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Sample records for 13c-metabolic flux analysis

  1. Non-stationary (13)C-metabolic flux ratio analysis.

    PubMed

    Hörl, Manuel; Schnidder, Julian; Sauer, Uwe; Zamboni, Nicola

    2013-12-01

    (13)C-metabolic flux analysis ((13)C-MFA) has become a key method for metabolic engineering and systems biology. In the most common methodology, fluxes are calculated by global isotopomer balancing and iterative fitting to stationary (13)C-labeling data. This approach requires a closed carbon balance, long-lasting metabolic steady state, and the detection of (13)C-patterns in a large number of metabolites. These restrictions mostly reduced the application of (13)C-MFA to the central carbon metabolism of well-studied model organisms grown in minimal media with a single carbon source. Here we introduce non-stationary (13)C-metabolic flux ratio analysis as a novel method for (13)C-MFA to allow estimating local, relative fluxes from ultra-short (13)C-labeling experiments and without the need for global isotopomer balancing. The approach relies on the acquisition of non-stationary (13)C-labeling data exclusively for metabolites in the proximity of a node of converging fluxes and a local parameter estimation with a system of ordinary differential equations. We developed a generalized workflow that takes into account reaction types and the availability of mass spectrometric data on molecular ions or fragments for data processing, modeling, parameter and error estimation. We demonstrated the approach by analyzing three key nodes of converging fluxes in central metabolism of Bacillus subtilis. We obtained flux estimates that are in agreement with published results obtained from steady state experiments, but reduced the duration of the necessary (13)C-labeling experiment to less than a minute. These results show that our strategy enables to formally estimate relative pathway fluxes on extremely short time scale, neglecting cellular carbon balancing. Hence this approach paves the road to targeted (13)C-MFA in dynamic systems with multiple carbon sources and towards rich media. PMID:23860906

  2. 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

  3. Fluxomers: a new approach for 13C metabolic flux analysis

    PubMed Central

    2011-01-01

    Background The ability to perform quantitative studies using isotope tracers and metabolic flux analysis (MFA) is critical for detecting pathway bottlenecks and elucidating network regulation in biological systems, especially those that have been engineered to alter their native metabolic capacities. Mathematically, MFA models are traditionally formulated using separate state variables for reaction fluxes and isotopomer abundances. Analysis of isotope labeling experiments using this set of variables results in a non-convex optimization problem that suffers from both implementation complexity and convergence problems. Results This article addresses the mathematical and computational formulation of 13C MFA models using a new set of variables referred to as fluxomers. These composite variables combine both fluxes and isotopomer abundances, which results in a simply-posed formulation and an improved error model that is insensitive to isotopomer measurement normalization. A powerful fluxomer iterative algorithm (FIA) is developed and applied to solve the MFA optimization problem. For moderate-sized networks, the algorithm is shown to outperform the commonly used 13CFLUX cumomer-based algorithm and the more recently introduced OpenFLUX software that relies upon an elementary metabolite unit (EMU) network decomposition, both in terms of convergence time and output variability. Conclusions Substantial improvements in convergence time and statistical quality of results can be achieved by applying fluxomer variables and the FIA algorithm to compute best-fit solutions to MFA models. We expect that the fluxomer formulation will provide a more suitable basis for future algorithms that analyze very large scale networks and design optimal isotope labeling experiments. PMID:21846358

  4. 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

  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. Parallel labeling experiments validate Clostridium acetobutylicum metabolic network model for (13)C metabolic flux analysis.

    PubMed

    Au, Jennifer; Choi, Jungik; Jones, Shawn W; Venkataramanan, Keerthi P; Antoniewicz, Maciek R

    2014-11-01

    In this work, we provide new insights into the metabolism of Clostridium acetobutylicum ATCC 824 obtained using a systematic approach for quantifying fluxes based on parallel labeling experiments and (13)C-metabolic flux analysis ((13)C-MFA). Here, cells were grown in parallel cultures with [1-(13)C]glucose and [U-(13)C]glucose as tracers and (13)C-MFA was used to quantify intracellular metabolic fluxes. Several metabolic network models were compared: an initial model based on current knowledge, and extended network models that included additional reactions that improved the fits of experimental data. While the initial network model did not produce a statistically acceptable fit of (13)C-labeling data, an extended network model with five additional reactions was able to fit all data with 292 redundant measurements. The model was subsequently trimmed to produce a minimal network model of C. acetobutylicum for (13)C-MFA, which could still reproduce all of the experimental data. The flux results provided valuable new insights into the metabolism of C. acetobutylicum. First, we found that TCA cycle was effectively incomplete, as there was no measurable flux between α-ketoglutarate and succinyl-CoA, succinate and fumarate, and malate and oxaloacetate. Second, an active pathway was identified from pyruvate to fumarate via aspartate. Third, we found that isoleucine was produced exclusively through the citramalate synthase pathway in C. acetobutylicum and that CAC3174 was likely responsible for citramalate synthase activity. These model predictions were confirmed in several follow-up tracer experiments. The validated metabolic network model established in this study can be used in future investigations for unbiased (13)C-flux measurements in C. acetobutylicum. PMID:25183671

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

    PubMed Central

    2011-01-01

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

  9. 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.

  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. 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/ PMID:23893473

  12. (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. PMID:26318243

  13. 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

  14. 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

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

    DOE PAGESBeta

    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

  16. 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

  17. 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.

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

    PubMed

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

    2016-09-01

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

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

    PubMed

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

    2012-12-01

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

  20. 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

  1. 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

  2. 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

  3. Non-stationary 13C metabolic flux analysis of Chinese hamster ovary cells in batch culture using extracellular labeling highlights metabolic reversibility and compartmentation

    PubMed Central

    2014-01-01

    Background Mapping the intracellular fluxes for established mammalian cell lines becomes increasingly important for scientific and economic reasons. However, this is being hampered by the high complexity of metabolic networks, particularly concerning compartmentation. Results Intracellular fluxes of the CHO-K1 cell line central carbon metabolism were successfully determined for a complex network using non-stationary 13C metabolic flux analysis. Mass isotopomers of extracellular metabolites were determined using [U-13C6] glucose as labeled substrate. Metabolic compartmentation and extracellular transport reversibility proved essential to successfully reproduce the dynamics of the labeling patterns. Alanine and pyruvate reversibility changed dynamically even if their net production fluxes remained constant. Cataplerotic fluxes of cytosolic phosphoenolpyruvate carboxykinase and mitochondrial malic enzyme and pyruvate carboxylase were successfully determined. Glycolytic pyruvate channeling to lactate was modeled by including a separate pyruvate pool. In the exponential growth phase, alanine, glycine and glutamate were excreted, and glutamine, aspartate, asparagine and serine were taken up; however, all these amino acids except asparagine were exchanged reversibly with the media. High fluxes were determined in the pentose phosphate pathway and the TCA cycle. The latter was fueled mainly by glucose but also by amino acid catabolism. Conclusions The CHO-K1 central metabolism in controlled batch culture proves to be robust. It has the main purpose to ensure fast growth on a mixture of substrates and also to mitigate oxidative stress. It achieves this by using compartmentation to control NADPH and NADH availability and by simultaneous synthesis and catabolism of amino acids. PMID:24773761

  4. 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

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

    PubMed

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

    2016-09-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  7. 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. PMID:27342798

  8. 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

  9. ¹³C-metabolic flux analysis for Escherichia coli.

    PubMed

    Matsuoka, Yu; Shimizu, Kazuyuki

    2014-01-01

    (13)C-Metabolic flux analysis ((13)C-MFA) is used here to study the effects of the knockout of such genes as pgi, zwf, gnd, ppc, pck, pyk, and lpdA on the metabolic changes in Escherichia coli cultivated under aerobic condition. The metabolic regulation mechanisms were clarified by integrating such information as fermentation data, gene expression, enzyme activities, and metabolite concentrations as well the result of (13)C-MFA. PMID:25178796

  10. Simultaneous imaging of 13C metabolism and 1H structure: technical considerations and potential applications.

    PubMed

    Gordon, Jeremy W; Fain, Sean B; Niles, David J; Ludwig, Kai D; Johnson, Kevin M; Peterson, Eric T

    2015-05-01

    Real-time imaging of (13)C metabolism in vivo has been enabled by recent advances in hyperpolarization. As a result of the inherently low natural abundance of endogenous (13)C nuclei, hyperpolarized (13)C images lack structural information that could be used to aid in motion detection and anatomical registration. Motion before or during the (13)C acquisition can therefore result in artifacts and misregistration that may obscure measures of metabolism. In this work, we demonstrate a method to simultaneously image both (1)H and (13)C nuclei using a dual-nucleus spectral-spatial radiofrequency excitation and a fully coincident readout for rapid multinuclear spectroscopic imaging. With the appropriate multinuclear hardware, and the means to simultaneously excite and receive on both channels, this technique is straightforward to implement requiring little to no increase in scan time. Phantom and in vivo experiments were performed with both Cartesian and spiral trajectories to validate and illustrate the utility of simultaneous acquisitions. Motion compensation of dynamic metabolic measurements acquired during free breathing was demonstrated using motion tracking derived from (1)H data. Simultaneous multinuclear imaging provides structural (1)H and metabolic (13)C images that are correlated both spatially and temporally, and are therefore amenable to joint (1)H and (13)C analysis and correction of structure-function images. PMID:25810146

  11. 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

  12. 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

  13. 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.

  14. Isotopically nonstationary 13C flux analysis of Myc-induced metabolic reprogramming in B-cells

    PubMed Central

    Murphy, Taylor A.; Dang, Chi V.; Young, Jamey D.

    2012-01-01

    We assessed several methods of 13C metabolic flux analysis (MFA) and found that isotopically nonstationary MFA achieved maximum flux resolution in cultured P493-6 B-cells, which have been engineered to provide tunable expression of the Myc oncoprotein. Comparison of metabolic flux maps obtained under oncogenic (High) and endogenous (Low) Myc expression levels revealed network-wide reprogramming in response to ectopic Myc expression. High Myc cells relied more heavily on mitochondrial oxidative metabolism than Low Myc cells and globally upregulated their consumption of amino acids relative to glucose. TCA cycle and amphibolic mitochondrial pathways exhibited 2- to 4-fold flux increases in High Myc cells, in contrast to modest increases in glucose uptake and lactate excretion. Because our MFA approach relied exclusively upon isotopic measurements of protein-bound amino acids and RNA-bound ribose, it is readily applicable to more complex tumor models that are not amenable to direct extraction and isotopic analysis of free intracellular metabolites. PMID:22898717

  15. Proteome and carbon flux analysis of Pseudomonas aeruginosa clinical isolates from different infection sites.

    PubMed

    Lassek, Christian; Berger, Antje; Zühlke, Daniela; Wittmann, Christoph; Riedel, Katharina

    2016-05-01

    Pseudomonas aeruginosa is known as opportunistic pathogen frequently isolated from different infection sites. To investigate the expression rates of P. aeruginosa proteins commonly expressed by different clinical isolates, absolute protein quantities were determined employing a gel-free and data-independent LC-IMS(E) approach. Moreover, the metabolic diversity of these isolates was investigated by (13) C-metabolic flux analyses. 812 proteins were reproducibly identified and absolutely quantified for the reference strain P. aeruginosa PAO1, 363 of which were also identified and relatively quantified in all isolates. Whilst the majority of these proteins were expressed in constant amounts, expression rates of 42 proteins were highly variable between the isolates. Notably, the outer membrane protein OprH and the response regulator PhoP were strongly expressed in burned wounds isolates compared to lung/urinary tract isolates. Moreover, proteins involved in iron/amino acids uptake were found to be highly abundant in urinary tract isolates. The fluxome data revealed a conserved glycolysis, and a niche-specific divergence in fluxes through the glyoxylate shunt and the TCA cycle among the isolates. The integrated proteome/fluxome analysis did not indicate straightforward correlation between the protein amount and flux, but rather points to additional layers of regulation that mediate metabolic adaption of P. aeruginosa to different host environments. All MS data have been deposited in the ProteomeXchange with identifier PXD002373 (http://proteomecentral.proteomexchange.org/dataset/PXD002373). PMID:26959854

  16. 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. PMID:23954952

  17. 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.

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

    DOE PAGESBeta

    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

  19. 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

  20. Strategies for investigating the plant metabolic network with steady-state metabolic flux analysis: lessons from an Arabidopsis cell culture and other systems.

    PubMed

    Kruger, N J; Masakapalli, S K; Ratcliffe, R G

    2012-03-01

    Steady-state (13)C metabolic flux analysis (MFA) is currently the experimental method of choice for generating flux maps of the compartmented network of primary metabolism in heterotrophic and mixotrophic plant tissues. While statistically robust protocols for the application of steady-state MFA to plant tissues have been developed by several research groups, the implementation of the method is still far from routine. The effort required to produce a flux map is more than justified by the information that it contains about the metabolic phenotype of the system, but it remains the case that steady-state MFA is both analytically and computationally demanding. This article provides an overview of principles that underpin the implementation of steady-state MFA, focusing on the definition of the metabolic network responsible for redistribution of the label, experimental considerations relating to data collection, the modelling process that allows a set of metabolic fluxes to be deduced from the labelling data, and the interpretation of flux maps. The article draws on published studies of Arabidopsis cell cultures and other systems, including developing oilseeds, with the aim of providing practical guidance and strategies for handling the issues that arise when applying steady-state MFA to the complex metabolic networks encountered in plants. PMID:22140245

  1. 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

  2. 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

  3. 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

  4. 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

  5. Stochastic flux analysis of chemical reaction networks

    PubMed Central

    2013-01-01

    Background Chemical reaction networks provide an abstraction scheme for a broad range of models in biology and ecology. The two common means for simulating these networks are the deterministic and the stochastic approaches. The traditional deterministic approach, based on differential equations, enjoys a rich set of analysis techniques, including a treatment of reaction fluxes. However, the discrete stochastic simulations, which provide advantages in some cases, lack a quantitative treatment of network fluxes. Results We describe a method for flux analysis of chemical reaction networks, where flux is given by the flow of species between reactions in stochastic simulations of the network. Extending discrete event simulation algorithms, our method constructs several data structures, and thereby reveals a variety of statistics about resource creation and consumption during the simulation. We use these structures to quantify the causal interdependence and relative importance of the reactions at arbitrary time intervals with respect to the network fluxes. This allows us to construct reduced networks that have the same flux-behavior, and compare these networks, also with respect to their time series. We demonstrate our approach on an extended example based on a published ODE model of the same network, that is, Rho GTP-binding proteins, and on other models from biology and ecology. Conclusions We provide a fully stochastic treatment of flux analysis. As in deterministic analysis, our method delivers the network behavior in terms of species transformations. Moreover, our stochastic analysis can be applied, not only at steady state, but at arbitrary time intervals, and used to identify the flow of specific species between specific reactions. Our cases study of Rho GTP-binding proteins reveals the role played by the cyclic reverse fluxes in tuning the behavior of this network. PMID:24314153

  6. 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.

  7. '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.

  8. Software applications for flux balance analysis.

    PubMed

    Lakshmanan, Meiyappan; Koh, Geoffrey; Chung, Bevan K S; Lee, Dong-Yup

    2014-01-01

    Flux balance analysis (FBA) is a widely used computational method for characterizing and engineering intrinsic cellular metabolism. The increasing number of its successful applications and growing popularity are possibly attributable to the availability of specific software tools for FBA. Each tool has its unique features and limitations with respect to operational environment, user-interface and supported analysis algorithms. Presented herein is an in-depth evaluation of currently available FBA applications, focusing mainly on usability, functionality, graphical representation and inter-operability. Overall, most of the applications are able to perform basic features of model creation and FBA simulation. COBRA toolbox, OptFlux and FASIMU are versatile to support advanced in silico algorithms to identify environmental and genetic targets for strain design. SurreyFBA, WEbcoli, Acorn, FAME, GEMSiRV and MetaFluxNet are the distinct tools which provide the user friendly interfaces in model handling. In terms of software architecture, FBA-SimVis and OptFlux have the flexible environments as they enable the plug-in/add-on feature to aid prospective functional extensions. Notably, an increasing trend towards the implementation of more tailored e-services such as central model repository and assistance to collaborative efforts was observed among the web-based applications with the help of advanced web-technologies. Furthermore, most recent applications such as the Model SEED, FAME, MetaFlux and MicrobesFlux have even included several routines to facilitate the reconstruction of genome-scale metabolic models. Finally, a brief discussion on the future directions of FBA applications was made for the benefit of potential tool developers. PMID:23131418

  9. 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.

  10. FAME, the Flux Analysis and Modeling Environment

    PubMed Central

    2012-01-01

    Background The creation and modification of genome-scale metabolic models is a task that requires specialized software tools. While these are available, subsequently running or visualizing a model often relies on disjoint code, which adds additional actions to the analysis routine and, in our experience, renders these applications suboptimal for routine use by (systems) biologists. Results The Flux Analysis and Modeling Environment (FAME) is the first web-based modeling tool that combines the tasks of creating, editing, running, and analyzing/visualizing stoichiometric models into a single program. Analysis results can be automatically superimposed on familiar KEGG-like maps. FAME is written in PHP and uses the Python-based PySCeS-CBM for its linear solving capabilities. It comes with a comprehensive manual and a quick-start tutorial, and can be accessed online at http://f-a-m-e.org/. Conclusions With FAME, we present the community with an open source, user-friendly, web-based "one stop shop" for stoichiometric modeling. We expect the application will be of substantial use to investigators and educators alike. PMID:22289213

  11. 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

  12. Digital flux-gate magnetometer structural analysis

    NASA Astrophysics Data System (ADS)

    Korepanov, Valery; Berkman, Rikhard

    1999-08-01

    Analogue and digital structures of the flux-gate magnetometer are compared. The main disturbing factors in digital circuit were singled out and the additional errors associated with the digital structure are estimated. The reader's attention is drawn to some specific problems associated with digital circuits - the special influence of the unbalanced voltage amplitude at the flux-gate-sensor output and ADC-DAC switching-time instabilities. The given analytical results could be useful for the designer when it is necessary to make a choice of the structural type of magnetometer.

  13. Time series analysis of electron flux at geostationary orbit

    SciTech Connect

    Szita, S.; Rodgers, D.J.; Johnstone, A.D.

    1996-07-01

    Time series of energetic (42.9{endash}300 keV) electron flux data from the geostationary satellite Meteosat-3 shows variability over various timescales. Of particular interest are the strong local time dependence of the flux data and the large flux peaks associated with particle injection events which occur over a timescale of a few hours. Fourier analysis has shown that for this energy range, the average electron flux diurnal variation can be approximated by a combination of two sine waves with periods of 12 and 24 hours. The data have been further examined using wavelet analysis, which shows how the diurnal variation changes and where it appears most significant. The injection events have a characteristic appearance but do not occur in phase with one another and therefore do not show up in a Fourier spectrum. Wavelet analysis has been used to look for characteristic time scales for these events. {copyright} {ital 1996 American Institute of Physics.}

  14. Metabolic flux analysis of diterpene biosynthesis pathway in rice.

    PubMed

    Chang, Yung-Jin; Kim, Bo-Ra; Kim, Soo-Un

    2005-09-01

    Relative transcript levels of eight rice diterpene cyclases at the branch points of gibberellins and phytoalexins biosynthesis pathway were measured by reverse transcription quantitative PCR. Metabolic flux analysis by the distribution ratio of common substrate showed that UV-irradiation of etiolated rice seedlings decreased the flux for primary metabolism of gibberellins biosynthesis by half (from 62 to 27%) and 41% of geranylgeranyl pyrophosphate was used for induction of pimaradiene intermediate as the major phytoalexin. In comparison, light-illumination used almost all geranylgeranyl pyrophosphate (96%) for gibberellin biosynthesis to stimulate the plant growth and strongly repressed the metabolic flux for phytoalexins biosynthesis. PMID:16215852

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

    PubMed

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

    2011-11-01

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

  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. Towards dynamic metabolic flux analysis in CHO cell cultures.

    PubMed

    Ahn, Woo Suk; Antoniewicz, Maciek R

    2012-01-01

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

  18. 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.

  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. Dynamic flux balance analysis for synthetic microbial communities.

    PubMed

    Henson, Michael A; Hanly, Timothy J

    2014-10-01

    Dynamic flux balance analysis (DFBA) is an extension of classical flux balance analysis that allows the dynamic effects of the extracellular environment on microbial metabolism to be predicted and optimised. Recently this computational framework has been extended to microbial communities for which the individual species are known and genome-scale metabolic reconstructions are available. In this review, the authors provide an overview of the emerging DFBA approach with a focus on two case studies involving the conversion of mixed hexose/pentose sugar mixtures by synthetic microbial co-culture systems. These case studies illustrate the key requirements of the DFBA approach, including the incorporation of individual species metabolic reconstructions, formulation of extracellular mass balances, identification of substrate uptake kinetics, numerical solution of the coupled linear program/differential equations and model adaptation for common, suboptimal growth conditions and identified species interactions. The review concludes with a summary of progress to date and possible directions for future research. PMID:25257022

  1. Structural analysis of metabolic networks based on flux centrality.

    PubMed

    Koschützki, Dirk; Junker, Björn H; Schwender, Jörg; Schreiber, Falk

    2010-08-01

    Metabolic reactions are fundamental to living organisms, and a large number of reactions simultaneously occur at a given time in living cells transforming diverse metabolites into each other. There has been an ongoing debate on how to classify metabolites with respect to their importance for metabolic performance, usually based on the analysis of topological properties of genome scale metabolic networks. However, none of these studies have accounted quantitatively for flux in metabolic networks, thus lacking an important component of a cell's biochemistry. We therefore analyzed a genome scale metabolic network of Escherichia coli by comparing growth under 19 different growth conditions, using flux balance analysis and weighted network centrality investigation. With this novel concept of flux centrality we generated metabolite rankings for each particular growth condition. In contrast to the results of conventional analysis of genome scale metabolic networks, different metabolites were top-ranking dependent on the growth condition. At the same time, several metabolites were consistently among the high ranking ones. Those are associated with pathways that have been described by biochemists as the most central part of metabolism, such as glycolysis, tricarboxylic acid cycle and pentose phosphate pathway. The values for the average path length of the analyzed metabolite networks were between 10.5 and 12.6, supporting recent findings that the metabolic network of E. coli is not a small-world network. PMID:20471988

  2. Metabolic fluxes in Corynebacterium glutamicum during lysine production with sucrose as carbon source.

    PubMed

    Wittmann, Christoph; Kiefer, Patrick; Zelder, Oskar

    2004-12-01

    Metabolic fluxes in the central metabolism were determined for lysine-producing Corynebacterium glutamicum ATCC 21526 with sucrose as a carbon source, providing an insight into molasses-based industrial production processes with this organism. For this purpose, 13C metabolic flux analysis with parallel studies on [1-(13C)Fru]sucrose, [1-(13C)Glc]sucrose, and [13C6Fru]sucrose was carried out. C. glutamicum directed 27.4% of sucrose toward extracellular lysine. The strain exhibited a relatively high flux of 55.7% (normalized to an uptake flux of hexose units of 100%) through the pentose phosphate pathway (PPP). The glucose monomer of sucrose was completely channeled into the PPP. After transient efflux, the fructose residue was mainly taken up by the fructose-specific phosphotransferase system (PTS) and entered glycolysis at the level of fructose-1,6-bisphosphate. Glucose-6-phosphate isomerase operated in the gluconeogenetic direction from fructose-6-phosphate to glucose-6-phosphate and supplied additional carbon (7.2%) from the fructose part of the substrate toward the PPP. This involved supply of fructose-6-phosphate from the fructose part of sucrose either by PTS(Man) or by fructose-1,6-bisphosphatase. C. glutamicum further exhibited a high tricarboxylic acid (TCA) cycle flux of 78.2%. Isocitrate dehydrogenase therefore significantly contributed to the total NADPH supply of 190%. The demands for lysine (110%) and anabolism (32%) were lower than the supply, resulting in an apparent NADPH excess. The high TCA cycle flux and the significant secretion of dihydroxyacetone and glycerol display interesting targets to be approached by genetic engineers for optimization of the strain investigated. PMID:15574927

  3. Partitioning Carbon Dioxide and Water Vapor Fluxes Using Correlation Analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Partitioning of eddy covariance flux measurements is routinely done to quantify the contributions of separate processes to the overall fluxes. Measurements of carbon dioxide fluxes represent the difference between gross ecosystem photosynthesis and total respiration, while measurements of water vapo...

  4. A high heat flux experiment for verification of thermostructural analysis

    NASA Technical Reports Server (NTRS)

    Gladden, Herbert J.; Melis, Matthew E.

    1988-01-01

    A major concern in advancing the state of the art technologies for hypersonic vehicles is the development of an aeropropulsion system capable of handling the high heat fluxes during flight. The leading edges of such systems must not only tolerate the maximum heating rates, but must also minimize distortions to the flow field due to excessive blunting and/or thermal warping of the compression surface to achieve the high inlet performance required. A combined analytical and experimental effort to study the aerothermodynamic loads on actively cooled structures for hypersonic applications was established. A hydrogen/oxygen rocket engine was modified to establish a high enthalpy high heat flux environment. The facility provides heat flux levels from about 200 up to 10000 Btu/sq ft/sec. Cross flow and parallel flow regeneratively cooled model can be tested and analyzed by using cooling fluids of water and hydrogen. Results are presented of the experiment and the characteristics of the Hot Gas Test Facility. The predicted temperature results of the cross flow model are compared with the experimental data on the first monolithic specimens and are found to be in good agreement. Thermal stress analysis results are also presented.

  5. Dissolved organic nitrogen in precipitation: Collection, analysis and atmospheric flux

    SciTech Connect

    Scudlark, J.R.; Church, T.M.; Russell, K.M.; Montag, J.A.; Maben, J.R.; Keene, W.C.; Galloway, J.N.

    1995-12-31

    Recent studies have documented the importance of atmosphere inorganic nitrogen deposition to coastal waters. However, due to the limited number of field measurements and concerns about the reliability of measurement techniques, the aeolian flux of organic N is very uncertain. Coordinated studies have been initiated at Lewes, DE and Charlottesville, VA to evaluate collection and analysis techniques for dissolved organic nitrogen (DON) in precipitation and to provide preliminary estimate of DON wet fluxes. Sampling was conducted both manually and employing an automated wet-only collector (ACM) on a daily basis. A total of 37 events were analyzed from October 1993 through December 1994. Side-by-side comparisons of standard white HDPE buckets and stainless steel and glass collection vessels indicate sampling artifacts associate with plastic buckets. DON in precipitation appears to be highly labile, with significant losses observed in some samples within 12 hours. Analytical methods evaluated include persulfate wet chemical oxidation, UV photo-oxidation and a modified high temperature instrumental (ANTEK 7000) technique. Based on preliminary results, the volume-weighted average concentration of DON in precipitation at the mid-Atlantic coast is 9.1 {micro}moles/1. On an annual basis, DON compromises 23% of the total dissolved nitrogen in precipitation, varying from 0--64% on an event basis. From an ecological perspective, DON wet flux represents a quantitatively important exogenous source of N to coastal waters such as Chesapeake Bay.

  6. 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.

  7. Wavelet analysis of solar wind ion flux fluctuations.

    NASA Astrophysics Data System (ADS)

    Astaf'eva, N. M.; Zastenker, G. N.; Ehjges, P. E.

    1996-08-01

    The authors analyse solar wind ion flux data measured by Monitor instrument at satellite Prognoz-8: the set about 30 - 70 h duration with 10, 24 s time-resolution and the set about 3 - 10 h with 1.28 s resolution. They present power spectra and results of wavelet analysis. They determine the set of temporal (from 11 h to 20 s) or spatial (from 17×106 to 10×103km) scales which may be typical for two processes: Alfvén waves and convective structures moving from upper corona of the Sun.

  8. Analysis of experiments on stainless steel flux welds

    SciTech Connect

    Wilkowski, G.; Ahmad, J.; Brust, F.; Guerrieri, D.; Kramer, G.; Kulhowvick, G.; Landow, M.; Marschall, C.; Nakagaki, M.; Papaspyropoulos, V.

    1987-04-01

    This report describes experimental and analytical efforts to evaluate fracture of stainless steel flux-welded pipe. Seven pipe fracture experiments (four with through-wall circumferential cracks and three with circumferential internal surface cracks) were conducted at 550/sup 0/F (288/sup 0/C). Material characterization efforts involved laboratory specimen tests to assess specimen size effects, effects of solution-annealing, and crack-growth behavior in the HAZ, along the fusion line, and in the weld metal. Efforts involved assessing the net-section-collapse analysis, the plastic-zone screening criterion, inherent safety margins in the IWB-3640 flux weld analysis, through-wall-cracked pipe predictive J-estimation schemes for LBB analyses, eta-factor J-R curves calculated from the pipe experiments for comparison to C(T) specimen results, and finite element analysis of C(T) specimens and one pipe experiment. This report also evaluates the technical significance of these results and their significance relative to licensing decisions.

  9. Multiresolution Analysis and Prediction of Solar Magnetic Flux

    NASA Astrophysics Data System (ADS)

    Wik, Magnus

    Synoptic maps of the solar magnetic field provide an important visualization of the global transport and evolution of the large-scale magnetic flux. The solar dynamo picture is dependent on both the spatial and time resolution. It is therefore interesting to study the solar magnetic activity for many resolutions at the same time. A multi-resolution analysis gives us the possibility to study the synoptic solar magnetic fields for several resolutions at the same time. In this study we have first carried out a wavelet based multiresolution analysis (MRA) of the longitudinally averaged photospheric synoptic magnetograms. Magnetograms of Wilcox Solar Observatory (WSO), Stanford and of Michelson Doppler Imager (MDI) onboard SOHO of ESA/NASA were used. WSO data enabled a study of cycle 21,22 and 23 and MDI data a more detailed study of cycle 23. The result reveals a complex picture of the solar magnetic activity on different scales. For resolutions around 1-2 years and 6-7 years we observe strong transports of fluxes to the polar regions. Around 11 years we observe a very regular pattern which resembles a wave from the polar to the sunspot regions. We also see that a large range of latitudes vary in phase. A large asymmetry between solar northern and southern hemispheres is also seen. We have also developed a multilayer back propagation neural network for prediction of the solar magnetic flux. The inputs to the model are the polar and sunspot magnetic field in WSO longitudinally averaged solar magnetic fields.

  10. Metabolic network analysis of lysine producing Corynebacterium glutamicum at a miniaturized scale.

    PubMed

    Wittmann, Christoph; Kim, Hyung Min; Heinzle, Elmar

    2004-07-01

    We present a straightforward approach comprising (13)C tracer experiments at 200-microL volume in 96-well microtiter plates with on-line measurement of dissolved oxygen for quantitative high-throughput metabolic network analysis at a miniaturized scale. This method was successfully applied for cultivation and (13)C metabolic flux analysis of two mutants of lysine producing Corynebacterium glutamicum (ATCC 13287 and ATCC 21543). Microtiter-plate cultivations showed excellent accordance in kinetics and stoichiometry of growth and product formation as well as in intracellular flux distributions as compared with parallel shake-flask experiments. These cultivations further allowed clear identification of strain-specific flux differences such as increased flux toward lysine, increased flux through the pentose phosphate pathway (PPP), decreased flux through the tricarboxylic (TCA) cycle, and increased dihydroxyacetone formation in C. glutamicum ATCC 21543 compared with ATCC 13287. The present approach has strong potential for broad quantitative screening of metabolic network activities, especially those involving high-cost tracer substrates. PMID:15211482

  11. Metabolic flux analysis of the halophilic archaeon Haladaptatus paucihalophilus.

    PubMed

    Liu, Guangxiu; Zhang, Manxiao; Mo, Tianlu; He, Lian; Zhang, Wei; Yu, Yi; Zhang, Qi; Ding, Wei

    2015-11-27

    This work reports the (13)C-assisted metabolic flux analysis of Haladaptatus paucihalophilus, a halophilic archaeon possessing an intriguing osmoadaption mechanism. We showed that the carbon flow is through the oxidative tricarboxylic acid (TCA) cycle whereas the reductive TCA cycle is not operative in H. paucihalophilus. In addition, both threonine and the citramalate pathways contribute to isoleucine biosynthesis, whereas lysine is synthesized through the diaminopimelate pathway and not through the α-aminoadipate pathway. Unexpected, the labeling patterns of glycine from the cells grown on [1-(13)C]pyruvate and [2-(13)C]pyruvate suggest that, unlike all the organisms investigated so far, in which glycine is produced exclusively from the serine hydroxymethyltransferase (SHMT) pathway, glycine biosynthesis in H. paucihalophilus involves different pathways including SHMT, threonine aldolase (TA) and the reverse reaction of glycine cleavage system (GCS), demonstrating for the first time that other pathways instead of SHMT can also make a significant contribution to the cellular glycine pool. Transcriptional analysis confirmed that both TA and GCS genes were transcribed in H. paucihalophilus, and the transcriptional level is independent of salt concentrations in the culture media. This study expands our understanding of amino acid biosynthesis and provides valuable insights into the metabolism of halophilic archaea. PMID:26441084

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

    PubMed Central

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

    2015-01-01

    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. PMID:25754258

  13. Amplified expression of fructose 1,6-bisphosphatase in Corynebacterium glutamicum increases in vivo flux through the pentose phosphate pathway and lysine production on different carbon sources.

    PubMed

    Becker, Judith; Klopprogge, Corinna; Zelder, Oskar; Heinzle, Elmar; Wittmann, Christoph

    2005-12-01

    The overexpression of fructose 1,6-bisphosphatase (FBPase) in Corynebacterium glutamicum leads to significant improvement of lysine production on different sugars. Amplified expression of FBPase via the promoter of the gene encoding elongation factor TU (EFTU) increased the lysine yield in the feedback-deregulated lysine-producing strain C. glutamicum lysCfbr by 40% on glucose and 30% on fructose or sucrose. Additionally formation of the by-products glycerol and dihydroxyacetone was significantly reduced in the PEFTUfbp mutant. As revealed by 13C metabolic flux analysis on glucose the overexpression of FBPase causes a redirection of carbon flux from glycolysis toward the pentose phosphate pathway (PPP) and thus leads to increased NADPH supply. Normalized to an uptake flux of glucose of 100%, the relative flux into the PPP was 56% for C. glutamicum lysCfbr PEFTUfbp and 46% for C. glutamicum lysCfbr. The flux for NADPH supply was 180% in the PEFTUfbp strain and only 146% in the parent strain. Amplification of FBPase increases the production of lysine via an increased supply of NADPH. Comparative studies with another mutant containing the sod promoter upstream of the fbp gene indicate that the expression level of FBPase relates to the extent of the metabolic effects. The overexpression of FBPase seems useful for starch- and molasses-based industrial lysine production with C. glutamicum. The redirection of flux toward the PPP should also be interesting for the production of other NADPH-demanding compounds as well as for products directly stemming from the PPP. PMID:16332851

  14. Isotopomer Spectral Analysis: Utilizing Nonlinear Models in Isotopic Flux Studies.

    PubMed

    Kelleher, Joanne K; Nickol, Gary B

    2015-01-01

    We present the principles underlying the isotopomer spectral analysis (ISA) method for evaluating biosynthesis using stable isotopes. ISA addresses a classic conundrum encountered in the use of radioisotopes to estimate biosynthesis rates whereby the information available is insufficient to estimate biosynthesis. ISA overcomes this difficulty capitalizing on the additional information available from the mass isotopomer labeling profile of a polymer. ISA utilizes nonlinear regression to estimate the two unknown parameters of the model. A key parameter estimated by ISA represents the fractional contribution of the tracer to the precursor pool for the biosynthesis, D. By estimating D in cells synthesizing lipids, ISA quantifies the relative importance of two distinct pathways for flux of glutamine to lipid, reductive carboxylation, and glutaminolysis. ISA can also evaluate the competition between different metabolites, such as glucose and acetoacetate, as precursors for lipogenesis and thereby reveal regulatory properties of the biosynthesis pathway. The model is flexible and may be expanded to quantify sterol biosynthesis allowing tracer to enter the pathway at three different positions, acetyl CoA, acetoacetyl CoA, and mevalonate. The nonlinear properties of ISA provide a method of testing for the presence of gradients of precursor enrichment illustrated by in vivo sterol synthesis. A second ISA parameter provides the fraction of the polymer that is newly synthesized over the time course of the experiment. In summary, ISA is a flexible framework for developing models of polymerization biosynthesis providing insight into pools and pathway that are not easily quantified by other techniques. PMID:26358909

  15. 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.

  16. 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.

  17. 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%).

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Dimensional Analysis of Thermoelectric Modules Under Constant Heat Flux

    NASA Astrophysics Data System (ADS)

    Suzuki, Ryosuke O.; Fujisaka, Takeyuki; Ito, Keita O.; Meng, Xiangning; Sui, Hong-Tao

    2015-01-01

    Thermoelectric power generation is examined in the case of radiative heating. A constant heat flux is assumed in addition to consideration of the Seebeck effect, Peltier effect, and Joule heating with temperature-dependent material properties. Numerical evaluations are conducted using a combination of the finite-volume method and an original simultaneous solver for the heat transfer, thermoelectric, and electric transportation phenomena. Comparison with experimental results shows that the new solver could work well in the numerical calculations. The calculations predict that the Seebeck effect becomes larger for longer thermoelectric elements because of the larger temperature difference. The heat transfer to the cold surface is critical to determine the junction temperatures under a constant heat flux from the hot surface. The negative contribution from Peltier cooling and heating can be minimized when the current is smaller for longer elements. Therefore, a thicker TE module can generate more electric power even under a constant heat flux.

  3. 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...

  4. A Preliminary Low-Frequency Electromagnetic Analysis of a Flux Concentrator

    SciTech Connect

    Mayhall, D J

    2006-06-07

    The objective of this investigation was to conduct a quick, preliminary transient magnetostatic analysis of a Brechna-type[1] flux concentrator to determine its feasibility for collecting positrons in the International Linear Collider. The magnetostatic transient module of Maxwell 3D, Version 10, from the Ansoft Corporation was used to model the flux concentrator.

  5. 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.

  6. 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

  7. Geomagnetic field analysis. IV - Testing the frozen-flux hypothesis

    NASA Astrophysics Data System (ADS)

    Bloxham, J.; Gubbins, D.

    1986-01-01

    Magnetic field models at the core-mantle boundary are presented for three epochs: 1959.5, 1969.5, and 1980.0. The hypothesis that the field has been frozen into the core fluid throughout this 20-yr time span is tested by comparing the changes in the flux integrals over the three epochs with error estimates for the field at the core surface. It is found that the hypothesis can be rejected with 95 percent confidence.

  8. Insights into primary metabolism in oilseeds from labeling and flux analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Labeling investigations along with metabolic flux analysis have enabled quantification of important cellular phenotypes. These descriptions have documented uses of enzymes in unique ways and characterized the contributions of pathways to oil, protein and carbohydrate compositions in seeds. The diffe...

  9. 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.

  10. Performance analysis of a PM motor by changing the magnitude and the path of flux

    NASA Astrophysics Data System (ADS)

    Lee, Hyung-Woo; Lee, Ki-Doek; Kim, Mi-Jung; Lee, Jae-Jun; Han, Jung-Ho; Jeong, Tae-Chul; Lee, Ho-Joon; Ryu, Gwang-Hyeon; Park, Hyun-Jong; Lee, Ju

    2013-01-01

    In an electric motor in which permanent magnets are used, the magnetic flux is caused by the magneto-motive force of the permanent magnets of the rotor and the stator winding wire, and the performance of the electric motor is determined by the scale of the magnetic flux and the magnetic circuit. This thesis is aimed at introducing electric motors in which permanent magnets are used and focuses on a performance analysis of said electric motors according to the scale of the magnetic flux and changes in the magnetic circuit. The analysis was carried out by separating the magnetic flux occurring at the stator winding wire into the magnetic flux of axis d and that of q axis, so that the impact of the magnetic flux on the performance of the electric motor could be analyzed. In addition, the impact of changes in the magnetic circuit, which were caused by the magnetic flux at the permanent magnet of the rotator, on the electric motor was analyzed. Finally, the results of the analysis were verified by performing experiments on a model made by using selected analysis results.

  11. Multiple Triangulation Analysis: another approach to determine the orientation of magnetic flux ropes

    NASA Astrophysics Data System (ADS)

    Zhou, X.-Z.; Zong, Q.-G.; Pu, Z. Y.; Fritz, T. A.; Dunlop, M. W.; Shi, Q. Q.; Wang, J.; Wei, Y.

    2006-07-01

    Another approach (Multiple Triangulation Analysis, MTA) is presented to determine the orientation of magnetic flux rope, based on 4-point measurements. A 2-D flux rope model is used to examine the accuracy of the MTA technique in a theoretical way. It is found that the precision of the estimated orientation is dependent on both the spacecraft separation and the constellation path relative to the flux rope structure. However, the MTA error range can be shown to be smaller than that of the traditional MVA technique. As an application to real Cluster data, several flux rope events on 26 January 2001 are analyzed using MTA, to obtain their orientations. The results are compared with the ones obtained by several other methods which also yield flux rope orientation. The estimated axis orientations are shown to be fairly close, suggesting the reliability of the MTA method.

  12. 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

  13. 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

  14. 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. PMID:23065402

  15. 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

  16. Numerical analysis of TDS spectra under high and low flux plasma exposure conditions

    NASA Astrophysics Data System (ADS)

    Grigorev, P.; Buzi, L.; Bakaeva, A.; Terentyev, D.; De Temmerman, G.; Van Oost, G.; Noterdaeme, J.-M.

    2016-02-01

    A recently developed numerical model, based on the dislocation-driven nucleation of gas bubbles, is used to analyse experimental results on deuterium retention in tungsten under ITER relevant plasma exposure conditions. Focus is placed on understanding the relation between exposure temperature and flux on primary features of thermal desorption spectra: peak positions and intensities of the desorption flux. The model allows one to relate the peak positions with the size of plasma induced deuterium bubbles and envisage exposure conditions (temperature and flux) for their formation. Based on the performed analysis, dedicated experimental conditions to validate the model are proposed.

  17. 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

  18. Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism

    PubMed Central

    Gatto, Francesco; Miess, Heike; Schulze, Almut; Nielsen, Jens

    2015-01-01

    Flux balance analysis is the only modelling approach that is capable of producing genome-wide predictions of gene essentiality that may aid to unveil metabolic liabilities in cancer. Nevertheless, a systemic validation of gene essentiality predictions by flux balance analysis is currently missing. Here, we critically evaluated the accuracy of flux balance analysis in two cancer types, clear cell renal cell carcinoma (ccRCC) and prostate adenocarcinoma, by comparison with large-scale experiments of gene essentiality in vitro. We found that in ccRCC, but not in prostate adenocarcinoma, flux balance analysis could predict essential metabolic genes beyond random expectation. Five of the identified metabolic genes, AGPAT6, GALT, GCLC, GSS, and RRM2B, were predicted to be dispensable in normal cell metabolism. Hence, targeting these genes may selectively prevent ccRCC growth. Based on our analysis, we discuss the benefits and limitations of flux balance analysis for gene essentiality predictions in cancer metabolism, and its use for exposing metabolic liabilities in ccRCC, whose emergent metabolic network enforces outstanding anabolic requirements for cellular proliferation. PMID:26040780

  19. 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.

  20. 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.

  1. An improved path flux analysis with multi generations method for mechanism reduction

    NASA Astrophysics Data System (ADS)

    Wang, Wei; Gou, Xiaolong

    2016-03-01

    An improved path flux analysis with a multi generations (IMPFA) method is proposed to eliminate unimportant species and reactions, and to generate skeletal mechanisms. The production and consumption path fluxes of each species at multiple reaction paths are calculated and analysed to identify the importance of the species and of the elementary reactions. On the basis of the indexes of each reaction path of the first, second, and third generations, the improved path flux analysis with two generations (IMPFA2) and improved path flux analysis with three generations (IMPFA3) are used to generate skeletal mechanisms that contain different numbers of species. The skeletal mechanisms are validated in the case of homogeneous autoignition and perfectly stirred reactor of methane and n-decane/air mixtures. Simulation results of the skeletal mechanisms generated by IMPFA2 and IMPFA3 are compared with those obtained by path flux analysis (PFA) with two and three generations, respectively. The comparisons of ignition delay times, final temperatures, and temperature dependence on flow residence time show that the skeletal mechanisms generated by the present IMPFA method are more accurate than those obtained by the PFA method, with almost the same number of species under a range of initial conditions. By considering the accuracy and computational efficiency, when using the IMPFA (or PFA) method, three generations may be the best choice for the reduction of large-scale detailed chemistry.

  2. 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.

  3. Nonlinear analysis of blood flux in human vessels.

    PubMed

    Bräuer, K; Hahn, M

    1999-07-01

    Laser Doppler fluxmetry (LDF) is frequently used in research on microcirculation of blood. Usually LDF time series are analysed by conventional linear methods, mainly Fourier analysis. These methods may not be optimal for the investigation of nonlinear effects of vasomotion, heartbeat or vessels. Nonlinear methods are based on a reconstruction of the system trajectory in an embedding space describing not only the measured time series but the behaviour of the whole system. The fill factor is a tool for displaying the main properties of this attractor in two dimensions and for determining diverse parameters for further analysis. A quantitative characterization of the system is possible by the distribution of correlation dimensions in the embedding space. The singular value decomposition (SVD) can be used to display and characterize individual degrees of freedom. These methods were applied to LDF time series from nine healthy controls and nine patients with Raynaud's phenomenon due to connective tissue disease. The fill factor and the SVD indicate qualitatively that in the controls vasomotion and heartbeat are the main influences on blood flow and act fairly independently of each other. In the patients there was a mixture of strong but irregular degrees of freedom. The mean and the maximal local correlation dimensions were significantly higher in the patient group. Nonlinear analysis of LDF time series provides additional information which cannot be detected using conventional approaches. PMID:10442708

  4. 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

  5. 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

  6. 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

  7. [Spectra and thermal analysis of the arc in activating flux plasma arc welding].

    PubMed

    Chai, Guo-Ming; Zhu, Yi-Feng

    2010-04-01

    In activating flux plasma arc welding the welding arc was analyzed by spectra analysis technique, and the welding arc temperature field was measured by the infrared sensing and computer image technique. The distribution models of welding arc heat flow density of activating flux PAW welding were developed. The composition of welding arc affected by activated flux was studied, and the welding arc temperature field was studied. The results show that the spectral lines of argon atom and ionized argon atom of primary ionization are the main spectra lines of the conventional plasma welding arc. The spectra lines of weld metal are inappreciable in the spectra lines of the conventional plasma welding arc. The gas particle is the main in the conventional plasma welding arc. The conventional plasma welding arc is gas welding arc. The spectra lines of argon atom and ionized argon atom of primary ionization are intensified in the activating flux plasma welding arc, and the spectra lines of Ti, Cr and Fe elements are found in the activating flux plasma welding arc. The welding arc temperature distribution in activating flux plasma arc welding is compact, the outline of the welding arc temperature field is narrow, the range of the welding arc temperature distribution is concentrated, the welding arc radial temperature gradient is large, and the welding arc radial temperature gradient shows normal Gauss distribution. PMID:20545181

  8. 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.

  9. Potassium Fluxes in Chlamydomonas reinhardtii (II. Compartmental Analysis).

    PubMed Central

    Malhotra, B.; Glass, ADM.

    1995-01-01

    42K+ and 86Rb+ were used to determine the subcellular distribution of potassium in Chlamydomonas reinhardtii by compartmental analysis. In both wild type and a mutant strain, three distinct compartments (referred to as I, II, and III) were apparent. Using 42K+, we found that these had half-lives for K+ exchange of 1.07 min, 12.8 min, and 2.9 h, respectively, in wild-type cells and 0.93 min, 14.7 min, and 9.8 h, respectively, for the mutants. Half-lives were not significantly different when 86Rb+ was used to trace K+. Compartments I and II probably correspond to the cell wall and cytoplasm, respectively. Based on the lack of a large central vacuole in Chlamydomonas, the effect of a dark pretreatment on the kinetic properties of compartment III and the similarity between the [K+] of compartment III and that of isolated chloroplasts, this slowly exchanging compartment was identified as the chloroplast. Growth of wild-type cells at 100 [mu]M (instead of 10 mM K+) caused no change of cytoplasmic [K+] but reduced chloroplast [K+] very substantially. The mutants failed to grow at 100 [mu]M K+. PMID:12228560

  10. 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.

  11. 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.

  12. 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

  13. Detection of stator winding faults in induction machines using flux and vibration analysis

    NASA Astrophysics Data System (ADS)

    Lamim Filho, P. C. M.; Pederiva, R.; Brito, J. N.

    2014-01-01

    This work aims at presenting the detection and diagnosis of electrical faults in the stator winding of three-phase induction motors using magnetic flux and vibration analysis techniques. A relationship was established between the main electrical faults (inter-turn short circuits and unbalanced voltage supplies) and the signals of magnetic flux and vibration, in order to identify the characteristic frequencies of those faults. The experimental results showed the efficiency of the conjugation of these techniques for detection, diagnosis and monitoring tasks. The results were undoubtedly impressive and can be adapted and used in real predictive maintenance programs in industries.

  14. 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

  15. 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

  16. 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

  17. 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

  18. Leonid Storm Flux Analysis from One Leonid Mac Video AL50R

    NASA Astrophysics Data System (ADS)

    Gural, Peter S.; Jenniskens, Peter

    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 are made for the optimal pointing directions for video camera meteor counts during future ground and airborne missions.

  19. 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.

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

    PubMed Central

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

    2007-01-01

    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

  1. 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

  2. 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

  3. Analysis of Material Interface Discontinuities and Superconvergent Fluxes in Finite Difference Theory

    NASA Astrophysics Data System (ADS)

    MacKinnon, R. J.; Carey, G. F.

    1988-03-01

    An analysis of material interface discontinuities is developed and applied in finite difference theory to determine mathematically rigorous averaging techniques for material properties. This result is compared with other averaging techniques, particularly harmonic averaging, which is often applied in practice. We also develop a class of formulas of high accuracy for post-processing the difference formula to compute derivatives (fluxes, stresses), and conduct supporting numerical studies.

  4. Photosensitivity in Smith-Lemli-Opitz syndrome: a flux balance analysis of altered metabolism.

    PubMed

    Eapen, Bell Raj

    2007-01-01

    Ultraviolet A photosensitivity is a debilitating symptom associated with the metabolic disorder Smith-Lemli-Opitz syndrome (SLOS). SLOS is a manifestation of the deficiency of 7-dehydrocholesterol reductase, an enzyme involved in the cholesterol biosynthesis. As a result several abnormal intermediary compounds are formed among which Cholesta 5, 7, 9(11)-trien-3beta-ol is the most likely cause of photosensitivity. The effect of various drugs acting on cholesterol biosynthetic pathway on SLOS is not clear as clinical trials are not available for this rare disorder. A Flux Balance Analysis (FBA) has been carried out using the software CellNetAnalyzer or FluxAnalyzer to gain insight into the probable effects of various drugs acting on cholesterol biosynthetic pathway on photosensitivity in SLOS. The model consisted of 44 metabolites and 40 reactions. The formation flux of Cholesta 5, 7, 9(11)-trien-3beta-ol increased in SLOS and remained unchanged on simulation of the effect of miconazole and SR31747. However zaragozic acid can potentially reduce the flux through the entire pathway. FBA predicts zaragozic acid along with cholesterol supplementation as an effective treatment for photosensitivity in SLOS. PMID:18188427

  5. 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

  6. Flux analysis of cholesterol biosynthesis in vivo reveals multiple tissue and cell-type specific pathways

    PubMed Central

    Mitsche, Matthew A; McDonald, Jeffrey G; Hobbs, Helen H; Cohen, Jonathan C

    2015-01-01

    Two parallel pathways produce cholesterol: the Bloch and Kandutsch-Russell pathways. Here we used stable isotope labeling and isotopomer analysis to trace sterol flux through the two pathways in mice. Surprisingly, no tissue used the canonical K–R pathway. Rather, a hybrid pathway was identified that we call the modified K–R (MK–R) pathway. Proportional flux through the Bloch pathway varied from 8% in preputial gland to 97% in testes, and the tissue-specificity observed in vivo was retained in cultured cells. The distribution of sterol isotopomers in plasma mirrored that of liver. Sterol depletion in cultured cells increased flux through the Bloch pathway, whereas overexpression of 24-dehydrocholesterol reductase (DHCR24) enhanced usage of the MK–R pathway. Thus, relative use of the Bloch and MK–R pathways is highly variable, tissue-specific, flux dependent, and epigenetically fixed. Maintenance of two interdigitated pathways permits production of diverse bioactive sterols that can be regulated independently of cholesterol. DOI: http://dx.doi.org/10.7554/eLife.07999.001 PMID:26114596

  7. Power Law Regression Analysis of Heat Flux Width in Type I ELMs

    NASA Astrophysics Data System (ADS)

    Stephens, C. D.; Makowski, M. A.; Leonard, A. W.; Osborne, T. H.

    2014-10-01

    In this project, a database of Type I ELM characteristics has been assembled and will be used to investigate possible dependencies of the heat flux width on physics and engineering parameters. At the edge near the divertor, high impulsive heat loads are imparted onto the surface. The impact of these ELMs can cause a reduction in divertor lifetime if the heat flux is great enough due to material erosion. A program will be used to analyze data, extract relevant, measurable quantities, and record the quantities in the table. Care is taken to accurately capture the complex space/time structure of the ELM. Then correlations between discharge and equilibrium parameters will be investigated. Power law regression analysis will be used to help determine the dependence of the heat flux width on these various measurable quantities and parameters. This will enable us to better understand the physics of heat flux at the edge. Work supported in part by the National Undergraduate Fellowship Program in Plasma Physics and Fusion Energy Sciences and the US DOE under DE-FG02-04ER54761, DE-AC52-07NA27344, DE-FC02-04ER54698.

  8. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

    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.

  10. Stoichiometry Based Steady-State Hepatic Flux Analysis: Computational and Experimental Aspects

    PubMed Central

    Orman, Mehmet A.; Mattick, John; Androulakis, Ioannis P.; Berthiaume, Francois; Ierapetritou, Marianthi G.

    2012-01-01

    : The liver has many complex physiological functions, including lipid, protein and carbohydrate metabolism, as well as bile and urea production. It detoxifies toxic substances and medicinal products. It also plays a key role in the onset and maintenance of abnormal metabolic patterns associated with various disease states, such as burns, infections and major traumas. Liver cells have been commonly used in in vitro experiments to elucidate the toxic effects of drugs and metabolic changes caused by aberrant metabolic conditions, and to improve the functions of existing systems, such as bioartificial liver. More recently, isolated liver perfusion systems have been increasingly used to characterize intrinsic metabolic changes in the liver caused by various perturbations, including systemic injury, hepatotoxin exposure and warm ischemia. Metabolic engineering tools have been widely applied to these systems to identify metabolic flux distributions using metabolic flux analysis or flux balance analysis and to characterize the topology of the networks using metabolic pathway analysis. In this context, hepatic metabolic models, together with experimental methodologies where hepatocytes or perfused livers are mainly investigated, are described in detail in this review. The challenges and opportunities are also discussed extensively. PMID:24957379

  11. 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

  12. 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

  13. Robust hyperpolarized (13)C metabolic imaging with selective non-excitation of pyruvate (SNEP).

    PubMed

    Chen, Way Cherng; Teo, Xing Qi; Lee, Man Ying; Radda, George K; Lee, Philip

    2015-08-01

    In vivo metabolic imaging using hyperpolarized [1-(13)C]pyruvate provides localized biochemical information and is particularly useful in detecting early disease changes, as well as monitoring disease progression and treatment response. However, a major limitation of hyperpolarized magnetization is its unrecoverable decay, due not only to T1 relaxation but also to radio-frequency (RF) excitation. RF excitation schemes used in metabolic imaging must therefore be able to utilize available hyperpolarized magnetization efficiently and robustly for the optimal detection of substrate and metabolite activities. In this work, a novel RF excitation scheme called selective non-excitation of pyruvate (SNEP) is presented. This excitation scheme involves the use of a spectral selective RF pulse to specifically exclude the excitation of [1-(13)C]pyruvate, while uniformly exciting the key metabolites of interest (namely [1-(13)C]lactate and [1-(13)C]alanine) and [1-(13)C]pyruvate-hydrate. By eliminating the loss of hyperpolarized [1-(13)C]pyruvate magnetization due to RF excitation, the signal from downstream metabolite pools is increased together with enhanced dynamic range. Simulation results, together with phantom measurements and in vivo experiments, demonstrated the improvement in signal-to-noise ratio (SNR) and the extension of the lifetime of the [1-(13)C]lactate and [1-(13)C]alanine pools when compared with conventional non-spectral selective (NS) excitation. SNEP has also been shown to perform comparably well with multi-band (MB) excitation, yet SNEP possesses distinct advantages, including ease of implementation, less stringent demands on gradient performance, increased robustness to frequency drifts and B0 inhomogeneity as well as easier quantification involving the use of [1-(13)C]pyruvate-hydrate as a proxy for the actual [1-(13)C] pyruvate signal. SNEP is therefore a promising alternative for robust hyperpolarized [1-(13)C]pyruvate metabolic imaging with high fidelity. PMID:26119950

  14. 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.

  15. 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

  16. 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

  17. 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

  18. 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.

  19. Quantitative analysis of bidirectional electron fluxes within coronal mass ejections at 1 AU

    NASA Technical Reports Server (NTRS)

    Phillips, J. L.; Gosling, J. T.; Mccomas, D. J.; Bame, S. J.; Feldman, W. C.

    1992-01-01

    The solar wind electron heat flux is carried primarily by suprathermal electrons beamed antisunward along the interplanetary magnetic field. However, analysis of electron observations at 1 AU has shown that counterstreaming electron beams, suggesting closed magnetic structures, prevail within coronal mass ejections (CMEs). These structures might be magnetic 'tongues', magnetically detached plasmoids, or complex flux ropes. Here we show results of analysis of ISEE-3 observations within 39 CMEs, including the asymmetry between the two beams, its control by magnetic field orientation, and the variation of the electron distributions as CMEs convect past the spacecraft. We find that some CMEs are strongly asymmetric, with the antisunward beam generally dominant, while others contain nearly symmetric beams. The beam asymmetries, and the magnetic field orientations, exhibit characteristic trends as CMEs pass over the spacecraft. We present an example of a distinctive 'strahl-on-strahl' distribution, suggesting continued magnetic connection to the corona, in which a narrow antisunward beam is superimposed on a broader beam. Our results favor continuing magnetic connection to the Sun in a tongue or flux rope geometry rather than a fully detached plasmoid.

  20. Modeling the optimal central carbon metabolic pathways under feedback inhibition using flux balance analysis.

    PubMed

    De, Rajat K; Tomar, Namrata

    2012-12-01

    Metabolism is a complex process for energy production for cellular activity. It consists of a cascade of reactions that form a highly branched network in which the product of one reaction is the reactant of the next reaction. Metabolic pathways efficiently produce maximal amount of biomass while maintaining a steady-state behavior. The steady-state activity of such biochemical pathways necessarily incorporates feedback inhibition of the enzymes. This observation motivates us to incorporate feedback inhibition for modeling the optimal activity of metabolic pathways using flux balance analysis (FBA). We demonstrate the effectiveness of the methodology on a synthetic pathway with and without feedback inhibition. Similarly, for the first time, the Central Carbon Metabolic (CCM) pathways of Saccharomyces cerevisiae and Homo sapiens have been modeled and compared based on the above understanding. The optimal pathway, which maximizes the amount of the target product(s), is selected from all those obtained by the proposed method. For this, we have observed the concentration of the product inhibited enzymes of CCM pathway and its influence on its corresponding metabolite/substrate. We have also studied the concentration of the enzymes which are responsible for the synthesis of target products. We further hypothesize that an optimal pathway would opt for higher flux rate reactions. In light of these observations, we can say that an optimal pathway should have lower enzyme concentration and higher flux rates. Finally, we demonstrate the superiority of the proposed method by comparing it with the extreme pathway analysis. PMID:22913632

  1. #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

  2. A Statistical Analysis on the Precipitated and Trapped Electron Fluxes Using Long-term POES Observations

    NASA Astrophysics Data System (ADS)

    Zhou, C.; Ni, B.; Li, W.; Zhao, Z.; Gu, X.; Shi, R.; Hu, Z.

    2013-12-01

    We present a statistical analysis on the electron precipitation and trapped fluxes using NOAA POES data from 1998 to 2013, which covers more than an entire solar circle. The data of precipitation and trapped electron fluxes and the ratios between them are comprehensively investigated as a function of L-shell, magnetic local time (MLT), and geomagnetic conditions. Our results will help establish the major features of precipitated and trapped electron dynamics in the inner magnetosphere and their dependence on the level of geomagnetic activity, spatial location and phase of a solar cycle. We also investigate electron precipitation near the area of the South Atlantic Anomaly and compare the results with other regions where the ambient magnetic field configuration is normal. By doing so, we intend to explore the effect of precipitation caused by drift loss cone in contrast to that caused by bounce loss cone.

  3. A New Technique for Analysis of Static Eccentricity in Axial Flux Resolver

    NASA Astrophysics Data System (ADS)

    Tootoonchian, F.; Abbaszadeh, K.; Ardebili, M.

    2012-01-01

    Resolvers have been widely used in motion control systems as position sensors. This paper deals with the analysis of Axial Flux Resolvers. Axial flux resolvers are a group of resolvers which can be used in high performance servomechanisms. The accuracy of resolver detected position is affected by errors. Some of these errors are caused by speed fluctuations, permeance ripples, unbalanced voltages, and eccentricity between rotor and stator. Among these errors the static eccentricity > and Lq values and then, the static eccentricity effect based on the developed model is studied. A novel algorithm is proposed for suppressing the eccentricity error. This method is based on analytical model and modern control fundamentals. In a comparison, simulation and experimental results show good agreement. Finally, the effect of air gap length, pole number and excitation voltage on position error of eccentric AFR is investigated, practically.

  4. Continuous-Time Markov Chain–Based Flux Analysis in Metabolism

    PubMed Central

    Ji, Ping

    2014-01-01

    Abstract Metabolic flux analysis (MFA), a key technology in bioinformatics, is an effective way of analyzing the entire metabolic system by measuring fluxes. Many existing MFA approaches are based on differential equations, which are complicated to be solved mathematically. So MFA requires some simple approaches to investigate metabolism further. In this article, we applied continuous-time Markov chain to MFA, called MMFA approach, and transformed the MFA problem into a set of quadratic equations by analyzing the transition probability of each carbon atom in the entire metabolic system. Unlike the other methods, MMFA analyzes the metabolic model only through the transition probability. This approach is very generic and it could be applied to any metabolic system if all the reaction mechanisms in the system are known. The results of the MMFA approach were compared with several chemical reaction equilibrium constants from early experiments by taking pentose phosphate pathway as an example. PMID:25089363

  5. 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

  6. (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

  7. 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

  8. Heterogeneity of membrane transport quantified by the analysis of a unidirectional flux transient of charged tracer.

    PubMed

    Bass, L; Maloney, L V; Young, M O

    1989-05-01

    A planar mosaic membrane consists of patches, each with a given area, diffusion coefficient, and mobility of charged tracer; a common electric field, constant in space and time, lies across all the patches. Given the properties of the patches, the transient of the total unidirectional flux (summed over the patches) is predictable. Here we deal with the inverse problem: Given only the observed transient of the total unidirectional flux (as defined experimentally by Ussing), the unknown transport heterogeneity of the mosaic membrane is to be analyzed. Results obtained previously for uncharged tracers are generalized to include effects of the field. In particular, the ratio of the arithmetic and harmonic means (both area-weighted) of the diffusion coefficients, evaluated over the membrane, is expressed in terms of only the observed transient and the field strength and is used to characterize the heterogeneity; and the unique exact solution of the inverse problem for two kinds of patches is recovered at any field strength. If the mosaic consists of n distinct kinds of patches, a sweep of the field strength from low to high values reveals (at most) n steplike shapes in the time course of the total unidirectional flux (normalized to its final steady value), which permit an approximate analysis of the heterogeneity by elementary means. PMID:2520165

  9. Core Fueling and Edge Particle Flux Analysis in Ohmically and Auxiliary Heated NSTX Plasmas

    SciTech Connect

    V.A. Soukhanovskii; R. Maingi; R. Raman; H.W. Kugel; B.P. LeBlanc; L. Roquemore; C.H. Skinner; NSTX Research Team

    2002-06-12

    The Boundary Physics program of the National Spherical Torus Experiment (NSTX) is focusing on optimization of the edge power and particle flows in b * 25% L- and H-mode plasmas of t {approx} 0.8 s duration heated by up to 6 MW of high harmonic fast wave and up to 5 MW of neutral beam injection. Particle balance and core fueling efficiencies of low and high field side gas fueling of L-mode homic and NBI heated plasmas have been compared using an analytical zero dimensional particle balance model and measured ion and neutral fluxes. Gas fueling efficiencies are in the range of 0.05-0.20 and do not depend on discharge magnetic configuration, density or poloidal location of the injector. The particle balance modeling indicates that the addition of HFS fueling results in a reversal of the wall loading rate and higher wall inventories. Initial particle source estimates obtained from neutral pressure and spectroscopic measurements indicate that ion flux into the divertor greatly exceeds midplane ion flux from the main plasma, suggesting that the scrape-off cross-field transport plays a minor role in diverted plasmas. Present analysis provides the basis for detailed fluid modeling of core and edge particle flows and particle confinement properties of NSTX plasmas. This research was supported by the U.S. Department of Energy under contracts No. DE-AC02-76CH03073, DE-AC05-00OR22725, and W-7405-ENG-36.

  10. 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. PMID:25634548

  11. Quantitative analysis of bidirectional electron fluxes within coronal mass ejections at 1 AU

    NASA Astrophysics Data System (ADS)

    Phillips, J. L.; Gosling, J. T.; McComas, D. J.; Bame, S. J.; Feldman, W. C.

    The solar wind electron heat flux is carried primarily by suprathermal 'halo' electrons beamed antisunward along the interplanetary magnetic field (IMF), indicating magnetic connection to the Sun only in one direction. However, electron observations at 1 AU show that counterstreaming halo beams, suggesting closed magnetic structures, prevail within coronal mass ejections (CME's). These structures might be magnetic 'tongues', tied to the Sun at both ends, magnetically detached plasmoids, or complex flux rope structures. Here, we present first results of analysis of ISEE-3 observations within 39 CME's, including the asymmetry between the counterstreaming beams and its control by the IMF orientation, and the variation of the electron distributions as CME's convect past the spacecraft. We find that some CME's contain nearly symmetric electron beams, while others are strongly asymmetric, and that the antisunward beam is generally dominant. The more nearly radial the IMF, the greater the asymmetry between outward and inward beams. We present an example of a distinctive 'strahl-on-strahl' distribution, suggesting continued magnetic connection to the corona, in which a narrow antisunward beam is superimposed on a broader beam. Taken as a whole, our results appear to favor a tongue or flux rope scenario rather than a fully detached plasmoid.

  12. 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. PMID:21807434

  13. Metabolic flux analysis of the mixotrophic metabolisms in the green sulfur bacterium Chlorobaculum tepidum.

    PubMed

    Feng, Xueyang; Tang, Kuo-Hsiang; Blankenship, Robert E; Tang, Yinjie J

    2010-12-10

    The photosynthetic green sulfur bacterium Chlorobaculum tepidum assimilates CO(2) and organic carbon sources (acetate or pyruvate) during mixotrophic growth conditions through a unique carbon and energy metabolism. Using a (13)C-labeling approach, this study examined biosynthetic pathways and flux distributions in the central metabolism of C. tepidum. The isotopomer patterns of proteinogenic amino acids revealed an alternate pathway for isoleucine synthesis (via citramalate synthase, CimA, CT0612). A (13)C-assisted flux analysis indicated that carbons in biomass were mostly derived from CO(2) fixation via three key routes: the reductive tricarboxylic acid (RTCA) cycle, the pyruvate synthesis pathway via pyruvate:ferredoxin oxidoreductase, and the CO(2)-anaplerotic pathway via phosphoenolpyruvate carboxylase. During mixotrophic growth with acetate or pyruvate as carbon sources, acetyl-CoA was mainly produced from acetate (via acetyl-CoA synthetase) or citrate (via ATP citrate lyase). Pyruvate:ferredoxin oxidoreductase converted acetyl-CoA and CO(2) to pyruvate, and this growth-rate control reaction is driven by reduced ferredoxin generated during phototrophic growth. Most reactions in the RTCA cycle were reversible. The relative fluxes through the RTCA cycle were 80∼100 units for mixotrophic cultures grown on acetate and 200∼230 units for cultures grown on pyruvate. Under the same light conditions, the flux results suggested a trade-off between energy-demanding CO(2) fixation and biomass growth rate; C. tepidum fixed more CO(2) and had a higher biomass yield (Y(X/S), mole carbon in biomass/mole substrate) in pyruvate culture (Y(X/S) = 9.2) than in acetate culture (Y(X/S) = 6.4), but the biomass growth rate was slower in pyruvate culture than in acetate culture. PMID:20937805

  14. 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

  15. 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.

  16. 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

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

    PubMed

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

    2013-11-01

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

  18. 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

  19. Glucose-methanol co-utilization in Pichia pastoris studied by metabolomics and instationary 13C flux analysis

    PubMed Central

    2013-01-01

    Background Several studies have shown that the utilization of mixed carbon feeds instead of methanol as sole carbon source is beneficial for protein production with the methylotrophic yeast Pichia pastoris. In particular, growth under mixed feed conditions appears to alleviate the metabolic burden related to stress responses triggered by protein overproduction and secretion. Yet, detailed analysis of the metabolome and fluxome under mixed carbon source metabolizing conditions are missing. To obtain a detailed flux distribution of central carbon metabolism, including the pentose phosphate pathway under methanol-glucose conditions, we have applied metabolomics and instationary 13C flux analysis in chemostat cultivations. Results Instationary 13C-based metabolic flux analysis using GC-MS and LC-MS measurements in time allowed for an accurate mapping of metabolic fluxes of glycolysis, pentose phosphate and methanol assimilation pathways. Compared to previous results from NMR-derived stationary state labelling data (proteinogenic amino acids, METAFoR) more fluxes could be determined with higher accuracy. Furthermore, using a thermodynamic metabolic network analysis the metabolite measurements and metabolic flux directions were validated. Notably, the concentration of several metabolites of the upper glycolysis and pentose phosphate pathway increased under glucose-methanol feeding compared to the reference glucose conditions, indicating a shift in the thermodynamic driving forces. Conversely, the extracellular concentrations of all measured metabolites were lower compared with the corresponding exometabolome of glucose-grown P. pastoris cells. The instationary 13C flux analysis resulted in fluxes comparable to previously obtained from NMR datasets of proteinogenic amino acids, but allowed several additional insights. Specifically, i) in vivo metabolic flux estimations were expanded to a larger metabolic network e.g. by including trehalose recycling, which accounted for

  20. 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.

  1. 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.

  2. Differential Bees Flux Balance Analysis with OptKnock for In Silico Microbial Strains Optimization

    PubMed Central

    Choon, Yee Wen; Mohamad, Mohd Saberi; Deris, Safaai; Illias, Rosli Md.; Chong, Chuii Khim; Chai, Lian En; Omatu, Sigeru; Corchado, Juan Manuel

    2014-01-01

    Microbial strains optimization for the overproduction of desired phenotype has been a popular topic in recent years. The strains can be optimized through several techniques in the field of genetic engineering. Gene knockout is a genetic engineering technique that can engineer the metabolism of microbial cells with the objective to obtain desirable phenotypes. However, the complexities of the metabolic networks have made the process to identify the effects of genetic modification on the desirable phenotypes challenging. Furthermore, a vast number of reactions in cellular metabolism often lead to the combinatorial problem in obtaining optimal gene deletion strategy. Basically, the size of a genome-scale metabolic model is usually large. As the size of the problem increases, the computation time increases exponentially. In this paper, we propose Differential Bees Flux Balance Analysis (DBFBA) with OptKnock to identify optimal gene knockout strategies for maximizing the production yield of desired phenotypes while sustaining the growth rate. This proposed method functions by improving the performance of a hybrid of Bees Algorithm and Flux Balance Analysis (BAFBA) by hybridizing Differential Evolution (DE) algorithm into neighborhood searching strategy of BAFBA. In addition, DBFBA is integrated with OptKnock to validate the results for improving the reliability the work. Through several experiments conducted on Escherichia coli, Bacillus subtilis, and Clostridium thermocellum as the model organisms, DBFBA has shown a better performance in terms of computational time, stability, growth rate, and production yield of desired phenotypes compared to the methods used in previous works. PMID:25047076

  3. Principal component analysis of solar flares in the soft X-ray flux

    NASA Technical Reports Server (NTRS)

    Teuber, D. L.; Reichmann, E. J.; Wilson, R. M.

    1979-01-01

    The paper considers principal component analysis of solar flares in the soft X-ray flux, a technique for extracting the salient features from a mass of data. The method applies particularly to the analysis of nonstationary ensembles, and its computations require the evaluation of eigenvalues of matrices. The Eispack matrix eigen system routines were used to analyze full-disk proportional-counter data from the X-ray event analyzer which was part of the Skylab experiment. Empirical orthogonal functions were derived for events in the soft X-ray spectrum between 2.5 and 20 A during different time periods, indicating that about 90% of the cumulative power of each analyzed flare is contained in the largest eigenvector. The first two largest eigenvectors are sufficient for an empirical curve fit through the raw data and a characterization of solar flares in the soft X-ray flux, and power spectra of two largest eigenvectors reveal a reported periodicity of about 5 min.

  4. 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

  5. Stoichiometric model and flux balance analysis for a mixed culture of Leptospirillum ferriphilum and Ferroplasma acidiphilum.

    PubMed

    Merino, M P; Andrews, B A; Asenjo, J A

    2015-01-01

    The oxidation process of sulfide minerals in natural environments is achieved by microbial communities from the Archaea and Bacteria domains. A metabolic reconstruction of two dominant species, Leptospirillum ferriphilum and Ferroplasma acidiphilum, which are always found together as a mixed culture in this natural environments, was made. The metabolic model, composed of 152 internal reactions and 29 transport reactions, describes the main interactions between these species, assuming that both use ferrous iron as energy source, and F. acidiphilum takes advantage of the organic compounds secreted by L. ferriphilum for chemomixotrophic growth. A first metabolic model for a mixed culture used in bacterial leaching is proposed in this article, which pretends to represent the characteristics of the mixed culture in a simplified manner. It was evaluated with experimental data through flux balance analysis (FBA) using as objective function the maximization of biomass. The growth yields on ferrous iron obtained for each microorganism are consistent with experimental data, and the flux distribution obtained allows understanding of the metabolic capabilities of both microorganisms growing together in a bioleaching process. The model was used to simulate the growth of F. acidiphilum on different substrates, to determine in silico which compounds maximize cell growth, and which are essential. Knockout simulations were carried out for L. ferriphilum and F. acidiphilum metabolic models, predicting key enzymes of central metabolism. The results of this analysis are consistent with experimental data from literature, showing a robust behavior of the metabolic model. PMID:25504621

  6. 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.

  7. 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

  8. 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. PMID:27140868

  9. Substrate cycles in Penicillium chrysogenum quantified by isotopic non-stationary flux analysis

    PubMed Central

    2012-01-01

    Background Penicillium chrysogenum, the main production strain for penicillin-G, has a high content of intracellular carbohydrates, especially reduced sugars such as mannitol, arabitol, erythritol, as well as trehalose and glycogen. In previous steady state 13C wash-in experiments a delay of labeling enrichments in glycolytic intermediates was observed, which suggests turnover of storage carbohydrates. The turnover of storage pools consumes ATP which is expected to reduce the product yield for energy demanding production pathways like penicillin-G. Results In this study, a 13C labeling wash-in experiment of 1 hour was performed to systematically quantify the intracellular flux distribution including eight substrate cycles. The experiments were performed using a mixed carbon source of 85% CmolGlc/CmolGlc+EtOH labeled glucose (mixture of 90% [1-13C1] and 10% [U-13C6]) and 15% ethanol [U-13C2]. It was found, that (1) also several extracellular pools are enriched with 13C labeling rapidly (trehalose, mannitol, and others), (2) the intra- to extracellular metabolite concentration ratios were comparable for a large set of metabolites while for some carbohydrates (mannitol, trehalose, and glucose) the measured ratios were much higher. Conclusions The fast enrichment of several extracellular carbohydrates and a concentration ratio higher than the ratio expected from cell lysis (2%) indicate active (e.g. ATP consuming) transport cycles over the cellular membrane. The flux estimation indicates, that substrate cycles account for about 52% of the gap in the ATP balance based on metabolic flux analysis. PMID:23098235

  10. 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.

  11. Heat-flux measurements and analysis for a rotating turbine stage

    NASA Astrophysics Data System (ADS)

    Dunn, M. G.

    1985-09-01

    A measurement and analysis program is descirbed which utilizes: (1) a Garrett TFE 731-2 high-pressure turbine stage and (2) a Garrett low aspect ratio turbine (LART) stage. The major emphasis of this program has been placed on obtaining accurate measurements of heat-flux distributions in the full-scale rotating turbine stage. The experimental technique being used is the short-duration, shock-tunnel approach, in which fast-response, thin-film thermometers are used to measure the surface temperature histories at prescribed positions on the various component parts. Heat flux values are then inferred from these temperature histories using standard data reduction procedures. A summary and discussion of the TFE 731-2 high pressure turbine results with particular emphasis on nozzle guide vane (NGV) tip endwall data not previously reported are provided. A significantly more brief discussion of the LART stage instrumentation is also included. In addition, a summary discussion of the experimental technique and the associated instrumentation is included.

  12. 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.

  13. 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.

  14. 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.

  15. Combining flux and energy balance analysis to model large-scale biochemical networks.

    PubMed

    Heuett, William J; Qian, Hong

    2006-12-01

    Stoichiometric Network Theory is a constraints-based, optimization approach for quantitative analysis of the phenotypes of large-scale biochemical networks that avoids the use of detailed kinetics. This approach uses the reaction stoichiometric matrix in conjunction with constraints provided by flux balance and energy balance to guarantee mass conserved and thermodynamically allowable predictions. However, the flux and energy balance constraints have not been effectively applied simultaneously on the genome scale because optimization under the combined constraints is non-linear. In this paper, a sequential quadratic programming algorithm that solves the non-linear optimization problem is introduced. A simple example and the system of fermentation in Saccharomyces cerevisiae are used to illustrate the new method. The algorithm allows the use of non-linear objective functions. As a result, we suggest a novel optimization with respect to the heat dissipation rate of a system. We also emphasize the importance of incorporating interactions between a model network and its surroundings. PMID:17245812

  16. Flux Analysis of the Trypanosoma brucei Glycolysis Based on a Multiobjective-Criteria Bioinformatic Approach

    PubMed Central

    Ghozlane, Amine; Bringaud, Frédéric; Soueidan, Hayssam; Dutour, Isabelle; Jourdan, Fabien; Thébault, Patricia

    2012-01-01

    Trypanosoma brucei is a protozoan parasite of major of interest in discovering new genes for drug targets. This parasite alternates its life cycle between the mammal host(s) (bloodstream form) and the insect vector (procyclic form), with two divergent glucose metabolism amenable to in vitro culture. While the metabolic network of the bloodstream forms has been well characterized, the flux distribution between the different branches of the glucose metabolic network in the procyclic form has not been addressed so far. We present a computational analysis (called Metaboflux) that exploits the metabolic topology of the procyclic form, and allows the incorporation of multipurpose experimental data to increase the biological relevance of the model. The alternatives resulting from the structural complexity of networks are formulated as an optimization problem solved by a metaheuristic where experimental data are modeled in a multiobjective function. Our results show that the current metabolic model is in agreement with experimental data and confirms the observed high metabolic flexibility of glucose metabolism. In addition, Metaboflux offers a rational explanation for the high flexibility in the ratio between final products from glucose metabolism, thsat is, flux redistribution through the malic enzyme steps. PMID:23097667

  17. 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. PMID:25757889

  18. 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

  19. 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

  20. Sensitivity Analysis of the Land Surface Model NOAH-MP for Different Model Fluxes

    NASA Astrophysics Data System (ADS)

    Thober, S.; Mai, J.; Samaniego, L. E.; Clark, M. P.; Mendoza, P. A.; Wulfmeyer, V. G.; Branch, O.; Attinger, S.; Kumar, R.; Cuntz, M.

    2014-12-01

    The land-atmosphere fluxes of water, energy and carbon, as computed by the Land Surface Model (LSM), are a critical component of Earth System Models and Numerical Weather Prediction models. Processes and parameters of LSMs are validated mostly against point measurements, for example from Eddy-covariance towers, with much attention given to biophysical processes and vegetation parameters. River discharge on the other hand is not considered very often although it provides an integrated signal of the hydrologic cycle over a catchment. Sensitivity analyses of hydrologic models have shown that soil parameters have then the largest impact on modeled river discharge. In this study, we quantify parametric sensitivities of the land surface model NOAH-MP simultaneously for model outputs at different spatial resolutions. NOAH-MP is a state-of-the-art LSM, which is used at regional scale as the land surface scheme of the atmospheric Weather Research and Forecasting Model (WRF). NOAH-MP contains multiple process parameterizations (hence MP), yielding a considerable amount of parameters (> 500). Standard methods for sensitivity analysis such as Sobol indexes require too many model evaluations in case of many parameters. We therefore use first a recently developed inexpensive screening method based on Elementary Effects that has proven to identify the same informative parameters as the Sobol method but requires only 1% of model evaluations. This reduces the number of parameters to a feasible amount for a thorough sensitivity analysis. The study is conducted on twelve Model Parameter Estimation Experiment (MOPEX) catchments. This allows investigation of parametric sensitivities for distinct hydro-climatic characteristics, emphasizing different land-surface processes. The river basins range in size from 1020 to 4421 km^2, allowing fast model evaluation. The screening and sensitivity analysis identifies the most informative parameters of NOAH-MP for different model output variables

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. Radiation flux and spectral analysis of the multi-temperature Z dynamic hohlraum.

    PubMed

    Lockard, T E; Idzorek, G C; Tierney, T E; Watt, R G

    2008-10-01

    Experiments performed at the Sandia National Laboratories (SNL) Z-machine, located in Albuquerque, New Mexico produce hot (approximately 220 eV) plasmas. X-ray emission from the plasma is used to drive radiation flow experiments. Our standard plasma diagnostic suite consists of x-ray diodes (XRDs), silicon photodiodes, and nickel thin film bolometers. Small diagnostic holes allow us to view the hot plasma from the side, top axial anode side, and bottom axial cathode side. Computer software has been written to process the raw data to calculate data quality, fold in detector spectral response and experiment geometry for emitted flux, calculate a multidetector spectral unfold, and yield an equivalent time-dependent Planckian temperature profile. Spectral unfolds of our XRD data generally yield a Planckian-like spectrum. In our presentation we will compare our diagnostic techniques, analysis, and results to more accurately characterize spectral unfolds in order to establish better drive conditions for our experiments. PMID:19044635

  6. Towards High Resolution Analysis of Metabolic Flux in Cells and Tissues

    PubMed Central

    Sims, James K; Manteiga, Sara; Lee, Kyongbum

    2013-01-01

    Metabolism extracts chemical energy from nutrients, uses this energy to form building blocks for biosynthesis, and interconverts between various small molecules that coordinate the activities of cellular pathways. The metabolic state of a cell is increasingly recognized to determine the phenotype of not only metabolically active cell types such as liver, muscle, and adipose, but also other specialized cell types such as neurons and immune cells. This review focuses on methods to quantify intracellular reaction flux as a measure of cellular metabolic activity, with emphasis on studies involving cells of mammalian tissue. Two key areas are highlighted for future development, single cell metabolomics and noninvasive imaging, which could enable spatiotemporally resolved analysis and thereby overcome issues of heterogeneity, a distinctive feature of tissue metabolism. PMID:23906926

  7. Equilibrium analysis of carbon pools and fluxes of forest biomes in the former Soviet Union

    SciTech Connect

    Kolchugina, T.P.; Vinson, T.S.

    1993-01-01

    Forests are an important component of the biosphere and sequestration of carbon in boreal forests may represent one of the few realistic alternatives to ameliorate changes in atmospheric chemistry. The former Soviet Union has the greatest expanse of boreal forests in the world; however, the role of these forests in the terrestrial carbon cycle is not fully understood because the carbon budget of the Soviet forest sector has not been established. In recognition of the need to determine the role of these forests in the global carbon cycle, the carbon budget of forest biomes in the former Soviet Union was assessed based on an equilibrium analysis of carbon cycle pools and fluxes. Net primary productivity was used to identify the rate of carbon turnover in the forest biomes.

  8. Metabolites production improvement by identifying minimal genomes and essential genes using flux balance analysis.

    PubMed

    Salleh, Abdul Hakim Mohamed; Mohamad, Mohd Saberi; Deris, Safaai; Illias, Rosli Md

    2015-01-01

    With the advancement in metabolic engineering technologies, reconstruction of the genome of host organisms to achieve desired phenotypes can be made. However, due to the complexity and size of the genome scale metabolic network, significant components tend to be invisible. We proposed an approach to improve metabolite production that consists of two steps. First, we find the essential genes and identify the minimal genome by a single gene deletion process using Flux Balance Analysis (FBA) and second by identifying the significant pathway for the metabolite production using gene expression data. A genome scale model of Saccharomyces cerevisiae for production of vanillin and acetate is used to test this approach. The result has shown the reliability of this approach to find essential genes, reduce genome size and identify production pathway that can further optimise the production yield. The identified genes and pathways can be extendable to other applications especially in strain optimisation. PMID:26489144

  9. 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

  10. Flux Balance Analysis of Mycolic Acid Pathway: Targets for Anti-Tubercular Drugs

    PubMed Central

    Raman, Karthik; Rajagopalan, Preethi; Chandra, Nagasuma

    2005-01-01

    Mycobacterium tuberculosis is the focus of several investigations for design of newer drugs, as tuberculosis remains a major epidemic despite the availability of several drugs and a vaccine. Mycobacteria owe many of their unique qualities to mycolic acids, which are known to be important for their growth, survival, and pathogenicity. Mycolic acid biosynthesis has therefore been the focus of a number of biochemical and genetic studies. It also turns out to be the pathway inhibited by front-line anti-tubercular drugs such as isoniazid and ethionamide. Recent years have seen the emergence of systems-based methodologies that can be used to study microbial metabolism. Here, we seek to apply insights from flux balance analyses of the mycolic acid pathway (MAP) for the identification of anti-tubercular drug targets. We present a comprehensive model of mycolic acid synthesis in the pathogen M. tuberculosis involving 197 metabolites participating in 219 reactions catalysed by 28 proteins. Flux balance analysis (FBA) has been performed on the MAP model, which has provided insights into the metabolic capabilities of the pathway. In silico systematic gene deletions and inhibition of InhA by isoniazid, studied here, provide clues about proteins essential for the pathway and hence lead to a rational identification of possible drug targets. Feasibility studies using sequence analysis of the M. tuberculosis H37Rv and human proteomes indicate that, apart from the known InhA, potential targets for anti-tubercular drug design are AccD3, Fas, FabH, Pks13, DesA1/2, and DesA3. Proteins identified as essential by FBA correlate well with those previously identified experimentally through transposon site hybridisation mutagenesis. This study demonstrates the application of FBA for rational identification of potential anti-tubercular drug targets, which can indeed be a general strategy in drug design. The targets, chosen based on the critical points in the pathway, form a ready shortlist

  11. 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. PMID:23036926

  12. 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.

  13. 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

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

    SciTech Connect

    Primm, Trent

    2008-01-01

    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. Such a model was built based on the available description parameters as provided by the latest version of the nuclear analysis software package called Program for the Analysis of Reactor Transients (PARET). Analysis performed with the model constructed was 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 making LEU fuel a safe alternative fuel for the reactor core.

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

    PubMed

    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

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. Analysis of the operational error of heat flux transducers placed on wall surfaces

    NASA Astrophysics Data System (ADS)

    Baba, Tetsuya; Ono, Akira; Hattori, Susumu

    1985-07-01

    The operational error in the heat flux measurements is theoretically investigated when the heat flux from a furnace wall to the environment is measured by a heat flux transducer. Change of the original heat flux, which is caused by placing a transducer on the furnace wall, is clarified by solving a three-dimensional heat transfer problem. The operational error is explicitly given by a simple equation taking into account the thermal properties of the furnace wall and the transducer. Numerical results are also provided for a typical application to industrial furnaces.

  1. 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

  2. Transient hot-spot analysis of the high-flux isotope reactor

    SciTech Connect

    Sofu, T.; Dodds, H.L. ); Cook, D.H. )

    1992-01-01

    Consideration of fuel element failure and the possibility of failure propagation is part of the overall safety approach for the Oak Ridge National Laboratory's High-Flux Isoptope Reactor (FHIR). There is a need to establish a technical basis for understanding the initiators that lead to fuel melting, the phenomena of fuel melting, and its consequences in order to reevaluate core damage criteria and to ensure that the HFIR core is designed to avoid or mitigate such accidents to the greatest extent possible. In this work, a computer model for the transient analysis of the HFIR is developed and applied for the study of hot-spot behavior during rapid HFIR transients. An earlier model that was developed for the analysis of reactivity transients of U-Al-dispersion-fueled research reactors is used as the base model. It includes point reactor kinetics for neutronics, a nonhomogeneous, nonequilibrium representation of the two-phase thermal hydraulics, and one-dimensional, spatially averaged heat conduction through fuel plates. The flow and heat transfer regimes considered are single-phase liquid flow, subcooled boiling, bulk boiling, film boiling, and single-phase vapor flow.

  3. 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.

  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. Climate-driven uncertainties in modeling terrestrial energy and water fluxes: a site-level to global-scale analysis.

    PubMed

    Barman, Rahul; Jain, Atul K; Liang, Miaoling

    2014-06-01

    We used a land surface model constrained using data from flux tower sites, to analyze the biases in ecosystem energy and water fluxes arising due to the use of meteorological reanalysis datasets. Following site-level model calibration encompassing major vegetation types from the tropics to the northern high-latitudes, we repeated the site and global simulations using two reanalysis datasets: the NCEP/NCAR and the CRUNCEP. In comparison with the model simulations using observed meteorology from sites, the reanalysis-driven simulations produced several systematic biases in net radiation (Rn ), latent heat (LE), and sensible heat (H) fluxes. These include: (i) persistently positive tropical/subtropical biases in Rn using the NCEP/NCAR, and gradually transitioning to negative Rn biases in the higher latitudes; (ii) large positive H biases in the tropics/subtropics using the NCEP/NCAR; (iii) negative LE biases using the NCEP/NCAR above 40°N; (iv) high tropical LE using the CRUNCEP in comparison with observationally derived global estimates; and (v) flux-partitioning biases from canopy and ground components. Across vegetation types, we investigated the role of the meteorological drivers (shortwave and longwave radiation, atmospheric humidity, temperature, precipitation) and their seasonal biases in controlling these reanalysis-driven uncertainties. At the global scale, our site-level analysis explains several model-data differences in the LE and H fluxes when compared with observationally derived global estimates of these fluxes. Using our results, we discuss the implications of site-level model calibration on subsequent regional/global applications to study energy and hydrological processes. The flux-partitioning biases presented in this study have potential implications on the couplings among terrestrial carbon, energy, and water fluxes, and for the calibration of land-atmosphere parameterizations that are dependent on LE/H partitioning. PMID:24273011

  6. 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.

  7. Does the Blazar Gamma-ray Spectrum Harden with Increasing Flux? - Analysis of Nine Years of EGRET Data

    NASA Technical Reports Server (NTRS)

    Nandikotkur, Giridhar; Jahoda, Keith M.; Hartman, R. C.; Mukherjee, R.; Sreekumar, P.; Boettcher, M.

    2007-01-01

    The Energetic Gamma Ray Experiment Telescope (EGRET) on the Compton Gamma Ray Observatory (CGRO) discovered gamma-ray emission from more than 67 blazars during its nine-year lifetime. We conducted an exhaustive search of the EGRET archives and selected all the blazars that were observed multiple times and were bright enough to enable a spectral analysis using standard powerlaw models. The sample consists of 18 flat-spectrum radio quasars (FSRQs), 6 low-frequency-peaked BL Lacs (LBLs) and 2 high-frequency-peaked BL Lacs (HBLs). We do not detect any clear pattern in'the variation of spectral index with flux. Some of the blazars do not show any statistical evidence for spectral variability. The spectrum hardens with increasing flux in a few cases. There is also evidence for a flux-hardness anticorrelation at lo\\v fluxes in five blazars. The well observed blazars (3C 279,3C 273, PKS 0528-i-134, PKS 1622-297, PKS 0208- 512) do not show any overall trend in the long-term spectral dependence on flux, but the sample shows a mixture of hard and soft states. We observed spectral hysteresis at weekly timescales in all the three FSRQs for which data from flares lasting for 3 approx. 4 weeks were available. All three sources show a counterclockwise rotation despite the widely different flux profiles. Hysteresis in the spectral index vs. flux space has never been observed in FSRQs in gamma-rays at weekly timescales. itre analyze the observed spectral behavior in the context of various inverse-Compton mechanisms believed to be responsible for emission in the EGRET energy range. Our analysis uses the EGRET skymaps that were regenerated to include the changes in performance during the mission.

  8. 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

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

    PubMed Central

    Shen, Tie; Zheng, Meijuan; Zhou, Wenwei; Du, Honglin; Fan, Yadong; Wang, Yongkang; Zhang, Zhengdong; Xu, Shengsheng; Liu, Zhijie; Wen, Han; Xie, Xiaoyao

    2015-01-01

    NADPH regeneration capacity is attracting growing research attention due to its important role in resisting oxidative stress. Besides, NADPH availability has been regarded as a limiting factor in production of industrially valuable compounds. The central carbon metabolism carries the carbon skeleton flux supporting the operation of NADPH-regenerating enzyme and offers flexibility in coping with NADPH demand for varied intracellular environment. To acquire an insightful understanding of its NADPH regeneration capacity, the elementary mode method was employed to compute all elementary flux modes (EFMs) of a network representative of central carbon metabolism. Based on the metabolic flux distributions of these modes, a cluster analysis of EFMs with high NADPH regeneration rate was conducted using the self-organizing map clustering algorithm. The clustering results were used to study the relationship between the flux of total NADPH regeneration and the flux in each NADPH producing enzyme. The results identified several reaction combinations supporting high NADPH regeneration, which are proven to be feasible in cells via thermodynamic analysis and coincident with a great deal of previous experimental report. Meanwhile, the reaction combinations showed some common characteristics: there were one or two decarboxylation oxidation reactions in the combinations that produced NADPH and the combination constitution included certain gluconeogenesis pathways. These findings suggested cyclization pathways as a powerful way for NADPH regeneration capacity of bacterial central carbon metabolism. PMID:26086807

  10. Accuracy and Precision Analysis of Chamber-Based Nitrous Oxide Gas Flux Estimates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Chamber-based estimates of soil-to-atmosphere nitrous oxide (N2O) gas flux tend to underestimate actual emission rates due to inherently non-linear time series data. In theory, this limitation can be minimized by adjusting measurement conditions to reduce non-linearity and/or by using flux-calculati...

  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. Steady-state and dynamic flux balance analysis of ethanol production by Saccharomyces cerevisiae.

    PubMed

    Hjersted, J L; Henson, M A

    2009-05-01

    Steady-state and dynamic flux balance analysis (DFBA) was used to investigate the effects of metabolic model complexity and parameters on ethanol production predictions for wild-type and engineered Saccharomyces cerevisiae. Three metabolic network models ranging from a single compartment representation of metabolism to a genome-scale reconstruction with seven compartments and detailed charge balancing were studied. Steady-state analysis showed that the models generated similar wild-type predictions for the biomass and ethanol yields, but for ten engineered strains the seven compartment model produced smaller ethanol yield enhancements. Simplification of the seven compartment model to two intracellular compartments produced increased ethanol yields, suggesting that reaction localisation had an impact on mutant phenotype predictions. Further analysis with the seven compartment model demonstrated that steady-state predictions can be sensitive to intracellular model parameters, with the biomass yield exhibiting high sensitivity to ATP utilisation parameters and the biomass composition. The incorporation of gene expression data through the zeroing of metabolic reactions associated with unexpressed genes was shown to produce negligible changes in steady-state predictions when the oxygen uptake rate was suitably constrained. Dynamic extensions of the single and seven compartment models were developed through the addition of glucose and oxygen uptake expressions and transient extracellular balances. While the dynamic models produced similar predictions of the optimal batch ethanol productivity for the wild type, the single compartment model produced significantly different predictions for four implementable gene insertions. A combined deletion/overexpression/insertion mutant with improved ethanol productivity capabilities was computationally identified by dynamically screening multiple combinations of the ten metabolic engineering strategies. The authors concluded that

  14. Analysis of Solar Receiver Flux Distributions for US/Russian Solar Dynamic System Demonstration on the MIR Space Station

    NASA Technical Reports Server (NTRS)

    1995-01-01

    Analyses have been performed at the NASA Lewis Research Center's Power Systems Project Office to support the design and development of the joint U.S./Russian Solar Dynamic Flight Demonstration Project. The optical analysis of the concentrator and solar flux predictions on target receiver surfaces have an important influence on receiver design and control of the Brayton engine.

  15. [Metabolic flux analysis of L-serine synthesis by Corynebacterium glutamicum SYPS-062].

    PubMed

    Zhang, Xiaomei; Dou, Wenfang; Xu, Hongyu; Xu, Zhenghong

    2010-10-01

    Corynebacterium glutamicum SYPS-062 was an L-serine producing strain stored at our lab and could produce L-serine directly from sugar. We studied the effects of cofactors in one carbon unit metabolism-folate and VB12 on the cell growth, sucrose consumption and L-serine production by SYPS-062. In the same time, the metabolic flux distribution was determined in different conditions. The supplementation of folate or VB12 enhanced the cell growth, energy synthesis, and finally increased the flux of pentose phosphate pathway (HMP), whereas the carbon flux to L-serine was decreased. The addition of VB12 not only increased the ratio of L-serine synthesis pathway on G3P joint, but also caused the insufficiency of tricarboxylic acid cycle (TCA) flux, which needed more anaplerotic reaction flux to replenish TCA cycle, that was an important limiting factor for the further increasing of the L-serine productivity. PMID:21218623

  16. Gene Knockout Identification Using an Extension of Bees Hill Flux Balance Analysis

    PubMed Central

    Choon, Yee Wen; Mohamad, Mohd Saberi; Deris, Safaai; Chong, Chuii Khim; Omatu, Sigeru; Corchado, Juan Manuel

    2015-01-01

    Microbial strain optimisation for the overproduction of a desired phenotype has been a popular topic in recent years. Gene knockout is a genetic engineering technique that can modify the metabolism of microbial cells to obtain desirable phenotypes. Optimisation algorithms have been developed to identify the effects of gene knockout. However, the complexities of metabolic networks have made the process of identifying the effects of genetic modification on desirable phenotypes challenging. Furthermore, a vast number of reactions in cellular metabolism often lead to a combinatorial problem in obtaining optimal gene knockout. The computational time increases exponentially as the size of the problem increases. This work reports an extension of Bees Hill Flux Balance Analysis (BHFBA) to identify optimal gene knockouts to maximise the production yield of desired phenotypes while sustaining the growth rate. This proposed method functions by integrating OptKnock into BHFBA for validating the results automatically. The results show that the extension of BHFBA is suitable, reliable, and applicable in predicting gene knockout. Through several experiments conducted on Escherichia coli, Bacillus subtilis, and Clostridium thermocellum as model organisms, extension of BHFBA has shown better performance in terms of computational time, stability, growth rate, and production yield of desired phenotypes. PMID:25874200

  17. 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

  18. 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.

  19. 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.

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

    PubMed

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

    2014-02-01

    Extracellular flux (XF) analysis has become a mainstream method for measuring mitochondrial function in cells and tissues. Although this technique is commonly used to measure bioenergetics in intact cells, we outline here a detailed XF protocol for measuring respiration in permeabilized cells. Cells are permeabilized using saponin (SAP), digitonin (DIG) or recombinant perfringolysin O (rPFO) (XF-plasma membrane permeabilizer (PMP) reagent), and they are provided with specific substrates to measure complex I- or complex 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 (FA) oxidation or glutamine oxidation, respectively. This protocol uses a minimal number of cells compared with other protocols and does not require isolation of mitochondria. The results are highly reproducible, and mitochondria remain well coupled. Collectively, this protocol provides comprehensive and detailed information regarding mitochondrial activity and efficiency, and, after preparative steps, it takes 6-8 h to complete. PMID:24457333

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

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

    PubMed

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

    2015-10-01

    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

  7. Skyshine analysis using energy and angular dependent dose-contribution fluxes obtained from air-over-ground adjoint calculation.

    PubMed

    Uematsu, Mikio; Kurosawa, Masahiko

    2005-01-01

    A generalised and convenient skyshine dose analysis method has been developed based on forward-adjoint folding technique. In the method, the air penetration data were prepared by performing an adjoint DOT3.5 calculation with cylindrical air-over-ground geometry having an adjoint point source (importance of unit flux to dose rate at detection point) in the centre. The accuracy of the present method was certified by comparing with DOT3.5 forward calculation. The adjoint flux data can be used as generalised radiation skyshine data for all sorts of nuclear facilities. Moreover, the present method supplies plenty of energy-angular dependent contribution flux data, which will be useful for detailed shielding design of facilities. PMID:16604693

  8. 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

  9. 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

  10. 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. PMID:23236266

  11. 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.

  12. Uncertainty analysis of heat flux measurements estimated using a one-dimensional, inverse heat-conduction program.

    SciTech Connect

    Nakos, James Thomas; Figueroa, Victor G.; Murphy, Jill E.

    2005-02-01

    The measurement of heat flux in hydrocarbon fuel fires (e.g., diesel or JP-8) is difficult due to high temperatures and the sooty environment. Un-cooled commercially available heat flux gages do not survive in long duration fires, and cooled gages often become covered with soot, thus changing the gage calibration. An alternate method that is rugged and relatively inexpensive is based on inverse heat conduction methods. Inverse heat-conduction methods estimate absorbed heat flux at specific material interfaces using temperature/time histories, boundary conditions, material properties, and usually an assumption of one-dimensional (1-D) heat flow. This method is commonly used at Sandia.s fire test facilities. In this report, an uncertainty analysis was performed for a specific example to quantify the effect of input parameter variations on the estimated heat flux when using the inverse heat conduction method. The approach used was to compare results from a number of cases using modified inputs to a base-case. The response of a 304 stainless-steel cylinder [about 30.5 cm (12-in.) in diameter and 0.32-cm-thick (1/8-in.)] filled with 2.5-cm-thick (1-in.) ceramic fiber insulation was examined. Input parameters of an inverse heat conduction program varied were steel-wall thickness, thermal conductivity, and volumetric heat capacity; insulation thickness, thermal conductivity, and volumetric heat capacity, temperature uncertainty, boundary conditions, temperature sampling period; and numerical inputs. One-dimensional heat transfer was assumed in all cases. Results of the analysis show that, at the maximum heat flux, the most important parameters were temperature uncertainty, steel thickness and steel volumetric heat capacity. The use of a constant thermal properties rather than temperature dependent values also made a significant difference in the resultant heat flux; therefore, temperature-dependent values should be used. As an example, several parameters were varied to

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

    DOE PAGESBeta

    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

  14. Elucidating rice cell metabolism under flooding and drought stresses using flux-based modeling and analysis.

    PubMed

    Lakshmanan, Meiyappan; Zhang, Zhaoyang; Mohanty, Bijayalaxmi; Kwon, Jun-Young; Choi, Hong-Yeol; Nam, Hyung-Jin; Kim, Dong-Il; Lee, Dong-Yup

    2013-08-01

    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

  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. Uncertainty analysis of modeled carbon and water fluxes in a subtropical coniferous plantation

    NASA Astrophysics Data System (ADS)

    Ren, Xiaoli; He, Honglin; Moore, David J. P.; Zhang, Li; Liu, Min; Li, Fan; Yu, Guirui; Wang, Huimin

    2013-12-01

    Estimating the exchanges of carbon and water between vegetation and the atmosphere requires process-based ecosystem models; however, uncertainty in model predictions is inevitable due to the uncertainties in model structure, model parameters, and driving variables. This paper proposes a methodological framework for analyzing prediction uncertainty of ecosystem models caused by parameters and applies it in Qianyanzhou subtropical coniferous plantation using the Simplified Photosynthesis and Evapotranspiration model. We selected 20 key parameters from 42 parameters of the model using one-at-a-time sensitivity analysis method and estimated their posterior distributions using Markov Chain Monte Carlo technique. Prediction uncertainty was quantified through Monte Carlo method and partitioned using Sobol' method by decomposing the total variance of model predictions into different components. The uncertainty in predicted net ecosystem CO2 exchange (NEE), gross primary production (GPP), ecosystem respiration (RE), evapotranspiration (ET), and transpiration (T), defined as the coefficient of variation, was 61.0%, 20.6%, 12.7%, 14.2%, and 19.9%, respectively. Modeled carbon and water fluxes were highly sensitive to two parameters, maximum net CO2 assimilation rate (Amax) and specific leaf weight (SLWC). They contributed more than two thirds of the uncertainty in predicted NEE, GPP, ET, and T and almost one third of the uncertainty in predicted RE, which should be focused on in further efforts to reduce uncertainty. The results indicated a direction for future model development and data collection. Although there were still limitations in the framework illustrated here, it did provide a paradigm for systematic quantification of ecosystem model prediction uncertainty.

  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. Analysis of Evaporative Flux Over Irrigated and Unirrigated Pasture in the Wood River Basin

    NASA Astrophysics Data System (ADS)

    Cuenca, R. H.; Mahrt, L.; Hagimoto, Y.; Peterson, S.

    2005-12-01

    The reduction in evaporative fluxes due to withholding irrigation water for pasture in the Wood River subbasin of the Upper Klamath Basin was evaluated to estimate the potential benefit in subsequent streamflow. Two Campbell Scientific (CSI) Bowen ratio - energy balance systems were installed, one over a fully irrigated site and one over a non-irrigated site separated by approximately 11 km. The systems were comprised of an infrared gas analyzer for water vapor gradients, fine-wire thermocouples for temperature gradients, net radiometer and soil heat flux sensors. Additional micrometeorological sensors for precipitation, solar radiation, air temperature and relative humidity, wind speed and direction enabled calculation of a Penman-Monteith reference evapotranspiration. Both sites had uniform fetch conditions in excess of 1 km in the predominant upwind direction. Bowen ratio data were quality controlled using the Ohmura algorithm and energy balance components and fluxes computed every 20-min. Soil temperature and soil moisture profile sensors in six depth layers down to 80 cm were installed at the same sites and monitored every 15-min. High frequency (10-min) recording piezometers for water table monitoring were also installed. Both irrigated and unirrigated sites started the 2004 growing season with virtually the same soil moisture conditions due to over winter precipitation and melting of the snowpack. The evaporative flux rates from the two sites were nearly identical early in the season, and the repeatability of the diurnal fluxes at the two sites during this period is excellent. Towards the middle of the growing season, the evaporative flux rate at the irrigated site increased relative to the unirrigated site until at the end of the season there was approximately a 40 percent unbiased (dividing by the mean) difference between the two sites. The micrometeorological data indicate nearly uniform atmospheric conditions at the two sites due to turbulent mixing of

  19. 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.

  20. Modelling and analysis of flux surface mapping experiments on W7-X

    NASA Astrophysics Data System (ADS)

    Lazerson, Samuel; Otte, Matthias; Bozhenkov, Sergey; Sunn Pedersen, Thomas; Bräuer, Torsten; Gates, David; Neilson, Hutch; W7-X Team

    2015-11-01

    The measurement and compensation of error fields in W7-X will be key to the device achieving high beta steady state operations. Flux surface mapping utilizes the vacuum magnetic flux surfaces, a feature unique to stellarators and heliotrons, to allow direct measurement of magnetic topology, and thereby allows a highly accurate determination of remnant magnetic field errors. As will be reported separately at this meeting, the first measurements confirming the existence of nested flux surfaces in W7-X have been made. In this presentation, a synthetic diagnostic for the flux surface mapping diagnostic is presented. It utilizes Poincaré traces to construct an image of the flux surface consistent with the measured camera geometry, fluorescent rod sweep plane, and emitter beam position. Forward modeling of the high-iota configuration will be presented demonstrating an ability to measure the intrinsic error field using the U.S. supplied trim coil system on W7-X, and a first experimental assessment of error fields in W7-X will be presented. This work has been authored by Princeton University under Contract Number DE-AC02-09CH11466 with the US Department of Energy.

  1. 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.

  2. Dynamic vacuum analysis for APS high heat flux beamline front ends using optical ray-tracing simulation methods

    SciTech Connect

    Xu, S.; Nielsen, R.W.

    1992-01-01

    The high-power and high-flux x-ray beams produced by third generation synchrotron radiation sources such as the Advanced Photon Source (APS) can cause significantly high gas desorption rates on beamline front-end components if beam missteering occurs. The effect of this gas desorption needs to be understood for dynamic vacuum analysis. To simulate beam missteering conditions, optical ray-tracing methods have been employed. The results of the ray-tracing analysis have been entered into a system-oriented vacuum program to provide dynamic vacuum calculations for determination of pumping requirements for the beamline front-ends. The APS will provide several types of synchrotron radiation sources, for example, undulators, wigglers, and bending magnets. For the purpose of this study, the wiggler source was chosen as a worst case'' scenario due to its high photon flux, high beam power, and relatively large beam cross section.

  3. Dynamic vacuum analysis for APS high heat flux beamline front ends using optical ray-tracing simulation methods

    SciTech Connect

    Xu, S.; Nielsen, R.W.

    1992-09-01

    The high-power and high-flux x-ray beams produced by third generation synchrotron radiation sources such as the Advanced Photon Source (APS) can cause significantly high gas desorption rates on beamline front-end components if beam missteering occurs. The effect of this gas desorption needs to be understood for dynamic vacuum analysis. To simulate beam missteering conditions, optical ray-tracing methods have been employed. The results of the ray-tracing analysis have been entered into a system-oriented vacuum program to provide dynamic vacuum calculations for determination of pumping requirements for the beamline front-ends. The APS will provide several types of synchrotron radiation sources, for example, undulators, wigglers, and bending magnets. For the purpose of this study, the wiggler source was chosen as a ``worst case`` scenario due to its high photon flux, high beam power, and relatively large beam cross section.

  4. 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

  5. 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.

  6. 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).

  7. Hierarchical flux-based thermal-structural finite element analysis method

    NASA Technical Reports Server (NTRS)

    Polesky, Sandra P.

    1992-01-01

    A hierarchical flux-based finite element method is developed for both a one and two dimensional thermal structural analyses. Derivation of the finite element equations is presented. The resulting finite element matrices associated with the flux based formulation are evaluated in a closed form. The hierarchical finite elements include additional degrees of freedom in the approximation of the element variable distributions by the use of nodeless variables. The nodeless variables offer increased solution accuracy without the need for defining actual nodes and rediscretizing the finite element model. Thermal and structural responses are obtained from a conventional linear finite element method and exact solutions. Results show that the hierarchical flux-based method can provide improved thermal and structural solution accuracy with fewer elements when compared to results for the conventional linear element method.

  8. 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.

  9. An analysis of return flux from the Space Shuttle Orbiter RCS engines

    NASA Technical Reports Server (NTRS)

    Ehlers, H. K. F.

    1984-01-01

    The return flux from the Space Shuttle Orbiter reaction control system (RCS) engines to sensors in the open payload bay has been analyzed on the basis of Shuttle/Payload Contamination Evaluation (SPACE II) model predictions and orbital flight measurements. Model data are presented showing the variations of molecular return flux values with Orbiter orientation and instrument direction. The effects of multiple molecular collisions within RCS engine plumes and in their vicinity are discussed. These collisions significantly influence the amount of plume molecules returning to payload instruments and, therefore, the amount of contaminants received.

  10. Effect of plasmid replication deregulation via inc mutations on E. coli proteome & simple flux model analysis.

    PubMed

    Meade, Jonathan; Bartlow, Patrick; Trivedi, Ram Narayan; Akhtar, Parvez; Ataai, Mohammad M; Khan, Saleem A; Domach, Michael M

    2015-01-01

    When the replication of a plasmid based on sucrose selection is deregulated via the inc1 and inc2 mutations, high copy numbers (7,000 or greater) are attained while the growth rate on minimal medium is negligibly affected. Adaptions were assumed to be required in order to sustain the growth rate. Proteomics indicated that indeed a number of adaptations occurred that included increased expression of ribosomal proteins and 2-oxoglutarate dehydrogenase. The operating space prescribed by a basic flux model that maintained phenotypic traits (e.g. growth, byproducts, etc.) within typical bounds of resolution was consistent with the flux implications of the proteomic changes. PMID:25890349

  11. 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

  12. 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. PMID:26066363

  13. 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

  14. 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

  15. 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

  16. 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

  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. Flux-torque cross-coupling analysis of FOC schemes: Novel perturbation rejection characteristics.

    PubMed

    Amezquita-Brooks, Luis; Liceaga-Castro, Eduardo; Liceaga-Castro, Jesús; Ugalde-Loo, Carlos E

    2015-09-01

    Field oriented control (FOC) is one of the most successful control schemes for electrical machines. In this article new properties of FOC schemes for induction motors (IMs) are revealed by studying the cross-coupling of the flux-torque subsystem. Through the use of frequency-based multivariable tools, it is shown that FOC has intrinsic stator currents disturbance rejection properties due to the existence of a transmission zero in the flux-torque subsystem. These properties can be exploited in order to select appropriate feedback loop configurations. One of the major drawbacks of FOC schemes is their high sensitivity to slip angular velocity perturbations. These perturbations are related to variations of the rotor time constant, which are known to be problematic for IM control. In this regard, the effect that slip angular velocity perturbations have over the newly found perturbation rejection properties is also studied. In particular, although perturbation rejection is maintained, deviations to the equilibrium point are induced; this introduces difficulties for simultaneous flux and torque control. The existence of equilibrium point issues when flux and torque are simultaneously controlled is documented for the first time in this article. PMID:26187346

  19. Metabolic Flux Analysis of Plastidic Isoprenoid Biosynthesis in Poplar Leaves Emitting and Nonemitting Isoprene1[W

    PubMed Central

    Ghirardo, Andrea; Wright, Louwrance Peter; Bi, Zhen; Rosenkranz, Maaria; Pulido, Pablo; Rodríguez-Concepción, Manuel; Niinemets, Ülo; Brüggemann, Nicolas; Gershenzon, Jonathan; Schnitzler, Jörg-Peter

    2014-01-01

    The plastidic 2-C-methyl-d-erythritol-4-phosphate (MEP) pathway is one of the most important pathways in plants and produces a large variety of essential isoprenoids. Its regulation, however, is still not well understood. Using the stable isotope 13C-labeling technique, we analyzed the carbon fluxes through the MEP pathway and into the major plastidic isoprenoid products in isoprene-emitting and transgenic isoprene-nonemitting (NE) gray poplar (Populus × canescens). We assessed the dependence on temperature, light intensity, and atmospheric [CO2]. Isoprene biosynthesis was by far (99%) the main carbon sink of MEP pathway intermediates in mature gray poplar leaves, and its production required severalfold higher carbon fluxes compared with NE leaves with almost zero isoprene emission. To compensate for the much lower demand for carbon, NE leaves drastically reduced the overall carbon flux within the MEP pathway. Feedback inhibition of 1-deoxy-d-xylulose-5-phosphate synthase activity by accumulated plastidic dimethylallyl diphosphate almost completely explained this reduction in carbon flux. Our data demonstrate that short-term biochemical feedback regulation of 1-deoxy-d-xylulose-5-phosphate synthase activity by plastidic dimethylallyl diphosphate is an important regulatory mechanism of the MEP pathway. Despite being relieved from the large carbon demand of isoprene biosynthesis, NE plants redirected only approximately 0.5% of this saved carbon toward essential nonvolatile isoprenoids, i.e. β-carotene and lutein, most probably to compensate for the absence of isoprene and its antioxidant properties. PMID:24590857

  20. Evapotranspiration and energy flux observations from a global tower network with a critical analysis of uncertainties

    NASA Astrophysics Data System (ADS)

    Stoy, P. C.

    2012-12-01

    Eddy covariance studies tend to focus on the flux of carbon dioxide despite the central role of surface-atmosphere water and energy exchange in the climate system. The under-utilization of water and energy flux data is due in part to uncertainties, including the lack of observed energy balance closure. Across 173 FLUXNET sites, energy balance closure averaged 0.84 with best average closure in evergreen broadleaf forests and savannas (0.91-0.94) and worst average closure in crops, deciduous broadleaf forests, mixed forests and wetlands (0.70-0.78). The simplest explanatory model using information criteria analyses cannot exclude landscape-level heterogeneity. This finding is in empirical agreement with studies that suggest that secondary circulations, likely attributable to landscape-scale variability, are related to lack of energy balance closure, although unmeasured storage terms cannot be ruled out as a dominant contributor. Keeping uncertainties in mind, evapotranspiration and sensible heat flux follow expected seasonal patterns, and the magnitude of evapotranspiration in temperate ecosystems approached that of tropical ecosystems during the peak growing season. Latent heat exchange is constrained by an exponentially-decreasing function of vapor pressure deficit, consistent with theories of optimal stomatal behavior. Forests tended to have cooler surface temperatures when controlled for net radiation than did short-statured ecosystems, and further investigations revealed the importance of efficient heat and water vapor transport in forest canopies that are well-coupled to the atmosphere. The value of energy and water flux data from FLUXNET increases as uncertainties become better-understood, and careful interpretations of tower-level water and energy flux data will ultimately improve our understanding of the role of terrestrial ecosystems in the Earth system.

  1. MEAN-FLUX-REGULATED PRINCIPAL COMPONENT ANALYSIS CONTINUUM FITTING OF SLOAN DIGITAL SKY SURVEY Ly{alpha} FOREST SPECTRA

    SciTech Connect

    Lee, Khee-Gan; Spergel, David N.; Suzuki, Nao

    2012-02-15

    Continuum fitting is an important aspect of Ly{alpha} forest science, since errors in the derived optical depths scale with the fractional continuum error. However, traditional methods of estimating continua in noisy and moderate-resolution spectra (e.g., Sloan Digital Sky Survey, SDSS; S/N {approx}< 10 pixel{sup -1} and R {approx} 2000), such as power-law extrapolation or dividing by the mean spectrum, achieve no better than {approx}15% rms accuracy. To improve on this, we introduce mean-flux-regulated principal component analysis (MF-PCA) continuum fitting. In this technique, PCA fitting is carried out redward of the quasar Ly{alpha} line in order to provide a prediction for the shape of the Ly{alpha} forest continuum. The slope and amplitude of this continuum prediction is then corrected using external constraints for the Ly{alpha} forest mean flux. This requires prior knowledge of the mean flux, (F), but significantly improves the accuracy of the flux transmission, F {identical_to} exp (- {tau}), estimated from each pixel. From tests on mock spectra, we find that MF-PCA reduces the errors to 8% rms in S/N {approx} 2 spectra, and <5% rms in spectra with S/N {approx}> 5. The residual Fourier power in the continuum is decreased by a factor of a few in comparison with dividing by the mean continuum, enabling Ly{alpha} flux power spectrum measurements to be extended to {approx}2 Multiplication-Sign larger scales. Using this new technique, we make available continuum fits for 12,069 z > 2.3 Ly{alpha} forest spectra from SDSS Data Release 7 for use by the community. This technique is also applicable to future releases of the ongoing Baryon Oscillations Spectroscopic Survey, which obtains spectra for {approx}150, 000 Ly{alpha} forest spectra at low signal-to-noise (S/N {approx} 2).

  2. 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

  3. 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.

  4. Ecological analysis of a boreal peatland CO2 flux based on eddy covariance data set from Ust Pojeg, Russia.

    NASA Astrophysics Data System (ADS)

    Gazovic, Michal; Kutzbach, Lars; Schneider, Julia; Wille, Christian; Wilmking, Martin

    2010-05-01

    Boreal peatlands are an important reservoir of carbon as they store one third of the terrestrial soil organic carbon (C) pool. In the last decades, more and more continuous measurements using eddy covariance technique were conducted in arctic and subarctic regions and these non-intrusive continuous measurements of C fluxes from boreal peatlands proved to be a valuable tool in peatland ecology studies. Results from such non-intrusive experiments were used to address possible changes in peatland functioning. Eddy covariance datasets typically suffer from gaps introduced during technical problems, or when the environmental conditions are not fulfilling the basic theory of eddy covariance. However, enough data points are usually left, to successfully model the missing values. Empirical models, using various environmental variables related to the measured fluxes are a common method. The carbon dioxide (CO2) flux, consistent with the term net ecosystem exchange (NEE), is composed of two reciprocal processes: C assimilation by photosynthesis and ecosystem respiration, consisting of plant and soil respiration. Generally, C accumulation is related to photosynthetically active radiation (PAR) through green leaf area and temperature. Plant respiration is related to temperature changes, and soil respiration additionally to carbon substrate concentrations in the soil solution. With such assumptions, the empirical models are created. However, these models are simple approximations of the world in which the conditions are not stable, but changing over shorter periods, and don't necessarily describe real changes in the environmental controls. Thus, important ecological processes might be "buried" in models integrating over long time periods. Year round measurements of CO2 fluxes from a Russian boreal peatland are presented here, and we test an alternative approach to understand the underlying ecological controls within the annual signal. Moving window regression analysis was used

  5. Sensitivity Analysis of the Land Surface Model NOAH-MP for Different Model Fluxes

    NASA Astrophysics Data System (ADS)

    Mai, Juliane; Thober, Stephan; Samaniego, Luis; Branch, Oliver; Wulfmeyer, Volker; Clark, Martyn; Attinger, Sabine; Kumar, Rohini; Cuntz, Matthias

    2015-04-01

    Land Surface Models (LSMs) use a plenitude of process descriptions to represent the carbon, energy and water cycles. They are highly complex and computationally expensive. Practitioners, however, are often only interested in specific outputs of the model such as latent heat or surface runoff. In model applications like parameter estimation, the most important parameters are then chosen by experience or expert knowledge. Hydrologists interested in surface runoff therefore chose mostly soil parameters while biogeochemists interested in carbon fluxes focus on vegetation parameters. However, this might lead to the omission of parameters that are important, for example, through strong interactions with the parameters chosen. It also happens during model development that some process descriptions contain fixed values, which are supposedly unimportant parameters. However, these hidden parameters remain normally undetected although they might be highly relevant during model calibration. Sensitivity analyses are used to identify informative model parameters for a specific model output. Standard methods for sensitivity analysis such as Sobol indexes require large amounts of model evaluations, specifically in case of many model parameters. We hence propose to first use a recently developed inexpensive sequential screening method based on Elementary Effects that has proven to identify the relevant informative parameters. This reduces the number parameters and therefore model evaluations for subsequent analyses such as sensitivity analysis or model calibration. In this study, we quantify parametric sensitivities of the land surface model NOAH-MP that is a state-of-the-art LSM and used at regional scale as the land surface scheme of the atmospheric Weather Research and Forecasting Model (WRF). NOAH-MP contains multiple process parameterizations yielding a considerable amount of parameters (˜ 100). Sensitivities for the three model outputs (a) surface runoff, (b) soil drainage

  6. 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

  7. 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

  8. 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.

  9. Time-series analysis of high-resolution ebullition fluxes from a stratified, freshwater lake

    NASA Astrophysics Data System (ADS)

    Varadharajan, Charuleka; Hemond, Harold F.

    2012-06-01

    Freshwater lakes can emit significant quantities of methane to the atmosphere by bubbling. The high spatial and temporal heterogeneity of ebullition, combined with a lack of high-resolution field measurements, has made it difficult to accurately estimate methane fluxes or determine the underlying mechanisms for bubble release. We use a high-temporal resolution data set of ebullitive fluxes from the eutrophic Upper Mystic Lake, Massachusetts to understand the triggers that lead to bubbling from submerged sediments. A wavelet approach is introduced to detect ebullition events for multiple time-scales, and is complemented with traditional statistical methods for data analyses. We show that bubble release from lake sediments occurred synchronously at several sites, and was closely associated with small, aperiodic drops in total hydrostatic pressure. Such results are essential to constrain mechanistic models and to design future measurement schemes, particularly with respect to the temporal scales that are needed to accurately observe and quantify ebullition in aquatic ecosystems.

  10. 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

  11. Combined multi-fluid and drift-flux approaches for analysis of pipe flows

    NASA Astrophysics Data System (ADS)

    Krasnopolsky, B.; Starostin, A.; Spesivtsev, P.; Shaposhnikov, D.; Osiptsov, A.

    2013-10-01

    We propose an approach for generalization of 1D transient model for multiphase flows. It allows to combine an arbitrary number of phases with interaction defined by multi-fluid and drift-flux models. Commonly a fluid carries a number of components. The model is based on a graph of fluids and components, where on higher level the flow of several fluids is governed by the multi-fluid approach, while on lower level the relative motion of components within each fluid is described by drift-flux relations. The proposed model is applied to flows in oil and gas wells. The model is implemented numerically using a SIMPLE-like iterative scheme with the geometry conservation based algorithm (GCBA). The numerical realization of the algorithm for an arbitrary number of fluids and components is presented. For illustration, particular cases are considered which are relevant to wellbore flows in oil and gas applications. The introduction of drift-flux correlations into the numerical implementation is discussed. The code is validated against experimental flow patterns and stability study of stratified flows. The typical graphs for gas/liquid transport are discussed. The simulation of phase segregation in a vertical pipe demonstrates the flexibility of model.

  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. 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).

  15. 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.

  16. 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

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

    PubMed

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

    2007-05-01

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

  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. Analysis of cell flux in the parallel plate flow chamber: implications for cell capture studies.

    PubMed Central

    Munn, L L; Melder, R J; Jain, R K

    1994-01-01

    The parallel plate flow chamber provides a controlled environment for determinations of the shear stress at which cells in suspension can bind to endothelial cell monolayers. By decreasing the flow rate of cell-containing media over the monolayer and assessing the number of cells bound at each wall shear stress, the relationship between shear force and binding efficiency can be determined. The rate of binding should depend on the delivery of cells to the surface as well as the intrinsic cell-surface interactions; thus, only if the cell flux to the surface is known can the resulting binding curves be interpreted correctly. We present the development and validation of a mathematical model based on the sedimentation rate and velocity profile in the chamber for the delivery of cells from a flowing suspension to the chamber surface. Our results show that the flux depends on the bulk cell concentration, the distance from the entrance point, and the flow rate of the cell-containing medium. The model was then used in a normalization procedure for experiments in which T cells attach to TNF-alpha-stimulated HUVEC monolayers, showing that a threshold for adhesion occurs at a shear stress of about 3 dyn/cm2. Images FIGURE 1 FIGURE 2 PMID:7948702

  2. Heat flux sensor calibration using noninteger system identification: Theory, experiment, and error analysis

    SciTech Connect

    Gardarein, Jean-Laurent; Battaglia, Jean-Luc; Loehle, Stefan

    2009-02-15

    This paper concerns the improvement of the calibration technique of null point calorimeters generally used in high enthalpy plasma flows. Based on the linearity assumption, this technique leads to calculate the impulse response that relates the heat flux at the tip of the sensor according to the temperature at the embedded thermocouple close to the heated surface. The noninteger system identification (NISI) procedure is applied. The NISI technique had been well described in previous study. The present work focuses on the accuracy of the identified system in terms of absorbed heat flux during the calibration experiment and of the estimated parameters in the model. The impulse response is thus calculated along with its associated standard deviation. Furthermore, this response is compared with that of the one-dimensional semi-infinite medium, which is classically used in practical applications. The asymptotic behavior of the identified system at the short times is analyzed for a better understanding of the noninteger identified system. Finally, the technique was applied to a new sensor geometry that has been developed particularly for high enthalpy plasma flows and it is shown that the method can be applied to any geometry suitable for a certain test configuration.

  3. Characteristic analysis and comparison of axial flux machines according to magnetization pattern for 500 W-class wind power generator application

    NASA Astrophysics Data System (ADS)

    Park, Yu-Seop; Jang, Seok-Myeong; Ko, Kyoung-Jin; Choi, Jang-Young; Sung, So-Young

    2012-04-01

    This paper presents the electromagnetic characteristic analysis of axial flux machines applied to 500(W) class wind power generators. For the dramatic analysis time reduction, analytical method is applied, and comparative analysis is performed according to magnetization patterns of permanent magnets. Due to their structural features, quasi 3-dimensional analysis is employed, and correction function is introduced to consider the flux leakage of the machines. The analysis results are compared with the results by finite element method and experiment to validate the suggested method performed in this paper showing high reliability.

  4. Natural Isotopic Signatures of Variations in Body Nitrogen Fluxes: A Compartmental Model Analysis

    PubMed Central

    Poupin, Nathalie; Mariotti, François; Huneau, Jean-François; Hermier, Dominique; Fouillet, Hélène

    2014-01-01

    Body tissues are generally 15N-enriched over the diet, with a discrimination factor (Δ15N) that varies among tissues and individuals as a function of their nutritional and physiopathological condition. However, both 15N bioaccumulation and intra- and inter-individual Δ15N variations are still poorly understood, so that theoretical models are required to understand their underlying mechanisms. Using experimental Δ15N measurements in rats, we developed a multi-compartmental model that provides the first detailed representation of the complex functioning of the body's Δ15N system, by explicitly linking the sizes and Δ15N values of 21 nitrogen pools to the rates and isotope effects of 49 nitrogen metabolic fluxes. We have shown that (i) besides urea production, several metabolic pathways (e.g., protein synthesis, amino acid intracellular metabolism, urea recycling and intestinal absorption or secretion) are most probably associated with isotope fractionation and together contribute to 15N accumulation in tissues, (ii) the Δ15N of a tissue at steady-state is not affected by variations of its P turnover rate, but can vary according to the relative orientation of tissue free amino acids towards oxidation vs. protein synthesis, (iii) at the whole-body level, Δ15N variations result from variations in the body partitioning of nitrogen fluxes (e.g., urea production, urea recycling and amino acid exchanges), with or without changes in nitrogen balance, (iv) any deviation from the optimal amino acid intake, in terms of both quality and quantity, causes a global rise in tissue Δ15N, and (v) Δ15N variations differ between tissues depending on the metabolic changes involved, which can therefore be identified using simultaneous multi-tissue Δ15N measurements. This work provides proof of concept that Δ15N measurements constitute a new promising tool to investigate how metabolic fluxes are nutritionally or physiopathologically reorganized or altered. The existence of such

  5. 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

  6. 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%).

  7. Heat-flux measurements for the rotor of a full-stage turbine. II - Description of analysis technique and typical time-resolved measurements

    NASA Technical Reports Server (NTRS)

    Dunn, M. G.; George, W. K.; Rae, W. J.; Woodward, S. H.; Moller, J. C.

    1986-01-01

    An analytical technique for obtaining the time-resolved heat flux of a turbine blade is applied to the case of a TFE 731-2 hp full-stage rotating turbine. In order to obtain the heat flux values from the thin film gage temperature histories, a finite difference procedure is used to solve the heat equation with variable thermal properties. After setting out the data acquisition and analysis procedures, their application is illustrated for three midspan locations on the blade and operation at the design flow function. Results demonstrate that the magnitude of the heat flux fluctuation due to vane-balde interaction is large by comparison to the time-averaged heat flux at all investigated locations; FFT of a portion of the heat flux record illustrates that the dominant frequencies occur at the wake-cutting frequency and its harmonics.

  8. Inference of physical phenomena from FFTF (Fast Flux Test Facility) noise analysis

    SciTech Connect

    Thie, J.A.; Damiano, B.; Campbell, L.R.

    1989-01-01

    The source of features observed in noise spectra collected by an automated data collection system operated by the Oak Ridge National Laboratory at the Fast Flux Test Facility (FFTF) can be identified using a methodology based on careful data observation and intuition. When a large collection of data is available, as in this case, automatic pattern recognition and parameter storage and retrieval using a data base can be used to extract useful information. However, results can be limited to empirical signature comparison monitoring unless an effort is made to determine the noise sources. This paper describes the identification of several FFTF noise data phenomena and suggests how this understanding may lead to new or enhanced monitoring. 13 refs., 4 figs.

  9. 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.

  10. 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

  11. Genome-scale metabolic network reconstruction and in silico flux analysis of the thermophilic bacterium Thermus thermophilus HB27

    PubMed Central

    2014-01-01

    Background Thermus thermophilus, an extremely thermophilic bacterium, has been widely recognized as a model organism for studying how microbes can survive and adapt under high temperature environment. However, the thermotolerant mechanisms and cellular metabolism still remains mostly unravelled. Thus, it is highly required to consider systems biological approaches where T. thermophilus metabolic network model can be employed together with high throughput experimental data for elucidating its physiological characteristics under such harsh conditions. Results We reconstructed a genome-scale metabolic model of T. thermophilus, iTT548, the first ever large-scale network of a thermophilic bacterium, accounting for 548 unique genes, 796 reactions and 635 unique metabolites. Our initial comparative analysis of the model with Escherichia coli has revealed several distinctive metabolic reactions, mainly in amino acid metabolism and carotenoid biosynthesis, producing relevant compounds to retain the cellular membrane for withstanding high temperature. Constraints-based flux analysis was, then, applied to simulate the metabolic state in glucose minimal and amino acid rich media. Remarkably, resulting growth predictions were highly consistent with the experimental observations. The subsequent comparative flux analysis under different environmental conditions highlighted that the cells consumed branched chain amino acids preferably and utilized them directly in the relevant anabolic pathways for the fatty acid synthesis. Finally, gene essentiality study was also conducted via single gene deletion analysis, to identify the conditional essential genes in glucose minimal and complex media. Conclusions The reconstructed genome-scale metabolic model elucidates the phenotypes of T. thermophilus, thus allowing us to gain valuable insights into its cellular metabolism through in silico simulations. The information obtained from such analysis would not only shed light on the

  12. 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 %. PMID:25563837

  13. 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.

  14. 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

  15. Analysis of carbon dioxide, water vapour and energy fluxes over an Indian teak mixed deciduous forest for winter and summer months using eddy covariance technique

    NASA Astrophysics Data System (ADS)

    Jha, Chandra Shekhar; Thumaty, Kiran Chand; Rodda, Suraj Reddy; Sonakia, Ajit; Dadhwal, Vinay Kumar

    2013-10-01

    In the present study, we report initial results on analysis of carbon dioxide (CO2), water vapour (H2O), and energy fluxes (sensible and latent heat flux) over teak mixed deciduous forests of Madhya Pradesh, central India, during winter (November 2011 and January 2012) and summer (February-May 2012) seasons using eddy covariance flux tower datasets. During the study period, continuous fast response measurements of CO2, H2O and heat fluxes above the canopy were carried out at 10 Hz and averaged for 30 minutes. Concurrently, slow response measurements of meteorological parameters are also being carried out. Diurnal and seasonal variations of CO2, H2O and heat fluxes were analysed and correlated with the meteorological variables. The study showed strong influence of leaf off and on scenario on the CO2, H2O and energy fluxes due to prevalence of deciduous vegetation type in the study area. Maximum amount of CO2 was sequestered for photosynthesis during winter (monthly mean of mol/m2/s) compared to summer (monthly mean of mol/m2/s). Energy flux analysis (weekly mean) showed more energy being portioned into latent heat during winter (668 W/m2) and sensible heat during summer (718 W/m2).

  16. Control analysis applied to the whole body: control by body organs over plasma concentrations and organ fluxes of substances in the blood.

    PubMed

    Brown, G C

    1994-01-01

    Metabolic control analysis is adapted as a method for describing and analysing the control by organs in the body over the fluxes and concentrations of substances carried in the blood. This physiological control analysis can most usefully be applied to substances with fluxes into and out of organs that are uniquely dependent only on their plasma concentrations. The organ flux of a substance is defined as the steady-state net flux of a substance into a particular organ. The organ flux control coefficients quantify the extent to which a particular organ controls the flux of a substance into the same or another particular organ. Organ concentration control coefficients quantify the extent to which an organ controls the steady-state concentration of a substance in the blood. The control coefficients are additive and obey summation, connectivity and branching theorems. Thus the control coefficients can be determined experimentally by measuring the sensitivities (elasticities) of organ fluxes to the plasma concentration of the substance. As an example of the application of these concepts, the control of ketone-body metabolism in vivo is analysed using data from the literature. PMID:8280089

  17. 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

  18. 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

  19. System Identification Algorithm Analysis of Acupuncture Effect on Mean Blood Flux of Contralateral Hegu Acupoint

    PubMed Central

    Wang, Guangjun; Han, Jianguo; Litscher, Gerhard; Zhang, Weibo

    2012-01-01

    Background. Acupoints (belonging to 12 meridians) which have the same names are symmetrically distributed on the body. It has been proved that acupoints have certain biological specificities different from the normal parts of the body. However, there is little evidence that acupoints which have the same name and are located bilaterally and symmetrically have lateralized specificity. Thus, researching the lateralized specificity and the relationship between left-side and right-side acupuncture is of special importance. Methodology and Principal Findings. The mean blood flux (MBF) in both Hegu acupoints was measured by Moor full-field laser perfusion imager. With the method of system identification algorithm, the output distribution in different groups was acquired, based on different acupoint stimulation and standard signal input. It is demonstrated that after stimulation of the right Hegu acupoint by needle, the output value of MBF in contralateral Hegu acupoint was strongly amplified, while after acupuncturing the left Hegu acupoint, the output value of MBF in either side Hegu acupoint was amplified moderately. Conclusions and Significance. This paper indicates that the Hegu acupoint has lateralized specificity. After stimulating the ipsilateral Hegu acupoint, symmetry breaking will be produced in contrast to contralateral Hegu acupoint stimulation. PMID:22693535

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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...

  5. 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

  6. 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

  7. 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.

  8. Predicting riverine dissolved silica fluxes by chemical weathering: results from a hyperactive region and analysis of first-order controls

    NASA Astrophysics Data System (ADS)

    Hartmann, Jens; Jansen, Nils; Dürr, Hans H.; Harashima, Akira; Okubo, Kenji; Kempe, Stephan

    2010-05-01

    misinterpreted land cover information from satellite images. Implications of results for chemical weathering rates based on lithological information applied are discussed. Reference: Hartmann, J., Jansen, N., Dürr, H.H., Harashima, A., Okubo, K., Kempe S. (2010) Predicting riverine dissolved silica fluxes into coastal zones from a hyperactive region and analysis of their first order controls. International Journal of Earth Sciences, 99(1), 207-230. doi:10.1007/s00531-008-0381-5.

  9. 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.

  10. Statistical analysis of the flux of micrometeoroids at Mercury from both cometary and asteroidal components

    NASA Astrophysics Data System (ADS)

    Borin, P.; Cremonese, G.; Marzari, F.

    2016-01-01

    Context. Meteoroid impacts are an important source of neutral atoms for the exosphere of Mercury. We previously estimated the contribution of meteoroids originating in the asteroid belt for vapor release. In this paper, we concentrate on the cometary component of particles impacting the planet. Comets and asteroids are considered to be the two major sources of interplanetary dust particles in the solar system. The debate about which source contributes most to dust populating the solar system is still ongoing. Aims: In this work, we compute the orbital evolution of dust particles produced by Jupiter-family comets (JFC) via N-body numerical integrations. From our numerical simulations, we compute the fraction of particles hitting Earth and Mercury's surface and the corresponding distribution of impact velocities. According to some authors more than 80% of all the incoming mass of meteoroids entering the Earth's atmosphere is concentrated in the mass range 10-7-10-3 g. In our model, we considered a slightly different range, 10-9 to 10-6 g, to include possible uncertainty. Methods: The orbital evolution of dust particles of different sizes is computed with a numerical integration code, which includes the effects of Poynting-Robertson drag, solar wind drag, and planetary perturbations. Results: By comparing the impact frequency of grains evolving either from main belt asteroids or JFC we find that the cometary component is significantly less efficient in releasing dust particles on Mercury than on the Earth. The opposite occurs in the case of dust coming from the main belt with a flux higher at Mercury than on the Earth. This is mostly due to the different dynamical histories of the grains from their release until impact. This may have important implications for the vapor production rate on Mercury. We compare our results with previous estimates given by different authors.

  11. Analysis of the relationship between photosynthetic photon flux density and natural Taxus baccata seedlings occurrence

    NASA Astrophysics Data System (ADS)

    Iszkuło, Grzegorz; Boratyński, Adam

    2006-01-01

    The aim of the present work was to analyse the relationship of seedlings and saplings of Taxus baccata to the photosynthetic photon flux density (PPFD) reaching the forest floor under natural conditions. Two permanent plots, subdivided into 1 × 1 m square plots, were established in a naturally regenerating population of T. baccata formed during last decades in the Kórnik Arboretum, Poland. All seedlings in every 1 × 1 m plots were counted. Relative PPFD was measured for every plot at the canopy height of the yew seedlings. The dependence of seedling density upon PPFD was examined. We found, that the frequency of the smallest seedlings (to 6.0 cm tall) was highest in the most shaded plots and decreased in plots with increasing PPFD. Thus, the youngest yew seedlings can germinate and grow in very shady conditions. However, the older seedlings (6.1-25.0 and 25.1-100.0 classes) were observed most frequently in 2-7% PPFD. The small numbers of older, taller seedlings in deep shade likely indicate a higher mortality rate of seedlings less than 6 cm in height without promotion to the next height class. Probably the low value of PPFD under the canopy of the stand significantly reduces the competition of other plants with the youngest yew seedlings. At higher light levels they may not be able to compete with more light-demanding plants, such as herbs and seedlings of broad-leaved trees. The seedlings of the second (6.1-25.0 cm) and third (25.1-100.0 cm) height classes were observed most frequently in the plots with 2-7% PPFD ( Fig. 1b and c).

  12. Effects of experimental nitrogen deposition on peatland carbon pools and fluxes: a modelling analysis

    NASA Astrophysics Data System (ADS)

    Wu, Y.; Blodau, C.; Moore, T. R.; Bubier, J.; Juutinen, S.; Larmola, T.

    2015-01-01

    Nitrogen (N) pollution of peatlands alters their carbon (C) balances, yet long-term effects and controls are poorly understood. We applied the model PEATBOG to explore impacts of long-term nitrogen (N) fertilization on C cycling in an ombrotrophic bog. Simulations of summer gross ecosystem production (GEP), ecosystem respiration (ER) and net ecosystem exchange (NEE) were evaluated against 8 years of observations and extrapolated for 80 years to identify potential effects of N fertilization and factors influencing model behaviour. The model successfully simulated moss decline and raised GEP, ER and NEE on fertilized plots. GEP was systematically overestimated in the model compared to the field data due to factors that can be related to differences in vegetation distribution (e.g. shrubs vs. graminoid vegetation) and to high tolerance of vascular plants to N deposition in the model. Model performance regarding the 8-year response of GEP and NEE to N input was improved by introducing an N content threshold shifting the response of photosynthetic capacity (GEPmax) to N content in shrubs and graminoids from positive to negative at high N contents. Such changes also eliminated the competitive advantages of vascular species and led to resilience of mosses in the long-term. Regardless of the large changes of C fluxes over the short-term, the simulated GEP, ER and NEE after 80 years depended on whether a graminoid- or shrub-dominated system evolved. When the peatland remained shrub-Sphagnum-dominated, it shifted to a C source after only 10 years of fertilization at 6.4 g N m-2 yr-1, whereas this was not the case when it became graminoid-dominated. The modelling results thus highlight the importance of ecosystem adaptation and reaction of plant functional types to N deposition, when predicting the future C balance of N-polluted cool temperate bogs.

  13. Effects of experimental nitrogen deposition on peatland carbon pools and fluxes: a modeling analysis

    NASA Astrophysics Data System (ADS)

    Wu, Y.; Blodau, C.; Moore, T. R.; Bubier, J. L.; Juutinen, S.; Larmola, T.

    2014-07-01

    Nitrogen (N) pollution of peatlands alters their carbon (C) balances, yet long-term effects and controls are poorly understood. We applied the model PEATBOG to analyze impacts of long-term nitrogen (N) fertilization on C cycling in an ombrotrophic bog. Simulations of summer gross ecosystem production (GEP), ecosystem respiration (ER) and net ecosystem exchange (NEE) were evaluated against 8 years of observations and extrapolated for 80 years to identify potential effects of N fertilization and factors influencing model behavior. The model successfully simulated moss decline and raised GEP, ER and NEE on fertilized plots. GEP was systematically overestimated in the model compared to the field data due to high tolerance of Sphagnum to N deposition in the model. Model performance regarding the 8 year response of GEP and NEE to N was improved by introducing an N content threshold shifting the response of photosynthesis capacity to N content in shrubs and graminoids from positive to negative at high N contents. Such changes also eliminated the competitive advantages of vascular species and led to resilience of mosses in the long-term. Regardless of the large changes of C fluxes over the short-term, the simulated GEP, ER and NEE after 80 years depended on whether a graminoid- or shrub-dominated system evolved. When the peatland remained shrub-Sphagnum dominated, it shifted to a C source after only 10 years of fertilization at 6.4 g N m-2 yr-1, whereas this was not the case when it became graminoid-dominated. The modeling results thus highlight the importance of ecosystem adaptation and reaction of plant functional types to N deposition, when predicting the future C balance of N-polluted cool temperate bogs.

  14. 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

  15. 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...

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

    PubMed

    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

  17. 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.

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

    NASA Astrophysics Data System (ADS)

    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.

  19. 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

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

    PubMed Central

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

    2012-01-01

    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

  1. A 25-Year Retrospective Analysis of River Nitrogen Fluxes in the Atchafalaya

    NASA Astrophysics Data System (ADS)

    Xu, Y.

    2005-05-01

    Nitrogen enrichment from the upper Mississippi River Basin has been attributed to be the major cause for the hypoxia in the Northern Gulf of Mexico. The hypoxia threatens not only the aquatic ecosystem health but Louisiana's fishery industry directly among other problems. Although fresh water diversion from the lower Mississippi River into the region's wetlands has been considered an alternative means for reducing nitrogen loading, it is largely uncertain how much nitrogen can actually be retained from the overflowing waters in these natural wetlands. Generally, there is a knowledge gap in what tools are available for accurate assessment of nitrogen inflow, outflow and removal potential for the complex and diverse coastal floodplain systems. This study is to seek answers to three critical questions: (1) Does the Atchafalaya River Swamp remove a significant amount of nitrogen from the overflowing water or release more nitrogen into the Gulf than removing it? (2) How seasonally and annually do the nitrogen removal or release rates fluctuate? (3) What are the relationships between the nitrogen removal capacity and the basin's hydrologic conditions such as river stage and discharge? By utilizing river's long-term discharge and water quality data (1978-2002), monthly and annual nitrogen fluxes were quantified, and their relationships with the basin's hydrologic conditions were investigated. A total Kjeldahl nitrogen (TKN) mass input-output balance between the upstream (Simmesport) and downstream (Morgan City and Wax Lake Outlet) locations was established to examine the organic nitrogen removal potential for this largest freshwater swamp basin in North America. The results showed that on average, TKN input into the Atchafalaya was 200,323 Mg yr-1 and TKN output leaving the basin was 145,917 Mg yr-1, resulting in a 27% removal rate of nitrogen. Monthly nitrogen input and output in the basin were highest from March to June (input vs. output: 25,000 vs. 18,000 Mg mon-1) and

  2. 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

  3. Metabolic flux and metabolic network analysis of Penicillium chrysogenum using 2D [13C, 1H] COSY NMR measurements and cumulative bondomer simulation.

    PubMed

    van Winden, Wouter A; van Gulik, Walter M; Schipper, Dick; Verheijen, Peter J T; Krabben, Preben; Vinke, Jacobus L; Heijnen, Joseph J

    2003-07-01

    At present two alternative methods are available for analyzing the fluxes in a metabolic network: (1) combining measurements of net conversion rates with a set of metabolite balances including the cofactor balances, or (2) leaving out the cofactor balances and fitting the resulting free fluxes to measured (13)C-labeling data. In this study these two approaches are applied to the fluxes in the glycolysis and pentose phosphate pathway of Penicillium chrysogenum growing on either ammonia or nitrate as the nitrogen source, which is expected to give different pentose phosphate pathway fluxes. The presented flux analyses are based on extensive sets of 2D [(13)C, (1)H] COSY data. A new concept is applied for simulation of this type of (13)C-labeling data: cumulative bondomer modeling. The outcomes of the (13)C-labeling based flux analysis substantially differ from those of the pure metabolite balancing approach. The fluxes that are determined using (13)C-labeling data are shown to be highly dependent on the chosen metabolic network. Extending the traditional nonoxidative pentose phosphate pathway with additional transketolase and transaldolase reactions, extending the glycolysis with a fructose 6-phosphate aldolase/dihydroxyacetone kinase reaction sequence or adding a phosphoenolpyruvate carboxykinase reaction to the model considerably improves the fit of the measured and the simulated NMR data. The results obtained using the extended version of the nonoxidative pentose phosphate pathway model show that the transketolase and transaldolase reactions need not be assumed reversible to get a good fit of the (13)C-labeling data. Strict statistical testing of the outcomes of (13)C-labeling based flux analysis using realistic measurement errors is demonstrated to be of prime importance for verifying the assumed metabolic model. PMID:12740935

  4. 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

  5. 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.

  6. Statistical Analysis of Peptide-Induced Graded and All-or-None Fluxes in Giant Vesicles

    PubMed Central

    Wheaten, Sterling A.; Lakshmanan, Aruna; Almeida, Paulo F.

    2013-01-01

    Antimicrobial, cytolytic, and cell-penetrating peptides induce pores or perturbations in phospholipid membranes that result in fluxes of dyes into or out of lipid vesicles. Here we examine the fluxes induced by four of these membrane-active peptides in giant unilamellar vesicles. The type of flux is determined from the modality of the distributions of vesicles as a function of their dye content using the statistical Hartigan dip test. Graded and all-or-none fluxes correspond to unimodal and bimodal distributions, respectively. To understand how these distributions arise, we perform Monte Carlo simulations of peptide-induced dye flux into vesicles using a very simple model. The modality of the distributions depends on the rate constants of pore opening and closing, and dye flux. If the rate constants of pore opening and closing are both much smaller than that of dye flux through the pore, all-or-none influx occurs. However, if one of them, especially the rate constant for pore opening, increases significantly relative to the flux rate constant, the process becomes graded. In the experiments, we find that the flux type is the same in giant and large vesicles, for all peptides except one. But this one exception indicates that the flux type cannot be used to unambiguously predict the mechanism of membrane permeabilization by the peptides. PMID:23870264

  7. 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

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

    SciTech Connect

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

    2012-11-07

    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)], 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)], 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 distribution of energy transfer pathways.

  9. 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

  10. 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

  11. 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

  12. Spectral index of solar cosmic-ray flux from the analysis of ground-level enhancements

    NASA Astrophysics Data System (ADS)

    Caballero-Lopez, R. A.; Moraal, H.

    2016-03-01

    In this work we analyze the ground-level enhancement of the cosmic-ray intensity due to solar energetic particles as observed on 29 September 1989, by using two pairs of standard and lead-free neutron monitors. This enables one to separate spectral and anisotropy effects. This has been done previously by several authors for other events, but in this paper we make use of the large size and long duration of this event, as well as the fact that it is perhaps the best-observed one in the whole data base since 1942. It is shown that the method is more sensitive than the standard method that uses neutron monitors at different locations. The analysis provides a prototype for what can potentially be achieved by a new generation of mini neutron monitors.

  13. 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

  14. CLUMPY: Jeans analysis, γ-ray and ν fluxes from dark matter (sub-)structures

    NASA Astrophysics Data System (ADS)

    Bonnivard, Vincent; Hütten, Moritz; Nezri, Emmanuel; Charbonnier, Aldée; Combet, Céline; Maurin, David

    2016-03-01

    We present an update of the CLUMPY code for the calculation of the astrophysical J-factors (from dark matter annihilation/decay) for any Galactic or extragalactic dark matter halo including substructures: halo-to-halo concentration scatter may now be enabled, boost factors can include several levels of substructures, and triaxiality is a new option for dark matter haloes. This new version takes advantage of the cfitsio and HEALPix libraries to propose fits output maps using the HEALPix pixelisation scheme. Skymaps for γ-ray and ν signals from generic annihilation/decay spectra are now direct outputs of CLUMPY. Making use of HEALPix routines, smoothing by a user-defined instrumental Gaussian beam and computing the angular power spectrum of the maps are now possible. In addition to these improvements, the main novelty is the implementation of a Jeans analysis module, to obtain dark matter density profiles from kinematic data in relaxed spherical systems (e.g., dwarf spheroidal galaxies). The code is also interfaced with the GreAT toolkit designed for Markov Chain Monte Carlo analyses, from which probability density functions and credible intervals can be obtained for velocity dispersions, dark matter profiles, and J-factors.

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. 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

  1. 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

  2. High-frequency analysis of the complex linkage between soil CO(2) fluxes, photosynthesis and environmental variables.

    PubMed

    Martin, Jonathan G; Phillips, Claire L; Schmidt, Andres; Irvine, James; Law, Beverly E

    2012-01-01

    High-frequency soil CO(2) flux data are valuable for providing new insights into the processes of soil CO(2) production. A record of hourly soil CO(2) fluxes from a semi-arid ponderosa pine stand was spatially and temporally deconstructed in attempts to determine if variation could be explained by logical drivers using (i) CO(2) production depths, (ii) relationships and lags between fluxes and soil temperatures, or (iii) the role of canopy assimilation in soil CO(2) flux variation. Relationships between temperature and soil fluxes were difficult to establish at the hourly scale because diel cycles of soil fluxes varied seasonally, with the peak of flux rates occurring later in the day as soil water content decreased. Using a simple heat transport/gas diffusion model to estimate the time and depth of CO(2) flux production, we determined that the variation in diel soil CO(2) flux patterns could not be explained by changes in diffusion rates or production from deeper soil profiles. We tested for the effect of gross ecosystem productivity (GEP) by minimizing soil flux covariance with temperature and moisture using only data from discrete bins of environmental conditions (±1 °C soil temperature at multiple depths, precipitation-free periods and stable soil moisture). Gross ecosystem productivity was identified as a possible driver of variability at the hourly scale during the growing season, with multiple lags between ~5, 15 and 23 days. Additionally, the chamber-specific lags between GEP and soil CO(2) fluxes appeared to relate to combined path length for carbon flow (top of tree to chamber center). In this sparse and heterogeneous forested system, the potential link between CO(2) assimilation and soil CO(2) flux may be quite variable both temporally and spatially. For model applications, it is important to note that soil CO(2) fluxes are influenced by many biophysical factors, which may confound or obscure relationships with logical environmental drivers and act at

  3. 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. PMID:26265776

  4. Fuel-Coolant-Interaction modeling and analysis work for the High Flux Isotope Reactor Safety Analysis Report

    SciTech Connect

    Taleyarkhan, R.P.; Georgevich, V.; Nestor, C.W.; Chang, S.J.; Freels, J.; Gat, U.; Lepard, B.L.; Gwaltney, R.C.; Luttrell, C.; Kirkpatrick, J.

    1993-07-01

    A brief historical background and a description of short- and long-term task plan development for effective closure of this important safety issue for the HFIR are given. Short-term aspects deal with Fuel-Coolant-Interaction (FCI) issues experimentation, modeling, and analysis for the flow-blockage-induced steam explosion events in direct support of the SAR. Long-term aspects deal with addressing FCI issues resulting from other accidents in conjunction with issues dealing with aluminum ignition, which can result in an order of magnitude increase in overall energetics. Problem formulation, modeling, and computer code simulation for the various phases of steam explosions are described. The evaluation of core melt initiation propagation, and melt superheat are described. Core melt initiation and propagation have been studied using simple conservative models as well as from modeling and analysis using RELAP5. Core debris coolability, heatup, and melting/freezing aspects have been studied by use of the two-dimensional melting/freezing analysis code 2DKO, which was also benchmarked with MELCOR code predictions. Descriptions are provided for the HM, BH, FCIMOD, and CTH computer codes that have been implemented for studying steam explosion energetics from the standpoint of evaluating bounding loads by thermodynamic models or best-estimate loads from one- and two-dimensional simulations of steam explosion energetics. Vessel failure modeling and analysis was conducted using the principles of probabilistic fracture mechanics in conjunction with ADINA code calculations. Top head bolts failure modeling has also been conducted where the failure criterion was based upon stresses in the bolts exceeding the material yield stress for a given time duration. Missile transport modeling and analysis was conducted by setting up a one-dimensional mathematical model that accounts for viscous dissipation, virtual mass effects, and material inertia.

  5. 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. PMID:26536879

  6. Wavelet analysis of Laser Doppler Flux time series of tumor and inflammatory associated neoangiogenesis. Differences in rhythmical behavior.

    PubMed

    Häfner, Hans-Martin; Bräuer, Kurt; Radke, Carolin; Eichner, Martin; Strölin, Anke

    2009-01-01

    We use continuous wavelet analysis (WA) of Laser Doppler Flux (LDF) time series measured in basal cell carcinomas (BCC) and plaque psoriasis (PP) in order to investigate the rhythmical behavior of blood flow in tumor or inflammatory associated neoangiogenesis.A total of 68 patients with primary BCCs and 40 patients with PP were included in the study. LDF time series were separated in four scaling levels corresponding to the influences of sympathetic activity (SL1), myogenic activity in the vessel wall (SL2), respiration (SL3) and heart beat (SL4).In BCC, SL1 decreased compared to healthy skin. In all other scaling levels, we found a statistically significant increase of the SLs compared to healthy skin. These increases were not found in PP.Rhythmical behavior of blood flow in malignant tumors is totally different from that in regions with inflammation. In BCCs, thermoregulatory processes, ascribed to sympathetic activity, decrease statistically significant. In contrast, inflammatory processes in PP do not substantially change sympathetic activity. WA of tumor perfusion could open a new noninvasive monitor system for controlling tumor therapy. PMID:19847053

  7. Design and analysis of a transverse flux permanent-magnet machine using three-dimensional scalar magnetic potential finite element method

    NASA Astrophysics Data System (ADS)

    Wang, Jiankuan; Chau, K. T.; Jiang, J. Z.; Yu, Chuang

    2008-04-01

    In this paper, a new transverse flux permanent-magnet machine is proposed and implemented. It features a unique configuration that it is composed of assembled stators and flux-concentrating rotor, hence offering low manufacturing cost while retaining high torque density and low cogging torque. Because of its unique configuration, the proposed machine is analyzed by a newly developed three-dimensional scalar magnetic potential finite element method. Both calculated and experimental results are given to support the validity of the proposed design and analysis.

  8. Ecosystem function and particle flux dynamics across the Mackenzie Shelf (Beaufort Sea, Arctic Ocean): an integrative analysis of spatial variability and biophysical forcings

    NASA Astrophysics Data System (ADS)

    Forest, A.; Babin, M.; Stemmann, L.; Picheral, M.; Sampei, M.; Fortier, L.; Gratton, Y.; Bélanger, S.; Devred, E.; Sahlin, J.; Doxaran, D.; Joux, F.; Ortega-Retuerta, E.; Jeffrey, W. H.; Martín, J.; Gasser, B.; Miquel, J. C.

    2012-08-01

    A better understanding of how environmental changes affect organic matter fluxes in Arctic marine ecosystems is sorely needed. Here, we combine mooring times-series, ship-based measurements and remote-sensing to assess the variability and forcing factors of vertical fluxes of particulate organic carbon (POC) across the Mackenzie Shelf in 2009. We developed a geospatial model of these fluxes to proceed to an integrative analysis of their biophysical determinants in summer. Flux data were obtained with sediment traps and via a regional empirical algorithm applied to particle size-distributions (17 classes from 0.08-4.2 mm) measured by an Underwater Vision Profiler 5. Redundancy analyses and forward selection of abiotic/biotic parameters, linear trends, and spatial structures (i.e. principal coordinates of neighbor matrices, PCNM), were conducted to partition the variation of POC flux size-classes. Flux variability was explained at 69.5 % by the addition of a linear temporal trend, 7 significant PCNM and 9 biophysical variables. The interaction of all these factors explained 27.8 % of the variability. The first PCNM canonical axis (44.4 % of spatial variance) reflected a shelf-basin gradient controlled by bottom depth and ice concentration (p < 0.01), but a complex assemblage of fine-to-broad scale patterns was also identified. Among biophysical parameters, bacterial production and northeasterly wind (upwelling-favorable) were the two strongest explanatory variables (r2 cum. = 0.37), suggesting that bacteria were associated with sinking material, which was itself partly linked to upwelling-induced productivity. The second most important spatial structure corresponded actually to the two areas where shelf break upwelling is known to occur under easterlies. Copepod biomass was negatively correlated (p < 0.05) with vertical POC fluxes, implying that metazoans played a significant role in the regulation of export fluxes. The low fractal dimension of settling particles (1

  9. A critical review and analysis of the use of exposure- and flux-based ozone indices for predicting vegetation effects

    NASA Astrophysics Data System (ADS)

    Musselman, Robert C.; Lefohn, Allen S.; Massman, William J.; Heath, Robert L.

    Early studies of plant response to ozone (O 3) utilized concentration-based metrics, primarily by summarizing the commonly monitored hourly average data sets. Research with the O 3 concentration parameter led to the recognition that both peak concentrations and cumulative effects are important when relating plant response to O 3. The US and Canada currently use O 3 concentration-based (exposure-based) parameters for ambient air quality standards for protecting vegetation; the European countries use exposure-based critical levels to relate O 3 to vegetation response. Because plant response is thought to be more closely related to O 3 absorbed into leaf tissue, recent research has been focused on flux-based O 3 parameters. Even though flux-based indices may appear to be more biologically relevant than concentration-based indices, there are limitations associated with their use. The current set of flux-based indices assumes that the plant has no defense mechanism to detoxify O 3. This is a serious limitation. In this paper, we review the literature on exposure- and flux-based indices for predicting plant response. Both exposure- and flux-based metrics may overestimate plant response. At this time, flux-based models that take into consideration detoxification mechanisms (referred to as effective flux) provide the best approach to relate O 3 to plant response. However, because there is considerable uncertainty in quantifying the various defense mechanisms, effective flux at this time is difficult to quantify. Without adequate effective-flux based models, exposure-based O 3 metrics appear to be the only practical measure for use in relating ambient air quality standards to vegetation response.

  10. Analysis of particles and carbon dioxide concentrations and fluxes in an urban area: Correlation with traffic rate and local micrometeorology

    NASA Astrophysics Data System (ADS)

    Contini, D.; Donateo, A.; Elefante, C.; Grasso, F. M.

    2012-01-01

    Number particle concentrations and fluxes were measured, synchronously with CO 2 concentrations and fluxes, in an urban area. Measurements were taken with an eddy-correlation station located near the busiest road of the town of Lecce (Italy). Upward fluxes dominate completely over deposition and the area behaved as a source of aerosol and CO 2 with an average particle flux F N = 71,100 #/cm 2 s (median 64,000 #/cm 2 s) and an average CO 2 flux F C = 0.76 mg/m 2 s (median 0.46 mg/m 2 s). Pronounced diurnal and weekly cycles of F N and F C were observed, well correlated with measured traffic rate, T R, indicating that traffic is the main source of CO 2 and particles in the area. Biogenic cycle on CO 2 fluxes and concentrations was also distinguishable, decreasing the correlation between F N and F C. The relationships between particle and CO 2 fluxes with T R, friction velocity and atmospheric stability were analysed. Measured F N/ T R increased when friction velocity increased and, correspondingly, number concentration decreased. Particle fluxes showed a dependence on the atmospheric stability. These dependencies were used to derive an empirical parameterisation of aerosol concentration and fluxes, based on T R and micrometeorological parameters, that could be used to estimate traffic emissions, in real operating conditions, for applications in dispersion and climate modelling. Measured F C/ T R showed a limited correlation with friction velocity and stability, because of the influence of the biogenic cycle, thereby micrometeorological parameters were not used in the parameterisation of F C.

  11. 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.

  12. Uncertainty analysis of eddy covariance CO2 flux measurements for different EC tower distances using an extended two-tower approach

    NASA Astrophysics Data System (ADS)

    Post, H.; Hendricks Franssen, H. J.; Graf, A.; Schmidt, M.; Vereecken, H.

    2014-08-01

    The use of eddy covariance CO2 flux measurements in data assimilation and other applications requires an estimate of the random uncertainty. In previous studies, the two-tower approach has yielded robust uncertainty estimates, but care must be taken to meet the often competing requirements of statistical independence (non-overlapping footprints) and ecosystem homogeneity when choosing an appropriate tower distance. The role of the tower distance was investigated with help of a roving station separated between 8 m and 34 km from a permanent EC grassland station. Random uncertainty was estimated for five separation distances with an extended two-tower approach which removed systematic differences of CO2 fluxes measured at two EC towers. This analysis was made for a dataset where (i) only similar weather conditions at the two sites were included and (ii) an unfiltered one. The extended approach, applied to weather-filtered data for separation distances of 95 m and 173 m gave uncertainty estimates in best correspondence with the independent reference method The introduced correction for systematic flux differences considerably reduced the overestimation of the two-tower based uncertainty of net CO2 flux measurements, e.g. caused by different environmental conditions at both EC towers. It is concluded that the extension of the two-tower approach can help to receive more reliable uncertainty estimates because systematic differences of measured CO2 fluxes which are not part of random error are filtered out.

  13. Uncertainty analysis of eddy covariance CO2 flux measurements for different EC tower distances using an extended two-tower approach

    NASA Astrophysics Data System (ADS)

    Post, H.; Hendricks Franssen, H. J.; Graf, A.; Schmidt, M.; Vereecken, H.

    2015-02-01

    The use of eddy covariance (EC) CO2 flux measurements in data assimilation and other applications requires an estimate of the random uncertainty. In previous studies, the (classical) two-tower approach has yielded robust uncertainty estimates, but care must be taken to meet the often competing requirements of statistical independence (non-overlapping footprints) and ecosystem homogeneity when choosing an appropriate tower distance. The role of the tower distance was investigated with help of a roving station separated between 8 m and 34 km from a permanent EC grassland station. Random uncertainty was estimated for five separation distances with the classical two-tower approach and an extended approach which removed systematic differences of CO2 fluxes measured at two EC towers. This analysis was made for a data set where (i) only similar weather conditions at the two sites were included, and (ii) an unfiltered one. The extended approach, applied to weather-filtered data for separation distances of 95 and 173 m gave uncertainty estimates in best correspondence with an independent reference method. The introduced correction for systematic flux differences considerably reduced the overestimation of the two-tower based uncertainty of net CO2 flux measurements and decreased the sensitivity of results to tower distance. We therefore conclude that corrections for systematic flux differences (e.g., caused by different environmental conditions at both EC towers) can help to apply the two-tower approach to more site pairs with less ideal conditions.

  14. 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

  15. 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

  16. Theoretical analysis of flux amplification by soft magnetic material in a putative biological magnetic-field receptor

    NASA Astrophysics Data System (ADS)

    Shcherbakov, Valera P.; Winklhofer, Michael

    2010-03-01

    Birds are endowed with a magnetic sense that allows them to detect Earth’s magnetic field and to use it for orientation. Physiological and behavioral experiments have shown the upper beak to host a magnetoreceptor. Putative magnetoreceptive structures in the beak are nerve terminals that each contain a dozen or so of micrometer-sized clusters of superparamagnetic nanocrystals made of magnetite/maghemite and numerous electron-opaque platelets filled with a so far unidentified, amorphous ferric iron compound. The platelets typically form chainlike structures, which have been proposed to function as magnetic flux focusers for detecting the intensity of the geomagnetic field. Here, we test that proposition from first principles and develop an unconstrained model to determine the equilibrium distribution of magnetization along a linear chain of platelets which we assume to behave magnetically soft and to have no magnetic remanence. Our analysis, which is valid for arbitrary values of the intrinsic magnetic susceptibility χ , shows that χ needs to be much greater than unity to amplify the external field by two orders of magnitude in a chain of platelets. However, the high amplification is confined to the central region of the chain and subsides quadratically toward the ends of the chain. For large values of χ , the possibility opens up of realizing magnetoreceptor mechanisms on the basis of attraction forces between adjacent platelets in a linear chain. The force in the central region of the chain may amount to several pN, which would be sufficient to convert magnetic input energy into mechanical output energy. The striking feature of an ensemble of platelets is its ability to organize into tightly spaced chains under the action of an external field of given strength. We discuss how this property can be exploited for a magnetoreception mechanism.

  17. 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. PMID:20597144

  18. 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.

  19. 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.

    2013-12-01

    Around 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 not well understood though. 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 v.3 model of the terrestrial biosphere and biomass burning driven by satellite observations and interannually varying meteorology. We also use measurement-based ocean flux estimates from Takahashi et al. [2009], and fixed fossil CO2 emissions from the CDIAC dataset. Here, we present preliminary results from our inversions that incorporate column CO2 measurements from the GOSAT satellite, ground-based observations (individual flask and afternoon-average continuous observations), and aircraft 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 obtain spatiotemporal distributions of fluxes resembling those from other inversions, including NOAA's CarbonTracker. We compare the a posteriori fluxes obtained with and without the addition of GOSAT observations to the in situ network, and discuss possible impacts of biases in the GOSAT data.

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

    PubMed

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

    2011-06-01

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

  1. 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

  2. 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

  3. 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

  4. Metabolic flux ratio analysis and multi-objective optimization revealed a globally conserved and coordinated metabolic response of E. coli to paraquat-induced oxidative stress.

    PubMed

    Shen, Tie; Rui, Bin; Zhou, Hong; Zhang, Ximing; Yi, Yin; Wen, Han; Zheng, Haoran; Wu, Jihui; Shi, Yunyu

    2013-01-27

    The ability of a microorganism to adapt to changes in the environment, such as in nutrient or oxygen availability, is essential for its competitive fitness and survival. The cellular objective and the strategy of the metabolic response to an extreme environment are therefore of tremendous interest and, thus, have been increasingly explored. However, the cellular objective of the complex regulatory structure of the metabolic changes has not yet been fully elucidated and more details regarding the quantitative behaviour of the metabolic flux redistribution are required to understand the systems-wide biological significance of this response. In this study, the intracellular metabolic flux ratios involved in the central carbon metabolism were determined by fractional (13)C-labeling and metabolic flux ratio analysis (MetaFoR) of the wild-type E. coli strain JM101 at an oxidative environment in a chemostat. We observed a significant increase in the flux through phosphoenolpyruvate carboxykinase (PEPCK), phosphoenolpyruvate carboxylase (PEPC), malic enzyme (MEZ) and serine hydroxymethyltransferase (SHMT). We applied an ε-constraint based multi-objective optimization to investigate the trade-off relationships between the biomass yield and the generation of reductive power using the in silico iJR904 genome-scale model of E. coli K-12. The theoretical metabolic redistribution supports that the trans-hydrogenase pathway should not play a direct role in the defence mounted by E. coli against oxidative stress. The agreement between the measured ratio and the theoretical redistribution established the significance of NADPH synthesis as the goal of the metabolic reprogramming that occurs in response to oxidative stress. Our work presents a framework that combines metabolic flux ratio analysis and multi-objective optimization to investigate the metabolic trade-offs that occur under varied environmental conditions. Our results led to the proposal that the metabolic response of E

  5. Statistical analysis of the sunspot area and magnetic flux variations in 1996 2005 extracted from the Solar Feature Catalogue

    NASA Astrophysics Data System (ADS)

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

    2006-01-01

    This research presents some statistical properties of sunspots and their magnetic fields extracted in from May 1996 to May 2005 from the SOHO/MDI full disk whitelight images and magnetograms for the searchable Solar Feature Catalogue (SFC) using the automated pattern recognition techniques. A comparison of the total sunspot areas on a given day from the SFC with the daily sunspot areas available from US AF SOON data for 2000-2004 reveal a very good correlation of the datasets with the correlation coefficient of ˜93%. The total sunspot areas in the Northern and Southern hemispheres measured from a single solar image and their cumulative areas during the whole cycle are shown to have a strong North-South asymmetry with the Northern hemisphere prevailing around and after the maximum while the Southern one Schatten taking over towards the coming solar minimum. The similar N-S asymmetry is observed in a total and resulting, or excess, magnetic fluxes. The former is found to follow closely the N-S asymmetry in the sunspot areas while the latter shows a very significant flux separation in the opposite hemispheres. The excess flux is negative in the Southern hemisphere and positive in the Northern one during a long period from 1997 until 2004. During the solar minimum in 1996, the signs of total excess fluxes in the hemispheres are changed to the opposite and a similar change appears in 2003-2004 towards the approaching solar minimum. Since the magnetic field in sunspots is those of the leading polarity, so the excess magnetic flux evolution is believed to show a change of the magnetic field leading polarity during the solar cycle minima, while the asymmetry of the total magnetic flux, possibly, reflects the asymmetry of a poloidal magnetic field, as it is predicted by the oscillatory dynamo models.

  6. Metabolic flux analysis of Arthrobacter sp. CGMCC 3584 for cAMP production based on 13C tracer experiments and gas chromatography-mass spectrometry.

    PubMed

    Niu, Huanqing; Chen, Yong; Yao, Shiwei; Liu, Lixia; Yang, Chen; Li, Bingbing; Liu, Dong; Xie, Jingjing; Chen, Xiaochun; Wu, Jinglan; Ying, Hanjie

    2013-12-01

    Arthrobacter sp. CGMCC 3584 are able to produce cAMP from glucose by the purine synthesis pathway via de novo or salvage biosynthesis. In order to gain an improved understanding of its metabolism, (13)C-labeling experiment and gas chromatography-mass spectrometry (GC-MS) analysis were employed to determine the metabolic network structure and estimate the intracellular fluxes. GC-MS analysis helps to reflect the activity of the intracellular pathways and reactions. The metabolic network mainly contains glycolytic and pentose phosphate pathways, the tricarboxylic acid cycle, and the inactive glyoxylate shunt. Hypoxanthine as a precursor of cAMP and sodium fluoride as an inhibitor of glycolysis were found to increase the cAMP production, as well as the flux through the PP pathway. The effects of adding hypoxanthine and sodium fluoride are discussed based on the enzyme assays and metabolic flux analysis. In conclusion, our results provide quantitative insights into how cells manipulate the metabolic network under different culture conditions and this may be of value in metabolic regulation for desirable production. PMID:24056081

  7. 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

  8. Analysis of neutron flux distribution for the validation of computational methods for the optimization of research reactor utilization.

    PubMed

    Snoj, L; Trkov, A; Jaćimović, R; Rogan, P; Zerovnik, G; Ravnik, M

    2011-01-01

    In order to verify and validate the computational methods for neutron flux calculation in TRIGA research reactor calculations, a series of experiments has been performed. The neutron activation method was used to verify the calculated neutron flux distribution in the TRIGA reactor. Aluminium (99.9 wt%)-Gold (0.1 wt%) foils (disks of 5mm diameter and 0.2mm thick) were irradiated in 33 locations; 6 in the core and 27 in the carrousel facility in the reflector. The experimental results were compared to the calculations performed with Monte Carlo code MCNP using detailed geometrical model of the reactor. The calculated and experimental normalized reaction rates in the core are in very good agreement for both isotopes indicating that the material and geometrical properties of the reactor core are modelled well. In conclusion one can state that our computational model describes very well the neutron flux and reaction rate distribution in the reactor core. In the reflector however, the accuracy of the epithermal and thermal neutron flux distribution and attenuation is lower, mainly due to lack of information about the material properties of the graphite reflector surrounding the core, but the differences between measurements and calculations are within 10%. Since our computational model properly describes the reactor core it can be used for calculations of reactor core parameters and for optimization of research reactor utilization. PMID:20855215

  9. 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...

  10. 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.

  11. 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...

  12. Ecosystem function and particle flux dynamics across the Mackenzie Shelf (Beaufort Sea, Arctic Ocean): an integrative analysis of spatial variability and biophysical forcings

    NASA Astrophysics Data System (ADS)

    Forest, A.; Babin, M.; Stemmann, L.; Picheral, M.; Sampei, M.; Fortier, L.; Gratton, Y.; Bélanger, S.; Devred, E.; Sahlin, J.; Doxaran, D.; Joux, F.; Ortega-Retuerta, E.; Martín, J.; Jeffrey, W. H.; Gasser, B.; Miquel, J. Carlos

    2013-05-01

    A better understanding of how environmental changes affect organic matter fluxes in Arctic marine ecosystems is sorely needed. Here we combine mooring times series, ship-based measurements and remote sensing to assess the variability and forcing factors of vertical fluxes of particulate organic carbon (POC) across the Mackenzie Shelf in 2009. We developed a geospatial model of these fluxes to proceed to an integrative analysis of their determinants in summer. Flux data were obtained with sediment traps moored around 125 m and via a regional empirical algorithm applied to particle size distributions (17 classes from 0.08-4.2 mm) measured by an Underwater Vision Profiler 5. The low fractal dimension (i.e., porous, fluffy particles) derived from the algorithm (1.26 ± 0.34) and the dominance (~ 77%) of rapidly sinking small aggregates (< 0.5 mm) in total fluxes suggested that settling material was the product of recent aggregation processes between marine detritus, gel-like substances, and ballast minerals. Modeled settling velocity of small and large aggregates was, respectively, higher and lower than in previous studies within which a high fractal dimension (i.e., more compact particles) was consequential of deep-trap collection (~400-1300 m). Redundancy analyses and forward selection of abiotic/biotic parameters, linear trends, and spatial structures (i.e., principal coordinates of neighbor matrices, PCNM) were conducted to partition the variation of the 17 POC flux size classes. Flux variability was explained at 69.5% by the addition of a temporal trend, 7 significant PCNM, and 9 biophysical variables. The first PCNM canonical axis (44.5% of spatial variance) reflected the total magnitude of POC fluxes through a shelf-basin gradient controlled by bottom depth and sea ice concentration (p < 0.01). The second most important spatial structure (5.0%) corresponded to areas where shelf break upwelling is known to occur under easterlies and where phytoplankton was

  13. 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.

  14. Establishing ozone flux-response relationships for winter wheat: Analysis of uncertainties based on data for UK and Polish genotypes

    NASA Astrophysics Data System (ADS)

    Gonzalez–Fernandez, Ignacio; Kaminska, Agnieszka; Dodmani, Mahmadali; Goumenaki, Eleni; Quarrie, Steve; Barnes, Jeremy D.

    2010-02-01

    The work outlined in this paper had three objectives. The first was to explore the effects of ozone pollution on grain yield and quality of commercially-grown winter wheat cultivars. The second was to derive a stomatal ozone flux model for winter wheat and compare with those already developed for spring wheat. The third was to evaluate exposure- versus flux-response approaches from a risk assessment perspective, and explore the implications of genetic variation in modelled ozone flux. Fifteen winter wheat cultivars were grown in open-top chambers where they were exposed to four levels of ozone. During fumigation, stomatal conductance measurements were made over the lifespan of the flag leaf across a range of environmental conditions. Although significant intra-specific variation in 'ozone sensitivity' (in terms of impacts on yield) was identified, yield was inversely related ( R2 = 0.63, P < 0.001) to the accumulated hourly averaged ozone exposure above 40 ppb during daylight hours (AOT40) across the dataset. The adverse effect of ozone on yield was principally due to a decline in seed weight. Algorithms defining the influence of environmental variables on stomatal uptake were subtly different from those currently in use, based on data for spring wheat, to map ozone impacts on pan-European cereal yield. Considerable intra-specific variation in phenological effects was identified. This meant that an 'average behaviour' had to be derived which reduced the predictive capability of the derived stomatal flux model ( R2 = 0.49, P < 0.001, 15 cultivars included). Indeed, given the intra-specific variability encountered, the flux model that was derived from the full dataset was no better in predicting O 3 impacts on wheat yield than was the AOT40 index. The study highlights the need to use ozone risk assessment tools appropriate to specific vegetation types when modelling and mapping ozone impacts at the regional level.

  15. 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. PMID:18320265

  16. Dynamics of multiple flux tubes in sawtoothing KSTAR plasmas heated by electron cyclotron waves: II. Theoretical and numerical analysis

    NASA Astrophysics Data System (ADS)

    Bierwage, Andreas; Yun, Gunsu S.; Hyuen Choe, Gyueng; Nam, Yoonbum; Lee, Woochang; Park, Hyeon K.; Bae, Youngsoon

    2015-01-01

    The dynamics of multiple closed flux tubes in the core of a sawtoothing tokamak plasma are studied using nonlinear simulations. This is motivated by recent observations of long-lived hot spots in the electron cyclotron emission (ECE) images of KSTAR plasmas with electron cyclotron heating (ECH) (Yun et al 2012 Phys. Rev. Lett. 109 145003). Using an empirical source term in a reduced set of MHD equations, it is shown that flux tubes with helicity h = 1 are easily produced and survive for the observed time intervals only if the safety factor is close to unity (|q - 1| ≪ 0.5%) and the magnetic shear is small (|s| ≪ 1). This suggests that sawteeth in KSTAR leave behind wide regions where q ≈ 1. On the basis of the relevant time scales, we discuss how this magnetic geometry and the spatial localization of the EC resonance may allow ECH to actively induce the formation of flux tubes. Using simulations with q profiles that possess a wide q = 1 region inside the sawtooth inversion radius, we examine how the flux tubes merge and annihilate, and how their dynamics depend on the strength of the drive. The phenomena seen in the simulations and experiments lead us to conclude that, during the sawtooth ramp phase, there is a dynamic competition between sources and sinks of thermal and magnetic energy, where the flux tubes may play an important role; both as carriers of and channels for energy. The development of self-consistent simulation models is motivated and directions for future experiments are given.

  17. SAMOS Surface Fluxes

    NASA Astrophysics Data System (ADS)

    Smith, Shawn; Bourassa, Mark

    2014-05-01

    observations and the choices of constants that are used. Analysis of the preliminary SAMOS flux products will be presented, including spatial and temporal coverage for each derived parameter. The unique quality and sampling locations of research vessel observations and their independence from many models and products makes them ideal for validation studies. The strengths and limitations of research observations for flux validation studies will be discussed. The authors welcome a discussion with the flux community regarding expansion of the SAMOS program to include additional international vessels, thus facilitating and expansion of this research vessel-based flux product.

  18. 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

  19. 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.

  20. Control analysis of lipid biosynthesis in tissue cultures from oil crops shows that flux control is shared between fatty acid synthesis and lipid assembly.

    PubMed Central

    Ramli, Umi S; Baker, Darren S; Quant, Patti A; Harwood, John L

    2002-01-01

    Top-Down (Metabolic) Control Analysis (TDCA) was used to examine, quantitatively, lipid biosynthesis in tissue cultures from two commercially important oil crops, olive (Olea europaea L.) and oil palm (Elaeis guineensis Jacq.). A conceptually simplified system was defined comprising two blocks of reactions: fatty acid synthesis (Block A) and lipid assembly (Block B), which produced and consumed, respectively, a common and unique system intermediate, cytosolic acyl-CoA. We manipulated the steady-state levels of the system intermediate by adding exogenous oleic acid and, using two independent assays, measured the effect of the addition on the system fluxes (J(A) and J(B)). These were the rate of incorporation of radioactivity: (i) through Block A from [1-(14)C]acetate into fatty acids and (ii) via Block B from [U-(14)C]glycerol into complex lipids respectively. The data showed that fatty acid formation (Block A) exerted higher control than lipid assembly (Block B) in both tissues with the following group flux control coefficients (C):(i) Oil palm: *C(J(TL))(BlkA)=0.64+/-0.05 and *C(J(TL))(BlkB)=0.36+/-0.05(ii) Olive: *C(J(TL))(BlkA)=0.57+/-0.10 and *C(J(TL))(BlkB)=0.43+/-0.10where *C indicates the group flux control coefficient over the lipid biosynthesis flux (J(TL)) and the subscripts BlkA and BlkB refer to defined blocks of the system, Block A and Block B. Nevertheless, because both parts of the lipid biosynthetic pathway exert significant flux control, we suggest strongly that manipulation of single enzyme steps will not affect product yield appreciably. The present study represents the first use of TDCA to examine the overall lipid biosynthetic pathway in any tissue, and its findings are of immediate academic and economic relevance to the yield and nutritional quality of oil crops. PMID:12023882

  1. 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.

  2. 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

  3. 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.

  4. Underestimation of the pentose–phosphate pathway in intact primary neurons as revealed by metabolic flux analysis

    PubMed Central

    Rodriguez-Rodriguez, Patricia; Fernandez, Emilio; Bolaños, Juan P

    2013-01-01

    The rates of glucose oxidized at glycolysis and pentose–phosphate pathway (PPP) in neurons are controversial. Using [3-3H]-, [1-14C]-, and [6-14C]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. PMID:24064491

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. An assessment of the critical heat flux approaches of thermal-hydraulic system analysis codes using bundle data from the Heat Transfer Research Facility

    SciTech Connect

    Min Lee . Dept. of Nuclear Engineering); Lihyih Liao )

    1994-02-01

    Critical heat flux (CHF) bundle data from the Heat Transfer Research Facility of Columbia University are used to check the validity of the CHF approaches used in thermal-hydraulic system analysis codes for light water reactors. The CHF approaches assessed include the Biasi et al. correlation of TRAC, the Groeneveld et al. CHF table lookup approach of RELAP5/MOD3, the CHF table lookup approach of CATHARE, and the CHF approach of RETRAN. Depending on system pressure, RETRAN uses the B and W2, Barnett, and modified Barnett correlations and a linear interpolation scheme to predict CHF. Results show that among these CHF approaches, the Groeneveld et al. approach has the best prediction accuracy and the smallest uncertainty in the estimation of the HTRF bundle data. On the average, the Groeneveld et al. approach overpredicts the uniform axial heat flux distribution by 3.6% and the nonuniform axial heat flux distribution by 0.9%. The performance of the RETRAN approach is comparable with that of the Groenevel et al. Approach for uniform axial heat flux. In general, the accuracy and the uncertainty of all the approaches, except that of CATHARE, are worse under a nonuniform axial heat distribution than under a uniform axial heat distribution. All the CHF approaches assessed have a tendency to overpredict the HTRF bundle data at low pressure, low measured CHF, and high CHF quality. The performance of the Groenevel et al. approach is improved through a CHF table update and modification of the bundle correction factor using the HTRF bundle data.

  10. [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. PMID:23898654

  11. 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.

  12. Permanent magnet online magnetization performance analysis of a flux mnemonic double salient motor using an improved hysteresis model

    NASA Astrophysics Data System (ADS)

    Zhu, Xiaoyong; Quan, Li; Chen, Yunyun; Liu, Guohai; Shen, Yue; Liu, Hui

    2012-04-01

    The concept of the memory motor is based on the fact that the magnetization level of the AlNiCo permanent magnet in the motor can be regulated by a temporary current pulse and memorized automatically. In this paper, a new type of memory motor is proposed, namely a flux mnemonic double salient motor drive, which is particularly attractive for electric vehicles. To accurately analyze the motor, an improved hysteresis model is employed in the time-stepping finite element method. Both simulation and experimental results are given to verify the validity of the new method.

  13. An improved spectral analysis of the stray flux component for the detection of air-gap irregularities in squirrel cage motors.

    PubMed

    Salah, Mohamed; Bacha, Khmais; Chaari, Abdelkader

    2014-05-01

    For machines׳ monitoring purpose, the classical motor current signature analysis has shown its weakness in distinguishing the eccentricity occurrence in presence of others mechanical faults. Although Park׳s vector approach can cover this drawback, the high cost due to the requirement to use three current sensors associated with an advanced processing technique, makes it less desired by industrialists. In this paper, we suggest an alternative diagnosis method based on a suitable processing of the stray flux data. The experimental results have revealed the potential of a simple search coil for the detection and the distinction of the accurate eccentricity nature even in presence of similar mechanical faults. PMID:24582300

  14. 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.

  15. Analysis of collective pinning and depinning of the flux line lattice in pristine 2H-NbSe2

    NASA Astrophysics Data System (ADS)

    Lee, Jonghee; Wang, Hui; Dreyer, Michael; Barker, Barry I.

    2007-03-01

    Larkin and Ovchinnikov predicted collective pinning of the flux line lattice (FLL) in type II superconductors several decades ago. The collective pinning results from the interplay between strong vortex-vortex interaction and randomly distributed weak pinning centers in a media. The evidence of collective pinning was previously observed at a magnetic field, H, close to Hc2 in current-driven transport experiments on the macroscopic scale. But there still exists a lack of understanding of collective pinning on the microscopic level. In this talk, we show collective pinning and depinning of the FLL in pristine 2H-NbSe2 in a long time series (15 days), measured by a low temperature scanning tunneling microscope. We observed the motion of the FLL within an area of 400 nm x 400 nm, with an initial magnetic field of 0.5 T. The motion was caused by the very slow decay of magnetic field (˜ 5 nT/s) in a defective superconducting magnet. The average speed of FLL was ˜ 2.5 pm/s, lower than previously reported. Using highly time resolved data, we will further discuss the average direction of motion, the strength of pinning centers in pristine 2H-NbSe2, flux line mass, and the difference between current-driven and field-driven FLL motions.

  16. 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.

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

    PubMed

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

    2001-03-01

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

  18. 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

  19. 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

  20. Carbon flux analysis by 13C nuclear magnetic resonance to determine the effect of CO2 on anaerobic succinate production by Corynebacterium glutamicum.

    PubMed

    Radoš, Dušica; Turner, David L; Fonseca, Luís L; Carvalho, Ana Lúcia; Blombach, Bastian; Eikmanns, Bernhard J; Neves, Ana Rute; Santos, Helena

    2014-05-01

    Wild-type Corynebacterium glutamicum produces a mixture of lactic, succinic, and acetic acids from glucose under oxygen deprivation. We investigated the effect of CO2 on the production of organic acids in a two-stage process: cells were grown aerobically in glucose, and subsequently, organic acid production by nongrowing cells was studied under anaerobic conditions. The presence of CO2 caused up to a 3-fold increase in the succinate yield (1 mol per mol of glucose) and about 2-fold increase in acetate, both at the expense of l-lactate production; moreover, dihydroxyacetone formation was abolished. The redistribution of carbon fluxes in response to CO2 was estimated by using (13)C-labeled glucose and (13)C nuclear magnetic resonance (NMR) analysis of the labeling patterns in end products. The flux analysis showed that 97% of succinate was produced via the reductive part of the tricarboxylic acid cycle, with the low activity of the oxidative branch being sufficient to provide the reducing equivalents needed for the redox balance. The flux via the pentose phosphate pathway was low (~5%) regardless of the presence or absence of CO2. Moreover, there was significant channeling of carbon to storage compounds (glycogen and trehalose) and concomitant catabolism of these reserves. The intracellular and extracellular pools of lactate and succinate were measured by in vivo NMR, and the stoichiometry (H(+):organic acid) of the respective exporters was calculated. This study shows that it is feasible to take advantage of natural cellular regulation mechanisms to obtain high yields of succinate with C. glutamicum without genetic manipulation. PMID:24610842

  1. Carbon Flux Analysis by 13C Nuclear Magnetic Resonance To Determine the Effect of CO2 on Anaerobic Succinate Production by Corynebacterium glutamicum

    PubMed Central

    Radoš, Dušica; Turner, David L.; Fonseca, Luís L.; Carvalho, Ana Lúcia; Blombach, Bastian; Eikmanns, Bernhard J.; Neves, Ana Rute

    2014-01-01

    Wild-type Corynebacterium glutamicum produces a mixture of lactic, succinic, and acetic acids from glucose under oxygen deprivation. We investigated the effect of CO2 on the production of organic acids in a two-stage process: cells were grown aerobically in glucose, and subsequently, organic acid production by nongrowing cells was studied under anaerobic conditions. The presence of CO2 caused up to a 3-fold increase in the succinate yield (1 mol per mol of glucose) and about 2-fold increase in acetate, both at the expense of l-lactate production; moreover, dihydroxyacetone formation was abolished. The redistribution of carbon fluxes in response to CO2 was estimated by using 13C-labeled glucose and 13C nuclear magnetic resonance (NMR) analysis of the labeling patterns in end products. The flux analysis showed that 97% of succinate was produced via the reductive part of the tricarboxylic acid cycle, with the low activity of the oxidative branch being sufficient to provide the reducing equivalents needed for the redox balance. The flux via the pentose phosphate pathway was low (∼5%) regardless of the presence or absence of CO2. Moreover, there was significant channeling of carbon to storage compounds (glycogen and trehalose) and concomitant catabolism of these reserves. The intracellular and extracellular pools of lactate and succinate were measured by in vivo NMR, and the stoichiometry (H+:organic acid) of the respective exporters was calculated. This study shows that it is feasible to take advantage of natural cellular regulation mechanisms to obtain high yields of succinate with C. glutamicum without genetic manipulation. PMID:24610842

  2. 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

  3. 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

  4. 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.

  5. Analysis of single pulse radio flux measurements of PSR B1133+16 at 4.85 and 8.35 GHz

    NASA Astrophysics Data System (ADS)

    Krzeszowski, K.; Maron, O.; Słowikowska, A.; Dyks, J.; Jessner, A.

    2014-05-01

    We show the results of microsecond resolution radio data analysis focused on flux measurements of single pulses of PSR B1133+16. The data were recorded at 4.85 and 8.35 GHz with 0.5- and 1.1-GHz bandwidth, respectively, using Radio Telescope Effelsberg (Max-Planck-Institut für Radioastronomie). The most important conclusion of the analysis is that the strongest single pulse emission at 4.85 and 8.35 GHz contributes almost exclusively to the trailing part of the leading component of the pulsar mean profile, whereas studies at lower frequencies report that the contribution is spread almost uniformly, covering all phases of the pulsar mean profile. We also estimate the radio emission heights to be around 1-2 per cent of the light-cylinder radius, which is in agreement with previous studies. Additionally, these observations allowed us to add two more measurements of the flux density to the PSR B1133+16 broad-band radio spectrum, covering frequencies from 16.7 MHz up to 32 GHz. We fit two different models to the spectrum: a broken power law and a spectrum based on the flicker-noise model, which represents the spectrum in a simpler, but similarly accurate, way.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  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. 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.

  18. A hybrid of bees algorithm and flux balance analysis with OptKnock as a platform for in silico optimization of microbial strains.

    PubMed

    Choon, Yee Wen; Mohamad, Mohd Saberi; Deris, Safaai; Illias, Rosli Md; Chong, Chuii Khim; Chai, Lian En

    2014-03-01

    Microbial strain optimization focuses on improving technological properties of the strain of microorganisms. However, the complexities of the metabolic networks, which lead to data ambiguity, often cause genetic modification on the desirable phenotypes difficult to predict. Furthermore, vast number of reactions in cellular metabolism lead to the combinatorial problem in obtaining optimal gene deletion strategy. Consequently, the computation time increases exponentially with the increase in the size of the problem. Hence, we propose an extension of a hybrid of Bees Algorithm and Flux Balance Analysis (BAFBA) by integrating OptKnock into BAFBA to validate the result. This paper presents a number of computational experiments to test on the performance and capability of BAFBA. Escherichia coli, Bacillus subtilis and Clostridium thermocellum are the model organisms in this paper. Also included is the identification of potential reactions to improve the production of succinic acid, lactic acid and ethanol, plus the discussion on the changes in the flux distribution of the predicted mutants. BAFBA shows potential in suggesting the non-intuitive gene knockout strategies and a low variability among the several runs. The results show that BAFBA is suitable, reliable and applicable in predicting optimal gene knockout strategy. PMID:23892659

  19. 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.

  20. 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.

  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 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

  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. 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. PMID:24141485

  4. 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.

  5. 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

  6. A new multivariate time series data analysis technique: Automated detection of flux transfer events using Cluster data

    NASA Astrophysics Data System (ADS)

    Karimabadi, H.; Sipes, T. B.; Wang, Y.; Lavraud, B.; Roberts, A.

    2009-06-01

    A new data mining technique called MineTool-TS is introduced which captures the time-lapse information in multivariate time series data through extraction of global features and metafeatures. This technique is developed into a JAVA-based data mining software which automates all the steps in the model building to make it more accessible to nonexperts. As its first application in space sciences, MineTool-TS is used to develop a model for automated detection of flux transfer events (FTEs) at Earth's magnetopause in the Cluster spacecraft time series data. The model classifies a given time series into one of three categories of non-FTE, magnetosheath FTE, or magnetospheric FTE. One important feature of MineTool-TS is the ability to explore the importance of each variable or combination of variables as indicators of FTEs. FTEs have traditionally been identified on the basis of their magnetic field signatures, but here we find that some plasma variables can also be effective indicators of FTEs. For example, the perpendicular ion temperature yields a model accuracy of ˜93%, while a model based solely on the normal magnetic field BN yields an accuracy of ˜95%. This opens up the possibility of searching for more unusual FTEs that may, for example, have no clear BN signature and create a more comprehensive and less biased list of FTEs for statistical studies. We also find that models using GSM coordinates yield comparable accuracy to those using boundary normal coordinates. This is useful since there are regions where magnetopause models are not accurate. Another surprising result is the finding that the algorithm can largely detect FTEs, and even distinguish between magnetosheath and magnetospheric FTEs, solely on the basis of models built from single parameters, something that experts may not do so straightforwardly on the basis of short time series intervals. The most accurate models use a combination of plasma and magnetic field variables and achieve a very high

  7. 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

  8. 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

  9. 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

  10. Plasmoids as magnetic flux ropes

    SciTech Connect

    Moldwin, M.B.; Hughes, W.J. )

    1991-08-01

    Observational constraints on the magnetic topology and orientation of plasmoids is examined using a magnetic field model. The authors develop a magnetic flux rope model to examine whether principal axis analysis (PAA) of magnetometer signatures from a single satellite pass is sufficient to determine the magnetic topology of plasmoids and if plasmoid observations are best explained by the flux rope, closed loop, or large-amplitude wave picture. Satellite data are simulated by extracting the magnetic field along a path through the model of a magnetic flux rope. They then examine the results using PAA. They find that the principal axis directions (and therefore the interpretation of structure orientation) is highly dependent on several parameters including the satellite trajectory through the structure. Because of this they conclude that PAA of magnetometer data from a single satellite pass is insufficient to differentiate between magnetic closed loop and flux rope models. They also compare the model results to ISEE 3 magnetometer data of plasmoid events in various coordinate frames including principal axis and geocentric solar magnetospheric. They find that previously identified plasmoid events that have been explained as closed loop structures can also be modeled as flux ropes. They also searched the literature for previously reported flux rope and closed loop plasmoid events to examine if these structures had any similarities and/or differences. The results of the modeling efforts and examination of both flux rope and plasmoid events lead them to favor the flux rope model of plasmoid formation, as it is better able to unify the observations of various magnetic structures observed by ISEE 3.

  11. 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

  12. Starch Biosynthesis and Intermediary Metabolism in Maize Kernels. Quantitative Analysis of Metabolite Flux by Nuclear Magnetic Resonance1

    PubMed Central

    Glawischnig, Erich; Gierl, Alfons; Tomas, Adriana; Bacher, Adelbert; Eisenreich, Wolfgang

    2002-01-01

    The seeds of cereals represent an important sink for metabolites during the accumulation of storage products, and seeds are an essential component of human and animal nutrition. Understanding the metabolic interconversions (networks) underpinning storage product formation could provide the foundation for effective metabolic engineering of these primary nutritional sources. In this paper, we describe the use of retrobiosynthetic nuclear magnetic resonance analysis to establish the metabolic history of the glucose (Glc) units of starch in maize (Zea mays) kernels. Maize kernel cultures were grown with [U-13C6]Glc, [U-13C12]sucrose, or [1,2-13C2]acetate as supplements. After 19 d, starch was hydrolyzed, and the isotopomer composition of the resulting Glc was determined by quantitative nuclear magnetic resonance analysis. [1,2-13C2]Acetate was not incorporated into starch. [U-13C6]Glc or [U-13C12]sucrose gave similar labeling patterns of polysaccharide Glc units, which were dominated by [1,2,3-13C3]- and [4,5,6-13C3]-isotopomers, whereas the [U-13C6]-, [3,4,5,6-13C4]-, [1,2-13C2]-, [5,6-13C2], [3-13C1], and [4-13C1]-isotopomers were present at lower levels. These isotopomer compositions indicate that there is extensive recycling of Glc before its incorporation into starch, via the enzymes of glycolytic, glucogenic, and pentose phosphate pathways. The relatively high abundance of the [5,6-13C2]-isotopomer can be explained by the joint operation of glycolysis/glucogenesis and the pentose phosphate pathway. PMID:12481054

  13. 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.

  14. Applications of the computer codes FLUX2D and PHI3D for the electromagnetic analysis of compressed magnetic field generators and power flow channels

    SciTech Connect

    Hodgdon, M.L.; Oona, H.; Martinez, A.R.; Salon, S.; Wendling, P.; Krahenbuhl, L.; Nicolas, A.; Nicolas, L.

    1989-01-01

    We present herein the results of three electromagnetic field problems for compressed magnetic field generators and their associated power flow channels. The first problem is the computation of the transient magnetic field in a two-dimensional model of helical generator during loading. The second problem is the three-dimensional eddy current patterns in a section of an armature beneath a bifurcation point of a helical winding. Our third problem is the calculation of the three-dimensional electrostatic fields in a region known as the post-hole convolute in which a rod connects the inner and outer walls of a system of three concentric cylinders through a hole in the middle cylinder. While analytic solutions exist for many electromagnetic field problems in cases of special and ideal geometries, the solutions of these and similar problems for the proper analysis and design of compressed magnetic field generators and their related hardware require computer simulations. In earlier studies, computer models have been proposed, several based on research oriented hydrocodes to which uncoupled or partially coupled Maxwell's equations solvers are added. Although the hydrocode models address the problem of moving, deformable conductors, they are not useful for electromagnetic analysis, nor can they be considered design tools. For our studies, we take advantage of the commercial, electromagnetic computer-aided design software packages FLUX2D nd PHI3D that were developed for motor manufacturers and utilities industries. 4 refs., 6 figs.

  15. 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. PMID:24862955

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Estimating surface fluxes using eddy covariance and numerical ogive optimization

    NASA Astrophysics Data System (ADS)

    Sievers, J.; Papakyriakou, T.; Larsen, S. E.; Jammet, M. M.; Rysgaard, S.; Sejr, M. K.; Sørensen, L. L.

    2015-02-01

    Estimating representative surface fluxes using eddy covariance leads invariably to questions concerning inclusion or exclusion of low-frequency flux contributions. For studies where fluxes are linked to local physical parameters and up-scaled through numerical modelling efforts, low-frequency contributions interfere with our ability to isolate local biogeochemical processes of interest, as represented by turbulent fluxes. No method currently exists to disentangle low-frequency contributions on flux estimates. Here, we present a novel comprehensive numerical scheme to identify and separate out low-frequency contributions to vertical turbulent surface fluxes. For high flux rates (|Sensible heat flux| > 40 Wm-2, |latent heat flux|> 20 Wm-2 and |CO2 flux|> 100 mmol m-2 d-1 we found that the average relative difference between fluxes estimated by ogive optimization and the conventional method was low (5-20%) suggesting negligible low-frequency influence and that both methods capture the turbulent fluxes equally well. For flux rates below these thresholds, however, the average relative difference between flux estimates was found to be very high (23-98%) suggesting non-negligible low-frequency influence and that the conventional method fails in separating low-frequency influences from the turbulent fluxes. Hence, the ogive optimization method is an appropriate method of flux analysis, particularly in low-flux environments.

  1. 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

  2. Identification of gene knockout strategies using a hybrid of an ant colony optimization algorithm and flux balance analysis to optimize microbial strains.

    PubMed

    Lu, Shi Jing; Salleh, Abdul Hakim Mohamed; Mohamad, Mohd Saberi; Deris, Safaai; Omatu, Sigeru; Yoshioka, Michifumi

    2014-09-28

    Reconstructions of genome-scale metabolic networks from different organisms have become popular in recent years. Metabolic engineering can simulate the reconstruction process to obtain desirable phenotypes. In previous studies, optimization algorithms have been implemented to identify the near-optimal sets of knockout genes for improving metabolite production. However, previous works contained premature convergence and the stop criteria were not clear for each case. Therefore, this study proposes an algorithm that is a hybrid of the ant colony optimization algorithm and flux balance analysis (ACOFBA) to predict near optimal sets of gene knockouts in an effort to maximize growth rates and the production of certain metabolites. Here, we present a case study that uses Baker's yeast, also known as Saccharomyces cerevisiae, as the model organism and target the rate of vanillin production for optimization. The results of this study are the growth rate of the model organism after gene deletion and a list of knockout genes. The ACOFBA algorithm was found to improve the yield of vanillin in terms of growth rate and production compared with the previous algorithms. PMID:25462325

  3. 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.

  4. Improved L-BFGS diagonal preconditioners for a large-scale 4D-Var inversion system: application to CO2 flux constraints and analysis error calculation

    NASA Astrophysics Data System (ADS)

    Bousserez, Nicolas; Henze, Daven; Bowman, Kevin; Liu, Junjie; Jones, Dylan; Keller, Martin; Deng, Feng

    2013-04-01

    large-scale 4D-Var system. The impact of using the diagonal preconditioners proposed by Gilbert and Le Maréchal (1989) instead of the usual Oren-Spedicato scalar will be first presented. We will also introduce new hybrid methods that combine randomization estimates of the analysis error variance with L-BFGS diagonal updates to improve the inverse Hessian approximation. Results from these new algorithms will be evaluated against standard large ensemble Monte-Carlo simulations. The methods explored here are applied to the problem of inferring global atmospheric CO2 fluxes using remote sensing observations, and are intended to be integrated with the future NASA Carbon Monitoring System.

  5. 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.

  6. 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

  7. 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...

  8. South Atlantic meridional fluxes

    NASA Astrophysics Data System (ADS)

    Garzoli, Silvia L.; Baringer, Molly O.; Dong, Shenfu; Perez, Renellys C.; Yao, Qi

    2013-01-01

    The properties of the meridional overturning circulation (MOC) and associated meridional heat transport (MHT) and salt fluxes are analyzed in the South Atlantic. The oceanographic data used for the study consist of Expendable bathythermograph (XBT) data collected along 27 sections at nominally 35°S for the period of time 2002-2011, and Argo profile data collected in the region. Previous estimates obtained with a shorter record are improved and extended, using new oceanographic sections and wind fields. Different wind products are analyzed to determine the uncertainty in the Ekman component of the MHT derived from their use. Results of the analysis provide a 9-year time series of MHT, and volume transport in the upper layer of the MOC. Salt fluxes at 35°S are estimated using a parameter introduced by numerical studies, the Mov that represents the salt flux and helps determine the basin scale salt feedback associated with the MOC. Volume and heat transport by the western and eastern boundary currents are estimated, and their covariablity is examined. Analysis of the data shows that the South Atlantic is responsible for a northward MHT with a mean value of 0.54±0.14 PW. The MHT exhibits no significant trend from 2002 to 2011. The MOC varies from 14.4 to 22.7 Sv with a mean value of 18.1±2.3 Sv and the maximum overturning transport is found at a mean depth of 1250 m. Statistical analysis suggests that an increase of 1 Sv in the MOC leads to an increase of the MHT of 0.04±0.02 PW. Estimates of the Mov from data collected from three different kinds of observations, contrary to those obtained from models, feature a positive salt advection feedback (Mov<0) suggesting that freshwater perturbations will be amplified and that the MOC is bistable. In other words, the MOC might collapse with a large enough freshwater perturbation. Observations indicate that the mean value of the Brazil Current is -8.6±4.1 Sv at 24°S and -19.4±4.3 Sv at 35°S, increasing towards the

  9. 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

  10. 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

  11. 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.

  12. PHOTOSPHERIC FLUX CANCELLATION AND THE BUILD-UP OF SIGMOIDAL FLUX ROPES ON THE SUN

    SciTech Connect

    Savcheva, A. S.; Van Ballegooijen, A. A.; DeLuca, E. E.; Green, L. M.

    2012-11-10

    In this study we explore the scenario of photospheric flux cancellation being the primary formation mechanism of sigmoidal flux ropes in decaying active regions. We analyze magnetogram and X-ray observations together with data-driven non-linear force-free field (NLFFF) models of observed sigmoidal regions to test this idea. We measure the total and canceled fluxes in the regions from MDI magnetograms, as well as the axial and poloidal flux content of the modeled NLFFF flux ropes for three sigmoids-2007 February, 2007 December, and 2010 February. We infer that the sum of the poloidal and axial flux in the flux ropes for most models amounts to about 60%-70% of the canceled flux and 30%-50% of the total flux in the regions. The flux measurements and the analysis of the magnetic field structure show that the sigmoids first develop a strong axial field manifested as a sheared arcade and then, as flux cancellation proceeds, form long S-shaped field lines that contribute to the poloidal flux. In addition, the dips in the S-shaped field lines are located at the sites of flux cancellation that have been identified from the MDI magnetograms. We find that the line-of-sight-integrated free energy is also concentrated at these locations for all three regions, which can be liberated in the process of eruption. Flare-associated brightenings and flare loops coincide with the location of the X-line topology that develops at the site of most vigorous flux cancellation.

  13. Polyamine flux analysis by determination of heavy isotope incorporation from 13C, 15N-enriched amino acids into polyamines by LC-MS/MS.

    PubMed

    Cerrada-Gimenez, Marc; Häkkinen, Merja R; Vepsäläinen, Jouko; Auriola, Seppo; Alhonen, Leena; Keinänen, Tuomo A

    2012-02-01

    The study of polyamine flux, i.e. the circulating flow of polyamines through the interconnected biosynthetic and catabolic pathways, is of considerable interest because of the established links between the polyamine metabolism and many diseases, such as cancer and diabetes. To study polyamine flux in detail, a novel method based on following the label incorporation from the (13)C, (15)N-labeled polyamine precursors, arginine, methionine and ornithine, into polyamines by LC-MS/MS was implemented. This methodology was tested on three distinct cell lines with different spermidine/spermine-N (1)-acetyltransferase (SSAT) expression levels, i.e. non-transgenic, transgenic and knockout. These trials allowed the identification of the critical conditions for the successful polyamine flux measurement, such as the functional time frame of label incorporation, until plateau phase with the selected precursor is reached. The novel LC-MS/MS-based method for polyamine flux overcame the limitations of previous existing methodologies, with baseline separation of the different polyamine species and the exact quantification of the incorporated label. Moreover, the obtained results clearly show that the increased SSAT expression is associated with accelerated polyamine flux. PMID:21818565

  14. The Net Carbon Flux due to Deforestation and Forest Re-Growth in the Brazilian Amazon: Analysis using a Process-Based Model

    NASA Technical Reports Server (NTRS)

    Hirsch, A. I.; Little, W. S.; Houghton, R. A.; Scott, N. A.; White, J. D.

    2004-01-01

    We developed a process-based model of forest growth, carbon cycling, and land cover dynamics named CARLUC (for CARbon and Land Use Change) to estimate the size of terrestrial carbon pools in terra firme (non-flooded) forests across the Brazilian Legal Amazon and the net flux of carbon resulting from forest disturbance and forest recovery from disturbance. Our goal in building the model was to construct a relatively simple ecosystem model that would respond to soil and climatic heterogeneity that allows us to study of the impact of Amazonian deforestation, selective logging, and accidental fire on the global carbon cycle. This paper focuses on the net flux caused by deforestation and forest re-growth over the period from 1970-1998. We calculate that the net flux to the atmosphere during this period reached a maximum of approx. 0.35 PgC/yr (1PgC = 1 x 10(exp I5) gC) in 1990, with a cumulative release of approx. 7 PgC from 1970- 1998. The net flux is higher than predicted by an earlier study by a total of 1 PgC over the period 1989-1 998 mainly because CARLUC predicts relatively high mature forest carbon storage compared to the datasets used in the earlier study. Incorporating the dynamics of litter and soil carbon pools into the model increases the cumulative net flux by approx. 1 PgC from 1970-1998, while different assumptions about land cover dynamics only caused small changes. The uncertainty of the net flux, calculated with a Monte-Carlo approach, is roughly 35% of the mean value (1 SD).

  15. 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 within the motor as well as simple configurations for any number of output shafts up to six. The changes allow for improved manufacturability and reliability within the design.

  16. Heat Flux Sensor

    NASA Technical Reports Server (NTRS)

    1994-01-01

    A heat flux microsensor developed under a NASP Small Business Innovation Research (SBIR) has a wide range of potential commercial applications. Vatell Corporation originally designed microsensors for use in very high temperatures. The company then used the technology to develop heat flux sensors to measure the rate of heat energy flowing in and out of a surface as well as readings on the surface temperature. Additional major advantages include response to heat flux in less than 10 microseconds and the ability to withstand temperatures up to 1,200 degrees centigrade. Commercial applications a