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Sample records for 13c-metabolic flux analysis

  1. 13C metabolic flux analysis at a genome-scale.

    PubMed

    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

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

    PubMed

    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.

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

    PubMed

    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

  4. SUMOFLUX: A Generalized Method for Targeted 13C Metabolic Flux Ratio Analysis

    PubMed Central

    Kogadeeva, Maria

    2016-01-01

    Metabolic fluxes are a cornerstone of cellular physiology that emerge from a complex interplay of enzymes, carriers, and nutrients. The experimental assessment of in vivo intracellular fluxes using stable isotopic tracers is essential if we are to understand metabolic function and regulation. Flux estimation based on 13C or 2H labeling relies on complex simulation and iterative fitting; processes that necessitate a level of expertise that ordinarily preclude the non-expert user. To overcome this, we have developed SUMOFLUX, a methodology that is broadly applicable to the targeted analysis of 13C-metabolic fluxes. By combining surrogate modeling and machine learning, we trained a predictor to specialize in estimating flux ratios from measurable 13C-data. SUMOFLUX targets specific flux features individually, which makes it fast, user-friendly, applicable to experimental design and robust in terms of experimental noise and exchange flux magnitude. Collectively, we predict that SUMOFLUX's properties realistically pave the way to high-throughput flux analyses. PMID:27626798

  5. SUMOFLUX: A Generalized Method for Targeted 13C Metabolic Flux Ratio Analysis.

    PubMed

    Kogadeeva, Maria; Zamboni, Nicola

    2016-09-01

    Metabolic fluxes are a cornerstone of cellular physiology that emerge from a complex interplay of enzymes, carriers, and nutrients. The experimental assessment of in vivo intracellular fluxes using stable isotopic tracers is essential if we are to understand metabolic function and regulation. Flux estimation based on 13C or 2H labeling relies on complex simulation and iterative fitting; processes that necessitate a level of expertise that ordinarily preclude the non-expert user. To overcome this, we have developed SUMOFLUX, a methodology that is broadly applicable to the targeted analysis of 13C-metabolic fluxes. By combining surrogate modeling and machine learning, we trained a predictor to specialize in estimating flux ratios from measurable 13C-data. SUMOFLUX targets specific flux features individually, which makes it fast, user-friendly, applicable to experimental design and robust in terms of experimental noise and exchange flux magnitude. Collectively, we predict that SUMOFLUX's properties realistically pave the way to high-throughput flux analyses. PMID:27626798

  6. A Peptide-Based Method for 13C Metabolic Flux Analysis in Microbial Communities

    PubMed Central

    Ghosh, Amit; Nilmeier, Jerome; Weaver, Daniel; Adams, Paul D.; Keasling, Jay D.; Mukhopadhyay, Aindrila; Petzold, Christopher J.; Martín, Héctor García

    2014-01-01

    The study of intracellular metabolic fluxes and inter-species metabolite exchange for microbial communities is of crucial importance to understand and predict their behaviour. The most authoritative method of measuring intracellular fluxes, 13C Metabolic Flux Analysis (13C MFA), uses the labeling pattern obtained from metabolites (typically amino acids) during 13C labeling experiments to derive intracellular fluxes. However, these metabolite labeling patterns cannot easily be obtained for each of the members of the community. Here we propose a new type of 13C MFA that infers fluxes based on peptide labeling, instead of amino acid labeling. The advantage of this method resides in the fact that the peptide sequence can be used to identify the microbial species it originates from and, simultaneously, the peptide labeling can be used to infer intracellular metabolic fluxes. Peptide identity and labeling patterns can be obtained in a high-throughput manner from modern proteomics techniques. We show that, using this method, it is theoretically possible to recover intracellular metabolic fluxes in the same way as through the standard amino acid based 13C MFA, and quantify the amount of information lost as a consequence of using peptides instead of amino acids. We show that by using a relatively small number of peptides we can counter this information loss. We computationally tested this method with a well-characterized simple microbial community consisting of two species. PMID:25188426

  7. 13CFLUX2—high-performance software suite for 13C-metabolic flux analysis

    PubMed Central

    Weitzel, Michael; Nöh, Katharina; Dalman, Tolga; Niedenführ, Sebastian; Stute, Birgit; Wiechert, Wolfgang

    2013-01-01

    Summary: 13C-based metabolic flux analysis (13C-MFA) is the state-of-the-art method to quantitatively determine in vivo metabolic reaction rates in microorganisms. 13CFLUX2 contains all tools for composing flexible computational 13C-MFA workflows to design and evaluate carbon labeling experiments. A specially developed XML language, FluxML, highly efficient data structures and simulation algorithms achieve a maximum of performance and effectiveness. Support of multicore CPUs, as well as compute clusters, enables scalable investigations. 13CFLUX2 outperforms existing tools in terms of universality, flexibility and built-in features. Therewith, 13CFLUX2 paves the way for next-generation high-resolution 13C-MFA applications on the large scale. Availability and implementation: 13CFLUX2 is implemented in C++ (ISO/IEC 14882 standard) with Java and Python add-ons to run under Linux/Unix. A demo version and binaries are available at www.13cflux.net. Contact: info@13cflux.net or k.noeh@fz-juelich.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23110970

  8. 13C metabolic flux analysis in Clostridium acetobutylicum during growth on L-arabinose

    NASA Astrophysics Data System (ADS)

    Hurley, Margaret; Sund, Christian; Liu, Sanchao; Germane, Katherine; Servinsky, Matthew; Gerlach, Elliot

    2015-03-01

    Clostridium acetobutylicum's metabolic pathways have been studied for decades due to its metabolic diversity and industrial value, yet many details of its metabolism are continuing to emerge. To elucidate the role of xylulose-5-P/fructose-6-P phosphoketolase (XFP), and the recently discovered Pentose Phosphate Pathway (PKP) in C. acetobutylicum, experimental and computational metabolic isotope analysis was performed under growth on glucose, xylose, and arabinose. Results indicate that PKP utilization increased with increasing xylose concentration and this trend was further pronounced during growth on arabinose. This was confirmed by mutation of the gene encoding XFP, which almost completely abolished flux through the PKP during growth on arabinose and resulted in decreased acetate:butyrate ratios. We discuss these experimental and computational results here, and the implications for our understanding of sugar metabolism in C. acetobutylicum.

  9. 13 C-metabolic flux analysis in heterologous cellulase production by Bacillus subtilis genome-reduced strain.

    PubMed

    Toya, Yoshihiro; Hirasawa, Takashi; Morimoto, Takuya; Masuda, Kenta; Kageyama, Yasushi; Ozaki, Katsuya; Ogasawara, Naotake; Shimizu, Hiroshi

    2014-06-10

    The great potential of Bacillus subtilis to produce biomaterials would be further enhanced by the development of strains with deletions of non-essential genomic regions. Here, using stationary (13)C-metabolic flux analysis ((13)C-MFA), we investigated the metabolism during cellulase production by the genome-reduced B. subtilis strain MGB874. We transformed MGB874 and wild-type strains with the heterologous cellulase gene, and cultured these on a synthetic medium containing glucose as carbon source. The addition of glutamate and the genome reduction enhanced cellulase production, which led us to use (13)C-MFA to assess the effects of glutamate addition and gene deletions on metabolism. We found that there was a significant increase in the flux in the pentose phosphate (PP) pathway, whereas the fluxes of reactions from acetyl-CoA to α-ketoglutarate were repressed in the presence of glutamate. We hypothesize that the increase in the PP pathway flux was caused by the decrease of citrate synthase flux through the accumulation of glycolytic intermediates. Excess NADPH produced by the PP pathway may affect the increase in cellulase production. Furthermore, the fluxes on glycolysis and the acetate formation of the cellulase-producing wild-type strain were significantly larger than that of the cellulase-producing MGB874 strain when the strains were cultured with glucose and glutamate.

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

    PubMed

    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

  11. (13)C-metabolic flux analysis of lipid accumulation in the oleaginous fungus Mucor circinelloides.

    PubMed

    Zhao, Lina; Zhang, Huaiyuan; Wang, Liping; Chen, Haiqin; Chen, Yong Q; Chen, Wei; Song, Yuanda

    2015-12-01

    The oleaginous fungus Mucor circinelloides is of industrial interest because it can produce high levels of polyunsaturated fatty acid γ-linolenic acid. M. circinelloides CBS 277.49 is able to accumulate less than 15% of cell dry weight as lipids, while M. circinelloides WJ11 can accumulate lipid up to 36%. In order to better understand the mechanisms behind the differential lipid accumulation in these two strains, tracer experiments with (13)C-glucose were performed with the growth of M. circinelloides and subsequent gas chromatography-mass spectrometric detection of (13)C-patterns in proteinogenic amino acids was carried out to identify the metabolic network topology and estimate intracellular fluxes. Our results showed that the high oleaginous strain WJ11 had higher flux of pentose phosphate pathway and malic enzyme, lower flux in tricarboxylic acid cycle, higher flux in glyoxylate cycle and ATP: citrate lyase, together, it might provide more NADPH and substrate acetyl-CoA for fatty acid synthesis.

  12. Comparative 13C metabolic flux analysis of pyruvate dehydrogenase complex-deficient, L-valine-producing Corynebacterium glutamicum.

    PubMed

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

    2011-09-01

    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 (13)C 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 of 113% ± 22%. The shift in the split ratio can be explained by an increased demand of NADPH for l-valine formation. In accordance, the introduction of the Escherichia coli transhydrogenase PntAB, catalyzing the reversible conversion of NADH to NADPH, into an L-valine-producing C. glutamicum strain caused the PPP flux to decrease to 57% ± 6%, which is below the wild-type split ratio. Hence, transhydrogenase activity offers an alternative perspective for sufficient NADPH supply, which is relevant for most amino acid production systems. Moreover, as demonstrated for L-valine, this bypass leads to a significant increase of product yield due to a concurrent reduction in carbon dioxide formation via the PPP.

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

    PubMed

    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/

  14. Central metabolic responses to the overproduction of fatty acids in Escherichia coli based on 13C-metabolic flux analysis.

    PubMed

    He, Lian; Xiao, Yi; Gebreselassie, Nikodimos; Zhang, Fuzhong; Antoniewiez, Maciek R; Tang, Yinjie J; Peng, Lifeng

    2014-03-01

    We engineered a fatty acid overproducing Escherichia coli strain through overexpressing tesA (“pull”) and fadR (“push”) and knocking out fadE (“block”). This “pull-push-block” strategy yielded 0.17 g of fatty acids (C12–C18) per gram of glucose (equivalent to 48% of the maximum theoretical yield) in batch cultures during the exponential growth phase under aerobic conditions. Metabolic fluxes were determined for the engineered E. coli and its control strain using tracer ([1,2-13C]glucose) experiments and 13C-metabolic flux analysis. Cofactor (NADPH) and energy (ATP) balances were also investigated for both strains based on estimated fluxes. Compared to the control strain, fatty acid overproduction led to significant metabolic responses in the central metabolism: (1) Acetic acid secretion flux decreased 10-fold; (2) Pentose phosphate pathway and Entner–Doudoroff pathway fluxes increased 1.5- and 2.0-fold, respectively; (3) Biomass synthesis flux was reduced 1.9-fold; (4) Anaplerotic phosphoenolpyruvate carboxylation flux decreased 1.7-fold; (5) Transhydrogenation flux converting NADH to NADPH increased by 1.7-fold. Real-time quantitative RT-PCR analysis revealed the engineered strain increased the transcription levels of pntA (encoding the membrane-bound transhydrogenase) by 2.1-fold and udhA (encoding the soluble transhydrogenase) by 1.4-fold, which is in agreement with the increased transhydrogenation flux. Cofactor and energy balances analyses showed that the fatty acid overproducing E. coli consumed significantly higher cellular maintenance energy than the control strain. We discussed the strategies to future strain development and process improvements for fatty acid production in E. coli.

  15. Investigate the Metabolic Reprogramming of Saccharomyces cerevisiae for Enhanced Resistance to Mixed Fermentation Inhibitors via 13C Metabolic Flux Analysis.

    PubMed

    Guo, Weihua; Chen, Yingying; Wei, Na; Feng, Xueyang

    2016-01-01

    The fermentation inhibitors from the pretreatment of lignocellulosic materials, e.g., acetic acid and furfural, are notorious due to their negative effects on the cell growth and chemical production. However, the metabolic reprogramming of the cells under these stress conditions, especially metabolic response for resistance to mixed inhibitors, has not been systematically investigated and remains mysterious. Therefore, in this study, 13C metabolic flux analysis (13C-MFA), a powerful tool to elucidate the intracellular carbon flux distributions, has been applied to two Saccharomyces cerevisiae strains with different tolerances to the inhibitors under acetic acid, furfural, and mixed (i.e., acetic acid and furfural) stress conditions to unravel the key metabolic responses. By analyzing the intracellular carbon fluxes as well as the energy and cofactor utilization under different conditions, we uncovered varied metabolic responses to different inhibitors. Under acetate stress, ATP and NADH production was slightly impaired, while NADPH tended towards overproduction. Under furfural stress, ATP and cofactors (including both NADH and NADPH) tended to be overproduced. However, under dual-stress condition, production of ATP and cofactors was severely impaired due to synergistic stress caused by the simultaneous addition of two fermentation inhibitors. Such phenomenon indicated the pivotal role of the energy and cofactor utilization in resisting the mixed inhibitors of acetic acid and furfural. Based on the discoveries, valuable insights are provided to improve the tolerance of S. cerevisiae strain and further enhance lignocellulosic fermentation.

  16. Investigate the Metabolic Reprogramming of Saccharomyces cerevisiae for Enhanced Resistance to Mixed Fermentation Inhibitors via 13C Metabolic Flux Analysis

    PubMed Central

    Guo, Weihua; Chen, Yingying; Wei, Na; Feng, Xueyang

    2016-01-01

    The fermentation inhibitors from the pretreatment of lignocellulosic materials, e.g., acetic acid and furfural, are notorious due to their negative effects on the cell growth and chemical production. However, the metabolic reprogramming of the cells under these stress conditions, especially metabolic response for resistance to mixed inhibitors, has not been systematically investigated and remains mysterious. Therefore, in this study, 13C metabolic flux analysis (13C-MFA), a powerful tool to elucidate the intracellular carbon flux distributions, has been applied to two Saccharomyces cerevisiae strains with different tolerances to the inhibitors under acetic acid, furfural, and mixed (i.e., acetic acid and furfural) stress conditions to unravel the key metabolic responses. By analyzing the intracellular carbon fluxes as well as the energy and cofactor utilization under different conditions, we uncovered varied metabolic responses to different inhibitors. Under acetate stress, ATP and NADH production was slightly impaired, while NADPH tended towards overproduction. Under furfural stress, ATP and cofactors (including both NADH and NADPH) tended to be overproduced. However, under dual-stress condition, production of ATP and cofactors was severely impaired due to synergistic stress caused by the simultaneous addition of two fermentation inhibitors. Such phenomenon indicated the pivotal role of the energy and cofactor utilization in resisting the mixed inhibitors of acetic acid and furfural. Based on the discoveries, valuable insights are provided to improve the tolerance of S. cerevisiae strain and further enhance lignocellulosic fermentation. PMID:27532329

  17. Investigate the Metabolic Reprogramming of Saccharomyces cerevisiae for Enhanced Resistance to Mixed Fermentation Inhibitors via 13C Metabolic Flux Analysis.

    PubMed

    Guo, Weihua; Chen, Yingying; Wei, Na; Feng, Xueyang

    2016-01-01

    The fermentation inhibitors from the pretreatment of lignocellulosic materials, e.g., acetic acid and furfural, are notorious due to their negative effects on the cell growth and chemical production. However, the metabolic reprogramming of the cells under these stress conditions, especially metabolic response for resistance to mixed inhibitors, has not been systematically investigated and remains mysterious. Therefore, in this study, 13C metabolic flux analysis (13C-MFA), a powerful tool to elucidate the intracellular carbon flux distributions, has been applied to two Saccharomyces cerevisiae strains with different tolerances to the inhibitors under acetic acid, furfural, and mixed (i.e., acetic acid and furfural) stress conditions to unravel the key metabolic responses. By analyzing the intracellular carbon fluxes as well as the energy and cofactor utilization under different conditions, we uncovered varied metabolic responses to different inhibitors. Under acetate stress, ATP and NADH production was slightly impaired, while NADPH tended towards overproduction. Under furfural stress, ATP and cofactors (including both NADH and NADPH) tended to be overproduced. However, under dual-stress condition, production of ATP and cofactors was severely impaired due to synergistic stress caused by the simultaneous addition of two fermentation inhibitors. Such phenomenon indicated the pivotal role of the energy and cofactor utilization in resisting the mixed inhibitors of acetic acid and furfural. Based on the discoveries, valuable insights are provided to improve the tolerance of S. cerevisiae strain and further enhance lignocellulosic fermentation. PMID:27532329

  18. Integration of a constraint-based metabolic model of Brassica napus developing seeds with 13C-metabolic flux analysis

    DOE PAGES

    Hay, Jordan O.; Shi, Hai; Heinzel, Nicolas; Hebbelmann, Inga; Rolletschek, Hardy; Schwender, Jorg

    2014-12-19

    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) modelmore » 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 (GPR) associations resolving subcellular localization. Detailed mass and charge balancing and confidence scoring were applied to all reactions. Using B. 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). In conclusion, using this combined approach we characterize the difference in metabolic flux of developing seeds of two B. napus genotypes contrasting in starch

  19. Integration of a constraint-based metabolic model of Brassica napus developing seeds with 13C-metabolic flux analysis

    PubMed Central

    Hay, Jordan O.; Shi, Hai; Heinzel, Nicolas; Hebbelmann, Inga; Rolletschek, Hardy; Schwender, Jorg

    2014-01-01

    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 (GPR) associations resolving subcellular localization. Detailed mass and charge balancing and confidence scoring were applied to all reactions. Using B. 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 B. napus genotypes contrasting in starch and oil content. PMID

  20. (13)C metabolic flux analysis of the extremely thermophilic, fast growing, xylose-utilizing Geobacillus strain LC300.

    PubMed

    Cordova, Lauren T; Antoniewicz, Maciek R

    2016-01-01

    Thermophiles are increasingly used as versatile hosts in the biotechnology industry. One of the key advantages of thermophiles is the potential to achieve high rates of feedstock conversion at elevated temperatures. The recently isolated Geobacillus strain LC300 grows extremely fast on xylose, with a doubling time of less than 30 min. In the accompanying paper, the genome of Geobacillus LC300 was sequenced and annotated. In this work, we have experimentally validated the metabolic network model using parallel (13)C-labeling experiments and applied (13)C-metabolic flux analysis to quantify precise metabolic fluxes. Specifically, the complete set of singly labeled xylose tracers, [1-(13)C], [2-(13)C], [3-(13)C], [4-(13)C], and [5-(13)C]xylose, was used for the first time. Isotopic labeling of biomass amino acids was measured by gas chromatography mass spectrometry (GC-MS). Isotopic labeling of carbon dioxide in the off-gas was also measured by an on-line mass spectrometer. The (13)C-labeling data was then rigorously integrated for flux elucidation using the COMPLETE-MFA approach. The results provided important new insights into the metabolism of Geobacillus LC300, its efficient xylose utilization pathways, and the balance between carbon, redox and energy fluxes. The pentose phosphate pathway, glycolysis and TCA cycle were found to be highly active in Geobacillus LC300. The oxidative pentose phosphate pathway was also active and contributed significantly to NADPH production. No transhydrogenase activity was detected. Results from this work provide a solid foundation for future studies of this strain and its metabolic engineering and biotechnological applications.

  1. Metabolic network reconstruction, growth characterization and 13C-metabolic flux analysis of the extremophile Thermus thermophilus HB8.

    PubMed

    Swarup, Aditi; Lu, Jing; DeWoody, Kathleen C; Antoniewicz, Maciek R

    2014-07-01

    Thermus thermophilus is an extremely thermophilic bacterium with significant biotechnological potential. In this work, we have characterized aerobic growth characteristics of T. thermophilus HB8 at temperatures between 50 and 85°C, constructed a metabolic network model of its central carbon metabolism and validated the model using (13)C-metabolic flux analysis ((13)C-MFA). First, cells were grown in batch cultures in custom constructed mini-bioreactors at different temperatures to determine optimal growth conditions. The optimal temperature for T. thermophilus grown on defined medium with glucose was 81°C. The maximum growth rate was 0.25h(-1). Between 50 and 81°C the growth rate increased by 7-fold and the temperature dependence was described well by an Arrhenius model with an activation energy of 47kJ/mol. Next, we performed a (13)C-labeling experiment with [1,2-(13)C] glucose as the tracer and calculated intracellular metabolic fluxes using (13)C-MFA. The results provided support for the constructed network model and highlighted several interesting characteristics of T. thermophilus metabolism. We found that T. thermophilus largely uses glycolysis and TCA cycle to produce biosynthetic precursors, ATP and reducing equivalents needed for cells growth. Consistent with its proposed metabolic network model, we did not detect any oxidative pentose phosphate pathway flux or Entner-Doudoroff pathway activity. The biomass precursors erythrose-4-phosphate and ribose-5-phosphate were produced via the non-oxidative pentose phosphate pathway, and largely via transketolase, with little contribution from transaldolase. The high biomass yield on glucose that was measured experimentally was also confirmed independently by (13)C-MFA. The results presented here provide a solid foundation for future studies of T. thermophilus and its metabolic engineering applications.

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

    SciTech Connect

    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.

  3. 13C Metabolic Flux Analysis for Systematic Metabolic Engineering of S. cerevisiae for Overproduction of Fatty Acids

    PubMed Central

    Ghosh, Amit; Ando, David; Gin, Jennifer; Runguphan, Weerawat; Denby, Charles; Wang, George; Baidoo, Edward E. K.; Shymansky, Chris; Keasling, Jay D.; García Martín, Héctor

    2016-01-01

    Efficient redirection of microbial metabolism into the abundant production of desired bioproducts remains non-trivial. Here, we used flux-based modeling approaches to improve yields of fatty acids in Saccharomyces cerevisiae. We combined 13C labeling data with comprehensive genome-scale models to shed light onto microbial metabolism and improve metabolic engineering efforts. We concentrated on studying the balance of acetyl-CoA, a precursor metabolite for the biosynthesis of fatty acids. A genome-wide acetyl-CoA balance study showed ATP citrate lyase from Yarrowia lipolytica as a robust source of cytoplasmic acetyl-CoA and malate synthase as a desirable target for downregulation in terms of acetyl-CoA consumption. These genetic modifications were applied to S. cerevisiae WRY2, a strain that is capable of producing 460 mg/L of free fatty acids. With the addition of ATP citrate lyase and downregulation of malate synthase, the engineered strain produced 26% more free fatty acids. Further increases in free fatty acid production of 33% were obtained by knocking out the cytoplasmic glycerol-3-phosphate dehydrogenase, which flux analysis had shown was competing for carbon flux upstream with the carbon flux through the acetyl-CoA production pathway in the cytoplasm. In total, the genetic interventions applied in this work increased fatty acid production by ~70%. PMID:27761435

  4. 13C metabolic flux analysis for larger scale cultivation using gas chromatography-combustion-isotope ratio mass spectrometry.

    PubMed

    Yuan, Yongbo; Yang, Tae Hoon; Heinzle, Elmar

    2010-07-01

    (13)C-based metabolic flux analysis ((13)CMFA) is limited to smaller scale experiments due to very high costs of labeled substrates. We measured (13)C enrichment in proteinogenic amino acid hydrolyzates using gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS) from a series of parallel batch cultivations of Corynebacterium glutamicum utilizing mixtures of natural glucose and [1-(13)C] glucose, containing 0%, 0.5%, 1%, 2%, and 10% [1-(13)C] glucose. Decreasing the [1-(13)C] glucose content, kinetic isotope effects played an increasing role but could be corrected. From the corrected (13)C enrichments in vivo fluxes in the central metabolism were determined by numerical optimization. The obtained flux distribution was very similar to those obtained from parallel labeling experiments using conventional high labeling GC-MS method and to published results. The GC-C-IRMS-based method involving low labeling degree of expensive tracer substrate, e.g. 1%, is well suited for larger laboratory and industrial pilot scale fermentations.

  5. Metabolomic and (13)C-metabolic flux analysis of a xylose-consuming Saccharomyces cerevisiae strain expressing xylose isomerase.

    PubMed

    Wasylenko, Thomas M; Stephanopoulos, Gregory

    2015-03-01

    Over the past two decades, significant progress has been made in the engineering of xylose-consuming Saccharomyces cerevisiae strains for production of lignocellulosic biofuels. However, the ethanol productivities achieved on xylose are still significantly lower than those observed on glucose for reasons that are not well understood. We have undertaken an analysis of central carbon metabolite pool sizes and metabolic fluxes on glucose and on xylose under aerobic and anaerobic conditions in a strain capable of rapid xylose assimilation via xylose isomerase in order to investigate factors that may limit the rate of xylose fermentation. We find that during xylose utilization the flux through the non-oxidative Pentose Phosphate Pathway (PPP) is high but the flux through the oxidative PPP is low, highlighting an advantage of the strain employed in this study. Furthermore, xylose fails to elicit the full carbon catabolite repression response that is characteristic of glucose fermentation in S. cerevisiae. We present indirect evidence that the incomplete activation of the fermentation program on xylose results in a bottleneck in lower glycolysis, leading to inefficient re-oxidation of NADH produced in glycolysis. PMID:25311863

  6. Metabolomic and 13C-Metabolic Flux Analysis of a Xylose-Consuming Saccharomyces cerevisiae Strain Expressing Xylose Isomerase

    PubMed Central

    Wasylenko, Thomas M.; Stephanopoulos, Gregory

    2016-01-01

    Over the past two decades significant progress has been made in the engineering of xylose-consuming Saccharomyces cerevisiae strains for production of lignocellulosic biofuels. However, the ethanol productivities achieved on xylose are still significantly lower than those observed on glucose for reasons that are not well understood. We have undertaken an analysis of central carbon metabolite pool sizes and metabolic fluxes on glucose and on xylose under aerobic and anaerobic conditions in a strain capable of rapid xylose assimilation via xylose isomerase in order to investigate factors that may limit the rate of xylose fermentation. We find that during xylose utilization the flux through the non-oxidative PPP is high but the flux through the oxidative PPP is low, highlighting an advantage of the strain employed in this study. Furthermore, xylose fails to elicit the full carbon catabolite repression response that is characteristic of glucose fermentation in S. cerevisiae. We present indirect evidence that the incomplete activation of the fermentation program on xylose results in a bottleneck in lower glycolysis, leading to inefficient re-oxidation of NADH produced in glycolysis. PMID:25311863

  7. Impacts of high β-galactosidase expression on central metabolism of recombinant Pichia pastoris GS115 using glucose as sole carbon source via (13)C metabolic flux analysis.

    PubMed

    Nie, Yongsheng; Huang, Mingzhi; Lu, Junjie; Qian, Jiangchao; Lin, Weilu; Chu, Ju; Zhuang, Yingping; Zhang, Siliang

    2014-10-10

    The yeast Pichia pastoris GS115 is a widely used microbial cell factory for the production of heterologous protein. In order to reveal the impacts of high heterologous protein expression on the central metabolism of Pichia pastoris GS115 using glucose as sole carbon source, we engineered a high β-galactosidase expression strain P. pastoris G1HL and a low expression control strain P. pastoris GHL through controlling the initiation strength of constitutive promoter pGAP. The carbon flux distributions in these two strains were quantified via (13)C metabolic flux analysis. Compared to the control strain, G1HL showed a lower growth rate, a higher flux through glycolysis pathway, a higher flux through pentose phosphate pathway, and a lower flux through by-products secretion pathway. The metabolic flux redistribution in G1HL was thought to compensate the increased redox cofactors and energy demands caused by the high protein expression. Although the fluxes through Krebs cycle in two engineered strains were almost the same, they were significantly lower than those in wild strain. The enhanced expression of β-galactosidase by glutamate supplementation demonstrated the potential of P. pastoris GS115 to catabolize more carbon through the Krebs cycle for even higher protein expression. In conclusion, our work indicates that P. pastoris GS115 can readjusts the central metabolism for higher heterologous protein expression and provides strategies for strain development or process optimization for enhancing production of heterologous protein.

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

    PubMed

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

    2014-05-05

    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 observation is further confirmed by 13C-based metabolic flux analysis. In particular, the flux through the methanol oxidation pathway and the TCA cycle was increased in the Rol-producing strain compared to the reference strain. Next to changes in the flux distribution, significant variations in intracellular metabolite concentrations were observed. Most notably, the pools of trehalose, which is related to cellular stress response, and xylose, which is linked to methanol assimilation, were significantly increased in the recombinant strain.

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

    PubMed Central

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

    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 observation is further confirmed by 13C-based metabolic flux analysis. In particular, the flux through the methanol oxidation pathway and the TCA cycle was increased in the Rol-producing strain compared to the reference strain. Next to changes in the flux distribution, significant variations in intracellular metabolite concentrations were observed. Most notably, the pools of trehalose, which is related to cellular stress response, and xylose, which is linked to methanol assimilation, were significantly increased in the recombinant strain. PMID:24957027

  10. 13C metabolic flux analysis shows that resistin impairs the metabolic response to insulin in L6E9 myotubes

    PubMed Central

    2014-01-01

    Background It has been suggested that the adipokine resistin links obesity and insulin resistance, although how resistin acts on muscle metabolism is controversial. We aimed to quantitatively analyse the effects of resistin on the glucose metabolic flux profile and on insulin response in L6E9 myotubes at the metabolic level using a tracer-based metabolomic approach and our in-house developed software, Isodyn. Results Resistin significantly increased glucose uptake and glycolysis, altering pyruvate utilisation by the cell. In the presence of resistin, insulin only slightly increased glucose uptake and glycolysis, and did not alter the flux profile around pyruvate induced by resistin. Resistin prevented the increase in gene expression in pyruvate dehydrogenase-E1 and the sharp decrease in gene expression in cytosolic phosphoenolpyruvate carboxykinase-1 induced by insulin. Conclusions These data suggest that resistin impairs the metabolic activation of insulin. This impairment cannot be explained by the activity of a single enzyme, but instead due to reorganisation of the whole metabolic flux distribution. PMID:25217974

  11. 13C Metabolic Flux Analysis Identifies an Unusual Route for Pyruvate Dissimilation in Mycobacteria which Requires Isocitrate Lyase and Carbon Dioxide Fixation

    PubMed Central

    Beste, Dany J. V.; Bonde, Bhushan; Hawkins, Nathaniel; Ward, Jane L.; Beale, Michael H.; Noack, Stephan; Nöh, Katharina; Kruger, Nicholas J.; Ratcliffe, R. George; McFadden, Johnjoe

    2011-01-01

    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. PMID:21814509

  12. (13)C metabolic flux analysis in neurons utilizing a model that accounts for hexose phosphate recycling within the pentose phosphate pathway.

    PubMed

    Gebril, Hoda M; Avula, Bharathi; Wang, Yan-Hong; Khan, Ikhlas A; Jekabsons, Mika B

    2016-02-01

    Glycolysis, mitochondrial substrate oxidation, and the pentose phosphate pathway (PPP) are critical for neuronal bioenergetics and oxidation-reduction homeostasis, but quantitating their fluxes remains challenging, especially when processes such as hexose phosphate (i.e., glucose/fructose-6-phosphate) recycling in the PPP are considered. A hexose phosphate recycling model was developed which exploited the rates of glucose consumption, lactate production, and mitochondrial respiration to infer fluxes through the major glucose consuming pathways of adherent cerebellar granule neurons by replicating [(13)C]lactate labeling from metabolism of [1,2-(13)C2]glucose. Flux calculations were predicated on a steady-state system with reactions having known stoichiometries and carbon atom transitions. Non-oxidative PPP activity and consequent hexose phosphate recycling, as well as pyruvate production by cytoplasmic malic enzyme, were optimized by the model and found to account for 28 ± 2% and 7.7 ± 0.2% of hexose phosphate and pyruvate labeling, respectively. From the resulting fluxes, 52 ± 6% of glucose was metabolized by glycolysis, compared to 19 ± 2% by the combined oxidative/non-oxidative pentose cycle that allows for hexose phosphate recycling, and 29 ± 8% by the combined oxidative PPP/de novo nucleotide synthesis reactions. By extension, 62 ± 6% of glucose was converted to pyruvate, the metabolism of which resulted in 16 ± 1% of glucose oxidized by mitochondria and 46 ± 6% exported as lactate. The results indicate a surprisingly high proportion of glucose utilized by the pentose cycle and the reactions synthesizing nucleotides, and exported as lactate. While the in vitro conditions to which the neurons were exposed (high glucose, no lactate or other exogenous substrates) limit extrapolating these results to the in vivo state, the approach provides a means of assessing a number of metabolic fluxes within the context of hexose phosphate recycling in the PPP from a

  13. GC-MS/MS survey of collision-induced dissociation of tert-butyldimethylsilyl-derivatized amino acids and its application to (13)C-metabolic flux analysis of Escherichia coli central metabolism.

    PubMed

    Okahashi, Nobuyuki; Kawana, Shuichi; Iida, Junko; Shimizu, Hiroshi; Matsuda, Fumio

    2016-09-01

    Stable isotope labeling experiments using mass spectrometry have been employed to investigate carbon flow levels (metabolic flux) in mammalian, plant, and microbial cells. To achieve a more precise (13)C-metabolic flux analysis ((13)C-MFA), novel fragmentations of tert-butyldimethylsilyl (TBDMS)-amino acids were investigated by gas chromatography-tandem mass spectrometry (GC-MS/MS). The product ion scan analyses of 15 TBDMS-amino acids revealed 24 novel fragment ions. The amino acid-derived carbons included in the five fragment ions were identified by the analyses of (13)C-labeled authentic standards. The identification of the fragment ion at m/z 170 indicated that the isotopic abundance of S-methyl carbon in methionine could be determined from the cleavage of C5 in the precursor of [M-159](+) (m/z 218). It was also confirmed that the precision of (13)C-MFA in Escherichia coli central carbon metabolism could be improved by introducing (13)C-labeling data derived from novel fragmentations. Graphical Abstract Novel collision-induced dissociation fragmentations of tert-butyldimethylsilyl amino acids were investigated and identified by GC-MS/MS.

  14. Gas Chromatography-Quadrupole Time-of-Flight Mass Spectrometry-Based Determination of Isotopologue and Tandem Mass Isotopomer Fractions of Primary Metabolites for (13)C-Metabolic Flux Analysis.

    PubMed

    Mairinger, Teresa; Steiger, Matthias; Nocon, Justyna; Mattanovich, Diethard; Koellensperger, Gunda; Hann, Stephan

    2015-12-01

    For the first time an analytical work flow based on accurate mass gas chromatography-quadrupole time-of-flight mass spectrometry (GC-QTOFMS) with chemical ionization for analysis providing a comprehensive picture of (13)C distribution along the primary metabolism is elaborated. The method provides a powerful new toolbox for (13)C-based metabolic flux analysis, which is an emerging strategy in metabolic engineering. In this field, stable isotope tracer experiments based on, for example, (13)C are central for providing characteristic patterns of labeled metabolites, which in turn give insights into the regulation of metabolic pathway kinetics. The new method enables the analysis of isotopologue fractions of 42 free intracellular metabolites within biotechnological samples, while tandem mass isotopomer information is also accessible for a large number of analytes. Hence, the method outperforms previous approaches in terms of metabolite coverage, while also providing rich isotopomer information for a significant number of key metabolites. Moreover, the established work flow includes novel evaluation routines correcting for isotope interference of naturally distributed elements, which is crucial following derivatization of metabolites. Method validation in terms of trueness, precision, and limits of detection was performed, showing excellent analytical figures of merit with an overall maximum bias of 5.8%, very high precision for isotopologue and tandem mass isotopomer fractions representing >10% of total abundance, and absolute limits of detection in the femtomole range. The suitability of the developed method is demonstrated on a flux experiment of Pichia pastoris employing two different tracers, i.e., 1,6(13)C2-glucose and uniformly labeled (13)C-glucose. PMID:26513365

  15. Flux analysis in plant metabolic networks: increasing throughput and coverage.

    PubMed

    Junker, Björn H

    2014-04-01

    Quantitative information about metabolic networks has been mainly obtained at the level of metabolite contents, transcript abundance, and enzyme activities. However, the active process of metabolism is represented by the flow of matter through the pathways. These metabolic fluxes can be predicted by Flux Balance Analysis or determined experimentally by (13)C-Metabolic Flux Analysis. These relatively complicated and time-consuming methods have recently seen significant improvements at the level of coverage and throughput. Metabolic models have developed from single cell models into whole-organism dynamic models. Advances in lab automation and data handling have significantly increased the throughput of flux measurements. This review summarizes advances to increase coverage and throughput of metabolic flux analysis in plants.

  16. Chemical Shift Separation with Controlled Aliasing for Hyperpolarized 13C Metabolic Imaging

    PubMed Central

    Shin, Peter J.; Larson, Peder E.Z.; Uecker, Martin; Reed, Galen D.; Kerr, Adam B.; Tropp, James; Ohliger, Michael A.; Nelson, Sarah J.; Pauly, John M.; Lustig, Michael; Vigneron, Daniel B.

    2014-01-01

    Purpose A chemical shift separation technique for hyperpolarized 13C metabolic imaging with high spatial and temporal resolution was developed. Specifically, a fast 3D pulse sequence and a reconstruction method were implemented to acquire signals from multiple 13C species simultaneously with subsequent separation into individual images. Methods A stack of flyback-EPI readouts and a set of multiband excitation RF pulses were designed to spatially modulate aliasing patterns of the acquired metabolite images, which translated the chemical shift separation problem into parallel imaging reconstruction problem. An eight-channel coil array was used for data acquisition and a parallel imaging method based on nonlinear inversion was developed to separate the aliased images. Results Simultaneous acquisitions of pyruvate and lactate in a phantom study and in vivo rat experiments were performed. The results demonstrated successful separation of the metabolite distributions into individual images having high spatial resolution. Conclusion This method demonstrated the ability to provide accelerated metabolite imaging in hyperpolarized 13C MR utilizing multi-channel coils, tailored readout, and specialized RF pulses. PMID:25298086

  17. Carbon 13-Metabolic Flux Analysis derived constraint-based metabolic modelling of Clostridium acetobutylicum in stressed chemostat conditions.

    PubMed

    Wallenius, Janne; Maaheimo, Hannu; Eerikäinen, Tero

    2016-11-01

    The metabolism of butanol producing bacteria Clostridium acetobutylicum was studied in chemostat with glucose limited conditions, butanol stimulus, and as a reference cultivation. COnstraint-Based Reconstruction and Analysis (COBRA) was applied using additional constraints from (13)C Metabolic Flux Analysis ((13)C-MFA) and experimental measurement results. A model consisting of 451 metabolites and 604 reactions was utilized in flux balance analysis (FBA). The stringency of the flux spaces considering different optimization objectives, i.e. growth rate maximization, ATP maintenance, and NADH/NADPH formation, for flux variance analysis (FVA) was studied in the different modelled conditions. Also a previously uncharacterized exopolysaccharide (EPS) produced by C. acetobutylicum was characterized on monosaccharide level. The major monosaccharide components of the EPS were 40n-% rhamnose, 34n-% glucose, 13n-% mannose, 10n-% galactose, and 2n-% arabinose. The EPS was studied to have butanol adsorbing property, 70(butanol)mg(EPS)g(-1) at 37°C. PMID:27501035

  18. Flux-p: automating metabolic flux analysis.

    PubMed

    Ebert, Birgitta E; Lamprecht, Anna-Lena; Steffen, Bernhard; Blank, Lars M

    2012-11-12

    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.

  19. Radiative Flux Analysis

    DOE Data Explorer

    Long, Chuck [NOAA

    2008-05-14

    The Radiative Flux Analysis is a technique for using surface broadband radiation measurements for detecting periods of clear (i.e. cloudless) skies, and using the detected clear-sky data to fit functions which are then used to produce continuous clear-sky estimates. The clear-sky estimates and measurements are then used in various ways to infer cloud macrophysical properties.

  20. Achieving Metabolic Flux Analysis for S. cerevisiae at a Genome-Scale: Challenges, Requirements, and Considerations

    PubMed Central

    Gopalakrishnan, Saratram; Maranas, Costas D.

    2015-01-01

    Recent advances in 13C-Metabolic flux analysis (13C-MFA) have increased its capability to accurately resolve fluxes using a genome-scale model with narrow confidence intervals without pre-judging the activity or inactivity of alternate metabolic pathways. However, the necessary precautions, computational challenges, and minimum data requirements for successful analysis remain poorly established. This review aims to establish the necessary guidelines for performing 13C-MFA at the genome-scale for a compartmentalized eukaryotic system such as yeast in terms of model and data requirements, while addressing key issues such as statistical analysis and network complexity. We describe the various approaches used to simplify the genome-scale model in the absence of sufficient experimental flux measurements, the availability and generation of reaction atom mapping information, and the experimental flux and metabolite labeling distribution measurements to ensure statistical validity of the obtained flux distribution. Organism-specific challenges such as the impact of compartmentalization of metabolism, variability of biomass composition, and the cell-cycle dependence of metabolism are discussed. Identification of errors arising from incorrect gene annotation and suggested alternate routes using MFA are also highlighted. PMID:26393660

  1. OpenMebius: An Open Source Software for Isotopically Nonstationary 13C-Based Metabolic Flux Analysis

    PubMed Central

    Furusawa, Chikara

    2014-01-01

    The in vivo measurement of metabolic flux by 13C-based metabolic flux analysis (13C-MFA) provides valuable information regarding cell physiology. Bioinformatics tools have been developed to estimate metabolic flux distributions from the results of tracer isotopic labeling experiments using a 13C-labeled carbon source. Metabolic flux is determined by nonlinear fitting of a metabolic model to the isotopic labeling enrichment of intracellular metabolites measured by mass spectrometry. Whereas 13C-MFA is conventionally performed under isotopically constant conditions, isotopically nonstationary 13C metabolic flux analysis (INST-13C-MFA) has recently been developed for flux analysis of cells with photosynthetic activity and cells at a quasi-steady metabolic state (e.g., primary cells or microorganisms under stationary phase). Here, the development of a novel open source software for INST-13C-MFA on the Windows platform is reported. OpenMebius (Open source software for Metabolic flux analysis) provides the function of autogenerating metabolic models for simulating isotopic labeling enrichment from a user-defined configuration worksheet. Analysis using simulated data demonstrated the applicability of OpenMebius for INST-13C-MFA. Confidence intervals determined by INST-13C-MFA were less than those determined by conventional methods, indicating the potential of INST-13C-MFA for precise metabolic flux analysis. OpenMebius is the open source software for the general application of INST-13C-MFA. PMID:25006579

  2. OpenMebius: an open source software for isotopically nonstationary 13C-based metabolic flux analysis.

    PubMed

    Kajihata, Shuichi; Furusawa, Chikara; Matsuda, Fumio; Shimizu, Hiroshi

    2014-01-01

    The in vivo measurement of metabolic flux by (13)C-based metabolic flux analysis ((13)C-MFA) provides valuable information regarding cell physiology. Bioinformatics tools have been developed to estimate metabolic flux distributions from the results of tracer isotopic labeling experiments using a (13)C-labeled carbon source. Metabolic flux is determined by nonlinear fitting of a metabolic model to the isotopic labeling enrichment of intracellular metabolites measured by mass spectrometry. Whereas (13)C-MFA is conventionally performed under isotopically constant conditions, isotopically nonstationary (13)C metabolic flux analysis (INST-(13)C-MFA) has recently been developed for flux analysis of cells with photosynthetic activity and cells at a quasi-steady metabolic state (e.g., primary cells or microorganisms under stationary phase). Here, the development of a novel open source software for INST-(13)C-MFA on the Windows platform is reported. OpenMebius (Open source software for Metabolic flux analysis) provides the function of autogenerating metabolic models for simulating isotopic labeling enrichment from a user-defined configuration worksheet. Analysis using simulated data demonstrated the applicability of OpenMebius for INST-(13)C-MFA. Confidence intervals determined by INST-(13)C-MFA were less than those determined by conventional methods, indicating the potential of INST-(13)C-MFA for precise metabolic flux analysis. OpenMebius is the open source software for the general application of INST-(13)C-MFA.

  3. Evaluation of 13C isotopic tracers for metabolic flux analysis in mammalian cells

    PubMed Central

    Metallo, Christian M.; Walther, Jason L.; Stephanopoulos, Gregory

    2009-01-01

    13C metabolic flux analysis (MFA) is the most comprehensive means of characterizing cellular metabolic states. Uniquely labeled isotopic tracers enable more focused analyses to probe specific reactions within the network. As a result, the choice of tracer largely determines the precision with which one can estimate metabolic fluxes, especially in complex mammalian systems that require multiple substrates. Here we have experimentally determined metabolic fluxes in a tumor cell line, successfully recapitulating the hallmarks of cancer cell metabolism. Using these data, we computationally evaluated specifically labeled 13C glucose and glutamine tracers for their ability to precisely and accurately estimate fluxes in central carbon metabolism. These methods enabled us to to identify the optimal tracer for analyzing individual fluxes, specific pathways, and central carbon metabolism as a whole. [1,2-13C2]glucose provided the most precise estimates for glycolysis, the pentose phosphate pathway, and the overall network. Tracers such as [2-13C]glucose and [3-13C]glucose also outperformed the more commonly used [1-13C]glucose. [U-13C5]glutamine emerged as the preferred isotopic tracer for analysis of the tricarboxylic acid (TCA) cycle. These results provide valuable, quantitative information on the performance of 13C-labeled substrates and can aid in the design of more informative MFA experiments in mammalian cell culture. PMID:19622376

  4. In vivo application of sub-second spiral chemical shift imaging (CSI) to hyperpolarized 13C metabolic imaging: Comparison with phase-encoded CSI

    NASA Astrophysics Data System (ADS)

    Mayer, Dirk; Yen, Yi-Fen; Levin, Yakir S.; Tropp, James; Pfefferbaum, Adolf; Hurd, Ralph E.; Spielman, Daniel M.

    2010-06-01

    A fast spiral chemical shift imaging (CSI) has been developed to address the challenge of the limited acquisition window in hyperpolarized 13C metabolic imaging. The sequence exploits the sparsity of the spectra and prior knowledge of resonance frequencies to reduce the measurement time by undersampling the data in the spectral domain. As a consequence, multiple reconstructions are necessary for any given data set as only frequency components within a selected bandwidth are reconstructed "in-focus" while components outside that band are severely blurred ("spectral tomosynthesis"). A variable-flip-angle scheme was used for optimal use of the longitudinal magnetization. The sequence was applied to sub-second metabolic imaging of the rat in vivo after injection of hyperpolarized [1- 13C]-pyruvate on a clinical 3T MR scanner. The comparison with conventional CSI based on phase encoding showed similar signal-to-noise ratio (SNR) and spatial resolution in metabolic maps for the substrate and its metabolic products lactate, alanine, and bicarbonate, despite a 50-fold reduction in scan time for the spiral CSI acquisition. The presented results demonstrate that dramatic reductions in scan time are feasible in hyperpolarized 13C metabolic imaging without a penalty in SNR or spatial resolution.

  5. Metabolic flux analysis of Cyanothece sp. ATCC 51142 under mixotrophic conditions.

    PubMed

    Alagesan, Swathi; Gaudana, Sandeep B; Sinha, Avinash; Wangikar, Pramod P

    2013-11-01

    Cyanobacteria are a group of photosynthetic prokaryotes capable of utilizing solar energy to fix atmospheric carbon dioxide to biomass. Despite several "proof of principle" studies, low product yield is an impediment in commercialization of cyanobacteria-derived biofuels. Estimation of intracellular reaction rates by (13)C metabolic flux analysis ((13)C-MFA) would be a step toward enhancing biofuel yield via metabolic engineering. We report (13)C-MFA for Cyanothece sp. ATCC 51142, a unicellular nitrogen-fixing cyanobacterium, known for enhanced hydrogen yield under mixotrophic conditions. Rates of reactions in the central carbon metabolism under nitrogen-fixing and -non-fixing conditions were estimated by monitoring the competitive incorporation of (12)C and (13)C from unlabeled CO2 and uniformly labeled glycerol, respectively, into terminal metabolites such as amino acids. The observed labeling patterns suggest mixotrophic growth under both the conditions, with a larger fraction of unlabeled carbon in nitrate-sufficient cultures asserting a greater contribution of carbon fixation by photosynthesis and an anaplerotic pathway. Indeed, flux analysis complements the higher growth observed under nitrate-sufficient conditions. On the other hand, the flux through the oxidative pentose phosphate pathway and tricarboxylic acid cycle was greater in nitrate-deficient conditions, possibly to supply the precursors and reducing equivalents needed for nitrogen fixation. In addition, an enhanced flux through fructose-6-phosphate phosphoketolase possibly suggests the organism's preferred mode under nitrogen-fixing conditions. The (13)C-MFA results complement the reported predictions by flux balance analysis and provide quantitative insight into the organism's distinct metabolic features under nitrogen-fixing and -non-fixing conditions.

  6. Mapping cancer cell metabolism with13C flux analysis: Recent progress and future challenges

    PubMed Central

    Duckwall, Casey Scott; Murphy, Taylor Athanasaw; Young, Jamey Dale

    2013-01-01

    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 of13C 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. PMID:23961260

  7. Experimental flux measurements on a network scale

    SciTech Connect

    Schwender, J.

    2011-10-11

    Metabolic flux is a fundamental property of living organisms. In recent years, methods for measuring metabolic flux in plants on a network scale have evolved further. One major challenge in studying flux in plants is the complexity of the plant's metabolism. In particular, in the presence of parallel pathways in multiple cellular compartments, the core of plant central metabolism constitutes a complex network. Hence, a common problem with the reliability of the contemporary results of {sup 13}C-Metabolic Flux Analysis in plants is the substantial reduction in complexity that must be included in the simulated networks; this omission partly is due to limitations in computational simulations. Here, I discuss recent emerging strategies that will better address these shortcomings.

  8. Genome-based metabolic mapping and 13C flux analysis reveal systematic properties of an oleaginous microalga Chlorella protothecoides.

    PubMed

    Wu, Chao; Xiong, Wei; Dai, Junbiao; Wu, Qingyu

    2015-02-01

    Integrated and genome-based flux balance analysis, metabolomics, and (13)C-label profiling of phototrophic and heterotrophic metabolism in Chlorella protothecoides, an oleaginous green alga for biofuel. The green alga Chlorella protothecoides, capable of autotrophic and heterotrophic growth with rapid lipid synthesis, is a promising candidate for biofuel production. Based on the newly available genome knowledge of the alga, we reconstructed the compartmentalized metabolic network consisting of 272 metabolic reactions, 270 enzymes, and 461 encoding genes and simulated the growth in different cultivation conditions with flux balance analysis. Phenotype-phase plane analysis shows conditions achieving theoretical maximum of the biomass and corresponding fatty acid-producing rate for phototrophic cells (the ratio of photon uptake rate to CO2 uptake rate equals 8.4) and heterotrophic ones (the glucose uptake rate to O2 consumption rate reaches 2.4), respectively. Isotope-assisted liquid chromatography-mass spectrometry/mass spectrometry reveals higher metabolite concentrations in the glycolytic pathway and the tricarboxylic acid cycle in heterotrophic cells compared with autotrophic cells. We also observed enhanced levels of ATP, nicotinamide adenine dinucleotide (phosphate), reduced, acetyl-Coenzyme A, and malonyl-Coenzyme A in heterotrophic cells consistently, consistent with a strong activity of lipid synthesis. To profile the flux map in experimental conditions, we applied nonstationary (13)C metabolic flux analysis as a complementing strategy to flux balance analysis. The result reveals negligible photorespiratory fluxes and a metabolically low active tricarboxylic acid cycle in phototrophic C. protothecoides. In comparison, high throughput of amphibolic reactions and the tricarboxylic acid cycle with no glyoxylate shunt activities were measured for heterotrophic cells. Taken together, the metabolic network modeling assisted by experimental metabolomics and (13)C

  9. Genome-Based Metabolic Mapping and 13C Flux Analysis Reveal Systematic Properties of an Oleaginous Microalga Chlorella protothecoides

    DOE PAGES

    Wu, Chao; Xiong, Wei; Dai, Junbiao; Wu, Qingyu

    2014-12-15

    We report that integrated and genome-based flux balance analysis, metabolomics, and 13C-label profiling of phototrophic and heterotrophic metabolism in Chlorella protothecoides, an oleaginous green alga for biofuel. The green alga Chlorella protothecoides, capable of autotrophic and heterotrophic growth with rapid lipid synthesis, is a promising candidate for biofuel production. Based on the newly available genome knowledge of the alga, we reconstructed the compartmentalized metabolic network consisting of 272 metabolic reactions, 270 enzymes, and 461 encoding genes and simulated the growth in different cultivation conditions with flux balance analysis. Phenotype-phase plane analysis shows conditions achieving theoretical maximum of the biomass andmore » corresponding fatty acid-producing rate for phototrophic cells (the ratio of photon uptake rate to CO2 uptake rate equals 8.4) and heterotrophic ones (the glucose uptake rate to O2 consumption rate reaches 2.4), respectively. Isotope-assisted liquid chromatography-mass spectrometry/mass spectrometry reveals higher metabolite concentrations in the glycolytic pathway and the tricarboxylic acid cycle in heterotrophic cells compared with autotrophic cells. We also observed enhanced levels of ATP, nicotinamide adenine dinucleotide (phosphate), reduced, acetyl-Coenzyme A, and malonyl-Coenzyme A in heterotrophic cells consistently, consistent with a strong activity of lipid synthesis. To profile the flux map in experimental conditions, we applied nonstationary 13C metabolic flux analysis as a complementing strategy to flux balance analysis. We found that the result reveals negligible photorespiratory fluxes and a metabolically low active tricarboxylic acid cycle in phototrophic C. protothecoides. In comparison, high throughput of amphibolic reactions and the tricarboxylic acid cycle with no glyoxylate shunt activities were measured for heterotrophic cells. Lastly, taken together, the metabolic network modeling assisted

  10. Analysis of metabolic flux phenotypes for two Arabidopsis mutants with severe impairment in seed storage lipid synthesis

    SciTech Connect

    Lonien, J.; Schwender, J.

    2009-11-01

    Major storage reserves of Arabidopsis (Arabidopsis thaliana) seeds are triacylglycerols (seed oils) and proteins. Seed oil content is severely reduced for the regulatory mutant wrinkled1 (wri1-1; At3g54320) and for a double mutant in two isoforms of plastidic pyruvate kinase (pkp{beta}{sub 1}pkp{alpha}; At5g52920 and At3g22960). Both already biochemically well-characterized mutants were now studied by {sup 13}C metabolic flux analysis of cultured developing embryos based on comparison with their respective genetic wild-type backgrounds. For both mutations, in seeds as well as in cultured embryos, the oil fraction was strongly reduced while the fractions of proteins and free metabolites increased. Flux analysis in cultured embryos revealed changes in nutrient uptakes and fluxes into biomass as well as an increase in tricarboxylic acid cycle activity for both mutations. While in both wild types plastidic pyruvate kinase (PK{sub p}) provides most of the pyruvate for plastidic fatty acid synthesis, the flux through PK{sub p} is reduced in pkp{beta}{sub 1}pkp{alpha} by 43% of the wild-type value. In wri1-1, PK{sub p} flux is even more reduced (by 82%), although the genes PKp{beta}{sub 1} and PKp{alpha} are still expressed. Along a common paradigm of metabolic control theory, it is hypothesized that a large reduction in PK{sub p} enzyme activity in pkp{beta}{sub 1}pkp{alpha} has less effect on PK{sub p} flux than multiple smaller reductions in glycolytic enzymes in wri1-1. In addition, only in the wri1-1 mutant is the large reduction in PK{sub p} flux compensated in part by an increased import of cytosolic pyruvate and by plastidic malic enzyme. No such limited compensatory bypass could be observed in pkp{beta}{sub 1}pkp{alpha}.

  11. Flux balance analysis accounting for metabolite dilution.

    PubMed

    Benyamini, Tomer; Folger, Ori; Ruppin, Eytan; Shlomi, Tomer

    2010-01-01

    Flux balance analysis is a common method for predicting steady-state flux distributions within metabolic networks, accounting for the growth demand for the synthesis of a predefined set of essential biomass precursors. Ignoring the growth demand for the synthesis of intermediate metabolites required for balancing their dilution leads flux balance analysis to false predictions in some cases. Here, we present metabolite dilution flux balance analysis, which addresses this problem, resulting in improved metabolic phenotype predictions. PMID:20398381

  12. Flux balance analysis accounting for metabolite dilution.

    PubMed

    Benyamini, Tomer; Folger, Ori; Ruppin, Eytan; Shlomi, Tomer

    2010-01-01

    Flux balance analysis is a common method for predicting steady-state flux distributions within metabolic networks, accounting for the growth demand for the synthesis of a predefined set of essential biomass precursors. Ignoring the growth demand for the synthesis of intermediate metabolites required for balancing their dilution leads flux balance analysis to false predictions in some cases. Here, we present metabolite dilution flux balance analysis, which addresses this problem, resulting in improved metabolic phenotype predictions.

  13. Constrained Allocation Flux Balance Analysis.

    PubMed

    Mori, Matteo; Hwa, Terence; Martin, Olivier C; De Martino, Andrea; Marinari, Enzo

    2016-06-01

    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.

  14. Constrained Allocation Flux Balance Analysis.

    PubMed

    Mori, Matteo; Hwa, Terence; Martin, Olivier C; De Martino, Andrea; Marinari, Enzo

    2016-06-01

    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

  15. Constrained Allocation Flux Balance Analysis

    PubMed Central

    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

  16. Multi-objective experimental design for (13)C-based metabolic flux analysis.

    PubMed

    Bouvin, Jeroen; Cajot, Simon; D'Huys, Pieter-Jan; Ampofo-Asiama, Jerry; Anné, Jozef; Van Impe, Jan; Geeraerd, Annemie; Bernaerts, Kristel

    2015-10-01

    (13)C-based metabolic flux analysis is an excellent technique to resolve fluxes in the central carbon metabolism but costs can be significant when using specialized tracers. This work presents a framework for cost-effective design of (13)C-tracer experiments, illustrated on two different networks. Linear and non-linear optimal input mixtures are computed for networks for Streptomyces lividans and a carcinoma cell line. If only glucose tracers are considered as labeled substrate for a carcinoma cell line or S. lividans, the best parameter estimation accuracy is obtained by mixtures containing high amounts of 1,2-(13)C2 glucose combined with uniformly labeled glucose. Experimental designs are evaluated based on a linear (D-criterion) and non-linear approach (S-criterion). Both approaches generate almost the same input mixture, however, the linear approach is favored due to its low computational effort. The high amount of 1,2-(13)C2 glucose in the optimal designs coincides with a high experimental cost, which is further enhanced when labeling is introduced in glutamine and aspartate tracers. Multi-objective optimization gives the possibility to assess experimental quality and cost at the same time and can reveal excellent compromise experiments. For example, the combination of 100% 1,2-(13)C2 glucose with 100% position one labeled glutamine and the combination of 100% 1,2-(13)C2 glucose with 100% uniformly labeled glutamine perform equally well for the carcinoma cell line, but the first mixture offers a decrease in cost of $ 120 per ml-scale cell culture experiment. We demonstrated the validity of a multi-objective linear approach to perform optimal experimental designs for the non-linear problem of (13)C-metabolic flux analysis. Tools and a workflow are provided to perform multi-objective design. The effortless calculation of the D-criterion can be exploited to perform high-throughput screening of possible (13)C-tracers, while the illustrated benefit of multi

  17. Genome-Based Metabolic Mapping and 13C Flux Analysis Reveal Systematic Properties of an Oleaginous Microalga Chlorella protothecoides1[OPEN

    PubMed Central

    Wu, Chao; Xiong, Wei; Dai, Junbiao; Wu, Qingyu

    2015-01-01

    Integrated and genome-based flux balance analysis, metabolomics, and 13C-label profiling of phototrophic and heterotrophic metabolism in Chlorella protothecoides, an oleaginous green alga for biofuel. The green alga Chlorella protothecoides, capable of autotrophic and heterotrophic growth with rapid lipid synthesis, is a promising candidate for biofuel production. Based on the newly available genome knowledge of the alga, we reconstructed the compartmentalized metabolic network consisting of 272 metabolic reactions, 270 enzymes, and 461 encoding genes and simulated the growth in different cultivation conditions with flux balance analysis. Phenotype-phase plane analysis shows conditions achieving theoretical maximum of the biomass and corresponding fatty acid-producing rate for phototrophic cells (the ratio of photon uptake rate to CO2 uptake rate equals 8.4) and heterotrophic ones (the glucose uptake rate to O2 consumption rate reaches 2.4), respectively. Isotope-assisted liquid chromatography-mass spectrometry/mass spectrometry reveals higher metabolite concentrations in the glycolytic pathway and the tricarboxylic acid cycle in heterotrophic cells compared with autotrophic cells. We also observed enhanced levels of ATP, nicotinamide adenine dinucleotide (phosphate), reduced, acetyl-Coenzyme A, and malonyl-Coenzyme A in heterotrophic cells consistently, consistent with a strong activity of lipid synthesis. To profile the flux map in experimental conditions, we applied nonstationary 13C metabolic flux analysis as a complementing strategy to flux balance analysis. The result reveals negligible photorespiratory fluxes and a metabolically low active tricarboxylic acid cycle in phototrophic C. protothecoides. In comparison, high throughput of amphibolic reactions and the tricarboxylic acid cycle with no glyoxylate shunt activities were measured for heterotrophic cells. Taken together, the metabolic network modeling assisted by experimental metabolomics and 13C labeling

  18. Characterization of the metabolic shift between oxidative and fermentative growth in Saccharomyces cerevisiae by comparative 13C flux analysis

    PubMed Central

    Frick, Oliver; Wittmann, Christoph

    2005-01-01

    Background One of the most fascinating properties of the biotechnologically important organism Saccharomyces cerevisiae is its ability to perform simultaneous respiration and fermentation at high growth rate even under fully aerobic conditions. In the present work, this Crabtree effect called phenomenon was investigated in detail by comparative 13C metabolic flux analysis of S. cerevisiae growing under purely oxidative, respiro-fermentative and predominantly fermentative conditions. Results The metabolic shift from oxidative to fermentative growth was accompanied by complex changes of carbon flux throughout the whole central metabolism. This involved a flux redirection from the pentose phosphate pathway (PPP) towards glycolysis, an increased flux through pyruvate carboxylase, the fermentative pathways and malic enzyme, a flux decrease through the TCA cycle, and a partial relocation of alanine biosynthesis from the mitochondrion to the cytosol. S. cerevisiae exhibited a by-pass of pyruvate dehydrogenase in all physiological regimes. During oxidative growth this by-pass was mainly provided via pyruvate decarboxylase, acetaldehyde dehydrogenase, acetyl-CoA synthase and transport of acetyl-CoA into the mitochondrion. During fermentative growth this route, however, was saturated due to limited enzyme capacity. Under these conditions the cells exhibited high carbon flux through a chain of reactions involving pyruvate carboxylase, the oxaloacetate transporter and malic enzyme. During purely oxidative growth the PPP alone was sufficient to completely supply NADPH for anabolism. During fermentation, it provided only 60 % of the required NADPH. Conclusion We conclude that, in order to overcome the limited capacity of pyruvate dehydrogenase, S. cerevisiae possesses different metabolic by-passes to channel carbon into the mitochondrion. This involves the conversion of cytosolic pyruvate either into acetyl CoA or oxaloacetate followed by intercompartmental transport of these

  19. Metabolic flux pattern of glucose utilization by Xanthomonas campestris pv. campestris: prevalent role of the Entner-Doudoroff pathway and minor fluxes through the pentose phosphate pathway and glycolysis.

    PubMed

    Schatschneider, Sarah; Huber, Claudia; Neuweger, Heiko; Watt, Tony Francis; Pühler, Alfred; Eisenreich, Wolfgang; Wittmann, Christoph; Niehaus, Karsten; Vorhölter, Frank-Jörg

    2014-10-01

    The well-studied plant pathogenic bacterium Xanthomonas campestris pv. campestris (Xcc) synthesizes the biotechnologically important polysaccharide xanthan gum, which is also regarded as a virulence factor in plant interactions. In Xcc, sugars like glucose are utilized as a source to generate energy and biomass for growth and pathogenicity. In this study, we used [1-(13)C]glucose as a tracer to analyze the fluxes in the central metabolism of the bacterium growing in a minimal medium. (13)C-Metabolic flux analysis based on gas chromatography-mass spectrometry (GC-MS) confirmed the prevalent catabolic role of the Entner-Doudoroff pathway. Comparative nuclear magnetic resonance (NMR)-based isotopologue profiling of a mutant deficient in glycolysis gave evidence for a moderate flux via glycolysis in the wild-type. In addition to reconfirming the Entner-Doudoroff pathway as a catabolic main route, this approach affirmed a numerically minor but important flux via the pentose phosphate pathway.

  20. Conditional flux analysis and stable isotopes

    NASA Astrophysics Data System (ADS)

    Zeeman, M. J.; Knohl, A.; Sturm, P.; Buchmann, N. C.; Thomas, C. K.

    2009-12-01

    We propose to investigate to what extend conditional flux analysis can benefit from the addition of stable isotope information. Stable isotopes have been recognized for their potential as process tracer, and could add an extra dimension to the conditional flux concept, which aims at directly quantifying component fluxes and identifying their sources. Differences in 13C abundance in carbon dioxide can be used to distinguish assimilation or respiration sources, whereas the 18O abundance expresses differences in water exchange, for instance between canopy and soil. Lending to recent advances in measurement technology, stable isotopes can now be measured at high temporal resolutions (10Hz) required for commonly applied micrometeorological methods such as the eddy-covariance technique, or related conditional flux methods. We will present current ideas on how the conditional flux method, as recently proposed and evaluated by Thomas et al. (2008), Scanlon & Sahu (2008), to perform daytime flux partitioning at the ecosystem level, can be refined by stable isotope analysis (13C and 18O) of carbon dioxide as additional dimension for identification of fluxes.

  1. Integration of in vivo and in silico metabolic fluxes for improvement of recombinant protein production.

    PubMed

    Driouch, Habib; Melzer, Guido; Wittmann, Christoph

    2012-01-01

    The filamentous fungus Aspergillus niger is an efficient host for the recombinant production of the glycosylated enzyme fructofuranosidase, a biocatalyst of commercial interest for the synthesis of pre-biotic sugars. In batch culture on a minimal glucose medium, the recombinant strain A. niger SKAn1015, expressing the fructofuranosidase encoding suc1 gene secreted 45U/mL of the target enzyme, whereas the parent wild type SKANip8 did not exhibit production. The production of the recombinant enzyme induced a significant change of in vivo fluxes in central carbon metabolism, as assessed by (13)C metabolic flux ratio analysis. Most notably, the flux redistribution enabled an elevated supply of NADPH via activation of the cytosolic pentose phosphate pathway (PPP) and mitochondrial malic enzyme, whereas the flux through energy generating TCA cycle was reduced. In addition, the overall possible flux space of fructofuranosidase producing A. niger was investigated in silico by elementary flux mode analysis. This provided theoretical flux distributions for multiple scenarios with differing production capacities. Subsequently, the measured flux changes linked to improved production performance were projected into the in silico flux space. This provided a quantitative evaluation of the achieved optimization and a priority ranked target list for further strain engineering. Interestingly, the metabolism was shifted largely towards the optimum flux pattern by sole expression of the recombinant enzyme, which seems an inherent attractive property of A. niger. Selected fluxes, however, changed contrary to the predicted optimum and thus revealed novel targets-including reactions linked to NADPH metabolism and gluconate formation.

  2. Recurrence Analysis of Eddy Covariance Fluxes

    NASA Astrophysics Data System (ADS)

    Lange, Holger; Flach, Milan; Foken, Thomas; Hauhs, Michael

    2015-04-01

    The eddy covariance (EC) method is one key method to quantify fluxes in biogeochemical cycles in general, and carbon and energy transport across the vegetation-atmosphere boundary layer in particular. EC data from the worldwide net of flux towers (Fluxnet) have also been used to validate biogeochemical models. The high resolution data are usually obtained at 20 Hz sampling rate but are affected by missing values and other restrictions. In this contribution, we investigate the nonlinear dynamics of EC fluxes using Recurrence Analysis (RA). High resolution data from the site DE-Bay (Waldstein-Weidenbrunnen) and fluxes calculated at half-hourly resolution from eight locations (part of the La Thuile dataset) provide a set of very long time series to analyze. After careful quality assessment and Fluxnet standard gapfilling pretreatment, we calculate properties and indicators of the recurrent structure based both on Recurrence Plots as well as Recurrence Networks. Time series of RA measures obtained from windows moving along the time axis are presented. Their interpretation is guided by three different questions: (1) Is RA able to discern periods where the (atmospheric) conditions are particularly suitable to obtain reliable EC fluxes? (2) Is RA capable to detect dynamical transitions (different behavior) beyond those obvious from visual inspection? (3) Does RA contribute to an understanding of the nonlinear synchronization between EC fluxes and atmospheric parameters, which is crucial for both improving carbon flux models as well for reliable interpolation of gaps? (4) Is RA able to recommend an optimal time resolution for measuring EC data and for analyzing EC fluxes? (5) Is it possible to detect non-trivial periodicities with a global RA? We will demonstrate that the answers to all five questions is affirmative, and that RA provides insights into EC dynamics not easily obtained otherwise.

  3. 'Wave' analysis of Venus ionospheric flux ropes

    NASA Technical Reports Server (NTRS)

    Luhmann, J. G.

    1990-01-01

    The behavior of the general field fluctuations observed by the Pioneer Venus Orbiter magnetometer in the Venusian ionosphere is approached via the application of wave-analysis techniques to their compressional amplitude, ellipticity, and polarization. The most marked change in these properties occurs within about 15 deg of the terminator; ellipticity and compressional power plummet, implying that flux ropes either drastically change in character there or are confined to the dayside hemisphere, within about 75 percent of the subsolar point. Attention is given to a heuristic model which attempts to unify dayside flux-rope and 'terminator wave' interpretations.

  4. Robustness and Plasticity of Metabolic Pathway Flux among Uropathogenic Isolates of Pseudomonas aeruginosa

    PubMed Central

    Berger, Antje; Dohnt, Katrin; Tielen, Petra; Jahn, Dieter; Becker, Judith; Wittmann, Christoph

    2014-01-01

    Pseudomonas aeruginosa is a human pathogen that frequently causes urinary tract and catheter-associated urinary tract infections. Here, using 13C-metabolic flux analysis, we conducted quantitative analysis of metabolic fluxes in the model strain P. aeruginosa PAO1 and 17 clinical isolates. All P. aeruginosa strains catabolized glucose through the Entner-Doudoroff pathway with fully respiratory metabolism and no overflow. Together with other NADPH supplying reactions, this high-flux pathway provided by far more NADPH than needed for anabolism: a benefit for the pathogen to counteract oxidative stress imposed by the host. P. aeruginosa recruited the pentose phosphate pathway exclusively for biosynthesis. In contrast to glycolytic metabolism, which was conserved among all isolates, the flux through pyruvate metabolism, the tricarboxylic acid cycle, and the glyoxylate shunt was highly variable, likely caused by adaptive processes in individual strains during infection. This aspect of metabolism was niche-specific with respect to the corresponding flux because strains isolated from the urinary tract clustered separately from those originating from catheter-associated infections. Interestingly, most glucose-grown strains exhibited significant flux through the glyoxylate shunt. Projection into the theoretical flux space, which was computed using elementary flux-mode analysis, indicated that P. aeruginosa metabolism is optimized for efficient growth and exhibits significant potential for increasing NADPH supply to drive oxidative stress response. PMID:24709961

  5. Lithium metaborate flux in silicate analysis

    USGS Publications Warehouse

    Ingamells, C.O.

    1970-01-01

    Lithium metaborate is an effective flux for silicates and other rock-forming minerals. The glass resulting from fusion is mechanically strong, reasonably nonhygroscopic, and is readily soluble in dilute acids. These characteristics lead to its use in X-ray spectrography and in methods which require whole-rock solutions, such as atomic absorption and emission spectrometry. Difficulties have been encountered in the use of such techniques : a high-quality reagent has been difficult to obtain ; fusion conditions must be rather closely controlled; graphite crucibles used in the fusions need special treatment. Methods for overcoming these difficulties are outlined. Selected procedures for various instrumental methods of analysis are described. ?? 1970.

  6. Comparison and analysis of objective functions in flux balance analysis.

    PubMed

    García Sánchez, Carlos Eduardo; Torres Sáez, Rodrigo Gonzalo

    2014-01-01

    Flux balance analysis (FBA) is currently one of the most important and used techniques for estimation of metabolic reaction rates (fluxes). This mathematical approach utilizes an optimization criterion in order to select a distribution of fluxes from the feasible space delimited by the metabolic reactions and some restrictions imposed over them, assuming that cellular metabolism is in steady state. Therefore, the obtained flux distribution depends on the specific objective function used. Multiple studies have been aimed to compare distinct objective functions at given conditions, in order to determine which of those functions produces values of fluxes closer to real data when used as objective in the FBA; in other words, what is the best objective function for modeling cell metabolism at a determined environmental condition. However, these comparative studies have been designed in very dissimilar ways, and in general, several factors that can change the ideal objective function in a cellular condition have not been adequately considered. Additionally, most of them have used only one dataset for representing one condition of cell growth, and different measuring techniques have been used. For these reasons, a rigorous study on the effect of factors such as the quantity of used data, the number and type of fluxes utilized as input data, and the selected classification of growth conditions, are required in order to obtain useful conclusions for these comparative studies, allowing limiting clearly the application range on any of those results. PMID:25044958

  7. Comparison and analysis of objective functions in flux balance analysis.

    PubMed

    García Sánchez, Carlos Eduardo; Torres Sáez, Rodrigo Gonzalo

    2014-01-01

    Flux balance analysis (FBA) is currently one of the most important and used techniques for estimation of metabolic reaction rates (fluxes). This mathematical approach utilizes an optimization criterion in order to select a distribution of fluxes from the feasible space delimited by the metabolic reactions and some restrictions imposed over them, assuming that cellular metabolism is in steady state. Therefore, the obtained flux distribution depends on the specific objective function used. Multiple studies have been aimed to compare distinct objective functions at given conditions, in order to determine which of those functions produces values of fluxes closer to real data when used as objective in the FBA; in other words, what is the best objective function for modeling cell metabolism at a determined environmental condition. However, these comparative studies have been designed in very dissimilar ways, and in general, several factors that can change the ideal objective function in a cellular condition have not been adequately considered. Additionally, most of them have used only one dataset for representing one condition of cell growth, and different measuring techniques have been used. For these reasons, a rigorous study on the effect of factors such as the quantity of used data, the number and type of fluxes utilized as input data, and the selected classification of growth conditions, are required in order to obtain useful conclusions for these comparative studies, allowing limiting clearly the application range on any of those results.

  8. Flux Coupling Analysis of Genome-Scale Metabolic Network Reconstructions

    PubMed Central

    Burgard, Anthony P.; Nikolaev, Evgeni V.; Schilling, Christophe H.; Maranas, Costas D.

    2004-01-01

    In this paper, we introduce the Flux Coupling Finder (FCF) framework for elucidating the topological and flux connectivity features of genome-scale metabolic networks. The framework is demonstrated on genome-scale metabolic reconstructions of Helicobacter pylori, Escherichia coli, and Saccharomyces cerevisiae. The analysis allows one to determine whether any two metabolic fluxes, v1 and v2, are (1) directionally coupled, if a non-zero flux for v1 implies a non-zero flux for v2 but not necessarily the reverse; (2) partially coupled, if a non-zero flux for v1 implies a non-zero, though variable, flux for v2 and vice versa; or (3) fully coupled, if a non-zero flux for v1 implies not only a non-zero but also a fixed flux for v2 and vice versa. Flux coupling analysis also enables the global identification of blocked reactions, which are all reactions incapable of carrying flux under a certain condition; equivalent knockouts, defined as the set of all possible reactions whose deletion forces the flux through a particular reaction to zero; and sets of affected reactions denoting all reactions whose fluxes are forced to zero if a particular reaction is deleted. The FCF approach thus provides a novel and versatile tool for aiding metabolic reconstructions and guiding genetic manipulations. PMID:14718379

  9. Reliable Metabolic Flux Estimation in Escherichia coli Central Carbon Metabolism Using Intracellular Free Amino Acids

    PubMed Central

    Okahashi, Nobuyuki; Kajihata, Shuichi; Furusawa, Chikara; Shimizu, Hiroshi

    2014-01-01

    13C metabolic flux analysis (MFA) is a tool of metabolic engineering for investigation of in vivo flux distribution. A direct 13C enrichment analysis of intracellular free amino acids (FAAs) is expected to reduce time for labeling experiments of the MFA. Measurable FAAs should, however, vary among the MFA experiments since the pool sizes of intracellular free metabolites depend on cellular metabolic conditions. In this study, minimal 13C enrichment data of FAAs was investigated to perform the FAAs-based MFA. An examination of a continuous culture of Escherichia coli using 13C-labeled glucose showed that the time required to reach an isotopically steady state for FAAs is rather faster than that for conventional method using proteinogenic amino acids (PAAs). Considering 95% confidence intervals, it was found that the metabolic flux distribution estimated using FAAs has a similar reliability to that of the PAAs-based method. The comparative analysis identified glutamate, aspartate, alanine and phenylalanine as the common amino acids observed in E. coli under different culture conditions. The results of MFA also demonstrated that the 13C enrichment data of the four amino acids is required for a reliable analysis of the flux distribution. PMID:24957033

  10. Kinetic isotope effects significantly influence intracellular metabolite 13C labeling patterns and flux determination

    PubMed Central

    Wasylenko, Thomas M.; Stephanopoulos, Gregory

    2014-01-01

    Rigorous mathematical modeling of carbon-labeling experiments allows estimation of fluxes through the pathways of central carbon metabolism, yielding powerful information for basic scientific studies as well as for a wide range of applications. However, the mathematical models that have been developed for flux determination from 13C labeling data have commonly neglected the influence of kinetic isotope effects on the distribution of 13C label in intracellular metabolites, as these effects have often been assumed to be inconsequential. We have used measurements of the 13C isotope effects on the pyruvate dehydrogenase enzyme from the literature to model isotopic fractionation at the pyruvate node and quantify the modeling errors expected to result from the assumption that isotope effects are negligible. We show that under some conditions kinetic isotope effects have a significant impact on the 13C labeling patterns of intracellular metabolites, and the errors associated with neglecting isotope effects in 13C-metabolic flux analysis models can be comparable in size to measurement errors associated with GC–MS. Thus, kinetic isotope effects must be considered in any rigorous assessment of errors in 13C labeling data, goodness-of-fit between model and data, confidence intervals of estimated metabolic fluxes, and statistical significance of differences between estimated metabolic flux distributions. PMID:23828762

  11. Software applications toward quantitative metabolic flux analysis and modeling.

    PubMed

    Dandekar, Thomas; Fieselmann, Astrid; Majeed, Saman; Ahmed, Zeeshan

    2014-01-01

    Metabolites and their pathways are central for adaptation and survival. Metabolic modeling elucidates in silico all the possible flux pathways (flux balance analysis, FBA) and predicts the actual fluxes under a given situation, further refinement of these models is possible by including experimental isotopologue data. In this review, we initially introduce the key theoretical concepts and different analysis steps in the modeling process before comparing flux calculation and metabolite analysis programs such as C13, BioOpt, COBRA toolbox, Metatool, efmtool, FiatFlux, ReMatch, VANTED, iMAT and YANA. Their respective strengths and limitations are discussed and compared to alternative software. While data analysis of metabolites, calculation of metabolic fluxes, pathways and their condition-specific changes are all possible, we highlight the considerations that need to be taken into account before deciding on a specific software. Current challenges in the field include the computation of large-scale networks (in elementary mode analysis), regulatory interactions and detailed kinetics, and these are discussed in the light of powerful new approaches.

  12. Dynamic Modeling of Aerobic Growth of Shewanella oneidensis. Predicting Triauxic Growth, Flux Distributions and Energy Requirement for Growth

    SciTech Connect

    Song, Hyun-Seob; Ramkrishna, Doraiswami; Pinchuk, Grigoriy E.; Beliaev, Alex S.; Konopka, Allan; Fredrickson, Jim K.

    2013-01-01

    A model-based analysis is conducted to investigate metabolism of Shewanella oneidensis MR-1 strain in aerobic batch culture, which exhibits an intriguing growth pattern by sequentially consuming substrate (i.e., lactate) and by-products (i.e., pyruvate and acetate). A general protocol is presented for developing a detailed network-based dynamic model for S. oneidensis based on the Lumped Hybrid Cybernetic Model (LHCM) framework. The L-HCM, although developed from only limited data, is shown to accurately reproduce exacting dynamic metabolic shifts, and provide reasonable estimates of energy requirement for growth. Flux distributions in S. oneidensis predicted by the L-HCM compare very favorably with 13C-metabolic flux analysis results reported in the literature. Predictive accuracy is enhanced by incorporating measurements of only a few intracellular fluxes, in addition to extracellular metabolites. The L-HCM developed here for S. oneidensis is consequently a promising tool for the analysis of intracellular flux distribution and metabolic engineering.

  13. 13C-based metabolic flux analysis: fundamentals and practice.

    PubMed

    Yang, Tae Hoon

    2013-01-01

    Isotope-based metabolic flux analysis is one of the emerging technologies applied to system level metabolic phenotype characterization in metabolic engineering. Among the developed approaches, (13)C-based metabolic flux analysis has been established as a standard tool and has been widely applied to quantitative pathway characterization of diverse biological systems. To implement (13)C-based metabolic flux analysis in practice, comprehending the underlying mathematical and computational modeling fundamentals is of importance along with carefully conducted experiments and analytical measurements. Such knowledge is also crucial when designing (13)C-labeling experiments and properly acquiring key data sets essential for in vivo flux analysis implementation. In this regard, the modeling fundamentals of (13)C-labeling systems and analytical data processing are the main topics we will deal with in this chapter. Along with this, the relevant numerical optimization techniques are addressed to help implementation of the entire computational procedures aiming at (13)C-based metabolic flux analysis in vivo.

  14. Steady-state flux ratio analysis: application to biological transport.

    PubMed

    Wagg, J; Chapman, J B

    1995-05-01

    A thermodynamically constrained method of flux ratio analysis, based upon a previously developed thermodynamic rate ratio equation has been developed. In this paper it is demonstrated that, for a complex reaction, application of the thermodynamic rate ratio equation may provide a useful tool for the interpretation of unidirectional flux data thought to be mediated by the reaction, provided that: (i) a clearly defined mechanism for the reaction has been proposed; (ii) a set of partial reaction components may be defined for the reaction from the proposed mechanism, with the rate ratio of at least one of these components being amenable to experimental measurement. This paper defines the conditions for which the rate ratio of a component reaction may be measured, and illustrates the basic principles underlying this approach to flux ratio analysis by direct application to a number of hypothetical mechanisms for biological transport phenomena.

  15. An Analysis of Moisture Fluxes into the Gulf of California

    NASA Technical Reports Server (NTRS)

    Wu, Man-Li C.; Schubert, Siegfried D.; Suarez, Max J.; Huang, Norden E.

    2009-01-01

    This study examines the nature of episodes of enhanced warm-season moisture flux into the Gulf of California. Both spatial structure and primary time scales of the fluxes are examined using the 40-yr ECMWF Re-Analysis data for the period 1980-2001. The analysis approach consists of a compositing technique that is keyed on the low-level moisture fluxes into the Gulf of California. The results show that the fluxes have a rich spectrum of temporal variability, with periods of enhanced transport over the gulf linked to African easterly waves on subweekly (3-8 day) time scales, the Madden-Julian oscillation (MJO) at intraseasonal time scales (20-90 day), and intermediate (10-15 day) time-scale disturbances that appear to originate primarily in the Caribbean Sea-western Atlantic Ocean. In the case of the MJO, enhanced low-level westerlies and large-scale rising motion provide an environment that favors large-scale cyclonic development near the west coast of Central America that, over the course of about 2 weeks, expands northward along the coast eventually reaching the mouth of the Gulf of California where it acts to enhance the southerly moisture flux in that region. On a larger scale, the development includes a northward shift in the eastern Pacific ITCZ, enhanced precipitation over much of Mexico and the southwestern United States, and enhanced southerly/southeasterly fluxes from the Gulf of Mexico into Mexico and the southwestern and central United States. In the case of the easterly waves, the systems that reach Mexico appear to redevelop/reorganize on the Pacific coast and then move rapidly to the northwest to contribute to the moisture flux into the Gulf of California. The most intense fluxes into the gulf on these time scales appear to be synchronized with a midlatitude short-wave trough over the U.S. West Coast and enhanced low-level southerly fluxes over the U.S. Great Plains. The intermediate (10-15 day) time-scale systems have zonal wavelengths roughly twice

  16. E-Flux2 and SPOT: Validated Methods for Inferring Intracellular Metabolic Flux Distributions from Transcriptomic Data

    PubMed Central

    Kim, Min Kyung; Lane, Anatoliy; Kelley, James J.; Lun, Desmond S.

    2016-01-01

    Background Several methods have been developed to predict system-wide and condition-specific intracellular metabolic fluxes by integrating transcriptomic data with genome-scale metabolic models. While powerful in many settings, existing methods have several shortcomings, and it is unclear which method has the best accuracy in general because of limited validation against experimentally measured intracellular fluxes. Results We present a general optimization strategy for inferring intracellular metabolic flux distributions from transcriptomic data coupled with genome-scale metabolic reconstructions. It consists of two different template models called DC (determined carbon source model) and AC (all possible carbon sources model) and two different new methods called E-Flux2 (E-Flux method combined with minimization of l2 norm) and SPOT (Simplified Pearson cOrrelation with Transcriptomic data), which can be chosen and combined depending on the availability of knowledge on carbon source or objective function. This enables us to simulate a broad range of experimental conditions. We examined E. coli and S. cerevisiae as representative prokaryotic and eukaryotic microorganisms respectively. The predictive accuracy of our algorithm was validated by calculating the uncentered Pearson correlation between predicted fluxes and measured fluxes. To this end, we compiled 20 experimental conditions (11 in E. coli and 9 in S. cerevisiae), of transcriptome measurements coupled with corresponding central carbon metabolism intracellular flux measurements determined by 13C metabolic flux analysis (13C-MFA), which is the largest dataset assembled to date for the purpose of validating inference methods for predicting intracellular fluxes. In both organisms, our method achieves an average correlation coefficient ranging from 0.59 to 0.87, outperforming a representative sample of competing methods. Easy-to-use implementations of E-Flux2 and SPOT are available as part of the open

  17. Structural analysis of airborne flux estimates over a region

    NASA Technical Reports Server (NTRS)

    Caramori, Paulo; Schuepp, Peter; Desjardins, Raymond; Macpherson, Ian

    1994-01-01

    Aircraft-based observations of turbulence fields of velocity, moisture, and temperature are used to study coherent turbulent structures that dominate turbulent transfer of moisture and heat above three different eco-systems. Flux traces are defragmented, to reconstruct the presumed full size (along the sampled transect) of these structures, and flux traces are simplified by elimination of those that contribute negligibly to the flux estimate. Structures are analyzed in terms of size, spatial distribution, and contribution to the flux, in the four 'quadrant' modes of eddy-covariance transfer (excess up/down and deficit up/down). The effect of nonlinear detrending of moisture and temperature data on this 'structural analysis,' over surfaces with heterogeneous surface wetness, is also examined. Results over grassland, wetland, and moist and dry agricultural land, show that nonlinear detrending may provide a more physically realistic description of structures. Significant differences are observed between structure size and associated relative flux contribution, between moist and dry areas, with smaller structures playing a more important role over the moist areas. Structure size generally increases with height, as spatial reorganization from smaller structures into larger ones takes place. This coincides with a gradual loss of surface 'signature' (position and clustering of plumes above localized source areas). The data are expected to provide a basis for an eventual statistical description of boundary-layer transfer events , and help to interpret the link between boundary-layer transfer and hydrological surface conditions.

  18. Regional flux analysis of longitudinal atrophy in Alzheimer's disease.

    PubMed

    Lorenzi, Marco; Ayache, Nicholas; Xavier, Pennec

    2012-01-01

    The longitudinal analysis of the brain morphology in Alzheimer's disease(AD) is fundamental for understanding and quantifying the dynamics of the pathology. This study provides a new measure of the brain longitudinal changes based on the Helmholtz decomposition of deformation fields. We used the scalar pressure map associated to the irrotational component in order to identify a consistent group-wise set of areas of maximal volume change. The atrophy was then quantified in these areas for each subject by the probabilistic integration of the flux of the longitudinal deformations across the boundaries. The presented framework unifies voxel-based and regional approaches, and robustly describes the longitudinal atrophy at group level as a spatial process governed by consistently defined regions. Our experiments showed that the resulting regional flux analysis is able to detect the differential atrophy patterns across populations, and leads to precise and statistically powered quantifications of the longitudinal changes in AD, even in mild/premorbid cases.

  19. Metabolic flux profiling of MDCK cells during growth and canine adenovirus vector production

    PubMed Central

    Carinhas, Nuno; Pais, Daniel A. M.; Koshkin, Alexey; Fernandes, Paulo; Coroadinha, Ana S.; Carrondo, Manuel J. T.; Alves, Paula M.; Teixeira, Ana P.

    2016-01-01

    Canine adenovirus vector type 2 (CAV2) represents an alternative to human adenovirus vectors for certain gene therapy applications, particularly neurodegenerative diseases. However, more efficient production processes, assisted by a greater understanding of the effect of infection on producer cells, are required. Combining [1,2-13C]glucose and [U-13C]glutamine, we apply for the first time 13C-Metabolic flux analysis (13C-MFA) to study E1-transformed Madin-Darby Canine Kidney (MDCK) cells metabolism during growth and CAV2 production. MDCK cells displayed a marked glycolytic and ammoniagenic metabolism, and 13C data revealed a large fraction of glutamine-derived labelling in TCA cycle intermediates, emphasizing the role of glutamine anaplerosis. 13C-MFA demonstrated the importance of pyruvate cycling in balancing glycolytic and TCA cycle activities, as well as occurrence of reductive alphaketoglutarate (AKG) carboxylation. By turn, CAV2 infection significantly upregulated fluxes through most central metabolism, including glycolysis, pentose-phosphate pathway, glutamine anaplerosis and, more prominently, reductive AKG carboxylation and cytosolic acetyl-coenzyme A formation, suggestive of increased lipogenesis. Based on these results, we suggest culture supplementation strategies to stimulate nucleic acid and lipid biosynthesis for improved canine adenoviral vector production. PMID:27004747

  20. Structural analysis of airborne flux estimates over a region

    SciTech Connect

    Caramori, P.; Schuepp, P. ); Desjardins, R. ); MacPherson, I. )

    1994-05-01

    Aircraft-based observations of turbulence fields of velocity, moisture, and temperature are used to study coherent turbulent structures that dominate turbulent transfer of moisture and heat above three different ecosystems. Flux traces are defragmented, to reconstruct the presumed full size (along the sampled transect) of these structures, and flux traces are simplified by elimination of those that contribute negligibly to the flux estimates. Structures are analyzed in terms of size, spatial distribution, and contribution to the flux, in the four [open quotes]quadrant[close quotes] modes of eddy-covariance transfer (excess up/down and deficit up/down). The effect of nonlinear detrending of moisture and temperature data on this [open quotes]structural analysis,[close quotes] over surfaces with heterogeneous surface wetness, is also examined. Results over grassland, wetland, and moist and dry agricultural land, show that nonlinear detrending may provide a more physically realistic description of structures. Significant difference are observed between structure size and associated relative flux contribution, between moist and dry areas, with smaller structures playing a more important role over the moist areas. Structure size generally increases with height, as spatial reorganization from smaller structures into larger ones takes place. This coincides with a gradual loss of surface [open quotes]signature[close quotes] (position and clustering of plumes above localized source area). The data are expected to provide a basis for an eventual statistical description of boundary-layer transfer events, and help to interpret the link between boundary-layer transfer and hydrological surface conditions. 48 refs., 15 figs. 2 tabs.

  1. Dynamic analysis of CO₂ labeling and cell respiration using membrane-inlet mass spectrometry.

    PubMed

    Yang, Tae Hoon

    2014-01-01

    Here, we introduce a mass spectrometry-based analytical method and relevant technical details for dynamic cell respiration and CO2 labeling analysis. Such measurements can be utilized as additional information and constraints for model-based (13)C metabolic flux analysis. Dissolved dynamics of oxygen consumption and CO2 mass isotopomer evolution from (13)C-labeled tracer substrates through different cellular processes can be precisely measured on-line using a miniaturized reactor system equipped with a membrane-inlet mass spectrometer. The corresponding specific rates of physiologically relevant gases and CO2 mass isotopomers can be quantified within a short-term range based on the liquid-phase dynamics of dissolved fermentation gases.

  2. Analysis of metabolic flux using dynamic labelling and metabolic modelling.

    PubMed

    Fernie, A R; Morgan, J A

    2013-09-01

    Metabolic fluxes and the capacity to modulate them are a crucial component of the ability of the plant cell to react to environmental perturbations. Our ability to quantify them and to attain information concerning the regulatory mechanisms that control them is therefore essential to understand and influence metabolic networks. For all but the simplest of flux measurements labelling methods have proven to be the most informative. Both steady-state and dynamic labelling approaches have been adopted in the study of plant metabolism. Here the conceptual basis of these complementary approaches, as well as their historical application in microbial, mammalian and plant sciences, is reviewed, and an update on technical developments in label distribution analyses is provided. This is supported by illustrative cases studies involving the kinetic modelling of secondary metabolism. One issue that is particularly complex in the analysis of plant fluxes is the extensive compartmentation of the plant cell. This problem is discussed from both theoretical and experimental perspectives, and the current approaches used to address it are assessed. Finally, current limitations and future perspectives of kinetic modelling of plant metabolism are discussed. PMID:23421750

  3. Fast Flux Test Facility final safety analysis report. Amendment 73

    SciTech Connect

    Gantt, D.A.

    1993-08-01

    This report provides Final Safety Analysis Report (FSAR) Amendment 73 for incorporation into the Fast Flux Test Facility (FFTR) FSAR set. This page change incorporates Engineering Change Notices (ECNs) issued subsequent to Amendment 72 and approved for incorparoration before May 6, 1993. These changes include: Chapter 3, design criteria structures, equipment, and systems; chapter 5B, reactor coolant system; chapter 7, instrumentation and control systems; chapter 9, auxiliary systems; chapter 11, reactor refueling system; chapter 12, radiation protection and waste management; chapter 13, conduct of operations; chapter 17, technical specifications; chapter 20, FFTF criticality specifications; appendix C, local fuel failure events; and appendix Fl, operation at 680{degrees}F inlet temperature.

  4. Metabolic flux analysis of Gluconacetobacter xylinus for bacterial cellulose production.

    PubMed

    Zhong, Cheng; Zhang, Gui-Cai; Liu, Miao; Zheng, Xin-Tong; Han, Pei-Pei; Jia, Shi-Ru

    2013-07-01

    Metabolic flux analysis was used to reveal the metabolic distributions in Gluconacetobacter xylinus (CGMCC no. 2955) cultured on different carbon sources. Compared with other sources, glucose, fructose, and glycerol could achieve much higher bacterial cellulose (BC) yields from G. xylinus (CGMCC no. 2955). The glycerol led to the highest BC production with a metabolic yield of 14.7 g/mol C, which was approximately 1.69-fold and 2.38-fold greater than that produced using fructose and glucose medium, respectively. The highest BC productivity from G. xylinus CGMCC 2955 was 5.97 g BC/L (dry weight) when using glycerol as the sole carbon source. Metabolic flux analysis for the central carbon metabolism revealed that about 47.96 % of glycerol was transformed into BC, while only 19.05 % of glucose and 24.78 % of fructose were transformed into BC. Instead, when glucose was used as the sole carbon source, 40.03 % of glucose was turned into the by-product gluconic acid. Compared with BC from glucose and fructose, BC from the glycerol medium showed the highest tensile strength at 83.5 MPa, with thinner fibers and lower porosity. As a main byproduct of biodiesel production, glycerol holds great potential to produce BC with superior mechanical and microstructural characteristics.

  5. PAH fluxes to Siskiwit revisted: trends in fluxes and sources of pyrogenic PAH and perylene constrained via radiocarbon analysis.

    PubMed

    Slater, G F; Benson, A A; Marvin, C; Muir, D

    2013-05-21

    Trends in concentrations and radiocarbon content of pyrogenic PAHs and perylene were determined 20 years after a previous study by Mcveety and Hites (1988). Pyrogenic PAH fluxes to sediments were observed to continue to decrease over the period from 1980 to 2000 at this remote site in contrast to observations in more urban areas. Radiocarbon analysis of pyrogenic PAHs showed a 50% decrease in the proportion of pyrogenic PAH derived from fossil fuel combustion over the past 50 years, consistent with decreasing emissions from regional coal-fired power-generating plants. Fluxes of pyrogenic PAHs related to biomass burning were consistent over this same period and found to exceed fossil fuel sources in the most recent samples. Fluxes of biomass-derived pyrogenic PAHs were similar in magnitude to total pyrogenic PAH fluxes in early 1900, suggesting that these fluxes may represent wildfire inputs. Not only did perylene concentrations in these sediments increase with depth as previously observed but also concentrations from the same sedimentary layers analyzed 20 years previously showed large increases in perylene concentrations. Radiocarbon analysis of perylene indicated that 70-85% of perylene observed in the deeper sediments could be explained by production from total organic carbon. PMID:23582045

  6. Finding elementary flux modes in metabolic networks based on flux balance analysis and flux coupling analysis: application to the analysis of Escherichia coli metabolism.

    PubMed

    Tabe-Bordbar, Shayan; Marashi, Sayed-Amir

    2013-12-01

    Elementary modes (EMs) are steady-state metabolic flux vectors with minimal set of active reactions. Each EM corresponds to a metabolic pathway. Therefore, studying EMs is helpful for analyzing the production of biotechnologically important metabolites. However, memory requirements for computing EMs may hamper their applicability as, in most genome-scale metabolic models, no EM can be computed due to running out of memory. In this study, we present a method for computing randomly sampled EMs. In this approach, a network reduction algorithm is used for EM computation, which is based on flux balance-based methods. We show that this approach can be used to recover the EMs in the medium- and genome-scale metabolic network models, while the EMs are sampled in an unbiased way. The applicability of such results is shown by computing “estimated” control-effective flux values in Escherichia coli metabolic network.

  7. Metabolomics integrated elementary flux mode analysis in large metabolic networks.

    PubMed

    Gerstl, Matthias P; Ruckerbauer, David E; Mattanovich, Diethard; Jungreuthmayer, Christian; Zanghellini, Jürgen

    2015-03-10

    Elementary flux modes (EFMs) are non-decomposable steady-state pathways in metabolic networks. They characterize phenotypes, quantify robustness or identify engineering targets. An EFM analysis (EFMA) is currently restricted to medium-scale models, as the number of EFMs explodes with the network's size. However, many topologically feasible EFMs are biologically irrelevant. We present thermodynamic EFMA (tEFMA), which calculates only the small(er) subset of thermodynamically feasible EFMs. We integrate network embedded thermodynamics into EFMA and show that we can use the metabolome to identify and remove thermodynamically infeasible EFMs during an EFMA without losing biologically relevant EFMs. Calculating only the thermodynamically feasible EFMs strongly reduces memory consumption and program runtime, allowing the analysis of larger networks. We apply tEFMA to study the central carbon metabolism of E. coli and find that up to 80% of its EFMs are thermodynamically infeasible. Moreover, we identify glutamate dehydrogenase as a bottleneck, when E. coli is grown on glucose and explain its inactivity as a consequence of network embedded thermodynamics. We implemented tEFMA as a Java package which is available for download at https://github.com/mpgerstl/tEFMA.

  8. Fast Flux Test Facility final safety analysis report. Amendment 72

    SciTech Connect

    Gantt, D. A.

    1992-08-01

    This document provides the Final Safety Analysis Report (FSAR) Amendment 72 for incorporation into the Fast Flux Test Facility (FFTF) FSAR set. This amendment change incorporates Engineering Change Notices issued subsequent to Amendment 71 and approved for incorporation before June 24, 1992. These include changes in: Chapter 2, Site Characteristics; Chapter 3, Design Criteria Structures, Equipment, and Systems; Chapter 5B, Reactor Coolant System; Chapter 7, Instrumentation and Control Systems; Chapter 8, Electrical Systems - The description of the Class 1E, 125 Vdc systems is updated for the higher capacity of the newly installed, replacement batteries; Chapter 9, Auxiliary Systems - The description of the inert cell NASA systems is corrected to list the correct number of spare sample points; Chapter 11, Reactor Refueling System; Chapter 12, Radiation Protection and Waste Management; Chapter 13, Conduct of Operations; Chapter 16, Quality Assurance; Chapter 17, Technical Specifications; Chapter 19, FFTF Fire Specifications for Fire Detection, Alarm, and Protection Systems; Chapter 20, FFTF Criticality Specifications; and Appendix B, Primary Piping Integrity Evaluation.

  9. Analysis of actinic flux profiles measured from an ozonesonde balloon

    NASA Astrophysics Data System (ADS)

    Wang, P.; Allaart, M.; Knap, W. H.; Stammes, P.

    2015-04-01

    A green light sensor has been developed at KNMI to measure actinic flux profiles using an ozonesonde balloon. In total, 63 launches with ascending and descending profiles were performed between 2006 and 2010. The measured uncalibrated actinic flux profiles are analysed using the Doubling-Adding KNMI (DAK) radiative transfer model. Values of the cloud optical thickness (COT) along the flight track were taken from the Spinning Enhanced Visible and Infrared Imager (SEVIRI) Cloud Physical Properties (CPP) product. The impact of clouds on the actinic flux profile is evaluated on the basis of the cloud modification factor (CMF) at the cloud top and cloud base, which is the ratio between the actinic fluxes for cloudy and clear-sky scenes. The impact of clouds on the actinic flux is clearly detected: the largest enhancement occurs at the cloud top due to multiple scattering. The actinic flux decreases almost linearly from cloud top to cloud base. Above the cloud top the actinic flux also increases compared to clear-sky scenes. We find that clouds can increase the actinic flux to 2.3 times the clear-sky value at cloud top and decrease it to about 0.05 at cloud base. The relationship between CMF and COT agrees well with DAK simulations, except for a few outliers. Good agreement is found between the DAK-simulated actinic flux profiles and the observations for single-layer clouds in fully overcast scenes. The instrument is suitable for operational balloon measurements because of its simplicity and low cost. It is worth further developing the instrument and launching it together with atmospheric chemistry composition sensors.

  10. Shortwave flux profile analysis at the Cabauw BSRN site

    NASA Astrophysics Data System (ADS)

    Wang, P.; Baltink, H. Klein; Knap, W. H.; Stammes, P.

    2013-05-01

    The vertical distribution of the shortwave flux in the atmosphere is important for understanding the energy budget and the validation of climate models. We calculated shortwave flux profiles for cloudy cases by using the Doubling-Adding KNMI radiative transfer model with water vapour and cloud liquid water profiles derived from the Integrated Profiling Technique (IPT). As an example, we will show the approach for 3 March 2012. The calculated downward flux at the surface for this day compares well with measurements made at the Cabauw Baseline Surface Radiation Network (BSRN) site (51.97°N, 4.93°E), the Netherlands.

  11. Flux effect analysis in WWER-440 reactor pressure vessel steels

    NASA Astrophysics Data System (ADS)

    Kryukov, A.; Blagoeva, D.; Debarberis, L.

    2013-11-01

    The results of long term research programme concerning the determination of irradiation embrittlement dependence on fast neutron flux for WWER-440 reactor pressure vessel steels before and after annealing are presented in this paper. The study of flux effect was carried out on commercial WWER-440 steels which differ significantly in phosphorous (0.013-0.036 wt%) and copper (0.08-0.20 wt%) contents. All specimens were irradiated in surveillance channel positions under similar conditions at high ˜4 × 1012 сm-2 s-1 and low ˜6 × 1011 сm-2 s-1 fluxes (E > 0.5 MeV) at a temperature of 270 °С. The radiation embrittlement was evaluated by transition temperature shift on the basis of Charpy specimens test results. In case of low flux, the measured Tk shifts could be 25-50 °C bigger than the Tk shifts obtained from high flux data. A significant flux effect is observed in WWER-440 reactor pressure vessel steels with higher copper content (>0.13 wt%).

  12. Autonomous Particle Recognition and Analysis of Carbon Flux Explorer Imagery

    NASA Astrophysics Data System (ADS)

    Hamilton, C. M.; Bishop, J. K.; Wood, T.

    2013-12-01

    The biologically mediated export, or sedimentation, of particulate organic carbon to ocean depths below 100 m is approximately 10 Pg C per year and is highly variable in space and time. Despite the need to understand the biological drivers for export and the depth dependence of carbon remineralization for carbon cycle prediction, there are scant observations of sedimentation dynamics in the upper 1000 m. The Carbon Flux Explorer (CFE) is a robotic ocean profiling system, which combines the Scripps Sounding Oceanographic Lagrangian Observer (SOLO) and the LBNL/Berkeley optical sedimentation recorder. The CFE is designed to conduct high-frequency (hourly) observations of particulate organic and inorganic carbon sedimentation to kilometer depths, absent of ships, in all sea conditions, be reprogrammable and adaptive once deployed, and relay data to shore in near real time via Iridium satellite links for seasons to years. The CFE operates by sequentially imaging settled particles at ~15 micrometer size resolution in transmitted, transmitted cross-polarized, and dark field illumination. At present, these images must be stored on the CFE until recovery. In other words, the CFE is deployable in the context of multi-month long process studies. Here we present progress on particle recognition and quantification methodology, which will enable a 100,000:1 compression of image data needed for efficient satellite telemetry and fully autonomous real-time operation. Our methodology includes corrective thresh-holding, cross imaging comparison, distinction of aggregates from organisms, and the classification of particle properties including particle fractal dimension. We also look at these findings in context of particle vertical velocity, float performance, and oceanic conditions. Data analysis examples drawing on recent CFE missions to California coastal and offshore waters and to the subarctic N Pacific ocean, some lasting 41 days, will be presented.

  13. Quantitative flux analysis reveals folate-dependent NADPH production

    NASA Astrophysics Data System (ADS)

    Fan, Jing; Ye, Jiangbin; Kamphorst, Jurre J.; Shlomi, Tomer; Thompson, Craig B.; Rabinowitz, Joshua D.

    2014-06-01

    ATP is the dominant energy source in animals for mechanical and electrical work (for example, muscle contraction or neuronal firing). For chemical work, there is an equally important role for NADPH, which powers redox defence and reductive biosynthesis. The most direct route to produce NADPH from glucose is the oxidative pentose phosphate pathway, with malic enzyme sometimes also important. Although the relative contribution of glycolysis and oxidative phosphorylation to ATP production has been extensively analysed, similar analysis of NADPH metabolism has been lacking. Here we demonstrate the ability to directly track, by liquid chromatography-mass spectrometry, the passage of deuterium from labelled substrates into NADPH, and combine this approach with carbon labelling and mathematical modelling to measure NADPH fluxes. In proliferating cells, the largest contributor to cytosolic NADPH is the oxidative pentose phosphate pathway. Surprisingly, a nearly comparable contribution comes from serine-driven one-carbon metabolism, in which oxidation of methylene tetrahydrofolate to 10-formyl-tetrahydrofolate is coupled to reduction of NADP+ to NADPH. Moreover, tracing of mitochondrial one-carbon metabolism revealed complete oxidation of 10-formyl-tetrahydrofolate to make NADPH. As folate metabolism has not previously been considered an NADPH producer, confirmation of its functional significance was undertaken through knockdown of methylenetetrahydrofolate dehydrogenase (MTHFD) genes. Depletion of either the cytosolic or mitochondrial MTHFD isozyme resulted in decreased cellular NADPH/NADP+ and reduced/oxidized glutathione ratios (GSH/GSSG) and increased cell sensitivity to oxidative stress. Thus, although the importance of folate metabolism for proliferating cells has been long recognized and attributed to its function of producing one-carbon units for nucleic acid synthesis, another crucial function of this pathway is generating reducing power.

  14. Numerical Analysis of a Radiant Heat Flux Calibration System

    NASA Technical Reports Server (NTRS)

    Jiang, Shanjuan; Horn, Thomas J.; Dhir, V. K.

    1998-01-01

    A radiant heat flux gage calibration system exists in the Flight Loads Laboratory at NASA's Dryden Flight Research Center. This calibration system must be well understood if the heat flux gages calibrated in it are to provide useful data during radiant heating ground tests or flight tests of high speed aerospace vehicles. A part of the calibration system characterization process is to develop a numerical model of the flat plate heater element and heat flux gage, which will help identify errors due to convection, heater element erosion, and other factors. A 2-dimensional mathematical model of the gage-plate system has been developed to simulate the combined problem involving convection, radiation and mass loss by chemical reaction. A fourth order finite difference scheme is used to solve the steady state governing equations and determine the temperature distribution in the gage and plate, incident heat flux on the gage face, and flat plate erosion. Initial gage heat flux predictions from the model are found to be within 17% of experimental results.

  15. Observational & modeling analysis of surface heat and moisture fluxes

    SciTech Connect

    Smith, E.

    1995-09-01

    An observational and modeling study was conducted to help assess how well current GCMs are predicting surface fluxes under the highly variable cloudiness and flow conditions characteristic of the real atmosphere. The observational data base for the study was obtained from a network of surface flux stations operated during the First ISLSCP Field Experiment (FIFE). The study included examination of a surface-driven secondary circulation in the boundary layer resulting from a persistent cross-site gradient in soil moisture, to demonstrate the sensitivity of boundary layer dynamics to heterogeneous surface fluxes, The performance of a biosphere model in reproducing the measured surface fluxes was evaluated with and without the use of satellite retrieval of three key canopy variables with RMS uncertainties commensurate with those of the measurements themselves. Four sensible heat flux closure schemes currently being used in GCMs were then evaluated against the FIFE observations. Results indicate that the methods by which closure models are calibrated lead to exceedingly large errors when the schemes are applied to variable boundary layer conditions. 4 refs., 2 figs.

  16. Quantifying plant phenotypes with isotopic labeling and metabolic flux analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Analyses of metabolic flux using stable isotopes in plants have traditionally been restricted to tissues with presumed homogeneous cell populations such as developing seeds, cell suspensions, or cultured roots and root tips. It is now possible to describe these and other more complex tissues such a...

  17. Synthesis: comparing effects of resource and consumer fluxes into recipient food webs using meta-analysis.

    PubMed

    Allen, Daniel C; Wesner, Jeff S

    2016-03-01

    Here we synthesize empirical research using meta-analysis to compare how consumer and resource fluxes affect recipient food webs. We tested the following hypotheses: (H1) The direct effects of resource fluxes (bottom-up) should be stronger than the direct effects of consumer fluxes (top-down), because resource fluxes are permanent (do not return to the food web in which they were produced) but consumer fluxes may not be (consumers can leave). (H2) Following H1, the indirect effects should attenuate (weaken) more quickly for consumer fluxes than for resource fluxes due to their direct effects being weaker, (H3) The effects of resource fluxes should be stronger when recipient food webs are in different ecosystems than donor food webs due to differences in elevation that accompany cross-ecosystem food web interfaces, often increasing flux quantity due to gravity, while the effects of consumer fluxes should be stronger when donor and recipient food webs are in the same ecosystem as they should more easily assimilate into the recipient food web. We found no differences in the magnitude of bottom-up and top-down direct effects for resource and consumer fluxes, but top-down direct effects were 122% stronger than top-down indirect effects. Indirect effects of prey and predator fluxes quickly attenuated while indirect effects of non-prey resource and herbivore fluxes did not, as the overall direct effects of prey and predator fluxes were 123% and 163% stronger than their indirect effects, respectively. This result suggests that the magnitude of indirect effects decrease as the trophic level of resource and consumer fluxes increases, and also contrasts with results from studies showing in situ top-down indirect effects are stronger than in situ bottom-up indirect effects. We found that resource and consumer flux effect sizes were similar when they occurred between ecosystems, but when they occurred within ecosystems predator flux effects were 107% stronger than nutrient flux

  18. Synthesis: comparing effects of resource and consumer fluxes into recipient food webs using meta-analysis.

    PubMed

    Allen, Daniel C; Wesner, Jeff S

    2016-03-01

    Here we synthesize empirical research using meta-analysis to compare how consumer and resource fluxes affect recipient food webs. We tested the following hypotheses: (H1) The direct effects of resource fluxes (bottom-up) should be stronger than the direct effects of consumer fluxes (top-down), because resource fluxes are permanent (do not return to the food web in which they were produced) but consumer fluxes may not be (consumers can leave). (H2) Following H1, the indirect effects should attenuate (weaken) more quickly for consumer fluxes than for resource fluxes due to their direct effects being weaker, (H3) The effects of resource fluxes should be stronger when recipient food webs are in different ecosystems than donor food webs due to differences in elevation that accompany cross-ecosystem food web interfaces, often increasing flux quantity due to gravity, while the effects of consumer fluxes should be stronger when donor and recipient food webs are in the same ecosystem as they should more easily assimilate into the recipient food web. We found no differences in the magnitude of bottom-up and top-down direct effects for resource and consumer fluxes, but top-down direct effects were 122% stronger than top-down indirect effects. Indirect effects of prey and predator fluxes quickly attenuated while indirect effects of non-prey resource and herbivore fluxes did not, as the overall direct effects of prey and predator fluxes were 123% and 163% stronger than their indirect effects, respectively. This result suggests that the magnitude of indirect effects decrease as the trophic level of resource and consumer fluxes increases, and also contrasts with results from studies showing in situ top-down indirect effects are stronger than in situ bottom-up indirect effects. We found that resource and consumer flux effect sizes were similar when they occurred between ecosystems, but when they occurred within ecosystems predator flux effects were 107% stronger than nutrient flux

  19. Theoretical analysis of integral neutron transport equation using collision probability method with quadratic flux approach

    SciTech Connect

    Shafii, Mohammad Ali Meidianti, Rahma Wildian, Fitriyani, Dian; Tongkukut, Seni H. J.; Arkundato, Artoto

    2014-09-30

    Theoretical analysis of integral neutron transport equation using collision probability (CP) method with quadratic flux approach has been carried out. In general, the solution of the neutron transport using the CP method is performed with the flat flux approach. In this research, the CP method is implemented in the cylindrical nuclear fuel cell with the spatial of mesh being conducted into non flat flux approach. It means that the neutron flux at any point in the nuclear fuel cell are considered different each other followed the distribution pattern of quadratic flux. The result is presented here in the form of quadratic flux that is better understanding of the real condition in the cell calculation and as a starting point to be applied in computational calculation.

  20. Novel biological insights through metabolomics and 13C-flux analysis.

    PubMed

    Zamboni, Nicola; Sauer, Uwe

    2009-10-01

    Metabolomics and (13)C-flux analysis have become instrumental for analyzing cellular metabolism and its regulation. Driven primarily by technical advances in mass spectrometry-based analytics, they provide unmatched readouts on metabolic state and activity. Functional genomics leverages metabolomics for the discovery of novel enzymes and unexpected secondary activities of annotated enzymes. (13)C-flux analyses are frequently used for empirical elucidation of pathways in poorly characterized species and for network-wide analysis of mechanisms that realize energy and redox balancing. Integration of metabolomics, (13)C-flux analysis and other data enable the condition-dependent characterization of regulatory circuits that ultimately govern the metabolic phenotype.

  1. Quantifying plant phenotypes with isotopic labeling & metabolic flux analysis.

    PubMed

    Allen, Doug K

    2016-02-01

    Analyses of metabolic flux using stable isotopes in plants have traditionally been restricted to tissues with presumed homogeneous cell populations and long metabolic steady states such as developing seeds, cell suspensions, or cultured roots and root tips. It is now possible to describe these and other metabolically more dynamic tissues such as leaves in greater detail using novel methods in mass spectrometry, isotope labeling strategies, and transient labeling-based flux analyses. Such studies are necessary for a systems level description of plant function that more closely represents biological reality, and provides insights into the genes that will need to be modified as natural resources become ever more limited and environments change. PMID:26613198

  2. Flux and reflux: metabolite reflux in plant suspension cells and its implications for isotope-assisted metabolic flux analysis.

    PubMed

    Nargund, Shilpa; Misra, Ashish; Zhang, Xiaofeng; Coleman, Gary D; Sriram, Ganesh

    2014-06-01

    Isotope-assisted metabolic flux analysis (MFA) is a powerful methodology to quantify intracellular fluxes via isotope labeling experiments (ILEs). In batch cultures, which are often convenient, inexpensive or inevitable especially for eukaryotic systems, MFA is complicated by the presence of the initially present biomass. This unlabeled biomass may either mix with the newly synthesized labeled biomass or reflux into the metabolic network, thus masking the true labeling patterns in the newly synthesized biomass. Here, we report a detailed investigation of such metabolite reflux in cell suspensions of the tree poplar. In ILEs supplying 28% or 98% U-(13)C glucose as the sole organic carbon source, biomass components exhibited lower (13)C enrichments than the supplied glucose as well as anomalous isotopomers not explainable by simple mixing of the initial and newly synthesized biomass. These anomalous labeling patterns were most prominent in a 98% U-(13)C glucose ILE. By comparing the performance of light- and dark-grown cells as well as by analyzing the isotope labeling patterns in aspartic and glutamic acids, we eliminated photosynthetic or anaplerotic fixation of extracellular (12)CO2 as explanations for the anomalous labeling patterns. We further investigated four different metabolic models for interpreting the labeling patterns and evaluating fluxes: (i) a carbon source (glucose) dilution model, (ii) an isotopomer correction model with uniform dilution for all amino acids, (iii) an isotopomer correction model with variable dilution for different amino acids, and (iv) a comprehensive metabolite reflux model. Of these, the metabolite reflux model provided a substantially better fit for the observed labeling patterns (sum of squared residues: 538) than the other three models whose sum of squared residues were (i) 4626, (ii) 4983, and (iii) 1748, respectively. We compared fluxes determined using the metabolite reflux model to those determined using an independent

  3. Empirical predictive models of daily relativistic electron flux at geostationary orbit: Multiple regression analysis

    NASA Astrophysics Data System (ADS)

    Simms, Laura E.; Engebretson, Mark J.; Pilipenko, Viacheslav; Reeves, Geoffrey D.; Clilverd, Mark

    2016-04-01

    The daily maximum relativistic electron flux at geostationary orbit can be predicted well with a set of daily averaged predictor variables including previous day's flux, seed electron flux, solar wind velocity and number density, AE index, IMF Bz, Dst, and ULF and VLF wave power. As predictor variables are intercorrelated, we used multiple regression analyses to determine which are the most predictive of flux when other variables are controlled. Empirical models produced from regressions of flux on measured predictors from 1 day previous were reasonably effective at predicting novel observations. Adding previous flux to the parameter set improves the prediction of the peak of the increases but delays its anticipation of an event. Previous day's solar wind number density and velocity, AE index, and ULF wave activity are the most significant explanatory variables; however, the AE index, measuring substorm processes, shows a negative correlation with flux when other parameters are controlled. This may be due to the triggering of electromagnetic ion cyclotron waves by substorms that cause electron precipitation. VLF waves show lower, but significant, influence. The combined effect of ULF and VLF waves shows a synergistic interaction, where each increases the influence of the other on flux enhancement. Correlations between observations and predictions for this 1 day lag model ranged from 0.71 to 0.89 (average: 0.78). A path analysis of correlations between predictors suggests that solar wind and IMF parameters affect flux through intermediate processes such as ring current (Dst), AE, and wave activity.

  4. Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis

    PubMed Central

    Dantas, Gautam; Church, George M.; Galagan, James; Lehár, Joseph; Sommer, Morten O. A.

    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 most widely used antibiotic treatments. Here we extend FBA modeling to simulate responses to chemical inhibitors at varying concentrations, by diverting enzymatic flux to a waste reaction. This flux diversion yields very similar qualitative predictions to prior methods for single target activity. 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 possibility for more accurate genome-scale predictions of drug synergies, which can be used to suggest treatments for infections and other diseases. PMID:26821252

  5. Genome-scale metabolic flux analysis of Streptomyces lividans growing on a complex medium.

    PubMed

    D'Huys, Pieter-Jan; Lule, Ivan; Vercammen, Dominique; Anné, Jozef; Van Impe, Jan F; Bernaerts, Kristel

    2012-09-15

    Constraint-based metabolic modeling comprises various excellent tools to assess experimentally observed phenotypic behavior of micro-organisms in terms of intracellular metabolic fluxes. In combination with genome-scale metabolic networks, micro-organisms can be investigated in much more detail and under more complex environmental conditions. Although complex media are ubiquitously applied in industrial fermentations and are often a prerequisite for high protein secretion yields, such multi-component conditions are seldom investigated using genome-scale flux analysis. In this paper, a systematic and integrative approach is presented to determine metabolic fluxes in Streptomyces lividans TK24 grown on a nutritious and complex medium. Genome-scale flux balance analysis and randomized sampling of the solution space are combined to extract maximum information from exometabolome profiles. It is shown that biomass maximization cannot predict the observed metabolite production pattern as such. Although this cellular objective commonly applies to batch fermentation data, both input and output constraints are required to reproduce the measured biomass production rate. Rich media hence not necessarily lead to maximum biomass growth. To eventually identify a unique intracellular flux vector, a hierarchical optimization of cellular objectives is adopted. Out of various tested secondary objectives, maximization of the ATP yield per flux unit returns the closest agreement with the maximum frequency in flux histograms. This unique flux estimation is hence considered as a reasonable approximation for the biological fluxes. Flux maps for different growth phases show no active oxidative part of the pentose phosphate pathway, but NADPH generation in the TCA cycle and NADPH transdehydrogenase activity are most important in fulfilling the NADPH balance. Amino acids contribute to biomass growth by augmenting the pool of available amino acids and by boosting the TCA cycle, particularly

  6. Metabolic networks in motion: 13C-based flux analysis.

    PubMed

    Sauer, Uwe

    2006-01-01

    Many properties of complex networks cannot be understood from monitoring the components--not even when comprehensively monitoring all protein or metabolite concentrations--unless such information is connected and integrated through mathematical models. The reason is that static component concentrations, albeit extremely informative, do not contain functional information per se. The functional behavior of a network emerges only through the nonlinear gene, protein, and metabolite interactions across multiple metabolic and regulatory layers. I argue here that intracellular reaction rates are the functional end points of these interactions in metabolic networks, hence are highly relevant for systems biology. Methods for experimental determination of metabolic fluxes differ fundamentally from component concentration measurements; that is, intracellular reaction rates cannot be detected directly, but must be estimated through computer model-based interpretation of stable isotope patterns in products of metabolism.

  7. Metabolic flux and nodes control analysis of brewer's yeasts under different fermentation temperature during beer brewing.

    PubMed

    Yu, Zhimin; Zhao, Haifeng; Zhao, Mouming; Lei, Hongjie; Li, Huiping

    2012-12-01

    The aim of this work was to further investigate the glycolysis performance of lager and ale brewer's yeasts under different fermentation temperature using a combined analysis of metabolic flux, glycolytic enzyme activities, and flux control. The results indicated that the fluxes through glycolytic pathway decreased with the change of the fermentation temperature from 15 °C to 10 °C, which resulted in the prolonged fermentation times. The maximum activities (V (max)) of hexokinase (HK), phosphofructokinase (PFK), and pyruvate kinase (PK) at key nodes of glycolytic pathway decreased with decreasing fermentation temperature, which was estimated to have different control extent (22-84 %) on the glycolytic fluxes in exponential or flocculent phase. Moreover, the decrease of V (max) of PFK or PK displayed the crucial role in down-regulation of flux in flocculent phase. In addition, the metabolic state of ale strain was more sensitive to the variation of temperature than that of lager strain. The results of the metabolic flux and nodes control analysis in brewer's yeasts under different fermentation temperature may provide an alternative approach to regulate glycolytic flux by changing V (max) and improve the production efficiency and beer quality.

  8. Flux balance analysis in the production of clavulanic acid by Streptomyces clavuligerus.

    PubMed

    Sánchez, Claudia; Quintero, Juan Carlos; Ochoa, Silvia

    2015-01-01

    In this work, in silico flux balance analysis is used for predicting the metabolic behavior of Streptomyces clavuligerus during clavulanic acid production. To choose the best objective function for use in the analysis, three different optimization problems are evaluated inside the flux balance analysis formulation: (i) maximization of the specific growth rate, (ii) maximization of the ATP yield, and (iii) maximization of clavulanic acid production. Maximization of ATP yield showed the best predictions for the cellular behavior. Therefore, flux balance analysis using ATP as objective function was used for analyzing different scenarios of nutrient limitations toward establishing the effect of limiting the carbon, nitrogen, phosphorous, and oxygen sources on the growth and clavulanic acid production rates. Obtained results showed that ammonia and phosphate limitations are the ones most strongly affecting clavulanic acid biosynthesis. Furthermore, it was possible to identify the ornithine flux from the urea cycle and the α-ketoglutarate flux from the TCA cycle as the most determinant internal fluxes for promoting clavulanic acid production.

  9. RELATIONSHIP BETWEEN MASS FLUX REDUCTION AND SOURCE-ZONE MASS REMOVAL: ANALYSIS OF FIELD DATA

    PubMed Central

    DiFilippo, Erica L.

    2010-01-01

    The magnitude of contaminant mass flux reduction associated with a specific amount of contaminant mass removed is a key consideration for evaluating the effectiveness of a source-zone remediation effort. Thus, there is great interest in characterizing, estimating, and predicting relationships between mass flux reduction and mass removal. Published data collected for several field studies were examined to evaluate relationships between mass flux reduction and source-zone mass removal. The studies analyzed herein represent a variety of source-zone architectures, immiscible-liquid compositions, and implemented remediation technologies. There are two general approaches to characterizing the mass-flux-reduction/mass-removal relationship, end-point analysis and time-continuous analysis. End-point analysis, based on comparing masses and mass fluxes measured before and after a source-zone remediation effort, was conducted for 21 remediation projects. Mass removals were greater than 60% for all but three of the studies. Mass flux reductions ranging from slightly less than to slightly greater than one-to-one were observed for the majority of the sites. However, these single-snapshot characterizations are limited in that the antecedent behavior is indeterminate. Time-continuous analysis, based on continuous monitoring of mass removal and mass flux, was performed for two sites, both for which data were obtained under water-flushing conditions. The reductions in mass flux were significantly different for the two sites (90% vs. ~8%) for similar mass removals (~40%). These results illustrate the dependence of the mass-flux-reduction/mass-removal relationship on source-zone architecture and associated mass-transfer processes. Minimal mass flux reduction was observed for a system wherein mass removal was relatively efficient (ideal mass transfer and displacement). Conversely, a significant degree of mass flux reduction was observed for a site wherein mass removal was inefficient

  10. INCA: a computational platform for isotopically non-stationary metabolic flux analysis

    PubMed Central

    2014-01-01

    Summary: 13C flux analysis studies have become an essential component of metabolic engineering research. The scope of these studies has gradually expanded to include both isotopically steady-state and transient labeling experiments, the latter of which are uniquely applicable to photosynthetic organisms and slow-to-label mammalian cell cultures. Isotopomer network compartmental analysis (INCA) is the first publicly available software package that can perform both steady-state metabolic flux analysis and isotopically non-stationary metabolic flux analysis. The software provides a framework for comprehensive analysis of metabolic networks using mass balances and elementary metabolite unit balances. The generation of balance equations and their computational solution is completely automated and can be performed on networks of arbitrary complexity. Availability and implementation: MATLAB p-code files are freely available for non-commercial use and can be downloaded at http://mfa.vueinnovations.com. Commercial licenses are also available. Contact: j.d.young@vanderbilt.edu PMID:24413674

  11. Oxygen flux analysis to understand the biological function of sirtuins.

    PubMed

    Wang, Dongning; Green, Michelle F; McDonnell, Eoin; Hirschey, Matthew D

    2013-01-01

    The sirtuins are a family of highly conserved NAD(+)-dependent lysine deacylases with important roles in metabolic regulation. Of the seven mammalian sirtuins, three localize to the mitochondria: SIRT3, SIRT4, and SIRT5. Mitochondrial sirtuins are crucial regulators of the metabolic network that controls energy homeostasis and impacts cancer, obesity, diabetes, mitochondrial diseases, metabolic disorders, and many other human diseases of aging. To best study the mitochondrial function of the sirtuins, we have employed an oxygen flux analyzer as a tool to track and record the extracellular oxygen consumption rate and acidification rate that reflects mitochondrial respiration and glycolysis, respectfully. Here we described the methods using this assay to study the substrate utilization and mitochondrial function in a human hepatocellular carcinoma cell line, Huh7. Additionally, we have generated a stable SIRT4 knocked-down Huh7 cell line. With this cell line, we evaluated how the absence of SIRT4 affects mitochondrial function, glucose utilization, glutamine oxidation, and fatty acid oxidation in these cells. PMID:24014411

  12. Analysis of field measurements of carbon dioxide and water vapor fluxes

    NASA Technical Reports Server (NTRS)

    Verma, Shashi B.

    1991-01-01

    Analysis of the field measurements of carbon dioxide and water vapor fluxes is discussed. These data were examined in conjunction with reflectance obtained from helicopter mounted Modular Multiband Radiometer. These measurements are representative of the canopy scale (10 to 100 m)(exp 2) and provide a good basis for investigating the hypotheses/relationship potentially useful in remote sensing applications. All the micrometeorological data collected during FIFE-89 were processed and fluxes of CO2, water vapor, and sensible heat were calculated. Soil CO2 fluxes were also estimated. Employing these soil CO2 flux values, in conjunction with micrometeorological measurements, canopy photosynthesis is being estimated. A biochemical model of leaf photosynthesis was adapted to the prairie vegetation. The modeled leaf photosynthesis rates were scaled up to the canopy level. This model and a multiplicative stomatal conductance model are also used to calculate canopy conductance.

  13. The relative importance of head, flux, and prior information in hydraulic tomography analysis

    NASA Astrophysics Data System (ADS)

    Michael Tso, Chak-Hau; Zha, Yuanyuan; Jim Yeh, Tian-Chyi; Wen, Jet-Chau

    2016-01-01

    Using cross-correlation analysis, we demonstrate that flux measurements at observation locations during hydraulic tomography (HT) surveys carry nonredundant information about heterogeneity that are complementary to head measurements at the same locations. We then hypothesize that a joint interpretation of head and flux data, even when the same observation network as head has been used, can enhance the resolution of HT estimates. Subsequently, we use numerical experiments to test this hypothesis and investigate the impact of flux conditioning and prior information (such as correlation lengths and initial mean models (i.e., uniform mean or distributed means)) on the HT estimates of a nonstationary, layered medium. We find that the addition of flux conditioning to HT analysis improves the estimates in all of the prior models tested. While prior information on geologic structures could be useful, its influence on the estimates reduces as more nonredundant data (i.e., flux) are used in the HT analysis. Lastly, recommendations for conducting HT surveys and analysis are presented.

  14. Bayesian Statistical Analysis Applied to NAA Data for Neutron Flux Spectrum Determination

    NASA Astrophysics Data System (ADS)

    Chiesa, D.; Previtali, E.; Sisti, M.

    2014-04-01

    In this paper, we present a statistical method, based on Bayesian statistics, to evaluate the neutron flux spectrum from the activation data of different isotopes. The experimental data were acquired during a neutron activation analysis (NAA) experiment [A. Borio di Tigliole et al., Absolute flux measurement by NAA at the Pavia University TRIGA Mark II reactor facilities, ENC 2012 - Transactions Research Reactors, ISBN 978-92-95064-14-0, 22 (2012)] performed at the TRIGA Mark II reactor of Pavia University (Italy). In order to evaluate the neutron flux spectrum, subdivided in energy groups, we must solve a system of linear equations containing the grouped cross sections and the activation rate data. We solve this problem with Bayesian statistical analysis, including the uncertainties of the coefficients and the a priori information about the neutron flux. A program for the analysis of Bayesian hierarchical models, based on Markov Chain Monte Carlo (MCMC) simulations, is used to define the problem statistical model and solve it. The energy group fluxes and their uncertainties are then determined with great accuracy and the correlations between the groups are analyzed. Finally, the dependence of the results on the prior distribution choice and on the group cross section data is investigated to confirm the reliability of the analysis.

  15. TNA4OptFlux – a software tool for the analysis of strain optimization strategies

    PubMed Central

    2013-01-01

    Background Rational approaches for Metabolic Engineering (ME) deal with the identification of modifications that improve the microbes’ production capabilities of target compounds. One of the major challenges created by strain optimization algorithms used in these ME problems is the interpretation of the changes that lead to a given overproduction. Often, a single gene knockout induces changes in the fluxes of several reactions, as compared with the wild-type, and it is therefore difficult to evaluate the physiological differences of the in silico mutant. This is aggravated by the fact that genome-scale models per se are difficult to visualize, given the high number of reactions and metabolites involved. Findings We introduce a software tool, the Topological Network Analysis for OptFlux (TNA4OptFlux), a plug-in which adds to the open-source ME platform OptFlux the capability of creating and performing topological analysis over metabolic networks. One of the tool’s major advantages is the possibility of using these tools in the analysis and comparison of simulated phenotypes, namely those coming from the results of strain optimization algorithms. We illustrate the capabilities of the tool by using it to aid the interpretation of two E. coli strains designed in OptFlux for the overproduction of succinate and glycine. Conclusions Besides adding new functionalities to the OptFlux software tool regarding topological analysis, TNA4OptFlux methods greatly facilitate the interpretation of non-intuitive ME strategies by automating the comparison between perturbed and non-perturbed metabolic networks. The plug-in is available on the web site http://www.optflux.org, together with extensive documentation. PMID:23641878

  16. Global analysis of seasonality in the shell flux of extant planktonic Foraminifera

    NASA Astrophysics Data System (ADS)

    Jonkers, L.; Kučera, M.

    2015-04-01

    Shell fluxes of planktonic Foraminifera species vary intra-annually in a pattern that appears to follow the seasonal cycle. However, the variation in the timing and prominence of seasonal flux maxima in space and among species remains poorly constrained. Thus, although changing seasonality may result in a flux-weighted temperature offset of more than 5° C within a species, this effect is often ignored in the interpretation of Foraminifera-based paleoceanographic records. To address this issue we present an analysis of the intra-annual pattern of shell flux variability in 37 globally distributed time series. The existence of a seasonal component in flux variability was objectively characterised using periodic regression. This analysis yielded estimates of the number, timing and prominence of seasonal flux maxima. Over 80% of the flux series across all species showed a statistically significant periodic component, indicating that a considerable part of the intra-annual flux variability is predictable. Temperature appears to be a powerful predictor of flux seasonality, but its effect differs among species. Three different modes of seasonality are distinguishable. Tropical and subtropical species (Globigerinoides ruber (white and pink varieties), Neogloboquadrina dutertrei, Globigerinoides sacculifer, Orbulina universa, Globigerinella siphonifera, Pulleniatina obliquiloculata, Globorotalia menardii, Globoturborotalita rubescens, Globoturborotalita tenella and Globigerinoides conglobatus) appear to have a less predictable flux pattern, with random peak timing in warm waters. In colder waters, seasonality is more prevalent: peak fluxes occur shortly after summer temperature maxima and peak prominence increases. This tendency is stronger in species with a narrower temperature range, implying that warm-adapted species find it increasingly difficult to reproduce outside their optimum temperature range and that, with decreasing mean temperature, their flux is progressively

  17. Analysis of Atmosphere-Ocean Surface Flux Feedbacks in Recent Satellite and Model Reanalysis Products

    NASA Technical Reports Server (NTRS)

    Roberts, J. Brent; Robertson, F. R.; Clayson, C. A.

    2010-01-01

    Recent investigations have examined observations in an attempt to determine when and how the ocean forces the atmosphere, and vice versa. These studies focus primarily on relationships between sea surface temperature anomalies and the turbulent and radiative surface heat fluxes. It has been found that both positive and negative feedbacks, which enhance or reduce sea surface temperature anomaly amplitudes, can be generated through changes in the surface boundary layer. Consequent changes in sea surface temperature act to change boundary layer characteristics through changes in static stability or turbulent fluxes. Previous studies over the global oceans have used coarse-resolution observational and model products such as ICOADS and the NCEP Reanalysis. This study focuses on documenting the atmosphere ocean feedbacks that exist in recently produced higher resolution products, namely the SeaFlux v1.0 product and the NASA Modern Era Retrospective-Analysis for Research and Applications (MERRA). It has been noted in recent studies that evidence of oceanic forcing of the atmosphere exists on smaller scales than the usually more dominant atmospheric forcing of the ocean, particularly in higher latitudes. It is expected that use of these higher resolution products will allow for a more comprehensive description of these small-scale ocean-atmosphere feedbacks. The SeaFlux intercomparisons have revealed large scatter between various surface flux climatologies. This study also investigates the uncertainty in surface flux feedbacks based on several of these recent satellite based climatologies

  18. Micrometeorological measurement and source region analysis of nitrous oxide fluxes from an agricultural soil

    NASA Astrophysics Data System (ADS)

    Wienhold, F. G.; Welling, M.; Harris, G. W.

    Nitrous oxide (N 2O) fluxes were measured by eddy correlation during a field experiment in August 1993. The measurements took place on a harvested wheat field located in northwest Sealand (Denmark). A. tunable diode laser absorption spectrometer (TDLAS) was used for N 2O detection. The N 2O mixing ratio was sampled at a rate of 10 Hz synchronously with the three-dimensional wind data, air temperature, water vapour and carbon dioxide (CO 2) concentrations. Fast Fourier transform methods were applied to analyse spectral and co-spectral power distributions and to compute the fluxes from the covariance functions. Balance of the energy budget indicated adequate frequency coverage of the flux contributions. Continuous measurements were carried out in half hour intervals during daytime and fluxes in the range of 40-120 ng N m -2 s -1 were obtained. The footprint regions for the individual measurements were estimated by Markovian trajectory simulations taking into account the atmospheric stability conditions and wind distributions inferred from the micrometeorological measurements. The influence of adjoining fields with different crops was evident in the Bowen ratio and CO 2 flux, but not noticeable in the N 2O flux. This observation is consistent with supporting analysis of the soil depth dependence of the nitrous oxide production, which indicates that the major contributions arise from levels below 0.9 m.

  19. Development of high flux thermal neutron generator for neutron activation analysis

    NASA Astrophysics Data System (ADS)

    Vainionpaa, Jaakko H.; Chen, Allan X.; Piestrup, Melvin A.; Gary, Charles K.; Jones, Glenn; Pantell, Richard H.

    2015-05-01

    The new model DD110MB neutron generator from Adelphi Technology produces thermal (<0.5 eV) neutron flux that is normally achieved in a nuclear reactor or larger accelerator based systems. Thermal neutron fluxes of 3-5 · 107 n/cm2/s are measured. This flux is achieved using four ion beams arranged concentrically around a target chamber containing a compact moderator with a central sample cylinder. Fast neutron yield of ∼2 · 1010 n/s is created at the titanium surface of the target chamber. The thickness and material of the moderator is selected to maximize the thermal neutron flux at the center. The 2.5 MeV neutrons are quickly thermalized to energies below 0.5 eV and concentrated at the sample cylinder. The maximum flux of thermal neutrons at the target is achieved when approximately half of the neutrons at the sample area are thermalized. In this paper we present simulation results used to characterize performance of the neutron generator. The neutron flux can be used for neutron activation analysis (NAA) prompt gamma neutron activation analysis (PGNAA) for determining the concentrations of elements in many materials. Another envisioned use of the generator is production of radioactive isotopes. DD110MB is small enough for modest-sized laboratories and universities. Compared to nuclear reactors the DD110MB produces comparable thermal flux but provides reduced administrative and safety requirements and it can be run in pulsed mode, which is beneficial in many neutron activation techniques.

  20. AN ANALYSIS OF MAGNETOHYDRODYNAMIC INVARIANTS OF MAGNETIC FLUCTUATIONS WITHIN INTERPLANETARY FLUX ROPES

    SciTech Connect

    Telloni, D.; Perri, S.; Carbone, V.; Bruno, R.; D Amicis, R.

    2013-10-10

    A statistical analysis of magnetic flux ropes, identified by large-amplitude, smooth rotations of the magnetic field vector and a low level of both proton density and temperature, has been performed by computing the invariants of the ideal magnetohydrodynamic (MHD) equations, namely the magnetic helicity, the cross-helicity, and the total energy, via magnetic field and plasma fluctuations in the interplanetary medium. A technique based on the wavelet spectrograms of the MHD invariants allows the localization and characterization of those structures in both scales and time: it has been observed that flux ropes show, as expected, high magnetic helicity states (|σ{sub m}| in [0.6: 1]), but extremely variable cross-helicity states (|σ{sub c}| in [0: 0.8]), which, however, are not independent of the magnetic helicity content of the flux rope itself. The two normalized MHD invariants observed within the flux ropes tend indeed to distribute, neither trivially nor automatically, along the √(σ{sub m}{sup 2}+σ{sub c}{sup 2})=1 curve, thus suggesting that some constraint should exist between the magnetic and cross-helicity content of the structures. The analysis carried out has further showed that the flux rope properties are totally independent of their time duration and that they are detected either as a sort of interface between different portions of solar wind or as isolated structures embedded in the same stream.

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

    NASA Astrophysics Data System (ADS)

    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.

  2. Metabolic Flux Ratio Analysis of Genetic and Environmental Modulations of Escherichia coli Central Carbon Metabolism

    PubMed Central

    Sauer, Uwe; Lasko, Daniel R.; Fiaux, Jocelyne; Hochuli, Michel; Glaser, Ralf; Szyperski, Thomas; Wüthrich, Kurt; Bailey, James E.

    1999-01-01

    The response of Escherichia coli central carbon metabolism to genetic and environmental manipulation has been studied by use of a recently developed methodology for metabolic flux ratio (METAFoR) analysis; this methodology can also directly reveal active metabolic pathways. Generation of fluxome data arrays by use of the METAFoR approach is based on two-dimensional 13C-1H correlation nuclear magnetic resonance spectroscopy with fractionally labeled biomass and, in contrast to metabolic flux analysis, does not require measurements of extracellular substrate and metabolite concentrations. METAFoR analyses of E. coli strains that moderately overexpress phosphofructokinase, pyruvate kinase, pyruvate decarboxylase, or alcohol dehydrogenase revealed that only a few flux ratios change in concert with the overexpression of these enzymes. Disruption of both pyruvate kinase isoenzymes resulted in altered flux ratios for reactions connecting the phosphoenolpyruvate (PEP) and pyruvate pools but did not significantly alter central metabolism. These data indicate remarkable robustness and rigidity in central carbon metabolism in the presence of genetic variation. More significant physiological changes and flux ratio differences were seen in response to altered environmental conditions. For example, in ammonia-limited chemostat cultures, compared to glucose-limited chemostat cultures, a reduced fraction of PEP molecules was derived through at least one transketolase reaction, and there was a higher relative contribution of anaplerotic PEP carboxylation than of the tricarboxylic acid (TCA) cycle for oxaloacetate synthesis. These two parameters also showed significant variation between aerobic and anaerobic batch cultures. Finally, two reactions catalyzed by PEP carboxykinase and malic enzyme were identified by METAFoR analysis; these had previously been considered absent in E. coli cells grown in glucose-containing media. Backward flux from the TCA cycle to glycolysis, as

  3. Analysis of Voyager Observed High-Energy Electron Fluxes in the Heliosheath Using MHD Simulations

    NASA Technical Reports Server (NTRS)

    Washimi, Haruichi; Webber, W. R.; Zank, Gary P.; Hu, Qiang; Florinski, Vladimir; Adams, James; Kubo, Yuki

    2011-01-01

    The Voyager spacecraft (V1 and V2) observed electrons of 6-14 MeV in the heliosheath which showed several incidences of flux variation relative to a background of gradually increasing flux with distance from the Sun. The increasing flux of background electrons is thought to result from inward radial diffusion. We compare the temporal electron flux variation with dynamical phenomena in the heliosheath that are obtained from our MHD simulations. Because our simulation is based on V2 observed plasma data before V2 crossed the termination shock, this analysis is effective up to late 2008, i.e., about a year after the V2-crossing, during which disturbances, driven prior to the crossing time, survived in the heliosheath. Several electron flux variations correspond to times directly associated with interplanetary shock events. One noteworthy example corresponds to various times associated with the March 2006 interplanetary shock, these being the collision with the termination shock, the passage past the V1 spacecraft, and the collision with the region near the heliopause, as identified by W.R. Webber et al. for proton/helium of 7-200 MeV. Our simulations indicate that all other electron flux variations, except one, correspond well to the times when a shock-driven magneto-sonic pulse and its reflection in the heliosheath either passed across V1/V2, or collided with the termination shock or with the plasma sheet near the heliopause. This result suggests that variation in the electron flux should be due to either direct or indirect effects of magnetosonic pulses in the heliosheath driven by interplanetary shocks

  4. Elucidation of intrinsic biosynthesis yields using 13C-based metabolism analysis

    PubMed Central

    2014-01-01

    This paper discusses the use of 13C-based metabolism analysis for the assessment of intrinsic product yields — the actual carbon contribution from a single carbon substrate to the final product via a specific biosynthesis route — in the following four cases. First, undefined nutrients (such as yeast extract) in fermentation may contribute significantly to product synthesis, which can be quantified through an isotopic dilution method. Second, product and biomass synthesis may be dependent on the co-metabolism of multiple-carbon sources. 13C labeling experiments can track the fate of each carbon substrate in the cell metabolism and identify which substrate plays a main role in product synthesis. Third, 13C labeling can validate and quantify the contribution of the engineered pathway (versus the native pathway) to the product synthesis. Fourth, the loss of catabolic energy due to cell maintenance (energy used for functions other than production of new cell components) and low P/O ratio (Phosphate/Oxygen Ratio) significantly reduces product yields. Therefore, 13C-metabolic flux analysis is needed to assess the influence of suboptimal energy metabolism on microbial productivity, and determine how ATP/NAD(P)H are partitioned among various cellular functions. Since product yield is a major determining factor in the commercialization of a microbial cell factory, we foresee that 13C-isotopic labeling experiments, even without performing extensive flux calculations, can play a valuable role in the development and verification of microbial cell factories. PMID:24642094

  5. Elucidation of intrinsic biosynthesis yields using 13C-based metabolism analysis.

    PubMed

    Varman, Arul M; He, Lian; You, Le; Hollinshead, Whitney; Tang, Yinjie J

    2014-03-19

    This paper discusses the use of 13C-based metabolism analysis for the assessment of intrinsic product yields - the actual carbon contribution from a single carbon substrate to the final product via a specific biosynthesis route - in the following four cases. First, undefined nutrients (such as yeast extract) in fermentation may contribute significantly to product synthesis, which can be quantified through an isotopic dilution method. Second, product and biomass synthesis may be dependent on the co-metabolism of multiple-carbon sources. 13C labeling experiments can track the fate of each carbon substrate in the cell metabolism and identify which substrate plays a main role in product synthesis. Third, 13C labeling can validate and quantify the contribution of the engineered pathway (versus the native pathway) to the product synthesis. Fourth, the loss of catabolic energy due to cell maintenance (energy used for functions other than production of new cell components) and low P/O ratio (Phosphate/Oxygen Ratio) significantly reduces product yields. Therefore, 13C-metabolic flux analysis is needed to assess the influence of suboptimal energy metabolism on microbial productivity, and determine how ATP/NAD(P)H are partitioned among various cellular functions. Since product yield is a major determining factor in the commercialization of a microbial cell factory, we foresee that 13C-isotopic labeling experiments, even without performing extensive flux calculations, can play a valuable role in the development and verification of microbial cell factories.

  6. Quadrant analysis of turbulent pollution flux above the modelled street intersection

    NASA Astrophysics Data System (ADS)

    Kukačka, L.; Nosek, Š.; Kellnerová, R.; Jurčáková, K.; Jaňour, Z.

    2013-04-01

    The objective of this experimental study is to determine processes of a vertical turbulent pollution transport above the X-shaped street intersection in an idealised symmetric urban area for several approach flow directions. An experimental set-up for simultaneous measurement of the flow velocity and the tracer gas concentration in a high temporal resolution is assembled. Vertical turbulent scalar fluxes are computed from the measured data in a horizontal plane above the street intersection. The quadrant analysis was applied to the vertical turbulent pollution fluxes data. Events with dominant contribution to vertical turbulent pollution flux were detected. The mean duration, repetition frequency and the duration percentage were computed for these events. A strong influence of the approach flow direction on the the type of dominant events and their characteristics was resolved.

  7. Theoretical Analysis of Interferometer Wave Front Tilt and Fringe Radiant Flux on a Rectangular Photodetector

    PubMed Central

    Smith, Robert; Fuss, Franz Konstantin

    2013-01-01

    This paper is a theoretical analysis of mirror tilt in a Michelson interferometer and its effect on the radiant flux over the active area of a rectangular photodetector or image sensor pixel. It is relevant to sensor applications using homodyne interferometry where these opto-electronic devices are employed for partial fringe counting. Formulas are derived for radiant flux across the detector for variable location within the fringe pattern and with varying wave front angle. The results indicate that the flux is a damped sine function of the wave front angle, with a decay constant of the ratio of wavelength to detector width. The modulation amplitude of the dynamic fringe pattern reduces to zero at wave front angles that are an integer multiple of this ratio and the results show that the polarity of the radiant flux changes exclusively at these multiples. Varying tilt angle causes radiant flux oscillations under an envelope curve, the frequency of which is dependent on the location of the detector with the fringe pattern. It is also shown that a fringe count of zero can be obtained for specific photodetector locations and wave front angles where the combined effect of fringe contraction and fringe tilt can have equal and opposite effects. Fringe tilt as a result of a wave front angle of 0.05° can introduce a phase measurement difference of 16° between a photodetector/pixel located 20 mm and one located 100 mm from the optical origin. PMID:24018954

  8. Theoretical analysis of interferometer wave front tilt and fringe radiant flux on a rectangular photodetector.

    PubMed

    Smith, Robert; Fuss, Franz Konstantin

    2013-09-06

    This paper is a theoretical analysis of mirror tilt in a Michelson interferometer and its effect on the radiant flux over the active area of a rectangular photodetector or image sensor pixel. It is relevant to sensor applications using homodyne interferometry where these opto-electronic devices are employed for partial fringe counting. Formulas are derived for radiant flux across the detector for variable location within the fringe pattern and with varying wave front angle. The results indicate that the flux is a damped sine function of the wave front angle, with a decay constant of the ratio of wavelength to detector width. The modulation amplitude of the dynamic fringe pattern reduces to zero at wave front angles that are an integer multiple of this ratio and the results show that the polarity of the radiant flux changes exclusively at these multiples. Varying tilt angle causes radiant flux oscillations under an envelope curve, the frequency of which is dependent on the location of the detector with the fringe pattern. It is also shown that a fringe count of zero can be obtained for specific photodetector locations and wave front angles where the combined effect of fringe contraction and fringe tilt can have equal and opposite effects. Fringe tilt as a result of a wave front angle of 0.05° can introduce a phase measurement difference of 16° between a photodetector/pixel located 20 mm and one located 100 mm from the optical origin.

  9. Metabolic flux analysis with a comprehensive isotopomer model in Bacillus subtilis.

    PubMed

    Dauner, M; Bailey, J E; Sauer, U

    2001-09-01

    Fluxes in central carbon metabolism of a genetically engineered, riboflavin-producing Bacillus subtilis strain were investigated in glucose-limited chemostat cultures at low (0.11 h(-1)) and high (0.44 h(-1)) dilution rates. Using a mixture of 10% [U-(13)C] and 90% glucose labeled at natural abundance, (13)C-labeling experiments were carried out to provide additional information for metabolic flux balancing. The resulting labeling pattern in the proteinogenic amino acids were analyzed by two-dimensional [(13)C, (1)H] nuclear magnetic resonance (NMR) spectroscopy. To account rigorously for all available data from these experiments, we developed a comprehensive isotopomer model of B. subtilis central metabolism. Using this model, intracellular carbon net and exchange fluxes were estimated on the basis of validated physiological data and biomass composition in combination with 2D NMR data from 45 individual carbon atom spectra in the amino acids. Glucose catabolism proceeded primarily via glycolysis but pentose phosphate pathway fluxes increased with increasing growth rate. Moreover, significant back fluxes from the TCA cycle to the lower part of glycolysis via the gluconeogenic PEP carboxykinase were detected. The malic enzyme reaction, in contrast, was found to be inactive. A thorough statistical analysis was performed to prove the reliability of the isotopomer balance model and the obtained results. Specifically, a chi(2) test was applied to validate the model and the chi-square criterion was used to explore the sensitivity of model predictions to the experimental data.

  10. Combined analysis of neutron and photon flux measurements for the Jules Horowitz reactor core mapping

    SciTech Connect

    Fourmentel, D.; Villard, J. F.; Lyoussi, A.; Reynard-Carette, C.; Bignan, G.; Chauvin, J. P.; Gonnier, C.; Guimbal, P.; Malo, J. Y.; Carette, M.; Janulyte, A.; Merroun, O.; Brun, J.; Zerega, Y.; Andre, J.

    2011-07-01

    We study the combined analysis of nuclear measurements to improve the knowledge of the irradiation conditions in the experimental locations of the future Jules Horowitz Reactor (JHR). The goal of the present work is to measure more accurately neutron flux, photon flux and nuclear heating in the reactor. In a Material Testing Reactor (MTR), nuclear heating is a crucial parameter to design the experimental devices to be irradiated in harsh nuclear conditions. This parameter drives the temperature of the devices and of the samples. The numerical codes can predict this parameter but in-situ measurements are necessary to reach the expected accuracy. For this reason, one objective of the IN-CORE program [1] is to study the combined measurements of neutron and photon flux and their cross advanced interpretation. It should be reminded that both neutron and photon sensors are not totally selective as their signals are due to neutron and photon interactions. We intend to measure the neutron flux by three different kinds of sensors (Uranium Fission chamber, Plutonium Fission chamber and Self Powered Neutron Detector), the photon flux by two different sensors (Ionization chamber and Self Powered Gamma Detector) and the nuclear heating by two different ones (Differential calorimeter and Gamma Thermometer). For the same parameter, we expect that the use of different kinds of sensors will allow a better estimation of the aimed parameter by mixing different spectrum responses and different neutron and gamma contributions. An experimental test called CARMEN-1 is scheduled in OSIRIS reactor (CEA Saclay - France) at the end of 2011, with the goal to map irradiation locations in the reactor reflector to get a first validation of the analysis model. This article focuses on the sensor selection for CARMEN-1 experiment and to the way to link neutron and photon flux measurements in view to reduce their uncertainties but also to better assess the neutron and photon contributions to nuclear

  11. Efficient Modeling of MS/MS Data for Metabolic Flux Analysis

    PubMed Central

    Tepper, Naama; Shlomi, Tomer

    2015-01-01

    Metabolic flux analysis (MFA) is a widely used method for quantifying intracellular metabolic fluxes. It works by feeding cells with isotopic labeled nutrients, measuring metabolite isotopic labeling, and computationally interpreting the measured labeling data to estimate flux. Tandem mass-spectrometry (MS/MS) has been shown to be useful for MFA, providing positional isotopic labeling data. Specifically, MS/MS enables the measurement of a metabolite tandem mass-isotopomer distribution, representing the abundance in which certain parent and product fragments of a metabolite have different number of labeled atoms. However, a major limitation in using MFA with MS/MS data is the lack of a computationally efficient method for simulating such isotopic labeling data. Here, we describe the tandemer approach for efficiently computing metabolite tandem mass-isotopomer distributions in a metabolic network, given an estimation of metabolic fluxes. This approach can be used by MFA to find optimal metabolic fluxes, whose induced metabolite labeling patterns match tandem mass-isotopomer distributions measured by MS/MS. The tandemer approach is applied to simulate MS/MS data in a small-scale metabolic network model of mammalian methionine metabolism and in a large-scale metabolic network model of E. coli. It is shown to significantly improve the running time by between two to three orders of magnitude compared to the state-of-the-art, cumomers approach. We expect the tandemer approach to promote broader usage of MS/MS technology in metabolic flux analysis. Implementation is freely available at www.cs.technion.ac.il/~tomersh/methods.html PMID:26230524

  12. Extreme relativistic electron fluxes at geosynchronous orbit: Analysis of GOES E > 2 MeV electrons

    NASA Astrophysics Data System (ADS)

    Meredith, Nigel P.; Horne, Richard B.; Isles, John D.; Rodriguez, Juan V.

    2015-03-01

    Relativistic electrons (E > 1 MeV) cause internal charging on satellites and are an important space weather hazard. A key requirement in space weather research concerns extreme events and knowledge of the largest flux expected to be encountered over the lifetime of a satellite mission. This is interesting both from scientific and practical points of view since satellite operators, engineers, and the insurance industry need this information to better evaluate the effects of extreme events on their spacecraft. Here we conduct an extreme value analysis of daily averaged E > 2 MeV electron fluxes from the Geostationary Operational Environmental Satellites (GOES) during the 19.5 year period from 1 January 1995 to 30 June 2014. We find that the daily averaged flux measured at GOES West is typically a factor of about 2.5 higher than that measured at GOES East, and we conduct independent analyses for these two locations. The 1 in 10, 1 in 50, and 1 in 100 year daily averaged E > 2 MeV electron fluxes at GOES West are 1.84 ×105, 5.00 ×105, and 7.68 ×105 cm-2 s-1 sr-1, respectively. The corresponding fluxes at GOES East are 6.53 ×104, 1.98 ×105, and 3.25 ×105 cm-2 s-1 sr-1, respectively. The largest fluxes seen during the 19.5 year period on 29 July 2004 were particularly extreme and were seen by satellites at GOES West and GOES East. The extreme value analysis suggests that this event was a 1 in 50 year event.

  13. Analysis of 13C labeling enrichment in microbial culture applying metabolic tracer experiments using gas chromatography-combustion-isotope ratio mass spectrometry.

    PubMed

    Heinzle, Elmar; Yuan, Yongbo; Kumar, Sathish; Wittmann, Christoph; Gehre, Matthias; Richnow, Hans-Herrmann; Wehrung, Patrick; Adam, Pierre; Albrecht, Pierre

    2008-09-15

    The applicability of gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS) for the quantification of 13C enrichment of proteinogenic amino acids in metabolic tracer experiments was evaluated. Measurement of the 13C enrichment of proteinogenic amino acids from cell hydrolyzates of Corynebacterium glutamicum growing on different mixtures containing between 0.5 and 10% [1-13C]glucose shows the significance of kinetic isotope effects in metabolic flux studies at low degree of labeling. We developed a method to calculate the 13C enrichment. The approach to correct for these effects in metabolic flux studies using delta13C measurement by GC-C-IRMS uses two parallel experiments applying substrate with natural abundance and 13C-enriched tracer substrate, respectively. The fractional enrichment obtained in natural substrate is subtracted from that of the enriched one. Tracer studies with C. glutamicum resulted in a statistically identical relative fractional enrichment of 13C in proteinogenic amino acids over the whole range of applied concentrations of [1-13C]glucose. The current findings indicate a great potential of GC-C-IRMS for labeling quantification in 13C metabolic flux analysis with low labeling degree of tracer substrate directly in larger scale bioreactors.

  14. Analysis of the PKT correction for direct CO2 flux measurements over the ocean

    NASA Astrophysics Data System (ADS)

    Landwehr, S.; Miller, S. D.; Smith, M. J.; Saltzman, E. S.; Ward, B.

    2013-10-01

    Eddy covariance measurements of air-sea CO2 fluxes can be affected by cross-sensitivities of the CO2 measurement to water vapour, resulting in order-of-magnitude biases. Well established causes for these biases are (i) cross-sensitivity of the broadband non-dispersive infrared sensors due to band-broadening and spectral overlap (commercial sensors typically correct for this) and (ii) the effect of air density fluctuations (removed by determining the CO2 mixing ratio respective to dry air). However, another bias related to water vapour fluctuations has recently been observed with open-path sensors, and was attributed to sea salt build-up and water films on sensor optics. Two very different approaches have been used to deal with these water vapour-related biases. Miller et al. (2010) employed a membrane drier to physically eliminate 97% of the water vapour fluctuations in the sample air before it enters the gas analyser. Prytherch et al. (2010a) on the other hand, employed the empirical (Peter K. Taylor, PKT) post-processing correction to correct open-path sensor data. In this paper, we test these methods side by side using data from the Surface Ocean Aerosol Production (SOAP) experiment in the Southern Ocean. The air-sea CO2 flux was directly measured with four closed-path analysers, two of which were positioned down-stream of a membrane dryer. The CO2 fluxes from the two dried gas analysers matched each other and were in general agreement with common parametrisations. The flux estimates from the un-dried sensors agreed with the dried sensors only during periods with low latent heat flux (≤ 7 W m-2). When latent heat flux was higher, CO2 flux estimates from the un-dried sensors exhibited large scatter and an order-of magnitude bias. We applied the PKT correction to the flux data from the un-dried analysers and found that it did not remove the bias when compared to the data from the dried gas analyser. Our detailed analysis of the correction algorithm reveals

  15. Leonid Storm Flux Analysis From One Leonid MAC Video AL50R

    NASA Technical Reports Server (NTRS)

    Gural, Peter S.; Jenniskens, Peter; DeVincenzi, Donald L. (Technical Monitor)

    2000-01-01

    A detailed meteor flux analysis is presented of a seventeen-minute portion of one videotape, collected on November 18, 1999, during the Leonid Multi-instrument Aircraft Campaign. The data was recorded around the peak of the Leonid meteor storm using an intensified CCD camera pointed towards the low southern horizon. Positions of meteors on the sky were measured. These measured meteor distributions were compared to a Monte Carlo simulation, which is a new approach to parameter estimation for mass ratio and flux. Comparison of simulated flux versus observed flux levels, seen between 1:50:00 and 2:06:41 UT, indicate a magnitude population index of r = 1.8 +/- 0.1 and mass ratio of s = 1.64 +/- 0.06. The average spatial density of the material contributing to the Leonid storm peak is measured at 0.82 +/- 0.19 particles per square kilometer per hour for particles of at least absolute visual magnitude +6.5. Clustering analysis of the arrival times of Leonids impacting the earth's atmosphere over the total observing interval shows no enhancement or clumping down to time scales of the video frame rate. This indicates a uniformly random temporal distribution of particles in the stream encountered during the 1999 epoch. Based on the observed distribution of meteors on the sky and the model distribution, recommendations am made for the optimal pointing directions for video camera meteor counts during future ground and airborne missions.

  16. Bayesian flux balance analysis applied to a skeletal muscle metabolic model.

    PubMed

    Heino, Jenni; Tunyan, Knarik; Calvetti, Daniela; Somersalo, Erkki

    2007-09-01

    In this article, the steady state condition for the multi-compartment models for cellular metabolism is considered. The problem is to estimate the reaction and transport fluxes, as well as the concentrations in venous blood when the stoichiometry and bound constraints for the fluxes and the concentrations are given. The problem has been addressed previously by a number of authors, and optimization-based approaches as well as extreme pathway analysis have been proposed. These approaches are briefly discussed here. The main emphasis of this work is a Bayesian statistical approach to the flux balance analysis (FBA). We show how the bound constraints and optimality conditions such as maximizing the oxidative phosphorylation flux can be incorporated into the model in the Bayesian framework by proper construction of the prior densities. We propose an effective Markov chain Monte Carlo (MCMC) scheme to explore the posterior densities, and compare the results with those obtained via the previously studied linear programming (LP) approach. The proposed methodology, which is applied here to a two-compartment model for skeletal muscle metabolism, can be extended to more complex models. PMID:17568615

  17. Hands-on metabolism analysis of complex biochemical networks using elementary flux modes.

    PubMed

    Schäuble, Sascha; Schuster, Stefan; Kaleta, Christoph

    2011-01-01

    The aim of this chapter is to discuss the basic principles and reasoning behind elementary flux mode analysis (EFM analysis)--an important tool for the analysis of metabolic networks. We begin with a short introduction into metabolic pathway analysis and subsequently outline in detail fundamentals of EFM analysis by way of a small example network. We discuss issues arising in the reconstruction of metabolic networks required for EFM analysis and how they can be circumvented. Subsequently, we analyze a more elaborate example network representing photosynthate metabolism. Finally, we give an overview of applications of EFM analysis in biotechnology and other fields and discuss issues arising when applying methods from metabolic pathway analysis to genome-scale metabolic networks.

  18. High-throughput data pipelines for metabolic flux analysis in plants.

    PubMed

    Poskar, C Hart; Huege, Jan; Krach, Christian; Shachar-Hill, Yair; Junker, Björn H

    2014-01-01

    In this chapter we illustrate the methodology for high-throughput metabolic flux analysis. Central to this is developing an end to end data pipeline, crucial for integrating the wet lab experiments and analytics, combining hardware and software automation, and standardizing data representation providing importers and exporters to support third party tools. The use of existing software at the start, data extraction from the chromatogram, and the end, MFA analysis, allows for the most flexibility in this workflow. Developing iMS2Flux provided a standard, extensible, platform independent tool to act as the "glue" between these end points. Most importantly this tool can be easily adapted to support different data formats, data verification and data correction steps allowing it to be central to managing the data necessary for high-throughput MFA. An additional tool was needed to automate the MFA software and in particular to take advantage of the course grained parallel nature of high-throughput analysis and available high performance computing facilities.In combination these methods show the development of high-throughput pipelines that allow metabolic flux analysis to join as a full member of the omics family.

  19. Impact of water use efficiency on eddy covariance flux partitioning using correlation structure analysis

    NASA Astrophysics Data System (ADS)

    Anderson, Ray; Skaggs, Todd; Alfieri, Joseph; Kustas, William; Wang, Dong; Ayars, James

    2016-04-01

    Partitioned land surfaces fluxes (e.g. evaporation, transpiration, photosynthesis, and ecosystem respiration) are needed as input, calibration, and validation data for numerous hydrological and land surface models. However, one of the most commonly used techniques for measuring land surface fluxes, Eddy Covariance (EC), can directly measure net, combined water and carbon fluxes (evapotranspiration and net ecosystem exchange/productivity). Analysis of the correlation structure of high frequency EC time series (hereafter flux partitioning or FP) has been proposed to directly partition net EC fluxes into their constituent components using leaf-level water use efficiency (WUE) data to separate stomatal and non-stomatal transport processes. FP has significant logistical and spatial representativeness advantages over other partitioning approaches (e.g. isotopic fluxes, sap flow, microlysimeters), but the performance of the FP algorithm is reliant on the accuracy of the intercellular CO2 (ci) concentration used to parameterize WUE for each flux averaging interval. In this study, we tested several parameterizations for ci as a function of atmospheric CO2 (ca), including (1) a constant ci/ca ratio for C3 and C4 photosynthetic pathway plants, (2) species-specific ci/ca-Vapor Pressure Deficit (VPD) relationships (quadratic and linear), and (3) generalized C3 and C4 photosynthetic pathway ci/ca-VPD relationships. We tested these ci parameterizations at three agricultural EC towers from 2011-present in C4 and C3 crops (sugarcane - Saccharum officinarum L. and peach - Prunus persica), and validated again sap-flow sensors installed at the peach site. The peach results show that the species-specific parameterizations driven FP algorithm came to convergence significantly more frequently (~20% more frequently) than the constant ci/ca ratio or generic C3-VPD relationship. The FP algorithm parameterizations with a generic VPD relationship also had slightly higher transpiration (5 Wm-2

  20. An analysis of turbulent sensible heat fluxes within a heterogeneous black spruce boreal forest in Alaska

    NASA Astrophysics Data System (ADS)

    Starkenburg, Derek

    Turbulent sensible heat fluxes within the heterogeneous canopy of a black spruce boreal forest in Interior Alaska are evaluated at three different scales in order to assess their spatial variability, and to determine the feasibility of upscaling locally measured flux values to the landscape scale for modeling applications and climate studies. The first evaluation is performed locally at a single micrometeorological tower in an area of the boreal forest with a mean canopy height of 4.7 m. The data were taken across winter, spring and summer of 2012 from two sonic anemometers, one below the canopy at 3 m above ground, and one above the canopy at 12 m above ground. A multiresolution analysis is used to isolate coherent structures from the turbulent temperature time series at both instruments. When mean global statistics of coherent structures are analyzed at the two levels independently, results show an average of 8 structures per period, a mean duration of 85 s, and a mean sensible heat flux contribution of 48%. A spectral version of the Stokes parameters is applied to the turbulent horizontal wind components to show that 31% of the coherent turbulent structures detected at 12 m, and 13% at 3 m, may be complicated by canopy waves due to the prevalence of stable flows at this high latitude location. The second evaluation quantifies differences in turbulent sensible heat fluxes horizontally between two micrometeorological towers 600 m apart, one in a denser canopy (DC) and the other in a sparser canopy (SC), but under approximately similar atmospheric boundary layer conditions. Results show that SC is ˜ 3 °C cooler and more stably stratified than DC during nighttime. This suggests that changes in the height and density of the canopy impact local temperature and stability regimes. Most importantly, the sensible heat flux at DC is greater during midday periods, with that difference exceeding 30% of the measured flux and over 30 W m-2 in magnitude more than 60% of the

  1. Metabolic Flux Analysis -application in plant metabolic modelling for advanced life support systems

    NASA Astrophysics Data System (ADS)

    Sasidharan L, Swathy; Hezard, Pauline; Poughon, Laurent; Dussap, Claude-Gilles

    Plants have an important role in providing food and fresh oxygen for humans in a closed environment during long duration missions to Mars or Moon. Also, plants play an important role for recycling water. Thus, plant modelling (crop composition, yield prediction and the responses to its environment within the closed loop) gets much attention in the development of closed ecological life support systems. In order to achieve this, metabolic flux computation methods accounting for reactions stoichiometry and chemical energy conservation obtained from metabolic pathways description of different plant parts are required. The basic ideas of metabolic modelling and their application to various plant parts will be discussed. Metabolic systems consist of a set of metabolites and reactions that consume or produce them. The metabolic pathways within a metabolic network for each plant part or sub level are characterised and the metabolic fluxes, defined as the amount of converted metabolite per unit time and per unit mass of tissue (or per plant part), can be calculated. MBA (Metabolic flux analysis) which is a constraint based approach is effective at calculating flux distributions through bio-chemical networks. This methodology can be applied to several plants' growth situations. In terms of space appli-cations, it is shown how this approach could bring valuable tools for assessing and quantifying the effects of the environment of a close system on growth rate and conversion yields.

  2. The avian cell line AGE1.CR.pIX characterized by metabolic flux analysis

    PubMed Central

    2014-01-01

    Background In human vaccine manufacturing some pathogens such as Modified Vaccinia Virus Ankara, measles, mumps virus as well as influenza viruses are still produced on primary material derived from embryonated chicken eggs. Processes depending on primary cell culture, however, are difficult to adapt to modern vaccine production. Therefore, we derived previously a continuous suspension cell line, AGE1.CR.pIX, from muscovy duck and established chemically-defined media for virus propagation. Results To better understand vaccine production processes, we developed a stoichiometric model of the central metabolism of AGE1.CR.pIX cells and applied flux variability and metabolic flux analysis. Results were compared to literature dealing with mammalian and insect cell culture metabolism focusing on the question whether cultured avian cells differ in metabolism. Qualitatively, the observed flux distribution of this avian cell line was similar to distributions found for mammalian cell lines (e.g. CHO, MDCK cells). In particular, glucose was catabolized inefficiently and glycolysis and TCA cycle seem to be only weakly connected. Conclusions A distinguishing feature of the avian cell line is that glutaminolysis plays only a minor role in energy generation and production of precursors, resulting in low extracellular ammonia concentrations. This metabolic flux study is the first for a continuous avian cell line. It provides a basis for further metabolic analyses to exploit the biotechnological potential of avian and vertebrate cell lines and to develop specific optimized cell culture processes, e.g. vaccine production processes. PMID:25077436

  3. Extensive exometabolome analysis reveals extended overflow metabolism in various microorganisms

    PubMed Central

    2012-01-01

    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. PMID:22963408

  4. The relevance of particle flux monitors in accelerator-based activation analysis

    SciTech Connect

    Segebade, Chr.; Maimaitimin, M.; Sun Zaijing

    2013-04-19

    One of the most critical parameters in activation analysis is the flux density of the activating radiation, its spatial distribution in particular. The validity of the basic equation for calculating the activity induced to the exposed item depends upon the fulfilment of several conditions, the most relevant of them being equal doses of incident activating radiation received by the unknown sample, the calibration material and the reference material, respectively. This requirement is most problematic if accelerator-produced radiation is used for activation. Whilst nuclear research reactors usually are equipped with exposure positions that provide fairly homogenous activation fields for thermal neutron activation analysis accelerator-generated particle beams (neutrons, photons, charged particles) usually exhibit axial and, in particular, sharp radial flux gradients. Different experimental procedures have been developed to fulfil the condition mentioned above. In this paper, three variants of the application of flux monitors in photon activation analysis are discussed (external monitor, additive and inherent internal monitor). Experiments have indicated that the latter technique yields highest quality of the analytical results.

  5. Extraction, purification, methylation and GC-MS analysis of short-chain carboxylic acids for metabolic flux analysis.

    PubMed

    Tivendale, Nathan D; Jewett, Erin M; Hegeman, Adrian D; Cohen, Jerry D

    2016-08-15

    Dynamic metabolic flux analysis requires efficient and effective methods for extraction, purification and analysis of a plethora of naturally-occurring compounds. One area of metabolism that would be highly informative to study using metabolic flux analysis is the tricarboxylic acid (TCA) cycle, which consists of short-chain carboxylic acids. Here, we describe a newly-developed method for extraction, purification, derivatization and analysis of short-chain carboxylic acids involved in the TCA cycle. The method consists of snap-freezing the plant material, followed by maceration and a 12-15h extraction at -80 °C. The extracts are then subject to reduction (to stabilize β-keto acids), purified by strong anion exchange solid phase extraction and methylated with methanolic HCl. This method could also be readily adapted to quantify many other short-chain carboxylic acids.

  6. Extraction, purification, methylation and GC-MS analysis of short-chain carboxylic acids for metabolic flux analysis.

    PubMed

    Tivendale, Nathan D; Jewett, Erin M; Hegeman, Adrian D; Cohen, Jerry D

    2016-08-15

    Dynamic metabolic flux analysis requires efficient and effective methods for extraction, purification and analysis of a plethora of naturally-occurring compounds. One area of metabolism that would be highly informative to study using metabolic flux analysis is the tricarboxylic acid (TCA) cycle, which consists of short-chain carboxylic acids. Here, we describe a newly-developed method for extraction, purification, derivatization and analysis of short-chain carboxylic acids involved in the TCA cycle. The method consists of snap-freezing the plant material, followed by maceration and a 12-15h extraction at -80 °C. The extracts are then subject to reduction (to stabilize β-keto acids), purified by strong anion exchange solid phase extraction and methylated with methanolic HCl. This method could also be readily adapted to quantify many other short-chain carboxylic acids. PMID:27348709

  7. Uncertainty analysis of the Operational Simplified Surface Energy Balance (SSEBop) model at multiple flux tower sites

    NASA Astrophysics Data System (ADS)

    Chen, Mingshi; Senay, Gabriel B.; Singh, Ramesh K.; Verdin, James P.

    2016-05-01

    Evapotranspiration (ET) is an important component of the water cycle - ET from the land surface returns approximately 60% of the global precipitation back to the atmosphere. ET also plays an important role in energy transport among the biosphere, atmosphere, and hydrosphere. Current regional to global and daily to annual ET estimation relies mainly on surface energy balance (SEB) ET models or statistical and empirical methods driven by remote sensing data and various climatological databases. These models have uncertainties due to inevitable input errors, poorly defined parameters, and inadequate model structures. The eddy covariance measurements on water, energy, and carbon fluxes at the AmeriFlux tower sites provide an opportunity to assess the ET modeling uncertainties. In this study, we focused on uncertainty analysis of the Operational Simplified Surface Energy Balance (SSEBop) model for ET estimation at multiple AmeriFlux tower sites with diverse land cover characteristics and climatic conditions. The 8-day composite 1-km MODerate resolution Imaging Spectroradiometer (MODIS) land surface temperature (LST) was used as input land surface temperature for the SSEBop algorithms. The other input data were taken from the AmeriFlux database. Results of statistical analysis indicated that the SSEBop model performed well in estimating ET with an R2 of 0.86 between estimated ET and eddy covariance measurements at 42 AmeriFlux tower sites during 2001-2007. It was encouraging to see that the best performance was observed for croplands, where R2 was 0.92 with a root mean square error of 13 mm/month. The uncertainties or random errors from input variables and parameters of the SSEBop model led to monthly ET estimates with relative errors less than 20% across multiple flux tower sites distributed across different biomes. This uncertainty of the SSEBop model lies within the error range of other SEB models, suggesting systematic error or bias of the SSEBop model is within the

  8. Uncertainty analysis of the Operational Simplified Surface Energy Balance (SSEBop) model at multiple flux tower sites

    USGS Publications Warehouse

    Chen, Mingshi; Senay, Gabriel B.; Singh, Ramesh K.; Verdin, James P.

    2016-01-01

    Evapotranspiration (ET) is an important component of the water cycle – ET from the land surface returns approximately 60% of the global precipitation back to the atmosphere. ET also plays an important role in energy transport among the biosphere, atmosphere, and hydrosphere. Current regional to global and daily to annual ET estimation relies mainly on surface energy balance (SEB) ET models or statistical and empirical methods driven by remote sensing data and various climatological databases. These models have uncertainties due to inevitable input errors, poorly defined parameters, and inadequate model structures. The eddy covariance measurements on water, energy, and carbon fluxes at the AmeriFlux tower sites provide an opportunity to assess the ET modeling uncertainties. In this study, we focused on uncertainty analysis of the Operational Simplified Surface Energy Balance (SSEBop) model for ET estimation at multiple AmeriFlux tower sites with diverse land cover characteristics and climatic conditions. The 8-day composite 1-km MODerate resolution Imaging Spectroradiometer (MODIS) land surface temperature (LST) was used as input land surface temperature for the SSEBop algorithms. The other input data were taken from the AmeriFlux database. Results of statistical analysis indicated that the SSEBop model performed well in estimating ET with an R2 of 0.86 between estimated ET and eddy covariance measurements at 42 AmeriFlux tower sites during 2001–2007. It was encouraging to see that the best performance was observed for croplands, where R2 was 0.92 with a root mean square error of 13 mm/month. The uncertainties or random errors from input variables and parameters of the SSEBop model led to monthly ET estimates with relative errors less than 20% across multiple flux tower sites distributed across different biomes. This uncertainty of the SSEBop model lies within the error range of other SEB models, suggesting systematic error or bias of the SSEBop model is within

  9. k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design

    PubMed Central

    Chowdhury, Anupam; Zomorrodi, Ali R.; Maranas, Costas D.

    2014-01-01

    Computational strain design protocols aim at the system-wide identification of intervention strategies for the enhanced production of biochemicals in microorganisms. Existing approaches relying solely on stoichiometry and rudimentary constraint-based regulation overlook the effects of metabolite concentrations and substrate-level enzyme regulation while identifying metabolic interventions. In this paper, we introduce k-OptForce, which integrates the available kinetic descriptions of metabolic steps with stoichiometric models to sharpen the prediction of intervention strategies for improving the bio-production of a chemical of interest. It enables identification of a minimal set of interventions comprised of both enzymatic parameter changes (for reactions with available kinetics) and reaction flux changes (for reactions with only stoichiometric information). Application of k-OptForce to the overproduction of L-serine in E. coli and triacetic acid lactone (TAL) in S. cerevisiae revealed that the identified interventions tend to cause less dramatic rearrangements of the flux distribution so as not to violate concentration bounds. In some cases the incorporation of kinetic information leads to the need for additional interventions as kinetic expressions render stoichiometry-only derived interventions infeasible by violating concentration bounds, whereas in other cases the kinetic expressions impart flux changes that favor the overproduction of the target product thereby requiring fewer direct interventions. A sensitivity analysis on metabolite concentrations shows that the required number of interventions can be significantly affected by changing the imposed bounds on metabolite concentrations. Furthermore, k-OptForce was capable of finding non-intuitive interventions aiming at alleviating the substrate-level inhibition of key enzymes in order to enhance the flux towards the product of interest, which cannot be captured by stoichiometry-alone analysis. This study paves

  10. Comprehensive Analysis of Convective Heat Transfer in Parallel Plate Microchannel with Viscous Dissipation and Constant Heat Flux Boundary Conditions

    NASA Astrophysics Data System (ADS)

    Kushwaha, Hari Mohan; Sahu, Santosh Kumar

    2016-06-01

    This paper reports the hydrodynamically and thermally fully developed, laminar, incompressible, forced convective heat transfer characteristics of gaseous flows through a parallel plate microchannel with different constant heat flux boundary conditions. The first order velocity slip and viscous dissipation effects are considered in the analysis. Here, three different thermal boundary conditions such as: both plates kept at different constant heat fluxes, both plates kept at equal constant heat fluxes and one plate kept at constant heat flux and other one insulated are considered for the analysis. The deviation in Nusselt number between the model that considers both first order velocity slip and temperature jump and the one that considers only velocity slip is reported. Also, the effect of various heat flux ratios on the Nusselt number is reported in this analysis. In addition, the deviation in Nusselt number between first and second order slip model is discussed in this study.

  11. Methane flux in non-wetland soils in response to nitrogen addition: a meta-analysis.

    PubMed

    Aronson, E L; Helliker, B R

    2010-11-01

    The controls on methane (CH4) flux into and out of soils are not well understood. Environmental variables including temperature, precipitation, and nitrogen (N) status can have strong effects on the magnitude and direction (e.g., uptake vs. release) of CH4 flux. To better understand the interactions between CH4-cycling microorganisms and N in the non-wetland soil system, a meta-analysis was performed on published literature comparing CH4 flux in N amended and matched control plots. An appropriate study index was developed for this purpose. It was found that smaller amounts of N tended to stimulate CH4 uptake while larger amounts tended to inhibit uptake by the soil. When all other variables were accounted for, the switch occurred at 100 kg N x ha(-1) x yr(-1). Managed land and land with a longer duration of fertilization showed greater inhibition of CH4 uptake with added N. These results support the hypotheses that large amounts of available N can inhibit methanotrophy, but also that methanotrophs in upland soils can be N limited in their consumption of CH4 from the atmosphere. There were interactions between other variables and N addition on the CH4 flux response: lower temperature and, to a lesser extent, higher precipitation magnified the inhibition of CH4 uptake due to N addition. Several mechanisms that may cause these trends are discussed, but none could be conclusively supported with this approach. Further controlled and in situ study should be undertaken to isolate the correct mechanism(s) responsible and to model upland CH4 flux. PMID:21141185

  12. Analysis of a Multi-Machine Database on Divertor Heat Fluxes

    NASA Astrophysics Data System (ADS)

    Makowski, M. A.

    2011-10-01

    A coordinated effort to measure divertor heat flux characteristics in fully attached, similarly shaped H-mode plasmas on C-Mod, DIII-D and NSTX was carried out in 2010 in order to construct a predictive scaling relation applicable to next step devices including ITER, FNSF, and DEMO. Few published scaling laws are available and those that have been published were obtained under widely varying conditions and divertor geometries, leading to conflicting predictions for this critically important quantity. This study was designed to overcome these deficiencies. Corresponding plasma parameters were systematically varied in each tokamak, resulting in a combined data set in which Ip varies by a factor 3, Bt varies by a factor of 14.5, and major radius varies by a factor of 2.6. The derived scaling relation consistently predicts narrower heat flux widths than relations currently in use. Analysis of the combined data set reveals that the primary dependence of the parallel heat flux width is robustly inverse with Ip. All three tokamaks independently demonstrate this dependence. The midplane SOL profiles in DIII-D are also found to steepen with higher Ip, similar to the divertor heat flux profiles. Weaker dependencies on the toroidal field and normalized Greenwald density, fGW, are also found, but vary across devices and with the measure of the heat flux width used, either FWHM or integral width. In the combined data set, the strongest size scaling is with minor radius resulting in an approximately linear dependence on a /Ip . This suggests a scaling correlated with the inverse of the poloidal field, as would be expected for critical gradient or drift-based transport. Supported by the US DOE under DE-AC52-07NA27344 and DE-FC02-04ER54698.

  13. Some advance on the comprehension of SR analysis for estimating the flux of a scalar

    NASA Astrophysics Data System (ADS)

    Castellví, Dr

    2009-04-01

    In agronomy, the eddy covariance, EC, method likely is the preferred for measuring surface scalar fluxes. For latent heat flux, however, weighing lysimeters maybe preferred in agriculture, but they are rarely affordable and not portable. The dissipation method, DM, is considered the most reliable technique for measuring scalar fluxes over open water because instrument motion contaminates the EC measurements. The main advantage of DM over EC is that it is less sensitive to low frequency instrument platform motions (such as ship and buoys), sensor alignment, precise orientation and stringent steadiness in the mean meteorological conditions (Fairall and Larsen, 1986; Kader, 1992; Edson and Fairall, 1998). Over land, keeping in mind that the EC and DM methods require the same measurements for scalar flux measurement, the DM has several disadvantages versus the EC. Direct measurement of the scalar variance dissipation rate, VDR, requires to capture eddies in the Kolmogorov's microscale (thus scalar time series measured at frequencies in the order of kHz are needed). Therefore, it is not practical. Indirect methods to estimate VDR (such as spectral analysis and second or third order structure functions) requires implementing iterative methods involving similarity relationships that are not well established (Hsieh and Katul, 1997; Castellvi and Snyder, 2008). Currently, there is ample evidence that the DM as explained in traditional micrometeorological books (such as, Panofsky and Dutton, 1984; Brutsaert, 1988; Kaimal and Finnigan; 1994) is, in general, not correct. Accordingly, it likely explains why DM is typically omitted in revisits of micrometeorological methods for estimating scalar fluxes in agronomy. Within the last decade, over some agricultural surfaces, evidence has been shown on the advantages over other micrometeorological methods and the reliability (i.e., close performance to the EC method) of Surface Renewal, SR, theory in conjunction with the Analysis of

  14. #FluxFlow: Visual Analysis of Anomalous Information Spreading on Social Media.

    PubMed

    Zhao, Jian; Cao, Nan; Wen, Zhen; Song, Yale; Lin, Yu-Ru; Collins, Christopher

    2014-12-01

    We present FluxFlow, an interactive visual analysis system for revealing and analyzing anomalous information spreading in social media. Everyday, millions of messages are created, commented, and shared by people on social media websites, such as Twitter and Facebook. This provides valuable data for researchers and practitioners in many application domains, such as marketing, to inform decision-making. Distilling valuable social signals from the huge crowd's messages, however, is challenging, due to the heterogeneous and dynamic crowd behaviors. The challenge is rooted in data analysts' capability of discerning the anomalous information behaviors, such as the spreading of rumors or misinformation, from the rest that are more conventional patterns, such as popular topics and newsworthy events, in a timely fashion. FluxFlow incorporates advanced machine learning algorithms to detect anomalies, and offers a set of novel visualization designs for presenting the detected threads for deeper analysis. We evaluated FluxFlow with real datasets containing the Twitter feeds captured during significant events such as Hurricane Sandy. Through quantitative measurements of the algorithmic performance and qualitative interviews with domain experts, the results show that the back-end anomaly detection model is effective in identifying anomalous retweeting threads, and its front-end interactive visualizations are intuitive and useful for analysts to discover insights in data and comprehend the underlying analytical model. PMID:26356891

  15. #FluxFlow: Visual Analysis of Anomalous Information Spreading on Social Media.

    PubMed

    Zhao, Jian; Cao, Nan; Wen, Zhen; Song, Yale; Lin, Yu-Ru; Collins, Christopher

    2014-12-01

    We present FluxFlow, an interactive visual analysis system for revealing and analyzing anomalous information spreading in social media. Everyday, millions of messages are created, commented, and shared by people on social media websites, such as Twitter and Facebook. This provides valuable data for researchers and practitioners in many application domains, such as marketing, to inform decision-making. Distilling valuable social signals from the huge crowd's messages, however, is challenging, due to the heterogeneous and dynamic crowd behaviors. The challenge is rooted in data analysts' capability of discerning the anomalous information behaviors, such as the spreading of rumors or misinformation, from the rest that are more conventional patterns, such as popular topics and newsworthy events, in a timely fashion. FluxFlow incorporates advanced machine learning algorithms to detect anomalies, and offers a set of novel visualization designs for presenting the detected threads for deeper analysis. We evaluated FluxFlow with real datasets containing the Twitter feeds captured during significant events such as Hurricane Sandy. Through quantitative measurements of the algorithmic performance and qualitative interviews with domain experts, the results show that the back-end anomaly detection model is effective in identifying anomalous retweeting threads, and its front-end interactive visualizations are intuitive and useful for analysts to discover insights in data and comprehend the underlying analytical model.

  16. (13)C MRS and LC-MS Flux Analysis of Tumor Intermediary Metabolism.

    PubMed

    Shestov, Alexander A; Lee, Seung-Cheol; Nath, Kavindra; Guo, Lili; Nelson, David S; Roman, Jeffrey C; Leeper, Dennis B; Wasik, Mariusz A; Blair, Ian A; Glickson, Jerry D

    2016-01-01

    We present the first validated metabolic network model for analysis of flux through key pathways of tumor intermediary metabolism, including glycolysis, the oxidative and non-oxidative arms of the pentose pyrophosphate shunt, the TCA cycle as well as its anaplerotic pathways, pyruvate-malate shuttling, glutaminolysis, and fatty acid biosynthesis and oxidation. The model that is called Bonded Cumomer Analysis for application to (13)C magnetic resonance spectroscopy ((13)C MRS) data and Fragmented Cumomer Analysis for mass spectrometric data is a refined and efficient form of isotopomer analysis that can readily be expanded to incorporate glycogen, phospholipid, and other pathways thereby encompassing all the key pathways of tumor intermediary metabolism. Validation was achieved by demonstrating agreement of experimental measurements of the metabolic rates of oxygen consumption, glucose consumption, lactate production, and glutamate pool size with independent measurements of these parameters in cultured human DB-1 melanoma cells. These cumomer models have been applied to studies of DB-1 melanoma and DLCL2 human diffuse large B-cell lymphoma cells in culture and as xenografts in nude mice at 9.4 T. The latter studies demonstrate the potential translation of these methods to in situ studies of human tumor metabolism by MRS with stable (13)C isotopically labeled substrates on instruments operating at high magnetic fields (≥7 T). The melanoma studies indicate that this tumor line obtains 51% of its ATP by mitochondrial metabolism and 49% by glycolytic metabolism under both euglycemic (5 mM glucose) and hyperglycemic conditions (26 mM glucose). While a high level of glutamine uptake is detected corresponding to ~50% of TCA cycle flux under hyperglycemic conditions, and ~100% of TCA cycle flux under euglycemic conditions, glutaminolysis flux and its contributions to ATP synthesis were very small. Studies of human lymphoma cells demonstrated that inhibition of

  17. 13C MRS and LC–MS Flux Analysis of Tumor Intermediary Metabolism

    PubMed Central

    Shestov, Alexander A.; Lee, Seung-Cheol; Nath, Kavindra; Guo, Lili; Nelson, David S.; Roman, Jeffrey C.; Leeper, Dennis B.; Wasik, Mariusz A.; Blair, Ian A.; Glickson, Jerry D.

    2016-01-01

    We present the first validated metabolic network model for analysis of flux through key pathways of tumor intermediary metabolism, including glycolysis, the oxidative and non-oxidative arms of the pentose pyrophosphate shunt, the TCA cycle as well as its anaplerotic pathways, pyruvate–malate shuttling, glutaminolysis, and fatty acid biosynthesis and oxidation. The model that is called Bonded Cumomer Analysis for application to 13C magnetic resonance spectroscopy (13C MRS) data and Fragmented Cumomer Analysis for mass spectrometric data is a refined and efficient form of isotopomer analysis that can readily be expanded to incorporate glycogen, phospholipid, and other pathways thereby encompassing all the key pathways of tumor intermediary metabolism. Validation was achieved by demonstrating agreement of experimental measurements of the metabolic rates of oxygen consumption, glucose consumption, lactate production, and glutamate pool size with independent measurements of these parameters in cultured human DB-1 melanoma cells. These cumomer models have been applied to studies of DB-1 melanoma and DLCL2 human diffuse large B-cell lymphoma cells in culture and as xenografts in nude mice at 9.4 T. The latter studies demonstrate the potential translation of these methods to in situ studies of human tumor metabolism by MRS with stable 13C isotopically labeled substrates on instruments operating at high magnetic fields (≥7 T). The melanoma studies indicate that this tumor line obtains 51% of its ATP by mitochondrial metabolism and 49% by glycolytic metabolism under both euglycemic (5 mM glucose) and hyperglycemic conditions (26 mM glucose). While a high level of glutamine uptake is detected corresponding to ~50% of TCA cycle flux under hyperglycemic conditions, and ~100% of TCA cycle flux under euglycemic conditions, glutaminolysis flux and its contributions to ATP synthesis were very small. Studies of human lymphoma cells demonstrated that inhibition of

  18. Open-Source Automated Parahydrogen Hyperpolarizer for Molecular Imaging Using (13)C Metabolic Contrast Agents.

    PubMed

    Coffey, Aaron M; Shchepin, Roman V; Truong, Milton L; Wilkens, Ken; Pham, Wellington; Chekmenev, Eduard Y

    2016-08-16

    An open-source hyperpolarizer producing (13)C hyperpolarized contrast agents using parahydrogen induced polarization (PHIP) for biomedical and other applications is presented. This PHIP hyperpolarizer utilizes an Arduino microcontroller in conjunction with a readily modified graphical user interface written in the open-source processing software environment to completely control the PHIP hyperpolarization process including remotely triggering an NMR spectrometer for efficient production of payloads of hyperpolarized contrast agent and in situ quality assurance of the produced hyperpolarization. Key advantages of this hyperpolarizer include: (i) use of open-source software and hardware seamlessly allowing for replication and further improvement as well as readily customizable integration with other NMR spectrometers or MRI scanners (i.e., this is a multiplatform design), (ii) relatively low cost and robustness, and (iii) in situ detection capability and complete automation. The device performance is demonstrated by production of a dose (∼2-3 mL) of hyperpolarized (13)C-succinate with %P13C ∼ 28% and 30 mM concentration and (13)C-phospholactate at %P13C ∼ 15% and 25 mM concentration in aqueous medium. These contrast agents are used for ultrafast molecular imaging and spectroscopy at 4.7 and 0.0475 T. In particular, the conversion of hyperpolarized (13)C-phospholactate to (13)C-lactate in vivo is used here to demonstrate the feasibility of ultrafast multislice (13)C MRI after tail vein injection of hyperpolarized (13)C-phospholactate in mice. PMID:27478927

  19. High-throughput hyperpolarized 13C metabolic investigations using a multi-channel acquisition system

    NASA Astrophysics Data System (ADS)

    Lee, Jaehyuk; Ramirez, Marc S.; Walker, Christopher M.; Chen, Yunyun; Yi, Stacey; Sandulache, Vlad C.; Lai, Stephen Y.; Bankson, James A.

    2015-11-01

    Magnetic resonance imaging and spectroscopy of hyperpolarized (HP) compounds such as [1-13C]-pyruvate have shown tremendous potential for offering new insight into disease and response to therapy. New applications of this technology in clinical research and care will require extensive validation in cells and animal models, a process that may be limited by the high cost and modest throughput associated with dynamic nuclear polarization. Relatively wide spectral separation between [1-13C]-pyruvate and its chemical endpoints in vivo are conducive to simultaneous multi-sample measurements, even in the presence of a suboptimal global shim. Multi-channel acquisitions could conserve costs and accelerate experiments by allowing acquisition from multiple independent samples following a single dissolution. Unfortunately, many existing preclinical MRI systems are equipped with only a single channel for broadband acquisitions. In this work, we examine the feasibility of this concept using a broadband multi-channel digital receiver extension and detector arrays that allow concurrent measurement of dynamic spectroscopic data from ex vivo enzyme phantoms, in vitro anaplastic thyroid carcinoma cells, and in vivo in tumor-bearing mice. Throughput and the cost of consumables were improved by up to a factor of four. These preliminary results demonstrate the potential for efficient multi-sample studies employing hyperpolarized agents.

  20. Flux and energy analysis of species in hollow cathode magnetron ionized physical vapor deposition of copper

    NASA Astrophysics Data System (ADS)

    Wu, L.; Ko, E.; Dulkin, A.; Park, K. J.; Fields, S.; Leeser, K.; Meng, L.; Ruzic, D. N.

    2010-12-01

    To meet the stringent requirements of interconnect metallization for sub-32 nm technologies, an unprecedented level of flux and energy control of film forming species has become necessary to further advance ionized physical vapor deposition technology. Such technology development mandates improvements in methods to quantify the metal ion fraction, the gas/metal ion ratio, and the associated ion energies in the total ion flux to the substrate. In this work, a novel method combining planar Langmuir probes, quartz crystal microbalance (QCM), and gridded energy analyzer (GEA) custom instrumentation is developed to estimate the plasma density and temperature as well as to measure the metal ion fraction and ion energy. The measurements were conducted in a Novellus Systems, Inc. Hollow Cathode Magnetron (HCMTM) physical vapor deposition source used for deposition of Cu seed layer for 65-130 nm technology nodes. The gridded energy analyzer was employed to measure ion flux and ion energy, which was compared to the collocated planar Langmuir probe data. The total ion-to-metal neutral ratio was determined by the QCM combined with GEA. The data collection technique and the corresponding analysis are discussed. The effect of concurrent resputtering during the deposition process on film thickness profile is also discussed.

  1. Modelling osmotic stress by Flux Balance Analysis at the genomic scale.

    PubMed

    Metris, Aline; George, Susan; Baranyi, József

    2012-01-16

    Predictive microbiology for food safety is still primarily based on empirical models describing the effect of the environmental conditions of the food on the kinetics of the growth of foodborne pathogens. One way to make these models more mechanistic is to use systems biology methods such as Flux Balance Analysis (FBA). FBA consists of evaluating the possible fluxes through the metabolic reactions taking place in a cell. Using this method, the specific growth rate of Escherichia coli can be predicted by assuming, as an objective function, that the cells maximise their biomass production during balanced growth. Whilst this works under favourable environmental conditions, our simulations show that this objective function is not sufficient to explain the decrease of the growth rate due to osmotic stress. One feature of the FBA models is that the parameters and objective function in general refer to chemostat experiments where the carbon source is the main limiting factor. This may be relevant to some foods where the carbon to nitrogen balance is limiting but, in general, it is the physico-chemical conditions which are the most stringent. We therefore need to examine the effect of such constraints on the fluxes and/or modify the objective function, or to elaborate the metabolic model by taking into account other functional levels of the cell in order to develop mechanistic predictive models for osmotic stress conditions.

  2. Metabolic Flux Analysis during the Exponential Growth Phase of Saccharomyces cerevisiae in Wine Fermentations

    PubMed Central

    Quirós, Manuel; Martínez-Moreno, Rubén; Albiol, Joan; Morales, Pilar; Vázquez-Lima, Felícitas; Barreiro-Vázquez, Antonio; Ferrer, Pau; Gonzalez, Ramon

    2013-01-01

    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. PMID:23967264

  3. Flux and energy analysis of species in hollow cathode magnetron ionized physical vapor deposition of copper

    SciTech Connect

    Wu, L.; Ko, E.; Dulkin, A.; Park, K. J.; Fields, S.; Leeser, K.; Meng, L.; Ruzic, D. N.

    2010-12-15

    To meet the stringent requirements of interconnect metallization for sub-32 nm technologies, an unprecedented level of flux and energy control of film forming species has become necessary to further advance ionized physical vapor deposition technology. Such technology development mandates improvements in methods to quantify the metal ion fraction, the gas/metal ion ratio, and the associated ion energies in the total ion flux to the substrate. In this work, a novel method combining planar Langmuir probes, quartz crystal microbalance (QCM), and gridded energy analyzer (GEA) custom instrumentation is developed to estimate the plasma density and temperature as well as to measure the metal ion fraction and ion energy. The measurements were conducted in a Novellus Systems, Inc. Hollow Cathode Magnetron (HCM{sup TM}) physical vapor deposition source used for deposition of Cu seed layer for 65-130 nm technology nodes. The gridded energy analyzer was employed to measure ion flux and ion energy, which was compared to the collocated planar Langmuir probe data. The total ion-to-metal neutral ratio was determined by the QCM combined with GEA. The data collection technique and the corresponding analysis are discussed. The effect of concurrent resputtering during the deposition process on film thickness profile is also discussed.

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

    PubMed

    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.

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

    PubMed

    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.

  6. Segregated flux balance analysis constrained by population structure/function data: the case of PHA production by mixed microbial cultures.

    PubMed

    Pardelha, F; Albuquerque, M G E; Carvalho, G; Reis, M A M; Dias, J M L; Oliveira, R

    2013-08-01

    In this study we developed a segregated flux balance analysis (FBA) method to calculate metabolic flux distributions of the individual populations present in a mixed microbial culture (MMC). Population specific flux data constraints were derived from the raw data typically obtained by the fluorescence in situ hybridization (FISH) and microautoradiography (MAR)-FISH techniques. This method was applied to study the metabolic heterogeneity of a MMC that produces polyhydroxyalkanoates (PHA) from fermented sugar cane molasses. Three populations were identified by FISH, namely Paracoccus sp., Thauera sp., and Azoarcus sp. The segregated FBA method predicts a flux distribution for each of the identified populations. The method is shown to predict with high accuracy the average PHA storage flux and the respective monomeric composition for 16 independent experiments. Moreover, flux predictions by segregated FBA were slightly better than those obtained by nonsegregated FBA, and also highly concordant with metabolic flux analysis (MFA) estimated fluxes. The segregated FBA method can be of high value to assess metabolic heterogeneity in MMC systems and to derive more efficient eco-engineering strategies. For the case of PHA-producing MMC considered in this work, it becomes apparent that the PHA average monomeric composition might be controlled not only by the volatile fatty acids (VFA) feeding profile but also by the population composition present in the MMC. PMID:23475571

  7. Poynting flux analysis of whistler-mode chorus using THEMIS data

    NASA Astrophysics Data System (ADS)

    Taubenschuss, U.; Santolik, O.; Macusova, E.; Breuillard, H.; Hanzelka, M.

    2015-12-01

    We present a statistical analysis of Poynting fluxes for magnetospheric whistler-mode chorus emission observed on THEMIS (Time History of Events and Macroscale Interactions during Substorms). Results are shown for chorus rising and falling tones. The aim of this study is to clearly distinguish between chorus from equatorial source regions and from sources at higher magnetic latitudes, i.e., from dayside pockets of minimum magnetic field. Furthermore, the topic of magnetospherically reflected chorus as a possible process to produce falling tones will be discussed.

  8. Nonequilibrium, Drift-Flux Code System for Two-Phase Flow Network Analysis

    2000-08-01

    Version: 00 SOLA-LOOP is designed for the solution of transient two-phase flow in networks composed of one-dimensional components. The fluid dynamics is described by a nonequilibrium, drift-flux formulation of the fluid conservation laws. Although developed for nuclear reactor safety analysis, SOLA-LOOP may be used as the basis for other types of special-purpose network codes. The program can accommodate almost any set of constitutive relations, property tables, or other special features required for different applications.

  9. Exploiting diurnal variations to evaluate the ISCCP-FD flux calculations and radiative-flux-analysis-processed surface observations from BSRN, ARM, and SURFRAD

    SciTech Connect

    Zhang, Yuanchong; Long, Charles N.; Rossow, William B.; Dutton, Ellsworth G.

    2010-01-01

    Based on monthly-3-hourly and 3-hourly mean surface radiative fluxes and their associated meteorological parameters for 2004 from the International Satellite Cloud Climatology Project-FD (ISCCP-FD) and the Radiative Flux Analysis method-Produced Surface Observations (RFA-PSO) for 15 high-quality-controlled surface stations, operated by the Baseline Surface Radiation Network (BSRN), the Atmospheric Radiation Measurement (ARM) and the National Oceanic and Atmospheric Administration's Surface Radiation budget network (SURFRAD), this work, goes beyond the previous validation for FD against surface observation by introducing the Meteorological Similarity Comparison Method (MSCM) to make a more precise, mutual evaluation of both FD and PSO products. The comparison results in substantial uncertainty reduction and provides reasonable physical explanations for the flux differences. This approach compares fluxes for cases where the atmospheric and surface physical properties (specifically, the input parameters for radiative transfer model) are as close as possible to the values determined at the observational sites by matching the RFA-produced cloud fraction (CF) and/or optical thickness (Tau), etc., or alternatively, by directly changing the model input variables for FD to match PSO values, and using such-produced matched sub-datasets to make more accurate comparisons based on more similar meteorological environments between FD and PSO. The crucial part is the availability of flux-associated meteorological parameters from RFA-PSO, which was only recently made available that makes this work possible. For surface downwelling shortwave(SW) flux (SWdn) and its two components, diffuse (Dif) and direct (Dir), uncertainty for monthly mean is 15, 15 and 17 W/m2, respectively, smaller than the separately estimated uncertainty values from both FD and PSO. When applying MSCM by reducing their CF difference, the differences can be reduced by a factor of 2. The strength of

  10. Some advance on the comprehension of SR analysis for estimating the flux of a scalar

    NASA Astrophysics Data System (ADS)

    Castellví, Dr

    2009-04-01

    In agronomy, the eddy covariance, EC, method likely is the preferred for measuring surface scalar fluxes. For latent heat flux, however, weighing lysimeters maybe preferred in agriculture, but they are rarely affordable and not portable. The dissipation method, DM, is considered the most reliable technique for measuring scalar fluxes over open water because instrument motion contaminates the EC measurements. The main advantage of DM over EC is that it is less sensitive to low frequency instrument platform motions (such as ship and buoys), sensor alignment, precise orientation and stringent steadiness in the mean meteorological conditions (Fairall and Larsen, 1986; Kader, 1992; Edson and Fairall, 1998). Over land, keeping in mind that the EC and DM methods require the same measurements for scalar flux measurement, the DM has several disadvantages versus the EC. Direct measurement of the scalar variance dissipation rate, VDR, requires to capture eddies in the Kolmogorov's microscale (thus scalar time series measured at frequencies in the order of kHz are needed). Therefore, it is not practical. Indirect methods to estimate VDR (such as spectral analysis and second or third order structure functions) requires implementing iterative methods involving similarity relationships that are not well established (Hsieh and Katul, 1997; Castellvi and Snyder, 2008). Currently, there is ample evidence that the DM as explained in traditional micrometeorological books (such as, Panofsky and Dutton, 1984; Brutsaert, 1988; Kaimal and Finnigan; 1994) is, in general, not correct. Accordingly, it likely explains why DM is typically omitted in revisits of micrometeorological methods for estimating scalar fluxes in agronomy. Within the last decade, over some agricultural surfaces, evidence has been shown on the advantages over other micrometeorological methods and the reliability (i.e., close performance to the EC method) of Surface Renewal, SR, theory in conjunction with the Analysis of

  11. Analysis of the influence of rainfall variables on urban effluents concentrations and fluxes in wet weather

    NASA Astrophysics Data System (ADS)

    Gooré Bi, Eustache; Monette, Frédéric; Gasperi, Johnny

    2015-04-01

    Urban rainfall runoff has been a topic of increasing importance over the past years, a result of both the increase in impervious land area arising from constant urban growth and the effects of climate change on urban drainage. The main goal of the present study is to assess and analyze the correlations between rainfall variables and common indicators of urban water quality, namely event mean concentrations (EMCs) and event fluxes (EFs), in order to identify and explain the impacts of each of the main rainfall variables on the generation process of urban pollutants during wet periods. To perform this analysis, runoff from eight summer rainfall events that resulted in combined sewer overflow (CSO) was sampled simultaneously from two distinct catchment areas in order to quantify discharges at the respective outfalls. Pearson statistical analysis of total suspended solids (TSS), chemical oxygen demand (COD), carbonaceous biochemical oxygen demand at 5 days (CBOD5), total phosphorus (Ptot) and total kedjal nitrogen (N-TKN) showed significant correlations (ρ = 0.05) between dry antecedent time (DAT) and EMCs on one hand, and between total rainfall (TR) and the volume discharged (VD) during EFs, on the other. These results show that individual rainfall variables strongly affect either EMCs or EFs and are good predictors to consider when selecting variables for statistical modeling of urban runoff quality. The results also show that in a combined sewer network, there is a linear relationship between TSS event fluxes and COD, CBOD5, Ptot, and N-TKN event fluxes; this explains 97% of the variability of these pollutants which adsorb onto TSS during wet weather, which therefore act as tracers. Consequently, the technological solution selected for TSS removal will also lead to a reduction of these pollutants. Given the huge volumes involved, urban runoffs contribute substantially to pollutant levels in receiving water bodies, a situation which, in a climate change context, may

  12. Quantitative analysis of the high temperature-induced glycolytic flux increase in Saccharomyces cerevisiae reveals dominant metabolic regulation.

    PubMed

    Postmus, Jarne; Canelas, André B; Bouwman, Jildau; Bakker, Barbara M; van Gulik, Walter; de Mattos, M Joost Teixeira; Brul, Stanley; Smits, Gertien J

    2008-08-29

    A major challenge in systems biology lies in the integration of processes occurring at different levels, such as transcription, translation, and metabolism, to understand the functioning of a living cell in its environment. We studied the high temperature-induced glycolytic flux increase in Saccharomyces cerevisiae and investigated the regulatory mechanisms underlying this increase. We used glucose-limited chemostat cultures to separate regulatory effects of temperature from effects on growth rate. Growth at increased temperature (38 degrees C versus 30 degrees C) resulted in a strongly increased glycolytic flux, accompanied by a switch from respiration to a partially fermentative metabolism. We observed an increased flux through all enzymes, ranging from 5- to 10-fold. We quantified the contributions of direct temperature effects on enzyme activities, the gene expression cascade and shifts in the metabolic network, to the increased flux through each enzyme. To do this we adapted flux regulation analysis. We show that the direct effect of temperature on enzyme kinetics can be included as a separate term. Together with hierarchical regulation and metabolic regulation, this term explains the total flux change between two steady states. Surprisingly, the effect of the cultivation temperature on enzyme catalytic capacity, both directly through the Arrhenius effect and indirectly through adapted gene expression, is only a moderate contribution to the increased glycolytic flux for most enzymes. The changes in flux are therefore largely caused by changes in the interaction of the enzymes with substrates, products, and effectors.

  13. Job/task analysis for I C (Instrumentation and Controls) instrument technicians at the High Flux Isotope Reactor

    SciTech Connect

    Duke, L.L.

    1989-09-01

    To comply with Department of Energy Order 5480.XX (Draft), a job/task analysis was initiated by the Maintenance Management Department at Oak Ridge National Laboratory (ORNL). The analysis was applicable to instrument technicians working at the ORNL High Flux Isotope Reactor (HFIR). This document presents the procedures and results of that analysis. 2 refs., 2 figs.

  14. Arrangement Analysis of Leaves Optimized on Photon Flux Density or Photosynthetic Rate

    NASA Astrophysics Data System (ADS)

    Obara, Shin'ya; Tanno, Itaru

    By clarifying a plant evolutive process, useful information may be obtained on engineering. Consequently, an analysis algorithm that investigates the optimal arrangement of plant leaves was developed. In the developed algorithm, the Monte Carlo method is introduced and sunlight is simulated. Moreover, the arrangement optimization of leaves is analyzed using a Genetic Algorithm (GA). The number of light quanta (photon flux density) that reaches leaves, or the average photosynthetic rate of the same was set as the objective function, and leaf models of a dogwood and a ginkgo tree were analyzed. The number of leaf models was set between two to four, and the position of the leaf was expressed in terms of the angle of direction, elevation angle, rotation angle, and the representative length of the branch of a leaf. The chromosome model introduced into GA consists of information concerning the position of the leaf. Based on the analysis results, the characteristics of the leaf of an actual plant could be simulated by ensuring the algorithm had multiple constrained conditions. The optimal arrangement of leaves differs in maximization of the photon flux density, and that of the average value of a photosynthetic rate. Furthermore, the leaf form affecting the optimal arrangement of leave and also having a significant influence also on a photosynthetic rate was shown.

  15. Insights into pH-induced metabolic switch by flux balance analysis.

    PubMed

    Ivarsson, Marija; Noh, Heeju; Morbidelli, Massimo; Soos, Miroslav

    2015-01-01

    Lactate accumulation in mammalian cell culture is known to impede cellular growth and productivity. The control of lactate formation and consumption in a hybridoma cell line was achieved by pH alteration during the early exponential growth phase. In particular, lactate consumption was induced even at high glucose concentrations at pH 6.8, whereas highly increased production of lactate was obtained at pH 7.8. Consequently, constraint-based metabolic flux analysis was used to examine pH-induced metabolic states in the same growth state. We demonstrated that lactate influx at pH 6.8 led cells to maintain high fluxes in the TCA cycle and malate-aspartate shuttle resulting in a high ATP production rate. In contrast, under increased pH conditions, less ATP was generated and different ATP sources were utilized. Gene expression analysis led to the conclusion that lactate formation at high pH was enabled by gluconeogenic pathways in addition to facilitated glucose uptake. The obtained results provide new insights into the influence of pH on cellular metabolism, and are of importance when considering pH heterogeneities typically present in large scale industrial bioreactors. PMID:25906421

  16. Elementary Flux Mode Analysis of Acetyl-CoA Pathway in Carboxydothermus hydrogenoformans Z-2901

    PubMed Central

    Chinnasamy Perumal, Rajadurai; Selvaraj, Ashok; Ramesh Kumar, Gopal

    2014-01-01

    Carboxydothermus hydrogenoformans is a carboxydotrophic hydrogenogenic bacterium species that produces hydrogen molecule by utilizing carbon monoxide (CO) or pyruvate as a carbon source. To investigate the underlying biochemical mechanism of hydrogen production, an elementary mode analysis of acetyl-CoA pathway was performed to determine the intermediate fluxes by combining linear programming (LP) method available in CellNetAnalyzer software. We hypothesized that addition of enzymes necessary for carbon monoxide fixation and pyruvate dissimilation would enhance the theoretical yield of hydrogen. An in silico gene knockout of pyk, pykC, and mdh genes of modeled acetyl-CoA pathway allows the maximum theoretical hydrogen yield of 47.62 mmol/gCDW/h for 1 mole of carbon monoxide (CO) uptake. The obtained hydrogen yield is comparatively two times greater than the previous experimental data. Therefore, it could be concluded that this elementary flux mode analysis is a crucial way to achieve efficient hydrogen production through acetyl-CoA pathway and act as a model for strain improvement. PMID:24822064

  17. Surface renewal analysis to obtain sensible heat flux in rice, maize and soybean canopies

    NASA Astrophysics Data System (ADS)

    Maruyama, A.; Paw U, K.; Snyder, R. L.

    2013-12-01

    The thermal environment in the plant canopy affects plants' growth processes such as flowering and ripening. High temperatures often cause grain sterility and poor filling, and reduce crop production in tropical and temperate regions. With global warming predicted, these effects have become a major concern worldwide. In this study, surface renewal analysis, which is a novel method for estimating scalar fluxes, was applied to rice, maize and soybean canopies to understand the dynamics of sensible heat in crop canopies. Surface renewal analysis has advantages of (1) lower cost of equipment, (2) a shorter fetch requirement and (3) less disturbance in the field. The temperature of the atmosphere (T) at multiple heights was measured at 10 Hz with fine-wire thermocouples to calculate sensible heat flux (H) from the ramp pattern of T. Variations in H determined from the T measurements at canopy top was from -80 to 120 Wm-2 for rice, and it showed reasonable diurnal variation. However, H values determined from the T measurements within the canopies were smaller because of differences in temperature ramp frequency with height. These results suggest that not all turbulent structures penetrate deeply into canopies. The results for rice, maize and soybean canopies will be presented at the meeting.

  18. Insights into pH-induced metabolic switch by flux balance analysis.

    PubMed

    Ivarsson, Marija; Noh, Heeju; Morbidelli, Massimo; Soos, Miroslav

    2015-01-01

    Lactate accumulation in mammalian cell culture is known to impede cellular growth and productivity. The control of lactate formation and consumption in a hybridoma cell line was achieved by pH alteration during the early exponential growth phase. In particular, lactate consumption was induced even at high glucose concentrations at pH 6.8, whereas highly increased production of lactate was obtained at pH 7.8. Consequently, constraint-based metabolic flux analysis was used to examine pH-induced metabolic states in the same growth state. We demonstrated that lactate influx at pH 6.8 led cells to maintain high fluxes in the TCA cycle and malate-aspartate shuttle resulting in a high ATP production rate. In contrast, under increased pH conditions, less ATP was generated and different ATP sources were utilized. Gene expression analysis led to the conclusion that lactate formation at high pH was enabled by gluconeogenic pathways in addition to facilitated glucose uptake. The obtained results provide new insights into the influence of pH on cellular metabolism, and are of importance when considering pH heterogeneities typically present in large scale industrial bioreactors.

  19. Carbon material distribution and flux analysis under varying glucose concentrations in hydrogen-producing Clostridium tyrobutyricum JM1.

    PubMed

    Jo, Ji Hye; Kim, Woong

    2016-06-20

    Anaerobic glucose metabolism in hydrogen-producing Clostridium tyrobutyricum was investigated in batch culture with varying initial glucose concentrations (27.8-333.6mM). To understand the regulation of metabolism, the carbon material and reduction balances were applied to estimate the carbon flux distribution for the first time, and metabolic flux analysis (MFA) was used to provide qualitative information and guidance for effective metabolic design. The overall flux distribution suggested that C. tyrobutyricum metabolism has a high capacity for the production of butyrate and hydrogen at an initial glucose concentration of 222.4mM, with balanced activities of NADH and ATP.

  20. LES of large wind farm during a diurnal cycle: Analysis of Energy and Scalar flux budgets

    NASA Astrophysics Data System (ADS)

    Sharma, V.; Calaf, M.; Parlange, M. B.

    2014-12-01

    With an expanding role of wind energy in satisfying energy demands around the world, wind farms are covering increasingly larger surfaces to the point where interaction between wind farms and the atmospheric boundary layer (ABL) might have significant implications. Furthermore, many wind farm sites lie over existing farmland for which water is a precious resource. In this context, a relevant question yet to be fully understood, is whether large wind farms alter near surface temperatures and evaporation rates and if so, by how much. In the present study, Large Eddy Simulation (LES) of a geostrophic wind driven ABL with two active scalars, temperature and specific humidity, in the presence of Coriolis forces with an embedded wind farm are performed. Multiple 'synthetic' diurnal cycles are simulated by imposing a time-varying surface temperature and specific humidity. Wind turbines are modeled using the "actuator disk" approach along with the flexibility to reorient according to varying flow directions. LES is performed using the "pseudo-spectral" approach implying that an infinitely large wind farm is simulated. Comparison of simulations with and without wind farms show clear differences in vertical profiles of horizontal velocity magnitude and direction, turbulent kinetic energy and scalar fluxes. To better understand these differences, a detailed analysis of the constituent terms of budget equations of mean and turbulent kinetic energy and sensible and latent heat fluxes has been performed for different stratification regimes as the ABL evolves during the diurnal cycle. The analyses help explain the effect of wind farms on the characteristics of the low-level jet, depth of the stable boundary layer, formation and growth of the convective boundary layer (CBL) and scalar fluxes at the surface.

  1. Isotopically nonstationary 13C flux analysis of changes in Arabidopsis thaliana leaf metabolism due to high light acclimation.

    PubMed

    Ma, Fangfang; Jazmin, Lara J; Young, Jamey D; Allen, Doug K

    2014-11-25

    Improving plant productivity is an important aim for metabolic engineering. There are few comprehensive methods that quantitatively describe leaf metabolism, although such information would be valuable for increasing photosynthetic capacity, enhancing biomass production, and rerouting carbon flux toward desirable end products. Isotopically nonstationary metabolic flux analysis (INST-MFA) has been previously applied to map carbon fluxes in photoautotrophic bacteria, which involves model-based regression of transient (13)C-labeling patterns of intracellular metabolites. However, experimental and computational difficulties have hindered its application to terrestrial plant systems. We performed in vivo isotopic labeling of Arabidopsis thaliana rosettes with (13)CO2 and estimated fluxes throughout leaf photosynthetic metabolism by INST-MFA. Plants grown at 200 µmol m(-2)s(-1) light were compared with plants acclimated for 9 d at an irradiance of 500 µmol⋅m(-2)⋅s(-1). Approximately 1,400 independent mass isotopomer measurements obtained from analysis of 37 metabolite fragment ions were regressed to estimate 136 total fluxes (54 free fluxes) under each condition. The results provide a comprehensive description of changes in carbon partitioning and overall photosynthetic flux after long-term developmental acclimation of leaves to high light. Despite a doubling in the carboxylation rate, the photorespiratory flux increased from 17 to 28% of net CO2 assimilation with high-light acclimation (Vc/Vo: 3.5:1 vs. 2.3:1, respectively). This study highlights the potential of (13)C INST-MFA to describe emergent flux phenotypes that respond to environmental conditions or plant physiology and cannot be obtained by other complementary approaches. PMID:25368168

  2. The analysis of two-dimensional two-phase flow in horizontal heated tube bundles using drift flux model

    NASA Astrophysics Data System (ADS)

    Yang, Ruichang; Zheng, Rongchuan; Wang, Yanwu

    This paper presents the experimental study and numerical simulation of two-dimensional two-phase flow in horizontal heated tube bundles. In the experiments, two advanced measuring systems with a single-fibre optical probe and a tri-fibre-optical-probe were developed to measure respectively the local void fraction and vapor bubble velocities among the heated tube bundles. In accordance with the internal circulation characteristics of two-phase flow in the tube bundles, a mathematical model of two-dimensional two-phase low Reynolds number turbulent flow based on the modified drift flux model and the numerical simulation method to analyze the two-phase flow structures have been developed. The modified drift flux model in which both the acceleration by gravity and the acceleration of the average volumetric flow are taken into account for the calculation of the drift velocities enables its application to the analysis of multi-dimensional two-phase flow. In the analysis the distributions of the vapor-phase velocity, liquid-phase velocity and void fraction were numerically obtained by using the modified drift flux model and conventional drift flux model respectively and compared with the experimental results. The numerical analysis results by using the modified drift flux model agree reasonably well with the experimental investigation. It is confirmed that the modified drift flux model has the capability of correctly simulating the two-dimensional two-phase flow.

  3. Coordinated analysis and quantification of sedimentary fluxes and budgets in cold environments: The SEDIBUD Programme

    NASA Astrophysics Data System (ADS)

    Beylich, Achim A.; Lamoureux, Scott F.

    2010-05-01

    Amplified climate change and ecological sensitivity of polar and high-altitude cold environments has been highlighted as a key global environmental issue. Projected climate change in cold climate environments is expected to alter melt season duration and intensity, along with the number of extreme rainfall events, total annual precipitation and the balance between snowfall and rainfall. Similarly, changes to the thermal balance are expected to reduce the extent of permafrost and seasonal ground frost and increase active layer depth. These effects will undoubtedly change surface environments in cold environments and alter fluxes of sediments, nutrients and solutes, but the absense of data and coordinated analysis to understand the sensitivity of the surface environment are acute in cold climate environments. The SEDIBUD (Sediment Budgets in Cold Environments) Programme of the International Association of Geomorphologists (I.A.G./A.I.G.) was formed in 2005 to address this key knowledge gap. SEDIBUD has currently about 400 members worldwide and the Steering Committee of this international programme is composed of ten scientists from nine different countries. The central research question of this global group of scientists is to Assess the contemporary sedimentary fluxes in cold climates, with emphasis on both particulate and dissolved components. Research carried out at currently 38 defined SEDIBUD Key Test Sites varies by programme, logistics and available ressources, but typically represent interdisciplinary collaborations of geomorphologists, hydrologists, ecologists, and permafrost scientists and glaciologists with different levels of detail. SEDIBUD key test sites provide data on annual climate conditions, total runoff and particulate and dissolved fluxes as well as information on other relevant surface processes. A number of selected key test sites are providing high-resolution data on climatic conditions, runoff and fluvial fluxes, which in addition to the

  4. Metabolic flux analysis of Saccharomyces cerevisiae in a sealed winemaking fermentation system.

    PubMed

    Li, Hua; Su, Jing; Ma, Wen; Guo, Anque; Shan, Zuhua; Wang, Hua

    2015-03-01

    A sealed fermentation (SF) system and an anaerobic fermentation (AF) system (under normal atmospheric pressure conditions) were employed to study the influence of endogenous carbon dioxide (CO2) on the metabolism of Saccharomyces cerevisiae. The results showed that the fermentation stopped when 82.0 g L(-1) glucose was consumed and the endogenously produced CO2: pressure reached to 14.3 MPa in SF system, while the sugar was used up during AF. The total yeast viable count in the end of AF was higher than that of SF. It was also observed that the ethanol yield in AF and SF was similar, the glycerol yield in AF was 1.26 times higher than that in SF, while the succinic acid and acetic acid yields in SF were 24.7 and 26 times higher than that in AF, respectively. Additionally, this work provides a stoichiometric model used for metabolic flux analysis of S. cerevisiae to compare the flux distribution in SF and AF. The results showed that CO2 had an important effect on the pathways of oxaloacetic acid formation from pyruvic acid and ribose-5-phosphate formation from glucose-6-phosphate. However, the pathway of ethanol formation from pyruvic acid (decarboxylation reaction), catalyzed by pyruvate decarboxylase, was insensitive to CO2.

  5. Two-Flux Green's Function Analysis for Transient Spectral Radiation in a Composite

    NASA Technical Reports Server (NTRS)

    Siegel, Robert

    1996-01-01

    An analysis is developed for obtaining transient temperatures in a two-layer semitransparent composite with spectrally dependent properties. Each external boundary of the composite is subjected to radiation and convection. The two-flux radiative transfer equations are solved by deriving a Green's function. This yields the local radiative heat source needed to numerically solve the transient energy equation. An advantage of the two-flux method is that isotropic scattering is included without added complexity. The layer refractive indices are larger than one. This produces internal reflections at the boundaries and the internal interface; the reflections are assumed diffuse. Spectral results using the Green's function method are verified by comparing with numerical solutions using the exact radiative transfer equations. Transient temperature distributions are given to illustrate the effect of radiative heating on one side of a composite with external convective cooling. The protection of a material from incident radiation is illustrated by adding scattering to the layer adjacent to the radiative source.

  6. Mass analysis addition to the Differential Ion Flux Probe (DIFP) study

    NASA Technical Reports Server (NTRS)

    Wright, K. H., Jr.; Jolley, Richard

    1994-01-01

    The objective of this study is to develop a technique to measure the characteristics of space plasmas under highly disturbed conditions; e.g., non-Maxwellian plasmas with strong drifting populations and plasmas contaminated by spacecraft outgassing. The approach, conducted in conjunction with current MSFC activities, is to extend the capabilities of the Differential Ion Flux Probe (DIFP) to include a high throughput mass measurement that does not require either high voltage or contamination sensitive devices such as channeltron electron multipliers or microchannel plates. This will significantly reduce the complexity and expense of instrument fabrication, testing, and integration of flight hardware compared to classical mass analyzers. The feasibility of the enhanced DIFP has been verified by using breadboard test models in a controlled plasma environment. The ability to manipulate particles through the instrument regardless of incident angle, energy, or ionic component has been amply demonstrated. The energy analysis mode is differential and leads directly to a time-of-flight mass measurement. With the new design, the DIFP will separate multiple ion streams and analyze each stream independently for ion flux intensity, velocity (including direction of motion), mass, and temperature (or energy distribution). In particular, such an instrument will be invaluable on follow-on electrodynamic TSS missions and, possibly, for environmental monitoring on the space station.

  7. Gamma scintigraphic analysis of albumin flux in patients with acute respiratory distress syndrome

    SciTech Connect

    Sugerman, H.J.; Tatum, J.L.; Burke, T.S.; Strash, A.M.; Glauser, F.L.

    1984-06-01

    Computerized gamma-scintigraphy provides a new method for the analysis of albumin flux in patients with pulmonary permeability edema. In this technique, 10 mCi of /sup 99/mTc -tagged human serum albumin is administered and lung:heart radioactivity ratios are determined. This ratio remains constant unless there is a leak of albumin, when a rising ratio with time, called the ''slope index'' (SI), is seen. Thirty-five scintigraphic studies were obtained in 28 patients by means of a portable computerized gamma-camera. Thirteen of these patients had clinical evidence of the acute respiratory distress syndrome (ARDS) and six had or were recovering from left ventricular induced congestive heart failure (CHF). Five of the patients with CHF and pulmonary capillary wedge pressure (PCWP) below 30 mm Hg had normal scintigraphic studies. The patients with ARDS were found to have significantly higher SIs than patients who did not have, or had recovered from, ARDS. Positive SIs were present from 1 to 8 days following the apparent onset of ARDS in seven studies in five patients. Recovery of gas exchange was associated with a return to a normal SI in four patients. In conclusion, computerized gamma-scintigraphy was a sensitive, noninvasive tool for the detection of a pathologic increase in pulmonary protein flux. Positive scintigraphic findings were associated with significantly impaired gas exchange. The method documented that the leak of albumin in patients with ARDS may last for days but resolves with recovery.

  8. The Infrared Astronomical Satellite /IRAS/ Scientific Data Analysis System /SDAS/ sky flux subsystem

    NASA Technical Reports Server (NTRS)

    Stagner, J. R.; Girard, M. A.

    1980-01-01

    The sky flux subsystem of the Infrared Astronomical Satellite Scientific Data Analysis System is described. Its major output capabilities are (1) the all-sky lune maps (8-arcminute pixel size), (2) galactic plane maps (2-arcminute pixel size) and (3) regional maps of small areas such as extended sources greater than 1-degree in extent. The major processing functions are to (1) merge the CRDD and pointing data, (2) phase the detector streams, (3) compress the detector streams in the in-scan and cross-scan directions, and (4) extract data. Functional diagrams of the various capabilities of the subsystem are given. Although this device is inherently nonimaging, various calibrated and geometrically controlled imaging products are created, suitable for quantitative and qualitative scientific interpretation.

  9. Comprehensive measurement of respiratory activity in permeabilized cells using extracellular flux analysis

    PubMed Central

    Salabei, Joshua K.; Gibb, Andrew A.; Hill, Bradford G.

    2014-01-01

    Extracellular flux (XF) analysis has become a mainstream method to measure bioenergetic function in cells and tissues. While this technique is commonly used to measure energetics in intact cells, we outline here a detailed XF protocol for measuring respiration in permeabilized cells. Cells are permeabilized using saponin, digitonin, or recombinant perfringolysin O (XF PMP reagent) and provided with specific substrates to measure complex I- or II-mediated respiratory activity, Complex III+IV respiratory activity, or Complex IV activity. Medium- and long-chain acylcarnitines or glutamine may also be provided for measuring fatty acid oxidation or glutamine oxidation, respectively. This protocol allows for such measurements using a minimal number of cells compared with other protocols, without the need for mitochondrial isolation. The results are highly reproducible, and mitochondria remain well coupled. Collectively, this protocol provides comprehensive and detailed information regarding mitochondrial activity and efficiency, and, following preparative steps, takes approximately 6 hours to complete. PMID:24457333

  10. Risk analysis of environmental hazards at the High Flux Beam Reactor

    SciTech Connect

    Boccio, J.L.; Ho, V.S.; Johnson, D.H.

    1994-01-01

    In the late 1980s, a Level 1 internal event probabilistic risk assessment (PRA) was performed for the High-Flux Beam Reactor (HFBR), a US Department of Energy research reactor located at Brookhaven National Laboratory. Prior to the completion of that study, a level 1 PRA for external events was initiated, including environmental hazards such as fire, internal flooding, etc. Although this paper provides a brief summary of the risks from environmental hazards, emphasis will be placed on the methodology employed in utilizing industrial event databases for event frequency determination for the HFBR complex. Since the equipment in the HFBR is different from that of, say, a commercial nuclear power plant, the current approach is to categorize the industrial events according to the hazard initiators instead of categorizing by initiator location. But first a general overview of the analysis.

  11. Tidal frequencies in the spectral analysis of time series muon flux measurements

    NASA Astrophysics Data System (ADS)

    Feldman, Catherine; Takai, Helio

    2016-03-01

    Tidal frequencies are observed in the spectral analysis of time series muon flux measurements performed by the MARIACHI experiment over a period of seven years. The prominent peaks from the frequency spectrum correspond to tidal frequencies S1,S2,S3,K1,P1 and Ψ1 . We will present these results and compare them to the regular density oscillations from balloon sounding data. We interpret the observed data as being the effect of regular atmospheric density oscillations induced by the thermal heating of layers in Earth's atmosphere. As the density of the atmosphere varies, the altitude where particles are produced varies accordingly. As a consequence, the muon decay path elongates or contracts, modulating the number of muons detected at ground level. The role of other tidal effects, including geomagnetic tides, will also be discussed.

  12. The May 17, 2012 solar event: back-tracing analysis and flux reconstruction with PAMELA

    NASA Astrophysics Data System (ADS)

    Bruno, A.; Adriani, O.; Barbarino, G. C.; Bazilevskaya, G. A.; Bellotti, R.; Boezio, M.; Bogomolov, E. A.; Bongi, M.; Bonvicini, V.; Bottai, S.; Bravar, U.; Cafagna, F.; Campana, D.; Carbone, R.; Carlson, P.; Casolino, M.; Castellini, G.; Christian, E. C.; De Donato, C.; de Nolfo, G. A.; De Santis, C.; De Simone, N.; Di Felice, V.; Formato, V.; Galper, A. M.; Karelin, A. V.; Koldashov, S. V.; Koldobskiy, S.; Krutkov, S. Y.; Kvashnin, A. N.; Lee, M.; Leonov, A.; Malakhov, V.; Marcelli, L.; Martucci, M.; Mayorov, A. G.; Menn, W.; Mergè, M.; Mikhailov, V. V.; Mocchiutti, E.; Monaco, A.; Mori, N.; Munini, R.; Osteria, G.; Palma, F.; Panico, B.; Papini, P.; Pearce, M.; Picozza, P.; Ricci, M.; Ricciarini, S. B.; Ryan, J. M.; Sarkar, R.; Scotti, V.; Simon, M.; Sparvoli, R.; Spillantini, P.; Stochaj, S.; Stozhkov, Y. I.; Vacchi, A.; Vannuccini, E.; Vasilyev, G. I.; Voronov, S. A.; Yurkin, Y. T.; Zampa, G.; Zampa, N.; Zverev, V. G.

    2016-02-01

    The PAMELA space experiment is providing first direct observations of Solar Energetic Particles (SEPs) with energies from about 80 MeV to several GeV in near-Earth orbit, bridging the low energy measurements by other spacecrafts and the Ground Level Enhancement (GLE) data by the worldwide network of neutron monitors. Its unique observational capabilities include the possibility of measuring the flux angular distribution and thus investigating possible anisotropies associated to SEP events. The analysis is supported by an accurate back-tracing simulation based on a realistic description of the Earth's magnetosphere, which is exploited to estimate the SEP energy spectra as a function of the asymptotic direction of arrival with respect to the Interplanetary Magnetic Field (IMF). In this work we report the results for the May 17, 2012 event.

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

    SciTech Connect

    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.

  14. Flux balance analysis of mixed microbial cultures: application to the production of polyhydroxyalkanoates from complex mixtures of volatile fatty acids.

    PubMed

    Pardelha, Filipa; Albuquerque, Maria G E; Reis, Maria A M; Dias, João M L; Oliveira, Rui

    2012-12-31

    Fermented agro-industrial wastes are potential low cost substrates for polyhydroxyalkanoates (PHA) production by mixed microbial cultures (MMC). The use of complex substrates has however profound implications in the PHA metabolism. In this paper we investigate PHA accumulation using a lumped metabolic model that describes PHA storage from arbitrary mixtures of volatile fatty acids (VFA). Experiments were conducted using synthetic and complex VFA mixtures obtained from the fermentation of sugar cane molasses. Metabolic flux analysis (MFA) and flux balance analysis (FBA) were performed at different stages of culture enrichment in order to investigate the effect of VFA composition and time of enrichment in PHA storage efficiency. Substrate uptake and PHA storage fluxes increased over enrichment time by 70% and 73%, respectively. MFA calculations show that higher PHA storage fluxes are associated to an increase in the uptake of VFA with even number of carbon atoms and a more effective synthesis of hydroxyvalerate (HV) precursors from VFA with odd number of carbons. Furthermore, FBA shows that the key metabolic objective of a MMC subjected to the feast and famine regimen is the minimization of the tricarboxylic acid cycle fluxes. The PHA flux and biopolymer composition (hydroxybutyrate (HB): HV) could be accurately predicted in several independent experiments.

  15. OM-FBA: Integrate Transcriptomics Data with Flux Balance Analysis to Decipher the Cell Metabolism

    PubMed Central

    Guo, Weihua; Feng, Xueyang

    2016-01-01

    Constraint-based metabolic modeling such as flux balance analysis (FBA) has been widely used to simulate cell metabolism. Thanks to its simplicity and flexibility, numerous algorithms have been developed based on FBA and successfully predicted the phenotypes of various biological systems. However, their phenotype predictions may not always be accurate in FBA because of using the objective function that is assumed for cell metabolism. To overcome this challenge, we have developed a novel computational framework, namely omFBA, to integrate multi-omics data (e.g. transcriptomics) into FBA to obtain omics-guided objective functions with high accuracy. In general, we first collected transcriptomics data and phenotype data from published database (e.g. GEO database) for different microorganisms such as Saccharomyces cerevisiae. We then developed a “Phenotype Match” algorithm to derive an objective function for FBA that could lead to the most accurate estimation of the known phenotype (e.g. ethanol yield). The derived objective function was next correlated with the transcriptomics data via regression analysis to generate the omics-guided objective function, which was next used to accurately simulate cell metabolism at unknown conditions. We have applied omFBA in studying sugar metabolism of S. cerevisiae and found that the ethanol yield could be accurately predicted in most of the cases tested (>80%) by using transcriptomics data alone, and revealed valuable metabolic insights such as the dynamics of flux ratios. Overall, omFBA presents a novel platform to potentially integrate multi-omics data simultaneously and could be incorporated with other FBA-derived tools by replacing the arbitrary objective function with the omics-guided objective functions. PMID:27100883

  16. OM-FBA: Integrate Transcriptomics Data with Flux Balance Analysis to Decipher the Cell Metabolism.

    PubMed

    Guo, Weihua; Feng, Xueyang

    2016-01-01

    Constraint-based metabolic modeling such as flux balance analysis (FBA) has been widely used to simulate cell metabolism. Thanks to its simplicity and flexibility, numerous algorithms have been developed based on FBA and successfully predicted the phenotypes of various biological systems. However, their phenotype predictions may not always be accurate in FBA because of using the objective function that is assumed for cell metabolism. To overcome this challenge, we have developed a novel computational framework, namely omFBA, to integrate multi-omics data (e.g. transcriptomics) into FBA to obtain omics-guided objective functions with high accuracy. In general, we first collected transcriptomics data and phenotype data from published database (e.g. GEO database) for different microorganisms such as Saccharomyces cerevisiae. We then developed a "Phenotype Match" algorithm to derive an objective function for FBA that could lead to the most accurate estimation of the known phenotype (e.g. ethanol yield). The derived objective function was next correlated with the transcriptomics data via regression analysis to generate the omics-guided objective function, which was next used to accurately simulate cell metabolism at unknown conditions. We have applied omFBA in studying sugar metabolism of S. cerevisiae and found that the ethanol yield could be accurately predicted in most of the cases tested (>80%) by using transcriptomics data alone, and revealed valuable metabolic insights such as the dynamics of flux ratios. Overall, omFBA presents a novel platform to potentially integrate multi-omics data simultaneously and could be incorporated with other FBA-derived tools by replacing the arbitrary objective function with the omics-guided objective functions. PMID:27100883

  17. Comprehensive Method for Culturing Embryonic Dorsal Root Ganglion Neurons for Seahorse Extracellular Flux XF24 Analysis.

    PubMed

    Lange, Miranda; Zeng, Yan; Knight, Andrew; Windebank, Anthony; Trushina, Eugenia

    2012-01-01

    Changes in mitochondrial dynamics and function contribute to progression of multiple neurodegenerative diseases including peripheral neuropathies. The Seahorse Extracellular Flux XF24 analyzer provides a comprehensive assessment of the relative state of glycolytic and aerobic metabolism in live cells making this method instrumental in assessing mitochondrial function. One of the most important steps in the analysis of mitochondrial respiration using the Seahorse XF24 analyzer is plating a uniform monolayer of firmly attached cells. However, culturing of primary dorsal root ganglion (DRG) neurons is associated with multiple challenges, including their propensity to form clumps and detach from the culture plate. This could significantly interfere with proper analysis and interpretation of data. We have tested multiple cell culture parameters including coating substrates, culture medium, XF24 microplate plastics, and plating techniques in order to optimize plating conditions. Here we describe a highly reproducible method to obtain neuron-enriched monolayers of securely attached dissociated primary embryonic (E15) rat DRG neurons suitable for analysis with the Seahorse XF24 platform.

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

    PubMed Central

    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 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. PMID:23843751

  19. Flux balance analysis reveals acetate metabolism modulates cyclic electron flow and alternative glycolytic pathways in Chlamydomonas reinhardtii

    PubMed Central

    Chapman, Stephen P.; Paget, Caroline M.; Johnson, Giles N.; Schwartz, Jean-Marc

    2015-01-01

    Cells of the green alga Chlamydomonas reinhardtii cultured in the presence of acetate perform mixotrophic growth, involving both photosynthesis and organic carbon assimilation. Under such conditions, cells exhibit a reduced capacity for photosynthesis but a higher growth rate, compared to phototrophic cultures. Better understanding of the down regulation of photosynthesis would enable more efficient conversion of carbon into valuable products like biofuels. In this study, Flux Balance Analysis (FBA) and Flux Variability Analysis (FVA) have been used with a genome scale model of C. reinhardtii to examine changes in intracellular flux distribution in order to explain their changing physiology. Additionally, a reaction essentiality analysis was performed to identify which reaction subsets are essential for a given growth condition. Our results suggest that exogenous acetate feeds into a modified tricarboxylic acid (TCA) cycle, which bypasses the CO2 evolution steps, explaining increases in biomass, consistent with experimental data. In addition, reactions of the oxidative pentose phosphate and glycolysis pathways, inactive under phototrophic conditions, show substantial flux under mixotrophic conditions. Importantly, acetate addition leads to an increased flux through cyclic electron flow (CEF), but results in a repression of CO2 fixation via Rubisco, explaining the down regulation of photosynthesis. However, although CEF enhances growth on acetate, it is not essential—impairment of CEF results in alternative metabolic pathways being increased. We have demonstrated how the reactions of photosynthesis interconnect with carbon metabolism on a global scale, and how systems approaches play a viable tool in understanding complex relationships at the scale of the organism. PMID:26175742

  20. Effects of measurement resolution on the analysis of temperature time series for stream-aquifer flux estimation

    NASA Astrophysics Data System (ADS)

    Soto-López, Carlos D.; Meixner, Thomas; Ferré, Ty P. A.

    2011-12-01

    From its inception in the mid-1960s, the use of temperature time series (thermographs) to estimate vertical fluxes has found increasing use in the hydrologic community. Beginning in 2000, researchers have examined the impacts of measurement and parameter uncertainty on the estimates of vertical fluxes. To date, the effects of temperature measurement discretization (resolution), a characteristic of all digital temperature loggers, on the determination of vertical fluxes has not been considered. In this technical note we expand the analysis of recently published work to include the effects of temperature measurement resolution on estimates of vertical fluxes using temperature amplitude and phase shift information. We show that errors in thermal front velocity estimation introduced by discretizing thermographs differ when amplitude or phase shift data are used to estimate vertical fluxes. We also show that under similar circumstances sensor resolution limits the range over which vertical velocities are accurately reproduced more than uncertainty in temperature measurements, uncertainty in sensor separation distance, and uncertainty in the thermal diffusivity combined. These effects represent the baseline error present and thus the best-case scenario when discrete temperature measurements are used to infer vertical fluxes. The errors associated with measurement resolution can be minimized by using the highest-resolution sensors available. But thoughtful experimental design could allow users to select the most cost-effective temperature sensors to fit their measurement needs.

  1. Inverse modeling analysis of regional methane fluxes using GOSAT retrievals in 2010-2012

    NASA Astrophysics Data System (ADS)

    KIM, H. S.; Maksyutov, S. S.; Belikov, D.; Ito, A.; Morino, I.; Yoshida, Y.; Yokota, T.; Sasakawa, M.; Machida, T.

    2015-12-01

    Our inverse modeling system estimated monthly regional CH4 fluxes during the period 2010-2012, based on ground-based observations and GOSAT retrievals (called Inv.GG). With adding GOSAT retrievals to the flux estimation, we found enhanced fluxes in tropical Africa (17% from a priori and 10% from flux estimates using ground-based observations only, called Inv.GB), tropical and subtropical South America (12% and 9% respectively), and East Asia (21% and 6% respectively), but lowered fluxes in South and Southeast Asia (12% and 14% respectively). Overall, a larger year-to-year variation of estimated fluxes was found in Inv.GG. In 2010, raging fires occurred in Brazil and Bolivia under severe drought, and the highest biomass burning fluxes in central part of South America were estimated in 2010 during the simulation period 2010-2012. The intensity of the 2010 biomass burning flux was enhanced in Inv.GG compared with a priori of GFED v3.1 and Inv.GB. In Russia, two fire events occurred in 2010 and 2012 under very hot and relatively dry condition. The 2010 fires occurred over European Russia, and a large departure from the GFED estimates was not shown in both Inv.GB and Inv.GG. For the 2012 fires in eastern and central Russia, the severity was explained by the 2012 highest biomass burning fluxes over Siberia during the simulation period 2010-2012. The biomass burning fluxes in Inv.GG were similar to a priori, but lower than Inv.GB (particularly in the eastern part of Siberia). In Inv.GG, the Jun-Aug biomass burning fluxes account for ~14% of the annual mean Siberian total flux in 2010-2012.

  2. In-depth performance analysis of the HyperFlux spectrometer

    NASA Astrophysics Data System (ADS)

    Meade, Jeffrey T.; Behr, Bradford B.; Bismilla, Yusuf; Cenko, Andrew T.; Hajian, Arsen R.

    2013-03-01

    Tornado Spectral Systems introduced the HyperFluxTM spectrometer to the market in early 2012. The Hyper- Flux is the world's first HTVS (high-throughput virtual slit) enabled spectrometer and is able to achieve much greater system flux compared to slit-based spectrometers. Since the HyperFlux's debut extensive studies into the manufacturability, stability, and detector electronic performance have been performed and are presented in this paper. A generalized quantitative approach to spectrometer comparison by using a clearly-defined Quality Factor is presented at the end of the paper.

  3. Integrated, Step-Wise, Mass-Isotopomeric Flux Analysis of the TCA Cycle.

    PubMed

    Alves, Tiago C; Pongratz, Rebecca L; Zhao, Xiaojian; Yarborough, Orlando; Sereda, Sam; Shirihai, Orian; Cline, Gary W; Mason, Graeme; Kibbey, Richard G

    2015-11-01

    Mass isotopomer multi-ordinate spectral analysis (MIMOSA) is a step-wise flux analysis platform to measure discrete glycolytic and mitochondrial metabolic rates. Importantly, direct citrate synthesis rates were obtained by deconvolving the mass spectra generated from [U-(13)C6]-D-glucose labeling for position-specific enrichments of mitochondrial acetyl-CoA, oxaloacetate, and citrate. Comprehensive steady-state and dynamic analyses of key metabolic rates (pyruvate dehydrogenase, β-oxidation, pyruvate carboxylase, isocitrate dehydrogenase, and PEP/pyruvate cycling) were calculated from the position-specific transfer of (13)C from sequential precursors to their products. Important limitations of previous techniques were identified. In INS-1 cells, citrate synthase rates correlated with both insulin secretion and oxygen consumption. Pyruvate carboxylase rates were substantially lower than previously reported but showed the highest fold change in response to glucose stimulation. In conclusion, MIMOSA measures key metabolic rates from the precursor/product position-specific transfer of (13)C-label between metabolites and has broad applicability to any glucose-oxidizing cell. PMID:26411341

  4. Partial Safety Analysis for a Reduced Uranium Enrichment Core for the High Flux Isotope Reactor

    SciTech Connect

    Primm, Trent; Gehin, Jess C

    2009-04-01

    A computational model of the reactor core of the High Flux Isotope Rector (HFIR) was developed in order to analyze non-destructive accidents caused by transients during reactor operation. The reactor model was built for the latest version of the nuclear analysis software package called Program for the Analysis of Reactor Transients (PARET). Analyses performed with the model constructed were compared with previous data obtained with other tools in order to benchmark the code. Finally, the model was used to analyze the behavior of the reactor under transients using a different nuclear fuel with lower enrichment of uranium (LEU) than the fuel currently used, which has a high enrichment of uranium (HEU). The study shows that the presence of fertile isotopes in LEU fuel, which increases the neutron resonance absorption, reduces the impact of transients on the fuel and enhances the negative reactivity feedback, thus, within the limitations of this study, making LEU fuel appear to be a safe alternative fuel for the reactor core.

  5. A system analysis computer model for the High Flux Isotope Reactor (HFIRSYS Version 1)

    SciTech Connect

    Sozer, M.C.

    1992-04-01

    A system transient analysis computer model (HFIRSYS) has been developed for analysis of small break loss of coolant accidents (LOCA) and operational transients. The computer model is based on the Advanced Continuous Simulation Language (ACSL) that produces the FORTRAN code automatically and that provides integration routines such as the Gear`s stiff algorithm as well as enabling users with numerous practical tools for generating Eigen values, and providing debug outputs and graphics capabilities, etc. The HFIRSYS computer code is structured in the form of the Modular Modeling System (MMS) code. Component modules from MMS and in-house developed modules were both used to configure HFIRSYS. A description of the High Flux Isotope Reactor, theoretical bases for the modeled components of the system, and the verification and validation efforts are reported. The computer model performs satisfactorily including cases in which effects of structural elasticity on the system pressure is significant; however, its capabilities are limited to single phase flow. Because of the modular structure, the new component models from the Modular Modeling System can easily be added to HFIRSYS for analyzing their effects on system`s behavior. The computer model is a versatile tool for studying various system transients. The intent of this report is not to be a users manual, but to provide theoretical bases and basic information about the computer model and the reactor.

  6. Integrated, Step-Wise, Mass-Isotopomeric Flux Analysis of the TCA Cycle.

    PubMed

    Alves, Tiago C; Pongratz, Rebecca L; Zhao, Xiaojian; Yarborough, Orlando; Sereda, Sam; Shirihai, Orian; Cline, Gary W; Mason, Graeme; Kibbey, Richard G

    2015-11-01

    Mass isotopomer multi-ordinate spectral analysis (MIMOSA) is a step-wise flux analysis platform to measure discrete glycolytic and mitochondrial metabolic rates. Importantly, direct citrate synthesis rates were obtained by deconvolving the mass spectra generated from [U-(13)C6]-D-glucose labeling for position-specific enrichments of mitochondrial acetyl-CoA, oxaloacetate, and citrate. Comprehensive steady-state and dynamic analyses of key metabolic rates (pyruvate dehydrogenase, β-oxidation, pyruvate carboxylase, isocitrate dehydrogenase, and PEP/pyruvate cycling) were calculated from the position-specific transfer of (13)C from sequential precursors to their products. Important limitations of previous techniques were identified. In INS-1 cells, citrate synthase rates correlated with both insulin secretion and oxygen consumption. Pyruvate carboxylase rates were substantially lower than previously reported but showed the highest fold change in response to glucose stimulation. In conclusion, MIMOSA measures key metabolic rates from the precursor/product position-specific transfer of (13)C-label between metabolites and has broad applicability to any glucose-oxidizing cell.

  7. Analysis of Soil Vapor Extraction Data to Evaluate Mass-Transfer Constraints and Estimate Source-Zone Mass Flux

    SciTech Connect

    Brusseau, Mark; Rohay, Virginia J.; Truex, Michael J.

    2010-06-01

    Methods are developed to use data collected during cyclic operation of soil vapor extraction (SVE) systems to help characterize the magnitudes and timescales of mass flux associated with vadose zone contaminant sources. Operational data collected at the Department of Energy’s Hanford site are used to illustrate the use of such data. An analysis was conducted of carbon tetrachloride vapor concentrations collected during and between SVE operations. The objective of the analysis was to evaluate changes in concentrations measured during periods of operation and non-operation of SVE, with a focus on quantifying temporal dynamics of the vadose zone contaminant mass flux, and associated source strength. Three mass-flux terms, representing mass flux during the initial period of a SVE cycle, during the asymptotic period of a cycle, and representing mass flux during the rebound periods, were calculated and compared. It was shown that it is possible to use the rebound data to estimate time frames for effective operation of an SVE system if a sufficient set of historical cyclic operational data exists. This information could then be used to help evaluate changes in SVE operations, including system closure.

  8. ANALYSIS OF SOIL VAPOR EXTRACTION DATA TO EVALUATE MASS-TRANSFER CONSTRAINTS AND ESTIMATE SOURCE-ZONE MASS FLUX.

    PubMed

    Brusseau, Mark L; Rohay, Virginia; Truex, Michael J

    2010-01-01

    Methods are developed to use data collected during cyclic operation of soil vapor extraction (SVE) systems to help characterize the magnitudes and timescales of mass flux associated with vadose zone contaminant sources. Operational data collected at the Department of Energy's Hanford site are used to illustrate the use of such data. An analysis was conducted of carbon tetrachloride vapor concentrations collected during and between SVE operations. The objective of the analysis was to evaluate changes in concentrations measured during periods of operation and non-operation of SVE, with a focus on quantifying temporal dynamics of the vadose zone contaminant mass flux, and associated source strength. Three mass-flux terms, representing mass flux during the initial period of a SVE cycle, during the asymptotic period of a cycle, and during the rebound period, were calculated and compared. It was shown that it is possible to use the data to estimate time frames for effective operation of an SVE system if a sufficient set of historical cyclic operational data exists. This information could then be used to help evaluate changes in SVE operations, including system closure. The mass-flux data would also be useful for risk assessments of the impact of vadose-zone sources on groundwater contamination or vapor intrusion.

  9. ANALYSIS OF SOIL VAPOR EXTRACTION DATA TO EVALUATE MASS-TRANSFER CONSTRAINTS AND ESTIMATE SOURCE-ZONE MASS FLUX

    PubMed Central

    Rohay, Virginia; Truex, Michael J.

    2013-01-01

    Methods are developed to use data collected during cyclic operation of soil vapor extraction (SVE) systems to help characterize the magnitudes and timescales of mass flux associated with vadose zone contaminant sources. Operational data collected at the Department of Energy’s Hanford site are used to illustrate the use of such data. An analysis was conducted of carbon tetrachloride vapor concentrations collected during and between SVE operations. The objective of the analysis was to evaluate changes in concentrations measured during periods of operation and non-operation of SVE, with a focus on quantifying temporal dynamics of the vadose zone contaminant mass flux, and associated source strength. Three mass-flux terms, representing mass flux during the initial period of a SVE cycle, during the asymptotic period of a cycle, and during the rebound period, were calculated and compared. It was shown that it is possible to use the data to estimate time frames for effective operation of an SVE system if a sufficient set of historical cyclic operational data exists. This information could then be used to help evaluate changes in SVE operations, including system closure. The mass-flux data would also be useful for risk assessments of the impact of vadose-zone sources on groundwater contamination or vapor intrusion. PMID:23516336

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

    NASA Technical Reports Server (NTRS)

    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.

  11. Entropy Analysis of Kinetic Flux Vector Splitting Schemes for the Compressible Euler Equations

    NASA Technical Reports Server (NTRS)

    Shiuhong, Lui; Xu, Jun

    1999-01-01

    Flux Vector Splitting (FVS) scheme is one group of approximate Riemann solvers for the compressible Euler equations. In this paper, the discretized entropy condition of the Kinetic Flux Vector Splitting (KFVS) scheme based on the gas-kinetic theory is proved. The proof of the entropy condition involves the entropy definition difference between the distinguishable and indistinguishable particles.

  12. Impact of water use efficiency on eddy covariance flux partitioning using correlation structure analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Partitioned land surfaces fluxes (e.g. evaporation, transpiration, photosynthesis, and ecosystem respiration) are needed as input, calibration, and validation data for numerous hydrological and land surface models. However, one of the most commonly used techniques for measuring land surface fluxes,...

  13. Perturbation analysis of rail guns powered by explosive magnetic flux compression

    SciTech Connect

    Peterson, D.R.; Fowler, C.M.

    1980-01-01

    Perturbation methods are used to predict the performance of rail guns powered by explosive magnetic flux compression, and the results are compared with experimental data. The problem of designing explosive magnetic flux compression generators for optimum rail gun performance is also discussed.

  14. Cost-effectiveness analysis of online hemodiafiltration versus high-flux hemodialysis

    PubMed Central

    Ramponi, Francesco; Ronco, Claudio; Mason, Giacomo; Rettore, Enrico; Marcelli, Daniele; Martino, Francesca; Neri, Mauro; Martin-Malo, Alejandro; Canaud, Bernard; Locatelli, Francesco

    2016-01-01

    Background Clinical studies suggest that hemodiafiltration (HDF) may lead to better clinical outcomes than high-flux hemodialysis (HF-HD), but concerns have been raised about the cost-effectiveness of HDF versus HF-HD. Aim of this study was to investigate whether clinical benefits, in terms of longer survival and better health-related quality of life, are worth the possibly higher costs of HDF compared to HF-HD. Methods The analysis comprised a simulation based on the combined results of previous published studies, with the following steps: 1) estimation of the survival function of HF-HD patients from a clinical trial and of HDF patients using the risk reduction estimated in a meta-analysis; 2) simulation of the survival of the same sample of patients as if allocated to HF-HD or HDF using three-state Markov models; and 3) application of state-specific health-related quality of life coefficients and differential costs derived from the literature. Several Monte Carlo simulations were performed, including simulations for patients with different risk profiles, for example, by age (patients aged 40, 50, and 60 years), sex, and diabetic status. Scatter plots of simulations in the cost-effectiveness plane were produced, incremental cost-effectiveness ratios were estimated, and cost-effectiveness acceptability curves were computed. Results An incremental cost-effectiveness ratio of €6,982/quality-adjusted life years (QALY) was estimated for the baseline cohort of 50-year-old male patients. Given the commonly accepted threshold of €40,000/QALY, HDF is cost-effective. The probabilistic sensitivity analysis showed that HDF is cost-effective with a probability of ~81% at a threshold of €40,000/QALY. It is fundamental to measure the outcome also in terms of quality of life. HDF is more cost-effective for younger patients. Conclusion HDF can be considered cost-effective compared to HF-HD. PMID:27703388

  15. Quantitative analysis of autophagic flux by confocal pH-imaging of autophagic intermediates

    PubMed Central

    Maulucci, Giuseppe; Chiarpotto, Michela; Papi, Massimiliano; Samengo, Daniela; Pani, Giovambattista; De Spirito, Marco

    2015-01-01

    Although numerous techniques have been developed to monitor autophagy and to probe its cellular functions, these methods cannot evaluate in sufficient detail the autophagy process, and suffer limitations from complex experimental setups and/or systematic errors. Here we developed a method to image, contextually, the number and pH of autophagic intermediates by using the probe mRFP-GFP-LC3B as a ratiometric pH sensor. This information is expressed functionally by AIPD, the pH distribution of the number of autophagic intermediates per cell. AIPD analysis reveals how intermediates are characterized by a continuous pH distribution, in the range 4.5–6.5, and therefore can be described by a more complex set of states rather than the usual biphasic one (autophagosomes and autolysosomes). AIPD shape and amplitude are sensitive to alterations in the autophagy pathway induced by drugs or environmental states, and allow a quantitative estimation of autophagic flux by retrieving the concentrations of autophagic intermediates. PMID:26506895

  16. The flux of organic matter through a peatland ecosystem - evidence from thermogravimetric analysis

    NASA Astrophysics Data System (ADS)

    Worrall, Fred; Moody, Catherine; Clay, Gareth

    2016-04-01

    Carbon budgets of peatlands are now common and studies have considered nitrogen, oxygen and energy budgets, but no study has considered the whole composition of the organic matter as it transfers through and into a peatland. Organic matter samples were taken from each organic matter reservoir found in and each fluvial flux from a peatland and analysed the samples by thermogravimetric analysis. The samples analysed were: aboveground, belowground, heather, mosses and sedges, litter layer, a peat core, and monthly samples of particulate and dissolved organic matter. All organic matter samples were taken from a 100% peat catchment within Moor House National Nature Reserve in the North Pennines, UK, and collected samples were compared to standards of lignin, cellulose, humic acid and plant protein. Results showed that the thermogravimetric trace of the sampled organic matter were distinctive with the DOM traces being marked out by very low thermal stability relative other organic matter types. The peat profile shows a significant trend with depth from vegetation- to lignin-like composition. When all traces are weighted according to the observed dry matter and carbon budgets for the catchment then it is possible to judge what has been lost in the transition through and into the ecosystem. By plotting this "lost" trace it possible to assess its composition which is either 97% cellulose and 3% humic acid or 92% and 8% lignin. This has important implications for what controls the organic matter balance of peatlands and it suggests that the oxidation state (OR) of peatland is less than 1.

  17. Simplified Analysis of Airspike Heat Flux Into Lightcraft Thermal Management System

    NASA Astrophysics Data System (ADS)

    Head, Dean R.; Seo, Junghwa; Cassenti, Brice N.; Myrabo, Leik N.

    2005-04-01

    An approximate method is presented for estimating the airspike heat flux into a 9-meter diameter lightcraft, integrated over its flight to low Earth orbit. The super-pressure lightcraft's exotic twin-hull, sandwich structure is assumed to be fabricated from SiC/SiC thin-film ceramic matrix composites of semiconductor grade purity, giving superior structural properties while being transparent to 35-GHz microwave radiation. The vehicle's MHD slipstream accelerator engine is energized by an annular microwave power beam — converted on-board into DC electric power by two concentric, water-cooled microwave rectenna arrays. The vehicle's airspike is created by a central 3-m diameter laser beam that sustains a laser-supported detonation wave at a distance of 10-m ahead of the craft; the LSD wave propagates up the beam with a velocity that matches the lightcraft's flight speed. The simplified analysis, which is based on aerodynamic heating during re-entry, shows that helium flowing at a velocity of 10 m/s through the lightcraft's double-hull is sufficient to keep the outer, 0.13-mm thick SiC skin safely under its maximum service temperature. The interior helium pressurant that maintains the structural integrity of this exotic pressure-airship, increases in temperature by only 25 K during the flight to LEO.

  18. Magnetic Flux Leakage and Principal Component Analysis for metal loss approximation in a pipeline

    NASA Astrophysics Data System (ADS)

    Ruiz, M.; Mujica, L. E.; Quintero, M.; Florez, J.; Quintero, S.

    2015-07-01

    Safety and reliability of hydrocarbon transportation pipelines represent a critical aspect for the Oil an Gas industry. Pipeline failures caused by corrosion, external agents, among others, can develop leaks or even rupture, which can negatively impact on population, natural environment, infrastructure and economy. It is imperative to have accurate inspection tools traveling through the pipeline to diagnose the integrity. In this way, over the last few years, different techniques under the concept of structural health monitoring (SHM) have continuously been in development. This work is based on a hybrid methodology that combines the Magnetic Flux Leakage (MFL) and Principal Components Analysis (PCA) approaches. The MFL technique induces a magnetic field in the pipeline's walls. The data are recorded by sensors measuring leakage magnetic field in segments with loss of metal, such as cracking, corrosion, among others. The data provide information of a pipeline with 15 years of operation approximately, which transports gas, has a diameter of 20 inches and a total length of 110 km (with several changes in the topography). On the other hand, PCA is a well-known technique that compresses the information and extracts the most relevant information facilitating the detection of damage in several structures. At this point, the goal of this work is to detect and localize critical loss of metal of a pipeline that are currently working.

  19. Hydrogen Explosion Analysis for Cold Source Installation at the High Flux Isotope Reactor

    SciTech Connect

    Cook, David Howard

    2008-01-01

    Installation of a cold neutron source in the High Flux Isotope Reactor (HFIR) involved introduction of pressurized, cryogenic hydrogen into the facility and created explosion hazards to reactor safety-related equipment and personnel. Evaluation of potential hydrogen releases and facility/personnel consequences as a result of explosions was a key part of the safety analyses submitted to the DOE to obtain approval for testing and operation with hydrogen. This paper involves a description of the various hydrogen release and explosion consequence analyses that were performed. The range of explosion calculations involved (1) a detonation analysis using a 2D-transient CTH code model, (2) various BLAST/FX code models to estimate structural damage from equivalent point TNT sources, (3) a BLASTX code model to propagate shock and gas flow overpressures from a point TNT source, (4) a spreadsheet that combined a TNT-quivalence model and strong deflagration methods, and (5) a hydrogen jet model to evaluate potential high pressure jet releases.

  20. ¹³C-based metabolic flux analysis of recombinant Pichia pastoris.

    PubMed

    Ferrer, Pau; Albiol, Joan

    2014-01-01

    Overexpression of a foreign protein may negatively affect several cell growth parameters, as well as cause cellular stress. Central (or core) metabolism plays a crucial role since it supplies energy, reduction equivalents, and precursor molecules for the recombinant product, cell's maintenance, and growth needs. However, the number of quantitative physiology studies of the impact of recombinant protein production on the central metabolic pathways of yeast cell factories has been traditionally rather limited, thereby hampering the application of rational strain engineering strategies targeting central metabolism.The development and application of quantitative physiology and modelling tools and methodologies is allowing for a systems-level understanding of the effect of bioprocess parameters such as growth rate, temperature, oxygen availability, and substrate(s) choice on metabolism, and its subsequent interactions with recombinant protein synthesis, folding, and secretion.Here, we review the recent developments and applications of (13)C-based metabolic flux analysis ((13)C-MFA) of Pichia pastoris and the gained understanding of the metabolic behavior of this yeast in recombinant protein production bioprocesses. We also discuss the potential of multilevel studies integrating (13)C-MFA with other omics analyses, as well as future perspectives on the metabolic modelling approaches to study and design metabolic engineering strategies for improved protein production.

  1. Constrictor: Flux Balance Analysis Constraint Modification Provides Insight for Design of Biochemical Networks

    NASA Astrophysics Data System (ADS)

    Erickson, Keesha; Chatterjee, Anushree

    2014-03-01

    The use of in silico methods has become standard practice to correlate the structure of a biochemical network to the expression of a desired phenotype. Flux balance analysis (FBA) is one of the most prevalent techniques for modeling metabolism. FBA models have been successfully applied to obtain growth predictions, theoretical product yields from heterologous pathways, and genome engineering targets. We take inspiration from high-throughput recombineering techniques, which show that combinatorial exploration can reveal optimal mutants, and apply the advantages of computational techniques to analyze these combinations. We introduce Constrictor, an in silico tool for FBA that allows gene mutations to be analyzed in a combinatorial fashion, by applying simulated constraints accounting for regulation of gene expression. We apply this algorithm to study ethylene production in E. coli through the addition of the heterologous ethylene-forming enzyme from P. syringae. Targeting individual reactions as well as sets of reactions results in theoretical ethylene yields that are as much 65% greater than yields calculated using typical FBA. Constrictor is an adaptable technique that can be used to generate and analyze disparate populations of in silico mutants & select gene expression levels.

  2. Implicit flux-split Euler schemes for unsteady aerodynamic analysis involving unstructured dynamic meshes

    NASA Technical Reports Server (NTRS)

    Batina, John T.

    1990-01-01

    Improved algorithm for the solution of the time-dependent Euler equations are presented for unsteady aerodynamic analysis involving unstructured dynamic meshes. The improvements were developed recently to the spatial and temporal discretizations used by unstructured grid flow solvers. The spatial discretization involves a flux-split approach which is naturally dissipative and captures shock waves sharply with at most one grid point within the shock structure. The temporal discretization involves an implicit time-integration scheme using a Gauss-Seidel relaxation procedure which is computationally efficient for either steady or unsteady flow problems. For example, very large time steps may be used for rapid convergence to steady state, and the step size for unsteady cases may be selected for temporal accuracy rather than for numerical stability. Steady and unsteady flow results are presented for the NACA 0012 airfoil to demonstrate applications of the new Euler solvers. The unsteady results were obtained for the airfoil pitching harmonically about the quarter chord. The resulting instantaneous pressure distributions and lift and moment coefficients during a cycle of motion compare well with experimental data. A description of the Euler solvers is presented along with results and comparisons which assess the capability.

  3. Implicit flux-split Euler schemes for unsteady aerodynamic analysis involving unstructured dynamic meshes

    NASA Technical Reports Server (NTRS)

    Batina, John T.

    1990-01-01

    Improved algorithms for the solution of the time-dependent Euler equations are presented for unsteady aerodynamic analysis involving unstructured dynamic meshes. The improvements have been developed recently to the spatial and temporal discretizations used by unstructured grid flow solvers. The spatial discretization involves a flux-split approach which is naturally dissipative and captures shock waves sharply with at most one grid point within the shock structure. The temporal discretization involves an implicit time-integration shceme using a Gauss-Seidel relaxation procedure which is computationally efficient for either steady or unsteady flow problems. For example, very large time steps may be used for rapid convergence to steady state, and the step size for unsteady cases may be selected for temporal accuracy rather than for numerical stability. Steady and unsteady flow results are presented for the NACA 0012 airfoil to demonstrate applications of the new Euler solvers. The unsteady results were obtained for the airfoil pitching harmonically about the quarter chord. The resulting instantaneous pressure distributions and lift and moment coefficients during a cycle of motion compare well with experimental data. The paper presents a description of the Euler solvers along with results and comparisons which assess the capability.

  4. Analysis of actinic flux profiles measured from an ozone sonde balloon

    NASA Astrophysics Data System (ADS)

    Wang, P.; Allaart, M.; Knap, W. H.; Stammes, P.

    2014-12-01

    A green light sensor has been developed at KNMI to measure actinic flux profiles using an ozone sonde balloon. In total, 63 launches with ascending and descending profiles were performed between 2006 and 2010. The measured uncalibrated actinic flux profiles are analyzed using the Doubling Adding KNMI (DAK) radiative transfer model. Values of the cloud optical thickness (COT) along the flight track were taken from the Spinning Enhanced Visible and Infrared Imager (SEVIRI) Cloud Physical Properties (CPP) product. The impact of clouds on the actinic flux profile is evaluated on the basis of the cloud modification factor (CMF) at the cloud top and cloud base, which is the ratio between the actinic fluxes for cloudy and clear-sky scenes. The impact of clouds on the actinic flux is clearly detected: the largest enhancement occurs at the cloud top due to multiple scattering. The actinic flux decreases almost linearly from cloud top to cloud base. Above the cloud top the actinic flux also increases compared to clear-sky scenes. We find that clouds can increase the actinic flux to 2.3 times of the clear-sky value at cloud top and decrease it to about 0.05 at cloud base. The relationship between CMF and COT agrees well with DAK simulations, except for a few outliers. Good agreement is found between the DAK simulated actinic flux profiles and the observations for single layer clouds in fully overcast scenes. The instrument is suitable for operational balloon measurements because of its simplicity and low cost. It is worth to further develop the instrument and launch it together with atmospheric chemistry composition sensors.

  5. Flux Balance Analysis of Plant Metabolism: The Effect of Biomass Composition and Model Structure on Model Predictions

    PubMed Central

    Yuan, Huili; Cheung, C. Y. Maurice; Hilbers, Peter A. J.; van Riel, Natal A. W.

    2016-01-01

    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 modeling constraints and objective function showed that model predictions were sensitive to the structure of the models, highlighting large discrepancies between the published models. PMID:27200014

  6. Analysis of the transient calibration of heat flux sensors: One dimensional case

    NASA Technical Reports Server (NTRS)

    Dybbs, A.; Ling, J. X.

    1989-01-01

    The effect of transient heat flux on heat flux sensor response and calibration is analyzed. A one dimensional case was studied in order to elucidate the key parameters and trends for the problem. It has the added advantage that the solutions to the governing equations can be obtained by analytic means. The analytical results obtained to date indicate that the transient response of a heat flux sensor depends on the thermal boundary conditions, the geometry and the thermal properties of the sensor. In particular it was shown that if the thermal diffusivity of the sensor is small, then the transient behavior must be taken into account.

  7. Pool size measurements facilitate the determination of fluxes at branching points in non-stationary metabolic flux analysis: the case of Arabidopsis thaliana.

    PubMed

    Heise, Robert; Fernie, Alisdair R; Stitt, Mark; Nikoloski, Zoran

    2015-01-01

    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 labeling pattern. Therefore, our findings indicate the necessity for development of techniques for accurate pool size measurements to improve the quality of flux estimates from non-stationary flux estimates in intact plant cells in the absence of alternative flux measurements.

  8. Pool size measurements facilitate the determination of fluxes at branching points in non-stationary metabolic flux analysis: the case of Arabidopsis thaliana

    PubMed Central

    Heise, Robert; Fernie, Alisdair R.; Stitt, Mark; Nikoloski, Zoran

    2015-01-01

    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 labeling pattern. Therefore, our findings indicate the necessity for development of techniques for accurate pool size measurements to improve the quality of flux estimates from non-stationary flux estimates in intact plant cells in the absence of alternative flux measurements. PMID:26082786

  9. Sensitivity analysis of flux determination in heart by H₂ ¹⁸O -provided labeling using a dynamic Isotopologue model of energy transfer pathways.

    PubMed

    Schryer, David W; Peterson, Pearu; Illaste, Ardo; Vendelin, Marko

    2012-01-01

    To characterize intracellular energy transfer in the heart, two organ-level methods have frequently been employed: ³¹P − NMR inversion and saturation transfer, and dynamic ¹⁸O labeling. Creatine kinase (CK) fluxes obtained by following oxygen labeling have been considerably smaller than the fluxes determined by ³¹P − NMR saturation transfer. It has been proposed that dynamic ¹⁸O labeling determines net flux through CK shuttle, whereas ³¹P − NMR saturation transfer measures total unidirectional flux. However, to our knowledge, no sensitivity analysis of flux determination by oxygen labeling has been performed, limiting our ability to compare flux distributions predicted by different methods. Here we analyze oxygen labeling in a physiological heart phosphotransfer network with active CK and adenylate kinase (AdK) shuttles and establish which fluxes determine the labeling state. A mathematical model consisting of a system of ordinary differential equations was composed describing ¹⁸O enrichment in each phosphoryl group and inorganic phosphate. By varying flux distributions in the model and calculating the labeling, we analyzed labeling sensitivity to different fluxes in the heart. We observed that the labeling state is predominantly sensitive to total unidirectional CK and AdK fluxes and not to net fluxes. We conclude that measuring dynamic incorporation of ¹⁸O into the high-energy phosphotransfer network in heart does not permit unambiguous determination of energetic fluxes with a higher magnitude than the ATP synthase rate when the bidirectionality of fluxes is taken into account. Our analysis suggests that the flux distributions obtained using dynamic ¹⁸O labeling, after removing the net flux assumption, are comparable with those from ³¹P − NMR inversion and saturation transfer.

  10. Blocking laws analysis of dead-end constant flux microfiltration of compressible cakes.

    PubMed

    Chellam, Shankararaman; Xu, Wendong

    2006-09-01

    New blocking law models for dead-end constant flux microfiltration of colloids forming cakes that compressed in a linear and power law manner were derived. Constant pressure and constant flux experiments were performed using bacteria, colloidal silica, and treated natural waters to validate these new models and quantitatively verify blocking law predictions on the role of cake compressibility in microfilter fouling. Statistically invariant values of cake specific resistance and compressibility were obtained for constant flux and constant pressure operation for each feed suspension. This suggests that colloids formed cakes whose hydraulic resistance is dominated by a morphology that did not depend on their mode of deposition, confirming that the cake permeability was determined by the instantaneous pressure. Additionally, an inverse relationship between extracellular polymeric substances (EPS) secreted by bacteria and hydrodynamic flux restoration procedures was obtained demonstrating the importance of linking EPS to backwashing frequency when bacteria are present in the feed water.

  11. Three-axis magnetic flux leakage in-line inspection simulation based on finite-element analysis

    NASA Astrophysics Data System (ADS)

    Feng, Jian; Zhang, Jun-Feng; Lu, Sen-Xiang; Wang, Hong-Yang; Ma, Rui-Ze

    2013-01-01

    With the increase of pipelines, corrosion leakage accidents happen frequently. Therefore, nondestructive testing technology is important for ensuring the safe operation of the pipelines and energy mining. In this paper, the structure and principle of magnetic flux leakage (MFL) in-line inspection system is introduced first. Besides, a mathematic model of the system according to the ampere circuit rule, flux continuity theorem, and column coordinate transform is built, and the magnetic flux density in every point of space is calculated based on the theory of finite element analysis. Then we analyze and design the disposition of measurement section probes and sensors combining both three-axis MFL in-line inspection and multi-sensor fusion technology. Its advantage is that the three-axis changes of magnetic flux leakage field are measured by the multi-probes at the same time, so we can determine various defects accurately. Finally, the theory of finite element analysis is used to build a finite element simulation model, and the relationship between defects and MFL inspection signals is studied. Simulation and experiment results verify that the method not only enhances the detection ability to different types of defects but also improves the precision and reliability of the inspection system.

  12. Analysis of solar receiver flux distributions for US/Russian solar dynamic system demonstration on the MIR Space Station

    NASA Technical Reports Server (NTRS)

    Kerslake, Thomas W.; Fincannon, James

    1995-01-01

    The United States and Russia have agreed to jointly develop a solar dynamic (SD) system for flight demonstration on the Russian MIR space station starting in late 1997. Two important components of this SD system are the solar concentrator and heat receiver provided by Russia and the U.S., respectively. This paper describes optical analysis of the concentrator and solar flux predictions on target receiver surfaces. The optical analysis is performed using the code CIRCE2. These analyses account for finite sun size with limb darkening, concentrator surface slope and position errors, concentrator petal thermal deformation, gaps between petals, and the shading effect of the receiver support struts. The receiver spatial flux distributions are then combined with concentrator shadowing predictions. Geometric shadowing patterns are traced from the concentrator to the target receiver surfaces. These patterns vary with time depending on the chosen MIR flight attitude and orbital mechanics of the MIR spacecraft. The resulting predictions provide spatial and temporal receiver flux distributions for any specified mission profile. The impact these flux distributions have on receiver design and control of the Brayton engine are discussed.

  13. Analysis of the PKT correction for direct CO2 flux measurements over the ocean

    NASA Astrophysics Data System (ADS)

    Landwehr, S.; Miller, S. D.; Smith, M. J.; Saltzman, E. S.; Ward, B.

    2014-04-01

    Eddy covariance measurements of air-sea CO2 fluxes can be affected by cross-sensitivities of the CO2 measurement to water vapour, resulting in order-of-magnitude biases. Well-established causes for these biases are (i) cross-sensitivity of the broadband non-dispersive infrared sensors due to band-broadening and spectral overlap (commercial sensors typically correct for this) and (ii) the effect of air density fluctuations (removed by determining the dry air CO2 mixing ratio). Another bias related to water vapour fluctuations has recently been observed with open-path sensors, attributed to sea salt build-up and water films on sensor optics. Two very different approaches have been used to deal with these water vapour-related biases. Miller et al. (2010) employed a membrane drier to physically eliminate 97% of the water vapour fluctuations in the sample air before it entered a closed-path gas analyser. Prytherch et al. (2010a) employed the empirical (Peter K. Taylor, PKT) post-processing correction to correct open-path sensor data. In this paper, we test these methods side by side using data from the Surface Ocean Aerosol Production (SOAP) experiment in the Southern Ocean. The air-sea CO2 flux was directly measured with four closed-path analysers, two of which were positioned down-stream of a membrane dryer. The CO2 fluxes from the two dried gas analysers matched each other and were in general agreement with common parameterisations. The flux estimates from the un-dried sensors agreed with the dried sensors only during periods with low latent heat flux (≤7 W m-2). When latent heat flux was higher, CO2 flux estimates from the un-dried sensors exhibited large scatter and an order-of-magnitude bias. Applying the PKT correction to the flux data from the un-dried analysers did not remove the bias when compared to the data from the dried gas analyser. The results of this study demonstrate the validity of measuring CO2 fluxes using a pre-dried air stream and show that

  14. Simulating cyanobacterial phenotypes by integrating flux balance analysis, kinetics, and a light distribution function

    DOE PAGES

    He, Lian; Wu, Stephen G.; Wan, Ni; Reding, Adrienne C.; Tang, Yinjie J.

    2015-12-24

    In this study, genome-scale models (GSMs) are widely used to predict cyanobacterial phenotypes in photobioreactors (PBRs). However, stoichiometric GSMs mainly focus on fluxome that result in maximal yields. Cyanobacterial metabolism is controlled by both intracellular enzymes and photobioreactor conditions. To connect both intracellular and extracellular information and achieve a better understanding of PBRs productivities, this study integrates a genome-scale metabolic model of Synechocystis 6803 with growth kinetics, cell movements, and a light distribution function. The hybrid platform not only maps flux dynamics in cells of sub-populations but also predicts overall production titer and rate in PBRs. Analysis of the integratedmore » GSM demonstrates several results. First, cyanobacteria are capable of reaching high biomass concentration (>20 g/L in 21 days) in PBRs without light and CO2 mass transfer limitations. Second, fluxome in a single cyanobacterium may show stochastic changes due to random cell movements in PBRs. Third, insufficient light due to cell self-shading can activate the oxidative pentose phosphate pathway in subpopulation cells. Fourth, the model indicates that the removal of glycogen synthesis pathway may not improve cyanobacterial bio-production in large-size PBRs, because glycogen can support cell growth in the dark zones. Based on experimental data, the integrated GSM estimates that Synechocystis 6803 in shake flask conditions has a photosynthesis efficiency of ~2.7 %. Conclusions: The multiple-scale integrated GSM, which examines both intracellular and extracellular domains, can be used to predict production yield/rate/titer in large-size PBRs. More importantly, genetic engineering strategies predicted by a traditional GSM may work well only in optimal growth conditions. In contrast, the integrated GSM may reveal mutant physiologies in diverse bioreactor conditions, leading to the design of robust strains with high chances of success in

  15. Simulating cyanobacterial phenotypes by integrating flux balance analysis, kinetics, and a light distribution function

    SciTech Connect

    He, Lian; Wu, Stephen G.; Wan, Ni; Reding, Adrienne C.; Tang, Yinjie J.

    2015-12-24

    In this study, genome-scale models (GSMs) are widely used to predict cyanobacterial phenotypes in photobioreactors (PBRs). However, stoichiometric GSMs mainly focus on fluxome that result in maximal yields. Cyanobacterial metabolism is controlled by both intracellular enzymes and photobioreactor conditions. To connect both intracellular and extracellular information and achieve a better understanding of PBRs productivities, this study integrates a genome-scale metabolic model of Synechocystis 6803 with growth kinetics, cell movements, and a light distribution function. The hybrid platform not only maps flux dynamics in cells of sub-populations but also predicts overall production titer and rate in PBRs. Analysis of the integrated GSM demonstrates several results. First, cyanobacteria are capable of reaching high biomass concentration (>20 g/L in 21 days) in PBRs without light and CO2 mass transfer limitations. Second, fluxome in a single cyanobacterium may show stochastic changes due to random cell movements in PBRs. Third, insufficient light due to cell self-shading can activate the oxidative pentose phosphate pathway in subpopulation cells. Fourth, the model indicates that the removal of glycogen synthesis pathway may not improve cyanobacterial bio-production in large-size PBRs, because glycogen can support cell growth in the dark zones. Based on experimental data, the integrated GSM estimates that Synechocystis 6803 in shake flask conditions has a photosynthesis efficiency of ~2.7 %. Conclusions: The multiple-scale integrated GSM, which examines both intracellular and extracellular domains, can be used to predict production yield/rate/titer in large-size PBRs. More importantly, genetic engineering strategies predicted by a traditional GSM may work well only in optimal growth conditions. In contrast, the integrated GSM may reveal mutant physiologies in diverse bioreactor conditions, leading to the design of robust strains with high

  16. Production process monitoring by serial mapping of microbial carbon flux distributions using a novel Sensor Reactor approach: II--(13)C-labeling-based metabolic flux analysis and L-lysine production.

    PubMed

    Drysch, A; El Massaoudi, M; Mack, C; Takors, R; de Graaf, A A; Sahm, H

    2003-04-01

    Corynebacterium glutamicum is intensively used for the industrial large-scale (fed-) batch production of amino acids, especially glutamate and lysine. However, metabolic flux analyses based on 13C-labeling experiments of this organism have hitherto been restricted to small-scale batch conditions and carbon-limited chemostat cultures, and are therefore of questionable relevance for industrial fermentations. To lever flux analysis to the industrial level, a novel Sensor Reactor approach was developed (El Massaoudi et al., Metab. Eng., submitted), in which a 300-L production reactor and a 1-L Sensor Reactor are run in parallel master/slave modus, thus enabling 13C-based metabolic flux analysis to generate a series of flux maps that document large-scale fermentation courses in detail. We describe the successful combination of this technology with nuclear magnetic resonance (NMR) analysis, metabolite balancing methods and a mathematical description of 13C-isotope labelings resulting in a powerful tool for quantitative pathway analysis during a batch fermentation. As a first application, 13C-based metabolic flux analysis was performed on exponentially growing, lysine-producing C. glutamicum MH20-22B during three phases of a pilot-scale batch fermentation. By studying the growth, (co-) substrate consumption and (by-) product formation, the similarity of the fermentations in production and Sensor Reactor was verified. Applying a generally applicable mathematical model, which included metabolite and carbon labeling balances for the analysis of proteinogenic amino acid 13C-isotopomer labeling data, the in vivo metabolic flux distribution was investigated during subsequent phases of exponential growth. It was shown for the first time that the in vivo reverse C(4)-decarboxylation flux at the anaplerotic node in C. glutamicum significantly decreased (70%) in parallel with threefold increased lysine formation during the investigated subsequent phases of exponential growth.

  17. ANALYSIS OF WATER AND ENERGY FLUXES USING SATELLITE, ENERGY BALANCE MODELING AND OBSERVATIONS (Invited)

    NASA Astrophysics Data System (ADS)

    Irmak, A.

    2009-12-01

    Surface energy fluxes, including net radiation (Rn), sensible heat (H), latent heat (LE), and soil heat flux (G) are critical in surface energy balance of any terrain or landscapes. Estimation or measurement of these energy fluxes is important for completing the water balance in terrestrial ecosystems, and therefore accurately predicting the effects of global climate and land use change. The objectives of this study were to (1) use METRICtm (Mapping Evapotranspiration at high Resolution using Internalized Calibration) model for estimating land surface energy fluxes in Nebraska (NE) by utilizing satellite remote sensing data, (2) identify model bias in energy balance components compared with measurements from Bowen Ratio Energy Balance System (BREBS) in a subsurface drip-irrigated maize field in South-central Nebraska, and (3) understand the partitioning of available energy into latent heat for corn and soybean cropping systems at large scale. A total of 15 Landsat images were processed to estimate instantaneous surface energy fluxes at Landsat overpasses with METRIC model. Results showed that the model predictions of the surface energy fluxes and daily evapotranspiration were correlated well with the BREBS measurements. There is a need, however, to test the performance of the model with in-situ observations in other locations with different dataset before utilizing it for crucial water regulatory and policy decisions. The METRICtm approach illustrated how an ‘off-the-shelf’ model can be applied operationally over a significant time period and how that model behaves. The findings makes considerable contribution to our understanding of estimating land surface energy fluxes using remote sensing approach and experimentally describes the operational characteristics of METRICtm and presents its limitations.

  18. Fed-batch culture of Escherichia coli for L-valine production based on in silico flux response analysis.

    PubMed

    Park, Jin Hwan; Kim, Tae Yong; Lee, Kwang Ho; Lee, Sang Yup

    2011-04-01

    We have previously reported the development of a 100% genetically defined engineered Escherichia coli strain capable of producing L-valine from glucose with a high yield of 0.38 g L-valine per gram glucose (0.58 mol L-valine per mol glucose) by batch culture. Here we report a systems biological strategy of employing flux response analysis in bioprocess development using L-valine production by fed-batch culture as an example. Through the systems-level analysis, the source of ATP was found to be important for efficient L-valine production. There existed a trade-off between L-valine production and biomass formation, which was optimized for the most efficient L-valine production. Furthermore, acetic acid feeding strategy was optimized based on flux response analysis. The final fed-batch cultivation strategy allowed production of 32.3 g/L L-valine, the highest concentration reported for E. coli. This approach of employing systems-level analysis of metabolic fluxes in developing fed-batch cultivation strategy would also be applicable in developing strategies for the efficient production of other bioproducts.

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

    SciTech Connect

    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.

  20. Uncertainty analysis of steady state incident heat flux measurements in hydrocarbon fuel fires.

    SciTech Connect

    Nakos, James Thomas

    2005-12-01

    The objective of this report is to develop uncertainty estimates for three heat flux measurement techniques used for the measurement of incident heat flux in a combined radiative and convective environment. This is related to the measurement of heat flux to objects placed inside hydrocarbon fuel (diesel, JP-8 jet fuel) fires, which is very difficult to make accurately (e.g., less than 10%). Three methods will be discussed: a Schmidt-Boelter heat flux gage; a calorimeter and inverse heat conduction method; and a thin plate and energy balance method. Steady state uncertainties were estimated for two types of fires (i.e., calm wind and high winds) at three times (early in the fire, late in the fire, and at an intermediate time). Results showed a large uncertainty for all three methods. Typical uncertainties for a Schmidt-Boelter gage ranged from {+-}23% for high wind fires to {+-}39% for low wind fires. For the calorimeter/inverse method the uncertainties were {+-}25% to {+-}40%. The thin plate/energy balance method the uncertainties ranged from {+-}21% to {+-}42%. The 23-39% uncertainties for the Schmidt-Boelter gage are much larger than the quoted uncertainty for a radiative only environment (i.e ., {+-}3%). This large difference is due to the convective contribution and because the gage sensitivities to radiative and convective environments are not equal. All these values are larger than desired, which suggests the need for improvements in heat flux measurements in fires.

  1. Mathematical analysis for internal filtration of convection-enhanced high-flux hemodialyzer.

    PubMed

    Lee, Jung Chan; Lee, Kyungsoo; Kim, Hee Chan

    2012-10-01

    Structural modifications using a conventional hemodialyzer improved the internal filtration and clearance of middle molecular weight wastes by enhanced convection effect. In this study, we employed a mathematical model describing the internal filtration rate as well as the hemodynamic and hematologic parameters in highflux dialyzer to interpret the previous reported experimental results. Conventional high-flux hemodialysis and convection-enhanced high-flux hemodialysis were configured in the mathematical forms and integrated into the iterative numerical method to predict the internal filtration phenomena inside the dialyzers during dialysis. The distributions of blood pressure, dialysate pressure, oncotic pressure, blood flow rates, dialysate flow rates, local ultrafiltration, hematocrit, protein concentration and blood viscosity along the axial length of dialyzer were calculated in order to estimate the internal filtration volume. The results show that the filtration volumes by internal filtration is two times higher in a convection-enhanced high-flux hemodialyzer than in a conventional high-flux hemodialzer and explains the experimental result of improved clearance of middle molecular size waste in convection-enhanced high-flux hemodialyzer.

  2. As-Run Thermal Analysis of the GTL-1 Experiment Irradiated in the ATR South Flux Trap

    SciTech Connect

    Donna P. Guillen

    2011-05-01

    The GTL-1 experiment was conducted to assess corrosion the performance of the proposed Boosted Fast Flux Loop booster fuel at heat flux levels {approx}30% above the design operating condition. Sixteen miniplates fabricated from 25% enriched, high-density U3Si2/Al dispersion fuel with 6061 aluminum cladding were subjected to peak beginning of cycle (BOC) heat fluxes ranging from 411 W/cm2 to 593 W/cm2. Miniplates fabricated with three different fuel variations (without fines, annealed, and with standard powder) performed equally well, with negligible irradiation-induced swelling and a normal fission density gradient. Both the standard and the modified prefilm procedures produced hydroxide films that adequately protected the miniplates from failure. A detailed finite element model was constructed to calculate temperatures and heat flux for an as-run cycle average effective south lobe power of 25.4 MW(t). Results of the thermal analysis are given at four times during the cycle: BOC at 0 effective full power days (EFPD), middle of cycle (MOC) at 18 EFPD, MOC at 36 EFPD, and end of cycle at 48.9 EFPD. The highest temperatures and heat fluxes occur at the BOC and decrease in a linear manner throughout the cycle. Miniplate heat flux levels and fuel, cladding, hydroxide, and coolant-hydroxide interface temperatures were calculated using the average measured hydroxide thickness on each miniplate. The hydroxide layers are the largest on miniplates nearest to the core midplane, where heat flux and temperature are highest. The hydroxide layer thickness averages 20.4 {mu}m on the six hottest miniplates (B3, B4, C1, C2, C3, and C4). This tends to exacerbate the heating of these miniplates, since a thicker hydroxide layer reduces the heat transfer from the fuel to the coolant. These six hottest miniplates have the following thermal characteristics at BOC: (1) Peak fuel centerline temperature >300 C; (2) Peak cladding temperature >200 C; (3) Peak hydroxide temperature >190 C; (4

  3. Flux Balance Analysis with Objective Function Defined by Proteomics Data-Metabolism of Mycobacterium tuberculosis Exposed to Mefloquine.

    PubMed

    Montezano, Daniel; Meek, Laura; Gupta, Rashmi; Bermudez, Luiz E; Bermudez, José C M

    2015-01-01

    We present a study of the metabolism of the Mycobacterium tuberculosis after exposure to antibiotics using proteomics data and flux balance analysis (FBA). The use of FBA to study prokaryotic organisms is well-established and allows insights into the metabolic pathways chosen by the organisms under different environmental conditions. To apply FBA a specific objective function must be selected that represents the metabolic goal of the organism. FBA estimates the metabolism of the cell by linear programming constrained by the stoichiometry of the reactions in an in silico metabolic model of the organism. It is assumed that the metabolism of the organism works towards the specified objective function. A common objective is the maximization of biomass. However, this goal is not suitable for situations when the bacterium is exposed to antibiotics, as the goal of organisms in these cases is survival and not necessarily optimal growth. In this paper we propose a new approach for defining the FBA objective function in studies when the bacterium is under stress. The function is defined based on protein expression data. The proposed methodology is applied to the case when the bacterium is exposed to the drug mefloquine, but can be easily extended to other organisms, conditions or drugs. We compare our method with an alternative method that uses experimental data for adjusting flux constraints. We perform comparisons in terms of essential enzymes and agreement using enzyme abundances. Results indicate that using proteomics data to define FBA objective functions yields less essential reactions with zero flux and lower error rates in prediction accuracy. With flux variability analysis we observe that overall variability due to alternate optima is reduced with the incorporation of proteomics data. We believe that incorporating proteomics data in the objective function used in FBA may help obtain metabolic flux representations that better support experimentally observed features

  4. Reconstruction of heat flux profile on the HL-2A divertor plate with a three-dimensional analysis model

    NASA Astrophysics Data System (ADS)

    Gao, Jin-Ming; Li, Wei; Xia, Zhi-Wei; Pan, Yu-Dong; Lu, Jie; Yi, Ping; Liu, Yi

    2013-01-01

    A three-dimensional analysis model based on the finite element method (FEM) is developed, which can derive the evolution and distribution characteristics of heat flux deposited on the divertor plate from the surface temperature measured by infrared thermography diagnostics. The numerical simulations of surface heating due to localized power bursts and the power deposition calculations demonstrate that this analysis can provide accurate results and useful information about localized hot spots compared with the normal one- and two-dimensional calculations. In this paper, the details of this three-dimensional analysis are presented, and some results in ohmic heating and electron cyclotron resonant heating (ECRH) discharge on HL-2A are given.

  5. An Analysis of Turbulent Heat Fluxes and the Energy Balance During the REFLEX Campaign

    NASA Astrophysics Data System (ADS)

    Tol, Christiaan van der; Timmermans, Wim; Corbari, Chiara; Carrara, Arnaud; Timmermans, Joris; Su, Zhongbo

    2015-12-01

    Three eddy covariance stations were installed at the Barrax experimental farm during the Land-Atmosphere Exchanges (REFLEX) airborne training and measurement campaign to provide ground truth data of energy balance fluxes and vertical temperature and wind profiles. The energy balance closure ratio (EBR) was 105% for a homogeneous camelina site, 86% at a sparse reforestation site, and 73% for a vineyard. We hypothesize that the lower closure in the last site was related to the limited fetch. Incorporating a vertical gradient of soil thermal properties decreased the RMSE of the energy balance at the camelina site by 16 W m-2. At the camelina site, eddy covariance estimates of sensible and latent heat fluxes could be reproduced well using mean vertical profiles of wind and temperature, provided that the Monin-Obukhov length is known. Measured surface temperature and sensible heat fluxes suggested high excess resistance for heat (kB-1 = 17).

  6. Computational Platform for Flux Analysis Using 13C-Label Tracing- Phase I SBIR Final Report

    SciTech Connect

    Van Dien, Stephen J.

    2005-04-12

    Isotopic label tracing is a powerful experimental technique that can be combined with metabolic models to quantify metabolic fluxes in an organism under a particular set of growth conditions. In this work we constructed a genome-scale metabolic model of Methylobacterium extorquens, a facultative methylotroph with potential application in the production of useful chemicals from methanol. A series of labeling experiments were performed using 13C-methanol, and the resulting distribution of labeled carbon in the proteinogenic amino acids was determined by mass spectrometry. Algorithms were developed to analyze this data in context of the metabolic model, yielding flux distributions for wild-type and several engineered strains of M. extorquens. These fluxes were compared to those predicted by model simulation alone, and also integrated with microarray data to give an improved understanding of the metabolic physiology of this organism.

  7. A benchmark analysis of radiation flux distribution for Boron Neutron Capture Therapy of canine brain tumors

    SciTech Connect

    Moran, J.M.

    1992-02-01

    Calculations of radiation flux and dose distributions for Boron Neutron Capture Therapy (BNCT) of brain tumors are typically performed using sophisticated three-dimensional analytical models based on either a homogeneous approximation or a simplified few-region approximation to the actual highly-heterogeneous geometry of the irradiation volume. Such models should be validated by comparison with calculations using detailed models in which all significant macroscopic tissue heterogeneities and geometric structures are explicitly represented as faithfully as possible. This work describes a validation exercise for BNCT of canine brain tumors. Geometric measurements of the canine anatomical structures of interest for this work were performed by dissecting and examining two essentially identical Labrador Retriever heads. Chemical analyses of various tissue samples taken during the dissections were conducted to obtain measurements of elemental compositions for tissues of interest. The resulting geometry and tissue composition data were then used to construct a detailed heterogeneous calculational model of the Labrador Retriever head. Calculations of three-dimensional radiation flux distributions pertinent to BNCT were performed for the model using the TORT discrete-ordinates radiation transport code. The calculations were repeated for a corresponding volume-weighted homogeneous tissue model. Comparison of the results showed that the peak neutron and photon flux magnitudes were quite similar for the two models (within 5%), but that the spatial flux profiles were shifted in the heterogeneous model such that the fluxes in some locations away from the peak differed from the corresponding fluxes in the homogeneous model by as much as 10-20%. Differences of this magnitude can be therapeutically significant, emphasizing the need for proper validation of simplified treatment planning models.

  8. Suspended sediment fluxes in a tidal wetland: Measurement, controlling factors, and error analysis

    USGS Publications Warehouse

    Ganju, N.K.; Schoellhamer, D.H.; Bergamaschi, B.A.

    2005-01-01

    Suspended sediment fluxes to and from tidal wetlands are of increasing concern because of habitat restoration efforts, wetland sustainability as sea level rises, and potential contaminant accumulation. We measured water and sediment fluxes through two channels on Browns Island, at the landward end of San Francisco Bay, United States, to determine the factors that control sediment fluxes on and off the island. In situ instrumentation was deployed between October 10 and November 13, 2003. Acoustic Doppler current profilers and the index velocity method were employed to calculate water fluxes. Suspended sediment concentrations (SSC) were determined with optical sensors and cross-sectional water sampling. All procedures were analyzed for their contribution to total error in the flux measurement. The inability to close the water balance and determination of constituent concentration were identified as the main sources of error; total error was 27% for net sediment flux. The water budget for the island was computed with an unaccounted input of 0.20 m 3 s-1 (22% of mean inflow), after considering channel flow, change in water storage, evapotranspiration, and precipitation. The net imbalance may be a combination of groundwater seepage, overland flow, and flow through minor channels. Change of island water storage, caused by local variations in water surface elevation, dominated the tidalty averaged water flux. These variations were mainly caused by wind and barometric pressure change, which alter regional water levels throughout the Sacramento-San Joaquin River Delta. Peak instantaneous ebb flow was 35% greater than peak flood flow, indicating an ebb-dominant system, though dominance varied with the spring-neap cycle. SSC were controlled by wind-wave resuspension adjacent to the island and local tidal currents that mobilized sediment from the channel bed. During neap tides sediment was imported onto the island but during spring tides sediment was exported because the main

  9. Recent advances in elementary flux modes and yield space analysis as useful tools in metabolic network studies.

    PubMed

    Horvat, Predrag; Koller, Martin; Braunegg, Gerhart

    2015-09-01

    A review of the use of elementary flux modes (EFMs) and their applications in metabolic engineering covered with yield space analysis (YSA) is presented. EFMs are an invaluable tool in mathematical modeling of biochemical processes. They are described from their inception in 1994, followed by various improvements of their computation in later years. YSA constitutes another precious tool for metabolic network modeling, and is presented in details along with EFMs in this article. The application of these techniques is discussed for several case studies of metabolic network modeling provided in respective original articles. The article is concluded by some case studies in which the application of EFMs and YSA turned out to be most useful, such as the analysis of intracellular polyhydroxyalkanoate (PHA) formation and consumption in Cupriavidus necator, including the constraint-based description of the steady-state flux cone of the strain's metabolic network, the profound analysis of a continuous five-stage bioreactor cascade for PHA production by C. necator using EFMs and, finally, the study of metabolic fluxes in the metabolic network of C. necator cultivated on glycerol.

  10. Analysis of Relevant Parameters for Autophagic Flux Using HeLa Cells Expressing EGFP-LC3.

    PubMed

    Muñoz-Braceras, Sandra; Escalante, Ricardo

    2016-01-01

    Macroautophagy (called just autophagy hereafter) is an intracellular degradation machinery essential for cell survival under stress conditions and for the maintenance of cellular homeostasis. The hallmark of autophagy is the formation of double membrane vesicles that engulf cytoplasmic material. These vesicles, called autophagosomes, mature by fusion with endosomes and lysosomes that allows the degradation of the cargo. Autophagy is a dynamic process regulated at multiple steps. Assessment of autophagy is not trivial because the number autophagosomes might not necessarily reflect the real level of autophagic degradation, the so-called autophagic flux. Here, we describe an optimized protocol for the analysis of relevant parameters of autophagic flux using HeLa cells stably expressing EGFP-LC3. These cells are a convenient tool to determine the influence of the downregulation or overexpression of specific proteins in the autophagic flux as well as the analysis of autophagy-modulating compounds. Western blot analysis of relevant parameters, such as the levels of EGFP-LC3, free EGFP generated by autophagic degradation and endogenous LC3·I-II are analyzed in the presence and absence of the autophagic inhibitor chloroquine. PMID:27613046

  11. Failure analysis of beryllium tile assembles following high heat flux testing for the ITER program

    SciTech Connect

    B. C. Odegard, Jr.; C. H. Cadden; N. Y. C. Yang

    2000-05-01

    The following document describes the processing, testing and post-test analysis of two Be-Cu assemblies that have successfully met the heat load requirements for the first wall and dome sections for the ITER (International Thermonuclear Experimental Reactor) fusion reactor. Several different joint assemblies were evaluated in support of a manufacturing technology investigation aimed at diffusion bonding or brazing a beryllium armor tile to a copper alloy heat sink for fusion reactor applications. Judicious selection of materials and coatings for these assemblies was essential to eliminate or minimize interactions with the highly reactive beryllium armor material. A thin titanium layer was used as a diffusion barrier to isolate the copper heat sink from the beryllium armor. To reduce residual stresses produced by differences in the expansion coefficients between the beryllium and copper, a compliant layer of aluminum or aluminum-beryllium (AlBeMet-150) was used. Aluminum was chosen because it does not chemically react with, and exhibits limited volubility in, beryllium. Two bonding processes were used to produce the assemblies. The primary process was a diffusion bonding technique. In this case, undesirable metallurgical reactions were minimized by keeping the materials in a solid state throughout the fabrication cycle. The other process employed an aluminum-silicon layer as a brazing filler material. In both cases, a hot isostatic press (HIP) furnace was used in conjunction with vacuum-canned assemblies in order to minimize oxidation and provide sufficient pressure on the assemblies for full metal-to-metal contact and subsequent bonding. The two final assemblies were subjected to a suite of tests including: tensile tests and electron and optical metallography. Finally, high heat flux testing was conducted at the electron beam testing system (EBTS) at Sandia National Laboratories, New Mexico. Here, test mockups were fabricated and subjected to normal heat loads to

  12. Uncertainty analysis of a coupled ecosystem response model simulating greenhouse gas fluxes from a temperate grassland

    NASA Astrophysics Data System (ADS)

    Liebermann, Ralf; Kraft, Philipp; Houska, Tobias; Breuer, Lutz; Müller, Christoph; Kraus, David; Haas, Edwin; Klatt, Steffen

    2015-04-01

    Among anthropogenic greenhouse gas emissions, CO2 is the dominant driver of global climate change. Next to its direct impact on the radiation budget, it also affects the climate system by triggering feedback mechanisms in terrestrial ecosystems. Such mechanisms - like stimulated photosynthesis, increased root exudations and reduced stomatal transpiration - influence both the input and the turnover of carbon and nitrogen compounds in the soil. The stabilization and decomposition of these compounds determines how increasing CO2 concentrations change the terrestrial trace gas emissions, especially CO2, N2O and CH4. To assess the potential reaction of terrestrial greenhouse gas emissions to rising tropospheric CO2 concentration, we make use of a comprehensive ecosystem model integrating known processes and fluxes of the carbon-nitrogen cycle in soil, vegetation and water. We apply a state-of-the-art ecosystem model with measurements from a long term field experiment of CO2 enrichment. The model - a grassland realization of LandscapeDNDC - simulates soil chemistry coupled with plant physiology, microclimate and hydrology. The data - comprising biomass, greenhouse gas emissions, management practices and soil properties - has been attained from a FACE (Free Air Carbon dioxide Enrichment) experiment running since 1997 on a temperate grassland in Giessen, Germany. Management and soil data, together with weather records, are used to drive the model, while cut biomass as well as CO2 and N2O emissions are used for calibration and validation. Starting with control data from installations without CO2 enhancement, we begin with a GLUE (General Likelihood Uncertainty Estimation) assessment using Latin Hypercube to reduce the range of the model parameters. This is followed by a detailed sensitivity analysis, the application of DREAM-ZS for model calibration, and an estimation of the effect of input uncertainty on the simulation results. Since first results indicate problems with

  13. Power Distribution Analysis for the ORNL High Flux Isotope Reactor Critical Experiment 3

    SciTech Connect

    Chandler, David; Primm, Trent; Maldonado, G Ivan

    2010-01-01

    The mission of the Reduced Enrichment for Research and Test Reactors Program is to minimize and, to the extent possible, eliminate the use of highly enriched uranium (HEU) in civilian nuclear applications by working to convert research and test reactors, as well as radioisotope production processes, to low-enriched uranium (LEU) fuel and targets. Oak Ridge National Laboratory (ORNL) is currently reviewing the design bases and key operating criteria including fuel operating parameters, enrichment-related safety analyses, fuel performance, and fuel fabrication in regard to converting the fuel of the High Flux Isotope Reactor (HFIR) from HEU to LEU. The purpose of this study is to validate Monte Carlo methods currently in use for conversion analyses. The methods have been validated for the prediction offlux values in the reactor target, reflector, and beam tubes, but this study focuses on the prediction of the power density profile in the core. Power distributions were calculated in the fuel elements of the HFIR, a research reactor at ORNL, via MCNP and were compared to experimentally obtained data. This study was performed to validate Monte Carlo methods for power density calculations and to observe biases. A current three-dimensional MCNP model was modified to replicate the 1965 HFIR Critical Experiment 3 (HFIRCE-3). In this experiment, the power profile was determined by counting the gamma activity at selected locations in the core. 'Foils' (chunks of fuel meat and clad) were punched out of the fuel elements in HFIRCE-3 following irradiation, and experimental relative power densities were obtained by measuring the activity of these foils and comparing each foil's activity to the activity of a normalizing foil. This analysis consisted of calculating corresponding activities by inserting volume tallies into the modified MCNP model to represent the punchings. The average fission density was calculated for each foil location and then normalized to the reference foil

  14. Statistical analysis of sunspot area and magnetic flux variations in 2001-2003

    NASA Astrophysics Data System (ADS)

    Zharkov, S. I.; Zharkova, V. V.

    This paper utilizes a searchable Solar Feature Catalogue (SFC) for sunspots created from the SOHO/MDI whitelight images and magnetograms in 2001-2003 using the automated pattern recognition techniques described at http://www.cyber.brad.ac.uk/egso/. Comparison of sunspot areas taklen from the SFC with the daily sunspot numbers published in the Sunspot Index Data Centre (SIDC) shows very good correlation of 78-86%. The total magnetic flux from sunspot areas, measured from a single solar image, is shown to have a strong northern-southern asymmetry revealing magnetic flux decrease in the northern hemisphere and an increase in the southern one with the solar cycle descendence towards the period end (year 2003). The resulting, or excess, flux has also demonstrated very significant asymmetry being negative in the southern hemisphere and positive in the northern at the beginning of the period (solar maximum, 2001)with its amplitude descreasing towards the the period end (2003), or the solar minimum. Also, in 2003 there are signs of change in the excess flux polarity between the northern and southern hemispheres.

  15. Analytical analysis of the Pennes bioheat transfer equation with sinusoidal heat flux condition on skin surface.

    PubMed

    Shih, Tzu-Ching; Yuan, Ping; Lin, Win-Li; Kou, Hong-Sen

    2007-11-01

    This study focuses on the effect of the temperature response of a semi-infinite biological tissue due to a sinusoidal heat flux at the skin. The Pennes bioheat transfer equation such as rho(t)c(t)( partial differentialT/ partial differentialt)+W(b)c(b)(T-T(a))=k partial differential(2)T/ partial differentialx(2) with the oscillatory heat flux boundary condition such as q(0,t)=q(0)e(iomegat) was investigated. By using the Laplace transform, the analytical solution of the Pennes bioheat transfer equation with surface sinusoidal heating condition is found. This analytical expression is suitable for describing the transient temperature response of tissue for the whole time domain from the starting periodic oscillation to the final steady periodic oscillation. The results show that the temperature oscillation due to the sinusoidal heating on the skin surface is unstable in the initial period. Further, it is unavailable to predict the blood perfusion rate via the phase shifting between the surface heat flux and the surface temperature. Moreover, the lower frequency of sinusoidal heat flux on the skin surface induces a more sensitive phase shift response to the blood perfusion rate change, but extends the beginning time of sampling because of the avoidance of the unavailable first cyclic oscillation.

  16. Analysis of autophagic flux in response to sulforaphane in metastatic prostate cancer cells

    PubMed Central

    Watson, Gregory W; Wickramasekara, Samanthi; Fang, Yufeng; Palomera-Sanchez, Zoraya; Maier, Claudia S; Williams, David E; Dashwood, Roderick H; Perez, Viviana I; Ho, Emily

    2015-01-01

    Scope The phytochemical sulforaphane has been shown to decrease prostate cancer metastases in a genetic mouse model of prostate carcinogenesis, though the mechanism of action is not fully known. Sulforaphane has been reported to stimulate autophagy, and modulation of autophagy has been proposed to influence sulforaphane cytotoxicity; however, no conclusions about autophagy can be drawn without assessing autophagic flux, which has not been characterized in prostate cancer cells following sulforaphane treatment. Methods and Results We conducted an investigation to assess the impact of sulforaphane on autophagic flux in two metastatic prostate cancer cell lines at a concentration shown to decrease metastasis in vivo. Autophagic flux was assessed by multiple autophagy related proteins and substrates. We found that sulforaphane can stimulate autophagic flux and cell death only at high concentrations, above what has been observed in vivo. Conclusion These results suggest that sulforaphane does not directly stimulate autophagy or cell death in metastatic prostate cancer cells under physiologically relevant conditions, but instead supports the involvement of in vivo factors as important effectors of sulforaphane- mediated prostate cancer suppression. PMID:26108801

  17. Flux balance analysis of primary metabolism in the diatom Phaeodactylum tricornutum.

    PubMed

    Kim, Joomi; Fabris, Michele; Baart, Gino; Kim, Min K; Goossens, Alain; Vyverman, Wim; Falkowski, Paul G; Lun, Desmond S

    2016-01-01

    Diatoms (Bacillarophyceae) are photosynthetic unicellular microalgae that have risen to ecological prominence in oceans over the past 30 million years. They are of interest as potential feedstocks for sustainable biofuels. Maximizing production of these feedstocks will require genetic modifications and an understanding of algal metabolism. These processes may benefit from genome-scale models, which predict intracellular fluxes and theoretical yields, as well as the viability of knockout and knock-in transformants. Here we present a genome-scale metabolic model of a fully sequenced and transformable diatom: Phaeodactylum tricornutum. The metabolic network was constructed using the P. tricornutum genome, biochemical literature, and online bioinformatic databases. Intracellular fluxes in P. tricornutum were calculated for autotrophic, mixotrophic and heterotrophic growth conditions, as well as knockout conditions that explore the in silico role of glycolytic enzymes in the mitochondrion. The flux distribution for lower glycolysis in the mitochondrion depended on which transporters for TCA cycle metabolites were included in the model. The growth rate predictions were validated against experimental data obtained using chemostats. Two published studies on this organism were used to validate model predictions for cyclic electron flow under autotrophic conditions, and fluxes through the phosphoketolase, glycine and serine synthesis pathways under mixotrophic conditions. Several gaps in annotation were also identified. The model also explored unusual features of diatom metabolism, such as the presence of lower glycolysis pathways in the mitochondrion, as well as differences between P. tricornutum and other photosynthetic organisms. PMID:26590126

  18. Predictive Potential of Flux Balance Analysis of Saccharomyces cerevisiae Using as Optimization Function Combinations of Cell Compartmental Objectives

    PubMed Central

    García Sánchez, Carlos Eduardo; Vargas García, César Augusto; Torres Sáez, Rodrigo Gonzalo

    2012-01-01

    Background The main objective of flux balance analysis (FBA) is to obtain quantitative predictions of metabolic fluxes of an organism, and it is necessary to use an appropriate objective function to guarantee a good estimation of those fluxes. Methodology In this study, the predictive performance of FBA was evaluated, using objective functions arising from the linear combination of different cellular objectives. This approach is most suitable for eukaryotic cells, owing to their multiplicity of cellular compartments. For this reason, Saccharomyces cerevisiae was used as model organism, and its metabolic network was represented using the genome-scale metabolic model iMM904. As the objective was to evaluate the predictive performance from the FBA using the kind of objective function previously described, substrate uptake and oxygen consumption were the only input data used for the FBA. Experimental information about microbial growth and exchange of metabolites with the environment was used to assess the quality of the predictions. Conclusions The quality of the predictions obtained with the FBA depends greatly on the knowledge of the oxygen uptake rate. For the most of studied classifications, the best predictions were obtained with “maximization of growth”, and with some combinations that include this objective. However, in the case of exponential growth with unknown oxygen exchange flux, the objective function “maximization of growth, plus minimization of NADH production in cytosol, plus minimization of NAD(P)H consumption in mitochondrion” gave much more accurate estimations of fluxes than the obtained with any other objective function explored in this study. PMID:22912775

  19. Analysis of metabolic pathways and fluxes in a newly discovered thermophilic and ethanol-tolerant Geobacillus strain.

    PubMed

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

    2009-04-01

    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 (10%, 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 accurately determined 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 to ethanol, L-lactate (> 99% optical purity), acetate, and 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 yield by approximately threefold, thus indicating that both pathways should be modified to maximize ethanol production.

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

    SciTech Connect

    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.

  1. Regional flux analysis for discovering and quantifying anatomical changes: An application to the brain morphometry in Alzheimer's disease.

    PubMed

    Lorenzi, M; Ayache, N; Pennec, X

    2015-07-15

    In this study we introduce the regional flux analysis, a novel approach to deformation based morphometry based on the Helmholtz decomposition of deformations parameterized by stationary velocity fields. We use the scalar pressure map associated to the irrotational component of the deformation to discover the critical regions of volume change. These regions are used to consistently quantify the associated measure of volume change by the probabilistic integration of the flux of the longitudinal deformations across the boundaries. The presented framework unifies voxel-based and regional approaches, and robustly describes the volume changes at both group-wise and subject-specific level as a spatial process governed by consistently defined regions. Our experiments on the large cohorts of the ADNI dataset show that the regional flux analysis is a powerful and flexible instrument for the study of Alzheimer's disease in a wide range of scenarios: cross-sectional deformation based morphometry, longitudinal discovery and quantification of group-wise volume changes, and statistically powered and robust quantification of hippocampal and ventricular atrophy.

  2. Serial 13C-based flux analysis of an L-phenylalanine-producing E. coli strain using the sensor reactor.

    PubMed

    Wahl, Aljoscha; El Massaoudi, Mohamed; Schipper, Dick; Wiechert, Wolfgang; Takors, Ralf

    2004-01-01

    With the aid of the recently developed Sensor reactor system, a series of three subsequent (13)C labeling experiments was performed mirroring the l-phenylalanine (l-Phe) production phase of a recombinant E. coli strain that was cultivated under industry-like conditions in a 300 L bioreactor. On the basis of the data from NMR labeling analysis, three subsequent flux patterns were successfully derived monitoring the l-Phe formation during an observation window from 14 to 23.3 h process time. Linear programming was performed to identify optimal flux patterns for l-Phe formation. Additionally, flux sensitivity analysis was used to identify the most promising metabolic engineering target. As a result, high rates of phosphoenolpyruvate (PEP) to pyruvate (PYR) conversion were identified as the most important reason for deterioration of the l-Phe/glucose yield from 20 to finally 11 mol %. Considering the characteristics of the enzyme kinetics involved, the working hypothesis was formulated that phosphoenolpyruvate synthase activity was increasingly hampered by rising oxaloacetate and 2-oxoglutarate concentrations, while at the same time pyruvate kinase activity arose due to activation by fructose 1,6-diphosphate. Hence, pps overexpression should be performed to optimize the existing production strain.

  3. Regional flux analysis for discovering and quantifying anatomical changes: An application to the brain morphometry in Alzheimer's disease.

    PubMed

    Lorenzi, M; Ayache, N; Pennec, X

    2015-07-15

    In this study we introduce the regional flux analysis, a novel approach to deformation based morphometry based on the Helmholtz decomposition of deformations parameterized by stationary velocity fields. We use the scalar pressure map associated to the irrotational component of the deformation to discover the critical regions of volume change. These regions are used to consistently quantify the associated measure of volume change by the probabilistic integration of the flux of the longitudinal deformations across the boundaries. The presented framework unifies voxel-based and regional approaches, and robustly describes the volume changes at both group-wise and subject-specific level as a spatial process governed by consistently defined regions. Our experiments on the large cohorts of the ADNI dataset show that the regional flux analysis is a powerful and flexible instrument for the study of Alzheimer's disease in a wide range of scenarios: cross-sectional deformation based morphometry, longitudinal discovery and quantification of group-wise volume changes, and statistically powered and robust quantification of hippocampal and ventricular atrophy. PMID:25963734

  4. Flux balance analysis of CHO cells before and after a metabolic switch from lactate production to consumption.

    PubMed

    Martínez, Verónica S; Dietmair, Stefanie; Quek, Lake-Ee; Hodson, Mark P; Gray, Peter; Nielsen, Lars K

    2013-02-01

    Mammalian cell cultures typically exhibit an energy inefficient phenotype characterized by the consumption of large quantities of glucose and the concomitant production of large quantities of lactate. Under certain conditions, mammalian cells can switch to a more energy efficient state during which lactate is consumed. Using a metabolic model derived from a mouse genome scale model we performed flux balance analysis of Chinese hamster ovary cells before and after a metabolic switch from lactate production (in the presence of glucose) to lactate consumption (after glucose depletion). Despite a residual degree of freedom after accounting for measurements, the calculated flux ranges and associated errors were narrow enough to enable investigation of metabolic changes across the metabolic switch. Surprisingly, the fluxes through the lower part of the TCA cycle from oxoglutarate to malate were very similar (around 60 µmol/gDW/h) for both phases. A detailed analysis of the energy metabolism showed that cells consuming lactate have an energy efficiency (total ATP produced per total C-mol substrate consumed) six times greater than lactate producing cells.

  5. Potential emission flux to aerosol pollutants over Bengal Gangetic plain through combined trajectory clustering and aerosol source fields analysis

    NASA Astrophysics Data System (ADS)

    Kumar, D. Bharath; Verma, S.

    2016-09-01

    A hybrid source-receptor analysis was carried out to evaluate the potential emission flux to winter monsoon (WinMon) aerosols over Bengal Gangetic plain urban (Kolkata, Kol) and semi-urban atmospheres (Kharagpur, Kgp). This was done through application of fuzzy c-mean clustering to back-trajectory data combined with emission flux and residence time weighted aerosols analysis. WinMon mean aerosol optical depth (AOD) and angstrom exponent (AE) at Kol (AOD: 0.77; AE: 1.17) were respectively slightly higher than and nearly equal to that at Kgp (AOD: 0.71; AE: 1.18). Out of six source region clusters over Indian subcontinent and two over Indian oceanic region, the cluster mean AOD was the highest when associated with the mean path of air mass originating from the Bay of Bengal and the Arabian sea clusters at Kol and that from the Indo-Gangetic plain (IGP) cluster at Kgp. Spatial distribution of weighted AOD fields showed the highest potential source of aerosols over the IGP, primarily over upper IGP (e.g. Punjab, Haryana), lower IGP (e.g. Uttarpradesh) and eastern region (e.g. west Bengal, Bihar, northeast India) clusters. The emission flux contribution potential (EFCP) of fossil fuel (FF) emissions at surface (SL) of Kol/Kgp, elevated layer (EL) of Kol, and of biomass burning (BB) emissions at SL of Kol were primarily from upper, lower, upper/lower IGP clusters respectively. The EFCP of FF/BB emissions at Kgp-EL/SL, and that of BB at EL of Kol/Kgp were mainly from eastern region and Africa (AFR) clusters respectively. Though the AFR cluster was constituted of significantly high emission flux source potential of dust emissions, the EFCP of dust from northwest India (NWI) was comparable to that from AFR at Kol SL/EL.

  6. 13C-flux Analysis Reveals NADPH-balancing Transhydrogenation Cycles in Stationary Phase of Nitrogen-starving Bacillus subtilis *

    PubMed Central

    Rühl, Martin; Le Coq, Dominique; Aymerich, Stéphane; Sauer, Uwe

    2012-01-01

    In their natural habitat, microorganisms are typically confronted with nutritional limitations that restrict growth and force them to persevere in a stationary phase. Despite the importance of this phase, little is known about the metabolic state(s) that sustains it. Here, we investigate metabolically active but non-growing Bacillus subtilis during nitrogen starvation. In the absence of biomass formation as the major NADPH sink, the intracellular flux distribution in these resting B. subtilis reveals a large apparent catabolic NADPH overproduction of 5.0 ± 0.6 mmol·g−1·h−1 that was partly caused by high pentose phosphate pathway fluxes. Combining transcriptome analysis, stationary 13C-flux analysis in metabolic deletion mutants, 2H-labeling experiments, and kinetic flux profiling, we demonstrate that about half of the catabolic excess NADPH is oxidized by two transhydrogenation cycles, i.e. isoenzyme pairs of dehydrogenases with different cofactor specificities that operate in reverse directions. These transhydrogenation cycles were constituted by the combined activities of the glyceraldehyde 3-phosphate dehydrogenases GapA/GapB and the malic enzymes MalS/YtsJ. At least an additional 6% of the overproduced NADPH is reoxidized by continuous cycling between ana- and catabolism of glutamate. Furthermore, in vitro enzyme data show that a not yet identified transhydrogenase could potentially reoxidize ∼20% of the overproduced NADPH. Overall, we demonstrate the interplay between several metabolic mechanisms that concertedly enable network-wide NADPH homeostasis under conditions of high catabolic NADPH production in the absence of cell growth in B. subtilis. PMID:22740702

  7. 13C-flux analysis reveals NADPH-balancing transhydrogenation cycles in stationary phase of nitrogen-starving Bacillus subtilis.

    PubMed

    Rühl, Martin; Le Coq, Dominique; Aymerich, Stéphane; Sauer, Uwe

    2012-08-10

    In their natural habitat, microorganisms are typically confronted with nutritional limitations that restrict growth and force them to persevere in a stationary phase. Despite the importance of this phase, little is known about the metabolic state(s) that sustains it. Here, we investigate metabolically active but non-growing Bacillus subtilis during nitrogen starvation. In the absence of biomass formation as the major NADPH sink, the intracellular flux distribution in these resting B. subtilis reveals a large apparent catabolic NADPH overproduction of 5.0 ± 0.6 mmol g(-1)h(-1) that was partly caused by high pentose phosphate pathway fluxes. Combining transcriptome analysis, stationary (13)C-flux analysis in metabolic deletion mutants, (2)H-labeling experiments, and kinetic flux profiling, we demonstrate that about half of the catabolic excess NADPH is oxidized by two transhydrogenation cycles, i.e. isoenzyme pairs of dehydrogenases with different cofactor specificities that operate in reverse directions. These transhydrogenation cycles were constituted by the combined activities of the glyceraldehyde 3-phosphate dehydrogenases GapA/GapB and the malic enzymes MalS/YtsJ. At least an additional 6% of the overproduced NADPH is reoxidized by continuous cycling between ana- and catabolism of glutamate. Furthermore, in vitro enzyme data show that a not yet identified transhydrogenase could potentially reoxidize ∼20% of the overproduced NADPH. Overall, we demonstrate the interplay between several metabolic mechanisms that concertedly enable network-wide NADPH homeostasis under conditions of high catabolic NADPH production in the absence of cell growth in B. subtilis.

  8. Comparative analysis of matter and energy fluxes determined by Bowen Ratio and Eddy Covariance techniques at a crop site in eastern Germany

    NASA Astrophysics Data System (ADS)

    Brust, K.; Hehn, M.; Bernhofer, C.

    2012-04-01

    The measurement of atmospheric fluxes is an important means to evaluate ecosystem exchanges. In 2009 and 2010, fluxes and gradients of heat, water vapour, and CO2 over winter barley and rapeseed were measured simultaneously at the Klingenberg cropland site in Germany. A Bowen Ratio (BR) system was employed alongside to an existing Eddy Covariance (EC) tower. The BR system is required to account for the longer response time of the chemiluminescence analysers measuring other trace gases, e.g. NOx. To test and evaluate the application of the NOx measurement setup, the two independent systems (BR/EC) are compared with respect to energy and CO2 fluxes. We show a regression and differences analysis, diurnal cycles of the obtained fluxes, and interpret their coherence to the growth stage of the crops. The regression analysis depicts that differences between the systems are largest for latent heat LE (BR detects apparently higher LE due to the forced closure of energy balance), whereby the matter fluxes of CO2 show fairly little differences. Both measurement systems are able to capture the fluctuations of fluxes adequately well. Additionally, a multiple linear regression revealed that differences between the obtained fluxes are not induced by atmospheric conditions. The results of the differences analysis for sensible and latent heat point out that the observed differences of fluxes between both systems are mainly due to deviations in the mean, while differences in variability and timing/shape are of smaller importance. The differences of CO2 fluxes between both measurement systems are particularly caused by deviations in timing and shape, which can be explained with the linear cross-correlation coefficient (R2=0.8). From the good results of the comparison of matter fluxes (CO2) we conclude that the use of the Bowen Ratio method is applicable to other matter fluxes (like NOx).

  9. FluxCTTX: A LIMS-based tool for management and analysis of cytotoxicity assays data

    PubMed Central

    2015-01-01

    Background Cytotoxicity assays have been used by researchers to screen for cytotoxicity in compound libraries. Researchers can either look for cytotoxic compounds or screen "hits" from initial high-throughput drug screens for unwanted cytotoxic effects before investing in their development as a pharmaceutical. These assays may be used as an alternative to animal experimentation and are becoming increasingly important in modern laboratories. However, the execution of these assays in large scale and different laboratories requires, among other things, the management of protocols, reagents, cell lines used as well as the data produced, which can be a challenge. The management of all this information is greatly improved by the utilization of computational tools to save time and guarantee quality. However, a tool that performs this task designed specifically for cytotoxicity assays is not yet available. Results In this work, we have used a workflow based LIMS -- the Flux system -- and the Together Workflow Editor as a framework to develop FluxCTTX, a tool for management of data from cytotoxicity assays performed at different laboratories. The main work is the development of a workflow, which represents all stages of the assay and has been developed and uploaded in Flux. This workflow models the activities of cytotoxicity assays performed as described in the OECD 129 Guidance Document. Conclusions FluxCTTX presents a solution for the management of the data produced by cytotoxicity assays performed at Interlaboratory comparisons. Its adoption will contribute to guarantee the quality of activities in the process of cytotoxicity tests and enforce the use of Good Laboratory Practices (GLP). Furthermore, the workflow developed is complete and can be adapted to other contexts and different tests for management of other types of data. PMID:26696462

  10. Dynamic flux balance analysis for pharmaceutical protein production by Pichia pastoris: human growth hormone.

    PubMed

    Calık, Pınar; Sahin, Merve; Taşpınar, Hatice; Soyaslan, Elif Ş; Inankur, Bahar

    2011-03-01

    The influence of methanol feeding rate on intracellular reaction network of recombinant human growth hormone (rhGH) producing Pichia pastoris was investigated at three different specific growth rates, namely, 0.02 (MS-0.02), 0.03 (MS-0.03), and 0.04 h(-1) (MS-0.04) where Period-I (33 ≤ t <42 h) includes the early exponential growth phase; Period-II (42 ≤ t<48 h) is the exponential growth phase where the specific cell growth rate decreases; Period-III (48 ≤ t ≤51 h) is the exponential growth phase where rhGH concentration was the highest; and Period-IV (t>51 h) is the diminution phase for rhGH and cell synthesis. In Period-I, almost all of the formaldehyde entered the assimilatory pathway, at MS-0.02 and MS-0.03, whereas, at MS-0.04 high methanol feeding rate resulted in an adaptation problem. In Period-III, only at MS-0.02 co-carbon source sorbitol uptake-flux was active showing that sorbitol uptake does not affected from the predetermined feeding rate of methanol at μ(0)>0.02 h(-1). The biomass synthesis flux value was the highest in Period-I, -II and -III, respectively at MS-0.03 & MS-0.04, MS-0.04 and MS-0.02; whereas, rhGH flux was the highest in Period-I, -II, and -III, respectively at MS-0.03, MS-0.02 and MS-0.03. Based on the fluxes, Period-I should start with MS-0.03 methanol feeding rate and starting from the middle of Period-II methanol feeding rate should be shifted to MS-0.02.

  11. Analysis of recoverable current from one component of magnetic flux density in MREIT and MRCDI.

    PubMed

    Park, Chunjae; Lee, Byung Il; Kwon, Oh In

    2007-06-01

    Magnetic resonance current density imaging (MRCDI) provides a current density image by measuring the induced magnetic flux density within the subject with a magnetic resonance imaging (MRI) scanner. Magnetic resonance electrical impedance tomography (MREIT) has been focused on extracting some useful information of the current density and conductivity distribution in the subject Omega using measured B(z), one component of the magnetic flux density B. In this paper, we analyze the map Tau from current density vector field J to one component of magnetic flux density B(z) without any assumption on the conductivity. The map Tau provides an orthogonal decomposition J = J(P) + J(N) of the current J where J(N) belongs to the null space of the map Tau. We explicitly describe the projected current density J(P) from measured B(z). Based on the decomposition, we prove that B(z) data due to one injection current guarantee a unique determination of the isotropic conductivity under assumptions that the current is two-dimensional and the conductivity value on the surface is known. For a two-dimensional dominating current case, the projected current density J(P) provides a good approximation of the true current J without accumulating noise effects. Numerical simulations show that J(P) from measured B(z) is quite similar to the target J. Biological tissue phantom experiments compare J(P) with the reconstructed J via the reconstructed isotropic conductivity using the harmonic B(z) algorithm.

  12. Numerical Analysis on the Vortex Pattern and Flux Particle Dispersion in KR Method Using MPS Method

    NASA Astrophysics Data System (ADS)

    Hirata, N.; Xu, Y.; Anzai, K.

    2015-06-01

    The mechanically-stirring vessel is widely used in many fields, such as chemical reactor, bioreactor, and metallurgy, etc. The type of vortex mode that formed during impeller stirring has great effect on stirring efficiency, chemical reacting rate and air entrapment. Many efforts have been made to numerically simulate the fluid flow in the stirring vessel with classical Eulerian method. However, it is difficult to directly investigate the vortex mode and flux particle dispersion. Therefore, moving particle semi-implicit (MPS) method, which is based on Lagrangian method, is applied to simulate the fluid flow in a KR method in this practice. Top height and bottom heights of vortex surface in a steady state under several rotation speed was taken as key parameters to compare the results of numerical and published results. Flux particle dispersion behaviour under a rotation speed range from 80 to 480 rpm was also compared with the past study. The result shows that the numerical calculation has high consistency with experimental results. It is confirmed that the calculation using MPS method well reflected the vortex mode and flux particle dispersion in a mechanically-stirring vessel.

  13. Heat Flux Analysis of a Reacting Thermite Spray Impingent on a Substrate

    SciTech Connect

    Eric S. Collins; Michelle L. Pantoya; Michael A. Daniels; Daniel J. Prentice; Eric D. Steffler; Steven P. D'Arche

    2012-03-01

    Spray combustion from a thermite reaction is a new area of research relevant to localized energy generation applications, such as welding or cutting. In this study, we characterized the heat flux of combustion spray impinging on a target from a nozzle for three thermite mixtures. The reactions studied include aluminum (Al) with iron oxide (Fe2O3), Al with copper oxide (CuO), and Al with molybdenum oxide (MoO3). Several standoff distances (i.e., distance from the nozzle exit to the target) were analyzed. A fast response heat flux sensor was engineered for this purpose and is discussed in detail. Results correlated substrate damage to a threshold heat flux of 4550 W/cm2 for a fixed-nozzle configuration. Also, higher gas-generating thermites were shown to produce a widely dispersed spray and be less effective at imparting kinetic energy damage to a target. These results provide an understanding of the role of thermal and physical properties (i.e., such as heat of combustion, gas generation, and particle size) on thermite spray combustion performance measured by damaging a target substrate.

  14. A Sensitivity Analysis of the Impact of Rain on Regional and Global Sea-Air Fluxes of CO2

    PubMed Central

    Shutler, J. D.; Land, P. E.; Woolf, D. K.; Quartly, G. D.

    2016-01-01

    The global oceans are considered a major sink of atmospheric carbon dioxide (CO2). Rain is known to alter the physical and chemical conditions at the sea surface, and thus influence the transfer of CO2 between the ocean and atmosphere. It can influence gas exchange through enhanced gas transfer velocity, the direct export of carbon from the atmosphere to the ocean, by altering the sea skin temperature, and through surface layer dilution. However, to date, very few studies quantifying these effects on global net sea-air fluxes exist. Here, we include terms for the enhanced gas transfer velocity and the direct export of carbon in calculations of the global net sea-air fluxes, using a 7-year time series of monthly global climate quality satellite remote sensing observations, model and in-situ data. The use of a non-linear relationship between the effects of rain and wind significantly reduces the estimated impact of rain-induced surface turbulence on the rate of sea-air gas transfer, when compared to a linear relationship. Nevertheless, globally, the rain enhanced gas transfer and rain induced direct export increase the estimated annual oceanic integrated net sink of CO2 by up to 6%. Regionally, the variations can be larger, with rain increasing the estimated annual net sink in the Pacific Ocean by up to 15% and altering monthly net flux by > ± 50%. Based on these analyses, the impacts of rain should be included in the uncertainty analysis of studies that estimate net sea-air fluxes of CO2 as the rain can have a considerable impact, dependent upon the region and timescale. PMID:27673683

  15. Uncertainties in Eddy Covariance fluxes due to post-field data processing: a multi-site, full factorial analysis

    NASA Astrophysics Data System (ADS)

    Sabbatini, S.; Fratini, G.; Arriga, N.; Papale, D.

    2012-04-01

    Eddy Covariance (EC) is the only technologically available direct method to measure carbon and energy fluxes between ecosystems and atmosphere. However, uncertainties related to this method have not been exhaustively assessed yet, including those deriving from post-field data processing. The latter arise because there is no exact processing sequence established for any given situation, and the sequence itself is long and complex, with many processing steps and options available. However, the consistency and inter-comparability of flux estimates may be largely affected by the adoption of different processing sequences. The goal of our work is to quantify the uncertainty introduced in each processing step by the fact that different options are available, and to study how the overall uncertainty propagates throughout the processing sequence. We propose an easy-to-use methodology to assign a confidence level to the calculated fluxes of energy and mass, based on the adopted processing sequence, and on available information such as the EC system type (e.g. open vs. closed path), the climate and the ecosystem type. The proposed methodology synthesizes the results of a massive full-factorial experiment. We use one year of raw data from 15 European flux stations and process them so as to cover all possible combinations of the available options across a selection of the most relevant processing steps. The 15 sites have been selected to be representative of different ecosystems (forests, croplands and grasslands), climates (mediterranean, nordic, arid and humid) and instrumental setup (e.g. open vs. closed path). The software used for this analysis is EddyPro™ 3.0 (www.licor.com/eddypro). The critical processing steps, selected on the basis of the different options commonly used in the FLUXNET community, are: angle of attack correction; coordinate rotation; trend removal; time lag compensation; low- and high- frequency spectral correction; correction for air density

  16. Analysis of the Effects of Vitiates on Surface Heat Flux in Ground Tests of Hypersonic Vehicles

    NASA Technical Reports Server (NTRS)

    Cuda, Vincent; Gaffney, Richard L

    2008-01-01

    To achieve the high enthalpy conditions associated with hypersonic flight, many ground test facilities burn fuel in the air upstream of the test chamber. Unfortunately, the products of combustion contaminate the test gas and alter gas properties and the heat fluxes associated with aerodynamic heating. The difference in the heating rates between clean air and a vitiated test medium needs to be understood so that the thermal management system for hypersonic vehicles can be properly designed. This is particularly important for advanced hypersonic vehicle concepts powered by air-breathing propulsion systems that couple cooling requirements, fuel flow rates, and combustor performance by flowing fuel through sub-surface cooling passages to cool engine components and preheat the fuel prior to combustion. An analytical investigation was performed comparing clean air to a gas vitiated with methane/oxygen combustion products to determine if variations in gas properties contributed to changes in predicted heat flux. This investigation started with simple relationships, evolved into writing an engineering-level code, and ended with running a series of CFD cases. It was noted that it is not possible to simultaneously match all of the gas properties between clean and vitiated test gases. A study was then conducted selecting various combinations of freestream properties for a vitiated test gas that matched clean air values to determine which combination of parameters affected the computed heat transfer the least. The best combination of properties to match was the free-stream total sensible enthalpy, dynamic pressure, and either the velocity or Mach number. This combination yielded only a 2% difference in heating. Other combinations showed departures of up to 10% in the heat flux estimate.

  17. Leakage effects in car underhood aerothermal management: temperature and heat flux analysis

    NASA Astrophysics Data System (ADS)

    Khaled, Mahmoud; Habchi, Charbel; Harambat, Fabien; Elmarakbi, Ahmed; Peerhossaini, Hassan

    2014-10-01

    Air leakage from the engine compartment of a vehicle comes mainly from the junctions of the vehicle hood and the front end grill, the vehicle wings, the optical and the windshield. The present paper studies the thermal impact of these air leakage zones on the components of the vehicle engine compartment through temperature and heat-flux measurements. The front wheels of the test vehicle are positioned on a dynamometer and driven by the vehicle engine. The engine compartment is instrumented with almost 100 surface and air thermocouples and 20 fluxmeters of normal gradients. Measurements were made for three different thermal operating points. Five leak-sealing configurations are studied.

  18. Structure Function Analysis of Two-Scale Scalar Ramps. Part II: Ramp Characteristics and Surface Renewal Flux Estimation

    NASA Astrophysics Data System (ADS)

    Shapland, T. M.; McElrone, A. J.; Snyder, R. L.; Paw U, K. T.

    2012-10-01

    Ramp features in the turbulent scalar field are associated with turbulent coherent structures, which dominate energy and mass fluxes in the atmospheric surface layer. Although finer scale ramp-like shapes embedded within larger scale ramp-like shapes can readily be perceived in turbulent scalar traces, their presence has largely been overlooked in the literature. We demonstrate the signature of more than one ramp scale in structure functions of the turbulent scalar field measured from above bare ground and two types of short plant canopies, using structure-function time lags ranging in scale from isotropic to larger than the characteristic coherent structures. Spectral analysis of structure functions was used to characterize different scales of turbulent structures. By expanding structure function analysis to include two ramp scales, we characterized the intermittency, duration, and surface renewal flux contribution of the smallest (i.e., Scale One) and the dominant (i.e., Scale Two) coherent structure scales. The frequencies of the coherent structure scales increase with mean wind shear, implying that both Scale One and Scale Two are shear-driven. The embedded Scale One turbulent structure scale is ineffectual in the surface-layer energy and mass transport process. The new method reported here for obtaining surface renewal-based scalar exchange works well over bare ground and short canopies under unstable conditions, effectively eliminating the α calibration for these conditions and forming the foundation for analysis over taller and more complex surfaces.

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

    SciTech Connect

    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.

  20. Validation of the MCNP computational model for neutron flux distribution with the neutron activation analysis measurement

    NASA Astrophysics Data System (ADS)

    Tiyapun, K.; Chimtin, M.; Munsorn, S.; Somchit, S.

    2015-05-01

    The objective of this work is to demonstrate the method for validating the predication of the calculation methods for neutron flux distribution in the irradiation tubes of TRIGA research reactor (TRR-1/M1) using the MCNP computer code model. The reaction rate using in the experiment includes 27Al(n, α)24Na and 197Au(n, γ)198Au reactions. Aluminium (99.9 wt%) and gold (0.1 wt%) foils and the gold foils covered with cadmium were irradiated in 9 locations in the core referred to as CT, C8, C12, F3, F12, F22, F29, G5, and G33. The experimental results were compared to the calculations performed using MCNP which consisted of the detailed geometrical model of the reactor core. The results from the experimental and calculated normalized reaction rates in the reactor core are in good agreement for both reactions showing that the material and geometrical properties of the reactor core are modelled very well. The results indicated that the difference between the experimental measurements and the calculation of the reactor core using the MCNP geometrical model was below 10%. In conclusion the MCNP computational model which was used to calculate the neutron flux and reaction rate distribution in the reactor core can be used for others reactor core parameters including neutron spectra calculation, dose rate calculation, power peaking factors calculation and optimization of research reactor utilization in the future with the confidence in the accuracy and reliability of the calculation.

  1. ) Mold Fluxes

    NASA Astrophysics Data System (ADS)

    Seo, Myung-Duk; Shi, Cheng-Bin; Cho, Jung-Wook; Kim, Seon-Hyo

    2014-10-01

    The effects of basicity (CaO/SiO2), B2O3, and Li2O addition on the crystallization behaviors of lime-silica-based mold fluxes have been investigated by non-isothermal differential scanning calorimetry (DSC), field emission scanning electron microscopy, X-ray diffraction (XRD), and single hot thermocouple technique. It was found that the crystallization temperature of cuspidine increased with increasing the basicity of mold fluxes. The crystallization of wollastonite was suppressed with increasing the mold flux basicity due to the enhancement of cuspidine crystallization. The addition of B2O3 suppresses the crystallization of mold flux. The crystallization temperature of mold flux decreases with Li2O addition. The size of cuspidine increases, while the number of cuspidine decreases with increasing mold flux basicity. The morphology of cuspidine in mold fluxes with lower basicity is largely dendritic. The dendritic cuspidine in mold fluxes is composed of many fine cuspidine crystals. On the contrary, in mold fluxes with higher basicity, the cuspidine crystals are larger in size with mainly faceted morphology. The crystalline phase evolution was also calculated using a thermodynamic database, and compared with the experimental results determined by DSC and XRD. The results of thermodynamic calculation of crystalline phase formation are in accordance with the results determined by DSC and XRD.

  2. NASA's Carbon Monitoring System Flux-Pilot Project: A Multi-Component Analysis System for Carbon-Cycle Research and Monitoring

    NASA Technical Reports Server (NTRS)

    Pawson, S.; Gunson, M.; Potter, C.; Jucks, K.

    2012-01-01

    The importance of greenhouse gas increases for climate motivates NASA s observing strategy for CO2 from space, including the forthcoming Orbiting Carbon Observatory (OCO-2) mission. Carbon cycle monitoring, including attribution of atmospheric concentrations to regional emissions and uptake, requires a robust modeling and analysis infrastructure to optimally extract information from the observations. NASA's Carbon-Monitoring System Flux-Pilot Project (FPP) is a prototype for such analysis, combining a set of unique tools to facilitate analysis of atmospheric CO2 along with fluxes between the atmosphere and the terrestrial biosphere or ocean. NASA's analysis system is unique, in that it combines information and expertise from the land, oceanic, and atmospheric branches of the carbon cycle and includes some estimates of uncertainty. Numerous existing space-based missions provide information of relevance to the carbon cycle. This study describes the components of the FPP framework, assessing the realism of computed fluxes, thus providing the basis for research and monitoring applications. Fluxes are computed using data-constrained terrestrial biosphere models and physical ocean models, driven by atmospheric observations and assimilating ocean-color information. Use of two estimates provides a measure of uncertainty in the fluxes. Along with inventories of other emissions, these data-derived fluxes are used in transport models to assess their consistency with atmospheric CO2 observations. Closure is achieved by using a four-dimensional data assimilation (inverse) approach that adjusts the terrestrial biosphere fluxes to make them consistent with the atmospheric CO2 observations. Results will be shown, illustrating the year-to-year variations in land biospheric and oceanic fluxes computed in the FPP. The signals of these surface-flux variations on atmospheric CO2 will be isolated using forward modeling tools, which also incorporate estimates of transport error. The

  3. A Combined Maximum-likelihood Analysis of the High-energy Astrophysical Neutrino Flux Measured with IceCube

    NASA Astrophysics Data System (ADS)

    Aartsen, M. G.; Abraham, K.; Ackermann, M.; Adams, J.; Aguilar, J. A.; Ahlers, M.; Ahrens, M.; Altmann, D.; Anderson, T.; Archinger, M.; Arguelles, C.; Arlen, T. C.; Auffenberg, J.; Bai, X.; Barwick, S. W.; Baum, V.; Bay, R.; Beatty, J. J.; Becker Tjus, J.; Becker, K.-H.; Beiser, E.; BenZvi, S.; Berghaus, P.; Berley, D.; Bernardini, E.; Bernhard, A.; Besson, D. Z.; Binder, G.; Bindig, D.; Bissok, M.; Blaufuss, E.; Blumenthal, J.; Boersma, D. J.; Bohm, C.; Börner, M.; Bos, F.; Bose, D.; Böser, S.; Botner, O.; Braun, J.; Brayeur, L.; Bretz, H.-P.; Brown, A. M.; Buzinsky, N.; Casey, J.; Casier, M.; Cheung, E.; Chirkin, D.; Christov, A.; Christy, B.; Clark, K.; Classen, L.; Coenders, S.; Cowen, D. F.; Cruz Silva, A. H.; Daughhetee, J.; Davis, J. C.; Day, M.; de André, J. P. A. M.; De Clercq, C.; Dembinski, H.; De Ridder, S.; Desiati, P.; de Vries, K. D.; de Wasseige, G.; de With, M.; DeYoung, T.; Díaz-Vélez, J. C.; Dumm, J. P.; Dunkman, M.; Eagan, R.; Eberhardt, B.; Ehrhardt, T.; Eichmann, B.; Euler, S.; Evenson, P. A.; Fadiran, O.; Fahey, S.; Fazely, A. R.; Fedynitch, A.; Feintzeig, J.; Felde, J.; Filimonov, K.; Finley, C.; Fischer-Wasels, T.; Flis, S.; Fuchs, T.; Gaisser, T. K.; Gaior, R.; Gallagher, J.; Gerhardt, L.; Ghorbani, K.; Gier, D.; Gladstone, L.; Glagla, M.; Glüsenkamp, T.; Goldschmidt, A.; Golup, G.; Gonzalez, J. G.; Goodman, J. A.; Góra, D.; Grant, D.; Gretskov, P.; Groh, J. C.; Gross, A.; Ha, C.; Haack, C.; Haj Ismail, A.; Hallgren, A.; Halzen, F.; Hansmann, B.; Hanson, K.; Hebecker, D.; Heereman, D.; Helbing, K.; Hellauer, R.; Hellwig, D.; Hickford, S.; Hignight, J.; Hill, G. C.; Hoffman, K. D.; Hoffmann, R.; Holzapfel, K.; Homeier, A.; Hoshina, K.; Huang, F.; Huber, M.; Huelsnitz, W.; Hulth, P. O.; Hultqvist, K.; In, S.; Ishihara, A.; Jacobi, E.; Japaridze, G. S.; Jero, K.; Jurkovic, M.; Kaminsky, B.; Kappes, A.; Karg, T.; Karle, A.; Kauer, M.; Keivani, A.; Kelley, J. L.; Kemp, J.; Kheirandish, A.; Kiryluk, J.; Kläs, J.; Klein, S. R.; Kohnen, G.; Kolanoski, H.; Konietz, R.; Koob, A.; Köpke, L.; Kopper, C.; Kopper, S.; Koskinen, D. J.; Kowalski, M.; Krings, K.; Kroll, G.; Kroll, M.; Kunnen, J.; Kurahashi, N.; Kuwabara, T.; Labare, M.; Lanfranchi, J. L.; Larson, M. J.; Lesiak-Bzdak, M.; Leuermann, M.; Leuner, J.; Lünemann, J.; Madsen, J.; Maggi, G.; Mahn, K. B. M.; Maruyama, R.; Mase, K.; Matis, H. S.; Maunu, R.; McNally, F.; Meagher, K.; Medici, M.; Meli, A.; Menne, T.; Merino, G.; Meures, T.; Miarecki, S.; Middell, E.; Middlemas, E.; Miller, J.; Mohrmann, L.; Montaruli, T.; Morse, R.; Nahnhauer, R.; Naumann, U.; Niederhausen, H.; Nowicki, S. C.; Nygren, D. R.; Obertacke, A.; Olivas, A.; Omairat, A.; O'Murchadha, A.; Palczewski, T.; Paul, L.; Pepper, J. A.; Pérez de los Heros, C.; Pfendner, C.; Pieloth, D.; Pinat, E.; Posselt, J.; Price, P. B.; Przybylski, G. T.; Pütz, J.; Quinnan, M.; Rädel, L.; Rameez, M.; Rawlins, K.; Redl, P.; Reimann, R.; Relich, M.; Resconi, E.; Rhode, W.; Richman, M.; Richter, S.; Riedel, B.; Robertson, S.; Rongen, M.; Rott, C.; Ruhe, T.; Ruzybayev, B.; Ryckbosch, D.; Saba, S. M.; Sabbatini, L.; Sander, H.-G.; Sandrock, A.; Sandroos, J.; Sarkar, S.; Schatto, K.; Scheriau, F.; Schimp, M.; Schmidt, T.; Schmitz, M.; Schoenen, S.; Schöneberg, S.; Schönwald, A.; Schukraft, A.; Schulte, L.; Seckel, D.; Seunarine, S.; Shanidze, R.; Smith, M. W. E.; Soldin, D.; Spiczak, G. M.; Spiering, C.; Stahlberg, M.; Stamatikos, M.; Stanev, T.; Stanisha, N. A.; Stasik, A.; Stezelberger, T.; Stokstad, R. G.; Stössl, A.; Strahler, E. A.; Ström, R.; Strotjohann, N. L.; Sullivan, G. W.; Sutherland, M.; Taavola, H.; Taboada, I.; Ter-Antonyan, S.; Terliuk, A.; Tešić, G.; Tilav, S.; Toale, P. A.; Tobin, M. N.; Tosi, D.; Tselengidou, M.; Unger, E.; Usner, M.; Vallecorsa, S.; Vandenbroucke, J.; van Eijndhoven, N.; Vanheule, S.; van Santen, J.; Veenkamp, J.; Vehring, M.; Voge, M.; Vraeghe, M.; Walck, C.; Wallace, A.; Wallraff, M.; Wandkowsky, N.; Weaver, Ch.; Wendt, C.; Westerhoff, S.; Whelan, B. J.; Whitehorn, N.; Wichary, C.; Wiebe, K.; Wiebusch, C. H.; Wille, L.; Williams, D. R.; Wissing, H.; Wolf, M.; Wood, T. R.; Woschnagg, K.; Xu, D. L.; Xu, X. W.; Xu, Y.; Yanez, J. P.; Yodh, G.; Yoshida, S.; Zarzhitsky, P.; Zoll, M.; IceCube Collaboration

    2015-08-01

    Evidence for an extraterrestrial flux of high-energy neutrinos has now been found in multiple searches with the IceCube detector. The first solid evidence was provided by a search for neutrino events with deposited energies ≳ 30 TeV and interaction vertices inside the instrumented volume. Recent analyses suggest that the extraterrestrial flux extends to lower energies and is also visible with throughgoing, νμ-induced tracks from the Northern Hemisphere. Here, we combine the results from six different IceCube searches for astrophysical neutrinos in a maximum-likelihood analysis. The combined event sample features high-statistics samples of shower-like and track-like events. The data are fit in up to three observables: energy, zenith angle, and event topology. Assuming the astrophysical neutrino flux to be isotropic and to consist of equal flavors at Earth, the all-flavor spectrum with neutrino energies between 25 TeV and 2.8 PeV is well described by an unbroken power law with best-fit spectral index -2.50 ± 0.09 and a flux at 100 TeV of ({6.7}-1.2+1.1)× {10}-18 {{GeV}}-1 {{{s}}}-1 {{sr}}-1 {{cm}}-2. Under the same assumptions, an unbroken power law with index -2 is disfavored with a significance of 3.8σ (p = 0.0066%) with respect to the best fit. This significance is reduced to 2.1σ (p = 1.7%) if instead we compare the best fit to a spectrum with index -2 that has an exponential cut-off at high energies. Allowing the electron-neutrino flux to deviate from the other two flavors, we find a νe fraction of 0.18 ± 0.11 at Earth. The sole production of electron neutrinos, which would be characteristic of neutron-decay-dominated sources, is rejected with a significance of 3.6σ (p = 0.014%).

  4. Controls on the seasonality of photosynthesis across the Amazon basin -A cross-site analysis of eddy flux tower measurements from the Brasil flux network

    NASA Astrophysics Data System (ADS)

    Restrepo-Coupe, N.; Saleska, S. R.; Da Rocha, H. R.

    2009-04-01

    The Amazon Basin is categorized as a terrestrial biogeochemical "hotspot" where climate change and deforestation can trigger substantial changes on atmospheric CO. However, model skill at predicting seasonality of photosynthetic metabolism and ecosystem productivity in the Amazon is limited. To enhance our understanding of these processes, we investigated the seasonal and spatial patterns of Amazonian forest photosynthetic activity by integrating data from a network of ground-based eddy flux towers in Brazil established as part of the ‘Large-Scale Biosphere Atmosphere Experiment in Amazonia' project. We present the results of a simple model of leaf-flush for two central Amazon BrasilFlux sites, based on the eddy covariance estimates of canopy photosynthetic capacity (Pc) and measured canopy structure parameters. We found that in contrast to studies of Amazon evapotranspiration, which is highly correlated with available energy, Amazon ecosystem photosynthetic flux surprisingly showed no simple relationship with measures of available energy. We hypothesize that the seasonality of Amazon photosynthesis is controlled by the interaction of adaptive mechanisms (which biologically determine photosynthetic capacity through leaf flush and litter fall seasonality) and sunlight availability (which determines the fraction of photosynthetic capacity utilized). Equatorial climates advantage vegetation that can grow leaves in the dry season, when surface solar radiation peaks, but southerly sites may not because of reduced seasonality in surface radiation.

  5. Seahorse Xfe 24 Extracellular Flux Analyzer-Based Analysis of Cellular Respiration in Caenorhabditis elegans.

    PubMed

    Luz, Anthony L; Smith, Latasha L; Rooney, John P; Meyer, Joel N

    2015-01-01

    Mitochondria are critical for their role in ATP production as well as multiple nonenergetic functions, and mitochondrial dysfunction is causal in myriad human diseases. Less well appreciated is the fact that mitochondria integrate environmental and intercellular as well as intracellular signals to modulate function. Because mitochondria function in an organismal milieu, there is need for assays capable of rapidly assessing mitochondrial health in vivo. Here, using the Seahorse XF(e) 24 Extracellular Flux Analyzer and the pharmacological inhibitors dicyclohexylcarbodiimide (DCCD, ATP synthase inhibitor), carbonyl cyanide-p-trifluoromethoxyphenylhydrazone (FCCP, mitochondrial uncoupler), and sodium azide (cytochrome c oxidase inhibitor), we describe how to obtain in vivo measurements of the fundamental parameters [basal oxygen consumption rate (OCR), ATP-linked respiration, maximal OCR, spare respiratory capacity, and proton leak] of the mitochondrial respiratory chain in the model organism Caenorhabditis elegans. PMID:26523474

  6. Seahorse Xfe24 Extracellular Flux Analyzer-based analysis of cellular respiration in Caenorhabditis elegans

    PubMed Central

    Luz, Anthony L.; Smith, Latasha L.; Rooney, John P.

    2015-01-01

    Mitochondria are critical for their role in ATP production as well as multiple nonenergetic functions, and mitochondrial dysfunction is causal in myriad human diseases. Less well appreciated is the fact that mitochondria integrate environmental and inter- as well as intracellular signals to modulate function. Because mitochondria function in an organismal milieu, there is need for assays capable of rapidly assessing mitochondrial health in vivo. Here, using the Seahorse XFe24 Extracellular Flux Analyzer and the pharmacological inhibitors dicyclohexylcarbodiimide (DCCD, ATP synthase inhibitor), carbonyl cyanide-p-trifluoromethoxyphenylhydrazone (FCCP, mitochondrial uncoupler) and sodium azide (cytochrome c oxidase inhibitor), we describe how to obtain in vivo measurements of the fundamental parameters (basal oxygen consumption rate (OCR), ATP-linked respiration, maximal OCR, spare respiratory capacity and proton leak) of the mitochondrial respiratory chain in the model organism Caenorhabditis elegans. PMID:26523474

  7. Seahorse Xfe 24 Extracellular Flux Analyzer-Based Analysis of Cellular Respiration in Caenorhabditis elegans.

    PubMed

    Luz, Anthony L; Smith, Latasha L; Rooney, John P; Meyer, Joel N

    2015-11-02

    Mitochondria are critical for their role in ATP production as well as multiple nonenergetic functions, and mitochondrial dysfunction is causal in myriad human diseases. Less well appreciated is the fact that mitochondria integrate environmental and intercellular as well as intracellular signals to modulate function. Because mitochondria function in an organismal milieu, there is need for assays capable of rapidly assessing mitochondrial health in vivo. Here, using the Seahorse XF(e) 24 Extracellular Flux Analyzer and the pharmacological inhibitors dicyclohexylcarbodiimide (DCCD, ATP synthase inhibitor), carbonyl cyanide-p-trifluoromethoxyphenylhydrazone (FCCP, mitochondrial uncoupler), and sodium azide (cytochrome c oxidase inhibitor), we describe how to obtain in vivo measurements of the fundamental parameters [basal oxygen consumption rate (OCR), ATP-linked respiration, maximal OCR, spare respiratory capacity, and proton leak] of the mitochondrial respiratory chain in the model organism Caenorhabditis elegans.

  8. High Flux Isotope Reactor Core Analysis-Challenges and Recent Enhancements in Modeling and Simulation

    SciTech Connect

    Ilas, Germina

    2016-01-01

    A concerted effort over the past few years has focused on enhancing the core depletion models for the High Flux Isotope Reactor (HFIR) as part of a comprehensive study for designing a HFIR core that would use low-enriched uranium (LEU) fuel. A HFIR core depletion model that is based on current state-of-the-art methods and nuclear data was needed for use as a reference for the design of an LEU fuel for HFIR and to improve the basis for analyses that support HFIR s current operation with high-enriched uranium (HEU) fuel. This paper summarizes the recent improvements in modeling and simulation for HFIR core analyses, with a focus on core depletion models.

  9. Hydroacoustic and spatial analysis of sediment fluxes and accumulation rates in two Virginia reservoirs, USA.

    PubMed

    Clark, E V; Odhiambo, B K; Yoon, S; Pilati, L

    2015-06-01

    Watershed sediment fluxes and reservoir sediment accumulation rates were analyzed in two contrasting reservoir systems in central and western Virginia. Lake Pelham, located in the Piedmont geologic province, is a human-impacted reservoir with a watershed dominated by agricultural, residential and industrial land uses. Conversely, Lake Moomaw has a largely undeveloped watershed characterized by very steep slopes and forested land use located in the Valley and Ridge province. The Revised Universal Soil Loss Equation (RUSLE) and sediment delivery ratios (SDRs) were used to estimate soil losses in the two watersheds. Bathymetric and sediment accumulation surveys of the two reservoirs were also conducted using a multi-frequency hydroacoustic surveying system. The RUSLE/SDR erosion model estimates 2150 kg ha(-1) year(-1) for Lake Pelham and 2720 kg ha(-1) year(-1) for Lake Moomaw, a 410 and 13 % increase from assumed pristine (100 % forested) land use for the respective basins. Mean sediment accumulation rates of 1.51 and 0.60 cm year(-1) were estimated from the hydroacoustic survey of Lake Pelham and Lake Moomaw, respectively. Overall, Lake Moomaw has relatively low sediment accumulation rates; however, the reservoir is vulnerable to increases in sediment fluxes with further human development due to the steep slopes and highly erodible colluvial soils that characterize the basin. Higher erosion and sediment accumulation rates in Lake Pelham are most likely reflecting the impact of human development on sedimentation processes, where the loss of vegetal buffers and increase in impervious surfaces exacerbates both the surficial soil losses as well as intrinsic stream sediment production leading to the current annual reservoir capacity loss of 0.4 %.

  10. Multi-technique Analysis of the Solar 10.7 cm Radio Flux Time-Series in Relation to Predictability

    NASA Astrophysics Data System (ADS)

    Ghosh, Oindrilla; Ghosh, Tanushree; Chatterjee, T. N.

    2014-06-01

    We studied the predictability of the 10.7 cm solar radio flux by using stationary and non-stationary time-series analysis techniques of fractal theory to find the correlation exponent, the spectral exponent, the Hurst exponent, and the fluctuation exponent of the time series. The Hurst exponent was determined, from which the fractal dimension and consequently the predictability was evaluated. The results suggest that stationary methods of analysis yield inconsistent result, that is, amongst the four techniques used, the values of the exponents show great disparity. While two of the techniques, namely the auto-correlation function analysis and the spectral analysis, indicate long-term positive correlation, the other two methods, specifically the Hurst rescaled range-analysis and the fluctuation analysis, clearly exhibit the anti-correlated nature of the time series. The two non-stationary methods, that is, the discrete wavelet transform and the centered moving-average analysis, yielded values of the Hurst exponent that are indicative of positive correlation, of persistent behavior, and also showed that the time series is predictable to a certain extent.

  11. Intensive flux measurements and analysis of greenhouse gases from an upland cabbage field at Kunsan, Korea

    NASA Astrophysics Data System (ADS)

    Kim, D.; Na, U.

    2010-12-01

    It has been recognized that intensively managed agricultural soil is a dominant source of atmospheric N2O through increase in use of nitrogen fertilizer and soil microbial processes, contributing to about 57% (9Tg y-1) of total N2O annual global emission. Organic carbons in soil and wetland sediment including tidal flat affect the CO2 and CH4 emission in such environments depending on their physicochemical conditions. From October 2009 to June 2010, CO2, CH4, and N2O (GHG) soil emission measurements were conducted from upland cabbage field at Kunsan (35o56’23’’N, 126o43’14’’E), Korea by using closed static chamber method. During the experimental period, hourly GHG emissions were conducted mostly from 1000 to 1800LST in each field measurement day (total 28 days). After placing each chamber over soil surface of two neighboring plots, 50 ml of air sample inside the chambers was taken for every 15 min over a 30 min period by using plastic syringes (total of three samples). GHG concentrations were simultaneously analyzed in the laboratory by using a GC equipped with a methanizer, FID and ECD (Varian CP3800). The GHG fluxes were calculated from a linear regression of the changes in the concentrations. Negative values indicate GHG uptake by the soil surface, and positive values indicate GHG emission to the atmosphere. In addition, soil parameters (e.g. soil moisture, temperature, pH, organic C, soil N) were measured at the sampling plot. The average soil pH and soil moisture during the experimental period was ~pH5.4±0.4 and 70.0±19.7 %WFPS, respectively. The average fluxes and ranges of GHG during the experimental period were -0.004±0.032 mg-m-2 hr-1 (-0.087 ~ 0.045 mg-m-2 hr-1) for CH4, 5.32±57.63 mg-m-2 hr-1 (-92.96 ~ 139.38 mg-m-2 hr-1) for CO2, and 1.119±1.918 mg-m-2 hr-1 (0.077 ~ 8.409 mg-m-2 hr-1) for N2O, respectively. Monthly base flux measurement results revealed that monthly means of CO2 and CH4 flux during October (fall) was positive and

  12. Endogenous and exogenous dynamics in the fluctuations of capital fluxes. An empirical analysis of the Chinese stock market

    NASA Astrophysics Data System (ADS)

    Jiang, Z.-Q.; Guo, L.; Zhou, W.-X.

    2007-06-01

    A phenomenological investigation of the endogenous and exogenous dynamics in the fluctuations of capital fluxes is carried out on the Chinese stock market using mean-variance analysis, fluctuation analysis, and their generalizations to higher orders. Non-universal dynamics have been found not only in the scaling exponent α, which is different from the universal values 1/2 and 1, but also in the distributions of the ratio η= σexo / σendo of individual stocks. Both the scaling exponent α of fluctuations and the Hurst exponent Hi increase in logarithmic form with the time scale Δt and the mean traded value per minute , respectively. We find that the scaling exponent αendo of the endogenous fluctuations is independent of the time scale. Multiscaling and multifractal features are observed in the data as well. However, the inhomogeneous impact model is not verified.

  13. Altered swelling and ion fluxes in articular cartilage as a biomarker in osteoarthritis and joint immobilization: a computational analysis

    PubMed Central

    Manzano, Sara; Manzano, Raquel; Doblaré, Manuel; Doweidar, Mohamed Hamdy

    2015-01-01

    In healthy cartilage, mechano-electrochemical phenomena act together to maintain tissue homeostasis. Osteoarthritis (OA) and degenerative diseases disrupt this biological equilibrium by causing structural deterioration and subsequent dysfunction of the tissue. Swelling and ion flux alteration as well as abnormal ion distribution are proposed as primary indicators of tissue degradation. In this paper, we present an extension of a previous three-dimensional computational model of the cartilage behaviour developed by the authors to simulate the contribution of the main tissue components in its behaviour. The model considers the mechano-electrochemical events as concurrent phenomena in a three-dimensional environment. This model has been extended here to include the effect of repulsion of negative charges attached to proteoglycans. Moreover, we have studied the fluctuation of these charges owning to proteoglycan variations in healthy and pathological articular cartilage. In this sense, standard patterns of healthy and degraded tissue behaviour can be obtained which could be a helpful diagnostic tool. By introducing measured properties of unhealthy cartilage into the computational model, the severity of tissue degeneration can be predicted avoiding complex tissue extraction and subsequent in vitro analysis. In this work, the model has been applied to monitor and analyse cartilage behaviour at different stages of OA and in both short (four, six and eight weeks) and long-term (11 weeks) fully immobilized joints. Simulation results showed marked differences in the corresponding swelling phenomena, in outgoing cation fluxes and in cation distributions. Furthermore, long-term immobilized patients display similar swelling as well as fluxes and distribution of cations to patients in the early stages of OA, thus, preventive treatments are highly recommended to avoid tissue deterioration. PMID:25392400

  14. Wavelet and Fractal Analysis of Remotely Sensed Surface Temperature with Applications to Estimation of Surface Sensible Heat Flux Density

    NASA Technical Reports Server (NTRS)

    Schieldge, John

    2000-01-01

    Wavelet and fractal analyses have been used successfully to analyze one-dimensional data sets such as time series of financial, physical, and biological parameters. These techniques have been applied to two-dimensional problems in some instances, including the analysis of remote sensing imagery. In this respect, these techniques have not been widely used by the remote sensing community, and their overall capabilities as analytical tools for use on satellite and aircraft data sets is not well known. Wavelet and fractal analyses have the potential to provide fresh insight into the characterization of surface properties such as temperature and emissivity distributions, and surface processes such as the heat and water vapor exchange between the surface and the lower atmosphere. In particular, the variation of sensible heat flux density as a function of the change In scale of surface properties Is difficult to estimate, but - in general - wavelets and fractals have proved useful in determining the way a parameter varies with changes in scale. We present the results of a limited study on the relationship between spatial variations in surface temperature distribution and sensible heat flux distribution as determined by separate wavelet and fractal analyses. We analyzed aircraft imagery obtained in the thermal infrared (IR) bands from the multispectral TIMS and hyperspectral MASTER airborne sensors. The thermal IR data allows us to estimate the surface kinetic temperature distribution for a number of sites in the Midwestern and Southwestern United States (viz., San Pedro River Basin, Arizona; El Reno, Oklahoma; Jornada, New Mexico). The ground spatial resolution of the aircraft data varied from 5 to 15 meters. All sites were instrumented with meteorological and hydrological equipment including surface layer flux measuring stations such as Bowen Ratio systems and sonic anemometers. The ground and aircraft data sets provided the inputs for the wavelet and fractal analyses

  15. Assessing the spatial representativeness of eddy-covariance measurements of AmeriFlux network based on remote sensing and footprint analysis

    NASA Astrophysics Data System (ADS)

    Fu, D.; Zhang, L.; Chen, B.

    2015-12-01

    The eddy-covariance towers of AmeriFlux network are important for the analysis of terrestrial ecosystem-atmosphere interactions, and they have been used to improve our understanding of the mechanism behind terrestrial carbon cycle and upscaling from site to landscape and regional scales. However, the spatial representativeness of AmeriFlux network has not been assessed, especially accounting for the effects of land cover change on it using high spatial resolution data. Here we demonstrated an approach for evaluating the spatial representativeness of flux tower measurements based on footprint climatology analyses, land cover change data and remotely sensed vegetation indices. This method was applied to 79 flux towers of AmeriFlux network located in the continental United States, covering evergreen forest, deciduous forest, mixed forest, grass, cropland, shrub, and wetland biomes. For each site, monthly and annual footprint climatologies (i.e. monthly or annual accumulative footprints) were calculated using the Simple Analytical Footprint model on Eulerian coordinates (SAFE-f). The footprint climatologies were then overlaid on the images of Normalized Difference Vegetation Index (NDVI) and National Land Cover Database (NLCD) for the years (2001, 2006 and 2011), which were used as surrogates of land surface fluxes to assess the spatial representativeness. For most sites of AmeriFlux network, the results show that (i) the percentages of the target vegetation functional type (dominant land cover) observed by the AmeriFlux towers were higher than 60%; (ii) to some extent, most of the AmeriFlux sites presented anisotropically distributed patterns of NDVI within the 90% annual footprint climatology area; (iii) the land surface heterogeneity within the flux footprint area differed among sites; and (iv) the land cover types had changed higher than 10% within 6 km*6 km area centered at the flux tower for 5 AmeriFlux sites. We conclude that the footprint modeling based on high

  16. ANALYSIS OF THE FLUX OF AN ENDOCRINE DISRUPTING DICARBOXIMIDE AND ITS DEGRADATION PRODUCTS FROM THE SOIL TO THE LOWER TROPOSPHERE

    EPA Science Inventory

    A method for measuring the atmospheric flux of the antiandrogenic dicarboxirnide, vinclozolin, and its degradation products was investigated. A nitric oxide laboratory chamber was modified to measure the flux of semi-volatile compounds. Pesticide application systems and soil in...

  17. A Data-Centered Collaboration Portal to Support Global Carbon-Flux Analysis

    SciTech Connect

    Agarwal, Deborah A.; Humphrey, Marty; Beekwilder, Norm; Jackson, Keith; Goode, Monte; van Ingen, Catharine

    2009-04-07

    Carbon-climate, like other environmental sciences, has been changing. Large-scalesynthesis studies are becoming more common. These synthesis studies are often conducted by science teams that are geographically distributed and on datasets that are global in scale. A broad array of collaboration and data analytics tools are now available that could support these science teams. However, building tools that scientists actually use is hard. Also, moving scientists from an informal collaboration structure to one mediated by technology often exposes inconsistencies in the understanding of the rules of engagement between collaborators. We have developed a scientific collaboration portal, called fluxdata.org, which serves the community of scientists providing and analyzing the global FLUXNET carbon-flux synthesis dataset. Key things we learned or re-learned during our portal development include: minimize the barrier to entry, provide features on a just-in-time basis, development of requirements is an on-going process, provide incentives to change leaders and leverage the opportunity they represent, automate as much as possible, and you can only learn how to make it better if people depend on it enough to give you feedback. In addition, we also learned that splitting the portal roles between scientists and computer scientists improved user adoption and trust. The fluxdata.org portal has now been in operation for ~;;1.5 years and has become central to the FLUXNET synthesis efforts.

  18. Analysis of summer phosphorus fluxes within the pelagic zone of Eau Galle Reservoir, Wisconsin

    USGS Publications Warehouse

    James, W.F.; Barko, J.W.

    1993-01-01

    Major phosphorus (P) fluxes to and from the pelagic zone (i.e., open water region including epilimnion, metalimnion, and hypolimnion) were estimated from data collected over a 6 year period during the summer in Eau Galle Reservoir, Wisconsin. P inputs to the pelagic zone included profundal sediments, the watershed, groundwater, and transport of P from the littoral zone. P outputs from the pelagic zone included discharge from the reservoir, deposition, and transport of P to the littoral zone. Nighttime convective circulation was assumed to be the dominant mechanism of P exchange between the littoral and pelagic zones. Littoral P inputs, often neglected from budgetary analyses, accounted for 15% of the total measured P input and 25% of the internal P input to the pelagic zone. External P inputs were greatest, accounting for 42% of the total measured P input to the pelagic zone. These results emphasize the need for control of various sources of P inputs in the development of lake and reservoir management strategies.

  19. Design, simulation and analysis of 3 kW low speed axial flux permanent magnet generator

    NASA Astrophysics Data System (ADS)

    Kasim, Muhammad; Irasari, Pudji; Hikmawan, Muhammad Fathul

    2016-03-01

    Design and simulation of an axial flux permanent magnet generator (AFPMG) have been described in this paper. It was designed using the single rotor - single stator construction. The analytical method was using in the design process. The design process also employed the simulation using Finite Element Method Magnetics (FEMM) 4.2 software for identifying the magnetic characteristic and heat transfer. The effect of fill factor (FF) variation on the generator performances also observed in this paper. The design result shows that using the selected FF, the conductor diameter, power output, efficiency and heat distribution are affected but not for the Bg. The generator output can achieve up to 5.2 kW using the FF 0.4 which is more than assumed power output at the pre-design using FF 0.3. It also can be seen that the increasing FF will increase the power output and the efficiency. Despite a higher temperature compared with FF 0.3 and 0.35, the value of 0.4 is the most appropriate FF for designing the AFPMG.

  20. Extracellular flux analysis to monitor glycolytic rates and mitochondrial oxygen consumption.

    PubMed

    Pelletier, Martin; Billingham, Leah K; Ramaswamy, Madhu; Siegel, Richard M

    2014-01-01

    Evidence accumulating over the past decade has linked alterations in bioenergetic metabolism to the pathogenesis of several diseases, including inflammatory conditions and cancer. However, the mutual relationship between the effector functions and the metabolism of immune cells has begun to emerge only recently. Similar to malignant cells, both innate and adaptive immune cells undergo a metabolic reprogramming that is required for effector functions, de facto underlying the elicitation of a robust immune response. These changes allow immune cells not only to rapidly respond to pathogens or (pre)malignant cells but also to adapt to changing microenvironmental conditions. Targeting the metabolic alterations of malignant cells has been the subject of an intense wave of investigation, resulting in the identification of promising therapeutic strategies. Since the inflammatory milieu and the tumor microenvironment are similar, the metabolism of immune cells and its regulation has recently come under renewed interest as a target for immunotherapy. Here, we describe different tools and techniques to study the bioenergetic metabolism of cultured cells, using immune cells as a model. Our methodological approach relies on an extracellular flux analyzer, an instrument that enables the real-time measurement of the two central pathways used by living cells to generate adenosine triphosphate: glycolysis and oxidative phosphorylation. This instrument and similar technological innovations have transformed the study of cellular metabolism, unveiling its profound impact on various immunologic and oncological disorders.

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

    PubMed Central

    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

  2. Metabolic pathway analysis of Scheffersomyces (Pichia) stipitis: effect of oxygen availability on ethanol synthesis and flux distributions.

    PubMed

    Unrean, Pornkamol; Nguyen, Nhung H A

    2012-06-01

    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.

  3. Design study and performance analysis of 12S-14P field excitation flux switching motor for hybrid electric vehicle

    NASA Astrophysics Data System (ADS)

    Husin, Zhafir Aizat; Sulaiman, Erwan; Khan, Faisal; Mazlan, Mohamed Mubin Aizat; Othman, Syed Muhammad Naufal Syed

    2015-05-01

    This paper presents a new structure of 12slot-14pole field excitation flux switching motor (FEFSM) as an alternative candidate of non-Permanent Magnet (PM) machine for HEV drives. Design study, performance analysis and optimization of field excitation flux switching machine with non-rare-earth magnet for hybrid electric vehicle drive applications is done. The stator of projected machine consists of iron core made of electromagnetic steels, armature coils and field excitation coils as the only field mmf source. The rotor is consisted of only stack of iron and hence, it is reliable and appropriate for high speed operation. The design target is a machine with the maximum torque, power and power density, more than 210Nm, 123kW and 3.5kW/kg, respectively, which competes with interior permanent magnet synchronous machine used in existing hybrid electric vehicle. Some design feasibility studies on FEFSM based on 2D-FEA and deterministic optimization method will be applied to design the proposed machine.

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

    PubMed

    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

  5. Estimating regional greenhouse gas fluxes: An uncertainty analysis of planetary boundary layer techniques and bottom-up inventories

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Quantification of regional greenhouse gas (GHG) fluxes is essential for establishing mitigation strategies and evaluating their effectiveness. Here, we used multiple top-down approaches and multiple trace gas observations at a tall tower to estimate GHG regional fluxes and evaluate the GHG fluxes de...

  6. CeCaFDB: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13C-fluxomics

    PubMed Central

    Zhang, Zhengdong; Shen, Tie; Rui, Bin; Zhou, Wenwei; Zhou, Xiangfei; Shang, Chuanyu; Xin, Chenwei; Liu, Xiaoguang; Li, Gang; Jiang, Jiansi; Li, Chao; Li, Ruiyuan; Han, Mengshu; You, Shanping; Yu, Guojun; Yi, Yin; Wen, Han; Liu, Zhijie; Xie, Xiaoyao

    2015-01-01

    The Central Carbon Metabolic Flux Database (CeCaFDB, available at http://www.cecafdb.org) is a manually curated, multipurpose and open-access database for the documentation, visualization and comparative analysis of the quantitative flux results of central carbon metabolism among microbes and animal cells. It encompasses records for more than 500 flux distributions among 36 organisms and includes information regarding the genotype, culture medium, growth conditions and other specific information gathered from hundreds of journal articles. In addition to its comprehensive literature-derived data, the CeCaFDB supports a common text search function among the data and interactive visualization of the curated flux distributions with compartmentation information based on the Cytoscape Web API, which facilitates data interpretation. The CeCaFDB offers four modules to calculate a similarity score or to perform an alignment between the flux distributions. One of the modules was built using an inter programming algorithm for flux distribution alignment that was specifically designed for this study. Based on these modules, the CeCaFDB also supports an extensive flux distribution comparison function among the curated data. The CeCaFDB is strenuously designed to address the broad demands of biochemists, metabolic engineers, systems biologists and members of the -omics community. PMID:25392417

  7. GRACE Mass Flux Measurements of Inland and Marginal Seas from Mascons: Analysis and Validation

    NASA Astrophysics Data System (ADS)

    Loomis, B.; Luthcke, S. B.; Sabaka, T. J.

    2015-12-01

    The latest GRACE time-variable gravity mascon solution from the NASA Goddard Space Flight Center (GSFC) applies an optimized set of models and constraints towards the direct measurement of 1-arc-degree global mass flux parameters each month. Separate mascon spatial constraint regions have been defined for the largest inland and marginal seas: Mediterranean Sea, Black Sea, Caspian Sea, Red Sea, and Hudson Bay. The mascon estimation approach, when applied with well-designed constraints, minimizes signal leakage across regional boundaries and eliminates the need for post-processing strategies. These post-processing techniques (e.g. smoothed averaging kernels) are necessary for computing regional mass change from the unconstrained spherical harmonics provided by the GRACE project to reduce the effect of noisy high degree and order terms, but introduce signal leakage into and out of the considered region. These mass signals are also difficult to obtain from altimetry measurements due to the comparatively sparse temperature and salinity data in these regions, which is needed to compute and remove the steric component of sea level variations. We provide new GSFC mascon measurements of these inland and marginal seas and compare to results obtained from kernel-averaged spherical harmonic solutions and steric-corrected altimetry measurements. The relative accuracy of the various solutions is determined by incorporating their output into the set of forward models applied in our processing of the GRACE Level-1B data and analyzing the effect on the inter-satellite range-rate residuals, where a reduction in residuals is a direct validation of improved solution quality.

  8. Reactor physics input to the safety analysis report for the High Flux Isotope Reactor

    SciTech Connect

    Primm, R.T. III.

    1992-03-01

    HFIR specific, few group neutron and coupled neutron-gamma libraries have been prepared. These are based on data from ENDF/B-V and beginning-of-life (BOL) conditions. The neutron library includes actinide data for curium target rods. Six critical experiments, collectively designated HFIR critical experiment 4, were analyzed. Calculated k-effective was 2% high at BOL-typical conditions but was 1.0 at end-of-life-typical conditions. The local power density distributions were calculated for each of the critical experiments. The axially averaged values at a given radius were frequently within experimental error. However at individual points, the calculated local power densities were significantly different from the experimentally derived values (several times greater than experimental uncertainty). A reassessment of the foil activation data with transport theory techniques seems desirable. Using the results of the critical experiments study, a model of current HFIR configuration was prepared. As with the critical experiments, BOL k-effective was high (3%). However, end-of-life k-effective was high (2%). The end-of-life concentrations of fission products were compared to those generated using the ORIGEN code. Agreement was generally good through differences in the inventories of some important nuclides, Xe and I, need to be understood. End-of-cycle curium target isotopics based on measured, discharged target rods were compared to calculated values and agreement was good. Axial flux plots at various irradiation positions were generated. Time-dependent power distributions based on two-dimensional calculations were provided.

  9. Neonatal infrared thermography imaging: Analysis of heat flux during different clinical scenarios

    NASA Astrophysics Data System (ADS)

    Abbas, Abbas K.; Heimann, Konrad; Blazek, Vladimir; Orlikowsky, Thorsten; Leonhardt, Steffen

    2012-11-01

    IntroductionAn accurate skin temperature measurement of Neonatal Infrared Thermography (NIRT) imaging requires an appropriate calibration process for compensation of external effects (e.g. variation of environmental temperature, variable air velocity or humidity). Although modern infrared cameras can perform such calibration, an additional compensation is required for highly accurate thermography. This compensation which corrects any temperature drift should occur during the NIRT imaging process. We introduce a compensation technique which is based on modeling the physical interactions within the measurement scene and derived the detected temperature signal of the object. Materials and methodsIn this work such compensation was performed for different NIRT imaging application in neonatology (e.g. convective incubators, kangaroo mother care (KMC), and an open radiant warmer). The spatially distributed temperatures of 12 preterm infants (average gestation age 31 weeks) were measured under these different infant care arrangements (i.e. closed care system like a convective incubator, and open care system like kangaroo mother care, and open radiant warmer). ResultsAs errors in measurement of temperature were anticipated, a novel compensation method derived from infrared thermography of the neonate's skin was developed. Moreover, the differences in temperature recording for the 12 preterm infants varied from subject to subject. This variation could be arising from individual experimental setting applied to the same region of interest over the neonate's body. The experimental results for the model-based corrections is verified over the selected patient group. ConclusionThe proposed technique relies on applying model-based correction to the measured temperature and reducing extraneous errors during NIRT. This application specific method is based on different heat flux compartments present in neonatal thermography scene. Furthermore, these results are considered to be

  10. Organic matter remineralisation and biogenic silica dissolution in a deep fjord in British Columbia, Canada: a regression analysis of upper ocean sediment-trap fluxes

    NASA Astrophysics Data System (ADS)

    Timothy, David A.

    2004-03-01

    Remineralisation of sinking particulate matter can be inferred from sediment-trap studies where fluxes decrease with depth. However, during a 4-year experiment of monthly sediment-trap deployments at two stations in Jervis Inlet, British Columbia, Canada, fluxes often increased with depth, a common observation in coastal and some oceanic settings. A regression analysis that simultaneously estimates the composition of 'additional' fluxes to deep sediment traps and inverse decay length (IDL) scales of the primary (operationally termed 'anticipated') flux is applied to the data from Jervis Inlet. IDL scales for organic carbon (OC), nitrogen (N) and biogenic silica (BSi) decreased with depth in a manner well described by the power function, and are used to generated curves of flux versus depth in the absence of additional fluxes. The curve for OC flux is comparable to previously published models, but in Jervis Inlet remineralisation was somewhat higher in the upper water column, and lower in deep waters, than implied from open-ocean curves. The first upper-ocean estimates for dissolution rates of sinking BSi are presented; conversion to time-dependent rate constants shows that BSi dissolution in Jervis Inlet was similar to results from other studies where dissolution was rapid. A fitting of the flux curves to the reactive continuum model demonstrates that settling organic matter in Jervis Inlet had 3-4 reactive components, while BSi had 6-7 reactive components and over-all was less susceptible to decay. Additional fluxes to deep sediment traps in Jervis Inlet appear to have resulted partly from resuspended sediment increasingly winnowed with distance from topographic boundaries. Resuspended fluxes were particularly abundant during deepwater renewals, and another source supplied additional fluxes to mid-depth and deep traps on a continual basis. Included in the analysis is an error term, which is interpreted as the degree to which anticipated fluxes were over- or under

  11. Characteristic and magnetic field analysis of a high temperature superconductor axial-flux coreless induction maglev motor.

    PubMed

    Wei, Qin; Yu, Fan; Jin, Fang; Shuo, Li; Guoguo, Li; Gang, Lv

    2012-04-01

    A new high temperature superconductor axial-flux coreless maglev motor (HTS AFIM) is proposed, of which the primary windings are made of HTS tapes and the secondary is a non-magnetic conductor. The main works of this paper are the magnetic-field computation and characteristics analysis of HTS AFIM. For the first one, the reduction of magnetic fields near outer and inner radius of the HTS AFIM is solved by introducing the sub-loop electro-magnetic model along the radial position. For the second one, the AC losses of HTS coils are calculated. The relationships between the device's characteristics and device parameters are presented, and the results indicate that under certain frequency and current levitation device can output enough lift force. The conclusions are verified by finite element calculations. PMID:22393268

  12. Analysis of the cumulative neutrino flux from Fermi LAT blazar populations using 3 years of IceCube data

    NASA Astrophysics Data System (ADS)

    Glüsenkamp, Thorsten

    2016-07-01

    The recent discovery of a diffuse neutrino flux up to PeV energies raises the question of which populations of astrophysical sources contribute to this diffuse signal. One extragalactic candidate source population to produce high-energy neutrinos are Blazars. We present results from a likelihood analysis searching for cumulative neutrino emission from Blazar populations selected with the 2nd Fermi LAT AGN catalogue (2LAC) using an IceCube data set that has been optimized for the detection of individual sources. In contrast to previous searches with IceCube, the investigated populations contain up to hundreds of sources, the biggest one being the entire Blazar sample measured by the Fermi-LAT. No significant neutrino signal was found from any of these populations. Some implications of this non-observation for the origin of the observed PeV diffuse signal will be discussed.

  13. A method for accounting for maintenance costs in flux balance analysis improves the prediction of plant cell metabolic phenotypes under stress conditions.

    PubMed

    Cheung, C Y Maurice; Williams, Thomas C R; Poolman, Mark G; Fell, David A; Ratcliffe, R George; Sweetlove, Lee J

    2013-09-01

    Flux balance models of metabolism generally utilize synthesis of biomass as the main determinant of intracellular fluxes. However, the biomass constraint alone is not sufficient to predict realistic fluxes in central heterotrophic metabolism of plant cells because of the major demand on the energy budget due to transport costs and cell maintenance. This major limitation can be addressed by incorporating transport steps into the metabolic model and by implementing a procedure that uses Pareto optimality analysis to explore the trade-off between ATP and NADPH production for maintenance. This leads to a method for predicting cell maintenance costs on the basis of the measured flux ratio between the oxidative steps of the oxidative pentose phosphate pathway and glycolysis. We show that accounting for transport and maintenance costs substantially improves the accuracy of fluxes predicted from a flux balance model of heterotrophic Arabidopsis cells in culture, irrespective of the objective function used in the analysis. Moreover, when the new method was applied to cells under control, elevated temperature and hyper-osmotic conditions, only elevated temperature led to a substantial increase in cell maintenance costs. It is concluded that the hyper-osmotic conditions tested did not impose a metabolic stress, in as much as the metabolic network is not forced to devote more resources to cell maintenance.

  14. Detailed study of the Abelian-projected SU(2) flux tube and its dual Ginzburg-Landau analysis

    NASA Astrophysics Data System (ADS)

    Koma, Y.; Koma, M.; Ilgenfritz, E.-M.; Suzuki, T.

    2003-12-01

    The color-electric flux tube of Abelian-projected (AP) SU(2) lattice gauge theory in the maximally Abelian gauge (MAG) is examined. It is shown that the lattice Gribov copy effect in the MAG is crucial for the monopole-related parts of the flux-tube profiles. Taking into account both the gauge fixing procedure and the effect of finite quark-antiquark distance properly, the scaling property of the flux-tube profile is confirmed. The quantitative relation between the measured AP flux tube and the flux-tube solution of the U(1) dual Abelian Higgs (DAH) model is also discussed. The fitting of the AP flux tube in terms of the DAH flux tube indicates that the vacuum can be classified as a weakly type-I dual superconductor.

  15. A Mass Balance Analysis of Total Mercury Flux Through a Large, Managed Floodplain

    NASA Astrophysics Data System (ADS)

    Springborn, M.; Singer, M. B.; Dunne, T.

    2005-05-01

    The fate and transport of mercury are of critical concern in lowland floodplains worldwide. Increasing attention has been paid to the uncertainty of mercury sources and sinks in the Sacramento Valley, which is still recovering from decades of gold mining that used mercury for gold separation. Active in floods, Yolo Bypass is the largest flood-control bypass (or conveyance floodway) on the Sacramento River and is a key conduit for flow (up to 15,000 m(3)s(-1)) and the transport of fine sediment and adsorbed mercury to the San Francisco-Sacramento Bay-Delta. The 24,000 hectare bypass located in the lower Sacramento Valley has been recently implicated as a likely storage site for mercury with a high risk for methylation and transmission into the food chain at the primary wintering stop on the Pacific Flyway. In order to assess contaminant risk in the bypass, quantitative relationships between (1) total mercury concentration and suspended sediment concentration and (2) suspended sediment concentration and flow were developed for each of its major inputs and outputs using event-based sample data from various sources. These relationships were improved by incorporating dynamics of seasonal exhaustion and intraflood exhaustion (hysteresis) of sediment and mercury. From this characterization of how the flow-sediment-mercury transport system functions we were able to characterize the relative contributions of the various inputs. While the main inflow to the bypass is via flood weirs along the Sacramento River, two major creeks and an agricultural runoff canal made significant contributions to flow, sediment and mercury loads. Using the continuous record of flow to estimate sediment transport and sediment transport to estimate mercury flux we computed the net transfer of mercury through the bypass over a five-year period. Based on the volume and source of the expected change in flow and sediment, we were able to evaluate how mercury loading might change in the future due to

  16. Single-step enantioselective amino acid flux analysis by capillary electrophoresis using on-line sample preconcentration with chemical derivatization.

    PubMed

    Ptolemy, Adam S; Tran, Lara; Britz-McKibbin, Philip

    2006-07-15

    Capillary electrophoresis (CE) represents a versatile platform for integrating sample pretreatment with chemical analysis because of its ability to tune analyte electromigration and band dispersion properties in discontinuous electrolyte systems. In this article, a single-step method that combines on-line sample preconcentration with in-capillary chemical derivatization is developed for rapid, sensitive, and enantioselective analysis of micromolar levels of amino acids that lack intrinsic chromophores by CE with UV detection. Time-resolved electrophoretic studies revealed two distinct stages of amino acid band narrowing within the original long sample injection plug occurring both prior to and after in-capillary labeling via zone passing by ortho-phthalaldehyde/N-acetyl l-cysteine (OPA/NAC). This technique enabled direct analysis of d-amino acids in a 95% enantiomeric excess mixture with sub-micromolar detection limits and minimal sample handling, where the capillary functions as a preconcentrator, microreactor, and chiral selector. On-line sample preconcentration with chemical derivatization CE (SPCD-CE) was applied to study the enantioselective amino acid flux in Escherichia coli bacteria cultures, which demonstrated a unique l-Ala efflux into the extracellular medium. New strategies for high-throughput analyses of low-abundance metabolites are important for understanding fundamental physiological processes in bacteria required for screening the efficacy of new classes of antibiotics as well as altered metabolism in genetically modified mutant strains.

  17. Single-step enantioselective amino acid flux analysis by capillary electrophoresis using on-line sample preconcentration with chemical derivatization.

    PubMed

    Ptolemy, Adam S; Tran, Lara; Britz-McKibbin, Philip

    2006-07-15

    Capillary electrophoresis (CE) represents a versatile platform for integrating sample pretreatment with chemical analysis because of its ability to tune analyte electromigration and band dispersion properties in discontinuous electrolyte systems. In this article, a single-step method that combines on-line sample preconcentration with in-capillary chemical derivatization is developed for rapid, sensitive, and enantioselective analysis of micromolar levels of amino acids that lack intrinsic chromophores by CE with UV detection. Time-resolved electrophoretic studies revealed two distinct stages of amino acid band narrowing within the original long sample injection plug occurring both prior to and after in-capillary labeling via zone passing by ortho-phthalaldehyde/N-acetyl l-cysteine (OPA/NAC). This technique enabled direct analysis of d-amino acids in a 95% enantiomeric excess mixture with sub-micromolar detection limits and minimal sample handling, where the capillary functions as a preconcentrator, microreactor, and chiral selector. On-line sample preconcentration with chemical derivatization CE (SPCD-CE) was applied to study the enantioselective amino acid flux in Escherichia coli bacteria cultures, which demonstrated a unique l-Ala efflux into the extracellular medium. New strategies for high-throughput analyses of low-abundance metabolites are important for understanding fundamental physiological processes in bacteria required for screening the efficacy of new classes of antibiotics as well as altered metabolism in genetically modified mutant strains. PMID:16753129

  18. Advanced digital methods for blood flow flux analysis using µPIV approach

    NASA Astrophysics Data System (ADS)

    Kurochkin, Maxim A.; Timoshina, Polina A.; Fedosov, Ivan V.; Tuchin, Valery V.

    2015-03-01

    A digital optical system focused on work with laboratory animals for intravital capillaroscopy has been developed. It implements the particle image velocimetry (PIV) based approach for measurements of red blood cells velocity in laboratory rat stomach capillaries. We propose a method of involuntary displacement compensation of the capillary network images. Image stabilization algorithm is based on correlation of feature tracking. The efficiency of designed image stabilization algorithm was experimentally demonstrated. The results of capillary blood flow analysis are demonstrated.

  19. Efficient energy transfer in light-harvesting systems: Quantum-classical comparison, flux network, and robustness analysis

    NASA Astrophysics Data System (ADS)

    Wu, Jianlan; Liu, Fan; Ma, Jian; Silbey, Robert J.; Cao, Jianshu

    2012-11-01

    Following the calculation of optimal energy transfer in thermal environment in our first paper [J. L. Wu, F. Liu, Y. Shen, J. S. Cao, and R. J. Silbey, New J. Phys. 12, 105012 (2010), 10.1088/1367-2630/12/10/105012], full quantum dynamics and leading-order "classical" hopping kinetics are compared in the seven-site Fenna-Matthews-Olson (FMO) protein complex. The difference between these two dynamic descriptions is due to higher-order quantum corrections. Two thermal bath models, classical white noise (the Haken-Strobl-Reineker (HSR) model) and quantum Debye model, are considered. In the seven-site FMO model, we observe that higher-order corrections lead to negligible changes in the trapping time or in energy transfer efficiency around the optimal and physiological conditions (2% in the HSR model and 0.1% in the quantum Debye model for the initial site at BChl 1). However, using the concept of integrated flux, we can identify significant differences in branching probabilities of the energy transfer network between hopping kinetics and quantum dynamics (26% in the HSR model and 32% in the quantum Debye model for the initial site at BChl 1). This observation indicates that the quantum coherence can significantly change the distribution of energy transfer pathways in the flux network with the efficiency nearly the same. The quantum-classical comparison of the average trapping time with the removal of the bottleneck site, BChl 4, demonstrates the robustness of the efficient energy transfer by the mechanism of multi-site quantum coherence. To reconcile with the latest eight-site FMO model which is also investigated in the third paper [J. Moix, J. L. Wu, P. F. Huo, D. F. Coker, and J. S. Cao, J. Phys. Chem. Lett. 2, 3045 (2011), 10.1021/jz201259v], the quantum-classical comparison with the flux network analysis is summarized in Appendix C. The eight-site FMO model yields similar trapping time and network structure as the seven-site FMO model but leads to a more disperse

  20. Genome-Based Metabolic Mapping and 13C Flux Analysis Reveal Systematic Properties of an Oleaginous Microalga Chlorella protothecoides

    SciTech Connect

    Wu, Chao; Xiong, Wei; Dai, Junbiao; Wu, Qingyu

    2014-12-15

    We report that integrated and genome-based flux balance analysis, metabolomics, and 13C-label profiling of phototrophic and heterotrophic metabolism in Chlorella protothecoides, an oleaginous green alga for biofuel. The green alga Chlorella protothecoides, capable of autotrophic and heterotrophic growth with rapid lipid synthesis, is a promising candidate for biofuel production. Based on the newly available genome knowledge of the alga, we reconstructed the compartmentalized metabolic network consisting of 272 metabolic reactions, 270 enzymes, and 461 encoding genes and simulated the growth in different cultivation conditions with flux balance analysis. Phenotype-phase plane analysis shows conditions achieving theoretical maximum of the biomass and corresponding fatty acid-producing rate for phototrophic cells (the ratio of photon uptake rate to CO2 uptake rate equals 8.4) and heterotrophic ones (the glucose uptake rate to O2 consumption rate reaches 2.4), respectively. Isotope-assisted liquid chromatography-mass spectrometry/mass spectrometry reveals higher metabolite concentrations in the glycolytic pathway and the tricarboxylic acid cycle in heterotrophic cells compared with autotrophic cells. We also observed enhanced levels of ATP, nicotinamide adenine dinucleotide (phosphate), reduced, acetyl-Coenzyme A, and malonyl-Coenzyme A in heterotrophic cells consistently, consistent with a strong activity of lipid synthesis. To profile the flux map in experimental conditions, we applied nonstationary 13C metabolic flux analysis as a complementing strategy to flux balance analysis. We found that the result reveals negligible photorespiratory fluxes and a metabolically low active tricarboxylic acid cycle in phototrophic C. protothecoides. In comparison, high throughput of amphibolic reactions and the tricarboxylic acid cycle with no glyoxylate shunt activities were measured for heterotrophic cells. Lastly, taken together, the

  1. Greenhouse gas fluxes from agricultural soils under organic and non-organic management--a global meta-analysis.

    PubMed

    Skinner, Colin; Gattinger, Andreas; Muller, Adrian; Mäder, Paul; Flieβbach, Andreas; Stolze, Matthias; Ruser, Reiner; Niggli, Urs

    2014-01-15

    It is anticipated that organic farming systems provide benefits concerning soil conservation and climate protection. A literature search on measured soil-derived greenhouse gas (GHG) (nitrous oxide and methane) fluxes under organic and non-organic management from farming system comparisons was conducted and followed by a meta-analysis. Up to date only 19 studies based on field measurements could be retrieved. Based on 12 studies that cover annual measurements, it appeared with a high significance that area-scaled nitrous oxide emissions from organically managed soils are 492 ± 160 kg CO2 eq. ha(-1) a(-1) lower than from non-organically managed soils. For arable soils the difference amounts to 497 ± 162 kg CO2 eq. ha(-1) a(-1). However, yield-scaled nitrous oxide emissions are higher by 41 ± 34 kg CO2 eq. t(-1) DM under organic management (arable and use). To equalize this mean difference in yield-scaled nitrous oxide emissions between both farming systems, the yield gap has to be less than 17%. Emissions from conventionally managed soils seemed to be influenced mainly by total N inputs, whereas for organically managed soils other variables such as soil characteristics seemed to be more important. This can be explained by the higher bioavailability of the synthetic N fertilisers in non-organic farming systems while the necessary mineralisation of the N sources under organic management leads to lower and retarded availability. Furthermore, a higher methane uptake of 3.2 ± 2.5 kg CO2 eq. ha(-1) a(-1) for arable soils under organic management can be observed. Only one comparative study on rice paddies has been published up to date. All 19 retrieved studies were conducted in the Northern hemisphere under temperate climate. Further GHG flux measurements in farming system comparisons are required to confirm the results and close the existing knowledge gaps.

  2. Systematic Analysis of the Effect of Small Scale Permeability Heterogeneity on Hyporheic Exchange Flux and Residence Times

    NASA Astrophysics Data System (ADS)

    Laube, G.; Schmidt, C.; Fleckenstein, J. H.

    2014-12-01

    The hyporheic zone (HZ) contributes significantly to whole stream biogeochemical cycling. Biogeochemical reactions within the HZ are often transport limited, thus, understanding these reactions requires knowledge about the magnitude of hyporheic fluxes (HF) and the residence time (RT) of these fluxes within the HZ. While the hydraulics of HF are relatively well understood, studies addressing the influence of permeability heterogeneity lack systematic analysis and have even produced contradictory results (e.g. [1] vs. [2]). In order to close this gap, this study uses a statistical numerical approach to elucidate the influence of permeability heterogeneity on HF and RT. We simulated and evaluated 3750 2D-scenarios of sediment heterogeneity by means of Gaussian random fields with focus on total HF and RT distribution. The scenarios were based on ten realizations of each of all possible combinations of 15 different correlation lengths, 5 dipping angles and 5 permeability variances. Roughly 500 hyporheic stream traces were analyzed per simulation, for a total of almost two million stream traces analyzed for correlations between permeability heterogeneity, HF, and RT. Total HF and the RT variance positively correlated with permeability variance while the mean RT negatively correlated with permeability variance. In contrast, changes in correlation lengths and dipping angles had little effect on the examined properties RT and HF. These results provide a possible explanation of the seemingly contradictory conclusions of recent studies, given that the permeability variances in these studies differ by several orders of magnitude. [1] Bardini, L., Boano, F., Cardenas, M.B, Sawyer, A.H, Revelli, R. and Ridolfi, L. "Small-Scale Permeability Heterogeneity Has Negligible Effects on Nutrient Cycling in Streambeds." Geophysical Research Letters, 2013. doi:10.1002/grl.50224. [2] Zhou, Y., Ritzi, R. W., Soltanian, M. R. and Dominic, D. F. "The Influence of Streambed Heterogeneity on

  3. Hybrid metabolic flux analysis and recombinant protein prediction in Pichia pastoris X-33 cultures expressing a single-chain antibody fragment.

    PubMed

    Isidro, Inês A; Portela, Rui M; Clemente, João J; Cunha, António E; Oliveira, Rui

    2016-09-01

    Despite the growing importance of the Pichia pastoris expression system as industrial workhorse, the literature is almost absent in systematic studies on how culture medium composition affects central carbon fluxes and heterologous protein expression. In this study we investigate how 26 variations of the BSM+PTM1 medium impact central carbon fluxes and protein expression in a P. pastoris X-33 strain expressing a single-chain antibody fragment. To achieve this goal, we adopted a hybrid metabolic flux analysis (MFA) methodology, which is a modification of standard MFA to predict the rate of synthesis of recombinant proteins. Hybrid MFA combines the traditional parametric estimation of central carbon fluxes with non-parametric statistical modeling of product-related quantitative or qualitative measurements as a function of central carbon fluxes. It was observed that protein yield variability was 53.6 % (relative standard deviation) among the different experiments. Protein yield is much more sensitive to medium composition than biomass growth, which is mainly determined by the carbon source availability and main salts. Hybrid MFA was able to describe accurately the protein yield with normalized RMSE of 6.3 % over 5 independent experiments. The metabolic state that promotes high protein yields is characterized by high overall metabolic rates through main central carbon pathways concomitantly with a relative shift of carbon flux from biosynthetic towards energy generating pathways. PMID:27129458

  4. Analysis of a link of embrittlement mechanisms and neutron flux effect as applied to reactor pressure vessel materials of WWER

    NASA Astrophysics Data System (ADS)

    Margolin, B. Z.; Yurchenko, E. V.; Morozov, A. M.; Pirogova, N. E.; Brumovsky, M.

    2013-03-01

    The effect of neutron flux on embrittlement of WWER RPV materials is analyzed for cases when different radiation defects prevail. Data bases on the ductile-brittle transition temperature shifts obtained in the surveillance specimens programs and the research programs are used. The material embrittlement mechanisms for which the flux effect is practically absent and for which the flux effect is remarkable are determined. For case when the phosphorus segregation mechanism dominates the theoretical justification of the absence of the flux effect is performed on the basis of the theory of radiation-enhanced diffusion.

  5. Bioremediation in marine ecosystems: a computational study combining ecological modeling and flux balance analysis

    PubMed Central

    Taffi, Marianna; Paoletti, Nicola; Angione, Claudio; Pucciarelli, Sandra; Marini, Mauro; Liò, Pietro

    2014-01-01

    The pressure to search effective bioremediation methodologies for contaminated ecosystems has led to the large-scale identification of microbial species and metabolic degradation pathways. However, minor attention has been paid to the study of bioremediation in marine food webs and to the definition of integrated strategies for reducing bioaccumulation in species. We propose a novel computational framework for analysing the multiscale effects of bioremediation at the ecosystem level, based on coupling food web bioaccumulation models and metabolic models of degrading bacteria. The combination of techniques from synthetic biology and ecological network analysis allows the specification of arbitrary scenarios of contaminant removal and the evaluation of strategies based on natural or synthetic microbial strains. In this study, we derive a bioaccumulation model of polychlorinated biphenyls (PCBs) in the Adriatic food web, and we extend a metabolic reconstruction of Pseudomonas putida KT2440 (iJN746) with the aerobic pathway of PCBs degradation. We assess the effectiveness of different bioremediation scenarios in reducing PCBs concentration in species and we study indices of species centrality to measure their importance in the contaminant diffusion via feeding links. The analysis of the Adriatic sea case study suggests that our framework could represent a practical tool in the design of effective remediation strategies, providing at the same time insights into the ecological role of microbial communities within food webs. PMID:25309577

  6. Overcoming the metabolic burden of protein secretion in Schizosaccharomyces pombe--a quantitative approach using 13C-based metabolic flux analysis.

    PubMed

    Klein, Tobias; Lange, Sabrina; Wilhelm, Nadine; Bureik, Matthias; Yang, Tae-Hoon; Heinzle, Elmar; Schneider, Konstantin

    2014-01-01

    Protein secretion in yeast is generally associated with a burden to cellular metabolism. To investigate this metabolic burden in Schizosaccharomyces pombe, we constructed a set of strains secreting the model protein maltase in different amounts. We quantified the influence of protein secretion on the metabolism applying (13)C-based metabolic flux analysis in chemostat cultures. Analysis of the macromolecular biomass composition revealed an increase in cellular lipid content at elevated levels of protein secretion and we observed altered metabolic fluxes in the pentose phosphate pathway, the TCA cycle, and around the pyruvate node including mitochondrial NADPH supply. Supplementing acetate to glucose or glycerol minimal media was found to improve protein secretion, accompanied by an increased cellular lipid content and carbon flux through the TCA cycle as well as increased mitochondrial NADPH production. Thus, systematic metabolic analyses can assist in identifying factors limiting protein secretion and in deriving strategies to overcome these limitations.

  7. Analysis of shape of porous cooled medium for an imposed surface heat flux and temperature

    NASA Technical Reports Server (NTRS)

    Siegel, R.

    1973-01-01

    The surface of a porous cooled medium is to be maintained at a specified design temperature while being subjected to uniform heating by an external source. An analytical method is given for determining the shape of the medium surface that will satisfy these boundary conditions. The analysis accounts for temperature dependent variations of fluid density and viscosity and for temperature dependent matrix thermal conductivity. The energy equation is combined with Darcy's law in such a way that a potential can be defined that satisfies Laplace's equation. All of the heat-transfer and flow quantities are expressed in terms of this potential. The determination of the shape of the porous cooled region is thereby reduced to a free-boundary problem such as in inviscid free jet theory. Two illustrative examples are carried out: a porous leading edge with coolant supplied through a slot and a porous cooled duct with a rectangular outer boundary.

  8. Multiscale Metabolic Modeling: Dynamic Flux Balance Analysis on a Whole-Plant Scale1[W][OPEN

    PubMed Central

    Grafahrend-Belau, Eva; Junker, Astrid; Eschenröder, André; Müller, Johannes; Schreiber, Falk; Junker, Björn H.

    2013-01-01

    Plant metabolism is characterized by a unique complexity on the cellular, tissue, and organ levels. On a whole-plant scale, changing source and sink relations accompanying plant development add another level of complexity to metabolism. With the aim of achieving a spatiotemporal resolution of source-sink interactions in crop plant metabolism, a multiscale metabolic modeling (MMM) approach was applied that integrates static organ-specific models with a whole-plant dynamic model. Allowing for a dynamic flux balance analysis on a whole-plant scale, the MMM approach was used to decipher the metabolic behavior of source and sink organs during the generative phase of the barley (Hordeum vulgare) plant. It reveals a sink-to-source shift of the barley stem caused by the senescence-related decrease in leaf source capacity, which is not sufficient to meet the nutrient requirements of sink organs such as the growing seed. The MMM platform represents a novel approach for the in silico analysis of metabolism on a whole-plant level, allowing for a systemic, spatiotemporally resolved understanding of metabolic processes involved in carbon partitioning, thus providing a novel tool for studying yield stability and crop improvement. PMID:23926077

  9. Analysis and modeling of flow blockage-induced steam explosion events in the High-Flux Isotope Reactor

    SciTech Connect

    Taleyarkhan, R.P.; Georgevich, V.; Lestor, C.W.; Gat, U.; Lepard, B.L.; Cook, D.H.; Freels, J.; Chang, S.J.; Luttrell, C.; Gwaltney, R.C.; Kirkpatrick, J.

    1993-06-01

    This paper provides a perspective overview of the analysis and modeling work done to evaluate the threat from steam explosion loads in the High-Flux Isotope Reactor during flow blockage events. The overall workscope included modeling and analysis of core melt initiation, melt propagation, bounding and best-estimate steam explosion energetics, vessel failure from fracture, bolts failure from exceedance of elastic limits, and finally, missile evolution and transport. Aluminum ignition was neglected. Evaluations indicated that a thermally driven steam explosion with more than 65 MJ of energy insertion in the core region over several miliseconds would be needed to cause a sufficiently energetic missile with a capacity to cause early confinement failure. This amounts to about 65% of the HFIR core mass melting and participating in a steam explosion. Conservative melt propagation analyses have indicated that at most only 24% of the HFIR core mass could melt during flow blockage events under full-power conditions. Therefore, it is judged that the HFIR vessel and top head structure will be able to withstand loads generated from thermally driven steam explosions initiated by any credible flow blockage event. A substantial margin to safety was demonstrated.

  10. Analysis and modeling of flow blockage-induced steam explosion events in the High-Flux Isotope Reactor

    SciTech Connect

    Taleyarkhan, R.P.; Georgevich, V.; Lestor, C.W.; Gat, U.; Lepard, B.L.; Cook, D.H.; Freels, J.; Chang, S.J.; Luttrell, C.; Gwaltney, R.C.; Kirkpatrick, J.

    1993-01-01

    This paper provides a perspective overview of the analysis and modeling work done to evaluate the threat from steam explosion loads in the High-Flux Isotope Reactor during flow blockage events. The overall workscope included modeling and analysis of core melt initiation, melt propagation, bounding and best-estimate steam explosion energetics, vessel failure from fracture, bolts failure from exceedance of elastic limits, and finally, missile evolution and transport. Aluminum ignition was neglected. Evaluations indicated that a thermally driven steam explosion with more than 65 MJ of energy insertion in the core region over several miliseconds would be needed to cause a sufficiently energetic missile with a capacity to cause early confinement failure. This amounts to about 65% of the HFIR core mass melting and participating in a steam explosion. Conservative melt propagation analyses have indicated that at most only 24% of the HFIR core mass could melt during flow blockage events under full-power conditions. Therefore, it is judged that the HFIR vessel and top head structure will be able to withstand loads generated from thermally driven steam explosions initiated by any credible flow blockage event. A substantial margin to safety was demonstrated.

  11. In situ measurement of methane fluxes and analysis of transcribed particulate methane monooxygenase in desert soils.

    PubMed

    Angel, Roey; Conrad, Ralf

    2009-10-01

    Aerated soils are a biological sink for atmospheric methane. However, the activity of desert soils and the presence of methanotrophs in these soils have hardly been studied. We studied on-site atmospheric methane consumption rates as well as the diversity and expression of the pmoA gene, coding for a subunit of the particulate methane monooxygenase, in arid and hyperarid soils in the Negev Desert, Israel. Methane uptake was only detected in undisturbed soils in the arid region (approximately 90 mm year(-1)) and vertical methane profiles in soil showed the active layer to be at 0-20 cm depth. No methane uptake was detected in the hyperarid soils (approximately 20 mm year(-1)) as well as in disturbed soils in the arid region (i.e. agricultural field and a mini-catchment). Molecular analysis of the methanotrophic community using terminal restriction fragment length polymorphism (T-RFLP) and cloning/sequencing of the pmoA gene detected methanotrophs in the active soils, whereas the inactive ones were dominated by sequences of the homologous gene amoA, coding for a subunit of the ammonia monooxygenase. Even in the active soils, methanotrophs (as well as in situ activity) could not be detected in the soil crust, which is the biologically most important layer in desert soils. All pmoA sequences belonged to yet uncultured strains. Transcript analysis showed dominance of sequences clustering within the JR3, formerly identified in Californian grassland soils. Our results show that although active methanotrophs are prevalent in arid soils they seem to be absent or inactive in hyperarid and disturbed arid soils. Furthermore, we postulate that methanotrophs of the yet uncultured JR3 cluster are the dominant atmospheric methane oxidizers in this ecosystem.

  12. Development and analysis of prognostic equations for mesoscale kinetic energy and mesoscale (subgrid scale) fluxes for large-scale atmospheric models

    NASA Technical Reports Server (NTRS)

    Avissar, Roni; Chen, Fei

    1993-01-01

    Generated by landscape discontinuities (e.g., sea breezes) mesoscale circulation processes are not represented in large-scale atmospheric models (e.g., general circulation models), which have an inappropiate grid-scale resolution. With the assumption that atmospheric variables can be separated into large scale, mesoscale, and turbulent scale, a set of prognostic equations applicable in large-scale atmospheric models for momentum, temperature, moisture, and any other gaseous or aerosol material, which includes both mesoscale and turbulent fluxes is developed. Prognostic equations are also developed for these mesoscale fluxes, which indicate a closure problem and, therefore, require a parameterization. For this purpose, the mean mesoscale kinetic energy (MKE) per unit of mass is used, defined as E-tilde = 0.5 (the mean value of u'(sub i exp 2), where u'(sub i) represents the three Cartesian components of a mesoscale circulation (the angle bracket symbol is the grid-scale, horizontal averaging operator in the large-scale model, and a tilde indicates a corresponding large-scale mean value). A prognostic equation is developed for E-tilde, and an analysis of the different terms of this equation indicates that the mesoscale vertical heat flux, the mesoscale pressure correlation, and the interaction between turbulence and mesoscale perturbations are the major terms that affect the time tendency of E-tilde. A-state-of-the-art mesoscale atmospheric model is used to investigate the relationship between MKE, landscape discontinuities (as characterized by the spatial distribution of heat fluxes at the earth's surface), and mesoscale sensible and latent heat fluxes in the atmosphere. MKE is compared with turbulence kinetic energy to illustrate the importance of mesoscale processes as compared to turbulent processes. This analysis emphasizes the potential use of MKE to bridge between landscape discontinuities and mesoscale fluxes and, therefore, to parameterize mesoscale fluxes

  13. Aerodynamic gradient measurements of the NH3-HNO3-NH4NO3 triad using a wet chemical instrument: an analysis of precision requirements and flux errors

    NASA Astrophysics Data System (ADS)

    Wolff, V.; Trebs, I.; Ammann, C.; Meixner, F. X.

    2010-02-01

    The aerodynamic gradient method is widely used for flux measurements of ammonia, nitric acid, particulate ammonium nitrate (the NH3-HNO3-NH4NO3 triad) and other water-soluble reactive trace compounds. The surface exchange flux is derived from a measured concentration difference and micrometeorological quantities (turbulent exchange coefficient). The significance of the measured concentration difference is crucial for the significant determination of surface exchange fluxes. Additionally, measurements of surface exchange fluxes of ammonia, nitric acid and ammonium nitrate are often strongly affected by phase changes between gaseous and particulate compounds of the triad, which make measurements of the four individual species (NH3, HNO3, NH4+, NO3- necessary for a correct interpretation of the measured concentration differences. We present here a rigorous analysis of results obtained with a multi-component, wet-chemical instrument, able to simultaneously measure gradients of both gaseous and particulate trace substances. Basis for our analysis are two field experiments, conducted above contrasting ecosystems (grassland, forest). Precision requirements of the instrument as well as errors of concentration differences and micrometeorological exchange parameters have been estimated, which, in turn, allows the establishment of thorough error estimates of the derived fluxes of NH3, HNO3, NH4+, and NO3-. Derived median flux errors for the grassland and forest field experiments were: 39% and 50% (NH3), 31% and 38% (HNO3), 62% and 57% (NH4+), and 47% and 68% (NO3-), respectively. Additionally, we provide the basis for using field data to characterize the instrument performance, as well as subsequent quantification of surface exchange fluxes and underlying mechanistic processes under realistic ambient measurement conditions.

  14. Aerodynamic gradient measurements of the NH3-HNO3-NH4NO3 triad using a wet chemical instrument: an analysis of precision requirements and flux errors

    NASA Astrophysics Data System (ADS)

    Wolff, V.; Trebs, I.; Ammann, C.; Meixner, F. X.

    2009-10-01

    The aerodynamic gradient method is widely used for flux measurements of ammonia, nitric acid, particulate ammonium nitrate (the NH3-HNO3-NH4NO3 triad) and other water-soluble reactive trace compounds. The surface exchange flux is derived from a measured concentration difference and micrometeorological quantities (turbulent exchange coefficient). The significance of the measured concentration difference is crucial for the significant determination of surface exchange fluxes. Additionally, measurements of surface exchange fluxes of ammonia, nitric acid and ammonium nitrate are often strongly affected by phase changes between gaseous and particulate compounds of the triad, which make measurements of the four individual species (NH3, HNO3, NH4+, NO3-) necessary for a correct interpretation of the measured concentration differences. We present here a rigorous analysis of results obtained with a multi-component, wet-chemical instrument, able to simultaneously measure gradients of both gaseous and particulate trace substances. Basis for our analysis are two field experiments, conducted above contrasting ecosystems (grassland, forest). Precision requirements of the instrument as well as errors of concentration differences and micrometeorological exchange parameters have been estimated, which, in turn, allows the establishment of thorough error estimates of the derived fluxes of NH3, HNO3, NH4+, and NO3-. Derived median flux errors for the grassland and forest field experiments were: 39 and 50% (NH3), 31 and 38% (HNO3), 62 and 57% (NH4+), and 47 and 68% (NO3-), respectively. Additionally, we provide the basis for using field data to characterize the instrument performance, as well as subsequent quantification of surface exchange fluxes and underlying mechanistic processes under realistic ambient measurement conditions.

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

    PubMed

    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

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

    PubMed Central

    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

  17. Metabolic evolution and (13) C flux analysis of a succinate dehydrogenase deficient strain of Yarrowia lipolytica.

    PubMed

    Yuzbashev, Tigran V; Bondarenko, Pavel Yu; Sobolevskaya, Tatiana I; Yuzbasheva, Evgeniya Yu; Laptev, Ivan A; Kachala, Vadim V; Fedorov, Alexander S; Vybornaya, Tatiana V; Larina, Anna S; Sineoky, Sergey P

    2016-11-01

    Bio-based succinic acid production can redirect industrial chemistry processes from using limited hydrocarbons to renewable carbohydrates. A fermentation process that does not require pH-titrating agents will be advantageous to the industry. Previously, a Yarrowia lipolytica strain that was defective for succinate dehydrogenase was constructed and was found to accumulate up to 17.5 g L(-1) of succinic acid when grown on glycerol without buffering. Here, a derivative mutant was isolated that produced 40.5 g L(-1) of succinic acid in 36 h with a yield of 0.32 g g(-1) glycerol. A combination approach of induced mutagenesis and metabolic evolution allowed isolation of another derivative that could utilize glucose efficiently and accumulated 50.2 g L(-1) succinic acid in 54 h with a yield of 0.43 g g(-1) . The parent strain of these isolated mutants was used for [1,6-(13) C2 ]glucose assimilation analysis. At least 35% glucose was estimated to be utilized through the pentose phosphate pathway, while ≥84% succinic acid was formed through the oxidative branch of the tricarboxylic acid cycle. Biotechnol. Bioeng. 2016;113: 2425-2432. © 2016 Wiley Periodicals, Inc. PMID:27182846

  18. Uncertainty Analysis on an Operational Simplified Surface Energy Balance algorithm for Estimation of Evapotranspiration at Multiple Flux Tower Sites

    NASA Astrophysics Data System (ADS)

    Chen, M.; Senay, G. B.; Verdin, J. P.; Rowland, J.

    2014-12-01

    Current regional to global and daily to annual Evapotranspiration ( ET) estimation mainly relies on surface energy balance (SEB) ET models or statistical empirical methods driven by remote sensing data and various meteorology databases. However, these ET models face challenging issues—large uncertainties from inevitable input errors, poorly defined parameters, and inadequate model structures. The eddy covariance measurements on water, energy, and carbon fluxes at globally available FLUXNET tower sites provide a feasible opportunity to assess the ET modelling uncertainties. In this study, we focused on uncertainty analysis on an operational simplified surface energy balance (SSEBop) algorithm for ET estimation at multiple Ameriflux tower sites with diverse land cover characteristics and climatic conditions. The input land surface temperature (LST) data of the algorithm were adopted from the 8-day composite1-km Moderate Resolution Imaging Spectroradiometer (MODIS) land surface temperature. The other input data were taken from the Ameriflux database. Results of statistical analysis indicated that uncertainties or random errors from input variables and parameters of SSEBop led to daily and seasonal ET estimates with relative errors around 20% across multiple flux tower sites distributed across different biomes. This uncertainty of SSEBop lies in the error range of 20-30% of similar SEB-based ET algorithms, such as, Surface Energy Balance System and Surface Energy Balance Algorithm for Land. The R2 between daily and seasonal ET estimates by SSEBop and ET eddy covariance measurements at multiple Ameriflux tower sites exceed 0.7, and even up to 0.9 for croplands, grasslands, and forests, suggesting systematic error or bias of the SSEBop is acceptable. In summary, the uncertainty assessment verifies that the SSEBop is a reliable method for wide-area ET calculation and especially useful for detecting drought years and relative drought severity for agricultural production

  19. Tropospheric ozone reduces carbon assimilation in trees: estimates from analysis of continuous flux measurements.

    PubMed

    Fares, Silvano; Vargas, Rodrigo; Detto, Matteo; Goldstein, Allen H; Karlik, John; Paoletti, Elena; Vitale, Marcello

    2013-08-01

    High ground-level ozone concentrations are typical of Mediterranean climates. Plant exposure to this oxidant is known to reduce carbon assimilation. Ozone damage has been traditionally measured through manipulative experiments that do not consider long-term exposure and propagate large uncertainty by up-scaling leaf-level observations to ecosystem-level interpretations. We analyzed long-term continuous measurements (>9 site-years at 30 min resolution) of environmental and eco-physiological parameters at three Mediterranean ecosystems: (i) forest site dominated by Pinus ponderosa in the Sierra Mountains in California, USA; (ii) forest site composed of a mixture of Quercus spp. and P. pinea in the Tyrrhenian sea coast near Rome, Italy; and (iii) orchard site of Citrus sinensis cultivated in the California Central Valley, USA. We hypothesized that higher levels of ozone concentration in the atmosphere result in a decrease in carbon assimilation by trees under field conditions. This hypothesis was tested using time series analysis such as wavelet coherence and spectral Granger causality, and complemented with multivariate linear and nonlinear statistical analyses. We found that reduction in carbon assimilation was more related to stomatal ozone deposition than to ozone concentration. The negative effects of ozone occurred within a day of exposure/uptake. Decoupling between carbon assimilation and stomatal aperture increased with the amount of ozone pollution. Up to 12-19% of the carbon assimilation reduction in P. ponderosa and in the Citrus plantation was explained by higher stomatal ozone deposition. In contrast, the Italian site did not show reductions in gross primary productivity either by ozone concentration or stomatal ozone deposition, mainly due to the lower ozone concentrations in the periurban site over the shorter period of investigation. These results highlight the importance of plant adaptation/sensitivity under field conditions, and the importance of

  20. Characterization of energy conversion based on metabolic flux analysis in mixotrophic liverwort cells, Marchantia polymorpha.

    PubMed

    Hata; Hua; Yang; Shimizu; Taya

    2000-08-01

    In order to characterize the contributions of respiratory and photosynthetic actions to energy conversions, the mixotrophic cells of Marchantia polymorpha were cultivated in the medium containing 10kg/m(3) glucose as an organic carbon source. The cultures were conducted with the supply of ordinary air (0.03% CO(2)) at constant incident light intensities of 50 and 180W/m(2). From the results of metabolic analysis, it was found that the cell yield based on ATP synthesis was estimated to be 6.3x10(-3)kg-dry cells/mol-ATP in these cultures. Under the examined conditions, energy conversion efficiency through respiration was larger than that through photosynthesis, and efficiency of overall energy conversion to ATP was maximized when the sum of energies from glucose and light captured by the cells was approximately 7.2x10(5)J/(hkg-dry cells). Taking into account the efficiency of overall energy conversion, a batch culture of M. polymorpha in a bioreactor was carried out by regulating incident light intensity ranging from 9 to 58W/m(2). In the culture with light regulation, the cell yield of 6.2x10(-9)kg-dry cells/J was achieved on the basis of energy provided to the system throughout the culture, and this value was 2.3 and 9.3 times as large as those obtained in the cultures under constant incident light intensities of 50 and 180W/m(2), respectively.

  1. A Method of Accounting for Enzyme Costs in Flux Balance Analysis Reveals Alternative Pathways and Metabolite Stores in an Illuminated Arabidopsis Leaf.

    PubMed

    Cheung, C Y Maurice; Ratcliffe, R George; Sweetlove, Lee J

    2015-11-01

    Flux balance analysis of plant metabolism is an established method for predicting metabolic flux phenotypes and for exploring the way in which the plant metabolic network delivers specific outcomes in different cell types, tissues, and temporal phases. A recurring theme is the need to explore the flexibility of the network in meeting its objectives and, in particular, to establish the extent to which alternative pathways can contribute to achieving specific outcomes. Unfortunately, predictions from conventional flux balance analysis minimize the simultaneous operation of alternative pathways, but by introducing flux-weighting factors to allow for the variable intrinsic cost of supporting each flux, it is possible to activate different pathways in individual simulations and, thus, to explore alternative pathways by averaging thousands of simulations. This new method has been applied to a diel genome-scale model of Arabidopsis (Arabidopsis thaliana) leaf metabolism to explore the flexibility of the network in meeting the metabolic requirements of the leaf in the light. This identified alternative flux modes in the Calvin-Benson cycle revealed the potential for alternative transitory carbon stores in leaves and led to predictions about the light-dependent contribution of alternative electron flow pathways and futile cycles in energy rebalancing. Notable features of the analysis include the light-dependent tradeoff between the use of carbohydrates and four-carbon organic acids as transitory storage forms and the way in which multiple pathways for the consumption of ATP and NADPH can contribute to the balancing of the requirements of photosynthetic metabolism with the energy available from photon capture.

  2. A Method of Accounting for Enzyme Costs in Flux Balance Analysis Reveals Alternative Pathways and Metabolite Stores in an Illuminated Arabidopsis Leaf1[OPEN

    PubMed Central

    Cheung, C.Y. Maurice; Ratcliffe, R. George; Sweetlove, Lee J.

    2015-01-01

    Flux balance analysis of plant metabolism is an established method for predicting metabolic flux phenotypes and for exploring the way in which the plant metabolic network delivers specific outcomes in different cell types, tissues, and temporal phases. A recurring theme is the need to explore the flexibility of the network in meeting its objectives and, in particular, to establish the extent to which alternative pathways can contribute to achieving specific outcomes. Unfortunately, predictions from conventional flux balance analysis minimize the simultaneous operation of alternative pathways, but by introducing flux-weighting factors to allow for the variable intrinsic cost of supporting each flux, it is possible to activate different pathways in individual simulations and, thus, to explore alternative pathways by averaging thousands of simulations. This new method has been applied to a diel genome-scale model of Arabidopsis (Arabidopsis thaliana) leaf metabolism to explore the flexibility of the network in meeting the metabolic requirements of the leaf in the light. This identified alternative flux modes in the Calvin-Benson cycle revealed the potential for alternative transitory carbon stores in leaves and led to predictions about the light-dependent contribution of alternative electron flow pathways and futile cycles in energy rebalancing. Notable features of the analysis include the light-dependent tradeoff between the use of carbohydrates and four-carbon organic acids as transitory storage forms and the way in which multiple pathways for the consumption of ATP and NADPH can contribute to the balancing of the requirements of photosynthetic metabolism with the energy available from photon capture. PMID:26265776

  3. Understanding the relationship between actual and potential evapotranspirations from long- term water balance analysis and flux observation

    NASA Astrophysics Data System (ADS)

    Yang, D.; Yang, H.; Sun, F.

    2007-12-01

    Increase in air temperature and decrease in pan evaporation was found to be common worldwide during the past half century. This results in controversy in view of the changes to the hydrological cycle. Increases in precipitation have been expected due to the Clausius¡§CClapyeron relation in that the specific humidity increases exponentially with the greenhouse-gas induced temperature increasing and confirmed by measurements over northern extratropical land areas. The hydrologic cycle is expected to be intensified (or accelerated). However, the decreased pan evaporation is found to be well related to the global dimming, i.e., the decreased solar radiation induced by the pollution increasing, thus evaporation (i.e., the latent heat flux) should be steadily decreasing from the energy balance perspective. Many researchers explained that the potential evaporation (usually measured by pan) is decreased with increasing of precipitation; however, the increased soil moisture (due to precipitation increasing) can be evaporated because of extra energy available. Therefore, the actual and potential evaporation are in complementary relationship, which is expected to unify the controversy between global warming and dimming. This means that pan evaporation decrease implicates acceleration of the global hydrologic cycle, i.e., increase in the terrestrial evaporation. Based on the complementary theory, many operational formulae have been introduced to estimated actual evaporation from the potential evaporation. Our recent water balance analysis of 108 catchments in non-humid regions of China has shown that there are no general opposite trends between potential and actual evaporation in the same period. A novel phenomenon has been found that the complementary relationships in evaporation are distinctly confirmed when the annual actual and potential evaporation are plotted against annual precipitation; However, complementary relationships disappear in many catchments when actual and

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

    PubMed

    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.

  5. Flux balance analysis of genome-scale metabolic model of rice (Oryza sativa): aiming to increase biomass.

    PubMed

    Shaw, Rahul; Kundu, Sudip

    2015-10-01

    Due to socio-economic reasons, it is essential to design efficient stress-tolerant, more nutritious, high yielding rice varieties. A systematic understanding of the rice cellular metabolism is essential for this purpose. Here, we analyse a genome-scale metabolic model of rice leaf using Flux Balance Analysis to investigate whether it has potential metabolic flexibility to increase the biosynthesis of any of the biomass components. We initially simulate the metabolic responses under an objective to maximize the biomass components. Using the estimated maximum value of biomass synthesis as a constraint, we further simulate the metabolic responses optimizing the cellular economy. Depending on the physiological conditions of a cell, the transport capacities of intracellular transporters (ICTs) can vary. To mimic this physiological state, we randomly vary the ICTs' transport capacities and investigate their effects. The results show that the rice leaf has the potential to increase glycine and starch in a wide range depending on the ICTs' transport capacities. The predicted biosynthesis pathways vary slightly at the two different optimization conditions. With the constraint of biomass composition, the cell also has the metabolic plasticity to fix a wide range of carbon-nitrogen ratio.

  6. 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.

    PubMed

    McCloskey, Douglas; Young, Jamey D; Xu, Sibei; Palsson, Bernhard O; Feist, Adam M

    2016-01-19

    The analytical challenges to acquire accurate isotopic data of intracellular metabolic intermediates for stationary, nonstationary, and dynamic metabolic flux analysis (MFA) are numerous. This work presents MID Max, a novel LC-MS/MS workflow, acquisition, and isotopomer deconvolution method for MFA 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 estimations and number of resolved exchange fluxes for wild-type E. coli compared to traditional methods and previously published data sets.

  7. Estimating regional greenhouse gas fluxes: an uncertainty analysis of planetary boundary layer techniques and bottom-up inventories

    NASA Astrophysics Data System (ADS)

    Zhang, X.; Lee, X.; Griffis, T. J.; Baker, J. M.; Xiao, W.

    2014-10-01

    Quantification of regional greenhouse gas (GHG) fluxes is essential for establishing mitigation strategies and evaluating their effectiveness. Here, we used multiple top-down approaches and multiple trace gas observations at a tall tower to estimate regional-scale GHG fluxes and evaluate the GHG fluxes derived from bottom-up approaches. We first applied the eddy covariance, equilibrium, inverse modeling (CarbonTracker), and flux aggregation methods using 3 years of carbon dioxide (CO2) measurements on a 244 m tall tower in the upper Midwest, USA. We then applied the equilibrium method for estimating CH4 and N2O fluxes with 1-month high-frequency CH4 and N2O gradient measurements on the tall tower and 1-year concentration measurements on a nearby tall tower, and evaluated the uncertainties of this application. The results indicate that (1) the flux aggregation, eddy covariance, the equilibrium method, and the CarbonTracker product all gave similar seasonal patterns of the regional CO2 flux (105-106 km2, but that the equilibrium method underestimated the July CO2 flux by 52-69%. (2) The annual budget varied among these methods from -54 to -131 g C-CO2 m-2 yr-1, indicating a large uncertainty in the annual CO2 flux estimation. (3) The regional CH4 and N2O emissions according to a top-down method were at least 6 and 2 times higher than the emissions from a bottom-up inventory (Emission Database for Global Atmospheric Research), respectively. (4) The global warming potentials of the CH4 and N2O emissions were equal in magnitude to the cooling benefit of the regional CO2 uptake. The regional GHG budget, including both biological and anthropogenic origins, is estimated at 7 ± 160 g CO2 equivalent m-2 yr-1.

  8. Integration of a constraint-based metabolic model of Brassica napus developing seeds with 13C-metabolic flux analysis

    SciTech Connect

    Hay, Jordan O.; Shi, Hai; Heinzel, Nicolas; Hebbelmann, Inga; Rolletschek, Hardy; Schwender, Jorg

    2014-12-19

    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 (GPR) associations resolving subcellular localization. Detailed mass and charge balancing and confidence scoring were applied to all reactions. Using B. 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). In conclusion, using this combined approach we characterize the difference in metabolic flux of developing seeds of two B. napus

  9. An analysis on the influence of spatial scales on sensible heat fluxes in the north Tibetan Plateau based on Eddy covariance and large aperture scintillometer data

    NASA Astrophysics Data System (ADS)

    Sun, Genhou; Hu, Zeyong; Sun, Fanglin; Wang, Jiemin; Xie, Zhipeng; Lin, Yun; Huang, Fangfang

    2016-05-01

    The influence of spatial scales on surface fluxes is an interesting but not fully investigated question. This paper presents an analysis on the influence of spatial scales on surface fluxes in the north Tibetan Plateau based on eddy covariance (EC) and large aperture scintillometer (LAS) data at site Nagqu/BJ, combined with the land surface temperature (LST) and normalized difference vegetation index (NDVI) of moderate-resolution imaging spectroradiometer (MODIS). The analysis shows that sensible heat fluxes calculated with LAS data (H_LAS) agree reasonably well with sensible heat fluxes calculated with EC data (H_EC) in the rain and dry seasons. The difference in their footprints due to the wind direction is an important reason for the differences in H_EC and H_LAS. The H_LAS are statistically more consistent with H_EC when their footprints overlap than when their footprints do not. A detailed analysis on H_EC and H_LAS changes with net radiation and wind direction in rain and dry season indicates that the spatial heterogeneity in net radiation created by clouds contributes greatly to the differences in H_EC and H_LAS in short-term variations. A significant relationship between the difference in footprint-weighted averages of LST and difference in H_EC and H_LAS suggests that the spatial heterogeneity in LST at two spatial scales is a reason for the differences in H_EC and H_LAS and that LST has a positive correlation with the differences in H_EC and H_LAS. A significant relationship between the footprint-weighted averages of NDVI and the ratio of sensible heat fluxes at two spatial scales to net radiation (H/Rn) in the rain season supports the analysis that the spatial heterogeneity in canopy at two spatial scales is another reason for differences in H_EC and H_LAS and that canopy has a negative correlation with (H/Rn). An analysis on the influence of the difference in aerodynamic roughness lengths at two spatial scales on sensible heat fluxes shows that the

  10. Metabolic flux responses to genetic modification for shikimic acid production by Bacillus subtilis strains

    PubMed Central

    2014-01-01

    Background Shikimic acid (SA) is a key chiral starting molecule for the synthesis of the neuramidase inhibitor GS4104 against viral influenza. Microbial production of SA has been extensively investigated in Escherichia coli, and to a less extent in Bacillus subtilis. However, metabolic flux of the high SA-producing strains has not been explored. In this study, we constructed with genetic manipulation and further determined metabolic flux with 13C-labeling test of high SA-producing B. subtilis strains. Results B. subtilis 1A474 had a mutation in SA kinase gene (aroI) and accumulated 1.5 g/L of SA. Overexpression of plasmid-encoded aroA, aroB, aroC or aroD in B. subtilis revealed that aroD had the most significantly positive effects on SA production. Simultaneous overexpression of genes for 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (aroA) and SA dehydrogenase (aroD) in B. subtilis BSSA/pSAAroA/pDGSAAroD resulted in SA production of 3.2 g/L. 13C-Metabolic flux assay (MFA) on the two strains BSSA/pHCMC04/pDG148-stu and BSSA/pSAAroA/pDGSAAroD indicated the carbon flux from glucose to SA increased to 4.6% in BSSA/pSAAroA/pDGSAAroD from 1.9% in strain BSSA/pHCMC04/pDG148-stu. The carbon flux through tricarboxylic acid cycle significantly reduced, while responses of the pentose phosphate pathway and the glycolysis to high SA production were rather weak, in the strain BSSA/pSAAroA/pDGSAAroD. Based on the results from MFA, two potential targets for further optimization of SA production were identified. Experiments on genetic deletion of phosphoenoylpyruvate kinase gene confirmed its positive influence on SA production, while the overexpression of the transketolase gene did not lead to increase in SA production. Conclusion Of the genes involved in shikimate pathway in B. subtilis, aroD exerted most significant influence on SA accumulation. Overexpression of plasmid-encoded aroA and aroD doubled SA production than its parent strain. MFA revealed metabolic flux

  11. Flux amplification in SSPX

    NASA Astrophysics Data System (ADS)

    Lodestro, Lynda; Hooper, E. B.; Jayakumar, R. J.; Pearlstein, L. D.; Wood, R. D.; McLean, H. S.

    2007-11-01

    Flux amplification---the ratio of poloidal flux enclosed between the magnetic and geometric axes to that between the separatrix and the geometric axis---is a key measure of efficiency for edge-current-driven spheromaks. With the new, modular capacitor bank, permitting flexible programming of the gun current, studies of flux amplification under various drive scenarios can be performed. Analysis of recent results of pulsed operation with the new bank finds an efficiency ˜ 0.2, in selected shots, of the conversion of gun energy to confined magnetic energy during the pulses, and suggests a route toward sustained efficiency at 0.2. Results of experiments, a model calculation of field build-up, and NIMROD simulations exploring this newly suggested scenario will be presented.

  12. Levels, fluxes and time trends of persistent organic pollutants in Lake Thun, Switzerland: combining trace analysis and multimedia modeling.

    PubMed

    Bogdal, Christian; Scheringer, Martin; Schmid, Peter; Bläuenstein, Markus; Kohler, Martin; Hungerbühler, Konrad

    2010-08-01

    Levels, mass fluxes, and time trends of polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs) in Lake Thun, a peri-Alpine lake, are investigated. We present measurements of PBDEs and PCBs in air, lake water, lake sediment, and tributary water. These measurements are combined with a multimedia fate model, based on site-specific environmental parameters from the lake catchment. Measured loadings of PBDEs and PCBs in air and tributaries were used to drive the model. The model satisfactorily reproduces PBDE and PCB congener patterns in water and sediment, but it tends to yield concentrations in water below the measurements and concentrations in sediment exceeding the measurements. A sensitivity analysis reveals that partitioning of PBDEs and PCBs between the aqueous dissolved phase and suspended particulate matter in the water column strongly affects the model results, in particular the concentrations in water and sediment. For lower-brominated PBDEs, approximately 70% and 30% of input into the lake stems from atmospheric deposition and from tributaries, respectively. For heavier PBDEs and all PCBs, rivers appear to deliver the major load (64-92%). Waste water effluents are of minor importance. 50-90% of the total input is buried in the permanent sediment. Sediment burial makes PBDEs and PCBs less available for recycling in the environment, and reduces concentrations in the outflowing river. If use of deca-BDE increases in the future, levels in Lake Thun will follow the same trend. If the use and resulting environmental emissions decrease, concentrations in water will rapidly decline, according to our calculations, while sediment levels will decrease at a considerably slower rate.

  13. A Global Synthesis Inversion Analysis of Recent Variability in Natural CO2 Fluxes Using Gosat and in Situ Observations

    NASA Astrophysics Data System (ADS)

    Wang, J. S.; Kawa, S. R.; Collatz, G. J.

    2014-12-01

    About one-half of the CO2 emissions from fossil fuel combustion and deforestation accumulates in the atmosphere, where it contributes to global warming. The rest is taken up by vegetation and the ocean. The precise contribution of the two, and the location and year-to-year variability of the CO2 sinks are, however, not well understood. We use a batch Bayesian inversion approach to deduce the global spatiotemporal distributions of CO2 fluxes during 2009-2010. For prior constraints, we utilize fluxes from the CASA-GFED model of the terrestrial biosphere and biomass burning driven by satellite observations and interannually varying meteorology. We also use measurement-based ocean flux estimates, and fixed fossil CO2 emissions. Here, we present results from our inversions that incorporate column CO2 measurements from the GOSAT satellite (ACOS retrieval, filtered and bias-corrected) and in situ observations (individual flask and afternoon-average continuous observations) to estimate fluxes in 108 regions over 8-day intervals. Relationships between fluxes and atmospheric concentrations are derived using the PCTM atmospheric transport model run at 2° x 2.5° (latitude/longitude) resolution driven by meteorology from the MERRA reanalysis. We evaluate the posterior CO2 concentrations using independent aircraft and other data sets. The optimized fluxes generally resemble those from other inversion systems using different techniques, for example indicating a net terrestrial biospheric CO2 sink, and a shift in the sink from tropics to northern high latitudes when going from an in-situ-only inversion to a GOSAT inversion. We show that in this inversion framework, GOSAT provides better flux estimates in most regions with its greater spatial coverage, but we also discuss impacts of possible remaining biases in the data.

  14. A control analysis exploration of the role of ATP utilisation in glycolytic-flux control and glycolytic-metabolite-concentration regulation.

    PubMed

    Thomas, S; Fell, D A

    1998-12-15

    A theoretical metabolic-control-analysis approach has been used to study aspects of glycolytic-flux control and carbon-metabolite regulation, particularly the role of ATP demand (ATPase), in order to determine what general features of the regulation of energy metabolism would be consistent with good carbon-metabolite homeostasis in the face of large changes in carbon flux. On the basis of a semi-quantitative control-analysis model, incorporating estimates of substrate, product and effector actions on the enzymes, the experimentally observed characteristics of glycolytic-flux changes prove to impose constraints on the feasible ranges of these estimates. This leads to the identification of several features of energy metabolism, each of which is necessary but not sufficient to explain the observations; although most of these have been advocated previously (such as AMP activation of phosphofructokinase (PFK), ADP inhibition of ATPase and the role of energy charge or ATP/ADP ratio), our analysis allows their relative importance to be assessed. In the model, the distribution of flux control depends primarily on ADP inhibition of ATPase, and on the activation of PFK by AMP; increase in ADP inhibition of ATPase increases the control on PFK; increase in AMP activation of PFK increases control on ATPase. PFK exerts greater flux control than does ATPase over approximately 50% of the ranges (parameter space) studied, but its control is sufficiently high to achieve sizeable flux increases over less than 20% of the space. Furthermore, control by alteration in PFK activity is shown to result in poor glycolytic metabolite homeostasis over the entire parameter space studied. However, over a large proportion of the parameter space, control by activation of ATPase can lead to large flux changes, i.e. high flux control, coupled with excellent glycolytic-metabolite homeostasis, similar to that observed in working muscle. As well as altering the relative degrees of flux control invested

  15. An Inversion Analysis of Recent Variability in Natural CO2 Fluxes Using GOSAT and In Situ Observations

    NASA Technical Reports Server (NTRS)

    Wang, James S.; Kawa, S. Randolph; Collatz, G. James; Baker, David F.; Ott, Lesley

    2015-01-01

    About one-half of the global CO2 emissions from fossil fuel combustion and deforestation accumulates in the atmosphere, where it contributes to global warming. The rest is taken up by vegetation and the ocean. The precise contribution of the two sinks, and their location and year-to-year variability are, however, not well understood. We use two different approaches, batch Bayesian synthesis inversion and variational data assimilation, to deduce the global spatiotemporal distributions of CO2 fluxes during 2009-2010. One of our objectives is to assess different sources of uncertainties in inferred fluxes, including uncertainties in prior flux estimates and observations, and differences in inversion techniques. For prior constraints, we utilize fluxes and uncertainties from the CASA-GFED model of the terrestrial biosphere and biomass burning driven by satellite observations and interannually varying meteorology. We also use measurement-based ocean flux estimates and two sets of fixed fossil CO2 emissions. Here, our inversions incorporate column CO2 measurements from the GOSAT satellite (ACOS retrieval, filtered and bias-corrected) and in situ observations (individual flask and afternoon-average continuous observations) to estimate fluxes in 108 regions over 8-day intervals for the batch inversion and at 3 x 3.75 weekly for the variational system. Relationships between fluxes and atmospheric concentrations are derived consistently for the two inversion systems using the PCTM atmospheric transport model driven by meteorology from the MERRA reanalysis. We compare the posterior fluxes and uncertainties derived using different data sets and the two inversion approaches, and evaluate the posterior atmospheric concentrations against independent data including aircraft measurements. The optimized fluxes generally resemble those from other studies. For example, the results indicate that the terrestrial biosphere is a net CO2 sink, and a GOSAT-only inversion suggests a shift in

  16. An Inversion Analysis of Recent Variability in Natural CO2 Fluxes Using GOSAT and In Situ Observations

    NASA Astrophysics Data System (ADS)

    Wang, J. S.; Kawa, S. R.; Baker, D. F.; Collatz, G. J.; Ott, L. E.

    2015-12-01

    About one-half of the global CO2 emissions from fossil fuel combustion and deforestation accumulates in the atmosphere, where it contributes to global warming. The rest is taken up by vegetation and the ocean. The precise contribution of the two sinks, and their location and year-to-year variability are, however, not well understood. We use two different approaches, batch Bayesian synthesis inversion and variational data assimilation, to deduce the global spatiotemporal distributions of CO2 fluxes during 2009-2010. One of our objectives is to assess different sources of uncertainties in inferred fluxes, including uncertainties in prior flux estimates and observations, and differences in inversion techniques. For prior constraints, we utilize fluxes and uncertainties from the CASA-GFED model of the terrestrial biosphere and biomass burning driven by satellite observations and interannually varying meteorology. We also use measurement-based ocean flux estimates and two sets of fixed fossil CO2 emissions. Here, our inversions incorporate column CO2 measurements from the GOSAT satellite (ACOS retrieval, filtered and bias-corrected) and in situ observations (individual flask and afternoon-average continuous observations) to estimate fluxes in 108 regions over 8-day intervals for the batch inversion and at 3° x 3.75° weekly for the variational system. Relationships between fluxes and atmospheric concentrations are derived consistently for the two inversion systems using the PCTM atmospheric transport model driven by meteorology from the MERRA reanalysis. We compare the posterior fluxes and uncertainties derived using different data sets and the two inversion approaches, and evaluate the posterior atmospheric concentrations against independent data including aircraft measurements. The optimized fluxes generally resemble those from other studies. For example, the results indicate that the terrestrial biosphere is a net CO2 sink, and a GOSAT-only inversion suggests a

  17. Introduction of J-OFURO version 2 surface heat flux data set and its analysis over the North Pacific

    NASA Astrophysics Data System (ADS)

    Tomita, H.; Jubota, M.; Iwasaki, S.; Hihara, T.; Kawatsura, A.

    2007-05-01

    Japanese Ocean Flux Data Sets with Use of Remote Sensing Observations (J-OFURO) includes global ocean surface heat flux data derived from satellite data and are used in many studies related to air-sea interaction. Recently new surface heat flux data was constructed in J-OFURO as the version 2. In the version 2 many points are improved compared with the version 1. Since we used wind speed and specific humidity data derived from one DMSP/SSMI sensor in the version 1, we obtained two data at most one day. Therefore, there may be large sampling errors for the daily-mean value. In order to escape this problem, multi-satellite data (DMSP/SSMI F08- 15, Aqua/AMSR-E, TRMM/TMI, ERS/AMI and QuikScat/SeaWinds) are used in the version 2. As a result we could improve accuracy and temporal resolution from 3-days mean value in version 1 to daily-mean value in version 2. Also we used an Optimum Interpolation method to estimate specific humidity data instead of a simple mean method. We basically need sea surface temperature (SST), specific humidity and wind speed data for estimation of latent heat flux. In version 1 we used NCEP data (Reynolds and Smith, 1994) as SST data. However, the temporal resolution of the data is based on weekly and considerably low. Recently there are many kinds of global SST data because we can obtain SST data using a microwave radiometer sensor such as TRMM/MI and Aqua/AMSR-E. Therefore, we compared many SST products and determined to use Merged satellite and in situ data Global Daily (MGD) SST provided by Japan Meteorological Agency. A bulk algorithm used for estimation of turbulent heat flux is changed from Kondo (1975) to COASRE 3.0(Fairall et al., 2003). Shortwave and longwave radiation data are based on the ISCCP product and some modifications are carried out for longwave radiation. Finally surface latent and sensible flux data and shortwave and longwave radiation data are extended to1989- 2004. In this presentation we will introduce surface heat flux

  18. The 2010 Eyjafjallajökull volcanic summit eruption: evidences from ash-leachates analysis and ground deposition fluxes

    NASA Astrophysics Data System (ADS)

    Bagnato, E.; Aiuppa, A.; Bertagnini, A.; Bonadonna, C.; Cioni, R.; Pedone, M.; Pistolesi, M.

    2012-04-01

    The Eyjafjallajökull 2010 eruption was an extraordinary event in that it led to widespread over Europe. Volcanic processes which lead to eruptions can be investigated by monitoring a variety of parameters, including the composition of ash leachates. Fine-grained tephra erupted from active vents, and transported through volcanic plumes, can adsorbs, and therefore rapidly scavenge, volatile elements such as S, halogens, and metal species in the form of soluble salts adhering to ash surfaces. Analysis of such water-soluble phases is a suitable complement for the remote sensing of volcanic gases at inaccessible volcanoes, like Eyjafjallajökull. The 2010 Eyjafjallajökull eruption developed in four main phases, whose difference in gas chemistry and products has been marked in ash-leachates data too. The recurrent ash fallout provided a unique opportunity to characterize the compositional features of ash leachates, and to identify their relation (if any) with the eruptive activity styles of the volcano. By these considerations, we report on the chemical composition of leachates of 20 volcanic ash samples deposited during the most explosive Eyjafjallajökull activities (from 14 April to 8 May) and during the lava fountaining event (on 26th March 2010). We found that ash-leachate solutions are dominated - among cations - by Na and Ca, while they display nearly equal S : Cl : F abundances (mean S/Cl and S/F molar ratios of 0.85 and 0.33, respectively), as characteristic of divergent-plate and within-plate volcanism. The strong correlations between leached Ca - F , Ca - SO4, and Na - Cl (r2 = 0.7 - 0.9), suggest that fluorite, anhydrite, and halite are the most likely soluble surface minerals formed in the plume (and therefore leached during our experiments), as also reported at many active volcanoes. Our data bring evidence for variations in S and halogens proportions, with samples from 5 - 8th May which show the highest S/Cl and lowest Cl/F ratios. By combining the

  19. Analysis of the biases in the downward shortwave surface flux in the GFDL CM2.1 general circulation model

    NASA Astrophysics Data System (ADS)

    Freidenreich, Stuart M.; Ramaswamy, V.

    2011-04-01

    Simulations of downward shortwave surface fluxes by the coupled Geophysical Fluid Dynamics Laboratory (GFDL) CM2.1 general circulation model are compared against climatology derived from the Baseline Surface Radiation Network (BSRN), Global Energy Balance Archive, and International Satellite Cloud Climatology Project ISCCP-FD data sets. The spatial pattern of the model's biases is evaluated. An investigation is made of how these relate to accompanying biases in total cloud amount and aerosol optical depth and how they affect the surface temperature simulation. Comparing CM2.1's clear-sky fluxes against BSRN site values, for European, Asian, and North American locations, there are underestimates in the direct and overestimates in the diffuse, resulting in underestimates in the total flux. These are related to overestimates of sulfate aerosol optical depth, arising owing to the behavior of the parameterization function for hygroscopic growth of these aerosols at very high relative humidity. Contrastingly, flux overestimate biases at lower latitude locations are associated with underestimates in sea-salt and carbonaceous aerosol amounts. All-sky flux biases consist of underestimates for North America, Eurasia, southern Africa, and northern oceanic regions and overestimates for the Amazon region, equatorial Africa, off the west coast of the Americas, and southern oceanic regions. These biases show strong correlations with cloud amount biases. There are modest correlations of the flux biases with cool surface temperature biases over North America and Eurasia, warm biases over the Amazon region, and cool (warm) biases over the northern (southern) oceanic regions. Analyses assuming nonhygroscopicity illustrate that there is a reduction of surface temperature biases accompanying a reduction of sulfate aerosol optical depth biases, whereas a more significant improvement in the temperature simulation requires refining the model's simulation of cloudiness.

  20. Metabolic Changes in Klebsiella oxytoca in Response to Low Oxidoreduction Potential, as Revealed by Comparative Proteomic Profiling Integrated with Flux Balance Analysis

    PubMed Central

    Zhu, Yan; Li, Dan; Bao, Guanhui; Wang, Shaohua; Mao, Shaoming; Song, Jiangning; Li, Yin

    2014-01-01

    Oxidoreduction potential (ORP) is an important physiological parameter for biochemical production in anaerobic or microaerobic processes. However, the effect of ORP on cellular physiology remains largely unknown, which hampers the design of engineering strategies targeting proteins associated with ORP response. Here we characterized the effect of altering ORP in a 1,3-propanediol producer, Klebsiella oxytoca, by comparative proteomic profiling combined with flux balance analysis. Decreasing the extracellular ORP from −150 to −240 mV retarded cell growth and enhanced 1,3-propanediol production. Comparative proteomic analysis identified 61 differentially expressed proteins, mainly involved in carbohydrate catabolism, cellular constituent biosynthesis, and reductive stress response. A hypothetical oxidoreductase (HOR) that catalyzes 1,3-propanediol production was markedly upregulated, while proteins involved in biomass precursor synthesis were downregulated. As revealed by subsequent flux balance analysis, low ORP induced a metabolic shift from glycerol oxidation to reduction and rebalancing of redox and energy metabolism. From the integrated protein expression profiles and flux distributions, we can construct a rational analytic framework that elucidates how (facultative) anaerobes respond to extracellular ORP changes. PMID:24584239

  1. Metabolic changes in Klebsiella oxytoca in response to low oxidoreduction potential, as revealed by comparative proteomic profiling integrated with flux balance analysis.

    PubMed

    Zhu, Yan; Li, Dan; Bao, Guanhui; Wang, Shaohua; Mao, Shaoming; Song, Jiangning; Li, Yin; Zhang, Yanping

    2014-05-01

    Oxidoreduction potential (ORP) is an important physiological parameter for biochemical production in anaerobic or microaerobic processes. However, the effect of ORP on cellular physiology remains largely unknown, which hampers the design of engineering strategies targeting proteins associated with ORP response. Here we characterized the effect of altering ORP in a 1,3-propanediol producer, Klebsiella oxytoca, by comparative proteomic profiling combined with flux balance analysis. Decreasing the extracellular ORP from -150 to -240 mV retarded cell growth and enhanced 1,3-propanediol production. Comparative proteomic analysis identified 61 differentially expressed proteins, mainly involved in carbohydrate catabolism, cellular constituent biosynthesis, and reductive stress response. A hypothetical oxidoreductase (HOR) that catalyzes 1,3-propanediol production was markedly upregulated, while proteins involved in biomass precursor synthesis were downregulated. As revealed by subsequent flux balance analysis, low ORP induced a metabolic shift from glycerol oxidation to reduction and rebalancing of redox and energy metabolism. From the integrated protein expression profiles and flux distributions, we can construct a rational analytic framework that elucidates how (facultative) anaerobes respond to extracellular ORP changes.

  2. OAFlux Satellite-Based High-Resolution Analysis of Air-Sea Turbulent Heat, Moisture, and Momentum Fluxes

    NASA Astrophysics Data System (ADS)

    Yu, Lisan

    2016-04-01

    The Objectively Analyzed air-sea Fluxes (OAFlux) project at the Woods Hole Oceanographic Institution has recently developed a new suite of products: the satellite-based high-resolution (HR) air-sea turbulent heat, moisture, and momentum fluxes over the global ocean from 1987 to the present. The OAFlux-HR fluxes are computed from the COARE bulk algorithm using air-sea variables (vector wind, near-surface humidity and temperature, and ocean surface temperature) derived from multiple satellite sensors and multiple missions. The vector wind time series are merged from 14 satellite sensors, including 4 scatterometers and 10 passive microwave radiometers. The near-surface humidity and temperature time series are retrieved from 11 satellite sensors, including 7 microwave imagers and 4 microwave sounders. The endeavor has greatly improved the depiction of the air-sea turbulent exchange on the frontal and meso-scales. The OAFlux-HR turbulent flux products are valuable datasets for a broad range of studies, including the study of the long-term change and variability in the oean-surface forcing functions, quantification of the large-scale budgets of mass, heat, and freshwater, and assessing the role of the ocean in the change and variability of the Earth's climate.

  3. Soil heat flux calculation for sunlit and shaded surfaces under row crops: 1 - Model Development and sensitivity analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil heat flux at the surface (G0) is strongly influenced by whether the soil is shaded or sunlit, and therefore can have large spatial variability for incomplete vegetation cover, such as across the interrows of row crops. Most practical soil-plant-atmosphere energy balance models calculate G0 as a...

  4. Neural network analysis on the effect of heat fluxes on greenhouse gas emissions from anaerobic swine waste treatment lagoon

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this study, we examined the various meteorological factors (i.e., air temperatures, solar radiation, and heat fluxes) that potentially affect greenhouse gas (GHG) emissions from swine waste lagoon. GHG concentrations (methane, carbon dioxide, and nitrous oxide) were monitored using a photoacous...

  5. An investigation of the neutron flux in bone-fluorine phantoms comparing accelerator based in vivo neutron activation analysis and FLUKA simulation data

    NASA Astrophysics Data System (ADS)

    Mostafaei, F.; McNeill, F. E.; Chettle, D. R.; Matysiak, W.; Bhatia, C.; Prestwich, W. V.

    2015-01-01

    We have tested the Monte Carlo code FLUKA for its ability to assist in the development of a better system for the in vivo measurement of fluorine. We used it to create a neutron flux map of the inside of the in vivo neutron activation analysis irradiation cavity at the McMaster Accelerator Laboratory. The cavity is used in a system that has been developed for assessment of fluorine levels in the human hand. This study was undertaken to (i) assess the FLUKA code, (ii) find the optimal hand position inside the cavity and assess the effects on precision of a hand being in a non-optimal position and (iii) to determine the best location for our γ-ray detection system within the accelerator beam hall. Simulation estimates were performed using FLUKA. Experimental measurements of the neutron flux were performed using Mn wires. The activation of the wires was measured inside (1) an empty bottle, (2) a bottle containing water, (3) a bottle covered with cadmium and (4) a dry powder-based fluorine phantom. FLUKA was used to simulate the irradiation cavity, and used to estimate the neutron flux in different positions both inside, and external to, the cavity. The experimental results were found to be consistent with the Monte Carlo simulated neutron flux. Both experiment and simulation showed that there is an optimal position in the cavity, but that the effect on the thermal flux of a hand being in a non-optimal position is less than 20%, which will result in a less than 10% effect on the measurement precision. FLUKA appears to be a code that can be useful for modeling of this type of experimental system.

  6. Transition of an Anaerobic Escherichia coli Culture to Aerobiosis: Balancing mRNA and Protein Levels in a Demand-Directed Dynamic Flux Balance Analysis.

    PubMed

    von Wulffen, Joachim; Sawodny, Oliver; Feuer, Ronny

    2016-01-01

    The facultative anaerobic bacterium Escherichia coli is frequently forced to adapt to changing environmental conditions. One important determinant for metabolism is the availability of oxygen allowing a more efficient metabolism. Especially in large scale bioreactors, the distribution of oxygen is inhomogeneous and individual cells encounter frequent changes. This might contribute to observed yield losses during process upscaling. Short-term gene expression data exist of an anaerobic E. coli batch culture shifting to aerobic conditions. The data reveal temporary upregulation of genes that are less efficient in terms of energy conservation than the genes predicted by conventional flux balance analyses. In this study, we provide evidence for a positive correlation between metabolic fluxes and gene expression. We then hypothesize that the more efficient enzymes are limited by their low expression, restricting flux through their reactions. We define a demand that triggers expression of the demanded enzymes that we explicitly include in our model. With these features we propose a method, demand-directed dynamic flux balance analysis, dddFBA, bringing together elements of several previously published methods. The introduction of additional flux constraints proportional to gene expression provoke a temporary demand for less efficient enzymes, which is in agreement with the transient upregulation of these genes observed in the data. In the proposed approach, the applied objective function of growth rate maximization together with the introduced constraints triggers expression of metabolically less efficient genes. This finding is one possible explanation for the yield losses observed in large scale bacterial cultivations where steady oxygen supply cannot be warranted. PMID:27384956

  7. Transition of an Anaerobic Escherichia coli Culture to Aerobiosis: Balancing mRNA and Protein Levels in a Demand-Directed Dynamic Flux Balance Analysis

    PubMed Central

    von Wulffen, Joachim; Sawodny, Oliver; Feuer, Ronny

    2016-01-01

    The facultative anaerobic bacterium Escherichia coli is frequently forced to adapt to changing environmental conditions. One important determinant for metabolism is the availability of oxygen allowing a more efficient metabolism. Especially in large scale bioreactors, the distribution of oxygen is inhomogeneous and individual cells encounter frequent changes. This might contribute to observed yield losses during process upscaling. Short-term gene expression data exist of an anaerobic E. coli batch culture shifting to aerobic conditions. The data reveal temporary upregulation of genes that are less efficient in terms of energy conservation than the genes predicted by conventional flux balance analyses. In this study, we provide evidence for a positive correlation between metabolic fluxes and gene expression. We then hypothesize that the more efficient enzymes are limited by their low expression, restricting flux through their reactions. We define a demand that triggers expression of the demanded enzymes that we explicitly include in our model. With these features we propose a method, demand-directed dynamic flux balance analysis, dddFBA, bringing together elements of several previously published methods. The introduction of additional flux constraints proportional to gene expression provoke a temporary demand for less efficient enzymes, which is in agreement with the transient upregulation of these genes observed in the data. In the proposed approach, the applied objective function of growth rate maximization together with the introduced constraints triggers expression of metabolically less efficient genes. This finding is one possible explanation for the yield losses observed in large scale bacterial cultivations where steady oxygen supply cannot be warranted. PMID:27384956

  8. Use of spectral analysis method to evaluate the precision of different fast response ozone sonde and the effect on ozone fluxes

    NASA Astrophysics Data System (ADS)

    Zhu, Z.; Tsokankunku, A.; Andreae, M. O.; Fpken, T.; Meixner, F. X.

    2009-04-01

    High concentration ozone in the troposphere has negative effect on human health and plant tissue. To investigate the vertical changes of ozone fluxes at different heights, 4-layer ozone fluxes were measured by using eddy covariance method above and below the canopy of a 55 yr old spruce forest (Fichtelgebirge, Germany). The heights are 1m 17m 25m and 32m above ground. The mean tree height is about 21m. The sonic anemometers are 3 Gill R2 and 1 CSAT3, and fast ozone sonde are also made in different companies or home-built. As ozone sondes at different heights are not the same, to eliminate the error caused by instruments, side-by-side comparison was also executed. The results show there was lager difference in ozone flux measured by different sondes located at the same position. The biggest relative error can reach as high as 40 standard, spectral analysis method was used to evaluate their precisions and uncertainties. In this study, we calculated the power spectra and cospectra (with vertical speed) of 5 sondes using 72 run half-hourly 20Hz raw data. All normalized spectral density was averaged according to different frequency range. By analyzing spectral density distribution with frequency and comparing to theoretic curve, we determined the best one as the relative standard. Meanwhile, the relationships between the standard and other sondes were calculated. Finally, we compared the ozone fluxes before and after correction. The corrected fluxes at different heights are more reasonable compared with that before.

  9. Spatial analysis of soil erosion and sediment fluxes: a paired watershed study of two Rappahannock River tributaries, Stafford County, Virginia.

    PubMed

    Ricker, Matthew C; Odhiambo, Ben K; Church, Joseph M

    2008-05-01

    Soil erosion is a serious problem in areas with expanding construction, agricultural production, and improper storm water management. It is important to understand the major processes affecting sediment delivery to surficial water bodies in order to tailor effective mitigation and outreach activities. This study analyzes how naturally occurring and anthropogenic influences, such as urbanization and soil disturbance on steep slopes, are reflected in the amount of soil erosion and sediment delivery within sub-watershed-sized areas. In this study, two sub-watersheds of the Rappahannock River, Horsepen Run and Little Falls Run, were analyzed using the Revised Universal Soil Loss Equation (RUSLE) and a sediment delivery ratio (SDR) to estimate annual sediment flux rates. The RUSLE/SDR analyses for Horsepen Run and Little Falls Run predicted 298 Mg/y and 234 Mg/y, respectively, but nearly identical per-unit-area sediment flux rates of 0.15 Mg/ha/y and 0.18 Mg/ha/y. Suspended sediment sampling indicated greater amounts of sediment in Little Falls Run, which is most likely due to anthropogenic influences. Field analyses also suggest that all-terrain vehicle crossings represent the majority of sediment flux derived from forested areas of Horsepen Run. The combined RUSLE/SDR and field sampling data indicate that small-scale anthropogenic disturbances (ATV trails and construction sites) play a major role in overall sediment flux rates for both basins and that these sites must be properly accounted for when evaluating sediment flux rates at a sub-watershed scale.

  10. A priori analysis of subgrid scale pressure and heat flux in high pressure mixing and reacting shear layers

    NASA Astrophysics Data System (ADS)

    Ma, Zhiyuan; Korucu, Ayse; Miller, Richard Steven

    2015-11-01

    Direct Numerical Simulation (DNS) data on high pressure H2/O2 and H2/air flames using the compressible flow formulation, detailed kinetics, a real fluid equation of state, and generalised diffusion are analysed. The DNS is filtered over a range of filter widths to provide exact terms in the Large Eddy Simulation (LES) governing equations, including unclosed terms. The filtered pressure and the filtered heat flux vector are extensively compared with the pressure and the heat flux vector calculated as a function of the filtered primitive variables (i.e. the exact LES term is compared with its form available within an actual LES). The difference between these forms defines the subgrid pressure and the subgrid heat flux vector. The analyses are done both globally across the entire flame, as well as by conditionally averaging over specific regions of the flame; including regions of large subgrid kinetic energy, subgrid scalar dissipation, subgrid temperature variance, flame temperature, etc. In this work, although negligible for purely mixing cases, the gradient of the subgrid pressure is shown to be of the same order as, and larger than, the corresponding divergence of the turbulent subgrid stresses for reacting cases. This is despite the fact that all species behave essentially as ideal gases for this flame and holds true even when the ideal gas law is used to calculate the pressure. The ratio of the subgrid pressure gradient to the subgrid stress tensor divergence is shown to increase with increasing Reynolds number. Both the subgrid heat flux vector and its divergence are found to be substantially larger in reacting flows in comparison with mixing due to the associated larger temperature gradients. However, the divergence of the subgrid heat flux vector tends to be significantly smaller than other unclosed terms in the energy equation with decreasing significance with increasing Reynolds number.

  11. Analysis of the Variation of Energetic Electron Flux with Respect to Longitude and Distance Normal to the Magnetic Equatorial Plane for Galileo Energetic Particle Detector Data

    NASA Technical Reports Server (NTRS)

    Swimm, Randall; Garrett, Henry B.; Jun, Insoo; Evans, Robin W.

    2004-01-01

    In this study we examine ten-minute omni-directional averages of energetic electron data measured by the Galileo spacecraft Energetic Particle Detector (EPD). Count rates from electron channels B1, DC2, and DC3 are evaluated using a power law model to yield estimates of the differential electron fluxes from 1 MeV to 11 MeV at distances between 8 and 51 Jupiter radii. Whereas the orbit of the Galileo spacecraft remained close to the rotational equatorial plane of Jupiter, the approximately 11 degree tilt of the magnetic axis of Jupiter relative to its rotational axis allowed the EPD instrument to sample high energy electrons at limited distances normal to the magnetic equatorial plane. We present a Fourier analysis of the semi-diurnal variation of electron fluxes with longitude.

  12. Cyclical patterns in volcanic degassing revealed by SO2 flux timeseries analysis: An application to Soufrière Hills Volcano, Montserrat

    NASA Astrophysics Data System (ADS)

    Nicholson, E. J.; Mather, T. A.; Pyle, D. M.; Odbert, H. M.; Christopher, T.

    2013-08-01

    Cyclical patterns of behaviour in timeseries of seismic and geodetic data at volcanoes are frequently observed during lava dome-building eruptions, and are particularly well-documented from the current eruption of the Soufrière Hills Volcano (SHV), Montserrat. However, the discontinuous nature of many SO2 measurements often preclude the identification and quantitative analysis of cyclical patterns in degassing data. Here, using a long SO2 timeseries from SHV, with continuous measurements since 2002, we explore for the first time degassing behaviour at a resolution comparable to that possible for seismic and deformation datasets. Timeseries analysis of flux data spanning 2002-2011 reveals that SO2 emissions at SHV exhibit complex cyclicity, with dominant cycles evident on both multi-year and multi-week (~50 day) timescales. These cycles persist through phases of both active extrusion and eruptive pause, and show close similarities to periodic components previously identified at SHV in timeseries of seismicity, ground deformation and lava extrusion. The strength of expression or amplitude of degassing cycles, particularly on multi-week timescales, shows distinct temporal variation, and appears to correlate with the occurrence and nature of explosive activity occurring in 2002-2009. This suggests that the amplitude of surface gas flux cycles is modulated by physical conditions within the conduit. Direct quantitative comparison between seismicity, dome growth, and degassing for eruptive Phases 2 (2002-2003) and 3 (2005-2007) reveals that peaks in SO2 flux appear to correspond broadly to enhanced lava extrusion and elevated seismicity within cycles of 30-50 days. However, time lags of 2, 4 and 7 days are observed between initial low-frequency seismic swarms and peaks in dome growth, SO2 flux and rockfall event rate respectively. Multi-parameter correlations offer valuable insights into the controls on subsurface gas ascent, but further research is required to fully

  13. Assessment of energetic costs of AhR activation by β-naphthoflavone in rainbow trout (Oncorhynchus mykiss) hepatocytes using metabolic flux analysis

    SciTech Connect

    Nault, Rance; Abdul-Fattah, Hiba; Mironov, Gleb G.; Berezovski, Maxim V.; Moon, Thomas W.

    2013-08-15

    Exposure to environmental contaminants such as activators of the aryl hydrocarbon receptor (AhR) leads to the induction of defense and detoxification mechanisms. While these mechanisms allow organisms to metabolize and excrete at least some of these environmental contaminants, it has been proposed that these mechanisms lead to significant energetic challenges. This study tests the hypothesis that activation of the AhR by the model agonist β-naphthoflavone (βNF) results in increased energetic costs in rainbow trout (Oncorhynchus mykiss) hepatocytes. To address this hypothesis, we employed traditional biochemical approaches to examine energy allocation and metabolism including the adenylate energy charge (AEC), protein synthesis rates, Na{sup +}/K{sup +}-ATPase activity, and enzyme activities. Moreover, we have used for the first time in a fish cell preparation, metabolic flux analysis (MFA) an in silico approach for the estimation of intracellular metabolic fluxes. Exposure of trout hepatocytes to 1 μM βNF for 48 h did not alter hepatocyte AEC, protein synthesis, or Na{sup +}/K{sup +}-ATPase activity but did lead to sparing of glycogen reserves and changes in activities of alanine aminotransferase and citrate synthase suggesting altered metabolism. Conversely, MFA did not identify altered metabolic fluxes, although we do show that the dynamic metabolism of isolated trout hepatocytes poses a significant challenge for this type of approach which should be considered in future studies. - Highlights: • Energetic costs of AhR activation by βNF was examined in rainbow trout hepatocytes. • Metabolic flux analysis was performed on a fish cell preparation for the first time. • Exposure to βNF led to sparing of glycogen reserves and altered enzyme activities. • Adenylate energy charge was maintained despite temporal changes in metabolism.

  14. Combined trajectory clustering and aerosol fields analysis to evaluate the potential emission flux to aerosol pollutants in an urban and semi-urban atmospheres in eastern India

    NASA Astrophysics Data System (ADS)

    Kumar, B. D.; Verma, S.

    2015-12-01

    A hybrid source-receptor analysis was carried out to evaluate the potential emission flux to winter monsoon (WinMon) aerosols over eastern India urban (Kolkata, Kol) and semi-urban atmospheres (Kharagpur, Kgp). This was done through application of fuzzy c-mean clustering to back-trajectory data combined with emission flux and residence time weighted aerosols analysis. WinMon mean aerosol optical depth (AOD) and angstrom exponent (AE) at Kol were respectively slightly higher than and nearly equal to that at Kgp. Out of six source region clusters over Indian subcontinent and two over Indian oceanic region, the cluster mean AOD was the highest when associated with the mean path of air mass originating from the Bay of Bengal (BoB) and the Arabian sea (AS) clusters at Kol and that from the Indo-Gangetic plain (IGP)cluster at Kgp. Spatial distribution of weighted AOD fields showed the highest potential source of aerosols over the IGP, majorly over upper IGP (IGP-U), lower IGP (IGP-L) and eastern region (ER) clusters. The emission flux contribution potential (EFCP) of fossil fuel (FF) emissions at surface (SL) of Kol/Kgp , elevated layer (EL) of Kol, and of biomass burning (BB) emissions at SL of Kol were majorly from IGP-U, IGP-L and IGP-U/L clusters respectively. The EFCP of FF/BB emissions at Kgp-EL/SL, and that of BB at EL of Kol/Kgp were mainly from ER and Africa (AFR) clusters respectively. Though the AFR cluster was constituted of significantly high emission flux source potential of dust emissions, the EFCP of dust from NWI was comparable to that from AFR at Kol SL/EL.

  15. Underestimation of the pentose-phosphate pathway in intact primary neurons as revealed by metabolic flux analysis.

    PubMed

    Rodriguez-Rodriguez, Patricia; Fernandez, Emilio; Bolaños, Juan P

    2013-12-01

    The rates of glucose oxidized at glycolysis and pentose-phosphate pathway (PPP) in neurons are controversial. Using [3-(3)H]-, [1-(14)C]-, and [6-(14)C]glucose to estimate fluxes through these pathways in resting, intact rat cortical primary neurons, we found that the rate of glucose oxidized through PPP was, apparently, ∼14% of total glucose metabolized. However, inhibition of PPP rate-limiting step, glucose-6-phosphate (G6P) dehydrogenase, increased approximately twofold the glycolytic rate; and, knockdown of phosphoglucose isomerase increased ∼1.8-fold the PPP rate. Thus, in neurons, a considerable fraction of fructose-6-phosphate returning from the PPP contributes to the G6P pool that re-enters PPP, largely underestimating its flux.

  16. Unusual flux-distance relationship for pulsars suggested by analysis of the Australia national telescopy facility pulsar catalogue

    SciTech Connect

    Singleton, John; Perez, M R; Singleton, J; Ardavan, H; Ardavan, A

    2009-01-01

    We analyze pulsar fluxes at 1400 MHz (S(1400)) and distances d taken from the Australia National Telescope Facility (ATNF) Pulsar Catalogue. Under the assumption that pulsar populations in different parts of the Galaxy are similar, we find that either (a) pulsar fluxes diminish with distance according to a non-standard power law (we suggest S(1400){proportional_to} 1/d rather than {proportional_to} 1/d{sup 2}) or (b) that there are very significant (i.e. order of magnitude) errors in the distance estimates quoted in the ATNF Catalogue. The former conclusion (a) supports a recent model for pulsar emission that has also successfully explained the frequency spectrum of the Crab pulsar over 16 orders of magnitude of frequency, whilst alternative (b) would necessitate a radical re-evaluation of both the dispersion method for estimating pulsar distances and current ideas about the distribution of pulsars within our Galaxy.

  17. Designing with null flux coils

    SciTech Connect

    Davey, K.R.

    1997-09-01

    Null flux were suggested by Danby and Powell in the late 1960`s as a useful means for realizing induced lift with little drag. As an array of alternating magnets is translated past a set of null flux coils, the currents induced in these coils act to vertically center the magnets on those coils. At present, one Japanese MAGLEV system company and two American-based companies are employing either null flux or flux eliminating coils in their design for high speed magnetically levitated transportation. The principle question addressed in paper is: what is the proper choice of coil length to magnet length in a null flux system? A generic analysis in the time and frequency domain is laid out with the intent of showing the optimal design specification in terms of coil parameters.

  18. Interannual Variability in Soil Trace Gas (CO2, N2O, NO) Fluxes and Analysis of Controllers

    NASA Technical Reports Server (NTRS)

    Potter, C.; Klooster, S.; Peterson, David L. (Technical Monitor)

    1997-01-01

    Interannual variability in flux rates of biogenic trace gases must be quantified in order to understand the differences between short-term trends and actual long-term change in biosphere-atmosphere interactions. We simulated interannual patterns (1983-1988) of global trace gas fluxes from soils using the NASA Ames model version of CASA (Carnegie-Ames-Stanford Approach) in a transient simulation mode. This ecosystem model has been recalibrated for simulations driven by satellite vegetation index data from the NOAA Advanced Very High Resolution Radiometer (AVHRR) over the mid-1980s. The predicted interannual pattern of soil heterotropic CO2 emissions indicates that relatively large increases in global carbon flux from soils occurred about three years following the strong El Nino Southern Oscillation (ENSO) event of 1983. Results for the years 1986 and 1987 showed an annual increment of +1 Pg (1015 g) C-CO2 emitted from soils, which tended to dampen the estimated global increase in net ecosystem production with about a two year lag period relative to plant carbon fixation. Zonal discrimination of model results implies that 80-90 percent of the yearly positive increments in soil CO2 emission during 1986-87 were attributable to soil organic matter decomposition in the low-latitudes (between 30 N and 30 S). Soils of the northern middle-latitude zone (between 30 N and 60 N) accounted for the residual of these annual increments. Total annual emissions of nitrogen trace gases (N2O and NO) from soils were estimated to vary from 2-4 percent over the time period modeled, a level of variability which is consistent with predicted interannual fluctuations in global soil CO2 fluxes. Interannual variability of precipitation in tropical and subtropical zones (30 N to 20 S appeared to drive the dynamic inverse relationship between higher annual emissions of NO versus emissions of N2O. Global mean emission rates from natural (heterotrophic) soil sources over the period modeled (1983

  19. Numerical prediction of heat-flux to massive calorimeters engulfed in regulatory fires with the cask analysis fire environment (CAFE) model

    SciTech Connect

    KOSKI,JORMAN A.; SUO-ANTITLA,AHTI; KRAMER,M. ALEX; GREINER,MILES

    2000-05-11

    Recent observations show that the thermal boundary conditions within large-scale fires are significantly affected by the presence of thermally massive objects. These objects cool the soot and gas near their surfaces, and these effects reduce the incoming radiant heat-flux to values lower than the levels expected from simple {sigma}T{sub fire}{sup 4} models. They also affect the flow and temperature fields in the fire far from their surfaces. The Cask Analysis Fire Environment (CAFE) code has been developed at Sandia National Laboratories to provide an enhanced fire boundary condition for the design of radioactive material packages. CAFE is a set of computer subroutines that use computational fluid mechanics methods to predict convective heat transfer and mixing. It also includes models for fuel and oxygen transport, chemical reaction, and participating-media radiation heat transfer. This code uses two-dimensional computational models so that it has reasonably short turnaround times on standard workstations and is well suited for design and risk studies. In this paper, CAFE is coupled with a commercial finite-element program to model a large cylindrical calorimeter fully engulfed in a pool fire. The time-dependent heat-flux to the calorimeter and the calorimeter surface temperature are determined for several locations around the calorimeter circumference. The variation of heat-flux with location is determined for calorimeters with different diameters and wall thickness, and the observed effects discussed.

  20. Application of the Principles of Systems Biology and Wiener’s Cybernetics for Analysis of Regulation of Energy Fluxes in Muscle Cells in Vivo

    PubMed Central

    Guzun, Rita; Saks, Valdur

    2010-01-01

    The mechanisms of regulation of respiration and energy fluxes in the cells are analyzed based on the concepts of systems biology, non-equilibrium steady state kinetics and applications of Wiener’s cybernetic principles of feedback regulation. Under physiological conditions cardiac function is governed by the Frank-Starling law and the main metabolic characteristic of cardiac muscle cells is metabolic homeostasis, when both workload and respiration rate can be changed manifold at constant intracellular level of phosphocreatine and ATP in the cells. This is not observed in skeletal muscles. Controversies in theoretical explanations of these observations are analyzed. Experimental studies of permeabilized fibers from human skeletal muscle vastus lateralis and adult rat cardiomyocytes showed that the respiration rate is always an apparent hyperbolic but not a sigmoid function of ADP concentration. It is our conclusion that realistic explanations of regulation of energy fluxes in muscle cells require systemic approaches including application of the feedback theory of Wiener’s cybernetics in combination with detailed experimental research. Such an analysis reveals the importance of limited permeability of mitochondrial outer membrane for ADP due to interactions of mitochondria with cytoskeleton resulting in quasi-linear dependence of respiration rate on amplitude of cyclic changes in cytoplasmic ADP concentrations. The system of compartmentalized creatine kinase (CK) isoenzymes functionally coupled to ANT and ATPases, and mitochondrial-cytoskeletal interactions separate energy fluxes (mass and energy transfer) from signalling (information transfer) within dissipative metabolic structures – intracellular energetic units (ICEU). Due to the non-equilibrium state of CK reactions, intracellular ATP utilization and mitochondrial ATP regeneration are interconnected by the PCr flux from mitochondria. The feedback regulation of respiration occurring via cyclic fluctuations

  1. The Virtual Observatory Service TheoSSA: Establishing a Database of Synthetic Stellar Flux Standards II. NLTE Spectral Analysis of the OB-Type Subdwarf Feige 110

    NASA Technical Reports Server (NTRS)

    Rauch, T.; Rudkowski, A.; Kampka, D.; Werner, K.; Kruk, J. W.; Moehler, S.

    2014-01-01

    Context. In the framework of the Virtual Observatory (VO), the German Astrophysical VO (GAVO) developed the registered service TheoSSA (Theoretical Stellar Spectra Access). It provides easy access to stellar spectral energy distributions (SEDs) and is intended to ingest SEDs calculated by any model-atmosphere code, generally for all effective temperatures, surface gravities, and elemental compositions. We will establish a database of SEDs of flux standards that are easily accessible via TheoSSA's web interface. Aims. The OB-type subdwarf Feige 110 is a standard star for flux calibration. State-of-the-art non-local thermodynamic equilibrium stellar-atmosphere models that consider opacities of species up to trans-iron elements will be used to provide a reliable synthetic spectrum to compare with observations. Methods. In case of Feige 110, we demonstrate that the model reproduces not only its overall continuum shape from the far-ultraviolet (FUV) to the optical wavelength range but also the numerous metal lines exhibited in its FUV spectrum. Results. We present a state-of-the-art spectral analysis of Feige 110. We determined Teff =47 250 +/- 2000 K, log g=6.00 +/- 0.20, and the abundances of He, N, P, S, Ti, V, Cr, Mn, Fe, Co, Ni, Zn, and Ge. Ti, V, Mn, Co, Zn, and Ge were identified for the first time in this star. Upper abundance limits were derived for C, O, Si, Ca, and Sc. Conclusions. The TheoSSA database of theoretical SEDs of stellar flux standards guarantees that the flux calibration of astronomical data and cross-calibration between different instruments can be based on models and SEDs calculated with state-of-the-art model atmosphere codes.

  2. Application of the principles of systems biology and Wiener's cybernetics for analysis of regulation of energy fluxes in muscle cells in vivo.

    PubMed

    Guzun, Rita; Saks, Valdur

    2010-03-08

    The mechanisms of regulation of respiration and energy fluxes in the cells are analyzed based on the concepts of systems biology, non-equilibrium steady state kinetics and applications of Wiener's cybernetic principles of feedback regulation. Under physiological conditions cardiac function is governed by the Frank-Starling law and the main metabolic characteristic of cardiac muscle cells is metabolic homeostasis, when both workload and respiration rate can be changed manifold at constant intracellular level of phosphocreatine and ATP in the cells. This is not observed in skeletal muscles. Controversies in theoretical explanations of these observations are analyzed. Experimental studies of permeabilized fibers from human skeletal muscle vastus lateralis and adult rat cardiomyocytes showed that the respiration rate is always an apparent hyperbolic but not a sigmoid function of ADP concentration. It is our conclusion that realistic explanations of regulation of energy fluxes in muscle cells require systemic approaches including application of the feedback theory of Wiener's cybernetics in combination with detailed experimental research. Such an analysis reveals the importance of limited permeability of mitochondrial outer membrane for ADP due to interactions of mitochondria with cytoskeleton resulting in quasi-linear dependence of respiration rate on amplitude of cyclic changes in cytoplasmic ADP concentrations. The system of compartmentalized creatine kinase (CK) isoenzymes functionally coupled to ANT and ATPases, and mitochondrial-cytoskeletal interactions separate energy fluxes (mass and energy transfer) from signalling (information transfer) within dissipative metabolic structures - intracellular energetic units (ICEU). Due to the non-equilibrium state of CK reactions, intracellular ATP utilization and mitochondrial ATP regeneration are interconnected by the PCr flux from mitochondria. The feedback regulation of respiration occurring via cyclic fluctuations of

  3. [Error analysis of CO2 storage flux in a temperate deciduous broadleaved forest based on different scalar variables].

    PubMed

    Wang, Jing; Wang, Xing-chang; Wang, Chuan-kuan

    2013-04-01

    Using the measurement data from an 8-level vertical profile of CO2/H2 0 in a temperate deciduous broadleaved forest at the Maoershan Forest Ecosystem Research Station, Northeast China, this paper quantified the errors of CO2 storage flux (Fs ) calculated with three scalar variables, i. e. , CO2 density (rho c), molar fraction (cc), and molar mixing ratio relative to dry air (Xc). The dry air storage in the control volume of flux measurement was not a constant, and thus, the fluctuation of the dry air storage could cause the CO2 molecules transporting out of or into the control volume, i. e. , the variation of the dry air storage adjustment term (Fsd). During nighttime and day-night transition periods, the relative magnitude of Fsd to eddy flux was larger, and ignoring the Fsd could introduce errors in calculating the net CO2 exchange between the forest ecosystem and the atmosphere. Three error sources in the Fs calculation could be introduced from the atmospheric hydrothermal processes, i. e. , 1) air temperature fluctuation, which could cause the largest error, with one order of magnitude larger than that caused by atmospheric pressure (P) , 2) water vapor, its effect being larger than that of P in warm and moist summer but smaller in cold and dry winter, and 3) P, whose effect was generally smaller throughout the year. In estimating the effective CO2 storage (Fs_E) , the Fs value calculated with rho c, cc, and Xc was overestimated averagely by 8. 5%, suggested that in the calculation of Fs, adopting the Xc conservation to atmospheric hydrothermal processes could be more appropriate to minimize the potential errors.

  4. Fast flux locked loop

    DOEpatents

    Ganther, Jr., Kenneth R.; Snapp, Lowell D.

    2002-09-10

    A flux locked loop for providing an electrical feedback signal, the flux locked loop employing radio-frequency components and technology to extend the flux modulation frequency and tracking loop bandwidth. The flux locked loop of the present invention has particularly useful application in read-out electronics for DC SQUID magnetic measurement systems, in which case the electrical signal output by the flux locked loop represents an unknown magnetic flux applied to the DC SQUID.

  5. Atomic force microscopy surface analysis of layered perovskite La2Ti2O7 particles grown by molten flux method

    NASA Astrophysics Data System (ADS)

    Orum, Aslihan; Takatori, Kazumasa; Hori, Shigeo; Ikeda, Tomiko; Yoshimura, Masamichi; Tani, Toshihiko

    2016-08-01

    Rectangular platelike particles of La2Ti2O7, a layered perovskite, were synthesized in KCl, NaCl, and LiCl by the molten flux method. The formation mechanism of the equilibrium shape in these alkali chloride fluxes was discussed in terms of the surface and interfacial energies of crystallographic planes. The atomic force microscopy (AFM) observations revealed that the developed plane of the platelike particles is along the interlayers in the {110}-type layered crystal structure, and is considered to represent the lowest surface energy plane in which strong, periodic Ti–O bond chains terminate. Herein, for the first time, a growth mechanism for La2Ti2O7 particles is proposed and discussed. Triangular prism structures along the c-axis were observed on the developed planes of KCl-grown particles whereas no such structures were found on those of LiCl-grown ones. AFM measurements suggest that the prism facets are {210}-La2Ti2O7, which results in lower interfacial energy within KCl.

  6. Analysis of junction temperature and modification of luminous flux degradation for white LEDs in a thermal accelerated reliability test.

    PubMed

    Ke, Hong-Liang; Jing, Lei; Hao, Jian; Gao, Qun; Wang, Yao; Wang, Xiao-Xun; Sun, Qiang; Xu, Zhi-Jun

    2016-08-01

    An accelerated aging test is the main method in evaluation of the reliability of light-emitting diodes (LEDs), and the first goal of this study is to investigate how the junction temperature (Tj) of the LED varies during accelerated aging. The Tj measured by the forward voltage method shows an upward trend over the aging time, which gives a variation about 6°C-8°C after 3,000 h of aging under an ambient temperature of 80°C. The second goal is to investigate how the variation of Tj affects the lifetime estimation. It is verified that at a certain aging stage, as Tj increases, the normalized luminous flux linearly decreases with variation rate of microns (μ) (1/°C). Then, we propose a method to modify the luminous flux degradation with the Tj and μ to meet the requirements of a constant degradation rate in the data fitting. The experimental results show that with the proposed method, the accelerated lifetimes of samples are bigger than that of the current method with increment values from 8.8% to 21.4% in this research. PMID:27505370

  7. Atomic force microscopy surface analysis of layered perovskite La2Ti2O7 particles grown by molten flux method

    NASA Astrophysics Data System (ADS)

    Orum, Aslihan; Takatori, Kazumasa; Hori, Shigeo; Ikeda, Tomiko; Yoshimura, Masamichi; Tani, Toshihiko

    2016-08-01

    Rectangular platelike particles of La2Ti2O7, a layered perovskite, were synthesized in KCl, NaCl, and LiCl by the molten flux method. The formation mechanism of the equilibrium shape in these alkali chloride fluxes was discussed in terms of the surface and interfacial energies of crystallographic planes. The atomic force microscopy (AFM) observations revealed that the developed plane of the platelike particles is along the interlayers in the {110}-type layered crystal structure, and is considered to represent the lowest surface energy plane in which strong, periodic Ti-O bond chains terminate. Herein, for the first time, a growth mechanism for La2Ti2O7 particles is proposed and discussed. Triangular prism structures along the c-axis were observed on the developed planes of KCl-grown particles whereas no such structures were found on those of LiCl-grown ones. AFM measurements suggest that the prism facets are {210}-La2Ti2O7, which results in lower interfacial energy within KCl.

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

    SciTech Connect

    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.

  9. Coupling river hydrochemical information with catchment properties for multi-scale-analysis of lateral matter fluxes in the Earth system

    NASA Astrophysics Data System (ADS)

    Hartmann, Jens; Lauerwald, Ronny; Moosdorf, Nils

    2016-04-01

    Over the last decade the number of regional to global scale studies of river chemical fluxes and their steering factors increased rapidly, entailing a growing demand for appropriate databases to calculate mass budgets, to calibrate models, or to test hypotheses [1, 2]. Research applying compilations of hydrochemical data are related to questions targeting different time and spatial scales, as for example the annual to centennial scale. In focus are often the alteration of land-ocean matter fluxes due anthropogenic disturbance, the climate sensitivity of chemical weathering fluxes [3], or nutrient fluxes and their evolution [2, 4]. We present an overview of the GLObal RIver CHemistry database GLORICH, which combines an assemblage of hydrochemical data from varying sources with catchment characteristics of the sampling locations [1]. The information provided include e.g. catchment size, lithology, soil, climate, land cover, net primary production, population density and average slope gradient. The data base comprises 1.27 million samples distributed over 17,000 sampling locations [1]. It will be shown how large assemblages of data are useful to target some major questions about the alteration of land ocean element fluxes due to climate or land use change while coupling hydrochemical data with catchment properties in a homogenized database. An extension by isotopic data will be in the focus of future work [c.f. 5]. Further, applications in climate change studies for understanding feedbacks in the Earth system will be discussed [6]. References: [1] Hartmann, J., Lauerwald, R., & Moosdorf, N. (2014). A brief overview of the GLObal RIver CHemistry Database, GLORICH. Procedia Earth and Planetary Science, 10, 23-27. [2] Hartmann, J., Levy, J., & Kempe, S. (2011). Increasing dissolved silica trends in the Rhine River: an effect of recovery from high P loads?. Limnology, 12(1), 63-73. [3] Hartmann, J., Moosdorf, N., Lauerwald, R., Hinderer, M., & West, A. J. (2014). Global

  10. Metabolic Profiling and Flux Analysis of MEL-2 Human Embryonic Stem Cells during Exponential Growth at Physiological and Atmospheric Oxygen Concentrations

    PubMed Central

    Titmarsh, Drew; Krömer, Jens O.; Kao, Li-Pin; Nielsen, Lars; Wolvetang, Ernst; Cooper-White, Justin

    2014-01-01

    As human embryonic stem cells (hESCs) steadily progress towards regenerative medicine applications there is an increasing emphasis on the development of bioreactor platforms that enable expansion of these cells to clinically relevant numbers. Surprisingly little is known about the metabolic requirements of hESCs, precluding the rational design and optimisation of such platforms. In this study, we undertook an in-depth characterisation of MEL-2 hESC metabolic behaviour during the exponential growth phase, combining metabolic profiling and flux analysis tools at physiological (hypoxic) and atmospheric (normoxic) oxygen concentrations. To overcome variability in growth profiles and the problem of closing mass balances in a complex environment, we developed protocols to accurately measure uptake and production rates of metabolites, cell density, growth rate and biomass composition, and designed a metabolic flux analysis model for estimating internal rates. hESCs are commonly considered to be highly glycolytic with inactive or immature mitochondria, however, whilst the results of this study confirmed that glycolysis is indeed highly active, we show that at least in MEL-2 hESC, it is supported by the use of oxidative phosphorylation within the mitochondria utilising carbon sources, such as glutamine to maximise ATP production. Under both conditions, glycolysis was disconnected from the mitochondria with all of the glucose being converted to lactate. No difference in the growth rates of cells cultured under physiological or atmospheric oxygen concentrations was observed nor did this cause differences in fluxes through the majority of the internal metabolic pathways associated with biogenesis. These results suggest that hESCs display the conventional Warburg effect, with high aerobic activity despite high lactate production, challenging the idea of an anaerobic metabolism with low mitochondrial activity. The results of this study provide new insight that can be used in

  11. Metabolic profiling and flux analysis of MEL-2 human embryonic stem cells during exponential growth at physiological and atmospheric oxygen concentrations.

    PubMed

    Turner, Jennifer; Quek, Lake-Ee; Titmarsh, Drew; Krömer, Jens O; Kao, Li-Pin; Nielsen, Lars; Wolvetang, Ernst; Cooper-White, Justin

    2014-01-01

    As human embryonic stem cells (hESCs) steadily progress towards regenerative medicine applications there is an increasing emphasis on the development of bioreactor platforms that enable expansion of these cells to clinically relevant numbers. Surprisingly little is known about the metabolic requirements of hESCs, precluding the rational design and optimisation of such platforms. In this study, we undertook an in-depth characterisation of MEL-2 hESC metabolic behaviour during the exponential growth phase, combining metabolic profiling and flux analysis tools at physiological (hypoxic) and atmospheric (normoxic) oxygen concentrations. To overcome variability in growth profiles and the problem of closing mass balances in a complex environment, we developed protocols to accurately measure uptake and production rates of metabolites, cell density, growth rate and biomass composition, and designed a metabolic flux analysis model for estimating internal rates. hESCs are commonly considered to be highly glycolytic with inactive or immature mitochondria, however, whilst the results of this study confirmed that glycolysis is indeed highly active, we show that at least in MEL-2 hESC, it is supported by the use of oxidative phosphorylation within the mitochondria utilising carbon sources, such as glutamine to maximise ATP production. Under both conditions, glycolysis was disconnected from the mitochondria with all of the glucose being converted to lactate. No difference in the growth rates of cells cultured under physiological or atmospheric oxygen concentrations was observed nor did this cause differences in fluxes through the majority of the internal metabolic pathways associated with biogenesis. These results suggest that hESCs display the conventional Warburg effect, with high aerobic activity despite high lactate production, challenging the idea of an anaerobic metabolism with low mitochondrial activity. The results of this study provide new insight that can be used in

  12. Quantitative analysis of some mechanisms affecting the yield of oxidative phosphorylation: dependence upon both fluxes and forces.

    PubMed

    Rigoulet, M; Leverve, X; Fontaine, E; Ouhabi, R; Guérin, B

    1998-07-01

    The purpose of this work was to show how the quantitative definition of the different parameters involved in mitochondrial oxidative phosphorylation makes it possible to characterize the mechanisms by which the yield of ATP synthesis is affected. Three different factors have to be considered: (i) the size of the different forces involved (free energy of redox reactions and ATP synthesis, proton electrochemical difference); (ii) the physical properties of the inner mitochondrial membrane in terms of leaks (H+ and cations); and finally (iii) the properties of the different proton pumps involved in this system (kinetic properties, regulation, modification of intrinsic stoichiometry). The data presented different situations where one or more of these parameters are affected, leading to a different yield of oxidative phosphorylation. (1) By manipulating the actual flux through each of the respiratory chain units at constant protonmotive force in yeast mitochondria, we show that the ATP/O ratio decreases when the flux increases. Moreover, the highest efficiency was obtained when the respiratory rate was low and almost entirely controlled by the electron supply. (2) By using almitrine in different kinds of mitochondria, we show that this drug leads to a decrease in ATP synthesis efficiency by increasing the H+/ATP stoichiometry ofATP synthase (Rigoulet M et al. Biochim Biophys Acta 1018: 91-97, 1990). Since this enzyme is reversible, it was possible to test the effect of this drug on the reverse reaction of the enzyme i.e. extrusion of protons catalyzed by ATP hydrolysis. Hence, we are able to prove that, in this case, the decrease in efficiency of oxidative phosphorylation is due to a change in the mechanistic stoichiometry of this proton pump. To our knowledge, this is the first example of a modification in oxidative phosphorylation yield by a change in mechanistic stoichiometry of one of the proton pumps involved. (3) In a model of polyunsaturated fatty acid deficiency

  13. Bioenergetic analysis of intact mammalian cells using the Seahorse XF24 Extracellular Flux analyzer and a luciferase ATP assay.

    PubMed

    de Moura, Michelle Barbi; Van Houten, Bennett

    2014-01-01

    Metabolic pathways and bioenergetics were described in great detail over half a century ago, and during the past decade there has been a resurgence in integrating these cellular processes with other biological properties of the cell, including growth control, protein kinase cascade signaling, cell cycle division, and autophagy. Since many disease conditions are associated with altered metabolism and production of energy, it is important to develop new approaches to measure these cellular parameters. This chapter summarizes a new and exciting approach based on the Seahorse XF24 Extracelluar Flux analyzer, which takes real time measurements of oxidative phosphorylation and glycolysis in living cells. These bioenergetic profiles are then compared with steady-state levels of cellular ATP as measured by a luciferase assay.

  14. Analysis of TLR-Induced Metabolic Changes in Dendritic Cells Using the Seahorse XF(e)96 Extracellular Flux Analyzer.

    PubMed

    Pelgrom, Leonard R; van der Ham, Alwin J; Everts, Bart

    2016-01-01

    Engagement of Toll-like receptors (TLRs) on dendritic cells (DCs) triggers the expression of a large set of genes involved in DC activation and maturation, which allow them to act efficiently as antigen-presenting cells. Recently, it has become clear that TLR signalling in DCs also results in dramatic metabolic changes that are integral to their changed biology. Here, we describe a detailed protocol on how DC metabolism can be studied after TLR stimulation using the 96-well format Extracellular Flux (XF(e)96) Analyzer from Seahorse Bioscience, a machine that allows one to simultaneously assess rates of oxidative phosphorylation and glycolysis in real-time, in live cells and in a high-throughput manner.

  15. Modeling and Simulation of Optimal Resource Management during the Diurnal Cycle in Emiliania huxleyi by Genome-Scale Reconstruction and an Extended Flux Balance Analysis Approach.

    PubMed

    Knies, David; Wittmüß, Philipp; Appel, Sebastian; Sawodny, Oliver; Ederer, Michael; Feuer, Ronny

    2015-01-01

    The coccolithophorid unicellular alga Emiliania huxleyi is known to form large blooms, which have a strong effect on the marine carbon cycle. As a photosynthetic organism, it is subjected to a circadian rhythm due to the changing light conditions throughout the day. For a better understanding of the metabolic processes under these periodically-changing environmental conditions, a genome-scale model based on a genome reconstruction of the E. huxleyi strain CCMP 1516 was created. It comprises 410 reactions and 363 metabolites. Biomass composition is variable based on the differentiation into functional biomass components and storage metabolites. The model is analyzed with a flux balance analysis approach called diurnal flux balance analysis (diuFBA) that was designed for organisms with a circadian rhythm. It allows storage metabolites to accumulate or be consumed over the diurnal cycle, while keeping the structure of a classical FBA problem. A feature of this approach is that the production and consumption of storage metabolites is not defined externally via the biomass composition, but the result of optimal resource management adapted to the diurnally-changing environmental conditions. The model in combination with this approach is able to simulate the variable biomass composition during the diurnal cycle in proximity to literature data. PMID:26516924

  16. Modeling and Simulation of Optimal Resource Management during the Diurnal Cycle in Emiliania huxleyi by Genome-Scale Reconstruction and an Extended Flux Balance Analysis Approach

    PubMed Central

    Knies, David; Wittmüß, Philipp; Appel, Sebastian; Sawodny, Oliver; Ederer, Michael; Feuer, Ronny

    2015-01-01

    The coccolithophorid unicellular alga Emiliania huxleyi is known to form large blooms, which have a strong effect on the marine carbon cycle. As a photosynthetic organism, it is subjected to a circadian rhythm due to the changing light conditions throughout the day. For a better understanding of the metabolic processes under these periodically-changing environmental conditions, a genome-scale model based on a genome reconstruction of the E. huxleyi strain CCMP 1516 was created. It comprises 410 reactions and 363 metabolites. Biomass composition is variable based on the differentiation into functional biomass components and storage metabolites. The model is analyzed with a flux balance analysis approach called diurnal flux balance analysis (diuFBA) that was designed for organisms with a circadian rhythm. It allows storage metabolites to accumulate or be consumed over the diurnal cycle, while keeping the structure of a classical FBA problem. A feature of this approach is that the production and consumption of storage metabolites is not defined externally via the biomass composition, but the result of optimal resource management adapted to the diurnally-changing environmental conditions. The model in combination with this approach is able to simulate the variable biomass composition during the diurnal cycle in proximity to literature data. PMID:26516924

  17. Fine-Scale Community Structure Analysis of ANME in Nyegga Sediments with High and Low Methane Flux

    PubMed Central

    Roalkvam, Irene; Dahle, Håkon; Chen, Yifeng; Jørgensen, Steffen Leth; Haflidason, Haflidi; Steen, Ida Helene

    2012-01-01

    To obtain knowledge on how regional variations in methane seepage rates influence the stratification, abundance, and diversity of anaerobic methanotrophs (ANME), we analyzed the vertical microbial stratification in a gravity core from a methane micro-seeping area at Nyegga by using 454-pyrosequencing of 16S rRNA gene tagged amplicons and quantitative PCR. These data were compared with previously obtained data from the more active G11 pockmark, characterized by higher methane flux. A down core stratification and high relative abundance of ANME were observed in both cores, with transition from an ANME-2a/b dominated community in low-sulfide and low methane horizons to ANME-1 dominance in horizons near the sulfate-methane transition zone. The stratification was over a wider spatial region and at greater depth in the core with lower methane flux, and the total 16S rRNA copy numbers were two orders of magnitude lower than in the sediments at G11 pockmark. A fine-scale view into the ANME communities at each location was achieved through operational taxonomical units (OTU) clustering of ANME-affiliated sequences. The majority of ANME-1 sequences from both sampling sites clustered within one OTU, while ANME-2a/b sequences were represented in unique OTUs. We suggest that free-living ANME-1 is the most abundant taxon in Nyegga cold seeps, and also the main consumer of methane. The observation of specific ANME-2a/b OTUs at each location could reflect that organisms within this clade are adapted to different geochemical settings, perhaps due to differences in methane affinity. Given that the ANME-2a/b population could be sustained in less active seepage areas, this subgroup could be potential seed populations in newly developed methane-enriched environments. PMID:22715336

  18. Comparison and analysis of empirical equations for soil heat flux for different cropping systems and irrigation methods

    USGS Publications Warehouse

    Irmak, A.; Singh, R.K.; Walter-Shea, Elizabeth; Verma, S.B.; Suyker, A.E.

    2011-01-01

    We evaluated the performance of four models for estimating soil heat flux density (G) in maize (Zea mays L.) and soybean (Glycine max L.) fields under different irrigation methods (center-pivot irrigated fields at Mead, Nebraska, and subsurface drip irrigated field at Clay Center, Nebraska) and rainfed conditions at Mead. The model estimates were compared against measurements made during growing seasons of 2003, 2004, and 2005 at Mead and during 2005, 2006, and 2007 at Clay Center. We observed a strong relationship between the G and net radiation (Rn) ratio (G/Rn) and the normalized difference vegetation index (NDVI). When a significant portion of the ground was bare soil, G/Rn ranged from 0.15 to 0.30 and decreased with increasing NDVI. In contrast to the NDVI progression, the G/Rn ratio decreased with crop growth and development. The G/Rn ratio for subsurface drip irrigated crops was smaller than for the center-pivot irrigated crops. The seasonal average G was 13.1%, 15.2%, 10.9%, and 12.8% of Rn for irrigated maize, rainfed maize, irrigated soybean, and rainfed soybean, respectively. Statistical analyses of the performance of the four models showed a wide range of variation in G estimation. The root mean square error (RMSE) of predictions ranged from 15 to 81.3 W m-2. Based on the wide range of RMSE, it is recommended that local calibration of the models should be carried out for remote estimation of soil heat flux. ?? 2011 American Society of Agricultural and Biological Engineers.

  19. Fine-Scale Community Structure Analysis of ANME in Nyegga Sediments with High and Low Methane Flux.

    PubMed

    Roalkvam, Irene; Dahle, Håkon; Chen, Yifeng; Jørgensen, Steffen Leth; Haflidason, Haflidi; Steen, Ida Helene

    2012-01-01

    To obtain knowledge on how regional variations in methane seepage rates influence the stratification, abundance, and diversity of anaerobic methanotrophs (ANME), we analyzed the vertical microbial stratification in a gravity core from a methane micro-seeping area at Nyegga by using 454-pyrosequencing of 16S rRNA gene tagged amplicons and quantitative PCR. These data were compared with previously obtained data from the more active G11 pockmark, characterized by higher methane flux. A down core stratification and high relative abundance of ANME were observed in both cores, with transition from an ANME-2a/b dominated community in low-sulfide and low methane horizons to ANME-1 dominance in horizons near the sulfate-methane transition zone. The stratification was over a wider spatial region and at greater depth in the core with lower methane flux, and the total 16S rRNA copy numbers were two orders of magnitude lower than in the sediments at G11 pockmark. A fine-scale view into the ANME communities at each location was achieved through operational taxonomical units (OTU) clustering of ANME-affiliated sequences. The majority of ANME-1 sequences from both sampling sites clustered within one OTU, while ANME-2a/b sequences were represented in unique OTUs. We suggest that free-living ANME-1 is the most abundant taxon in Nyegga cold seeps, and also the main consumer of methane. The observation of specific ANME-2a/b OTUs at each location could reflect that organisms within this clade are adapted to different geochemical settings, perhaps due to differences in methane affinity. Given that the ANME-2a/b population could be sustained in less active seepage areas, this subgroup could be potential seed populations in newly developed methane-enriched environments.

  20. Fine-Scale Community Structure Analysis of ANME in Nyegga Sediments with High and Low Methane Flux.

    PubMed

    Roalkvam, Irene; Dahle, Håkon; Chen, Yifeng; Jørgensen, Steffen Leth; Haflidason, Haflidi; Steen, Ida Helene

    2012-01-01

    To obtain knowledge on how regional variations in methane seepage rates influence the stratification, abundance, and diversity of anaerobic methanotrophs (ANME), we analyzed the vertical microbial stratification in a gravity core from a methane micro-seeping area at Nyegga by using 454-pyrosequencing of 16S rRNA gene tagged amplicons and quantitative PCR. These data were compared with previously obtained data from the more active G11 pockmark, characterized by higher methane flux. A down core stratification and high relative abundance of ANME were observed in both cores, with transition from an ANME-2a/b dominated community in low-sulfide and low methane horizons to ANME-1 dominance in horizons near the sulfate-methane transition zone. The stratification was over a wider spatial region and at greater depth in the core with lower methane flux, and the total 16S rRNA copy numbers were two orders of magnitude lower than in the sediments at G11 pockmark. A fine-scale view into the ANME communities at each location was achieved through operational taxonomical units (OTU) clustering of ANME-affiliated sequences. The majority of ANME-1 sequences from both sampling sites clustered within one OTU, while ANME-2a/b sequences were represented in unique OTUs. We suggest that free-living ANME-1 is the most abundant taxon in Nyegga cold seeps, and also the main consumer of methane. The observation of specific ANME-2a/b OTUs at each location could reflect that organisms within this clade are adapted to different geochemical settings, perhaps due to differences in methane affinity. Given that the ANME-2a/b population could be sustained in less active seepage areas, this subgroup could be potential seed populations in newly developed methane-enriched environments. PMID:22715336

  1. A Water Balance Model for Hill reservoir - Aquifer Exchange Water Flux Quantification and Uncertainty Analysis - Application to the Kamech catchment, Tunisia

    NASA Astrophysics Data System (ADS)

    Bouteffeha, Maroua; Dagès, Cécile; Bouhlila, Rachida; Raclot, Damien; Molénat, Jérôme

    2013-04-01

    hydrological years (09/2009-08/2010 and 09/2010-08/2011) shows that the net surface-subsurface exchange flux is positive, i.e. the infiltration from the hill reservoir to the aquifer predominates the discharge from the aquifer to the reservoir. Moreover the surface-subsurface exchange constitutes the main output component in the water balance. The annual surface-subsurface exchange flux appeared almost constant from one year to the other one whatever the hydrological conditions variability over the catchment. Moreover, the analysis of the intra-annual variability shows that the flux was nearly constant within every year. Reference: Voltz , M. and Albergel , J., 2002. OMERE : Observatoire Méditerranéen de l'Environnement Rural et de l'Eau - Impact des actions anthropiques sur les transferts de masse dans les hydrosystèmes méditerranéens ruraux. Proposition d'Observatoire de Recherche en Environnement, Ministère de la Recherche.

  2. Magnetic-flux pump

    NASA Technical Reports Server (NTRS)

    Hildebrandt, A. F.; Elleman, D. D.; Whitmore, F. C. (Inventor)

    1966-01-01

    A magnetic flux pump is described for increasing the intensity of a magnetic field by transferring flux from one location to the magnetic field. The device includes a pair of communicating cavities formed in a block of superconducting material, and a piston for displacing the trapped magnetic flux into the secondary cavity producing a field having an intense flux density.

  3. Extreme energetic electron fluxes in low Earth orbit: Analysis of POES E > 30, E > 100, and E > 300 keV electrons

    NASA Astrophysics Data System (ADS)

    Meredith, Nigel P.; Horne, Richard B.; Isles, John D.; Green, Janet C.

    2016-02-01

    Energetic electrons are an important space weather hazard. Electrons with energies less than about 100 keV cause surface charging, while higher-energy electrons can penetrate materials and cause internal charging. In this study we conduct an extreme value analysis of the maximum 3-hourly flux of E > 30 keV, E > 100 keV, and E > 300 keV electrons in low Earth orbit as a function of L∗, for geomagnetic field lines that map to the outer radiation belt, using data from the National Oceanic and Atmospheric Administration Polar Operational Environmental Satellites (POES) from July 1998 to June 2014. The 1 in 10 year flux of E > 30 keV electrons shows a general increasing trend with distance ranging from 1.8 × 107 cm-2 s-1 sr-1 at L∗=3.0 to 6.6 × 107 cm-2 s-1 sr-1 at L∗=8.0. The 1 in 10 year flux of E > 100 keV electrons peaks at L∗=4.5-5.0 at 1.9 × 107 cm-2 s-1 sr-1 decreasing to minima of 7.1 × 106 and 8.7 × 106 cm-2 s-1 sr-1 at L∗=3.0 and 8.0, respectively. In contrast to the E > 30 keV electrons, the 1 in 10 year flux of E > 300 keV electrons shows a general decreasing trend with distance, ranging from 2.4 × 106 cm-2 s-1 sr-1 at L∗=3.0 to 1.2 × 105 cm-2 s-1 sr-1 at L∗=8.0. Our analysis suggests that there is a limit to the E > 30 keV electrons with an upper bound in the range 5.1 × 107 to 8.8 × 107 cm-2 s-1 sr-1. However, the results suggest that there is no upper bound for the E > 100 keV and E > 300 keV electrons.

  4. An Improved Analysis onTrends and Uncertainties of Carbon Stocks and Fluxes in the Piedmont Ecoregion of the United States Using Data Assimilation

    NASA Astrophysics Data System (ADS)

    Chen, M.; Liu, S.; Young, C.; Tieszen, L. L.

    2011-12-01

    Accurate quantification of carbon fluxes and stocks in the terrestrial ecoregions can improve our understanding of carbon sequestration processes and further help address global climate change issues. However, two current principal approaches, modeling and measuring, have inherent limitations that usually lead to uncertainties of quantification. Such limitations include poorly defined parameters, model input errors, and spatially patchy and multi-resolution characteristics of measurements. Advanced data assimilation techniques can mitigate these limitations by combining a series of measurements with dynamic models. In this study, we used a sequential data assimilation method, the Smoothed Ensemble Kalman Filter (SEnKF), to assimilate the data from various sources into the General Ensemble Biogeochemical Modeling System (GEMS). This method (1) optimally estimates trends of carbon fluxes and stocks in the Piedmont ecoregion of the United States from the 1970s to the 2000s, and (2) simultaneously constrains several key model parameters (e.g., maximum potential production) for various types of land covers for improving the model prediction. Assimilated data included gross primary production, net primary production, and leaf area index from the Moderate Resolution Imaging Spectroradiometer (MODIS), grain yields at the county level from the U.S. Department of Agriculture (USDA), and forest characteristics from the USDA Forest Service's Forest Inventory and Analysis database. Our preliminary analyses indicated that carbon sequestration in the Piedmont ecoregion gradually decreased in the past three decades, and the interannual variability was strongly affected by climate variability. Our approach reduced uncertainties in the estimated carbon fluxes and stocks in forests, croplands, and grasslands by 50 percent compared to the estimates using originally defined parameters.

  5. Analysis of riverine suspended particulate matter fluxes (Gulf of Lion, Mediterranean Sea) using a synergy of ocean color observations with a 3-D hydrodynamic sediment transport model

    NASA Astrophysics Data System (ADS)

    Le Fouest, Vincent; Chami, Malik; Verney, Romaric

    2015-02-01

    The export of riverine suspended particulate matter (SPM) in the coastal ocean has major implications for the biogeochemical cycles. In the Mediterranean Sea (France), the Rhone River inputs of SPM into the Gulf of Lion (GoL) are highly variable in time, which severely impedes the assessment of SPM fluxes. The objectives of this study are (i) to investigate the prediction of the land-to-ocean flux of SPM using the complementarity (i.e., synergy) between a hydrodynamic sediment transport model and satellite observations, and (ii) to analyze the spatial distribution of the SPM export. An original approach that combines the MARS-3D model with satellite ocean color data is proposed. Satellite-derived SPM and light penetration depth are used to initialize MARS-3D and to validate its predictions. A sensitivity analysis is performed to quantify the impact of riverine SPM size composition and settling rate on the horizontal export of SPM. The best agreement between the model and the satellite in terms of SPM spatial distribution and export is obtained for two conditions: (i) when the relative proportion of "heavy and fast" settling particles significantly increases relative to the "light and slow" ones, and (ii) when the settling rate of heavy and light SPM increases by fivefold. The synergy between MARS-3D and the satellite data improved the SPM flux predictions by 48% near the Rhone River mouth. Our results corroborate the importance of implementing satellite observations within initialization procedures of ocean models since data assimilation techniques may fail for river floods showing strong seasonal variability.

  6. Analysis and results of a hydrogen-moderated isotope production assembly in the Fast Flux Test Facility

    SciTech Connect

    Wootan, D.W.; Rawlins, J.A.; Carter, L.L.; Brager, H.R.; Schenter, R.E. )

    1989-10-01

    This paper reports on a cobalt test assembly containing yttrium hydride pins for neutron moderation irradiated in the Fast Flux Test Facility (FFTF) during cycle 9A for 137.7 equivalent full-power days at a power level of 291 MW. The 36 test pins consisted of a batch of 32 pins containing cobalt metal used to produce {sup 60}Co and a set of four pins with europium oxide to produce {sup 153}Gd, a radioisotope used in detection of the bone disease osteoporosis. Postirradiation examination of the cobalt pins determined the {sup 60}Co production to be predictable to an accuracy of {approximately} 5%. The measured {sup 60}Co spatially distributed concentrations were within 20% of the calculated concentrations. The assembly average {sup 60}Co measured activity was 4% less than the calculated value. The europium oxide pins were gamma scanned for the europium isotopes {sup 152}Eu and {sup 154}Eu to an absolute accuracy of {approx equal} 10%. The measured europium radioisotope and {sup 153}Gd concentrations were within 20% of calculated values. The hydride assembly performed well and is an excellent vehicle for many FFTF isotope production applications. The results also demonstrate the accuracy of the calculational methods developed by the Westinghouse Hanford Company for predicting isotope production rates in this type of assembly.

  7. A high continental weathering flux into Paleoarchean seawater revealed by strontium isotope analysis of 3.26 Ga barite

    NASA Astrophysics Data System (ADS)

    Satkoski, Aaron M.; Lowe, Donald R.; Beard, Brian L.; Coleman, Max L.; Johnson, Clark M.

    2016-11-01

    Controls on Archean seawater chemistry remain controversial. Many studies have suggested that it was largely controlled by oceanic hydrothermal fluid circulation. Recent work, however, from clastic sequences, Hf-O isotope data from detrital zircons, and models for the Rb/Sr evolution of the continental crust suggest that intense continental weathering and low-temperature surface alteration were more important than previously thought during the early Archean. This is consistent with biogeochemical studies that suggest the Archean had a diverse microbial ecology, which would, in part, need to be sustained by nutrients (e.g., phosphorus) that were derived from continental weathering. To further quantify continental weathering during the early Archean, we analyzed 3.26 Ga barite from the Fig Tree Group, South Africa for strontium, oxygen, and sulfur isotope compositions. We propose that the seawater component of the barite is characterized by 87Sr/86Sr ratios >0.701, which is significantly more radiogenic than contemporaneous mantle (∼0.7007-0.7008). The radiogenic nature of seawater at this time suggests that the continental weathering flux at 3.26 Ga had a large impact on ocean chemistry 400 million years earlier than previously suggested.

  8. Statistical analysis of short-term water stress conditions at Riggs Creek OzFlux tower site

    NASA Astrophysics Data System (ADS)

    Azmi, Mohammad; Rüdiger, Christoph; Walker, Jeffrey P.

    2016-08-01

    A large range of indices and proxies are available to describe the water stress conditions of an area subject to different applications, which have varying capabilities and limitations depending on the prevailing local climatic conditions and land cover. The present study uses a range of spatio-temporally high-resolution (daily and within daily) data sources to evaluate a number of drought indices (DIs) for the Riggs Creek OzFlux tower site in southeastern Australia. Therefore, the main aim of this study is to evaluate the statistical characteristics of individual DIs subject to short-term water stress conditions. In order to derive a more general and therefore representative DI, a new criterion is required to specify the statistical similarity between each pair of indices to allow determining the dominant drought types along with their representative DIs. The results show that the monitoring of water stress at this case study area can be achieved by evaluating the individual behaviour of three clusters of (i) vegetation conditions, (ii) water availability and (iii) water consumptions. This indicates that it is not necessary to assess all individual DIs one by one to derive a comprehensive and informative data set about the water stress of an area; instead, this can be achieved by analysing one of the DIs from each cluster or deriving a new combinatory index for each cluster, based on established combination methods.

  9. Lunar impact flashes from Geminids: analysis of luminous efficiencies and the flux of large meteoroids on Earth

    NASA Astrophysics Data System (ADS)

    Ortiz, J. L.; Madiedo, J. M.; Morales, N.; Santos-Sanz, P.; Aceituno, F. J.

    2015-11-01

    We analyse lunar impact flashes recorded by our team during runs in December 2007, 2011, 2013 and 2014. In total, 12 impact flashes with magnitudes ranging between 7.1 and 9.3 in V band were identified. From these, nine events could be linked to the Geminid stream. Using these observations, the ratio of luminous energy emitted in the flashes with respect to the kinetic energy of the impactors for meteoroids of the Geminid stream is estimated. By making use of the known Geminids meteoroid flux on Earth we found this ratio to be 2.1 × 10-3 on average. We compare this luminous efficiency with other estimations derived in the past for other meteoroid streams and also compare it with other estimations that we present here for the first time by making use of crater diameter measurements. We think that the luminous efficiency has to be revised downwards, not upwards, at least for sporadic impacts. This implies an increase in the influx of kilogram-sized and larger bodies on Earth that has been derived thus far through the lunar impact flash monitoring technique.

  10. Is reduced benthic flux related to the Diporeia decline? Analysis of spring blooms and whiting events in Lake Ontario

    USGS Publications Warehouse

    Watkins, James M.; Rudstam, Lars G.; Crabtree, Darran L.; Walsh, Maureen

    2013-01-01

    Benthic monitoring by USGS off the southern shore of Lake Ontario from October 1993 to October 1995 provides a detailed view of the early stages of the decline of the native amphipod Diporeia. A loss of the 1994 and 1995 year classes of Diporeia preceded the disappearance of the native amphipod at sites near Oswego and Rochester at depths from 55 to 130 m. In succeeding years, Diporeia populations continued to decline in Lake Ontario and were nearly extirpated by 2008. Explanations for Diporeia 's decline in the Great Lakes include several hypotheses often linked to the introduction and expansion of exotic zebra and quagga mussels (Dreissena sp.). We compare the timeline of the Diporeia decline in Lake Ontario with trends in two sources of organic matter to the sediments — spring diatom blooms and late summer whiting events. The 1994–95 decline of Diporeia coincided with localized dreissenid effects on phytoplankton in the nearshore and a year (April 1994 to May 1995) of decreased flux of organic carbon recorded by sediment traps moored offshore of Oswego. Later declines of profundal (> 90 m) Diporeia populations in 2003 were poorly associated with trends in spring algal blooms and late summer whiting events. Lake Ontario/Diporeia/Dreissena/remote sensing.

  11. The virtual observatory service TheoSSA: Establishing a database of synthetic stellar flux standards . II. NLTE spectral analysis of the OB-type subdwarf Feige 110

    NASA Astrophysics Data System (ADS)

    Rauch, T.; Rudkowski, A.; Kampka, D.; Werner, K.; Kruk, J. W.; Moehler, S.

    2014-06-01

    Context. In the framework of the Virtual Observatory (VO), the German Astrophysical VO (GAVO) developed the registered service TheoSSA (Theoretical Stellar Spectra Access). It provides easy access to stellar spectral energy distributions (SEDs) and is intended to ingest SEDs calculated by any model-atmosphere code, generally for all effective temperatures, surface gravities, and elemental compositions. We will establish a database of SEDs of flux standards that are easily accessible via TheoSSA's web interface. Aims: The OB-type subdwarf Feige 110 is a standard star for flux calibration. State-of-the-art non-local thermodynamic equilibrium stellar-atmosphere models that consider opacities of species up to trans-iron elements will be used to provide a reliable synthetic spectrum to compare with observations. Methods: In case of Feige 110, we demonstrate that the model reproduces not only its overall continuum shape from the far-ultraviolet (FUV) to the optical wavelength range but also the numerous metal lines exhibited in its FUV spectrum. Results: We present a state-of-the-art spectral analysis of Feige 110. We determined , log g = 6.00 ± 0.20, and the abundances of He, N, P, S, Ti, V, Cr, Mn, Fe, Co, Ni, Zn, and Ge. Ti, V, Mn, Co, Zn, and Ge were identified for the first time in this star. Upper abundance limits were derived for C, O, Si, Ca, and Sc. Conclusions: The TheoSSA database of theoretical SEDs of stellar flux standards guarantees that the flux calibration of astronomical data and cross-calibration between different instruments can be based on models and SEDs calculated with state-of-the-art model-atmosphere codes. Based on observations with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS5-26666. Based on observations made with the NASA-CNES-CSA Far Ultraviolet Spectroscopic Explorer. Table 2, Figs. 3 and

  12. The Mimas ghost revisited - An analysis of the electron flux and electron microsignatures observed in the vicinity of Mimas at Saturn

    NASA Technical Reports Server (NTRS)

    Chenette, D. L.; Stone, E. C.

    1983-01-01

    An analysis of the electron-absorption signature observed by the cosmic-ray system on Voyager 2 near the orbit of Mimas is presented. It is found that these observations cannot be explained as the absorption signature of Mimas. By combining Pioneer 11 and Voyager 2 measurements of the electron flux at Mimas's orbit (L = 3.1), an electron spectrum is found in which most of the flux above about 100 keV is concentrated near 1 to 3 MeV. This spectral form is qualitatively consistent with the bandpass filter model of Van Allen et al. (1980). The expected Mimas absorption signature is calculated from this spectrum neglecting radial diffusion. Since no Mimas absorption signature was observed in the inbound Voyager 2 data, a lower limit on the diffusion coefficient for MeV electrons at L = 3.1 of D greater than 10 to the -8th sq Saturn radii/sec is obtained. With a diffusion coefficient this large, both the Voyager 2 and the Pioneer 11 small-scale electron-absorption-signature observations in Mimas's orbit are enigmatic. Thus the mechanism for producing these signatures is referred to as the Mimas ghost. A cloud of material in orbit with Mimas may account for the observed electron signature if the cloud is at least 1-percent opaque to electrons across a region extending over a few hundred kilometers.

  13. The Mimas ghost revisited: An analysis of the electron flux and electron microsignatures observed in the vicinity of Mimas at Saturn

    NASA Technical Reports Server (NTRS)

    Chenette, D. L.; Stone, E. C.

    1983-01-01

    An analysis of the electron absorption signature observed by the Cosmic Ray System (CRS) on Voyage 2 near the orbit of Mimas is presented. We find that these observations cannot be explained as the absorption signature of Mimas. Combing Pioneer 11 and Voyager 2 measurements of the electron flux at Mimas's orbit (L=3.1), we find an electron spectrum where most of the flux above approx 100 keV is concentrated near 1 to 3 MeV. The expected Mimas absorption signature is calculated from this spectrum neglecting radial diffusion. A lower limit on the diffusion coefficient for MeV electrons is obtained. With a diffusion coefficient this large, both the Voyager 2 and the Pioneer 11 small-scale electron absorption signature observations in Mimas's orbit are enigmatic. Thus we refer to the mechanism for producing these signatures as the Mimas ghost. A cloud of material in orbit with Mimas may account for the observed electron signature if the cloud is at least 1% opaque to electrons across a region extending over a few hundred kilometers.

  14. Evaluation of neutron flux parameters in irradiation sites of research reactor using the Westcott-formalism for the k0 neutron activation analysis method

    NASA Astrophysics Data System (ADS)

    Kasban, H.; Hamid, Ashraf

    2015-12-01

    Instrumental Neutron Activation Analysis using k0 (k0-INAA) method has been used to determine a number of elements in sediment samples collected from El-Manzala Lake in Egypt. k0-INAA according to Westcott's formalism has been implemented using the complete irradiation kit of the fast pneumatic rabbit and some selected manually loaded irradiation sites for short and long irradiation at Egypt Second Research Reactor (ETRR-2). Zr-Au and Co sets as neutron flux monitors are used to determine the neutron flux parameters (f and α) in each irradiation sites. Two reference materials IAEA Soil-7 samples have been inserted and implemented for data validation and an internal monostandard multi monitor used (k0 based IM-NAA). It was given a good agreement between the experimental analyzed values and that obtained of the certified values. The major and trace elements in the sediment samples have been evaluated with the use of Co as an internal and Au as an external monostandard comparators. The concentrations of the elements (Cr, Mn and Zn) in the sediment samples of the present work are discussed regarding to those obtained from other sites.

  15. Application of Karhunen-Loève Expansions for the Dynamic Analysis of a Natural Convection Loop for Known Heat Flux

    NASA Astrophysics Data System (ADS)

    Hummel, Tobias; Pacheco-Vega, Arturo

    2012-11-01

    In the present study we use Karhunen-Loève (KL) expansions to model the dynamic behavior of a single-phase natural convection loop. The loop is filled with an incompressible fluid that exchanges heat through the walls of its toroidal shape. Influx and efflux of energy take place at different parts of the loop. The focus here is a sinusoidal variation of the heat flux exchanged with the environment for three different scenarios; i.e., stable, limit cycles and chaos. For the analysis, one-dimensional models, in which the tilt angle and the amplitude of the heat flux are used as parameters, were first developed under suitable assumptions and then solved numerically to generate the data from which the KL-based models could be constructed. The method of snapshots, along with a Galerkin projection, was then used to find the basis functions and corresponding constants of each expansion, thus producing the optimal representation of the system. Results from this study indicate that the dimension of the KL-based dynamical system depends on the linear stability of the steady states; the number of basis functions necessary to describe the system increases with increased complexity of the system operation. When compared to typical dynamical systems based on Fourier expansions the KL-based models are, in general, more compact and equally accurate in the dynamic description of the natural convection loop.

  16. Correlating two-photon excited fluorescence imaging of breast cancer cellular redox state with seahorse flux analysis of normalized cellular oxygen consumption

    NASA Astrophysics Data System (ADS)

    Hou, Jue; Wright, Heather J.; Chan, Nicole; Tran, Richard; Razorenova, Olga V.; Potma, Eric O.; Tromberg, Bruce J.

    2016-06-01

    Two-photon excited fluorescence (TPEF) imaging of the cellular cofactors nicotinamide adenine dinucleotide and oxidized flavin adenine dinucleotide is widely used to measure cellular metabolism, both in normal and pathological cells and tissues. When dual-wavelength excitation is used, ratiometric TPEF imaging of the intrinsic cofactor fluorescence provides a metabolic index of cells-the "optical redox ratio" (ORR). With increased interest in understanding and controlling cellular metabolism in cancer, there is a need to evaluate the performance of ORR in malignant cells. We compare TPEF metabolic imaging with seahorse flux analysis of cellular oxygen consumption in two different breast cancer cell lines (MCF-7 and MDA-MB-231). We monitor metabolic index in living cells under both normal culture conditions and, for MCF-7, in response to cell respiration inhibitors and uncouplers. We observe a significant correlation between the TPEF-derived ORR and the flux analyzer measurements (R=0.7901, p<0.001). Our results confirm that the ORR is a valid dynamic index of cell metabolism under a range of oxygen consumption conditions relevant for cancer imaging.

  17. Metabolic control analysis of the penicillin biosynthetic pathway: the influence of the LLD-ACV:bisACV ratio on the flux control.

    PubMed

    Theilgaard, H A; Nielsen, J

    1999-01-01

    An extended kinetic model for the first two steps of the penicillin biosynthetic pathway in Penicillium chrysogenum is set up. It includes the formation and reduction of the dimer bis-delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine (bisACV) from the first pathway intermediate LLD-ACV and their parallel inhibition of the enzyme ACV synthetase (ACVS). The kinetic model is based on Michaelis-Menten type kinetics, with non-competitive inhibition of the ACVS by both LLD-ACV and bisACV, and competitive inhibition of the isopenicillin N synthetase (IPNS) by glutathione. The inhibition constant of LLD-ACV, KACV is determined to be 0.54 mm. With the kinetic model metabolic control analysis is performed to identify the distribution of rate-control in the pathway at all ratios of LLD-ACV:bisACV. It is concluded that the flux control totally resides at the IPNS. This is a result of the regulation of the ACVS by both the LLD-ACV and bisACV demanding a higher flux through the IPNS enzyme to alleviate their inhibition. The measurement of an intracellular ratio of LLD-ACV:bisACV to be in the range of 1-2 moles per moles emphasises the importance of a fast conversion of LLD-ACV to IPN, and accumulation of LLD-ACV above the K(m)-value of the IPNS should therefore be avoided.

  18. Metabolomics-on-a-chip and metabolic flux analysis for label-free modeling of the internal metabolism of HepG2/C3A cells.

    PubMed

    Ouattara, Djomangan Adama; Prot, Jean-Matthieu; Bunescu, Andrei; Dumas, Marc-Emmanuel; Elena-Herrmann, Bénédicte; Leclerc, Eric; Brochot, Céline

    2012-07-01

    In vitro microfluidic systems are increasingly used as an alternative to standard Petri dishes in bioengineering and metabolomic investigations, as they are expected to provide cellular environments close to the in vivo conditions. In this work, we combined the recently developed "metabolomics-on-a-chip" approach with metabolic flux analysis to model the metabolic network of the hepatoma HepG2/C3A cell line and to infer the distribution of intracellular metabolic fluxes in standard Petri dishes and microfluidic biochips. A high pyruvate reduction to lactate was observed in both systems, suggesting that the cells operate in oxygen-limited environments. Our results also indicate that HepG2/C3A cells in the biochip are characterized by a higher consumption rate of oxygen, presumably due to a higher oxygenation rate in the microfluidic environment. This leads to a higher entry of the ultimate glycolytic product, acetyl-CoA, into the Krebs cycle. These findings are supported by the transcriptional activity of HepG2/C3A cells in both systems since we observed that genes regulated by a HIF-1 (hypoxia-regulated factor-1) transcriptional factor were over expressed under the Petri conditions, but to a lesser extent in the biochip. PMID:22618574

  19. Soil erosion and sediment fluxes analysis: a watershed study of the Ni Reservoir, Spotsylvania County, VA, USA.

    PubMed

    Pope, Ian C; Odhiambo, Ben K

    2014-03-01

    Anthropogenic forces that alter the physical landscape are known to cause significant soil erosion, which has negative impact on surface water bodies, such as rivers, lakes/reservoirs, and coastal zones, and thus sediment control has become one of the central aspects of catchment management planning. The revised universal soil loss equation empirical model, erosion pins, and isotopic sediment core analyses were used to evaluate watershed erosion, stream bank erosion, and reservoir sediment accumulation rates for Ni Reservoir, in central Virginia. Land-use and land cover seems to be dominant control in watershed soil erosion, with barren land and human-disturbed areas contributing the most sediment, and forest and herbaceous areas contributing the least. Results show a 7 % increase in human development from 2001 (14 %) to 2009 (21.6 %), corresponding to an increase in soil loss of 0.82 Mg ha(-1) year(-1) in the same time period. (210)Pb-based sediment accumulation rates at three locations in Ni Reservoir were 1.020, 0.364, and 0.543 g cm(-2) year(-1) respectively, indicating that sediment accumulation and distribution in the reservoir is influenced by reservoir configuration and significant contributions from bedload. All three locations indicate an increase in modern sediment accumulation rates. Erosion pin results show variability in stream bank erosion with values ranging from 4.7 to 11.3 cm year(-1). These results indicate that urban growth and the decline in vegetative cover has increased sediment fluxes from the watershed and poses a significant threat to the long-term sustainability of the Ni Reservoir as urbanization continues to increase.

  20. IMFIT Integrated Modeling Applications Supporting Experimental Analysis: Multiple Time-Slice Kinetic EFIT Reconstructions, MHD Stability Limits, and Energy and Momentum Flux Analyses

    NASA Astrophysics Data System (ADS)

    Collier, A.; Lao, L. L.; Abla, G.; Chu, M. S.; Prater, R.; Smith, S. P.; St. John, H. E.; Guo, W.; Li, G.; Pan, C.; Ren, Q.; Park, J. M.; Bisai, N.; Srinivasan, R.; Sun, A. P.; Liu, Y.; Worrall, M.

    2010-11-01

    This presentation summarizes several useful applications provided by the IMFIT integrated modeling framework to support DIII-D and EAST research. IMFIT is based on Python and utilizes modular task-flow architecture with a central manager and extensive GUI support to coordinate tasks among component modules. The kinetic-EFIT application allows multiple time-slice reconstructions by fetching pressure profile data directly from MDS+ or from ONETWO or PTRANSP. The stability application analyzes a given reference equilibrium for stability limits by performing parameter perturbation studies with MHD codes such as DCON, GATO, ELITE, or PEST3. The transport task includes construction of experimental energy and momentum fluxes from profile analysis and comparison against theoretical models such as MMM95, GLF23, or TGLF.

  1. Flux analysis of the Lactobacillus reuteri propanediol-utilization pathway for production of 3-hydroxypropionaldehyde, 3-hydroxypropionic acid and 1,3-propanediol from glycerol

    PubMed Central

    2014-01-01

    Background Lactobacillus reuteri converts glycerol to 3-hydroxypropionic acid (3HP) and 1,3-propanediol (1,3PDO) via 3-hydroxypropionaldehyde (3HPA) as an intermediate using enzymes encoded in its propanediol-utilization (pdu) operon. Since 3HP, 1,3PDO and 3HPA are important building blocks for the bio-based chemical industry, L. reuteri can be an attractive candidate for their production. However, little is known about the kinetics of glycerol utilization in the Pdu pathway in L. reuteri. In this study, the metabolic fluxes through the Pdu pathway were determined as a first step towards optimizing the production of 3HPA, and co-production of 3HP and 1,3PDO from glycerol. Resting cells of wild-type (DSM 20016) and recombinant (RPRB3007, with overexpressed pdu operon) strains were used as biocatalysts. Results The conversion rate of glycerol to 3HPA by the resting cells of L. reuteri was evaluated by in situ complexation of the aldehyde with carbohydrazide to avoid the aldehyde-mediated inactivation of glycerol dehydratase. Under operational conditions, the specific 3HPA production rate of the RPRB3007 strain was 1.9 times higher than that of the wild-type strain (1718.2 versus 889.0 mg/gCDW.h, respectively). Flux analysis of glycerol conversion to 1,3PDO and 3HP in the cells using multi-step variable-volume fed-batch operation showed that the maximum specific production rates of 3HP and 1,3PDO were 110.8 and 93.7 mg/gCDW.h, respectively, for the wild-type strain, and 179.2 and 151.4 mg/gCDW.h, respectively, for the RPRB3007 strain. The cumulative molar yield of the two compounds was ~1 mol/mol glycerol and their molar ratio was ~1 mol3HP/mol1,3PDO. A balance of redox equivalents between the glycerol oxidative and reductive pathway branches led to equimolar amounts of the two products. Conclusions Metabolic flux analysis was a useful approach for finding conditions for maximal conversion of glycerol to 3HPA, 3HP and 1,3PDO. Improved specific production rates were

  2. Analysis of leaf area index in the ECMWF land surface model and impact on latent heat and carbon fluxes: Application to West Africa

    NASA Astrophysics Data System (ADS)

    Jarlan, L.; Balsamo, G.; Lafont, S.; Beljaars, A.; Calvet, J. C.; Mougin, E.

    2008-12-01

    A new version of the land surface model of the European Centre for Medium-Range Weather Forecasts (Carbon-TESSEL, or CTESSEL) includes a vegetation growth model. This study describes a leaf area index (LAI) data assimilation system (LDAS) based on CTESSEL and satellite LAI for operational Net Ecosystem Exchange (NEE) predictions. The LDAS is evaluated over West Africa. A preliminary experiment shows a significant impact of the LAI on the CTESSEL NEE. The LAI is compared to two satellite products: the predicted annual cycle is delayed over the Sahel and savannah, and the LAI values differ from the satellite products. Preliminary to their use in the LDAS, the LAI products are rescaled to the CTESSEL predictions. The LDAS simulations are confronted to measurements of biomass and LAI for a site in Mali. The LAI analysis is shown to improve the predicted biomass and the annual cycles of the water (latent heat flux, or LE) and carbon (NEE) fluxes. Afterward, the LDAS is run over West Africa with the Moderate-Resolution Imaging Spectroradiometer products (2001-2005). The analysis of LAI shows a limited impact on LE, but it impacts strongly on NEE. Finally, the CTESSEL NEE are compared to two other models' outputs (simple biosphere (SIB) and Carnegie-Ames-Stanford (CASA)). The order of magnitude of the three data sets agrees well, and the shift in annual cycle of CTESSEL is reduced by the LDAS. It is concluded that a LAI data assimilation system is essential for NEE prediction at seasonal and interannual timescales, while a LAI satellite-based climatology may be sufficient for accurate LE predictions.

  3. Fast flux module detection using matroid theory.

    PubMed

    Reimers, Arne C; Bruggeman, Frank J; Olivier, Brett G; Stougie, Leen

    2015-05-01

    Flux balance analysis (FBA) is one of the most often applied methods on genome-scale metabolic networks. Although FBA uniquely determines the optimal yield, the pathway that achieves this is usually not unique. The analysis of the optimal-yield flux space has been an open challenge. Flux variability analysis is only capturing some properties of the flux space, while elementary mode analysis is intractable due to the enormous number of elementary modes. However, it has been found by Kelk et al. (2012) that the space of optimal-yield fluxes decomposes into flux modules. These decompositions allow a much easier but still comprehensive analysis of the optimal-yield flux space. Using the mathematical definition of module introduced by Müller and Bockmayr (2013b), we discovered useful connections to matroid theory, through which efficient algorithms enable us to compute the decomposition into modules in a few seconds for genome-scale networks. Using that every module can be represented by one reaction that represents its function, in this article, we also present a method that uses this decomposition to visualize the interplay of modules. We expect the new method to replace flux variability analysis in the pipelines for metabolic networks. PMID:25565150

  4. Analysis of energy fluxes and vegetation-atmosphere parameters in irrigated and natural ecosystems of semi-arid Brazil

    NASA Astrophysics Data System (ADS)

    Teixeira, A. H. de Castro; Bastiaanssen, W. G. M.; Ahmad, M. D.; Moura, M. S. B.; Bos, M. G.

    2008-11-01

    SummaryKnowledge on evapotranspiration is essential in quantifying water use depletion and to allocate scarce water resources to competing uses. Despite that an extensive literature describes the theoretical mechanisms of turbulent water vapour transport above and within crop canopies fewer studies have examined land surface parameters within composite landscapes of irrigated crops and semi-arid natural vegetation. Aiming to improve parameterizations of the radiation and energy balance in irrigated crops and natural vegetation, micro-climatic measurements were carried out on irrigated land (vineyards and mango orchard) and natural vegetation (caatinga) in the semi-arid zone of the São Francisco River basin (Brazil) from 2002 to 2005. The fractions of 24 h incident solar radiation available for net radiation were 46%, 55%, 51% and 53%, for wine grape, table grape, mango orchard and caatinga, respectively. Daily evaporative fractions of the net available energy used as latent heat flux ( λE) were 0.80, 0.88, 0.75 and 0.33 respectively. The daylight values of bulk surface resistances ( rs) averaged 128 s m -1, 73 s m -1, 133 s m -1 and 1940 s m -1 for wine grape, table grape, mango orchard and caatinga, respectively. Simplified parameterizations on roughness and evaporation resistances were performed. It could be concluded that net radiation can be estimated by means of a linear expression with incident global solar radiation depending on the type of vegetation. The variability of aerodynamic resistance ( ra) could be mainly explained by the friction velocity ( u ∗) which on turn depends on the surface roughness length for momentum transport ( z 0m). The experimental data showed that for sparse canopies z 0m being 9% of the mean vegetation height is a doable operational rule for the semi-arid region of São Francisco River basin. The seasonal values of rs for irrigated crops were highly correlated with water vapour pressure deficit. The availability of analytical

  5. 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.

    PubMed

    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

  6. Comparative Analysis of Genomics and Proteomics in the New Isolated Bacillus thuringiensis X022 Revealed the Metabolic Regulation Mechanism of Carbon Flux Following Cu2+ Treatment

    PubMed Central

    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

  7. Physiological characterization of recombinant Saccharomyces cerevisiae expressing the Aspergillus nidulans phosphoketolase pathway: validation of activity through 13C-based metabolic flux analysis.

    PubMed

    Papini, Marta; Nookaew, Intawat; Siewers, Verena; Nielsen, Jens

    2012-08-01

    Several bacterial species and filamentous fungi utilize the phosphoketolase pathway (PHK) for glucose dissimilation as an alternative to the Embden-Meyerhof-Parnas pathway. In Aspergillus nidulans, the utilization of this metabolic pathway leads to increased carbon flow towards acetate and acetyl CoA. In the first step of the PHK, the pentose phosphate pathway intermediate xylulose-5-phosphate is converted into acetylphosphate and glyceraldehyde-3-phosphate through the action of xylulose-5-phosphate phosphoketolase, and successively acetylphosphate is converted into acetate by the action of acetate kinase. In the present work, we describe a metabolic engineering strategy used to express the fungal genes of the phosphoketolase pathway in Saccharomyces cerevisiae and the effects of the expression of this recombinant route in yeast. The phenotype of the engineered yeast strain MP003 was studied during batch and chemostat cultivations, showing a reduced biomass yield and an increased acetate yield during batch cultures. To establish whether the observed effects in the recombinant strain MP003 were due directly or indirectly to the expression of the phosphoketolase pathway, we resolved the intracellular flux distribution based on (13)C labeling during chemostat cultivations. From flux analysis it is possible to conclude that yeast is able to use the recombinant pathway. Our work indicates that the utilization of the phosphoketolase pathway does not interfere with glucose assimilation through the Embden-Meyerhof-Parnas pathway and that the expression of this route can contribute to increase the acetyl CoA supply, therefore holding potential for future metabolic engineering strategies having acetyl CoA as precursor for the biosynthesis of industrially relevant compounds.

  8. Concentration, flux, and the analysis of trends of total and dissolved phosphorus, total nitrogen, and chloride in 18 tributaries to Lake Champlain, Vermont and New York, 1990–2011

    USGS Publications Warehouse

    Medalie, Laura

    2013-01-01

    Annual concentration, flux, and yield for total phosphorus, dissolved phosphorus, total nitrogen, and chloride for 18 tributaries to Lake Champlain were estimated for 1990 through 2011 using a weighted regression method based on time, tributary streamflows (discharges), and seasonal factors. The weighted regression method generated two series of daily estimates of flux and concentration during the period of record: one based on observed discharges and a second based on a flow-normalization procedure that removes random variation due to year-to-year climate-driven effects. The flownormalized estimate for a given date is similar to an average estimate of concentration or flux that would be made if all of the observed discharges for that date were equally likely to have occurred. The flux bias statistic showed that 68 of the 72 flux regression models were minimally biased. Temporal trends in the concentrations and fluxes were determined by calculating percent changes in flow-normalized annual fluxes for the full period of analysis (1990 through 2010) and for the decades 1990–2000 and 2000–2010. Basinwide, flow-normalized total phosphorus flux decreased by 42 metric tons per year (t/yr) between 1990 and 2010. This net result reflects a basinwide decrease in flux of 21 metric tons (t) between 1990 and 2000, followed by a decrease of 20 t between 2000 and 2010; both results were largely influenced by flux patterns in the large tributaries on the eastern side of the basin. A comparison of results for total phosphorus for the two separate decades of analysis found that more tributaries had decreasing concentrations and flux rates in the second decade than the first. An overall reduction in dissolved phosphorus flux of 0.7 t/yr was seen in the Lake Champlain Basin during the full period of analysis. That very small net change in flux reflects substantial reductions between 1990 and 2000 from eastern tributaries, especially in Otter Creek and the LaPlatte and Winooski

  9. Patterns of Flux Emergence

    NASA Astrophysics Data System (ADS)

    Title, A.; Cheung, M.

    2008-05-01

    The high spatial resolution and high cadence of the Solar Optical Telescope on the JAXA Hinode spacecraft have allowed capturing many examples of magnetic flux emergence from the scale of granulation to active regions. The observed patterns of emergence are quite similar. Flux emerges as a array of small bipoles on scales from 1 to 5 arc seconds throughout the region that the flux eventually condenses. Because the fields emerging from the underlying flux rope my appear many in small segments and the total flux (absolute sum) is not a conserved quantity the amount of total flux on the surface may vary significantly during the emergence process. Numerical simulations of flux emergence exhibit patterns similar to observations. Movies of both observations and numerical simulations will be presented.

  10. Convective and large-scale mass flux profiles over tropical oceans determined from synergistic analysis of a suite of satellite observations

    NASA Astrophysics Data System (ADS)

    Masunaga, Hirohiko; Luo, Zhengzhao Johnny

    2016-07-01

    A new, satellite-based methodology is developed to evaluate convective mass flux and large-scale total mass flux. To derive the convective mass flux, candidate profiles of in-cloud vertical velocity are first constructed with a simple plume model under the constraint of ambient sounding and then narrowed down to the solution that matches satellite-derived cloud top buoyancy. Meanwhile, the large-scale total mass flux is provided separately from satellite soundings by a method developed previously. All satellite snapshots are sorted into a composite time series that delineates the evolution of a vigorous and organized convective system. Principal findings are the following. First, convective mass flux is modulated primarily by convective cloud cover, with the intensity of individual convection being less variable over time. Second, convective mass flux dominates the total mass flux only during the early hours of the convective evolution; as convective system matures, a residual mass flux builds up in the mass flux balance that is reminiscent of stratiform dynamics. The method developed in this study is expected to be of unique utility for future observational diagnosis of tropical convective dynamics and for evaluation of global climate model cumulus parameterizations in a global sense.

  11. Clarifying the regulation of NO/N2O production in Nitrosomonas europaea during anoxic-oxic transition via flux balance analysis of a metabolic network model.

    PubMed

    Perez-Garcia, Octavio; Villas-Boas, Silas G; Swift, Simon; Chandran, Kartik; Singhal, Naresh

    2014-09-01

    The metabolic mechanism regulating the production of nitric and nitrous oxide (NO, N2O) in ammonia oxidizing bacteria (AOB) was characterized by flux balance analysis (FBA) of a stoichiometric metabolic network (SMN) model. The SMN model was created using 51 reactions and 44 metabolites of the energy metabolism in Nitrosomonas europaea, a widely studied AOB. FBA of model simulations provided estimates for reaction rates and yield ratios of intermediate metabolites, substrates, and products. These estimates matched well, deviating on average by 15% from values for 17 M yield ratios reported for non-limiting oxygen and ammonium concentrations. A sensitivity analysis indicated that the reactions catalysed by cytochromes aa3 and P460 principally regulate the pathways of NO and N2O production (hydroxylamine oxidoreductase mediated and nitrifier denitrification). FBA of simulated N. europaea exposure to oxic-anoxic-oxic transition indicated that NO and N2O production primarily resulted from an intracellular imbalance between the production and consumption of electron equivalents during NH3 oxidation, and that NO and N2O are emitted when the sum of their production rates is greater than half the rate of NO oxidation by cytochrome P460.

  12. Statistical analysis of solar EUV and X-ray flux enhancements induced by solar flares and its implication to upper atmosphere

    NASA Astrophysics Data System (ADS)

    Le, Huijun; Liu, Libo; He, Han; Wan, Weixing

    2011-11-01

    The 0.1-0.8 nm X-ray flux data and 26-34 nm EUV flux data are used to statistically analyze the relationship between enhancement in X-ray flux and that in EUV flux during solar flares in 1996-2006. The EUV enhancement does not linearly increase with X-ray flux from C-class to X-class flares. Its uprising amplitude decreases with X-ray flux. The correlation coefficients between enhancements in EUV and X-ray flux for X, M and C-class flares are only 0.66, 0.58 and 0.54, respectively, which suggests that X-ray flux is not a good index for EUV flux during solar flares. Thus, for studying more accurately solar flare effect on the ionosphere/thermosphere system, one needs to use directly EUV flux measurements. One of important reasons for depressing relationship between X-ray and EUV is that the central meridian distance (CMD) of flare location can significantly affect EUV flux variation particularly for X-class flares: the larger value of CMD results in the smaller EUV enhancement. However, there are much smaller CMD effects on EUV enhancement for M and C-class flares. The solar disc images from SOHO/EIT are utilized to estimate the percentage contribution to total EUV enhancement from the flare region and from other region. The results show the larger percentage contribution from other region for the weaker flares, which would reduce the loss of EUV radiation due to limb location of flare and then weaken the CMD effect for weaker flares like M and C-class.

  13. Concentration, flux, and the analysis of trends of total and dissolved phosphorus, total nitrogen, and chloride in 18 tributaries to Lake Champlain, Vermont and New York, 1990–2011

    USGS Publications Warehouse

    Medalie, Laura

    2013-01-01

    Annual concentration, flux, and yield for total phosphorus, dissolved phosphorus, total nitrogen, and chloride for 18 tributaries to Lake Champlain were estimated for 1990 through 2011 using a weighted regression method based on time, tributary streamflows (discharges), and seasonal factors. The weighted regression method generated two series of daily estimates of flux and concentration during the period of record: one based on observed discharges and a second based on a flow-normalization procedure that removes random variation due to year-to-year climate-driven effects. The flownormalized estimate for a given date is similar to an average estimate of concentration or flux that would be made if all of the observed discharges for that date were equally likely to have occurred. The flux bias statistic showed that 68 of the 72 flux regression models were minimally biased. Temporal trends in the concentrations and fluxes were determined by calculating percent changes in flow-normalized annual fluxes for the full period of analysis (1990 through 2010) and for the decades 1990–2000 and 2000–2010. Basinwide, flow-normalized total phosphorus flux decreased by 42 metric tons per year (t/yr) between 1990 and 2010. This net result reflects a basinwide decrease in flux of 21 metric tons (t) between 1990 and 2000, followed by a decrease of 20 t between 2000 and 2010; both results were largely influenced by flux patterns in the large tributaries on the eastern side of the basin. A comparison of results for total phosphorus for the two separate decades of analysis found that more tributaries had decreasing concentrations and flux rates in the second decade than the first. An overall reduction in dissolved phosphorus flux of 0.7 t/yr was seen in the Lake Champlain Basin during the full period of analysis. That very small net change in flux reflects substantial reductions between 1990 and 2000 from eastern tributaries, especially in Otter Creek and the LaPlatte and Winooski

  14. Conception and development of a bibliographic database of blood nutrient fluxes across organs and tissues in ruminants: data gathering and management prior to meta-analysis.

    PubMed

    Vernet, Jean; Ortigues-Marty, Isabelle

    2006-01-01

    In the organism, nutrient exchanges among tissues and organs are subject to numerous sources of physiological or nutritional variation, and the contribution of individual factors needs to be quantified before establishing general response laws. To achieve this, meta-analysis of data from publications is a useful tool. The objective of this work was to develop a bibliographic database of nutrient fluxes across organs and tissues of ruminant animals (Flora) under Access using the Merise method. The most important criteria for Flora were the ease to relate the various information, the exhaustivity and the accuracy of the data input, a complete description of the diets, taking into account the methods of the methodological procedures of measurement and analysis of blood nutrients and the traceability of the information. The conceptual data model was built in 6 parts. The first part describes the authors and source of publication, and the person in charge of data input. It clearly separates and identifies the experiments, the groups of animals and the treatments within a publication. The second part is concerned with feeds, diets and their chemical composition and nutritional value. The third and fourth parts describe the infusion of any substrates and the methods employed, respectively. The fifth part is devoted to the results of blood flows and nutrient fluxes. The sixth part gathers miscellaneous experimental information. All these parts are inter-connected. To model this database, the Merise method was utilised and 26 entities and 32 relationships were created. At the physical level, 93 tables were created, corresponding, for the majority, to entities and relationships of the data model. They were divided into reference tables (n = 65) and data tables (n = 28). Data processing was developed in Flora and included the control of the data, generic calculations of unknown data from given data, the automation of the estimation of the missing data or the chemical

  15. Dynamics of multiple flux tubes in sawtoothing KSTAR plasmas heated by electron cyclotron waves: I. Experimental analysis of the tube structure

    NASA Astrophysics Data System (ADS)

    Choe, G. H.; Yun, G. S.; Nam, Y.; Lee, W.; Park, H. K.; Bierwage, A.; Domier, C. W.; Luhmann, N. C., Jr.; Jeong, J. H.; Bae, Y. S.; the KSTAR Team

    2015-01-01

    Multiple (two or more) flux tubes are commonly observed inside and/or near the q = 1 flux surface in KSTAR tokamak plasmas with localized electron cyclotron resonance heating and current drive (ECH/CD). Detailed 2D and quasi-3D images of the flux tubes obtained by an advanced imaging diagnostic system showed that the flux tubes are m/n = 1/1 field-aligned structures co-rotating around the magnetic axis. The flux tubes typically merge together and become like the internal kink mode of the usual sawtooth, which then collapses like a usual sawtooth crash. A systematic scan of ECH/CD beam position showed a strong correlation with the number of flux tubes. In the presence of multiple flux tubes close to the q = 1 surface, the radially outward heat transport was enhanced, which explains naturally temporal changes of electron temperature. We emphasize that the multiple flux tubes are a universal feature distinct from the internal kink instability and play a critical role in the control of sawteeth using ECH/CD.

  16. Design and demonstration of an analysis Information system for magnetic flux leakage inspection of natural gas pipeline. Final letter report

    SciTech Connect

    Schuster, G.J.; Saffell, B.A.

    1996-10-01

    A staff exchange was conducted for the mutual benefit of the Department of Energy, the Gas Research Institute (GRI), Vetco Pipeline Services Inc. (VPSI), and the Pacific Northwest National Laboratory. This staff exchange provided direct exposure by a Laboratory staff member knowledgeable in inspection, integrity assessment, and robotic capabilities of the Laboratory to the needs of the natural gas pipeline industry. The project included an assignment to the GRI Pipeline Simulation Facility (PSF) during the period preceding the commissioning of the flow loop. GRI is interested in exploiting advanced technology at the National Laboratories. To provide a sense of the market impact, it is estimated that $3 billion was spent in 1993 for the repair, renovation, and replacement of distribution piping. GRI has goals of saving the distribution industry $500 million in Operations and Maintenance costs and having an additional $250M savings impact on transmission pipelines. The objectives of the project included: (1) For PNNL staff to present technology to GRI and PSF staff on non- destructive evaluation, robotics, ground penetrating radar, and risk based inspection guidelines for application to the operation and maintenance of natural gas pipelines. (2) For GRI and PSF staff to discuss with PNNL staff opportunities for improving the industrial competitiveness of operation and maintenance services. (3) To explore the basis for partnership with GRI and PSF staff on technology transfer topics. In this project, staff exchanges were conducted to GRI`s Pipeline Simulation Facility and to VPSI. PNNL . staff had access to the $10M GRI Pipeline Simulation Facility (PSF) at West Jefferson, Ohio. The facility has a 4,700-ft. long pipe loop, an NDE laboratory, and a data analysis laboratory. PNNL staff had access to the VPSI`s facility in Houston, TX. VPSI has developed some of the most sophisticated inspection tools currently used in the pipeline inspection industry.

  17. Do Australian sclerophyll forests exhibit seasonality? an analysis with phenocam, eddy covariance fluxes, and satellite derived phenology.

    NASA Astrophysics Data System (ADS)

    Restrepo-Coupe, N.; Huete, A. R.; Davies, K.; Macfarlane, C.; Beringer, J.; Van Gorsel, E.; Maier, C.; Resco de Dios, V.

    2014-12-01

    Temperate broadleaf evergreen forests in Australia exhibit characteristically unique and contradictory seasonality behaviors with strongly seasonal gross primary productivity (GPP) values and weak to no seasonality in satellite-derived vegetation indices (VIs), leaf area index (LAI), and fraction of absorbed photosynthetically active radiation (fPAR). As part of adaptation strategies to highly variable rainfall and water balance deficit conditions, sclerophyll forests allocate carbon to long-lived, thick leaves with low water content, and generally exhibit small seasonal changes in canopy infrastructure (LAI). Erectophile leaf angle distributions, and/or differences in leaf adaxial and abaxial optical properties allow the leaves to achieve thermal protection. However, these leaf traits complicate any spectral analysis and the study of sclerophyll forest phenology. Our goal was to utilize tower mounted phenocam imagery of whole-canopy, multiple tree crowns, and understory layers to trace multi-functional phenology profiles at three sclerophyll forest sites (one banksia dominated and two eucalyptus dominated) all part of the Terrestrial Ecosystem Research Network (TERN). We contrast and compare in-situ phenocam time series data with satellite vegetation products from the Moderate Resolution Imaging Spectroradiometer (MODIS), and eddy covariance measures of ecosystem built photosynthetic capacity (ecosystem light use efficiency, LUE, and chlorophyll fPAR). We found that at sclerophyll forests, despite ecosystem photosynthetic capacity exhibiting weak seasonality, climate and in particular rainfall pulses, drove diverse responses over each of the different forest components (e.g. overstory and understory). Interestingly, tree and understory growing and browning cycles were out-of phase, and contributed to the characteristic VI seasonality behavior of the whole ecosystem.

  18. Return flux experiment

    NASA Technical Reports Server (NTRS)

    Tveekrem, June L.

    1992-01-01

    All spacecraft emit molecules via outgassing, thruster plumes, vents, etc. The return flux is the portion of those molecules that scatter from the ambient atmosphere and return to the spacecraft. Return flux allows critical spacecraft surfaces to become contaminated even when there is no direct line of sight between the contamination source and the critical surface. Data from the Long Duration Exposure Facility (LDEF) show that contamination of LDEF surfaces could not have come entirely from direct flux. The data suggest significant return flux. Several computer models have been developed to simulate return flux, but the predictions have never been verified in orbit. Large uncertainties in predictions lead to overly conservative spacecraft designs. The purpose of the REturn FLux EXperiment (REFLEX) is to fly a controlled experiment that can be directly compared with predictions from several models.

  19. Return flux experiment

    NASA Astrophysics Data System (ADS)

    Tveekrem, June L.

    All spacecraft emit molecules via outgassing, thruster plumes, vents, etc. The return flux is the portion of those molecules that scatter from the ambient atmosphere and return to the spacecraft. Return flux allows critical spacecraft surfaces to become contaminated even when there is no direct line of sight between the contamination source and the critical surface. Data from the Long Duration Exposure Facility (LDEF) show that contamination of LDEF surfaces could not have come entirely from direct flux. The data suggest significant return flux. Several computer models have been developed to simulate return flux, but the predictions have never been verified in orbit. Large uncertainties in predictions lead to overly conservative spacecraft designs. The purpose of the REturn FLux EXperiment (REFLEX) is to fly a controlled experiment that can be directly compared with predictions from several models.

  20. Heat flux measurements

    NASA Technical Reports Server (NTRS)

    Liebert, Curt H.; Weikle, Donald H.

    1989-01-01

    A new automated, computer controlled heat flux measurement facility is described. Continuous transient and steady-state surface heat flux values varying from about 0.3 to 6 MW/sq m over a temperature range of 100 to 1200 K can be obtained in the facility. An application of this facility is the development of heat flux gauges for continuous fast transient surface heat flux measurement on turbine blades operating in space shuttle main engine turbopumps. The facility is useful for durability testing at fast temperature transients.

  1. Aspects of flux compactification

    NASA Astrophysics Data System (ADS)

    Liu, Tao

    In this thesis, we study three main aspects of flux compactifications: (1) classify supergravity solutions from flux compactification; (2) construct flux-deformed geometry and 4D low-energy theory to describe these flux vacua; and (3) study 4D particle phenomenology and cosmology of flux vacua. In the first part, we review G-structure, the basic tool to study supersymmetric flux solutions, and some typical solutions obtained in heterotic, type IIA and type IIB string theories. Then we present a comprehensive classification of supersymmetric vacua of M-theory compactification on 7D manifolds with general four-form fluxes. We analyze the cases where the resulting four-dimensional vacua have N = 1, 2, 3, 4 supersymmetry and the internal space allows for SU(2)-, SU(3)- or G 2-structures. In particular, we find for N = 2 supersymmetry, that the external space-time is Minkowski and the base manifold of the internal space is conformally Kahler for SU(2) structures, while for SU(3) structures the internal space has to be Einstein-Sasaki and no internal fluxes are allowed. Moreover, we provide a new vacuum with N = 1 supersymmetry and SU(3) structure, where all fluxes are non-zero and the first order differential equations are solved. In the second part, we simply review the methods used to construct one subclass of fluxed-deformed geometry or the so-called "twisted manifold", and the associated 4D effective theory describing these flux vacua. Then by employing (generalized) Scherk-Schwarz reduction, we construct the geometric twisting for Calabi-Yau manifolds of Voisin-Borcea type (K 3 x T2)/ Z2 and study the superpotential in a type IIA orientifold based on this geometry. The twists modify the direct product by fibering the K 3 over T2 while preserving the Z2 involution. As an important application, the Voisin-Borcea class contains T6/( Z2 x Z2 ), the usual setting for intersecting D6 brane model building. Past work in this context considered only those twists inherited

  2. Kinetic analysis of electron flux in cytochrome P450 reductases reveals differences in rate-determining steps in plant and mammalian enzymes.

    PubMed

    Whitelaw, Douglas A; Tonkin, Rochelle; Meints, Carla E; Wolthers, Kirsten R

    2015-10-15

    Herein, we compare the kinetic properties of CPR from Arabidopsis thaliana (ATR2), with CPR from Artemisia annua (aaCPR) and human CPR (hCPR). While all three CPR forms elicit comparable rates for cytochrome c(3+) turnover, NADPH reduction of the FAD cofactor is ∼50-fold faster in aaCPR and ATR2 compared to hCPR, with a kobs of ∼500 s(-1) (6 °C). Stopped-flow analysis of the isolated FAD-domains reveals that NADP(+)-FADH2 charge-transfer complex formation is also significantly faster in the plant enzymes, but the rate of its decay is comparable for all three proteins. In hCPR, transfer of a hydride ion from NADPH to FAD is tightly coupled to subsequent FAD to FMN electron transfer, indicating that the former catalytic event is slow relative to the latter. In contrast, interflavin electron transfer is slower than NADPH hydride transfer in aaCPR and ATR2, occurring with an observed rate constant of ∼50 s(-1). Finally, the transfer of electrons from FMN to cytochrome c(3+) is rapid (>10(3) s(-1)) in all three enzymes and does not limit catalytic turnover. In combination, the data reveal differences in rate-determining steps between plant CPR and their mammalian equivalent in mediating the flux of reducing equivalents from NADPH to external electron acceptors. PMID:26361974

  3. Video Meteor Fluxes

    NASA Technical Reports Server (NTRS)

    Campbell-Brown, M. D.; Braid, D.

    2011-01-01

    The flux of meteoroids, or number of meteoroids per unit area per unit time, is critical for calibrating models of meteoroid stream formation and for estimating the hazard to spacecraft from shower and sporadic meteors. Although observations of meteors in the millimetre to centimetre size range are common, flux measurements (particularly for sporadic meteors, which make up the majority of meteoroid flux) are less so. It is necessary to know the collecting area and collection time for a given set of observations, and to correct for observing biases and the sensitivity of the system. Previous measurements of sporadic fluxes are summarized in Figure 1; the values are given as a total number of meteoroids striking the earth in one year to a given limiting mass. The Gr n et al. (1985) flux model is included in the figure for reference. Fluxes for sporadic meteoroids impacting the Earth have been calculated for objects in the centimeter size range using Super-Schmidt observations (Hawkins & Upton, 1958); this study used about 300 meteors, and used only the physical area of overlap of the cameras at 90 km to calculate the flux, corrected for angular speed of meteors, since a large angular speed reduces the maximum brightness of the meteor on the film, and radiant elevation, which takes into account the geometric reduction in flux when the meteors are not perpendicular to the horizontal. They bring up corrections for both partial trails (which tends to increase the collecting area) and incomplete overlap at heights other than 90 km (which tends to decrease it) as effects that will affect the flux, but estimated that the two effects cancelled one another. Halliday et al. (1984) calculated the flux of meteorite-dropping fireballs with fragment masses greater than 50 g, over the physical area of sky accessible to the MORP fireball cameras, counting only observations in clear weather. In the micron size range, LDEF measurements of small craters on spacecraft have been used to

  4. LCLS Spectral Flux Viewer

    2005-10-25

    This application (FluxViewer) is a tool for displaying spectral flux data for the Linac Coherent Light Source (LCLS). This tool allows the user to view sliced spatial and energy distributions of the photons selected for specific energies and positions transverse to the beam axis.

  5. DETERMINATION OF AMMONIA MASS EMISSION FLUX FROM HOG WASTE EFFLUENT SPRAYING OPERATION USING OPEN PATH TUNABLE DIODE LASER SPECTROSCOPY WITH VERTICAL RADIAL PLUME MAPPING ANALYSIS

    EPA Science Inventory

    Emission of ammonia from concentrated animal feeding operations represents an increasingly important environmental issue. Determination of total ammonia mass emission flux from extended area sources such as waste lagoons and waste effluent spraying operations can be evaluated usi...

  6. Analysis of the effectiveness of ground-based VLF wave observations for predicting or nowcasting relativistic electron flux at geostationary orbit

    NASA Astrophysics Data System (ADS)

    Simms, Laura E.; Engebretson, Mark J.; Smith, A. J.; Clilverd, Mark; Pilipenko, Viacheslav; Reeves, Geoffrey D.

    2015-03-01

    Poststorm relativistic electron flux enhancement at geosynchronous orbit has shown correlation with very low frequency (VLF) waves measured by satellite in situ. However, our previous study found little correlation between electron flux and VLF measured by a ground-based instrument at Halley, Antarctica. Here we explore several possible explanations for this low correlation. Using 220 storms (1992-2002), our previous work developed a predictive model of the poststorm flux at geosynchronous orbit based on explanatory variables measured a day or two before the flux increase. In a nowcast model, we use averages of variables from the time period when flux is rising during the recovery phase of geomagnetic storms and limit the VLF (1.0 kHz) measure to the dawn period at Halley (09:00-12:00 UT). This improves the simple correlation of VLF wave intensity with flux, although the VLF effect in an overall multiple regression is still much less than that of other factors. When analyses are performed separately for season and interplanetary magnetic field (IMF) Bz orientation, VLF outweighs the influence of other factors only during winter months when IMF Bz is in an average northward orientation.

  7. Structural Control of Metabolic Flux

    PubMed Central

    Sajitz-Hermstein, Max; Nikoloski, Zoran

    2013-01-01

    Organisms have to continuously adapt to changing environmental conditions or undergo developmental transitions. To meet the accompanying change in metabolic demands, the molecular mechanisms of adaptation involve concerted interactions which ultimately induce a modification of the metabolic state, which is characterized by reaction fluxes and metabolite concentrations. These state transitions are the effect of simultaneously manipulating fluxes through several reactions. While metabolic control analysis has provided a powerful framework for elucidating the principles governing this orchestrated action to understand metabolic control, its applications are restricted by the limited availability of kinetic information. Here, we introduce structural metabolic control as a framework to examine individual reactions' potential to control metabolic functions, such as biomass production, based on structural modeling. The capability to carry out a metabolic function is determined using flux balance analysis (FBA). We examine structural metabolic control on the example of the central carbon metabolism of Escherichia coli by the recently introduced framework of functional centrality (FC). This framework is based on the Shapley value from cooperative game theory and FBA, and we demonstrate its superior ability to assign “share of control” to individual reactions with respect to metabolic functions and environmental conditions. A comparative analysis of various scenarios illustrates the usefulness of FC and its relations to other structural approaches pertaining to metabolic control. We propose a Monte Carlo algorithm to estimate FCs for large networks, based on the enumeration of elementary flux modes. We further give detailed biological interpretation of FCs for production of lactate and ATP under various respiratory conditions. PMID:24367246

  8. Intramolecular Nuclear Flux Densities

    NASA Astrophysics Data System (ADS)

    Barth, I.; Daniel, C.; Gindensperger, E.; Manz, J.; PéRez-Torres, J. F.; Schild, A.; Stemmle, C.; Sulzer, D.; Yang, Y.

    The topic of this survey article has seen a renaissance during the past couple of years. Here we present and extend the results for various phenomena which we have published from 2012-2014, with gratitude to our coauthors. The new phenomena include (a) the first reduced nuclear flux densities in vibrating diatomic molecules or ions which have been deduced from experimental pump-probe spectra; these "experimental" nuclear flux densities reveal several quantum effects including (b) the "quantum accordion", i.e., during the turn from bond stretch to bond compression, the diatomic system never stands still — instead, various parts of it with different bond lengths flow into opposite directions. (c) Wavepacket interferometry has been extended from nuclear densities to flux densities, again revealing new phenomena: For example, (d) a vibrating nuclear wave function with compact initial shape may split into two partial waves which run into opposite directions, thus causing interfering flux densities. (e) Tunneling in symmetric 1-dimensional double-well systems yields maximum values of the associated nuclear flux density just below the potential barrier; this is in marked contrast with negligible values of the nuclear density just below the barrier. (f) Nuclear flux densities of pseudorotating nuclei may induce huge magnetic fields. A common methodologic theme of all topics is the continuity equation which connects the time derivative of the nuclear density to the divergence of the flux density, subject to the proper boundary conditions. (g) Nearly identical nuclear densities with different boundary conditions may be related to entirely different flux densities, e.g., during tunneling in cyclic versus non-cyclic systems. The original continuity equation, density and flux density of all nuclei, or of all nuclear degrees of freedom, may be reduced to the corresponding quantities for just a single nucleus, or just a single degree of freedom.

  9. Elucidating Rice Cell Metabolism under Flooding and Drought Stresses Using Flux-Based Modeling and Analysis1[C][W][OPEN

    PubMed Central

    Lakshmanan, Meiyappan; Zhang, Zhaoyang; Mohanty, Bijayalaxmi; Kwon, Jun-Young; Choi, Hong-Yeol; Nam, Hyung-Jin; Kim, Dong-Il; Lee, Dong-Yup

    2013-01-01

    Rice (Oryza sativa) is one of the major food crops in world agriculture, especially in Asia. However, the possibility of subsequent occurrence of flood and drought is a major constraint to its production. Thus, the unique behavior of rice toward flooding and drought stresses has required special attention to understand its metabolic adaptations. However, despite several decades of research investigations, the cellular metabolism of rice remains largely unclear. In this study, in order to elucidate the physiological characteristics in response to such abiotic stresses, we reconstructed what is to our knowledge the first metabolic/regulatory network model of rice, representing two tissue types: germinating seeds and photorespiring leaves. The phenotypic behavior and metabolic states simulated by the model are highly consistent with our suspension culture experiments as well as previous reports. The in silico simulation results of seed-derived rice cells indicated (1) the characteristic metabolic utilization of glycolysis and ethanolic fermentation based on oxygen availability and (2) the efficient sucrose breakdown through sucrose synthase instead of invertase. Similarly, flux analysis on photorespiring leaf cells elucidated the crucial role of plastid-cytosol and mitochondrion-cytosol malate transporters in recycling the ammonia liberated during photorespiration and in exporting the excess redox cofactors, respectively. The model simulations also unraveled the essential role of mitochondrial respiration during drought stress. In the future, the combination of experimental and in silico analyses can serve as a promising approach to understand the complex metabolism of rice and potentially help in identifying engineering targets for improving its productivity as well as enabling stress tolerance. PMID:23753178

  10. Directed flux motor

    NASA Technical Reports Server (NTRS)

    Wilson, Andrew (Inventor); Punnoose, Andrew (Inventor); Strausser, Katherine (Inventor); Parikh, Neil (Inventor)

    2011-01-01

    A directed flux motor described utilizes the directed magnetic flux of at least one magnet through ferrous material to drive different planetary gear sets to achieve capabilities in six actuated shafts that are grouped three to a side of the motor. The flux motor also utilizes an interwoven magnet configuration which reduces the overall size of the motor. The motor allows for simple changes to modify the torque to speed ratio of the gearing contained withi