WorldWideScience

Sample records for metabolic flux distribution

  1. Metabolic flux distribution and mathematical models for dynamic ...

    African Journals Online (AJOL)

    A simple model was build for the metabolic flux determination based on published articles. A method for metabolic flux determination by carbon labeling experiments was described and developed here in the first part of this study that allows mathematical description relating the measured quantities and the intracellular ...

  2. Metabolic flux distribution and mathematical models for dynamic ...

    African Journals Online (AJOL)

    user

    2011-03-21

    Mar 21, 2011 ... for metabolic flux determination by carbon labeling experiments was described and developed here in the first part of this study that allows mathematical description relating the measured quantities and the intracellular fluxes. The described method was used to investigate the central carbon metabolism of.

  3. Diversity of flux distribution in central carbon metabolism of S. cerevisiae strains from diverse environments.

    Science.gov (United States)

    Nidelet, Thibault; Brial, Pascale; Camarasa, Carole; Dequin, Sylvie

    2016-04-05

    S. cerevisiae has attracted considerable interest in recent years as a model for ecology and evolutionary biology, revealing a substantial genetic and phenotypic diversity. However, there is a lack of knowledge on the diversity of metabolic networks within this species. To identify the metabolic and evolutionary constraints that shape metabolic fluxes in S. cerevisiae, we used a dedicated constraint-based model to predict the central carbon metabolism flux distribution of 43 strains from different ecological origins, grown in wine fermentation conditions. In analyzing these distributions, we observed a highly contrasted situation in flux variability, with quasi-constancy of the glycolysis and ethanol synthesis yield yet high flexibility of other fluxes, such as the pentose phosphate pathway and acetaldehyde production. Furthermore, these fluxes with large variability showed multimodal distributions that could be linked to strain origin, indicating a convergence between genetic origin and flux phenotype. Flux variability is pathway-dependent and, for some flux, a strain origin effect can be found. These data highlight the constraints shaping the yeast operative central carbon network and provide clues for the design of strategies for strain improvement.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-04-21

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

  5. Bacterial adaptation through distributed sensing of metabolic fluxes

    NARCIS (Netherlands)

    Kotte, Oliver; Zaugg, Judith B.; Heinemann, Matthias

    The recognition of carbon sources and the regulatory adjustments to recognized changes are of particular importance for bacterial survival in fluctuating environments. Despite a thorough knowledge base of Escherichia coli’s central metabolism and its regulation, fundamental aspects of the employed

  6. Prediction of Metabolic Flux Distribution from Gene Expression Data Based on the Flux Minimization Principle

    Science.gov (United States)

    2014-11-14

    Saccharomyces cerevisiae , and wild-type and mutant Escherichia coli strains, our method achieved high prediction accuracy, as gauged by correlation...the aerobic growth of S. cerevisiae . We used experimental data collected by Lee et al., which included RNA-seq transcriptomic data and exchange flux...measurements of S. cerevisiae aerobically growing in chemostat cultures. This study provides data under two different growth conditions, i.e., glucose

  7. Investigation of useful carbon tracers for 13C-metabolic flux analysis of Escherichia coli by considering five experimentally determined flux distributions.

    Science.gov (United States)

    Maeda, Kousuke; Okahashi, Nobuyuki; Toya, Yoshihiro; Matsuda, Fumio; Shimizu, Hiroshi

    2016-12-01

    The 13 C-MFA experiments require an optimal design since the precision or confidence intervals of the estimated flux levels depends on factors such as the composition of 13 C-labeled carbon sources, as well as the metabolic flux distribution of interest. In this study, useful compositions of 13 C-labeled glucose for 13 C-metabolic flux analysis ( 13 C-MFA) of Escherichia coli are investigated using a computer simulation of the stable isotope labeling experiment. Following the generation of artificial mass spectra datasets of amino acid fragments using five literature-reported flux distributions of E. coli , the best fitted flux distribution and the 95% confidence interval were estimated by the 13 C-MFA procedure. A comparison of the precision scores showed that [1, 2- 13 C]glucose and a mixture of [1- 13 C] and [U- 13 C]glucose at 8:2 are one of the best carbon sources for a precise estimation of flux levels of the pentose phosphate pathway, glycolysis and the TCA cycle. Although the precision scores of the anaplerotic and glyoxylate pathway reactions were affected by both the carbon source and flux distribution, it was also shown that the mixture of non-labeled, [1- 13 C], and [U- 13 C]glucose at 4:1:5 was specifically effective for the flux estimation of the glyoxylate pathway reaction. These findings were confirmed by wet 13 C-MFA experiments.

  8. A kinetic model describes metabolic response to perturbations and distribution of flux control in the benzenoid network of Petunia hybrida.

    Science.gov (United States)

    Colón, Amy Marshall; Sengupta, Neelanjan; Rhodes, David; Dudareva, Natalia; Morgan, John

    2010-04-01

    In recent years there has been much interest in the genetic enhancement of plant metabolism; however, attempts at genetic modification are often unsuccessful due to an incomplete understanding of network dynamics and their regulatory properties. Kinetic modeling of plant metabolic networks can provide predictive information on network control and response to genetic perturbations, which allow estimation of flux at any concentration of intermediate or enzyme in the system. In this research, a kinetic model of the benzenoid network was developed to simulate whole network responses to different concentrations of supplied phenylalanine (Phe) in petunia flowers and capture flux redistributions caused by genetic manipulations. Kinetic parameters were obtained by network decomposition and non-linear least squares optimization of data from petunia flowers supplied with either 75 or 150 mm(2)H(5)-Phe. A single set of kinetic parameters simultaneously accommodated labeling and pool size data obtained for all endogenous and emitted volatiles at the two concentrations of supplied (2)H(5)-Phe. The generated kinetic model was validated using flowers from transgenic petunia plants in which benzyl CoA:benzyl alcohol/phenylethanol benzoyltransferase (BPBT) was down-regulated via RNAi. The determined in vivo kinetic parameters were used for metabolic control analysis, in which flux control coefficients were calculated for fluxes around the key branch point at Phe and revealed that phenylacetaldehyde synthase activity is the primary controlling factor for the phenylacetaldehyde branch of the benzenoid network. In contrast, control of flux through the beta-oxidative and non-beta-oxidative pathways is highly distributed.

  9. Metabolic engineering of Synechococcus elongatus PCC 7942 for improvement of 1,3-propanediol and glycerol production based on in silico simulation of metabolic flux distribution.

    Science.gov (United States)

    Hirokawa, Yasutaka; Matsuo, Shingo; Hamada, Hiroyuki; Matsuda, Fumio; Hanai, Taizo

    2017-11-25

    Production directly from carbon dioxide by engineered cyanobacteria is one of the promising technologies for sustainable future. Previously, we have successfully achieved 1,3-propanediol (1,3-PDO) production using Synechococcus elongatus PCC 7942 with a synthetic metabolic pathway. The strain into which the synthetic metabolic pathway was introduced produced 3.48 mM (0.265 g/L) 1,3-PDO and 14.3 mM (1.32 g/L) glycerol during 20 days of incubation. In this study, the productivities of 1,3-PDO were improved by gene disruption selected by screening with in silico simulation. First, a stoichiometric metabolic model was applied to prediction of cellular metabolic flux distribution in a 1,3-PDO-producing strain of S. elongatus PCC 7942. A genome-scale model of S. elongatus PCC 7942 constructed by Knoop was modified by the addition of a synthetic metabolic pathway for 1,3-PDO production. Next, the metabolic flux distribution predicted by metabolic flux balance analysis (FBA) was used for in silico simulation of gene disruption. As a result of gene disruption simulation, NADPH dehydrogenase 1 (NDH-1) complexes were found by screening to be the most promising candidates for disruption to improve 1,3-PDO production. The effect of disruption of the gene encoding a subunit of the NDH-1 complex was evaluated in the 1,3-PDO-producing strain. During 20 days of incubation, the ndhF1-null 1,3-PDO-producing strain showed the highest titers: 4.44 mM (0.338 g/L) 1,3-PDO and 30.3 mM (2.79 g/L) glycerol. In this study, we successfully improved 1,3-PDO productivity on the basis of in silico simulation of gene disruption.

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

    Science.gov (United States)

    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. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. Carbon-flux distribution within Streptomyces coelicolor metabolism: a comparison between the actinorhodin-producing strain M145 and its non-producing derivative M1146.

    Directory of Open Access Journals (Sweden)

    Fabien Coze

    Full Text Available Metabolic Flux Analysis is now viewed as essential to elucidate the metabolic pattern of cells and to design appropriate genetic engineering strategies to improve strain performance and production processes. Here, we investigated carbon flux distribution in two Streptomyces coelicolor A3 (2 strains: the wild type M145 and its derivative mutant M1146, in which gene clusters encoding the four main antibiotic biosynthetic pathways were deleted. Metabolic Flux Analysis and (13C-labeling allowed us to reconstruct a flux map under steady-state conditions for both strains. The mutant strain M1146 showed a higher growth rate, a higher flux through the pentose phosphate pathway and a higher flux through the anaplerotic phosphoenolpyruvate carboxylase. In that strain, glucose uptake and the flux through the Krebs cycle were lower than in M145. The enhanced flux through the pentose phosphate pathway in M1146 is thought to generate NADPH enough to face higher needs for biomass biosynthesis and other processes. In both strains, the production of NADPH was higher than NADPH needs, suggesting a key role for nicotinamide nucleotide transhydrogenase for redox homeostasis. ATP production is also likely to exceed metabolic ATP needs, indicating that ATP consumption for maintenance is substantial.Our results further suggest a possible competition between actinorhodin and triacylglycerol biosynthetic pathways for their common precursor, acetyl-CoA. These findings may be instrumental in developing new strategies exploiting S. coelicolor as a platform for the production of bio-based products of industrial interest.

  12. Principal Metabolic Flux Mode Analysis.

    Science.gov (United States)

    Bhadra, Sahely; Blomberg, Peter; Castillo, Sandra; Rousu, Juho; Wren, Jonathan

    2018-02-06

    In the analysis of metabolism, two distinct and complementary approaches are frequently used: Principal component analysis (PCA) and stoichiometric flux analysis. PCA is able to capture the main modes of variability in a set of experiments and does not make many prior assumptions about the data, but does not inherently take into account the flux mode structure of metabolism. Stoichiometric flux analysis methods, such as Flux Balance Analysis (FBA) and Elementary Mode Analysis, on the other hand, are able to capture the metabolic flux modes, however, they are primarily designed for the analysis of single samples at a time, and not best suited for exploratory analysis on a large sets of samples. We propose a new methodology for the analysis of metabolism, called Principal Metabolic Flux Mode Analysis (PMFA), which marries the PCA and stoichiometric flux analysis approaches in an elegant regularized optimization framework. In short, the method incorporates a variance maximization objective form PCA coupled with a stoichiometric regularizer, which penalizes projections that are far from any flux modes of the network. For interpretability, we also introduce a sparse variant of PMFA that favours flux modes that contain a small number of reactions. Our experiments demonstrate the versatility and capabilities of our methodology. The proposed method can be applied to genome-scale metabolic network in efficient way as PMFA does not enumerate elementary modes. In addition, the method is more robust on out-of-steady steady-state experimental data than competing flux mode analysis approaches. Matlab software for PMFA and SPMFA and data set used for experiments are available in https://github.com/aalto-ics-kepaco/PMFA. sahely@iitpkd.ac.in, juho.rousu@aalto.fi, Peter.Blomberg@vtt.fi, Sandra.Castillo@vtt.fi. Detailed results are in Supplementary files. Supplementary data are available at https://github.com/aalto-ics-kepaco/PMFA/blob/master/Results.zip.

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

    Directory of Open Access Journals (Sweden)

    Gabriel Yarmush

    2016-01-01

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

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

    Science.gov (United States)

    Vallino, J J; Stephanopoulos, G

    2000-03-20

    The two main contributions of this article are the solidification of Corynebacterium glutamicum biochemistry guided by bioreaction network analysis, and the determination of basal metabolic flux distributions during growth and lysine synthesis. Employed methodology makes use of stoichiometrically based mass balances to determine flux distributions in the C. glutamicum metabolic network. Presented are a brief description of the methodology, a thorough literature review of glutamic acid bacteria biochemistry, and specific results obtained through a combination of fermentation studies and analysis-directed intracellular assays. The latter include the findings of the lack of activity of glyoxylate shunt, and that phosphoenolpyruvate carboxylase (PPC) is the only anaplerotic reaction expressed in C. glutamicum cultivated on glucose minimal media. Network simplifications afforded by the above findings facilitated the determination of metabolic flux distributions under a variety of culture conditions and led to the following conclusions. Both the pentose phosphate pathway and PPC support significant fluxes during growth and lysine overproduction, and that flux partitioning at the glucosa-6-phosphate branch point does not appear to limit lysine synthesis. Copyright 1993 John Wiley & Sons, Inc.

  15. Continuous and batch cultures of Escherichia coli KJ134 for succinic acid fermentation: metabolic flux distributions and production characteristics.

    Science.gov (United States)

    van Heerden, Carel D; Nicol, Willie

    2013-09-17

    Succinic acid (SA) has become a prominent biobased platform chemical with global production quantities increasing annually. Numerous genetically modified E. coli strains have been developed with the main aim of increasing the SA yield of the organic carbon source. In this study, a promising SA-producing strain, E. coli KJ134 [Biotechnol. Bioeng. 101:881-893, 2008], from the Department of Microbiology and Cell Science of the University of Florida was evaluated under continuous and batch conditions using D-glucose and CO2 in a mineral salt medium. Production characteristics entailing growth and maintenance rates, growth termination points and metabolic flux distributions under growth and non-growth conditions were determined. The culture remained stable for weeks under continuous conditions. Under growth conditions the redox requirements of the reductive tricarboxylic acid (TCA) cycle was solely balanced by acetic acid (AcA) production via the pyruvate dehydrogenase route resulting in a molar ratio of SA:AcA of two. A maximum growth rate of 0.22 h(-1) was obtained, while complete growth inhibition occurred at a SA concentration of 18 g L(-1). Batch culture revealed that high-yield succinate production (via oxidative TCA or glyoxylate redox balancing) occurred under non-growth conditions where a SA:AcA molar ratio of up to five was attained, with a final SA yield of 0.94 g g(-1). Growth termination of the batch culture was in agreement with that of the continuous culture. The maximum maintenance production rate of SA under batch conditions was found to be 0.6 g g(-1) h(-1). This is twice the maintenance rate observed in the continuous runs. The study revealed that the metabolic flux of E. coli KJ134 differs significantly for growth and non-growth conditions, with non-growth conditions resulting in higher SA:AcA ratios and SA yields. Bioreaction characteristics entailing growth and maintenance rates, as well as growth termination markers will guide future fermentor

  16. Optimal flux patterns in cellular metabolic networks

    Energy Technology Data Exchange (ETDEWEB)

    Almaas, E

    2007-01-20

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

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

    Directory of Open Access Journals (Sweden)

    Cheng Zhong

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

  18. Assessment of metabolic flux distribution in the thermophilic hydrogen producer Caloramator celer as affected by external pH and hydrogen partial pressure.

    Science.gov (United States)

    Ciranna, Alessandro; Pawar, Sudhanshu S; Santala, Ville; Karp, Matti; van Niel, Ed W J

    2014-03-28

    Caloramator celer is a strict anaerobic, alkalitolerant, thermophilic bacterium capable of converting glucose to hydrogen (H2), carbon dioxide, acetate, ethanol and formate by a mixed acid fermentation. Depending on the growth conditions C. celer can produce H2 at high yields. For a biotechnological exploitation of this bacterium for H2 production it is crucial to understand the factors that regulate carbon and electron fluxes and therefore the final distribution of metabolites to channel the metabolic flux towards the desired product. Combining experimental results from batch fermentations with genome analysis, reconstruction of central carbon metabolism and metabolic flux analysis (MFA), this study shed light on glucose catabolism of the thermophilic alkalitolerant bacterium C. celer. Two innate factors pertaining to culture conditions have been identified to significantly affect the metabolic flux distribution: culture pH and partial pressures of H2 (PH2). Overall, at alkaline to neutral pH the rate of biomass synthesis was maximized, whereas at acidic pH the lower growth rate and the less efficient biomass formation are accompanied with more efficient energy recovery from the substrate indicating high cell maintenance possibly to sustain intracellular pH homeostasis. Higher H2 yields were associated with fermentation at acidic pH as a consequence of the lower synthesis of other reduced by-products such as formate and ethanol. In contrast, PH2 did not affect the growth of C. celer on glucose. At high PH2 the cellular redox state was balanced by rerouting the flow of carbon and electrons to ethanol and formate production allowing unaltered glycolytic flux and growth rate, but resulting in a decreased H2 synthesis. C. celer possesses a flexible fermentative metabolism that allows redistribution of fluxes at key metabolic nodes to simultaneously control redox state and efficiently harvest energy from substrate even under unfavorable conditions (i.e. low pH and high

  19. Oxygen-enriched fermentation of sodium gluconate by Aspergillus niger and its impact on intracellular metabolic flux distributions.

    Science.gov (United States)

    Shen, Yuting; Tian, Xiwei; Zhao, Wei; Hang, Haifeng; Chu, Ju

    2018-01-01

    Different concentrations of oxygen-enriched air were utilized for sodium gluconate (SG) fermentation by Aspergillus niger. The fermentation time shortened from 20 to 15.5 h due to the increase of volumetric oxygen transfer coefficient (K L a) and the formation of more dispersed mycelia when inlet oxygen concentration ascended from 21 to 32%. According to metabolic flux analysis, during the growth phase, extracellular glucose for SG synthesis accounted for 79.0 and 85.3% with air and oxygen-enriched air (25%), respectively, whereas the proportions were 89.4 and 93.0% in the stationary phase. Intracellular glucose consumption decreased in oxygen-enriched fermentation, as cell respiration was more high-efficiently performed. Metabolic profiling indicated that most intermediates in TCA cycle and EMP pathway had smaller pool sizes in oxygen-enriched fermentations. Moreover, the main by-product of citric acid dramatically decreased from 1.36 to 0.34 g L -1 in oxygen-enriched fermentation. And the sodium gluconate yield increased from 0.856 to 0.903 mol mol -1 .

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

    Directory of Open Access Journals (Sweden)

    Nielsen Lars K

    2009-05-01

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

  1. Primary Metabolic Pathways and Metabolic Flux Analysis

    DEFF Research Database (Denmark)

    Villadsen, John

    2015-01-01

    his chapter introduces the metabolic flux analysis (MFA) or stoichiometry-based MFA, and describes the quantitative basis for MFA. It discusses the catabolic pathways in which free energy is produced to drive the cell-building anabolic pathways. An overview of these primary pathways provides...... the reader who is primarily trained in the engineering sciences with atleast a preliminary introduction to biochemistry and also shows how carbon is drained off the catabolic pathways to provide precursors for cell mass building and sometimes for important industrial products. The primary pathways...... to be examined in the following are: glycolysis, primarily by the EMP pathway, but other glycolytic pathways is also mentioned; fermentative pathways in which the redox generated in the glycolytic reactions are consumed; reactions in the tricarboxylic acid (TCA) cycle, which produce biomass precursors and redox...

  2. Consequences of phosphoenolpyruvate:sugar phosphotranferase system and pyruvate kinase isozymes inactivation in central carbon metabolism flux distribution in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Meza Eugenio

    2012-09-01

    Full Text Available Abstract Background In Escherichia coli phosphoenolpyruvate (PEP is a key central metabolism intermediate that participates in glucose transport, as precursor in several biosynthetic pathways and it is involved in allosteric regulation of glycolytic enzymes. In this work we generated W3110 derivative strains that lack the main PEP consumers PEP:sugar phosphotransferase system (PTS- and pyruvate kinase isozymes PykA and PykF (PTS-pykA- and PTS-pykF-. To characterize the effects of these modifications on cell physiology, carbon flux distribution and aromatics production capacity were determined. Results When compared to reference strain W3110, strain VH33 (PTS- displayed lower specific rates for growth, glucose consumption and acetate production as well as a higher biomass yield from glucose. These phenotypic effects were even more pronounced by the additional inactivation of PykA or PykF. Carbon flux analysis revealed that PTS inactivation causes a redirection of metabolic flux towards biomass formation. A cycle involving PEP carboxylase (Ppc and PEP carboxykinase (Pck was detected in all strains. In strains W3110, VH33 (PTS- and VH35 (PTS-, pykF-, the net flux in this cycle was inversely correlated with the specific rate of glucose consumption and inactivation of Pck in these strains caused a reduction in growth rate. In the PTS- background, inactivation of PykA caused a reduction in Ppc and Pck cycling as well as a reduction in flux to TCA, whereas inactivation of PykF caused an increase in anaplerotic flux from PEP to OAA and an increased flux to TCA. The wild-type and mutant strains were modified to overproduce L-phenylalanine. In resting cells experiments, compared to reference strain, a 10, 4 and 7-fold higher aromatics yields from glucose were observed as consequence of PTS, PTS PykA and PTS PykF inactivation. Conclusions Metabolic flux analysis performed on strains lacking the main activities generating pyruvate from PEP revealed the high

  3. Controlling fluxes for microbial metabolic engineering

    OpenAIRE

    Sachdeva, Gairik

    2014-01-01

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

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

    Science.gov (United States)

    Beurton-Aimar, Marie; Beauvoit, Bertrand; Monier, Antoine; Vallée, François; Dieuaide-Noubhani, Martine; Colombié, Sophie

    2011-06-20

    (13)C 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. 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. 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 (13)C metabolic flux analysis

  5. Derivative processes for modelling metabolic fluxes

    Science.gov (United States)

    Žurauskienė, Justina; Kirk, Paul; Thorne, Thomas; Pinney, John; Stumpf, Michael

    2014-01-01

    Motivation: One of the challenging questions in modelling biological systems is to characterize the functional forms of the processes that control and orchestrate molecular and cellular phenotypes. Recently proposed methods for the analysis of metabolic pathways, for example, dynamic flux estimation, can only provide estimates of the underlying fluxes at discrete time points but fail to capture the complete temporal behaviour. To describe the dynamic variation of the fluxes, we additionally require the assumption of specific functional forms that can capture the temporal behaviour. However, it also remains unclear how to address the noise which might be present in experimentally measured metabolite concentrations. Results: Here we propose a novel approach to modelling metabolic fluxes: derivative processes that are based on multiple-output Gaussian processes (MGPs), which are a flexible non-parametric Bayesian modelling technique. The main advantages that follow from MGPs approach include the natural non-parametric representation of the fluxes and ability to impute the missing data in between the measurements. Our derivative process approach allows us to model changes in metabolite derivative concentrations and to characterize the temporal behaviour of metabolic fluxes from time course data. Because the derivative of a Gaussian process is itself a Gaussian process, we can readily link metabolite concentrations to metabolic fluxes and vice versa. Here we discuss how this can be implemented in an MGP framework and illustrate its application to simple models, including nitrogen metabolism in Escherichia coli. Availability and implementation: R code is available from the authors upon request. Contact: j.norkunaite@imperial.ac.uk; m.stumpf@imperial.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24578401

  6. From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints

    Science.gov (United States)

    Klamt, Steffen; Gerstl, Matthias P.; Jungreuthmayer, Christian; Mahadevan, Radhakrishnan; Müller, Stefan

    2017-01-01

    Elementary flux modes (EFMs) emerged as a formal concept to describe metabolic pathways and have become an established tool for constraint-based modeling and metabolic network analysis. EFMs are characteristic (support-minimal) vectors of the flux cone that contains all feasible steady-state flux vectors of a given metabolic network. EFMs account for (homogeneous) linear constraints arising from reaction irreversibilities and the assumption of steady state; however, other (inhomogeneous) linear constraints, such as minimal and maximal reaction rates frequently used by other constraint-based techniques (such as flux balance analysis [FBA]), cannot be directly integrated. These additional constraints further restrict the space of feasible flux vectors and turn the flux cone into a general flux polyhedron in which the concept of EFMs is not directly applicable anymore. For this reason, there has been a conceptual gap between EFM-based (pathway) analysis methods and linear optimization (FBA) techniques, as they operate on different geometric objects. One approach to overcome these limitations was proposed ten years ago and is based on the concept of elementary flux vectors (EFVs). Only recently has the community started to recognize the potential of EFVs for metabolic network analysis. In fact, EFVs exactly represent the conceptual development required to generalize the idea of EFMs from flux cones to flux polyhedra. This work aims to present a concise theoretical and practical introduction to EFVs that is accessible to a broad audience. We highlight the close relationship between EFMs and EFVs and demonstrate that almost all applications of EFMs (in flux cones) are possible for EFVs (in flux polyhedra) as well. In fact, certain properties can only be studied with EFVs. Thus, we conclude that EFVs provide a powerful and unifying framework for constraint-based modeling of metabolic networks. PMID:28406903

  7. PFA toolbox: a MATLAB tool for Metabolic Flux Analysis.

    Science.gov (United States)

    Morales, Yeimy; Bosque, Gabriel; Vehí, Josep; Picó, Jesús; Llaneras, Francisco

    2016-07-11

    Metabolic Flux Analysis (MFA) is a methodology that has been successfully applied to estimate metabolic fluxes in living cells. However, traditional frameworks based on this approach have some limitations, particularly when measurements are scarce and imprecise. This is very common in industrial environments. The PFA Toolbox can be used to face those scenarios. Here we present the PFA (Possibilistic Flux Analysis) Toolbox for MATLAB, which simplifies the use of Interval and Possibilistic Metabolic Flux Analysis. The main features of the PFA Toolbox are the following: (a) It provides reliable MFA estimations in scenarios where only a few fluxes can be measured or those available are imprecise. (b) It provides tools to easily plot the results as interval estimates or flux distributions. (c) It is composed of simple functions that MATLAB users can apply in flexible ways. (d) It includes a Graphical User Interface (GUI), which provides a visual representation of the measurements and their uncertainty. (e) It can use stoichiometric models in COBRA format. In addition, the PFA Toolbox includes a User's Guide with a thorough description of its functions and several examples. The PFA Toolbox for MATLAB is a freely available Toolbox that is able to perform Interval and Possibilistic MFA estimations.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-08-19

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

  9. EL-2 reactor: Thermal neutron flux distribution

    International Nuclear Information System (INIS)

    Rousseau, A.; Genthon, J.P.

    1958-01-01

    The flux distribution of thermal neutrons in EL-2 reactor is studied. The reactor core and lattices are described as well as the experimental reactor facilities, in particular, the experimental channels and special facilities. The measurement shows that the thermal neutron flux increases in the central channel when enriched uranium is used in place of natural uranium. However the thermal neutron flux is not perturbed in the other reactor channels by the fuel modification. The macroscopic flux distribution is measured according the radial positioning of fuel rods. The longitudinal neutron flux distribution in a fuel rod is also measured and shows no difference between enriched and natural uranium fuel rods. In addition, measurements of the flux distribution have been effectuated for rods containing other material as steel or aluminium. The neutron flux distribution is also studied in all the experimental channels as well as in the thermal column. The determination of the distribution of the thermal neutron flux in all experimental facilities, the thermal column and the fuel channels has been made with a heavy water level of 1825 mm and is given for an operating power of 1000 kW. (M.P.)

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

    Directory of Open Access Journals (Sweden)

    Nobuyuki Okahashi

    2014-05-01

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

  11. FluxFix: automatic isotopologue normalization for metabolic tracer analysis.

    Science.gov (United States)

    Trefely, Sophie; Ashwell, Peter; Snyder, Nathaniel W

    2016-11-25

    Isotopic tracer analysis by mass spectrometry is a core technique for the study of metabolism. Isotopically labeled atoms from substrates, such as [ 13 C]-labeled glucose, can be traced by their incorporation over time into specific metabolic products. Mass spectrometry is often used for the detection and differentiation of the isotopologues of each metabolite of interest. For meaningful interpretation, mass spectrometry data from metabolic tracer experiments must be corrected to account for the naturally occurring isotopologue distribution. The calculations required for this correction are time consuming and error prone and existing programs are often platform specific, non-intuitive, commercially licensed and/or limited in accuracy by using theoretical isotopologue distributions, which are prone to artifacts from noise or unresolved interfering signals. Here we present FluxFix ( http://fluxfix.science ), an application freely available on the internet that quickly and reliably transforms signal intensity values into percent mole enrichment for each isotopologue measured. 'Unlabeled' data, representing the measured natural isotopologue distribution for a chosen analyte, is entered by the user. This data is used to generate a correction matrix according to a well-established algorithm. The correction matrix is applied to labeled data, also entered by the user, thus generating the corrected output data. FluxFix is compatible with direct copy and paste from spreadsheet applications including Excel (Microsoft) and Google sheets and automatically adjusts to account for input data dimensions. The program is simple, easy to use, agnostic to the mass spectrometry platform, generalizable to known or unknown metabolites, and can take input data from either a theoretical natural isotopologue distribution or an experimentally measured one. Our freely available web-based calculator, FluxFix ( http://fluxfix.science ), quickly and reliably corrects metabolic tracer data for

  12. Regulation of flux through metabolic cycles

    International Nuclear Information System (INIS)

    Walsh, K.

    1984-01-01

    The branchpoint of the tricarboxylic acid and glyoxylate shunt was characterized in the intact organism by a multidimensional approach. Theory and methodology were developed to determine velocities for the net flow of carbon through the major steps of acetate metabolism in E. coli. Rates were assigned based on the 13 C-NMR spectrum of intracellular glutamate, measured rates of substrate incorporation into end products, the constituent composition of E. coli and a series of conservation equations which described the system at steady state. The in vivo fluxes through the branchpoint of the tricarboxylic acid and glyoxylate cycles were compared to rates calculated from the kinetic constants of the branchpoint enzymes and the intracellular concentrations of their substrates. These studies elucidated the role of isocitrate dehydrogenase phosphorylation in the Krebs cycle and led to the development of a generalized mathematical description of the sensitivity of branchpoints to regulatory control. This theoretical analysis was termed the branchpoint effect and it describes conditions which result in large changes in the flux through an enzyme even though that enzyme is not subject to direct regulatory control. The theoretical and experimental characterization of this system provided a framework to study the effects of enzyme overproduction and underproduction on metabolic processes in the cell. An in vivo method was developed to determine the extent to which an enzyme catalyzes a rate-controlling reaction. The enzyme chosen for this study was citrate synthase

  13. Heat Flux Distribution of Antarctica Unveiled

    Science.gov (United States)

    Martos, Yasmina M.; Catalán, Manuel; Jordan, Tom A.; Golynsky, Alexander; Golynsky, Dmitry; Eagles, Graeme; Vaughan, David G.

    2017-11-01

    Antarctica is the largest reservoir of ice on Earth. Understanding its ice sheet dynamics is crucial to unraveling past global climate change and making robust climatic and sea level predictions. Of the basic parameters that shape and control ice flow, the most poorly known is geothermal heat flux. Direct observations of heat flux are difficult to obtain in Antarctica, and until now continent-wide heat flux maps have only been derived from low-resolution satellite magnetic and seismological data. We present a high-resolution heat flux map and associated uncertainty derived from spectral analysis of the most advanced continental compilation of airborne magnetic data. Small-scale spatial variability and features consistent with known geology are better reproduced than in previous models, between 36% and 50%. Our high-resolution heat flux map and its uncertainty distribution provide an important new boundary condition to be used in studies on future subglacial hydrology, ice sheet dynamics, and sea level change.

  14. Metabolic fuels: regulating fluxes to select mix.

    Science.gov (United States)

    Weber, Jean-Michel

    2011-01-15

    Animals must regulate the fluxes of multiple fuels to support changing metabolic rates that result from variation in physiological circumstances. The aim of fuel selection strategies is to exploit the advantages of individual substrates while minimizing the impact of disadvantages. All exercising mammals share a general pattern of fuel selection: at the same %V(O(2,max)) they oxidize the same ratio of lipids to carbohydrates. However, highly aerobic species rely more on intramuscular fuels because energy supply from the circulation is constrained by trans-sarcolemmal transfer. Fuel selection is performed by recruiting different muscles, different fibers within the same muscles or different pathways within the same fibers. Electromyographic analyses show that shivering humans can modulate carbohydrate oxidation either through the selective recruitment of type II fibers within the same muscles or by regulating pathway recruitment within type I fibers. The selection patterns of shivering and exercise are different: at the same %V(O(2,max)), a muscle producing only heat (shivering) or significant movement (exercise) strikes a different balance between lipid and carbohydrate oxidation. Long-distance migrants provide an excellent model to characterize how to increase maximal substrate fluxes. High lipid fluxes are achieved through the coordinated upregulation of mobilization, transport and oxidation by activating enzymes, lipid-solubilizing proteins and membrane transporters. These endurance athletes support record lipolytic rates in adipocytes, use lipoprotein shuttles to accelerate transport and show increased capacity for lipid oxidation in muscle mitochondria. Some migrant birds use dietary omega-3 fatty acids as performance-enhancing agents to boost their ability to process lipids. These dietary fatty acids become incorporated in membrane phospholipids and bind to peroxisome proliferator-activated receptors to activate membrane proteins and modify gene expression.

  15. Phototransduction Influences Metabolic Flux and Nucleotide Metabolism in Mouse Retina.

    Science.gov (United States)

    Du, Jianhai; Rountree, Austin; Cleghorn, Whitney M; Contreras, Laura; Lindsay, Ken J; Sadilek, Martin; Gu, Haiwei; Djukovic, Danijel; Raftery, Dan; Satrústegui, Jorgina; Kanow, Mark; Chan, Lawrence; Tsang, Stephen H; Sweet, Ian R; Hurley, James B

    2016-02-26

    Production of energy in a cell must keep pace with demand. Photoreceptors use ATP to maintain ion gradients in darkness, whereas in light they use it to support phototransduction. Matching production with consumption can be accomplished by coupling production directly to consumption. Alternatively, production can be set by a signal that anticipates demand. In this report we investigate the hypothesis that signaling through phototransduction controls production of energy in mouse retinas. We found that respiration in mouse retinas is not coupled tightly to ATP consumption. By analyzing metabolic flux in mouse retinas, we also found that phototransduction slows metabolic flux through glycolysis and through intermediates of the citric acid cycle. We also evaluated the relative contributions of regulation of the activities of α-ketoglutarate dehydrogenase and the aspartate-glutamate carrier 1. In addition, a comprehensive analysis of the retinal metabolome showed that phototransduction also influences steady-state concentrations of 5'-GMP, ribose-5-phosphate, ketone bodies, and purines. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  16. Metabolic cartography: experimental quantification of metabolic fluxes from isotopic labelling studies

    Energy Technology Data Exchange (ETDEWEB)

    O' Grady J.; Schwender J.; Shachar-Hill, Y.; Morgan, J. A.

    2012-03-01

    For the past decade, flux maps have provided researchers with an in-depth perspective on plant metabolism. As a rapidly developing field, significant headway has been made recently in computation, experimentation, and overall understanding of metabolic flux analysis. These advances are particularly applicable to the study of plant metabolism. New dynamic computational methods such as non-stationary metabolic flux analysis are finding their place in the toolbox of metabolic engineering, allowing more organisms to be studied and decreasing the time necessary for experimentation, thereby opening new avenues by which to explore the vast diversity of plant metabolism. Also, improved methods of metabolite detection and measurement have been developed, enabling increasingly greater resolution of flux measurements and the analysis of a greater number of the multitude of plant metabolic pathways. Methods to deconvolute organelle-specific metabolism are employed with increasing effectiveness, elucidating the compartmental specificity inherent in plant metabolism. Advances in metabolite measurements have also enabled new types of experiments, such as the calculation of metabolic fluxes based on {sup 13}CO{sub 2} dynamic labelling data, and will continue to direct plant metabolic engineering. Newly calculated metabolic flux maps reveal surprising and useful information about plant metabolism, guiding future genetic engineering of crops to higher yields. Due to the significant level of complexity in plants, these methods in combination with other systems biology measurements are necessary to guide plant metabolic engineering in the future.

  17. Metabolic cartography: experimental quantification of metabolic fluxes from isotopic labelling studies

    Energy Technology Data Exchange (ETDEWEB)

    O' Grady, J; Schwender, J; Shachar-Hill, Y; Morgan, JA

    2012-03-26

    For the past decade, flux maps have provided researchers with an in-depth perspective on plant metabolism. As a rapidly developing field, significant headway has been made recently in computation, experimentation, and overall understanding of metabolic flux analysis. These advances are particularly applicable to the study of plant metabolism. New dynamic computational methods such as non-stationary metabolic flux analysis are finding their place in the toolbox of metabolic engineering, allowing more organisms to be studied and decreasing the time necessary for experimentation, thereby opening new avenues by which to explore the vast diversity of plant metabolism. Also, improved methods of metabolite detection and measurement have been developed, enabling increasingly greater resolution of flux measurements and the analysis of a greater number of the multitude of plant metabolic pathways. Methods to deconvolute organelle-specific metabolism are employed with increasing effectiveness, elucidating the compartmental specificity inherent in plant metabolism. Advances in metabolite measurements have also enabled new types of experiments, such as the calculation of metabolic fluxes based on (CO2)-C-13 dynamic labelling data, and will continue to direct plant metabolic engineering. Newly calculated metabolic flux maps reveal surprising and useful information about plant metabolism, guiding future genetic engineering of crops to higher yields. Due to the significant level of complexity in plants, these methods in combination with other systems biology measurements are necessary to guide plant metabolic engineering in the future.

  18. Metabolic cartography: experimental quantification of metabolic fluxes from isotopic labelling studies.

    Science.gov (United States)

    O'Grady, John; Schwender, Jörg; Shachar-Hill, Yair; Morgan, John A

    2012-03-01

    For the past decade, flux maps have provided researchers with an in-depth perspective on plant metabolism. As a rapidly developing field, significant headway has been made recently in computation, experimentation, and overall understanding of metabolic flux analysis. These advances are particularly applicable to the study of plant metabolism. New dynamic computational methods such as non-stationary metabolic flux analysis are finding their place in the toolbox of metabolic engineering, allowing more organisms to be studied and decreasing the time necessary for experimentation, thereby opening new avenues by which to explore the vast diversity of plant metabolism. Also, improved methods of metabolite detection and measurement have been developed, enabling increasingly greater resolution of flux measurements and the analysis of a greater number of the multitude of plant metabolic pathways. Methods to deconvolute organelle-specific metabolism are employed with increasing effectiveness, elucidating the compartmental specificity inherent in plant metabolism. Advances in metabolite measurements have also enabled new types of experiments, such as the calculation of metabolic fluxes based on (13)CO(2) dynamic labelling data, and will continue to direct plant metabolic engineering. Newly calculated metabolic flux maps reveal surprising and useful information about plant metabolism, guiding future genetic engineering of crops to higher yields. Due to the significant level of complexity in plants, these methods in combination with other systems biology measurements are necessary to guide plant metabolic engineering in the future.

  19. Metabolic flux analysis of heterotrophic growth in Chlamydomonas reinhardtii.

    Directory of Open Access Journals (Sweden)

    Nanette R Boyle

    Full Text Available Despite the wealth of knowledge available for C. reinhardtii, the central metabolic fluxes of growth on acetate have not yet been determined. In this study, 13C-metabolic flux analysis (13C-MFA was used to determine and quantify the metabolic pathways of primary metabolism in C. reinhardtii cells grown under heterotrophic conditions with acetate as the sole carbon source. Isotopic labeling patterns of compartment specific biomass derived metabolites were used to calculate the fluxes. It was found that acetate is ligated with coenzyme A in the three subcellular compartments (cytosol, mitochondria and plastid included in the model. Two citrate synthases were found to potentially be involved in acetyl-coA metabolism; one localized in the mitochondria and the other acting outside the mitochondria. Labeling patterns demonstrate that Acetyl-coA synthesized in the plastid is directly incorporated in synthesis of fatty acids. Despite having a complete TCA cycle in the mitochondria, it was also found that a majority of the malate flux is shuttled to the cytosol and plastid where it is converted to oxaloacetate providing reducing equivalents to these compartments. When compared to predictions by flux balance analysis, fluxes measured with 13C-MFA were found to be suboptimal with respect to biomass yield; C. reinhardtii sacrifices biomass yield to produce ATP and reducing equivalents.

  20. Effect of amino acid supplementation on titer and glycosylation distribution in hybridoma cell cultures-Systems biology-based interpretation using genome-scale metabolic flux balance model and multivariate data analysis.

    Science.gov (United States)

    Reimonn, Thomas M; Park, Seo-Young; Agarabi, Cyrus D; Brorson, Kurt A; Yoon, Seongkyu

    2016-09-01

    Genome-scale flux balance analysis (FBA) is a powerful systems biology tool to characterize intracellular reaction fluxes during cell cultures. FBA estimates intracellular reaction rates by optimizing an objective function, subject to the constraints of a metabolic model and media uptake/excretion rates. A dynamic extension to FBA, dynamic flux balance analysis (DFBA), can calculate intracellular reaction fluxes as they change during cell cultures. In a previous study by Read et al. (2013), a series of informed amino acid supplementation experiments were performed on twelve parallel murine hybridoma cell cultures, and this data was leveraged for further analysis (Read et al., Biotechnol Prog. 2013;29:745-753). In order to understand the effects of media changes on the model murine hybridoma cell line, a systems biology approach is applied in the current study. Dynamic flux balance analysis was performed using a genome-scale mouse metabolic model, and multivariate data analysis was used for interpretation. The calculated reaction fluxes were examined using partial least squares and partial least squares discriminant analysis. The results indicate media supplementation increases product yield because it raises nutrient levels extending the growth phase, and the increased cell density allows for greater culture performance. At the same time, the directed supplementation does not change the overall metabolism of the cells. This supports the conclusion that product quality, as measured by glycoform assays, remains unchanged because the metabolism remains in a similar state. Additionally, the DFBA shows that metabolic state varies more at the beginning of the culture but less by the middle of the growth phase, possibly due to stress on the cells during inoculation. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1163-1173, 2016. © 2016 American Institute of Chemical Engineers.

  1. Metabolic flux prediction in cancer cells with altered substrate uptake.

    Science.gov (United States)

    Schwartz, Jean-Marc; Barber, Michael; Soons, Zita

    2015-12-01

    Proliferating cells, such as cancer cells, are known to have an unusual metabolism, characterized by an increased rate of glycolysis and amino acid metabolism. Our understanding of this phenomenon is limited but could potentially be used in order to develop new therapies. Computational modelling techniques, such as flux balance analysis (FBA), have been used to predict fluxes in various cell types, but remain of limited use to explain the unusual metabolic shifts and altered substrate uptake in human cancer cells. We implemented a new flux prediction method based on elementary modes (EMs) and structural flux (StruF) analysis and tested them against experimentally measured flux data obtained from (13)C-labelling in a cancer cell line. We assessed the quality of predictions using different objective functions along with different techniques in normalizing a metabolic network with more than one substrate input. Results show a good correlation between predicted and experimental values and indicate that the choice of cellular objective critically affects the quality of predictions. In particular, lactate gives an excellent correlation and correctly predicts the high flux through glycolysis, matching the observed characteristics of cancer cells. In contrast with FBA, which requires a priori definition of all uptake rates, often hard to measure, atomic StruFs (aStruFs) are able to predict uptake rates of multiple substrates. © 2015 Authors; published by Portland Press Limited.

  2. Constraining genome-scale models to represent the bow tie structure of metabolism for 13C metabolic flux analysis

    DEFF Research Database (Denmark)

    Backman, Tyler W.H.; Ando, David; Singh, Jahnavi

    2018-01-01

    Determination of internal metabolic fluxes is crucial for fundamental and applied biology because they map how carbon and electrons flow through metabolism to enable cell function. 13C Metabolic Flux Analysis (13C MFA) and Two-Scale 13C Metabolic Flux Analysis (2S-13C MFA) are two techniques used...

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

    Science.gov (United States)

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

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

    Science.gov (United States)

    Tabe-Bordbar, Shayan; Marashi, Sayed-Amir

    2013-12-01

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

  5. Multiobjective flux balancing using the NISE method for metabolic network analysis.

    Science.gov (United States)

    Oh, Young-Gyun; Lee, Dong-Yup; Lee, Sang Yup; Park, Sunwon

    2009-01-01

    Flux balance analysis (FBA) is well acknowledged as an analysis tool of metabolic networks in the framework of metabolic engineering. However, FBA has a limitation for solving a multiobjective optimization problem which considers multiple conflicting objectives. In this study, we propose a novel multiobjective flux balance analysis method, which adapts the noninferior set estimation (NISE) method (Solanki et al., 1993) for multiobjective linear programming (MOLP) problems. NISE method can generate an approximation of the Pareto curve for conflicting objectives without redundant iterations of single objective optimization. Furthermore, the flux distributions at each Pareto optimal solution can be obtained for understanding the internal flux changes in the metabolic network. The functionality of this approach is shown by applying it to a genome-scale in silico model of E. coli. Multiple objectives for the poly(3-hydroxybutyrate) [P(3HB)] production are considered simultaneously, and relationships among them are identified. The Pareto curve for maximizing succinic acid production vs. maximizing biomass production is used for the in silico analysis of various combinatorial knockout strains. This proposed method accelerates the strain improvement in the metabolic engineering by reducing computation time of obtaining the Pareto curve and analysis time of flux distribution at each Pareto optimal solution. (c) 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009.

  6. Modelling central metabolic fluxes by constraint-based optimization reveals metabolic reprogramming of developing Solanum lycopersicum (tomato) fruit.

    Science.gov (United States)

    Colombié, Sophie; Nazaret, Christine; Bénard, Camille; Biais, Benoît; Mengin, Virginie; Solé, Marion; Fouillen, Laëtitia; Dieuaide-Noubhani, Martine; Mazat, Jean-Pierre; Beauvoit, Bertrand; Gibon, Yves

    2015-01-01

    Modelling of metabolic networks is a powerful tool to analyse the behaviour of developing plant organs, including fruits. Guided by our current understanding of heterotrophic metabolism of plant cells, a medium-scale stoichiometric model, including the balance of co-factors and energy, was constructed in order to describe metabolic shifts that occur through the nine sequential stages of Solanum lycopersicum (tomato) fruit development. The measured concentrations of the main biomass components and the accumulated metabolites in the pericarp, determined at each stage, were fitted in order to calculate, by derivation, the corresponding external fluxes. They were used as constraints to solve the model by minimizing the internal fluxes. The distribution of the calculated fluxes of central metabolism were then analysed and compared with known metabolic behaviours. For instance, the partition of the main metabolic pathways (glycolysis, pentose phosphate pathway, etc.) was relevant throughout fruit development. We also predicted a valid import of carbon and nitrogen by the fruit, as well as a consistent CO2 release. Interestingly, the energetic balance indicates that excess ATP is dissipated just before the onset of ripening, supporting the concept of the climacteric crisis. Finally, the apparent contradiction between calculated fluxes with low values compared with measured enzyme capacities suggest a complex reprogramming of the metabolic machinery during fruit development. With a powerful set of experimental data and an accurate definition of the metabolic system, this work provides important insight into the metabolic and physiological requirements of the developing tomato fruits. © 2014 The Authors The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

  7. The measurements of thermal neutron flux distribution in a paraffin

    Indian Academy of Sciences (India)

    The term `thermal flux' implies a Maxwellian distribution of velocity and energy corresponding to the most probable velocity of 2200 ms-1 at 293.4 K. In order to measure the thermal neutron flux density, the foil activation method was used. Thermal neutron flux determination in paraffin phantom by counting the emitted rays of ...

  8. The measurements of thermal neutron flux distribution in a paraffin ...

    Indian Academy of Sciences (India)

    The term `thermal flux' implies a Maxwellian distribution of velocity and energy corresponding to the most probable velocity of 2200 ms-1 at 293.4 K. In order to measure the thermal neutron flux density, the foil activation method was used. Thermal neutron flux determination in paraffin phantom by counting the emitted rays of ...

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

    Directory of Open Access Journals (Sweden)

    Jordan eHay

    2014-12-01

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

  10. Designing metabolic engineering strategies with genome-scale metabolic flux modeling

    Directory of Open Access Journals (Sweden)

    Yen JY

    2015-01-01

    Full Text Available Jiun Y Yen,1,2 Imen Tanniche,1 Amanda K Fisher,1–3 Glenda E Gillaspy,2 David R Bevan,2,3 Ryan S Senger1 1Department of Biological Systems Engineering, 2Department of Biochemistry, 3Genomics, Bioinformatics, and Computational Biology Interdisciplinary Program, Virginia Tech, Blacksburg, VA, USA Abstract: New in silico tools that make use of genome-scale metabolic flux modeling are improving the design of metabolic engineering strategies. This review highlights the latest developments in this area, explains the interface between these in silico tools and the experimental implementation tools of metabolic engineers, and provides a way forward so that in silico predictions can better mimic reality and more experimental methods can be considered in simulation studies. The several methodologies for solving genome-scale models (eg, flux balance analysis [FBA], parsimonious FBA, flux variability analysis, and minimization of metabolic adjustment all have unique advantages and applications. There are two basic approaches to designing metabolic engineering strategies in silico, and both have demonstrated success in the literature. The first involves: 1 making a genetic manipulation in a model; 2 testing for improved performance through simulation; and 3 iterating the process. The second approach has been used in more recently designed in silico tools and involves: 1 comparing metabolic flux profiles of a wild-type and ideally engineered state and 2 designing engineering strategies based on the differences in these flux profiles. Improvements in genome-scale modeling are anticipated in areas such as the inclusion of all relevant cellular machinery, the ability to understand and anticipate the results of combinatorial enrichment experiments, and constructing dynamic and flexible biomass equations that can respond to environmental and genetic manipulations. Keywords: genome-scale modeling, genome-scale modeling, flux balance analysis, flux variability

  11. Two-Scale 13C Metabolic Flux Analysis for Metabolic Engineering.

    Science.gov (United States)

    Ando, David; Garcia Martin, Hector

    2018-01-01

    Accelerating the Design-Build-Test-Learn (DBTL) cycle in synthetic biology is critical to achieving rapid and facile bioengineering of organisms for the production of, e.g., biofuels and other chemicals. The Learn phase involves using data obtained from the Test phase to inform the next Design phase. As part of the Learn phase, mathematical models of metabolic fluxes give a mechanistic level of comprehension to cellular metabolism, isolating the principle drivers of metabolic behavior from the peripheral ones, and directing future experimental designs and engineering methodologies. Furthermore, the measurement of intracellular metabolic fluxes is specifically noteworthy as providing a rapid and easy-to-understand picture of how carbon and energy flow throughout the cell. Here, we present a detailed guide to performing metabolic flux analysis in the Learn phase of the DBTL cycle, where we show how one can take the isotope labeling data from a 13 C labeling experiment and immediately turn it into a determination of cellular fluxes that points in the direction of genetic engineering strategies that will advance the metabolic engineering process.For our modeling purposes we use the Joint BioEnergy Institute (JBEI) Quantitative Metabolic Modeling (jQMM) library, which provides an open-source, python-based framework for modeling internal metabolic fluxes and making actionable predictions on how to modify cellular metabolism for specific bioengineering goals. It presents a complete toolbox for performing different types of flux analysis such as Flux Balance Analysis, 13 C Metabolic Flux Analysis, and it introduces the capability to use 13 C labeling experimental data to constrain comprehensive genome-scale models through a technique called two-scale 13 C Metabolic Flux Analysis (2S- 13 C MFA) [1]. In addition to several other capabilities, the jQMM is also able to predict the effects of knockouts using the MoMA and ROOM methodologies. The use of the jQMM library is

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

    DEFF Research Database (Denmark)

    Machado, Daniel; Herrgard, Markus; Rocha, Isabel

    2015-01-01

    contribution to the metabolic flux changes. Inspired by these results, we develop a constraint-based method (arFBA) for simulation of metabolic flux distributions that accounts for allosteric interactions. This method can be used for systematic prediction of potential allosteric regulation under the given...... the metabolic flux. Accounting for allosteric interactions in metabolic reconstructions reveals a hidden topology in metabolic networks, improving our understanding of cellular metabolism and fostering the development of novel simulation methods that account for this type of regulation....

  13. An observer-theoretic approach to estimating neutron flux distribution

    International Nuclear Information System (INIS)

    Park, Young Ho; Cho, Nam Zin

    1989-01-01

    State feedback control provides many advantages such as stabilization and improved transient response. However, when the state feedback control is considered for spatial control of a nuclear reactor, it requires complete knowledge of the distributions of the system state variables. This paper describes a method for estimating the flux spatial distribution using only limited flux measurements. It is based on the Luenberger observer in control theory, extended to the distributed parameter systems such as the space-time reactor dynamics equation. The results of the application of the method to simple reactor models showed that the flux distribution is estimated by the observer very efficiently using information from only a few sensors

  14. Maintenance metabolism and carbon fluxes in Bacillus species

    Directory of Open Access Journals (Sweden)

    Decasper Seraina

    2008-06-01

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

  15. Metabolic flux profiling of recombinant protein secreting Pichia pastoris growing on glucose:methanol mixtures

    Science.gov (United States)

    2012-01-01

    Background The methylotrophic yeast Pichia pastoris has emerged as one of the most promising yeast hosts for the production of heterologous proteins. Mixed feeds of methanol and a multicarbon source instead of methanol as sole carbon source have been shown to improve product productivities and alleviate metabolic burden derived from protein production. Nevertheless, systematic quantitative studies on the relationships between the central metabolism and recombinant protein production in P. pastoris are still rather limited, particularly when growing this yeast on mixed carbon sources, thus hampering future metabolic network engineering strategies for improved protein production. Results The metabolic flux distribution in the central metabolism of P. pastoris growing on a mixed feed of glucose and methanol was analyzed by Metabolic Flux Analysis (MFA) using 13C-NMR-derived constraints. For this purpose, we defined new flux ratios for methanol assimilation pathways in P. pastoris cells growing on glucose:methanol mixtures. By using this experimental approach, the metabolic burden caused by the overexpression and secretion of a Rhizopus oryzae lipase (Rol) in P. pastoris was further analyzed. This protein has been previously shown to trigger the unfolded protein response in P. pastoris. A series of 13C-tracer experiments were performed on aerobic chemostat cultivations with a control and two different Rol producing strains growing at a dilution rate of 0.09 h−1 using a glucose:methanol 80:20 (w/w) mix as carbon source. The MFA performed in this study reveals a significant redistristribution of carbon fluxes in the central carbon metabolism when comparing the two recombinant strains vs the control strain, reflected in increased glycolytic, TCA cycle and NADH regeneration fluxes, as well as higher methanol dissimilation rates. Conclusions Overall, a further 13C-based MFA development to characterise the central metabolism of methylotrophic yeasts when growing on mixed

  16. Metabolic flux profiling of recombinant protein secreting Pichia pastoris growing on glucose:methanol mixtures

    Directory of Open Access Journals (Sweden)

    Jordà Joel

    2012-05-01

    Full Text Available Abstract Background The methylotrophic yeast Pichia pastoris has emerged as one of the most promising yeast hosts for the production of heterologous proteins. Mixed feeds of methanol and a multicarbon source instead of methanol as sole carbon source have been shown to improve product productivities and alleviate metabolic burden derived from protein production. Nevertheless, systematic quantitative studies on the relationships between the central metabolism and recombinant protein production in P. pastoris are still rather limited, particularly when growing this yeast on mixed carbon sources, thus hampering future metabolic network engineering strategies for improved protein production. Results The metabolic flux distribution in the central metabolism of P. pastoris growing on a mixed feed of glucose and methanol was analyzed by Metabolic Flux Analysis (MFA using 13C-NMR-derived constraints. For this purpose, we defined new flux ratios for methanol assimilation pathways in P. pastoris cells growing on glucose:methanol mixtures. By using this experimental approach, the metabolic burden caused by the overexpression and secretion of a Rhizopus oryzae lipase (Rol in P. pastoris was further analyzed. This protein has been previously shown to trigger the unfolded protein response in P. pastoris. A series of 13C-tracer experiments were performed on aerobic chemostat cultivations with a control and two different Rol producing strains growing at a dilution rate of 0.09 h−1 using a glucose:methanol 80:20 (w/w mix as carbon source. The MFA performed in this study reveals a significant redistristribution of carbon fluxes in the central carbon metabolism when comparing the two recombinant strains vs the control strain, reflected in increased glycolytic, TCA cycle and NADH regeneration fluxes, as well as higher methanol dissimilation rates. Conclusions Overall, a further 13C-based MFA development to characterise the central metabolism of methylotrophic

  17. WUFlux: an open-source platform for 13C metabolic flux analysis of bacterial metabolism.

    Science.gov (United States)

    He, Lian; Wu, Stephen G; Zhang, Muhan; Chen, Yixin; Tang, Yinjie J

    2016-11-04

    Flux analyses, including flux balance analysis (FBA) and 13 C-metabolic flux analysis ( 13 C-MFA), offer direct insights into cell metabolism, and have been widely used to characterize model and non-model microbial species. Nonetheless, constructing the 13 C-MFA model and performing flux calculation are demanding for new learners, because they require knowledge of metabolic networks, carbon transitions, and computer programming. To facilitate and standardize the 13 C-MFA modeling work, we set out to publish a user-friendly and programming-free platform (WUFlux) for flux calculations in MATLAB ® . We constructed an open-source platform for steady-state 13 C-MFA. Using GUIDE (graphical user interface design environment) in MATLAB, we built a user interface that allows users to modify models based on their own experimental conditions. WUFlux is capable of directly correcting mass spectrum data of TBDMS (N-tert-butyldimethylsilyl-N-methyltrifluoroacetamide)-derivatized proteinogenic amino acids by removing background noise. To simplify 13 C-MFA of different prokaryotic species, the software provides several metabolic network templates, including those for chemoheterotrophic bacteria and mixotrophic cyanobacteria. Users can modify the network and constraints, and then analyze the microbial carbon and energy metabolisms of various carbon substrates (e.g., glucose, pyruvate/lactate, acetate, xylose, and glycerol). WUFlux also offers several ways of visualizing the flux results with respect to the constructed network. To validate our model's applicability, we have compared and discussed the flux results obtained from WUFlux and other MFA software. We have also illustrated how model constraints of cofactor and ATP balances influence fluxome results. Open-source software for 13 C-MFA, WUFlux, with a user-friendly interface and easy-to-modify templates, is now available at http://www.13cmfa.org /or ( http://tang.eece.wustl.edu/ToolDevelopment.htm ). We will continue

  18. Device for measuring neutron-flux distribution density

    International Nuclear Information System (INIS)

    Rozenbljum, N.D.; Mitelman, M.G.; Kononovich, A.A.; Kirsanov, V.S.; Zagadkin, V.A.

    1977-01-01

    An arrangement is described for measuring the distribution of neutron flux density over the height of a nuclear reactor core and which may be used for monitoring energy release or for detecting deviations of neutron flux from an optimal level so that subsequent balance can be achieved. It avoids mutual interference of detectors. Full constructional details are given. (UK)

  19. Modeling of Drift Effects on Solar Tower Concentrated Flux Distributions

    Directory of Open Access Journals (Sweden)

    Luis O. Lara-Cerecedo

    2016-01-01

    Full Text Available A novel modeling tool for calculation of central receiver concentrated flux distributions is presented, which takes into account drift effects. This tool is based on a drift model that includes different geometrical error sources in a rigorous manner and on a simple analytic approximation for the individual flux distribution of a heliostat. The model is applied to a group of heliostats of a real field to obtain the resulting flux distribution and its variation along the day. The distributions differ strongly from those obtained assuming the ideal case without drift or a case with a Gaussian tracking error function. The time evolution of peak flux is also calculated to demonstrate the capabilities of the model. The evolution of this parameter also shows strong differences in comparison to the case without drift.

  20. Estimation of flux distributions with Monte Carlo functional expansion tallies

    International Nuclear Information System (INIS)

    Griesheimer, D. P.; Martin, W. R.; Holloway, J. P.

    2005-01-01

    Monte Carlo methods provide a powerful technique for estimating the average radiation flux in a volume (or across a surface) in cases where analytical solutions may not be possible. Unfortunately, Monte Carlo simulations typically provide only integral results and do not offer any further details about the distribution of the flux with respect to space, angle, time or energy. In the functional expansion tally (FET) a Monte Carlo simulation is used to estimate the functional expansion coefficients for flux distributions with respect to an orthogonal set of basis functions. The expansion coefficients are then used in post-processing to reconstruct a series approximation to the true distribution. Discrete event FET estimators are derived and their application in estimating radiation flux or current distributions is demonstrated. Sources of uncertainty in the FET are quantified and estimators for the statistical and truncation errors are derived. Numerical results are presented to support the theoretical development. (authors)

  1. Physiology and genetics of metabolic flux control in Zymomonas mobilis

    Energy Technology Data Exchange (ETDEWEB)

    Conway, T.

    1992-01-01

    This work seeks to understand the role of gene expression in regulating glycolytic enzyme synthesis in a balance that allows proper glycoltic flux control. The seven genes targeted for study in this laboratory have been cloned and sequenced, and molecular details of regulation have been investigated. Clear that glycolytic enzyme synthesis is coordinated to prevent the build up of toxic metabolic intermediates. The genetic mechanisms responsible for regulating balanced expression of the EntnerDoudoroff and glycolytic genes in Z. mobilis are beginning to be understood. Several layers of genetic control, perhaps in a hierarchal arrangement act in concert to determine the relative abundance of the glycolytic enzymes. These genetic controls involve differential translational efficiency, highly conserved promoter sequences, transcription factors, differential mRNA stabilities, and nucleolytic mRNA processing. The serendipitous cloning of the glucose facilitator, glf, as a result of linkage to several other genes of interest will have a significant impact on the study of Z. mobilis metabolism. The glucose facilitator is being characterized in a genetically reconstituted system in E. coli. Molecular genetic studies indicate that the ratio of glf expression to that of glk, zmf, and edd is carefully regulated, and suggests a critical role in metabolic control. Regulation of glycolytic gene expression is now sufficiently well understood to allow use of the glycolytic genes as tools to manipulate specified enzyme levels for the purpose of analyzing metabolic flux control. The critical genes have been subcloned for stable expression in Z. mobilis and placed under control of a regulated promoter system involving the tac promoter, the lacI repressor, and gene induction in by IPTG. HPLC methods have been developed that allow quantitation of virtually all of the metabolic intermediates in the cell pool.

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

    Directory of Open Access Journals (Sweden)

    Akιn Ata

    2007-12-01

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

  3. Constraining Genome-Scale Models to Represent the Bow Tie Structure of Metabolism for 13C Metabolic Flux Analysis

    Directory of Open Access Journals (Sweden)

    Tyler W. H. Backman

    2018-01-01

    Full Text Available Determination of internal metabolic fluxes is crucial for fundamental and applied biology because they map how carbon and electrons flow through metabolism to enable cell function. 13 C Metabolic Flux Analysis ( 13 C MFA and Two-Scale 13 C Metabolic Flux Analysis (2S- 13 C MFA are two techniques used to determine such fluxes. Both operate on the simplifying approximation that metabolic flux from peripheral metabolism into central “core” carbon metabolism is minimal, and can be omitted when modeling isotopic labeling in core metabolism. The validity of this “two-scale” or “bow tie” approximation is supported both by the ability to accurately model experimental isotopic labeling data, and by experimentally verified metabolic engineering predictions using these methods. However, the boundaries of core metabolism that satisfy this approximation can vary across species, and across cell culture conditions. Here, we present a set of algorithms that (1 systematically calculate flux bounds for any specified “core” of a genome-scale model so as to satisfy the bow tie approximation and (2 automatically identify an updated set of core reactions that can satisfy this approximation more efficiently. First, we leverage linear programming to simultaneously identify the lowest fluxes from peripheral metabolism into core metabolism compatible with the observed growth rate and extracellular metabolite exchange fluxes. Second, we use Simulated Annealing to identify an updated set of core reactions that allow for a minimum of fluxes into core metabolism to satisfy these experimental constraints. Together, these methods accelerate and automate the identification of a biologically reasonable set of core reactions for use with 13 C MFA or 2S- 13 C MFA, as well as provide for a substantially lower set of flux bounds for fluxes into the core as compared with previous methods. We provide an open source Python implementation of these algorithms at https://github.com/JBEI/limitfluxtocore.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Manuel Quirós

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

  6. Metabolic process engineering of Clostridium tyrobutyricum Δack-adhE2 for enhanced n-butanol production from glucose: effects of methyl viologen on NADH availability, flux distribution, and fermentation kinetics.

    Science.gov (United States)

    Du, Yinming; Jiang, Wenyan; Yu, Mingrui; Tang, I-Ching; Yang, Shang-Tian

    2015-04-01

    Butanol biosynthesis through aldehyde/alcohol dehydrogenase (adhE2) is usually limited by NADH availability, resulting in low butanol titer, yield, and productivity. To alleviate this limitation and improve n-butanol production by Clostridium tyrobutyricum Δack-adhE2 overexpressing adhE2, the NADH availability was increased by using methyl viologen (MV) as an artificial electron carrier to divert electrons from ferredoxin normally used for H2 production. In the batch fermentation with the addition of 500 μM MV, H2 , acetate, and butyrate production was reduced by more than 80-90%, while butanol production increased more than 40% to 14.5 g/L. Metabolic flux analysis revealed that butanol production increased in the fermentation with MV because of increased NADH availability as a result of reduced H2 production. Furthermore, continuous butanol production of ∼55 g/L with a high yield of ∼0.33 g/g glucose and extremely low ethanol, acetate, and butyrate production was obtained in fed-batch fermentation with gas stripping for in situ butanol recovery. This study demonstrated a stable and reliable process for high-yield and high-titer n-butanol production by metabolically engineered C. tyrobutyricum by applying MV as an electron carrier to increase butanol biosynthesis. © 2014 Wiley Periodicals, Inc.

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

    Directory of Open Access Journals (Sweden)

    Chou I-Chun

    2012-07-01

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

  8. Tropical Gravity Wave Momentum Fluxes and Latent Heating Distributions

    Science.gov (United States)

    Geller, Marvin A.; Zhou, Tiehan; Love, Peter T.

    2015-01-01

    Recent satellite determinations of global distributions of absolute gravity wave (GW) momentum fluxes in the lower stratosphere show maxima over the summer subtropical continents and little evidence of GW momentum fluxes associated with the intertropical convergence zone (ITCZ). This seems to be at odds with parameterizations forGWmomentum fluxes, where the source is a function of latent heating rates, which are largest in the region of the ITCZ in terms of monthly averages. The authors have examined global distributions of atmospheric latent heating, cloud-top-pressure altitudes, and lower-stratosphere absolute GW momentum fluxes and have found that monthly averages of the lower-stratosphere GW momentum fluxes more closely resemble the monthly mean cloud-top altitudes rather than the monthly mean rates of latent heating. These regions of highest cloud-top altitudes occur when rates of latent heating are largest on the time scale of cloud growth. This, plus previously published studies, suggests that convective sources for stratospheric GW momentum fluxes, being a function of the rate of latent heating, will require either a climate model to correctly model this rate of latent heating or some ad hoc adjustments to account for shortcomings in a climate model's land-sea differences in convective latent heating.

  9. Magnesium - distribution and basic metabolism

    African Journals Online (AJOL)

    Magnesium is extensively distributed in soil, water and plants. It is essential for ehzymatic reactions requiring adenosine triphosphate, and the recom- mended dietary allowance in man is 5 - 10 mg/kg/d. About 50% of magnesium in man is stored ~n bone, where it is regulated by parathyroid hormone'and. 1,25(OHb-D3.

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

    Directory of Open Access Journals (Sweden)

    Jörg eSchwender

    2014-11-01

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

  11. Critical sizes and flux distributions in the shut down pile

    International Nuclear Information System (INIS)

    Banchereau, A.; Berthier, P.; Genthon, J.P.; Gourdon, C.; Lattes, R.; Martelly, J.; Mazancourt, R. de; Portes, L.; Sagot, M.; Schmitt, A.P.; Tanguy, P.; Teste du Bailler, A.; Veyssiere, A.

    1957-01-01

    An important part of the experiments carried out on the reactor G1 during a period of shut-down has consisted in determinations of critical sizes, and measurements of flux distribution by irradiations of detectors. This report deals with the following points: 1- Critical sizes of the flat pile, the long pile and the uranium-thorium pile. 2- Flux charts of the same piles, and study of an exponential experiment. 3- Determination of the slit effect. 4- Calculation of the anisotropy of the lattice. 5- Description of the experimental apparatus of the irradiation measurements. (author) [fr

  12. Metabolic Flux Analysis of the Synechocystis sp. PCC 6803 ΔnrtABCD Mutant Reveals a Mechanism for Metabolic Adaptation to Nitrogen-Limited Conditions.

    Science.gov (United States)

    Nakajima, Tsubasa; Yoshikawa, Katsunori; Toya, Yoshihiro; Matsuda, Fumio; Shimizu, Hiroshi

    2017-03-01

    Metabolic flux redirection during nitrogen-limited growth was investigated in the Synechocystis sp. PCC 6803 glucose-tolerant (GT) strain under photoautotrophic conditions by isotopically non-stationary metabolic flux analysis (INST-MFA). A ΔnrtABCD mutant of Synechocystis sp. PCC 6803 was constructed to reproduce phenotypes arising during nitrogen starvation. The ΔnrtABCD mutant and the wild-type GT strain were cultured under photoautotrophic conditions by a photobioreactor. Intracellular metabolites were labeled over a time course using NaH13CO3 as a carbon source. Based on these data, the metabolic flux distributions in the wild-type and ΔnrtABCD cells were estimated by INST-MFA. The wild-type GT and ΔnrtABCD strains displayed similar distribution patterns, although the absolute levels of metabolic flux were lower in ΔnrtABCD. Furthermore, the relative flux levels for glycogen metabolism, anaplerotic reactions and the oxidative pentose phosphate pathway were increased in ΔnrtABCD. This was probably due to the increased expression of enzyme genes that respond to nitrogen depletion. Additionally, we found that the ratio of ATP/NADPH demand increased slightly in the ΔnrtABCD mutant. These results indicated that futile ATP consumption increases under nitrogen-limited conditions because the Calvin-Benson cycle and the oxidative pentose phosphate pathway form a metabolic futile cycle that consumes ATP without CO2 fixation and NADPH regeneration. © The Author 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  13. Metabolic flux analysis of the halophilic archaeon Haladaptatus paucihalophilus

    International Nuclear Information System (INIS)

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

    2015-01-01

    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. - Highlights: • Serine hydroxymethyltransferase, threonine aldolase, and glycine cleavage system all contribute to the glycine pool of H. paucihalophilus. • Threonine and the citramalate pathways contribute equally to the isoleucine biosynthesis in H. paucihalophilus. • Lysine in H. paucihalophilus is synthesized through the diaminopimelate pathway and not through the α-aminoadipate pathway. • Glycine biosynthesis is likely unrelated to the cell osmoadaption mechanism.

  14. Metabolic flux analysis of the halophilic archaeon Haladaptatus paucihalophilus

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Guangxiu; Zhang, Manxiao [Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000 (China); Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou, 730000 (China); Mo, Tianlu [Department of Chemistry, Fudan University, Shanghai, 200433 (China); He, Lian [Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071 (China); Zhang, Wei [Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000 (China); Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou, 730000 (China); Yu, Yi, E-mail: yu_yi@whu.edu.cn [Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071 (China); Zhang, Qi, E-mail: qizhang@sioc.ac.cn [Department of Chemistry, Fudan University, Shanghai, 200433 (China); Ding, Wei, E-mail: dingw@lzu.edu.cn [Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000 (China); Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou, 730000 (China); Department of Chemistry, Fudan University, Shanghai, 200433 (China)

    2015-11-27

    This work reports the {sup 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-{sup 13}C]pyruvate and [2-{sup 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. - Highlights: • Serine hydroxymethyltransferase, threonine aldolase, and glycine cleavage system all contribute to the glycine pool of H. paucihalophilus. • Threonine and the citramalate pathways contribute equally to the isoleucine biosynthesis in H. paucihalophilus. • Lysine in H. paucihalophilus is synthesized through the diaminopimelate pathway and not through the α-aminoadipate pathway. • Glycine biosynthesis is likely unrelated to the cell osmoadaption mechanism.

  15. Lunar impact flux distribution and global asymmetry revisited

    Science.gov (United States)

    Pinet, P.

    1985-10-01

    The author reinvestigates the hypothesis of an early lunar bombardment (≡4 aeons ago) by geocentric projectiles. These projectiles may have originated either as Earth satellites or as heliocentric planetoids later captured by the Earth's gravitational field and possibly fragmented by tidal forces inside the Roche limit. A 3-d numerical simulation is used to compute the trajectories of an initial set of projectiles, under the attraction of Earth and Moon, and to determine the loci of impacts, on the lunar surface, of colliding bodies. The simulation end-product is the local flux of impacts, normalized to the mean total flux over the whole lunar surface. The computed distributions meet main features of the observed lunar distribution of large craters and might give a mechanical explanation to the reported polar impact excess.

  16. Optimization of neutron flux distribution in Isotope Production Reactor

    International Nuclear Information System (INIS)

    Valladares, G.L.

    1988-01-01

    In order to optimize the thermal neutrons flux distribution in a Radioisotope Production and Research Reactor, the influence of two reactor parameters was studied, namely the Vmod / Vcomb ratio and the core volume. The reactor core is built with uranium oxide pellets (UO 2 ) mounted in rod clusters, with an enrichment level of ∼3 %, similar to LIGHT WATER POWER REATOR (LWR) fuel elements. (author) [pt

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

    Directory of Open Access Journals (Sweden)

    Feng Xueyang

    2012-08-01

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

  18. Determination of soil evaporation fluxes using distributed temperature sensing methods

    Science.gov (United States)

    Serna, J. L.; Cristi Matte, F.; Munoz, J. F.; Suarez, F. I.

    2014-12-01

    The dynamics of evaporation fluxes in arid soils is an unresolved complex phenomenon that has a major impact on the basin's water availability. In arid zones, evaporation controls moisture contents near the soil surface and drives liquid water and water vapor fluxes through the vadose zone, playing a critical role in both the hydrological cycle and energy balance. However, determining soil evaporation in arid zones is a difficult undertaking. Thus, it is important to develop new measuring techniques that can determine evaporation fluxes. In the last decade, distributed temperature sensing (DTS) methods have been successfully used to investigate a wide range of hydrologic applications. In particular, DTS methods have been used indirectly to monitor soil moisture. Two methods have been developed: the passive and the active method. In the active mode, the DTS system uses cables with metal elements and a voltage difference is applied at the two ends to of the cable to heat it up for a defined time-period. Then, the cumulative temperature increase along the cable is computed and soil moisture is determined by using an empirical relation. DTS technology has also been used to determine water fluxes in porous media, but so far no efforts have been made to determine evaporation fluxes. Here, we investigate the feasibility of using the active DTS method to determine soil evaporation fluxes. To achieve this objective, column experiments were designed to study evaporation from sandy soils with shallow water tables. The soil columns were instrumented with traditional temperature and time-domain-reflectometry probes, and an armored fiber-optic cable that allows using the active method to estimate the soil moisture profile. In the experiments, the water table can be fixed at different depths and soil evaporation can be estimated by measuring the water added to the constant-head reservoir that feeds the column. Thus, allowing the investigation of soil evaporation fluxes from DTS

  19. Flux balance analysis of genome-scale metabolic model of rice ...

    Indian Academy of Sciences (India)

    Here, we analyse a genome-scale metabolic model of rice leaf using Flux Balance Analysis to investigate whether it has potential metabolic flexibility to increase the biosynthesis of any of the biomass components. We initially simulate the metabolic responses under an objective to maximize the biomass components.

  20. Rerouting of carbon flux in a glycogen mutant of cyanobacteria assessed via isotopically non-stationary13C metabolic flux analysis.

    Science.gov (United States)

    Hendry, John I; Prasannan, Charulata; Ma, Fangfang; Möllers, K Benedikt; Jaiswal, Damini; Digmurti, Madhuri; Allen, Doug K; Frigaard, Niels-Ulrik; Dasgupta, Santanu; Wangikar, Pramod P

    2017-10-01

    Cyanobacteria, which constitute a quantitatively dominant phylum, have attracted attention in biofuel applications due to favorable physiological characteristics, high photosynthetic efficiency and amenability to genetic manipulations. However, quantitative aspects of cyanobacterial metabolism have received limited attention. In the present study, we have performed isotopically non-stationary 13 C metabolic flux analysis (INST- 13 C-MFA) to analyze rerouting of carbon in a glycogen synthase deficient mutant strain (glgA-I glgA-II) of the model cyanobacterium Synechococcus sp. PCC 7002. During balanced photoautotrophic growth, 10-20% of the fixed carbon is stored in the form of glycogen via a pathway that is conserved across the cyanobacterial phylum. Our results show that deletion of glycogen synthase gene orchestrates cascading effects on carbon distribution in various parts of the metabolic network. Carbon that was originally destined to be incorporated into glycogen gets partially diverted toward alternate storage molecules such as glucosylglycerol and sucrose. The rest is partitioned within the metabolic network, primarily via glycolysis and tricarboxylic acid cycle. A lowered flux toward carbohydrate synthesis and an altered distribution at the glucose-1-phosphate node indicate flexibility in the network. Further, reversibility of glycogen biosynthesis reactions points toward the presence of futile cycles. Similar redistribution of carbon was also predicted by Flux Balance Analysis. The results are significant to metabolic engineering efforts with cyanobacteria where fixed carbon needs to be re-routed to products of interest. Biotechnol. Bioeng. 2017;114: 2298-2308. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  1. Random sampling of elementary flux modes in large-scale metabolic networks.

    Science.gov (United States)

    Machado, Daniel; Soons, Zita; Patil, Kiran Raosaheb; Ferreira, Eugénio C; Rocha, Isabel

    2012-09-15

    The description of a metabolic network in terms of elementary (flux) modes (EMs) provides an important framework for metabolic pathway analysis. However, their application to large networks has been hampered by the combinatorial explosion in the number of modes. In this work, we develop a method for generating random samples of EMs without computing the whole set. Our algorithm is an adaptation of the canonical basis approach, where we add an additional filtering step which, at each iteration, selects a random subset of the new combinations of modes. In order to obtain an unbiased sample, all candidates are assigned the same probability of getting selected. This approach avoids the exponential growth of the number of modes during computation, thus generating a random sample of the complete set of EMs within reasonable time. We generated samples of different sizes for a metabolic network of Escherichia coli, and observed that they preserve several properties of the full EM set. It is also shown that EM sampling can be used for rational strain design. A well distributed sample, that is representative of the complete set of EMs, should be suitable to most EM-based methods for analysis and optimization of metabolic networks. Source code for a cross-platform implementation in Python is freely available at http://code.google.com/p/emsampler. dmachado@deb.uminho.pt Supplementary data are available at Bioinformatics online.

  2. Study of the neutron flux distribution in acylindrical reactor

    Directory of Open Access Journals (Sweden)

    A. Vidal-Ferràndiz

    2017-08-01

    Full Text Available In the Energy Engineering Degree of the Universitat Politècnica de València, the students attend to the Nuclear Technology course, in which the basic knowledge of this technology is presented. A main objective of this technology is to obtain neutron population distribution inside a reactor core, in order to maintain the fission reaction chain. As this activity cannot be experimentally developed, mathematical modelling is of great importance to achieve such objective.  One of the computer laboratories proposed consists in the neutron flux determination analytically and numerically in a cylindrical geometry. The analytical solution makes use of the Bessel functions and is a good example of their applications. Alternatively, a numerical solution based on finite differences is used to obtain an approximate solution of the neutron flux. In this work, different discretizations of the cylindrical geometry are implemented and their results are compared.

  3. Distribution of thermal neutron flux around a PET cyclotron.

    Science.gov (United States)

    Ogata, Yoshimune; Ishigure, Nobuhito; Mochizuki, Shingo; Ito, Kengo; Hatano, Kentaro; Abe, Junichiro; Miyahara, Hiroshi; Masumoto, Kazuyoshi; Nakamura, Hajime

    2011-05-01

    The number of positron emission tomography (PET) examinations has greatly increased world-wide. Since positron emission nuclides for the PET examinations have short half-lives, they are mainly produced using on-site cyclotrons. During the production of the nuclides, significant quantities of neutrons are generated from the cyclotrons. Neutrons have potential to activate the materials around the cyclotrons and cause exposure to the staff. To investigate quantities and distribution of the thermal neutrons, thermal neutron fluxes were measured around a PET cyclotron in a laboratory associating with a hospital. The cyclotron accelerates protons up to 18 MeV, and the mean particle current is 20 μA. The neutron fluxes were measured during both 18F production and C production. Gold foils and thermoluminescent dosimeter (TLD) badges were used to measure the neutron fluxes. The neutron fluxes in the target box averaged 9.3 × 10(6) cm(-2) s(-1) and 1.7 × 10(6) cm(-2) s(-1) during 18F and 11C production, respectively. Those in the cyclotron room averaged 4.1 × 10(5) cm(-2) s(-1) and 1.2 × 10(5) cm(-2) s(-1), respectively. Those outside the concrete wall shielding were estimated as being equal to or less than ∼3 cm s, which corresponded to 0.1 μSv h(-1) in effective dose. The neutron fluxes outside the concrete shielding were confirmed to be quite low compared to the legal limit.

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

    Science.gov (United States)

    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. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.

  5. Flux balance analysis of genome-scale metabolic model of rice ...

    Indian Academy of Sciences (India)

    2015-09-28

    Sep 28, 2015 ... genome-scale metabolic model of rice leaf using Flux Balance Analysis to investigate whether it has potential .... is number of reactions. In steady state. S.v = 0. (2) where v is the flux vector of reactions (Kauffman et al. 2003). Objective function is. Z = w.v. (3). 820 .... All the reactions are not included.

  6. Detecting the Significant Flux Backbone of Escherichia coli metabolism.

    Science.gov (United States)

    Güell, Oriol; Sagués, Francesc; Serrano, M Ángeles

    2017-05-01

    The heterogeneity of computationally predicted reaction fluxes in metabolic networks within a single flux state can be exploited to detect their significant flux backbone. Here, we disclose the backbone of Escherichia coli, and compare it with the backbones of other bacteria. We find that, in general, the core of the backbones is mainly composed of reactions in energy metabolism corresponding to ancient pathways. In E. coli, the synthesis of nucleotides and the metabolism of lipids form smaller cores which rely critically on energy metabolism. Moreover, the consideration of different media leads to the identification of pathways sensitive to environmental changes. The metabolic backbone of an organism is thus useful to trace simultaneously both its evolution and adaptation fingerprints. © 2017 The Authors FEBS Letters published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.

  7. COMPLETE-MFA: complementary parallel labeling experiments technique for metabolic flux analysis.

    Science.gov (United States)

    Leighty, Robert W; Antoniewicz, Maciek R

    2013-11-01

    We have developed a novel approach for measuring highly accurate and precise metabolic fluxes in living cells, termed COMPLETE-MFA, short for complementary parallel labeling experiments technique for metabolic flux analysis. The COMPLETE-MFA method is based on combined analysis of multiple isotopic labeling experiments, where the synergy of using complementary tracers greatly improves the precision of estimated fluxes. In this work, we demonstrate the COMPLETE-MFA approach using all singly labeled glucose tracers, [1-(13)C], [2-(13)C], [3-(13)C], [4-(13)C], [5-(13)C], and [6-(13)C]glucose to determine precise metabolic fluxes for wild-type Escherichia coli. Cells were grown in six parallel cultures on defined medium with glucose as the only carbon source. Mass isotopomers of biomass amino acids were measured by gas chromatography-mass spectrometry (GC-MS). The data from all six experiments were then fitted simultaneously to a single flux model to determine accurate intracellular fluxes. We obtained a statistically acceptable fit with more than 300 redundant measurements. The estimated flux map is the most precise flux result obtained thus far for E. coli cells. To our knowledge, this is the first time that six isotopic labeling experiments have been successfully integrated for high-resolution (13)C-flux analysis. Copyright © 2013 Elsevier Inc. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Joel Jordà

    2014-05-01

    Full Text Available Pichia pastoris has been recognized as an effective host for recombinant protein production. In this work, we combine metabolomics and instationary 13C metabolic flux analysis (INST 13C-MFA using GC-MS and LC-MS/MS to evaluate the potential impact of the production of a Rhizopus oryzae lipase (Rol on P. pastoris central carbon metabolism. Higher oxygen uptake and CO2 production rates and slightly reduced biomass yield suggest an increased energy demand for the producing strain. This observation is further confirmed by 13C-based metabolic flux analysis. In particular, the flux through the methanol oxidation pathway and the TCA cycle was increased in the Rol-producing strain compared to the reference strain. Next to changes in the flux distribution, significant variations in intracellular metabolite concentrations were observed. Most notably, the pools of trehalose, which is related to cellular stress response, and xylose, which is linked to methanol assimilation, were significantly increased in the recombinant strain.

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

    Science.gov (United States)

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

    2009-11-01

    (13)C metabolic flux analysis (MFA) is the most comprehensive means of characterizing cellular metabolic states. Uniquely labeled isotopic tracers enable more focused analyses to probe specific reactions within the network. As a result, the choice of tracer largely determines the precision with which one can estimate metabolic fluxes, especially in complex mammalian systems that require multiple substrates. Here we have experimentally determined metabolic fluxes in a tumor cell line, successfully recapitulating the hallmarks of cancer cell metabolism. Using these data, we computationally evaluated specifically labeled (13)C glucose and glutamine tracers for their ability to precisely and accurately estimate fluxes in central carbon metabolism. These methods enabled us to identify the optimal tracer for analyzing individual fluxes, specific pathways, and central carbon metabolism as a whole. [1,2-(13)C(2)]glucose provided the most precise estimates for glycolysis, the pentose phosphate pathway, and the overall network. Tracers such as [2-(13)C]glucose and [3-(13)C]glucose also outperformed the more commonly used [1-(13)C]glucose. [U-(13)C(5)]glutamine emerged as the preferred isotopic tracer for the analysis of the tricarboxylic acid (TCA) cycle. These results provide valuable, quantitative information on the performance of (13)C-labeled substrates and can aid in the design of more informative MFA experiments in mammalian cell culture.

  10. Flux analysis uncovers key role of functional redundancy in formaldehyde metabolism.

    Directory of Open Access Journals (Sweden)

    Christopher J Marx

    2005-02-01

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

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

    Science.gov (United States)

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

    2011-12-01

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

  12. Flux-Enabled Exploration of the Role of Sip1 in galactose yeast metabolism

    DEFF Research Database (Denmark)

    Shymansky, Christopher M.; Wang, George; Baidoo, Edward E. K.

    2017-01-01

    13C metabolic flux analysis (13C MFA) is an important systems biology technique that has been used to investigate microbial metabolism for decades. The heterotrimer Snf1 kinase complex plays a key role in the preference Saccharomyces cerevisiae exhibits for glucose over galactose, a phenomenon kn...

  13. Isotopically nonstationary metabolic flux analysis (INST-MFA) of photosynthesis and photorespiration in plants

    Science.gov (United States)

    Photorespiration is a central component of photosynthesis; however to better understand its role it should be viewed in the context of an integrated metabolic network rather than a series of individual reactions that operate independently. Isotopically nonstationary 13C metabolic flux analysis (INST...

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

    LENUS (Irish Health Repository)

    Burleigh, Susan C

    2011-10-18

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

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

    Directory of Open Access Journals (Sweden)

    Maria Kogadeeva

    2016-09-01

    Full Text Available 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.

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

    Directory of Open Access Journals (Sweden)

    Richard A Notebaart

    2008-01-01

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

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

    DEFF Research Database (Denmark)

    Østergaard, Simon; Olsson, Lisbeth; Nielsen, Jens

    2001-01-01

    the flux entering the TCA cycle was low and acetate and ethanol started to be excreted to the extracellular medium. During recovery of cell growth the flux entering the TCA cycle increased again, and at t = 30 this flux exceeded the corresponding steady-state flux. During the pulse an enhanced level of Gal...

  18. Genealogy profiling through strain improvement by using metabolic network analysis: metabolic flux genealogy of several generations of lysine-producing corynebacteria.

    Science.gov (United States)

    Wittmann, Christoph; Heinzle, Elmar

    2002-12-01

    A comprehensive approach of metabolite balancing, (13)C tracer studies, gas chromatography-mass spectrometry, matrix-assisted laser desorption ionization-time of flight mass spectrometry, and isotopomer modeling was applied for comparative metabolic network analysis of a genealogy of five successive generations of lysine-producing Corynebacterium glutamicum. The five strains examined (C. glutamicum ATCC 13032, 13287, 21253, 21526, and 21543) were previously obtained by random mutagenesis and selection. Throughout the genealogy, the lysine yield in batch cultures increased markedly from 1.2 to 24.9% relative to the glucose uptake flux. Strain optimization was accompanied by significant changes in intracellular flux distributions. The relative pentose phosphate pathway (PPP) flux successively increased, clearly corresponding to the product yield. Moreover, the anaplerotic net flux increased almost twofold as a consequence of concerted regulation of C(3) carboxylation and C(4) decarboxylation fluxes to cover the increased demand for lysine formation; thus, the overall increase was a consequence of concerted regulation of C(3) carboxylation and C(4) decarboxylation fluxes. The relative flux through isocitrate dehydrogenase dropped from 82.7% in the wild type to 59.9% in the lysine-producing mutants. In contrast to the NADPH demand, which increased from 109 to 172% due to the increasing lysine yield, the overall NADPH supply remained constant between 185 and 196%, resulting in a decrease in the apparent NADPH excess through strain optimization. Extrapolated to industrial lysine producers, the NADPH supply might become a limiting factor. The relative contributions of PPP and the tricarboxylic acid cycle to NADPH generation changed markedly, indicating that C. glutamicum is able to maintain a constant supply of NADPH under completely different flux conditions. Statistical analysis by a Monte Carlo approach revealed high precision for the estimated fluxes, underlining the

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    Verónica S. Martínez

    2015-12-01

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

  1. Integrated analysis of gene expression and metabolic fluxes in PHA-producing Pseudomonas putida grown on glycerol.

    Science.gov (United States)

    Beckers, Veronique; Poblete-Castro, Ignacio; Tomasch, Jürgen; Wittmann, Christoph

    2016-05-03

    Given its high surplus and low cost, glycerol has emerged as interesting carbon substrate for the synthesis of value-added chemicals. The soil bacterium Pseudomonas putida KT2440 can use glycerol to synthesize medium-chain-length poly(3-hydroxyalkanoates) (mcl-PHA), a class of biopolymers of industrial interest. Here, glycerol metabolism in P. putida KT2440 was studied on the level of gene expression (transcriptome) and metabolic fluxes (fluxome), using precisely adjusted chemostat cultures, growth kinetics and stoichiometry, to gain a systematic understanding of the underlying metabolic and regulatory network. Glycerol-grown P. putida KT2440 has a maintenance energy requirement [0.039 (mmolglycerol (gCDW h)(-1))] that is about sixteen times lower than that of other bacteria, such as Escherichia coli, which provides a great advantage to use this substrate commercially. The shift from carbon (glycerol) to nitrogen (ammonium) limitation drives the modulation of specific genes involved in glycerol metabolism, transport electron chain, sensors to assess the energy level of the cell, and PHA synthesis, as well as changes in flux distribution to increase the precursor availability for PHA synthesis (Entner-Doudoroff pathway and pyruvate metabolism) and to reduce respiration (glyoxylate shunt). Under PHA-producing conditions (N-limitation), a higher PHA yield was achieved at low dilution rate (29.7 wt% of CDW) as compared to a high rate (12.8 wt% of CDW). By-product formation (succinate, malate) was specifically modulated under these regimes. On top of experimental data, elementary flux mode analysis revealed the metabolic potential of P. putida KT2440 to synthesize PHA and identified metabolic engineering targets towards improved production performance on glycerol. This study revealed the complex interplay of gene expression levels and metabolic fluxes under PHA- and non-PHA producing conditions using the attractive raw material glycerol as carbon substrate. This

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

    Directory of Open Access Journals (Sweden)

    Pinto José P

    2010-04-01

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

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

    Science.gov (United States)

    Rocha, Isabel; Maia, Paulo; Evangelista, Pedro; Vilaça, Paulo; Soares, Simão; Pinto, José P; Nielsen, Jens; Patil, Kiran R; Ferreira, Eugénio C; Rocha, Miguel

    2010-04-19

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

  4. Analysis of polyhydroxybutyrate flux limitations by systematic genetic and metabolic perturbations.

    Science.gov (United States)

    Tyo, Keith E J; Fischer, Curt R; Simeon, Fritz; Stephanopoulos, Gregory

    2010-05-01

    Poly-3-hydroxybutyrate (PHB) titers in Escherichia coli have benefited from 10+ years of metabolic engineering. In the majority of studies, PHB content, expressed as percent PHB (dry cell weight), is increased, although this increase can be explained by decreases in growth rate or increases in PHB flux. In this study, growth rate and PHB flux were quantified directly in response to systematic manipulation of (1) gene expression in the product-forming pathway and (2) growth rates in a nitrogen-limited chemostat. Gene expression manipulation revealed acetoacetyl-CoA reductase (phaB) limits flux to PHB, although overexpression of the entire pathway pushed the flux even higher. These increases in PHB flux are accompanied by decreases in growth rate, which can be explained by carbon diversion, rather than toxic effects of the PHB pathway. In chemostats, PHB flux was insensitive to growth rate. These results imply that PHB flux is primarily controlled by the expression levels of the product forming pathway and not by the availability of precursors. These results confirm prior in vitro measurements and metabolic models and show expression level is a major affecter of PHB flux. 2009 Elsevier Inc. All rights reserved.

  5. Investigating The Neutron Flux Distribution Of The Miniature Neutron Source Reactor MNSR Type

    International Nuclear Information System (INIS)

    Nguyen Hoang Hai; Do Quang Binh

    2011-01-01

    Neutron flux distribution is the important characteristic of nuclear reactor. In this article, four energy group neutron flux distributions of the miniature neutron source reactor MNSR type versus radial and axial directions are investigated in case the control rod is fully withdrawn. In addition, the effect of control rod positions on the thermal neutron flux distribution is also studied. The group constants for all reactor components are generated by the WIMSD code, and the neutron flux distributions are calculated by the CITATION code. The results show that the control rod positions only affect in the planning area for distribution in the region around the control rod. (author)

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

    Directory of Open Access Journals (Sweden)

    Robert eHeise

    2015-06-01

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

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

    Science.gov (United States)

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

    2014-07-01

    Thermus thermophilus is an extremely thermophilic bacterium with significant biotechnological potential. In this work, we have characterized aerobic growth characteristics of T. thermophilus HB8 at temperatures between 50 and 85°C, constructed a metabolic network model of its central carbon metabolism and validated the model using (13)C-metabolic flux analysis ((13)C-MFA). First, cells were grown in batch cultures in custom constructed mini-bioreactors at different temperatures to determine optimal growth conditions. The optimal temperature for T. thermophilus grown on defined medium with glucose was 81°C. The maximum growth rate was 0.25h(-1). Between 50 and 81°C the growth rate increased by 7-fold and the temperature dependence was described well by an Arrhenius model with an activation energy of 47kJ/mol. Next, we performed a (13)C-labeling experiment with [1,2-(13)C] glucose as the tracer and calculated intracellular metabolic fluxes using (13)C-MFA. The results provided support for the constructed network model and highlighted several interesting characteristics of T. thermophilus metabolism. We found that T. thermophilus largely uses glycolysis and TCA cycle to produce biosynthetic precursors, ATP and reducing equivalents needed for cells growth. Consistent with its proposed metabolic network model, we did not detect any oxidative pentose phosphate pathway flux or Entner-Doudoroff pathway activity. The biomass precursors erythrose-4-phosphate and ribose-5-phosphate were produced via the non-oxidative pentose phosphate pathway, and largely via transketolase, with little contribution from transaldolase. The high biomass yield on glucose that was measured experimentally was also confirmed independently by (13)C-MFA. The results presented here provide a solid foundation for future studies of T. thermophilus and its metabolic engineering applications. Copyright © 2014 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  8. Detection of Metabolic Fluxes of O and H Atoms into Intracellular Water in Mammalian Cells

    Science.gov (United States)

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

    2012-01-01

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

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

    DEFF Research Database (Denmark)

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

    1998-01-01

    through the pentose phosphate pathway. Hence, wrong assumptions on the presence or activity of transhydrogenation reactions will result in wrong estimations of the intracellular flux distribution. Using C-13 tracer experiments and NMR analysis, flux analysis can be performed on the basis of only well...

  10. Metabolic implications of body fat distribution.

    Science.gov (United States)

    Björntorp, P

    1991-12-01

    Insulin resistance is the cornerstone for the development of non-insulin-dependent diabetes mellitus (NIDDM). Free fatty acids (FFAs) cause insulin resistance in muscle and liver and increase hepatic gluconeogenesis and lipoprotein production and perhaps decrease hepatic clearance of insulin. It is suggested that the depressing effect of insulin on circulating FFA concentration is dependent on the fraction derived from visceral adipocytes, which have a low responsiveness to the antilipolytic effect of insulin. Elevated secretion of cortisol and/or testosterone induces insulin resistance in muscle. This also seems to be the case for low testosterone concentrations in men. In addition, cortisol increases hepatic gluconeogenesis. Cortisol and testosterone have "permissive" effect on adipose lipolysis and therefore amplify lipolytic stimulation; FFA, cortisol, and testosterone thus have powerful combined effects, resulting in insulin resistance and increased hepatic gluconeogenesis. All these factors promoting insulin resistance are active in abdominal visceral obesity, which is closely associated with insulin resistance, NIDDM, and the "metabolic syndrome." In addition, the endocrine aberrations may provide a cause for visceral fat accumulation, probably due to regional differences in steroid-hormone-receptor density. In addition to the increased activity along the adrenocorticosteroid axis, there also seem to be signs of increased activity from the central sympathetic nervous system. These are the established endocrine consequences of hypothalamic arousal in the defeat and defense reactions. There is some evidence that suggests an increased prevalence of psychosocial stress factors is associated with visceral distribution of body fat. Therefore, it is hypothesized that such factors might provide a background not only to a defense reaction and primary hypertension, suggested previously, but also to a defeat reaction, which contributes to an endocrine aberration

  11. 13C Metabolic Flux Analysis for systematic metabolic engineering of S. cerevisiae for overproduction of fatty acids.

    Directory of Open Access Journals (Sweden)

    Amit Ghosh

    2016-10-01

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

  12. Understanding the anisotropic ion distributions within magnetotail dipolarizing flux bundles

    Science.gov (United States)

    Zhou, X.; Runov, A.; Angelopoulos, V.; Birn, J.

    2017-12-01

    Dipolarizing flux bundles (DFBs), earthward-propagating structures with enhanced northward magnetic field (Bz) component, are usually believed to carry a different plasma population from that in the ambient magnetotail plasma sheet. The ion distribution functions within the DFB, however, are recently found to be largely controlled by the ion adiabaticity parameter κ in the ambient plasma sheet outside the DFBs. According to these observations, the ambient κ values of 2-3 usually correspond to a strong perpendicular anisotropy of suprathermal ions within the DFBs, whereas for lower κ values the ions inside the DFBs become more isotropic. Here we utilize a simple, test-particle model to explore the nature of the anisotropy and its dependence on the ambient κ values. We find that the ion anisotropy originates from successive ion reflections and reentries to the DFBs, during which the ions can be consecutively accelerated in the perpendicular direction by the DFB-carried electric field. This acceleration process may be interrupted, however, when the magnetic field lines are highly curved in the ambient plasma sheet. In this case, the ion trajectories are most stochastic outside the DFB region, which makes the reflected ions less likely to return to the DFBs for another cycle of acceleration; as a consequence, the perpendicular ion anisotropy does not appear. Given that the DFB ions are a free energy source for instabilities when they are injected towards Earth, our simple model (that reproduces most observational features on the anisotropic DFB ion distributions) may shed new lights on the coupling process between the magnetotail and the inner magneosphere.

  13. The measurements of thermal neutron flux distribution in a paraffin ...

    Indian Academy of Sciences (India)

    neutron flux density, the foil activation method was used. Thermal neutron flux determination in paraffin phantom by counting the emitted rays of indium foils with two different detectors (Geiger–. Muller counter and NaI(Tl)) was the aim of this project. The relative differences of the outcome of the experiments were between ...

  14. The measurements of thermal neutron flux distribution in a paraffin ...

    Indian Academy of Sciences (India)

    at 293.4 K. In order to measure the thermal neutron flux density, the foil activation method was used. Thermal neutron flux determination in paraffin phantom by counting the emitted rays of indium foils with two different detectors (Geiger–. Muller counter and NaI(Tl)) was the aim of this project. The relative differences of the ...

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

    DEFF Research Database (Denmark)

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

    2016-01-01

    accumulation in Y. lipolytica does not involve transcriptional regulation of lipid metabolism but is associated with regulation of amino-acid biosynthesis, resulting in redirection of carbon flux during nitrogen limitation from amino acids to lipids. Lipid accumulation in Y. lipolytica at nitrogen limitation...

  16. Optimization of 13C isotopic tracers for metabolic flux analysis in mammalian cells.

    Science.gov (United States)

    Walther, Jason L; Metallo, Christian M; Zhang, Jie; Stephanopoulos, Gregory

    2012-03-01

    Mammalian cells consume and metabolize various substrates from their surroundings for energy generation and biomass synthesis. Glucose and glutamine, in particular, are the primary carbon sources for proliferating cancer cells. While this combination of substrates generates static labeling patterns for use in (13)C metabolic flux analysis (MFA), the inability of single tracers to effectively label all pathways poses an obstacle for comprehensive flux determination within a given experiment. To address this issue we applied a genetic algorithm to optimize mixtures of (13)C-labeled glucose and glutamine for use in MFA. We identified tracer combinations that minimized confidence intervals in an experimentally determined flux network describing central carbon metabolism in tumor cells. Additional simulations were used to determine the robustness of the [1,2-(13)C(2)]glucose/[U-(13)C(5)]glutamine tracer combination with respect to perturbations in the network. Finally, we experimentally validated the improved performance of this tracer set relative to glucose tracers alone in a cancer cell line. This versatile method allows researchers to determine the optimal tracer combination to use for a specific metabolic network, and our findings applied to cancer cells significantly enhance the ability of MFA experiments to precisely quantify fluxes in higher organisms. Copyright © 2011 Elsevier Inc. All rights reserved.

  17. Aerobic glucose metabolism of Saccharomyces kluyveri: Growth, metabolite production, and quantification of metabolic fluxes

    DEFF Research Database (Denmark)

    Møller, Kasper; Christensen, B.; Förster, Jochen

    2002-01-01

    growth in aerobic glucose-limited continuous cultivation. It was found that in S. kluyveri the flux into the pentose phosphate pathway was 18.8 mmole per 100 mmole glucose consumed during respiratory growth in aerobic glucose-limited continuous cultivation. Such a low flux into the pentose phosphate...

  18. The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization.

    Directory of Open Access Journals (Sweden)

    Elad Noor

    2016-11-01

    Full Text Available Bacterial growth depends crucially on metabolic fluxes, which are limited by the cell's capacity to maintain metabolic enzymes. The necessary enzyme amount per unit flux is a major determinant of metabolic strategies both in evolution and bioengineering. It depends on enzyme parameters (such as kcat and KM constants, but also on metabolite concentrations. Moreover, similar amounts of different enzymes might incur different costs for the cell, depending on enzyme-specific properties such as protein size and half-life. Here, we developed enzyme cost minimization (ECM, a scalable method for computing enzyme amounts that support a given metabolic flux at a minimal protein cost. The complex interplay of enzyme and metabolite concentrations, e.g. through thermodynamic driving forces and enzyme saturation, would make it hard to solve this optimization problem directly. By treating enzyme cost as a function of metabolite levels, we formulated ECM as a numerically tractable, convex optimization problem. Its tiered approach allows for building models at different levels of detail, depending on the amount of available data. Validating our method with measured metabolite and protein levels in E. coli central metabolism, we found typical prediction fold errors of 4.1 and 2.6, respectively, for the two kinds of data. This result from the cost-optimized metabolic state is significantly better than randomly sampled metabolite profiles, supporting the hypothesis that enzyme cost is important for the fitness of E. coli. ECM can be used to predict enzyme levels and protein cost in natural and engineered pathways, and could be a valuable computational tool to assist metabolic engineering projects. Furthermore, it establishes a direct connection between protein cost and thermodynamics, and provides a physically plausible and computationally tractable way to include enzyme kinetics into constraint-based metabolic models, where kinetics have usually been ignored or

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

    Science.gov (United States)

    Bates, Philip D

    2016-09-01

    Plant oil biosynthesis involves a complex metabolic network with multiple subcellular compartments, parallel pathways, cycles, and pathways that have a dual function to produce essential membrane lipids and triacylglycerol. Modern molecular biology techniques provide tools to alter plant oil compositions through bioengineering, however with few exceptions the final composition of triacylglycerol cannot be predicted. One reason for limited success in oilseed bioengineering is the inadequate understanding of how to control the flux of fatty acids through various fatty acid modification, and triacylglycerol assembly pathways of the lipid metabolic network. This review focuses on the mechanisms of acyl flux through the lipid metabolic network, and highlights where uncertainty resides in our understanding of seed oil biosynthesis. This article is part of a Special Issue entitled: Plant Lipid Biology edited by Kent D. Chapman and Ivo Feussner. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. Correlation of the space distribution of the neutron flux and power in the reactor RA in Vinca

    International Nuclear Information System (INIS)

    Martinc, R.; Marinkov, L.; Bikit, I.; Kocic, A.; Veskovic, M.; Zivotic, Z.

    1984-01-01

    The neutron flux distribution in the reactor RA has been measured by the neutron activation detectors Zr, Dy and Co. The correlation of the neutron flux distribution and power distribution has been established by the homogeneous approach. (author)

  1. Changes of in vivo fluxes through central metabolic pathways during the production of nystatin by Streptomyces noursei in batch culture

    DEFF Research Database (Denmark)

    Jonsbu, E.; Christensen, Bjarke; Nielsen, Jens

    2001-01-01

    of the amino acids and calculated fluxes of the central metabolism showed that changes in the primary and secondary metabolisms occurred simultaneously. Changes in the profiles for the integrated fluxes showed a decreased flux through the pentose phosphate pathway and an increased flux in the tricarboxylic...... acid cycle relative to the glucose uptake rate when the culture entered a phase with reduced specific growth rate and enhanced nystatin yield. The flux through the pentose phosphate pathway seemed to be adjusted according to the NADPH requirement during the different phases of the batch fermentation....

  2. Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism

    Directory of Open Access Journals (Sweden)

    Christopher M. Shymansky

    2017-05-01

    Full Text Available 13C metabolic flux analysis (13C MFA is an important systems biology technique that has been used to investigate microbial metabolism for decades. The heterotrimer Snf1 kinase complex plays a key role in the preference Saccharomyces cerevisiae exhibits for glucose over galactose, a phenomenon known as glucose repression or carbon catabolite repression. The SIP1 gene, encoding a part of this complex, has received little attention, presumably, because its knockout lacks a growth phenotype. We present a fluxomic investigation of the relative effects of the presence of galactose in classically glucose-repressing media and/or knockout of SIP1 using a multi-scale variant of 13C MFA known as 2-Scale 13C metabolic flux analysis (2S-13C MFA. In this study, all strains have the galactose metabolism deactivated (gal1Δ background so as to be able to separate the metabolic effects purely related to glucose repression from those arising from galactose metabolism. The resulting flux profiles reveal that the presence of galactose in classically glucose-repressing conditions, for a CEN.PK113-7D gal1Δ background, results in a substantial decrease in pentose phosphate pathway (PPP flux and increased flow from cytosolic pyruvate and malate through the mitochondria toward cytosolic branched-chain amino acid biosynthesis. These fluxomic redistributions are accompanied by a higher maximum specific growth rate, both seemingly in violation of glucose repression. Deletion of SIP1 in the CEN.PK113-7D gal1Δ cells grown in mixed glucose/galactose medium results in a further increase. Knockout of this gene in cells grown in glucose-only medium results in no change in growth rate and a corresponding decrease in glucose and ethanol exchange fluxes and flux through pathways involved in aspartate/threonine biosynthesis. Glucose repression appears to be violated at a 1/10 ratio of galactose-to-glucose. Based on the scientific literature, we may have conducted our experiments

  3. Radial Flux Distribution of Low-Energy Neutrons.

    Science.gov (United States)

    Higinbotham, J.

    1979-01-01

    Describes an experiment designed to illustrate the basic principle involved in the process of moderation of fast neutrons by water, and the monitoring of the low-energy neutron flux using indium as a probe. (GA)

  4. Distribution Functions of Sizes and Fluxes Determined from Supra-Arcade Downflows

    Science.gov (United States)

    McKenzie, D.; Savage, S.

    2011-01-01

    The frequency distributions of sizes and fluxes of supra-arcade downflows (SADs) provide information about the process of their creation. For example, a fractal creation process may be expected to yield a power-law distribution of sizes and/or fluxes. We examine 120 cross-sectional areas and magnetic flux estimates found by Savage & McKenzie for SADs, and find that (1) the areas are consistent with a log-normal distribution and (2) the fluxes are consistent with both a log-normal and an exponential distribution. Neither set of measurements is compatible with a power-law distribution nor a normal distribution. As a demonstration of the applicability of these findings to improved understanding of reconnection, we consider a simple SAD growth scenario with minimal assumptions, capable of producing a log-normal distribution.

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

    Energy Technology Data Exchange (ETDEWEB)

    Maranas, Costas D

    2012-05-21

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

  6. To be certain about the uncertainty: Bayesian statistics for 13 C metabolic flux analysis.

    Science.gov (United States)

    Theorell, Axel; Leweke, Samuel; Wiechert, Wolfgang; Nöh, Katharina

    2017-11-01

    13 C Metabolic Fluxes Analysis ( 13 C MFA) remains to be the most powerful approach to determine intracellular metabolic reaction rates. Decisions on strain engineering and experimentation heavily rely upon the certainty with which these fluxes are estimated. For uncertainty quantification, the vast majority of 13 C MFA studies relies on confidence intervals from the paradigm of Frequentist statistics. However, it is well known that the confidence intervals for a given experimental outcome are not uniquely defined. As a result, confidence intervals produced by different methods can be different, but nevertheless equally valid. This is of high relevance to 13 C MFA, since practitioners regularly use three different approximate approaches for calculating confidence intervals. By means of a computational study with a realistic model of the central carbon metabolism of E. coli, we provide strong evidence that confidence intervals used in the field depend strongly on the technique with which they were calculated and, thus, their use leads to misinterpretation of the flux uncertainty. In order to provide a better alternative to confidence intervals in 13 C MFA, we demonstrate that credible intervals from the paradigm of Bayesian statistics give more reliable flux uncertainty quantifications which can be readily computed with high accuracy using Markov chain Monte Carlo. In addition, the widely applied chi-square test, as a means of testing whether the model reproduces the data, is examined closer. © 2017 Wiley Periodicals, Inc.

  7. Enthalpy Distributions of Arc Jet Flow Based on Measured Laser Induced Fluorescence, Heat Flux and Stagnation Pressure Distributions

    Science.gov (United States)

    Suess, Leonard E.; Milhoan, James D.; Oelke, Lance; Godfrey, Dennis; Larin, Maksim Y.; Scott, Carl D.; Grinstead, Jay H.; DelPapa, Steven

    2011-01-01

    The centerline total enthalpy of arc jet flow is determined using laser induced fluorescence of oxygen and nitrogen atoms. Each component of the energy, kinetic, thermal, and chemical can be determined from LIF measurements. Additionally, enthalpy distributions are inferred from heat flux and pressure probe distribution measurements using an engineering formula. Average enthalpies are determined by integration over the radius of the jet flow, assuming constant mass flux and a mass flux distribution estimated from computational fluid dynamics calculations at similar arc jet conditions. The trends show favorable agreement, but there is an uncertainty that relates to the multiple individual measurements and assumptions inherent in LIF measurements.

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

    Science.gov (United States)

    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.

  9. Infrared radiometric technique for rapid quantitative evaluation of heat flux distribution over large areas

    Science.gov (United States)

    Glazer, Stuart; Siebes, Georg

    1989-01-01

    This paper describes a novel approach for rapid, quantitative measurement of spatially distributed heat flux incident on a plane. The technique utilizes the spatial temperature distribution on an opaque thin film at the location of interest, as measured by an imaging infrared radiometer. Knowledge of film radiative properties, plus quantitative estimates of convection cooling permit the steady state energy balance at any location on the film sheet to be solved for the incident heat flux. Absolute accuracies on the order of 10-15 percent have been obtained in tests performed in air. The method is particularly useful for evaluation of spatial heat flux uniformity from distributed heat sources over large areas. It has recently been used in several applications at the Jet Propulsion Laboratory, including flux uniformity measurements from large distributed quartz lamp arrays used during thermal vacuum testing of several spacecraft components, and flux mapping of a low power NdYg laser beam.

  10. Nitrogen Flux in Watersheds: The Role of Soil Distributions and Climate in Nitrogen Flux to the Coastal Ecosystems

    Science.gov (United States)

    Showers, W. J.; Reyes, M. M.; Genna, B. J.

    2009-12-01

    Quantifying the flux of nitrate from different landscape sources in watersheds is important to understand the increased flux of nitrogen to coastal ecosystems. Recent technological advances in chemical sensor networks has demonstrated that chemical variability in aquatic environments are chronically under-sampled, and that many nutrient monitoring programs with monthly or daily sampling rates are inadequate to characterize the dominate seasonal, daily or semi-diurnal fluxes in watersheds. The RiverNet program has measured the nitrate flux in the Neuse River Basin, NC on a 15 minute interval over the past eight years. Significant diurnal variation has been observed in nitrate concentrations during high and low flow periods associated with waste water treatment plants in urban watersheds that are not present in agricultural watersheds. Discharge and N flux in the basin also has significant inter-annual variations associated with El Nino oscillations modified by the North Atlantic oscillation. Positive JMA and NAO indexes are associated with increased groundwater levels, nutrient fluxes, and estuary fish kills. To understand how climate oscillation affect discharge and nutrient fluxes, we have monitored runoff/drainages and groundwater inputs adjacent to a large waste application field over the past 4 years, and used the nitrate inputs as a tracer. Surface water run off is well correlated to precipitation patterns and is the largest nutrient flux into the river. Groundwater inputs are variable spatially and temporally, and are controlled by geology and groundwater levels. Hydric soil spatial distributions are an excellent predictor of nutrient transport across landscapes, and is related to the distribution of biogeochemical “hotspots” The isotopic composition of oxygen and nitrogen in dissolved nitrate indicate that sources change with discharge state, and that atmospherically deposited nitrogen is only important to river fluxes in forested and urban watersheds

  11. Tissue-specific metabolic reprogramming drives nutrient flux in diabetic complications

    Science.gov (United States)

    Sas, Kelli M.; Kayampilly, Pradeep; Byun, Jaeman; Nair, Viji; Hinder, Lucy M.; Zhang, Hongyu; Lin, Chengmao; Qi, Nathan R.; Michailidis, George; Groop, Per-Henrik; Nelson, Robert G.; Darshi, Manjula; Sharma, Kumar; Schelling, Jeffrey R.; Sedor, John R.; Pop-Busui, Rodica; Weinberg, Joel M.; Soleimanpour, Scott A.; Abcouwer, Steven F.; Gardner, Thomas W.; Burant, Charles F.; Feldman, Eva L.; Kretzler, Matthias; Brosius, Frank C.

    2016-01-01

    Diabetes is associated with altered cellular metabolism, but how altered metabolism contributes to the development of diabetic complications is unknown. We used the BKS db/db diabetic mouse model to investigate changes in carbohydrate and lipid metabolism in kidney cortex, peripheral nerve, and retina. A systems approach using transcriptomics, metabolomics, and metabolic flux analysis identified tissue-specific differences, with increased glucose and fatty acid metabolism in the kidney, a moderate increase in the retina, and a decrease in the nerve. In the kidney, increased metabolism was associated with enhanced protein acetylation and mitochondrial dysfunction. To confirm these findings in human disease, we analyzed diabetic kidney transcriptomic data and urinary metabolites from a cohort of Southwestern American Indians. The urinary findings were replicated in 2 independent patient cohorts, the Finnish Diabetic Nephropathy and the Family Investigation of Nephropathy and Diabetes studies. Increased concentrations of TCA cycle metabolites in urine, but not in plasma, predicted progression of diabetic kidney disease, and there was an enrichment of pathways involved in glycolysis and fatty acid and amino acid metabolism. Our findings highlight tissue-specific changes in metabolism in complication-prone tissues in diabetes and suggest that urinary TCA cycle intermediates are potential prognostic biomarkers of diabetic kidney disease progression. PMID:27699244

  12. Enhancement of magnetic flux distribution in a DC superconducting electric motor

    International Nuclear Information System (INIS)

    Hamid, N A; Ewe, L S; Chin, K M

    2013-01-01

    Most motor designs require an air gap between the rotor and stator to enable the armature to rotate freely. The interaction of magnetic flux from rotor and stator within the air gap will provide the thrust for rotational motion. Thus, the understanding of magnetic flux in the vicinity of the air gap is very important to mathematically calculate the magnetic flux generated in the area. In this work, a finite element analysis was employed to study the behavior of the magnetic flux in view of designing a synchronous DC superconducting electric motor. The analysis provides an ideal magnetic flux distribution within the components of the motor. From the flux plot analysis, it indicates that flux losses are mainly in the forms of leakage and fringe effect. The analysis also shows that the flux density is high at the area around the air gap and the rotor. The high flux density will provide a high force area that enables the rotor to rotate. In contrast, the other parts of the motor body do not show high flux density indicating low distribution of flux. Consequently, a bench top model of a DC superconducting motor was developed where by motor with a 2-pole type winding was chosen. Each field coil was designed with a racetrack-shaped double pancake wound using DI-BSCCO Bi-2223 superconducting tapes. The performance and energy efficiency of the superconducting motor was superior when compared to the conventional motor with similar capacity.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-01-01

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

  14. 13CFLUX2--high-performance software suite for (13)C-metabolic flux analysis.

    Science.gov (United States)

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

    2013-01-01

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

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

    DEFF Research Database (Denmark)

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

    2010-01-01

    software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets, using Evolutionary Algorithms/Simulated Annealing metaheuristics or the previously proposed Opt...... to address industrial goals. However, the use of these methods has been restricted to bioinformaticians or other expert researchers. The main aim of this work is, therefore, to provide a user-friendly computational tool for Metabolic Engineering applications. Results: OptFlux is an open-source and modular...... algorithms. The software supports importing/exporting to several flat file formats and it is compatible with the SBML standard. OptFlux has a visualization module that allows the analysis of the model structure that is compatible with the layout information of Cell Designer, allowing the superimposition...

  16. Identifying model error in metabolic flux analysis - a generalized least squares approach.

    Science.gov (United States)

    Sokolenko, Stanislav; Quattrociocchi, Marco; Aucoin, Marc G

    2016-09-13

    The estimation of intracellular flux through traditional metabolic flux analysis (MFA) using an overdetermined system of equations is a well established practice in metabolic engineering. Despite the continued evolution of the methodology since its introduction, there has been little focus on validation and identification of poor model fit outside of identifying "gross measurement error". The growing complexity of metabolic models, which are increasingly generated from genome-level data, has necessitated robust validation that can directly assess model fit. In this work, MFA calculation is framed as a generalized least squares (GLS) problem, highlighting the applicability of the common t-test for model validation. To differentiate between measurement and model error, we simulate ideal flux profiles directly from the model, perturb them with estimated measurement error, and compare their validation to real data. Application of this strategy to an established Chinese Hamster Ovary (CHO) cell model shows how fluxes validated by traditional means may be largely non-significant due to a lack of model fit. With further simulation, we explore how t-test significance relates to calculation error and show that fluxes found to be non-significant have 2-4 fold larger error (if measurement uncertainty is in the 5-10 % range). The proposed validation method goes beyond traditional detection of "gross measurement error" to identify lack of fit between model and data. Although the focus of this work is on t-test validation and traditional MFA, the presented framework is readily applicable to other regression analysis methods and MFA formulations.

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

    Directory of Open Access Journals (Sweden)

    Edwards Jeremy S

    2000-07-01

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

  18. Measurement and simulation of thermal neutron flux distribution in the RTP core

    Science.gov (United States)

    Rabir, Mohamad Hairie B.; Jalal Bayar, Abi Muttaqin B.; Hamzah, Na’im Syauqi B.; Mustafa, Muhammad Khairul Ariff B.; Karim, Julia Bt. Abdul; Zin, Muhammad Rawi B. Mohamed; Ismail, Yahya B.; Hussain, Mohd Huzair B.; Mat Husin, Mat Zin B.; Dan, Roslan B. Md; Ismail, Ahmad Razali B.; Husain, Nurfazila Bt.; Jalil Khan, Zareen Khan B. Abdul; Yakin, Shaiful Rizaide B. Mohd; Saad, Mohamad Fauzi B.; Masood, Zarina Bt.

    2018-01-01

    The in-core thermal neutron flux distribution was determined using measurement and simulation methods for the Malaysian’s PUSPATI TRIGA Reactor (RTP). In this work, online thermal neutron flux measurement using Self Powered Neutron Detector (SPND) has been performed to verify and validate the computational methods for neutron flux calculation in RTP calculations. The experimental results were used as a validation to the calculations performed with Monte Carlo code MCNP. The detail in-core neutron flux distributions were estimated using MCNP mesh tally method. The neutron flux mapping obtained revealed the heterogeneous configuration of the core. Based on the measurement and simulation, the thermal flux profile peaked at the centre of the core and gradually decreased towards the outer side of the core. The results show a good agreement (relatively) between calculation and measurement where both show the same radial thermal flux profile inside the core: MCNP model over estimation with maximum discrepancy around 20% higher compared to SPND measurement. As our model also predicts well the neutron flux distribution in the core it can be used for the characterization of the full core, that is neutron flux and spectra calculation, dose rate calculations, reaction rate calculations, etc.

  19. Calibration of a distributed hydrology and land surface model using energy flux measurements

    DEFF Research Database (Denmark)

    Larsen, Morten Andreas Dahl; Refsgaard, Jens Christian; Jensen, Karsten H.

    2016-01-01

    In this study we develop and test a calibration approach on a spatially distributed groundwater-surface water catchment model (MIKE SHE) coupled to a land surface model component with particular focus on the water and energy fluxes. The model is calibrated against time series of eddy flux measure...

  20. The flow distribution in the parallel tubes of the cavity receiver under variable heat flux

    International Nuclear Information System (INIS)

    Hao, Yun; Wang, Yueshe; Hu, Tian

    2016-01-01

    Highlights: • An experimental loop is built to find the flow distribution in the parallel tubes. • With the concentration of heat flux, two-phase flow makes distribution more uneven. • The total flow rate is chosen appropriately for a wider heat flux distribution. • A suitable system pressure is essential for the optimization of flow distribution. - Abstract: As an optical component of tower solar thermal power station, the heliostat mirror reflects sunlight to one point of the heated surface in the solar cavity receiver, called as one-point focusing system. The radiation heat flux concentrated in the cavity receiver is always non-uniform temporally and spatially, which may lead to extremely local over-heat on the receiver evaporation panels. In this paper, an electrical heated evaporating experimental loop, including five parallel vertical tubes, is set up to evaluate the hydrodynamic characteristics of evaporation panels in a solar cavity receiver under various non-uniform heat flux. The influence of the heat flux concentration ratio, total flow rate, and system pressure on the flow distribution of parallel tubes is discussed. It is found that the flow distribution becomes significantly worse with the increase of heat flux and concentration ratio; and as the system pressure decreased, the flow distribution is improved. It is extremely important to obtain these interesting findings for the safe and stable operation of solar cavity receiver, and can also provide valuable references for the design and optimization of operating parameters solar tower power station system.

  1. Amino Acid Flux from Metabolic Network Benefits Protein Translation: the Role of Resource Availability.

    Science.gov (United States)

    Hu, Xiao-Pan; Yang, Yi; Ma, Bin-Guang

    2015-06-09

    Protein translation is a central step in gene expression and affected by many factors such as codon usage bias, mRNA folding energy and tRNA abundance. Despite intensive previous studies, how metabolic amino acid supply correlates with protein translation efficiency remains unknown. In this work, we estimated the amino acid flux from metabolic network for each protein in Escherichia coli and Saccharomyces cerevisiae by using Flux Balance Analysis. Integrated with the mRNA expression level, protein abundance and ribosome profiling data, we provided a detailed description of the role of amino acid supply in protein translation. Our results showed that amino acid supply positively correlates with translation efficiency and ribosome density. Moreover, with the rank-based regression model, we found that metabolic amino acid supply facilitates ribosome utilization. Based on the fact that the ribosome density change of well-amino-acid-supplied genes is smaller than poorly-amino-acid-supply genes under amino acid starvation, we reached the conclusion that amino acid supply may buffer ribosome density change against amino acid starvation and benefit maintaining a relatively stable translation environment. Our work provided new insights into the connection between metabolic amino acid supply and protein translation process by revealing a new regulation strategy that is dependent on resource availability.

  2. An analytical transport theory method for calculating flux distribution in slab cells

    International Nuclear Information System (INIS)

    AbdelKrim, M.S.

    2000-01-01

    A transport theory method for calculating flux distributions in slab fuel cell is described. Two coupled integral equations for flux in fuel and moderator are obtained; assuming partial reflection at moderator external boundaries. Galerkin technique is used to solve these equations. N umerical results for average fluxes in fuel and moderator also the disadvantage factor are given. Comparison with exact numerical methods, that is for total reflection moderator outer boundaries, show that Galerkin technique gives accurate results for the disadvantage factor and average fluxes

  3. An analytical transport theory method for calculating flux distribution in slab cells

    International Nuclear Information System (INIS)

    Abdel Krim, M.S.

    2001-01-01

    A transport theory method for calculating flux distributions in slab fuel cell is described. Two coupled integral equations for flux in fuel and moderator are obtained; assuming partial reflection at moderator external boundaries. Galerkin technique is used to solve these equations. Numerical results for average fluxes in fuel and moderator and the disadvantage factor are given. Comparison with exact numerical methods, that is for total reflection moderator outer boundaries, show that the Galerkin technique gives accurate results for the disadvantage factor and average fluxes. (orig.)

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

    Czech Academy of Sciences Publication Activity Database

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

    2013-01-01

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

  5. Tracking the metabolic pulse of plant lipid production with isotopic labeling and flux analyses: Past, present and future.

    Science.gov (United States)

    Allen, Doug K; Bates, Philip D; Tjellström, Henrik

    2015-04-01

    Metabolism is comprised of networks of chemical transformations, organized into integrated biochemical pathways that are the basis of cellular operation, and function to sustain life. Metabolism, and thus life, is not static. The rate of metabolites transitioning through biochemical pathways (i.e., flux) determines cellular phenotypes, and is constantly changing in response to genetic or environmental perturbations. Each change evokes a response in metabolic pathway flow, and the quantification of fluxes under varied conditions helps to elucidate major and minor routes, and regulatory aspects of metabolism. To measure fluxes requires experimental methods that assess the movements and transformations of metabolites without creating artifacts. Isotopic labeling fills this role and is a long-standing experimental approach to identify pathways and quantify their metabolic relevance in different tissues or under different conditions. The application of labeling techniques to plant science is however far from reaching it potential. In light of advances in genetics and molecular biology that provide a means to alter metabolism, and given recent improvements in instrumentation, computational tools and available isotopes, the use of isotopic labeling to probe metabolism is becoming more and more powerful. We review the principal analytical methods for isotopic labeling with a focus on seminal studies of pathways and fluxes in lipid metabolism and carbon partitioning through central metabolism. Central carbon metabolic steps are directly linked to lipid production by serving to generate the precursors for fatty acid biosynthesis and lipid assembly. Additionally some of the ideas for labeling techniques that may be most applicable for lipid metabolism in the future were originally developed to investigate other aspects of central metabolism. We conclude by describing recent advances that will play an important future role in quantifying flux and metabolic operation in plant

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

    Directory of Open Access Journals (Sweden)

    Picó Jesús

    2007-10-01

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

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

    Science.gov (United States)

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

    2016-05-01

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

  8. Magnesium - distribution and basic metabolism | Olhaberry | South ...

    African Journals Online (AJOL)

    Magnesium is extensively distributed in soil, water and plants. It is essential for ehzymatic reactions requiring adenosine triphosphate, and the recommended dietary allowance in man is 5 - 10 mg/kg/d. About 50% of magnesium in man is stored in bone, where it is regulated by parathyroid hormone'and 1,25(OH)2-D3.

  9. Surface flux density distribution characteristics of bulk high-T c superconductor in external magnetic field

    International Nuclear Information System (INIS)

    Nishikawa, H.; Torii, S.; Yuasa, K.

    2005-01-01

    This paper describes the measured results of the two-dimensional flux density distribution of a YBCO bulk under applied AC magnetic fields with various frequency. Melt-processed oxide superconductors have been developed in order to obtain strong pinning forces. Various electric mechanical systems or magnetic levitation systems use those superconductors. The major problem is that cracks occur because the bulk superconductors are brittle. The bulk may break in magnetizing process after cracks make superconducting state instable. The trapped flux density and the permanent current characteristics of bulk superconductors have been analyzed, so as to examine the magnetizing processes or superconducting states of the bulk. In those studies, the two-dimensional surface flux density distributions of the bulk in static fields are discussed. On the other hand, the distributions in dynamic fields are little discussed. We attempted to examine the states of the bulk in the dynamic fields, and made a unique experimental device which has movable sensors synchronized with AC applied fields. As a result, the two-dimensional distributions in the dynamic fields are acquired by recombining the one-dimensional distributions. The dynamic states of the flux of the bulk and the influences of directions of cracks are observed from the distributions. In addition, a new method for measuring two-dimensional flux density distribution under dynamic magnetic fields is suggested

  10. Vertical distribution and fluxes of ammonia at Great Dun Fell

    Science.gov (United States)

    Sutton, M. A.; Perthue, E.; Fowler, D.; Storeton-West, R. L.; Cape, J. N.; Arends, B. G.; Möls, J. J.

    As part of the study of the ammonia budget over Great Dun Fell, measurements of fluxes of gaseous ammonia (NH 3) with the hill surface (grass moorland and blanket bog) were made using micrometeorological techniques, to provide information on NH 3 removal by the hill surface and on vertical concentration gradients. Measurements of vertical concentration, χ, profiles of NH 3 concentration were coupled with turbulent diffusivities to determine fluxes, Fg deposition velocities, and canopy resistances, Rc to uptake by the ground. Consistent with published measurements for this site, NH 3 was generally found to deposit efficiently to the vegetation canopy, with mean Rc of 5 and 27 s m - for example days shown. However, short periods of NH 3 emission from the moorland were also observed at small χ (cloud processing: depletion of χ by in-cloud reaction would be expected to favour NH 3 emission from down-wind agricultural land and moorland, though emission from the hill itself during immersion in cloud is unlikely. Comparison of two measurement techniques to determine air concentrations (batch wet rotating denuder, inlet 0.5 m height; continuous wet denuder, inlets 0.3, 2 m heights) showed acceptable agreement, although because vertical concentration gradients were large (small Rc) the height of sampling had a substantial effect. Vertical gradients are also relevant to the use of the measured concentrations as estimates of NH 3 in the air mass passing over the hill, for modelling atmospheric budgets. Where NH 3 deposition occurs at the maximum rate, concentrations measured at 1 m require a 35% correction in neutral conditions when scaling to a reference height of 10 m.

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

    Science.gov (United States)

    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

  12. A minimal growth medium for the basidiomycetePleurotus sapidusfor metabolic flux analysis.

    Science.gov (United States)

    Fraatz, Marco A; Naeve, Stefanie; Hausherr, Vanessa; Zorn, Holger; Blank, Lars M

    2014-01-01

    Pleurotus sapidus secretes a huge enzymatic repertoire including hydrolytic and oxidative enzymes and is an example for higher basidiomycetes being interesting for biotechnology. The complex growth media used for submerged cultivation limit basic physiological analyses of this group of organisms. Using undefined growth media, only little insights into the operation of central carbon metabolism and biomass formation, i.e. , the interplay of catabolic and anabolic pathways, can be gained. The development of a chemically defined growth medium allowed rapid growth of P. sapidus in submerged cultures. As P. sapidus grew extremely slow in salt medium, the co-utilization of amino acids using 13 C-labelled glucose was investigated by gas chromatography-mass spectrometry (GC-MS) analysis. While some amino acids were synthesized up to 90% in vivo from glucose ( e.g., alanine), asparagine and/or aspartate were predominantly taken up from the medium. With this information in hand, a defined yeast free salt medium containing aspartate and ammonium nitrate as a nitrogen source was developed. The observed growth rates of P. sapidus were well comparable with those previously published for complex media. Importantly, fast growth could be observed for 4 days at least, up to cell wet weights (CWW) of 400 g L -1 . The chemically defined medium was used to carry out a 13 C-based metabolic flux analysis, and the in vivo reactions rates in the central carbon metabolism of P. sapidus were investigated. The results revealed a highly respiratory metabolism with high fluxes through the pentose phosphate pathway and TCA cycle. The presented chemically defined growth medium enables researchers to study the metabolism of P. sapidus , significantly enlarging the analytical capabilities. Detailed studies on the production of extracellular enzymes and of secondary metabolites of P. sapidus may be designed based on the reported data.

  13. Physiology and genetics of metabolic flux control in Zymomonas mobilis. Progress report

    Energy Technology Data Exchange (ETDEWEB)

    Conway, T.

    1992-08-01

    This work seeks to understand the role of gene expression in regulating glycolytic enzyme synthesis in a balance that allows proper glycoltic flux control. The seven genes targeted for study in this laboratory have been cloned and sequenced, and molecular details of regulation have been investigated. Clear that glycolytic enzyme synthesis is coordinated to prevent the build up of toxic metabolic intermediates. The genetic mechanisms responsible for regulating balanced expression of the EntnerDoudoroff and glycolytic genes in Z. mobilis are beginning to be understood. Several layers of genetic control, perhaps in a hierarchal arrangement act in concert to determine the relative abundance of the glycolytic enzymes. These genetic controls involve differential translational efficiency, highly conserved promoter sequences, transcription factors, differential mRNA stabilities, and nucleolytic mRNA processing. The serendipitous cloning of the glucose facilitator, glf, as a result of linkage to several other genes of interest will have a significant impact on the study of Z. mobilis metabolism. The glucose facilitator is being characterized in a genetically reconstituted system in E. coli. Molecular genetic studies indicate that the ratio of glf expression to that of glk, zmf, and edd is carefully regulated, and suggests a critical role in metabolic control. Regulation of glycolytic gene expression is now sufficiently well understood to allow use of the glycolytic genes as tools to manipulate specified enzyme levels for the purpose of analyzing metabolic flux control. The critical genes have been subcloned for stable expression in Z. mobilis and placed under control of a regulated promoter system involving the tac promoter, the lacI repressor, and gene induction in by IPTG. HPLC methods have been developed that allow quantitation of virtually all of the metabolic intermediates in the cell pool.

  14. Aerobic glucose metabolism of Saccharomyces kluyveri: Growth, metabolite production, and quantification of metabolic fluxes

    DEFF Research Database (Denmark)

    Møller, Kasper; Christensen, B.; Förster, Jochen

    2002-01-01

    The growth and product formation of Saccharomyces kluyveri was characterized in aerobic batch cultivation on glucose. At these conditions it was found that ethyl acetate was a major overflow metabolite in S. kluyveri. During the exponential-growth phase on glucose ethyl acetate was produced...... at a constant specific rate of 0.12 g ethyl acetate per g dry weight per hour. The aerobic glucose metabolism in S. kluyveri was found to be less fermentative than in S. cerevisiae, as illustrated by the comparably low yield of ethanol on glucose (0.08 +/- 0.02 g/g), and high yield of biomass on glucose (0...

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

    Science.gov (United States)

    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. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Poskar C Hart

    2012-11-01

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

  17. Flux

    DEFF Research Database (Denmark)

    Ravn, Ib

    . FLUX betegner en flyden eller strømmen, dvs. dynamik. Forstår man livet som proces og udvikling i stedet for som ting og mekanik, får man et andet billede af det gode liv end det, som den velkendte vestlige mekanicisme lægger op til. Dynamisk forstået indebærer det gode liv den bedst mulige...... kanalisering af den flux eller energi, der strømmer igennem os og giver sig til kende i vore daglige aktiviteter. Skal vores tanker, handlinger, arbejde, samvær og politiske liv organiseres efter stramme og faste regelsæt, uden slinger i valsen? Eller skal de tværtimod forløbe ganske uhindret af regler og bånd...

  18. A robust and efficient method for estimating enzyme complex abundance and metabolic flux from expression data.

    Science.gov (United States)

    Barker, Brandon E; Sadagopan, Narayanan; Wang, Yiping; Smallbone, Kieran; Myers, Christopher R; Xi, Hongwei; Locasale, Jason W; Gu, Zhenglong

    2015-12-01

    A major theme in constraint-based modeling is unifying experimental data, such as biochemical information about the reactions that can occur in a system or the composition and localization of enzyme complexes, with high-throughput data including expression data, metabolomics, or DNA sequencing. The desired result is to increase predictive capability and improve our understanding of metabolism. The approach typically employed when only gene (or protein) intensities are available is the creation of tissue-specific models, which reduces the available reactions in an organism model, and does not provide an objective function for the estimation of fluxes. We develop a method, flux assignment with LAD (least absolute deviation) convex objectives and normalization (FALCON), that employs metabolic network reconstructions along with expression data to estimate fluxes. In order to use such a method, accurate measures of enzyme complex abundance are needed, so we first present an algorithm that addresses quantification of complex abundance. Our extensions to prior techniques include the capability to work with large models and significantly improved run-time performance even for smaller models, an improved analysis of enzyme complex formation, the ability to handle large enzyme complex rules that may incorporate multiple isoforms, and either maintained or significantly improved correlation with experimentally measured fluxes. FALCON has been implemented in MATLAB and ATS, and can be downloaded from: https://github.com/bbarker/FALCON. ATS is not required to compile the software, as intermediate C source code is available. FALCON requires use of the COBRA Toolbox, also implemented in MATLAB. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Color flux distribution in pure SU(2) Lattice Gauge Theory

    International Nuclear Information System (INIS)

    Haymaker, R.W.; Peng, Yingcai; Singh, V.

    1990-01-01

    The color field distribution around a static q bar q pair is studied in detail for pure SU(2) Lattice Gauge Theory in four dimensions. As a result of large cancellations between electric and magnetic components, the action density dominates the energy density typically by an order of magnitude, at points far from the quarks

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

    Science.gov (United States)

    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

  1. Metabolism drives distribution and abundance in extremophile fish.

    Directory of Open Access Journals (Sweden)

    Richard S A White

    Full Text Available Differences in population density between species of varying size are frequently attributed to metabolic rates which are assumed to scale with body size with a slope of 0.75. This assumption is often criticised on the grounds that 0.75 scaling of metabolic rate with body size is not universal and can vary significantly depending on species and life-history. However, few studies have investigated how interspecific variation in metabolic scaling relationships affects population density in different sized species. Here we predict inter-specific differences in metabolism from niche requirements, thereby allowing metabolic predictions of species distribution and abundance at fine spatial scales. Due to the differences in energetic efficiency required along harsh-benign gradients, an extremophile fish (brown mudfish, Neochanna apoda living in harsh environments had slower metabolism, and thus higher population densities, compared to a fish species (banded kōkopu, Galaxias fasciatus in physiologically more benign habitats. Interspecific differences in the intercepts for the relationship between body and density disappeared when species mass-specific metabolic rates, rather than body sizes, were used to predict density, implying population energy use was equivalent between mudfish and kōkopu. Nevertheless, despite significant interspecific differences in the slope of the metabolic scaling relationships, mudfish and kōkopu had a common slope for the relationship between body size and population density. These results support underlying logic of energetic equivalence between different size species implicit in metabolic theory. However, the precise slope of metabolic scaling relationships, which is the subject of much debate, may not be a reliable indicator of population density as expected under metabolic theory.

  2. Metabolism drives distribution and abundance in extremophile fish.

    Science.gov (United States)

    White, Richard S A; McHugh, Peter A; Glover, Chris N; McIntosh, Angus R

    2017-01-01

    Differences in population density between species of varying size are frequently attributed to metabolic rates which are assumed to scale with body size with a slope of 0.75. This assumption is often criticised on the grounds that 0.75 scaling of metabolic rate with body size is not universal and can vary significantly depending on species and life-history. However, few studies have investigated how interspecific variation in metabolic scaling relationships affects population density in different sized species. Here we predict inter-specific differences in metabolism from niche requirements, thereby allowing metabolic predictions of species distribution and abundance at fine spatial scales. Due to the differences in energetic efficiency required along harsh-benign gradients, an extremophile fish (brown mudfish, Neochanna apoda) living in harsh environments had slower metabolism, and thus higher population densities, compared to a fish species (banded kōkopu, Galaxias fasciatus) in physiologically more benign habitats. Interspecific differences in the intercepts for the relationship between body and density disappeared when species mass-specific metabolic rates, rather than body sizes, were used to predict density, implying population energy use was equivalent between mudfish and kōkopu. Nevertheless, despite significant interspecific differences in the slope of the metabolic scaling relationships, mudfish and kōkopu had a common slope for the relationship between body size and population density. These results support underlying logic of energetic equivalence between different size species implicit in metabolic theory. However, the precise slope of metabolic scaling relationships, which is the subject of much debate, may not be a reliable indicator of population density as expected under metabolic theory.

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

    DEFF Research Database (Denmark)

    Montagud, Arnau; Zelezniak, Aleksej; Navarro, Emilio

    2011-01-01

    Synechocystis sp. PCC6803 is a model cyanobacterium capable of producing biofuels with CO2 as carbon source and with its metabolism fueled by light, for which it stands as a potential production platform of socio-economic importance. Compilation and characterization of Synechocystis genome...... networks, surrounded by a stable core of pathways leading to biomass building blocks. This analysis identified potential bottlenecks for hydrogen and ethanol production. Integration of transcriptomic data with the Synechocystis flux coupling networks lead to identification of reporter flux coupling pairs...... and reporter flux coupling groups - regulatory hot spots during metabolic shifts triggered by the availability of light. Overall, flux coupling analysis provided insight into the structural organization of Synechocystis sp. PCC6803 metabolic network toward designing of a photosynthesis-based production...

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

    Energy Technology Data Exchange (ETDEWEB)

    Hay, J.; Schwender, J.

    2011-08-01

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

  5. An investigation of the effect of axial heat-flux distribution on critical heat flux in tubes

    International Nuclear Information System (INIS)

    Yang, J.; Groeneveld, D.C.; Cheng, S.C.; Leung, L.K.H.; El Nakla, M.A.

    2004-01-01

    The effect of axial heat flux distribution (AFD) on critical heat flux (CHF) in tubes was investigated. CHF measurements were obtained with three HFC-134a cooled vertical tubes. One of these tubes was axially uniform-heated. The other two tubes exhibited non-uniform axial power profile and were also tested in reversed positions providing four different profiles. In general, the observed AFD effect on critical power is small at high inlet subcoolings. At low inlet subcoolings, the critical power for the inlet-peak profile is up to 15% higher than that for the outlet-peak profile. A local conditions analysis showed that the AFD has the strongest effect on CHF at high dryout qualities. CHF values for non-uniform AFDs could be 50% lower than those for the uniform AFD. The AFD effect on CHF becomes diminished with decreasing dryout quality. Four different approaches to account for the effect of AFD on CHF were assessed against the experimental values from the current experiment. The boiling-length-average heat-flux approach with the boiling-length starting point at the onset of annular flow provided the best prediction of the critical power and the CHF location. (author)

  6. Diverging polygon-based modeling (DPBM) of concentrated solar flux distributions

    OpenAIRE

    Loomis, James; Weinstein, Lee; Boriskina, Svetlana V.; Huang, Xiaopeng; Chiloyan, Vazrik; Chen, Gang

    2015-01-01

    This paper presents an efficient and robust methodology for modeling concentrated solar flux distributions. Compared to ray tracing methods, which provide high accuracy but can be computationally intensive, this approach makes a number of simplifying assumptions in order to reduce complexity by modeling incident and reflected flux as a series of simple geometric diverging polygons, then applying shading and blocking effects. A reduction in processing time (as compared to ray tracing) allows f...

  7. Nutrient fluxes and net metabolism in a coastal lagoon SW peninsula of Baja California, Mexico

    Directory of Open Access Journals (Sweden)

    Cervantes Duarte, R.

    2016-09-01

    Full Text Available Fluxes of nutrients and net metabolism were estimated in coastal lagoon Magdalena Bay using LOICZ biogeochemical model. In situ data were obtained from 14 sites in the lagoon and also from a fixed site in the adjacent ocean area. Intense upwelling (February to July and faint upwelling (August to January were analyzed from monthly time series. The Temperature, nitrite + nitrate, ammonium and phosphate within the lagoon showed significant differences (p<0.05 between the two periods. Salinity (p=0.408 was more homogeneous (no significantly different due to mixing processes. During the intense upwelling period, nutrients increased in and out of the lagoon due to the influence of Transitional Water and Subartic Water transported by the California Current. However, during the faint upwelling, from August to January, the Transition Water and Subtropical Surface Water were predominant. Magdalena Bay showed denitrification processes of throughout the year as it occurred in other semi-arid coastal lagoons. It also showed a net autotrophic metabolism during intense upwelling and heterotrophic metabolism during faint upwelling. Understanding nutrient flows and net metabolism through simple biogeochemical models can provide tools for better management of the coastal zone.

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

    Science.gov (United States)

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

    2016-01-01

    Metabolic network rewiring is the rerouting of metabolism through the use of alternate enzymes to adjust pathway flux and accomplish specific anabolic or catabolic objectives. Here, we report the first characterization of two parallel pathways for the breakdown of the short chain fatty acid propionate in Caenorhabditis elegans. Using genetic interaction mapping, gene co-expression analysis, pathway intermediate quantification and carbon tracing, we uncover a vitamin B12-independent propionate breakdown shunt that is transcriptionally activated on vitamin B12 deficient diets, or under genetic conditions mimicking the human diseases propionic- and methylmalonic acidemia, in which the canonical B12-dependent propionate breakdown pathway is blocked. Our study presents the first example of transcriptional vitamin-directed metabolic network rewiring to promote survival under vitamin deficiency. The ability to reroute propionate breakdown according to B12 availability may provide C. elegans with metabolic plasticity and thus a selective advantage on different diets in the wild. DOI: http://dx.doi.org/10.7554/eLife.17670.001 PMID:27383050

  9. Visualization of neutron flux and power distributions in TRIGA Mark II reactor as an educational tool

    International Nuclear Information System (INIS)

    Snoj, Luka; Ravnik, Matjaz; Lengar, Igor

    2008-01-01

    Modern Monte Carlo computer codes (e.g. MCNP) for neutron transport allow calculation of detailed neutron flux and power distribution in complex geometries with resolution of ∼1 mm. Moreover they enable the calculation of individual particle tracks, scattering and absorption events. With the use of advanced software for 3D visualization (e.g. Amira, Voxler, etc.) one can create and present neutron flux and power distribution in a 'user friendly' way convenient for educational purposes. One can view axial, radial or any other spatial distribution of the neutron flux and power distribution in a nuclear reactor from various perspectives and in various modalities of presentation. By visualizing the distribution of scattering and absorption events and individual particle tracks one can visualize neutron transport parameters (mean free path, diffusion length, macroscopic cross section, up-scattering, thermalization, etc.) from elementary point of view. Most of the people remember better, if they visualize the processes. Therefore the representation of the reactor and neutron transport parameters is a convenient modern educational tool for the (nuclear power plant) operators, nuclear engineers, students and specialists involved in reactor operation and design. The visualization of neutron flux and power distributions in Jozef Stefan Institute TRIGA Mark II research reactor is treated in the paper. The distributions are calculated with MCNP computer code and presented using Amira and Voxler software. The results in the form of figures are presented in the paper together with comments qualitatively explaining the figures. (authors)

  10. An analytical method based on multipole moment expansion to calculate the flux distribution in Gammacell-220

    Science.gov (United States)

    Rezaeian, P.; Ataenia, V.; Shafiei, S.

    2017-12-01

    In this paper, the flux of photons inside the irradiation cell of the Gammacell-220 is calculated using an analytical method based on multipole moment expansion. The flux of the photons inside the irradiation cell is introduced as the function of monopole, dipoles and quadruples in the Cartesian coordinate system. For the source distribution of the Gammacell-220, the values of the multipole moments are specified by direct integrating. To confirm the validation of the presented methods, the flux distribution inside the irradiation cell was determined utilizing MCNP simulations as well as experimental measurements. To measure the flux inside the irradiation cell, Amber dosimeters were employed. The calculated values of the flux were in agreement with the values obtained by simulations and measurements, especially in the central zones of the irradiation cell. In order to show that the present method is a good approximation to determine the flux in the irradiation cell, the values of the multipole moments were obtained by fitting the simulation and experimental data using Levenberg-Marquardt algorithm. The present method leads to reasonable results for the all source distribution even without any symmetry which makes it a powerful tool for the source load planning.

  11. Predicting growth conditions from internal metabolic fluxes in an in-silico model of E. coli.

    Directory of Open Access Journals (Sweden)

    Viswanadham Sridhara

    Full Text Available A widely studied problem in systems biology is to predict bacterial phenotype from growth conditions, using mechanistic models such as flux balance analysis (FBA. However, the inverse prediction of growth conditions from phenotype is rarely considered. Here we develop a computational framework to carry out this inverse prediction on a computational model of bacterial metabolism. We use FBA to calculate bacterial phenotypes from growth conditions in E. coli, and then we assess how accurately we can predict the original growth conditions from the phenotypes. Prediction is carried out via regularized multinomial regression. Our analysis provides several important physiological and statistical insights. First, we show that by analyzing metabolic end products we can consistently predict growth conditions. Second, prediction is reliable even in the presence of small amounts of impurities. Third, flux through a relatively small number of reactions per growth source (∼10 is sufficient for accurate prediction. Fourth, combining the predictions from two separate models, one trained only on carbon sources and one only on nitrogen sources, performs better than models trained to perform joint prediction. Finally, that separate predictions perform better than a more sophisticated joint prediction scheme suggests that carbon and nitrogen utilization pathways, despite jointly affecting cellular growth, may be fairly decoupled in terms of their dependence on specific assortments of molecular precursors.

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-11-15

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

  14. Fat distribution, androgens, and metabolism in nonobese women

    NARCIS (Netherlands)

    Seidell, J C; Cigolini, M; Deurenberg, P.; Oosterlee, A.; Doornbos, G

    Eighty-five randomly selected women, all born in 1948, were studied. All were nonobese (body mass index [BMI], 23.3 +/- 0.3 (means +/- SD]). The relationships between three indicators of fat distribution (waist-hip, waist-thigh, and subscapular-triceps ratios) and hormonal and metabolic variables

  15. Investigating the impact of uneven magnetic flux density distribution on core loss estimation

    DEFF Research Database (Denmark)

    Niroumand, Farideh Javidi; Nymand, Morten; Wang, Yiren

    2017-01-01

    . The presented work in this paper has been carried out for two common excitation waveforms in power electronics applications, sinusoid and square-wave and for two different core shapes, toroid and E-cores. Results show that ±10% discrepancy should be expected in loss estimation of the core using effective...... is calculated according to an effective flux density value and the macroscopic dimensions of the cores. However, the flux distribution in the core can alter by core shapes and/or operating conditions due to nonlinear material properties. This paper studies the element-wise estimation of the loss in magnetic...... cores. FEM has been used to investigate the flux density distribution in the core and the loss has been estimated considering this distribution. Finally, comparative results are shown between the classical macroscopic core loss estimation using effective dimensions and the element-wise loss estimation...

  16. What determines the distribution of shallow convective mass flux through cloud base?

    Science.gov (United States)

    Sakradzija, Mirjana; Hohenegger, Cathy

    2017-04-01

    The distribution of cumulus cloud population is studied using large-eddy simulations of two shallow cumulus cases, one representing conditions over the tropical ocean, and another representing mid-latitude conditions over land. In particular, the distribution of mass flux through cloud base differs among these two cases on a log-log plot. The case over the ocean shows a concave shape, while the case over land shows a straight line shape. The question of this study is what sets these differences. We find that the magnitude of the surface fluxes and its variation over the diurnal cycle do not influence the distribution shape. The latter is also not controlled by the level of organization in the cloud filed. It is instead controlled by the ratio of the surface sensible heat flux to the surface latent heat flux, the Bowen ratio B. Using a theoretical thermodynamic cycle, we explain why B controls the distribution shape and how it connects to the average mass flux per cloud ⟨m⟩.

  17. Calculation of neutron flux distributions in BNCT using removal-diffusion theory

    Energy Technology Data Exchange (ETDEWEB)

    Niemkiewicz, J.; Blue, T.E.; Gupta, N.

    1994-12-31

    Boron neutron capture therapy (BNCT) is under investigation as a treatment modality for brain tumors. Successful routine use of BNCT will require a knowledge of the radiation dose distribution in a patient`s head prior to treatment. This will allow optimization of the treatment to fit the needs of individual patients. Determination of the dose distribution begins with calculation of the neutron flux distribution in the head. Most efforts to date have relied on Monte Carlo or discrete ordinates techniques to calculate this flux distribution. Use of removal-diffusion theory has the advantage of a relatively short computer time to complete a calculation. Previous work by our group has shown good agreement between neutron flux distributions calculated using removal-diffusion theory and Monte Carlo methods for parallel incident neutrons and a rectangular parallelepiped water phantom. This work compares neutron flux distributions calculated using removal-diffusion theory and Monte Carlo methods for a homogeneous ellipsoidal water phantom that models the human head.

  18. Optimal tracers for parallel labeling experiments and13C metabolic flux analysis: A new precision and synergy scoring system.

    Science.gov (United States)

    Crown, Scott B; Long, Christopher P; Antoniewicz, Maciek R

    2016-11-01

    13 C-Metabolic flux analysis ( 13 C-MFA) is a widely used approach in metabolic engineering for quantifying intracellular metabolic fluxes. The precision of fluxes determined by 13 C-MFA depends largely on the choice of isotopic tracers and the specific set of labeling measurements. A recent advance in the field is the use of parallel labeling experiments for improved flux precision and accuracy. However, as of today, no systemic methods exist for identifying optimal tracers for parallel labeling experiments. In this contribution, we have addressed this problem by introducing a new scoring system and evaluating thousands of different isotopic tracer schemes. Based on this extensive analysis we have identified optimal tracers for 13 C-MFA. The best single tracers were doubly 13 C-labeled glucose tracers, including [1,6- 13 C]glucose, [5,6- 13 C]glucose and [1,2- 13 C]glucose, which consistently produced the highest flux precision independent of the metabolic flux map (here, 100 random flux maps were evaluated). Moreover, we demonstrate that pure glucose tracers perform better overall than mixtures of glucose tracers. For parallel labeling experiments the optimal isotopic tracers were [1,6- 13 C]glucose and [1,2- 13 C]glucose. Combined analysis of [1,6- 13 C]glucose and [1,2- 13 C]glucose labeling data improved the flux precision score by nearly 20-fold compared to widely use tracer mixture 80% [1- 13 C]glucose +20% [U- 13 C]glucose. Copyright © 2016 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    Moxley, Joel F; Jewett, Michael C; Antoniewicz, Maciek R; Villas-Boas, Silas G; Alper, Hal; Wheeler, Robert T; Tong, Lily; Hinnebusch, Alan G; Ideker, Trey; Nielsen, Jens; Stephanopoulos, Gregory

    2009-04-21

    Genome sequencing dramatically increased our ability to understand cellular response to perturbation. Integrating system-wide measurements such as gene expression with networks of protein-protein interactions and transcription factor binding revealed critical insights into cellular behavior. However, the potential of systems biology approaches is limited by difficulties in integrating metabolic measurements across the functional levels of the cell despite their being most closely linked to cellular phenotype. To address this limitation, we developed a model-based approach to correlate mRNA and metabolic flux data that combines information from both interaction network models and flux determination models. We started by quantifying 5,764 mRNAs, 54 metabolites, and 83 experimental (13)C-based reaction fluxes in continuous cultures of yeast under stress in the absence or presence of global regulator Gcn4p. Although mRNA expression alone did not directly predict metabolic response, this correlation improved through incorporating a network-based model of amino acid biosynthesis (from r = 0.07 to 0.80 for mRNA-flux agreement). The model provides evidence of general biological principles: rewiring of metabolic flux (i.e., use of different reaction pathways) by transcriptional regulation and metabolite interaction density (i.e., level of pairwise metabolite-protein interactions) as a key biosynthetic control determinant. Furthermore, this model predicted flux rewiring in studies of follow-on transcriptional regulators that were experimentally validated with additional (13)C-based flux measurements. As a first step in linking metabolic control and genetic regulatory networks, this model underscores the importance of integrating diverse data types in large-scale cellular models. We anticipate that an integrated approach focusing on metabolic measurements will facilitate construction of more realistic models of cellular regulation for understanding diseases and constructing

  20. Metabolic flux ratio analysis and cell staining suggest the existence of C4 photosynthesis in Phaeodactylum tricornutum.

    Science.gov (United States)

    Huang, A; Liu, L; Zhao, P; Yang, C; Wang, G C

    2016-03-01

    Mechanisms for carbon fixation via photosynthesis in the diatom Phaeodactylum tricornutum Bohlin were studied recently but there remains a long-standing debate concerning the occurrence of C4 photosynthesis in this species. A thorough investigation of carbon metabolism and the evidence for C4 photosynthesis based on organelle partitioning was needed. In this study, we identified the flux ratios between C3 and C4 compounds in P. tricornutum using (13)C-labelling metabolic flux ratio analysis, and stained cells with various cell-permeant fluorescent probes to investigate the likely organelle partitioning required for single-cell C4 photosynthesis. Metabolic flux ratio analysis indicated the C3/C4 exchange ratios were high. Cell staining indicated organelle partitioning required for single-cell C4 photosynthesis might exist in P. tricornutum. The results of (13)C-labelling metabolic flux ratio analysis and cell staining suggest single-cell C4 photosynthesis exists in P. tricornutum. This study provides insights into photosynthesis patterns of P. tricornutum and the evidence for C4 photosynthesis based on (13)C-labelling metabolic flux ratio analysis and organelle partitioning. © 2015 The Society for Applied Microbiology.

  1. Subchannel measurements of the equilibrium quality and mass flux distribution in a rod bundle

    International Nuclear Information System (INIS)

    Lahey, R.T. Jr.

    1986-01-01

    An experiment was performed to measure the equilibrium subchannel void and mass flux distribution in a simulated BWR rod bundle. These new equilibrium subchannel data are unique and represent an excellent basis for subchannel ''void drift'' model development and assessment. Equilibrium subchannel void and mass flux distributions have been determined from the data presented herein. While the form of these correlations agree with the results of previous theoretical investigations, they should be generalized with caution since the current data base has been taken at only one (low) system pressure. Clearly there is a need for equilibrium subchannel data at higher system pressures if mechanistic subchannel models are to be developed

  2. Ideal free distribution of metabolic activity: Implications of seasonal metabolic-activity patterns on competitive coexistence.

    Science.gov (United States)

    Szabó, Péter

    2016-10-01

    The seasonal distribution of metabolic activity determines how much individuals experience different aspects of a periodically changing environment. Seasonal metabolic-activity patterns of coexisting species may differ significantly despite their shared environmental conditions, suggesting that interspecific diversification of this trait has a major role in the coexistence of competing species. In the present study the effect of the seasonal distribution of metabolic activity on intra- and interspecific competition is investigated in a consumer-resource model. It is shown that, in a periodically changing environment, for each environmental preference pattern there is an ideal seasonal distribution of metabolic activity, which results in maximum resource utilisation efficiency and competitive superiority. Contrary to the common interpretation of temporal niche segregation, opposing species-specific seasonal preferences are not a sufficient condition for the coexistence of two species on a population dynamical time scale. A necessary and sufficient condition for coexistence is the temporal segregation of the species via different seasonal activity distributions. However, coexistence is evolutionarily stable only if seasonal metabolic activities and preferences are positively correlated. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. A Correction for IUE UV Flux Distributions from Comparisons with CALSPEC

    Science.gov (United States)

    Bohlin, Ralph C.; Bianchi, Luciana

    2018-04-01

    A collection of spectral energy distributions (SEDs) is available in the Hubble Space Telescope (HST) CALSPEC database that is based on calculated model atmospheres for pure hydrogen white dwarfs (WDs). A much larger set (∼100,000) of UV SEDs covering the range (1150–3350 Å) with somewhat lower quality are available in the IUE database. IUE low-dispersion flux distributions are compared with CALSPEC to provide a correction that places IUE fluxes on the CALSPEC scale. While IUE observations are repeatable to only 4%–10% in regions of good sensitivity, the average flux corrections have a precision of 2%–3%. Our re-calibration places the IUE flux scale on the current UV reference standard and is relevant for any project based on IUE archival data, including our planned comparison of GALEX to the corrected IUE fluxes. IUE SEDs may be used to plan observations and cross-calibrate data from future missions, so the IUE flux calibration must be consistent with HST instrumental calibrations to the best possible precision.

  4. Spatial distribution of potential near surface moisture flux at Yucca Mountain

    International Nuclear Information System (INIS)

    Flint, A.L.; Flint, L.E.

    1994-01-01

    An estimate of the areal distribution of present-day surface liquid moisture flux at Yucca Mountain was made using field measured water contents and laboratory measured rock properties. Using available data for physical and hydrologic properties (porosity, saturated hydraulic conductivity, moisture retention functions) of the volcanic rocks, surface lithologic units that are hydrologically similar were delineated. Moisture retention and relative permeability functions were assigned to each surface unit based on the similarity of the mean porosity and saturated hydraulic conductivity of the surface unit to laboratory samples of the same lithology. The potential flux into the mountain was estimated for each surface hydrologic unit using the mean saturated hydraulic conductivity for each unit and assuming all matrix flow. Using measured moisture profiles for each of the surface units, estimates were made of the depth at which seasonal fluctuations diminish and steady state downward flux conditions are likely to exist. The hydrologic properties at that depth were used with the current relative saturation of the tuff, to estimate flux as the unsaturated hydraulic conductivity. This method assumes a unit gradient. The range in estimated flux was 0.02 mm/yr for the welded Tiva Canyon to 13.4 mm/yr for the nonwelded Paintbrush Tuff. The areally averaged flux was 1.4 mm/yr. The major zones of high flux occur to the north of the potential repository boundary where the nonwelded tuffs are exposed in the major drainages

  5. Spatial distribution of potential near surface moisture flux at Yucca Mountain

    International Nuclear Information System (INIS)

    Flint, A.L.; Flint, L.E.

    1994-01-01

    An estimate of the areal distribution of present-day surface liquid moisture flux at Yucca Mountain was made using field measured water contents and laboratory measured rock properties. Using available data for physical and hydrologic properties (porosity, saturated hydraulic conductivity moisture retention functions) of the volcanic rocks, surface lithologic units that are hydrologically similar were delineated. Moisture retention and relative permeability functions were assigned to each surface unit based on the similarity of the mean porosity and saturated hydraulic conductivity of the surface unit to laboratory samples of the same lithology. The potential flux into the mountain was estimated for each surface hydrologic unit using the mean saturated hydraulic conductivity for each unit and assuming all matrix flow. Using measured moisture profiles for each of the surface units, estimates were made of the depth at which seasonal fluctuations diminish and steady state downward flux conditions are likely to exist. The hydrologic properties at that depth were used with the current relative saturation of the tuff, to estimate flux as the unsaturated hydraulic conductivity. This method assumes a unit gradient. The range in estimated flux was 0.02 mm/yr for the welded Tiva Canyon to 13.4 mm/yr for the nonwelded Paintbrush Tuff. The areally averaged flux was 1.4 mm/yr. The major zones of high flux occur to the north of the potential repository boundary where the nonwelded tuffs are exposed in the major drainages

  6. Modeling and analysis of flux distributions in the two branches of the phosphotransferase system in Pseudomonas putida

    Directory of Open Access Journals (Sweden)

    Kremling Andreas

    2012-12-01

    Full Text Available Abstract Background Signal transduction plays a fundamental role in the understanding of cellular physiology. The bacterial phosphotransferase system (PTS together with the PEP/pyruvate node in central metabolism represents a signaling unit that acts as a sensory element and measures the activity of the central metabolism. Pseudomonas putida possesses two PTS branches, the C-branch (PTSFru and a second branch (PTSNtr, which communicate with each other by phosphate exchange. Recent experimental results showed a cross talk between the two branches. However, the functional role of the crosstalk remains open. Results A mathematical model was set up to describe the available data of the state of phosphorylation of PtsN, one of the PTS proteins, for different environmental conditions and different strain variants. Additionally, data from flux balance analysis was used to determine some of the kinetic parameters of the involved reactions. Based on the calculated and estimated parameters, the flux distribution during growth of the wild type strain on fructose could be determined. Conclusion Our calculations show that during growth of the wild type strain on the PTS substrate fructose, the major part of the phosphoryl groups is provided by the second branch of the PTS. This theoretical finding indicates a new role of the second branch of the PTS and will serve as a basis for further experimental studies.

  7. Comprehensive analysis of glucose and xylose metabolism in Escherichia coli under aerobic and anaerobic conditions by13C metabolic flux analysis.

    Science.gov (United States)

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

    2017-01-01

    Glucose and xylose are the two most abundant sugars derived from the breakdown of lignocellulosic biomass. While aerobic glucose metabolism is relatively well understood in E. coli, until now there have been only a handful of studies focused on anaerobic glucose metabolism and no 13 C-flux studies on xylose metabolism. In the absence of experimentally validated flux maps, constraint-based approaches such as MOMA and RELATCH cannot be used to guide new metabolic engineering designs. In this work, we have addressed this critical gap in current understanding by performing comprehensive characterizations of glucose and xylose metabolism under aerobic and anaerobic conditions, using recent state-of-the-art techniques in 13 C metabolic flux analysis ( 13 C-MFA). Specifically, we quantified precise metabolic fluxes for each condition by performing parallel labeling experiments and analyzing the data through integrated 13 C-MFA using the optimal tracers [1,2- 13 C]glucose, [1,6- 13 C]glucose, [1,2- 13 C]xylose and [5- 13 C]xylose. We also quantified changes in biomass composition and confirmed turnover of macromolecules by applying [U- 13 C]glucose and [U- 13 C]xylose tracers. We demonstrated that under anaerobic growth conditions there is significant turnover of lipids and that a significant portion of CO 2 originates from biomass turnover. Using knockout strains, we also demonstrated that β-oxidation is critical for anaerobic growth on xylose. Quantitative analysis of co-factor balances (NADH/FADH 2 , NADPH, and ATP) for different growth conditions provided new insights regarding the interplay of energy and redox metabolism and the impact on E. coli cell physiology. Copyright © 2016 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  8. DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees.

    Science.gov (United States)

    Foret, Sylvain; Kucharski, Robert; Pellegrini, Matteo; Feng, Suhua; Jacobsen, Steven E; Robinson, Gene E; Maleszka, Ryszard

    2012-03-27

    In honey bees (Apis mellifera), the development of a larva into either a queen or worker depends on differential feeding with royal jelly and involves epigenomic modifications by DNA methyltransferases. To understand the role of DNA methylation in this process we sequenced the larval methylomes in both queens and workers. We show that the number of differentially methylated genes (DMGs) in larval head is significantly increased relative to adult brain (2,399 vs. 560) with more than 80% of DMGs up-methylated in worker larvae. Several highly conserved metabolic and signaling pathways are enriched in methylated genes, underscoring the connection between dietary intake and metabolic flux. This includes genes related to juvenile hormone and insulin, two hormones shown previously to regulate caste determination. We also tie methylation data to expressional profiling and describe a distinct role for one of the DMGs encoding anaplastic lymphoma kinase (ALK), an important regulator of metabolism. We show that alk is not only differentially methylated and alternatively spliced in Apis, but also seems to be regulated by a cis-acting, anti-sense non-protein-coding transcript. The unusually complex regulation of ALK in Apis suggests that this protein could represent a previously unknown node in a process that activates downstream signaling according to a nutritional context. The correlation between methylation and alternative splicing of alk is consistent with the recently described mechanism involving RNA polymerase II pausing. Our study offers insights into diet-controlled development in Apis.

  9. Bacterial persistence is an active σS stress response to metabolic flux limitation.

    Science.gov (United States)

    Radzikowski, Jakub Leszek; Vedelaar, Silke; Siegel, David; Ortega, Álvaro Dario; Schmidt, Alexander; Heinemann, Matthias

    2016-09-21

    While persisters are a health threat due to their transient antibiotic tolerance, little is known about their phenotype and what actually causes persistence. Using a new method for persister generation and high-throughput methods, we comprehensively mapped the molecular phenotype of Escherichia coli during the entry and in the state of persistence in nutrient-rich conditions. The persister proteome is characterized by σ(S)-mediated stress response and a shift to catabolism, a proteome that starved cells tried to but could not reach due to absence of a carbon and energy source. Metabolism of persisters is geared toward energy production, with depleted metabolite pools. We developed and experimentally verified a model, in which persistence is established through a system-level feedback: Strong perturbations of metabolic homeostasis cause metabolic fluxes to collapse, prohibiting adjustments toward restoring homeostasis. This vicious cycle is stabilized and modulated by high ppGpp levels, toxin/anti-toxin systems, and the σ(S)-mediated stress response. Our system-level model consistently integrates past findings with our new data, thereby providing an important basis for future research on persisters. © 2016 The Authors. Published under the terms of the CC BY 4.0 license.

  10. The Red MSX Source survey: the bolometric fluxes and luminosity distributions of young massive stars

    Science.gov (United States)

    Mottram, J. C.; Hoare, M. G.; Urquhart, J. S.; Lumsden, S. L.; Oudmaijer, R. D.; Robitaille, T. P.; Moore, T. J. T.; Davies, B.; Stead, J.

    2011-01-01

    Context. The Red MSX Source (RMS) survey is returning a large sample of massive young stellar objects (MYSOs) and ultra-compact (UC) H ii regions using follow-up observations of colour-selected candidates from the MSX point source catalogue. Aims: We obtain the bolometric fluxes and, using kinematic distance information, the luminosities for young RMS sources with far-infrared fluxes. Methods: We use a model spectral energy distribution (SED) fitter to obtain the bolometric flux for our sources, given flux data from our work and the literature. The inputs to the model fitter were optimised by a series of investigations designed to reveal the effect varying these inputs had on the resulting bolometric flux. Kinematic distances derived from molecular line observations were then used to calculate the luminosity of each source. Results: Bolometric fluxes are obtained for 1173 young RMS sources, of which 1069 have uniquely constrained kinematic distances and good SED fits. A comparison of the bolometric fluxes obtained using SED fitting with trapezium rule integration and two component greybody fits was also undertaken, and showed that both produce considerable scatter compared to the method used here. Conclusions: The bolometric flux results allowed us to obtain the luminosity distributions of YSOs and UCH ii regions in the RMS sample, which we find to be different. We also find that there are few MYSOs with L ≥ 105 L⊙, despite finding many MYSOs with 104 L⊙ ≥ L ≥ 105 L⊙. Full Tables 1 and 2 are only available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.125.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/525/A149

  11. Multidimensional optimality of microbial metabolism

    NARCIS (Netherlands)

    Schuetz, Robert; Zamboni, Nicola; Zampieri, Mattia; Heinemann, Matthias; Sauer, Uwe

    2012-01-01

    Although the network topology of metabolism is well known, understanding the principles that govern the distribution of fluxes through metabolism lags behind. Experimentally, these fluxes can be measured by (13)C-flux analysis, and there has been a long-standing interest in understanding this

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

    Directory of Open Access Journals (Sweden)

    Leandro Rodríguez-Viera

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

  13. Resuscitation of ischemic donor livers with normothermic machine perfusion: a metabolic flux analysis of treatment in rats.

    Directory of Open Access Journals (Sweden)

    Maria-Louisa Izamis

    Full Text Available Normothermic machine perfusion has previously been demonstrated to restore damaged warm ischemic livers to transplantable condition in animal models. However, the mechanisms of recovery are unclear, preventing rational optimization of perfusion systems and slowing clinical translation of machine perfusion. In this study, organ recovery time and major perfusate shortcomings were evaluated using a comprehensive metabolic analysis of organ function in perfusion prior to successful transplantation. Two groups, Fresh livers and livers subjected to 1 hr of warm ischemia (WI received perfusion for a total preservation time of 6 hrs, followed by successful transplantation. 24 metabolic fluxes were directly measured and 38 stoichiometrically-related fluxes were estimated via a mass balance model of the major pathways of energy metabolism. This analysis revealed stable metabolism in Fresh livers throughout perfusion while identifying two distinct metabolic states in WI livers, separated at t = 2 hrs, coinciding with recovery of oxygen uptake rates to Fresh liver values. This finding strongly suggests successful organ resuscitation within 2 hrs of perfusion. Overall perfused livers regulated metabolism of perfusate substrates according to their metabolic needs, despite supraphysiological levels of some metabolites. This study establishes the first integrative metabolic basis for the dynamics of recovery during perfusion treatment of marginal livers. Our initial findings support enhanced oxygen delivery for both timely recovery and long-term sustenance. These results are expected to lead the optimization of the treatment protocols and perfusion media from a metabolic perspective, facilitating translation to clinical use.

  14. A transmission probability method for calculation of neutron flux distributions in hexagonal geometry

    International Nuclear Information System (INIS)

    Wasastjerna, F.; Lux, I.

    1980-03-01

    A transmission probability method implemented in the program TPHEX is described. This program was developed for the calculation of neutron flux distributions in hexagonal light water reactor fuel assemblies. The accuracy appears to be superior to diffusion theory, and the computation time is shorter than that of the collision probability method. (author)

  15. Seasonal variability in distribution and fluxes of methane in the Arabian Sea

    Digital Repository Service at National Institute of Oceanography (India)

    Patra, P.K.; Lal, S.; Venkataramani, S.; Gauns, M.; Sarma, V.V.S.S.

    Study (India). These observations record its distributions in the water column asd well as its fluxes and their seasonal variations. Methane is mainly produced in subsurface water, and its supersaturation occurs in the upper 400 m. The CH@ sub(4) peak...

  16. Evaporation Flux Distribution of Drops on a Hydrophilic or Hydrophobic Flat Surface by Molecular Simulations.

    Science.gov (United States)

    Xie, Chiyu; Liu, Guangzhi; Wang, Moran

    2016-08-16

    The evaporation flux distribution of sessile drops is investigated by molecular dynamic simulations. Three evaporating modes are classified, including the diffusion dominant mode, the substrate heating mode, and the environment heating mode. Both hydrophilic and hydrophobic drop-substrate interactions are considered. To count the evaporation flux distribution, which is position dependent, we proposed an azimuthal-angle-based division method under the assumption of spherical crown shape of drops. The modeling results show that the edge evaporation, i.e., near the contact line, is enhanced for hydrophilic drops in all the three modes. The surface diffusion of liquid molecular absorbed on solid substrate for hydrophilic cases plays an important role as well as the space diffusion on the enhanced evaporation rate at the edge. For hydrophobic drops, the edge evaporation flux is higher for the substrate heating mode, but lower than elsewhere of the drop for the diffusion dominant mode; however, a nearly uniform distribution is found for the environment heating mode. The evidence shows that the temperature distribution inside drops plays a key role in the position-dependent evaporation flux.

  17. [Metabolic mechanisms underlying reparative action of metal-dependent spectral light flux from a hollow cathode lamp (experimental study)].

    Science.gov (United States)

    Pusyreva, G A; Frolkov, V K; Bobrovnitskiĭ, I P

    2010-01-01

    The objective of the present study was to evaluate the influence of serial irradiation of experimental animals with a visible light flow showing spectral lines of copper and manganese on the rate of reparative processes and the associated metabolic events. The cathode of the lamp that contained both microelements generated the light flux possessed of significant biological activity. Specifically, it accelerated reduction of the wound surface area and optimized regulation of carbohydrate metabolism in the lipid peroxidation system by insulin and cotisol. The light flux emitted by the cathode containing only one of the two elements (either copper or manganese) produced a similar but less pronounced effect.

  18. Zenith distribution and flux of atmospheric muons measured with the 5-line ANTARES detector

    Science.gov (United States)

    ANTARES Collaboration; Aguilar, J. A.; Albert, A.; Anton, G.; Anvar, S.; Ardid, M.; Assis Jesus, A. C.; Astraatmadja, T.; Aubert, J.-J.; Auer, R.; Baret, B.; Basa, S.; Bazzotti, M.; Bertin, V.; Biagi, S.; Bigongiari, C.; Bou-Cabo, M.; Bouwhuis, M. C.; Brown, A. M.; Brunner, J.; Busto, J.; Camarena, F.; Capone, A.; Carminati, G.; Carr, J.; Castel, D.; Castorina, E.; Cavasinni, V.; Cecchini, S.; Charvis, Ph.; Chiarusi, T.; Circella, M.; Coniglione, R.; Costantini, H.; Cottini, N.; Coyle, P.; Curtil, C.; de Bonis, G.; Decowski, M. P.; Dekeyser, I.; Deschamps, A.; Distefano, C.; Donzaud, C.; Dornic, D.; Drouhin, D.; Eberl, T.; Emanuele, U.; Ernenwein, J.-P.; Escoffier, S.; Fehr, F.; Flaminio, V.; Fratini, K.; Fritsch, U.; Fuda, J.-L.; Giacomelli, G.; Gómez-González, J. P.; Graf, K.; Guillard, G.; Halladjian, G.; Hallewell, G.; van Haren, H.; Heijboer, A. J.; Hello, Y.; Hernández-Rey, J. J.; Hößl, J.; de Jong, M.; Kalantar-Nayestanaki, N.; Kalekin, O.; Kappes, A.; Katz, U.; Kooijman, P.; Kopper, C.; Kouchner, A.; Kretschmer, W.; Lahmann, R.; Lamare, P.; Lambard, G.; Larosa, G.; Laschinsky, H.; Lefèvre, D.; Lelaizant, G.; Lim, G.; Lo Presti, D.; Loehner, H.; Loucatos, S.; Lucarelli, F.; Lyons, K.; Mangano, S.; Marcelin, M.; Margiotta, A.; Martinez-Mora, J. A.; Maurin, G.; Mazure, A.; Melissas, M.; Montaruli, T.; Morganti, M.; Moscoso, L.; Motz, H.; Naumann, C.; Neff, M.; Ostasch, R.; Palioselitis, D.; Păvălaş, G. E.; Payre, P.; Petrovic, J.; Piattelli, P.; Picot-Clemente, N.; Picq, C.; Pillet, R.; Popa, V.; Pradier, T.; Presani, E.; Racca, C.; Radu, A.; Reed, C.; Richardt, C.; Rujoiu, M.; Russo, G. V.; Salesa, F.; Sapienza, P.; Schöck, F.; Schuller, J.-P.; Shanidze, R.; Simeone, F.; Spurio, M.; Steijger, J. J. M.; Stolarczyk, Th.; Taiuti, M.; Tamburini, C.; Tasca, L.; Toscano, S.; Vallage, B.; van Elewyck, V.; Vecchi, M.; Vernin, P.; Wijnker, G.; de Wolf, E.; Yepes, H.; Zaborov, D.; Zornoza, J. D.; Zúñiga, J.; ANTARES Collaboration

    2010-10-01

    The ANTARES high-energy neutrino telescope is a three-dimensional array of about 900 photomultipliers distributed over 12 mooring lines installed in the Mediterranean Sea. Between February and November 2007 it acquired data in a 5-line configuration. The zenith angular distribution of the atmospheric muon flux and the associated depth-intensity relation are measured and compared with previous measurements and Monte Carlo expectations. An evaluation of the systematic effects due to uncertainties on environmental and detector parameters is presented.

  19. Producing Acetic Acid of Acetobacter pasteurianus by Fermentation Characteristics and Metabolic Flux Analysis.

    Science.gov (United States)

    Wu, Xuefeng; Yao, Hongli; Liu, Qing; Zheng, Zhi; Cao, Lili; Mu, Dongdong; Wang, Hualin; Jiang, Shaotong; Li, Xingjiang

    2018-03-19

    The acetic acid bacterium Acetobacter pasteurianus plays an important role in acetic acid fermentation, which involves oxidation of ethanol to acetic acid through the ethanol respiratory chain under specific conditions. In order to obtain more suitable bacteria for the acetic acid industry, A. pasteurianus JST-S screened in this laboratory was compared with A. pasteurianus CICC 20001, a current industrial strain in China, to determine optimal fermentation parameters under different environmental stresses. The maximum total acid content of A. pasteurianus JST-S was 57.14 ± 1.09 g/L, whereas that of A. pasteurianus CICC 20001 reached 48.24 ± 1.15 g/L in a 15-L stir stank. Metabolic flux analysis was also performed to compare the reaction byproducts. Our findings revealed the potential value of the strain in improvement of industrial vinegar fermentation.

  20. Conical pitch angle distributions of very-low energy ion fluxes observed by ISEE 1

    International Nuclear Information System (INIS)

    Horowitz, J.L.; Baugher, C.R.; Chappell, C.R.; Shelley, E.G.; Young, D.T.

    1982-01-01

    Observations of low-energy ionospheric ions by the plasma composition experiment abroad ISEE 1 often show conical pitch angle distributions, that is, peak fluxes between 0 0 and 90 0 to the directions parallel or antiparallel to the magnetic field. Frequently, all three primary ionospheric ion species (H + , He + , and O + ) simultaneously exhibit conical distributions with peak fluxes at essentially the same pitch angle. A distinction is made here between unidirectional, or streaming, distributions, in which ions are traveling essentially from only one hemisphere, and symmetrical distributions, in which significant fluxes are observed traveling from both hemispheres. The orbital coverage for this survey was largely restricted to the night sector, approximately 2100--0600 LT, and moderate geomagnetic latitudes of 20 0 --40 0 . Also, lack of complete pitch angle coverage at all times may have reduced detection for conics with small cone angles. However, we may conclude that the unidirectional conical distributions observed in the northern hemisphere are always observed to be traveling from the northern hemisphere and that they exhibit the following characteristics relative to the symmetric distributions, in that they (1) are typically observed on higher L shells (that is, higher geomagnetic latitudes or larger geocentric distances or both), (2) tend to have significantly larger cone angles, and (3), are associated with higher magnetic activity levels

  1. Integrating flux balance analysis into kinetic models to decipher the dynamic metabolism of Shewanella oneidensis MR-1.

    Directory of Open Access Journals (Sweden)

    Xueyang Feng

    2012-02-01

    Full Text Available Shewanella oneidensis MR-1 sequentially utilizes lactate and its waste products (pyruvate and acetate during batch culture. To decipher MR-1 metabolism, we integrated genome-scale flux balance analysis (FBA into a multiple-substrate Monod model to perform the dynamic flux balance analysis (dFBA. The dFBA employed a static optimization approach (SOA by dividing the batch time into small intervals (i.e., ∼400 mini-FBAs, then the Monod model provided time-dependent inflow/outflow fluxes to constrain the mini-FBAs to profile the pseudo-steady-state fluxes in each time interval. The mini-FBAs used a dual-objective function (a weighted combination of "maximizing growth rate" and "minimizing overall flux" to capture trade-offs between optimal growth and minimal enzyme usage. By fitting the experimental data, a bi-level optimization of dFBA revealed that the optimal weight in the dual-objective function was time-dependent: the objective function was constant in the early growth stage, while the functional weight of minimal enzyme usage increased significantly when lactate became scarce. The dFBA profiled biologically meaningful dynamic MR-1 metabolisms: 1. the oxidative TCA cycle fluxes increased initially and then decreased in the late growth stage; 2. fluxes in the pentose phosphate pathway and gluconeogenesis were stable in the exponential growth period; and 3. the glyoxylate shunt was up-regulated when acetate became the main carbon source for MR-1 growth.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-07-01

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

  3. Effects of drugs in subtoxic concentrations on the metabolic fluxes in human hepatoma cell line Hep G2

    International Nuclear Information System (INIS)

    Niklas, Jens; Noor, Fozia; Heinzle, Elmar

    2009-01-01

    Commonly used cytotoxicity assays assess the toxicity of a compound by measuring certain parameters which directly or indirectly correlate to the viability of the cells. However, the effects of a given compound at concentrations considerably below EC 50 values are usually not evaluated. These subtoxic effects are difficult to identify but may eventually cause severe and costly long term problems such as idiosyncratic hepatotoxicity. We determined the toxicity of three hepatotoxic compounds, namely amiodarone, diclofenac and tacrine on the human hepatoma cell line Hep G2 using an online kinetic respiration assay and analysed the effects of subtoxic concentrations of these drugs on the cellular metabolism by using metabolic flux analysis. Several changes in the metabolism could be detected upon exposure to subtoxic concentrations of the test compounds. Upon exposure to diclofenac and tacrine an increase in the TCA-cycle activity was observed which could be a signature of an uncoupling of the oxidative phosphorylation. The results indicate that metabolic flux analysis could serve as an invaluable novel tool for the investigation of the effects of drugs. The described methodology enables tracking the toxicity of compounds dynamically using the respiration assay in a range of concentrations and the metabolic flux analysis permits interesting insights into the changes in the central metabolism of the cell upon exposure to drugs.

  4. Equilibrium quality and mass flux distributions in an adiabatic three-subchannel test section

    International Nuclear Information System (INIS)

    Yadigaroglu, G.; Maganas, A.

    1993-01-01

    An experiment was designed to measure the fully-developed quality and mass flux distributions in an adiabatic three-subchannel test section. The three subchannels had the geometrical characteristics of the corner, side, and interior subchannels of a BWR-5 rod bundle. Data collected with Refrigerant-144 at pressures ranging from 7 to 14 bar, simulating operation with water in the range 55 to 103 bar are reported. The average mass flux and quality in the test section were in the ranges 1300 to 1750 kg/m s and -0.03 to 0.25, respectively. The data are analyzed and presented in various forms

  5. Metabolic engineering of Synechocystis sp. PCC 6803 for enhanced ethanol production based on flux balance analysis.

    Science.gov (United States)

    Yoshikawa, Katsunori; Toya, Yoshihiro; Shimizu, Hiroshi

    2017-05-01

    Synechocystis sp. PCC 6803 is an attractive host for bio-ethanol production due to its ability to directly convert atmospheric carbon dioxide into ethanol using photosystems. To enhance ethanol production in Synechocystis sp. PCC 6803, metabolic engineering was performed based on in silico simulations, using the genome-scale metabolic model. Comprehensive reaction knockout simulations by flux balance analysis predicted that the knockout of NAD(P)H dehydrogenase enhanced ethanol production under photoautotrophic conditions, where ammonium is the nitrogen source. This deletion inhibits the re-oxidation of NAD(P)H, which is generated by ferredoxin-NADP + reductase and imposes re-oxidation in the ethanol synthesis pathway. The effect of deleting the ndhF1 gene, which encodes NADH dehydrogenase subunit 5, on ethanol production was experimentally evaluated using ethanol-producing strains of Synechocystis sp. PCC 6803. The ethanol titer of the ethanol-producing ∆ndhF1 strain increased by 145%, compared with that of the control strain.

  6. Direct calculation of elementary flux modes satisfying several biological constraints in genome-scale metabolic networks.

    Science.gov (United States)

    Pey, Jon; Planes, Francisco J

    2014-08-01

    The concept of Elementary Flux Mode (EFM) has been widely used for the past 20 years. However, its application to genome-scale metabolic networks (GSMNs) is still under development because of methodological limitations. Therefore, novel approaches are demanded to extend the application of EFMs. A novel family of methods based on optimization is emerging that provides us with a subset of EFMs. Because the calculation of the whole set of EFMs goes beyond our capacity, performing a selective search is a proper strategy. Here, we present a novel mathematical approach calculating EFMs fulfilling additional linear constraints. We validated our approach based on two metabolic networks in which all the EFMs can be obtained. Finally, we analyzed the performance of our methodology in the GSMN of the yeast Saccharomyces cerevisiae by calculating EFMs producing ethanol with a given minimum carbon yield. Overall, this new approach opens new avenues for the calculation of EFMs in GSMNs. Matlab code is provided in the supplementary online materials fplanes@ceit.es. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  7. Histone Deacetylase AtSRT1 Links Metabolic Flux and Stress Response in Arabidopsis.

    Science.gov (United States)

    Liu, Xiaoyun; Wei, Wei; Zhu, Wenjun; Su, Lufang; Xiong, Zeyang; Zhou, Man; Zheng, Yu; Zhou, Dao-Xiu

    2017-12-04

    How plant metabolic flux alters gene expression to optimize plant growth and response to stress remains largely unclear. Here, we report that Arabidopsis thaliana NAD + -dependent histone deacetylase AtSRT1 negatively regulates plant tolerance to stress and glycolysis but stimulates mitochondrial respiration. We found that AtSRT1 interacts with Arabidopsis cMyc-Binding Protein 1 (AtMBP-1), a transcriptional repressor produced by alternative translation of the cytosolic glycolytic enolase gene LOS2/ENO2. We demonstrated that AtSRT1 could associate with the chromatin of AtMBP-1 targets LOS2/ENO2 and STZ/ZAT10, both of which encode key stress regulators, and reduce the H3K9ac levels at these genes to repress their transcription. Overexpression of both AtSRT1 and AtMBP-1 had synergistic effects on the expression of glycolytic genes, glycolytic enzymatic activities, and mitochondrial respiration. Furthermore, we found that AtMBP-1 is lysine-acetylated and vulnerable to proteasomal protein degradation, while AtSRT1 could remove its lysine acetylation and significantly enhance its stability in vivo. Taken together, these results indicate that AtSRT1 regulates primary metabolism and stress response by both epigenetic regulation and modulation of AtMBP-1 transcriptional activity in Arabidopsis. Copyright © 2017 The Author. Published by Elsevier Inc. All rights reserved.

  8. Gamma-Ray Flux Distribution and Nonlinear Behavior of Four LAT Bright AGNs

    Science.gov (United States)

    Kushwaha, Pankaj; Sinha, Atreyee; Misra, Ranjeev; Singh, K. P.; de Gouveia Dal Pino, E. M.

    2017-11-01

    We present a statistical characterization of the γ-ray emission from the four Fermi-LAT sources: FR I radio galaxy NGC 1275, BL Lac Mrk 421, FSRQs B2 1520+31, and PKS 1510-089 detected almost continuously over a time integration of three days between 2008 August and 2015 October. The observed flux variation is large, spanning ≳ 2 orders of magnitude between the extremes, except for Mrk 421. We compute the flux distributions and compare with Gaussian and lognormal ones. We find that the three blazars have distributions consistent with a lognormal, suggesting that the variability is of a nonlinear, multiplicative nature. This is further supported by the computation of the flux-rms relation, which is observed to be linear for the three blazars. However, for NGC 1275, the distribution does not seem to be represented either by a lognormal or a Gaussian, while its flux-rms relation is still found to be linear. We also compute the power spectra, which suggest the presence of a break, but are consistent with typical scale-free power-law shot noise. The results are broadly consistent with the statistical properties of the magnetic reconnection powered minijets-in-a-jet model. We discuss other possible scenarios and implications of these observations on jet processes and connections with the central engine.

  9. 13C Metabolic Flux Analysis for Systematic Metabolic Engineering of S. cerevisiae for Overproduction of Fatty Acids

    DEFF Research Database (Denmark)

    Ghosh, Amit; Ando, David; Gin, Jennifer

    2016-01-01

    Efficient redirection of microbial metabolism into the abundant production of desired bioproducts remains non-trivial. Here, we used flux-based modeling approaches to improve yields of fatty acids in Saccharomyces cerevisiae. We combined 13C labeling data with comprehensive genome-scale models to...

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

    NARCIS (Netherlands)

    Jorda, J.; Cueto Rojas, H.F.; Carnicer, M.; Wahl, S.A.; Ferrer, P.; Albiol, J.

    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)

  11. Beaver-mediated lateral hydrologic connectivity, fluvial carbon and nutrient flux, and aquatic ecosystem metabolism

    Science.gov (United States)

    Wegener, Pam; Covino, Tim; Wohl, Ellen

    2017-06-01

    River networks that drain mountain landscapes alternate between narrow and wide valley segments. Within the wide segments, beaver activity can facilitate the development and maintenance of complex, multithread planform. Because the narrow segments have limited ability to retain water, carbon, and nutrients, the wide, multithread segments are likely important locations of retention. We evaluated hydrologic dynamics, nutrient flux, and aquatic ecosystem metabolism along two adjacent segments of a river network in the Rocky Mountains, Colorado: (1) a wide, multithread segment with beaver activity; and, (2) an adjacent (directly upstream) narrow, single-thread segment without beaver activity. We used a mass balance approach to determine the water, carbon, and nutrient source-sink behavior of each river segment across a range of flows. While the single-thread segment was consistently a source of water, carbon, and nitrogen, the beaver impacted multithread segment exhibited variable source-sink dynamics as a function of flow. Specifically, the multithread segment was a sink for water, carbon, and nutrients during high flows, and subsequently became a source as flows decreased. Shifts in river-floodplain hydrologic connectivity across flows related to higher and more variable aquatic ecosystem metabolism rates along the multithread relative to the single-thread segment. Our data suggest that beaver activity in wide valleys can create a physically complex hydrologic environment that can enhance hydrologic and biogeochemical buffering, and promote high rates of aquatic ecosystem metabolism. Given the widespread removal of beaver, determining the cumulative effects of these changes is a critical next step in restoring function in altered river networks.

  12. Absorption, tissue distribution, excretion, and metabolism of clothianidin in rats.

    Science.gov (United States)

    Yokota, Tokunori; Mikata, Kazuki; Nagasaki, Hiromi; Ohta, Kazunari

    2003-11-19

    Absorption, distribution, excretion, and metabolism of clothianidin [(E)-1-(2-chloro-1,3-thiazol-5-ylmethyl)-3-methyl-2-nitroguanidine] were investigated after a single oral administration of [nitroimino-(14)C]- or [thiazolyl-2-(14)C]clothianidin to male and female rats at a dose of 5 mg/kg of body weight (bw) (low dose) or 250 mg/kg of bw (high dose). The maximum concentration of carbon-14 in blood occurred 2 h after administration of the low oral dose for both labeled clothianidins, and then the concentration of carbon-14 in blood decreased with a half-life of 2.9-4.0 h. The orally administered carbon-14 was rapidly and extensively distributed to all tissues and organs within 2 h after administration, especially to the kidney and liver, but was rapidly and almost completely eliminated from all tissues and organs with no evidence of accumulation. The orally administered carbon-14 was almost completely excreted into urine and feces within 2 days after administration, and approximately 90% of the administered dose was excreted via urine. The major compound in excreta was clothianidin, accounting for >60% of the administered dose. The major metabolic reactions of clothianidin in rats were oxidative demethylation to form N-(2-chlorothiazol-5-ylmethyl)-N'-nitroguanidine and the cleavage of the carbon-nitrogen bond between the thiazolylmethyl moiety and the nitroguanidine moiety. The part of the molecule containing the nitroguanidine moiety was transformed mainly to N-methyl-N'-nitroguanidine, whereas the thiazol moiety was further metabolized to 2-(methylthio)thiazole-5-carboxylic acid. With the exception of the transiently delayed excretion of carbon-14 at the high-dose level, the rates of biokinetics, excretion, distribution, and metabolism of clothianidin were not markedly influenced by dose level and sex.

  13. Metabolic flux rearrangement in the amino acid metabolism reduces ammonia stress in the α1-antitrypsin producing human AGE1.HN cell line.

    Science.gov (United States)

    Priesnitz, Christian; Niklas, Jens; Rose, Thomas; Sandig, Volker; Heinzle, Elmar

    2012-03-01

    This study focused on metabolic changes in the neuronal human cell line AGE1.HN upon increased ammonia stress. Batch cultivations of α(1)-antitrypsin (A1AT) producing AGE1.HN cells were carried out in media with initial ammonia concentrations ranging from 0mM to 5mM. Growth, A1AT production, metabolite dynamics and finally metabolic fluxes calculated by metabolite balancing were compared. Growth and A1AT production decreased with increasing ammonia concentration. The maximum A1AT concentration decreased from 0.63g/l to 0.51g/l. Central energy metabolism remained relatively unaffected exhibiting only slightly increased glycolytic flux at high initial ammonia concentration in the medium. However, the amino acid metabolism was significantly changed. Fluxes through transaminases involved in amino acid degradation were reduced concurrently with a reduced uptake of amino acids. On the other hand fluxes through transaminases working in the direction of amino acid synthesis, i.e., alanine and phosphoserine, were increased leading to increased storage of excess nitrogen in extracellular alanine and serine. Glutamate dehydrogenase flux was reversed increasingly fixing free ammonia with increasing ammonia concentration. Urea production additionally observed was associated with arginine uptake by the cells and did not increase at high ammonia stress. It was therefore not used as nitrogen sink to remove excess ammonia. The results indicate that the AGE1.HN cell line can adapt to ammonia concentrations usually present during the cultivation process to a large extent by changing metabolism but with slightly reduced A1AT production and growth. Copyright © 2012 Elsevier Inc. All rights reserved.

  14. Two dimensional electron transport in disordered and ordered distributions of magnetic flux vortices

    International Nuclear Information System (INIS)

    Nielsen, M.; Hedegaard, P.

    1994-04-01

    We have considered the conductivity properties of a two dimensional electron gas (2DEG) in two different kinds of inhomogeneous magnetic fields, i.e. a disordered distribution of magnetic flux vortices, and a periodic array of magnetic flux vortices. The work falls in two parts. In the first part we show how the phase shifts for an electron scattering on an isolated vortex, can be calculated analytically, and related to the transport properties through the differential cross section. In the second part we present numerical results for the Hall conductivity of the 2DEG in a periodic array of flux vortices found by exact diagonalization. We find characteristic spikes in the Hall conductance, when it is plotted against the filling fraction. It is argued that the spikes can be interpreted in terms of ''topological charge'' piling up across local and global gaps in the energy spectrum. (au) (23 refs.)

  15. Tracking the metabolic pulse of plant lipid production with isotopic labeling and flux analyses: Past, present and future

    Science.gov (United States)

    Metabolic networks are comprised of chemical transformations that are the basis of cellular operation and function to sustain life. The molecular rate of transitioning through biochemical pathways (i.e. flux) establishes cellular phenotypes that can be studied in response to genetic or environmental...

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

    DEFF Research Database (Denmark)

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

    2009-01-01

    Gcn4p. Although mRNA expression alone did not directly predict metabolic response, this correlation improved through incorporating a network-based model of amino acid biosynthesis (from r = 0.07 to 0.80 for mRNA-flux agreement). The model provides evidence of general biological principles: rewiring...

  17. Optimal heliostat aiming strategy for uniform distribution of heat flux on the receiver of a solar power tower plant

    International Nuclear Information System (INIS)

    Besarati, Saeb M.; Yogi Goswami, D.; Stefanakos, Elias K.

    2014-01-01

    Highlights: • The HFLCAL method is used to find the flux distribution of individual heliostats. • An optimization algorithm is developed based on the principles of genetic algorithm. • The objective is to minimize the standard deviation of flux density distribution. • The optimization algorithm finds which heliostats should aim at which point. • By using the new algorithm the maximum flux is reduced by an order of magnitude. - Abstract: Temperature distribution on the receiver surface of a solar power tower plant is of great importance. High temperature gradients may lead to local hot spots and consequently failure of the receiver. The temperature distribution can be controlled by defining several aiming points on the receiver surface and adjusting the heliostats accordingly. In this paper, a new optimization algorithm which works based on the principles of genetic algorithm is developed to find the optimal flux distribution on the receiver surface. The objective is to minimize the standard deviation of the flux density distribution by changing the aiming points of individual heliostats. Flux distribution of each heliostat is found by using the HFLCAL model [1], which is validated against experimental data. The results show that after employing the new algorithm the maximum flux density is reduced by an order of magnitude. The effects of number of aiming points and size of the aiming surface on the flux density distribution are investigated in detail

  18. The effects of off-center pellets on the temperature distribution and the heat flux distribution of fuel rods in nuclear reactors

    International Nuclear Information System (INIS)

    Peng Muzhang; Xing Jianhua

    1986-01-01

    This paper analyzes the effects of off-center pellets on the steady state temperature distribution and heat flux distribution of fuel rods in the nuclear reactors, and derives the dimensionless temperature distribution relationships and the dimensionless heat flux distribution relationship from the fuel rods with off-center pellets. The calculated results show that the effects of off-center will result in not only deviations of the highest temperature placement in the fuel pellets, but also the circumferentially nonuniform distributions of the temperatures and heat fluxes of the fuel rod surfaces

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

    International Nuclear Information System (INIS)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  1. Estimation of electrical conductivity distribution within the human head from magnetic flux density measurement

    Science.gov (United States)

    Gao, Nuo; Zhu, S. A.; He, Bin

    2005-06-01

    We have developed a new algorithm for magnetic resonance electrical impedance tomography (MREIT), which uses only one component of the magnetic flux density to reconstruct the electrical conductivity distribution within the body. The radial basis function (RBF) network and simplex method are used in the present approach to estimate the conductivity distribution by minimizing the errors between the 'measured' and model-predicted magnetic flux densities. Computer simulations were conducted in a realistic-geometry head model to test the feasibility of the proposed approach. Single-variable and three-variable simulations were performed to estimate the brain-skull conductivity ratio and the conductivity values of the brain, skull and scalp layers. When SNR = 15 for magnetic flux density measurements with the target skull-to-brain conductivity ratio being 1/15, the relative error (RE) between the target and estimated conductivity was 0.0737 ± 0.0746 in the single-variable simulations. In the three-variable simulations, the RE was 0.1676 ± 0.0317. Effects of electrode position uncertainty were also assessed by computer simulations. The present promising results suggest the feasibility of estimating important conductivity values within the head from noninvasive magnetic flux density measurements.

  2. Measurements of neutron flux distributions in the core of the Ljubljana TRIGA Mark II Reactor

    International Nuclear Information System (INIS)

    Rant, J.; Ravnik, M.; Mele, I.; Dimic, V.

    2008-01-01

    Recently the Ljubljana TRIGA Mark II Reactor has been refurbished and upgraded to pulsed operation. To verify the core design calculations using TRIGAP and PULSTR1 codes and to obtain necessary data for future irradiation and neutron beam experiments, an extensive experimental program of neutron flux mapping and neutron field characterization was carried out. Using the existing neutron measuring thimbles complete axial and radial distributions in two radial directions were determined for two different core configurations. For one core configuration the measurements were also carried out in the pulsed mode. For flux distributions thin Cu (relative measurements) and diluted Au wires (absolute values) were used. For each radial position the cadmium ratio was determined in two axial levels. The core configuration was rather uniform, well defined (fresh fuel of a single type, including fuelled followers) and compact (no irradiation channels or gaps), offering unique opportunity to test the computer codes for TRIGA reactor calculations. The neutron flux measuring procedures and techniques are described and the experimental results are presented. The agreement between the predicted and measured power peaking factors are within the error limits of the measurements (<±5%) and calculations (±10%). Power peaking occurs in the B ring, and in the A ring (centre) there is a significant flux depression. (authors)

  3. Noninvasive ultrasonic measurements of temperature distribution and heat fluxes in nuclear systems

    International Nuclear Information System (INIS)

    Jia, Yunlu; Skliar, Mikhail

    2015-01-01

    Measurements of temperature and heat fluxes through structural materials are important in many nuclear systems. One such example is dry storage casks (DSC) that are built to store highly radioactive materials, such as spent nuclear reactor fuel. The temperature inside casks must be maintained within allowable limits of the fuel assemblies and the DSC components because many degradation mechanisms are thermally controlled. In order to obtain direct, real-time measurements of temperature distribution without insertion of sensing elements into harsh environment of storage casks, we are developing noninvasive ultrasound (US) methods for measuring spatial distribution of temperature inside solid materials, such as concrete overpacks, steel casings, thimbles, and rods. The measured temperature distribution can then be used to obtain heat fluxes that provide calorimetric characterisation of the fuel decay, fuel distribution inside the cask, its integrity, and accounting of nuclear materials. The physical basis of the proposed approach is the temperature dependence of the speed of sound in solids. By measuring the time it takes an ultrasound signal to travel a known distance between a transducer and a receiver, the indication about the temperature distribution along the path of the ultrasound propagation may be obtained. However, when temperature along the path of US propagation is non-uniform, the overall time of flight of an ultrasound signal depends on the temperature distribution in a complex and unknown way. To overcome this difficulty, the central idea of our method is to create an US propagation path inside material of interest which incorporates partial ultrasound reflectors (back scatterers) at known locations and use the train of created multiple echoes to estimate the temperature distribution. In this paper, we discuss experimental validation of this approach, the achievable accuracy and spatial resolution of the measured temperature profile, and stress the

  4. Effects of temperature and UVR on organic matter fluxes and the metabolic activity of Acropora muricata

    Directory of Open Access Journals (Sweden)

    Lucile Courtial

    2017-08-01

    Full Text Available Coral bleaching events are predicted to occur more frequently in the coming decades with global warming. The susceptibility of corals to bleaching during thermal stress episodes depends on many factors, including the magnitude of thermal stress and irradiance. The interactions among these two factors, and in particular with ultra-violet radiation (UVR, the most harmful component of light, are more complex than assumed, and are not yet well understood. This paper explores the individual and combined effects of temperature and UVR on the metabolism of Acropora muricata, one of the most abundant coral species worldwide. Particulate and dissolved organic matter (POM/DOM fluxes and organic matter (OM degradation by the mucus-associated bacteria were also monitored in all conditions. The results show that UVR exposure exacerbated the temperature-induced bleaching, but did not affect OM fluxes, which were only altered by seawater warming. Temperature increase induced a shift from POM release and DOM uptake in healthy corals to POM uptake and DOM release in stressed ones. POM uptake was linked to a significant grazing of pico- and nanoplankton particles during the incubation, to fulfil the energetic requirements of A. muricata in the absence of autotrophy. Finally, OM degradation by mucus-associated bacterial activity was unaffected by UVR exposure, but significantly increased under high temperature. Altogether, our results demonstrate that seawater warming and UVR not only affect coral physiology, but also the way corals interact with the surrounding seawater, with potential consequences for coral reef biogeochemical cycles and food webs.

  5. Calculation of Stationary, Free Molecular Flux Distributions in General 3D Environments

    Science.gov (United States)

    Labello, Jesse

    2011-10-01

    This article presents an application of the angular coefficient method for diffuse reflection to calculate stationary molecular flux distributions in general three dimensional environments. The method of angular coefficients is reviewed and the integration of the method into Blender, a free, open-source, 3D modeling software package, is described. Some example calculations are compared to analytical and Direct Simulation Monte Carlo (DSMC) results with excellent agreement.

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

    Directory of Open Access Journals (Sweden)

    Eddy J Bautista

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

  7. Interaction of storage carbohydrates and other cyclic fluxes with central metabolism: A quantitative approach by non-stationary 13C metabolic flux analysis

    Directory of Open Access Journals (Sweden)

    C.A. Suarez-Mendez

    2016-12-01

    Full Text Available 13C labeling experiments in aerobic glucose limited cultures of Saccharomyces cerevisiae at four different growth rates (0.054; 0.101, 0.207, 0.307 h−1 are used for calculating fluxes that include intracellular cycles (e.g., storage carbohydrate cycles, exchange fluxes with amino acids, which are rearranged depending on the growth rate. At low growth rates the impact of the storage carbohydrate recycle is relatively more significant than at high growth rates due to a higher concentration of these materials in the cell (up to 560-fold and higher fluxes relative to the glucose uptake rate (up to 16%. Experimental observations suggest that glucose can be exported to the extracellular space, and that its source is related to storage carbohydrates, most likely via the export and subsequent extracellular breakdown of trehalose. This hypothesis is strongly supported by 13C-labeling experimental data, measured extracellular trehalose, and the corresponding flux estimations. Keywords: Non-stationary 13C labeling, Flux estimation, Trehalose, Glycogen, Amino acids

  8. Phase transitions and flux distributions of SU(2) lattice gauge theory

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Yingcai

    1993-12-31

    The strong interactions between quarks are believed to be described by Quantum Chromodynamics (QCD), which is a non-abelian SU(3) gauge theory. It is known that QCD undergoes a deconfining phase transition at very high temperatures, that is, at low temperatures QCD is in confined phase, at sufficient high temperatures it is in an unconfined phase. Also, quark confinement is believed to be due to string formation. In this dissertation the authors studied SU(2) gauge theory using numerical methods of LGT, which will provide some insights about the properties of QCD because SU(2) is similar to SU(3). They measured the flux distributions of a q{bar q} pair at various temperatures in different volumes. They find that in the limit of infinite volumes the flux distribution is different in the two phases. In the confined phase strong evidence is found for the string formation, however, in the unconfined phase there is no string formation. On the other hand, in the limit of zero temperature and finite volumes they find a clear signal for string formation in the large volume region, however, the string tension measured in intermediate volumes is due to finite volume effects, there is no intrinsic string formation. The color flux energies (action) of the q{bar q} pair are described by Michael sum rules. The original Michael sum rules deal with a static q{bar q} pair at zero temperature in infinite volumes. To check these sum rules with flux data at finite temperatures, they present a complete derivation for the sum rules, thus generalizing them to account for finite temperature effects. They find that the flux data are consistent with the prediction of generalized sum rules. The study elucidates the rich structures of QCD, and provides evidence for quark confinement and string formation. This supports the belief that QCD is a correct theory for strong interactions, and quark confinement can be explained by QCD.

  9. A Numerical Method for Obtaining Monoenergetic Neutron Flux Distributions and Transmissions in Multiple-Region Slabs

    Science.gov (United States)

    Schneider, Harold

    1959-01-01

    This method is investigated for semi-infinite multiple-slab configurations of arbitrary width, composition, and source distribution. Isotropic scattering in the laboratory system is assumed. Isotropic scattering implies that the fraction of neutrons scattered in the i(sup th) volume element or subregion that will make their next collision in the j(sup th) volume element or subregion is the same for all collisions. These so-called "transfer probabilities" between subregions are calculated and used to obtain successive-collision densities from which the flux and transmission probabilities directly follow. For a thick slab with little or no absorption, a successive-collisions technique proves impractical because an unreasonably large number of collisions must be followed in order to obtain the flux. Here the appropriate integral equation is converted into a set of linear simultaneous algebraic equations that are solved for the average total flux in each subregion. When ordinary diffusion theory applies with satisfactory precision in a portion of the multiple-slab configuration, the problem is solved by ordinary diffusion theory, but the flux is plotted only in the region of validity. The angular distribution of neutrons entering the remaining portion is determined from the known diffusion flux and the remaining region is solved by higher order theory. Several procedures for applying the numerical method are presented and discussed. To illustrate the calculational procedure, a symmetrical slab ia vacuum is worked by the numerical, Monte Carlo, and P(sub 3) spherical harmonics methods. In addition, an unsymmetrical double-slab problem is solved by the numerical and Monte Carlo methods. The numerical approach proved faster and more accurate in these examples. Adaptation of the method to anisotropic scattering in slabs is indicated, although no example is included in this paper.

  10. Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit.

    Science.gov (United States)

    Gupta, Apoorv; Reizman, Irene M Brockman; Reisch, Christopher R; Prather, Kristala L J

    2017-03-01

    Metabolic engineering of microorganisms to produce desirable products on an industrial scale can result in unbalanced cellular metabolic networks that reduce productivity and yield. Metabolic fluxes can be rebalanced using dynamic pathway regulation, but few broadly applicable tools are available to achieve this. We present a pathway-independent genetic control module that can be used to dynamically regulate the expression of target genes. We apply our module to identify the optimal point to redirect glycolytic flux into heterologous engineered pathways in Escherichia coli, resulting in titers of myo-inositol increased 5.5-fold and titers of glucaric acid increased from unmeasurable to >0.8 g/L, compared to the parent strains lacking dynamic flux control. Scaled-up production of these strains in benchtop bioreactors resulted in almost ten- and fivefold increases in specific titers of myo-inositol and glucaric acid, respectively. We also used our module to control flux into aromatic amino acid biosynthesis to increase titers of shikimate in E. coli from unmeasurable to >100 mg/L.

  11. Effect of Particle Size Distribution on Wall Heat Flux in Pulverized-Coal Furnaces and Boilers

    Science.gov (United States)

    Lu, Jun

    A mathematical model of combustion and heat transfer within a cylindrical enclosure firing pulverized coal has been developed and tested against two sets of measured data (one is 1993 WSU/DECO Pilot test data, the other one is the International Flame Research Foundation 1964 Test (Beer, 1964)) and one independent code FURN3D from the Argonne National Laboratory (Ahluwalia and IM, 1992). The model called PILC assumes that the system is a sequence of many well-stirred reactors. A char burnout model combining diffusion to the particle surface, pore diffusion, and surface reaction is employed for predicting the char reaction, heat release, and evolution of char. The ash formation model included relates the ash particle size distribution to the particle size distribution of pulverized coal. The optical constants of char and ash particles are calculated from dispersion relations derived from reflectivity, transmissivity and extinction measurements. The Mie theory is applied to determine the extinction and scattering coefficients. The radiation heat transfer is modeled using the virtual zone method, which leads to a set of simultaneous nonlinear algebraic equations for the temperature field within the furnace and on its walls. This enables the heat fluxes to be evaluated. In comparisons with the experimental data and one independent code, the model is successful in predicting gas temperature, wall temperature, and wall radiative flux. When the coal with greater fineness is burnt, the particle size of pulverized coal has a consistent influence on combustion performance: the temperature peak was higher and nearer to burner, the radiation flux to combustor wall increased, and also the absorption and scattering coefficients of the combustion products increased. The effect of coal particle size distribution on absorption and scattering coefficients and wall heat flux is significant. But there is only a small effect on gas temperature and fuel fraction burned; it is speculated

  12. Measured and Predicted Neutron Flux Distributions in a Material Surrounding a Cylindrical Duct

    Energy Technology Data Exchange (ETDEWEB)

    Nilsson, J.; Sandlin, R.

    1966-03-15

    The radial fast neutron flux attenuations in the material (iron) surrounding ducts of diameters 7, 9, and 15 cm and total duct length of about 1.5 m have been investigated with and without neutron scattering cans filled with D{sub 2}O in the duct. Experimentally the problem was solved by the use of foil activation techniques. Theoretically it was attacked by, in the first place, a Monte Carlo program specially written for this purpose and utilizing an importance sampling technique. In the second place non- and single-scattering removal flux codes were tried, and also simple hand calculations. The Monte Carlo results accounted well for the fast flux attenuation, while the non- and single-scattering methods overestimated the attenuation generally by a factor of 10 or less. Simple hand calculations using three empirical parameters could be fitted to the measured data within a factor of 1.2 - 1.3 at penetration depths greater than 3 - 4 cm. The distribution of the D{sub 2}O-scattered flux could well be described in terms of single scattering.

  13. Thermal and epithermal neutron flux distributions measurement in thermal column of TRR using an experimental-simulation method.

    Science.gov (United States)

    Adeli, Ruhollah; Kasesaz, Yaser; Shirmardi, Seyed Pezhman; Ezaty, Arsalan

    2018-03-01

    For designing an appropriate neutron beam, the determination of neutron flux at any irradiation facility is an important key factor. Due to the importance of determining the thermal and epithermal neutron fluxes in a typical thermal column of a reactor, a simple and accurate technique is introduced in this study. Absolute thermal and epithermal fluxes were measured experimentally at a certain point using the foil activation method by neutron bombardment of bare and cadmium covered Au foils. The relative neutron fluxes were also derived simply by means of Monte Carlo simulation by accurate modelling of the reactor components. Finally, by normalization of the relative distribution flux with regard to information about the absolute neutron flux, the accurate thermal and epithermal neutron distributions were derived, separately. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    Energy Technology Data Exchange (ETDEWEB)

    Lonien, J.; Schwender, J.

    2009-11-01

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

  15. Transient critical heat flux under flow coast-down in vertical annulus with non-uniform heat flux distribution

    International Nuclear Information System (INIS)

    Moon, S.K.; Chun, S.Y.; Choi, K.Y.; Yang, S.K.

    2001-01-01

    An experimental study on transient critical heat flux (CHF) under flow coast-down has been performed for water flow in a non-uniformly heated vertical annulus under low flow and a wide range of pressure conditions. The objectives of this study are to systematically investigate the effect of the flow transient on the CHF and to compare the transient CHF with steady state CHF. The transient CHF experiments have been performed for three kinds of flow transient modes based on the coast-down data of the Kori 3/4 nuclear power plant reactor coolant pump. Most of the CHFs occurred in the annular-mist flow regime. Thus, it means that the possible CHF mechanism might be the liquid film dryout in the annular-mist flow regime. For flow transient mode with the smallest flow reduction rate, the time-to-CHF is the largest. At the same inlet subcooling, system pressure and heat flux, the effect of the initial mass flux on the critical mass flux can be negligible. However, the effect of the initial mass flux on the time-to-CHF becomes large as the heat flux decreases. Usually, the critical mass flux is large for slow flow reduction. There is a pressure effect on the ratio of the transient CHF data to steady state CHF data. Some conventional correlations show relatively better CHF prediction results for high system pressure, high quality and slow transient modes than for low system pressure, low quality and fast transient modes. (author)

  16. Development of a position-sensitive fission counter and measurement of neutron flux distributions

    International Nuclear Information System (INIS)

    Yamagishi, Hideshi; Soyama, Kazuhiko; Kakuta, Tsunemi

    2001-08-01

    A position-sensitive fission counter (PSFC) that operates in high neutron flux and high gamma-ray background such as at the side of a power reactor vessel has been developed. Neutron detection using the PSFC with a solenoid electrode is based on a delay-line method. The PSFC that has the outer diameter of 25 mm and the sensitive length of 1000 mm was manufactured for investigation of the performances. The PSFC provided output current pulses that were sufficiently higher than the alpha noise, though the PSFC has a solenoid electrode and large electrode-capacitance. The S/N ratio of PSFC outputs proved to be higher than that of ordinary fission counters with 200 mm sensitive length. A performance test to measure neutron flux distributions by a neutron measuring system with the PSFC was carried out by the side of a graphite pile, W2.4 x H1.4 x L1.2 m, with neutron sources, Am-Be 370 GBq x 2. It was confirmed that the neutron flux distribution was well measured with the system. (author)

  17. Intramolecular stable isotope distributions detect plant metabolic responses on century time scales

    Science.gov (United States)

    Schleucher, Jürgen; Ehlers, Ina; Augusti, Angela; Betson, Tatiana

    2014-05-01

    Plants respond to environmental changes on a vast range of time scales, and plant gas exchanges constitute important feedback mechanisms in the global C cycle. Responses on time scales of decades to centuries are most important for climate models, for prediction of crop productivity, and for adaptation to climate change. Unfortunately, responses on these timescale are least understood. We argue that the knowledge gap on intermediate time scales is due to a lack of adequate methods that can bridge between short-term manipulative experiments (e.g. FACE) and paleo research. Manipulative experiments in plant ecophysiology give information on metabolism on time scales up to years. However, this information cannot be linked to results from retrospective studies in paleo research, because little metabolic information can be derived from paleo archives. Stable isotopes are prominent tools in plant ecophysiology, biogeochemistry and in paleo research, but in all applications to date, isotope ratios of whole molecules are measured. However, it is well established that stable isotope abundance varies among intramolecular groups of biochemical metabolites, that is each so-called "isotopomer" has a distinct abundance. This intramolecular variation carries information on metabolic regulation, which can even be traced to individual enzymes (Schleucher et al., Plant, Cell Environ 1999). Here, we apply intramolecular isotope distributions to study the metabolic response of plants to increasing atmospheric [CO2] during the past century. Greenhouse experiments show that the deuterium abundance among the two positions in the C6H2 group of photosynthetic glucose depends on [CO2] during growth. This is observed for all plants using C3 photosynthesis, and reflects the metabolic flux ratio between photorespiration and photosynthesis. Photorespiration is a major C flux that limits assimilation in C3 plants, which encompass the overwhelming fraction of terrestrial photosynthesis and the

  18. Radar meteors range distribution model. II. Shower flux density and mass distribution index

    Czech Academy of Sciences Publication Activity Database

    Pecinová, Drahomíra; Pecina, Petr

    2007-01-01

    Roč. 37, č. 2 (2007), s. 107-124 ISSN 1335-1842 R&D Projects: GA ČR GA205/03/1405 Institutional research plan: CEZ:AV0Z10030501 Keywords : physics of meteors * radar meteors * range distribution Subject RIV: BN - Astronomy, Celestial Mechanics, Astrophysics

  19. Prompt neutrino fluxes in the atmosphere with PROSA parton distribution functions

    Energy Technology Data Exchange (ETDEWEB)

    Garzelli, M.V.; Moch, S.; Placakyte, R.; Sigl, G. [Hamburg Univ. (Germany). 2. Inst. for Theoretical Physics; Zenaiev, O.; Geiser, A.; Lipka, K. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Cooper-Sarkar, A. [Oxford Univ. (United Kingdom). Dept. of Physics; Collaboration: PROSA Collaboration

    2016-11-15

    Effects on atmospheric prompt neutrino fluxes of present uncertainties affecting the nucleon composition are studied by using the PROSA fit to parton distribution functions (PDFs). The PROSA fit extends the precision of the PDFs to low x, which is the kinematic region of relevance for high-energy neutrino production, by taking into account LHCb data on charm and bottom hadroproduction. In the range of neutrino energies explored by present Very Large Volume Neutrino Telescopes, it is found that PDF uncertainties are far smaller with respect to those due to renormalization and factorization scale variation and to assumptions on the cosmic ray composition, which at present dominate and limit our knowledge of prompt neutrino fluxes. A discussion is presented on how these uncertainties affect the expected number of atmospheric prompt neutrino events in the analysis of high-energy events characterized by interaction vertices fully contained within the instrumented volume of the detector, performed by the IceCube collaboration.

  20. Prompt neutrino fluxes in the atmosphere with PROSA parton distribution functions

    International Nuclear Information System (INIS)

    Garzelli, M.V.; Moch, S.; Placakyte, R.; Sigl, G.; Cooper-Sarkar, A.

    2016-11-01

    Effects on atmospheric prompt neutrino fluxes of present uncertainties affecting the nucleon composition are studied by using the PROSA fit to parton distribution functions (PDFs). The PROSA fit extends the precision of the PDFs to low x, which is the kinematic region of relevance for high-energy neutrino production, by taking into account LHCb data on charm and bottom hadroproduction. In the range of neutrino energies explored by present Very Large Volume Neutrino Telescopes, it is found that PDF uncertainties are far smaller with respect to those due to renormalization and factorization scale variation and to assumptions on the cosmic ray composition, which at present dominate and limit our knowledge of prompt neutrino fluxes. A discussion is presented on how these uncertainties affect the expected number of atmospheric prompt neutrino events in the analysis of high-energy events characterized by interaction vertices fully contained within the instrumented volume of the detector, performed by the IceCube collaboration.

  1. Equilibrium quality and mass flux distributions in an adiabatic three-subchannel test section

    International Nuclear Information System (INIS)

    Yadigaroglu, G.; Maganas, A.

    1995-01-01

    An experiment was designed to measure the fully developed quality and mass flux distributions in an adiabatic three-subchannel test section. The three subchannels had the geometrical characteristics of the corner, side, and interior subchannels of a boiling water reactor (BWR-5) rod bundle. Data collected with Refrigerant-114 at pressures ranging from 7 to 14 bars, simulating operation with water in the range 55 to 103 bars are reported. The average mass flux and quality in the test section were in the ranges 1,300 to 1,750 kg/m 2 · s and -0.03 to 0.25, respectively. The data are analyzed and presented in various forms

  2. Electron energy distribution control by fiat: breaking from the conventional flux ratio scaling rules in etch

    Science.gov (United States)

    Ranjan, Alok; Wang, Mingmei; Sherpa, Sonam; Ventzek, Peter

    2015-03-01

    With shrinking critical dimensions, minimizing each of aspect ratio dependent etching (ARDE), bowing, undercut, selectivity, and within die uniformly across a wafer is met by trading off one requirement against another. The problem of trade-offs is especially critical. At the root of the problem is that roles radical flux, ion flux and ion energy play may be both good and bad. Increasing one parameter helps meeting one requirement but hinders meeting the other. Managing process by managing flux ratios and ion energy alone with conventional sources is not adequate because surface chemistry is uncontrollable. At the root of lack of control is that the electron energy distribution function (eedf) has not been controlled. Fortunately the high density surface wave sources control the eedf by fiat. High density surface wave sources are characterized by distinct plasma regions: an active plasma generation region with high electron temperature (Te) and an ionization free but chemistry rich diffusive region (low Te region). Pressure aids is segregating the regions by proving a means for momentum relaxation between the source and downstream region. "Spatial pulsing" allows access to plasma chemistry with reasonably high ion flux, from the active plasma generation region, just above the wafer. Low plasma potential enables precise passivation of surfaces which is critical for atomic layer etch (ALE) or high precision etch where the roles of plasma species can be limited to their purposed roles. High precision etch need not be at the cost of speed and manufacturability. Large ion flux at precisely controlled ion energy with RLSATM realizes fast desorption steps for ALE without compromising process throughput and precision.

  3. Distributed Temperature Sensing as a tool for measuring soil heat flux

    Science.gov (United States)

    Jansen, J.; Steele-Dunne, S. C.; Van De Giesen, N.; Selker, J. S.

    2011-12-01

    Soil heat flux is an important component of the surface energy balance. It is typically measured at a point using heat flux plates. Spatial patterns as well as temporal variability can be measured using Distributed Temperature Sensing (DTS), in which fiber-optic cable is used as an environmental temperature sensor. Previous research has demonstrated that DTS can be used to monitor soil moisture patterns and soil thermal profiles. By using a custom-built mole-plow, fiber optic cables were installed at three depths within the top 15 centimeters of a grass plot in Delft, The Netherlands. DTS was used to measure temperatures along the cable with a spatial resolution of 1 meter and a temporal resolution 5 minutes along a cable of 84 meters length. In this cable the response of soil temperature to the diurnal cycle of net radiation was measured over three months (Passive DTS). By inverse modeling of the diffusion equation, thermal properties of the soil are determined from which soil heat flux is calculated. During several more intensive campaigns, active heating experiments (Active DTS) were also carried out. In this case, a controlled electrical pulse was applied to the stainless steel armoring on the cable. The thermal response of the cable is measured for pulses of different input power, and this is related to the thermal properties of the surrounding soil. Net radiation, thermal conductivity and sensible heat flux were also measured to quantify the surface energy balance during the intensive campaigns. Results will be presented to illustrate that DTS (Active and/or Passive) is a promising and relatively inexpensive tool to measure large scale spatial patterns in temperature, soil moisture and soil heat flux at high spatial and temporal resolution.

  4. A metabolic and body-size scaling framework for parasite within-host abundance, biomass, and energy flux.

    Science.gov (United States)

    Hechinger, Ryan F

    2013-08-01

    Energetics may provide a useful currency for studying the ecology of parasite assemblages within individual hosts. Parasite assemblages may also provide powerful models to study general principles of ecological energetics. Yet there has been little ecological research on parasite-host energetics, probably due to methodological difficulties. However, the scaling relationships of individual metabolic rate with body or cell size and temperature may permit us to tackle the energetics of parasite assemblages in hosts. This article offers the foundations and initial testing of a metabolic theory of ecology (MTE) framework for parasites in hosts. I first provide equations to estimate energetic flux through observed parasite assemblages. I then develop metabolic scaling theory for parasite abundance, energetics, and biomass in individual hosts. In contrast to previous efforts, the theory factors in both host and parasite metabolic scaling, how parasites use host space, and whether energy or space dictates carrying capacity. Empirical tests indicate that host energetic flux can set parasite carrying capacity, which decreases as predicted considering the scaling of host and parasite metabolic rates. The theory and results also highlight that the phenomenon of "energetic equivalence" is not an assumption of MTE but a possible outcome contingent on how species partition resources. Hence, applying MTE to parasites can lend mechanistic, quantitative, predictive insight into the nature of parasitism and can inform general ecological theory.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-01-20

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

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

    International Nuclear Information System (INIS)

    Tang, Yinjie; Pingitore, Francesco; Mukhopadhyay, Aindrila; Phan, Richard; Hazen, Terry C.; Keasling, Jay D.

    2007-01-01

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

  7. Ethanol-metabolizing pathways in deermice. Estimation of flux calculated from isotope effects

    International Nuclear Information System (INIS)

    Alderman, J.; Takagi, T.; Lieber, C.S.

    1987-01-01

    The apparent deuterium isotope effects on Vmax/Km (D(V/K] of ethanol oxidation in two deermouse strains (one having and one lacking hepatic alcohol dehydrogenase (ADH] were used to calculate flux through the ADH, microsomal ethanol-oxidizing system (MEOS), and catalase pathways. In vitro, D(V/K) values were 3.22 for ADH, 1.13 for MEOS, and 1.83 for catalase under physiological conditions of pH, temperature, and ionic strength. In vivo, in deermice lacking ADH (ADH-), D(V/K) was 1.20 +/- 0.09 (mean +/- S.E.) at 7.0 +/- 0.5 mM blood ethanol and 1.08 +/- 0.10 at 57.8 +/- 10.2 mM blood ethanol, consistent with ethanol oxidation principally by MEOS. Pretreatment of ADH- animals with the catalase inhibitor 3-amino-1,2,4-triazole did not significantly change D(V/K). ADH+ deermice exhibited D(V/K) values of 1.87 +/- 0.06 (untreated), 1.71 +/- 0.13 (pretreated with 3-amino-1,2,4-triazole), and 1.24 +/- 0.13 (after the ADH inhibitor, 4-methylpyrazole) at 5-7 mM blood ethanol levels. At elevated blood ethanol concentrations (58.1 +/- 2.4 mM), a D(V/K) of 1.37 +/- 0.21 was measured in the ADH+ strain. For measured D(V/K) values to accurately reflect pathway contributions, initial reaction conditions are essential. These were shown to exist by the following criteria: negligible fractional conversion of substrate to product and no measurable back reaction in deermice having a reversible enzyme (ADH). Thus, calculations from D(V/K) indicate that, even when ADH is present, non-ADH pathways (mostly MEOS) participate significantly in ethanol metabolism at all concentrations tested and play a major role at high levels

  8. Estimation of neutron flux and xenon distributions via observer-based control theory

    Energy Technology Data Exchange (ETDEWEB)

    Park, Y.H.; Cho, N.Z. (Korea Advanced Inst. of Science and Technology, Dept. of Nuclear Engineering, P.O. Box 150, Cheongryang, Seoul (KR))

    1992-05-01

    State feedback control provides many advantages, such as stabilization and improved transient response. However, when state feedback control is considered for spatial control of a nuclear reactor, it requires complete knowledge of the distributions of the system state variables. Also, if the reactor is in a transient, flux mapping systems that are based on steady-state conditions are not appropriate for an accurate representation of the operating state of the reactor. In this paper a method is described for reconstructing the measurable and unmeasurable state variables in a nuclear reactor from output measurement data, which can be used to generate input for a feedback control system or serve as a core observer (estimator) in a reactor transient. The method is based on a Luenberger-type observer theory that is extended to infinite-dimensional distributed parameter systems. The method was applied to a simple reactor model in one spatial dimension and one energy group with xenon dynamics that exhibited spatial oscillations. The resulting observer was tested by using model-based data for measurement output. The results show that the spatial distributions of iodine, xenon, and neutron flux are estimated very well be the observer using information from a finite number of sensors.

  9. Aboveground herbivory shapes the biomass distribution and flux of soil invertebrates.

    Directory of Open Access Journals (Sweden)

    Christian Mulder

    Full Text Available BACKGROUND: Living soil invertebrates provide a universal currency for quality that integrates physical and chemical variables with biogeography as the invertebrates reflect their habitat and most ecological changes occurring therein. The specific goal was the identification of "reference" states for soil sustainability and ecosystem functioning in grazed vs. ungrazed sites. METHODOLOGY/PRINCIPAL FINDINGS: Bacterial cells were counted by fluorescent staining and combined direct microscopy and automatic image analysis; invertebrates (nematodes, mites, insects, oligochaetes were sampled and their body size measured individually to allow allometric scaling. Numerical allometry analyses food webs by a direct comparison of weight averages of components and thus might characterize the detrital soil food webs of our 135 sites regardless of taxonomy. Sharp differences in the frequency distributions are shown. Overall higher biomasses of invertebrates occur in grasslands, and all larger soil organisms differed remarkably. CONCLUSIONS/SIGNIFICANCE: Strong statistical evidence supports a hypothesis explaining from an allometric perspective how the faunal biomass distribution and the energetic flux are affected by livestock, nutrient availability and land use. Our aim is to propose faunal biomass flux and biomass distribution as quantitative descriptors of soil community composition and function, and to illustrate the application of these allometric indicators to soil systems.

  10. Body fat distribution and inflammation among obese older adults with and without metabolic syndrome

    NARCIS (Netherlands)

    Koster, A.; Stenholm, S.; Alley, D.E.; Kim, L.J.; Simonsick, E.M.; Kanaya, A.M.; Visser, M.; Houston, D.K.; Nicklas, B.J.; Tylavsky, F.A.; Satterfield, S.; Goodpaster, B.H.; Ferrucci, L.; Harris, T.B.

    2010-01-01

    The protective mechanisms by which some obese individuals escape the detrimental metabolic consequences of obesity are not understood. This study examined differences in body fat distribution and adipocytokines in obese older persons with and without metabolic syndrome. Additionally, we examined

  11. Nested Global Inversion for the Carbon Flux Distribution in Canada and USA from 1994 to 2003

    Science.gov (United States)

    Chen, J. M.; Deng, F.; Ishizawa, M.; Ju, W.; Mo, G.; Chan, D.; Higuchi, K.; Maksyutov, S.

    2007-12-01

    Based on TransCom inverse modeling for 22 global regions, we developed a nested global inversion system for estimating carbon fluxes of 30 regions in North America (2 of the 22 regions are divided into 30). Irregular boundaries of these 30 regions are delineated based on ecosystem types and provincial/state borders. Synthesis Bayesian inversion is conducted in monthly steps using CO2 concentration measurements at 88 coastal and continental stations of the globe for the 1994-2003 period (NOAA GlobalView database). Responses of these stations to carbon fluxes from the 50 regions are simulated using the transport model of National Institute for Environmental Studies of Japan and reanalysis wind fields of the National Centers for Environmental Prediction (NCEP). Terrestrial carbon flux fields modeled using BEPS and Biome-BGC driven by NCEP reanalysis meteorological data are used as two different a priori to constrain the inversion. The inversion (top- down) results are compared with remote sensing-based ecosystem modeling (bottom-up) results in Canada's forests and wetlands. There is a broad consistency in the spatial pattern of the carbon source and sink distributions obtained using these two independent methods. Both sets of results also indicate that Canada's forests and wetlands are carbon sinks in 1994-2003, but the top-down method produces consistently larger sinks than the bottom-up results. Reasons for this discrepancy may lie in both methods, and several issues are identified for further investigation.

  12. Characterizing the Lyman-alpha forest flux probability distribution function using Legendre polynomials

    Science.gov (United States)

    Cieplak, Agnieszka; Slosar, Anze

    2018-01-01

    The Lyman-alpha forest has become a powerful cosmological probe at intermediate redshift. It is a highly non-linear field with much information present beyond the power spectrum. The flux probability flux distribution (PDF) in particular has been a successful probe of small scale physics. However, it is also sensitive to pixel noise, spectrum resolution, and continuum fitting, all of which lead to possible biased estimators. Here we argue that measuring the coefficients of the Legendre polynomial expansion of the PDF offers several advantages over measuring the binned values as is commonly done. Since the n-th Legendre coefficient can be expressed as a linear combination of the first n moments of the field, this allows for the coefficients to be measured in the presence of noise and allows for a clear route towards marginalization over the mean flux. Additionally, in the presence of noise, a finite number of these coefficients are well measured with a very sharp transition into noise dominance. This compresses the information into a small amount of well-measured quantities. Finally, we find that measuring fewer quasars with high signal-to-noise produces a higher amount of recoverable information.

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

    Science.gov (United States)

    Wierckx, Nick; Ruijssenaars, Harald J; de Winde, Johannes H; Schmid, Andreas; Blank, Lars M

    2009-08-20

    The physiological effects of genetic and transcriptional changes observed in a phenol producing mutant of the solvent-tolerant Pseudomonas putida S12 were assessed with metabolic flux analysis. The upregulation of a malate/lactate dehydrogenase encoding gene could be connected to a flux increase from malate to oxaloacetate. A mutation in the pykA gene decreased in vitro pyruvate kinase activity, which is consistent with a lower flux from phosphoenolpyruvate to pyruvate. Changes in the oprB-1, gntP and gnuK genes, encoding a glucose-selective porin, gluconokinase and a gluconate transporter respectively, altered the substrate uptake profile. Metabolic flux analysis furthermore revealed cellular events not predicted by the transcriptome analysis. Gluconeogenic formation of glucose-6-phosphate from triose-3-phosphate was abolished, in favour of increased phosphoenolpyruvate production. An increased pentose phosphate pathway flux resulted in higher erythrose-4-phosphate production. Thus, the availability of these two central phenol precursors was improved. Furthermore, metabolic fluxes were redistributed such that the overall TCA cycle flux was unaffected and energy production increased. Engineering P. putida S12 for phenol production has yielded a strain that channels carbon fluxes to previously unfavourable routes to reconcile the drain on metabolites required for phenol production, while maintaining basal flux levels through central carbon metabolism.

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

    Directory of Open Access Journals (Sweden)

    Wittmann Christoph

    2005-11-01

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

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2014-07-08

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

  17. Infinite-dimensional observer theory for dynamic estimation of neutron flux and xenon distributions

    Energy Technology Data Exchange (ETDEWEB)

    Park, Young Ho; Cho, Nam Zin [Korea Advanced Institute of Science and Technology, Taejon (Korea, Republic of)

    1991-07-01

    This paper describes a method for reconstructing the measurable and unmeasurable state variables in a nuclear reactor from output measurement data, which can be used to generate input of a feedback control system or to serve as a core observer (estimator) in reactor transient. The method is based on the Luenberger-type observer theory that is extended to infinite-dimensional distributed parameter systems. The method was applied to a simple reactor model in one spatial dimension and one energy group with xenon dynamics which exhibited spatial oscillations. The observer designed was tested by using model-based data for measurement output. The results showed that the spatial distributions of iodine, xenon and neutron flux were estimated by the observer very well using information from a finite number of sensors.

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

    Directory of Open Access Journals (Sweden)

    Sergio eRuiz-Halpern

    2014-12-01

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

  19. Analysis of Neutron Flux Distribution in Rsg-Gas Reactor With U-Mo Fuels

    Directory of Open Access Journals (Sweden)

    Taswanda Taryo

    2004-01-01

    Full Text Available The use of U-Mo fuels in research reactors seems to be promising and, recently, world researchers have carried out these such activities actively. The National Nuclear Energy Agency (BATAN which owns RSG-GAS reactor available in Serpong Research Center for Atomic Energy should anticipate this trend. It is, therefore, this research work on the use of U-Mo fuels in RSG-GAS reactor should be carried out. The work was focused on the analysis of neutron flux distribution in the RSG-GAS reactor using different content of molybdenum in U-Mo fuels. To begin with, RSG-GAS reactor core model was developed and simulated into X, Y and Z dimensions. Cross section of materials based on the developed cells of standard and control fuels was then generated using WIMS-D5-B. The criticality calculations were finally carried out applying BATAN-2DIFF code. The results showed that the neutron flux distribution obtained in U-Mo-fuel-based RSG-GAS core is very similar to those achieved in the 300-gram sillicide-fuel-based RSG-GAS reactor core. Indeed, the utilization of the U-Mo RSG-GAS core can be very similar to that of the high-density sillicide reactor core and even could be better in the future.

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

    Science.gov (United States)

    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. Magnetic Flux Distribution of Linear Machines with Novel Three-Dimensional Hybrid Magnet Arrays

    Directory of Open Access Journals (Sweden)

    Nan Yao

    2017-11-01

    Full Text Available The objective of this paper is to propose a novel tubular linear machine with hybrid permanent magnet arrays and multiple movers, which could be employed for either actuation or sensing technology. The hybrid magnet array produces flux distribution on both sides of windings, and thus helps to increase the signal strength in the windings. The multiple movers are important for airspace technology, because they can improve the system’s redundancy and reliability. The proposed design concept is presented, and the governing equations are obtained based on source free property and Maxwell equations. The magnetic field distribution in the linear machine is thus analytically formulated by using Bessel functions and harmonic expansion of magnetization vector. Numerical simulation is then conducted to validate the analytical solutions of the magnetic flux field. It is proved that the analytical model agrees with the numerical results well. Therefore, it can be utilized for the formulation of signal or force output subsequently, depending on its particular implementation.

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

    NARCIS (Netherlands)

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

    2009-01-01

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

  3. In vivo metabolic flux profiling with stable isotopes discriminates sites and quantifies effects of mitochondrial dysfunction in C. elegans

    Science.gov (United States)

    Ostrovsky, Julian; Clarke, Colleen; Preston, Judith; Bennett, Michael J.; Yudkoff, Marc; Xiao, Rui; Falk, Marni J.

    2014-01-01

    Mitochondrial respiratory chain (RC) disease diagnosis is complicated both by an absence of biomarkers that sufficiently divulge all cases and limited capacity to quantify adverse effects across intermediary metabolism. We applied high performance liquid chromatography (HPLC) and mass spectrometry (MS) studies of stable-isotope based precursor–product relationships in the nematode, C. elegans, to interrogate in vivo differences in metabolic flux among distinct genetic models of primary RC defects and closely related metabolic disorders. Methods C. elegans strains studied harbor single nuclear gene defects in complex I, II, or III RC subunits (gas-1, mev-1, isp-1); enzymes involved in coenzyme Q biosynthesis (clk-1), the tricarboxylic acid cycle (TCA, idh-1), or pyruvate metabolism (pdha-1); and central nodes of the nutrient-sensing signaling network that involve insulin response (daf-2) or the sirtuin homologue (sir-2.1). Synchronous populations of 2000 early larval stage worms were fed standard Escherichia coli on nematode growth media plates containing 1,6-13C2-glucose throughout their developmental period, with samples extracted on the first day of adult life in 4% perchloric acid with an internal standard. Quantitation of whole animal free amino acid concentrations and isotopic incorporation into amino and organic acids throughout development was performed in all strains by HPLC and isotope ratio MS, respectively. GC/MS analysis was also performed to quantify absolute isotopic incorporation in all molecular species of key TCA cycle intermediates in gas-1 and N2 adult worms. Results Genetic mutations within different metabolic pathways displayed distinct metabolic profiles. RC complex I (gas-1) and III (isp-1) subunit mutants, together with the coenzyme Q biosynthetic mutant (clk-1), shared a similar amino acid profile of elevated alanine and decreased glutamate. The metabolic signature of the complex II mutant (mev-1) was distinct from that of the other RC

  4. Distribution, regional sources and deposition fluxes of organochlorine pesticides in precipitation in Guangzhou, South China

    Science.gov (United States)

    Huang, De-Yin; Peng, Ping'an; Xu, Yi-Gang; Sun, Cui-Xiang; Deng, Hong-Mei; Deng, Yun-Yun

    2010-07-01

    We analyzed rainwater collected from multiple sites, Guangzhou, China, from March to August 2005, with the aim to characterize the distribution, regional sources and deposition fluxes of organochlorine pesticides (OCPs) in South China. Eight species of organochlorine pesticide were detected, including hexachlorocyclohexanes (HCHs), dichlorodiphenyltrichloroethanes (DDTs), and endosulfans. Volume-weighted mean monthly total concentrations varied from 3.65 ± 0.95 to 9.37 ± 2.63 ng L - 1 , and the estimated total wet deposition flux was about 11.43 ± 3.27 µg m - 2 during the monitoring period. Pesticides were mainly detected in the dissolved phase. Distribution coefficients between particulate and dissolved phases in March and April were generally higher than in other months. HCHs, p,p'-DDD and p,p'-DDT in precipitation were attributed to both the residues and present usage of insecticides in Pearl River Delta. The concentrations of p,p'-DDD + p,p'-DDT were relatively high from April to August, which were related to the usage of antifouling paints containing DDT for fishing ships in seaports of the South China Sea in summer. In contrast, endosulfans were relatively high in March, which was related to their seasonal atmospheric transport from cotton fields in eastern China by the Asian winter monsoon. The consistency of the variation of endosulfans, p,p'-DDD and p,p'-DDT concentrations with the alternation of summer and winter monsoon suggested that the Asian monsoon played an important role in the long-range transport of OCPs. In addition, the wet deposition of OCPs may influence not only Pearl River water but also the surface land distributions of pesticides in the Guangzhou area, especially for endosulfans, p,p'-DDD and p,p'-DDT.

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

    Directory of Open Access Journals (Sweden)

    Komi Nambou

    2015-12-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-08-13

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

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

    DEFF Research Database (Denmark)

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

    2004-01-01

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

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

    DEFF Research Database (Denmark)

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

    2004-01-01

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

  10. Far-ultraviolet spectra and flux distributions of some Orion stars

    International Nuclear Information System (INIS)

    Carruthers, G.R.; Heckathorn, H.M.; Opal, C.B.

    1981-01-01

    Far-ultraviolet (950--1800 A) spectra with about 2 A resolution were obtained of a number of stars in Orion during a sounding-rocket flight 1975 December 6. These spectra have been reduced to absolute flux distributions with the aid of preflight calibrations. The derived fluxes are in good agreement with model-atmosphere predictions and previous observations down to about 1200 A. In the 1200--1080 A range, the present results are in good agreement with model predictions but fall above the rocket measurements of Brune, Mount, and Feldman. Below 1080 A, our measurements fall below the model predictions, reaching a deviation of a factor of 2 near 1010 A and a factor of 4 near 950 A. The present results are compared with those of Brune et al. via Copernicus U2 observations in this spectral range, and possible sources of discrepancies between the various observations and model-atmosphere predictions are discussed. Other aspects of the spectra, particularly with regard to spectral classification, are briefly discussed

  11. Characterizing the Lyα forest flux probability distribution function using Legendre polynomials

    Energy Technology Data Exchange (ETDEWEB)

    Cieplak, Agnieszka M.; Slosar, Anže, E-mail: acieplak@bnl.gov, E-mail: anze@bnl.gov [Brookhaven National Laboratory, Bldg 510, Upton, NY, 11973 (United States)

    2017-10-01

    The Lyman-α forest is a highly non-linear field with considerable information available in the data beyond the power spectrum. The flux probability distribution function (PDF) has been used as a successful probe of small-scale physics. In this paper we argue that measuring coefficients of the Legendre polynomial expansion of the PDF offers several advantages over measuring the binned values as is commonly done. In particular, the n -th Legendre coefficient can be expressed as a linear combination of the first n moments, allowing these coefficients to be measured in the presence of noise and allowing a clear route for marginalisation over mean flux. Moreover, in the presence of noise, our numerical work shows that a finite number of coefficients are well measured with a very sharp transition into noise dominance. This compresses the available information into a small number of well-measured quantities. We find that the amount of recoverable information is a very non-linear function of spectral noise that strongly favors fewer quasars measured at better signal to noise.

  12. Effect of feed flow pattern on the distribution of permeate fluxes in desalination by direct contact membrane distillation

    KAUST Repository

    Soukane, Sofiane

    2017-05-31

    The current study aims to highlight the effect of flow pattern on the variations of permeate fluxes over the membrane surface during desalination in a direct contact membrane distillation (DCMD) flat module. To do so, a three dimensional (3D) Computational Fluid Dynamics (CFD) model with embedded pore scale calculations is implemented to predict flow, heat and mass transfer in the DCMD module. Model validation is carried out in terms of average permeate fluxes with experimental data of seawater desalination using two commercially available PTFE membranes. Average permeate fluxes agree within 6% and less with experimental values without fitting parameters. Simulation results show that the distribution of permeate fluxes and seawater salinity over the membrane surface are strongly dependent on momentum and heat transport and that temperature and concentration polarization follow closely the flow distribution. The analysis reveals a drastic effect of recirculation loops and dead zones on module performance and recommendations to improve MD flat module design are drawn consequently.

  13. The Martian hydrologic cycle - Effects of CO2 mass flux on global water distribution

    Science.gov (United States)

    James, P. B.

    1985-01-01

    The Martian CO2 cycle, which includes the seasonal condensation and subsequent sublimation of up to 30 percent of the planet's atmosphere, produces meridional winds due to the consequent mass flux of CO2. These winds currently display strong seasonal and hemispheric asymmetries due to the large asymmetries in the distribution of insolation on Mars. It is proposed that asymmetric meridional advection of water vapor on the planet due to these CO2 condensation winds is capable of explaining the observed dessication of Mars' south polar region at the current time. A simple model for water vapor transport is used to verify this hypothesis and to speculate on the effects of changes in orbital parameters on the seasonal water cycle.

  14. Flux balance analysis of genome-scale metabolic model of rice ...

    Indian Academy of Sciences (India)

    2015-09-28

    Sep 28, 2015 ... producing vitamin A–enriched golden rice (Beyer et al. 2002). On the other hand, metabolic engineering has been proven as a powerful technique for over or less production of specific metabolites in microbes (Peralta-Yahya et al. 2012). Modelling and analysis of the cellular metabolism is a key step in the ...

  15. Transorgan fluxes in a porcine model reveal a central role for liver in acylcarnitine metabolism

    NARCIS (Netherlands)

    Schooneman, Marieke G.; ten Have, Gabriella A. M.; van Vlies, Naomi; Houten, Sander M.; Deutz, Nicolaas E. P.; Soeters, Maarten R.

    2015-01-01

    Acylcarnitines are derived from mitochondrial acyl-CoA metabolism and have been associated with diet-induced insulin resistance. However, plasma acylcarnitine profiles have been shown to poorly reflect whole body acylcarnitine metabolism. We aimed to clarify the individual role of different organ

  16. Radiopharmaceuticals for Assessment of Altered Metabolism and Biometal Fluxes in Brain Aging and Alzheimer’s Disease with Positron Emission Tomography

    OpenAIRE

    Xie, Fang; Peng, Fangyu

    2017-01-01

    Aging is a risk factor for Alzheimer’s disease (AD). There are changes of brain metabolism and biometal fluxes due to brain aging, which may play a role in pathogenesis of AD. Positron emission tomography (PET) is a versatile tool for tracking alteration of metabolism and biometal fluxes due to brain aging and AD. Age-dependent changes in cerebral glucose metabolism can be tracked with PET using 2-deoxy-2-[18F]-fluoro-D-glucose (18F-FDG), a radiolabeled glucose analogue, as a radiotracer. Bas...

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

    Science.gov (United States)

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

    2014-10-01

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

  18. Cofactor engineering through heterologous expression of an NADH oxidase and its impact on metabolic flux redistribution in Klebsiella pneumoniae

    Directory of Open Access Journals (Sweden)

    Ji Xiao-Jun

    2013-01-01

    Full Text Available Abstract Background Acetoin is an important bio-based platform chemical. However, it is usually existed as a minor byproduct of 2,3-butanediol fermentation in bacteria. Results The present study reports introducing an exogenous NAD+ regeneration sysytem into a 2,3-butanediol producing strain Klebsiella pneumoniae to increse the accumulation of acetoin. Batch fermentation suggested that heterologous expression of the NADH oxidase in K. pneumoniae resulted in large decreases in the intracellular NADH concentration (1.4 fold and NADH/NAD+ ratio (2.0 fold. Metabolic flux analysis revealed that fluxes to acetoin and acetic acid were enhanced, whereas, production of lactic acid and ethanol were decreased, with the accumualation of 2,3-butanediol nearly unaltered. By fed-batch culture of the recombinant, the highest reported acetoin production level (25.9 g/L by Klebsiella species was obtained. Conclusions The present study indicates that microbial production of acetoin could be improved by decreasing the intracellular NADH/NAD+ ratio in K. pneumoniae. It demonstrated that the cofactor engineering method, which is by manipulating the level of intracellular cofactors to redirect cellular metabolism, could be employed to achieve a high efficiency of producing the NAD+-dependent microbial metabolite.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    Wasylenko, Thomas M; Stephanopoulos, Gregory

    2015-03-01

    Over the past two decades, significant progress has been made in the engineering of xylose-consuming Saccharomyces cerevisiae strains for production of lignocellulosic biofuels. However, the ethanol productivities achieved on xylose are still significantly lower than those observed on glucose for reasons that are not well understood. We have undertaken an analysis of central carbon metabolite pool sizes and metabolic fluxes on glucose and on xylose under aerobic and anaerobic conditions in a strain capable of rapid xylose assimilation via xylose isomerase in order to investigate factors that may limit the rate of xylose fermentation. We find that during xylose utilization the flux through the non-oxidative Pentose Phosphate Pathway (PPP) is high but the flux through the oxidative PPP is low, highlighting an advantage of the strain employed in this study. Furthermore, xylose fails to elicit the full carbon catabolite repression response that is characteristic of glucose fermentation in S. cerevisiae. We present indirect evidence that the incomplete activation of the fermentation program on xylose results in a bottleneck in lower glycolysis, leading to inefficient re-oxidation of NADH produced in glycolysis. © 2014 Wiley Periodicals, Inc.

  1. Metabolic control analysis of the penicillin biosynthetic pathway: the influence of the LLD-ACV:bisACV ratio on the flux control.

    Science.gov (United States)

    Theilgaard, H A; Nielsen, J

    1999-01-01

    An extended kinetic model for the first two steps of the penicillin biosynthetic pathway in Penicillium chrysogenum is set up. It includes the formation and reduction of the dimer bis-delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine (bisACV) from the first pathway intermediate LLD-ACV and their parallel inhibition of the enzyme ACV synthetase (ACVS). The kinetic model is based on Michaelis-Menten type kinetics, with non-competitive inhibition of the ACVS by both LLD-ACV and bisACV, and competitive inhibition of the isopenicillin N synthetase (IPNS) by glutathione. The inhibition constant of LLD-ACV, KACV is determined to be 0.54 mm. With the kinetic model metabolic control analysis is performed to identify the distribution of rate-control in the pathway at all ratios of LLD-ACV:bisACV. It is concluded that the flux control totally resides at the IPNS. This is a result of the regulation of the ACVS by both the LLD-ACV and bisACV demanding a higher flux through the IPNS enzyme to alleviate their inhibition. The measurement of an intracellular ratio of LLD-ACV:bisACV to be in the range of 1-2 moles per moles emphasises the importance of a fast conversion of LLD-ACV to IPN, and accumulation of LLD-ACV above the K(m)-value of the IPNS should therefore be avoided.

  2. The Distribution and Flux of Fish in the Forebay of The Dalles Dam in 2003

    Energy Technology Data Exchange (ETDEWEB)

    Faber, Derrek M.; Hanks, Michael E.; Zimmerman, Shon A.; Skalski, John R.; Dillingham, Peter W.

    2005-04-29

    In spring and summer 2003, the Pacific Northwest National Laboratory led a team that conducted mobile and fixed hydroacoustic surveys in the forebay of The Dalles Dam for the U.S. Army Corps of Engineers - Portland District, for the Anadromous Fish Evaluation Program. The surveys provided information on the distribution and movement of smolt-sized fish relative to ambient factors such as flow, bathymetry, or diel cycle in the forebay at The Dalles Dam. This information is intended to provide baseline data for the development of a surface bypass alternative for juvenile salmon at The Dalles Dam. We sampled the forebay of The Dallas Dam one day and night each week for six weeks in the spring and another six weeks in the summer. In general, during the day in the spring, the greatest densities of smolt-sized fish were observed in the thalweg of the main channel from the Washington bank, to the east side of the powerhouse, along the powerhouse, and concentrated in the areas next to the sluiceway. Fish density was lower on the Washington side of the river and west of mid-powerhouse (north spillway side). The spring night distribution was similar, with a few notable differences. The density of fish was high on the east side of the powerhouse and along the face of the powerhouse, and more fish were detected on the north spillway side. The distribution of sub-yearling sized fish in summer followed the same general patterns as spring, except that summer fish had a greater presence on the east side of the powerhouse and on the north spillway side. The vertical distribution of fish was also determined. In spring 80% of fish were above 5.6 m of depth during the day and above 4.7 m in the night. The summer fish were similarly distributed in the day and night with 80% of the fish in the upper 4.5 m and 4.7 m of the water column respectively. In general the smolt-sized fish were distributed deeper in the water column in the center of the channel than near the edges. The net

  3. SU-G-TeP3-10: Radiation Induces Prompt Live-Cell Metabolic Fluxes

    Energy Technology Data Exchange (ETDEWEB)

    Campos, D [University of Wisconsin Madison, Madison, WI (United States); Peeters, W; Bussink, J [Radboud University Medical Center, Nijmegen, GA (United States); Nickel, K [University of Wisconsin - Madison, Madison, Wisconsin (United States); Burkel, B; Kimple, R; Kogel, A van der; Eliceiri, K [University of Wisconsin - Madison, Madison, WI (United States); Kissick, M [University of Wisconsin, Madison, WI (United States)

    2016-06-15

    Purpose: To compare metabolic dynamics and HIF-1α expression following radiation between a cancerous cell line (UM-SCC-22B) and a normal, immortalized cell line, NOK (Normal Oral Keratinocyte). HIF-1 is a key factor in metabolism and radiosensitivity. A better understanding of how radiation affects the interplay of metabolism and HIF-1 might give a better understanding of the mechanisms responsible for radiosensitivity. Methods: Changes in cellular metabolism in response to radiation are tracked by fluorescence lifetime of NADH. Expression of HIF-1α was measured by immunofluorescence for both cell lines with and without irradiation. Radiation response is also monitored with additional treatment of a HIF-1α inhibitor (chrysin) as well as a radical scavenger (glutathione). Changes in oxygen consumption and respiratory capacity are also monitored using the Seahorse XF analyzer. Results: An increase in HIF-1α was found to be in response to radiation for the cancer cell line, but not the normal cell line. Radiation was found to shift metabolism toward glycolytic pathways in cancer cells as measured by oxygen consumption and respiratory capacity. Radiation response was found to be muted by addition of glutathione to cell media. HIF-1α inhibition similarly muted radiation response in cancer. Conclusion: The HIF-1 protein complex is a key regulator cellular metabolism through the regulation of glycolysis and glucose transport enzymes. Moreover, HIF-1 has shown radio-protective effects in tumor vascular endothelia, and has been implicated in metastatic aggression. Monitoring interplay between metabolism and the HIF-1 protein complex can give a more fundamental understanding of radiotherapy response.

  4. Feasibility study of Self Powered Neutron Detectors in Fast Reactors for detecting local change in neutron flux distribution

    International Nuclear Information System (INIS)

    Jammes, Christian; Filliatre, Philippe; Verma, Vasudha; Hellesen, Carl; Jacobsson Svard, Staffan

    2015-01-01

    Neutron flux monitoring system forms an integral part of the design of a Generation IV sodium cooled fast reactor system. Diverse possibilities of detector systems installation have to be investigated with respect to practicality and feasibility according to the detection parameters. In this paper, we demonstrate the feasibility of using self powered neutron detectors as in-core detectors in fast reactors for detecting local change in neutron flux distribution. We show that the gamma contribution from fission products decay in the fuel and activation of structural materials is very small compared to the fission gammas. Thus, it is possible for the in-core SPND signal to follow changes in local neutron flux as they are proportional to each other. This implies that the signal from an in-core SPND can provide dynamic information on the neutron flux perturbations occurring inside the reactor core. (authors)

  5. Consequences of gas flux model choice on the interpretation of metabolic balance across 15 lakes

    Science.gov (United States)

    Dugan, Hilary; Woolway, R. Iestyn; Santoso, Arianto; Corman, Jessica; Jaimes, Aline; Nodine, Emily; Patil, Vijay; Zwart, Jacob A.; Brentrup, Jennifer A.; Hetherington, Amy; Oliver, Samantha K.; Read, Jordan S.; Winters, Kirsten; Hanson, Paul; Read, Emily; Winslow, Luke; Weathers, Kathleen

    2016-01-01

    Ecosystem metabolism and the contribution of carbon dioxide from lakes to the atmosphere can be estimated from free-water gas measurements through the use of mass balance models, which rely on a gas transfer coefficient (k) to model gas exchange with the atmosphere. Theoretical and empirically based models of krange in complexity from wind-driven power functions to complex surface renewal models; however, model choice is rarely considered in most studies of lake metabolism. This study used high-frequency data from 15 lakes provided by the Global Lake Ecological Observatory Network (GLEON) to study how model choice of kinfluenced estimates of lake metabolism and gas exchange with the atmosphere. We tested 6 models of k on lakes chosen to span broad gradients in surface area and trophic states; a metabolism model was then fit to all 6 outputs of k data. We found that hourly values for k were substantially different between models and, at an annual scale, resulted in significantly different estimates of lake metabolism and gas exchange with the atmosphere.

  6. An integrative machine learning strategy for improved prediction of essential genes in Escherichia coli metabolism using flux-coupled features.

    Science.gov (United States)

    Nandi, Sutanu; Subramanian, Abhishek; Sarkar, Ram Rup

    2017-07-25

    Prediction of essential genes helps to identify a minimal set of genes that are absolutely required for the appropriate functioning and survival of a cell. The available machine learning techniques for essential gene prediction have inherent problems, like imbalanced provision of training datasets, biased choice of the best model for a given balanced dataset, choice of a complex machine learning algorithm, and data-based automated selection of biologically relevant features for classification. Here, we propose a simple support vector machine-based learning strategy for the prediction of essential genes in Escherichia coli K-12 MG1655 metabolism that integrates a non-conventional combination of an appropriate sample balanced training set, a unique organism-specific genotype, phenotype attributes that characterize essential genes, and optimal parameters of the learning algorithm to generate the best machine learning model (the model with the highest accuracy among all the models trained for different sample training sets). For the first time, we also introduce flux-coupled metabolic subnetwork-based features for enhancing the classification performance. Our strategy proves to be superior as compared to previous SVM-based strategies in obtaining a biologically relevant classification of genes with high sensitivity and specificity. This methodology was also trained with datasets of other recent supervised classification techniques for essential gene classification and tested using reported test datasets. The testing accuracy was always high as compared to the known techniques, proving that our method outperforms known methods. Observations from our study indicate that essential genes are conserved among homologous bacterial species, demonstrate high codon usage bias, GC content and gene expression, and predominantly possess a tendency to form physiological flux modules in metabolism.

  7. Metabolic flux of the oxidative pentose phosphate pathway under low light conditions in Synechocystis sp. PCC 6803.

    Science.gov (United States)

    Ueda, Kentaro; Nakajima, Tsubasa; Yoshikawa, Katsunori; Toya, Yoshihiro; Matsuda, Fumio; Shimizu, Hiroshi

    2018-02-27

    The role of the oxidative pentose phosphate pathway (oxPPP) in Synechocystis sp. PCC 6803 under mixotrophic conditions was investigated by 13 C metabolic flux analysis. Cells were cultured under low (10 μmol m -2  s -1 ) and high light intensities (100 μmol m -2  s -1 ) in the presence of glucose. The flux of CO 2 fixation by ribulose bisphosphate carboxylase/oxygenase under the high light condition was approximately 3-fold higher than that under the low light condition. Although no flux of the oxPPP was observed under the high light condition, flux of 0.08-0.19 mmol gDCW -1  h -1 in the oxPPP was observed under the low light condition. The balance between the consumption and production of NADPH suggested that approximately 10% of the total NADPH production was generated by the oxPPP under the low light condition. The growth phenotype of a mutant with deleted zwf, which encodes glucose-6-phosphate dehydrogenase in the oxPPP, was compared to that of the parental strain under low and high light conditions. Growth of the Δzwf mutant nearly stopped during the late growth phase under the low light condition, whereas the growth rates of the two strains were identical under the high light condition. These results indicate that NADPH production in the oxPPP is essential for anabolism under low light conditions. The oxPPP appears to play an important role in producing NADPH from glucose and ATP to compensate for NADPH shortage under low light conditions. Copyright © 2018 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  8. Radiopharmaceuticals for Assessment of Altered Metabolism and Biometal Fluxes in Brain Aging and Alzheimer's Disease with Positron Emission Tomography.

    Science.gov (United States)

    Xie, Fang; Peng, Fangyu

    2017-01-01

    Aging is a risk factor for Alzheimer's disease (AD). There are changes of brain metabolism and biometal fluxes due to brain aging, which may play a role in pathogenesis of AD. Positron emission tomography (PET) is a versatile tool for tracking alteration of metabolism and biometal fluxes due to brain aging and AD. Age-dependent changes in cerebral glucose metabolism can be tracked with PET using 2-deoxy-2-[18F]-fluoro-D-glucose (18F-FDG), a radiolabeled glucose analogue, as a radiotracer. Based on different patterns of altered cerebral glucose metabolism, 18F-FDG PET was clinically used for differential diagnosis of AD and Frontotemporal dementia (FTD). There are continued efforts to develop additional radiopharmaceuticals or radiotracers for assessment of age-dependent changes of various metabolic pathways and biometal fluxes due to brain aging and AD with PET. Elucidation of age-dependent changes of brain metabolism and altered biometal fluxes is not only significant for a better mechanistic understanding of brain aging and the pathophysiology of AD, but also significant for identification of new targets for the prevention, early diagnosis, and treatment of AD.

  9. Estimation of surface heat flux and temperature distributions in a multilayer tissue based on the hyperbolic model of heat conduction.

    Science.gov (United States)

    Lee, Haw-Long; Chen, Wen-Lih; Chang, Win-Jin; Yang, Yu-Ching

    2015-01-01

    In this study, an inverse algorithm based on the conjugate gradient method and the discrepancy principle is applied to solve the inverse hyperbolic heat conduction problem in estimating the unknown time-dependent surface heat flux in a skin tissue, which is stratified into epidermis, dermis, and subcutaneous layers, from the temperature measurements taken within the medium. Subsequently, the temperature distributions in the tissue can be calculated as well. The concept of finite heat propagation velocity is applied to the modeling of the bioheat transfer problem. The inverse solutions will be justified based on the numerical experiments in which two different heat flux distributions are to be determined. The temperature data obtained from the direct problem are used to simulate the temperature measurements. The influence of measurement errors on the precision of the estimated results is also investigated. Results show that an excellent estimation on the time-dependent surface heat flux can be obtained for the test cases considered in this study.

  10. The key to acetate: metabolic fluxes of acetic acid bacteria under cocoa pulp fermentation-simulating conditions.

    Science.gov (United States)

    Adler, Philipp; Frey, Lasse Jannis; Berger, Antje; Bolten, Christoph Josef; Hansen, Carl Erik; Wittmann, Christoph

    2014-08-01

    Acetic acid bacteria (AAB) play an important role during cocoa fermentation, as their main product, acetate, is a major driver for the development of the desired cocoa flavors. Here, we investigated the specialized metabolism of these bacteria under cocoa pulp fermentation-simulating conditions. A carefully designed combination of parallel 13C isotope labeling experiments allowed the elucidation of intracellular fluxes in the complex environment of cocoa pulp, when lactate and ethanol were included as primary substrates among undefined ingredients. We demonstrate that AAB exhibit a functionally separated metabolism during coconsumption of two-carbon and three-carbon substrates. Acetate is almost exclusively derived from ethanol, while lactate serves for the formation of acetoin and biomass building blocks. Although this is suboptimal for cellular energetics, this allows maximized growth and conversion rates. The functional separation results from a lack of phosphoenolpyruvate carboxykinase and malic enzymes, typically present in bacteria to interconnect metabolism. In fact, gluconeogenesis is driven by pyruvate phosphate dikinase. Consequently, a balanced ratio of lactate and ethanol is important for the optimum performance of AAB. As lactate and ethanol are individually supplied by lactic acid bacteria and yeasts during the initial phase of cocoa fermentation, respectively, this underlines the importance of a well-balanced microbial consortium for a successful fermentation process. Indeed, AAB performed the best and produced the largest amounts of acetate in mixed culture experiments when lactic acid bacteria and yeasts were both present.

  11. Human taurine metabolism: fluxes and fractional extraction rates of the gut, liver, and kidneys

    NARCIS (Netherlands)

    van Stijn, Mireille F. M.; Vermeulen, Mechteld A. R.; Siroen, Michiel P. C.; Wong, Leanne N.; van den Tol, M. Petrousjka; Ligthart-Melis, Gerdien C.; Houdijk, Alexander P. J.; van Leeuwen, Paul A. M.

    2012-01-01

    Taurine is involved in numerous biological processes. However, taurine plasma level decreases in response to pathological conditions, suggesting an increased need. Knowledge on human taurine metabolism is scarce and only described by arterial-venous differences across a single organ. Here we present

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

    Czech Academy of Sciences Publication Activity Database

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

    2014-01-01

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

  13. The flux distribution from a 1.25m2 target aligned heliostat: comparison of ray tracing and experimental results

    CSIR Research Space (South Africa)

    Maliage, M

    2012-05-01

    Full Text Available The purpose of this paper is to validate SolTrace for concentrating solar investigations at CSIR by means of a test case: the comparison of the flux distribution in the focal spot of a 1.25 m2 target aligned heliostat predicted by the ray tracing...

  14. {sup 13}C dynamic nuclear polarization for measuring metabolic flux in endothelial progenitor cells

    Energy Technology Data Exchange (ETDEWEB)

    Nielsen, Nathalie; Laustsen, Christoffer; Bertelsen, Lotte Bonde, E-mail: Lotte@clin.au.dk

    2016-11-15

    Endothelial progenitor cells (EPCs) represent a heterogeneous cell population that is believed to be involved in vasculogenesis. With the purpose of enhancing endothelial repair, EPCs could have a potential for future cell therapies. Due to the low amount of EPCs in the peripheral circulating blood, in vitro expansion is needed before administration to recipients and the effects of in vitro culturing is still an under-evaluated field with little knowledge of how the cells change over time in culture. The aim of this study was to use hyperpolarised carbon-13 magnetic resonance spectroscopy to profile important metabolic pathways in a population of progenitor cells and to show that cell culturing in 3D scaffolds seem to block the metabolic processes that leads to cell senescence. The metabolic breakdown of hyperpolarized [1-{sup 13}C]pyruvate was followed after injection of the substrate to a bioreactor system with EPCs either adhered to 3D printed scaffolds or kept in cell suspension. The pyruvate-to-lactate conversion was elevated in suspension of EPCs compared to the EPCs adhered to scaffolds. Furthermore in the setup with EPCs in suspension, an increase in lactate production was seen over time indicating that the older the cultures of EPCs was before using the cells for cell suspension experiments, the more lactate they produce, compared to a constant lactate level in the cells adhered to scaffolds. It could therefore be stated that cells grown first in 2D culture and subsequent prepared for cell suspension show a metabolism with higher lactate production consistent with cells senescence processes compared to cells grown first at 2D culture and subsequent in the 3D printed scaffolds, where metabolism shows no sign of metabolic shifting during the monitored period. - Highlights: • Hyperpolarized 13C MRS detects EPCs metabolic changes associated with ageing and cultivating conditions. • Increased lactate production in EPC’s correlates positively with aging.

  15. Magnetic flux distribution in a ferromagnetic material magnetized by U-shaped electromagnets of different geometric dimensions types

    Directory of Open Access Journals (Sweden)

    Povolotskaya Anna

    2018-01-01

    Full Text Available A model experiment has been carried out on studying the type of changes in the magnetic induction in a homogeneous isotropic sample that is locally magnetized with attached U-type electromagnets of different geometrical dimensions. The study was aimed at finding out magnetic flux distribution at different locations within the sample and determining the effect that the geometry of attached electromagnets has on this distribution.

  16. Ion fluxes across the pitcher walls of three Bornean Nepenthes pitcher plant species: flux rates and gland distribution patterns reflect nitrogen sequestration strategies.

    Science.gov (United States)

    Moran, Jonathan A; Hawkins, Barbara J; Gowen, Brent E; Robbins, Samantha L

    2010-03-01

    Nepenthes pitcher plant species differ in their prey capture strategies, prey capture rates, and pitcher longevity. In this study, it is investigated whether or not interspecific differences in nutrient sequestration strategy are reflected in the physiology and microstructure of the pitchers themselves. Using a non-invasive technique (MIFE), ion fluxes in pitchers of Nepenthes ampullaria Jack, Nepenthes bicalcarata Hook.f., and Nepenthes rafflesiana Jack were measured. Scanning electron microscopy was also used to characterize the distribution of glandular and other structures on the inner pitcher walls. The results demonstrate that nutrient sequestration strategy is indeed mirrored in pitcher physiology and microstructure. Species producing long-lived pitchers with low prey capture rates (N. ampullaria, N. bicalcarata) showed lower rates of NH(4)(+) uptake than N. rafflesiana, a species producing short-lived pitchers with high capture rates. Crucially, species dependent upon aquatic commensals (N. ampullaria, N. bicalcarata) actively manipulated H(+) fluxes to maintain less acid pitcher fluid than found in 'typical' species; in addition, these species lacked the lunate cells and epicuticular waxes characteristic of 'typical' insectivorous congeners. An unexpected finding was that ion fluxes occurred in the wax-covered, non-glandular zones in N. rafflesiana. The only candidates for active transport of aqueous ions in these zones appear to be the epidermal cells lying beneath the lunate cells, as these are the only sites not visibly coated with epicuticular waxes.

  17. A New Stellar Atmosphere Grid and Comparisons with HST /STIS CALSPEC Flux Distributions

    Energy Technology Data Exchange (ETDEWEB)

    Bohlin, Ralph C.; Fleming, Scott W.; Gordon, Karl D.; Koekemoer, Anton M. [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Mészáros, Szabolcs; Kovács, József [ELTE Gothard Astrophysical Observatory, H-9700 Szombathely, Szent Imre Herceg St. 112 (Hungary)

    2017-05-01

    The Space Telescope Imaging Spectrograph has measured the spectral energy distributions for several stars of types O, B, A, F, and G. These absolute fluxes from the CALSPEC database are fit with a new spectral grid computed from the ATLAS-APOGEE ATLAS9 model atmosphere database using a chi-square minimization technique in four parameters. The quality of the fits are compared for complete LTE grids by Castelli and Kurucz (CK04) and our new comprehensive LTE grid (BOSZ). For the cooler stars, the fits with the MARCS LTE grid are also evaluated, while the hottest stars are also fit with the NLTE Lanz and Hubeny OB star grids. Unfortunately, these NLTE models do not transition smoothly in the infrared to agree with our new BOSZ LTE grid at the NLTE lower limit of T {sub eff} = 15,000 K. The new BOSZ grid is available via the Space Telescope Institute MAST archive and has a much finer sampled IR wavelength scale than CK04, which will facilitate the modeling of stars observed by the James Webb Space Telescope . Our result for the angular diameter of Sirius agrees with the ground-based interferometric value.

  18. Measurement of two-dimensional thermal neutron flux in a water phantom and evaluation of dose distribution characteristics

    International Nuclear Information System (INIS)

    Yamamoto, Kazuyoshi; Kumada, Hiroaki; Kishi, Toshiaki; Torii, Yoshiya; Horiguchi, Yoji

    2001-03-01

    To evaluate nitrogen dose, boron dose and gamma-ray dose occurred by neutron capture reaction of the hydrogen at the medical irradiation, two-dimensional distribution of the thermal neutron flux is very important because these doses are proportional to the thermal neutron distribution. This report describes the measurement of the two-dimensional thermal neutron distribution in a head water phantom by neutron beams of the JRR-4 and evaluation of the dose distribution characteristic. Thermal neutron flux in the phantom was measured by gold wire placed in the spokewise of every 30 degrees in order to avoid the interaction. Distribution of the thermal neutron flux was also calculated using two-dimensional Lagrange's interpolation program (radius, angle direction) developed this time. As a result of the analysis, it was confirmed to become distorted distribution which has annular peak at outside of the void, though improved dose profile of the deep direction was confirmed in the case which the radiation field in the phantom contains void. (author)

  19. Assessment of energetic costs of AhR activation by β-naphthoflavone in rainbow trout (Oncorhynchus mykiss) hepatocytes using metabolic flux analysis

    Energy Technology Data Exchange (ETDEWEB)

    Nault, Rance, E-mail: naultran@msu.edu [Ottawa-Carleton Institute of Biology, Department of Biology and Centre for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Ontario, K1N 6N5 (Canada); Abdul-Fattah, Hiba [Ottawa-Carleton Institute of Biology, Department of Biology and Centre for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Ontario, K1N 6N5 (Canada); Mironov, Gleb G.; Berezovski, Maxim V. [Ottawa-Carleton Institute of Biology, Department of Biology and Centre for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Ontario, K1N 6N5 (Canada); Department of Chemistry, University of Ottawa, Ottawa, Ontario, K1N 6N5 (Canada); Moon, Thomas W. [Ottawa-Carleton Institute of Biology, Department of Biology and Centre for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Ontario, K1N 6N5 (Canada)

    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.

  20. Assessment of energetic costs of AhR activation by β-naphthoflavone in rainbow trout (Oncorhynchus mykiss) hepatocytes using metabolic flux analysis

    International Nuclear Information System (INIS)

    Nault, Rance; Abdul-Fattah, Hiba; Mironov, Gleb G.; Berezovski, Maxim V.; Moon, Thomas W.

    2013-01-01

    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 + /K + -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 + /K + -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

  1. Characterizing the roles of changing population size and selection on the evolution of flux control in metabolic pathways.

    Science.gov (United States)

    Orlenko, Alena; Chi, Peter B; Liberles, David A

    2017-05-25

    Understanding the genotype-phenotype map is fundamental to our understanding of genomes. Genes do not function independently, but rather as part of networks or pathways. In the case of metabolic pathways, flux through the pathway is an important next layer of biological organization up from the individual gene or protein. Flux control in metabolic pathways, reflecting the importance of mutation to individual enzyme genes, may be evolutionarily variable due to the role of mutation-selection-drift balance. The evolutionary stability of rate limiting steps and the patterns of inter-molecular co-evolution were evaluated in a simulated pathway with a system out of equilibrium due to fluctuating selection, population size, or positive directional selection, to contrast with those under stabilizing selection. Depending upon the underlying population genetic regime, fluctuating population size was found to increase the evolutionary stability of rate limiting steps in some scenarios. This result was linked to patterns of local adaptation of the population. Further, during positive directional selection, as with more complex mutational scenarios, an increase in the observation of inter-molecular co-evolution was observed. Differences in patterns of evolution when systems are in and out of equilibrium, including during positive directional selection may lead to predictable differences in observed patterns for divergent evolutionary scenarios. In particular, this result might be harnessed to detect differences between compensatory processes and directional processes at the pathway level based upon evolutionary observations in individual proteins. Detecting functional shifts in pathways reflects an important milestone in predicting when changes in genotypes result in changes in phenotypes.

  2. Fermentation Process and Metabolic Flux of Ethanol Production from the Detoxified Hydrolyzate of Cassava Residue

    Directory of Open Access Journals (Sweden)

    Xingjiang Li

    2017-08-01

    Full Text Available With the growth of the world population, energy problems are becoming increasingly severe; therefore, sustainable energy sources have gained enormous importance. With respect to ethanol fuel production, biomass is gradually replacing grain as the main raw material. In this study, we explored the fermentation of five- and six-carbon sugars, the main biomass degradation products, into alcohol. We conducted mutagenic screening specifically for Candida tropicalis CICC1779 to obtain a strain that effectively used xylose (Candida tropicalis CICC1779-Dyd. By subsequently studying fermentation conditions under different initial liquid volume oxygen transfer coefficients (kLα, and coupling control of the aeration rate and agitation speed under optimal conditions, the optimal dissolved oxygen change curve was obtained. In addition, we constructed metabolic flow charts and equations to obtain a better understanding of the fermentation mechanism and to improve the ethanol yield. In our experiment, the ethanol production of the wild type stain was 17.58 g·L−1 at a kLα of 120. The highest ethanol yield of the mutagenic strains was 24.85 g·L−1. The ethanol yield increased to 26.56 g·L−1 when the dissolved oxygen content was optimized, and the conversion of sugar into alcohol reached 0.447 g·g−1 glucose (the theoretical titer of yeast-metabolized xylose was 0.46 g ethanol/g xylose and the glucose ethanol fermentation titer was 0.51 g ethanol/g glucose. Finally, the detected activity of xylose reductase and xylose dehydrogenase was higher in the mutant strain than in the original, which indicated that the mutant strain (CICC1779-Dyd could effectively utilize xylose for metabolism.

  3. Experimental investigation on distribution of mass flux and gas/liquid mixture ratio of airblast coaxial atomizers

    Science.gov (United States)

    Wu, Jinxiang; Liu, Weidong; Zhuang, Fengchen

    1993-06-01

    Airblast coaxial atomizers are widely used in combustion chambers of liquid rocket engines, and the distributions of mass flux and gas/liquid mixture ratio in the downstream of the atomizers are one of the important parameters which influence the performance of combustion. A two-phase impact probe designed by the authors was employed to measure these parameters in a type of airblast coaxial atomizer. Graphs from experimental results show the details of the distribution in the downstream of the atomizers and the influences of the configuration parameters on distribution. The results provides important references for understanding the structure of gas/liquid flow fields and for designing and improving such atomizers.

  4. Development of a screening approach for exploring cell factory potential through metabolic flux analysis and physiology

    DEFF Research Database (Denmark)

    Knudsen, Peter Boldsen; Nielsen, Kristian Fog; Thykær, Jette

    2012-01-01

    of the recombinant strains in order to evaluate their potential as fungal cell factories and for guiding further metabolic engineering strategies. To meet the demand for a fast and reliable method for physiological characterisation of fungal strains, a screening approach using a micro titer format was developed...... of the validation, already well described fungal strains were selected and tested using the described method and the developed method was subsequently used to test recombinant fungal strains producing the model polyketide 6-methylsalicylic acid. Diligent application of this strategy significantly reduces the cost...

  5. Next-Generation Angular Distribution Models for Top-of-Atmosphere Radiative Flux Calculation from CERES Instruments: Validation

    Science.gov (United States)

    Su, W.; Corbett, J.; Eitzen, Z.; Liang, L.

    2015-01-01

    Radiative fluxes at the top of the atmosphere (TOA) from the Clouds and the Earth's Radiant Energy System (CERES) instrument are fundamental variables for understanding the Earth's energy balance and how it changes with time. TOA radiative fluxes are derived from the CERES radiance measurements using empirical angular distribution models (ADMs). This paper evaluates the accuracy of CERES TOA fluxes using direct integration and flux consistency tests. Direct integration tests show that the overall bias in regional monthly mean TOA shortwave (SW) flux is less than 0.2Wm(exp -2) and the RMSE is less than 1.1Wm(exp -2). The bias and RMSE are very similar between Terra and Aqua. The bias in regional monthly mean TOA LW fluxes is less than 0.5Wm(exp -2) and the RMSE is less than 0.8Wm(exp -)2 for both Terra and Aqua. The accuracy of the TOA instantaneous flux is assessed by performing tests using fluxes inverted from nadir- and oblique-viewing angles using CERES along-track observations and temporally and spatially matched MODIS observations, and using fluxes inverted from multi-angle MISR observations. The averaged TOA instantaneous SW flux uncertainties from these two tests are about 2.3% (1.9Wm(exp -2) over clear ocean, 1.6% (4.5Wm(exp -2) over clear land, and 2.0% (6.0Wm(exp -) over clear snow/ice; and are about 3.3% (9.0Wm(exp -2), 2.7% (8.4Wm(exp -2), and 3.7% (9.9Wm(exp -2) over ocean, land, and snow/ice under all-sky conditions. The TOA SW flux uncertainties are generally larger for thin broken clouds than for moderate and thick overcast clouds. The TOA instantaneous daytime LW flux uncertainties derived from the CERESMODIS test are 0.5% (1.5Wm(exp -2), 0.8% (2.4Wm(exp -2), and 0.7% (1.3Wm(exp -2) over clear ocean, land, and snow/ice; and are about 1.5% (3.5Wm(exp -2), 1.0% (2.9Wm(exp -2), and 1.1% (2.1Wm(exp -2) over ocean, land, and snow/ice under all-sky conditions. The TOA instantaneous nighttime LW flux uncertainties are about 0.5-1% (<2.0Wm(exp -2) for all

  6. Joint Bayesian Estimation of Quasar Continua and the Lyα Forest Flux Probability Distribution Function

    Science.gov (United States)

    Eilers, Anna-Christina; Hennawi, Joseph F.; Lee, Khee-Gan

    2017-08-01

    We present a new Bayesian algorithm making use of Markov Chain Monte Carlo sampling that allows us to simultaneously estimate the unknown continuum level of each quasar in an ensemble of high-resolution spectra, as well as their common probability distribution function (PDF) for the transmitted Lyα forest flux. This fully automated PDF regulated continuum fitting method models the unknown quasar continuum with a linear principal component analysis (PCA) basis, with the PCA coefficients treated as nuisance parameters. The method allows one to estimate parameters governing the thermal state of the intergalactic medium (IGM), such as the slope of the temperature-density relation γ -1, while marginalizing out continuum uncertainties in a fully Bayesian way. Using realistic mock quasar spectra created from a simplified semi-numerical model of the IGM, we show that this method recovers the underlying quasar continua to a precision of ≃ 7 % and ≃ 10 % at z = 3 and z = 5, respectively. Given the number of principal component spectra, this is comparable to the underlying accuracy of the PCA model itself. Most importantly, we show that we can achieve a nearly unbiased estimate of the slope γ -1 of the IGM temperature-density relation with a precision of +/- 8.6 % at z = 3 and +/- 6.1 % at z = 5, for an ensemble of ten mock high-resolution quasar spectra. Applying this method to real quasar spectra and comparing to a more realistic IGM model from hydrodynamical simulations would enable precise measurements of the thermal and cosmological parameters governing the IGM, albeit with somewhat larger uncertainties, given the increased flexibility of the model.

  7. Effect of Magnetic Flux Density and Applied Current on Temperature, Velocity and Entropy Generation Distributions in MHD Pumps

    Directory of Open Access Journals (Sweden)

    M. Kiyasatfar

    2011-01-01

    Full Text Available In the present study, simulation of steady state, incompressible and fully developed laminar flow has been conducted in a magneto hydrodynamic (MHD pump. The governing equations are solved numerically by finite-difference method. The effect of the magnetic flux density and current on the flow and temperature distributions in a MHD pump is investigated. The obtained results showed that controlling the flow and the temperature is possible through the controlling of the applied current and the magnetic flux. Furthermore, the effects of the magnetic flux density and current on entropy generation in MHD pump are considered. Our presented numerical results are in good agreement with the experimental data showed in literature.

  8. Flow under standing waves Part 1. Shear stress distribution, energy flux and steady streaming

    DEFF Research Database (Denmark)

    Gislason, Kjartan; Fredsøe, Jørgen; Deigaard, Rolf

    2009-01-01

    The conditions for energy flux, momentum flux and the resulting streaming velocity are analysed for standing waves formed in front of a fully reflecting wall. The exchange of energy between the outer wave motion and the near bed oscillatory boundary layer is considered, determining the horizontal...... energy flux inside and outside the boundary layer. The momentum balance, the mean shear stress and the resulting time averaged streaming velocities are determined. For a laminar bed boundary layer the analysis of the wave drift gives results similar to the original work of Longuet-Higgins from 1953...

  9. Determination and analysis of neutron flux distribution on radial Piercing beam port for utilization of Kartini research reactor

    International Nuclear Information System (INIS)

    Widarto

    2002-01-01

    Determination and analysis of neutron flux measurements on radial piercing beam port have been done as completion experimental data document and progressing on utilization of the Kartini research reactor purposes. The analysis and determination of the neutron flux have been carried out by using Au foils detector neutron activation analysis method which put on the radius of cross section (19 cm) and a long of radial piercing beam port (310 cm) Based on the calculation, distribution of the thermal neutron flux is around (8.3 ± 0.9) x 10 5 ncm -2 s -1 to (6.8 ± 0.5) x 10 7 ncm -2 s -1 and fast neutron is (5.0 ± 0.2) x 10 5 ncm -2 s -1 to (1.43 ± 0.6) x 10 7 ncm -2 s -1 . Analyzing by means of curve fitting method could be concluded that the neutron flux distribution on radial piercing beam port has profiled as a polynomial curve. (author)

  10. Simultaneous investigation of cardiac pyruvate dehydrogenase flux, Krebs cycle metabolism and pH, using hyperpolarized [1,2-(13)C2]pyruvate in vivo.

    Science.gov (United States)

    Chen, Albert P; Hurd, Ralph E; Schroeder, Marie A; Lau, Angus Z; Gu, Yi-ping; Lam, Wilfred W; Barry, Jennifer; Tropp, James; Cunningham, Charles H

    2012-02-01

    (13)C MR spectroscopy studies performed on hearts ex vivo and in vivo following perfusion of prepolarized [1-(13)C]pyruvate have shown that changes in pyruvate dehydrogenase (PDH) flux may be monitored non-invasively. However, to allow investigation of Krebs cycle metabolism, the (13)C label must be placed on the C2 position of pyruvate. Thus, the utilization of either C1 or C2 labeled prepolarized pyruvate as a tracer can only afford a partial view of cardiac pyruvate metabolism in health and disease. If the prepolarized pyruvate molecules were labeled at both C1 and C2 positions, then it would be possible to observe the downstream metabolites that were the results of both PDH flux ((13)CO(2) and H(13)CO(3)(-)) and Krebs cycle flux ([5-(13)C]glutamate) with a single dose of the agent. Cardiac pH could also be monitored in the same experiment, but adequate SNR of the (13)CO(2) resonance may be difficult to obtain in vivo. Using an interleaved selective RF pulse acquisition scheme to improve (13)CO(2) detection, the feasibility of using dual-labeled hyperpolarized [1,2-(13)C(2)]pyruvate as a substrate for dynamic cardiac metabolic MRS studies to allow simultaneous investigation of PDH flux, Krebs cycle flux and pH, was demonstrated in vivo. Copyright © 2011 John Wiley & Sons, Ltd.

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Huaiyuan Zhang

    Full Text Available 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.

  13. Novel use of Tat components to increase metabolic flux in light-driven biosynthesis

    DEFF Research Database (Denmark)

    Henriques de Jesus, Maria Perestrello Ramos

    Oxygenic photosynthesis provides plants, algae and cyanobacteria the ability to convert solar energy and CO2 into complex organic molecules. Thus tapping into photosynthesis for synthetic biology efforts has a huge potential for the industrial production of fuels and high value bioactive compounds...... relocating a biosynthetic pathway into the chloroplast, as well as possible solutions. Paper I compares the potential of chloroplasts and cyanobacteria as sustainable biosynthetic compartments and hosts for metabolic engineering. An estimation of the percentage of photosynthetic electrons that can...... be redirected into the biosynthesis of products is given. The availability of photosynthetic reducing power appears to be non-limiting whereas the redirection of the fixed carbon seems to be main challenge for achieving higher product yields. On paper II a novel strategy where the membrane anchors...

  14. Thermal neutron flux distribution in ET-RR-2 reactor thermal column

    Directory of Open Access Journals (Sweden)

    Imam Mahmoud M.

    2002-01-01

    Full Text Available The thermal column in the ET-RR-2 reactor is intended to promote a thermal neutron field of high intensity and purity to be used for following tasks: (a to provide a thermal neutron flux in the neutron transmutation silicon doping, (b to provide a thermal flux in the neutron activation analysis position, and (c to provide a thermal neutron flux of high intensity to the head of one of the beam tubes leading to the room specified for boron thermal neutron capture therapy. It was, therefore, necessary to determine the thermal neutron flux at above mentioned positions. In the present work, the neutron flux in the ET-RR-2 reactor system was calculated by applying the three dimensional diffusion depletion code TRITON. According to these calculations, the reactor system is composed of the core, surrounding external irradiation grid, beryllium block, thermal column and the water reflector in the reactor tank next to the tank wall. As a result of these calculations, the thermal neutron fluxes within the thermal column and at irradiation positions within the thermal column were obtained. Apart from this, the burn up results for the start up core calculated according to the TRITION code were compared with those given by the reactor designer.

  15. Estimating the amount and distribution of radon flux density from the soil surface in China

    International Nuclear Information System (INIS)

    Zhuo Weihai; Guo Qiuju; Chen Bo; Cheng Guan

    2008-01-01

    Based on an idealized model, both the annual and the seasonal radon ( 222 Rn) flux densities from the soil surface at 1099 sites in China were estimated by linking a database of soil 226 Ra content and a global ecosystems database. Digital maps of the 222 Rn flux density in China were constructed in a spatial resolution of 25 km x 25 km by interpolation among the estimated data. An area-weighted annual average 222 Rn flux density from the soil surface across China was estimated to be 29.7 ± 9.4 mBq m -2 s -1 . Both regional and seasonal variations in the 222 Rn flux densities are significant in China. Annual average flux densities in the southeastern and northwestern China are generally higher than those in other regions of China, because of high soil 226 Ra content in the southeastern area and high soil aridity in the northwestern one. The seasonal average flux density is generally higher in summer/spring than winter, since relatively higher soil temperature and lower soil water saturation in summer/spring than other seasons are common in China

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

    Czech Academy of Sciences Publication Activity Database

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

    2005-01-01

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

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

    DEFF Research Database (Denmark)

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

    2008-01-01

    The hydrolytic F-1-part of the F1F0-ATPase was over-expressed in Lactobacillus (L.) plantarum NC8 and L. sakei Lb790x during fermentation of glucose or ribose, in order to study how changes in the intracellular levels of ATP and ADP affect the metabolic fluxes. The uncoupled ATPase activity resul...

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

    Energy Technology Data Exchange (ETDEWEB)

    Wetzel, R.G.

    1992-12-31

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

  19. Survey of the thermal and fast neutron flux distribution in the core of IPR-R1 reactor

    International Nuclear Information System (INIS)

    Guimaraes, R.R.R.

    1985-01-01

    A methodology to obtain the neutron flux distribution inside the core of a reactor is presented, aiming to analyze specifications for increasing reactor power. The activation measurement technique with irradiation of steel eletrodes of 700 mm of lenght, put in acrylic rods was used. In the detection process and in the counting of activation product, a Ge (Li) detector with high resolution and a scanning mechanical system, constructed and projected in CDTN (Nuclear Technology Development Center) were used. (E.G.) [pt

  20. Measurement and analysis of neutron flux distribution of STACY heterogeneous core by position sensitive proportional counter. Contract research

    CERN Document Server

    Murazaki, M; Uno, Y

    2003-01-01

    We have measured neutron flux distribution around the core tank of STACY heterogeneous core by position sensitive proportional counter (PSPC) to develop the method to measure reactivity for subcritical systems. The neutron flux distribution data in the position accuracy of +-13 mm have been obtained in the range of uranium concentration of 50g/L to 210g/L both in critical and in subcritical state. The prompt neutron decay constant, alpha, was evaluated from the measurement data of pulsed neutron source experiments. We also calculated distribution of neutron flux and sup 3 He reaction rates at the location of PSPC by using continuous energy Monte Carlo code MCNP. The measurement data was compared with the calculation results. As results of comparison, calculated values agreed generally with measurement data of PSPC with Cd cover in the region above half of solution height, but the difference between calculated value and measurement data was large in the region below half of solution height. On the other hand, ...

  1. Revised methane emissions factors and spatially distributed annual carbon fluxes for global livestock.

    Science.gov (United States)

    Wolf, Julie; Asrar, Ghassem R; West, Tristram O

    2017-09-29

    Livestock play an important role in carbon cycling through consumption of biomass and emissions of methane. Recent research suggests that existing bottom-up inventories of livestock methane emissions in the US, such as those made using 2006 IPCC Tier 1 livestock emissions factors, are too low. This may be due to outdated information used to develop these emissions factors. In this study, we update information for cattle and swine by region, based on reported recent changes in animal body mass, feed quality and quantity, milk productivity, and management of animals and manure. We then use this updated information to calculate new livestock methane emissions factors for enteric fermentation in cattle, and for manure management in cattle and swine. Using the new emissions factors, we estimate global livestock emissions of 119.1 ± 18.2 Tg methane in 2011; this quantity is 11% greater than that obtained using the IPCC 2006 emissions factors, encompassing an 8.4% increase in enteric fermentation methane, a 36.7% increase in manure management methane, and notable variability among regions and sources. For example, revised manure management methane emissions for 2011 in the US increased by 71.8%. For years through 2013, we present (a) annual livestock methane emissions, (b) complete annual livestock carbon budgets, including carbon dioxide emissions, and (c) spatial distributions of livestock methane and other carbon fluxes, downscaled to 0.05 × 0.05 degree resolution. Our revised bottom-up estimates of global livestock methane emissions are comparable to recently reported top-down global estimates for recent years, and account for a significant part of the increase in annual methane emissions since 2007. Our results suggest that livestock methane emissions, while not the dominant overall source of global methane emissions, may be a major contributor to the observed annual emissions increases over the 2000s to 2010s. Differences at regional and local scales may help

  2. Distribution and metabolism of ascorbic acid in pear fruits ( Pyrus ...

    African Journals Online (AJOL)

    Ascorbate accumulation levels, distribution and key enzyme activities involved in synthesizing via Smirnoff-Wheeler pathway and recycling in different pear fruit tissues during development were studied. Results show that the ascorbate contents increased with the fruit development, and reached the highest titers in 30 days ...

  3. Distribution and metabolism of ascorbic acid in pear fruits (Pyrus ...

    African Journals Online (AJOL)

    ajl user 1

    2013-04-17

    Apr 17, 2013 ... (100 rpm) at 25°C, incubated samples were washed with the sterile water and surface-dried on filter paper, followed by immersion in liquid nitrogen. Total AsA concentration was determined by a spectrophotometer as described above. RESULTS. Distribution of AsA during fruit development and ripening.

  4. Determination of neutron flux with an arbitrary energy distribution by measurement of irradiated foils activity

    International Nuclear Information System (INIS)

    Ljubenov, V.; Milosevic, M.

    2003-01-01

    A procedure for the neutron flux determination in a neutron field with an arbitrary energy spectrum, based on the using of standard methods for the measurement of irradiated foils activity and on the application of the SCALE-4.4a code system for averaged cross section calculation is described in this paper. Proposed procedure allows to include the energy spectrum of neutron flux reestablished in the location of irradiated foils and the resonance self-shielding effects in the foils also. Example application of this procedure is given for the neutron flux determination inside the neutron filter with boron placed in the centre of heavy water critical assembly RB at the Vinca Institute (author)

  5. Systematic assembly homogenization and local flux reconstruction for nodal method calculations of fast reactor power distributions

    International Nuclear Information System (INIS)

    Dorning, J.J.

    1991-01-01

    A simultaneous pin lattice cell and fuel bundle homogenization theory has been developed for use with nodal diffusion calculations of practical reactors. The theoretical development of the homogenization theory, which is based on multiple-scales asymptotic expansion methods carried out through fourth order in a small parameter, starts from the transport equation and systematically yields: a cell-homogenized bundled diffusion equation with self-consistent expressions for the cell-homogenized cross sections and diffusion tensor elements; and a bundle-homogenized global reactor diffusion equation with self-consistent expressions for the bundle-homogenized cross sections and diffusion tensor elements. The continuity of the angular flux at cell and bundle interfaces also systematically yields jump conditions for the scaler flux or so-called flux discontinuity factors on the cell and bundle interfaces in terms of the two adjacent cell or bundle eigenfunctions. The expressions required for the reconstruction of the angular flux or the 'de-homogenization' theory were obtained as an integral part of the development; hence the leading order transport theory angular flux is easily reconstructed throughout the reactor including the regions in the interior of the fuel bundles or computational nodes and in the interiors of the pin lattice cells. The theoretical development shows that the exact transport theory angular flux is obtained to first order from the whole-reactor nodal diffusion calculations, done using the homogenized nuclear data and discontinuity factors, is a product of three computed quantities: a ''cell shape function''; a ''bundle shape function''; and a ''global shape function''. 10 refs

  6. Determination of fast neutron flux distribution in irradiation sites of the Malaysian Nuclear Agency research reactor

    International Nuclear Information System (INIS)

    Yavar, A.R.; Sarmani, S.B.; Wood, A.K.; Fadzil, S.M.; Radir, M.H.; Khoo, K.S.

    2011-01-01

    Determination of thermal to fast neutron flux ratio (f fast ) and fast neutron flux (φ fast ) is required for fast neutron reactions, fast neutron activation analysis, and for correcting interference reactions. The f fast and subsequently φ fast were determined using the absolute method. The f fast ranged from 48 to 155, and the φ fast was found in the range 1.03x10 10 -4.89x10 10 n cm -2 s -1 . These values indicate an acceptable conformity and applicable for installation of the fast neutron facility at the MNA research reactor.

  7. Modelisation and distribution of neutron flux in radium-beryllium source (226Ra-Be)

    Science.gov (United States)

    Didi, Abdessamad; Dadouch, Ahmed; Jai, Otman

    2017-09-01

    Using the Monte Carlo N-Particle code (MCNP-6), to analyze the thermal, epithermal and fast neutron fluxes, of 3 millicuries of radium-beryllium, for determine the qualitative and quantitative of many materials, using method of neutron activation analysis. Radium-beryllium source of neutron is established to practical work and research in nuclear field. The main objective of this work was to enable us harness the profile flux of radium-beryllium irradiation, this theoretical study permits to discuss the design of the optimal irradiation and performance for increased the facility research and education of nuclear physics.

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

    Science.gov (United States)

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

    2012-12-01

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

  9. Moderate DNA damage promotes metabolic flux into PPP via PKM2 Y-105 phosphorylation: a feature that favours cancer cells.

    Science.gov (United States)

    Kumar, Bhupender; Bamezai, Rameshwar N K

    2015-08-01

    Pyruvate kinase M2, an important metabolic enzyme, promotes aerobic glycolysis (Warburg effect) to facilitate cancer cell proliferation. Unravelling the status of this important glycolytic pathway enzyme under sub-lethal doses of etoposide, a commonly used anti-proliferative genotoxic drug to induce mild/moderate DNA damage in HeLa cells as a model system and discern its effect on: PKM2 expression, phosphorylation, dimer: tetramer ratio, activity and associated effects, was pertinent. Protein expression and phosphorylation of PKM2 from HeLa cells was estimated using Western blotting. Same protein lysate was also used to estimate total pyruvate kinase activity and the total dimer: tetramer content evaluated using glycerol gradient ultra-centrifugation. Intracellular PEP was estimated manually using standard curve; while NADPH was assessed by NADPH estimation kit. Unpaired t test and two-way-ANOVA was used for statistical analysis. A relative decrease in PKM2 expression and a subsequent dose and time dependent increase in Y105-phosphorylation were observed. A concomitant increase in PKM2 dimer content and Y105-phosphorylation responsible for reduced PKM2 activity promoted PEP accumulation and NADPH production, representing increased metabolic flux into PPP, a feature that favours cancer cells. It was apparent that the sub-lethal doses of etoposide induced inadequate damage to DNA in cancer cells in culture promoted pro-survival conditions due to Y105-phosphorylation of PKM2, its stable dimerization and inactivation, a unique association not known earlier, indicating what might happen in tumour revivals or recurrences.

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

    NARCIS (Netherlands)

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

    2001-01-01

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

  11. Determination of metabolic fluxes during glucose catabolism in Propionibacterium freudenreichii subsp. shermanii.

    Science.gov (United States)

    Meurice, G; Bondon, A; Deborde, C; Boyaval, P

    2001-01-01

    In vivo 13C Nuclear Magnetic Resonance (NMR) spectroscopy was used to investigate the pathways of glucose metabolism, non-invasively, in living cell suspensions of Propionibacterium freudenreichii subsp. shermanii. This species is the main ripening flora of the Swiss-type cheeses and is widely used as propionic acid and vitamin B12 industrial producer. The flow of labelled [1-13C]glucose was monitored in living cell suspensions and enrichment was detected in main products like [1-13C]glycogen, [6-13C]lycogen, [1-13C]trehalose, [6-13C]trehalose, [1-13C]propionate, [2-13C]propionate, [3-13C]propionate, [1-13C]acetate, [2-13C]acetate, [1-13C]succinate, [2-13C]succinate and [1-13C]CO2. alpha and beta glucose consumption could be examined separately and were catabolized at the same rate. Three intermediates were also found out, namely [1-13C]glucose-6-phosphate, [6-13C]glucose-6-phosphate and [1-13C]glucose-1-phosphate. From the formation of intermediates such as [6-3C]glucose-6-phosphate and products like [6-13C]glycogen from [1-13C]glucose we concluded the bidirectionality of reactions in the first part of glycolysis and the isomerization at the triose-phosphate level. Comparison of spectra obtained after addition of [1-13C]glucose or [U-12C]glucose revealed production of [1-13C]CO2 which means that pentose phosphates pathway is active under our experimental conditions. From the isotopic pattern of trehalose, it could be postulated that trehalose biosynthesis occurred either by direct condensation of two glucose molecules or by gluconeogenesis. A chemically defined medium was elaborated for the study and trehalose was the main osmolyte found in the intracellular fraction of P. shermanii grown in this medium.

  12. Viscous flux flow velocity and stress distribution in the Kim model of a long rectangular slab superconductor

    Science.gov (United States)

    Yang, Yong; Chai, Xueguang

    2018-05-01

    When a bulk superconductor endures the magnetization process, enormous mechanical stresses are imposed on the bulk, which often leads to cracking. In the present work, we aim to resolve the viscous flux flow velocity υ 0/w, i.e. υ 0 (because w is a constant) and the stress distribution in a long rectangular slab superconductor for the decreasing external magnetic field (B a ) after zero-field cooling (ZFC) and field cooling (FC) using the Kim model and viscous flux flow equation simultaneously. The viscous flux flow velocity υ 0/w and the magnetic field B* at which the body forces point away in all of the slab volumes during B a reduction, are determined by both B a and the decreasing rate (db a /dt) of the external magnetic field normalized by the full penetration field B p . In previous studies, υ 0/w obtained by the Bean model with viscous flux flow is only determined by db a /dt, and the field B* that is derived only from the Kim model is a positive constant when the maximum external magnetic field is chosen. This means that the findings in this paper have more physical contents than the previous results. The field B* stress changing with decreasing field B a after ZFC if B* ≤ 0. The effect of db a /dt on the stress is significant in the cases of both ZFC and FC.

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

    International Nuclear Information System (INIS)

    Cooper, P.D.

    1981-01-01

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

  14. Transport calculation of neutron flux distribution in reflector of PW reactor

    International Nuclear Information System (INIS)

    Remec, I.

    1982-01-01

    Two-dimensional transport calculation of the neutron flux and spectrum in the equatorial plain of PW reactor, using computer program DOT 3, is presented. Results show significant differences between neutron fields in which test samples and reactor vessel are exposed. (author)

  15. Spatial distribution of regional whole tree carbon stocks and fluxes of forests in Europe

    NARCIS (Netherlands)

    Schelhaas, M.J.; Nabuurs, G.J.

    2001-01-01

    This report presents carbon stocks and fluxes of the whole-tree biomass of European forests and other wooded land, distinguished into coniferous, deciduous and mixed forests. The results are presented at the European, the national and (where possible)the regional level. Results concerning carbon

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

    DEFF Research Database (Denmark)

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

    1999-01-01

    positive linear correlation of percentage (14C) wax alcohols with log [22Na efflux]. Based on the observed parallel between Naf flux and gill lipid metabolism, it is suggested that the eel reacts at first to a loss of Na+ by synthesizing wax alcohols that can tighten the gill membrane. (C) 1999 Elsevier......+ uptake rate was 12 mu mol kg(-1) h(-1), i.e., the general picture in DW was a net Na+ loss. In another similar experiment, groups of three FW-adapted eels were incubated in vivo for up to 24 h with (C-14) acetate added as lipid precursor to the ambient water. Incubation in FW showed about 20......% of the total C-14-activity incorporated into gill lipids as (C-14) wax alcohols (WA; octadecanol and eicosanol). This percentage went up to 50% shortly after transfer to DW and came down again to about 20% after 2 weeks in DW. Single eels labelled with Na-22 in the plasma showed a statistically significant...

  17. TGF location, flux and fluence distribution with off-axis angle derived from FERMI data and WWLLN locations

    Science.gov (United States)

    Connell, Paul

    2017-04-01

    The FERMI science support centre has published an online catalogue of 3356 TGFs, along with a subset of 1049 TGFs with a WWLLN temporal association. We have used these tables to create scatter plots and the angular distribution of TGF angles in the FERMI nadir FOV - originally to see what the ASIM/MXGS gamma-ray imager could expect to observe in its FOV. We have also used photon counts from the two FERMI BGO detectors to derive an estimate of TGF flux distribution and fluence with nadir angle. One interesting result is the observation of TGFs out to 50 degrees off-axis, but even more interesting is an angular flux distribution which seems to indicate that a TGF has either a very wide beam angle or that TGFs are narrow beams whose axis has a very wide angular distribution from the earth radial. Whether this indicates TGFs originate by acceleration in macro scale electric fields in storm clouds, or in the micro scale electric fields in lightning leaders, is not clear but the results do call for a more detailed analysis taking FERMI orientation into account. We have not seen any publication of this TGF off-axis angle analysis and show our results for the interest of the TGF research community.

  18. Metabolism of cerium 144 in rat. Distribution - elimination - dosimetry

    International Nuclear Information System (INIS)

    Remy, Jacques

    1959-01-01

    This academic report concerns a study during which cerium 144 has been intravenously injected to three-month old rats under the form of cerium chloride in aqueous solution with pH of 9,5. Rats have then been sacrificed at different times after the injection, and organ or tissue samplings have been performed to study the isotope distribution in their bodies. This allowed the calculation of internal irradiation doses locally received by the animal, and also to identify critical organs with respect to cerium 144. Thus, until the twentieth day after injection, liver is the critical organ. After, it is the skeleton, for the rest of the animal's life. The bone internal irradiation is the highest danger for an internal cerium 144 contamination, due to threats on body hematopoietic functions [fr

  19. Morphology and magnetic flux distribution in superparamagnetic, single-crystalline Fe{sub 3}O{sub 4} nanoparticle rings

    Energy Technology Data Exchange (ETDEWEB)

    Takeno, Yumu [Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577 (Japan); Murakami, Yasukazu, E-mail: murakami@tagen.tohoku.ac.jp, E-mail: kannanmk@uw.edu; Shindo, Daisuke [Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577 (Japan); Center for Emergent Matter Science, RIKEN, Wako 351-0198 (Japan); Sato, Takeshi [Hitachi High-Technologies Corporation, 1040 Ichige, Hitachinaka-shi, Ibaraki 312-0033 (Japan); Tanigaki, Toshiaki [Center for Emergent Matter Science, RIKEN, Wako 351-0198 (Japan); Central Research Laboratory, Hitachi, Ltd., Hatoyama 350-0395 (Japan); Park, Hyun Soon [Center for Emergent Matter Science, RIKEN, Wako 351-0198 (Japan); Department of Materials Science and Engineering, Dong-A University, Busan 604-714, Republic of South Korea (Korea, Republic of); Ferguson, R. Matthew [LodeSpin Labs, P.O. Box 95632, Seattle, Washington 91845 (United States); Krishnan, Kannan M., E-mail: murakami@tagen.tohoku.ac.jp, E-mail: kannanmk@uw.edu [Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195-2120 (United States)

    2014-11-03

    This study reports on the correlation between crystal orientation and magnetic flux distribution of Fe{sub 3}O{sub 4} nanoparticles in the form of self-assembled rings. High-resolution transmission electron microscopy demonstrated that the nanoparticles were single-crystalline, highly monodispersed, (25 nm average diameter), and showed no appreciable lattice imperfections such as twins or stacking faults. Electron holography studies of these superparamagnetic nanoparticle rings indicated significant fluctuations in the magnetic flux lines, consistent with variations in the magnetocrystalline anisotropy of the nanoparticles. The observations provide useful information for a deeper understanding of the micromagnetics of ultrasmall nanoparticles, where the magnetic dipolar interaction competes with the magnetic anisotropy.

  20. Metabolic profiling and flux analysis of MEL-2 human embryonic stem cells during exponential growth at physiological and atmospheric oxygen concentrations.

    Directory of Open Access Journals (Sweden)

    Jennifer Turner

    Full Text Available As human embryonic stem cells (hESCs steadily progress towards regenerative medicine applications there is an increasing emphasis on the development of bioreactor platforms that enable expansion of these cells to clinically relevant numbers. Surprisingly little is known about the metabolic requirements of hESCs, precluding the rational design and optimisation of such platforms. In this study, we undertook an in-depth characterisation of MEL-2 hESC metabolic behaviour during the exponential growth phase, combining metabolic profiling and flux analysis tools at physiological (hypoxic and atmospheric (normoxic oxygen concentrations. To overcome variability in growth profiles and the problem of closing mass balances in a complex environment, we developed protocols to accurately measure uptake and production rates of metabolites, cell density, growth rate and biomass composition, and designed a metabolic flux analysis model for estimating internal rates. hESCs are commonly considered to be highly glycolytic with inactive or immature mitochondria, however, whilst the results of this study confirmed that glycolysis is indeed highly active, we show that at least in MEL-2 hESC, it is supported by the use of oxidative phosphorylation within the mitochondria utilising carbon sources, such as glutamine to maximise ATP production. Under both conditions, glycolysis was disconnected from the mitochondria with all of the glucose being converted to lactate. No difference in the growth rates of cells cultured under physiological or atmospheric oxygen concentrations was observed nor did this cause differences in fluxes through the majority of the internal metabolic pathways associated with biogenesis. These results suggest that hESCs display the conventional Warburg effect, with high aerobic activity despite high lactate production, challenging the idea of an anaerobic metabolism with low mitochondrial activity. The results of this study provide new insight that

  1. A DETERMINATION OF THE FLUX DENSITY IN CORE OF DISTRIBUTION TRANSFORMERS, WHAT BUILT WITH THE COMMON USING OF GRAIN AND NON GRAIN ORIENTED MAGNETIC STEELS

    Directory of Open Access Journals (Sweden)

    I.V. Pentegov

    2015-12-01

    Full Text Available Purpose. The development of calculation method to determinate the flux densities in different parts of the magnetic cores of distribution transformers, what built from different types magnetic steel (mixed core. Methodology. The method is based on the scientific positions of Theoretical Electrical Engineering – the theory of the electromagnetic field in nonlinear mediums to determine the distribution of magnetic flux in mixed core of transformer, what are using different types of steel what have the different magnetic properties. Results. The developed method gives possible to make calculation of the flux density and influence of skin effect in different parts of the magnetic cores of distribution transformer, where are used mix of grain oriented (GO and non grain oriented (NGO steels. Was determinate the general basic conditions for the calculation of flux density in the laminations from grain and non grain oriented steels of the magnetic core: the strength of magnetic field for the laminations of particular part of mixed core is the same; the sum of the magnetic fluxes in GO and NGO steels in particular part of mixed core is equal with the designed magnetic flux in this part of mixed core. Discover, the magnetic flux in mixed core of the transformer has specific distribution between magnetic steels. The flux density is higher in laminations from GO steel and smaller in laminations from the NGO steel. That is happened because for magnetic flux is easier pass through laminations from GO steel, what has better magnetic conductance than laminations from NGO steel. Originality. The common using of different types of magnetic steels in cores for distribution transformers gives possibility to make design of transformer with low level of no load losses, high efficiency and with optimal cost. Practical value. The determination of the flux density in different parts of magnetic core with GO and NGO steels gives possibility make accurate calculation of

  2. Measurement of angular distribution of neutron flux for the 6MeV race-track microtron based pulsed neutron source.

    Science.gov (United States)

    Patil, B J; Chavan, S T; Pethe, S N; Krishnan, R; Dhole, S D

    2010-09-01

    The 6MeV race track microtron based pulsed neutron source has been designed specifically for the elemental analysis of short lived activation products, where the low neutron flux requirement is desirable. Electrons impinges on a e-gamma target to generate bremsstrahlung radiations, which further produces neutrons by photonuclear reaction in gamma-n target. The optimisation of these targets along with their spectra were estimated using FLUKA code. The measurement of neutron flux was carried out by activation of vanadium at different scattering angles. Angular distribution of neutron flux indicates that the flux decreases with increase in the angle and are in good agreement with the FLUKA simulation.

  3. Analytical Calculation of the Magnetic Field distribution in a Flux-Modulated Permanent-Magnet Brushless Motor

    DEFF Research Database (Denmark)

    Zhang, Xiaoxu; Liu, Xiao; Chen, Zhe

    2015-01-01

    This paper presents a rapid approach to compute the magnetic field distribution in a flux-modulated permanent-magnet brushless motor. Partial differential equations are used to describe the magnet field behavior in terms of magnetic vector potentials. The whole computational domain is divided...... into several regions, i.e., magnet, air-gaps, slot-openings, and slots. The numerical solution could be obtained by applying the boundary constraints on the interfaces between these regions. The accuracy of the proposed analytical model is verified by comparing the no-load magnetic field and armature reaction...... magnetic field with those calculated by finite element method....

  4. A one-dimensional, one-group absorption-production nodal method for neutron flux and power distributions calculations

    International Nuclear Information System (INIS)

    Ferreira, C.R.

    1984-01-01

    It is presented the absorption-production nodal method for steady and dynamical calculations in one-dimension and one group energy. It was elaborated the NOD1D computer code (in FORTRAN-IV language). Calculations of neutron flux and power distributions, burnup, effective multiplication factors and critical boron concentration were made with the NOD1D code and compared with results obtained through the CITATION code, which uses the finite difference method. The nuclear constants were produced by the LEOPARD code. (M.C.K.) [pt

  5. Effects of experimental nitrogen fertilization on planktonic metabolism and CO2 flux in a hypereutrophic hardwater lake.

    Directory of Open Access Journals (Sweden)

    Matthew J Bogard

    Full Text Available Hardwater lakes are common in human-dominated regions of the world and often experience pollution due to agricultural and urban effluent inputs of inorganic and organic nitrogen (N. Although these lakes are landscape hotspots for CO2 exchange and food web carbon (C cycling, the effect of N enrichment on hardwater lake food web functioning and C cycling patterns remains unclear. Specifically, it is unknown if different eutrophication scenarios (e.g., modest non point vs. extreme point sources yield consistent effects on auto- and heterotrophic C cycling, or how biotic responses interact with the inorganic C system to shape responses of air-water CO2 exchange. To address this uncertainty, we induced large metabolic gradients in the plankton community of a hypereutrophic hardwater Canadian prairie lake by adding N as urea (the most widely applied agricultural fertilizer at loading rates of 0, 1, 3, 8 or 18 mg N L-1 week-1 to 3240-L, in-situ mesocosms. Over three separate 21-day experiments, all treatments of N dramatically increased phytoplankton biomass and gross primary production (GPP two- to six-fold, but the effects of N on autotrophs plateaued at ~3 mg N L-1. Conversely, heterotrophic metabolism increased linearly with N fertilization over the full treatment range. In nearly all cases, N enhanced net planktonic uptake of dissolved inorganic carbon (DIC, and increased the rate of CO2 influx, while planktonic heterotrophy and CO2 production only occurred in the highest N treatments late in each experiment, and even in these cases, enclosures continued to in-gas CO2. Chemical effects on CO2 through calcite precipitation were also observed, but similarly did not change the direction of net CO2 flux. Taken together, these results demonstrate that atmospheric exchange of CO2 in eutrophic hardwater lakes remains sensitive to increasing N loading and eutrophication, and that even modest levels of N pollution are capable of enhancing autotrophy and CO

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

    Directory of Open Access Journals (Sweden)

    Dany J V Beste

    2011-07-01

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

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

    OpenAIRE

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

    1996-01-01

    The Flux Control Coefficients of mitochondrial outer membrane carnitine palmitoyltransferase (CPT I) with respect to the overall rates of beta-oxidation, ketogenesis and tricarboxylic acid cycle activity were measured in hepatocytes isolated from rats in different metabolic states (fed, 24 h-starved, starved-refed and starved/insulin-treated). These conditions were chosen because there is controversy as to whether, when significant control ceases to be exerted by CPT I over the rate of fatty ...

  8. Prediction of Flow and Temperature Distributions in a High Flux Research Reactor Using the Porous Media Approach

    Directory of Open Access Journals (Sweden)

    Shanfang Huang

    2017-01-01

    Full Text Available High thermal neutron fluxes are needed in some research reactors and for irradiation tests of materials. A High Flux Research Reactor (HFRR with an inverse flux trap-converter target structure is being developed by the Reactor Engineering Analysis Lab (REAL at Tsinghua University. This paper studies the safety of the HFRR core by full core flow and temperature calculations using the porous media approach. The thermal nonequilibrium model is used in the porous media energy equation to calculate coolant and fuel assembly temperatures separately. The calculation results show that the coolant temperature keeps increasing along the flow direction, while the fuel temperature increases first and decreases afterwards. As long as the inlet coolant mass flow rate is greater than 450 kg/s, the peak cladding temperatures in the fuel assemblies are lower than the local saturation temperatures and no boiling exists. The flow distribution in the core is homogeneous with a small flow rate variation less than 5% for different assemblies. A large recirculation zone is observed in the outlet region. Moreover, the porous media model is compared with the exact model and found to be much more efficient than a detailed simulation of all the core components.

  9. Effects of ocean acidification and hydrodynamic conditions on carbon metabolism and dissolved organic carbon (DOC) fluxes in seagrass populations.

    Science.gov (United States)

    Egea, Luis G; Jiménez-Ramos, Rocío; Hernández, Ignacio; Bouma, Tjeerd J; Brun, Fernando G

    2018-01-01

    Global change has been acknowledged as one of the main threats to the biosphere and its provision of ecosystem services, especially in marine ecosystems. Seagrasses play a critical ecological role in coastal ecosystems, but their responses to ocean acidification (OA) and climate change are not well understood. There have been previous studies focused on the effects of OA, but the outcome of interactions with co-factors predicted to alter during climate change still needs to be addressed. For example, the impact of higher CO2 and different hydrodynamic regimes on seagrass performance remains unknown. We studied the effects of OA under different current velocities on productivity of the seagrass Zostera noltei, using changes in dissolved oxygen as a proxy for the seagrass carbon metabolism, and release of dissolved organic carbon (DOC) in a four-week experiment using an open-water outdoor mesocosm. Under current pH conditions, increasing current velocity had a positive effect on productivity, but this depended on shoot density. However, this positive effect of current velocity disappeared under OA conditions. OA conditions led to a significant increase in gross production rate and respiration, suggesting that Z. noltei is carbon-limited under the current inorganic carbon concentration of seawater. In addition, an increase in non-structural carbohydrates was found, which may lead to better growing conditions and higher resilience in seagrasses subjected to environmental stress. Regarding DOC flux, a direct and positive relationship was found between current velocity and DOC release, both under current pH and OA conditions. We conclude that OA and high current velocity may lead to favourable growth scenarios for Z. noltei populations, increasing their productivity, non-structural carbohydrate concentrations and DOC release. Our results add new dimensions to predictions on how seagrass ecosystems will respond to climate change, with important implications for the

  10. Effects of ocean acidification and hydrodynamic conditions on carbon metabolism and dissolved organic carbon (DOC fluxes in seagrass populations.

    Directory of Open Access Journals (Sweden)

    Luis G Egea

    Full Text Available Global change has been acknowledged as one of the main threats to the biosphere and its provision of ecosystem services, especially in marine ecosystems. Seagrasses play a critical ecological role in coastal ecosystems, but their responses to ocean acidification (OA and climate change are not well understood. There have been previous studies focused on the effects of OA, but the outcome of interactions with co-factors predicted to alter during climate change still needs to be addressed. For example, the impact of higher CO2 and different hydrodynamic regimes on seagrass performance remains unknown. We studied the effects of OA under different current velocities on productivity of the seagrass Zostera noltei, using changes in dissolved oxygen as a proxy for the seagrass carbon metabolism, and release of dissolved organic carbon (DOC in a four-week experiment using an open-water outdoor mesocosm. Under current pH conditions, increasing current velocity had a positive effect on productivity, but this depended on shoot density. However, this positive effect of current velocity disappeared under OA conditions. OA conditions led to a significant increase in gross production rate and respiration, suggesting that Z. noltei is carbon-limited under the current inorganic carbon concentration of seawater. In addition, an increase in non-structural carbohydrates was found, which may lead to better growing conditions and higher resilience in seagrasses subjected to environmental stress. Regarding DOC flux, a direct and positive relationship was found between current velocity and DOC release, both under current pH and OA conditions. We conclude that OA and high current velocity may lead to favourable growth scenarios for Z. noltei populations, increasing their productivity, non-structural carbohydrate concentrations and DOC release. Our results add new dimensions to predictions on how seagrass ecosystems will respond to climate change, with important

  11. Axial and radial distribution of neutron fluxes in the irradiation channels of the Ghana Research Reactor-1 using foil activation analysis and Monte Carlo

    International Nuclear Information System (INIS)

    Abrefah, G.R.

    2009-02-01

    The Monte-Carlo method and experimental methods were used to determine the neutron fluxes in the irradiation channels of the Ghana Research Reactor -1. The MCNP5 code was used for this purpose to simulate the radial and axial distribution of the neutron fluxes within all the ten irradiation channels. The results obtained were compared with the experimental results. After the MCNP simulation and experimental procedure, it was observed that axially, the fluxes rise to a peak before falling and then finally leveling out. Axially and radially, it was also observed that the fluxes in the centre of the channels were lower than on the sides. Radially, the fluxes dip in the centre while it increases steadily towards the sides of the channels. The results have shown that there are flux variations within the irradiation channels both axially and radially. (au)

  12. A dynamic metabolic flux analysis of ABE (acetone-butanol-ethanol) fermentation by Clostridium acetobutylicum ATCC 824, with riboflavin as a by-product.

    Science.gov (United States)

    Zhao, Xinhe; Kasbi, Mayssa; Chen, Jingkui; Peres, Sabine; Jolicoeur, Mario

    2017-12-01

    The present study reveals that supplementing sodium acetate (NaAc) strongly stimulates riboflavin production in acetone-butanol-ethanol (ABE) fermentation by Clostridium acetobutylicum ATCC 824 with xylose as carbon source. Riboflavin production increased from undetectable concentrations to ∼0.2 g L -1 (0.53 mM) when supplementing 60 mM NaAc. Of interest, solvents production and biomass yield were also promoted with fivefold acetone, 2.6-fold butanol, and 2.4-fold biomass adding NaAc. A kinetic metabolic model, developed to simulate ABE biosystem, with riboflavin production, revealed from a dynamic metabolic flux analysis (dMFA) simultaneous increase of riboflavin (ribA) and GTP (precursor of riboflavin) (PurM) synthesis flux rates under NaAc supplementation. The model includes 23 fluxes, 24 metabolites, and 72 kinetic parameters. It also suggested that NaAc condition has first stimulated the accumulation of intracellular metabolite intermediates during the acidogenic phase, which have then fed the solventogenic phase leading to increased ABE production. In addition, NaAc resulted in higher intracellular levels of NADH during the whole culture. Moreover, lower GTP-to-adenosine phosphates (ATP, ADP, AMP) ratio under NaAc supplemented condition suggests that GTP may have a minor role in the cell energetic metabolism compared to its contribution to riboflavin synthesis. © 2017 Wiley Periodicals, Inc.

  13. Zenith distribution and flux of atmospheric muons measured with the 5-line ANTARES detector

    NARCIS (Netherlands)

    Aguilar, J.A.; et al., [Unknown; Kooijman, P.; Lim, G.; Palioselitis, D.; Presani, E.; Wijnker, G.; de Wolf, E.

    2010-01-01

    The ANTARES high-energy neutrino telescope is a three-dimensional array of about 900 photomultipliers distributed over 12 mooring lines installed in the Mediterranean Sea. Between February and November 2007 it acquired data in a 5-line configuration. The zenith angular distribution of the

  14. Vertical Distribution and Flux of Nutrients in the Sediments of the Mangrove Reclamation Region of Muara Angke Kapuk, Jakarta

    Directory of Open Access Journals (Sweden)

    Anna Ida Sunaryo Purwiyanto

    2012-12-01

    Full Text Available The reclaimed mangrove estuary in Muara Angke Kapuk is a reclaimed area that has not evaded the impacted of pollution and waste in the areas surrounding Cengkareng, Jakarta. This is apparent from the fact that almost all sediments under the mangrove trees are buried under heaps of plastic trash. However, the reclaimed region still has variety of organism, which indicating that the region still has an internal carrying capacity, especially nutrients from sediment. The purpose of this research was to examine the condition of sediment nutrients in this mangrove reclamation region. The research was conducted by taking water samples using a modification of the stratified cup at a sediment depth of 0-15 cm with depth intervals of 2.5 cm, and taking sediment samples using the sediment ring. Pore water samples were measured for dissolved oxygen (DO and concentrations of ammonia, nitrite, nitrate, and phosphate. Sediment samples were used to obtain porosity values. The data obtained is used to make vertical concentration profiles and analysis of vertical nutrient flux. Vertical nutrient flux analysis was performed with the aid of QUAL2K software version 2.11. The results showed different vertical distributions and flux of nutrients, where influx for ammonia and phosphate and an increase in line with increasing sediment depth, while nitrate efflux and a decreased concentration. The flux calculation of nitrite as transitory nutrient was not done, but the concentration decreased after a depth of 2.5 cm. This indicates that the high contamination on the surface does not prevent the natural chemical processes so the reclaimed region can still provide nutritional support for its organism.

  15. Estimation of In-canopy Flux Distributions of Reactive Nitrogen and Sulfur within a Mixed Hardwood Forest in Southern Appalachia

    Science.gov (United States)

    Wu, Z.; Walker, J. T.; Chen, X.; Oishi, A. C.; Duman, T.

    2017-12-01

    Estimating the source/sink distribution and vertical fluxes of air pollutants within and above forested canopies is critical for understanding biological, physical, and chemical processes influencing the soil-vegetation-atmosphere exchange. The vertical source-sink profiles of reactive nitrogen and sulfur were examined using multiple inverse modeling methods in a mixed hardwood forest in the southern Appalachian Mountains where the ecosystem is highly sensitive to loads of pollutant from atmospheric depositions. Measurements of the vertical concentration profiles of ammonia (NH3), nitric acid (HNO3), sulfur dioxide (SO2), and ammonium (NH4+), nitrate (NO3-), and sulfate (SO42-) in PM2.5 were measured during five study periods between May 2015 and August 2016. The mean concentration of NH3 decreased with height in the upper canopy and increased below the understory toward the forest floor, indicating that the canopy was a sink for NH3 but the forest floor was a source. All other species exhibited patterns of monotonically decreasing concentration from above the canopy to the forest floor. Using the measured concentration profiles, we simulated the within-canopy flow fields and estimated the vertical source-sink flux profiles using three inverse approaches: a Eulerian high-order closure model (EUL), a Lagrangian localized near-field (LNF) model, and a new full Lagrangian stochastic model (LSM). The models were evaluated using the within- and above-canopy eddy covariance flux measurements of heat, CO2 and H2O. Differences between models were analyzed and the flux profiles were used to investigate the origin and fate of reactive nitrogen and sulfur compounds within the canopy. The knowledge gained in this study will benefit the development of soil-vegetation-atmosphere models capable of partitioning canopy-scale deposition of nitrogen and sulfur to specific ecosystem compartments.

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

    Science.gov (United States)

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

    2018-01-01

    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 13C-metabolic flux analysis (13C-MFA) with [1,6-13C]glucose, [5-13C]xylose, and [1,6-13C]glucose + [5-13C]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 0.46 h−1, respectively. In medium containing glucose and xylose the strain efficiently co-utilized the two sugars. 13C-MFA results provided insights into the metabolism of T. thermophilus LC113 that allows efficient co-utilization of glucose and xylose. Specifically, 13C-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 5× multiplication of a region on the pVV8 plasmid that contains xylose isomerase and xylulokinase genes, the first two enzymes of xylose catabolism. Taken together, 13C-MFA and genome sequence analysis provided complementary insights into the physiology of the evolved strain. PMID:27164561

  17. Assessing HYDRUS-2D model to estimate soil water contents and olive tree transpiration fluxes under different water distribution systems

    Science.gov (United States)

    Autovino, Dario; Negm, Amro; Rallo, Giovanni; Provenzano, Giuseppe

    2016-04-01

    In Mediterranean countries characterized by limited water resources for agricultural and societal sectors, irrigation management plays a major role to improve water use efficiency at farm scale, mainly where irrigation systems are correctly designed to guarantee a suitable application efficiency and the uniform water distribution throughout the field. In the last two decades, physically-based agro-hydrological models have been developed to simulate mass and energy exchange processes in the soil-plant-atmosphere (SPA) system. Mechanistic models like HYDRUS 2D/3D (Šimunek et al., 2011) have been proposed to simulate all the components of water balance, including actual crop transpiration fluxes estimated according to a soil potential-dependent sink term. Even though the suitability of these models to simulate the temporal dynamics of soil and crop water status has been reported in the literature for different horticultural crops, a few researches have been considering arboreal crops where the higher gradients of root water uptake are the combination between the localized irrigation supply and the three dimensional root system distribution. The main objective of the paper was to assess the performance of HYDRUS-2D model to evaluate soil water contents and transpiration fluxes of an olive orchard irrigated with two different water distribution systems. Experiments were carried out in Castelvetrano (Sicily) during irrigation seasons 2011 and 2012, in a commercial farm specialized in the production of table olives (Olea europaea L., var. Nocellara del Belice), representing the typical variety of the surrounding area. During the first season, irrigation water was provided by a single lateral placed along the plant row with four emitters per plant (ordinary irrigation), whereas during the second season a grid of emitters laid on the soil was installed in order to irrigate the whole soil surface around the selected trees. The model performance was assessed based on the

  18. Enhanced H2 Production and Redirected Metabolic Flux via Overexpression of fhlA and pncB in Klebsiella HQ-3 Strain.

    Science.gov (United States)

    Jawed, Muhammad; Pi, Jian; Xu, Li; Zhang, Houjin; Hakeem, Abdul; Yan, Yunjun

    2016-03-01

    Genetic modifications are considered as one of the most important technologies for improving fermentative hydrogen yield. Herein, we overexpress fhlA and pncB genes from Klebsiella HQ-3 independently to enhance hydrogen molar yield. HQ-3-fhlA/pncB strain is developed by manipulation of pET28-Pkan/fhlA Kan(r) and pBBR1-MCS5/pncB Gm(r) as expression vectors to examine the synchronous effects of fhlA and pncB. Optimization of anaerobic batch fermentations is achieved and the maximum yield of biohydrogen (1.42 mol H2/mol of glucose) is produced in the range of pH 6.5-7.0 at 33-37 °C. Whole cell H2 yield is increased up to 40 % from HQ-3-fhlA/pncB, as compared with HQ-3-fhlA 20 % and HQ-3-pncB 12 % keeping HQ-3-C as a control. Mechanism of improved H2 yield is studied in combination with metabolic flux analysis by measuring glucose consumption and other metabolites including formate, succinate, 2,3 butanediol, lactate, acetate, ethanol, and hydrogen. The results suggest that under transient conditions, the increase in the total level of NAD by NAPRTase can enhance the rate of NADH-dependent pathways, and therefore, final distribution of metabolites is changed. Combined overexpression of fhlA and pncB eventually modifies the energy and carbon balance leading to enhanced H2 production from FHL as well as by NADH pathway.

  19. What can flux tracking teach us about water age distribution patterns and their temporal dynamics?

    NARCIS (Netherlands)

    Hrachowitz, M.; Savenije, H.; Bogaard, T.A.; Tetzlaff, D.; Soulsby, C.

    2013-01-01

    The complex interactions of runoff generation processes underlying the hydrological response of streams remain not entirely understood at the catchment scale. Extensive research has demonstrated the utility of tracers for both inferring flow path distributions and constraining model

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

    Directory of Open Access Journals (Sweden)

    Sugimoto Masahiro

    2006-07-01

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

  1. Metabolic flux analysis of Escherichia coli in glucose-limited continuous culture. I. Growth-rate-dependent metabolic efficiency at steady state.

    Science.gov (United States)

    Kayser, Anke; Weber, Jan; Hecht, Volker; Rinas, Ursula

    2005-03-01

    The Escherichia coli K-12 strain TG1 was grown at 28 degrees C in aerobic glucose-limited continuous cultures at dilution rates ranging from 0.044 to 0.415 h(-1). The rates of biomass formation, the specific rates of glucose, ammonium and oxygen uptake and the specific carbon dioxide evolution rate increased linearly with the dilution rate up to 0.3 h(-1). At dilution rates between 0.3 h(-1) and 0.4 h(-1), a strong deviation from the linear increase to lower specific oxygen uptake and carbon dioxide evolution rates occurred. The biomass formation rate and the specific glucose and ammonium uptake rates did not deviate that strongly from the linear increase up to dilution rates of 0.4 h(-1). An increasing percentage of glucose carbon flow towards biomass determined by a reactor mass balance and a decreasing specific ATP production rate concomitant with a decreasing adenylate energy charge indicated higher energetic efficiency of carbon substrate utilization at higher dilution rates. Estimation of metabolic fluxes by a stoichiometric model revealed an increasing activity of the pentose phosphate pathway and a decreasing tricarboxylic acid cycle activity with increasing dilution rates, indicative of the increased NADPH and precursor demand for anabolic purposes at the expense of ATP formation through catabolic activities. Thus, increasing growth rates first result in a more energy-efficient use of the carbon substrate for biomass production, i.e. a lower portion of the carbon substrate is channelled into the respiratory, energy-generating pathway. At dilution rates above 0.4 h(-1), close to the wash-out point, respiration rates dropped sharply and accumulation of glucose and acetic acid was observed. Energy generation through acetate formation yields less ATP compared with complete oxidation of the sugar carbon substrate, but is the result of maximized energy generation under conditions of restrictions in the tricarboxylic acid cycle or in respiratory NADH turnover

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

    Directory of Open Access Journals (Sweden)

    Hadi Nazem-Bokaee

    2015-09-01

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

  3. Uptake, Translocation, Metabolism, and Distribution of Glyphosate in Nontarget Tea Plant (Camellia sinensis L.).

    Science.gov (United States)

    Tong, Mengmeng; Gao, Wanjun; Jiao, Weiting; Zhou, Jie; Li, Yeyun; He, Lili; Hou, Ruyan

    2017-09-06

    The uptake, translocation, metabolism, and distribution behavior of glyphosate in nontarget tea plant were investigated. The negative effects appeared to grown tea saplings when the nutrient solution contained glyphosate above 200 mg L -1 . Glyphosate was highest in the roots of the tea plant, where it was also metabolized to aminomethyl phosphonic acid (AMPA). The glyphosate and AMPA in the roots were transported through the xylem or phloem to the stems and leaves. The amount of AMPA in the entire tea plant was less than 6.0% of the amount of glyphosate. The glyphosate level in fresh tea shoots was less than that in mature leaves at each day. These results indicated that free glyphosate in the soil can be continuously absorbed by, metabolized in, and transported from the roots of the tea tree into edible leaves, and therefore, free glyphosate residues in the soil should be controlled to produce teas free of glyphosate.

  4. A Diel Flux Balance Model Captures Interactions between Light and Dark Metabolism during Day-Night Cycles in C3 and Crassulacean Acid Metabolism Leaves1[C][W][OPEN

    Science.gov (United States)

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

    2014-01-01

    Although leaves have to accommodate markedly different metabolic flux patterns in the light and the dark, models of leaf metabolism based on flux-balance analysis (FBA) have so far been confined to consideration of the network under continuous light. An FBA framework is presented that solves the two phases of the diel cycle as a single optimization problem and, thus, provides a more representative model of leaf metabolism. The requirement to support continued export of sugar and amino acids from the leaf during the night and to meet overnight cellular maintenance costs forces the model to set aside stores of both carbon and nitrogen during the day. With only minimal constraints, the model successfully captures many of the known features of C3 leaf metabolism, including the recently discovered role of citrate synthesis and accumulation in the night as a precursor for the provision of carbon skeletons for amino acid synthesis during the day. The diel FBA model can be applied to other temporal separations, such as that which occurs in Crassulacean acid metabolism (CAM) photosynthesis, allowing a system-level analysis of the energetics of CAM. The diel model predicts that there is no overall energetic advantage to CAM, despite the potential for suppression of photorespiration through CO2 concentration. Moreover, any savings in enzyme machinery costs through suppression of photorespiration are likely to be offset by the higher flux demand of the CAM cycle. It is concluded that energetic or nitrogen use considerations are unlikely to be evolutionary drivers for CAM photosynthesis. PMID:24596328

  5. Applications of computational modeling in metabolic engineering of yeast

    DEFF Research Database (Denmark)

    Kerkhoven, Eduard J.; Lahtvee, Petri-Jaan; Nielsen, Jens

    2015-01-01

    Generally, a microorganism's phenotype can be described by its pattern of metabolic fluxes. Although fluxes cannot be measured directly, inference of fluxes is well established. In biotechnology the aim is often to increase the capacity of specific fluxes. For this, metabolic engineering methods...... a preferred flux distribution. These methods point to strategies for altering gene expression; however, fluxes are often controlled by post-transcriptional events. Moreover, GEMs are usually not taking into account metabolic regulation, thermodynamics and enzyme kinetics. To facilitate metabolic engineering......, tools from synthetic biology have emerged, enabling integration and assembly of naturally nonexistent, but well-characterized components into a living organism. To describe these systems kinetic models are often used and to integrate these systems with the standard metabolic engineering approach...

  6. Visualisation of flux distributions in high-temperature superconductors. Final report; Sichtbarmachung der Flussverteilung in Hochtemperatursupraleitern nach verschiedenen Mikrostrukturaenderungen. Abschlussbericht

    Energy Technology Data Exchange (ETDEWEB)

    Kuhn, H.; Kronmueller, H.

    1998-05-01

    Theoretical calculation models for current, magnetic and electric field distributions in thin superconductors of arbitrary shape in perpendicular magnetic field were developed. Calculations were done for inhomogeneous and anisotropic critical currents and compared with magnetooptical observations of flux penetration. Nice agreement of theory and experiment was found. Flux-line depinning and motion in superconductors with linear defects was investigated by magneto-optics. Depinning mechanisms were deduced from observations of high-temperature superconductors which are irradiated with swift heavy ions parallel and crosswisely at various angles to the surface normal. Magneto-optical investigations of flux penetration into (Bi,Pb){sub 2}Sr{sub 2}Ca{sub 2}Cu{sub 3}O{sub 10+{delta}} multifilament tapes showed a strong dependence of the current capability on the microstructure of single filaments. The different filament textures which are caused by the inhomogeneous deformation of the tape during thermomechanical treatment results in critical current densities varying by about one order of magnitude. (orig.) [Deutsch] Theoretische Modelle zur Berechnung von Strom-, Magnet- und elektrischen Feldverteilungen wurden fuer duenne Supraleiter beliebiger Geometrie mit inhomogener und anisotroper kritischer Stromdichte im senkrechten Magnetfeld entwickelt und mit magnetooptischen Beobachtungen des Flusseindringens verglichen, wobei eine hervorragende Uebereinstimmung zwischen Theorie und Experiment erzielt wurde. Mit Hilfe von magnetooptischen Untersuchungen des Flusseindringens in schwerionenbestrahlte Hochtemperatursupraleiter, die unter verschiedenen Winkeln zur Oberflaechennormalen parallel und kreuzweise bestrahlt wurden, konnten Bewegungs- und Entankerungsmechanismen von Flusslinien in Supraleitern mit linearen Defekten abgeleitet werden. Magnetooptische Untersuchungen des Flusseindringens in (Bi, Pb){sub 2}Sr{sub 2}Ca{sub 2}Cu{sub 3}O{sub 10+{delta

  7. Comparison between measured and computed magnetic flux density distribution of simulated transformer core joints assembled from grain-oriented and non-oriented electrical steel

    Science.gov (United States)

    Shahrouzi, Hamid; Moses, Anthony J.; Anderson, Philip I.; Li, Guobao; Hu, Zhuochao

    2018-04-01

    The flux distribution in an overlapped linear joint constructed in the central region of an Epstein Square was studied experimentally and results compared with those obtained using a computational magnetic field solver. High permeability grain-oriented (GO) and low permeability non-oriented (NO) electrical steels were compared at a nominal core flux density of 1.60 T at 50 Hz. It was found that the experimental results only agreed well at flux densities at which the reluctance of different paths of the flux are similar. Also it was revealed that the flux becomes more uniform when the working point of the electrical steel is close to the knee point of the B-H curve of the steel.

  8. Intracellular metabolic pathway distribution in diatoms and tools for genome-enabled experimental diatom research.

    Science.gov (United States)

    Gruber, Ansgar; Kroth, Peter G

    2017-09-05

    Diatoms are important primary producers in the oceans and can also dominate other aquatic habitats. One reason for the success of this phylogenetically relatively young group of unicellular organisms could be the impressive redundancy and diversity of metabolic isoenzymes in diatoms. This redundancy is a result of the evolutionary origin of diatom plastids by a eukaryote-eukaryote endosymbiosis, a process that implies temporary redundancy of functionally complete eukaryotic genomes. During the establishment of the plastids, this redundancy was partially reduced via gene losses, and was partially retained via gene transfer to the nucleus of the respective host cell. These gene transfers required re-assignment of intracellular targeting signals, a process that simultaneously altered the intracellular distribution of metabolic enzymes compared with the ancestral cells. Genome annotation, the correct assignment of the gene products and the prediction of putative function, strongly depends on the correct prediction of the intracellular targeting of a gene product. Here again diatoms are very peculiar, because the targeting systems for organelle import are partially different to those in land plants. In this review, we describe methods of predicting intracellular enzyme locations, highlight findings of metabolic peculiarities in diatoms and present genome-enabled approaches to study their metabolism.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'. © 2017 The Author(s).

  9. The effect of cadmium shielding on the spatial neutron flux distribution inside one of the outer irradiation sites

    International Nuclear Information System (INIS)

    Shaaban, I.

    2009-06-01

    A permanent epithermal neutron irradiation facility was designed in the Syrian Miniature Neutron Source Reactor (MNSR) by using the cadmium (cylindrical vial 1.0 mm in thickness, 38.50 mm in diameter and 180 mm in length) as thermal neutron shielding material, for a permanent epithermal neutron activation analysis (ENAA). This site was designed by shielding the internal surface of the aluminum tube of the first outer irradiation site in the MNSR reactor. I was used the activation detectors 0.1143% Au-Al alloy foils with 0.1 mm thickness and 2.0 mm diameter for measurement the thermal neutron flux, epithermal and R c d=A b are/A c over ratio in the outer irradiation site. Distribution of the thermal neutron flux in the outer irradiation capsule has been found numerically using MCNP-4C code with and without cadmium shield, and experimentally by irradiating five copper wires using the outer irradiation capsule. Good agreements were obtained between the calculated and the measured results. (author)

  10. Using a spatially-distributed hydrologic biogeochemistry model with nitrogen transport to study the spatial variation of carbon stocks and fluxes in a Critical Zone Observatory

    Science.gov (United States)

    Shi, Y.; Eissenstat, D. M.; He, Y.; Davis, K. J.

    2017-12-01

    Most current biogeochemical models are 1-D and represent one point in space. Therefore, they cannot resolve topographically driven land surface heterogeneity (e.g., lateral water flow, soil moisture, soil temperature, solar radiation) or the spatial pattern of nutrient availability. A spatially distributed forest biogeochemical model with nitrogen transport, Flux-PIHM-BGC, has been developed by coupling a 1-D mechanistic biogeochemical model Biome-BGC (BBGC) with a spatially distributed land surface hydrologic model, Flux-PIHM, and adding an advection dominated nitrogen transport module. Flux-PIHM is a coupled physically based model, which incorporates a land-surface scheme into the Penn State Integrated Hydrologic Model (PIHM). The land surface scheme is adapted from the Noah land surface model, and is augmented by adding a topographic solar radiation module. Flux-PIHM is able to represent the link between groundwater and the surface energy balance, as well as land surface heterogeneities caused by topography. In the coupled Flux-PIHM-BGC model, each Flux-PIHM model grid couples a 1-D BBGC model, while nitrogen is transported among model grids via surface and subsurface water flow. In each grid, Flux-PIHM provides BBGC with soil moisture, soil temperature, and solar radiation, while BBGC provides Flux-PIHM with spatially-distributed leaf area index. The coupled Flux-PIHM-BGC model has been implemented at the Susquehanna/Shale Hills Critical Zone Observatory. The model-predicted aboveground vegetation carbon and soil carbon distributions generally agree with the macro patterns observed within the watershed. The importance of abiotic variables (including soil moisture, soil temperature, solar radiation, and soil mineral nitrogen) in predicting aboveground carbon distribution is calculated using a random forest. The result suggests that the spatial pattern of aboveground carbon is controlled by the distribution of soil mineral nitrogen. A Flux-PIHM-BGC simulation

  11. Computational Flux Balance Analysis Predicts that Stimulation of Energy Metabolism in Astrocytes and their Metabolic Interactions with Neurons Depend on Uptake of K(+) Rather than Glutamate

    DEFF Research Database (Denmark)

    DiNuzzo, Mauro; Giove, Federico; Maraviglia, Bruno

    2017-01-01

    Brain activity involves essential functional and metabolic interactions between neurons and astrocytes. The importance of astrocytic functions to neuronal signaling is supported by many experiments reporting high rates of energy consumption and oxidative metabolism in these glial cells...... utilization. In order to examine the participation of astrocytic energy metabolism in brain ion homeostasis, here we attempted to devise a simple stoichiometric relation linking glutamatergic neurotransmission to Na(+) and K(+) ionic currents. To this end, we took into account ion pumps and voltage....../ligand-gated channels using the stoichiometry derived from available energy budget for neocortical signaling and incorporated this stoichiometric relation into a computational metabolic model of neuron-astrocyte interactions. We aimed at reproducing the experimental observations about rates of metabolic pathways...

  12. Flux and distribution of methane (CH4) in the Gunsan Basin of the southeastern Yellow Sea, off the Western Korea.

    Science.gov (United States)

    Lee, Jun-Ho; Woo, Han Jun; Son, Seung-Kyu; Kim, Moonkoo; Lee, Dong-Hun; Tsunogai, Urumu; Jeong, Kap-Sik

    2018-04-16

    The flux and distribution of methane (CH 4 ) was investigated in the seawater column at 14 stations in the Gunsan Basin, the southeastern part of Yellow Sea from 2013 to 2015. Here CH 4 is concentrated 2.4-4.7 (3.4 ± 0.7) nM in the surface and 2.5-7.4 (5.2 ± 1.7) nM in the bottom layer. The CH 4 saturation ratios ranged from 65.5% to 295.5% (162.6 ± 68.7), comprising the mean sea-to-air CH 4 flux of 3.8 to 25.3 (15.6 ± 5.5) µM m -2 d -1 . Methane concentration was largely different in the upper and the lower seawater layers that is separated by the thermocline of which depth is variable (20-60 m) depending on the time of sampling. The concentration of seawater dissolved CH 4 is high between the bottom surface of the thermocline layer and the sea floor. Generally it tends to decrease from the south-westernmost part of the basin toward the west coast of Korea. This distribution pattern of CH 4 seems to result from the CH 4 supply by decomposition of organic matters produced in the upper seawater layer that is superimposed by the larger supply from the underlying sediment layer especially beneath the thermocline. The latter is manifested by ubiquitous CH 4 seeps from the seafloor sediments.

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

    Science.gov (United States)

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

    2016-09-01

    We evolved Thermus thermophilus to efficiently co-utilize glucose and xylose, the two most abundant sugars in lignocellulosic biomass, at high temperatures without carbon catabolite repression. To generate the strain, T. thermophilus HB8 was first evolved on glucose to improve its growth characteristics, followed by evolution on xylose. The resulting strain, T. thermophilus LC113, was characterized in growth studies, by whole genome sequencing, and (13)C-metabolic flux analysis ((13)C-MFA) with [1,6-(13)C]glucose, [5-(13)C]xylose, and [1,6-(13)C]glucose+[5-(13)C]xylose as isotopic tracers. Compared to the starting strain, the evolved strain had an increased growth rate (~2-fold), increased biomass yield, increased tolerance to high temperatures up to 90°C, and gained the ability to grow on xylose in minimal medium. At the optimal growth temperature of 81°C, the maximum growth rate on glucose and xylose was 0.44 and 0.46h(-1), respectively. In medium containing glucose and xylose the strain efficiently co-utilized the two sugars. (13)C-MFA results provided insights into the metabolism of T. thermophilus LC113 that allows efficient co-utilization of glucose and xylose. Specifically, (13)C-MFA revealed that metabolic fluxes in the upper part of metabolism adjust flexibly to sugar availability, while fluxes in the lower part of metabolism remain relatively constant. Whole genome sequence analysis revealed two large structural changes that can help explain the physiology of the evolved strain: a duplication of a chromosome region that contains many sugar transporters, and a 5x multiplication of a region on the pVV8 plasmid that contains xylose isomerase and xylulokinase genes, the first two enzymes of xylose catabolism. Taken together, (13)C-MFA and genome sequence analysis provided complementary insights into the physiology of the evolved strain. Copyright © 2016 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  14. Water track distribution and effects on carbon dioxide flux in an eastern Siberian upland tundra landscape

    International Nuclear Information System (INIS)

    Curasi, Salvatore R; Loranty, Michael M; Natali, Susan M

    2016-01-01

    Shrub expansion in tundra ecosystems may act as a positive feedback to climate warming, the strength of which depends on its spatial extent. Recent studies have shown that shrub expansion is more likely to occur in areas with high soil moisture and nutrient availability, conditions typically found in sub-surface water channels known as water tracks. Water tracks are 5–15 m wide channels of subsurface water drainage in permafrost landscapes and are characterized by deeper seasonal thaw depth, warmer soil temperatures, and higher soil moisture and nutrient content relative to adjacent tundra. Consequently, enhanced vegetation productivity, and dominance by tall deciduous shrubs, are typical in water tracks. Quantifying the distribution of water tracks may inform investigations of the extent of shrub expansion and associated impacts on tundra ecosystem carbon cycling. Here, we quantify the distribution of water tracks and their contribution to growing season CO 2 dynamics for a Siberian tundra landscape using satellite observations, meteorological data, and field measurements. We find that water tracks occupy 7.4% of the 448 km 2 study area, and account for a slightly larger proportion of growing season carbon uptake relative to surrounding tundra. For areas inside water tracks dominated by shrubs, field observations revealed higher shrub biomass and higher ecosystem respiration and gross primary productivity relative to adjacent upland tundra. Conversely, a comparison of graminoid-dominated areas in water tracks and inter-track tundra revealed that water track locations dominated by graminoids had lower shrub biomass yet increased net uptake of CO 2 . Our results show water tracks are an important component of this landscape. Their distribution will influence ecosystem structural and functional responses to climate, and is therefore of importance for modeling. (letter)

  15. 13C based proteinogenic amino acid (PAA) and metabolic flux ratio analysis of Lactococcus lactis reveals changes in pentose phosphate (PP) pathway in response to agitation and temperature related stresses

    Science.gov (United States)

    2017-01-01

    Lactococcus lactis subsp. cremoris MG1363 is an important starter culture for dairy fermentation. During industrial fermentations, L. lactis is constantly exposed to stresses that affect the growth and performance of the bacterium. Although the response of L. lactis to several stresses has been described, the adaptation mechanisms at the level of in vivo fluxes have seldom been described. To gain insights into cellular metabolism, 13C metabolic flux analysis and gas chromatography mass spectrometry (GC-MS) were used to measure the flux ratios of active pathways in the central metabolism of L. lactis when subjected to three conditions varying in temperature (30°C, 37°C) and agitation (with and without agitation at 150 rpm). Collectively, the concentrations of proteinogenic amino acids (PAAs) and free fatty acids (FAAs) were compared, and Pearson correlation analysis (r) was calculated to measure the pairwise relationship between PAAs. Branched chain and aromatic amino acids, threonine, serine, lysine and histidine were correlated strongly, suggesting changes in flux regulation in glycolysis, the pentose phosphate (PP) pathway, malic enzyme and anaplerotic reaction catalysed by pyruvate carboxylase (pycA). Flux ratio analysis revealed that glucose was mainly converted by glycolysis, highlighting the stability of L. lactis’ central carbon metabolism despite different conditions. Higher flux ratios through oxaloacetate (OAA) from pyruvate (PYR) reaction in all conditions suggested the activation of pyruvate carboxylate (pycA) in L. lactis, in response to acid stress during exponential phase. Subsequently, more significant flux ratio differences were seen through the oxidative and non-oxidative pentose phosphate (PP) pathways, malic enzyme, and serine and C1 metabolism, suggesting NADPH requirements in response to environmental stimuli. These reactions could play an important role in optimization strategies for metabolic engineering in L. lactis. Overall, the

  16. 13C based proteinogenic amino acid (PAA and metabolic flux ratio analysis of Lactococcus lactis reveals changes in pentose phosphate (PP pathway in response to agitation and temperature related stresses

    Directory of Open Access Journals (Sweden)

    Kamalrul Azlan Azizan

    2017-07-01

    Full Text Available Lactococcus lactis subsp. cremoris MG1363 is an important starter culture for dairy fermentation. During industrial fermentations, L. lactis is constantly exposed to stresses that affect the growth and performance of the bacterium. Although the response of L. lactis to several stresses has been described, the adaptation mechanisms at the level of in vivo fluxes have seldom been described. To gain insights into cellular metabolism, 13C metabolic flux analysis and gas chromatography mass spectrometry (GC-MS were used to measure the flux ratios of active pathways in the central metabolism of L. lactis when subjected to three conditions varying in temperature (30°C, 37°C and agitation (with and without agitation at 150 rpm. Collectively, the concentrations of proteinogenic amino acids (PAAs and free fatty acids (FAAs were compared, and Pearson correlation analysis (r was calculated to measure the pairwise relationship between PAAs. Branched chain and aromatic amino acids, threonine, serine, lysine and histidine were correlated strongly, suggesting changes in flux regulation in glycolysis, the pentose phosphate (PP pathway, malic enzyme and anaplerotic reaction catalysed by pyruvate carboxylase (pycA. Flux ratio analysis revealed that glucose was mainly converted by glycolysis, highlighting the stability of L. lactis’ central carbon metabolism despite different conditions. Higher flux ratios through oxaloacetate (OAA from pyruvate (PYR reaction in all conditions suggested the activation of pyruvate carboxylate (pycA in L. lactis, in response to acid stress during exponential phase. Subsequently, more significant flux ratio differences were seen through the oxidative and non-oxidative pentose phosphate (PP pathways, malic enzyme, and serine and C1 metabolism, suggesting NADPH requirements in response to environmental stimuli. These reactions could play an important role in optimization strategies for metabolic engineering in L. lactis. Overall

  17. Distribution of carbon flux within fatty acid utilization during myocardial ischemia and reperfusion

    International Nuclear Information System (INIS)

    Nellis, S.H.; Liedtke, A.J.; Renstrom, B.

    1991-01-01

    Twenty-nine intact, working pig hearts were extracorporeally perfused and divided into two study groups (16 Aerobic and 13 Ischemic/Reflow hearts). Step function, equilibrium labeling with [14C]palmitate was used to develop uptake and washout curves of radioactive fatty acid products contained in coronary effluent during either aerobic perfusion or reperfusion after ischemia (60% reduction in left anterior descending coronary flow for 30 minutes). Left anterior descending control flows were slightly overperfused in Aerobic hearts (18% higher than in Ischemic/Reflow hearts); otherwise, circumflex and right coronary flows, left ventricular pressure, and serum fatty acids and blood sugar levels were comparable between groups. As expected in Ischemic/Reflow hearts, recovery of regional systolic shortening and myocardial oxygen consumption in reperfusion was only modestly impaired (-20% and -19%, respectively, not significant and p less than 0.011 compared with preischemic values, not significant from Aerobic hearts). The only significant metabolized product to be released from labeled fatty acid utilization in either group was 14CO2. A smaller fatty acid pool also was measured and accounted for by that contained in the coronary intravascular volume. The authors could determine no significant back diffusion of fatty acids from myocardium in either perfusion condition. Uptake time constants of the early phase of 14CO2 production also were virtually identical in both groups (19.9 ± 3.2 versus 16.7 ± 3.2 minutes in Aerobic and Ischemic/Reflow hearts, respectively) and strongly correlated with hemodynamics as described by heart rate. In washout studies, tissue radioactivity in the aqueous soluble and fatty acid pools declined in both study groups, and counts in complex lipids and cholesterol/cholesteryl esters remained steady, whereas those in triacylglycerols varied

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

    Directory of Open Access Journals (Sweden)

    Ahmad A Mannan

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

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

    Science.gov (United States)

    Mannan, Ahmad A.; Toya, Yoshihiro; Shimizu, Kazuyuki; McFadden, Johnjoe; Kierzek, Andrzej M.; Rocco, Andrea

    2015-01-01

    An understanding of the dynamics of the metabolic profile of a bacterial cell is sought from a dynamical systems analysis of kinetic models. This modelling formalism relies on a deterministic mathematical description of enzyme kinetics and their metabolite regulation. However, it is severely impeded by the lack of available kinetic information, limiting the size of the system that can be modelled. Furthermore, the subsystem of the metabolic network whose dynamics can be modelled is faced with three problems: how to parameterize the model with mostly incomplete steady state data, how to close what is now an inherently open system, and how to account for the impact on growth. In this study we address these challenges of kinetic modelling by capitalizing on multi-‘omics’ steady state data and a genome-scale metabolic network model. We use these to generate parameters that integrate knowledge embedded in the genome-scale metabolic network model, into the most comprehensive kinetic model of the central carbon metabolism of E. coli realized to date. As an application, we performed a dynamical systems analysis of the resulting enriched model. This revealed bistability of the central carbon metabolism and thus its potential to express two distinct metabolic states. Furthermore, since our model-informing technique ensures both stable states are constrained by the same thermodynamically feasible steady state growth rate, the ensuing bistability represents a temporal coexistence of the two states, and by extension, reveals the emergence of a phenotypically heterogeneous population. PMID:26469081

  20. A scaling theory for number-flux distributions generated during steady-state coagulation and settling and application to particles in Lake Zurich, Switzerland.

    Science.gov (United States)

    Boehm, Alexandria B

    2002-10-15

    In this study, we extend the established scaling theory for cluster size distributions generated during unsteady coagulation to number-flux distributions that arise during steady-state coagulation and settling in an unmixed water mass. The scaling theory predicts self-similar number-flux distributions and power-law decay of total number flux with depth. The shape of the number-flux distributions and the power-law exponent describing the decay of the total number flux are shown to depend on the homogeneity and small i/j limit of the coagulation kernel and the exponent kappa, which describes the variation in settling velocity with cluster volume. Particle field measurements from Lake Zurich, collected by U. Weilenmann and co-workers (Limnol. Oceanogr.34, 1 (1989)), are used to illustrate how the scaling predictions can be applied to a natural system. This effort indicates that within the mid-depth region of Lake Zurich, clusters of the same size preferentially interact and large clusters react with one another more quickly than small ones, indicative of clusters coagulating in a reaction-limited regime.

  1. Isometric size-scaling of metabolic rate and the size abundance distribution of phytoplankton

    Science.gov (United States)

    Huete-Ortega, María; Cermeño, Pedro; Calvo-Díaz, Alejandra; Marañón, Emilio

    2012-01-01

    The relationship between phytoplankton cell size and abundance has long been known to follow regular, predictable patterns in near steady-state ecosystems, but its origin has remained elusive. To explore the linkage between the size-scaling of metabolic rate and the size abundance distribution of natural phytoplankton communities, we determined simultaneously phytoplankton carbon fixation rates and cell abundance across a cell volume range of over six orders of magnitude in tropical and subtropical waters of the Atlantic Ocean. We found an approximately isometric relationship between carbon fixation rate and cell size (mean slope value: 1.16; range: 1.03–1.32), negating the idea that Kleiber's law is applicable to unicellular autotrophic protists. On the basis of the scaling of individual resource use with cell size, we predicted a reciprocal relationship between the size-scalings of phytoplankton metabolic rate and abundance. This prediction was confirmed by the observed slopes of the relationship between phytoplankton abundance and cell size, which have a mean value of −1.15 (range: −1.29 to −0.97), indicating that the size abundance distribution largely results from the size-scaling of metabolic rate. Our results imply that the total energy processed by carbon fixation is constant along the phytoplankton size spectrum in near steady-state marine ecosystems. PMID:22171079

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

    Science.gov (United States)

    Himeoka, Yusuke; Kaneko, Kunihiko

    2016-04-01

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

  3. Distributions and fluxes of methylmercury in the East/Japan Sea

    Science.gov (United States)

    Yang, Jisook; Kim, Hyunji; Kang, Chang-Keun; Kim, Kyung-Ryul; Han, Seunghee

    2017-12-01

    The East/Japan Sea (EJS) is well ventilated to deep water via brine rejection from ice formations and thermohaline convection, resulting in a short overturning period in several decades. Due to these characteristics, the dissolved oxygen concentration in the EJS deep water is much higher (190-200 μg L-1 at 3000 m water depth) than that found at the same depths of the Northwestern Pacific (30 μg L-1) or anywhere in the Pacific Ocean. The total mercury (THg) and methylmercury (MeHg) distributions, and MeHg mass budgets were investigated to identify how the EJS's distinct circulation pattern affects Hg speciation. Whereas the THg concentration in the surface seawater (ranging from 0.20 to 1.2 pM, mean 0.59 ± 0.24 pM) showed no site variation between the Japan Basin and the Ulleung Basin, the MeHg concentration in the surface seawater was significantly higher (p < 0.05) in the Japan Basin (32 ± 24 fM) than in the Ulleung Basin (12 fM), with a south to north increasing gradient. This observation was supported by the mass budget estimation showing that upward diffusion as well as net methylation of Hg(II) was the primary source of MeHg in the surface seawater; the upward diffusion value was higher in the Japan Basin (3.2 nmol m-2 yr-1) than in the Ulleung Basin (1.9 nmol m-2 yr-1) due to the shallow thermocline depths in the Japan Basin. In contrast, the MeHg concentration in deep seawater (1000-3000 m) was similar between the Japan Basin (530 ± 87 fM) and the Ulleung Basin (610 ± 99 fM) and significantly (p < 0.05) higher than in the North Pacific (24 ± 40 fM) or North Atlantic (87 ± 96 fM) deep seawater. The Hg(II) methylation capacity, represented by the MeHg concentration normalized to apparent oxygen utilization, was also higher for the EJS deep water (0.0048) than the Northeastern Pacific (0.0030) and Northwestern Pacific (0.0025) intermediate waters, implying that the short overturning period of EJS may cause exclusively high MeHg concentrations in the

  4. Thermal neutron diffusion parameters dependent on the flux energy distribution in finite hydrogenous media

    International Nuclear Information System (INIS)

    Drozdowicz, K.

    1999-01-01

    Macroscopic parameters for a description of the thermal neutron transport in finite volumes are considered. A very good correspondence between the theoretical and experimental parameters of hydrogenous media is attained. Thermal neutrons in the medium possess an energy distribution, which is dependent on the size (characterized by the geometric buckling) and on the neutron transport properties of the medium. In a hydrogenous material the thermal neutron transport is dominated by the scattering cross section which is strongly dependent on energy. A monoenergetic treatment of the thermal neutron group (admissible for other materials) leads in this case to a discrepancy between theoretical and experimental results. In the present paper the theoretical definitions of the pulsed thermal neutron parameters (the absorption rate, the diffusion coefficient, and the diffusion cooling coefficient) are based on Nelkin's analysis of the decay of a neutron pulse. Problems of the experimental determination of these parameters for a hydrogenous medium are discussed. A theoretical calculation of the pulsed parameters requires knowledge of the scattering kernel. For thermal neutrons it is individual for each hydrogenous material because neutron scattering on hydrogen nuclei bound in a molecule is affected by the molecular dynamics (characterized with internal energy modes which are comparable to the incident neutron energy). Granada's synthetic model for slow-neutron scattering is used. The complete up-dated formalism of calculation of the energy transfer scattering kernel after this model is presented in the paper. An influence of some minor variants within the model on the calculated differential and integral neutron parameters is shown. The theoretical energy-dependent scattering cross section (of Plexiglas) is compared to experimental results. A particular attention is paid to the calculation of the diffusion cooling coefficient. A solution of an equation, which determines the

  5. An overview of techniques for the measurement of calcium distribution, calcium fluxes, and cytosolic free calcium in mammalian cells

    International Nuclear Information System (INIS)

    Borle, A.B.

    1990-01-01

    An array of techniques can be used to study cell calcium metabolism that comprises several calcium compartments and many types of transport systems such as ion channels, ATP-dependent pumps, and antiporters. The measurement of total call calcium brings little information of value since 60 to 80% of total cell calcium is actually bound to the extracellular glycocalyx. Cell fractionation and differential centrifugation have been used to study intracellular Ca 2+ compartmentalization, but the methods suffer from the possibility of Ca 2+ loss or redistribution among cell fractions. Steady-state kinetic analyses of 45 Ca uptake or desaturation curves have been used to study the distribution of Ca 2+ among various kinetic pools in living cells and their rate of Ca 2+ exchange, but the analyses are constrained by many limitations. Nonsteady-state tracer studies can provide information about rapid changes in calcium influx or efflux in and out of the cell. Zero-time kinetics of 45 Ca uptake can detect instantaneous changes in calcium influx, while 45 Ca fractional efflux ratio, can detect rapid stimulations or inhibitions of calcium efflux out of cells. The best strategy to study cell calcium metabolism is to use several different methods that focus on a specific problem from widely different angles

  6. In vivo metabolism of organophosphate flame retardants and distribution of their main metabolites in adult zebrafish.

    Science.gov (United States)

    Wang, Guowei; Chen, Hanyan; Du, Zhongkun; Li, Jianhua; Wang, Zunyao; Gao, Shixiang

    2017-07-15

    Understanding the metabolism of chemicals as well as the distribution and depuration of their main metabolites in tissues are essential for evaluating their fate and potential toxicity in vivo. Herein, we investigated the metabolism of six typical organophosphate (OP) flame retardants (tripropyl phosphate (TPRP), tri-n-butyl phosphate (TNBP), tris(2-butoxyethyl) phosphate (TBOEP), tris(2-chloroethyl) phosphate (TCEP), tris(1,3-dichloro-2-propyl) phosphate (TDCIPP) and tri-p-cresyl phosphate (p-TCP)) in adult zebrafish in laboratory at three levels (0, 1/150 LC 50 (environmentally relevant level), and 1/30 LC 50 per OP analog). Twenty main metabolites were detected in the liver of OPs-exposed zebrafish using high resolution mass spectrometry (Q-TOF). The reaction pathways involving scission of the ester bond (hydrolysis), cleavage of the ether bond, oxidative hydroxylation, dechlorination, and coupling with glucuronic acid were proposed, and were further confirmed by the frontier electron density and point charge calculations. Tissue distribution of the twenty metabolites revealed that liver and intestine with the highest levels of metabolites were the most active organs for OPs biotransformation among the studied tissues of intestine, liver, roe, brain, muscle, and gill, which showed the importance of hepatobiliary system (liver-bile-intestine) in the metabolism and excretion of OPs in zebrafish. Fast depuration of metabolites from tissues indicated that the formed metabolites might be not persistent in fish, and easily released into water. This study provides comprehensive information on the metabolism of OPs in the tissue of zebrafish, which might give some hints for the exploration of their toxic mechanism in aquatic life. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Body fat distribution in pre-and post-menopausal women: metabolic and anthropometric variables.

    Science.gov (United States)

    Garaulet, M; Pérez-Llamas, F; Baraza, J C; Garcia-Prieto, M D; Fardy, P S; Tébar, F J; Zamora, S

    2002-01-01

    Abdominal obesity is associated with coronary risk although the causality is not well established. To compare body fat distribution and metabolic variables in obese pre- and post- menopausal women. The study was conducted in 55 obese female subjects (22 pre- and 33 post- menopausal) with body mass indices (BMI) from 27 to 35 Kg/m2. Body fat distribution was measured using waist and hip circumference and computerized tomography. Hormones such as estradiol, testosterone, androstenedione, dehydroepiandrosterone-sulfate, as well as plasma lipids such as triglycerides, total cholesterol, high density lipoprotein, low density lipoprotein, apoproteins A and B, were also determined. No significant differences were found between the two groups in BMI, percentage of body fat, waist circumference, triceps, biceps, suprailiac and abdominal skinfolds. Hip circumference, subscapular skinfold and subcutaneous abdominal adipose tissue area were significantly lower, and waist-hip ratio, visceral area and visceral to subcutaneous area ratios significantly higher in post- menopausal women (P low density lipoprotein, values were significantly higher in the post-menopausal group (P fat distribution changes according to menopausal status, with central obesity more pronounced in post- menopausal women. Metabolic abnormalities are related more to visceral adipose tissue and estrogen plasma levels than to BMI.

  8. Pressure Transient Analysis and Flux Distribution for Multistage Fractured Horizontal Wells in Triple-Porosity Reservoir Media with Consideration of Stress-Sensitivity Effect

    Directory of Open Access Journals (Sweden)

    Jingjing Guo

    2015-01-01

    Full Text Available Triple-porosity model is usually adopted to describe reservoirs with multiscaled pore spaces, including matrix pores, natural fractures, and vugs. Multiple fractures created by hydraulic fracturing can effectively improve the connectivity between existing natural fractures and thus increase well deliverability. However, little work has been done on pressure transient behavior of multistage fractured horizontal wells in triple-porosity reservoirs. Based on source/sink function method, this paper presents a triple-porosity model to investigate the transient pressure dynamics and flux distribution for multistage fractured horizontal wells in fractured-vuggy reservoirs with consideration of stress-dependent natural fracture permeability. The model is semianalytically solved by discretizing hydraulic fractures and Pedrosa’s transformation, perturbation theory, and integration transformation method. Type curves of transient pressure dynamics are generated, and flux distribution among hydraulic fractures for a fractured horizontal well with constant production rate is also discussed. Parametric study shows that major influential parameters on transient pressure responses are parameters pertinent to reservoir properties, interporosity mass transfer, and hydraulic fractures. Analysis of flux distribution indicates that flux density gradually increases from the horizontal wellbore to fracture tips, and the flux contribution of outermost fractures is higher than that of inner fractures. The model can also be extended to optimize hydraulic fracture parameters.

  9. Squeezing Flux Out of Fat

    DEFF Research Database (Denmark)

    Gonzalez-Franquesa, Alba; Patti, Mary-Elizabeth

    2018-01-01

    Merging transcriptomics or metabolomics data remains insufficient for metabolic flux estimation. Ramirez et al. integrate a genome-scale metabolic model with extracellular flux data to predict and validate metabolic differences between white and brown adipose tissue. This method allows both metab...

  10. SMALL-SCALE AND GLOBAL DYNAMOS AND THE AREA AND FLUX DISTRIBUTIONS OF ACTIVE REGIONS, SUNSPOT GROUPS, AND SUNSPOTS: A MULTI-DATABASE STUDY

    Energy Technology Data Exchange (ETDEWEB)

    Muñoz-Jaramillo, Andrés; Windmueller, John C.; Amouzou, Ernest C.; Longcope, Dana W. [Department of Physics, Montana State University, Bozeman, MT 59717 (United States); Senkpeil, Ryan R. [Department of Physics, Purdue University, West Lafayette, IN 47907 (United States); Tlatov, Andrey G. [Kislovodsk Mountain Astronomical Station of the Pulkovo Observatory, Kislovodsk 357700 (Russian Federation); Nagovitsyn, Yury A. [Pulkovo Astronomical Observatory, Russian Academy of Sciences, St. Petersburg 196140 (Russian Federation); Pevtsov, Alexei A. [National Solar Observatory, Sunspot, NM 88349 (United States); Chapman, Gary A.; Cookson, Angela M. [San Fernando Observatory, Department of Physics and Astronomy, California State University Northridge, Northridge, CA 91330 (United States); Yeates, Anthony R. [Department of Mathematical Sciences, Durham University, South Road, Durham DH1 3LE (United Kingdom); Watson, Fraser T. [National Solar Observatory, Tucson, AZ 85719 (United States); Balmaceda, Laura A. [Institute for Astronomical, Terrestrial and Space Sciences (ICATE-CONICET), San Juan (Argentina); DeLuca, Edward E. [Harvard-Smithsonian Center for Astrophysics, Cambridge, MA 02138 (United States); Martens, Petrus C. H., E-mail: munoz@solar.physics.montana.edu [Department of Physics and Astronomy, Georgia State University, Atlanta, GA 30303 (United States)

    2015-02-10

    In this work, we take advantage of 11 different sunspot group, sunspot, and active region databases to characterize the area and flux distributions of photospheric magnetic structures. We find that, when taken separately, different databases are better fitted by different distributions (as has been reported previously in the literature). However, we find that all our databases can be reconciled by the simple application of a proportionality constant, and that, in reality, different databases are sampling different parts of a composite distribution. This composite distribution is made up by linear combination of Weibull and log-normal distributions—where a pure Weibull (log-normal) characterizes the distribution of structures with fluxes below (above) 10{sup 21}Mx (10{sup 22}Mx). Additionally, we demonstrate that the Weibull distribution shows the expected linear behavior of a power-law distribution (when extended to smaller fluxes), making our results compatible with the results of Parnell et al. We propose that this is evidence of two separate mechanisms giving rise to visible structures on the photosphere: one directly connected to the global component of the dynamo (and the generation of bipolar active regions), and the other with the small-scale component of the dynamo (and the fragmentation of magnetic structures due to their interaction with turbulent convection)

  11. Estrogenic activity of flavonoids in mice. The importance of estrogen receptor distribution, metabolism and bioavailability

    DEFF Research Database (Denmark)

    Breinholt, Vibeke; Hossaini, A.; Svendsen, Gitte W.

    2000-01-01

    The in vivo estrogenic potential of the flavonoids apigenin, kaempferol, genistein and equol was investigated in immature female mice. Genistein and equol, administered by gavage for 4 consecutive days [post-natal day (PND) 17-20, 100 mg/kg body weight], was found to significantly increase uterine...... or lower potency. Bioavailability, metabolism, the ability to alter ER alpha distribution in the uterus and the estrogenic potential of parent compound and metabolites may thus contribute to the differences in in vivo estrogenicity of dietary flavonoids....

  12. Metabolism and distribution of guanosine given intraperitoneally: implications for spinal cord injury.

    Science.gov (United States)

    Jiang, Shucui; Fischione, Gemma; Giuliani, Patricia; Guiliani, Patricia; Romano, Silvia; Caciagli, Francesco; Di Iorio, Patrizia; Diiorio, Patrizia

    2008-06-01

    Intraperitoneal administration of guanosine to rats with chronic spinal cord injury stimulates remyelination and functional recovery. If guanosine produced its effects in the nervous system, it should enter it and elevate endogenous concentrations. [(3)H]-guanosine (8 mg/kg) was administered intraperitoneally to rats and its distribution and concentration in different sites determined. Guanosine rapidly entered all tissues; its concentration peaked at about 15 minutes except in adipose tissue and CNS where it continued to rise for 30 minutes. Its chief metabolic product in all sites was guanine with over twice as much guanine as guanosine present in CNS after 30 minutes.

  13. The use of thallium diethyldithiocarbamate for mapping CNS potassium metabolism and neuronal activity: Tl+ -redistribution, Tl+ -kinetics and Tl+ -equilibrium distribution.

    Science.gov (United States)

    Wanger, Tim; Scheich, Henning; Ohl, Frank W; Goldschmidt, Jürgen

    2012-07-01

    The potassium (K(+)) analogue thallium (Tl(+)) can be used as a tracer for mapping neuronal activity. However, because of the poor blood-brain barrier (BBB) K(+) -permeability, only minute amounts of Tl(+) enter the brain after systemic injection of Tl(+) -salts like thallium acetate (TlAc). We have recently shown that it is possible to overcome this limitation by injecting animals with the lipophilic chelate complex thallium diethyldithiocarbamate (TlDDC), that crosses the BBB and releases Tl(+) prior to neuronal or glial uptake. TlDDC can thus be used for mapping CNS K(+) metabolism and neuronal activity. Here, we analyze Tl(+) -kinetics in the rodent brain both experimentally and using simple mathematical models. We systemically injected animals either with TlAc or with TlDDC. Using an autometallographic method we mapped the brain Tl(+) -distribution at various time points after injection. We show that the patterns and kinetics of Tl(+) -redistribution in the brain are essentially the same irrespective of whether animals have been injected with TlAc or TlDDC. Data from modeling and experiments indicate that transmembrane Tl(+) -fluxes in cells within the CNS in vivo equilibrate at similar rates as K(+) -fluxes in vitro. This equilibration is much faster than and largely independent of the equilibration of Tl(+) -fluxes across the BBB. The study provides further proof-of-concept for the use of TlDDC for mapping neuronal activity and CNS K(+) -metabolism. A theoretical guideline is given for the use of K(+) -analogues for imaging neuronal activity with general implications for the use of metal ions in neuroimaging. © 2012 The Authors. Journal of Neurochemistry © 2012 International Society for Neurochemistry.

  14. Distribution of zooplankton biomass and potential metabolic activities across the northern Benguela upwelling system

    Science.gov (United States)

    Fernández-Urruzola, I.; Osma, N.; Packard, T. T.; Gómez, M.; Postel, L.

    2014-11-01

    The distribution of zooplankton biomass and potential metabolic rates, in terms of electron transport system (ETS) and glutamate dehydrogenase (GDH), were analyzed along a cross-shelf transect in waters off Namibia. The highly variable dynamics of upwelling filaments promoted short-term fluctuations in the zooplankton biomass and metabolism. Maximum values were characteristically found over the shelf-break, where zooplankton biomass as dry mass (DM) reached peaks of 64.5 mg m- 3 within the upper 200 m in late August. Two weeks later, the zooplankton-DM decreased by more than a third (19 mg DM m- 3). Zooplankton potential respiration and NH4+ excretion averaged 234 μmol O2 m- 3 d- 1 and 169 μmol NH4+ m- 3 d- 1 in the Namibian shelf, respectively. High protein-specific ETS activities even in the low-chlorophyll waters outside the filament suggested a shift into greater omnivory seaward. In this light, zooplankton elemental and isotopic compositions were used to investigate the pelagic food web interactions. They evidenced spatial changes in the carbon resource for zooplankton as well as changes in the form of nitrogen that fueled the biological production in aging advected waters. Overall, both aspects of zooplankton metabolism impacted the primary productivity at a level less than 10% under all the different oceanographic conditions.

  15. Metabolism and tissue distribution of sulforaphane in Nrf2 knockout and wild-type mice.

    Science.gov (United States)

    Clarke, John D; Hsu, Anna; Williams, David E; Dashwood, Roderick H; Stevens, Jan F; Yamamoto, Masayuki; Ho, Emily

    2011-12-01

    To determine the metabolism and tissue distribution of the dietary chemoprotective agent sulforaphane following oral administration to wild-type and Nrf2 knockout (Nrf2(-/-)) mice. Male and female wild-type and Nrf2(-/-) mice were given sulforaphane (5 or 20 μmoles) by oral gavage; plasma, liver, kidney, small intestine, colon, lung, brain and prostate were collected at 2, 6 and 24 h (h). The five major metabolites of sulforaphane were measured in tissues by high performance liquid chromatography coupled with tandem mass spectrometry. Sulforaphane metabolites were detected in all tissues at 2 and 6 h post gavage, with the highest concentrations in the small intestine, prostate, kidney and lung. A dose-dependent increase in sulforaphane concentrations was observed in all tissues except prostate. At 5 μmole, Nrf2(-/-) genotype had no effect on sulforaphane metabolism. Only Nrf2(-/-) females given 20 μmoles sulforaphane for 6 h exhibited a marked increase in tissue sulforaphane metabolite concentrations. The relative abundance of each metabolite was not strikingly different between genders and genotypes. Sulforaphane is metabolized and reaches target tissues in wild-type and Nrf2(-/-) mice. These data provide further evidence that sulforaphane is bioavailable and may be an effective dietary chemoprevention agent for several tissue sites.

  16. Atmospheric Inversion of the Global Surface Carbon Flux with Consideration of the Spatial Distributions of US Crop Production and Consumption

    Science.gov (United States)

    Fung, Jonathan Winston

    Carbon dioxide is taken up by crops during production and released back to the atmosphere at different geographical locations through respiration of consumed crop commodities. In this study, spatially distributed county-level US cropland net primary productivity, harvested biomass, changes in soil carbon, and human and livestock consumption data were integrated into the prior terrestrial biosphere flux generated by the Boreal Ecosystem Productivity Simulator (BEPS). A global time-dependent Bayesian synthesis inversion with a nested focus on North America was carried out based on CO2 observations at 210 stations. Overall, the inverted annual North American CO2 sink weakened by 6.5% over the period from 2002 to 2007 compared to simulations disregarding US crop statistical data. The US Midwest is found to be the major sink of 0.36±0.13 PgC yr-1 whereas the large sink in the US Southeast forests weakened to 0.16±0.12 PgC yr-1 partly due to local CO2 sources from crop consumption.

  17. Effects of Hyperglycemia and Effects of Ketosis on Cerebral Perfusion, Cerebral Water Distribution, and Cerebral Metabolism

    Science.gov (United States)

    Glaser, Nicole; Ngo, Catherine; Anderson, Steven; Yuen, Natalie; Trifu, Alexandra; O’Donnell, Martha

    2012-01-01

    Diabetic ketoacidosis (DKA) may cause brain injuries in children. The mechanisms responsible are difficult to elucidate because DKA involves multiple metabolic derangements. We aimed to determine the independent effects of hyperglycemia and ketosis on cerebral metabolism, blood flow, and water distribution. We used magnetic resonance spectroscopy to measure ratios of cerebral metabolites (ATP to inorganic phosphate [Pi], phosphocreatine [PCr] to Pi, N-acetyl aspartate [NAA] to creatine [Cr], and lactate to Cr) and diffusion-weighted imaging and perfusion-weighted imaging to assess cerebral water distribution (apparent diffusion coefficient [ADC] values) and cerebral blood flow (CBF) in three groups of juvenile rats (hyperglycemic, ketotic, and normal control). ATP-to-Pi ratio was reduced in both hyperglycemic and ketotic rats in comparison with controls. PCr-to-Pi ratio was reduced in the ketotic group, and there was a trend toward reduction in the hyperglycemic group. No significant differences were observed in NAA-to-Cr or lactate-to-Cr ratio. Cortical ADC was reduced in both groups (indicating brain cell swelling). Cortical CBF was also reduced in both groups. We conclude that both hyperglycemia and ketosis independently cause reductions in cerebral high-energy phosphates, CBF, and cortical ADC values. These effects may play a role in the pathophysiology of DKA-related brain injury. PMID:22498698

  18. PM2.5-bound metal metabolic distribution and coupled lipid abnormality at different developmental windows.

    Science.gov (United States)

    Ku, Tingting; Zhang, Yingying; Ji, Xiaotong; Li, Guangke; Sang, Nan

    2017-09-01

    Atmospheric fine particulate matter (PM 2.5 ) is a serious threat to human health. As a toxicant constituent, metal leads to significant health risks in a population, but exposure to PM 2.5 -bound metals and their biological impacts are not fully understood. In this study, we determined the metal contents of PM 2.5 samples collected from a typical coal-burning city and then investigated the metabolic distributions of six metals (Zn, Pb, Mn, As, Cu, and Cd) following PM 2.5 inhalation in mice in different developmental windows. The results indicate that fine particles were mainly deposited in the lung, but PM 2.5 -bound metals could reach and gather in secondary off-target tissues (the lung, liver, heart and brain) with a developmental window-dependent property. Furthermore, elevations in triglycerides and cholesterol levels in sensitive developmental windows (the young and elderly stages) occurred, and significant associations between metals (Pb, Mn, As and Cd) and cholesterol in the heart, brain, liver and lung were observed. These findings suggest that PM 2.5 inhalation caused selective metal metabolic distribution in tissues with a developmental window-dependent property and that the effects were associated with lipid alterations. This provides a foundation for the underlying systemic toxicity following PM 2.5 exposure based on metal components. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Spatio-temporal Model of Xenobiotic Distribution and Metabolism in an in Silico Mouse Liver Lobule

    Science.gov (United States)

    Fu, Xiao; Sluka, James; Clendenon, Sherry; Glazier, James; Ryan, Jennifer; Dunn, Kenneth; Wang, Zemin; Klaunig, James

    Our study aims to construct a structurally plausible in silico model of a mouse liver lobule to simulate the transport of xenobiotics and the production of their metabolites. We use a physiologically-based model to calculate blood-flow rates in a network of mouse liver sinusoids and simulate transport, uptake and biotransformation of xenobiotics within the in silico lobule. Using our base model, we then explore the effects of variations of compound-specific (diffusion, transport and metabolism) and compound-independent (temporal alteration of blood flow pattern) parameters, and examine their influence on the distribution of xenobiotics and metabolites. Our simulations show that the transport mechanism (diffusive and transporter-mediated) of xenobiotics and blood flow both impact the regional distribution of xenobiotics in a mouse hepatic lobule. Furthermore, differential expression of metabolic enzymes along each sinusoid's portal to central axis, together with differential cellular availability of xenobiotics, induce non-uniform production of metabolites. Thus, the heterogeneity of the biochemical and biophysical properties of xenobiotics, along with the complexity of blood flow, result in different exposures to xenobiotics for hepatocytes at different lobular locations. We acknowledge support from National Institute of Health GM 077138 and GM 111243.

  20. Neutron flux distribution inside the cylindrical core of minor excess of reactivity in the IPEN/MB-01 reactor and comparison with citation code and MCNP- 5 code

    Energy Technology Data Exchange (ETDEWEB)

    Aredes, Vitor Ottoni; Bitelli, Ulysses d' Utra; Mura, Luiz Ernesto C.; Santos, Diogo Feliciano dos; Lima, Ana Cecilia de Souza, E-mail: ubitelli@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2015-07-01

    This study aims to determine the distribution of thermal neutron flux in the IPEN/MB-01 nuclear reactor core assembled with cylindrical core configuration of minor excess of reactivity with 568 fuel rods (28 fuel rods in diameter). The thermal neutron flux at the positions of irradiation derive from the method of reaction rate using gold foils. The experiment consists in inserting gold activations foils with and without cadmium coverage (cadmium boxes with 0.0502 cm thickness) in several positions throughout the active core. After irradiation, activity induced by nuclear reaction rates over gold foils is assessed by gamma ray spectrometry using a high-purity germanium (HPGe) detector. Experimental results are compared to those derived from calculations performed using a three dimensional CITATION diffusion code and MCNP-5 code and a proper nuclear data library. While calculated neutron flux data shows good agreement with experimental values in regions with little disturbance in the neutron flux, also showing that in the region of the reflectors of neutrons and near the control rods, the diffusion theory is not very precise. The average value of thermal neutron flux obtained experimentally compared to the calculated value by CITATION code and MCNP-5 code respectively show a difference of 1.18% and 0.84% at a nuclear power level of 74.65 ± 3.28 % watts. The average measured value of thermal neutron flux is 4.10 10{sup 8} ± 5.25% n/cm{sup 2}s. (author)

  1. GreenLITE™: a novel approach for quantification of atmospheric methane concentrations, 2-D spatial distribution, and flux

    Science.gov (United States)

    Dobler, J. T.; Blume, N.; Pernini, T.; Zaccheo, T. S.; Braun, M.

    2017-12-01

    The Greenhouse Gas Laser Imaging Tomography Experiment (GreenLITE™) was originally developed by Harris and Atmospheric and Environmental Research (AER) under a cooperative agreement with the National Energy Technology Laboratory of the Department of Energy. The system, initially conceived in 2013, used a pair of high-precision intensity modulated continuous wave (IMCW) transceivers and a series of retroreflectors to generate overlapping atmospheric density measurements of carbon dioxide (CO2) for continuous monitoring of ground carbon storage sites. The overlapping measurements provide an estimate of the two-dimensional (2-D) spatial distribution of the gas within the area of interest using sparsely sampled tomography methods. GreenLITE™ is a full end-to-end system that utilizes standard 4G connectivity and an all cloud-based data storage, processing, and dissemination suite to provide autonomous, near-real-time data via a web-based user interface. The system has been demonstrated for measuring and mapping CO2 over areas from approximately 0.04 km2 to 25 km2 ( 200 m X 200 m, up to 5 km X 5 km), including a year-long demonstration over the city of Paris, France. In late 2016, the GreenLITE™ system was converted by Harris and AER to provide similar measurement capabilities for methane (CH4). Recent experiments have shown that GreenLITE™ CH4 retrieved concentrations agree with a Picarro cavity ring-down spectrometer, calibrated with World Meteorological Organization traceable gas, to within approximately 0.5% of background or 10-15 parts per billion. The system has been tested with several controlled releases over the past year, including a weeklong experiment at an industrial oil and gas facility. Recent experiments have been exploring the use of a box model-based approach for estimating flux, and the initial results are very promising. We will present a description of the instrument, share some recent methane experimental results, and describe the flux

  2. Metabolism

    Science.gov (United States)

    ... functions: Anabolism (uh-NAB-uh-liz-um), or constructive metabolism, is all about building and storing. It ... in infants and young children. Hypothyroidism slows body processes and causes fatigue (tiredness), slow heart rate, excessive ...

  3. Metabolism

    Science.gov (United States)

    ... a particular food provides to the body. A chocolate bar has more calories than an apple, so ... acid phenylalanine, needed for normal growth and protein production). Inborn errors of metabolism can sometimes lead to ...

  4. Effects of Citrus aurantium (bitter orange) fruit extracts and p-synephrine on metabolic fluxes in the rat liver.

    Science.gov (United States)

    Peixoto, Jéssica Sereno; Comar, Jurandir Fernando; Moreira, Caroline Tessaro; Soares, Andréia Assunção; de Oliveira, Andrea Luiza; Bracht, Adelar; Peralta, Rosane Marina

    2012-05-16

    The fruit extracts of Citrus aurantium (bitter orange) are traditionally used as weight-loss products and as appetite supressants. An important fruit component is p-synephrine, which is structurally similar to the adrenergic agents. Weight-loss and adrenergic actions are always related to metabolic changes and this work was designed to investigate a possible action of the C. aurantium extract on liver metabolism. The isolated perfused rat liver was used to measure catabolic and anabolic pathways, including oxygen uptake and perfusion pressure. The C. aurantium extract and p-synephrine increased glycogenolysis, glycolysis, oxygen uptake and perfusion pressure. These changes were partly sensitive to α- and β-adrenergic antagonists. p-Synephrine (200 μM) produced an increase in glucose output that was only 15% smaller than the increment caused by the extract containing 196 μM p-synephrine. At low concentrations the C. aurantium extract tended to increase gluconeogenesis, but at high concentrations it was inhibitory, opposite to what happened with p-synephrine. The action of the C. aurantium extract on liver metabolism is similar to the well known actions of adrenergic agents and can be partly attributed to its content in p-synephrine. Many of these actions are catabolic and compatible with the weight-loss effects usually attributed to C. aurantium.

  5. Spatial distribution of mechanical forces and ionic flux in electro-kinetic instability near a permselective membrane

    Science.gov (United States)

    Magnico, Pierre

    2018-01-01

    This paper is devoted to the numerical investigation of electro-kinetic instability in a polarization layer next to a cation-exchange membrane. An analysis of some properties of the electro-kinetic instability is followed by a detailed description of the fluid flow structure and of the spatial distribution of the ionic flux. In this aim, the Stokes-Poisson-Nernst-Planck equation set is solved until the Debye length scale. The results show that the potential threshold of the marginal instability and the current density depend on the logarithm of the concentration at the membrane surface. The size of the stable vortices seems to be an increasing function of the potential drop. The fluid motion is induced by the electric force along the maximum concentration in the extended space charge (ESC) region and by the pressure force in the region around the inner edge of the ESC layer. Two spots of kinetic energy are located in the ESC region and between the vortices. The cationic motion, controlled by the electric field and the convection, presents counter-rotating vortices in the stagnation zone located in the fluid ejection region. The anion transport is also characterized by two independent layers which contain counter-rotating vortices. The first one is in contact with the stationary reservoir. In the second layer against the membrane, the convection, and the electric field control, the transversal motion, the Fickian diffusion, and the convection are dominant in the longitudinal direction. Finally, the longitudinal disequilibrium of potential and pressure along the membrane is analyzed.

  6. Assessment of 12 CHF prediction methods, for an axially non-uniform heat flux distribution, with the RELAP5 computer code

    International Nuclear Information System (INIS)

    Ferrouk, M.; Aissani, S.; D'Auria, F.; DelNevo, A.; Salah, A. Bousbia

    2008-01-01

    The present article covers the evaluation of the performance of twelve critical heat flux methods/correlations published in the open literature. The study concerns the simulation of an axially non-uniform heat flux distribution with the RELAP5 computer code in a single boiling water reactor channel benchmark problem. The nodalization scheme employed for the considered particular geometry, as modelled in RELAP5 code, is described. For this purpose a review of critical heat flux models/correlations applicable to non-uniform axial heat profile is provided. Simulation results using the RELAP5 code and those obtained from our computer program, based on three type predictions methods such as local conditions, F-factor and boiling length average approaches were compared

  7. Energy distribution of the neutron flux measurements at the Chilean Reactor RECH-1 using multi-foil neutron activation and the Expectation Maximization unfolding algorithm.

    Science.gov (United States)

    Molina, F; Aguilera, P; Romero-Barrientos, J; Arellano, H F; Agramunt, J; Medel, J; Morales, J R; Zambra, M

    2017-11-01

    We present a methodology to obtain the energy distribution of the neutron flux of an experimental nuclear reactor, using multi-foil activation measurements and the Expectation Maximization unfolding algorithm, which is presented as an alternative to well known unfolding methods such as GRAVEL. Self-shielding flux corrections for energy bin groups were obtained using MCNP6 Monte Carlo simulations. We have made studies at the at the Dry Tube of RECH-1 obtaining fluxes of 1.5(4)×10 13 cm -2 s -1 for the thermal neutron energy region, 1.9(5)×10 12 cm -2 s -1 for the epithermal neutron energy region, and 4.3(11)×10 11 cm -2 s -1 for the fast neutron energy region. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Bi-Maxwellian electron energy distribution function in the vicinity of the last closed flux surface in fusion plasma

    Czech Academy of Sciences Publication Activity Database

    Popov, T.S.V.K.; Dimitrova, Miglena; Pedrosa, M. A.; López-Bruna, D.; Horáček, Jan; Kovačič, J.; Dejarnac, Renaud; Stöckel, Jan; Aftanas, Milan; Böhm, Petr; Bílková, Petra; Hidalgo, C.; Pánek, Radomír

    2015-01-01

    Roč. 57, č. 11 (2015), č. článku 115011. ISSN 0741-3335 R&D Projects: GA ČR(CZ) GAP205/12/2327; GA MŠk(CZ) LM2011021 Institutional support: RVO:61389021 Keywords : COMPASS tokamak, parallel power flux density * TJ-II stellarator * bi-Maxwellian EEDF * last closed flux surface * SOL * parallel power flux density Subject RIV: BL - Plasma and Gas Discharge Physics OBOR OECD: Fluids and plasma physics (including surface physics) Impact factor: 2.404, year: 2015

  9. Metabolic flux analysis of the phenylpropanoid pathway in wound-healing potato tuber tissue using stable isotope-labeled tracer and LC-MS spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Matsuda, Fumio; Morino, Keiko; Miyashita, Masahiro; Miyagawa, Hisashi [Kyoto Univ. (Japan). Department of Agriculture

    2003-05-01

    The metabolic flux of two phenylpropanoid metabolites, N-p-coumaroyloctopamine (p-CO) and chlorogenic acid (CGA), in the wound-healing potato tuber tissue was quantitatively analyzed by a newly developed method based upon the tracer experiment using stable isotope-labeled compounds and LC-MS. Tuber disks were treated with aqueous solution of L-phenyl-d{sub 5}-alanine, and the change in the ratio of stable isotope-labeled compound to non-labeled (isotope abundance) was monitored for p-CO and CGA in the tissue extract by LC-MS. The time-dependent change in the isotope abundance of each metabolite was fitted to an equation that was derived from the formation and conversion kinetics of each compound. Good correlations were obtained between the observed and calculated isotope abundances for both p-CO and CGA. The rates of p-CO formation and conversion (i.e. fluxes) were 1.15 and 0.96 nmol (g FW){sup -1}h{sup -1}, respectively, and for CGA, the rates 4.63 and 0.42 nmol (g FW){sup -1}h{sup -1}, respectively. This analysis enabled a direct comparison of the biosynthetic activity between these two compounds. (author)

  10. Flight muscle enzymes and metabolic flux rates during hovering flight of the nectar bat, Glossophaga soricina: further evidence of convergence with hummingbirds.

    Science.gov (United States)

    Suarez, R K; Welch, K C; Hanna, S K; Herrera M, L G

    2009-06-01

    Given their high metabolic rates, nectarivorous diet, and ability to directly fuel their energetically-expensive flight using recently-ingested sugar, we tested the hypothesis that Pallas long tongued nectar bats (Glossophaga soricina) possess flight muscles similar to those of hummingbirds with respect to enzymatic flux capacities in bioenergetic pathways. In addition, we compared these biochemical capacities with flux rates achieved in vivo during hovering flight. Rates of oxygen consumption (V(O(2))) were measured during hover-feeding and used to estimate rates of ATP turnover, glucose and long-chain fatty acid oxidation per unit mass of flight muscle. Enzyme V(max) values at key steps in glucose and fatty acid oxidation obtained in vitro from pectoralis muscle samples exceed those found in the locomotory muscles of other species of small mammals and resemble data obtained from hummingbird flight muscles. The ability of nectar bats and hummingbirds to hover in fed and fasted states, fueled almost exclusively by carbohydrate or fat, respectively, allowed the estimation of fractional velocities (v/V(max)) at both the hexokinase and carnitine palmitoyltransferase-2 steps in glucose and fatty acid oxidation, respectively. The results further support the hypothesis of convergent evolution in biochemical and physiological traits in nectar bats and hummingbirds.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  12. [Association of fat distribution with metabolic syndrome in patients with polycystic ovary syndrome].

    Science.gov (United States)

    Luo, Xiaoyan; Xu, Liangzhi

    2012-09-01

    To study the characteristics of the metabolic syndrome (MS) in patients with polycystic ovary syndrome (PCOS). Oral glucose tolerance test (OGTT) was performed in 336 patients with PCOS, and the serum levels triglycerides (TG), total cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol and testosterone were measured. The total incidence of MS was 18.8% in these 336 patients with PCOS. The incidence of MS increased with percent body fat (%BF) and lipid accumulation product (LAP) in patients with PCOS. The patients at child-bearing age appeared to have a higher incidence of MS than those in puberty. The muscle distribution coefficient, age, body mass index, and the metabolic parameters were all higher in patients with MS than in those without MS. The bilateral lower limb muscle strength were lower in patients with MS than in those without, but the level of testosterone showed no significant difference between them. The risk of MS increases with BF%, age and LAP in patients with PCOS.

  13. The role of Monosaccharide Transport Proteins in carbohydrate assimilation, distribution, metabolism and homeostasis

    Science.gov (United States)

    Cura, Anthony J.; Carruthers, Anthony

    2012-01-01

    The facilitated diffusion of glucose, galactose, fructose, urate, myoinositol and dehydroascorbic acid in mammals is catalyzed by a family of 14 monosaccharide transport proteins called GLUTs. These transporters may be divided into 3 classes according to sequence similarity and function/substrate specificity. GLUT1 appears to be highly expressed in glycolytically active cells and has been co-opted in vitamin C auxotrophs to maintain the redox state of the blood through transport of dehydroascorbate. Several GLUTs are definitive glucose/galactose transporters, GLUT2 and GLUT5 are physiologically important fructose transporters, GLUT9 appears to be a urate transporter while GLUT13 (HMIT1) is a proton/myoinositol co-transporter. The physiologic substrates of some GLUTs remain to be established. The GLUTs are expressed in a tissue specific manner where affinity, specificity and capacity for substrate transport are paramount for tissue function. Although great strides have been made in characterizing GLUT-catalyzed monosaccharide transport and mapping GLUT membrane topography and determinants of substrate specificity, a unifying model for GLUT structure and function remains elusive. The GLUTs play a major role in carbohydrate homeostasis and the redistribution of sugar-derived carbons among the various organ systems. This is accomplished through a multiplicity of GLUT-dependent glucose sensing and effector mechanisms that regulate monosaccharide ingestion, absorption, distribution, cellular transport and metabolism and recovery/retention. Glucose transport and metabolism have co-evolved in mammals to support cerebral glucose utilization. PMID:22943001

  14. Association of erythrocyte deformability with red blood cell distribution width in metabolic diseases and thalassemia trait.

    Science.gov (United States)

    Vayá, Amparo; Alis, Rafael; Suescún, Marta; Rivera, Leonor; Murado, Julian; Romagnoli, Marco; Solá, Eva; Hernandez-Mijares, Antonio

    2015-01-01

    Increased red blood distribution width (RDW) in anemia is related to disturbances in the cellular surface/volume ratio, usually accompanied by morphological alterations, while it has been shown in inflammatory diseases that the activity of pro-inflammatory cytokines disturbing erythropoiesis increases RDW. Recently it has been reported that higher RDW is related with decreased erythrocyte deformability, and that it could be related with the association of RDW and increased risk of cardiovascular diseases. In order to analyze the influence of morphological alterations and proinflammatory status on the relationship between RDW and erythrocyte deformability, we analyzed erythrocyte deformability along with RDW and other hematological and biochemical parameters in 36 α-thalassemia, 20 β-thalassemia, 20 δβ-thalassemia trait carriers, 61 metabolic syndrome patients and 76 morbidly obese patients. RDW correlated inversely with erythrocyte deformability in minor β-thalassemia (r =-0.530, p thalassemia is often accompanied by more marked cell-shaped perturbations than other thalassemia traits. This could be the reason for this negative association only in this setting. Higher anisocytosis seems to be associated with greater morphologic alterations (shape/volume), which reduce erythrocyte deformability. The proinflammatory profile in metabolic patients can be related to the positive association of RDW with erythrocyte deformability found in these patients. However, further research is needed to explain the mechanisms underlying this association.

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

    Directory of Open Access Journals (Sweden)

    F. Gazeau

    2005-01-01

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

  16. Evaluation of magnetic flux distribution from magnetic domains in [Co/Pd] nanowires by magnetic domain scope method using contact-scanning of tunneling magnetoresistive sensor

    Energy Technology Data Exchange (ETDEWEB)

    Okuda, Mitsunobu, E-mail: okuda.m-ky@nhk.or.jp; Miyamoto, Yasuyoshi; Miyashita, Eiichi; Hayashi, Naoto [NHK Science and Technology Research Laboratories, 1-10-11 Kinuta Setagaya, Tokyo 157-8510 (Japan)

    2014-05-07

    Current-driven magnetic domain wall motions in magnetic nanowires have attracted great interests for physical studies and engineering applications. The magnetic force microscope (MFM) is widely used for indirect verification of domain locations in nanowires, where relative magnetic force between the local domains and the MFM probe is used for detection. However, there is an occasional problem that the magnetic moments of MFM probe influenced and/or rotated the magnetic states in the low-moment nanowires. To solve this issue, the “magnetic domain scope for wide area with nano-order resolution (nano-MDS)” method has been proposed recently that could detect the magnetic flux distribution from the specimen directly by scanning of tunneling magnetoresistive field sensor. In this study, magnetic domain structure in nanowires was investigated by both MFM and nano-MDS, and the leakage magnetic flux density from the nanowires was measured quantitatively by nano-MDS. Specimen nanowires consisted from [Co (0.3)/Pd (1.2)]{sub 21}/Ru(3) films (units in nm) with perpendicular magnetic anisotropy were fabricated onto Si substrates by dual ion beam sputtering and e-beam lithography. The length and the width of the fabricated nanowires are 20 μm and 150 nm. We have succeeded to obtain not only the remanent domain images with the detection of up and down magnetizations as similar as those by MFM but also magnetic flux density distribution from nanowires directly by nano-MDS. The obtained value of maximum leakage magnetic flux by nano-MDS is in good agreement with that of coercivity by magneto-optical Kerr effect microscopy. By changing the protective diamond-like-carbon film thickness on tunneling magnetoresistive sensor, the three-dimensional spatial distribution of leakage magnetic flux could be evaluated.

  17. Androgenicity in relation to body fat distribution and metabolism in 38-year-old women--the European Fat Distribution Study

    NARCIS (Netherlands)

    Seidell, J C; Cigolini, M; Charzewska, J; Ellsinger, B M; Di Biase, G; Björntorp, P; Hautvast, J.G.A.J.; Contaldo, F; Szostak, V; Scuro, L A

    1990-01-01

    We studied fat distribution and metabolic risk factors in 434 38-year old women selected from population registrars in 5 cities in different parts of Europe. In the present study we focussed on the geographical variation in serum concentrations of free testosterone and its relation to measures of

  18. Uptake, tissue distribution and metabolism of the insecticide endosulfan in Jenynsia multidentata (Anablepidae, Cyprinodontiformes).

    Science.gov (United States)

    Ballesteros, M L; Gonzalez, M; Wunderlin, D A; Bistoni, M A; Miglioranza, K S B

    2011-06-01

    The study reports the accumulation, distribution and metabolism of technical endosulfan in Jenynsia multidentata. Adult females were exposed to acute sublethal concentrations (0.072, 0.288 and 1.4 μg L⁻¹). After 24 h, fish were sacrificed and gills, liver, brain, intestine and muscle were removed. Results show that both isomers of technical-grade endosulfan (α- and β-) are accumulated in fish tissues and biotransformation to endosulfan sulfate occurs at all concentrations tested. Significantly differences in endosulfan accumulation were only found at 1.4 μg L⁻¹ but not between the lowest concentrations. However a similar distribution pattern was observed at all exposure levels where liver, intestine and brain had the highest levels of α-, β-endosulfan and endosulfan sulfate. Moreover, liver and brain showed the highest endosulfan sulfate:α-endosulfan ratios due to high biotransfomation capacity. J. multidentata demonstrated to be a sensitive species under exposure to technical endosulfan and, therefore, could be used to assess aquatic pollution. Copyright © 2011 Elsevier Ltd. All rights reserved.

  19. Absorption, distribution, metabolism and excretion of 14C-chlorphenesin carbamate in rats

    International Nuclear Information System (INIS)

    Nozu, Takashi; Aoyagi, Tadao; Setoyama, Kageyoshi; Suwa, Toshio; Tanaka, Ichiro

    1977-01-01

    Absorption, distribution, metabolism and excretion of chlorphenesin carbamate (CPC), a central acting muscle relaxant, were investigated in rats by use of 14 C-labeled CPC. After oral administration, 14 C-CPC was well absorbed from gastrointestinal tract and about 90% of the given radioactivity was excreted in urine and 5% in feces during 5 days. Approximately 36% was recovered in bile during 8 hr after oral administration. The highest blood level of 14 C was observed at 3-8 hr after oral administration and decreased slowly. The radioactivity was distributed widely in almost all tissues. The highest concentration of 14 C was observed in the liver and the higher was detected in the brain and spinal cord, suggesting a pharmacological effect of CPC. In pregnant rats given 14 C-CPC orally, the radioactivity in the fetuses was below 0.8% of the dose at 1-24 hr. The major metabolites in 48 hr urine was identified as CPC-glucuronide and the acidic metabolites, p-chlorophenoxylactic acid, p-chlorophenoxyacetic acid and p-chlorophenol, were also detected. After intravenous injection of the 14 C-labeled acidic metabolites, the radioactivity was not detected in the central nervous system and excreted rapidly. In the case of repeated administration of CPC and 14 C-CPC for 21 days, the radioactivity did not accumulated in any tissue of rats. (auth.)

  20. Uptake, tissue distribution and metabolism of the insecticide endosulfan in Jenynsia multidentata (Anablepidae, Cyprinodontiformes)

    Energy Technology Data Exchange (ETDEWEB)

    Ballesteros, M.L., E-mail: mlballesteros@efn.uncor.edu [Universidad Nacional de Cordoba, Facultad de Ciencias Exactas Fisicas y Naturales, Catedra Diversidad Animal II, Av. Velez Sarsfield 299, 5000 Cordoba (Argentina); Universidad Nacional de Mar del Plata, Facultad de Ciencias Exactas y Naturales, Laboratorio de Ecotoxicologia, Funes 3350, 7600 Mar del Plata (Argentina); Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET) (Argentina); Gonzalez, M. [Universidad Nacional de Mar del Plata, Facultad de Ciencias Exactas y Naturales, Laboratorio de Ecotoxicologia, Funes 3350, 7600 Mar del Plata (Argentina); Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET) (Argentina); Wunderlin, D.A. [Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET) (Argentina); Universidad Nacional de Cordoba-CONICET, Facultad de Ciencias Quimicas, Dto. Quimica Organica-CIBICI, Haya de la Torre y Medina Allende, Ciudad Universitaria, 5000 Cordoba (Argentina); Bistoni, M.A. [Universidad Nacional de Cordoba, Facultad de Ciencias Exactas Fisicas y Naturales, Catedra Diversidad Animal II, Av. Velez Sarsfield 299, 5000 Cordoba (Argentina); Miglioranza, K.S.B. [Universidad Nacional de Mar del Plata, Facultad de Ciencias Exactas y Naturales, Laboratorio de Ecotoxicologia, Funes 3350, 7600 Mar del Plata (Argentina); Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET) (Argentina)

    2011-06-15

    The study reports the accumulation, distribution and metabolism of technical endosulfan in Jenynsia multidentata. Adult females were exposed to acute sublethal concentrations (0.072, 0.288 and 1.4 {mu}g L{sup -1}). After 24 h, fish were sacrificed and gills, liver, brain, intestine and muscle were removed. Results show that both isomers of technical-grade endosulfan ({alpha}- and {beta}-) are accumulated in fish tissues and biotransformation to endosulfan sulfate occurs at all concentrations tested. Significantly differences in endosulfan accumulation were only found at 1.4 {mu}g L{sup -1} but not between the lowest concentrations. However a similar distribution pattern was observed at all exposure levels where liver, intestine and brain had the highest levels of {alpha}-, {beta}-endosulfan and endosulfan sulfate. Moreover, liver and brain showed the highest endosulfan sulfate:{alpha}-endosulfan ratios due to high biotransfomation capacity. J. multidentata demonstrated to be a sensitive species under exposure to technical endosulfan and, therefore, could be used to assess aquatic pollution. - Highlights: > Acute exposure of Jenynsia multidentata to technical-grade endosulfan. > Endosulfan bioaccumulation in different organs of Jenynsia multidentata. > Technical-grade endosulfan biotransformation to endosulfan sulfate. - Endosulfan is accumulated in organs of J. multidentata as well as biotransformed to endosulfan sulfate, which relative abundance points out the time from exposure.

  1. Uptake, tissue distribution and metabolism of the insecticide endosulfan in Jenynsia multidentata (Anablepidae, Cyprinodontiformes)

    International Nuclear Information System (INIS)

    Ballesteros, M.L.; Gonzalez, M.; Wunderlin, D.A.; Bistoni, M.A.; Miglioranza, K.S.B.

    2011-01-01

    The study reports the accumulation, distribution and metabolism of technical endosulfan in Jenynsia multidentata. Adult females were exposed to acute sublethal concentrations (0.072, 0.288 and 1.4 μg L -1 ). After 24 h, fish were sacrificed and gills, liver, brain, intestine and muscle were removed. Results show that both isomers of technical-grade endosulfan (α- and β-) are accumulated in fish tissues and biotransformation to endosulfan sulfate occurs at all concentrations tested. Significantly differences in endosulfan accumulation were only found at 1.4 μg L -1 but not between the lowest concentrations. However a similar distribution pattern was observed at all exposure levels where liver, intestine and brain had the highest levels of α-, β-endosulfan and endosulfan sulfate. Moreover, liver and brain showed the highest endosulfan sulfate:α-endosulfan ratios due to high biotransfomation capacity. J. multidentata demonstrated to be a sensitive species under exposure to technical endosulfan and, therefore, could be used to assess aquatic pollution. - Highlights: → Acute exposure of Jenynsia multidentata to technical-grade endosulfan. → Endosulfan bioaccumulation in different organs of Jenynsia multidentata. → Technical-grade endosulfan biotransformation to endosulfan sulfate. - Endosulfan is accumulated in organs of J. multidentata as well as biotransformed to endosulfan sulfate, which relative abundance points out the time from exposure.

  2. The effects of the uncertainties in geothermal heat flux distribution on the present-day Greenland Ice Sheet

    Science.gov (United States)

    Rogozhina, I.; Hagedoorn, J. M.; Martinec, Z.; Fleming, K.; Soucek, O.; Greve, R.; Thomas, M.

    2012-04-01

    The thermodynamic state of basal ice layers determines to a large extent the overall dynamic behavior of grounded ice masses, especially by (i) the formation of basal temperate ice that undergoes enhanced deformation, and (ii) by the process of basal melting, which controls sliding processes and most basal transport phenomena. One of major uncertainties in understanding the basal thermal conditions of the Greenland Ice Sheet (GIS) originates from our poor knowledge of the geothermal heat flux (GHF) that enters basal ice layers from the underlying bedrock. This study analyzes the range of results that arise from the models of the present-day GIS due to ill-constrained GHF distribution in the Greenland region. Within the context of dynamic GIS modeling, we consider the following questions: (i) What is the significance of the differences between the existing GHF models for thermomechanical ice-sheet modeling studies dealing with the past evolution and present-day state of the GIS? (ii) How well do paleoclimatic simulations controlled by each GHF model agree with the today's knowledge of the GIS's thermal state and thickness? (iii) What portion of the misfit between the ice-sheet model results and observations can be attributed to other source of uncertainties, namely the GIS history. In order to answer these questions, we consider three GHF models available in the published literature, based on the tectonic-regionalization model (Pollack et al. [1993]), seismic-tomography model (Shapiro and Ritzwoller [2004]) and magnetic-data model (Fox Maule et al. [2009]) and use these models to force paleoclimatic ice-sheet simulations throughout the last 150 thousand years of the GIS history. From the results of paleoclimatic simulations and sensitivity experiments, we conclude that differences in the GHF maps have a major effect on the history and present-day state of the GIS, exerting a strong influence on the evolution and current thermal regime of its basal layer. The ice

  3. Stage-Specific Fatty Acid Fluxes Play a Regulatory Role in Glycerolipid Metabolism during Seed Development in Jatropha curcas L.

    Science.gov (United States)

    Chaitanya, Bharatula Sri Krishna; Kumar, Sumit; Kaki, Shiva Shanker; Balakrishna, Marrapu; Karuna, Mallampalli Sri Lakshmi; Prasad, Rachapudi Badari Narayana; Sastry, Pidaparty Seshadri; Reddy, Attipalli Ramachandra

    2015-12-23

    The present study describes the changes in lipid profile as well as fatty acid fluxes during seed development in Jatropha curcas L. Endosperm from 34, 37, and 40 days after anthesis (DAA), incubated with [(14)C]acetate, showed significant synthesis of phosphatidylcholine (PC) at seed maturation. The fatty acid methyl ester profile showed PC from 34 DAA was rich in palmitic acid (16:0), whereas PC from 37 and 40 DAA was rich in oleic acid (18:1n-9). Molecular species analysis of diacylglycerol (DAG) indicated DAG (16:0/18:2n-6) was in abundance at 34 DAA, whereas DAG (18:1n-9/18:2n-6) was significantly high at 40 DAA. Triacylglycerol (TAG) analysis revealed TAG (16:0/18:2n-6/16:0) was abundant at 34 DAA, whereas TAG (18:1n-9/18:2n-6/18:1n-9) formed the majority at 40 DAA. Expression of two types of diacylglycerol acyltransferases varied with seed maturation. These data demonstrate stage-specific distinct pools of PC and DAG synthesis during storage TAG accumulation in Jatropha seed.

  4. Validation of absolute axial neutron flux distribution calculations with MCNP with 197Au(n,γ)198Au reaction rate distribution measurements at the JSI TRIGA Mark II reactor.

    Science.gov (United States)

    Radulović, Vladimir; Štancar, Žiga; Snoj, Luka; Trkov, Andrej

    2014-02-01

    The calculation of axial neutron flux distributions with the MCNP code at the JSI TRIGA Mark II reactor has been validated with experimental measurements of the (197)Au(n,γ)(198)Au reaction rate. The calculated absolute reaction rate values, scaled according to the reactor power and corrected for the flux redistribution effect, are in good agreement with the experimental results. The effect of different cross-section libraries on the calculations has been investigated and shown to be minor. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. Distribution, Community Composition, and Potential Metabolic Activity of Bacterioplankton in an Urbanized Mediterranean Sea Coastal Zone.

    Science.gov (United States)

    Richa, Kumari; Balestra, Cecilia; Piredda, Roberta; Benes, Vladimir; Borra, Marco; Passarelli, Augusto; Margiotta, Francesca; Saggiomo, Maria; Biffali, Elio; Sanges, Remo; Scanlan, David J; Casotti, Raffaella

    2017-09-01

    Bacterioplankton are fundamental components of marine ecosystems and influence the entire biosphere by contributing to the global biogeochemical cycles of key elements. Yet, there is a significant gap in knowledge about their diversity and specific activities, as well as environmental factors that shape their community composition and function. Here, the distribution and diversity of surface bacterioplankton along the coastline of the Gulf of Naples (GON; Italy) were investigated using flow cytometry coupled with high-throughput sequencing of the 16S rRNA gene. Heterotrophic bacteria numerically dominated the bacterioplankton and comprised mainly Alphaproteobacteria , Gammaproteobacteria , and Bacteroidetes Distinct communities occupied river-influenced, coastal, and offshore sites, as indicated by Bray-Curtis dissimilarity, distance metric (UniFrac), linear discriminant analysis effect size (LEfSe), and multivariate analyses. The heterogeneity in diversity and community composition was mainly due to salinity and changes in environmental conditions across sites, as defined by nutrient and chlorophyll a concentrations. Bacterioplankton communities were composed of a few dominant taxa and a large proportion (92%) of rare taxa (here defined as operational taxonomic units [OTUs] accounting for bacterioplankton in coastal zones is of critical importance, considering that these areas are highly productive and anthropogenically impacted. Their richness and evenness, as well as their potential activity, are very important to assess ecosystem health and functioning. Here, we investigated bacterial distribution, community composition, and potential metabolic activity in the GON, which is an ideal test site due to its heterogeneous environment characterized by a complex hydrodynamics and terrestrial inputs of varied quantities and quality. Our study demonstrates that bacterioplankton communities in this region are highly diverse and strongly regulated by a combination of

  6. Local Neutron Flux Distribution Measurements by Wire-Dosimetry in the AMMON Experimental Program in the EOLE Reactor

    Directory of Open Access Journals (Sweden)

    Gruel A.

    2016-01-01

    Full Text Available Dosimetry measurements were carried out during the AMMON experimental program, in the EOLE facility. Al-0.1 wt% Au wires were positioned along curved fuel plates of JHR-type assemblies to investigate the azimuthal and axial gold capture rate profiles, directly linked to the thermal and epithermal flux. After irradiation, wires were cut into small segments (a few mm, and the gold capture rate of each part was measured by gamma spectrometry on the MADERE platform. This paper presents results in the “hafnium” configuration, and more specifically the azimuthal flux profile characterization. The final uncertainty on each measured wire lies below 1% (at 2 standard deviations. Experimental profiles are in a good agreement against Monte Carlo calculations, and the 4% capture rate increase at the plate edge is well observed. The flux dissymmetry due to assembly position in the core is also measured, and shows a 10% discrepancy between the two edges of the plate.

  7. Topographical body fat distribution links to amino acid and lipid metabolism in healthy obese women [corrected].

    Directory of Open Access Journals (Sweden)

    Francois-Pierre J Martin

    Full Text Available Visceral adiposity is increasingly recognized as a key condition for the development of obesity related disorders, with the ratio between visceral adipose tissue (VAT and subcutaneous adipose tissue (SAT reported as the best correlate of cardiometabolic risk. In this study, using a cohort of 40 obese females (age: 25-45 y, BMI: 28-40 kg/m(2 under healthy clinical conditions and monitored over a 2 weeks period we examined the relationships between different body composition parameters, estimates of visceral adiposity and blood/urine metabolic profiles. Metabonomics and lipidomics analysis of blood plasma and urine were employed in combination with in vivo quantitation of body composition and abdominal fat distribution using iDXA and computerized tomography. Of the various visceral fat estimates, VAT/SAT and VAT/total abdominal fat ratios exhibited significant associations with regio-specific body lean and fat composition. The integration of these visceral fat estimates with metabolic profiles of blood and urine described a distinct amino acid, diacyl and ether phospholipid phenotype in women with higher visceral fat. Metabolites important in predicting visceral fat adiposity as assessed by Random forest analysis highlighted 7 most robust markers, including tyrosine, glutamine, PC-O 44∶6, PC-O 44∶4, PC-O 42∶4, PC-O 40∶4, and PC-O 40∶3 lipid species. Unexpectedly, the visceral fat associated inflammatory profiles were shown to be highly influenced by inter-days and between-subject variations. Nevertheless, the visceral fat associated amino acid and lipid signature is proposed to be further validated for future patient stratification and cardiometabolic health diagnostics.

  8. Regional blood flow distribution and oxygen metabolism during mesenteric ischemia and congestion.

    Science.gov (United States)

    Cruz, Ruy J; Garrido, Alejandra G; Ribeiro, Cristiane M F; Harada, Tomoyuki; Rocha-e-Silva, Mauricio

    2010-06-01

    Acute mesenteric ischemia is a potentially fatal vascular emergency with mortality rates ranging between 60% and 80%. Several studies have extensively examined the hemodynamic and metabolic effects of superior mesenteric artery occlusion. On the other hand, the cardiocirculatory derangement and the tissue damage induced by intestinal outflow obstruction have not been investigated systematically. For these reasons we decided to assess the initial impact of venous mesenteric occlusion on intestinal blood flow distribution, and correlate these findings with other systemic and regional perfusion markers. Fourteen mongrel dogs were subjected to 45 min of superior mesenteric artery (SMAO) or vein occlusion (SMVO), and observed for 120 min after reperfusion. Systemic hemodynamics were evaluated using Swan-Ganz and arterial catheters. Regional blood flow (ultrasonic flow probes), intestinal O(2)-derived variables, and mesenteric-arterial and tonometric-arterial pCO(2) gradients (D(mv-a)pCO(2) and D(t-a)pCO(2)) were also calculated. SMVO was associated with hypotension and low cardiac output. A significant increase in the regional pCO(2) gradients was also observed in both groups during the ischemic period. After reperfusion, a progressive reduction in D(mv-a)pCO(2) occurred in the SMVO group; however, no improvement in D(t-a)pCO(2) was observed. The histopathologic injury scores were 2.7 +/- 0.5 and 4.8 +/- 0.2 for SMAO and SMVO, respectively. SMV occlusion promoted early and significant hemodynamic and metabolic derangement at systemic and regional levels. Additionally, systemic pCO(2) gradient is not a reliable parameter to evaluate the local intestinal oxygenation. Finally, the D(t-a)pCO(2) correlates with histologic changes during intestinal congestion or ischemia. However, minor histologic changes cannot be detected using this methodology. Copyright (c) 2010 Elsevier Inc. All rights reserved.

  9. Predicted Water and Carbon Fluxes as well as Vegetation Distribution on the Korean Peninsula in the Future with the Ecosystem Demography Model version 2

    Science.gov (United States)

    Kim, J. B.; Kim, Y.

    2017-12-01

    This study investigates how the water and carbon fluxes as well as vegetation distribution on the Korean peninsula would vary with climate change. Ecosystem Demography (ED) Model version 2 (ED2) is used in this study, which is an integrated terrestrial biosphere model that can utilize a set of size- and age- structured partial differential equations that track the changing structure and composition of the plant canopy. With using the vegetation distribution data of Jeju Island, located at the southern part of the Korean Peninsula, ED2 is setup and driven for the past 10 years. Then the results of ED2 are evaluated and adjusted with observed forestry data, i.e., growth and mortality, and the flux tower and MODIS satellite data, i.e., evapotranspiration (ET) and gross primary production (GPP). This adjusted ED2 are used to simulate the water and carbon fluxes as well as vegetation dynamics in the Korean Peninsula for the historical period with evaluating the model against the MODIS satellite data. Finally, the climate scenarios of RCP 2.6 and 6.0 are used to predict the fluxes and vegetation distribution of the Korean Peninsula in the future. With using the state-of-art terrestrial ecosystem model, this study would provide us better understanding of the future ecosystem vulnerability of the Korean Peninsula. AcknowledgementsThis work was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT & Future Planning (2015R1C1A2A01054800) and by the Korea Meteorological Administration R&D Program under Grant KMIPA 2015-6180. This work was also supported by the Yonsei University Future-leading Research Initiative of 2015(2016-22-0061).

  10. Mono-Heteromeric Configurations of Gap Junction Channels Formed by Connexin43 and Connexin45 Reduce Unitary Conductance and Determine both Voltage Gating and Metabolic Flux Asymmetry

    Science.gov (United States)

    Zhong, Guoqiang; Akoum, Nazem; Appadurai, Daniel A.; Hayrapetyan, Volodya; Ahmed, Osman; Martinez, Agustin D.; Beyer, Eric C.; Moreno, Alonso P.

    2017-01-01

    In cardiac tissues, the expression of multiple connexins (Cx40, Cx43, Cx45, and Cx30.2) is a requirement for proper development and function. Gap junctions formed by these connexins have distinct permeability and gating mechanisms. Since a single cell can express more than one connexin isoform, the formation of hetero-multimeric gap junction channels provides a tissue with an enormous repertoire of combinations to modulate intercellular communication. To study further the perm-selectivity and gating properties of channels containing Cx43 and Cx45, we studied two monoheteromeric combinations in which a HeLa cell co-transfected with Cx43 and Cx45 was paired with a cell expressing only one of these connexins. Macroscopic measurements of total conductance between cell pairs indicated a drastic reduction in total conductance for mono-heteromeric channels. In terms of Vj dependent gating, Cx43 homomeric connexons facing heteromeric connexons only responded weakly to voltage negativity. Cx45 homomeric connexons exhibited no change in Vj gating when facing heteromeric connexons. The distributions of unitary conductances (γj) for both mono-heteromeric channels were smaller than predicted, and both showed low permeability to the fluorescent dyes Lucifer yellow and Rhodamine123. For both mono-heteromeric channels, we observed flux asymmetry regardless of dye charge: flux was higher in the direction of the heteromeric connexon for MhetCx45 and in the direction of the homomeric Cx43 connexon for MhetCx43. Thus, our data suggest that co-expression of Cx45 and Cx43 induces the formation of heteromeric connexons with greatly reduced permeability and unitary conductance. Furthermore, it increases the asymmetry for voltage gating for opposing connexons, and it favors asymmetric flux of molecules across the junction that depends primarily on the size (not the charge) of the crossing molecules. PMID:28611680

  11. Common variants near MC4R in relation to body fat, body fat distribution, metabolic traits and energy expenditure

    DEFF Research Database (Denmark)

    Kring, Sofia Inez Iqbal; Holst, C; Toubro, Søren

    2010-01-01

    Common variants near melanocortin receptor 4 (MC4R) have been related to fatness and type 2 diabetes. We examined the associations of rs17782313 and rs17700633 in relation to body fat, body fat distribution, metabolic traits, weight development and energy expenditure....

  12. [Absorption, distribution, metabolism and excretion of T-3761, a new quinolone derivative, in experimental animals].

    Science.gov (United States)

    Minami, S; Takahata, M; Hayashi, T; Kumano, K; Ikeda, Y; Noumi, T; Takagi, S; Oogake, N; Tsuneda, R; Maehana, J

    1995-05-01

    We studied the absorption, distribution, metabolism and excretion of T-3761, a new quinolone derivative, in experimental animals. The following results were obtained. 1. The peak serum levels of T-3761 after a single oral administration to various fasting animals at a dose of 5 mg/kg were high in the order of rats, dogs, mice and rabbits, showing favorable absorption in all animals except for rabbits. In mice and rats, T-3761 showed higher peak serum levels than ofloxacin and ciprofloxacin but T-3761 were more rapidly eliminated from serum than ofloxacin and ciprofloxacin. 2. Tissue concentrations of T-3761 in rats were similar to those of ofloxacin but its ratio of tissue to serum levels were lower than those of ofloxacin. 3. Urinary excretion of T-3761 as active form until 24 hours after oral administration was 27.3%, 63.1%, 41.0% and 63.3% in mice, rats, rabbits and dogs, respectively. Only unchanged T-3761 was detected as active form in urine of all animals tested. In rats, urinary concentrations until 2 hours after administration were higher than those of ofloxacin. 4. Biliary excretion of T-3761 in mice and rats were 2.9% and 1.4% as active form. 5. The absorption of T-3761 was not different in male and female rats or 8 and 14 weeks old rats. The meal lowered absorption of T-3761 in rats. There was no significant difference in serum levels, urinary excretion and distribution to tissues after multiple administration of T-3761 comparing with its single administration. 6. In rats with liver dysfunction induced by D-galactosamine, the serum levels and urinary excretion were slightly higher than in normal rats. On the other hands, in rats with kidney dysfunction induced by HgCl2, the serum levels were significantly higher and urinary excretion of T-3761 was significantly lower than in normal rats. Above results show that T-3761 has unique characteristics in absorption, excretion and distribution after oral administration to animals among new quinolones, i.e., T

  13. Distinct clinical and metabolic deficits in PCA and AD are not related to amyloid distribution.

    Science.gov (United States)

    Rosenbloom, M H; Alkalay, A; Agarwal, N; Baker, S L; O'Neil, J P; Janabi, M; Yen, I V; Growdon, M; Jang, J; Madison, C; Mormino, E C; Rosen, H J; Gorno-Tempini, M L; Weiner, M W; Miller, B L; Jagust, W J; Rabinovici, G D

    2011-05-24

    Patients with posterior cortical atrophy (PCA) often have Alzheimer disease (AD) at autopsy, yet are cognitively and anatomically distinct from patients with clinical AD. We sought to compare the distribution of β-amyloid and glucose metabolism in PCA and AD in vivo using Pittsburgh compound B (PiB) and FDG-PET. Patients with PCA (n = 12, age 57.5 ± 7.4, Mini-Mental State Examination [MMSE] 22.2 ± 5.1), AD (n = 14, age 58.8 ± 9.6, MMSE 23.8 ± 6.7), and cognitively normal controls (NC, n = 30, age 73.6 ± 6.4) underwent PiB and FDG-PET. Group differences in PiB distribution volume ratios (DVR, cerebellar reference) and FDG uptake (pons-averaged) were assessed on a voxel-wise basis and by comparing binding in regions of interest (ROIs). Compared to NC, both patients with AD and patients with PCA showed diffuse PiB uptake throughout frontal, temporoparietal, and occipital cortex (p PCA and AD even after correcting for atrophy. FDG patterns in PCA and AD were distinct: while both groups showed hypometabolism compared to NC in temporoparietal cortex and precuneus/posterior cingulate, patients with PCA further showed hypometabolism in inferior occipitotemporal cortex compared to both NC and patients with AD (p PCA. Fibrillar amyloid deposition in PCA is diffuse and similar to AD, while glucose hypometabolism extends more posteriorly into occipital cortex. Further studies are needed to determine the mechanisms of selective network degeneration in focal variants of AD.

  14. Estimating the geographical distribution of the prevalence of the metabolic syndrome in young Mexicans

    Directory of Open Access Journals (Sweden)

    Miguel Murguía-Romero

    2012-09-01

    Full Text Available The geographical distribution of the metabolic syndrome (MetS prevalence in young Mexicans (aged 17-24 years was estimated stepwise starting from its prevalence based on the body mass index (BMI in a study of 3,176 undergraduate students of this age group from Mexico City. To estimate the number of people with MetS by state, we multiplied its prevalence derived from the BMI range found in the Mexico City sample by the BMI proportions (range and state obtained from the Mexico 2006 national survey on health and nutrition. Finally, to estimate the total number of young people with MetS in Mexico, its prevalence by state was multiplied by the share of young population in each state according to the National Population and Housing Census 2010. Based on these figures, we estimated the national prevalence of MetS at 15.8%, the average BMI at 24.1 (standard deviation = 4.2, and the prevalence of overweight people (BMI ≥25 of that age group at 39.0%. These results imply that 2,588,414 young Mexicans suffered from MetS in 2010. The Yucatan peninsula in the south and the Sonora state in the north showed the highest rates of MetS prevalence. The calculation of the MetS prevalence by BMI range in a sample of the population, and extrapolating it using the BMI proportions by range of the total population, was found to be a useful approach. We conclude that the BMI is a valuable public health tool to estimate MetS prevalence in the whole country, including its geographical distribution.

  15. Transcriptomics, Targeted Metabolomics and Gene Expression of Blackberry Leaves and Fruits Indicate Flavonoid Metabolic Flux from Leaf to Red Fruit.

    Science.gov (United States)

    Gutierrez, Enrique; García-Villaraco, Ana; Lucas, José A; Gradillas, Ana; Gutierrez-Mañero, F Javier; Ramos-Solano, Beatriz

    2017-01-01

    Blackberries ( Rubus spp.) are among the high added value food products relevant for human health due to the increasing evidence of the beneficial effects of polyphenols, which are very abundant in these fruits. Interestingly, these compounds also play a role on plant physiology, being especially relevant their role in plant defense against biotic and abiotic stress. Hence, we hypothesize that since blackberry fruits have high amounts of flavonols and anthocyanins, leaves would also have high amounts of these compounds, and can be studied as a source of active molecules; furthermore, leaf synthesis would support their high contents in fruits. To explore this hypothesis, the present study reports a de novo transcriptome analysis on field grown blackberry leaves and fruits at the same time point, to establish the metabolic relationship of these compounds in both organs. Transcripts were aligned against Fragaria vesca genome, and genes were identified and annotated in different databases; tissue expression pattern showed 20,463 genes common to leaves and fruits, while 6,604 genes were significantly overexpressed only in fruits, while another 6,599 genes were significantly overexpressed in leaves, among which flavonol-anthocyanin transporter genes were present. Bioactives characterization indicated that total phenolics in leaves were three-fold, and flavonols were six-fold than in fruits, while concentration of anthocyanins was higher in fruits; HPLC-MS analysis indicated different composition in leaves and fruits, with cyanidin-3-glucoside as the only common compound identified. Next, RT-qPCR of the core genes in the flavonol anthocyanin pathway and regulatory MYB genes were carried out. Interestingly, genes in the flavonol-anthocyanin pathway and flavonol-transport families were overexpressed in leaves, consistent with the higher bioactive levels. On the other hand, transcription factors were overexpressed in fruits anticipating an active anthocyanin biosynthesis

  16. Spatial distribution of atomic and ion hydrogen flux and its effect on hydrogen recycling in long duration confined and non-confined plasmas

    Directory of Open Access Journals (Sweden)

    A. Kuzmin

    2017-08-01

    Full Text Available In order to understand the atomic hydrogen distribution in different kinds of plasma and its influence on the recycling, two kinds of plasmas were used: non-confined annular electron cyclotron resonance (ECR and confined long duration plasmas. The permeation probes are used to measure directly the atomic hydrogen flux at several poloidal positions. The permeation through metals due to the ion and atom component of the hydrogen flux to the wall is indistinguishable. To estimate the contribution of the ions directly, Langmuir probes were used. The Гinc profile behind the plasma facing components (PFCs is almost constant, ∼2 ×1018 H/s/m2.

  17. Estimating spatially distributed turbulent heat fluxes from high-resolution thermal imagery acquired with a UAV system.

    Science.gov (United States)

    Brenner, Claire; Thiem, Christina Elisabeth; Wizemann, Hans-Dieter; Bernhardt, Matthias; Schulz, Karsten

    2017-05-19

    In this study, high-resolution thermal imagery acquired with a small unmanned aerial vehicle (UAV) is used to map evapotranspiration (ET) at a grassland site in Luxembourg. The land surface temperature (LST) information from the thermal imagery is the key input to a one-source and two-source energy balance model. While the one-source model treats the surface as a single uniform layer, the two-source model partitions the surface temperature and fluxes into soil and vegetation components. It thus explicitly accounts for the different contributions of both components to surface temperature as well as turbulent flux exchange with the atmosphere. Contrary to the two-source model, the one-source model requires an empirical adjustment parameter in order to account for the effect of the two components. Turbulent heat flux estimates of both modelling approaches are compared to eddy covariance (EC) measurements using the high-resolution input imagery UAVs provide. In this comparison, the effect of different methods for energy balance closure of the EC data on the agreement between modelled and measured fluxes is also analysed. Additionally, the sensitivity of the one-source model to the derivation of the empirical adjustment parameter is tested. Due to the very dry and hot conditions during the experiment, pronounced thermal patterns developed over the grassland site. These patterns result in spatially variable turbulent heat fluxes. The model comparison indicates that both models are able to derive ET estimates that compare well with EC measurements under these conditions. However, the two-source model, with a more complex treatment of the energy and surface temperature partitioning between the soil and vegetation, outperformed the simpler one-source model in estimating sensible and latent heat fluxes. This is consistent with findings from prior studies. For the one-source model, a time-variant expression of the adjustment parameter (to account for the difference between

  18. Study on the radiation flux and temperature distributions of the concentrator-receiver system in a solar dish/Stirling power facility

    International Nuclear Information System (INIS)

    Li Zhigang; Tang Dawei; Du Jinglong; Li Tie

    2011-01-01

    Uniform heater temperature and high optical-thermal efficiency are crucial for the reliable and economical operation of a Solar Dish/Stirling engine facility. The Monte-Carlo ray-tracing method is utilized to predict the radiation flux distributions of the concentrator-receiver system. The ray-tracing method is first validated by experiment, then the radiation flux profiles on the solar receiver surface for faceted real concentrator and ideal paraboloidal concentrator, irradiated by Xe-arc lamps and real sun, for different aperture positions and receiver shapes are analyzed, respectively. The resulted radiation flux profiles are subsequently transferred to a CFD code as boundary conditions to numerically simulate the fluid flow and conjugate heat transfer in the receiver cavity by coupling the radiation, natural convection and heat conduction together, and the CFD method is also validated through experiment. The results indicate that a faceted concentrator in combination with a solar simulator composed of 12 Xe-arc lamps is advantageous to drive the solar Stirling engine for all-weather indoor tests. Based on the simulation results, a solar receiver-Stirling heater configuration is designed to achieve a considerably uniform temperature distribution on the heater head tubes while maintaining a high efficiency of 60.7%. - Highlights: → Radiation flux in Dish/Stirling system is analyzed by validated ray-tracing method. → Temperature field on the solar receiver is analyzed by a validated CFD method. → Effects of Xe-arc lamp solar simulator and faceted real concentrator are analyzed. → Effects of different receiver positions and receiver shapes are investigated. → A Stirling heater configuration is presented with uniform temperature field.

  19. SVD identifies transcript length distribution functions from DNA microarray data and reveals evolutionary forces globally affecting GBM metabolism.

    Directory of Open Access Journals (Sweden)

    Nicolas M Bertagnolli

    Full Text Available To search for evolutionary forces that might act upon transcript length, we use the singular value decomposition (SVD to identify the length distribution functions of sets and subsets of human and yeast transcripts from profiles of mRNA abundance levels across gel electrophoresis migration distances that were previously measured by DNA microarrays. We show that the SVD identifies the transcript length distribution functions as "asymmetric generalized coherent states" from the DNA microarray data and with no a-priori assumptions. Comparing subsets of human and yeast transcripts of the same gene ontology annotations, we find that in both disparate eukaryotes, transcripts involved in protein synthesis or mitochondrial metabolism are significantly shorter than typical, and in particular, significantly shorter than those involved in glucose metabolism. Comparing the subsets of human transcripts that are overexpressed in glioblastoma multiforme (GBM or normal brain tissue samples from The Cancer Genome Atlas, we find that GBM maintains normal brain overexpression of significantly short transcripts, enriched in transcripts that are involved in protein synthesis or mitochondrial metabolism, but suppresses normal overexpression of significantly longer transcripts, enriched in transcripts that are involved in glucose metabolism and brain activity. These global relations among transcript length, cellular metabolism and tumor development suggest a previously unrecognized physical mode for tumor and normal cells to differentially regulate metabolism in a transcript length-dependent manner. The identified distribution functions support a previous hypothesis from mathematical modeling of evolutionary forces that act upon transcript length in the manner of the restoring force of the harmonic oscillator.

  20. Association mapping of starch chain length distribution and amylose content in pea (Pisum sativum L.) using carbohydrate metabolism candidate genes.

    Science.gov (United States)

    Carpenter, Margaret A; Shaw, Martin; Cooper, Rebecca D; Frew, Tonya J; Butler, Ruth C; Murray, Sarah R; Moya, Leire; Coyne, Clarice J; Timmerman-Vaughan, Gail M

    2017-08-01

    Although starch consists of large macromolecules composed of glucose units linked by α-1,4-glycosidic linkages with α-1,6-glycosidic branchpoints, variation in starch structural and functional properties is found both within and between species. Interest in starch genetics is based on the importance of starch in food and industrial processes, with the potential of genetics to provide novel starches. The starch metabolic pathway is complex but has been characterized in diverse plant species, including pea. To understand how allelic variation in the pea starch metabolic pathway affects starch structure and percent amylose, partial sequences of 25 candidate genes were characterized for polymorphisms using a panel of 92 diverse pea lines. Variation in the percent amylose composition of extracted seed starch and (amylopectin) chain length distribution, one measure of starch structure, were characterized for these lines. Association mapping was undertaken to identify polymorphisms associated with the variation in starch chain length distribution and percent amylose, using a mixed linear model that incorporated population structure and kinship. Associations were found for polymorphisms in seven candidate genes plus Mendel's r locus (which conditions the round versus wrinkled seed phenotype). The genes with associated polymorphisms are involved in the substrate supply, chain elongation and branching stages of the pea carbohydrate and starch metabolic pathways. The association of polymorphisms in carbohydrate and starch metabolic genes with variation in amylopectin chain length distribution and percent amylose may help to guide manipulation of pea seed starch structural and functional properties through plant breeding.

  1. Modulating the distribution of fluxes among respiration and fermentation by overexpression of HAP4 in Saccharomyces cerevisiae.

    NARCIS (Netherlands)

    van Maris, A.J.A.; Bakker, B.M.; Brandt, M.; Boorsma, A.; Teixeira de Mattos, M.J.; Grivell, L.A.; Pronk, J.T.

    2001-01-01

    The tendency of Saccharomyces cerevisiae to favor alcoholic fermentation over respiration is a complication in aerobic, biomass-directed applications of this yeast. Overproduction of Hap4p, a positive transcriptional regulator of genes involved in respiratory metabolism, has been reported to

  2. Contribution to the qualification of calculation methods of reactivity and of flux and power distributions in nuclear pressurized water reactor cores

    International Nuclear Information System (INIS)

    Abit, K.

    1984-01-01

    The last stage of the creation computer methods and calculations consists of verifying the running and qualifying the results obtained. The work of the present thesis consisted of improving a coupling method between radial and axial phenomena in a PWR core, refering to three-dimensional calculations, while ensuring a perfect coherence between the programmed physical models. The calculation results have been compared to measurements of reactivity and of flux distributions realized during start-up tests. Thus, the methods have been applied to the calculation of the evolution of a burnable poison (gadolinium) in view of operation in long campaign. 13 refs [fr

  3. Method of and device for determining the characteristics and flux distribution of micrometeorites. [scanning puncture holes in sheet material with photoelectric cell

    Science.gov (United States)

    Meissinger, H. F. (Inventor)

    1973-01-01

    A micrometeorite impact sensing method of and device for determining the characteristics and flux distribution of micrometeorites are discussed. The method consists of exposing to the micrometeorite environment, a panel of sheet material of a thickness to be punctured by impacting micrometeorites and then scanning the panel with a scanner which produces an output representing the number and size of the puncture holes in the panel. After, exposure, the panel is scanned for puncture holes by illuminating one side of the panel and retracting the panel into its stowage container past a photoelectric scanner which produces an output representing the incident light.

  4. The flux-based PIN allocation mechanism can generate either canalyzed or diffuse distribution patterns depending on geometry and boundary conditions.

    Directory of Open Access Journals (Sweden)

    Michael Luke Walker

    Full Text Available Growth and morphogenesis in plants require controlled transport of the plant hormone auxin. An important participant is the auxin effluxing protein PIN, whose polarized subcellular localization allows it to effectively transport auxin large distances through tissues. The flux-based model, in which auxin flux through a wall stimulates PIN allocation to that wall, is a dominant contender among models determining where and in what quantity PIN is allocated to cell walls. In this paper we characterise the behaviour of flux-based PIN allocation models in various tissues of the shoot apical meristem. Arguing from both mathematical analysis and computer simulations, we describe the natural behaviours of this class of models under various circumstances. In particular, we demonstrate the important dichotomy between sink- and source- driven systems, and show that both diffuse and canalized PIN distributions can be generated simultaneously in the same tissue, without model hybridization or variation of PIN-related parameters. This work is performed in the context of the shoot apical and floral meristems and is applicable to the construction of a unified PIN allocation model.

  5. Magnetic flux density distribution in superconducting cylinders of arbitrary cross section subjected to an axial magnetic field

    Science.gov (United States)

    Fournet, G.

    1982-07-01

    We show here how the application of the critical state model allows one to determine the magnetic flux density B⃗ in each point of a superconducting cylinder with an arbitrary cross section subjected to axial magnetic fields Hz; the B = 0 boundaries of the regions occupied by the vortices are so defined. We successively consider the cases where the critical current density Jc is either isotropic (constant or an arbitrary function of B) or tensorial, which means, for our problem, the use of two components Jcx and Jcy (either constant or depending on B but Jcx/Jcy remaining constant).

  6. Distribution and Metabolism of Bt-Cry1Ac Toxin in Tissues and Organs of the Cotton Bollworm, Helicoverpa armigera

    Directory of Open Access Journals (Sweden)

    Zhuoya Zhao

    2016-07-01

    Full Text Available Crystal (Cry proteins derived from Bacillus thuringiensis (Bt have been widely used in transgenic crops due to their toxicity against insect pests. However, the distribution and metabolism of these toxins in insect tissues and organs have remained obscure because the target insects do not ingest much toxin. In this study, several Cry1Ac-resistant strains of Helicoverpa armigera, fed artificial diets containing high doses of Cry1Ac toxin, were used to investigate the distribution and metabolism of Cry1Ac in their bodies. Cry1Ac was only detected in larvae, not in pupae or adults. Also, Cry1Ac passed through the midgut into other tissues, such as the hemolymph and fat body, but did not reach the larval integument. Metabolic tests revealed that Cry1Ac degraded most rapidly in the fat body, followed by the hemolymph, peritrophic membrane and its contents. The toxin was metabolized slowly in the midgut, but was degraded in all locations within 48 h. These findings will improve understanding of the functional mechanism of Bt toxins in target insects and the biotransfer and the bioaccumulation of Bt toxins in arthropod food webs in the Bt crop ecosystem.

  7. Controlling the transcription levels of argGH redistributed L-arginine metabolic flux in N-acetylglutamate kinase and ArgR-deregulated Corynebacterium crenatum.

    Science.gov (United States)

    Zhao, Qinqin; Luo, Yuchang; Dou, Wenfang; Zhang, Xian; Zhang, Xiaomei; Zhang, Weiwei; Xu, Meijuan; Geng, Yan; Rao, Zhiming; Xu, Zhenghong

    2016-01-01

    Corynebacterium crenatum SYPA5-5, an L-arginine high-producer obtained through multiple mutation-screening steps, had been deregulated by the repression of ArgR that inhibits L-arginine biosynthesis at genetic level. Further study indicated that feedback inhibition of SYPA5-5 N-acetylglutamate kinase (CcNAGK) by L-arginine, as another rate-limiting step, could be deregulated by introducing point mutations. Here, we introduced two of the positive mutations (H268N or R209A) of CcNAGK into the chromosome of SYPA5-5, however, resulting in accumulation of large amounts of the intermediates (L-citrulline and L-ornithine) and decreased production of L-arginine. Genetic and enzymatic levels analysis involved in L-arginine biosynthetic pathway of recombinants SYPA5-5-NAGKH268N (H-7) and SYPA5-5-NAGKR209A (R-8) showed that the transcription levels of argGH decreased accompanied with the reduction of argininosuccinate synthase and argininosuccinase activities, respectively, which led to the metabolic obstacle from L-citrulline to L-arginine. Co-expression of argGH with exogenous plasmid in H-7 and R-8 removed this bottleneck and increased L-arginine productivity remarkably. Compared with SYPA5-5, fermentation period of H-7/pDXW-10-argGH (H-7-GH) reduced to 16 h; meanwhile, the L-arginine productivity improved about 63.6%. Fed-batch fermentation of H-7-GH in 10 L bioreactor produced 389.9 mM L-arginine with the productivity of 5.42 mM h(-1). These results indicated that controlling the transcription of argGH was a key factor for regulating the metabolic flux toward L-arginine biosynthesis after deregulating the repression of ArgR and feedback inhibition of CcNAGK, and therefore functioned as another regulatory mode for L-arginine production. Thus, deregulating all these three regulatory modes was a powerful strategy to construct L-arginine high-producing C. crenatum.

  8. Determination of neutron flux distribution by using ANISN, a one-dimensional discrete S sub n ordinates transport code with anisotropic scattering

    Science.gov (United States)

    Ghorai, S. K.

    1983-01-01

    The purpose of this project was to use a one-dimensional discrete coordinates transport code called ANISN in order to determine the energy-angle-spatial distribution of neutrons in a 6-feet cube rock box which houses a D-T neutron generator at its center. The project was two-fold. The first phase of the project involved adaptation of the ANISN code written for an IBM 360/75/91 computer to the UNIVAC system at JSC. The second phase of the project was to use the code with proper geometry, source function and rock material composition in order to determine the neutron flux distribution around the rock box when a 14.1 MeV neutron generator placed at its center is activated.

  9. Neutronic characterization of cylindrical core of minor excess reactivity in the nuclear reactor IPEN/MB-01 from the measure of neutron flux distribution and its reactivity ratio

    Energy Technology Data Exchange (ETDEWEB)

    Bitelli, Ulysses d' Utra; Aredes, Vitor O.G.; Mura, Luiz E.C.; Santos, Diogo F. dos; Silva, Alexandre P. da, E-mail: ubitelli@ipen.br, E-mail: vitoraredes@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2013-07-01

    When compared to a rectangular parallelepiped configuration the cylindrical configuration of a nuclear reactor core has a better neutron economy because in this configuration the probability of the neutron leakage is smaller, causing an increase in overall reactivity in the system to the same amount of fuel used. In this work we obtained a critical cylindrical configuration with the control rods 89.50% withdraw from the active region of the IPEN/MB-01 core. This is the cylindrical configuration minimum possible excess of reactivity. Thus we obtained a cylindrical configuration with a diameter of only 28 fuel rods with lowest possible excess of reactivity. For this purpose, 112 peripheral fuel rods are removed from standard reactor core (rectangular parallelepiped of 28x28 fuel rods). In this configuration the excesses of reactivity is approximated 279 pcm. From there, we characterize the neutron field by measuring the spatial distribution of the thermal and epithermal neutron flux for the reactor operating power of 83 watts measured by neutron noise analysis technique and 92.08± 0.07 watts measured by activation technique [10]. The values of thermal and epithermal neutron flux in different directions, axial, radial north-south and radial east-west, are obtained in the asymptotic region of the reactor core, away from the disturbances caused by the reflector and control bar, by irradiating thin gold foils infinitely diluted (1% Au - 99% Al) with and without (bare) cadmium cover. In addition to the distribution of neutron flux, the moderator temperature coefficient, the void coefficient, calibration of the control rods were measured. (author)

  10. Hydrogeology, groundwater seepage, nitrate distribution, and flux at the Raleigh hydrologic research station, Wake County, North Carolina, 2005-2007

    Science.gov (United States)

    McSwain, Kristen Bukowski; Bolich, Richard E.; Chapman, Melinda J.

    2013-01-01

    median concentration of 79 milligrams per liter as nitrogen. On the opposite side of the dike, concentrations of nitrate in pore water samples ranged from 3 to 91 milligrams per liter as nitrogen with a median concentration of 52 milligrams per liter. At one of the multiport piezometers the vertical gradient of hydraulic head between the Neuse River and the groundwater was too small to measure. At the multiport piezometer located in the suspected seepage area, an upward gradient of about 0.1 was present and explains the occurrence of higher concentrations of nitrate near the sediment/water interface. Horizontal seepage flux from the surficial aquifer to the edge of the Neuse River was estimated for 2006. Along a 130-foot flow path, the estimated seepage flux ranged from –0.52 to 0.2 foot per day with a median of 0.09 foot per day. The estimated advective horizontal mass flux of nitrate along a 300-foot reach of the Neuse River ranged from –10.9 to 5 pounds per day with a median of 2.2 pounds per day. The total horizontal mass flux of nitrate from the surficial aquifer to the Neuse River along the 130-foot flow path was estimated to be about 750 pounds for all of 2006. Seepage meters were deployed on the bed of the Neuse River in the areas of the multiport piezometers on either side of the diabase dike to estimate rates of vertical groundwater discharge and flux of nitrate. The average estimated daily seepage flux differed by two orders of magnitude between seepage areas. The potential vertical flux of nitrate from groundwater to the Neuse River was estimated at an average of 2.5 grams per day near one of the multiport piezometers and an average of 784 grams per day at the other. These approximations suggest that under some hydrologic conditions there is the potential for substantial quantities of nitrate to discharge from the groundwater to the Neuse River.

  11. Procedure of calculation of the spatial distribution of temperatures and heat fluxes in the steam generator of a nuclear power installation with an RBEC fast-neutron reactor

    Science.gov (United States)

    Frolov, A. A.; Sedov, A. A.

    2016-08-01

    A method for combined 3D/1D-modeling of thermohydraulics of a once-through steam generator (SG) based on the joint analysis of three-dimensional thermo- and hydrodynamics of a single-phase heating coolant in the intertube space and one-dimensional thermohydraulics of steam-generating channels (tubes) with the use of well-known friction and heat-transfer correlations under various boiling conditions is discussed. This method allows one to determine the spatial distribution of temperatures and heat fluxes of heat-exchange surfaces of SGs with a single-phase heating coolant in the intertube space and with steam generation within tubes. The method was applied in the analytical investigation of typical operation of a once-through SG of a nuclear power installation with an RBEC fast-neutron heavy-metal reactor that is being designed by Kurchatov Institute in collaboration with OKB GIDROPRESS and Leipunsky Institute of Physics and Power Engineering. Flow pattern and temperature fields were obtained for the heavy-metal heating coolant in the intertube space. Nonuniformities of heating of the steam-water coolant in different heat-exchange tubes and nonuniformities in the distribution of heat fluxes at SG heat-exchange surfaces were revealed.

  12. BACILLUS SPECIES IN THE OCEANIC WATERS ADJACENT TO CUBA: ASSOCIATION BETWEEN THEIR DISTRIBUTION AND METABOLIC ACTIVITY

    Directory of Open Access Journals (Sweden)

    Gladys Margarita Lugioyo

    2011-07-01

    Full Text Available The aim of the present work was to identify spore-forming Gram-positive Bacillus strains isolated from oceanic waters adjacent to Cuba and to establish a possible relationship between their distribution and the metabolic activity of the isolates. Total protein patterns, derived from SDS-PAGE, were used to build a non-rooted dendrogram where the strains appeared clustered in three nodes. No direct relationship was observed between a node and particular species. In contrast, according to the physical and chemical characteristics of the zones, node I was different from node II and III, since it comprises strains from the farthest zones of the coast, poorer in nutrients. On the other hand, nodes II and III mainly collect strains isolated from nutrient and organic matter-enriched zones. Associating the node clustering with metabolic activities, it was found that in node I the ratio: number of positive activities/strain was 2.3, followed by node II with a ratio of 3.3, and finally node III exhibiting a ratio equal to 3.7. This could suggest that different total protein patterns in bacteria belonging to the same specie, but coming from environments with different degree of nutrient richness, could be an indicator of the capacities of these microorganisms to adapt and live in different environments.   El objetivo del presente trabajo fue la identificación de cepas de bacilos Gram-positivos esporulados aislados de las aguas oceánicas adyacentes a Cuba y el establecimiento de la posible relación entre la distribución y las actividades metabólicas de los aislados. A partir del patrón de proteínas obtenido mediante electroforesis SDS-PAGE, se construyó un dendrograma no enraizado, lo que permitió la agrupación de las cepas en tres nodos. No se observó una relación directa entre un nodo y especies particulares, sin embargo, se encontraron diferencias entre los nodos al considerar las características físicas y químicas de las zonas; el nodo I

  13. Framework for network modularization and Bayesian network analysis to investigate the perturbed metabolic network.

    Science.gov (United States)

    Kim, Hyun Uk; Kim, Tae Yong; Lee, Sang Yup

    2011-01-01

    Genome-scale metabolic network models have contributed to elucidating biological phenomena, and predicting gene targets to engineer for biotechnological applications. With their increasing importance, their precise network characterization has also been crucial for better understanding of the cellular physiology. We herein introduce a framework for network modularization and Bayesian network analysis (FMB) to investigate organism's metabolism under perturbation. FMB reveals direction of influences among metabolic modules, in which reactions with similar or positively correlated flux variation patterns are clustered, in response to specific perturbation using metabolic flux data. With metabolic flux data calculated by constraints-based flux analysis under both control and perturbation conditions, FMB, in essence, reveals the effects of specific perturbations on the biological system through network modularization and Bayesian network analysis at metabolic modular level. As a demonstration, this framework was applied to the genetically perturbed Escherichia coli metabolism, which is a lpdA gene knockout mutant, using its genome-scale metabolic network model. After all, it provides alternative scenarios of metabolic flux distributions in response to the perturbation, which are complementary to the data obtained from conventionally available genome-wide high-throughput techniques or metabolic flux analysis.

  14. Design and demonstration of a distributed sensor array for predicting water flow and nitrate flux in the Santa Fe Basin

    Science.gov (United States)

    Graham, W. D.; Cohen, M.; Delfino, J.; Martin, J.; Slatton, K. C.; Thomas, R.

    2006-12-01

    Watershed characterization requires well-planned sampling to track simultaneous time-variable fluxes and flowpaths of water, nutrients, sediments, and energy. In this research project legacy hydrologic, meteorologic and water quality data from the Santa Fe basin in the Suwannee river watershed will be assembled into a web- accessible digital watershed. These data, together with predictions from physically-based hydrologic models, will be used to develop a probabilistic algorithm to predict surface water stage and flux throughout the Santa Fe river basin and evaluate the accuracy of these predictions. Information on prediction uncertainty will be used to design a spatial network of new conductivity-temperature-depth (CTD) sensors to improve the predictions. The adequacy of the assembled data and the utility of the optimal estimation algorithm will be evaluated by comparing resulting predictions with observations of surface water stage and flux from the newly deployed CTD sondes. Field data collection will include evaluations of interferences and applicability of off-the-shelf optical and cadmium reduction continuous nitrate sensors. The best performing sensor will be identified and calibrated to conditions in the Santa Fe watershed. At least two nitrate sensors will be linked with the CTD sondes into sensor packages and deployed at selected locations in the Santa Fe watershed. The high frequency data collected by the sensors will be transmitted continuously via cell-phone technology to a central university computer. These new data will be used to improve local relationships among flow, stage, conductivity and nitrate. Information collected with the sensors will lay the groundwork for developing a general methodology to augment continuous measurement of nitrate with correlated surrogates (i.e., in this case flow and conductivity) to decrease the density of sensors needed to accurately predict the nitrate in the system over space and time. Furthermore, the data will

  15. Gas fluxing of aluminum: a bubble probe for optimization of bubbles/bubble distribution and minimization of splashing/droplet formation

    International Nuclear Information System (INIS)

    James W. Evans; Auitumn Fjeld

    2006-01-01

    totaling 1.549 million lbs. for only thirteen of the twenty three primary smelters then in operation in the US. The research work described in the body of this report (the doctoral dissertation of Dr. Autumn M. Fjeld) had as its objective the improvement of gas fluxing technology to reduce emissions while still maintaining fluxing unit metal throughput. A second objective was a better understanding of the splashing and droplet emission that occurs during fluxing at high gas throughput rates. In the extreme such droplets can form undesired accretions on the walls and gas exit lines of the fluxing unit. Consequently, the productivity of a fluxing unit is sometimes limited by the need to avoid such spraying of droplets produced as gas bubbles break at the metal surface. The approach used was a combination of experimental work in laboratories at UC Berkeley and at the Alcoa Technical Center. The experimental work was mostly on a bubble probe that could be used to determine the extent of dispersion of gas bubbles in the fluxing unit (a parameter affecting the utilization of the injected chlorine). Additionally a high speed digital movie camera was used to study droplet formation due to gas bubbles bursting at the surface of a low melting point alloy. The experimental work was supported by mathematical modeling. In particular, two FLUENT? base mathematical models were developed to compute the metal flow and distribution of the gas within a fluxing unit. Results from these models were then used in a third model to compute emissions and the progress of impurity removal as a function of parameters such as rotor speed. The project was successful in demonstrating that the bubble probe could detect bubbles in a gas fluxing unit at the Alcoa technical Center outside Pittsburgh, PA. This unit is a commercial sized one and the probe, with its associated electronics, was subjected to the hostile molten aluminum, electrical noise etc. Despite this the probes were, on several occasions

  16. Quantitative intracellular flux modeling and applications in biotherapeutic development and production using CHO cell cultures.

    Science.gov (United States)

    Huang, Zhuangrong; Lee, Dong-Yup; Yoon, Seongkyu

    2017-12-01

    Chinese hamster ovary (CHO) cells have been widely used for producing many recombinant therapeutic proteins. Constraint-based modeling, such as flux balance analysis (FBA) and metabolic flux analysis (MFA), has been developing rapidly for the quantification of intracellular metabolic flux distribution at a systematic level. Such methods would produce detailed maps of flows through metabolic networks, which contribute significantly to better understanding of metabolism in cells. Although these approaches have been extensively established in microbial systems, their application to mammalian cells is sparse. This review brings together the recent development of constraint-based models and their applications in CHO cells. The further development of constraint-based modeling approaches driven by multi-omics datasets is discussed, and a framework of potential modeling application in cell culture engineering is proposed. Improved cell culture system understanding will enable robust developments in cell line and bioprocess engineering thus accelerating consistent process quality control in biopharmaceutical manufacturing. © 2017 Wiley Periodicals, Inc.

  17. Radiocesium distribution and fluxes in the typical Cryptomeria japonica forest at the late stage after the accident at Fukushima Dai-Ichi Nuclear Power Plant.

    Science.gov (United States)

    Yoschenko, Vasyl; Takase, Tsugiko; Konoplev, Alexei; Nanba, Kenji; Onda, Yuichi; Kivva, Sergiy; Zheleznyak, Mark; Sato, Natsumi; Keitoku, Koji

    2017-01-01

    The Fukushima-derived radiocesium distribution in the typical Japanese cedar (Cryptomeria japonica D. Don) forest ecosystem was determined. In four years after the Fukushima accident, about 74% of the total radiocesium inventory was localized in soil, 20% was in the litter, and only 6% was associated with the aboveground biomass. Most of the radiocesium that was initially intercepted by the tree canopies has been already transported to the ground surface. The