded with beryllium reflectors. Each fuel bundle is composed of 25 nuclear fuel rods. The TRIGA 14 MW reactor was commissioned 28 years ago with HEU fuel rods. The conversion was gradually achieved, starting in February 1992 and completed in March 2006. The full conversion of the 14 MW TRIGA Research Reactor was completed in May 2006 and each step of the conversion was achieved by removal of HEU fuel, replaced by LEU fuel, accompanied by a large set of theoretical evaluation and physical measurements intended to confirm the performances of gradual conversion. After the core full conversion, a program of measurements and comparisons with previous results of core physics and measurements is underway, allowing data acquisition for normal operation, demonstration of safety and economics of the converted core. Neutron flux spectrum measurements in the XC in the XC-1 water 1 water-filled channel were performed using multi multi-foil activation techniques. The neutron spectra and flux are obtained by unfolding from measured reaction rates using SAND II computer code. The integral neutron flux value for LEU core is greater of 13% than for the standard HEU core. Also thermal neutron flux value for converted LEU core is smaller by 0.38% than for the standard HEU core. These differences appear because the foil activation detectors have been irradiated using a pneumatic rabbit having a diameter of 32 mm, whereas foil irradiations in standard HEU core has been performed with a pneumatic rabbit having a diameter of 14 mm, and therefore the neutron spectra in LEU core is less thermalized and the weight of fast neutron is greater.

  11. The Sinorhizobium meliloti RNA chaperone Hfq influences central carbon metabolism and the symbiotic interaction with alfalfa

    Directory of Open Access Journals (Sweden)

    Jiménez-Zurdo José I

    2010-03-01

    Full Text Available Abstract Background The bacterial Hfq protein is able to interact with diverse RNA molecules, including regulatory small non-coding RNAs (sRNAs, and thus it is recognized as a global post-transcriptional regulator of gene expression. Loss of Hfq has an extensive impact in bacterial physiology which in several animal pathogens influences virulence. Sinorhizobium meliloti is a model soil bacterium known for its ability to establish a beneficial nitrogen-fixing intracellular symbiosis with alfalfa. Despite the predicted general involvement of Hfq in the establishment of successful bacteria-eukaryote interactions, its function in S. meliloti has remained unexplored. Results Two independent S. meliloti mutants, 2011-3.4 and 1021Δhfq, were obtained by disruption and deletion of the hfq gene in the wild-type strains 2011 and 1021, respectively, both exhibiting similar growth defects as free-living bacteria. Transcriptomic profiling of 1021Δhfq revealed a general down-regulation of genes of sugar transporters and some enzymes of the central carbon metabolism, whereas transcripts specifying the uptake and metabolism of nitrogen sources (mainly amino acids were more abundant than in the wild-type strain. Proteomic analysis of the 2011-3.4 mutant independently confirmed these observations. Symbiotic tests showed that lack of Hfq led to a delayed nodulation, severely compromised bacterial competitiveness on alfalfa roots and impaired normal plant growth. Furthermore, a large proportion of nodules (55%-64% elicited by the 1021Δhfq mutant were non-fixing, with scarce content in bacteroids and signs of premature senescence of endosymbiotic bacteria. RT-PCR experiments on RNA from bacteria grown under aerobic and microoxic conditions revealed that Hfq contributes to regulation of nifA and fixK1/K2, the genes controlling nitrogen fixation, although the Hfq-mediated regulation of fixK is only aerobiosis dependent. Finally, we found that some of the recently

  12. An estimate of equatorial wave energy flux at 9- to 90-day periods in the Central Pacific

    Science.gov (United States)

    Eriksen, Charles C.; Richman, James G.

    1988-01-01

    Deep fluctuations in current along the equator in the Central Pacific are dominated by coherent structures which correspond closely to narrow-band propagating equatorial waves. Currents were measured roughly at 1500 and 3000 m depths at five moorings between 144 and 148 deg W from January 1981 to March 1983, as part of the Pacific Equatorial Ocean Dynamics program. In each frequency band resolved, a single complex empirical orthogonal function accounts for half to three quarters of the observed variance in either zonal or meridional current. Dispersion for equatorial first meridional Rossby and Rossby gravity waves is consistent with the observed vertical-zonal coherence structure. The observations indicate that energy flux is westward and downward in long first meridional mode Rossby waves at periods 45 days and longer, and eastward and downward in short first meridional mode Rossby waves and Rossby-gravity waves at periods 30 days and shorter. A local minimum in energy flux occurs at periods corresponding to a maximum in upper-ocean meridional current energy contributed by tropical instability waves. Total vertical flux across the 9- to 90-day period range is 2.5 kW/m.

  13. Seawater methane flux, methane oxidation rates, and methane sources on the Central US Beaufort Sea Continental Shelf

    Science.gov (United States)

    Pohlman, J.; Pack-Woo, M.; Xu, X.; Ruppel, C. D.; Casso, M.; Worley, C.

    2012-12-01

    Previous studies have shown that some shallow-water circum-Arctic Ocean continental shelves (e.g., the Laptev Sea) are releasing substantial methane to the atmosphere. A number of processes -- including microbial degradation of organic matter in shallow sediments or in deeper sediments that were only recently thawed from permafrost, the dissociation of gas hydrates that formed in association with permafrost, and leakage from deeper thermogenic reservoirs -- may contribute to these methane fluxes. In August 2012, the USGS Gas Hydrates Project, with sponsorship from the DOE Methane Hydrates R&D Program, conducted a cross-shelf survey of greenhouse gas fluxes, carbon isotopic signatures of methane and CO2, and methane oxidation rates on the Central US Beaufort Sea continental shelf. IODP drilling has been proposed for a shelf-to-upper continental slope transect on this part of the Alaskan Beaufort passive margin to unravel the history of late Pleistocene to contemporary climate warming and sea level rise. The work presented here complements a 2012 USGS multichannel seismic program intended as IODP site survey. The flux, isotopic, and oxidation rate surveys sampled nearshore areas still underlain by subsea permafrost, a location where relict gas hydrate previously associated with permafrost may still exist and extend across the shelf to where present-day methane release is likely dominated by microbial methane generated in situ. The new geochemical data were acquired using dedicated cavity ringdown spectrometers (CRDS) for the atmospheric and sea surface measurements. The seawater CRDS also characterized the carbon isotopic signature of the CO2 and CH4 in real-time. Oxidation rate measurements were carried out using the low level 14C-CH4 (LL 14C) tracer method. Continuous measurements of surface air and surface seawater methane and carbon dioxide concentration, in conjunction with relevant meteorological and water chemistry data, permit us to calculate sea

  14. Development of a kinetic metabolic model: application to Catharanthus roseus hairy root

    OpenAIRE

    Leduc, M.; Tikhomiroff, C.; Cloutier, M.; Perrier, M.; Jolicoeur, M.

    2006-01-01

    A kinetic metabolic model describing Catharanthus roseus hairy root growth and nutrition was developed. The metabolic network includes glycolysis, pentose-phosphate pathway, TCA cycle and the catabolic reactions leading to cell building blocks such as amino acids, organic acids, organic phosphates, lipids and structural hexoses. The central primary metabolic network was taken at pseudo-steady state and metabolic flux analysis technique allowed reducing from 31 metabolic fluxes to 20 independe...

  15. Central Russia agroecosystem monitoring with CO2 fluxes analysis by eddy covariance method

    Directory of Open Access Journals (Sweden)

    Joulia Meshalkina

    2015-07-01

    Full Text Available The eddy covariance (EC technique as a powerful statistics-based method of measurement and calculation the vertical turbulent fluxes of greenhouses gases within atmospheric boundary layers provides the continuous, long-term flux information integrated at the ecosystem scale. An attractive way to compare the agricultural practices influences on GHG fluxes is to divide a crop area into subplots managed in different ways. The research has been carried out in the Precision Farming Experimental Field of the Russian Timiryazev State Agricultural University (RTSAU, Moscow in 2013 under the support of RF Government grant # 11.G34.31.0079, EU grant # 603542 LUС4С (7FP and RF Ministry of education and science grant # 14-120-14-4266-ScSh. Arable Umbric Albeluvisols have around 1% of SOC, 5.4 pH (KCl and NPK medium-enhanced contents in sandy loam topsoil. The CO2 flux seasonal monitoring has been done by two eddy covariance stations located at the distance of 108 m. The LI-COR instrumental equipment was the same for the both stations. The stations differ only by current crop version: barley or vetch and oats. At both sites, diurnal patterns of NEE among different months were very similar in shape but varied slightly in amplitude. NEE values were about zero during spring time. CO2 fluxes have been intensified after crop emerging from values of 3 to 7 µmol/s∙m2 for emission, and from 5 to 20 µmol/s∙m2 for sink. Stabilization of the fluxes has come at achieving plants height of 10-12 cm. Average NEE was negative only in June and July. Maximum uptake was observed in June with average values about 8 µmol CO2 m−2 s−1. Although different kind of crops were planted on the fields A and B, GPP dynamics was quite similar for both sites: after reaching the peak values at the mid of June, GPP decreased from 4 to 0.5 g C CO2 m-2 d-1 at the end of July. The difference in crops harvesting time that was equal two weeks did not significantly influence the daily

  16. Determination of neutron flux distribution across the RB reactor with large central air hol

    International Nuclear Information System (INIS)

    The need for the irradiation of large samples in the fast neutron field was led to design of a strongly heterogeneous core at the RB heavy water reactor. This configuration, operates as the internal fast neutron converter, introduces many difficulties in reactor safety and criticality analysis. In this paper, the collision probability method in two-dimensional r-z geometry, implemented in the VEGA code is applied. The neutron flux calculated by the VEGA code is compared to the results obtained by the MCNP sup T sup M continuous-energy Monte Carlo code and to the measured distribution. Results of VEGA and MCNP codes show good agreement with measured values. (author)

  17. Lack of differential pattern in central adiposity and metabolic syndrome in Barrett's esophagus and gastroesophageal reflux disease.

    LENUS (Irish Health Repository)

    Healy, L A

    2012-02-01

    Obesity is an established risk factor for esophageal adenocarcinoma, although the mechanism is unclear. A pathway from reflux to inflammation through metaplasia is the dominant hypothesis, and an added role relating to visceral adiposity and the metabolic syndrome has been mooted in Barrett\\'s esophagus (BE) patients. Whether BE differs from gastroesophageal reflux disease (GERD) in obesity and metabolic syndrome profiles is unclear, and this was the focus of this study. Patients with proven BE or GERD were randomly selected from the unit data registry and invited to attend for metabolic syndrome screening, anthropometry studies including segmental body composition analysis, and laboratory tests including fasting lipids, insulin, and C-reactive protein. Metabolic syndrome was defined using the National Cholesterol Education Program (NCEP) and the International Diabetes Federation (IDF) criteria. One hundred and eighteen BE patients and 113 age- and sex-matched GERD controls were studied. The incidence of obesity (body mass index >30 kg\\/m(2)) was 36% and 38%, respectively, with the pattern of fat deposition predominantly central and an estimated trunk fat mass of 13 and 14 kg, respectively. Using the NCEP criteria, metabolic syndrome was significantly more common in the BE cohort (30% vs 20%, P < 0.05), but there was no significant difference using IDF criteria (42% vs 37%, P= 0.340). Central obesity and the metabolic syndrome are common in both Barrett\\'s and GERD cohorts, but not significantly different, suggesting that central obesity and the metabolic syndrome does not per se impact on the development of BE in a reflux population. In BE, the importance of obesity and the metabolic syndrome in disease progression merits further study.

  18. Metabolic Flux Distribution during Defatting of Steatotic Human Hepatoma (HepG2 Cells

    Directory of Open Access Journals (Sweden)

    Gabriel Yarmush

    2016-01-01

    Full Text Available Methods that rapidly decrease fat in steatotic hepatocytes may be helpful to recover severely fatty livers for transplantation. Defatting kinetics are highly dependent upon the extracellular medium composition; however, the pathways involved are poorly understood. Steatosis was induced in human hepatoma cells (HepG2 by exposure to high levels of free fatty acids, followed by defatting using plain medium containing no fatty acids, or medium supplemented with a cocktail of defatting agents previously described before. We measured the levels of 28 extracellular metabolites and intracellular triglyceride, and fed the data into a steady-state mass balance model to estimate strictly intracellular fluxes. We found that during defatting, triglyceride content decreased, while beta-oxidation, the tricarboxylic acid cycle, and the urea cycle increased. These fluxes were augmented by defatting agents, and even more so by hyperoxic conditions. In all defatting conditions, the rate of extracellular glucose uptake/release was very small compared to the internal supply from glycogenolysis, and glycolysis remained highly active. Thus, in steatotic HepG2 cells, glycolysis and fatty acid oxidation may co-exist. Together, these pathways generate reducing equivalents that are supplied to mitochondrial oxidative phosphorylation.

  19. Metabolic Flux Distribution during Defatting of Steatotic Human Hepatoma (HepG2) Cells.

    Science.gov (United States)

    Yarmush, Gabriel; Santos, Lucas; Yarmush, Joshua; Koundinyan, Srivathsan; Saleem, Mubasher; Nativ, Nir I; Schloss, Rene S; Yarmush, Martin L; Maguire, Timothy J; Berthiaume, Francois

    2016-01-01

    Methods that rapidly decrease fat in steatotic hepatocytes may be helpful to recover severely fatty livers for transplantation. Defatting kinetics are highly dependent upon the extracellular medium composition; however, the pathways involved are poorly understood. Steatosis was induced in human hepatoma cells (HepG2) by exposure to high levels of free fatty acids, followed by defatting using plain medium containing no fatty acids, or medium supplemented with a cocktail of defatting agents previously described before. We measured the levels of 28 extracellular metabolites and intracellular triglyceride, and fed the data into a steady-state mass balance model to estimate strictly intracellular fluxes. We found that during defatting, triglyceride content decreased, while beta-oxidation, the tricarboxylic acid cycle, and the urea cycle increased. These fluxes were augmented by defatting agents, and even more so by hyperoxic conditions. In all defatting conditions, the rate of extracellular glucose uptake/release was very small compared to the internal supply from glycogenolysis, and glycolysis remained highly active. Thus, in steatotic HepG2 cells, glycolysis and fatty acid oxidation may co-exist. Together, these pathways generate reducing equivalents that are supplied to mitochondrial oxidative phosphorylation. PMID:26742084

  20. The Short-Chain Fatty Acid Uptake Fluxes by Mice on a Guar Gum Supplemented Diet Associate with Amelioration of Major Biomarkers of the Metabolic Syndrome

    OpenAIRE

    den Besten, Gijs; Havinga, Rick; Bleeker, Aycha; Rao, Shodhan; Gerding, Albert; van Eunen, Karen; Albert K Groen; Reijngoud, Dirk-Jan; Bakker, Barbara M.

    2014-01-01

    Studies with dietary supplementation of various types of fibers have shown beneficial effects on symptoms of the metabolic syndrome. Short-chain fatty acids (SCFAs), the main products of intestinal bacterial fermentation of dietary fiber, have been suggested to play a key role. Whether the concentration of SCFAs or their metabolism drives these beneficial effects is not yet clear. In this study we investigated the SCFA concentrations and in vivo host uptake fluxes in the absence or presence o...

  1. Optimization of permeate flux produced by solar energy driven membrane distillation process using central composite design approach.

    Science.gov (United States)

    Bouguecha, Salah T; Boubakri, Ali; Aly, Samir E; Al-Beirutty, Mohammad H; Hamdi, Mohamed M

    2016-01-01

    Membrane distillation (MD) is considered as a relatively high-energy requirement. To overcome this drawback, it is recommended to couple the MD process with solar energy as the renewable energy source in order to provide heat energy required to optimize its performance to produce permeate flux. In the present work, an original solar energy driven direct contact membrane distillation (DCMD) pilot plant was built and tested under actual weather conditions at Jeddah, KSA, in order to model and optimize permeate flux. The dependency of permeate flux on various operating parameters such as feed temperature (46.6-63.4°C), permeate temperature (6.6-23.4°C), feed flow rate (199-451L/h) and permeate flow rate (199-451L/h) was studied by response surface methodology based on central composite design approach. The analysis of variance (ANOVA) confirmed that all independent variables had significant influence on the model (where P-value <0.05). The high coefficient of determination (R(2) = 0.9644 and R(adj)(2) = 0.9261) obtained by ANOVA demonstrated good correlation between experimental and predicted values of the response. The optimized conditions, determined using desirability function, were T(f) = 63.4°C, Tp = 6.6°C, Q(f) = 451L/h and Q(p) = 451L/h. Under these conditions, the maximum permeate flux of 6.122 kg/m(2).h was achieved, which was close to the predicted value of 6.398 kg/m(2).h. PMID:27386986

  2. The carbon assimilation network in Escherichia coli is densely connected and largely sign-determined by directions of metabolic fluxes.

    Directory of Open Access Journals (Sweden)

    Valentina Baldazzi

    2010-06-01

    Full Text Available Gene regulatory networks consist of direct interactions but also include indirect interactions mediated by metabolites and signaling molecules. We describe how these indirect interactions can be derived from a model of the underlying biochemical reaction network, using weak time-scale assumptions in combination with sensitivity criteria from metabolic control analysis. We apply this approach to a model of the carbon assimilation network in Escherichia coli. Our results show that the derived gene regulatory network is densely connected, contrary to what is usually assumed. Moreover, the network is largely sign-determined, meaning that the signs of the indirect interactions are fixed by the flux directions of biochemical reactions, independently of specific parameter values and rate laws. An inversion of the fluxes following a change in growth conditions may affect the signs of the indirect interactions though. This leads to a feedback structure that is at the same time robust to changes in the kinetic properties of enzymes and that has the flexibility to accommodate radical changes in the environment.

  3. Modeling the diversion of primary carbon flux into secondary metabolism under variable nitrate and light/dark conditions.

    Science.gov (United States)

    Larbat, Romain; Robin, Christophe; Lillo, Cathrine; Drengstig, Tormod; Ruoff, Peter

    2016-08-01

    In plants, the partitioning of carbon resources between growth and defense is detrimental for their development. From a metabolic viewpoint, growth is mainly related to primary metabolism including protein, amino acid and lipid synthesis, whereas defense is based notably on the biosynthesis of a myriad of secondary metabolites. Environmental factors, such as nitrate fertilization, impact the partitioning of carbon resources between growth and defense. Indeed, experimental data showed that a shortage in the nitrate fertilization resulted in a reduction of the plant growth, whereas some secondary metabolites involved in plant defense, such as phenolic compounds, accumulated. Interestingly, sucrose, a key molecule involved in the transport and partitioning of carbon resources, appeared to be under homeostatic control. Based on the inflow/outflow properties of sucrose homeostatic regulation we propose a global model on how the diversion of the primary carbon flux into the secondary phenolic pathways occurs at low nitrate concentrations. The model can account for the accumulation of starch during the light phase and the sucrose remobilization by starch degradation during the night. Day-length sensing mechanisms for variable light-dark regimes are discussed, showing that growth is proportional to the length of the light phase. The model can describe the complete starch consumption during the night for plants adapted to a certain light/dark regime when grown on sufficient nitrate and can account for an increased accumulation of starch observed under nitrate limitation. PMID:27164436

  4. Fructan biosynthesis and degradation as part of plant metabolism controlling sugar fluxes during durum wheat kernel maturation

    Directory of Open Access Journals (Sweden)

    Sara eCimini

    2015-02-01

    Full Text Available Wheat kernels contain fructans, fructose based oligosaccharides with prebiotic properties, in levels between 2 and 35 weight % depending on the developmental stage of the kernel. To improve knowledge on the metabolic pathways leading to fructan storage and degradation, carbohydrate fluxes occurring during durum wheat kernel development were analyzed. Kernels were collected at various developmental stages and quali-quantitative analysis of carbohydrates (mono- and di-saccharides, fructans, starch was performed, alongside analysis of the activities and gene expression of the enzymes involved in their biosynthesis and hydrolysis. High resolution HPAEC-PAD of fructan contained in durum wheat kernels revealed that fructan content is higher at the beginning of kernel development, when fructans with higher DP, such as bifurcose and 1,1-nystose, were mainly found. The changes in fructan pool observed during kernel maturation might be part of the signaling pathways influencing carbohydrate metabolism and storage in wheat kernels during development. During the first developmental stages fructan accumulation may contribute to make kernels more effective Suc sinks and to participate in osmotic regulation while the observed decrease in their content may mark the transition to later developmental stages, transition that is also orchestrated by changes in redox balance.

  5. Co-factor engineering in lactobacilli: Effects of uncoupled ATPase activity on metabolic fluxes in Lactobacillus (L.) plantarum and L. sakei

    DEFF Research Database (Denmark)

    Rud, Ida; Solem, Christian; Jensen, Peter Ruhdal;

    2008-01-01

    The hydrolytic F-1-part of the F1F0-ATPase was over-expressed in Lactobacillus (L.) plantarum NC8 and L. sakei Lb790x during fermentation of glucose or ribose, in order to study how changes in the intracellular levels of ATP and ADP affect the metabolic fluxes. The uncoupled ATPase activity resul...... have approximately 80% control on both the glycolytic and ribolytic flux in L. plantarum under these conditions. In contrast, the glycolytic and ribolytic flux decreased in L. sakei with uncoupled ATPase activity. (C) 2008 Elsevier Inc. All rights reserved....

  6. The Role of Airmass Types and Surface Energy Fluxes in Snow Cover Ablation in the Central Appalachians.

    Science.gov (United States)

    Leathers, Daniel J.; Graybeal, Daniel; Mote, Thomas; Grundstein, Andrew; Robinson, David

    2004-12-01

    A one-dimensional snowpack model, a unique airmass identification scheme, and surface weather observations are used to investigate large ablation events in the central Appalachian Mountains of North America. Data from cooperative observing stations are used to identify large ablation events within a 1° latitude × 1° longitude grid box that covers the majority of the Lycoming Creek basin in northern Pennsylvania. All 1-day ablation events greater than or equal to 7.6 cm (3 in.) are identified for the period of 1950 through 2001. Seventy-one events are identified, and these days are matched with a daily airmass type derived using the Spatial Synoptic Classification technique. Average meteorological characteristics on ablation days of each airmass type are calculated in an effort to understand the diverse meteorological influences that led to the large ablation events. A one-dimensional mass and energy balance snowpack model (“SNTHERM”) is used to calculate surface/atmosphere energy fluxes responsible for ablation under each airmass type. Results indicate that large ablation events take place under diverse airmass/synoptic conditions in the central Appalachians. Five airmass types account for the 71 large ablation events over the 52-yr period. Forty-three of the events occurred under “moist” airmass types and 28 under “dry” airmass conditions. Large ablation events under dry airmass types are driven primarily by daytime net radiation receipt, especially net solar radiation. These events tend to occur early and late in the snow cover season when solar radiation receipt is highest and are characterized by relatively clear skies, warm daytime temperatures, and low dewpoint temperatures. Moist airmass types are characterized by cloudy, windy conditions with higher dewpoint temperatures and often with liquid precipitation. During these events sensible heat flux is most often the dominant energy flux to the snowpack during ablation episodes. However, in many

  7. Elemental weathering fluxes and saprolite production rate in a Central African lateritic terrain (Nsimi, South Cameroon)

    Science.gov (United States)

    Braun, Jean-Jacques; Marechal, Jean-Christophe; Riotte, Jean; Boeglin, Jean-Loup; Bedimo Bedimo, Jean-Pierre; Ndam Ngoupayou, Jules Remy; Nyeck, Brunot; Robain, Henri; Sekhar, M.; Audry, Stéphane; Viers, Jérôme

    2012-12-01

    The comparison between contemporary and long-term weathering has been carried out in the Small Experimental Watershed (SEW) of Nsimi, South Cameroon in order to quantify the export fluxes of major and trace elements and the residence time of the lateritic weathering cover. We focus on the hillside system composed of a thick lateritic weathering cover topped by a soil layer. This study is built on the recent improvements of the hillside hydrological functioning and on the analyses of major and trace elements. The mass balance calculation at the weathering horizon scale performed with the parent rock as reference indicates (i) strong depletion profiles for alkalis (Na, K, Rb) and alkaline earths (Mg, Ca, Sr, Ba), (ii) moderate depletion profiles for Si, P, Cd, Cu, Zn, Ni and Co, (iii) depletion/enrichment profiles for Al, Ga, Ge, Sn, Pb, LREE, HREE, Y, U, Fe, V, Cr, Mn. It is noteworthy that (i) Mn and Ce are not significantly redistributed according to oxidative processes as it is the case for Fe, V and Cr, and (ii) Ge is fractionated compared to silica with enrichment in Fe-rich horizons. The calculations performed for the topsoil with iron crust as parent material reference reveal that the degradation of the iron crust is accompanied by the loss of most of the constituting elements, among which are those specifically accumulated as the redox sensitive elements (Fe, V, Cr) and iron oxide related elements like Th. The overall current elemental fluxes from the hillside system at the springs and the seepage zones are extremely low due to the inert lateritic mineralogy. Ninety-four percent of the whole Na flux generated from the hillside corrected from atmospheric deposits (77 mol/ha/yr) represents the current weathering rates of plagioclase (oligoclase) in the system, the other remaining 6% may be attributed to the dissolution of hornblende. The silica hillside flux is 300 mol/ha/yr and can be mostly attributed to the plagioclase and kaolinite dissolution. Al and Ga

  8. The Association of Glucose Metabolism and Eigenvector Centrality in Alzheimer's Disease.

    Science.gov (United States)

    Adriaanse, Sofie M; Wink, Alle Meije; Tijms, Betty M; Ossenkoppele, Rik; Verfaillie, Sander C J; Lammertsma, Adriaan A; Boellaard, Ronald; Scheltens, Philip; van Berckel, Bart N M; Barkhof, Frederik

    2016-02-01

    Both fluorine-18-labeled fluorodeoxyglucose ([(18)F]FDG) positron emission tomography, examining glucose metabolism, and resting-state functional magnetic resonance imaging (rs-fMRI), using covarying blood oxygen levels, can be used to explore neuronal dysfunction in Alzheimer's disease (AD). Both measures are reported to identify similar brain regions affected in AD patients. The spatial overlap and association of [(18)F]FDG with rs-fMRI in AD patients and controls were examined to investigate whether these two measures are associated, and if so, to what extent. For 24 AD patients and 18 controls, [(18)F]FDG and rs-fMRI data were available. [(18)F]FDG standardized uptake value ratios (SUVr), with cerebellar gray matter (GM) as reference tissue, were calculated. Eigenvector centrality (EC) mapping was used to spatially analyze the functional brain network. Group differences were calculated for [(18)F]FDG and eigenvector centrality mapping (ECM) values in four cortical regions (occipital, parietal, frontal, and temporal) and across voxels, with age, gender, and GM as covariates. Correlation of [(18)F]FDG with ECM was calculated within groups. Both lowered [(18)F]FDG SUVr and EC values were seen in the parietal and occipital cortex of AD patients. However, [(18)F]FDG yielded more robust and widespread brain areas affected in AD patients; hypometabolism was also observed in the temporal cortex and regions within frontal brain areas. Poor spatial overlap of both measures was observed. No associations were found between local [(18)F]FDG SUVr and ECM. In conclusion, agreement of [(18)F]FDG and ECM in AD patients seems moderate at best. [(18)F]FDG was most accurate in distinguishing AD patients from controls. PMID:26414628

  9. Energy exchanges in a Central Business District - Interpretation of Eddy Covariance and radiation flux measurements (London UK)

    Science.gov (United States)

    Kotthaus, S.; Grimmond, S.

    2013-12-01

    Global urbanisation brings increasingly dense and complex urban structures. To manage cities sustainably and smartly, currently and into the future under changing climates, urban climate research needs to advance in areas such as Central Business Districts (CBD) where human interactions with the environment are particularly concentrated. Measurement and modelling approaches may be pushed to their limits in dense urban settings, but if urban climate research is to contribute to the challenges of real cities those limits have to be addressed. The climate of cities is strongly governed by surface-atmosphere exchanges of energy, moisture and momentum. Observations of the relevant fluxes provide important information for improvement and evaluation of modelling approaches. Due to the CBD's heterogeneity, a very careful analysis of observations is required to understand the relevant processes. Current approaches used to interpret observations and set them in a wider context may need to be adapted for use in these more complex areas. Here, we present long-term observations of the radiation balance components and turbulent fluxes of latent heat, sensible heat and momentum in the city centre of London. This is one of the first measurement studies in a CBD covering multiple years with analysis at temporal scales from days to seasons. Data gathered at two sites in close vicinity, but with different measurement heights, are analysed to investigate the influence of source area characteristics on long-term radiation and turbulent fluxes. Challenges of source area modelling and the critical aspect of siting in such a complex environment are considered. Outgoing long- and short-wave radiation are impacted by the anisotropic nature of the urban surface and the high reflectance materials increasingly being used as building materials. Results highlight the need to consider the source area of radiometers in terms of diffuse and direct irradiance. Sensible heat fluxes (QH) are positive

  10. Tracer‐Based Metabolic NMR‐Based Flux Analysis in a Leukaemia Cell Line

    Science.gov (United States)

    Carrigan, John B.; Reed, Michelle A. C.; Ludwig, Christian; Khanim, Farhat L.; Bunce, Christopher M.

    2016-01-01

    Abstract High levels of reactive oxygen species (ROS) have a profound impact on acute myeloid leukaemia cells and can be used to specifically target these cells with novel therapies. We have previously shown how the combination of two redeployed drugs, the contraceptive steroid medroxyprogesterone and the lipid‐regulating drug bezafibrate exert anti‐leukaemic effects by producing ROS. Here we report a 13C‐tracer‐based NMR metabolic study to understand how these drugs work in K562 leukaemia cells. Our study shows that [1,2‐13C]glucose is incorporated into ribose sugars, indicating activity in oxidative and non‐oxidative pentose phosphate pathways alongside lactate production. There is little label incorporation into the tricarboxylic acid cycle from glucose, but much greater incorporation arises from the use of [3‐13C]glutamine. The combined medroxyprogesterone and bezafibrate treatment decreases label incorporation from both glucose and glutamine into α‐ketoglutarate and increased that for succinate, which is consistent with ROS‐mediated conversion of α‐ketoglutarate to succinate. Most interestingly, this combined treatment drastically reduced the production of several pyrimidine synthesis intermediates. PMID:27347458

  11. Rational Design of a Corynebacterium glutamicum Pantothenate Production Strain and Ins Characterization by Metabolic Flux Analysis and Genome-Wide Transcriptional Profiling

    Czech Academy of Sciences Publication Activity Database

    Hüser, A.T.; Chassagnole, Ch.; Lindley, N.D.; Merkamm, M.; Guyonvarch, A.; Elišáková, Veronika; Pátek, Miroslav; Kalinowski, J.; Brune, I.; Pühler, A.; Tauch, A.

    2005-01-01

    Roč. 71, č. 6 (2005), s. 3255-3268. ISSN 0099-2240 Institutional research plan: CEZ:AV0Z50200510 Keywords : corynebacterium glutamicum * metabolic flux Subject RIV: EE - Microbiology, Virology Impact factor: 3.818, year: 2005

  12. Regulation of bacterial sulfate reduction and hydrogen sulfide fluxes in the central Namibian coastal upwelling zone

    DEFF Research Database (Denmark)

    Bruchert, V.; Jørgensen, BB; Neumann, K.;

    2003-01-01

    low capacity to oxidize and trap sulfide. The inner shelf break marks the seaward border of sulfidic bottom waters, and separates two different regimes of bacterial sulfate reduction. In the sulfidic bottom waters on the shelf, up to 55% of sulfide oxidation is mediated by the large nitrate......The coastal upwelling system off central Namibia is one of the most productive regions of the oceans and is characterized by frequently occurring shelf anoxia with severe effects for the benthic life and fisheries. We present data on water column dissolved oxygen, sulfide, nitrate and nitrite, pore...... water profiles for dissolved,sulfide and sulfate, S-35-sulfate reduction rates, as well as bacterial counts of large sulfur bacteria from 20 stations across the continental shelf and slope. The stations covered two transects and included the inner shelf with its anoxic and extremely oxygen...

  13. Metabolic Flux Analysis of Lipid Biosynthesis in the Yeast Yarrowia lipolytica Using 13C-Labled Glucose and Gas Chromatography-Mass Spectrometry.

    Science.gov (United States)

    Zhang, Huaiyuan; Wu, Chao; Wu, Qingyu; Dai, Junbiao; Song, Yuanda

    2016-01-01

    The oleaginous yeast Yarrowia lipolytica has considerable potential for producing single cell oil, which can be converted to biodiesel, a sustainable alternative to fossil fuels. However, extensive fundamental and engineering efforts must be carried out before commercialized production become cost-effective. Therefore, in this study, metabolic flux analysis of Y. lipolytica was performed using 13C-labeled glucose as a sole carbon source in nitrogen sufficient and insufficient media. The nitrogen limited medium inhibited cell growth while promoting lipid accumulation (from 8.7% of their biomass to 14.3%). Metabolic flux analysis showed that flux through the pentose phosphate pathway was not significantly regulated by nitrogen concentration, suggesting that NADPH generation is not the limiting factor for lipid accumulation in Y. lipolytica. Furthermore, metabolic flux through malic enzyme was undetectable, confirming its non-regulatory role in lipid accumulation in this yeast. Nitrogen limitation significantly increased flux through ATP:citrate lyase (ACL), implying that ACL plays a key role in providing acetyl-CoA for lipid accumulation in Y. lipolytica. PMID:27454589

  14. Metabolic flux distributions in Corynebacterium glutamicum during growth and lysine overproduction. Reprinted from Biotechnology and Bioengineering, Vol. 41, Pp 633-646 (1993).

    Science.gov (United States)

    Vallino, J J; Stephanopoulos, G

    2000-03-20

    The two main contributions of this article are the solidification of Corynebacterium glutamicum biochemistry guided by bioreaction network analysis, and the determination of basal metabolic flux distributions during growth and lysine synthesis. Employed methodology makes use of stoichiometrically based mass balances to determine flux distributions in the C. glutamicum metabolic network. Presented are a brief description of the methodology, a thorough literature review of glutamic acid bacteria biochemistry, and specific results obtained through a combination of fermentation studies and analysis-directed intracellular assays. The latter include the findings of the lack of activity of glyoxylate shunt, and that phosphoenolpyruvate carboxylase (PPC) is the only anaplerotic reaction expressed in C. glutamicum cultivated on glucose minimal media. Network simplifications afforded by the above findings facilitated the determination of metabolic flux distributions under a variety of culture conditions and led to the following conclusions. Both the pentose phosphate pathway and PPC support significant fluxes during growth and lysine overproduction, and that flux partitioning at the glucosa-6-phosphate branch point does not appear to limit lysine synthesis. PMID:10699864

  15. Investigation of thermal energy transport from an anisotropic central heating element to the adjacent channels: A multipoint flux approximation

    KAUST Repository

    Salama, Amgad

    2015-02-01

    The problem of heat transfer from a central heating element pressed between two clad plates to cooling channels adjacent and outboard of the plates is investigated numerically. The aim of this work is to highlight the role of thermal conductivity anisotropy of the heating element and/or the encompassing plates on thermal energy transport to the fluid passing through the two channels. When the medium is anisotropic with respect to thermal conductivity; energy transport to the neighboring channels is no longer symmetric. This asymmetry in energy fluxes influence heat transfer to the coolant resulting in different patterns of temperature fields. In particular, it is found that the temperature fields are skewed towards the principal direction of anisotropy. In addition, the heat flux distributions along the edges of the heating element are also different as a manifestation of thermal conductivity anisotropy. Furthermore, the peak temperature at the channel walls change location and magnitude depending on the principal direction of anisotropy. Based on scaling arguments, it is found that, the ratio of width to the height of the heating system is a key parameter which can suggest when one may ignore the effect of the cross-diagonal terms of the full conductivity tensor. To account for anisotropy in thermal conductivity, the method of multipoint flux approximation (MPFA) is employed. Using this technique, it is possible to find a finite difference stencil which can handle full thermal conductivity tensor and in the same time enjoys the simplicity of finite difference approximation. Although the finite difference stencil based on MPFA is quite complex, in this work we apply the recently introduced experimenting field approach which construct the global problem automatically.

  16. Metabolism

    Science.gov (United States)

    ... also influenced by body composition — people with more muscle and less fat generally have higher BMRs. previous continue Things That Can Go Wrong With Metabolism Most of the time your metabolism works effectively ...

  17. Metabolism

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    2008255 Serum adiponectin level declines in the elderly with metabolic syndrome.WU Xiaoyan(吴晓琰),et al.Dept Geriatr,Huashan Hosp,Fudan UnivShanghai200040.Chin J Geriatr2008;27(3):164-167.Objective To investigate the correlation between ser-um adiponectin level and metabolic syndrome in the elderly·Methods Sixty-one subjects with metabolic syndrome and140age matched subjects without metabolic

  18. Dissolved organic matter and lake metabolism: Biogeochemistry and controls of nutrient flux dynamics to fresh waters. Technical progress report, January 1, 1990--December 31, 1991

    Energy Technology Data Exchange (ETDEWEB)

    Wetzel, R.G.

    1992-12-31

    The land-water interface region consists of two major components: the wetland, and the down-gradient adjacent littoral floating-leaved and submersed, macrophyte communities. Because of the importance of very high production and nutrient turnover of attached microbiota, a major emphasis of this investigation was placed upon these biota and their metabolic capacities for assimilation and release of organic compounds and nutrient retention and cycling. Examination of the capacities of wetland littoral communities to regulate fluxes of nutrients and organic compounds often has been limited to input-output analyses. These input-output data are an integral part of these investigations, but most of the research effort concentrated on the biotic and metabolic mechanisms that control fluxes and retention capacities and their effects upon biota in the down-gradient waters. The important regulatory capacities of dissolved organic compounds on enzyme reactivity was examined experimentally and coupled to the wetland-littoral organic carbon flux budgets.

  19. Prevalence of Central Obesity among Adults with Normal BMI and Its Association with Metabolic Diseases in Northeast China

    Science.gov (United States)

    Zhang, Peng; Wang, Rui; Gao, Chunshi; Jiang, Lingling; Lv, Xin; Song, Yuanyuan; Li, Bo

    2016-01-01

    Objectives The present study aimed to investigate the prevalence of central obesity among adults with normal BMI and its association with metabolic diseases in Jilin Province, China. Methods A population-based cross-sectional study was conducted in 2012 in Jilin Province of China. Information was collected by face to face interview. Descriptive data analysis and 95% confidence intervals (CI) of prevalence/frequency were conducted. Log-binomial regression analyses were used to find the independent factors associated with central obesity and to explore the adjusted association between central obesity and metabolic diseases among adults with normal BMI. Results Among the adult residents with normal BMI in Jilin Province, 55.6% of participants with central obesity self-assessed as normal weight and 27.0% thought their body weight were above normal. 12.7% of central obesity people took methods to lose weight, while 85.3% didn’t. Female, older people and non-manual worker had higher risk to be central obesity among adults with normal BMI. Hypertension, diabetes and hyperlipidemia were significantly associated with central obesity among adults with normal BMI, the PRs were 1.337 (1.224–1.461), 1.323 (1.193–1.456) and 1.261 (1.152–1.381) separately when adjusted for gender, age and BMI. Conclusions Hypertension, diabetes and hyperlipidemia were significantly associated with central obesity among adults with normal BMI in Jilin Province, China. The low rates of awareness and control of central obesity among adults with normal BMI should be improved by government and health department. PMID:27467819

  20. Metabolic-flux analysis of continuously cultured hybridoma cells using 13CO2 mass spectrometry in combination with 13C-lactate nuclear magnetic resonance spectroscopy and metabolic balancing

    NARCIS (Netherlands)

    Bonarius, H.P.J.; Ozemre, A.; Timmerarends, B.; Skrabal, P.; Tramper, J.; Schmid, G.; Heinzle, E.

    2001-01-01

    Protein production of mammalian-cell culture is limited due to accumulation of waste products such as lactate, CO2, and ammonia. In this study, the intracellular fluxes of hybridoma cells are measured to determine the amount by which various metabolic pathways contribute to the secretion of waste pr

  1. Metabolic engineering of proanthocyanidin production by repressing the isoflavone pathways and redirecting anthocyanidin precursor flux in legume.

    Science.gov (United States)

    Li, Penghui; Dong, Qiang; Ge, Shujun; He, Xianzhi; Verdier, Jerome; Li, Dongqin; Zhao, Jian

    2016-07-01

    MtPAR is a proanthocyanidin (PA) biosynthesis regulator; the mechanism underlying its promotion of PA biosynthesis is not fully understood. Here, we showed that MtPAR promotes PA production by a direct repression of biosynthesis of isoflavones, the major flavonoids in legume, and by redirecting immediate precursors, such as anthocyanidins, flux into PA pathway. Ectopic expression of MtPAR repressed isoflavonoid production by directly binding and suppressing isoflavone biosynthetic genes such as isoflavone synthase (IFS). Meanwhile, MtPAR up-regulated PA-specific genes and decreased the anthocyanin levels without altering the expression of anthocyanin biosynthetic genes. MtPAR may shift the anthocyanidin precursor flux from anthocyanin pathway to PA biosynthesis. MtPAR complemented PA-deficient phenotype of Arabidopsis tt2 mutant seeds, demonstrating their similar action on PA production. We showed the direct interactions between MtPAR, MtTT8 and MtWD40-1 proteins from Medicago truncatula and Glycine max, to form a ternary complex to trans-activate PA-specific ANR gene. Finally, MtPAR expression in alfalfa (Medicago sativa) hairy roots and whole plants only promoted the production of small amount of PAs, which was significantly enhanced by co-expression of MtPAR and MtLAP1. Transcriptomic and metabolite profiling showed an additive effect between MtPAR and MtLAP1 on the production of PAs, supporting that efficient PA production requires more anthocyanidin precursors. This study provides new insights into the role and mechanism of MtPAR in partitioning precursors from isoflavone and anthocyanin pathways into PA pathways for a specific promotion of PA production. Based on this, a strategy by combining MtPAR and MtLAP1 co-expression to effectively improve metabolic engineering performance of PA production in legume forage was developed. PMID:26806316

  2. Sources and the flux pattern of dissolved carbon in rivers of the Yenisey basin draining the Central Siberian Plateau

    International Nuclear Information System (INIS)

    Frequent measurements of dissolved organic (DOC) and inorganic (DIC) carbon concentrations in rivers during snowmelt, the entire ice-free season, and winter were made in five large watersheds (15 000–174 000 km2) of the Central Siberian Plateau (Yenisey River basin). These differ in the degree of continuous permafrost coverage, mean annual air temperature, and the proportion of tundra and forest vegetation. With an annual DOC export from the catchment areas of 2.8–4.7 gC m−2 as compared to an annual DIC export of 1.0–2.8 gC m−2, DOC was the dominant component of terrigenous C released to rivers. There was strong temporal variation in the discharge of DOC and DIC. Like for other rivers of the pan-arctic and boreal zones, snowmelt dominated annual fluxes, being 55–71% for water runoff, 64–82% for DOC and 37–41% for DIC. Likewise, DOC and DIC exhibited also a strong spatial variation in C fluxes, with both dissolved C species decreasing from south to north. The rivers of the southern part of the plateau had the largest flow-weighted DOC concentrations among those previously reported for Siberian rivers, but the smallest flow-weighted DIC concentrations. In the study area, DOC and DIC fluxes were negatively correlated with the distribution of continuous permafrost and positively correlated with mean annual air temperature. A synthesis of literature data shows similar trends from west to east, with an eastward decrease of dissolved C concentrations and an increased proportion of DOC in the total dissolved C flux. It appears that there are two contemporary limitations for river export of terrigenous C across Siberia: (1) low productivity of ecosystems with respect to potentially mobilizable organic C, slow weathering rates with concomitant small formation of bicarbonate, and/or wildfire disturbance limit the pools of organic and inorganic C that can be mobilized for transport in rivers (source-limited), and (2) mobilization of available pools of C is

  3. The short-chain fatty acid uptake fluxes by mice on a guar gum supplemented diet associate with amelioration of major biomarkers of the metabolic syndrome.

    Directory of Open Access Journals (Sweden)

    Gijs den Besten

    Full Text Available Studies with dietary supplementation of various types of fibers have shown beneficial effects on symptoms of the metabolic syndrome. Short-chain fatty acids (SCFAs, the main products of intestinal bacterial fermentation of dietary fiber, have been suggested to play a key role. Whether the concentration of SCFAs or their metabolism drives these beneficial effects is not yet clear. In this study we investigated the SCFA concentrations and in vivo host uptake fluxes in the absence or presence of the dietary fiber guar gum. C57Bl/6J mice were fed a high-fat diet supplemented with 0%, 5%, 7.5% or 10% of the fiber guar gum. To determine the effect on SCFA metabolism, 13C-labeled acetate, propionate or butyrate were infused into the cecum of mice for 6 h and the isotopic enrichment of cecal SCFAs was measured. The in vivo production, uptake and bacterial interconversion of acetate, propionate and butyrate were calculated by combining the data from the three infusion experiments in a single steady-state isotope model. Guar gum treatment decreased markers of the metabolic syndrome (body weight, adipose weight, triglycerides, glucose and insulin levels and HOMA-IR in a dose-dependent manner. In addition, hepatic mRNA expression of genes involved in gluconeogenesis and fatty acid synthesis decreased dose-dependently by guar gum treatment. Cecal SCFA concentrations were increased compared to the control group, but no differences were observed between the different guar gum doses. Thus, no significant correlation was found between cecal SCFA concentrations and metabolic markers. In contrast, in vivo SCFA uptake fluxes by the host correlated linearly with metabolic markers. We argue that in vivo SCFA fluxes, and not concentrations, govern the protection from the metabolic syndrome by dietary fibers.

  4. The short-chain fatty acid uptake fluxes by mice on a guar gum supplemented diet associate with amelioration of major biomarkers of the metabolic syndrome.

    Science.gov (United States)

    den Besten, Gijs; Havinga, Rick; Bleeker, Aycha; Rao, Shodhan; Gerding, Albert; van Eunen, Karen; Groen, Albert K; Reijngoud, Dirk-Jan; Bakker, Barbara M

    2014-01-01

    Studies with dietary supplementation of various types of fibers have shown beneficial effects on symptoms of the metabolic syndrome. Short-chain fatty acids (SCFAs), the main products of intestinal bacterial fermentation of dietary fiber, have been suggested to play a key role. Whether the concentration of SCFAs or their metabolism drives these beneficial effects is not yet clear. In this study we investigated the SCFA concentrations and in vivo host uptake fluxes in the absence or presence of the dietary fiber guar gum. C57Bl/6J mice were fed a high-fat diet supplemented with 0%, 5%, 7.5% or 10% of the fiber guar gum. To determine the effect on SCFA metabolism, 13C-labeled acetate, propionate or butyrate were infused into the cecum of mice for 6 h and the isotopic enrichment of cecal SCFAs was measured. The in vivo production, uptake and bacterial interconversion of acetate, propionate and butyrate were calculated by combining the data from the three infusion experiments in a single steady-state isotope model. Guar gum treatment decreased markers of the metabolic syndrome (body weight, adipose weight, triglycerides, glucose and insulin levels and HOMA-IR) in a dose-dependent manner. In addition, hepatic mRNA expression of genes involved in gluconeogenesis and fatty acid synthesis decreased dose-dependently by guar gum treatment. Cecal SCFA concentrations were increased compared to the control group, but no differences were observed between the different guar gum doses. Thus, no significant correlation was found between cecal SCFA concentrations and metabolic markers. In contrast, in vivo SCFA uptake fluxes by the host correlated linearly with metabolic markers. We argue that in vivo SCFA fluxes, and not concentrations, govern the protection from the metabolic syndrome by dietary fibers. PMID:25203112

  5. Land use change effects on trace gas fluxes in the forest margins of Central Sulawesi, Indonesia

    Science.gov (United States)

    Veldkamp, Edzo; Purbopuspito, Joko; Corre, Marife D.; Brumme, Rainer; Murdiyarso, Daniel

    2008-06-01

    Land use changes and land use intensification are considered important processes contributing to the increasing concentrations of the greenhouse gases nitrous oxide (N2O) and methane (CH4) and of nitric oxide (NO), a precursor of ozone. Studies on the effects of land use changes and land use intensification on soil trace gas emissions were mostly conducted in Latin America and only very few in Asia. Here we present results from Central Sulawesi where profound changes in land use and cultivation practices take place: traditional agricultural practices like shifting cultivation and slash-and-burn agriculture are replaced by permanent cultivation systems and introduction of income-generating cash crops like cacao. Our results showed that N2O emissions were higher from cacao agroforestry (35 ± 10 μg N m-2 h-1) than maize (9 ± 2 μg N m-2 h-1), whereas intermediate rates were observed from secondary forests (25 ± 11 μg N m-2 h-1). NO emissions did not differ among land use systems, ranging from 12 ± 2 μg N m-2 h-1 for cacao agroforestry and secondary forest to 18 ± 2 μg N m-2 h-1 for maize. CH4 uptake was higher for maize (-30 ± 4 μg C m-2 h-1) than cacao agroforestry (-18 ± 2 μg C m-2 h-1) and intermediate rates were measured from secondary forests (-25 ± 4 μg C m-2 h-1). Combining these data with results from other studies in this area, we present chronosequence effects of land use change on trace gas emissions from natural forest, through maize cultivation, to cacao agroforestry (with or without fertilizer). Compared to the original forests, this typical land use change in the study area clearly led to higher N2O emissions and lower CH4 uptake with age of cacao agroforestry systems. We conclude that this common land use sequence in the area combined with the increasing use of fertilizer will strongly increase soil trace gas emissions. We suggest that the future hot spot regions of high N2O (and to a lesser extend NO) emissions in the tropics are those

  6. Metabolic and transcriptional response of central metabolism affected by root endophytic fungus Piriformospora indica under salinity in barley.

    Science.gov (United States)

    Ghaffari, Mohammad Reza; Ghabooli, Mehdi; Khatabi, Behnam; Hajirezaei, Mohammad Reza; Schweizer, Patrick; Salekdeh, Ghasem Hosseini

    2016-04-01

    The root endophytic fungus Piriformospora indica enhances plant adaptation to environmental stress based on general and non-specific plant species mechanisms. In the present study, we integrated the ionomics, metabolomics, and transcriptomics data to identify the genes and metabolic regulatory networks conferring salt tolerance in P. indica-colonized barley plants. To this end, leaf samples were harvested at control (0 mM NaCl) and severe salt stress (300 mM NaCl) in P. indica-colonized and non-inoculated barley plants 4 weeks after fungal inoculation. The metabolome analysis resulted in an identification of a signature containing 14 metabolites and ions conferring tolerance to salt stress. Gene expression analysis has led to the identification of 254 differentially expressed genes at 0 mM NaCl and 391 genes at 300 mM NaCl in P. indica-colonized compared to non-inoculated samples. The integration of metabolome and transcriptome analysis indicated that the major and minor carbohydrate metabolism, nitrogen metabolism, and ethylene biosynthesis pathway might play a role in systemic salt-tolerance in leaf tissue induced by the root-colonized fungus. PMID:26951140

  7. Ecosystem-scale volatile organic compound fluxes during an extreme drought in a broadleaf temperate forest of the Missouri Ozarks (central USA).

    Science.gov (United States)

    Seco, Roger; Karl, Thomas; Guenther, Alex; Hosman, Kevin P; Pallardy, Stephen G; Gu, Lianhong; Geron, Chris; Harley, Peter; Kim, Saewung

    2015-10-01

    Considerable amounts and varieties of biogenic volatile organic compounds (BVOCs) are exchanged between vegetation and the surrounding air. These BVOCs play key ecological and atmospheric roles that must be adequately represented for accurately modeling the coupled biosphere-atmosphere-climate earth system. One key uncertainty in existing models is the response of BVOC fluxes to an important global change process: drought. We describe the diurnal and seasonal variation in isoprene, monoterpene, and methanol fluxes from a temperate forest ecosystem before, during, and after an extreme 2012 drought event in the Ozark region of the central USA. BVOC fluxes were dominated by isoprene, which attained high emission rates of up to 35.4 mg m(-2)  h(-1) at midday. Methanol fluxes were characterized by net deposition in the morning, changing to a net emission flux through the rest of the daylight hours. Net flux of CO2 reached its seasonal maximum approximately a month earlier than isoprenoid fluxes, which highlights the differential response of photosynthesis and isoprenoid emissions to progressing drought conditions. Nevertheless, both processes were strongly suppressed under extreme drought, although isoprene fluxes remained relatively high compared to reported fluxes from other ecosystems. Methanol exchange was less affected by drought throughout the season, confirming the complex processes driving biogenic methanol fluxes. The fraction of daytime (7-17 h) assimilated carbon released back to the atmosphere combining the three BVOCs measured was 2% of gross primary productivity (GPP) and 4.9% of net ecosystem exchange (NEE) on average for our whole measurement campaign, while exceeding 5% of GPP and 10% of NEE just before the strongest drought phase. The meganv2.1 model correctly predicted diurnal variations in fluxes driven mainly by light and temperature, although further research is needed to address model BVOC fluxes during drought events. PMID:25980459

  8. Ecosystem-scale volatile organic compound fluxes during an extreme drought in a broadleaf temperate forest of the Missouri Ozarks (central USA)

    Energy Technology Data Exchange (ETDEWEB)

    Seco, Roger [Univ. of California, Irvine, CA (United States); Karl, Thomas [Univ. of Innsbruck (Austria); Guenther, Alex B. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Washington State Univ., Pullman, WA (United States); Hosman, Kevin P. [Univ. of Missouri, Columbia, MO (United States); Pallardy, Stephen G. [Univ. of Missouri, Columbia, MO (United States); Gu, Lianhong [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Geron, Chris [U.S. Environmental Protection Agency, Research Triangle Park, NC (United States); Harley, Peter [National Center for Atmospheric Research, Boulder, CO (United States); Kim, Saewung [Univ. of California, Irvine, CA (United States)

    2015-07-07

    Considerable amounts and varieties of biogenic volatile organic compounds (BVOCs) are exchanged between vegeta-tion and the surrounding air. These BVOCs play key ecological and atmospheric roles that must be adequately repre-sented for accurately modeling the coupled biosphere–atmosphere–climate earth system. One key uncertainty in existing models is the response of BVOC fluxes to an important global change process: drought. We describe the diur-nal and seasonal variation in isoprene, monoterpene, and methanol fluxes from a temperate forest ecosystem before, during, and after an extreme 2012 drought event in the Ozark region of the central USA. BVOC fluxes were domi-nated by isoprene, which attained high emission rates of up to 35.4 mg m-2h-1 at midday. Methanol fluxes were characterized by net deposition in the morning, changing to a net emission flux through the rest of the daylight hours. Net flux of CO2 reached its seasonal maximum approximately a month earlier than isoprenoid fluxes, which high-lights the differential response of photosynthesis and isoprenoid emissions to progressing drought conditions. Never-theless, both processes were strongly suppressed under extreme drought, although isoprene fluxes remained relatively high compared to reported fluxes from other ecosystems. Methanol exchange was less affected by drought throughout the season, conflrming the complex processes driving biogenic methanol fluxes. The fraction of daytime (7–17 h) assimilated carbon released back to the atmosphere combining the three BVOCs measured was 2% of gross primary productivity (GPP) and 4.9% of net ecosystem exchange (NEE) on average for our whole measurement cam-paign, while exceeding 5% of GPP and 10% of NEE just before the strongest drought phase. The MEGANv2.1 model correctly predicted diurnal variations in fluxes driven mainly by light and temperature, although further research is needed to address model BVOC fluxes

  9. Validation of the doubly-labeled water (H/sup 3/H/sup 18/O) method for measuring water flux and energy metabolism in tenebrionid beetles

    Energy Technology Data Exchange (ETDEWEB)

    Cooper, P.D.

    1981-01-01

    Doubly-labeled water (H/sup 3/H/sup 18/O) has been used to determine water flux and energy metabolism in a variety of vertebrates. This study examines the applicability of this technique to arthropods. The theory of the technique depends upon the assumption that doubly-labeled water introduced into the animal's body water equilibrates with water and carbon dioxide by the action of carbonic anhydrase. Tritium (/sup 3/H) is lost from the animal only with water while oxygen-18 is lost with both water and carbon dioxide. The difference bwtween the rates of loss of the two isotopes is proportional to CO/sub 2/ loss rate. Validation of the use of tritiated water for measuring water flux was accomplished by comparing gravimetric measurements of water gain with flux rates determined by loss of tritiated water. At room humidity, an overestimate for influx calculated from labeled water calculations was found, averaging 12 mg H/sub 2/O (g.d)/sup -1/. Comparison of CO/sub 2/ loss rate determined isotopically with rates of CO/sub 2/ loss determined by standard metabolic rates also yielded overestimates for the isotopic technique, overestimates ranging between 20 and 30%. The relevance of this for studies using labeled water for studying water fluxes and free metabolism of free-ranging arthropods is discussed.

  10. Validation of the doubly-labeled water (H3H18O) method for measuring water flux and energy metabolism in tenebrionid beetles

    International Nuclear Information System (INIS)

    Doubly-labeled water (H3H18O) has been used to determine water flux and energy metabolism in a variety of vertebrates. This study examines the applicability of this technique to arthropods. The theory of the technique depends upon the assumption that doubly-labeled water introduced into the animal's body water equilibrates with water and carbon dioxide by the action of carbonic anhydrase. Tritium (3H) is lost from the animal only with water while oxygen-18 is lost with both water and carbon dioxide. The difference bwtween the rates of loss of the two isotopes is proportional to CO2 loss rate. Validation of the use of tritiated water for measuring water flux was accomplished by comparing gravimetric measurements of water gain with flux rates determined by loss of tritiated water. At room humidity, an overestimate for influx calculated from labeled water calculations was found, averaging 12 mg H2O (g.d)-1. Comparison of CO2 loss rate determined isotopically with rates of CO2 loss determined by standard metabolic rates also yielded overestimates for the isotopic technique, overestimates ranging between 20 and 30%. The relevance of this for studies using labeled water for studying water fluxes and free metabolism of free-ranging arthropods is discussed

  11. Interaction Between the Central and Peripheral Effects of Insulin in Controlling Hepatic Glucose Metabolism in the Conscious Dog

    OpenAIRE

    Ramnanan, Christopher J.; Kraft, Guillaume; Smith, Marta S.; Farmer, Ben; Neal, Doss; Williams, Phillip E.; Lautz, Margaret; Farmer, Tiffany; Donahue, E. Patrick; Cherrington, Alan D.; Edgerton, Dale S.

    2012-01-01

    The importance of hypothalamic insulin action to the regulation of hepatic glucose metabolism in the presence of a normal liver/brain insulin ratio (3:1) is unknown. Thus, we assessed the role of central insulin action in the response of the liver to normal physiologic hyperinsulinemia over 4 h. Using a pancreatic clamp, hepatic portal vein insulin delivery was increased three- or eightfold in the conscious dog. Insulin action was studied in the presence or absence of intracerebroventricularl...

  12. PI3K: An Attractive Candidate for the Central Integration of Metabolism and Reproduction

    OpenAIRE

    Maricedes eAcosta-Martinez

    2012-01-01

    In neurons, as in a variety of other cell types, the enzyme phosphatidylinositol-3-kinase (PI3K) is a key intermediate that is common to the signaling pathways of a number of peripheral metabolic cues, including insulin and leptin, which are well known to regulate both metabolic and reproductive functions. In this article, I explore the possibility that PI3K is a key integrator of metabolic and neural signals regulating gonadotropin releasing hormone (GnRH)/luteinizing hormone (LH) release a...

  13. Phosphorus fluxes in headwater streams draining non-research poultry-pasture operations in north-central Georgia, USA

    Science.gov (United States)

    Romeis, J. J.; Jackson, C. R.; Radcliffe, D. E.; Risse, M. L.; Bryant, J.

    2007-12-01

    Poultry production is the largest agricultural commodity in Georgia, USA. Due to inefficient utilization of the phosphorus (P) in poultry feed, the manure contains high concentrations of P. When used as fertilizer for crops and pasture, poultry manure may be washed from the soil surface and increase eutrophication risks to downstream lakes and reservoirs. Long term application of poultry manure may result in P saturation of the soils. In the upper Etowah River basin in north-central Georgia, a long history of poultry farming has resulted in high P levels in soils receiving regular poultry manure applications. Few studies to date have been performed on the estimation of P fluxes from operational commercial poultry farms in Georgia. In Fall 2006, a 20-month surface water quality monitoring program was completed that was aimed at estimating P and suspended sediment fluxes in nine headwater streams draining poultry-pasture operations in the upper Etowah River basin. The nine catchments differed in terms of land use history, soil P levels, best management practices and other factors. An additional three streams draining U.S. National Forest were also monitored to provide reference concentrations and loads. Monitoring data included continuous (5-minute) streamflow, rainfall, and water quality samples. Water quality samples included biweekly grab samples plus storm samples collected using conventional autosamplers. Storm sampling using autosamplers included collection of discrete samples and composite samples. In particular instances, the two types of storm sample were collected simultaneously. Discrete storm sampling methods enabled collection of both rising and falling hydrograph limb samples to identify potential hysteretic water quality effects. Water samples were analyzed for total P, filterable reactive P, and total suspended solids. We are using this data to compare different flux estimation methods with emphasis on regression models that utilize laboratory results

  14. Anaerobic central metabolic pathways active during polyhydroxyalkanoate production in uncultured cluster 1 Defluviicoccus enriched in activated sludge communities.

    Science.gov (United States)

    Burow, Luke C; Mabbett, Amanda N; Borrás, Luis; Blackall, Linda L

    2009-09-01

    A glycogen nonpolyphosphate-accumulating organism (GAO) enrichment culture dominated by the Alphaproteobacteria cluster 1 Defluviicoccus was investigated to determine the metabolic pathways involved in the anaerobic formation of polyhydroxyalkanoates, carbon storage polymers important for the proliferation of microorganisms in enhanced biological phosphorus removal processes. FISH-microautoradiography and post-FISH fluorescent chemical staining confirmed acetate assimilation as polyhydroxyalkanoates in cluster 1 Defluviicoccus under anaerobic conditions. Chemical inhibition of glycolysis using iodoacetate, and of isocitrate lyase by 3-nitropropionate and itaconate, indicated that carbon is likely to be channelled through both glycolysis and the glyoxylate cycle in cluster 1 Defluviicoccus. The effect of metabolic inhibitors of aconitase (monofluoroacetate) and succinate dehydrogenase (malonate) suggested that aconitase, but not succinate dehydrogenase, was active, providing further support for the role of the glyoxylate cycle in these GAOs. Metabolic inhibition of fumarate reductase using oxantel decreased polyhydroxyalkanoate production. This indicated reduction of fumarate to succinate and the operation of the reductive branch of the tricarboxylic acid cycle, which is possibly important in the production of the polyhydroxyvalerate component of polyhydroxyalkanoates observed in cluster 1 Defluviicoccus enrichment cultures. These findings were integrated with previous metabolic models for GAOs and enabled an anaerobic central metabolic pathway model for polyhydroxyalkanoate formation in cluster 1 Defluviicoccus to be proposed. PMID:19622073

  15. Equilibrium temperature as a parameter for estimating the net heat-flux at the air-sea interface in the central red-sea

    OpenAIRE

    Ahmad, F; Sultan, Sar

    1994-01-01

    The net rate of heat exchange at the water surface in the central Red Sea is calculated with reference to the equilibrium temperature and the thermal exchange coefficient, both of which depend on meteorological variables. The monthly means of this exchange agree well with the values computed on the basis of heat balance processes which include sensible, evaporative and radiative heat fluxes.

  16. PI3K: An attractive candidate for the central integration of metabolism and reproduction

    Directory of Open Access Journals (Sweden)

    Maricedes eAcosta-Martinez

    2012-01-01

    Full Text Available In neurons, as in a variety of other cell types, the enzyme phosphatidylinositol-3-kinase (PI3K is a key intermediate that is common to the signaling pathways of a number of peripheral metabolic cues, including insulin and leptin, which are well known to regulate both metabolic and reproductive functions. In this article, I explore the possibility that PI3K is a key integrator of metabolic and neural signals regulating gonadotropin releasing hormone (GnRH/luteinizing hormone (LH release and explore the hypothesis that this enzyme is pivotal in many disorders where gonadotropin release is at risk. Although the mechanisms mediating the influence of metabolism and nutrition on fertility are currently unclear, the strong association between metabolic disorders and infertility is undeniable. For example, women suffering from anorectic disorders experience amenorrhea as a consequence of malnutrition-induced impairment of LH release, and at the other extreme, obesity is also commonly co-morbid with menstrual dysfunction and infertility. Impaired hypothalamic insulin and leptin receptor signaling is thought to be at the core of reproductive disorders associated with metabolic dysfunction. While low levels of leptin and insulin characterize states of negative energy balance, prolonged nutrient excess is associated with insulin and leptin resistance. Metabolic models known to alter GnRH/LH release such as diabetes, diet-induced obesity, and caloric restriction are also accompanied by impairment of PI3K signaling in insulin and leptin sensitive tissues including the hypothalamus. However, a clear link between this signaling pathway and the control of GnRH release by peripheral metabolic cues has not been established. Investigating the role of the signaling pathways shared by metabolic cues that are critical for a normal reproductive state can help identify possible targets in the treatment of metabolic and reproductive disorders such as Polycystic Ovarian

  17. Localized Climate and Surface Energy Flux Alterations across an Urban Gradient in the Central U.S.

    Directory of Open Access Journals (Sweden)

    Jason A. Hubbart

    2014-03-01

    Full Text Available Long-term urban and rural climate data spanning January 1995 through October 2013 were analyzed to investigate the Urban Heat Island (UHI effect in a representative mid-sized city of the central US. Locally distributed climate data were also collected at nested low density urban, recently developed, and high density urban monitoring sites from June through September 2013 to improve mechanistic understanding of spatial variability of the UHI effect based upon urban land use intensity. Long-term analyses (1995–2013 indicate significant differences (p < 0.001 between average air temperature (13.47 and 12.89 °C, at the urban and rural site respectively, relative humidity (69.11% and 72.51%, urban and rural respectively, and average wind speed (2.05 and 3.15 m/s urban and rural respectively. Significant differences (p < 0.001 between urban monitoring sites indicate an urban microclimate gradient for all climate variables except precipitation. Results of analysis of net radiation and soil heat flux data suggest distinct localized alterations in urban energy budgets due to land use intensity. Study results hold important implications for urban planners and land managers seeking to improve and implement better urban management practices. Results also reinforce the need for distributed urban energy balance investigations.

  18. Redirection of metabolic flux for high levels of omega-7 monounsaturated fatty acid accumulation in camelina seeds.

    Science.gov (United States)

    Nguyen, Huu Tam; Park, Hyunwoo; Koster, Karen L; Cahoon, Rebecca E; Nguyen, Hanh T M; Shanklin, John; Clemente, Thomas E; Cahoon, Edgar B

    2015-01-01

    Seed oils enriched in omega-7 monounsaturated fatty acids, including palmitoleic acid (16:1∆9) and cis-vaccenic acid (18:1∆11), have nutraceutical and industrial value for polyethylene production and biofuels. Existing oilseed crops accumulate only small amounts (camelina (Camelina sativa) and soybean (Glycine max) that is dependent on redirection of metabolic flux from the typical ∆9 desaturation of stearoyl (18:0)-acyl carrier protein (ACP) to ∆9 desaturation of palmitoyl (16:0)-acyl carrier protein (ACP) and coenzyme A (CoA). This was achieved by seed-specific co-expression of a mutant ∆9-acyl-ACP and an acyl-CoA desaturase with high specificity for 16:0-ACP and CoA substrates, respectively. This strategy was most effective in camelina where seed oils with ~17% omega-7 monounsaturated fatty acids were obtained. Further increases in omega-7 fatty acid accumulation to 60-65% of the total fatty acids in camelina seeds were achieved by inclusion of seed-specific suppression of 3-keto-acyl-ACP synthase II and the FatB 16:0-ACP thioesterase genes to increase substrate pool sizes of 16:0-ACP for the ∆9-acyl-ACP desaturase and by blocking C18 fatty acid elongation. Seeds from these lines also had total saturated fatty acids reduced to ~5% of the seed oil versus ~12% in seeds of nontransformed plants. Consistent with accumulation of triacylglycerol species with shorter fatty acid chain lengths and increased monounsaturation, seed oils from engineered lines had marked shifts in thermotropic properties that may be of value for biofuel applications. PMID:25065607

  19. Co-utilization of glucose and xylose by evolved Thermus thermophilus LC113 strain elucidated by (13)C metabolic flux analysis and whole genome sequencing.

    Science.gov (United States)

    Cordova, Lauren T; Lu, Jing; Cipolla, Robert M; Sandoval, Nicholas R; Long, Christopher P; Antoniewicz, Maciek R

    2016-09-01

    We evolved Thermus thermophilus to efficiently co-utilize glucose and xylose, the two most abundant sugars in lignocellulosic biomass, at high temperatures without carbon catabolite repression. To generate the strain, T. thermophilus HB8 was first evolved on glucose to improve its growth characteristics, followed by evolution on xylose. The resulting strain, T. thermophilus LC113, was characterized in growth studies, by whole genome sequencing, and (13)C-metabolic flux analysis ((13)C-MFA) with [1,6-(13)C]glucose, [5-(13)C]xylose, and [1,6-(13)C]glucose+[5-(13)C]xylose as isotopic tracers. Compared to the starting strain, the evolved strain had an increased growth rate (~2-fold), increased biomass yield, increased tolerance to high temperatures up to 90°C, and gained the ability to grow on xylose in minimal medium. At the optimal growth temperature of 81°C, the maximum growth rate on glucose and xylose was 0.44 and 0.46h(-1), respectively. In medium containing glucose and xylose the strain efficiently co-utilized the two sugars. (13)C-MFA results provided insights into the metabolism of T. thermophilus LC113 that allows efficient co-utilization of glucose and xylose. Specifically, (13)C-MFA revealed that metabolic fluxes in the upper part of metabolism adjust flexibly to sugar availability, while fluxes in the lower part of metabolism remain relatively constant. Whole genome sequence analysis revealed two large structural changes that can help explain the physiology of the evolved strain: a duplication of a chromosome region that contains many sugar transporters, and a 5x multiplication of a region on the pVV8 plasmid that contains xylose isomerase and xylulokinase genes, the first two enzymes of xylose catabolism. Taken together, (13)C-MFA and genome sequence analysis provided complementary insights into the physiology of the evolved strain. PMID:27164561

  20. Metabolism

    Science.gov (United States)

    ... a particular food provides to the body. A chocolate bar has more calories than an apple, so ... More Common in People With Type 1 Diabetes Metabolic Syndrome Your Child's Weight Healthy Eating Endocrine System Blood ...

  1. Role of mesoscale eddies on the variability of biogenic flux in the northern and central Bay of Bengal

    Digital Repository Service at National Institute of Oceanography (India)

    Vidya, P.J.; PrasannaKumar, S.

    15 m with spatial resolution of 1o x 1o [Bonjean and Lagerloef, 2002]. 3 Results 3.1 Biogenic flux The time-series of biogenic flux at NBBT during the period 1994 February to 1998 November is presented in Figure 2a (black line). Biogenic flux... with low SSHA (Figure 2, black line). Interestingly, at both the locations, all the peaks in the biogenic flux showed an inverse relation with SSHA (negative). This indicates that biogenic flux at both the locations is someway related to negative SSHA...

  2. 13C-metabolic flux ratio and novel carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose

    Directory of Open Access Journals (Sweden)

    Saloheimo Markku

    2009-10-01

    Full Text Available Abstract Background The filamentous fungus Trichoderma reesei is an important host organism for industrial enzyme production. It is adapted to nutrient poor environments where it is capable of producing large amounts of hydrolytic enzymes. In its natural environment T. reesei is expected to benefit from high energy yield from utilization of respirative metabolic pathway. However, T. reesei lacks metabolic pathway reconstructions and the utilization of the respirative pathway has not been investigated on the level of in vivo fluxes. Results The biosynthetic pathways of amino acids in T. reesei supported by genome-level evidence were reconstructed with computational carbon path analysis. The pathway reconstructions were a prerequisite for analysis of in vivo fluxes. The distribution of in vivo fluxes in both wild type strain and cre1, a key regulator of carbon catabolite repression, deletion strain were quantitatively studied by performing 13C-labeling on both repressive carbon source glucose and non-repressive carbon source sorbitol. In addition, the 13C-labeling on sorbitol was performed both in the presence and absence of sophorose that induces the expression of cellulase genes. Carbon path analyses and the 13C-labeling patterns of proteinogenic amino acids indicated high similarity between biosynthetic pathways of amino acids in T. reesei and yeast Saccharomyces cerevisiae. In contrast to S. cerevisiae, however, mitochondrial rather than cytosolic biosynthesis of Asp was observed under all studied conditions. The relative anaplerotic flux to the TCA cycle was low and thus characteristic to respiratory metabolism in both strains and independent of the carbon source. Only minor differences were observed in the flux distributions of the wild type and cre1 deletion strain. Furthermore, the induction of the hydrolytic gene expression did not show altered flux distributions and did not affect the relative amino acid requirements or relative anabolic

  3. Central and Metabolic Effects of High Fructose Consumption: Evidence from Animal and Human Studies

    OpenAIRE

    Alexandra Stoianov; Khosrow Adeli

    2014-01-01

    Fructose consumption has increased dramatically in the last 40 years, and its role in the pathogenesis of the metabolic syndrome has been implicated by many studies. It is most often encountered in the diet as sucrose (glucose and fructose) or high-fructose corn syrup (55% fructose). At high levels, dietary exposure to fructose triggers a series of metabolic changes originating in the liver, leading to hepatic steatosis, hypertriglyceridemia, insulin resistance, and decreased leptin sensitivi...

  4. Central nervous system: a conductor orchestrating metabolic regulations harmed by both hyperglycaemia and hypoglycaemia.

    OpenAIRE

    Scheen, André

    2010-01-01

    Recent evidence suggests that the brain has a key role in the control of energy metabolism, body fat content and glucose metabolism. Neuronal systems, which regulate energy intake, energy expenditure, and endogenous glucose production, sense and respond to input from hormonal and nutrient-related signals that convey information regarding both body energy stores and current energy availability. In response to this input, adaptive changes occur that promote energy homeostasis and the maintenanc...

  5. A simplified method for power-law modelling of metabolic pathways from time-course data and steady-state flux profiles

    Directory of Open Access Journals (Sweden)

    Sugimoto Masahiro

    2006-07-01

    Full Text Available Abstract Background In order to improve understanding of metabolic systems there have been attempts to construct S-system models from time courses. Conventionally, non-linear curve-fitting algorithms have been used for modelling, because of the non-linear properties of parameter estimation from time series. However, the huge iterative calculations required have hindered the development of large-scale metabolic pathway models. To solve this problem we propose a novel method involving power-law modelling of metabolic pathways from the Jacobian of the targeted system and the steady-state flux profiles by linearization of S-systems. Results The results of two case studies modelling a straight and a branched pathway, respectively, showed that our method reduced the number of unknown parameters needing to be estimated. The time-courses simulated by conventional kinetic models and those described by our method behaved similarly under a wide range of perturbations of metabolite concentrations. Conclusion The proposed method reduces calculation complexity and facilitates the construction of large-scale S-system models of metabolic pathways, realizing a practical application of reverse engineering of dynamic simulation models from the Jacobian of the targeted system and steady-state flux profiles.

  6. Glutamate metabolism of astrocytes during hyperbaric oxygen exposure and its effects on central nervous system oxygen toxicity.

    Science.gov (United States)

    Chen, Yu-Liang; Li, Dan; Wang, Zhong-Zhuang; Xu, Wei-Gang; Li, Run-Ping; Zhang, Jun-Dong

    2016-01-20

    Hyperbaric oxygen (HBO) has been used widely in many underwater missions and clinical work. However, exposure to extremely high oxygen pressure may cause central nervous system oxygen toxicity (CNS-OT). The regulation of astrocyte glutamate metabolism is closely related to epilepsy. This study aimed to observe the effects of HBO exposure on glutamate metabolism in astrocytes and confirm the role of glutamate metabolism in CNS-OT. Anesthetized rats were exposed to 5 atmosphere absolute HBO for 80 min and microdialysis samples of brain interstitial fluid were continuously collected. Extracellular glutamate and glutamine concentrations were also detected. Freely moving rats were exposed to HBO of the same pressure for 20 min and glutamine synthetase (GS) activity in brain tissues was measured. Finally, we observed the effects of different doses of drugs related to glutamate metabolism on the latency of CNS-OT. Results showed that HBO exposure significantly increased glutamate content, whereas glutamine content was significantly reduced. Moreover, HBO exposure significantly reduced GS activity. Glutamate transporter-1 (GLT-1) selective antagonist ceftriaxone prolonged CNS-OT latency, whereas GLT-1 selective inhibitor dihydrokainate shortened CNS-OT latency. In summary, HBO exposure improved glutamate concentration and reduced glutamine concentration by inhibition of GS activity. GLT-1 activation also participated in the prevention of HBO-induced CNS-OT. Our research will provide a potential new target to terminate or attenuate CNS-OT. PMID:26619231

  7. Suppression of the External MitochondrialNADPH Dehydrogenase, NDB1, in Arabidopsisthaliana Affects Central Metabolism andVegetative Growth

    Institute of Scientific and Technical Information of China (English)

    2014-01-01

    Ca2+-dependent oxidation of cytosolic NADPH is mediated by NDB1, which is an external type II NADPHdehydrogenase in the plant mitochondrial electron transport chain. Using RNA interference, the NDB1 transcript wassuppressed by 80% in Arabidopsis thaliana plants, and external Ca2+-dependent NADPH dehydrogenase activity becameundetectable in isolated mitochondria. This was linked to a decreased level of NADP+ in rosettes of the transgenic lines.Sterile-grown transgenic seedlings displayed decreased growth specifically on glucose, and respiratory metabolism of 14C-glucose was increased. On soil, NDBl-suppressing plants had a decreased vegetative biomass, but leaf maximumquantum efficiency of photosystem Ⅱ and CO2 assimilation rates, as well as total respiration, were similar to the wild-type. The in vivo alternative oxidase activity and capacity were also similar in all genotypes. Metabolic profiling revealeddecreased levels of sugars, citric acid cycle intermediates, and amino acids in the transgenic lines. The NDBl-suppressioninduced transcriptomic changes associated with protein synthesis and glucosinolate and jasmonate metabolism. Thetranscriptomic changes also overlapped with changes observed in a mutant lacking ABAINSENSITIVE4 and in A. thalianaoverexpressing stress tolerance genes from rice. The results thus indicate that A. thaliana NDB1 modulates NADP(H)reduction levels, which in turn affect central metabolism and growth, and interact with defense signaling.

  8. Burial fluxes and sources of organic carbon in sediments of the central Yellow Sea mud area over the past 200 years

    Institute of Scientific and Technical Information of China (English)

    YANG Shu; YANG Qian; LIU Sai; CAI Deling; QU Keming; SUN Yao

    2015-01-01

    Long-term changes of composition, sources and burial fluxes of TOC (total organic carbon) in sediments of the central Yellow Sea mud area and their possible affecting factors are discussed in this paper. Firstly, similarity analysis is employed to confirm that the carbon burial features resulted from two collected cores are typical in the central Yellow Sea mud area where YSWC (Yellow Sea Warm Current) is prevalent. On this basis, the burial flux of TOC here was considered to be 235.5–488.4 μmol/(cm2∙a) since the first industrial revolution, accounting for about 70%–90% among burial fluxes of TC (total carbon) in the sediments. Compared TOC/TC ratio in the two cores with that in other marine sediments worldwide, we suggest that the growth of calcareous/non-calcareous organisms and dissolution of IC (inorganic carbon) are important factors controlling the TOC/TC ratio in sediment. Results of two-end mixed model based onδ13C data indicate that marine-derived organic carbon (OCa) is the main part among total burial organic carbon which accounts for a ratio over 85%. Due to the high TOC/TC ratio in the two cores, TC in the sediments also mainly exists as OCa, and the proportion of OCa is about 60%–80%. Away from the shore and relatively high primary production in upper waters are the main reasons that OCa is predominant among all burial OC in sediments of the central Yellow Sea mud area. Burial of OC in this mud area is probably mainly influenced by the human activities. Although the economic development during the late 19th century caused by the first industrial revolution in China did not obviously increase the TOC burial fluxes in the sediments, the rise of industry and agriculture after the founding of new China has clearly increased the TOC burial flux since 1950s. Otherwise, we also realize that among TC burial fluxes, TIC account for about 10%–30% in sediments of the central Yellow Sea mud area, so its burial could not be simply ignored here

  9. ToMI-FBA: A genome-scale metabolic flux based algorithm to select optimum hosts and media formulations for expressing pathways of interest

    Directory of Open Access Journals (Sweden)

    Hadi Nazem-Bokaee

    2015-09-01

    Full Text Available The Total Membrane Influx constrained Flux Balance Analysis (ToMI-FBA algorithm was developed in this research as a new tool to help researchers decide which microbial host and medium formulation are optimal for expressing a new metabolic pathway. ToMI-FBA relies on genome-scale metabolic flux modeling and a novel in silico cell membrane influx constraint that specifies the flux of atoms (not molecules into the cell through all possible membrane transporters. The ToMI constraint is constructed through the addition of an extra row and column to the stoichiometric matrix of a genome-scale metabolic flux model. In this research, the mathematical formulation of the ToMI constraint is given along with four case studies that demonstrate its usefulness. In Case Study 1, ToMI-FBA returned an optimal culture medium formulation for the production of isobutanol from Bacillus subtilis. Significant levels of L-valine were recommended to optimize production, and this result has been observed experimentally. In Case Study 2, it is demonstrated how the carbon to nitrogen uptake ratio can be specified as an additional ToMI-FBA constraint. This was investigated for maximizing medium chain length polyhydroxyalkanoates (mcl-PHA production from Pseudomonas putida KT2440. In Case Study 3, ToMI-FBA revealed a strategy of adding cellobiose as a means to increase ethanol selectivity during the stationary growth phase of Clostridium acetobutylicum ATCC 824. This strategy was also validated experimentally. Finally, in Case Study 4, B. subtilis was identified as a superior host to Escherichia coli, Saccharomyces cerevisiae, and Synechocystis PCC6803 for the production of artemisinate.

  10. Flow Cytometry Analysis of Pparα Receptors in Metabolic Syndrome / Studiul Receptorilor Pparα prin Metoda Citometriei în Flux în Sindromul Metabolic

    Directory of Open Access Journals (Sweden)

    Popa Elena

    2014-12-01

    Full Text Available Introducere. Sindromul metabolic (SM reprezintă o asociere de alterări metabolice independente cu risc cardiovascular crescut. Receptorii activați de inductorii proliferării peroxizomilor-alpha (PPARα, membri ai superfamiliei receptorilor nucleari cu rol de factori de transcripţie , sunt implicați în reglarea metabolismului lipidic și inflamație în diferite tipuri de celule și reprezintă una din țintele terapeutice în SM. Am analizat expresia PPARα în leucocitele pacienților cu SM, îndreptându-ne spre implicarea PPARα în această patologie. Material și metoda. Studiul s-a desfășurat pe un număr de 57 pacienți adulți recrutați după semnarea consimțământului informat, investigați pentru evidențierea SM conform criteriilor Federației Internaționale de Diabet (IDF și care au fost grupați în două loturi: lotul SM (26 pacienți și lotul de control, fără SM (31 subiecți. Au fost determinați parametrii clinici și de laborator utilizați curent în evaluarea SM. În populațiile de leucocite circulante ale pacienților au fost evaluate nivelurile de expresie a două molecule, PPARα și CD36, printr-o metodă optimizată de citometrie în flux . Semnificația diferențelor dintre valorile parametrilor măsurați a fost stabilită prin analiza statistică, utilizând programul SPSS și teste statistice simple (Pearson, t-Student, Chi-test. Rezultate și discuții. Când am comparat nivelul de expresie a PPARα în eozinofile, am obținut a reducere semnificativă a intensității medie de fluorescență (p<0.05 pentru PPARα în lotul MS versus lotul martor. Concluzii. Studiul nostru este primul care arată că nivelul de expresie a PPARα în eozinofile este diminuat semnificativ la pacienții cu SM. Diferențele de expresie ale acestor molecule cheie în leucocitele circulante (ca diferite specii de PPAR, CD36 și altele ar putea deveni evocatoare pentru disfuncția endotelială și obezitate și ar putea

  11. Differential metabolic rates among the school going boys of a Central Indian Town (Sagar

    Directory of Open Access Journals (Sweden)

    R. Thakur

    2016-05-01

    Full Text Available The prime objective of the present study was to estimate the basal metabolic rate (BMR and resting metabolic rate (RMR among school going boys of 5-18 year of age. The subjects were recruited from government schools of Sagar town of Madhya Pradesh state of Indian Union. Height and weight of the boys were measured using standard anthropometric techniques. Body mass index (BMI and metabolic rates (BMR/RMR were computed for each individual. It was found that mean of BMI varies from 13.8±1.6 Kg m- 2 among boys of 8 year of age to 19.0±1.9 Kg m- 2 among boys of 17 year of age. Similarly, mean of Basal metabolic rate (BMR varies from 1219.0±106.9 K cal/day among boys aged 5 year of age to 2296.3±255.9 K cal/day among 17 year of age. Pre pubertal and pubertal boys have significant difference in their basal metabolic rates as well as stunted, underweight and undernourished boys have significant low BMR. The linear bivariate regression analysis shows that the BMR is dependent on BMI, weight and height. The RMR have highest regression coefficient (r2=0.935 on BMR, followed by Height (r2=0.664, weight (r2=0.631 and body mass index (r2=0.368. The similar trends can be seen for RMR also. The BMR is highly dependent on RMR followed by height, weight and BMI.

  12. In-situ measurement of concentrated solar flux and distribution at the aperture of a central solar receiver

    Science.gov (United States)

    Ferriere, Alain; Volut, Mikael; Perez, Antoine; Volut, Yann

    2016-05-01

    A flux mapping system has been designed, implemented and experimented at the top of the Themis solar tower in France. This system features a moving bar associated to a CCD video camera and a flux gauge mounted onto the bar used as reference measurement for calibration purpose. Images and flux signal are acquired separately. The paper describes the equipment and focus on the data processing to issue the distribution of flux density and concentration at the aperture of the solar receiver. Finally, the solar power entering into the receiver is estimated by integration of flux density. The processing is largely automated in the form of a dedicated software with fast execution. A special attention is paid to the accuracy of the results, to the robustness of the algorithm and to the velocity of the processing.

  13. Metabolic syndrome in the rural population of Wardha, Central India: An exploratory factor analysis

    Directory of Open Access Journals (Sweden)

    Pradeep R Deshmukh

    2013-01-01

    Full Text Available Background and Objectives: Metabolic syndrome - a plausible precondition for type II diabetes and cardiovascular diseases is also on rise. To understand the mechanistic complexity of metabolic syndrome it is imperative to study the specific contribution of the determinants of metabolic syndrome. Such study can help to identify the most significant factor which may be of use in early detection as well as prevention efforts. Such information is scarcely available from India and especially from rural India. Hence, the present study was undertaken to explore for such factor which might be considered crucial for development of such pathogenesis particularly in rural population of Wardha. Methods: A cross-sectional study comprising of 300 subjects was carried out in rural area of Primary Health Center, attached to medical college with approximate 31,000 populations. The anthropometric parameters such as height, weight, waist circumference were measured. Overnight fasting samples were collected for lipid profile (total cholesterol, triglyceride, high density lipoproteins, low density lipoproteins, very low density lipoproteins and fasting blood glucose levels. The National Cholesterol Education Programme Adult Treatment Panel, ATP-III guidelines were used to categorize the study subjects. As many of the variables are highly intercorrelated, exploratory factor analysis was carried out to reduce the data to a smaller number of independent factors that accounts for the most of the variances in the data. Principal component analysis was used as a method of extraction. Results: For both sexes, three factors were extracted accounting for about 71% variance in the measured variables. An adiposity factor which accounted for highest explained variance (28%, was the initial factor extracted. It was loaded positively by waist circumference, triglyceride, and very low density lipoprotein and negatively loaded by high density lipoprotein. Second factor extracted

  14. Flux control exerted by mitochondrial outer membrane carnitine palmitoyltransferase over beta-oxidation, ketogenesis and tricarboxylic acid cycle activity in hepatocytes isolated from rats in different metabolic states.

    Science.gov (United States)

    Drynan, L; Quant, P A; Zammit, V A

    1996-01-01

    The Flux Control Coefficients of mitochondrial outer membrane carnitine palmitoyltransferase (CPT I) with respect to the overall rates of beta-oxidation, ketogenesis and tricarboxylic acid cycle activity were measured in hepatocytes isolated from rats in different metabolic states (fed, 24 h-starved, starved-refed and starved/insulin-treated). These conditions were chosen because there is controversy as to whether, when significant control ceases to be exerted by CPT I over the rate of fatty oxidation [Moir and Zammit (1994) Trends Biochem. Sci. 19, 313-317], this is transferred to one or more steps proximal to acylcarnitine synthesis (e.g. decreased delivery of fatty acids to the liver) or to the reaction catalysed by mitochondrial 3-hydroxy-3-methyl-glutaryl-CoA synthase [Hegardt (1995) Biochem. Soc. Trans. 23, 486-490]. Therefore isolated hepatocytes were used in the present study to exclude the involvement of changes in the rate of delivery of non-esterified fatty acids (NEFA) to the liver, such as occur in vivo, and to ascertain whether, under conditions of constant supply of NEFA, CPT I retains control over the relevant fluxes of fatty acid oxidation to ketones and carbon dioxide, or whether control is transferred to another (intrahepatocytic) site. The results clearly show that the Flux Control Coefficients of CPT I with respect to overall beta-oxidation and ketogenesis are very high under all conditions investigated, indicating that control is not lost to another intrahepatic site during the metabolic transitions studied. The control of CPT I over tricarboxylic acid cycle activity was always very low. The significance of these findings for the integration of fatty acid and carbohydrate metabolism in the liver is discussed. PMID:8760364

  15. Photobioreactor design for isotopic non-stationary 13C-metabolic flux analysis (INST 13C-MFA) under photoautotrophic conditions.

    Science.gov (United States)

    Martzolff, Arnaud; Cahoreau, Edern; Cogne, Guillaume; Peyriga, Lindsay; Portais, Jean-Charles; Dechandol, Emmanuel; Le Grand, Fabienne; Massou, Stéphane; Gonçalves, Olivier; Pruvost, Jérémy; Legrand, Jack

    2012-12-01

    Adaptive metabolic behavior of photoautotrophic microorganisms toward genetic and environmental perturbations can be interpreted in a quantitative depiction of carbon flow through a biochemical reaction network using isotopic non-stationary (13) C-metabolic flux analysis (INST (13) C-MFA). To evaluate (13) C-metabolic flux maps for Chlamydomonas reinhardtii, an original experimental framework was designed allowing rapid, reliable collection of high-quality isotopomer data against time. It involved (i) a short-time (13) C labeling injection device based on mixing control in a torus-shaped photobioreactor with plug-flow hydrodynamics allowing a sudden step-change in the (13) C proportion in the substrate feed and (ii) a rapid sampling procedure using an automatic fast filtration method coupled to a manual rapid liquid nitrogen quenching step. (13) C-substrate labeling enrichment was controlled through the total dissolved inorganic carbon concentration in the pulsed solution. First results were obtained from steady-state continuous culture measurements allowing the characterization of the kinetics of label incorporation into light-limited growing cells cultivated in a photobioreactor operating at the maximal biomass productivity for an incident photon flux density of 200 µmol m(-2) s(-1). (13)C label incorporation was measured for 21 intracellular metabolites using IC-MS/MS in 58 samples collected across a labeling experiment duration of 7 min. The fastest labeling rate was observed for 2/3-phosphoglycerate with an apparent isotopic stationary state reached after 300 s. The labeling rate was consistent with the optimized mixing time of about 4.9 s inside the reactor and the shortest reliable sampling period assessed at 5 s. PMID:22688667

  16. Enzyme oscillation can enhance the thermodynamic efficiency of cellular metabolism: consequence of anti-phase coupling between reaction flux and affinity

    Science.gov (United States)

    Himeoka, Yusuke; Kaneko, Kunihiko

    2016-04-01

    Cells generally convert nutrient resources to products via energy transduction. Accordingly, the thermodynamic efficiency of this conversion process is one of the most essential characteristics of living organisms. However, although these processes occur under conditions of dynamic metabolism, most studies of cellular thermodynamic efficiency have been restricted to examining steady states; thus, the relevance of dynamics to this efficiency has not yet been elucidated. Here, we develop a simple model of metabolic reactions with anabolism–catabolism coupling catalyzed by enzymes. Through application of external oscillation in the enzyme abundances, the thermodynamic efficiency of metabolism was found to be improved. This result is in strong contrast with that observed in the oscillatory input, in which the efficiency always decreased with oscillation. This improvement was effectively achieved by separating the anabolic and catabolic reactions, which tend to disequilibrate each other, and taking advantage of the temporal oscillations so that each of the antagonistic reactions could progress near equilibrium. In this case, anti-phase oscillation between the reaction flux and chemical affinity through oscillation of enzyme abundances is essential. This improvement was also confirmed in a model capable of generating autonomous oscillations in enzyme abundances. Finally, the possible relevance of the improvement in thermodynamic efficiency is discussed with respect to the potential for manipulation of metabolic oscillations in microorganisms.

  17. Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica

    DEFF Research Database (Denmark)

    Kerkhoven, Eduard J.; Pomraning, Kyle R.; Baker, Scott E.; Nielsen, Jens

    2016-01-01

    Yarrowia lipolytica is a promising microbial cell factory for the production of lipids to be used as fuels and chemicals, but there are few studies on regulation of its metabolism. Here we performed the first integrated data analysis of Y. lipolytica grown in carbon and nitrogen limited chemostat...... is similar to the overflow metabolism observed in many other microorganisms, e.g. ethanol production by Sacchromyces cerevisiae at nitrogen limitation....

  18. Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus

    Directory of Open Access Journals (Sweden)

    Kovaleva Galina

    2011-06-01

    Full Text Available Abstract Background Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in bacteria is one of the critical tasks of modern genomics. The Shewanella genus is comprised of metabolically versatile gamma-proteobacteria, whose lifestyles and natural environments are substantially different from Escherichia coli and other model bacterial species. The comparative genomics approaches and computational identification of regulatory sites are useful for the in silico reconstruction of transcriptional regulatory networks in bacteria. Results To explore conservation and variations in the Shewanella transcriptional networks we analyzed the repertoire of transcription factors and performed genomics-based reconstruction and comparative analysis of regulons in 16 Shewanella genomes. The inferred regulatory network includes 82 transcription factors and their DNA binding sites, 8 riboswitches and 6 translational attenuators. Forty five regulons were newly inferred from the genome context analysis, whereas others were propagated from previously characterized regulons in the Enterobacteria and Pseudomonas spp.. Multiple variations in regulatory strategies between the Shewanella spp. and E. coli include regulon contraction and expansion (as in the case of PdhR, HexR, FadR, numerous cases of recruiting non-orthologous regulators to control equivalent pathways (e.g. PsrA for fatty acid degradation and, conversely, orthologous regulators to control distinct pathways (e.g. TyrR, ArgR, Crp. Conclusions We tentatively defined the first reference collection of ~100 transcriptional regulons in 16 Shewanella genomes. The resulting regulatory network contains ~600 regulated genes per genome that are mostly involved in metabolism of carbohydrates, amino acids, fatty acids, vitamins, metals, and stress responses. Several reconstructed regulons including NagR for N-acetylglucosamine catabolism were experimentally validated in S

  19. Role of central nervous system in acute radiation syndrome functional metabolic encephalopathy

    International Nuclear Information System (INIS)

    In adult rabbit, the effect on the brain of a whole-body or encephalic gamma irradiation is a function of the absorbed dose and begins after 25 rads. Three phases are described in the mechanism of radiation effect. In the initial phase, irradiation acts as a direct stimulus of cerebral structures. The second phase is a response towards aggression which includes: the effect of stimulation of various cerebral structures; their response and the induced feed-back mechanism; the release of metabolites inducing a functional metabolic encephalopathy in which occur: modification of blood pressure; modification of pulmonary ventilation; modification of acido-basic blood equilibrium. The third phase consists of functional recovery

  20. Context-dependent metabolic networks

    CERN Document Server

    Beguerisse-Díaz, Mariano; Oyarzún, Diego; Picó, Jesús; Barahona, Mauricio

    2016-01-01

    Cells adapt their metabolism to survive changes in their environment. We present a framework for the construction and analysis of metabolic reaction networks that can be tailored to reflect different environmental conditions. Using context-dependent flux distributions from Flux Balance Analysis (FBA), we produce directed networks with weighted links representing the amount of metabolite flowing from a source reaction to a target reaction per unit time. Such networks are analyzed with tools from network theory to reveal salient features of metabolite flows in each biological context. We illustrate our approach with the directed network of the central carbon metabolism of Escherichia coli, and study its properties in four relevant biological scenarios. Our results show that both flow and network structure depend drastically on the environment: networks produced from the same metabolic model in different contexts have different edges, components, and flow communities, capturing the biological re-routing of metab...

  1. Lysine Malonylome May Affect the Central Metabolism and Erythromycin Biosynthesis Pathway in Saccharopolyspora erythraea.

    Science.gov (United States)

    Xu, Jun-Yu; Xu, Zhen; Zhou, Ying; Ye, Bang-Ce

    2016-05-01

    Lysine acylation is a dynamic, reversible post-translational modification that can regulate cellular and organismal metabolism in bacteria. Acetylome has been studied well in bacteria. However, to our knowledge, there are no proteomic data on the lysine malonylation in prokaryotes, especially in actinomycetes, which are the major producers of therapeutic antibiotics. In our study, the first malonylome of the erythromycin-producing Saccharopolyspora erythraea was described by using a high-resolution mass spectrometry-based proteomics approach and high-affinity antimalonyllysine antibodies. We identified 192 malonylated sites on 132 substrates. Malonylated proteins are enriched in many biological processes such as protein synthesis, glycolysis and gluconeogenesis, the TCA cycle, and the feeder metabolic pathways of erythromycin synthesis according to GO analysis and KEGG pathway analysis. A total of 238 S/T/Y/H-phosphorylated sites on 158 proteins were also identified in our study, which aimed to explore the potential cross-talk between acylation and phosphorylation. After that, site-specific mutations showed that malonylation is a negative regulatory modification on the enzymatic activity of the acetyl-CoA synthetase (Acs) and glutamine synthetase (Gs). Furthermore, we compared the malonylation levels of the two-growth state to explore the potential effect of malonylation on the erythromycin biosynthesis. These findings expand our current knowledge of the actinomycetes malonylome and supplement the acylproteome databases of the whole bacteria. PMID:27090497

  2. Genealogy Profiling through Strain Improvement by Using Metabolic Network Analysis: Metabolic Flux Genealogy of Several Generations of Lysine-Producing Corynebacteria

    OpenAIRE

    Wittmann, Christoph; Heinzle, Elmar

    2002-01-01

    A comprehensive approach of metabolite balancing, 13C tracer studies, gas chromatography-mass spectrometry, matrix-assisted laser desorption ionization-time of flight mass spectrometry, and isotopomer modeling was applied for comparative metabolic network analysis of a genealogy of five successive generations of lysine-producing Corynebacterium glutamicum. The five strains examined (C. glutamicum ATCC 13032, 13287, 21253, 21526, and 21543) were previously obtained by random mutagenesis and se...

  3. Nitrate addition to groundwater impacted by ethanol-blended fuel accelerates ethanol removal and mitigates the associated metabolic flux dilution and inhibition of BTEX biodegradation

    Science.gov (United States)

    Corseuil, Henry Xavier; Gomez, Diego E.; Schambeck, Cássio Moraes; Ramos, Débora Toledo; Alvarez, Pedro J. J.

    2015-03-01

    A comparison of two controlled ethanol-blended fuel releases under monitored natural attenuation (MNA) versus nitrate biostimulation (NB) illustrates the potential benefits of augmenting the electron acceptor pool with nitrate to accelerate ethanol removal and thus mitigate its inhibitory effects on BTEX biodegradation. Groundwater concentrations of ethanol and BTEX were measured 2 m downgradient of the source zones. In both field experiments, initial source-zone BTEX concentrations represented less than 5% of the dissolved total organic carbon (TOC) associated with the release, and measurable BTEX degradation occurred only after the ethanol fraction in the multicomponent substrate mixture decreased sharply. However, ethanol removal was faster in the nitrate amended plot (1.4 years) than under natural attenuation conditions (3.0 years), which led to faster BTEX degradation. This reflects, in part, that an abundant substrate (ethanol) can dilute the metabolic flux of target pollutants (BTEX) whose biodegradation rate eventually increases with its relative abundance after ethanol is preferentially consumed. The fate and transport of ethanol and benzene were accurately simulated in both releases using RT3D with our general substrate interaction module (GSIM) that considers metabolic flux dilution. Since source zone benzene concentrations are relatively low compared to those of ethanol (or its degradation byproduct, acetate), our simulations imply that the initial focus of cleanup efforts (after free-product recovery) should be to stimulate the degradation of ethanol (e.g., by nitrate addition) to decrease its fraction in the mixture and speed up BTEX biodegradation.

  4. Primary metabolism plays a central role in moulding silicon-inducible brown spot resistance in rice.

    Science.gov (United States)

    Van Bockhaven, Jonas; Steppe, Kathy; Bauweraerts, Ingvar; Kikuchi, Shoshi; Asano, Takayuki; Höfte, Monica; De Vleesschauwer, David

    2015-10-01

    Over recent decades, a multitude of studies have shown the ability of silicon (Si) to protect various plants against a range of microbial pathogens exhibiting different lifestyles and infection strategies. Despite this relative wealth of knowledge, an understanding of the action mechanism of Si is still in its infancy, which hinders its widespread application for agricultural purposes. In an attempt to further elucidate the molecular underpinnings of Si-induced disease resistance, we studied the transcriptome of control and Si-treated rice plants infected with the necrotrophic brown spot fungus Cochliobolus miyabeanus. Analysis of brown spot-infected control plants suggested that C. miyabeanus represses plant photosynthetic processes and nitrate reduction in order to trigger premature senescence and cause disease. In Si-treated plants, however, these pathogen-induced metabolic alterations are strongly impaired, suggesting that Si alleviates stress imposed by the pathogen. Interestingly, Si also significantly increased photorespiration rates in brown spot-infected plants. Although photorespiration is often considered as a wasteful process, recent studies have indicated that this metabolic bypass also enhances resistance during abiotic stress and pathogen attack by protecting the plant's photosynthetic machinery. In view of these findings, our results favour a scenario in which Si enhances brown spot resistance by counteracting C. miyabeanus-induced senescence and cell death via increased photorespiration. Moreover, our results shed light onto the mechanistic basis of Si-induced disease control and support the view that, in addition to activating plant immune responses, Si can also reduce disease severity by interfering with pathogen virulence strategies. PMID:25583155

  5. Transmutation of /sup 90/Sr and /sup 137/Cs in a high-flux fast reactor with a thermalized central region

    Energy Technology Data Exchange (ETDEWEB)

    Taube, M.

    1976-10-01

    The fission products /sup 90/Sr and /sup 137/Cs produced by fission reactors of 30 GW(th) can be transmutated into stable nuclides by neutron irradiation with a thermal flux of 2 x 10/sup 16/ n cm/sup -2/ s/sup -1/. The rates of transmutation are 15 and 3.3 times greater, respectively, than that of spontaneous beta decay. The transmutation would take place in a central thermalized region of a high-flux fast burner reactor of 7 GW(th). In the case where the power reactors of 23 GW(th) are breeders with a high breeding gain of G = 0.38, the total system, inclusive of the high-flux burner, remains a breeding system, with G/sub total/ = 0.09. Details of the neutronics calculations and simplified thermohydraulics are given. The high-flux burner is fueled with a molten salt of chlorides of plutonium and sodium with a power density of 10 kW cm/sup -3/. The ''self-liquidation'' of such a system is discussed.

  6. Testicular Metabolic Reprogramming in Neonatal Streptozotocin-Induced Type 2 Diabetic Rats Impairs Glycolytic Flux and Promotes Glycogen Synthesis

    OpenAIRE

    Rato, L; M. G. Alves; T. R. Dias; J. E. Cavaco; Oliveira, Pedro F.

    2015-01-01

    Defects in testicular metabolism are directly implicated with male infertility, but most of the mechanisms associated with type 2 diabetes- (T2DM) induced male infertility remain unknown. We aimed to evaluate the effects of T2DM on testicular glucose metabolism by using a neonatal-streptozotocin- (n-STZ) T2DM animal model. Plasma and testicular hormonal levels were evaluated using specific kits. mRNA and protein expression levels were assessed by real-time PCR and Western Blot, respectively. ...

  7. A VapBC Toxin-Antitoxin Module Is a Posttranscriptional Regulator of Metabolic Flux in Mycobacteria

    OpenAIRE

    McKenzie, Joanna L.; Robson, Jennifer; Berney, Michael; Smith, Tony C.; Ruthe, Alaine; Gardner, Paul P.; Vickery L Arcus; Cook, Gregory M.

    2012-01-01

    The largest family of toxin-antitoxin (TA) modules are encoded by the vapBC operons, but their roles in bacterial physiology remain enigmatic. Microarray analysis in Mycobacterium smegmatis overexpressing VapC/VapBC revealed a high percentage of downregulated genes with annotated roles in carbon transport and metabolism, suggesting that VapC was targeting specific metabolic mRNA transcripts. To validate this hypothesis, purified VapC was used to identify the RNA cleavage site in vitro. VapC h...

  8. Pyruvate Oxidoreductases Involved in Glycolytic Anaerobic Metabolism of Polychaetes from the Continental Shelf off Central-South Chile

    Science.gov (United States)

    González, R. R.; Quiñones, R. A.

    2000-10-01

    The presence of low oxygen conditions in extensive areas of the continental shelf off central-south Chile has important effects on the biochemical adaptations of the organisms living in this ecosystem. Polychaetes assemblages cohabit on the shelf with an extensively distributed prokaryotic community made up of giant filamentous sulfur bacteria (mainly Thioploca sp.). The aim of this research was to characterize the pyruvate oxidoreductases enzymes involved in the biochemical adaptation of these benthic polychaetes. Nine polychaete species ( Paraprionospio pinnata, Nephtys ferruginea, Glycera americana, Haploscoloplos sp., Lumbrineris composita, Sigambra bassi, Aricidea pigmentata , Cossura chilensis, and Pectinaria chilensis) were assayed for lactic dehydrogenase (LDH), octopine dehydrogenase (OPDH), strombine dehydrogenase (STRDH) and alanopine dehydrogenase (ALPDH). Each species had a characteristic number of the pyruvate oxidoreductases assayed ranging from 4 in Paraprionospio pinnata to 1 in Pectinaria chilensis . The pyruvate saturation curves obtained for the enzymes from all species analysed, except L. composita, suggest that NADH can be oxidized at different rates depending on the amino acid used in the reaction with pyruvate. Our results indicate that organisms having more that one pyruvate oxidoreductase present a greater metabolic capacity to cope with functional and environmental hypoxia because these enzymes would better regulate the pyruvate consumption rate during the transition period. Thus, the dominance of Paraprionospio pinnata in the study area and its worldwide distribution is consistent with its higher number of pyruvate oxidoreductases with different pyruvate consumption rates involved in anaerobic metabolism. Finally, a positive allometric relationship was found between body size and the specific activity of ALPDH, STRDH, and maximum pyruvate oxidoreductase specific activity. This latter result suggests a positive scaling of the specific

  9. Genetic analysis of central carbon metabolism unveils an amino acid substitution that alters maize NAD-dependent isocitrate dehydrogenase activity.

    Directory of Open Access Journals (Sweden)

    Nengyi Zhang

    Full Text Available BACKGROUND: Central carbon metabolism (CCM is a fundamental component of life. The participating genes and enzymes are thought to be structurally and functionally conserved across and within species. Association mapping utilizes a rich history of mutation and recombination to achieve high resolution mapping. Therefore, applying association mapping in maize (Zea mays ssp. mays, the most diverse model crop species, to study the genetics of CCM is a particularly attractive system. METHODOLOGY/PRINCIPAL FINDINGS: We used a maize diversity panel to test the CCM functional conservation. We found heritable variation in enzyme activity for every enzyme tested. One of these enzymes was the NAD-dependent isocitrate dehydrogenase (IDH, E.C. 1.1.1.41, in which we identified a novel amino-acid substitution in a phylogenetically conserved site. Using candidate gene association mapping, we identified that this non-synonymous polymorphism was associated with IDH activity variation. The proposed mechanism for the IDH activity variation includes additional components regulating protein level. With the comparison of sequences from maize and teosinte (Zea mays ssp. Parviglumis, the maize wild ancestor, we found that some CCM genes had also been targeted for selection during maize domestication. CONCLUSIONS/SIGNIFICANCE: Our results demonstrate the efficacy of association mapping for dissecting natural variation in primary metabolic pathways. The considerable genetic diversity observed in maize CCM genes underlies heritable phenotypic variation in enzyme activities and can be useful to identify putative functional sites.

  10. Molecular System Bioenergics of the Heart: Experimental Studies of Metabolic Compartmentation and Energy Fluxes versus Computer Modeling

    Directory of Open Access Journals (Sweden)

    Valdur Saks

    2011-12-01

    Full Text Available In this review we analyze the recent important and remarkable advancements in studies of compartmentation of adenine nucleotides in muscle cells due to their binding to macromolecular complexes and cellular structures, which results in non-equilibrium steady state of the creatine kinase reaction. We discuss the problems of measuring the energy fluxes between different cellular compartments and their simulation by using different computer models. Energy flux determinations by 18O transfer method have shown that in heart about 80% of energy is carried out of mitochondrial intermembrane space into cytoplasm by phosphocreatine fluxes generated by mitochondrial creatine kinase from adenosine triphosphate (ATP, produced by ATP Synthasome. We have applied the mathematical model of compartmentalized energy transfer for analysis of experimental data on the dependence of oxygen consumption rate on heart workload in isolated working heart reported by Williamson et al. The analysis of these data show that even at the maximal workloads and respiration rates, equal to 174 µmol O2 per min per g dry weight, phosphocreatine flux, and not ATP, carries about 80–85% percent of energy needed out of mitochondria into the cytosol. We analyze also the reasons of failures of several computer models published in the literature to correctly describe the experimental data.

  11. LAND-USE CHANGE AND CARBON FLUX BETWEEN 1970S AND 1990S IN CENTRAL HIGHLANDS OF CHIAPAS, MEXICO

    Science.gov (United States)

    We present results of a study in an intensively impacted and highly fragmented landscape in which we apply field-measured carbon (C) density values to land-use/land-cover (LU/LC) statistics to estimate the flux of C between terrestrial ecosystems and the atmosphere from the 1970s...

  12. Synoptic evaluation of carbon cycling in Beaufort Sea during summer: contrasting river inputs, ecosystem metabolism and air-sea CO2 fluxes

    Science.gov (United States)

    Forest, A.; Coupel, P.; Else, B.; Nahavandian, S.; Lansard, B.; Raimbault, P.; Papakyriakou, T.; Gratton, Y.; Fortier, L.; Tremblay, J.-É.; Babin, M.

    2013-10-01

    The accelerated decline in Arctic sea ice combined with an ongoing trend toward a more dynamic atmosphere is modifying carbon cycling in the Arctic Ocean. A critical issue is to understand how net community production (NCP; the balance between gross primary production and community respiration) responds to changes and modulates air-sea CO2 fluxes. Using data collected as part of the ArcticNet-Malina 2009 expedition in southeastern Beaufort Sea (Arctic Ocean), we synthesize information on sea ice, wind, river, water column properties, metabolism of the planktonic food web, organic carbon fluxes and pools, as well as air-sea CO2 exchange, with the aim of identifying indices of ecosystem response to environmental changes. Data were analyzed to develop a non-steady-state carbon budget and an assessment of NCP against air-sea CO2 fluxes. The mean atmospheric forcing was a mild upwelling-favorable wind (~5 km h-1) blowing from the N-E and a decaying ice cover (600 mg C m-2d-1) over the shelf prior to our survey, (2) freshwater dilution by river runoff and ice melt, and (3) the presence of cold surface waters offshore. Only the Mackenzie River delta and localized shelf areas directly affected by upwelling were identified as substantial sources of CO2 to the atmosphere (>10mmol C m-2d-1). Although generally state.

  13. Synoptic evaluation of carbon cycling in the Beaufort Sea during summer: contrasting river inputs, ecosystem metabolism and air-sea CO2 fluxes

    Science.gov (United States)

    Forest, A.; Coupel, P.; Else, B.; Nahavandian, S.; Lansard, B.; Raimbault, P.; Papakyriakou, T.; Gratton, Y.; Fortier, L.; Tremblay, J.-É.; Babin, M.

    2014-05-01

    The accelerated decline in Arctic sea ice and an ongoing trend toward more energetic atmospheric and oceanic forcings are modifying carbon cycling in the Arctic Ocean. A critical issue is to understand how net community production (NCP; the balance between gross primary production and community respiration) responds to changes and modulates air-sea CO2 fluxes. Using data collected as part of the ArcticNet-Malina 2009 expedition in the southeastern Beaufort Sea (Arctic Ocean), we synthesize information on sea ice, wind, river, water column properties, metabolism of the planktonic food web, organic carbon fluxes and pools, as well as air-sea CO2 exchange, with the aim of documenting the ecosystem response to environmental changes. Data were analyzed to develop a non-steady-state carbon budget and an assessment of NCP against air-sea CO2 fluxes. During the field campaign, the mean wind field was a mild upwelling-favorable wind (~ 5 km h-1) from the NE. A decaying ice cover ( 600 mg C m-2 d-1) over the shelf prior to our survey, (2) freshwater dilution by river runoff and ice melt, and (3) the presence of cold surface waters offshore. Only the Mackenzie River delta and localized shelf areas directly affected by upwelling were identified as substantial sources of CO2 to the atmosphere (> 10 mmol C m-2 d-1). Daily PP rates were generally state.

  14. Flux coupling and transcriptional regulation within the metabolic network of the photosynthetic bacterium Synechocystis sp. PCC6803

    DEFF Research Database (Denmark)

    Montagud, Arnau; Zelezniak, Aleksej; Navarro, Emilio;

    2011-01-01

    Synechocystis sp. PCC6803 is a model cyanobacterium capable of producing biofuels with CO2 as carbon source and with its metabolism fueled by light, for which it stands as a potential production platform of socio-economic importance. Compilation and characterization of Synechocystis genome-scale ...

  15. Modulating the metabolic flux through the biosynthesis pathways of branched-chain amino acids in corynebacterium glutamicum

    Czech Academy of Sciences Publication Activity Database

    Pátek, Miroslav; Elišáková, Veronika; Holátko, Jiří

    2004, s. 53. [Metabolic Engineering /5./. Squaw Creek (US), 19.09.2004-23.09.2004] R&D Projects: GA ČR GA525/04/0548 Institutional research plan: CEZ:AV0Z5020903 Keywords : corynebacterium glutamicum * pathway Subject RIV: EE - Microbiology, Virology

  16. Dust flux estimates for the Last Glacial Period in East Central Europe based on terrestrial records of loess deposits: a review

    Science.gov (United States)

    Újvári, Gábor; Kovács, János; Varga, György; Raucsik, Béla; Marković, Slobodan B.

    2010-11-01

    Loess-paleosol sequences are significant records of the mineral dust cycle of glacial-interglacial periods. As dust particles give rise to direct and indirect radiative forcing, obtaining a reliable picture of the global and regional patterns of mineral dust fluxes during glacial periods can lead to a better understanding of the contribution of mineral dust to past climate changes. Recent progress in absolute dating of loess deposits in the Carpathian Basin in East Central Europe made it possible to provide correct aeolian flux estimates for the Last Glacial period, marine isotope stage (MIS) 2. Mass accumulation rates (MARs) from chronological data of 33 loess sites exhibited a wide range of values, from 150 to 1422 g m -2 a -1, centered around median and mean values of 338 and 417 g m -2 a -1. MAR and MAR estimates have been also calculated using grain size measurements of many loess samples and loess MARs in order to facilitate comparison with models, and since particles larger than 10 μm have a negligible radiative effect. Here we show that some previous model simulations of the dust cycle at the Last Glacial Maximum (LGM) significantly underestimated the real aeolian flux (ranges of our estimates: MAR=34-324 and MAR=9.3-88.2 g m a) in East Central Europe. For this reason, some simulations of dust-induced direct radiative forcing of the LGM climate failed to yield reliable results for this mid-latitude region as they have been based on three-dimensional dust field models that are not capable of estimating the real aeolian fluxes in Central Europe. A recent global model of top of the atmosphere (TOA) radiative forcing by mineral aerosols at the LGM that has been based on more realistic parameterization of dust sources, transport, and deposition revealed zonally averaged surface cooling of -2 °C for the latitudes of our study area. This surface cooling and TOA radiative forcing (-2 to -3 W m -2) are greater than recognized in other models and draws our

  17. Fluxes of CO2, CH4 and N2O from soil of burned grassland savannah of central Africa

    Directory of Open Access Journals (Sweden)

    R. Valentini

    2010-06-01

    Full Text Available Grassland savannah ecosystems subject to frequent fires are considered to have an almost neutral carbon balance, as the C released during burning mostly balance the C fixed by the photosynthetic process. However, burning might modify the net soil-atmosphere exchange of GHGs in the post burning phase so that the radiative balance of the site might shift from neutrality. In the present study the impact of fire on soil fluxes of CO2, CH4 and N2O was investigated in a grassland savannah (Congo Brazzaville where high frequency burning is the typical management form of the region. An area was preserved for one season from annual burning and was used as "unburned" treatment. Two field campaigns were carried on at different time length from the fire event, 1 month, in the middle of the dry season, and 8 months after, at the end of the growing season. CO2, CH4 and N2O fluxes, as well as several soil parameters, were measured in each campaign from burned and unburned plots. Rain events were simulated at each campaign to evaluate magnitude and length of the generated GHG flux pulses. In laboratory experiments, on soil samples from the two treatments, microbial biomass, net N mineralization, net nitrification, N2O, NO and CO2 emissions were analyzed in function of soil water and/or temperature variations. Results showed that fire had a significant effect on GHG fluxes but the effect was transient, as after 8 months differences between treatments were no longer significant. One month after burning CO2 soil emissions were significantly lower in the burned plots, CH4 fluxes were dominated by net emissions rather than net consumption in the unburned area and fire shifted the CH4 flux distribution towards more negative values. No significant effect of fire was observed in the field on N2O fluxes. It was assumed that the low water content was the main limiting factor as in fact laboratory data showed that only above 75% of water saturation, N2O emissions

  18. Comparing surface and mid-troposphere CO2 concentration and fluxes from central U.S. grasslands

    Science.gov (United States)

    Cochran, F. V.; Brunsell, N. A.; Quick, A. T.

    2010-12-01

    Terrestrial ecosystem dynamics influence the Earth’s climate system, which is affected by variations in atmospheric carbon dioxide (CO2). Assessments of CO2 concentration and net fluxes at regional scales are needed to diminish uncertainties related to the effects of land-use change on ecosystem processes, to identify land management practices that have the potential to mitigate CO2 emissions, and to discern sources and sinks within geopolitical boundaries for reasons of carbon accountability. Understanding how surface CO2 concentration and flux dynamics within heterogeneous landscapes scale to mid-troposphere concentrations is the focus of this study. CO2 flux data from three eddy covariance (EC) towers in northeastern Kansas are compared to mid-tropospheric data collected by the Atmospheric Infrared Sounder (AIRS). EC tower data from two watershed sites on the Konza Prairie Biological Station (KPBS) for the period 2006-2010 and one study site at the Nelson Environmental Study Area (NESA) for the period 2007-2010 are examined. KPBS site 1D is primarily C4 grasses, burned annually; KPBS site 4B is a mix of C3 forbs and C4 grasses, burned every four years; and the NESA site is a mix of C3/C4 grasses, burned approximately every five years, and experiencing woody encroachment. Results show higher concentration of CO2 in the mid-troposphere. Furthermore, mid-troposphere CO2 exhibited daily and seasonal lags and decreased amplitude in flux dynamics compared to surface CO2. Long-term, combined observations of surface and atmospheric CO2 offer the potential for a better understanding of the natural processes and anthropogenic activities related to CO2 source-sink dynamics, seasonal and interannual variability, and climate forcings, including temperature and precipitation changes.

  19. NON-INVASIVE ESTIMATION OF METABOLIC FLUX AND BLOOD FLOW IN WORKING MUSCLE: EFFECT OF BLOOD-TISSUE DISTRIBUTION

    OpenAIRE

    Lai, Nicola; Saidel, Gerald M.; Iorio, Matthew; Cabrera, Marco E.

    2009-01-01

    Muscle oxygenation measurements by near infrared spectroscopy (NIRS) are frequently obtained in humans to make inferences about mechanisms of metabolic control of respiration in working skeletal muscle. However, these measurements have technical limitations that can mislead the evaluation of tissue processes. In particular, NIRS measurements of working muscle represent oxygenation of a mix of fibers with heterogeneous activation, perfusion and architecture. Specifically, the relative volume d...

  20. Pathway Pioneer: A Web-Based Graphical Tool for the Organization and Flux Analysis of Metabolic Networks

    OpenAIRE

    Singh, Sumit Kumar

    2014-01-01

    As stoichiometric metabolic models increase in complexity and delity, design and reconstruction tools are urgently needed to increase the productivity of this time-consuming process. Engineers require software for the exploration, evaluation, and rapid analysis of model alternatives within an intuitive visualization and data management framework. This thesis introduces such a tool: Pathway Pioneer (www.pathwaypioneer.org), a web based system built as a front-end graphical user interface to th...

  1. Osmotic Stress Response: Quantification of Cell Maintenance and Metabolic Fluxes in a Lysine-Overproducing Strain of Corynebacterium glutamicum

    OpenAIRE

    Varela, Cristian A.; Baez, Mauricio E.; Agosin, Eduardo

    2004-01-01

    Osmotic stress diminishes cell productivity and may cause cell inactivation in industrial fermentations. The quantification of metabolic changes under such conditions is fundamental for understanding and describing microbial behavior during bioprocesses. We quantified the gradual changes that take place when a lysine-overproducing strain of Corynebacterium glutamicum is grown in continuous culture with saline gradients at different dilution rates. The use of compatible solutes depended on env...

  2. Implications of central obesity-related variants in LYPLAL1, NRXN3, MSRA, and TFAP2B on quantitative metabolic traits in adult Danes

    DEFF Research Database (Denmark)

    Bille, Dorthe Sadowa; Banasik, Karina; Justesen, Johanne Marie; Sandholt, Camilla H; Sandbæk, Annelli; Lauritzen, Torsten; Jørgensen, Torben; Witte, Daniel Rinse; Holm, Jens-Christian; Hansen, Torben; Pedersen, Oluf

    2011-01-01

    -binding protein 2 beta (TFAP2B) associate with measures of central obesity. To elucidate potential underlying phenotypes we aimed to investigate whether these variants associated with: 1) quantitative metabolic traits, 2) anthropometric measures (waist circumference (WC), waist-hip ratio, and BMI), or 3) type 2...

  3. Issues in the in vivo measurement of glucose metabolism of human central nervous system tumors.

    Science.gov (United States)

    Di Chiro, G; Brooks, R A; Patronas, N J; Bairamian, D; Kornblith, P L; Smith, B H; Mansi, L; Barker, J

    1984-01-01

    Over 150 cases of central nervous system tumors have been studied with positron emission tomography using fluorine-18-labeled fluorodeoxyglucose (18FDG) as a tracer. From this material 100 consecutive cases of cerebral glioma have been reviewed and analyzed. The results show a strong correlation of tumor grade with glycolytic rate, with visual "hot spots" present in all high-grade neoplasms and in only four low-grade tumors. The quantitative accuracy is limited by three basic factors. First, the measurement of tissue uptake, as compared with the parent technique, autoradiography, is more difficult because detection must be done outside the body. Effects such as scattered radiation and self-attenuation introduce errors unless properly corrected. A more serious problem when measuring small structures, such as a rim-shaped high-grade glioma, is the limited spatial resolution. The most advanced scanner, the Neuro-PET, has a resolution of 6 to 7 mm. Second, corrections are needed for backflow, including free tracer at the time of the scan that will return to the blood and "trapped" tracer that will backflow because of the presence of phosphatase. These corrections are calculated from the blood activity using nominal rate constants for 18FDG. Our study found no significant alteration in rate constants between normal and tumoral tissue. Finally, a lumped constant is needed to correct for kinetic differences between 18FDG and glucose. If there is a change in the mechanism of either membrane transport or the hexokinase reaction, the lumped constant may change. However, measurements of actual glucose utilization in tissue culture lines from six patients support the 18FDG results. PMID:6331282

  4. New concepts of the central control of reproduction, integrating influence of stress, metabolic state, and season.

    Science.gov (United States)

    Clarke, I J; Arbabi, L

    2016-07-01

    Gonadotropin releasing hormone is the primary driver of reproductive function and pulsatile GnRH secretion from the brain causes the synthesis and secretion of LH and FSH from the pituitary gland. Recent work has revealed that the secretion of GnRH is controlled at the level of the GnRH secretory terminals in the median eminence. At this level, projections of kisspeptin cells from the arcuate nucleus of the hypothalamus are seen to be closely associated with fibers and terminals of GnRH cells. Direct application of kisspeptin into the median eminence causes release of GnRH. The kisspeptin cells are activated at the time of a natural "pulse" secretion of GnRH, as reflected in the secretion of LH. This appears to be due to input to the kisspeptin cells from glutamatergic cells in the basal hypothalamus, indicating that more than 1 neural element is involved in the secretion of GnRH. Because the GnRH secretory terminals are outside the blood-brain barrier, factors such as kisspeptin may be administered systemically to cause GnRH secretion; this offers opportunities for manipulation of the reproductive axis using factors that do not cross the blood-brain barrier. In particular, kisspeptin or analogs of the same may be used to activate reproduction in the nonbreeding season of domestic animals. Another brain peptide that influences reproductive function is gonadotropin inhibitory hormone (GnIH). Work in sheep shows that this peptide acts on GnRH neuronal perikarya, but projections to the median eminence also allow secretion into the hypophysial portal blood and action of GnIH on pituitary gonadotropes. GnIH cells are upregulated in anestrus, and infusion of GnIH can block the ovulatory surge in GnRH and/or LH secretion. Metabolic status may also affect the secretion of reproduction, and this could involve action of gut peptides and leptin. Neuropeptide Y and Y-receptor ligands have a negative impact on reproduction, and Neuropeptide Y production is markedly increased in

  5. Central Role of Glutamate Metabolism in the Maintenance of Nitrogen Homeostasis in Normal and Hyperammonemic Brain

    Directory of Open Access Journals (Sweden)

    Arthur J. L. Cooper

    2016-03-01

    enzyme pyruvate carboxylase. Here, we suggest that glutamate may constitute a buffer or bulwark against changes in cerebral amine and ammonia nitrogen. Although the glutamate transporters are briefly discussed, the major emphasis of the present review is on the enzymology contributing to the maintenance of glutamate levels under normal and hyperammonemic conditions. Emphasis will also be placed on the central role of glutamate in the glutamine-glutamate and glutamine-GABA neurotransmitter cycles between neurons and astrocytes. Finally, we provide a brief and selective discussion of neuropathology associated with altered cerebral glutamate levels.

  6. Central Role of Glutamate Metabolism in the Maintenance of Nitrogen Homeostasis in Normal and Hyperammonemic Brain.

    Science.gov (United States)

    Cooper, Arthur J L; Jeitner, Thomas M

    2016-01-01

    . Here, we suggest that glutamate may constitute a buffer or bulwark against changes in cerebral amine and ammonia nitrogen. Although the glutamate transporters are briefly discussed, the major emphasis of the present review is on the enzymology contributing to the maintenance of glutamate levels under normal and hyperammonemic conditions. Emphasis will also be placed on the central role of glutamate in the glutamine-glutamate and glutamine-GABA neurotransmitter cycles between neurons and astrocytes. Finally, we provide a brief and selective discussion of neuropathology associated with altered cerebral glutamate levels. PMID:27023624

  7. Whole-system metabolism and CO2 fluxes in a Mediterranean Bay dominated by seagrass beds (Palma Bay, NW Mediterranean

    Directory of Open Access Journals (Sweden)

    F. Gazeau

    2005-01-01

    Full Text Available Planktonic and benthic incubations (bare and Posidonia oceanica vegetated sediments were performed at monthly intervals from March 2001 to October 2002 in a seagrass vegetated area of the Bay of Palma (Mallorca, Spain. Results showed a contrast between the planktonic compartment, which was on average near metabolic balance (−4.6±5.9 mmol O2 m-2 d-1 and the benthic compartment, which was autotrophic (17.6±8.5 mmol O2 m-2 d-1. During two cruises in March and June 2002, planktonic and benthic incubations were performed at several stations in the bay to estimate the whole-system metabolism and to examine its relationship with partial pressure of CO2 (pCO2 and apparent oxygen utilisation (AOU spatial patterns. Moreover, during the second cruise, when the residence time of water was long enough, net ecosystem production (NEP estimates based on incubations were compared, over the Posidonia oceanica meadow, to rates derived from dissolved inorganic carbon (DIC and oxygen (O2 mass balance budgets. These budgets provided NEP estimates in fair agreement with those derived from direct metabolic estimates based on incubated samples over the Posidonia oceanica meadow. Whereas the seagrass community was autotrophic, the excess organic carbon production therein could only balance the planktonic heterotrophy in shallow waters relative to the maximum depth of the bay (55 m. This generated a horizontal gradient from autotrophic or balanced communities in the shallow seagrass-covered areas, to strongly heterotrophic communities in deeper areas of the bay. It seems therefore that, on an annual scale in the whole bay, the organic matter production by the Posidonia oceanica may not be sufficient to fully compensate the heterotrophy of the planktonic compartment, which may require external organic carbon inputs, most likely from land.

  8. A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria.

    Science.gov (United States)

    McKenzie, Joanna L; Robson, Jennifer; Berney, Michael; Smith, Tony C; Ruthe, Alaine; Gardner, Paul P; Arcus, Vickery L; Cook, Gregory M

    2012-05-01

    The largest family of toxin-antitoxin (TA) modules are encoded by the vapBC operons, but their roles in bacterial physiology remain enigmatic. Microarray analysis in Mycobacterium smegmatis overexpressing VapC/VapBC revealed a high percentage of downregulated genes with annotated roles in carbon transport and metabolism, suggesting that VapC was targeting specific metabolic mRNA transcripts. To validate this hypothesis, purified VapC was used to identify the RNA cleavage site in vitro. VapC had RNase activity that was sequence specific, cleaving single-stranded RNA substrates at AUAU and AUAA in vitro and in vivo (viz., MSMEG_2121 to MSMEG_2124). A bioinformatic analysis of these regions suggested that an RNA hairpin 3' of the AUA(U/A) motif is also required for efficient cleavage. VapC-mediated regulation in vivo was demonstrated by showing that MSMEG_2124 (dhaF) and MSMEG_2121 (dhaM) were upregulated in a ΔvapBC mutant growing on glycerol. The ΔvapBC mutant had a specific rate of glycerol consumption that was 2.4-fold higher than that of the wild type during exponential growth. This increased rate of glycerol consumption was not used for generating bacterial biomass, suggesting that metabolism by the ΔvapBC mutant was uncoupled from growth. These data suggest a model in which VapC regulates the rate of glycerol utilization to match the anabolic demands of the cell, allowing for fine-tuning of the catabolic rate at a posttranscriptional level. PMID:22366418

  9. Gill lipid metabolism and unidirectional Na+ flux in the European eel (Anguilla anguilla) after transfer to dilute media

    DEFF Research Database (Denmark)

    Hansen, H.J.M.; Grosell, M.; Rosenkilde, P.

    The present study investigated the mechanism involved when fish tighten their gill membrane after transfer to dilute media. Ten individually assayed eels adapted to fresh water (EW) and labelled with radioactive Na-22 in the plasma showed mean exchange rates in equilibrium with ambient radioactive...... total C-14-activity incorporated into gill lipids as (C-14) wax alcohols (WA; octadecanol and eicosanol). This percentage went up to 50% shortly after transfer to DW and came down again to about 20% after 2 weeks in DW. Single eels labelled with Na-22 in the plasma showed a statistically significant...... positive linear correlation of percentage (14C) wax alcohols with log [22Na efflux]. Based on the observed parallel between Naf flux and gill lipid metabolism, it is suggested that the eel reacts at first to a loss of Na+ by synthesizing wax alcohols that can tighten the gill membrane. (C) 1999 Elsevier...

  10. Isoprene and monoterpene fluxes from Central Amazonian rainforest inferred from tower-based and airborne measurements, and implications on the atmospheric chemistry and the local carbon budget

    Directory of Open Access Journals (Sweden)

    U. Kuhn

    2007-01-01

    Full Text Available We estimated the isoprene and monoterpene source strengths of a pristine tropical forest north of Manaus in the central Amazon Basin using three different micrometeorological flux measurement approaches. During the early dry season campaign of the Cooperative LBA Airborne Regional Experiment (LBA-CLAIRE-2001, a tower-based surface layer gradient (SLG technique was applied simultaneously with a relaxed eddy accumulation (REA system. Airborne measurements of vertical profiles within and above the convective boundary layer (CBL were used to estimate fluxes on a regional scale by application of the mixed layer gradient (MLG technique. The mean daytime fluxes of organic carbon measured by REA were 2.1 mg C m−2 h−1 for isoprene, 0.20 mg C m−2 h−1 for α-pinene, and 0.39 mg C m−2 h−1 for the sum of monoterpenes. These values are in reasonable agreement with fluxes determined with the SLG approach, which exhibited a higher scatter, as expected for the complex terrain investigated. The observed VOC fluxes are in good agreement with simulations using a single-column chemistry and climate model (SCM.

    In contrast, the model-derived mixing ratios of VOCs were by far higher than observed, indicating that chemical processes may not be adequately represented in the model. The observed vertical gradients of isoprene and its primary degradation products methyl vinyl ketone (MVK and methacrolein (MACR suggest that the oxidation capacity in the tropical CBL is much higher than previously assumed. A simple chemical kinetics model was used to infer OH radical concentrations from the vertical gradients of (MVK+MACR/isoprene. The estimated range of OH concentrations during the daytime was 3–8×106 molecules cm−3, i.e., an order of magnitude higher than is estimated for the tropical CBL by current state-of-the-art atmospheric chemistry and transport models

  11. Nitrous oxide flux in maize and wheat cropped soils in the central region of Mexico during El nino year 1998

    Energy Technology Data Exchange (ETDEWEB)

    Longoria Ramirez, R. [Centro Nacional de Investigaciones y Desarrollo Tecnologico, Mexico, D.F. (Mexico); Carbajal Benitez, G.; Mar Morales, B.E.; Ruiz Suarez, G. [Centro de Ciencias de la Atmosfera, Universidad Nacional Autonoma de Mexico, (UNAM), Mexico, D.F. (Mexico)

    2003-10-01

    Emissions of nitrous oxide (N{sub 2}O) were measured in agricultural lands used for farming wheat and maize during 1998 in the states of Hidalgo and Tlaxcala in Mexico. In an irrigated wheat field (El Tenhe, Hidalgo), an average flux of -10.85 {mu}g N{sub 2}O - N m{sup -}2 h{sup -}1 was obtained for the total cycle (155 days between December and May). There, high negative values were observed with Water Fill Porous Space (WFPS) close to 70%. The average flux of the complete cycle (269 days between March and December) in an irrigated maize field (El Progreso, Hidalgo) was 37.43 {mu}g N{sub 2}O - N m{sup -}2 h{sup -}1. In this case, more insignificant negative fluxes were found with WFPS close to 45% or less. These last results may have been influenced by the strong El Nino, which occurred in the middle of 1998. Twenty once percent of the measurements in the state of Hidalgo showed soil acting as a nitrous oxide sink. The samples from Tlaxcala showed that these fields acted as emitters. In the rain fed fields in the state of Tlaxcala, an average flux of 121 {mu}g N{sub 2}O - N m{sup -}2 h{sup -}1 was obtained for the wheat field. The farming season lasted 142 days, from July to December. In addition, for the maize field the averaged flux was 285.61 {mu}g N{sub 2}O - Nm{sup -}2h-1. The farming season lasted 246 days, from April to December. [Spanish] En 1998 se midieron las emisiones de oxido nitroso (N{sub 2}O) de suelos agricolas para cultivar trigo y maiz en los estados de Hidalgo y Tlaxcala, en Mexico. Para un campo irrigado de trigo (El Tenhe, Hidalgo), se obtuvo un flujo promedio de -10.85 {mu}g N{sub 2}O - N m{sup -}2 h{sup -}1 para el ciclo total (155 dias entre diciembre y mayo). En este caso se observaron valores negativos elevados en el espacio poroso relleno de agua (VFPS, pos sus siglas en ingles), cercanos a 70%. El flujo promedio para el ciclo completo (269 dias entre marzo y diciembre) en un campo irrigado de maiz fue de 37.43 {mu}g N{sub 2}O - N m

  12. Windthrow and fallow-forest successions impacts in soil carbon stocks and GHG fluxes spatial variability and dynamics in the Central Russia' reserve spruce ecosystems

    Science.gov (United States)

    Vasenev, Ivan; Ivanov, Alexey; Komarova, Tatyana; Valentini, Riccardo

    2015-04-01

    High spatial and temporal variability is mutual feature for most forest soils that is especially obvious in case of their carbon stocks and GHG fluxes. This phenomenon is generally well-known but not so often becomes the object of special precision investigation in detail and small scales so there are still serious gaps in its principal factors understanding due to their high bioclimatic, regional, landscape, tree species and temporal variability. Southern taiga is one of the most environmentally important world zonal forest ecosystems due to its still comparatively intensive carbon biogeochemical cycle and huge area in the northern Eurasia with strong anthropogenic impacts by Western & Central European and Southern & Eastern Asian regions. Central Forest Biospheric Reserve (Tver region, 360 km to North-West from Moscow) is the principal southern-taiga reserve in the European territory of Russia. Since start of its research activity in 1939 the reserve became the regional center of mature spruce ecosystem structure and dynamics investigation. In 1970-1980-s there have been done complex investigations of windthrow soil patterns and fallow-forest successions. Since middle of 1990-s the ecosystem-level GHG fluxes have been observed by eddy covariance method. Since 2012 the detailed year-round monitoring is running in the southern-taiga zonal station of the regional system RusFluxNet with especial attention on the soil carbon stocks and GHG fluxes spatial variability and dynamics due to windthrow and fallow-forest successions (in frame of RF Governmental projects #11.G34.31.0079 and #14.120.14.4266). Soil carbon dynamics is investigated in decades-hundred-year chronosequences of dominated parcels and different-size windthrow soil cover patterns, including direct investigation during last 33 years with detailed mapping, soil profile morphometrics and bulk density, morphogenetic and statistical analysis of mass data. Morphogenetic analysis of microrelief, soil profile

  13. Agricultural crops and soil treatment impacts on the daily and seasonal dynamics of CO2 fluxes in the field agroecosystems at the Central region of Russia

    Science.gov (United States)

    Mazirov, Ilya; Vasenev, Ivan; Meshalkina, Joulia; Yaroslavtsev, Alexis; Berezovskiy, Egor; Djancharov, Turmusbek

    2015-04-01

    The problem of greenhouse gases' concentrations increasing becomes more and more important due to global changes issues. The main component of greenhouse gases is carbon dioxide. The researches focused on its fluxes in natural and anthropogenic modified landscapes can help in this problem solution. Our research has been done with support of the RF Government grants # 11.G34.31.0079 and # 14.120.14.4266 and of FP7 Grant # 603542 LUC4C in the representative for Central Region of Russia field agroecosystems at the Precision Farming Experimental Field of Russian Timiryazev State Agrarian University with cultivated sod podzoluvisols, barley and oats - vetch grass mix (Moscow station of the RusFluxNet). The daily and seasonal dynamics of the carbon dioxide have been studied at the ecosystem level by the Eddy covariance method (2 stations) and at the soil level by the exposition chamber method (40 chambers) with mobile infra red gas analyzer (Li-Cor 820). The primary Eddy covariance monitoring data on CO2 fluxes and water vapor have been processed by EddyPro software developed by LI-COR Biosciences. According to the two-year monitoring data the daily CO2 sink during the vegetation season is usually approximately two times higher than its emission at night. Seasonal CO2 fluxes comparative stabilization has been fixed in case the plants height around 10-12 cm and it usually persist until the wax ripeness phase. There is strong dependence between the soil CO2 emission and the air temperature with the correlation coefficient 0.86 in average (due to strong input of the soil thin top functional subhorizon), but it drops essentially at the end of the season - till 0.38. The soil moisture impact on CO2 fluxes dynamics was less, with negative correlation at the end of the season. High daily dynamics of CO2 fluxes determines the protocol requirements for seasonal soil monitoring investigation with less limitation at the end of the season. The accumulated monitoring data will be

  14. Localized Climate and Surface Energy Flux Alterations across an Urban Gradient in the Central U.S.

    OpenAIRE

    Jason A. Hubbart; Elliott Kellner; Lynne Hooper; Anthony R. Lupo; Market, Patrick S.; Patrick E. Guinan; Kirsten Stephan; Neil I. Fox; Bohumil M. Svoma

    2014-01-01

    Long-term urban and rural climate data spanning January 1995 through October 2013 were analyzed to investigate the Urban Heat Island (UHI) effect in a representative mid-sized city of the central US. Locally distributed climate data were also collected at nested low density urban, recently developed, and high density urban monitoring sites from June through September 2013 to improve mechanistic understanding of spatial variability of the UHI effect based upon urban land use intensity. Long-te...

  15. Metabolic flux analysis of the phenylpropanoid pathway in wound-healing potato tuber tissue using stable isotope-labeled tracer and LC-MS spectroscopy

    International Nuclear Information System (INIS)

    The metabolic flux of two phenylpropanoid metabolites, N-p-coumaroyloctopamine (p-CO) and chlorogenic acid (CGA), in the wound-healing potato tuber tissue was quantitatively analyzed by a newly developed method based upon the tracer experiment using stable isotope-labeled compounds and LC-MS. Tuber disks were treated with aqueous solution of L-phenyl-d5-alanine, and the change in the ratio of stable isotope-labeled compound to non-labeled (isotope abundance) was monitored for p-CO and CGA in the tissue extract by LC-MS. The time-dependent change in the isotope abundance of each metabolite was fitted to an equation that was derived from the formation and conversion kinetics of each compound. Good correlations were obtained between the observed and calculated isotope abundances for both p-CO and CGA. The rates of p-CO formation and conversion (i.e. fluxes) were 1.15 and 0.96 nmol (g FW)-1h-1, respectively, and for CGA, the rates 4.63 and 0.42 nmol (g FW)-1h-1, respectively. This analysis enabled a direct comparison of the biosynthetic activity between these two compounds. (author)

  16. Composición, estructura y flujo energético del meiobentos frente a Chile central Composition, structure and energy flux of the meiobenthos off central Chile

    Directory of Open Access Journals (Sweden)

    JAVIER SELLANES

    2003-09-01

    Full Text Available Se estudió la estructura de la meiofauna metazoaria (a nivel de grandes grupos taxonómicos y su rol en el flujo de energía en el subsistema bentónico frente a Concepción (~3630' S. Las muestras se recolectaron en mayo y noviembre de 1997 y mayo de 1998 en cinco sitios correspondientes a: interior de la Bahía de Concepción (28 m, boca de la bahía (35 m, plataforma interior (64 m, plataforma intermedia (88 m y plataforma externa (120 m. El periodo de estudio coincidió con el evento El Niño 1997-1998 (EN. El meiobentos resultó ser poco diverso a nivel de grandes grupos, pero con abundancias y biomasas moderadas a altas, en comparación con los valores promedio reportados en la literatura para el sublitoral fangoso. Nematoda fue el grupo dominante, con más de un 95 % (10³­10(4 ind 10 cm­2 de la densidad total, seguidos por Copepoda y Polychaeta. Las mayores abundancias y biomasas totales se encontraron siempre en la boca de la bahía, seguida de su parte interior y de la plataforma interior, mientras que los menores valores se ubicaron en la plataforma intermedia y externa. Frente a Concepción el meiobentos juega un importante rol en el flujo de energía a través del subsistema bentónico. Se estimó que estos organismos podrían estar remineralizando y/o convirtiendo a biomasa hasta un 36 y 45 % del carbono orgánico que llega desde la columna de agua a los sedimentos en el centro y en la boca de la bahía, respectivamente.The general objective of this study was to determine the structure of metazoan meiofauna (at a high taxonomic level and to estimate its role in the energy flux of the benthic sub-system off Concepción, Chile (~3630' S. Samples were collected in May and November 1997 and May 1998 at five sites located at the: inner Bay of Concepción (28 m, bay-mouth (35 m, inner-shelf (64 m, mid-shelf (88 m and outer-shelf (120 m. The study period coincided with the El Niño 1997-1998 (EN event. The diversity of the meiobenthos

  17. Comparative Analysis of Genomics and Proteomics in the New Isolated Bacillus thuringiensis X022 Revealed the Metabolic Regulation Mechanism of Carbon Flux Following Cu2+ Treatment

    Science.gov (United States)

    Quan, Meifang; Xie, Junyan; Liu, Xuemei; Li, Yang; Rang, Jie; Zhang, Tong; Zhou, Fengjuan; Xia, Liqiu; Hu, Shengbiao; Sun, Yunjun; Ding, Xuezhi

    2016-01-01

    Bacillus thuringiensis (Bt) X022 is a novel strain isolated from soil in China, and showed strong insecticidal activity against several Lepidopteran pests. In this work, we performed whole genome sequencing of this Bt strain using the next-generation sequencing technology, and further conducted a comparative analysis with the proteomics data of the specific spore-release period based on LC-MS/MS approach. The Bt X022 genome consisted of one circular chromosomal DNA and seven plasmids, which were further functionally annotated using the RAST server. Comparative analysis of insecticidal substances showed that X022 contained genes coding for three Cry proteins (Cry1Ac, Cry1Ia and Cry2Ab) and a vegetative insecticidal protein (Vip3A). However, three insecticidal crystal proteins (ICPs) (Cry1Ca, Cry1Ac and Cry1Da) were detected by proteomics in the spore-release period. Moreover, a putative biosynthetic gene cluster and the metabolic pathway for poly-β-hydroxybutyrate in Bt X022 were deduced based on the comparative analysis of genomic and proteomic data, which revealed the metabolic regulation mechanism of carbon flux correlated with increased production of ICPs caused by Cu2+. Hence, these results provided a deeper understanding of the genetic background and protein expression profile of Bt X022. This study established a foundation for directed genetic modification and further application of this new isolated Bt strain. PMID:27303381

  18. Comparative Analysis of Genomics and Proteomics in the New Isolated Bacillus thuringiensis X022 Revealed the Metabolic Regulation Mechanism of Carbon Flux Following Cu(2+) Treatment.

    Science.gov (United States)

    Quan, Meifang; Xie, Junyan; Liu, Xuemei; Li, Yang; Rang, Jie; Zhang, Tong; Zhou, Fengjuan; Xia, Liqiu; Hu, Shengbiao; Sun, Yunjun; Ding, Xuezhi

    2016-01-01

    Bacillus thuringiensis (Bt) X022 is a novel strain isolated from soil in China, and showed strong insecticidal activity against several Lepidopteran pests. In this work, we performed whole genome sequencing of this Bt strain using the next-generation sequencing technology, and further conducted a comparative analysis with the proteomics data of the specific spore-release period based on LC-MS/MS approach. The Bt X022 genome consisted of one circular chromosomal DNA and seven plasmids, which were further functionally annotated using the RAST server. Comparative analysis of insecticidal substances showed that X022 contained genes coding for three Cry proteins (Cry1Ac, Cry1Ia and Cry2Ab) and a vegetative insecticidal protein (Vip3A). However, three insecticidal crystal proteins (ICPs) (Cry1Ca, Cry1Ac and Cry1Da) were detected by proteomics in the spore-release period. Moreover, a putative biosynthetic gene cluster and the metabolic pathway for poly-β-hydroxybutyrate in Bt X022 were deduced based on the comparative analysis of genomic and proteomic data, which revealed the metabolic regulation mechanism of carbon flux correlated with increased production of ICPs caused by Cu(2+.) Hence, these results provided a deeper understanding of the genetic background and protein expression profile of Bt X022. This study established a foundation for directed genetic modification and further application of this new isolated Bt strain. PMID:27303381

  19. Central obesity and atherogenic dyslipidemia in metabolic syndrome are associated with increased risk for colorectal adenoma in a Chinese population

    Directory of Open Access Journals (Sweden)

    Lin Tsann

    2010-05-01

    Full Text Available Abstract Background Metabolic syndrome (MetS is composed of cardiovascular risk factors including insulin resistance, obesity, dyslipidemia, and hypertension. Most of the components of MetS have been linked to the development of neoplasm. The purpose of this study was to evaluate the relationship between individual components of MetS and colorectal adenoma. Methods The study subjects were recruited from a pool of 4872 individuals who underwent a health check-up examination during the period January 2006 to May 2008. Each participant fulfilled a structured questionnaire. MetS was defined based on the America Heart Association and National Heart Lung Blood Institute criteria. Subjects with history of colon cancer, colon polyps, colitis, or prior colonic surgery were excluded. Results A total of 4122 subjects were included for final analysis (2367 men and 1755 women; mean age, 49.6 ± 11.7 years. Of them, MetS was diagnosed in 708 men (29.9% and in 367 women (20.9%. Among the patients with MetS, 34.6% had adenoma, 31.7% had hyperplastic polyps and 23.3% were polyp-free (p Conclusions Of the components of MetS analyzed in this study, central obesity and dyslipidemia are independent risk factors for colorectal adenoma. With regard to the prevention of colorectal neoplasm, life-style modification such as weight reduction is worthwhile.

  20. Metabolic engineering Corynebacterium glutamicum for the L-lysine production by increasing the flux into L-lysine biosynthetic pathway.

    Science.gov (United States)

    Xu, Jianzhong; Han, Mei; Zhang, Junlan; Guo, Yanfeng; Zhang, Weiguo

    2014-09-01

    The experiments presented here were based on the conclusions of our previous results. In order to avoid introduction of expression plasmid and to balance the NADH/NAD ratio, the NADH biosynthetic enzyme, i.e., NAD-dependent glyceraldehyde-3-phosphate dehydrogenase (GADPH), was replaced by NADP-dependent GADPH, which was used to biosynthesize NADPH rather than NADH. The results indicated that the NADH/NAD ratio significantly decreased, and glucose consumption and L-lysine production drastically improved. Moreover, increasing the flux through L-lysine biosynthetic pathway and disruption of ilvN and hom, which involve in the branched amino acid and L-methionine biosynthesis, further improved L-lysine production by Corynebacterium glutamicum. Compared to the original strain C. glutamicum Lys5, the L-lysine production and glucose conversion efficiency (α) were enhanced to 81.0 ± 6.59 mM and 36.45% by the resulting strain C. glutamicum Lys5-8 in shake flask. In addition, the by-products (i.e., L-threonine, L-methionine and L-valine) were significantly decreased as results of genetic modification in homoserine dehydrogenase (HSD) and acetohydroxyacid synthase (AHAS). In fed-batch fermentation, C. glutamicum Lys5-8 began to produce L-lysine at post-exponential growth phase and continuously increased over 36 h to a final titer of 896 ± 33.41 mM. The L-lysine productivity was 2.73 g l(-1) h(-1) and the α was 47.06% after 48 h. However, the attenuation of MurE was not beneficial to increase the L-lysine production because of decreasing the cell growth. Based on the above-mentioned results, we get the following conclusions: cofactor NADPH, precursor, the flux through L-lysine biosynthetic pathway and DCW are beneficial to improve L-lysine production in C. glutamicum. PMID:24879631

  1. QED electrons penetrating into the central part of ALICE and e+e- flux near the interaction region

    CERN Document Server

    CERN. Geneva

    1993-01-01

    Evaluation of number of QED - electronics and positrons produced at a single collision of two bunches of Pb ions in LHC and registered at a distance of 10 cm from the center of interaction region along the beam axis at different radii from the axis per cm2 . MeV and total number of e+ /e- per cm2 is done for magnetic field B=0.2 T inside the detector. The average energy spectrum of these particles reaching the wall of 22 cm long beam pipe central part and its integral per single collision of two ion bunches are calculated for B=0.2 T and 1T.

  2. Central metabolism in Mycobacterium smegmatis during the transition from O2-rich to O2-poor conditions as studied by isotopomer-assisted metabolite analysis.

    Science.gov (United States)

    Tang, Yinjie J; Shui, Wenqing; Myers, Samuel; Feng, Xueyang; Bertozzi, Carolyn; Keasling, Jay D

    2009-08-01

    Isotopomer-assisted metabolite analysis was used to investigate the central metabolism of Mycobacterium smegmatis and its transition from normal growth to a non-replicating state under a hypoxic environment. Tween 80 significantly promoted aerobic growth by improving O(2) transfer, while only small amount was degraded and metabolized via the TCA cycle for biomass synthesis. As the bacillus encountered hypoxic stress, isotopomer analysis suggested: (1) isocitrate lyase activity increased, which further induced glyoxylate pathway and glycine dehydrogenase for replenishing NAD(+); (2) the relative amount of acetyl-CoA entering the TCA cycle was doubled, whereas little entered the glycolytic and pentose phosphate pathways. PMID:19357814

  3. Stage-Specific Fatty Acid Fluxes Play a Regulatory Role in Glycerolipid Metabolism during Seed Development in Jatropha curcas L.

    Science.gov (United States)

    Chaitanya, Bharatula Sri Krishna; Kumar, Sumit; Kaki, Shiva Shanker; Balakrishna, Marrapu; Karuna, Mallampalli Sri Lakshmi; Prasad, Rachapudi Badari Narayana; Sastry, Pidaparty Seshadri; Reddy, Attipalli Ramachandra

    2015-12-23

    The present study describes the changes in lipid profile as well as fatty acid fluxes during seed development in Jatropha curcas L. Endosperm from 34, 37, and 40 days after anthesis (DAA), incubated with [(14)C]acetate, showed significant synthesis of phosphatidylcholine (PC) at seed maturation. The fatty acid methyl ester profile showed PC from 34 DAA was rich in palmitic acid (16:0), whereas PC from 37 and 40 DAA was rich in oleic acid (18:1n-9). Molecular species analysis of diacylglycerol (DAG) indicated DAG (16:0/18:2n-6) was in abundance at 34 DAA, whereas DAG (18:1n-9/18:2n-6) was significantly high at 40 DAA. Triacylglycerol (TAG) analysis revealed TAG (16:0/18:2n-6/16:0) was abundant at 34 DAA, whereas TAG (18:1n-9/18:2n-6/18:1n-9) formed the majority at 40 DAA. Expression of two types of diacylglycerol acyltransferases varied with seed maturation. These data demonstrate stage-specific distinct pools of PC and DAG synthesis during storage TAG accumulation in Jatropha seed. PMID:26628196

  4. Establishing research strategies, methodologies and technologies to link genomics and proteomics to seagrass productivity, community metabolism and ecosystem carbon fluxes

    Directory of Open Access Journals (Sweden)

    Silvia eMazzuca

    2013-03-01

    Full Text Available A complete understanding of the mechanistic basis of marine ecosystem functioning is only possible through integrative and interdisciplinary research. This enables the prediction of change and possibly the mitigation of the consequences of anthropogenic impacts. One major aim of the COST Action ES0609 Seagrasses productivity. From genes to ecosystem management, is the calibration and synthesis of various methods and the development of innovative techniques and protocols for studying seagrass ecosystems.During ten days, twenty researchers representing a range of disciplines (molecular biology, physiology, botany, ecology, oceanography, underwater acoustics gathered at the marine station of STARESO (Corsica to study together the nearby Posidonia oceanica meadow. The Station de Recherches Sous-marine et Océanographiques (STARESO is located in an oligotrophic area classified as "pristine site" where environmental disturbances caused by anthropogenic pressure are exceptionally low. The healthy P. oceanica meadow, that grows in front of the lab, colonizes the sea bottom from the surface to 37 m depth. During the study, genomic and proteomic approaches were integrated with ecophysiological and physical approaches with the aim of understanding changes in seagrass productivity and metabolism at different depths and along daily cycles. In this paper we report details on the approaches utilized and we forecast the potential of the data that will come from this synergistic approach not only for P. oceanica but for seagrasses in general.

  5. Measurements of radon flux and soil-gas radon concentration along the Main Central Thrust, Garhwal Himalaya, using SRM and RAD7 detectors

    Science.gov (United States)

    Bourai, Abhay; Aswal, Sunita; Dangwal, Anoop; Rawat, Mukesh; Prasad, Mukesh; Naithani, Nagendra; Joshi, Veena; Ramola, Rakesh

    2013-08-01

    Radon in the Earth's crust or soil matrix is free to move only if its atoms find their way into pores or capillaries of the matrix. 222Rn atoms from solid mineral grains get into air, filling pores through emanation process. Then 222Rn enters into the atmosphere from air-filled pores by exhalation process. The estimation of radon flux from soil surface is an important parameter for determining the source term for radon concentration modeling. In the present investigation, radon fluxes and soil-gas radon concentration have been measured along and around the Main Central Thrust (MCT) in Uttarkashi district of Garhwal Himalaya, India, by using Scintillation Radon Monitor (SRM) and RAD7 devices, respectively. The soil radon gas concentration measured by RAD7 with soil probe at the constant depth was found to vary from 12 ± 3 to 2330 ± 48 Bq·m-3 with geometrical mean value of 302 ± 84 Bq·m-3. Th significance of this work is its usefulness from radiation protection point of view.

  6. Simulation of Canopy CO2/H2O Fluxes for a Rubber (Hevea Brasiliensis) Plantation in Central Cambodia: The Effect of the Regular Spacing of Planted Trees

    Energy Technology Data Exchange (ETDEWEB)

    Kumagai, Tomo' omi; Mudd, Ryan; Miyazawa, Yoshiyuki; Liu, Wen; Giambelluca, Thomas; Kobayashi, N.; Lim, Tiva Khan; Jomura, Mayuko; Matsumoto, Kazuho; Huang, Maoyi; Chen, Qi; Ziegler, Alan; Yin, Song

    2013-09-10

    We developed a soil-vegetation-atmosphere transfer (SVAT) model applicable to simulating CO2 and H2O fluxes from the canopies of rubber plantations, which are characterized by distinct canopy clumping produced by regular spacing of plantation trees. Rubber (Hevea brasiliensis Müll. Arg.) plantations, which are rapidly expanding into both climatically optimal and sub-optimal environments throughout mainland Southeast Asia, potentially change the partitioning of water, energy, and carbon at multiple scales, compared with traditional land covers it is replacing. Describing the biosphere-atmosphere exchange in rubber plantations via SVAT modeling is therefore essential to understanding the impacts on environmental processes. The regular spacing of plantation trees creates a peculiar canopy structure that is not well represented in most SVAT models, which generally assumes a non-uniform spacing of vegetation. Herein we develop a SVAT model applicable to rubber plantation and an evaluation method for its canopy structure, and examine how the peculiar canopy structure of rubber plantations affects canopy CO2 and H2O exchanges. Model results are compared with measurements collected at a field site in central Cambodia. Our findings suggest that it is crucial to account for intensive canopy clumping in order to reproduce observed rubber plantation fluxes. These results suggest a potentially optimal spacing of rubber trees to produce high productivity and water use efficiency.

  7. The arogenate dehydratase gene family: towards understanding differential regulation of carbon flux through phenylalanine into primary versus secondary metabolic pathways.

    Science.gov (United States)

    Corea, Oliver R A; Bedgar, Diana L; Davin, Laurence B; Lewis, Norman G

    2012-10-01

    Phe is formed from arogenate in planta through the action of arogenate dehydratase (ADT), and there are six ADT isoenzymes in the "model" vascular plant species Arabidopsis thaliana. This raised the possibility that specific ADTs may be differentially regulated so as to control Phe biosynthesis for protein synthesis vs its much more massive deployment for phenylpropanoid metabolism. In our previous reverse genetics study using 25 single/multiple ADT knockout (KO) lines, a subset of these knockouts was differentially reduced in their lignin contents. In the current investigation, it was hypothesized that Phe pool sizes might correlate well with reduction in lignin contents in the affected KO lines. The free amino acid contents of these KO lines were thus comprehensively analyzed in stem, leaf and root tissues, over a growth/developmental time course from 3 to 8 weeks until senescence. The data obtained were then compared to, and contrasted with, the differential extent of lignin deposition occurring in the various lines. Relative changes in pool sizes were also analyzed by performing a pairwise confirmatory factor analysis for Phe:Tyr, Phe:Trp and Tyr:Trp, following determination of the deviation from the mean for Phe, Tyr and Trp in each plant line. It was found that the Phe pool sizes measured were differentially reduced only in lignin-deficient lines, and in tissues and at time points where lignin biosynthesis was constitutively highly active (in wild type lines) under the growth conditions employed. In contrast, this trend was not evident across all ADT KO lines, possibly due to maintenance of Phe pools by non-targeted isoenzymes, or by feedback mechanisms known to be in place. PMID:22818526

  8. The Yeast Cyclin-Dependent Kinase Routes Carbon Fluxes to Fuel Cell Cycle Progression.

    Science.gov (United States)

    Ewald, Jennifer C; Kuehne, Andreas; Zamboni, Nicola; Skotheim, Jan M

    2016-05-19

    Cell division entails a sequence of processes whose specific demands for biosynthetic precursors and energy place dynamic requirements on metabolism. However, little is known about how metabolic fluxes are coordinated with the cell division cycle. Here, we examine budding yeast to show that more than half of all measured metabolites change significantly through the cell division cycle. Cell cycle-dependent changes in central carbon metabolism are controlled by the cyclin-dependent kinase (Cdk1), a major cell cycle regulator, and the metabolic regulator protein kinase A. At the G1/S transition, Cdk1 phosphorylates and activates the enzyme Nth1, which funnels the storage carbohydrate trehalose into central carbon metabolism. Trehalose utilization fuels anabolic processes required to reliably complete cell division. Thus, the cell cycle entrains carbon metabolism to fuel biosynthesis. Because the oscillation of Cdk activity is a conserved feature of the eukaryotic cell cycle, we anticipate its frequent use in dynamically regulating metabolism for efficient proliferation. PMID:27203178

  9. The carbon storage regulator (Csr system exerts a nutrient-specific control over central metabolism in Escherichia coli strain Nissle 1917.

    Directory of Open Access Journals (Sweden)

    Olga Revelles

    Full Text Available The role of the post-transcriptional carbon storage regulator (Csr system in nutrient utilization and in the control of the central metabolism in E. coli reference commensal strain Nissle 1917 was investigated. Analysis of the growth capabilities of mutants altered for various components of the Csr system (csrA51, csrB, csrC and csrD mutations showed that only the protein CsrA - the key component of the system - exerts a marked role in carbon nutrition. Attenuation of CsrA activity in the csrA51 mutant affects the growth efficiency on a broad range of physiologically relevant carbon sources, including compounds utilized by the Entner-Doudoroff (ED pathway. Detailed investigations of the metabolomes and fluxomes of mutants and wild-type cells grown on carbon sources representative of glycolysis and of the ED pathway (glucose and gluconate, respectively, revealed significant re-adjusting of central carbon metabolism for both compounds in the csrA51 mutant. However, the metabolic re-adjusting observed on gluconate was strikingly different from that observed on glucose, indicating a nutrient-specific control of metabolism by the Csr system.

  10. The carbon storage regulator (Csr) system exerts a nutrient-specific control over central metabolism in Escherichia coli strain Nissle 1917.

    Science.gov (United States)

    Revelles, Olga; Millard, Pierre; Nougayrède, Jean-Philippe; Dobrindt, Ulrich; Oswald, Eric; Létisse, Fabien; Portais, Jean-Charles

    2013-01-01

    The role of the post-transcriptional carbon storage regulator (Csr) system in nutrient utilization and in the control of the central metabolism in E. coli reference commensal strain Nissle 1917 was investigated. Analysis of the growth capabilities of mutants altered for various components of the Csr system (csrA51, csrB, csrC and csrD mutations) showed that only the protein CsrA - the key component of the system - exerts a marked role in carbon nutrition. Attenuation of CsrA activity in the csrA51 mutant affects the growth efficiency on a broad range of physiologically relevant carbon sources, including compounds utilized by the Entner-Doudoroff (ED) pathway. Detailed investigations of the metabolomes and fluxomes of mutants and wild-type cells grown on carbon sources representative of glycolysis and of the ED pathway (glucose and gluconate, respectively), revealed significant re-adjusting of central carbon metabolism for both compounds in the csrA51 mutant. However, the metabolic re-adjusting observed on gluconate was strikingly different from that observed on glucose, indicating a nutrient-specific control of metabolism by the Csr system. PMID:23840455

  11. Determining the Central Atlantic Magmatic Province (CAMPS)'s Role in the Increased Flux of CO2 in the end-Triassic Mass Extinction

    Science.gov (United States)

    Srinivasan, P. S.; Bachan, A.; Stanford School of Earth Sciences Department of Paleobiology

    2011-12-01

    The Central Atlantic Magmatic Province (CAMP) is one of the largest flood basalt provinces known. Its empacement coincided with a period of major plant and animal extinctions-the end-Triassic mass extinction. It is postulated that the release of large amounts of carbon dioxide into the atmosphere from the volcanics was one of the causes of this mass extinction. However,the magnitude of impact on ocean chemistry, and timescales involved remain unclear. To determine CAMP's role in this increased flux of CO2, we studied the geochemistry of samples of rock from the Triassic-Jurassic boundary, in northern Italy. Specifically, by observing the ratios of carbon isotopes 12 and 13 in the organic carbon found in these limestone sedimentary rocks, we could determine the ratio of carbonate to organic burial fluxes globally. We drilled limestone rocks from two different sections in the Southern Alps-- Pozzo Glaciale and Val Adrara. Once they were drilled to a fine powder-like form, we acidified the CaCO3 with HCl to isolate the organic carbon. Then, the organic matter was cleaned to rid the acid, and eventually was placed into tin foil to be placed into the Elemental Analyzer, which determined the percent Carbon in each sample. We tested about 200 samples, and placed them into the Mass Spectrometer machine to determine the isotopic ratios of C12 and C13. According to the data, there was a positive excursion for both sample sets, which means that there was an increase in the amount of C13 in the organic matter. The duration of this excursion was at least a few hundred thousand years. This suggests a protracted increase in the burial flux of organic carbon globally, which is consistent with the hypothesized volcanically driven increase in CO2. This further bolsters the contention that CAMP was responsible, in part, for this mass extinction. By studying the earth's recovery from increased carbon fluxes in the past, we can predict the recovery path that our anthropogenically

  12. Functionally ecological assessment of C dominant pools and fluxes in field agroecosystems with sod-podzoluvosols at the Central Region of Russia

    Science.gov (United States)

    Mazirov, Ilya; Vizirskaya, Mariya; Epikhina, Anna; Vasenev, Ivan; Valentini, Riccardo; Meshalkina, Julia

    2014-05-01

    The Global Change problem has obvious interaction with greenhouse gases (GHG) emission. The principal GHG is carbon dioxide. There is a lot of data on its fluxes but the Central Region of Russia is still one of less investigated area especially in case of agroecosystem carbon dioxide fluxes monitoring by chambers and eddy covariance methods combined application. Our research has been at the representative key plots of cultivated sod-podzoluvosols located at the Precision Farming Experimental Field of the Russian Timiryazev State Agricultural University (Moscow) in 2012-2013 in frame of RF Government grant 11.G34.31.0079 and RFBR grant 11-04-01376 activities. The research include the detailed soil cover patterns morphogenetic investigation, soil C pools dynamic analysis, soil CO2 flux decade-based monitoring by method of exposition chambers with IRGA (infra red gas analyzer) and agroecosystem CO2 flux seasonal monitoring by two eddy covariance stations in frame of 4 ha experimental plot. There were two crop versions (barley and grass mixture), and in case of chamber analysis - also two agrotecnology versions (traditional and no-till ones) with soil temperature and moisture analysis too. The results have shown high daily and seasonal dynamic of soil and agroecosystem CO2 emission. The beginning of vegetation period (until plant height of 10-12 cm) is characterized by high average soil CO2 emission and adsorption at the same time. The adsorption is significantly higher. The resulted CO2 absorption during the day is approximately two times higher than emissions at night. After harvesting CO2 emission is becoming essentially higher than adsorption. In 2012 data have shown for barley the small predominance of CO2 emissions over the absorption. The daily dynamics of soil CO2 emissions depends on the air temperature dynamics with the correlation coefficient changes from 0.86 at the beginning of the season to 0.52 and 0.38 at the middle and at the end of one. Soil moisture

  13. A fuzzy logic controller based approach to model the switching mechanism of the mammalian central carbon metabolic pathway in normal and cancer cells.

    Science.gov (United States)

    Dasgupta, Abhijit; Paul, Debjyoti; De, Rajat K

    2016-07-19

    Dynamics of large nonlinear complex systems, like metabolic networks, depend on several parameters. A metabolic pathway may switch to another pathway in accordance with the current state of parameters in both normal and cancer cells. Here, most of the parameter values are unknown to us. A fuzzy logic controller (FLC) has been developed here for the purpose of modeling metabolic networks by approximating the reasons for the behaviour of a system and applying expert knowledge to track switching between metabolic pathways. The simulation results can track the switching between glycolysis and gluconeogenesis, as well as glycolysis and pentose phosphate pathways (PPP) in normal cells. Unlike normal cells, pyruvate kinase (M2 isoform) (PKM2) switches alternatively between its two oligomeric forms, i.e. an active tetramer and a relatively low activity dimer, in cancer cells. Besides, there is a coordination among PKM2 switching and enzymes catalyzing PPP. These phenomena help cancer cells to maintain their high energy demand and macromolecular synthesis. However, the reduction of initial adenosine triphosphate (ATP) to a very low concentration, decreasing initial glucose uptake, destroying coordination between glycolysis and PPP, and replacement of PKM2 by its relatively inactive oligomeric form (dimer) or inhibition of the translation of PKM2 may destabilize the mutated control mechanism of the mammalian central carbon metabolic (CCM) pathway in cancer cells. The performance of the model is compared appropriately with some existing ones. PMID:27225801

  14. Dissolved organic matter and lake metabolism: Biogeochemistry and controls of nutrient flux dynamics in lakes: Technical progress report, 1 July 1987--30 June 1988

    Energy Technology Data Exchange (ETDEWEB)

    Wetzel, R.G.

    1988-01-01

    Our work has continued and expanded in the region of nutrient fluxes, uptake mechanisms, and recycling in microcommunities on the plants and within the plants. Limiting nutrient factors are dissolved inorganic carbon, phosphorus, and in some cases, nitrogen. The macrophyte-epiphyte complex exists in a viscous medium where regions of greatly reduced flow and no turbulence occur at surfaces. As a result of the greatly reduced flow, lack of turbulence,and extremely slow rate of diffusion in water, diffusional processes predominate within the boundary layer. During periods of high metabolic activity (i.e., during photosynthesis) nutrients are likely to become depleted within the boundary layer, constraining production and placing the macrophyte and associated microflora in direct nutrient competition. Once nutrients have entered the complex via diffusion or sedimentation from the bulk phase, or uptake through the macrophyte rhizosphere, exit across the boundary layer is retarded. The close juxtaposition of the biota results in a rapid cycling and, ultimately, in concentration of nutrients. This occurs until the end of the macrophyte vegetative life span when the supporting macrophyte loses its integrity and release of dissolved matter exceeds the retentive capacity of the microbiota. A quantity of this material released by the macrophyte is retained in the epiphyton when the macrophyte-epiphyte complex sinks to the sediment. 324 refs., 6 figs.

  15. Rapid generation of CRISPR/dCas9-regulated, orthogonally repressible hybrid T7-lac promoters for modular, tuneable control of metabolic pathway fluxes in Escherichia coli.

    Science.gov (United States)

    Cress, Brady F; Jones, J Andrew; Kim, Daniel C; Leitz, Quentin D; Englaender, Jacob A; Collins, Shannon M; Linhardt, Robert J; Koffas, Mattheos A G

    2016-05-19

    Robust gene circuit construction requires use of promoters exhibiting low crosstalk. Orthogonal promoters have been engineered utilizing an assortment of natural and synthetic transcription factors, but design of large orthogonal promoter-repressor sets is complicated, labor-intensive, and often results in unanticipated crosstalk. The specificity and ease of targeting the RNA-guided DNA-binding protein dCas9 to any 20 bp user-defined DNA sequence makes it a promising candidate for orthogonal promoter regulation. Here, we rapidly construct orthogonal variants of the classic T7-lac promoter using site-directed mutagenesis, generating a panel of inducible hybrid promoters regulated by both LacI and dCas9. Remarkably, orthogonality is mediated by only two to three nucleotide mismatches in a narrow window of the RNA:DNA hybrid, neighboring the protospacer adjacent motif. We demonstrate that, contrary to many reports, one PAM-proximal mismatch is insufficient to abolish dCas9-mediated repression, and we show for the first time that mismatch tolerance is a function of target copy number. Finally, these promoters were incorporated into the branched violacein biosynthetic pathway as dCas9-dependent switches capable of throttling and selectively redirecting carbon flux in Escherichia coli We anticipate this strategy is relevant for any promoter and will be adopted for many applications at the interface of synthetic biology and metabolic engineering. PMID:27079979

  16. Particle fluxes and their drivers in the Avilés submarine canyon and adjacent slope, central Cantabrian margin, Bay of Biscay

    Science.gov (United States)

    Rumín-Caparrós, A.; Sanchez-Vidal, A.; González-Pola, C.; Lastras, G.; Calafat, A.; Canals, M.

    2016-05-01

    The Avilés Canyon in the central Cantabrian margin is one of the largest submarine canyons in Europe, extending from the shelf edge at 130 m depth to 4765 m depth in the Biscay abyssal plain. In this paper we present the results of a year-round (March 2012 to April 2013) study of particle fluxes in this canyon and the adjacent continental slope. Three mooring lines equipped with automated sequential sediment traps, high-accuracy conductivity-temperature recorders and current meters allowed measuring total mass fluxes and their major components (lithogenics, calcium carbonate, opal and organic matter) in the settling material jointly with a set of environmental parameters. The integrated analysis of the data obtained from the moorings together with remote sensing images and meteorological and hydrographical data has shed light on the sources of particles and the across- and along margin mechanisms involved in their transfer to the deep. Our results allow interpreting the dynamics of the sedimentary particles in the study area. Two factors play a critical role: (i) direct delivery of river-sourced material to the narrow continental shelf, and (ii) major resuspension events caused by large waves and near bottom currents developing at the occasion of the rather frequent severe storms that are typical of the Cantabrian Sea. Wind direction and subsequent wind-driven currents largely determine the way sedimentary particles reach the canyon. While westerly winds favour the injection of sediments into the Avilés Canyon mainly by building an offshore transport in the bottom Ekman layer, easterly winds ease the offshore advection of particulate matter towards the Avilés Canyon and its adjacent western slope principally through the surface Ekman layer. Furthermore, repeated cycles of semidiurnal tides add an extra amount of energy to the prevailing bottom currents and actively contribute to keep a permanent background of suspended particles in near-bottom waters. High

  17. Synoptic evaluation of carbon cycling in Beaufort Sea during summer: contrasting river inputs, ecosystem metabolism and air–sea CO2 fluxes

    Directory of Open Access Journals (Sweden)

    A. Forest

    2013-10-01

    Full Text Available The accelerated decline in Arctic sea ice combined with an ongoing trend toward a more dynamic atmosphere is modifying carbon cycling in the Arctic Ocean. A critical issue is to understand how net community production (NCP; the balance between gross primary production and community respiration responds to changes and modulates air–sea CO2 fluxes. Using data collected as part of the ArcticNet-Malina 2009 expedition in southeastern Beaufort Sea (Arctic Ocean, we synthesize information on sea ice, wind, river, water column properties, metabolism of the planktonic food web, organic carbon fluxes and pools, as well as air–sea CO2 exchange, with the aim of identifying indices of ecosystem response to environmental changes. Data were analyzed to develop a non-steady-state carbon budget and an assessment of NCP against air–sea CO2 fluxes. The mean atmospheric forcing was a mild upwelling-favorable wind (~5 km h−1 blowing from the N-E and a decaying ice cover (2 with a mean uptake rate of −2.0 ± 3.3 mmol C m−2d−1. We attribute this discrepancy to: (1 elevated PP rates (>600 mg C m−2d−1 over the shelf prior to our survey, (2 freshwater dilution by river runoff and ice melt, and (3 the presence of cold surface waters offshore. Only the Mackenzie River delta and localized shelf areas directly affected by upwelling were identified as substantial sources of CO2 to the atmosphere (>10mmol C m−2d−1. Although generally −2d−1, daily PP rates cumulated to a total PP of ~437.6 × 103 t C, which was roughly twice higher than the organic carbon delivery by river inputs (~241.2 × 103 t C. Subsurface PP represented 37.4% of total PP for the whole area and as much as ~72.0% seaward of the shelf break. In the upper 100 m, bacteria dominated (54% total community respiration (~250 mg C m−2d−1, whereas protozoans, metazoans, and benthos, contributed to 24%, 10%, and 12%, respectively. The range of production-to-biomass ratios of bacteria was

  18. Studies on the effect of cell cycle arrest on central metabolism in the diatom Phaeodactylum tricornutum, using physiological and systems biology approaches

    Science.gov (United States)

    Kim, Joomi

    Diatoms (Bacillarophyceae) are photosynthetic unicellular microalgae that have risen to ecological prominence in the modern oceans over the past 30 million years. They are excellent candidates for biodiesel feedstocks. Global climate change has led to an interest in algal triacylglycerols (TAGs) as feedstocks for sustainable biodiesel, and diatoms are attractive candidates for TAG production as one of the most productive and environmentally flexible algae in the contemporary oceans. For Chapter 2, a genome-scale metabolic model was constructed to calculate intracellular fluxes of a diatom under different growth conditions. The model identified enzymes that may be relevant to increasing lipid synthesis, explored how transporters affect flux outputs, and explored unusual features of diatoms, including the Entner-Douderoff and phosphoketolase pathways, and glycolytic enzymes in their mitochondria. Chapter 3 discusses how cell cycle arrest via cyclin-dependent kinase (Cdk) inhibition, can increase accumulation of TAGs, and shift metabolism away from protein synthesis. For Chapter 4, transcriptome analysis of cells under cell cycle arrest was performed to show that the pattern of gene expression was fundamentally different from nitrogen stress. Most of the genes related to fatty acid and TAG synthesis were up-regulated. The gene expression pattern for light harvesting complexes was similar to cells stressed by high light, suggesting that arrested cells have smaller sinks for photosynthetically generated electrons.

  19. Sources of methane and nitrous oxide in California's Central Valley estimated through direct airborne flux and positive matrix factorization source apportionment of groundbased and regional tall tower measurements

    Science.gov (United States)

    Guha, Abhinav

    concentration enhancements into major source categories along with direct emissions estimates from airborne observations. We perform high-precision measurements of greenhouse gases using gas analyzers based on absorption spectroscopy, and other source marker volatile organic compounds (VOCs) using state of the art VOC measurement systems (e.g. proton transfer reaction mass spectrometry). We combine these measurements with a statistical source apportionment technique called positive matrix factorization (PMF) to evaluate and investigate the major local sources of CH4 and N2O during CalNex and Walnut Grove campaigns. In the CABERNET study, we combine measurements with an airborne approach to a well-established micrometeorological technique (eddy-covariance method) to derive CH4 fluxes over different source regions in the Central Valley. In the CalNex experiments, we demonstrate that dairy and livestock remains the largest source sector of non-CO2 greenhouse gases in the San Joaquin Valley contributing most of the CH4 and much of the measured N2O at Bakersfield. Agriculture is observed to provide another major source of N2O, while vehicle emissions are found to be an insignificant source of N2O, contrary to the current statewide greenhouse gas inventory which includes vehicles as a major source. Our PMF source apportionment also produces an evaporative/fugitive factor but its relative lack of CH4 contributions points to removal processes from vented emissions in the surrounding O&G industry and the overwhelming dominance of the dairy CH4 source. In the CABERNET experiments, we report enhancements of CH4 from a number of sources spread across the spatial domain of the Central Valley that improves our understanding of their distribution and relative strengths. We observe large enhancements of CH4 mixing ratios over the dairy and feedlot intensive regions of Central Valley corresponding with significant flux estimates that are larger than CH4 emission rates reported in the greenhouse

  20. Metabolic Syndrome in Italian Obese Children and Adolescents: Stronger Association with Central Fat Depot than with Insulin Sensitivity and Birth Weight

    Directory of Open Access Journals (Sweden)

    Claudia Brufani

    2011-01-01

    Full Text Available Aim. To evaluate whether body fat distribution, birth weight, and family history for diabetes (FHD were associated with metabolic syndrome (MetS in children and adolescents. Methods. A total of 439 Italian obese children and adolescents (5–18 years were enrolled. Subjects were divided into 2 groups: prepubertal and pubertal. MetS was diagnosed according to the adapted National Cholesterol Education Program criteria. Birth weight percentile, central obesity index (measured by dual-energy X-ray absorptiometry, insulin sensitivity (ISI, and disposition index were evaluated. Multivariate logistic regression models were used to determine variables associated with MetS. Results. The prevalence of MetS was 17%, with higher percentage in adolescents than in children (21 versus 12%. In the overall population, central obesity index was a stronger predictor of MetS than insulin sensitivity and low birth weight. When the two groups were considered, central fat depot remained the strongest predictor of MetS, with ISI similarly influencing the probability of MetS in the two groups and birth weight being negatively associated to MetS only in pubertal individuals. Neither FHD nor degree of fatness was a significant predictor of MetS. Conclusion. Simple clinical parameters like increased abdominal adiposity and low birth weight could be useful tools to identify European obese adolescents at risk for metabolic complications.

  1. Pathway confirmation and flux analysis of central metabolicpathways in Desulfovibrio vulgaris Hildenborough using gaschromatography-mass spectrometry and fourier transform-ion cyclotronresonance mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Yinjie; Pingitore, Francesco; Mukhopadhyay, Aindrila; Phan,Richard; Hazen, Terry C.; Keasling, Jay D.

    2006-07-11

    It has been proposed that during growth under anaerobic oroxygen-limited conditions Shewanella oneidensis MR-1 uses theserine-isocitrate lyase pathway common to many methylotrophic anaerobes,in which formaldehyde produced from pyruvate is condensed with glycine toform serine. The serine is then transformed through hydroxypyruvate andglycerate to enter central metabolism at phosphoglycerate. To examine itsuse of the serine-isocitrate lyase pathway under anaerobic conditions, wegrew S. oneidensis MR-1 on [1-13C]lactate as the sole carbon source witheither trimethylamine N-oxide (TMAO) or fumarate as an electron acceptor.Analysis of cellular metabolites indicates that a large percentage(>75 percent) of lactate was partially oxidized to either acetate orpyruvate. The 13C isotope distributions in amino acids and other keymetabolites indicate that, under anaerobic conditions, a complete serinepathway is not present, and lactate is oxidized via a highly reversibleserine degradation pathway. The labeling data also suggest significantactivity in the anaplerotic (malic enzyme and phosphoenolpyruvatecarboxylase) and glyoxylate shunt (isocitrate lyase and malate synthase)reactions. Although the tricarboxylic acid (TCA) cycle is often observedto be incomplete in many other anaerobes (absence of 2-oxoglutaratedehydrogenase activity), isotopic labeling supports the existence of acomplete TCA cycle in S. oneidensis MR-1 under TMAO reductioncondition.

  2. Enhanced H2 Production and Redirected Metabolic Flux via Overexpression of fhlA and pncB in Klebsiella HQ-3 Strain.

    Science.gov (United States)

    Jawed, Muhammad; Pi, Jian; Xu, Li; Zhang, Houjin; Hakeem, Abdul; Yan, Yunjun

    2016-03-01

    Genetic modifications are considered as one of the most important technologies for improving fermentative hydrogen yield. Herein, we overexpress fhlA and pncB genes from Klebsiella HQ-3 independently to enhance hydrogen molar yield. HQ-3-fhlA/pncB strain is developed by manipulation of pET28-Pkan/fhlA Kan(r) and pBBR1-MCS5/pncB Gm(r) as expression vectors to examine the synchronous effects of fhlA and pncB. Optimization of anaerobic batch fermentations is achieved and the maximum yield of biohydrogen (1.42 mol H2/mol of glucose) is produced in the range of pH 6.5-7.0 at 33-37 °C. Whole cell H2 yield is increased up to 40 % from HQ-3-fhlA/pncB, as compared with HQ-3-fhlA 20 % and HQ-3-pncB 12 % keeping HQ-3-C as a control. Mechanism of improved H2 yield is studied in combination with metabolic flux analysis by measuring glucose consumption and other metabolites including formate, succinate, 2,3 butanediol, lactate, acetate, ethanol, and hydrogen. The results suggest that under transient conditions, the increase in the total level of NAD by NAPRTase can enhance the rate of NADH-dependent pathways, and therefore, final distribution of metabolites is changed. Combined overexpression of fhlA and pncB eventually modifies the energy and carbon balance leading to enhanced H2 production from FHL as well as by NADH pathway. PMID:26590848

  3. Changes in the Phosphoproteome and Metabolome Link Early Signaling Events to Rearrangement of Photosynthesis and Central Metabolism in Salinity and Oxidative Stress Response in Arabidopsis.

    Science.gov (United States)

    Chen, Yanmei; Hoehenwarter, Wolfgang

    2015-12-01

    Salinity and oxidative stress are major factors affecting and limiting the productivity of agricultural crops. The molecular and biochemical processes governing the plant response to abiotic stress have often been researched in a reductionist manner. Here, we report a systemic approach combining metabolic labeling and phosphoproteomics to capture early signaling events with quantitative metabolome analysis and enzyme activity assays to determine the effects of salt and oxidative stress on plant physiology. K(+) and Na(+) transporters showed coordinated changes in their phosphorylation pattern, indicating the importance of dynamic ion homeostasis for adaptation to salt stress. Unique phosphorylation sites were found for Arabidopsis (Arabidopsis thaliana) SNF1 kinase homolog10 and 11, indicating their central roles in the stress-regulated responses. Seven Sucrose Non-fermenting1-Related Protein Kinase2 kinases showed varying levels of phosphorylation at multiple serine/threonine residues in their kinase domain upon stress, showing temporally distinct modulation of the various isoforms. Salinity and oxidative stress also lead to changes in protein phosphorylation of proteins central to photosynthesis, in particular the kinase State Transition Protein7 required for state transition and light-harvesting II complex proteins. Furthermore, stress-induced changes of the phosphorylation of enzymes of central metabolism were observed. The phosphorylation patterns of these proteins were concurrent with changes in enzyme activity. This was reflected by altered levels of metabolites, such as the sugars sucrose and fructose, glycolysis intermediates, and amino acids. Together, our study provides evidence for a link between early signaling in the salt and oxidative stress response that regulates the state transition of photosynthesis and the rearrangement of primary metabolism. PMID:26471895

  4. The carbon storage regulator (Csr) system exerts a nutrient-specific control over central metabolism in Escherichia coli strain nissle 1917

    OpenAIRE

    Revelles, Olga; Millard, Pierre; Nougayrede, Jean-Philippe; Dobrindt, Ulrich; Oswald, Eric; Létisse, Fabien; Portais, Jean-Charles

    2013-01-01

    The role of the post-transcriptional carbon storage regulator (Csr) system in nutrient utilization and in the control of the central metabolism in E. coli reference commensal strain Nissle 1917 was investigated. Analysis of the growth capabilities of mutants altered for various components of the Csr system (csrA51, csrB, csrC and csrD mutations) showed that only the protein CsrA - the key component of the system - exerts a marked role in carbon nutrition. Attenuation of CsrA activity in the c...

  5. The glycolytic flux in Escherichia coli is controlled by the demand for ATP

    DEFF Research Database (Denmark)

    Købmann, Brian Jensen; Westerhoff, H.V.; Snoep, J.L.; Nilsson, D.; Jensen, Peter Ruhdal

    2002-01-01

    The nature of the control of glycolytic flux is one of the central, as-yet-uncharacterized issues in cellular metabolism. We developed a molecular genetic tool that specifically induces ATP hydrolysis in living cells without interfering with other aspects of metabolism. Genes encoding the F-1 par.......e., the cells are mostly "carbon" limited. Ways to increase the efficiency and productivity of industrial fermentation processes are discussed....... optimizing additional ATP hydrolysis, we increased the flux through glycolysis to 1.7 times that of the wild-type flux. The results demonstrate why attempts in the past to increase the glycolytic flux through overexpression of glycolytic enzymes have been unsuccessful: the majority of flux control (> 75...

  6. Long-term investigations of summertime chlorophyll a, particulate organic carbon and continuously observations of vertical particle flux in Fram Strait and the central Arctic Ocean

    Science.gov (United States)

    Nöthig, Eva-Maria; Bauerfeind, Eduard; Bracher, Astrid; Cherkasheva, Alexandra; Fahl, Kirsten; Lalande, Catherine; Metfies, Katja; Peeken, Ilka; Salter, Ian; Boetius, Antje; Soltwedel, Thomas

    2016-04-01

    The Arctic Ocean is one of the key regions where the effect of climate change is most pronounced due to massive reduction of sea ice volume and extent. Most of the sea ice is transported out of the Arctic Ocean with the cold East Greenland Current (EGC) in the western Fram Strait, while warm Atlantic water enters the Arctic Ocean with the West Spitsbergen Current (WSC) in the eastern Fram Strait. In this scenario we conducted several cruises to Fram Strait and the central Arctic Ocean (CAO) between 1991 and 2015 to monitor phytoplankton biomass, particulate organic carbon standing stocks during summer at discrete depth using water bottle samples, and the sedimentation of organic matter by means of moored sediment traps throughout the year. With our study we aim at tracing effects of environmental changes in the pelagic system and impacts on the fate of organic matter produced in the upper water column in a region that is anticipated to react rapidly to climate change. We will present data sets of phytoplankton biomass (chlorophyll a) and particulate organic carbon (POC) from the upper 100 m of the water column as well as results from vertical particle flux measurements with yearly deployed sediment traps at the LTER (Long-Term Ecological Research) observatory HAUSGARTEN in eastern Fram Strait (79°/4°E) between 2000 and 2012 and from two locations in the CAO close to the Lomonosov Ridge (1995/96) and the Gakkel Ridge (2011/12). Analyses of the material collected by the sediment traps allowed us to track seasonal and inter-annual changes in the upper water column at HAUSGARTEN and in the CAO. Whereas chlorophyll a (integrated values 0 -100 m) showed only a slight increase in eastern Fram Strait, it stayed more or less constant in the CAO and western Fram Strait, with the exception of 2015 exhibiting less biomass during late summer in the CAO. Highest biomass was found in the eastern Fram Strait and lowest in the heavily ice-covered regions. POC distribution

  7. Comparison of CO2 fluxes in a larch forest on permafrost and a pine forest on non-permafrost soils in Central Siberia

    Science.gov (United States)

    Zyryanov, V.; Tchebakova, N. M.; Nakai, Y.; Zyryanova, O.; Parfenova, E. I.; Matsuura, Y.; Vygodskaya, N.

    2013-12-01

    Inter-annual and seasonal variations of energy, water and carbon fluxes and associated climate variables in a middle taiga pine (Pinus sylvestris) forest on warm sandy soils and a northern taiga larch (Larix gmelini) forest on permafrost in Central Siberia were studied from eddy covariance measurements obtained during growing seasons of 1998-2000 and 2004-2008 (except 2006) respectively. Both naturally regenerated after fire forests grew in different environments and differed by their tree stand characteristics. The pure Gmelin larch stand was 105 yr old, stem density of living trees was about 5480 trees/ha, LAI was 0.6 m2/m2, biomass (dry weight) was 0.0044 kg/m2, with average diameter of the trees at breast height 7.1 cm and mean tree height 6.8 m. The pure Scots pine stand was 215 yr old, stand structure was relatively homogenous with a stem density of 468 living trees/ha, LAI was 1.5 m2/m2, biomass (dry weight) was 10.7 kg/m2, with average diameter of the trees at breast height 28 cm and mean tree height 23 m. The climatic and soil conditions of these ecosystems were very distinctive. The habitat of the larch forest was much colder and dryer than that of the pine forest: the growing season was 1 month shorter and growing-degree days 200°C less and winters were about one month longer and colder with January temperature -37°C versus -23°C; annual precipitation was 400 mm in the larch versus 650 mm in the pine forest and maximal snow pack was 40 cm vs 70 cm. The soils were Gelisols with permafrost table within the upper 1 m in the larch stand and Pergelic Cryochrept, alluvial sandy soil with no underlying permafrost. Average daily net ecosystem exchange (NEE) was significantly smaller in the larch ecosystem - (-3-6) μmol/m2s compared to that in the pine forest (-7-8) μmol/m2s, however daily maximal NEE was about the same. Seasonal NEE in the larch forest on continuous permafrost varied from -53 to -107 and in the pine forest on non-permafrost from -180 to

  8. Effects of wind farm construction on concentrations and fluxes of dissolved organic carbon and suspended sediment from peat catchments at Braes of Doune, central Scotland

    Directory of Open Access Journals (Sweden)

    I. Grieve

    2008-07-01

    Full Text Available This paper assesses the impacts of disturbance associated with the construction of a wind farm on fluxes of dissolved organic carbon (DOC and suspended sediment from a blanket peat catchment in central Scotland during the period immediately following completion of construction. Six streams draining the site were sampled on six dates from October 2006, when construction was completed, and an additional three control streams to the west of the site were sampled on the same dates. Turbidity and stage were recorded semi-continuously in the two largest streams (one disturbed and one control, which were also sampled during storm events. Absorbance (400 nm and DOC concentrations were determined on all samples, and suspended sediment was determined on the event samples. Absorbance and DOC were closely correlated in both the disturbed and undisturbed streams, with slightly greater absorbance per unit DOC in the disturbed streams. DOC concentrations in disturbed tributaries were always greater than those in undisturbed streams, with mean differences ranging from 2 to around 5 mg L-1. DOC and stage were positively correlated during events with maximum concentrations in excess of 30 mg L 1 at peak flow. Suspended sediment concentrations were markedly elevated in the disturbed stream with maximum concentrations at peak flow some 4–5 times greater than in the control. The colour of the sediment suggested that it was highly organic in nature at peak flow, and suspended particulate organic carbon represented a further loss of C from the site. Using flow-weighted mean DOC concentrations calculated for the storms monitored in autumn 2007, dissolved carbon losses can be estimated for the catchments of the disturbed and control streams. From these data the additional DOC loss related to disturbance associated with the wind farm is estimated at 5 g m-2.

  9. N2O and CH4 fluxes in Undisturbed and Burned Holm oak, Scots pine and Pyrenean oak forests in Central Spain

    OpenAIRE

    Inclán Cuartas, Rosa; Uribe Vallejos, Carla; Sánchez Martín, Laura; Sánchez Ledesma, Dolores María; Clavero Sánchez, M. Angeles; Fernández Díaz, Ana Maria; Morante Sánchez, Ramón; Blanco Andray, Alfredo; Jandl, Robert

    2010-01-01

    We investigated N2O and CH4 fluxes from soils of Quercus ilex, Quercus pyrenaica and Pinus sylvestris stands located in the surrounding area of Madrid (Spain). The fluxes were measured for 18 months from both mature stands and post fire stands using the static chamber technique. Simultaneously with gas fluxes, soil temperature, soil water content, soil C and soil N were measured in the stands. Nitrous oxide fluxes ranged from −11.43 to 8.34 μg N2O–N m−2 h−1 in Q.ilex, −7.74 to 13.52 μg N2O–N ...

  10. An Orange Ripening Mutant Links Plastid NAD(P)H Dehydrogenase Complex Activity to Central and Specialized Metabolism during Tomato Fruit Maturation[C][W

    Science.gov (United States)

    Nashilevitz, Shai; Melamed-Bessudo, Cathy; Izkovich, Yinon; Rogachev, Ilana; Osorio, Sonia; Itkin, Maxim; Adato, Avital; Pankratov, Ilya; Hirschberg, Joseph; Fernie, Alisdair R.; Wolf, Shmuel; Usadel, Björn; Levy, Avraham A.; Rumeau, Dominique; Aharoni, Asaph

    2010-01-01

    In higher plants, the plastidial NADH dehydrogenase (Ndh) complex supports nonphotochemical electron fluxes from stromal electron donors to plastoquinones. Ndh functions in chloroplasts are not clearly established; however, its activity was linked to the prevention of the overreduction of stroma, especially under stress conditions. Here, we show by the characterization of OrrDs, a dominant transposon-tagged tomato (Solanum lycopersicum) mutant deficient in the NDH-M subunit, that this complex is also essential for the fruit ripening process. Alteration to the NDH complex in fruit changed the climacteric, ripening-associated metabolites and transcripts as well as fruit shelf life. Metabolic processes in chromoplasts of ripening tomato fruit were affected in OrrDs, as mutant fruit were yellow-orange and accumulated substantially less total carotenoids, mainly β-carotene and lutein. The changes in carotenoids were largely influenced by environmental conditions and accompanied by modifications in levels of other fruit antioxidants, namely, flavonoids and tocopherols. In contrast with the pigmentation phenotype in mature mutant fruit, OrrDs leaves and green fruits did not display a visible phenotype but exhibited reduced Ndh complex quantity and activity. This study therefore paves the way for further studies on the role of electron transport and redox reactions in the regulation of fruit ripening and its associated metabolism. PMID:20571113

  11. Moderate voluntary exercise attenuates the metabolic syndrome in melanocortin-4 receptor-deficient rats showing central dopaminergic dysregulation

    Directory of Open Access Journals (Sweden)

    Silvana Obici

    2015-10-01

    Conclusions: Central dopamine dysregulation during VWR reinforces the link between MC4R function and molecular and behavioral responding to rewards. The data also suggest that exercise can be a successful lifestyle intervention in MC4R-haploinsufficient individuals despite reduced positive reinforcement during exercise training.

  12. Partial Amelioration of Peripheral and Central Symptoms of Huntington’s Disease via Modulation of Lipid Metabolism

    Science.gov (United States)

    Chen, Jane Y.; Tran, Conny; Hwang, Lin; Deng, Gang; Jung, Michael E.; Faull, Kym F.; Levine, Michael S.; Cepeda, Carlos

    2016-01-01

    Background Huntington’s disease (HD) is a fatal, inherited neurodegenerative disorder characterized by uncontrollable dance-like movements, as well as cognitive deficits and mood changes. A feature of HD is a metabolic disturbance that precedes neurological symptoms. In addition, brain cholesterol synthesis is significantly reduced, which could hamper synaptic transmission. Objective Alterations in lipid metabolism as a potential target for therapeutic intervention in the R6/2 mouse model of HD were examined. Methods Electrophysiological recordings in vitro examined the acute effects of cholesterol-modifying drugs. In addition, behavioral testing, effects on synaptic activity, and measurements of circulating and brain tissue concentrations of cholesterol and the ketone β-hydroxybutyrate (BHB), were examined in symptomatic R6/2 mice and littermate controls raised on normal chow or a ketogenic diet (KD). Results Whole-cell voltage clamp recordings of striatal medium-sized spiny neurons (MSNs) from symptomatic R6/2 mice showed increased frequency of spontaneous inhibitory postsynaptic currents (sIPSCs) compared with littermate controls. Incubation of slices in cholesterol reduced the frequency of large-amplitude sIPSCs. Addition of BHB or the Liver X Receptor (LXR) agonist T0901317 reduced the frequency and amplitude of sIPSCs. Surprisingly, incubation in simvastatin to reduce cholesterol levels also decreased the frequency of sIPSCs. HD mice fed the KD lost weight more gradually, performed better in an open field, had fewer stereotypies and lower brain levels of cholesterol than mice fed a regular diet. Conclusions Lipid metabolism represents a potential target for therapeutic intervention in HD. Modifying cholesterol or ketone levels acutely in the brain can partially rescue synaptic alterations, and the KD can prevent weight loss and improve some behavioral abnormalities. PMID:27031732

  13. Endothelial nitric oxide synthase is central to skeletal muscle metabolic regulation and enzymatic signaling during exercise in vivo

    OpenAIRE

    Lee-Young, Robert S.; Ayala, Julio E.; Hunley, Charles F.; James, Freyja D.; Bracy, Deanna P; Kang, Li; Wasserman, David H.

    2010-01-01

    Endothelial nitric oxide synthase (eNOS) is associated with a number of physiological functions involved in the regulation of metabolism; however, the functional role of eNOS is poorly understood. We tested the hypothesis that eNOS is critical to muscle cell signaling and fuel usage during exercise in vivo, using 16-wk-old catheterized (carotid artery and jugular vein) C57BL/6J mice with wild-type (WT), partial (+/−), or no expression (−/−) of eNOS. Quantitative reductions in eNOS expression ...

  14. Development of a kinetic metabolic model: application to Catharanthus roseus hairy root

    Science.gov (United States)

    Leduc, M.; Tikhomiroff, C.; Cloutier, M.; Perrier, M.

    2006-01-01

    A kinetic metabolic model describing Catharanthus roseus hairy root growth and nutrition was developed. The metabolic network includes glycolysis, pentose-phosphate pathway, TCA cycle and the catabolic reactions leading to cell building blocks such as amino acids, organic acids, organic phosphates, lipids and structural hexoses. The central primary metabolic network was taken at pseudo-steady state and metabolic flux analysis technique allowed reducing from 31 metabolic fluxes to 20 independent pathways. Hairy root specific growth rate was described as a function of intracellular concentration in cell building blocks. Intracellular transport and accumulation kinetics for major nutrients were included. The model uses intracellular nutrients as well as energy shuttles to describe metabolic regulation. Model calibration was performed using experimental data obtained from batch and medium exchange liquid cultures of C. roseus hairy root using a minimal medium in Petri dish. The model is efficient in estimating the growth rate. PMID:16453114

  15. Software applications for flux balance analysis.

    Science.gov (United States)

    Lakshmanan, Meiyappan; Koh, Geoffrey; Chung, Bevan K S; Lee, Dong-Yup

    2014-01-01

    Flux balance analysis (FBA) is a widely used computational method for characterizing and engineering intrinsic cellular metabolism. The increasing number of its successful applications and growing popularity are possibly attributable to the availability of specific software tools for FBA. Each tool has its unique features and limitations with respect to operational environment, user-interface and supported analysis algorithms. Presented herein is an in-depth evaluation of currently available FBA applications, focusing mainly on usability, functionality, graphical representation and inter-operability. Overall, most of the applications are able to perform basic features of model creation and FBA simulation. COBRA toolbox, OptFlux and FASIMU are versatile to support advanced in silico algorithms to identify environmental and genetic targets for strain design. SurreyFBA, WEbcoli, Acorn, FAME, GEMSiRV and MetaFluxNet are the distinct tools which provide the user friendly interfaces in model handling. In terms of software architecture, FBA-SimVis and OptFlux have the flexible environments as they enable the plug-in/add-on feature to aid prospective functional extensions. Notably, an increasing trend towards the implementation of more tailored e-services such as central model repository and assistance to collaborative efforts was observed among the web-based applications with the help of advanced web-technologies. Furthermore, most recent applications such as the Model SEED, FAME, MetaFlux and MicrobesFlux have even included several routines to facilitate the reconstruction of genome-scale metabolic models. Finally, a brief discussion on the future directions of FBA applications was made for the benefit of potential tool developers. PMID:23131418

  16. Radiohistochemical investigations into the central nervous sialoglycoconjugate metabolism of dormice (Glis glis) in different stages of adaptation

    International Nuclear Information System (INIS)

    Twenty adult dormice (Glis glis, Gliridae) were used to measure seasonal and temperature-related variations of sialoglycoconjugates in the central nervous system. The study had two different aims: On the one hand, biochemical and radiochemical methods of separation were used to investigate 10 cerebral regions for any changes in their individual contents of proteins and protein-bound sialic acids and for alterations in the ganglioside pattern of neurons as well as the time curves plotted for the uptake of a specific ganglioside tracer, 14C-N-Ac-mannosamine, that may possibly arise in response to seasonal and temperature-dependent adaptations. In addition, 32 central cerebral regions were examined for dormice showing different stages of adaptation (winter versus summer) to determine in autoradiograms that percentage share of integrated optical density (IOD), which accounts for the radioactively labelled proportions of TCA/PTA-soluble compounds, sialoglycolipids and sialoglycoproteins plus asialocompounds in the total radioactivity. (orig./ECB)

  17. Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis–Menten and approximate kinetic equations

    DEFF Research Database (Denmark)

    Costa, Rafael S.; Machado, Daniel; Rocha, Isabel;

    2010-01-01

    The construction of dynamic metabolic models at reaction network level requires the use of mechanistic enzymatic rate equations that comprise a large number of parameters. The lack of knowledge on these equations and the difficulty in the experimental identification of their associated parameters...... using the hybrid model composed of Michaelis–Menten and the approximate lin-log kinetics indicate that this is a possible suitable approach to model complex large-scale networks where the exact rate laws are unknown.......The construction of dynamic metabolic models at reaction network level requires the use of mechanistic enzymatic rate equations that comprise a large number of parameters. The lack of knowledge on these equations and the difficulty in the experimental identification of their associated parameters......, represent nowadays the limiting factor in the construction of such models. In this study, we compare four alternative modeling approaches based on Michaelis–Menten kinetics for the bi-molecular reactions and different types of simplified rate equations for the remaining reactions (generalized mass action...

  18. Increased lysine production by flux coupling of the tricarboxylic acid cycle and the lysine biosynthetic pathway--metabolic engineering of the availability of succinyl-CoA in Corynebacterium glutamicum.

    Science.gov (United States)

    Kind, Stefanie; Becker, Judith; Wittmann, Christoph

    2013-01-01

    In this study, we demonstrate increased lysine production by flux coupling using the industrial work horse bacterium Corynebacterium glutamicum, which was mediated by the targeted interruption of the tricarboxylic acid (TCA) cycle at the level of succinyl-CoA synthetase. The succinylase branch of the lysine production pathway functions as the bridging reaction to convert succinyl-CoA to succinate in this aerobic bacterium. The mutant C. glutamicum ΔsucCD showed a 60% increase in the yield of lysine when compared to the advanced lysine producer which was used as parent strain. This mutant was highly vital and exhibited only a slightly reduced specific growth rate. Metabolic flux analysis with (13)C isotope studies confirmed that the increase in lysine production was mediated by pathway coupling. The novel strain exhibited an exceptional flux profile, which was closer to the optimum performance predicted by in silico pathway analysis than to the large set of lysine-producing strains analyzed thus far. Fluxomics and transcriptomics were applied as further targets for next-level strain engineering to identify the back-up mechanisms that were activated upon deletion of the enzyme in the mutant strain. It seemed likely that the cells partly recruited the glyoxylate shunt as a by-pass route. Additionally, the α-ketoglutarate decarboxylase pathway emerged as the potential compensation mechanism. This novel strategy appears equally promising for Escherichia coli, which is used in the industrial production of lysine, wherein this bacterium synthesizes lysine exclusively by succinyl-CoA activation of pathway intermediates. The channeling of a high flux pathway into a production pathway by pathway coupling is an interesting metabolic engineering strategy that can be explored to optimize bio-production in the future. PMID:22871505

  19. In vivo cardiac glucose metabolism in the high-fat fed mouse: Comparison of euglycemic–hyperinsulinemic clamp derived measures of glucose uptake with a dynamic metabolomic flux profiling approach

    Energy Technology Data Exchange (ETDEWEB)

    Kowalski, Greg M., E-mail: greg.kowalski@deakin.edu.au [Centre for Physical Activity and Nutrition Research, School of Exercise and Nutrition Sciences, Deakin University, Burwood, Victoria 3125 (Australia); De Souza, David P. [Metabolomics Australia, Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria 3010 (Australia); Risis, Steve [Cellular and Molecular Metabolism Laboratory, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004 (Australia); Burch, Micah L. [Brigham and Women' s Hospital, Department of Medicine, Boston, MA (United States); Hamley, Steven [Centre for Physical Activity and Nutrition Research, School of Exercise and Nutrition Sciences, Deakin University, Burwood, Victoria 3125 (Australia); Kloehn, Joachim [Metabolomics Australia, Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria 3010 (Australia); Selathurai, Ahrathy [Centre for Physical Activity and Nutrition Research, School of Exercise and Nutrition Sciences, Deakin University, Burwood, Victoria 3125 (Australia); Lee-Young, Robert S. [Cellular and Molecular Metabolism Laboratory, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004 (Australia); Tull, Dedreia; O' Callaghan, Sean; McConville, Malcolm J. [Metabolomics Australia, Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria 3010 (Australia); Bruce, Clinton R. [Centre for Physical Activity and Nutrition Research, School of Exercise and Nutrition Sciences, Deakin University, Burwood, Victoria 3125 (Australia)

    2015-08-07

    Rationale: Cardiac metabolism is thought to be altered in insulin resistance and type 2 diabetes (T2D). Our understanding of the regulation of cardiac substrate metabolism and insulin sensitivity has largely been derived from ex vivo preparations which are not subject to the same metabolic regulation as in the intact heart in vivo. Studies are therefore required to examine in vivo cardiac glucose metabolism under physiologically relevant conditions. Objective: To determine the temporal pattern of the development of cardiac insulin resistance and to compare with dynamic approaches to interrogate cardiac glucose and intermediary metabolism in vivo. Methods and results: Studies were conducted to determine the evolution of cardiac insulin resistance in C57Bl/6 mice fed a high-fat diet (HFD) for between 1 and 16 weeks. Dynamic in vivo cardiac glucose metabolism was determined following oral administration of [U-{sup 13}C] glucose. Hearts were collected after 15 and 60 min and flux profiling was determined by measuring {sup 13}C mass isotopomers in glycolytic and tricarboxylic acid (TCA) cycle intermediates. Cardiac insulin resistance, determined by euglycemic–hyperinsulinemic clamp, was evident after 3 weeks of HFD. Despite the presence of insulin resistance, in vivo cardiac glucose metabolism following oral glucose administration was not compromised in HFD mice. This contrasts our recent findings in skeletal muscle, where TCA cycle activity was reduced in mice fed a HFD. Similar to our report in muscle, glucose derived pyruvate entry into the TCA cycle in the heart was almost exclusively via pyruvate dehydrogenase, with pyruvate carboxylase mediated anaplerosis being negligible after oral glucose administration. Conclusions: Under experimental conditions which closely mimic the postprandial state, the insulin resistant mouse heart retains the ability to stimulate glucose metabolism. - Highlights: • Insulin clamp was used to determine the evolution of cardiac

  20. In vivo cardiac glucose metabolism in the high-fat fed mouse: Comparison of euglycemic–hyperinsulinemic clamp derived measures of glucose uptake with a dynamic metabolomic flux profiling approach

    International Nuclear Information System (INIS)

    Rationale: Cardiac metabolism is thought to be altered in insulin resistance and type 2 diabetes (T2D). Our understanding of the regulation of cardiac substrate metabolism and insulin sensitivity has largely been derived from ex vivo preparations which are not subject to the same metabolic regulation as in the intact heart in vivo. Studies are therefore required to examine in vivo cardiac glucose metabolism under physiologically relevant conditions. Objective: To determine the temporal pattern of the development of cardiac insulin resistance and to compare with dynamic approaches to interrogate cardiac glucose and intermediary metabolism in vivo. Methods and results: Studies were conducted to determine the evolution of cardiac insulin resistance in C57Bl/6 mice fed a high-fat diet (HFD) for between 1 and 16 weeks. Dynamic in vivo cardiac glucose metabolism was determined following oral administration of [U-13C] glucose. Hearts were collected after 15 and 60 min and flux profiling was determined by measuring 13C mass isotopomers in glycolytic and tricarboxylic acid (TCA) cycle intermediates. Cardiac insulin resistance, determined by euglycemic–hyperinsulinemic clamp, was evident after 3 weeks of HFD. Despite the presence of insulin resistance, in vivo cardiac glucose metabolism following oral glucose administration was not compromised in HFD mice. This contrasts our recent findings in skeletal muscle, where TCA cycle activity was reduced in mice fed a HFD. Similar to our report in muscle, glucose derived pyruvate entry into the TCA cycle in the heart was almost exclusively via pyruvate dehydrogenase, with pyruvate carboxylase mediated anaplerosis being negligible after oral glucose administration. Conclusions: Under experimental conditions which closely mimic the postprandial state, the insulin resistant mouse heart retains the ability to stimulate glucose metabolism. - Highlights: • Insulin clamp was used to determine the evolution of cardiac insulin

  1. Cut off values for abdominal obesity as a criterion of metabolic syndrome in an ethnic Kyrgyz population (Central Asian region)

    OpenAIRE

    Mirrakhimov Aibek E; Lunegova Olga S; Kerimkulova Alina S; Moldokeeva Cholpon B; Nabiev Malik P; Mirrakhimov Erkin M

    2012-01-01

    Abstract Background People of different racial and ethnic backgrounds have a distinct pattern of central fat deposition, thus making it necessary to devise a race based approach for the diagnosis and evaluation of abdominal obesity (AO). This is the first study to determine the optimal waist circumference (WC) cutoff values for definition of AO in an ethnic Kyrgyz population. Methods 323 persons of Kyrgyz ethnicity (183 women and 140 men), with a mean age of 51.8 ± 9.5 years old were included...

  2. Central acylated ghrelin improves memory function and hippocampal AMPK activation and partly reverses the impairment of energy and glucose metabolism in rats infused with β-amyloid.

    Science.gov (United States)

    Kang, Suna; Moon, Na Rang; Kim, Da Sol; Kim, Sung Hoon; Park, Sunmin

    2015-09-01

    Ghrelin is a gastric hormone released during the fasting state that targets the hypothalamus where it induces hunger; however, emerging evidence suggests it may also affect memory function. We examined the effect of central acylated-ghrelin and DES-acetylated ghrelin (native ghrelin) on memory function and glucose metabolism in an experimentally induced Alzheimer's disease (AD) rat model. AD rats were divided into 3 groups and Non-AD rats were used as a normal-control group. Each rat in the AD groups had intracerebroventricular (ICV) infusion of β-amyloid (25-35; 16.8nmol/day) into the lateral ventricle for 3 days, and then the pumps were changed to infuse either acylated-ghrelin (0.2nmol/h; AD-G), DES-acylated ghrelin (0.2nmol/h; AD-DES-G), or saline (control; AD-C) for 3 weeks. The Non-AD group had ICV infusion of β-amyloid (35-25) which does not deposit in the hippocampus. During the next 3 weeks memory function, food intake, body weight gain, body fat composition, and glucose metabolism were measured. AD-C exhibited greater β-amyloid deposition compared to Non-AD-C, and AD-G suppressed the increased β-amyloid deposition and potentiated the phosphorylation AMPK. In addition, AD-G increased the phosphorylation GSK and decreased the phosphorylation of Tau in comparison to AD-C and AD-DES-G. Cognitive function, measured by passive avoidance and water maze tests, was much lower in AD-C than Non-AD-C whereas AD-G but not AD-DES-G prevented the decrease (pintermittent fasting to facilitate sustained elevations of acyl-ghrelin should be investigated for cognitive and metabolic benefits, especially in person with early symptoms of memory impairment. PMID:26188171

  3. Effects of sublethal fenitrothion ingestion on cholinesterase inhibition, standard metabolism, thermal preference, and prey-capture ability in the Australian central bearded dragon (Pogona vitticeps, Agamidae).

    Science.gov (United States)

    Bain, David; Buttemer, William A; Astheimer, Lee; Fildes, Karen; Hooper, Michael J

    2004-01-01

    The central bearded dragon (Pogona vitticeps) is a medium-sized lizard that is common in semiarid habitats in Australia and that potentially is at risk of fenitrothion exposure from use of the chemical in plague locust control. We examined the effects of single sublethal doses of this organophosphate (OP; low dose = 2.0 mg/kg; high dose = 20 mg/kg; control = vehicle alone) on lizard thermal preference, standard metabolic rate, and prey-capture ability. We also measured activities of plasma total cholinesterase (ChE) and acetylcholinesterase before and at 0, 2, 8, 24, 120, and 504 h after OP dosing. Predose plasma total ChE activity differed significantly between sexes and averaged 0.66 +/- 0.06 and 0.45 +/- 0.06 micromol/min/ml for males and females, respectively. Approximately 75% of total ChE activity was attributable to butyrylcholinesterase. Peak ChE inhibition reached 19% 2 h after OP ingestion in the low-dose group, and 68% 8 h after ingestion in high-dose animals. Neither OP doses significantly affected diurnal body temperature, standard metabolic rate, or feeding rate. Plasma total ChE levels remained substantially depressed up to 21 d after dosing in the high-dose group, making this species a useful long-term biomonitor of OP exposure in its habitat. PMID:14768874

  4. YANA – a software tool for analyzing flux modes, gene-expression and enzyme activities

    Directory of Open Access Journals (Sweden)

    Engels Bernd

    2005-06-01

    Full Text Available Abstract Background A number of algorithms for steady state analysis of metabolic networks have been developed over the years. Of these, Elementary Mode Analysis (EMA has proven especially useful. Despite its low user-friendliness, METATOOL as a reliable high-performance implementation of the algorithm has been the instrument of choice up to now. As reported here, the analysis of metabolic networks has been improved by an editor and analyzer of metabolic flux modes. Analysis routines for expression levels and the most central, well connected metabolites and their metabolic connections are of particular interest. Results YANA features a platform-independent, dedicated toolbox for metabolic networks with a graphical user interface to calculate (integrating METATOOL, edit (including support for the SBML format, visualize, centralize, and compare elementary flux modes. Further, YANA calculates expected flux distributions for a given Elementary Mode (EM activity pattern and vice versa. Moreover, a dissection algorithm, a centralization algorithm, and an average diameter routine can be used to simplify and analyze complex networks. Proteomics or gene expression data give a rough indication of some individual enzyme activities, whereas the complete flux distribution in the network is often not known. As such data are noisy, YANA features a fast evolutionary algorithm (EA for the prediction of EM activities with minimum error, including alerts for inconsistent experimental data. We offer the possibility to include further known constraints (e.g. growth constraints in the EA calculation process. The redox metabolism around glutathione reductase serves as an illustration example. All software and documentation are available for download at http://yana.bioapps.biozentrum.uni-wuerzburg.de. Conclusion A graphical toolbox and an editor for METATOOL as well as a series of additional routines for metabolic network analyses constitute a new user

  5. Study of Stationary Phase Metabolism Via Isotopomer Analysis of Amino Acids from an Isolated Protein

    Energy Technology Data Exchange (ETDEWEB)

    Shaikh, AfshanS.; Tang, YinjieJ.; Mukhopadhyay, Aindrila; Martin, Hector Garcia; Gin, Jennifer; Benke, Peter; Keasling, Jay D.

    2009-09-14

    Microbial production of many commercially important secondary metabolites occurs during stationary phase, and methods to measure metabolic flux during this growth phase would be valuable. Metabolic flux analysis is often based on isotopomer information from proteinogenic amino acids. As such, flux analysis primarily reflects the metabolism pertinent to the growth phase during which most proteins are synthesized. To investigate central metabolism and amino acids synthesis activity during stationary phase, addition of fully 13C-labeled glucose followed by induction of green fluorescent protein (GFP) expression during stationary phase was used. Our results indicate that Escherichia coli was able to produce new proteins (i.e., GFP) in the stationary phase, and the amino acids in GFP were mostly from degraded proteins synthesized during the exponential growth phase. Among amino acid biosynthetic pathways, only those for serine, alanine, glutamate/glutamine, and aspartate/asparagine had significant activity during the stationary phase.

  6. Compartmentation of glycogen metabolism revealed from 13C isotopologue distributions

    Directory of Open Access Journals (Sweden)

    Marin de Mas Igor

    2011-10-01

    Full Text Available Abstract Background Stable isotope tracers are used to assess metabolic flux profiles in living cells. The existing methods of measurement average out the isotopic isomer distribution in metabolites throughout the cell, whereas the knowledge of compartmental organization of analyzed pathways is crucial for the evaluation of true fluxes. That is why we accepted a challenge to create a software tool that allows deciphering the compartmentation of metabolites based on the analysis of average isotopic isomer distribution. Results The software Isodyn, which simulates the dynamics of isotopic isomer distribution in central metabolic pathways, was supplemented by algorithms facilitating the transition between various analyzed metabolic schemes, and by the tools for model discrimination. It simulated 13C isotope distributions in glucose, lactate, glutamate and glycogen, measured by mass spectrometry after incubation of hepatocytes in the presence of only labeled glucose or glucose and lactate together (with label either in glucose or lactate. The simulations assumed either a single intracellular hexose phosphate pool, or also channeling of hexose phosphates resulting in a different isotopic composition of glycogen. Model discrimination test was applied to check the consistency of both models with experimental data. Metabolic flux profiles, evaluated with the accepted model that assumes channeling, revealed the range of changes in metabolic fluxes in liver cells. Conclusions The analysis of compartmentation of metabolic networks based on the measured 13C distribution was included in Isodyn as a routine procedure. The advantage of this implementation is that, being a part of evaluation of metabolic fluxes, it does not require additional experiments to study metabolic compartmentation. The analysis of experimental data revealed that the distribution of measured 13C-labeled glucose metabolites is inconsistent with the idea of perfect mixing of hexose

  7. The impact of land use change on the energy and water fluxes between atmosphere and tropical vegetation in Central Sulawesi, Indonesia

    Science.gov (United States)

    Falk, U.; Ibrom, A.; Kreilein, H.; Oltchev, A.; Gravenhorst, G.

    2003-12-01

    The conversion of tropical rain forest to agriculturally used land is a widespread process throughout Indonesia. Besides the effects on the biological diversity and the hydrological functions of a forest, this also has an impact on the turbulent exchange processes between vegetation and atmosphere, the radiative properties of the surface and therefore on atmospheric boundary layer and local climate. Within the framework of the project STORMA "Stability of rain forest margins" (SFB 552, University Goettingen, financed by the German Research Foundation), the energy and water fluxes above one of the major land use types, a Cacao plantation, were investigated using the Eddy-Covariance method. Simultaneously meteorological measurements of the variables wind speed and velocity, temperature, humidity, rainfall, soil heat flux and the components of the radiation budget were performed, in order to complete the energy balance and investigate the dependencies of the turbulent exchange processes on the atmospheric boundary conditions. The measurements are being compared to a SVAT model, providing the heat flux into the vegetation. Energy balance closure is used as a means to check the quality of the measured fluxes. The comparison to measurements above undisturbed rain forest by means of the ratio of sensible to latent heat flux, the Bowen ratio, indicates a significantly different boundary layer regime of the atmosphere above the Cacao.

  8. Enzyme oscillation can enhance the thermodynamic efficiency of cellular metabolism: Consequence of anti-phase coupling between reaction flux and affinity

    CERN Document Server

    Himeoka, Yusuke

    2015-01-01

    Cells generally convert nutrient resources to useful products via energy transduction. Accordingly, the thermodynamic efficiency of this conversion process is one of the most essential characteristics of living organisms. However, although these processes occur under conditions of dynamic metabolism, most studies of cellular thermodynamic efficiency have been restricted to examining steady states; thus, the relevance of dynamics to this efficiency has not yet been elucidated. Here, we develop a simple model of metabolic reactions with anabolism-catabolism coupling catalysed by enzymes. Through application of external oscillation in the enzyme abundances, the thermodynamic efficiency of metabolism was found to be improved. This result is in strong contrast with that observed in the oscillatory input, in which the efficiency always decreased with oscillation. This improvement was effectively achieved by separating the anabolic and catabolic reactions, which tend to disequilibrate each other, and taking advantag...

  9. Flux Emergence (Theory)

    OpenAIRE

    Cheung, Mark C. M.; Hiroaki Isobe

    2014-01-01

    Magnetic flux emergence from the solar convection zone into the overlying atmosphere is the driver of a diverse range of phenomena associated with solar activity. In this article, we introduce theoretical concepts central to the study of flux emergence and discuss how the inclusion of different physical effects (e.g., magnetic buoyancy, magnetoconvection, reconnection, magnetic twist, interaction with ambient field) in models impact the evolution of the emerging field and plasma.

  10. Flux Emergence (Theory

    Directory of Open Access Journals (Sweden)

    Mark C. M. Cheung

    2014-07-01

    Full Text Available Magnetic flux emergence from the solar convection zone into the overlying atmosphere is the driver of a diverse range of phenomena associated with solar activity. In this article, we introduce theoretical concepts central to the study of flux emergence and discuss how the inclusion of different physical effects (e.g., magnetic buoyancy, magnetoconvection, reconnection, magnetic twist, interaction with ambient field in models impact the evolution of the emerging field and plasma.

  11. Perfil metabólico e antropométrico dos Suyá: Parque Indígena do Xingu, Brasil Central Metabolic and anthropometric profile of Suyá: Xingu Indigenous Park, Central Brazil

    Directory of Open Access Journals (Sweden)

    Vera Lúcia Morais Antonio de Salvo

    2009-09-01

    Full Text Available OBJETIVO: Descrever o perfil metabólico e antropométrico de índios Suyá que vivem no Parque Indígena do Xingu (Mato Grosso. MÉTODO: Neste estudo transversal foram avaliados 86 índios Suyá com idade de > 20 anos, de ambos os sexos. Durante o exame físico foram obtidos os valores de pressão arterial, peso, altura, perímetros corporais e dobras cutâneas. Amostras de sangue foram coletadas para dosagem de lipoproteínas, glicemia e ácido úrico. Na análise dos dados foram utilizados os testes estatísticos qui-quadrado (para proporções ou t de Student (para valores médios nas comparações das distribuições das variáveis relativas ao estado nutricional e perfil metabólico, segundo sexo e faixa etária dos sujeitos. RESULTADOS: As mulheres, quando comparadas aos homens, apresentaram valores médios estatisticamente menores das variáveis antropométricas (peso, índice de massa corporal, perímetro de cintura, do braço e dobras cutâneas, de pressão arterial, triglicérides, VLDL e ácido úrico. Foram encontrados, entre os Suyá, 46,5%, com excesso de peso, 12,8% com obesidade generalizada, 38,4% com obesidade central, 26,7%, apresentaram alterações pressóricas, 4% glicemia de jejum alterada, 63,9% dislipidemia e 21,9% síndrome metabólica. CONCLUSÃO: Foram observadas alterações metabólicas e antropométricas entre os índios Suyá. Intervenções educativas devem ser implementadas para resgatar hábitos e estilo de vida tradicionais a fim de conter o avanço deste quadro.OBJECTIVE: To describe the metabolic and anthropometric profile of Suyá people living in the Xingu Indigenous Park (Mato Grosso. METHOD: In this cross-sectional study, we evaluated 86 Suyá Indians aged >20 years, of both genders. During the physical examination, we measured blood pressure, weight, height, body perimeters, and skin fold thickness. Samples of blood were collected for lipoprotein, glucose, and uric acid dosage. Chi-square (proportions

  12. The Short-Chain Fatty Acid Uptake Fluxes by Mice on a Guar Gum Supplemented Diet Associate with Amelioration of Major Biomarkers of the Metabolic Syndrome

    NARCIS (Netherlands)

    den Besten, Gijs; Havinga, Rick; Bleeker, Aycha; Rao, Shodhan; Gerding, Albert; van Eunen, Karen; Groen, Albert K.; Reijngoud, Dirk-Jan; Bakker, Barbara M.

    2014-01-01

    Studies with dietary supplementation of various types of fibers have shown beneficial effects on symptoms of the metabolic syndrome. Short-chain fatty acids (SCFAs), the main products of intestinal bacterial fermentation of dietary fiber, have been suggested to play a key role. Whether the concentra

  13. Cut off values for abdominal obesity as a criterion of metabolic syndrome in an ethnic Kyrgyz population (Central Asian region

    Directory of Open Access Journals (Sweden)

    Mirrakhimov Aibek E

    2012-02-01

    Full Text Available Abstract Background People of different racial and ethnic backgrounds have a distinct pattern of central fat deposition, thus making it necessary to devise a race based approach for the diagnosis and evaluation of abdominal obesity (AO. This is the first study to determine the optimal waist circumference (WC cutoff values for definition of AO in an ethnic Kyrgyz population. Methods 323 persons of Kyrgyz ethnicity (183 women and 140 men, with a mean age of 51.8 ± 9.5 years old were included in the study. Measurement of blood pressure (BP, anthropometric data (including body mass index calculation and WC measurement, fasting blood sugar, serum lipid parameters and insulin were performed in all examined individuals. Insulin resistance (IR was considered as HOMA index (insulin × fasting glucose/22.5 ≥ 2.77. Sensitivity and specificity for the presence of IR or two other criteria of MS (according to the international classification, 2009 were calculated by using receiver operating characteristic (ROC curves for men and women separately. Results The optimal sensitivity and specificity obtained from the ROC curves for IR were 88 cm in women (sensitivity of 0.85, 95%CI (0.72-0.93, specificity of 0.58, 95%CI (0.49-0.66 and 94 cm for men (sensitivity of 0.8, 95% CI (0.65-0.91, specificity of 0.61, 95% CI (0.51-0.71. The data from the ROC curve for any two other MS criteria confirmed the results and the WC 88 cm in women (sensitivity of 0.82, 95% CI (0.72-0.9, specificity of 0.72, 95% CI (0.62-0.8 and 94 cm in men (sensitivity of 0.74, 95% CI (0.62-0.84, specificity of 0.73, 95% CI (0.61-0.83 were corresponded to the optimal sensitivity and specificity. Conclusion WC ≥ 88 cm and ≥ 94 cm should be used as a criterion for the diagnosis of AO for Kyrgyz women and men respectively based on these results.

  14. Tracer kinetic studies of the low density lipoprotein metabolism in the fetal rat: An example for estimation of flux rates in the nonsteady state

    International Nuclear Information System (INIS)

    To get insight into the low density lipoprotein (LDL)-apoB flux in the rat fetus near term and in the early postnatal period, homologous apoE-free 125I-labeled LDL was injected into the umbilical vein of the rat fetus immediately after Caesarean section. Since the serum LDL-apoB spontaneously declined after birth, a time-dependent two-pool model was used to calculate the flux rates in the neonate from the specific activities of LDL-apoB up to 15 h post partum. An approximate value of LDL-apoB flux in the fetus at birth was obtained by extrapolation of the kinetic data to the time of injection of the tracer. The data revealed that the turnover of LDL-apoB in the fetus (18.6 micrograms LDL-apoB/h per g body weight) exceeded that in the adult rat (0.4 microgram/h per g body weight) by at least one order of magnitude. Even 15 h after delivery, the LDL-apoB influx amounted to 2.5 micrograms/h per g body weight. The fractional catabolic rate of LDL-apoB in the fetus at term (0.39, h-1) slightly exceeded that in the adult animal (0.15, h-1) and reached the adult level within the first 3 h after birth and remained constant thereafter. In the rat fetus, LDL-apoB flux greatly exceeds that of VLDL-apoB. The data support the view of a direct synthesis and secretion of LDL, most probably by the fetal membranes

  15. Energy and water fluxes above a cacao agroforestry system in Central Sulawesi, Indonesia, indicate effects of land-use change on local climate

    Energy Technology Data Exchange (ETDEWEB)

    Falk, U.; Ibrom, A.; Oltchev, A.; Kreilein, H.; Merklein, J.; Gravenhorst, G. [Inst. of Bioclimatology, Univ. Goettingen (Germany); June, T. [Inst. Pertanian Bogor, BIOTROP-ICSEA, Bogor (Indonesia); Rauf, A. [Univ. Tadulako, Palu (Indonesia)

    2005-04-01

    Rapid conversion of tropical rainforests to agricultural land-use types occurs throughout Indonesia and South-East Asia. We hypothesize that these changes in land-use affect the turbulent heat exchange processes between vegetation and the atmosphere, and the radiative properties of the surface, and therefore, induce an impact on local climate and water flows. As part of the international research project (SFB 552, Stability of Rainforest Margins in Indonesia, STORMA) the turbulent heat fluxes over a cacao agroforestry system (AFS) were investigated, using the eddy covariance technique. These first heat flux observations above a cacao AFS showed an unexpectedly large contribution of the sensible heat flux to the total turbulent heat transport, resulting in an averaged day-time Bowen ratio of {beta} = H/{lambda}E {approx} 1. Seasonality of {beta} did mainly coincide with the seasonal course of precipitation, which amounted to 1970 mm yr{sup -1} during the investigated period. The findings are compared to investigations at four neotropical rain forests where daytime {beta} were substantially smaller than 1. All discussed sites received similar incident short wave radiation, however, precipitation at the neotropical sites was much higher. Our first observations in a nearby Indonesian upland rain forest where precipitation was comparable to that at the cacao AFS showed an intermediate behaviour. Differences in {beta} between the cacao AFS and the tropical forests are discussed as a consequence of differing precipitation amounts, and albedo. From these comparisons we conclude that conversion from tropical forests to cacao AFS affects the energy fluxes towards increased heating of the day-time convective boundary-layer. (orig.)

  16. Diverting the flux of the JA pathway in Nicotiana attenuata compromises the plant's defense metabolism and fitness in nature and glasshouse.

    Directory of Open Access Journals (Sweden)

    Michael Stitz

    Full Text Available A plant's inducible defenses against herbivores as well as certain developmental processes are known to be controlled by the jasmonic acid (JA pathway. We have previously shown that ectopically expressing Arabidopsis thaliana JA O-methyltransferase in Nicotiana attenuata (35S-jmt strongly reduces the herbivory-elicited jasmonate bursts by acting as metabolic sink that redirects free JA towards methylation; here we examine the consequences of this metabolic sink on N. attenuata's secondary metabolism and performance in nature. In the glasshouse, 35S-jmt plants produced fewer seed capsules due to shorter floral styles, which could be restored to wild type (WT levels after hand-pollination, and were more susceptible to Manduca sexta larvae attack. When transplanted into the Great Basin Desert in Utah, 35S-jmt plants grew as well as WT empty vector, but were highly attacked by native herbivores of different feeding guilds: leaf chewers, miners, and single cell feeders. This greater susceptibility was strongly associated with reduced emissions of volatile organic compounds (hexenylesters, monoterpenes and sesquiterpenes and profound alterations in the production of direct defenses (trypsin proteinase inhibitors [TPI], nicotine, diterpene glycosides [DTGs] and phenylpropanoid-polyamine conjugates as revealed by a combination of targeted and metabolomics analyses of field collected samples. Complementation experiments with JA-Ile, whose formation is outcompeted in 35S-jmt plants by the methylation reaction, restored the local TPI activation to WT levels and partially complemented nicotine and DTG levels in elicited but not systemic leaves. These findings demonstrate that MeJA, the major JA metabolite in 35S-jmt plants, is not an active signal in defense activation and highlights the value of creating JA sinks to disrupt JA signaling, without interrupting the complete octadecanoid pathway, in order to investigate the regulation of plants' defense

  17. Engineering of metabolic control

    Science.gov (United States)

    Liao, James C.

    2006-10-17

    The invention features a method of producing heterologous molecules in cells under the regulatory control of a metabolite and metabolic flux. The method can enhance the synthesis of heterologous polypeptides and metabolites.

  18. Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale.

    Science.gov (United States)

    McCloskey, Douglas; Young, Jamey D; Xu, Sibei; Palsson, Bernhard O; Feist, Adam M

    2016-04-01

    Metabolic flux analysis (MFA) is considered to be the gold standard for determining the intracellular flux distribution of biological systems. The majority of work using MFA has been limited to core models of metabolism due to challenges in implementing genome-scale MFA and the undesirable trade-off between increased scope and decreased precision in flux estimations. This work presents a tunable workflow for expanding the scope of MFA to the genome-scale without trade-offs in flux precision. The genome-scale MFA model presented here, iDM2014, accounts for 537 net reactions, which includes the core pathways of traditional MFA models and also covers the additional pathways of purine, pyrimidine, isoprenoid, methionine, riboflavin, coenzyme A, and folate, as well as other biosynthetic pathways. When evaluating the iDM2014 using a set of measured intracellular intermediate and cofactor mass isotopomer distributions (MIDs),1 it was found that a total of 232 net fluxes of central and peripheral metabolism could be resolved in the E. coli network. The increase in scope was shown to cover the full biosynthetic route to an expanded set of bioproduction pathways, which should facilitate applications such as the design of more complex bioprocessing strains and aid in identifying new antimicrobials. Importantly, it was found that there was no loss in precision of core fluxes when compared to a traditional core model, and additionally there was an overall increase in precision when considering all observable reactions. PMID:26981784

  19. Comparative ecosystem-atmosphere exchange of energy and mass in a European Russian and a central Siberian bog I. Interseasonal and interannual variability of energy and latent heat fluxes during the snowfree period

    International Nuclear Information System (INIS)

    Energy and latent heat fluxes λE were measured over ombrotrophic bogs in European Russia (Fyodorovskoye) and in central Siberia (Zotino) using the eddy covariance technique, as part of the EuroSiberian Carbonflux Project. The study covered most of the snowfree periods in 1998, 1999 and 2000; in addition some data were also collected under snow in early spring and late autumn 1999 and 2000. The snowfree period in European Russia exceeds the snowfree period in central Siberia by nearly 10 weeks. Marked seasonal and interannual differences in temperatures and precipitation, and hence energy partitioning, were observed at both sites. At both bogs latent heat fluxes ( E) exceeded sensible heat fluxes (H) during most of the snowfree period: maximum λE were between 10 and 12 MJ/m2/d while maximum H were between 3 and 5 MJ/m2/d. There was a tendency towards higher Bowen ratios at Fyodorovskoye. Net radiation was the most influential variable that regulated daily evaporation rates, with no obvious effects due to surface dryness during years with exceptionally dry summers. Total snowfree evaporation at Fyodorovskoye (320 mm) exceeded totals at Zotino (280 mm) by 15%. At the former site, evaporation was equal to or less than precipitation, contrasting the Zotino observations, where summer evaporation was distinctly higher than precipitation. During the entire observation period evaporation rates were less than 50% of their potential rate. These data suggest a strong 'mulching' effect of a rapidly drying peat surface on total evaporation, despite the substantial area of free water surfaces during parts of the year. This effect of surface dryness was also observed as close atmospheric coupling

  20. Uranium-throium isotopes and transition metal fluxes in two oriented manganese nodules from the Central Indian Basin: implications for nodule turnover

    Digital Repository Service at National Institute of Oceanography (India)

    Banakar, V.K.

    and associated sedi- crustations from the South China Sea. Geochim. Cos- ments from the Pacific ocean. Mar. Chem., 5: 43-74. mochim. Acta, 50:149-156. Dymond, J., Lyle, M., Finney, B., Piper, D.Z., Murphy, McCave, I.N., 1988. Biological pumping upward of the K....L., MacDougal, J.D., Burns, M.V., sediment-water interface. N.Z.J. Sci., 20: 187-190. Burns, R., Dymond, J., Lyle, M.W. and Piper, D.Z., Guichard, F., Reyss, J.L. and Yokoyama, Y., 1978. Growth 1981. Fluxes of metals to a manganese nodule: Radi- rate...

  1. Effects of Citrus aurantium (Bitter Orange Fruit Extracts and p-Synephrine on Metabolic Fluxes in the Rat Liver

    Directory of Open Access Journals (Sweden)

    Rosane Marina Peralta

    2012-05-01

    Full Text Available The fruit extracts of Citrus aurantium (bitter orange are traditionally used as weight-loss products and as appetite supressants. An important fruit component is p-synephrine, which is structurally similar to the adrenergic agents. Weight-loss and adrenergic actions are always related to metabolic changes and this work was designed to investigate a possible action of the C. aurantium extract on liver metabolism. The isolated perfused rat liver was used to measure catabolic and anabolic pathways, including oxygen uptake and perfusion pressure. The C. aurantium extract and p-synephrine increased glycogenolysis, glycolysis, oxygen uptake and perfusion pressure. These changes were partly sensitive to a- and b-adrenergic antagonists. p-Synephrine (200 mM produced an increase in glucose output that was only 15% smaller than the increment caused by the extract containing 196 mM p-synephrine. At low concentrations the C. aurantium extract tended to increase gluconeogenesis, but at high concentrations it was inhibitory, opposite to what happened with p-synephrine. The action of the C. aurantium extract on liver metabolism is similar to the well known actions of adrenergic agents and can be partly attributed to its content in p-synephrine. Many of these actions are catabolic and compatible with the weight-loss effects usually attributed to C. aurantium.

  2. Using a Regional Cluster of AmeriFlux Sites in Central California to Advance Our Knowledge on Decadal-Scale Ecosystem-Atmosphere Carbon Dioxide Exchange

    Energy Technology Data Exchange (ETDEWEB)

    Baldocchi, Dennis [Univ. of California, Berkeley, CA (United States)

    2015-03-24

    Continuous eddy convariance measurements of carbon dioxide, water vapor and heat were measured continuously between an oak savanna and an annual grassland in California over a 4 year period. These systems serve as representative sites for biomes in Mediterranean climates and experience much seasonal and inter-annual variability in temperature and precipitation. These sites hence serve as natural laboratories for how whole ecosystem will respond to warmer and drier conditions. The savanna proved to be a moderate sink of carbon, taking up about 150 gC m-2y-1 compared to the annual grassland, which tended to be carbon neutral and often a source during drier years. But this carbon sink by the savanna came at a cost. This ecosystem used about 100 mm more water per year than the grassland. And because the savanna was darker and rougher its air temperature was about 0.5 C warmer. In addition to our flux measurements, we collected vast amounts of ancillary data to interpret the site and fluxes, making this site a key site for model validation and parameterization. Datasets consist of terrestrial and airborne lidar for determining canopy structure, ground penetrating radar data on root distribution, phenology cameras monitoring leaf area index and its seasonality, predawn water potential, soil moisture, stem diameter and physiological capacity of photosynthesis.

  3. Linking metabolomics data to underlying metabolic regulation

    Directory of Open Access Journals (Sweden)

    Thomas eNägele

    2014-11-01

    Full Text Available The comprehensive experimental analysis of a metabolic constitution plays a central role in approaches of organismal systems biology.Quantifying the impact of a changing environment on the homeostasis of cellular metabolism has been the focus of numerous studies applying various metabolomics techniques. It has been proven that approaches which integrate different analytical techniques, e.g. LC-MS, GC-MS, CE-MS and H-NMR, can provide a comprehensive picture of a certain metabolic homeostasis. Identification of metabolic compounds and quantification of metabolite levels represent the groundwork for the analysis of regulatory strategies in cellular metabolism. This significantly promotes our current understanding of the molecular organization and regulation of cells, tissues and whole organisms.Nevertheless, it is demanding to elicit the pertinent information which is contained in metabolomics data sets.Based on the central dogma of molecular biology, metabolite levels and their fluctuations are the result of a directed flux of information from gene activation over transcription to translation and posttranslational modification.Hence, metabolomics data represent the summed output of a metabolic system comprising various levels of molecular organization.As a consequence, the inverse assignment of metabolomics data to underlying regulatory processes should yield information which-if deciphered correctly-provides comprehensive insight into a metabolic system.Yet, the deduction of regulatory principles is complex not only due to the high number of metabolic compounds, but also because of a high level of cellular compartmentalization and differentiation.Motivated by the question how metabolomics approaches can provide a representative view on regulatory biochemical processes, this article intends to present and discuss current metabolomics applications, strategies of data analysis and their limitations with respect to the interpretability in context of

  4. Dissolved organic matter and lake metabolism: Biogeochemistry and controls of nutrient flux dynamics in lakes: Technical progress report, 1 July 1986-30 June 1987

    International Nuclear Information System (INIS)

    Most lakes are small and possess large littoral and wetland components in the interface region between the open water per se and the drainage basin. Not only does the photosynthetic productivity of the surrounding littoral-wetland complex vastly exceed that of the pelagic zone, but the littoral-wetland vegetation and its intensive synthesis and decompositional metabolism regulate loading of inorganic nutrients passing to the open water (functioning as pulsed sources and sinks), and regulate loading of dissolved organic matter and particulate organic matter to the recipient open water, which by numerous complex pathways and mechanisms enhance or suppress pelagic productivity. Research emphasis was placed on the sources, fates, and interactions of dissolved and particulate organic matter in relation to inorganic chemical cycling: allochthonous loading to the lake system; and the coupled nutrient physiology and metabolism of phytoplankton, bacterial populations, macrophytes and attendant sessile algal-bacterial communities. Regulatory mechanisms of growth and rates of carbon and nutrient cycling were evaluated among the inorganic-organic influxes of allochthonous sources as they are controlled by wetland-littoral communities, the littoral photosynthetic producer-decomposer complex, the microflora of the sediment-water interface, and the microflora of the pelagic zone. 28 refs., 13 figs., 2 tabs

  5. Authigenic 10Be/9Be ratios and 10Be-fluxes (230Thxs-normalized) in central Baffin Bay sediments during the last glacial cycle: Paleoenvironmental implications

    Science.gov (United States)

    Simon, Quentin; Thouveny, Nicolas; Bourlès, Didier L.; Nuttin, Laurence; Hillaire-Marcel, Claude; St-Onge, Guillaume

    2016-05-01

    Authigenic 10Be/9Be ratios and 10Be-fluxes reconstructed using the 230Thxs normalization, proxies of the cosmogenic radionuclide 10Be production rate in the atmosphere, have been measured in a sedimentary core from Baffin Bay (North Atlantic) spanning the last 136 ka BP. The normalization applied on the exchangeable (authigenic) 10Be concentrations using the authigenic 9Be isotope and 230Thxs methods yield equivalent results strongly correlated with sedimentological parameters (grain-size and mineralogy). Lower authigenic beryllium (Be) concentrations and 10Be/9Be ratios are associated with coarse-grained carbonate-rich layers, while higher authigenic Be values are related to fine-grained felspar-rich sediments. This variability is due to: i) sediment composition control over beryllium-scavenging efficiency and, ii) glacial history that contributed to modify the 10Be concentration in Baffin Bay by input and boundary scavenging condition changes. Most paleo-denudation rates inferred from the 10Be/9Be ratio vary weakly around 220 ± 76 tons.km-2.yr-1 (0.09 ± 0.03 mm.yr-1) corresponding to relatively steady weathering fluxes over the last glacial cycle except for six brief intervals characterized by sharp increases of the denudation rate. These intervals are related to ice-surging episodes coeval with Heinrich events and the last deglaciation period. An average freshwater flux of 180.6 km3.yr-1 (0.006 Sv), consistent with recent models, has been calculated in order to sustain glacially-derived 10Be inputs into Baffin Bay. It is concluded that in such environments, the authigenic 10Be measured mainly depends on climatic effects related to the glacial dynamics, which masks the 10Be production variation modulated by geomagnetic field changes. Altogether, these results challenge the simple interpretation of 10Be-concentration variation as a proxy of Interglacial/Glacial (interstadial/stadial) cycles in Arctic and sub-Arctic regions. They rather suggest the effect

  6. Multi-Isotopic (o, H, Sr, Li) Tracing of the Fluxes Involved in the Water Status of a Peatland (la Sauvetat, Massif Central, France)

    Science.gov (United States)

    Agnès, B.; Negrel, P. J.; Millot, R.; Clotilde, B.

    2010-12-01

    The bio-diversity (vegetation and fauna) of peatlands, like all wetlands ecosystems, are strongly fragile as they are requiring very specific wet conditions. In the past 20 years, increasing efforts were engaged to restore degraded wetlands, to create new wetlands where they have been totally lost and to manage wetlands sustainably in order to assess their multiple benefits. However, engaging specific actions to restore and preserve wetlands require an important knowledge on the water cycle in such systems. In this study, we propose to use chemical and multi-isotopic approaches combined with hydrological measurements (piezometric level and stream flow measurements) to trace the fluxes of water and dissolved element involved in the “Narces de la Sauvetat” peatland (France) and for the stream draining the area. Aims are to evaluate the water status of this ecosystem as well as the origin of dissolved elements and possible anthropogenic impacts. These approaches clearly demonstrated their effectiveness to improve the knowledge on the hydrological functioning of wetlands ecosystems. Main results are (1) at least three fluxes with distinct chemical and isotopic signatures are providing water supplies to peatland (Sr and stable isotopes), (2) water flow that comes out of the peatland through the stream is certainly negligible (Li isotopes) and 3) water within the peat land exhibits Sr and Li -isotopes values consistent with carbonate amendments inputs used in local agriculture. The outcomes of this study are that peatland ecosystem water balance is poorly affected by its outlet but are strongly controlled by groundwater replenishment. This could lead to a better adjustment of decision maker choices to maintain the water balance of the peatland, which is essential for the preservation of this fragile ecosystem. This study also opens a new field for Li isotope investigations in hydro-systems and highlights the possibility of using Li isotopes as environmental tracers.

  7. Spring in the boreal environment: observations on pre- and post-melt energy and CO2 fluxes in two central Siberian ecosystems

    International Nuclear Information System (INIS)

    A range of observations points towards earlier onset of spring in northern high latitudes. However, despite the profound effects this may have on vegetation-atmosphere exchange of carbon (NEE), vegetation-atmosphere physical coupling, or the location of the tundra-taiga interface, the number of studies that investigate winter-spring transition fluxes in contrasting northern vegetation types is limited. Here, we examine spring ecosystem-atmosphere energy and carbon exchange in a Siberian pine forest and mire. Divergent surface albedo before and during snow-melt resulted in daytime net radiation (Rn) above the forest exceeding Rn above the mire by up to 10 MJ m-2. Until stomata could open, absorbed radiation by the green pine canopy caused substantial daytime sensible heat fluxes (H > 10MJ m-2). H above the mire was very low, even negative (-2), during that same period. Physiological activity in both ecosystems responded rapidly to warming temperatures and snow-melt, which is essential for survival in Siberia with its very short summers. On days with above-zero temperatures, before melt was complete, low rates of forest photosynthesis (1-2 μmol m-2 s-1) were discernible. Forest and mire NEE became negative the same day, or shortly after, photosynthesis commenced. The mire lagged by about two weeks behind the forest and regained its full carbon uptake capacity at a slower rate. Our data provide empirical evidence for the importance the timing of spring and the relative proportion of forest vs. mire has for late winter/spring boundary-layer growth, and production and surface-atmosphere mixing of trace gases. Models that seek to investigate effects of increasingly earlier spring in high latitudes must correctly account for contrasting physical and biogeochemical ecosystem-atmosphere exchange in heterogeneous landscapes. (orig.)

  8. Second Law of Thermodynamics Applied to Metabolic Networks

    Science.gov (United States)

    Nigam, R.; Liang, S.

    2003-01-01

    We present a simple algorithm based on linear programming, that combines Kirchoff's flux and potential laws and applies them to metabolic networks to predict thermodynamically feasible reaction fluxes. These law's represent mass conservation and energy feasibility that are widely used in electrical circuit analysis. Formulating the Kirchoff's potential law around a reaction loop in terms of the null space of the stoichiometric matrix leads to a simple representation of the law of entropy that can be readily incorporated into the traditional flux balance analysis without resorting to non-linear optimization. Our technique is new as it can easily check the fluxes got by applying flux balance analysis for thermodynamic feasibility and modify them if they are infeasible so that they satisfy the law of entropy. We illustrate our method by applying it to the network dealing with the central metabolism of Escherichia coli. Due to its simplicity this algorithm will be useful in studying large scale complex metabolic networks in the cell of different organisms.

  9. Depletion of the "gamma-type carbonic anhydrase-like" subunits of complex I affects central mitochondrial metabolism in Arabidopsis thaliana.

    Science.gov (United States)

    Fromm, Steffanie; Göing, Jennifer; Lorenz, Christin; Peterhänsel, Christoph; Braun, Hans-Peter

    2016-01-01

    "Gamma-type carbonic anhydrase-like" (CAL) proteins form part of complex I in plants. Together with "gamma carbonic anhydrase" (CA) proteins they form an extra domain which is attached to the membrane arm of complex I on its matrix exposed side. In Arabidopsis two CAL and three CA proteins are present, termed CAL1, CAL2, CA1, CA2 and CA3. It has been proposed that the carbonic anhydrase domain of complex I is involved in a process mediating efficient recycling of mitochondrial CO2 for photosynthetic carbon fixation which is especially important during growth conditions causing increased photorespiration. Depletion of CAL proteins has been shown to significantly affect plant development and photomorphogenesis. To better understand CAL function in plants we here investigated effects of CAL depletion on the mitochondrial compartment. In mutant lines and cell cultures complex I amount was reduced by 90-95% but levels of complexes III and V were unchanged. At the same time, some of the CA transcripts were less abundant. Proteome analysis of CAL depleted cells revealed significant reduction of complex I subunits as well as proteins associated with photorespiration, but increased amounts of proteins participating in amino acid catabolism and stress response reactions. Developmental delay of the mutants was slightly alleviated if plants were cultivated at high CO2. Profiling of selected metabolites revealed defined changes in intermediates of the citric acid cycle and amino acid catabolism. It is concluded that CAL proteins are essential for complex I assembly and that CAL depletion specifically affects central mitochondrial metabolism. PMID:26482706

  10. Flux imbalance analysis and the sensitivity of cellular growth to changes in metabolite pools.

    Directory of Open Access Journals (Sweden)

    Ed Reznik

    Full Text Available Stoichiometric models of metabolism, such as flux balance analysis (FBA, are classically applied to predicting steady state rates - or fluxes - of metabolic reactions in genome-scale metabolic networks. Here we revisit the central assumption of FBA, i.e. that intracellular metabolites are at steady state, and show that deviations from flux balance (i.e. flux imbalances are informative of some features of in vivo metabolite concentrations. Mathematically, the sensitivity of FBA to these flux imbalances is captured by a native feature of linear optimization, the dual problem, and its corresponding variables, known as shadow prices. First, using recently published data on chemostat growth of Saccharomyces cerevisae under different nutrient limitations, we show that shadow prices anticorrelate with experimentally measured degrees of growth limitation of intracellular metabolites. We next hypothesize that metabolites which are limiting for growth (and thus have very negative shadow price cannot vary dramatically in an uncontrolled way, and must respond rapidly to perturbations. Using a collection of published datasets monitoring the time-dependent metabolomic response of Escherichia coli to carbon and nitrogen perturbations, we test this hypothesis and find that metabolites with negative shadow price indeed show lower temporal variation following a perturbation than metabolites with zero shadow price. Finally, we illustrate the broader applicability of flux imbalance analysis to other constraint-based methods. In particular, we explore the biological significance of shadow prices in a constraint-based method for integrating gene expression data with a stoichiometric model. In this case, shadow prices point to metabolites that should rise or drop in concentration in order to increase consistency between flux predictions and gene expression data. In general, these results suggest that the sensitivity of metabolic optima to violations of the steady

  11. Constrained Allocation Flux Balance Analysis

    CERN Document Server

    Mori, Matteo; Martin, Olivier C; De Martino, Andrea; Marinari, Enzo

    2016-01-01

    New experimental results on bacterial growth inspire a novel top-down approach to study cell metabolism, combining mass balance and proteomic constraints to extend and complement Flux Balance Analysis. We introduce here Constrained Allocation Flux Balance Analysis, CAFBA, in which the biosynthetic costs associated to growth are accounted for in an effective way through a single additional genome-wide constraint. Its roots lie in the experimentally observed pattern of proteome allocation for metabolic functions, allowing to bridge regulation and metabolism in a transparent way under the principle of growth-rate maximization. We provide a simple method to solve CAFBA efficiently and propose an "ensemble averaging" procedure to account for unknown protein costs. Applying this approach to modeling E. coli metabolism, we find that, as the growth rate increases, CAFBA solutions cross over from respiratory, growth-yield maximizing states (preferred at slow growth) to fermentative states with carbon overflow (preferr...

  12. Towards Kinetic Modeling of Global Metabolic Networks Methylobacterium extorquens AM1 Growth as Validation

    Institute of Scientific and Technical Information of China (English)

    Ping Ao; Lik Wee Lee; Mary E. Lidstrom; Lan Yin; Xiaomei Zhu

    2008-01-01

    Here we report a systematic method for constructing a large scale kinetic metabolic model and its initial application to the modeling of central metabolism of Methylobacterium extorquens AM1, a methylotrophic and environmental important bacterium. Its central metabolic network includes formaldehyde metabolism, serine cycle, citric acid cycle, pentose phosphate pathway, ghiconeogensis, PHB synthesis and acetyl-CoA conversion pathway, respiration and energy metabolism. Through a systematic and consistent procedure of finding a set of parameters in the physiological range we overcome an outstanding difficulty in large scale kinetic modeling: the requirement for a massive number of enzymatic reaction parameters. We are able to construct the kinetic model based on general biological considerations and incomplete experimental kinetic parameters. Our method consists of the following major steps: 1) using a generic enzymatic rate equation to reduce the number of enzymatic parameters to a minimum set while still preserving their characteristics; 2) using a set of steady state fluxes and metabolite concenwations in the physiological range as the expected output steady state fluxes and metabolite concentrations for the kinetic model to restrict the parametric space of enzymatic reactions; 3) choosing enzyme constants K's and K'eqs optimized for reactions under physiological concentrations, if their experimental values are unknown; 4) for models which do not cover the entire metabolic network of the organisms, designing a dynamical exchange for the coupling between the metabolism represented in the model and the rest not included.

  13. Trace element fluxes and natural potential risks from 210Pb-dated sediment cores in lacustrine environments at the Central Mexican Plateau.

    Science.gov (United States)

    Ontiveros-Cuadras, J F; Ruiz-Fernández, A C; Sanchez-Cabeza, J A; Pérez-Bernal, L H; Sericano, J L; Preda, M; Wee Kwong, L Liong; Páez-Osuna, F

    2014-01-15

    The accumulation, enrichment and provenance of selected trace metals (Ag, As, Cd, Cr, Cu, Hg, Ni, Pb, V and Zn) were studied in sediment cores collected from three lakes located in the Central Mexican Plateau, selected on the basis of their contrasting degree of urbanization: Santa Elena Lake, in a rural and remote area; El Tule Lake, in a rural and slightly urbanized area; and Chapala Lake, in a highly urbanized area. Grain size, magnetic susceptibility and sedimentary constituents such as organic carbon, calcium carbonate, as well as major (Al, Fe, Mn) and minor (Ca, Li, Rb, Sr, Th) elements were analyzed to explain the concentration trends of trace metals. Factor analysis (FA) was used to assess the provenance of the trace elements. The highest metal enrichment factor (EF) above natural concentration levels was found at Chapala Lake for Ag (EF = 3.9), although other trace element EF in all lakes was lakes, Hg and Zn in Chapala Lake, Cu in El Tule Lake and As in Santa Elena Lake were above international benchmarks for which adverse effects are expected to occur frequently, even for those metals only slightly enriched (e.g. As, Cr). Through FA, the terrigenous contribution was identified as the most important source of trace metals to the three lakes, most likely related to deforestation and erosion of the surrounding areas, followed by atmospheric transport of volcanic ashes, rather than to direct sources. PMID:24061059

  14. Flux Creep and Flux Jumping

    CERN Document Server

    Mints, R G

    1995-01-01

    We consider the flux jump instability of the Bean's critical state arising in the flux creep regime in type-II superconductors. We find the flux jump field, $B_j$, that determines the superconducting state stability criterion. We calculate the dependence of $B_j$ on the external magnetic field ramp rate, magnetization experiments the slope of the current-voltage curve in the flux creep regime determines the stability of the Bean's critical state, {\\it i.e.}, the value of $B_j$. We show that a flux jump can be preceded by the magneto-thermal oscillations and find the frequency of these oscillations as a function of $\\dot B_e$.

  15. Methane Flux

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — Methane (CH4) flux is the net rate of methane exchange between an ecosystem and the atmosphere. Data of this variable were generated by the USGS LandCarbon project...

  16. Effects of Conservation Tillage on Topsoil Microbial Metabolic Characteristics and Organic Carbon within Aggregates under a Rice (Oryza sativa L.-Wheat (Triticum aestivum L. Cropping System in Central China.

    Directory of Open Access Journals (Sweden)

    Li-Jin Guo

    Full Text Available Investigating microbial metabolic characteristics and soil organic carbon (SOC within aggregates and their relationships under conservation tillage may be useful in revealing the mechanism of SOC sequestration in conservation tillage systems. However, limited studies have been conducted to investigate the relationship between SOC and microbial metabolic characteristics within aggregate fractions under conservation tillage. We hypothesized that close relationships can exist between SOC and microbial metabolic characteristics within aggregates under conservation tillage. In this study, a field experiment was conducted from June 2011 to June 2013 following a split-plot design of a randomized complete block with tillage practices [conventional intensive tillage (CT and no tillage (NT] as main plots and straw returning methods [preceding crop residue returning (S, 2100-2500 kg C ha-1 and removal (NS, 0 kg C ha(-1] as subplots with three replications. The objective of this study was to reveal the effects of tillage practices and residue-returning methods on topsoil microbial metabolic characteristics and organic carbon (SOC fractions within aggregates and their relationships under a rice-wheat cropping system in central China. Microbial metabolic characteristics investigated using the Biolog system was examined within two aggregate fractions (>0.25 and 0.25 aggregate, and 0.25 mm aggregate (11.3%, and 0.25 mm aggregate, and 0.25 mm aggregate, and 0.25 and 0.25 mm aggregate in the upper (0-5 cm soil layer under conservation tillage systems, as well as directly and indirectly by promoting DOC and MBC in <0.25 mm aggregate. Our results suggested that conservation tillage increased SOC in aggregates in the topsoil by improving microbial metabolic activities.

  17. Metabolic design based on a coupled gene expression-metabolic network model of tryptophan production in Escherichia coli.

    Science.gov (United States)

    Schmid, Joachim W; Mauch, Klaus; Reuss, Matthias; Gilles, Ernst D; Kremling, Andreas

    2004-10-01

    The presumably high potential of a holistic design approach for complex biochemical reaction networks is exemplified here for the network of tryptophan biosynthesis from glucose, a system whose components have been investigated thoroughly before. A dynamic model that combines the behavior of the trp operon gene expression with the metabolic network of central carbon metabolism and tryptophan biosynthesis is investigated. This model is analyzed in terms of metabolic fluxes, metabolic control, and nonlinear optimization. We compare two models for a wild-type strain and another model for a tryptophan producer. An integrated optimization of the whole network leads to a significant increase in tryptophan production rate for all systems under study. This enhancement is well above the increase that can be achieved by an optimization of subsystems. A constant ratio of control coefficients on tryptophan synthesis rate has been identified for the models regarding or disregarding trp operon expression. Although we found some examples where flux control coefficients even contradict the trends of enzyme activity changes in an optimized profile, flux control can be used as an indication for enzymes that have to be taken into account in optimization. PMID:15491865

  18. Differential effects of Th1, monocyte/macrophage and Th2 cytokine mixtures on early gene expression for molecules associated with metabolism, signaling and regulation in central nervous system mixed glial cell cultures

    Directory of Open Access Journals (Sweden)

    Studzinski Diane

    2009-01-01

    Full Text Available Abstract Background Cytokines secreted by immune cells and activated glia play central roles in both the pathogenesis of and protection from damage to the central nervous system (CNS in multiple sclerosis (MS. Methods We have used gene array analysis to identify the initial direct effects of cytokines on CNS glia by comparing changes in early gene expression in CNS glial cultures treated for 6 hours with cytokines typical of those secreted by Th1 and Th2 lymphocytes and monocyte/macrophages (M/M. Results In two previous papers, we summarized effects of these cytokines on immune-related molecules, and on neural and glial related proteins, including neurotrophins, growth factors and structural proteins. In this paper, we present the effects of the cytokines on molecules involved in metabolism, signaling and regulatory mechanisms in CNS glia. Many of the changes in gene expression were similar to those seen in ischemic preconditioning and in early inflammatory lesions in experimental autoimmune encephalomyelitis (EAE, related to ion homeostasis, mitochondrial function, neurotransmission, vitamin D metabolism and a variety of transcription factors and signaling pathways. Among the most prominent changes, all three cytokine mixtures markedly downregulated the dopamine D3 receptor, while Th1 and Th2 cytokines downregulated neuropeptide Y receptor 5. An unexpected finding was the large number of changes related to lipid metabolism, including several suggesting a switch from diacylglycerol to phosphatidyl inositol mediated signaling pathways. Using QRT-PCR we validated the results for regulation of genes for iNOS, arginase and P glycoprotein/multi-drug resistance protein 1 (MDR1 seen at 6 hours with microarray. Conclusion Each of the three cytokine mixtures differentially regulated gene expression related to metabolism and signaling that may play roles in the pathogenesis of MS, most notably with regard to mitochondrial function and neurotransmitter

  19. Robustness of metabolic networks

    Science.gov (United States)

    Jeong, Hawoong

    2009-03-01

    We investigated the robustness of cellular metabolism by simulating the system-level computational models, and also performed the corresponding experiments to validate our predictions. We address the cellular robustness from the ``metabolite''-framework by using the novel concept of ``flux-sum,'' which is the sum of all incoming or outgoing fluxes (they are the same under the pseudo-steady state assumption). By estimating the changes of the flux-sum under various genetic and environmental perturbations, we were able to clearly decipher the metabolic robustness; the flux-sum around an essential metabolite does not change much under various perturbations. We also identified the list of the metabolites essential to cell survival, and then ``acclimator'' metabolites that can control the cell growth were discovered. Furthermore, this concept of ``metabolite essentiality'' should be useful in developing new metabolic engineering strategies for improved production of various bioproducts and designing new drugs that can fight against multi-antibiotic resistant superbacteria by knocking-down the enzyme activities around an essential metabolite. Finally, we combined a regulatory network with the metabolic network to investigate its effect on dynamic properties of cellular metabolism.

  20. Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation

    Energy Technology Data Exchange (ETDEWEB)

    Bordbar, Aarash; Mo, Monica L.; Nakayasu, Ernesto S.; Rutledge, Alexandra C.; Kim, Young-Mo; Metz, Thomas O.; Jones, Marcus B.; Frank, Bryan C.; Smith, Richard D.; Peterson, Scott N.; Hyduke, Daniel R.; Adkins, Joshua N.; Palsson, Bernhard O.

    2012-06-26

    Macrophages are central players in the immune response, manifesting divergent phenotypes to control inflammation and innate immunity through the release of cytokines and other regulatory factor-dependent signaling pathways. In recent years, the focus on metabolism has been reemphasized as critical signaling and regulatory pathways of human pathophysiology, ranging from cancer to aging, often converge on metabolic responses. Here, we used genome-scale modeling and multi-omics (transcriptomics, proteomics, and metabolomics) analysis to assess metabolic features critical for macrophage functions. We constructed a genome-scale metabolic network for the RAW 264.7 cell line to determine metabolic modulators of macrophage activation. Metabolites well-known to be associated with immunoactivation (e.g., glucose and arginine) and immunosuppression (e.g., tryptophan and vitamin D3) were amongst the most critical effectors. Intracellular metabolic mechanisms linked to critical suppressive effectors were then assessed, identifying a suppressive role for de novo nucleotide synthesis. Finally, the underlying metabolic mechanisms of macrophage activation are identified by analyzing multi-omic data obtained from LPS-stimulated RAW cells in the context of our flux-based predictions. Our study demonstrates metabolism's role in regulating activation may be greater than previously anticipated and elucidates underlying metabolic connections between activation and metabolic effectors.

  1. Heat Flux Apportionment to Heterogeneous Surfaces Using Flux Footprint Analysis

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Heat flux data collected from the Baiyangdian Heterogeneous Field Experiment were analyzed using the footprint method. High resolution (25 m) Landsat-5 satellite imaging was used to determine the land cover as one of four surface types: farmland, lake, wetland, or village. Data from two observation sites in September 2005 were used. One site (Wangjiazhai) was characterized by highly heterogeneous surfaces in the central area of the Baiyangdian: lake/wetland. The other site (Xiongxian) was on land with more uniform surface cover. An improved Eulerian analytical flux footprint model was used to determine "source areas" of the heat fluxes measured at towers located at each site from surrounding landscapes of mixed surface types.In relative terms results show that wetland and lake areas generally contributed most to the observed heat flux at Wangjiazhai, while farmland contributed most at Xiongxian. Given the areal distribution of surface type contributions, calculations were made to obtain the magnitudes of the heat flux from lake, wetland and farmland to the total observed flux and apportioned contributions of each surface type to the sensible and latent heat fluxes. Results show that on average the sensible heat flux from wetland and farmland were comparable over the diurnal cycle, while the latent heat flux from farmland was somewhat larger by about 30-50 W m-2 during daytime. The latent and sensible fluxes from the lake source in daytime were about 50 W m-2 and 100 W m-2 less, respectively, than from wetland and farmland. The results are judged reasonable and serve to demonstrate the potential for flux apportionment over heterogeneous surfaces.

  2. Quantitative Tools for Dissection of Hydrogen-Producing Metabolic Networks-Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Rabinowitz, Joshua D.; Dismukes, G.Charles.; Rabitz, Herschel A.; Amador-Noguez, Daniel

    2012-10-19

    During this project we have pioneered the development of integrated experimental-computational technologies for the quantitative dissection of metabolism in hydrogen and biofuel producing microorganisms (i.e. C. acetobutylicum and various cyanobacteria species). The application of these new methodologies resulted in many significant advances in the understanding of the metabolic networks and metabolism of these organisms, and has provided new strategies to enhance their hydrogen or biofuel producing capabilities. As an example, using mass spectrometry, isotope tracers, and quantitative flux-modeling we mapped the metabolic network structure in C. acetobutylicum. This resulted in a comprehensive and quantitative understanding of central carbon metabolism that could not have been obtained using genomic data alone. We discovered that biofuel production in this bacterium, which only occurs during stationary phase, requires a global remodeling of central metabolism (involving large changes in metabolite concentrations and fluxes) that has the effect of redirecting resources (carbon and reducing power) from biomass production into solvent production. This new holistic, quantitative understanding of metabolism is now being used as the basis for metabolic engineering strategies to improve solvent production in this bacterium. In another example, making use of newly developed technologies for monitoring hydrogen and NAD(P)H levels in vivo, we dissected the metabolic pathways for photobiological hydrogen production by cyanobacteria Cyanothece sp. This investigation led to the identification of multiple targets for improving hydrogen production. Importantly, the quantitative tools and approaches that we have developed are broadly applicable and we are now using them to investigate other important biofuel producers, such as cellulolytic bacteria.

  3. Critical flux determination by flux-stepping

    DEFF Research Database (Denmark)

    Beier, Søren; Jonsson, Gunnar Eigil

    2010-01-01

    values are more or less useless in itself as critical flux predictors, and constant flux verification experiments have to be conducted to check if the determined critical fluxes call predict sustainable flux regimes. However, it is shown that using the step-by-step predicted critical fluxes as start...

  4. Obesity, metabolic syndrome and adipocytes

    Science.gov (United States)

    Obesity and metabolic syndrome are examples whereby excess energy consumption and energy flux disruptions are causative agents of increased fatness. Because other, as yet elucidated, cellular factors may be involved and because potential treatments of these metabolic problems involve systemic agents...

  5. Reluctance motor employing superconducting magnetic flux switches

    International Nuclear Information System (INIS)

    This paper reports that superconducting flux switches controlling the magnetic flux in the poles of a motor will enable the implementation of a reluctance motor using one central single phase winding. A superconducting flux switch consists of a ring of superconducting material surrounding a ferromagnetic pole of the motor. When in the superconducting state the switch will block all magnetic flux attempting to flow in the ferromagnetic core. When switched to the normal state the superconducting switch will allow the magnetic flux to flow freely in that pole. By using one high turns-count coil as a flux generator, and selectively channeling flux among the various poles using the superconducting flux switch, 3-phase operation can be emulated with a single-hase central AC source. The motor will also operate when the flux generating coil is driven by a DC current, provided the magnetic flux switches see a continuously varying magnetic flux. Rotor rotation provides this varying flux due to the change in stator pole inductance it produces

  6. Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis

    DEFF Research Database (Denmark)

    Krueger, Andrew S.; Munck, Christian; Dantas, Gautam;

    2016-01-01

    Flux balance analysis (FBA) is an increasingly useful approach for modeling the behavior of metabolic systems. However, standard FBA modeling of genetic knockouts cannot predict drug combination synergies observed between serial metabolic targets, even though such synergies give rise to some of the....... However, we find very different predictions for combinations, where flux diversion, which mimics the kinetics of competitive metabolic inhibitors, can explain serial target synergies between metabolic enzyme inhibitors that we confirmed in Escherichia coli cultures. FBA flux diversion opens the...

  7. Mapping the landscape of metabolic goals of a cell.

    Science.gov (United States)

    Zhao, Qi; Stettner, Arion I; Reznik, Ed; Paschalidis, Ioannis Ch; Segrè, Daniel

    2016-01-01

    Genome-scale flux balance models of metabolism provide testable predictions of all metabolic rates in an organism, by assuming that the cell is optimizing a metabolic goal known as the objective function. We introduce an efficient inverse flux balance analysis (invFBA) approach, based on linear programming duality, to characterize the space of possible objective functions compatible with measured fluxes. After testing our algorithm on simulated E. coli data and time-dependent S. oneidensis fluxes inferred from gene expression, we apply our inverse approach to flux measurements in long-term evolved E. coli strains, revealing objective functions that provide insight into metabolic adaptation trajectories. PMID:27215445

  8. On Functional Module Detection in Metabolic Networks

    Directory of Open Access Journals (Sweden)

    Ina Koch

    2013-08-01

    Full Text Available Functional modules of metabolic networks are essential for understanding the metabolism of an organism as a whole. With the vast amount of experimental data and the construction of complex and large-scale, often genome-wide, models, the computer-aided identification of functional modules becomes more and more important. Since steady states play a key role in biology, many methods have been developed in that context, for example, elementary flux modes, extreme pathways, transition invariants and place invariants. Metabolic networks can be studied also from the point of view of graph theory, and algorithms for graph decomposition have been applied for the identification of functional modules. A prominent and currently intensively discussed field of methods in graph theory addresses the Q-modularity. In this paper, we recall known concepts of module detection based on the steady-state assumption, focusing on transition-invariants (elementary modes and their computation as minimal solutions of systems of Diophantine equations. We present the Fourier-Motzkin algorithm in detail. Afterwards, we introduce the Q-modularity as an example for a useful non-steady-state method and its application to metabolic networks. To illustrate and discuss the concepts of invariants and Q-modularity, we apply a part of the central carbon metabolism in potato tubers (Solanum tuberosum as running example. The intention of the paper is to give a compact presentation of known steady-state concepts from a graph-theoretical viewpoint in the context of network decomposition and reduction and to introduce the application of Q-modularity to metabolic Petri net models.

  9. On functional module detection in metabolic networks.

    Science.gov (United States)

    Koch, Ina; Ackermann, Jörg

    2013-01-01

    Functional modules of metabolic networks are essential for understanding the metabolism of an organism as a whole. With the vast amount of experimental data and the construction of complex and large-scale, often genome-wide, models, the computer-aided identification of functional modules becomes more and more important. Since steady states play a key role in biology, many methods have been developed in that context, for example, elementary flux modes, extreme pathways, transition invariants and place invariants. Metabolic networks can be studied also from the point of view of graph theory, and algorithms for graph decomposition have been applied for the identification of functional modules. A prominent and currently intensively discussed field of methods in graph theory addresses the Q-modularity. In this paper, we recall known concepts of module detection based on the steady-state assumption, focusing on transition-invariants (elementary modes) and their computation as minimal solutions of systems of Diophantine equations. We present the Fourier-Motzkin algorithm in detail. Afterwards, we introduce the Q-modularity as an example for a useful non-steady-state method and its application to metabolic networks. To illustrate and discuss the concepts of invariants and Q-modularity, we apply a part of the central carbon metabolism in potato tubers (Solanum tuberosum) as running example. The intention of the paper is to give a compact presentation of known steady-state concepts from a graph-theoretical viewpoint in the context of network decomposition and reduction and to introduce the application of Q-modularity to metabolic Petri net models. PMID:24958145

  10. Adipose tissue remodeling: its role in energy metabolism and metabolic disorders

    Directory of Open Access Journals (Sweden)

    Sung Sik eChoe

    2016-04-01

    Full Text Available The adipose tissue is a central metabolic organ in the regulation of whole-body energy homeostasis. The white adipose tissue (WAT functions as a key energy reservoir for other organs, whereas the brown adipose tissue (BAT accumulates lipids for cold-induced adaptive thermogenesis. Adipose tissues secret various hormones, cytokines, and metabolites (termed as adipokines that control systemic energy balance by regulating appetitive signals from the central nerve system as well as metabolic activity in peripheral tissues. In response to changes in the nutritional status, the adipose tissue undergoes dynamic remodeling, including quantitative and qualitative alterations in adipose tissue resident cells. A growing body of evidence indicates that adipose tissue remodeling in obesity is closely associated with adipose tissue function. Changes in the number and size of the adipocytes affect the microenvironment of expanded fat tissues, accompanied by alterations in adipokine secretion, adipocyte death, local hypoxia, and fatty acid fluxes. Concurrently, stromal vascular cells in the adipose tissue, including immune cells, are involved in numerous adaptive processes, such as dead adipocyte clearance, adipogenesis, and angiogenesis, all of which are dysregulated in obese adipose tissue remodeling. Chronic over-nutrition triggers uncontrolled inflammatory responses, leading to systemic low-grade inflammation and metabolic disorders, such as insulin resistance. This review will discuss current mechanistic understandings of adipose tissue remodeling processes in adaptive energy homeostasis and pathological remodeling of adipose tissue in connection with immune response.

  11. Adipose Tissue Remodeling: Its Role in Energy Metabolism and Metabolic Disorders.

    Science.gov (United States)

    Choe, Sung Sik; Huh, Jin Young; Hwang, In Jae; Kim, Jong In; Kim, Jae Bum

    2016-01-01

    The adipose tissue is a central metabolic organ in the regulation of whole-body energy homeostasis. The white adipose tissue functions as a key energy reservoir for other organs, whereas the brown adipose tissue accumulates lipids for cold-induced adaptive thermogenesis. Adipose tissues secrete various hormones, cytokines, and metabolites (termed as adipokines) that control systemic energy balance by regulating appetitive signals from the central nerve system as well as metabolic activity in peripheral tissues. In response to changes in the nutritional status, the adipose tissue undergoes dynamic remodeling, including quantitative and qualitative alterations in adipose tissue-resident cells. A growing body of evidence indicates that adipose tissue remodeling in obesity is closely associated with adipose tissue function. Changes in the number and size of the adipocytes affect the microenvironment of expanded fat tissues, accompanied by alterations in adipokine secretion, adipocyte death, local hypoxia, and fatty acid fluxes. Concurrently, stromal vascular cells in the adipose tissue, including immune cells, are involved in numerous adaptive processes, such as dead adipocyte clearance, adipogenesis, and angiogenesis, all of which are dysregulated in obese adipose tissue remodeling. Chronic overnutrition triggers uncontrolled inflammatory responses, leading to systemic low-grade inflammation and metabolic disorders, such as insulin resistance. This review will discuss current mechanistic understandings of adipose tissue remodeling processes in adaptive energy homeostasis and pathological remodeling of adipose tissue in connection with immune response. PMID:27148161

  12. The central role of vascular extracellular matrix and basement membrane remodeling in metabolic syndrome and type 2 diabetes: the matrix preloaded

    Directory of Open Access Journals (Sweden)

    Tyagi Suresh C

    2005-06-01

    Full Text Available Abstract The vascular endothelial basement membrane and extra cellular matrix is a compilation of different macromolecules organized by physical entanglements, opposing ionic charges, chemical covalent bonding, and cross-linking into a biomechanically active polymer. These matrices provide a gel-like form and scaffolding structure with regional tensile strength provided by collagens, elasticity by elastins, adhesiveness by structural glycoproteins, compressibility by proteoglycans – hyaluronans, and communicability by a family of integrins, which exchanges information between cells and between cells and the extracellular matrix of vascular tissues. Each component of the extracellular matrix and specifically the capillary basement membrane possesses unique structural properties and interactions with one another, which determine the separate and combined roles in the multiple diabetic complications or diabetic opathies. Metabolic syndrome, prediabetes, type 2 diabetes mellitus, and their parallel companion (atheroscleropathy are associated with multiple metabolic toxicities and chronic injurious stimuli. The adaptable quality of a matrix or form genetically preloaded with the necessary information to communicate and respond to an ever-changing environment, which supports the interstitium, capillary and arterial vessel wall is individually examined.

  13. Rhizobium leguminosarum bv. viciae 3841 Adapts to 2,4-Dichlorophenoxyacetic Acid with "Auxin-Like" Morphological Changes, Cell Envelope Remodeling and Upregulation of Central Metabolic Pathways.

    Directory of Open Access Journals (Sweden)

    Supriya V Bhat

    Full Text Available There is a growing need to characterize the effects of environmental stressors at the molecular level on model organisms with the ever increasing number and variety of anthropogenic chemical pollutants. The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D, as one of the most widely applied pesticides in the world, is one such example. This herbicide is known to have non-targeted undesirable effects on humans, animals and soil microbes, but specific molecular targets at sublethal levels are unknown. In this study, we have used Rhizobium leguminosarum bv. viciae 3841 (Rlv as a nitrogen fixing, beneficial model soil organism to characterize the effects of 2,4-D. Using metabolomics and advanced microscopy we determined specific target pathways in the Rlv metabolic network and consequent changes to its phenotype, surface ultrastructure, and physical properties during sublethal 2,4-D exposure. Auxin and 2,4-D, its structural analogue, showed common morphological changes in vitro which were similar to bacteroids isolated from plant nodules, implying that these changes are related to bacteroid differentiation required for nitrogen fixation. Rlv showed remarkable adaptation capabilities in response to the herbicide, with changes to integral pathways of cellular metabolism and the potential to assimilate 2,4-D with consequent changes to its physical and structural properties. This study identifies biomarkers of 2,4-D in Rlv and offers valuable insights into the mode-of-action of 2,4-D in soil bacteria.

  14. Metabolic responses to pyruvate kinase deletion in lysine producing Corynebacterium glutamicum

    Directory of Open Access Journals (Sweden)

    Wittmann Christoph

    2008-03-01

    Full Text Available Abstract Background Pyruvate kinase is an important element in flux control of the intermediate metabolism. It catalyzes the irreversible conversion of phosphoenolpyruvate into pyruvate and is under allosteric control. In Corynebacterium glutamicum, this enzyme was regarded as promising target for improved production of lysine, one of the major amino acids in animal nutrition. In pyruvate kinase deficient strains the required equimolar ratio of the two lysine precursors oxaloacetate and pyruvate can be achieved through concerted action of the phosphotransferase system (PTS and phosphoenolpyruvate carboxylase (PEPC, whereby a reduced amount of carbon may be lost as CO2 due to reduced flux into the tricarboxylic acid (TCA cycle. In previous studies, deletion of pyruvate kinase in lysine-producing C. glutamicum, however, did not yield a clear picture and the exact metabolic consequences are not fully understood. Results In this work, deletion of the pyk gene, encoding pyruvate kinase, was carried out in the lysine-producing strain C. glutamicum lysCfbr, expressing a feedback resistant aspartokinase, to investigate the cellular response to deletion of this central glycolytic enzyme. Pyk deletion was achieved by allelic replacement, verified by PCR analysis and the lack of in vitro enzyme activity. The deletion mutant showed an overall growth behavior (specific growth rate, glucose uptake rate, biomass yield which was very similar to that of the parent strain, but differed in slightly reduced lysine formation, increased formation of the overflow metabolites dihydroxyacetone and glycerol and in metabolic fluxes around the pyruvate node. The latter involved a flux shift from pyruvate carboxylase (PC to PEPC, by which the cell maintained anaplerotic supply of the TCA cycle. This created a metabolic by-pass from PEP to pyruvate via malic enzyme demonstrating its contribution to metabolic flexibility of C. glutamicum on glucose. Conclusion The metabolic

  15. C. elegans Metabolic Gene Regulatory Networks Govern the Cellular Economy

    Science.gov (United States)

    Watson, Emma; Walhout, Albertha J.M.

    2014-01-01

    Diet greatly impacts metabolism in health and disease. In response to the presence or absence of specific nutrients, metabolic gene regulatory networks sense the metabolic state of the cell and regulate metabolic flux accordingly, for instance by the transcriptional control of metabolic enzymes. Here we discuss recent insights regarding metazoan metabolic regulatory networks using the nematode Caenorhabditis elegans as a model, including the modular organization of metabolic gene regulatory networks, the prominent impact of diet on the transcriptome and metabolome, specialized roles of nuclear hormone receptors in responding to dietary conditions, regulation of metabolic genes and metabolic regulators by microRNAs, and feedback between metabolic genes and their regulators. PMID:24731597

  16. The RabGAP TBC1D1 plays a central role in exercise-regulated glucose metabolism in skeletal muscle

    DEFF Research Database (Denmark)

    Stöckli, Jacqueline; Meoli, Christopher C; Hoffman, Nolan J;

    2015-01-01

    Insulin and exercise stimulate glucose uptake into skeletal muscle via different pathways. Both stimuli converge on the translocation of the glucose transporter GLUT4 from intracellular vesicles to the cell surface. Two Rab guanosine triphosphatases-activating proteins (GAPs) have been implicated...... in this process: AS160 for insulin stimulation and its homolog, TBC1D1, are suggested to regulate exercise-mediated glucose uptake into muscle. TBC1D1 has also been implicated in obesity in humans and mice. We investigated the role of TBC1D1 in glucose metabolism by generating TBC1D1(-/-) mice and...... analyzing body weight, insulin action, and exercise. TBC1D1(-/-) mice showed normal glucose and insulin tolerance, with no difference in body weight compared with wild-type littermates. GLUT4 protein levels were reduced by ∼40% in white TBC1D1(-/-) muscle, and TBC1D1(-/-) mice showed impaired exercise...

  17. Subcutaneous adipose tissue transplantation in diet-induced obese mice attenuates metabolic dysregulation while removal exacerbates it

    OpenAIRE

    Foster, Michelle T.; Softic, Samir; Caldwell, Jody; Kohli, Rohit; deKloet, Annette D; Seeley, Randy J.

    2013-01-01

    Adipose tissue distribution is an important determinant of obesity-related comorbidities. It is well established that central obesity (visceral adipose tissue accumulation) is a risk factor for many adverse health consequences such as dyslipidemia, insulin resistance, and type-2-diabetes. We hypothesize that the metabolic dysregulation that occurs following high fat diet-induced increases in adiposity are due to alterations in visceral adipose tissue function which influence lipid flux to the...

  18. Constrained Allocation Flux Balance Analysis

    Science.gov (United States)

    Mori, Matteo; Hwa, Terence; Martin, Olivier C.

    2016-01-01

    New experimental results on bacterial growth inspire a novel top-down approach to study cell metabolism, combining mass balance and proteomic constraints to extend and complement Flux Balance Analysis. We introduce here Constrained Allocation Flux Balance Analysis, CAFBA, in which the biosynthetic costs associated to growth are accounted for in an effective way through a single additional genome-wide constraint. Its roots lie in the experimentally observed pattern of proteome allocation for metabolic functions, allowing to bridge regulation and metabolism in a transparent way under the principle of growth-rate maximization. We provide a simple method to solve CAFBA efficiently and propose an “ensemble averaging” procedure to account for unknown protein costs. Applying this approach to modeling E. coli metabolism, we find that, as the growth rate increases, CAFBA solutions cross over from respiratory, growth-yield maximizing states (preferred at slow growth) to fermentative states with carbon overflow (preferred at fast growth). In addition, CAFBA allows for quantitatively accurate predictions on the rate of acetate excretion and growth yield based on only 3 parameters determined by empirical growth laws. PMID:27355325

  19. Metabolic acidosis

    Science.gov (United States)

    Acidosis - metabolic ... Metabolic acidosis occurs when the body produces too much acid. It can also occur when the kidneys are not ... the body. There are several types of metabolic acidosis. Diabetic acidosis develops when acidic substances, known as ...

  20. Do plant species influence soil CO2 and N2O fluxes in a diverse tropical forest?

    Science.gov (United States)

    van Haren, Joost L. M.; de Oliveira, R. Cosme; Restrepo-Coupe, Natalia; Hutyra, Lucy; de Camargo, Plinio B.; Keller, Michael; Saleska, Scott R.

    2010-09-01

    To test whether plant species influence greenhouse gas production in diverse ecosystems, we measured wet season soil CO2 and N2O fluxes close to ˜300 large (>35 cm in diameter at breast height (DBH)) trees of 15 species at three clay-rich forest sites in central Amazonia. We found that soil CO2 fluxes were 38% higher near large trees than at control sites >10 m away from any tree (P DBH explained 19% of remaining CO2 flux variability. Soil N2O fluxes adjacent to Caryocar villosum, Lecythis lurida, Schefflera morototoni, and Manilkara huberi were 84%-196% greater than Erisma uncinatum and Vochysia maxima, both Vochysiaceae. Tree species identity was the most important explanatory factor for N2O fluxes, accounting for more than twice the N2O flux variability as all other factors combined. Two observations suggest a mechanism for this finding: (1) sugar addition increased N2O fluxes near C. villosum twice as much (P < 0.05) as near Vochysiaceae and (2) species mean N2O fluxes were strongly negatively correlated with tree growth rate (P = 0.002). These observations imply that through enhanced belowground carbon allocation liana and tree species can stimulate soil CO2 and N2O fluxes (by enhancing denitrification when carbon limits microbial metabolism). Alternatively, low N2O fluxes potentially result from strong competition of tree species with microbes for nutrients. Species-specific patterns in CO2 and N2O fluxes demonstrate that plant species can influence soil biogeochemical processes in a diverse tropical forest.

  1. Phenotype prediction in regulated metabolic networks

    Directory of Open Access Journals (Sweden)

    Centler Florian

    2008-04-01

    Full Text Available Abstract Background Due to the growing amount of biological knowledge that is incorporated into metabolic network models, their analysis has become more and more challenging. Here, we examine the capabilities of the recently introduced chemical organization theory (OT to ease this task. Considering only network stoichiometry, the theory allows the prediction of all potentially persistent species sets and therewith rigorously relates the structure of a network to its potential dynamics. By this, the phenotypes implied by a metabolic network can be predicted without the need for explicit knowledge of the detailed reaction kinetics. Results We propose an approach to deal with regulation – and especially inhibitory interactions – in chemical organization theory. One advantage of this approach is that the metabolic network and its regulation are represented in an integrated way as one reaction network. To demonstrate the feasibility of this approach we examine a model by Covert and Palsson (J Biol Chem, 277(31, 2002 of the central metabolism of E. coli that incorporates the regulation of all involved genes. Our method correctly predicts the known growth phenotypes on 16 different substrates. Without specific assumptions, organization theory correctly predicts the lethality of knockout experiments in 101 out of 116 cases. Taking into account the same model specific assumptions as in the regulatory flux balance analysis (rFBA by Covert and Palsson, the same performance is achieved (106 correctly predicted cases. Two model specific assumptions had to be considered: first, we have to assume that secreted molecules do not influence the regulatory system, and second, that metabolites with increasing concentrations indicate a lethal state. Conclusion The introduced approach to model a metabolic network and its regulation in an integrated way as one reaction network makes organization analysis a universal technique to study the potential behavior of

  2. Analysis of Data on Xanthan Fermentation in Stationary Phase Using Black Box and Metabolic Network Models

    Institute of Scientific and Technical Information of China (English)

    马红武; 赵学明; 唐寅杰

    1999-01-01

    The xanthan fermentation data in the stationary phase was analyzed using the black box and the metabolic network models. The data consistency ls checked through the elemental balance in the black box model. In the metabolic network model, the metabolic flux distribution in the cell is calculated using the metabolic flux analysis method, then the maintenance coefficients is calculated.

  3. Extensive exometabolome analysis reveals extended overflow metabolism in various microorganisms

    Directory of Open Access Journals (Sweden)

    Paczia Nicole

    2012-09-01

    Full Text Available Abstract Overflow metabolism is well known for yeast, bacteria and mammalian cells. It typically occurs under glucose excess conditions and is characterized by excretions of by-products such as ethanol, acetate or lactate. This phenomenon, also denoted the short-term Crabtree effect, has been extensively studied over the past few decades, however, its basic regulatory mechanism and functional role in metabolism is still unknown. Here we present a comprehensive quantitative and time-dependent analysis of the exometabolome of Escherichia coli, Corynebacterium glutamicum, Bacillus licheniformis, and Saccharomyces cerevisiae during well-controlled bioreactor cultivations. Most surprisingly, in all cases a great diversity of central metabolic intermediates and amino acids is found in the culture medium with extracellular concentrations varying in the micromolar range. Different hypotheses for these observations are formulated and experimentally tested. As a result, the intermediates in the culture medium during batch growth must originate from passive or active transportation due to a new phenomenon termed “extended” overflow metabolism. Moreover, we provide broad evidence that this could be a common feature of all microorganism species when cultivated under conditions of carbon excess and non-inhibited carbon uptake. In turn, this finding has consequences for metabolite balancing and, particularly, for intracellular metabolite quantification and 13C-metabolic flux analysis.

  4. Regulation of terpene metabolism. Final technical report, March 15, 1988--March 14, 1996

    Energy Technology Data Exchange (ETDEWEB)

    Croteau, R.

    1996-12-31

    This research focuses on the following topics: the biosynthesis and catabolism of monoterpenes; the organization of monoterpene metabolism; the developmental regulation of monoterpene metabolism; the flux control of precursor supply; and the integration of monoterpene and higher terpenoid metabolism.

  5. The integrated analysis of metabolic and protein interaction networks reveals novel molecular organizing principles

    Directory of Open Access Journals (Sweden)

    Walther Dirk

    2008-11-01

    Full Text Available Abstract Background The study of biological interaction networks is a central theme of systems biology. Here, we investigate the relationships between two distinct types of interaction networks: the metabolic pathway map and the protein-protein interaction network (PIN. It has long been established that successive enzymatic steps are often catalyzed by physically interacting proteins forming permanent or transient multi-enzymes complexes. Inspecting high-throughput PIN data, it was shown recently that, indeed, enzymes involved in successive reactions are generally more likely to interact than other protein pairs. In our study, we expanded this line of research to include comparisons of the underlying respective network topologies as well as to investigate whether the spatial organization of enzyme interactions correlates with metabolic efficiency. Results Analyzing yeast data, we detected long-range correlations between shortest paths between proteins in both network types suggesting a mutual correspondence of both network architectures. We discovered that the organizing principles of physical interactions between metabolic enzymes differ from the general PIN of all proteins. While physical interactions between proteins are generally dissortative, enzyme interactions were observed to be assortative. Thus, enzymes frequently interact with other enzymes of similar rather than different degree. Enzymes carrying high flux loads are more likely to physically interact than enzymes with lower metabolic throughput. In particular, enzymes associated with catabolic pathways as well as enzymes involved in the biosynthesis of complex molecules were found to exhibit high degrees of physical clustering. Single proteins were identified that connect major components of the cellular metabolism and may thus be essential for the structural integrity of several biosynthetic systems. Conclusion Our results reveal topological equivalences between the protein

  6. NONLINEAR THREE-DIMENSIONAL MAGNETOCONVECTION AROUND MAGNETIC FLUX TUBES

    International Nuclear Information System (INIS)

    Magnetic flux in the solar photosphere forms concentrations from small scales, such as flux elements, to large scales, such as sunspots. This paper presents a study of the decay process of large magnetic flux tubes, such as sunspots, on a supergranular scale. Three-dimensional nonlinear resistive magnetohydrodynamic numerical simulations are performed in a cylindrical domain, initialized with axisymmetric solutions that consist of a well-defined central flux tube and an annular convection cell surrounding it. As the nonlinear convection evolves, the annular cell breaks up into many cells in the azimuthal direction, allowing magnetic flux to slip between cells away from the central flux tube (turbulent erosion). This lowers magnetic pressure in the central tube, and convection grows inside the tube, possibly becoming strong enough to push the tube apart. A remnant of the central flux tube persists with nonsymmetric perturbations caused by the convection surrounding it. Secondary flux concentrations form between convection cells away from the central tube. Tube decay is dependent on the convection around the tube. Convection cells forming inside the tube as time-dependent outflows will remove magnetic flux. (This is most pronounced for small tubes.) Flux is added to the tube when flux caught in the surrounding convection is pushed toward it. The tube persists when convection inside the tube is sufficiently suppressed by the remaining magnetic field. All examples of persistent tubes have the same effective magnetic field strength, consistent with the observation that pores and sunspot umbrae all have roughly the same magnetic field strength.

  7. Metabolic Burden: Cornerstones in Synthetic Biology and Metabolic Engineering Applications.

    Science.gov (United States)

    Wu, Gang; Yan, Qiang; Jones, J Andrew; Tang, Yinjie J; Fong, Stephen S; Koffas, Mattheos A G

    2016-08-01

    Engineering cell metabolism for bioproduction not only consumes building blocks and energy molecules (e.g., ATP) but also triggers energetic inefficiency inside the cell. The metabolic burdens on microbial workhorses lead to undesirable physiological changes, placing hidden constraints on host productivity. We discuss cell physiological responses to metabolic burdens, as well as strategies to identify and resolve the carbon and energy burden problems, including metabolic balancing, enhancing respiration, dynamic regulatory systems, chromosomal engineering, decoupling cell growth with production phases, and co-utilization of nutrient resources. To design robust strains with high chances of success in industrial settings, novel genome-scale models (GSMs), (13)C-metabolic flux analysis (MFA), and machine-learning approaches are needed for weighting, standardizing, and predicting metabolic costs. PMID:26996613

  8. SQUID With Integral Flux Concentrator

    Science.gov (United States)

    Peters, Palmer N.; Sisk, Robert C.

    1989-01-01

    In improved superconducting quantum interference device (SQUID), change in size and shape of superconducting ring improves coupling to external signal coil and eases coil-positioning tolerances. More rugged and easier to manufacture than conventional SQUID's with comparable electrical characteristics. Thin-film superconducting flux concentrator utilizes Meissner effect to deflect magnetic field of signal coil into central hole of SQUID. Used in magnetometers, ammeters, analog-to-digital converters, and related electronic applications in which high signal-to-noise ratios required.

  9. Applications of computational modeling in metabolic engineering of yeast

    DEFF Research Database (Denmark)

    Kerkhoven, Eduard J.; Lahtvee, Petri-Jaan; Nielsen, Jens

    2015-01-01

    Generally, a microorganism's phenotype can be described by its pattern of metabolic fluxes. Although fluxes cannot be measured directly, inference of fluxes is well established. In biotechnology the aim is often to increase the capacity of specific fluxes. For this, metabolic engineering methods...... preferred flux distribution. These methods point to strategies for altering gene expression; however, fluxes are often controlled by post-transcriptional events. Moreover, GEMs are usually not taking into account metabolic regulation, thermodynamics and enzyme kinetics. To facilitate metabolic engineering......, tools from synthetic biology have emerged, enabling integration and assembly of naturally nonexistent, but well-characterized components into a living organism. To describe these systems kinetic models are often used and to integrate these systems with the standard metabolic engineering approach, it is...

  10. Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications

    Directory of Open Access Journals (Sweden)

    Blake Robert

    2008-12-01

    Full Text Available Abstract Background Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining. It is a chemolithoautrophic, γ-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. It thrives at extremely low pH (pH 1–2 and fixes both carbon and nitrogen from the atmosphere. It solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemical cycling in acid environments. The lack of a well-developed system for genetic manipulation has prevented thorough exploration of its physiology. Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism. Results The genome of the type strain A. ferrooxidans ATCC 23270 was sequenced and annotated to identify general features and provide a framework for in silico metabolic reconstruction. Earlier models of iron and sulfur oxidation, biofilm formation, quorum sensing, inorganic ion uptake, and amino acid metabolism are confirmed and extended. Initial models are presented for central carbon metabolism, anaerobic metabolism (including sulfur reduction, hydrogen metabolism and nitrogen fixation, stress responses, DNA repair, and metal and toxic compound fluxes. Conclusion Bioinformatics analysis provides a valuable platform for gene discovery and functional prediction that helps explain the activity of A. ferrooxidans in industrial bioleaching and its role as a primary producer in acidic environments. An analysis of the genome of the type strain provides a coherent view of its gene content and metabolic potential.

  11. Physics of magnetic flux tubes

    CERN Document Server

    Ryutova, Margarita

    2015-01-01

    This book is the first account of the physics of magnetic flux tubes from their fundamental properties to collective phenomena in an ensembles of flux tubes. The physics of magnetic flux tubes is absolutely vital for understanding fundamental physical processes in the solar atmosphere shaped and governed by magnetic fields. High-resolution and high cadence observations from recent space and  ground-based instruments taken simultaneously at different heights and temperatures not only show the ubiquity of filamentary structure formation but also allow to study how various events are interconnected by system of magnetic flux tubes. The book covers both theory and observations. Theoretical models presented in analytical and phenomenological forms are tailored for practical applications. These are welded with state-of-the-art observations from early decisive ones to the most recent data that open a new phase-space for exploring the Sun and sun-like stars. Concept of magnetic flux tubes is central to various magn...

  12. Metabolic Disorders

    Science.gov (United States)

    ... as your liver, muscles, and body fat. A metabolic disorder occurs when abnormal chemical reactions in your body ... that produce the energy. You can develop a metabolic disorder when some organs, such as your liver or ...

  13. Metabolic Syndrome

    Science.gov (United States)

    Metabolic syndrome is a group of conditions that put you at risk for heart disease and diabetes. These ... doctors agree on the definition or cause of metabolic syndrome. The cause might be insulin resistance. Insulin is ...

  14. iSCHRUNK – In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks

    OpenAIRE

    Andreozzi, Stefano; Miskovic, Ljubisa; Hatzimanikatis, Vassily

    2016-01-01

    Accurate determination of physiological states of cellular metabolism requires detailed information about metabolic fluxes, metabolite concentrations and distribution of enzyme states. Integration of fluxomics and metabolomics data, and thermodynamics-based metabolic flux analysis contribute to improved understanding of steady-state properties of metabolism. However, knowledge about kinetics and enzyme activities though essential for quantitative understanding of metabolic dynamics remains sc...

  15. Nitrous oxide flux following tropical land clearing

    Science.gov (United States)

    Luizao, Flavio; Luizao, Regina; Matson, Pamela; Livingston, Gerald; Vitousek, Peter

    1989-01-01

    The importance of seasonal cycles of N2O flux from tropical ecosystems and the possibility that tropical deforestation could contribute to the ongoing global increase in N2O concentrations were assessed by measuring N2O flux from forest, cleared land, and pasture over an annual cycle in the central Amazon. A pasture that had been converted from tropical forest had threefold greater annual N2O flux than a paired forest site; similar results were obtained in spot measurements in other pastures. If these results are general, such tropical pastures represent a globally significant source of increased N2O.

  16. Metabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteria

    Directory of Open Access Journals (Sweden)

    Grammel Hartmut

    2011-09-01

    Full Text Available Abstract Background Purple nonsulfur bacteria (PNSB are facultative photosynthetic bacteria and exhibit an extremely versatile metabolism. A central focus of research on PNSB dealt with the elucidation of mechanisms by which they manage to balance cellular redox under diverse conditions, in particular under photoheterotrophic growth. Results Given the complexity of the central metabolism of PNSB, metabolic modeling becomes crucial for an integrated analysis of the accumulated biological knowledge. We reconstructed a stoichiometric model capturing the central metabolism of three important representatives of PNSB (Rhodospirillum rubrum, Rhodobacter sphaeroides and Rhodopseudomonas palustris. Using flux variability analysis, the model reveals key metabolic constraints related to redox homeostasis in these bacteria. With the help of the model we can (i give quantitative explanations for non-intuitive, partially species-specific phenomena of photoheterotrophic growth of PNSB, (ii reproduce various quantitative experimental data, and (iii formulate several new hypotheses. For example, model analysis of photoheterotrophic growth reveals that - despite a large number of utilizable catabolic pathways - substrate-specific biomass and CO2 yields are fixed constraints, irrespective of the assumption of optimal growth. Furthermore, our model explains quantitatively why a CO2 fixing pathway such as the Calvin cycle is required by PNSB for many substrates (even if CO2 is released. We also analyze the role of other pathways potentially involved in redox metabolism and how they affect quantitatively the required capacity of the Calvin cycle. Our model also enables us to discriminate between different acetate assimilation pathways that were proposed recently for R. sphaeroides and R. rubrum, both lacking the isocitrate lyase. Finally, we demonstrate the value of the metabolic model also for potential biotechnological applications: we examine the theoretical

  17. Central blood pressure and pulse wave velocity: relationship to target organ damage and cardiovascular morbidity-mortality in diabetic patients or metabolic syndrome. An observational prospective study. LOD-DIABETES study protocol

    Directory of Open Access Journals (Sweden)

    Castaño-Sánchez Carmen

    2010-03-01

    Full Text Available Abstract Background Diabetic patients show an increased prevalence of non-dipping arterial pressure pattern, target organ damage and elevated arterial stiffness. These alterations are associated with increased cardiovascular risk. The objectives of this study are the following: to evaluate the prognostic value of central arterial pressure and pulse wave velocity in relation to the incidence and outcome of target organ damage and the appearance of cardiovascular episodes (cardiovascular mortality, myocardial infarction, chest pain and stroke in patients with type 2 diabetes mellitus or metabolic syndrome. Methods/Design Design: This is an observational prospective study with 5 years duration, of which the first year corresponds to patient inclusion and initial evaluation, and the remaining four years to follow-up. Setting: The study will be carried out in the urban primary care setting. Study population: Consecutive sampling will be used to include patients diagnosed with type 2 diabetes between 20-80 years of age. A total of 110 patients meeting all the inclusion criteria and none of the exclusion criteria will be included. Measurements: Patient age and sex, family and personal history of cardiovascular disease, and cardiovascular risk factors. Height, weight, heart rate and abdominal circumference. Laboratory tests: hemoglobin, lipid profile, creatinine, microalbuminuria, glomerular filtration rate, blood glucose, glycosylated hemoglobin, blood insulin, fibrinogen and high sensitivity C-reactive protein. Clinical and 24-hour ambulatory (home blood pressure monitoring and self-measured blood pressure. Common carotid artery ultrasound for the determination of mean carotid intima-media thickness. Electrocardiogram for assessing left ventricular hypertrophy. Ankle-brachial index. Retinal vascular study based on funduscopy with non-mydriatic retinography and evaluation of pulse wave morphology and pulse wave velocity using the SphygmoCor system. The

  18. Towards stable kinetics of large metabolic networks: Nonequilibrium potential function approach

    Science.gov (United States)

    Chen, Yong-Cong; Yuan, Ruo-Shi; Ao, Ping; Xu, Min-Juan; Zhu, Xiao-Mei

    2016-06-01

    While the biochemistry of metabolism in many organisms is well studied, details of the metabolic dynamics are not fully explored yet. Acquiring adequate in vivo kinetic parameters experimentally has always been an obstacle. Unless the parameters of a vast number of enzyme-catalyzed reactions happened to fall into very special ranges, a kinetic model for a large metabolic network would fail to reach a steady state. In this work we show that a stable metabolic network can be systematically established via a biologically motivated regulatory process. The regulation is constructed in terms of a potential landscape description of stochastic and nongradient systems. The constructed process draws enzymatic parameters towards stable metabolism by reducing the change in the Lyapunov function tied to the stochastic fluctuations. Biologically it can be viewed as interplay between the flux balance and the spread of workloads on the network. Our approach allows further constraints such as thermodynamics and optimal efficiency. We choose the central metabolism of Methylobacterium extorquens AM1 as a case study to demonstrate the effectiveness of the approach. Growth efficiency on carbon conversion rate versus cell viability and futile cycles is investigated in depth.

  19. Clustering of Emerging Flux

    Science.gov (United States)

    Ruzmaikin, A.

    1997-01-01

    Observations show that newly emerging flux tends to appear on the Solar surface at sites where there is flux already. This results in clustering of solar activity. Standard dynamo theories do not predict this effect.

  20. Metabolic ecology.

    Science.gov (United States)

    Humphries, Murray M; McCann, Kevin S

    2014-01-01

    Ecological theory that is grounded in metabolic currencies and constraints offers the potential to link ecological outcomes to biophysical processes across multiple scales of organization. The metabolic theory of ecology (MTE) has emphasized the potential for metabolism to serve as a unified theory of ecology, while focusing primarily on the size and temperature dependence of whole-organism metabolic rates. Generalizing metabolic ecology requires extending beyond prediction and application of standardized metabolic rates to theory focused on how energy moves through ecological systems. A bibliometric and network analysis of recent metabolic ecology literature reveals a research network characterized by major clusters focused on MTE, foraging theory, bioenergetics, trophic status, and generalized patterns and predictions. This generalized research network, which we refer to as metabolic ecology, can be considered to include the scaling, temperature and stoichiometric models forming the core of MTE, as well as bioenergetic equations, foraging theory, life-history allocation models, consumer-resource equations, food web theory and energy-based macroecology models that are frequently employed in ecological literature. We conclude with six points we believe to be important to the advancement and integration of metabolic ecology, including nomination of a second fundamental equation, complementary to the first fundamental equation offered by the MTE. PMID:24028511

  1. Ventilatory response in metabolic acidosis and cerebral blood volume in humans.

    NARCIS (Netherlands)

    Ven, M.T.P. van de; Colier, W.N.J.M.; Sluijs, M.C. van der; Oeseburg, B.; Folgering, H.T.M.

    2001-01-01

    The relationship between alterations in cerebral blood volume (CBV) and central chemosensitivity regulation was studied under neutral metabolic conditions and during metabolic acidosis. Fifteen healthy subjects (5610 years) were investigated. To induce metabolic acidosis, ammonium chloride (NH(4)Cl)

  2. EL-2 reactor: Thermal neutron flux distribution

    International Nuclear Information System (INIS)

    The flux distribution of thermal neutrons in EL-2 reactor is studied. The reactor core and lattices are described as well as the experimental reactor facilities, in particular, the experimental channels and special facilities. The measurement shows that the thermal neutron flux increases in the central channel when enriched uranium is used in place of natural uranium. However the thermal neutron flux is not perturbed in the other reactor channels by the fuel modification. The macroscopic flux distribution is measured according the radial positioning of fuel rods. The longitudinal neutron flux distribution in a fuel rod is also measured and shows no difference between enriched and natural uranium fuel rods. In addition, measurements of the flux distribution have been effectuated for rods containing other material as steel or aluminium. The neutron flux distribution is also studied in all the experimental channels as well as in the thermal column. The determination of the distribution of the thermal neutron flux in all experimental facilities, the thermal column and the fuel channels has been made with a heavy water level of 1825 mm and is given for an operating power of 1000 kW. (M.P.)

  3. Improved L-lysine production with Corynebacterium glutamicum and systemic insight into citrate synthase flux and activity.

    Science.gov (United States)

    van Ooyen, Jan; Noack, Stephan; Bott, Michael; Reth, Alexander; Eggeling, Lothar

    2012-08-01

    We here developed a series of Corynebacterium glutamicum strains with gradual decreased specific citrate synthase (CS) activity and quantified in a multifaceted approach the consequences of residual activity on the transcriptome, metabolome, and fluxome level as well as on L-lysine formation and growth. We achieved an intended gradual L-lysine yield increase and recognized and overcame further new limitations in the L-lysine biosynthesis pathway to result in a strain with the highest yield reported so far when assayed under comparable conditions. As a non-intended outcome, a detailed flux analysis revealed an almost constant flux through CS at 10% remaining CS activity, whereas the metabolome data revealed an increase in the oxaloacetate and acetyl-CoA concentrations. Hence reduced CS activity is apparently efficiently buffered by increased concentrations of CS substrates, implying a certain robustness of the central metabolism in response of the imposed gene expressions. PMID:22392073

  4. Protostellar Accretion Flows Destabilized by Magnetic Flux Redistribution

    CERN Document Server

    Krasnopolsky, Ruben; Shang, Hsien; Zhao, Bo

    2012-01-01

    Magnetic flux redistribution lies at the heart of the problem of star formation in dense cores of molecular clouds that are magnetized to a realistic level. If all of the magnetic flux of a typical core were to be dragged into the central star, the stellar field strength would be orders of magnitude higher than the observed values. This well-known "magnetic flux problem" can in principle be resolved through non-ideal MHD effects. Two dimensional (axisymmetric) calculations have shown that ambipolar diffusion, in particular, can transport magnetic flux outward relative to matter, allowing material to enter the central object without dragging the field lines along. We show through simulations that such axisymmetric protostellar accretion flows are unstable in three dimensions to magnetic interchange instability in the azimuthal direction. The instability is driven by the magnetic flux redistributed from the matter that enters the central object. It typically starts to develop during the transition from the pres...

  5. Integration of gene expression data into genome-scale metabolic models

    DEFF Research Database (Denmark)

    Åkesson, M.; Förster, Jochen; Nielsen, Jens

    2004-01-01

    gene expression from chemostat and batch cultures of Saccharomyces cerevisiae were combined with a recently developed genome-scale model, and the computed metabolic flux distributions were compared to experimental values from carbon labeling experiments and metabolic network analysis. The integration...... of expression data resulted in improved predictions of metabolic behavior in batch cultures, enabling quantitative predictions of exchange fluxes as well as qualitative estimations of changes in intracellular fluxes. A critical discussion of correlation between gene expression and metabolic fluxes is......A framework for integration of transcriptome data into stoichiometric metabolic models to obtain improved flux predictions is presented. The key idea is to exploit the regulatory information in the expression data to give additional constraints on the metabolic fluxes in the model. Measurements of...

  6. FAME, the Flux Analysis and Modeling Environment

    OpenAIRE

    Boele Joost; Olivier Brett G; Teusink Bas

    2012-01-01

    Background The creation and modification of genome-scale metabolic models is a task that requires specialized software tools. While these are available, subsequently running or visualizing a model often relies on disjoint code, which adds additional actions to the analysis routine and, in our experience, renders these applications suboptimal for routine use by (systems) biologists. Results The Flux Analysis and Modeling Environment (FAME) is the first web-based modeling tool that combines th...

  7. DRUG METABOLISM

    Directory of Open Access Journals (Sweden)

    Deepak Singla

    2011-02-01

    Full Text Available The termmetabolism, derived from the Greek language, simply means change or transformation. It relates to various processes within the body that convert food and other substances into energy and other metabolic byproducts used by the body. Drug metabolism is the body’s way of transforming drugs, so they can be excreted from the body. Many drugs arenot active until they have been metabolized in the body by enzymes that transform them. Most drugs are lipophilic, meaning they pass through membranes to reach their target site. Most drugs are treated by the body like foreign substances, also known as xenobiotics. Humans have evolved a complex system for xenobiotic metabolism

  8. Metabolic neuropathies

    Science.gov (United States)

    ... body ( sepsis ) Thyroid disease Vitamin deficiencies (including vitamins B12 , B6 , E , and B1 ) Some metabolic disorders are ... by injection. Abnormal blood sugar level or thyroid function may need medicines to correct the problem. For ...

  9. Noise effect in metabolic networks

    International Nuclear Information System (INIS)

    Constraint-based models such as flux balance analysis (FBA) are a powerful tool to study biological metabolic networks. Under the hypothesis that cells operate at an optimal growth rate as the result of evolution and natural selection, this model successfully predicts most cellular behaviours in growth rate. However, the model ignores the fact that cells can change their cellular metabolic states during evolution, leaving optimal metabolic states unstable. Here, we consider all the cellular processes that change metabolic states into a single term 'noise', and assume that cells change metabolic states by randomly walking in feasible solution space. By simulating a state of a cell randomly walking in the constrained solution space of metabolic networks, we found that in a noisy environment cells in optimal states tend to travel away from these points. On considering the competition between the noise effect and the growth effect in cell evolution, we found that there exists a trade-off between these two effects. As a result, the population of the cells contains different cellular metabolic states, and the population growth rate is at suboptimal states. (cross-disciplinary physics and related areas of science and technology)

  10. Metabolic syndrome

    Directory of Open Access Journals (Sweden)

    Gogia Atul

    2006-02-01

    Full Text Available The Metabolic syndrome is a widely prevalent and multi-factorial disorder. The syndrome has been given several names, including- the metabolic syndrome, the insulin resistance syndrome, the plurimetabolic syndrome, and the deadly quartet. With the formulation of NCEP/ATP III guidelines, some uniformity and standardization has occurred in the definition of metabolic syndrome and has been very useful for epidemiological purposes. The mechanisms underlying the metabolic syndrome are not fully known; however resistance to insulin stimulated glucose uptake seems to modify biochemical responses in a way that predisposes to metabolic risk factors. The clinical relevance of the metabolic syndrome is related to its role in the development of cardiovascular disease. Management of the metabolic syndrome involves patient-education and intervention at various levels. Weight reduction is one of the main stays of treatment. In this article we comprehensively discuss this syndrome- the epidemiology, pathogenesis, clinical relevance and management. The need to do a comprehensive review of this particular syndrome has arisen in view of the ever increasing incidence of this entitiy. Soon, metabolic syndrome will overtake cigarette smoking as the number one risk factor for heart disease among the US population. Hardly any issue of any primary care medical journal can be opened without encountering an article on type 2 diabetes, dyslipidemia or hypertension. It is rare to see type 2 diabetes, dyslipidemia, obesity or hypertension in isolation. Insulin resistance and resulting hyperinsulinemia have been implicated in the development of glucose intolerance (and progression to type 2 diabetes, hypertriglyceridemia, hypertension, polycystic ovary yndrome, hypercoagulability and vascular inflammation, as well as the eventual development of atherosclerotic cardiovascular disease manifested as myocardial infarction, stroke and myriad end organ diseases. Conversely

  11. Lipid Metabolism

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    2008393 Effects of angiotensin Ⅱ type 1 receptor blocker on triglyceride metabolism in the liver: experiment with Zucker fatty rats. RAN Jianmin(冉建民), et al. Dept Endocrinol, Guangzhou Red Cross Hosp, 4th Hosp Med Coll, Jinan Univ, Guangzhou 510220. Natl Med J China 2008;88(22):1557-1561. Objective To investigate the effects of angiotensin receptor blocker (ARB) on triglyceride (TG) metabolism and mechanism thereof.

  12. Integration of Metabolic Modeling with Gene Co-expression Reveals Transcriptionally Programmed Reactions Explaining Robustness in Mycobacterium tuberculosis.

    Science.gov (United States)

    Puniya, Bhanwar Lal; Kulshreshtha, Deepika; Mittal, Inna; Mobeen, Ahmed; Ramachandran, Srinivasan

    2016-01-01

    Robustness of metabolic networks is accomplished by gene regulation, modularity, re-routing of metabolites and plasticity. Here, we probed robustness against perturbations of biochemical reactions of M. tuberculosis in the form of predicting compensatory trends. In order to investigate the transcriptional programming of genes associated with correlated fluxes, we integrated with gene co-expression network. Knock down of the reactions NADH2r and ATPS responsible for producing the hub metabolites, and Central carbon metabolism had the highest proportion of their associated genes under transcriptional co-expression with genes of their flux correlated reactions. Reciprocal gene expression correlations were observed among compensatory routes, fresh activation of alternative routes and in the multi-copy genes of Cysteine synthase and of Phosphate transporter. Knock down of 46 reactions caused the activation of Isocitrate lyase or Malate synthase or both reactions, which are central to the persistent state of M. tuberculosis. A total of 30 new freshly activated routes including Cytochrome c oxidase, Lactate dehydrogenase, and Glycine cleavage system were predicted, which could be responsible for switching into dormant or persistent state. Thus, our integrated approach of exploring transcriptional programming of flux correlated reactions has the potential to unravel features of system architecture conferring robustness. PMID:27000948

  13. Brain glucose sensing, glucokinase and neural control of metabolism and islet function.

    Science.gov (United States)

    Ogunnowo-Bada, E O; Heeley, N; Brochard, L; Evans, M L

    2014-09-01

    It is increasingly apparent that the brain plays a central role in metabolic homeostasis, including the maintenance of blood glucose. This is achieved by various efferent pathways from the brain to periphery, which help control hepatic glucose flux and perhaps insulin-stimulated insulin secretion. Also, critically important for the brain given its dependence on a constant supply of glucose as a fuel--emergency counter-regulatory responses are triggered by the brain if blood glucose starts to fall. To exert these control functions, the brain needs to detect rapidly and accurately changes in blood glucose. In this review, we summarize some of the mechanisms postulated to play a role in this and examine the potential role of the low-affinity hexokinase, glucokinase, in the brain as a key part of some of this sensing. We also discuss how these processes may become altered in diabetes and related metabolic diseases. PMID:25200293

  14. Animal metabolism

    International Nuclear Information System (INIS)

    Studies on placental transport included the following: clearance of tritiated water as a baseline measurement for transport of materials across perfused placentas; transport of organic and inorganic mercury across the perfused placenta of the guinea pig in late gestation; and transport of cadmium across the perfused placenta of the guinea pig in late gestation. Studies on cadmium absorption and metabolism included the following: intestinal absorption and retention of cadmium in neonatal rats; uptake and distribut