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Sample records for central carbon metabolism

  1. Metabolic Dysfunction in Parkinson's Disease: Bioenergetics, Redox Homeostasis and Central Carbon Metabolism.

    Science.gov (United States)

    Anandhan, Annadurai; Jacome, Maria S; Lei, Shulei; Hernandez-Franco, Pablo; Pappa, Aglaia; Panayiotidis, Mihalis I; Powers, Robert; Franco, Rodrigo

    2017-07-01

    The loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc) and the accumulation of protein inclusions (Lewy bodies) are the pathological hallmarks of Parkinson's disease (PD). PD is triggered by genetic alterations, environmental/occupational exposures and aging. However, the exact molecular mechanisms linking these PD risk factors to neuronal dysfunction are still unclear. Alterations in redox homeostasis and bioenergetics (energy failure) are thought to be central components of neurodegeneration that contribute to the impairment of important homeostatic processes in dopaminergic cells such as protein quality control mechanisms, neurotransmitter release/metabolism, axonal transport of vesicles and cell survival. Importantly, both bioenergetics and redox homeostasis are coupled to neuro-glial central carbon metabolism. We and others have recently established a link between the alterations in central carbon metabolism induced by PD risk factors, redox homeostasis and bioenergetics and their contribution to the survival/death of dopaminergic cells. In this review, we focus on the link between metabolic dysfunction, energy failure and redox imbalance in PD, making an emphasis in the contribution of central carbon (glucose) metabolism. The evidence summarized here strongly supports the consideration of PD as a disorder of cell metabolism. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Reconstruction of the central carbon metabolism of Aspergillus niger

    DEFF Research Database (Denmark)

    David, Helga; Åkesson, Mats Fredrik; Nielsen, Jens

    2003-01-01

    The topology of central carbon metabolism of Aspergillus niger was identified and the metabolic network reconstructed, by integrating genomic, biochemical and physiological information available for this microorganism and other related fungi. The reconstructed network may serve as a valuable...... of metabolic fluxes using metabolite balancing. This framework was employed to perform an in silico characterisation of the phenotypic behaviour of A. niger grown on different carbon sources. The effects on growth of single reaction deletions were assessed and essential biochemical reactions were identified...... for different carbon sources. Furthermore, application of the stoichiometric model for assessing the metabolic capabilities of A. niger to produce metabolites was evaluated by using succinate production as a case study....

  3. Central carbon metabolism influences cellulase production in Bacillus licheniformis.

    Science.gov (United States)

    Wang, J; Liu, S; Li, Y; Wang, H; Xiao, S; Li, C; Liu, B

    2018-01-01

    Bacillus licheniformis that can produce cellulase including endo glucanase and glucosidase is an important industrial microbe for cellulose degradation. The purpose of this research was to assess the effect of endo glucanase gene bglC and glucosidase gene bglH on the central metabolic flux in B. licheniformis. bglC and bglH were knocked out using homologous recombination method, respectively, and the corresponding knockout strains were obtained for 13 C metabolic flux analysis. A significant change was observed in metabolic fluxes after 13 C metabolic flux ratio analysis. In both of the knockout strains, the increased fluxes of the pentose phosphate pathway and malic enzyme reaction enabled an elevated supply of NADPH which provided enough reducing power for the in vivo synthesis reactions. The fluxes through tricarboxylic acid cycle and anaplerotic reactions increased fast in the two knockout strains, which meant more energy generated. The changed fluxes in central carbon metabolism provided a holistic view of the physiological status in B. licheniformis and possible targets for further strain engineering. Cellulase is very important in the field of agriculture and bioenergy because of its degrading effect on cellulosic biomass. This study presented the effect of central carbon metabolism on cellulase production in Bacillus licheniformis. The study also provided a holistic view of the physiological status in B. licheniformis. The shifted metabolism provided a quantitative evaluation of the biosynthesis of cellulase and a priority ranked target list for further strain engineering. © 2017 The Society for Applied Microbiology.

  4. Genetic response to metabolic fluctuations: correlation between central carbon metabolism and DNA replication in Escherichia coli

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    Szalewska-Pałasz Agnieszka

    2011-03-01

    Full Text Available Abstract Background Until now, the direct link between central carbon metabolism and DNA replication has been demonstrated only in Bacillus. subtilis. Therefore, we asked if this is a specific phenomenon, characteristic for this bacterium and perhaps for its close relatives, or a more general biological rule. Results We found that temperature-sensitivity of mutants in particular genes coding for replication proteins could be suppressed by deletions of certain genes coding for enzymes of the central carbon metabolism. Namely, the effects of dnaA46(ts mutation could be suppressed by dysfunction of pta or ackA, effects of dnaB(ts by dysfunction of pgi or pta, effects of dnaE486(ts by dysfunction of tktB, effects of dnaG(ts by dysfunction of gpmA, pta or ackA, and effects of dnaN159(ts by dysfunction of pta or ackA. The observed suppression effects were not caused by a decrease in bacterial growth rate. Conclusions The genetic correlation exists between central carbon metabolism and DNA replication in the model Gram-negative bacterium, E. coli. This link exists at the steps of initiation and elongation of DNA replication, indicating the important global correlation between metabolic status of the cell and the events leading to cell reproduction.

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

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    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.

  6. Metabolic fluxes in the central carbon metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis, two members of the marine Roseobacter clade

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    Rabus Ralf

    2009-09-01

    Full Text Available Abstract Background In the present work the central carbon metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis was studied at the level of metabolic fluxes. These two strains belong to the marine Roseobacter clade, a dominant bacterial group in various marine habitats, and represent surface-associated, biofilm-forming growth (P. gallaeciensis and symbiotic growth with eukaryotic algae (D. shibae. Based on information from recently sequenced genomes, a rich repertoire of pathways has been identified in the carbon core metabolism of these organisms, but little is known about the actual contribution of the various reactions in vivo. Results Using 13C labelling techniques in specifically designed experiments, it could be shown that glucose-grown cells of D. shibae catabolise the carbon source exclusively via the Entner-Doudoroff pathway, whereas alternative routes of glycolysis and the pentose phosphate pathway are obviously utilised for anabolic purposes only. Enzyme assays confirmed this flux pattern and link the lack of glycolytic flux to the absence of phosphofructokinase activity. The previously suggested formation of phosphoenolpyruvate from pyruvate during mixotrophic CO2 assimilation was found to be inactive under the conditions studied. Moreover, it could be shown that pyruvate carboxylase is involved in CO2 assimilation and that the cyclic respiratory mode of the TCA cycle is utilised. Interestingly, the use of intracellular pathways was highly similar for P. gallaeciensis. Conclusion The present study reveals the first insight into pathway utilisation within the Roseobacter group. Fluxes through major intracellular pathways of the central carbon metabolism, which are closely linked to the various important traits found for the Roseobacter clade, could be determined. The close similarity of fluxes between the two physiologically rather different species might provide the first indication of more general key properties among

  7. The carbon storage regulator (Csr) system exerts a nutrient-specific control over central metabolism in Escherichia coli strain Nissle 1917.

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    Revelles, Olga; Millard, Pierre; Nougayrède, Jean-Philippe; Dobrindt, Ulrich; Oswald, Eric; Létisse, Fabien; Portais, Jean-Charles

    2013-01-01

    The role of the post-transcriptional carbon storage regulator (Csr) system in nutrient utilization and in the control of the central metabolism in E. coli reference commensal strain Nissle 1917 was investigated. Analysis of the growth capabilities of mutants altered for various components of the Csr system (csrA51, csrB, csrC and csrD mutations) showed that only the protein CsrA - the key component of the system - exerts a marked role in carbon nutrition. Attenuation of CsrA activity in the csrA51 mutant affects the growth efficiency on a broad range of physiologically relevant carbon sources, including compounds utilized by the Entner-Doudoroff (ED) pathway. Detailed investigations of the metabolomes and fluxomes of mutants and wild-type cells grown on carbon sources representative of glycolysis and of the ED pathway (glucose and gluconate, respectively), revealed significant re-adjusting of central carbon metabolism for both compounds in the csrA51 mutant. However, the metabolic re-adjusting observed on gluconate was strikingly different from that observed on glucose, indicating a nutrient-specific control of metabolism by the Csr system.

  8. Carbon metabolic pathways in phototrophic bacteria and their broader evolutionary implications

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    Kuo-Hsiang eTang

    2011-08-01

    Full Text Available Photosynthesis is the biological process that converts solar energy to biomass, bio-products and biofuel. It is the only major natural solar energy storage mechanism on Earth. To satisfy the increased demand for sustainable energy sources and identify the mechanism of photosynthetic carbon assimilation, which is one of the bottlenecks in photosynthesis, it is essential to understand the process of solar energy storage and associated carbon metabolism in photosynthetic organisms. Researchers have employed physiological studies, microbiological chemistry, enzyme assays, genome sequencing, transcriptomics, and 13C-based metabolomics/fluxomics to investigate central carbon metabolism and enzymes that operate in phototrophs. In this report, we review diverse CO2 assimilation pathways, acetate assimilation, carbohydrate catabolism, the TCA cycle and some key and/or unconventional enzymes in central carbon metabolism of phototrophic microorganisms. We also discuss the reducing equivalent flow during photoautotrophic and photoheterotrophic growth, evolutionary links in the central carbon metabolic network, and correlations between photosynthetic and non-photosynthetic organisms. Considering the metabolic versatility in these fascinating and diverse photosynthetic bacteria, many essential questions in their central carbon metabolism still remain to be addressed.

  9. The depressed central carbon and energy metabolisms is associated to the acquisition of levofloxacin resistance in Vibrio alginolyticus.

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    Cheng, Zhi-Xue; Yang, Man-Jun; Peng, Bo; Peng, Xuan-Xian; Lin, Xiang-Min; Li, Hui

    2018-06-15

    The overuse and misuse of antibiotics lead to bacterial antibiotic resistance, challenging human health and intensive cultivation. It is especially required to understand for the mechanism of antibiotic resistance to control antibiotic-resistant pathogens. The present study characterized the differential proteome of levofloxacin-resistant Vibrio alginolyticus with the most advanced iTRAQ quantitative proteomics technology. A total of 160 proteins of differential abundance were identified, where 70 were decreased and 90 were increased. Further analysis demonstrated that crucial metabolic pathways like TCA cycle were significantly down-regulated. qRT-PCR analysis demonstrated the decreased gene expression of glycolysis/gluconeogenesis, the TCA cycle, and fatty acid biosynthesis. Moreover, Na(+)-NQR complex gene expression, membrane potential and the adenylate energy charge ratio were decreased, indicating that the decreased central carbon metabolism is associated to the acquisition of levofloxacin resistance. Therefore, the reduced central carbon and energy metabolisms form a characteristic feature as fitness costs of V. alginolyticus in resistance to levofloxacin. The overuse and misuse of antibiotics lead to bacterial antibiotic resistance, challenging human health and intensive cultivation. Understanding for the antibiotic resistance mechanisms is especially required to control these antibiotic-resistant pathogens. The present study characterized the differential proteome of levofloxacin-resistant Vibrio alginolyticus using the most advanced iTRAQ quantitative proteomics technology. A total of 160 differential abundance of proteins were identified with 70 decreases and 90 increases by liquid chromatography matrix assisted laser desorption ionization mass spectrometry. Most interestingly, crucial metabolic pathways such as the TCA cycle sharply fluctuated. This is the first report that the reduced central carbon and energy metabolisms form a characteristic feature

  10. Spatially resolved metabolic analysis reveals a central role for transcriptional control in carbon allocation to wood.

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    Roach, Melissa; Arrivault, Stéphanie; Mahboubi, Amir; Krohn, Nicole; Sulpice, Ronan; Stitt, Mark; Niittylä, Totte

    2017-06-15

    The contribution of transcriptional and post-transcriptional regulation to modifying carbon allocation to developing wood of trees is not well defined. To clarify the role of transcriptional regulation, the enzyme activity patterns of eight central primary metabolism enzymes across phloem, cambium, and developing wood of aspen (Populus tremula L.) were compared with transcript levels obtained by RNA sequencing of sequential stem sections from the same trees. Enzymes were selected on the basis of their importance in sugar metabolism and in linking primary metabolism to lignin biosynthesis. Existing enzyme assays were adapted to allow measurements from ~1 mm3 sections of dissected stem tissue. These experiments provided high spatial resolution of enzyme activity changes across different stages of wood development, and identified the gene transcripts probably responsible for these changes. In most cases, there was a clear positive relationship between transcripts and enzyme activity. During secondary cell wall formation, the increases in transcript levels and enzyme activities also matched with increased levels of glucose, fructose, hexose phosphates, and UDP-glucose, emphasizing an important role for transcriptional regulation in carbon allocation to developing aspen wood. These observations corroborate the efforts to increase carbon allocation to wood by engineering gene regulatory networks. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  11. Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP.

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    Kim, Donghyuk; Seo, Sang Woo; Gao, Ye; Nam, Hojung; Guzman, Gabriela I; Cho, Byung-Kwan; Palsson, Bernhard O

    2018-04-06

    Two major transcriptional regulators of carbon metabolism in bacteria are Cra and CRP. CRP is considered to be the main mediator of catabolite repression. Unlike for CRP, in vivo DNA binding information of Cra is scarce. Here we generate and integrate ChIP-exo and RNA-seq data to identify 39 binding sites for Cra and 97 regulon genes that are regulated by Cra in Escherichia coli. An integrated metabolic-regulatory network was formed by including experimentally-derived regulatory information and a genome-scale metabolic network reconstruction. Applying analysis methods of systems biology to this integrated network showed that Cra enables optimal bacterial growth on poor carbon sources by redirecting and repressing glycolysis flux, by activating the glyoxylate shunt pathway, and by activating the respiratory pathway. In these regulatory mechanisms, the overriding regulatory activity of Cra over CRP is fundamental. Thus, elucidation of interacting transcriptional regulation of core carbon metabolism in bacteria by two key transcription factors was possible by combining genome-wide experimental measurement and simulation with a genome-scale metabolic model.

  12. Dynamic Labeling Reveals Temporal Changes in Carbon Re-Allocation within the Central Metabolism of Developing Apple Fruit

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    Wasiye F. Beshir

    2017-10-01

    Full Text Available In recent years, the application of isotopically labeled substrates has received extensive attention in plant physiology. Measuring the propagation of the label through metabolic networks may provide information on carbon allocation in sink fruit during fruit development. In this research, gas chromatography coupled to mass spectrometry based metabolite profiling was used to characterize the changing metabolic pool sizes in developing apple fruit at five growth stages (30, 58, 93, 121, and 149 days after full bloom using 13C-isotope feeding experiments on hypanthium tissue discs. Following the feeding of [U-13C]glucose, the 13C-label was incorporated into the various metabolites to different degrees depending on incubation time, metabolic pathway activity, and growth stage. Evidence is presented that early in fruit development the utilization of the imported sugars was faster than in later developmental stages, likely to supply the energy and carbon skeletons required for cell division and fruit growth. The declined 13C-incorporation into various metabolites during growth and maturation can be associated with the reduced metabolic activity, as mirrored by the respiratory rate. Moreover, the concentration of fructose and sucrose increased during fruit development, whereas concentrations of most amino and organic acids and polyphenols declined. In general, this study showed that the imported compounds play a central role not only in carbohydrate metabolism, but also in the biosynthesis of amino acid and related protein synthesis and secondary metabolites at the early stage of fruit development.

  13. Molecular Basis of Microbial One-Carbon Metabolism 2008 Gordon Research Conference (July 20-25, 2008)

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    Stephen W. Ragsdale

    2009-08-12

    One-carbon (C-1) compounds play a central role in microbial metabolism. C-1 compounds include methane, carbon monoxide, CO2, and methanol as well as coenzyme-bound one-carbon compounds (methyl-B12, CH3-H4folate, etc). Such compounds are of broad global importance because several C-1 compounds (e.g., CH4) are important energy sources, some (e.g., CO2 and CH4) are potent greenhouse gases, and others (e.g., CH2Cl2) are xenobiotics. They are central in pathways of energy metabolism and carbon fixation by microbes and many are of industrial interest. Research on the pathways of one-carbon metabolism has added greatly to our understanding of evolution, structural biology, enzyme mechanisms, gene regulation, ecology, and applied biology. The 2008 meeting will include recent important findings in the following areas: (a) genomics, metagenomics, and proteomic studies that have expanded our understanding of autotrophy and C-1 metabolism and the evolution of these pathways; (b) redox regulation of carbon cycles and the interrelationship between the carbon cycle and other biogeochemical cycles (sulfur, nitrogen, oxygen); (c) novel pathways for carbon assimilation; (d) biotechnology related to C-1 metabolism; (e) novel enzyme mechanisms including channeling of C-1 intermediates during metabolism; and (f) the relationship between metal homeostasis and the global carbon cycle. The conference has a diverse and gender-balanced slate of speakers and session leaders. The wide variety of disciplines brought to the study of C-1 metabolism make the field an excellent one in which to train young researchers.

  14. Phosphoketolase pathway contributes to carbon metabolism in cyanobacteria.

    Science.gov (United States)

    Xiong, Wei; Lee, Tai-Chi; Rommelfanger, Sarah; Gjersing, Erica; Cano, Melissa; Maness, Pin-Ching; Ghirardi, Maria; Yu, Jianping

    2015-12-07

    Central carbon metabolism in cyanobacteria comprises the Calvin-Benson-Bassham (CBB) cycle, glycolysis, the pentose phosphate (PP) pathway and the tricarboxylic acid (TCA) cycle. Redundancy in this complex metabolic network renders the rational engineering of cyanobacterial metabolism for the generation of biomass, biofuels and chemicals a challenge. Here we report the presence of a functional phosphoketolase pathway, which splits xylulose-5-phosphate (or fructose-6-phosphate) to acetate precursor acetyl phosphate, in an engineered strain of the model cyanobacterium Synechocystis (ΔglgC/xylAB), in which glycogen synthesis is blocked, and xylose catabolism enabled through the introduction of xylose isomerase and xylulokinase. We show that this mutant strain is able to metabolise xylose to acetate on nitrogen starvation. To see whether acetate production in the mutant is linked to the activity of phosphoketolase, we disrupted a putative phosphoketolase gene (slr0453) in the ΔglgC/xylAB strain, and monitored metabolic flux using (13)C labelling; acetate and 2-oxoglutarate production was reduced in the light. A metabolic flux analysis, based on isotopic data, suggests that the phosphoketolase pathway metabolises over 30% of the carbon consumed by ΔglgC/xylAB during photomixotrophic growth on xylose and CO2. Disruption of the putative phosphoketolase gene in wild-type Synechocystis also led to a deficiency in acetate production in the dark, indicative of a contribution of the phosphoketolase pathway to heterotrophic metabolism. We suggest that the phosphoketolase pathway, previously uncharacterized in photosynthetic organisms, confers flexibility in energy and carbon metabolism in cyanobacteria, and could be exploited to increase the efficiency of cyanobacterial carbon metabolism and photosynthetic productivity.

  15. Photosynthetic carbon metabolism in freshwater phytoplankton

    International Nuclear Information System (INIS)

    Groeger, A.W.

    1986-01-01

    Photosynthetic carbon metabolism of natural assemblages of freshwater phytoplankton was measured by following the flow of inorganic 14 C into the photosynthetic end products polysaccharide protein, lipid, and soluble metabolites. Data were collected from a wide range of physical, chemical, and trophic conditions in six southern United States reservoirs, with the primary environmental variables of interest being light intensity and nutrient supply. Polysaccharide and protein were consistently the primary products of photosynthetic carbon metabolism, comprising an average of 70% of the total carbon fixation over a wide range of light intensities. Polysaccharide was quantitatively more important at higher light intensities, and protein at lower light intensities, as light intensity varied both with depth within the water column and over diurnal cycles. Polysaccharide synthesis was more variable over the diurnal period than was protein synthesis. Phytoplankton in the downlake epilimnion of Normandy Lake, a central Tennessee reservoir, responded to summer nitrogen (N) deficiency by increasing relative rates of lipid synthesis from 10-15% to 20-25% of the total photosynthetic carbon fixation. Phytoplankton in more nitrogen-sufficient areas of the reservoir maintained lower rates of lipid synthesis throughout the summer. These results document the occurrence in nature of a relationship between N-deficiency and increased lipid synthesis previously observed only in laboratory algal culture studies

  16. An Integrative Approach to Energy Carbon and Redox Metabolism In Cyanobacterium Synechocystis

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    Dr. Ross Overbeek

    2003-06-30

    The main objectives for the first year were to produce a detailed metabolic reconstruction of synechocystis sp.pcc6803 especially in interrelated arrears of photosynthesis respiration and central carbon metabolism to support a more complete understanding and modeling of this organism. Additionally, IG, Inc. provided detailed bioinformatic analysis of selected functional systems related to carbon and energy generation and utilization, and of the corresponding pathways functional roles and individual genes to support wet lab experiments by collaborators.

  17. γ-Aminobutyric acid transaminase deficiency impairs central carbon metabolism and leads to cell wall defects during salt stress in Arabidopsis roots.

    Science.gov (United States)

    Renault, Hugues; El Amrani, Abdelhak; Berger, Adeline; Mouille, Grégory; Soubigou-Taconnat, Ludivine; Bouchereau, Alain; Deleu, Carole

    2013-05-01

    Environmental constraints challenge cell homeostasis and thus require a tight regulation of metabolic activity. We have previously reported that the γ-aminobutyric acid (GABA) metabolism is crucial for Arabidopsis salt tolerance as revealed by the NaCl hypersensitivity of the GABA transaminase (GABA-T, At3g22200) gaba-t/pop2-1 mutant. In this study, we demonstrate that GABA-T deficiency during salt stress causes root and hypocotyl developmental defects and alterations of cell wall composition. A comparative genome-wide transcriptional analysis revealed that expression levels of genes involved in carbon metabolism, particularly sucrose and starch catabolism, were found to increase upon the loss of GABA-T function under salt stress conditions. Consistent with the altered mutant cell wall composition, a number of cell wall-related genes were also found differentially expressed. A targeted quantitative analysis of primary metabolites revealed that glutamate (GABA precursor) accumulated while succinate (the final product of GABA metabolism) significantly decreased in mutant roots after 1 d of NaCl treatment. Furthermore, sugar concentration was twofold reduced in gaba-t/pop2-1 mutant roots compared with wild type. Together, our results provide strong evidence that GABA metabolism is a major route for succinate production in roots and identify GABA as a major player of central carbon adjustment during salt stress. © 2012 Blackwell Publishing Ltd.

  18. The Essential Role of Cholesterol Metabolism in the Intracellular Survival of Mycobacterium leprae Is Not Coupled to Central Carbon Metabolism and Energy Production.

    Science.gov (United States)

    Marques, Maria Angela M; Berrêdo-Pinho, Marcia; Rosa, Thabatta L S A; Pujari, Venugopal; Lemes, Robertha M R; Lery, Leticia M S; Silva, Carlos Adriano M; Guimarães, Ana Carolina R; Atella, Georgia C; Wheat, William H; Brennan, Patrick J; Crick, Dean C; Belisle, John T; Pessolani, Maria Cristina V

    2015-12-01

    Mycobacterium leprae induces the formation of lipid droplets, which are recruited to pathogen-containing phagosomes in infected macrophages and Schwann cells. Cholesterol is among the lipids with increased abundance in M. leprae-infected cells, and intracellular survival relies on cholesterol accumulation. The present study investigated the capacity of M. leprae to acquire and metabolize cholesterol. In silico analyses showed that oxidation of cholesterol to cholest-4-en-3-one (cholestenone), the first step of cholesterol degradation catalyzed by the enzyme 3β-hydroxysteroid dehydrogenase (3β-HSD), is apparently the only portion of the cholesterol catabolic pathway seen in Mycobacterium tuberculosis preserved by M. leprae. Incubation of bacteria with radiolabeled cholesterol confirmed the in silico predictions. Radiorespirometry and lipid analyses performed after incubating M. leprae with [4-(14)C]cholesterol or [26-(14)C]cholesterol showed the inability of this pathogen to metabolize the sterol rings or the side chain of cholesterol as a source of energy and carbon. However, the bacteria avidly incorporated cholesterol and, as expected, converted it to cholestenone both in vitro and in vivo. Our data indicate that M. leprae has lost the capacity to degrade and utilize cholesterol as a nutritional source but retains the enzyme responsible for its oxidation to cholestenone. Thus, the essential role of cholesterol metabolism in the intracellular survival of M. leprae is uncoupled from central carbon metabolism and energy production. Further elucidation of cholesterol metabolism in the host cell during M. leprae infection will establish the mechanism by which this lipid supports M. leprae intracellular survival and will open new avenues for novel leprosy therapies. Our study focused on the obligate intracellular pathogen Mycobacterium leprae and its capacity to metabolize cholesterol. The data make an important contribution for those interested in understanding the

  19. Prioritizing Popular Proteins in Liver Cancer: Remodelling One-Carbon Metabolism.

    Science.gov (United States)

    Mora, María Isabel; Molina, Manuela; Odriozola, Leticia; Elortza, Félix; Mato, José María; Sitek, Barbara; Zhang, Pumin; He, Fuchu; Latasa, María Uxue; Ávila, Matías Antonio; Corrales, Fernando José

    2017-12-01

    Primary liver cancer (HCC) is recognized as the fifth most common neoplasm and the second leading cause of cancer death worldwide. Most risk factors are known, and the molecular pathogenesis has been widely studied in the past decade; however, the underlying molecular mechanisms remain to be unveiled, as they will facilitate the definition of novel biomarkers and clinical targets for more effective patient management. We utilize the B/D-HPP popular protein strategy. We report a list of popular proteins that have been highly cocited with the expression "liver cancer". Several enzymes highlight the known metabolic remodeling of liver cancer cells, four of which participate in one-carbon metabolism. This pathway is central to the maintenance of differentiated hepatocytes, as it is considered the connection between intermediate metabolism and epigenetic regulation. We designed a targeted selective reaction monitoring (SRM) method to follow up one-carbon metabolism adaptation in mouse HCC and in regenerating liver following exposure to CCl 4 . This method allows systematic monitoring of one-carbon metabolism and could prove useful in the follow-up of HCC and of chronically liver-diseased patients (cirrhosis) at risk of HCC. The SRM data are available via ProteomeXchange in PASSEL (PASS01060).

  20. Modeling of Zymomonas mobilis central metabolism for novel metabolic engineering strategies.

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    Kalnenieks, Uldis; Pentjuss, Agris; Rutkis, Reinis; Stalidzans, Egils; Fell, David A

    2014-01-01

    Mathematical modeling of metabolism is essential for rational metabolic engineering. The present work focuses on several types of modeling approach to quantitative understanding of central metabolic network and energetics in the bioethanol-producing bacterium Zymomonas mobilis. Combined use of Flux Balance, Elementary Flux Mode, and thermodynamic analysis of its central metabolism, together with dynamic modeling of the core catabolic pathways, can help to design novel substrate and product pathways by systematically analyzing the solution space for metabolic engineering, and yields insights into the function of metabolic network, hardly achievable without applying modeling tools.

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

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    Hammami Ines

    2012-07-01

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

  2. Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli.

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    Shimada, Tomohiro; Yamamoto, Kaneyoshi; Ishihama, Akira

    2011-02-01

    Cra (catabolite repressor activator) is a global regulator of the genes for carbon metabolism in Escherichia coli. To gain insights into the regulatory roles of Cra, attempts were made to identify the whole set of regulation targets using an improved genomic SELEX (systematic evolution of ligands by exponential enrichment) system. Surprisingly, a total of 164 binding sites were identified for Cra, 144 (88%) of which were newly identified. The majority of known targets were included in the SELEX chip pattern. The promoters examined by the lacZ reporter assay in vivo were all regulated by Cra. These two lines of evidence indicate that a total of as many as 178 promoters are under the control of Cra. The majority of Cra targets are the genes coding for the enzymes involved in central carbon metabolism, covering all the genes for the enzymes involved in glycolysis and metabolism downstream of glycolysis, including the tricarboxylic acid (TCA) cycle and aerobic respiration. Taken together, we propose that Cra plays a key role in balancing the levels of the enzymes for carbon metabolism.

  3. Novel Members of the Cra Regulon Involved in Carbon Metabolism in Escherichia coli▿ †

    Science.gov (United States)

    Shimada, Tomohiro; Yamamoto, Kaneyoshi; Ishihama, Akira

    2011-01-01

    Cra (catabolite repressor activator) is a global regulator of the genes for carbon metabolism in Escherichia coli. To gain insights into the regulatory roles of Cra, attempts were made to identify the whole set of regulation targets using an improved genomic SELEX (systematic evolution of ligands by exponential enrichment) system. Surprisingly, a total of 164 binding sites were identified for Cra, 144 (88%) of which were newly identified. The majority of known targets were included in the SELEX chip pattern. The promoters examined by the lacZ reporter assay in vivo were all regulated by Cra. These two lines of evidence indicate that a total of as many as 178 promoters are under the control of Cra. The majority of Cra targets are the genes coding for the enzymes involved in central carbon metabolism, covering all the genes for the enzymes involved in glycolysis and metabolism downstream of glycolysis, including the tricarboxylic acid (TCA) cycle and aerobic respiration. Taken together, we propose that Cra plays a key role in balancing the levels of the enzymes for carbon metabolism. PMID:21115656

  4. 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.

  5. An Integrative Approach to Energy, Carbon, and Redox Metabolism in the Cyanobacterium Synechocystis sp. PCC 6803. Special Report

    Energy Technology Data Exchange (ETDEWEB)

    Overbeek, R.

    2003-06-30

    The main objectives for the first year were to produce a detailed metabolic reconstruction of synechocystis sp. PCC 6803 especially in interrelated areas of photosynthesis, respiration, and central carbon metabolism to support a more complete understanding and modeling of this organism. Additionally, Integrated Genomics, Inc., provided detailed bioinformatic analysis of selected functional systems related to carbon and energy generation and utilization, and of the corresponding pathways, functional roles and individual genes to support wet lab experiments by collaborators.

  6. Engineering central metabolism – a grand challenge for plant biologists

    DEFF Research Database (Denmark)

    Sweetlove, Lee J.; Nielsen, Jens; Fernie, Alisdair R.

    2017-01-01

    The goal of increasing crop productivity and nutrient-use efficiency is being addressed by a number of ambitious research projects seeking to re-engineer photosynthetic biochemistry. Many of these projects will require the engineering of substantial changes in fluxes of central metabolism. However......, as has been amply demonstrated in simpler systems such as microbes, central metabolism is extremely difficult to rationally engineer. This is because of multiple layers of regulation that operate to maintain metabolic steady state and because of the highly connected nature of central metabolism....... In this review we discuss new approaches for metabolic engineering that have the potential to address these problems and dramatically improve the success with which we can rationally engineer central metabolism in plants. In particular, we advocate the adoption of an iterative ‘design-build-test-learn’ cycle...

  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. A Synthetic Alternative to Canonical One-Carbon Metabolism.

    Science.gov (United States)

    Bouzon, Madeleine; Perret, Alain; Loreau, Olivier; Delmas, Valérie; Perchat, Nadia; Weissenbach, Jean; Taran, Frédéric; Marlière, Philippe

    2017-08-18

    One-carbon metabolism is an ubiquitous metabolic pathway that encompasses the reactions transferring formyl-, hydroxymethyl- and methyl-groups bound to tetrahydrofolate for the synthesis of purine nucleotides, thymidylate, methionine and dehydropantoate, the precursor of coenzyme A. An alternative cyclic pathway was designed that substitutes 4-hydroxy-2-oxobutanoic acid (HOB), a compound absent from known metabolism, for the amino acids serine and glycine as one-carbon donors. It involves two novel reactions, the transamination of l-homoserine and the transfer of a one-carbon unit from HOB to tetrahydrofolate releasing pyruvate as coproduct. Since canonical reactions regenerate l-homoserine from pyruvate by carboxylation and subsequent reduction, every one-carbon moiety made available for anabolic reactions originates from CO 2 . The HOB-dependent pathway was established in an Escherichia coli auxotroph selected for prototrophy using long-term cultivation protocols. Genetic, metabolic and biochemical evidence support the emergence of a functional HOB-dependent one-carbon pathway achieved with the recruitment of the two enzymes l-homoserine transaminase and HOB-hydroxymethyltransferase and of HOB as an essential metabolic intermediate. Escherichia coli biochemical reprogramming was achieved by minimally altering canonical metabolism and leveraging on natural selection mechanisms, thereby launching the resulting strain on an evolutionary trajectory diverging from all known extant species.

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

    Science.gov (United States)

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

    2007-10-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-07-01

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

  11. Carbon Source-Dependent Inducible Metabolism of Veratryl Alcohol and Ferulic Acid in Pseudomonas putida CSV86

    Science.gov (United States)

    Mohan, Karishma

    2017-01-01

    ABSTRACT Pseudomonas putida CSV86 degrades lignin-derived metabolic intermediates, viz., veratryl alcohol, ferulic acid, vanillin, and vanillic acid, as the sole sources of carbon and energy. Strain CSV86 also degraded lignin sulfonate. Cell respiration, enzyme activity, biotransformation, and high-pressure liquid chromatography (HPLC) analyses suggest that veratryl alcohol and ferulic acid are metabolized to vanillic acid by two distinct carbon source-dependent inducible pathways. Vanillic acid was further metabolized to protocatechuic acid and entered the central carbon pathway via the β-ketoadipate route after ortho ring cleavage. Genes encoding putative enzymes involved in the degradation were found to be present at fer, ver, and van loci. The transcriptional analysis suggests a carbon source-dependent cotranscription of these loci, substantiating the metabolic studies. Biochemical and quantitative real-time (qRT)-PCR studies revealed the presence of two distinct O-demethylases, viz., VerAB and VanAB, involved in the oxidative demethylation of veratric acid and vanillic acid, respectively. This report describes the various steps involved in metabolizing lignin-derived aromatic compounds at the biochemical level and identifies the genes involved in degrading veratric acid and the arrangement of phenylpropanoid metabolic genes as three distinct inducible transcription units/operons. This study provides insight into the bacterial degradation of lignin-derived aromatics and the potential of P. putida CSV86 as a suitable candidate for producing valuable products. IMPORTANCE Pseudomonas putida CSV86 metabolizes lignin and its metabolic intermediates as a carbon source. Strain CSV86 displays a unique property of preferential utilization of aromatics, including for phenylpropanoids over glucose. This report unravels veratryl alcohol metabolism and genes encoding veratric acid O-demethylase, hitherto unknown in pseudomonads, thereby providing new insight into the

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

    Directory of Open Access Journals (Sweden)

    Nengyi Zhang

    2010-04-01

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

  13. 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.

  14. 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

    The central carbon metabolism of the nystatin-producing strain Streptomyces noursei ATCC 11455 was evaluated by C-13-labelling experiments. A batch fermentation was examined during the idiophase by GC-MS measurements of the labelling patterns of amino acids in the biomass. The labelling patterns...

  15. The Role of Diet in One-Carbon Metabolism and Epigenetics

    DEFF Research Database (Denmark)

    Lind, Mads Vendelbo

    Background: Dysregulation of one-carbon metabolism (OCM) is related to metabolic syndrome (MetS) through various mechanisms including epigenetics. Diet plays a central role in ensuring normal OCM regulation by supplying multiple nutrients. Foods such as whole grains and fish have been proposed...... acid (EPA) and docosahexaenoic acid (DHA) which might also play a role in OCM regulation and epigenetics. Aim: This PhD thesis investigates the role of diet in OCM regulation and the potential association between OCM and MetS. We further investigated whether a dietary intervention with high whole grain......-adenosylmethionine (SAM), s-adenosylhomocysteine (SAH) and Hcy, and diet. Associations between OCM metabolites and MetS features were also investigated. In an 8-week human cross-over intervention study we investigated whether a diet rich in whole grain compared to a diet rich in refined grain could affect OCM metabolites...

  16. Benthic metabolic feedbacks to carbonate chemistry on coral reefs:implications for ocean acidification

    Science.gov (United States)

    Price, N.; Rohwer, F. L.; Stuart, S. A.; Andersson, A.; Smith, J.

    2012-12-01

    The metabolic activity of resident organisms can cause spatio-temporal variability in carbonate chemistry within the benthic boundary layer, and thus potentially buffer the global impacts of ocean acidification. But, little is known about the capacity for particular species assemblages to contribute to natural daily variability in carbonate chemistry. We encapsulated replicate areas (~3m2) of reef across six Northern Line Islands in the central Pacific for 24 hrs to quantify feedbacks to carbonate chemistry within the benthic boundary layer from community metabolism. Underneath each 'tent', we quantified relative abundance and biomass of each species of corals and algae. We coupled high temporal resolution time series data on the natural diurnal variability in pH, dissolved oxygen, salinity, and temperature (using autonomous sensors) with resident organisms' net community calcification and productivity rates (using change in total dissolved carbon and total alkalinity over time) to examine feedbacks from reef metabolism to boundary layer carbonate chemistry. These reefs experienced large ranges in pH (> 0.2 amplitude) each day, similar to the magnitude of 'acidification' expected over the next century. Daily benthic pH, pCO2, and aragonite saturation state (Ωaragonite) were contrasted with seasonal threshold values estimated from open ocean climatological data extrapolated at each island to determine relative inter-island feedbacks. Diurnal amplitude in pH, pCO2, and Ωaragonite at each island was dependent upon the resident species assemblage of the benthos and was particularly reliant upon the biomass, productivity, and calcification rate of Halimeda. Net primary productivity of fleshy algae (algal turfs and Lobophora spp.) predominated on degraded, inhabited islands where net community calcification was negligible. In contrast, the chemistry over reefs on 'pristine', uninhabited islands was driven largely by net calcification of calcareous algae and stony

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

    Directory of Open Access Journals (Sweden)

    Hyun-Seob Song

    2015-03-01

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

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

    Science.gov (United States)

    LaRossa, Robert A

    2015-04-01

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

  19. One-Carbon Metabolism in Prostate Cancer: The Role of Androgen Signaling

    Directory of Open Access Journals (Sweden)

    Joshua M. Corbin

    2016-07-01

    Full Text Available Cancer cell metabolism differs significantly from the metabolism of non-transformed cells. This altered metabolic reprogramming mediates changes in the uptake and use of nutrients that permit high rates of proliferation, growth, and survival. The androgen receptor (AR plays an essential role in the establishment and progression of prostate cancer (PCa, and in the metabolic adaptation that takes place during this progression. In its role as a transcription factor, the AR directly affects the expression of several effectors and regulators of essential catabolic and biosynthetic pathways. Indirectly, as a modulator of the one-carbon metabolism, the AR can affect epigenetic processes, DNA metabolism, and redox balance, all of which are important factors in tumorigenesis. In this review, we focus on the role of AR-signaling on one-carbon metabolism in tumorigenesis. Clinical implications of one-carbon metabolism and AR-targeted therapies for PCa are discussed in this context.

  20. One-Carbon Metabolism in Prostate Cancer: The Role of Androgen Signaling

    Science.gov (United States)

    Corbin, Joshua M.; Ruiz-Echevarría, Maria J.

    2016-01-01

    Cancer cell metabolism differs significantly from the metabolism of non-transformed cells. This altered metabolic reprogramming mediates changes in the uptake and use of nutrients that permit high rates of proliferation, growth, and survival. The androgen receptor (AR) plays an essential role in the establishment and progression of prostate cancer (PCa), and in the metabolic adaptation that takes place during this progression. In its role as a transcription factor, the AR directly affects the expression of several effectors and regulators of essential catabolic and biosynthetic pathways. Indirectly, as a modulator of the one-carbon metabolism, the AR can affect epigenetic processes, DNA metabolism, and redox balance, all of which are important factors in tumorigenesis. In this review, we focus on the role of AR-signaling on one-carbon metabolism in tumorigenesis. Clinical implications of one-carbon metabolism and AR-targeted therapies for PCa are discussed in this context. PMID:27472325

  1. Effects of Conservation Tillage on Topsoil Microbial Metabolic Characteristics and Organic Carbon within Aggregates under a Rice (Oryza sativa L.) –Wheat (Triticum aestivum L.) Cropping System in Central China

    Science.gov (United States)

    Liu, Tian-Qi; Cao, Cou-Gui; Li, Cheng-Fang

    2016-01-01

    Investigating microbial metabolic characteristics and soil organic carbon (SOC) within aggregates and their relationships under conservation tillage may be useful in revealing the mechanism of SOC sequestration in conservation tillage systems. However, limited studies have been conducted to investigate the relationship between SOC and microbial metabolic characteristics within aggregate fractions under conservation tillage. We hypothesized that close relationships can exist between SOC and microbial metabolic characteristics within aggregates under conservation tillage. In this study, a field experiment was conducted from June 2011 to June 2013 following a split-plot design of a randomized complete block with tillage practices [conventional intensive tillage (CT) and no tillage (NT)] as main plots and straw returning methods [preceding crop residue returning (S, 2100−2500 kg C ha−1) and removal (NS, 0 kg C ha-1)] as subplots with three replications. The objective of this study was to reveal the effects of tillage practices and residue-returning methods on topsoil microbial metabolic characteristics and organic carbon (SOC) fractions within aggregates and their relationships under a rice–wheat cropping system in central China. Microbial metabolic characteristics investigated using the Biolog system was examined within two aggregate fractions (>0.25 and 0.25 aggregate, and 0.25 mm aggregate (11.3%), and 0.25 mm aggregate, and 0.25 mm aggregate, and tillage (NT and S) increased microbial metabolic activities and Shannon index in >0.25 and directly improved SOC by promoting DOC in >0.25 mm aggregate in the upper (0−5 cm) soil layer under conservation tillage systems, as well as directly and indirectly by promoting DOC and MBC in tillage increased SOC in aggregates in the topsoil by improving microbial metabolic activities. PMID:26731654

  2. Nonstructural leaf carbohydrates dynamics of Pinus edulis during drought-induced tree mortality reveal role for carbon metabolism in mortality mechanism

    Science.gov (United States)

    Adams, Henry D.; Germino, Matthew J.; Breshears, David D.; Barron-Gafford, Greg A.; Guardiola-Claramonte, Maite; Zou, Chris B.; Huxman, Travis E.

    2013-01-01

    * Vegetation change is expected with global climate change, potentially altering ecosystem function and climate feedbacks. However, causes of plant mortality, which are central to vegetation change, are understudied, and physiological mechanisms remain unclear, particularly the roles of carbon metabolism and xylem function.

  3. The Central Nervous System and Bone Metabolism: An Evolving Story.

    Science.gov (United States)

    Dimitri, Paul; Rosen, Cliff

    2017-05-01

    Our understanding of the control of skeletal metabolism has undergone a dynamic shift in the last two decades, primarily driven by our understanding of energy metabolism. Evidence demonstrating that leptin not only influences bone cells directly, but that it also plays a pivotal role in controlling bone mass centrally, opened up an investigative process that has changed the way in which skeletal metabolism is now perceived. Other central regulators of bone metabolism have since been identified including neuropeptide Y (NPY), serotonin, endocannabinoids, cocaine- and amphetamine-regulated transcript (CART), adiponectin, melatonin and neuromedin U, controlling osteoblast and osteoclast differentiation, proliferation and function. The sympathetic nervous system was originally identified as the predominant efferent pathway mediating central signalling to control skeleton metabolism, in part regulated through circadian genes. More recent evidence points to a role of the parasympathetic nervous system in the control of skeletal metabolism either through muscarinic influence of sympathetic nerves in the brain or directly via nicotinic receptors on osteoclasts, thus providing evidence for broader autonomic skeletal regulation. Sensory innervation of bone has also received focus again widening our understanding of the complex neuronal regulation of bone mass. Whilst scientific advance in this field of bone metabolism has been rapid, progress is still required to understand how these model systems work in relation to the multiple confounders influencing skeletal metabolism, and the relative balance in these neuronal systems required for skeletal growth and development in childhood and maintaining skeletal integrity in adulthood.

  4. Suppression of the Escherichia coli dnaA46 mutation by changes in the activities of the pyruvate-acetate node links DNA replication regulation to central carbon metabolism.

    Science.gov (United States)

    Tymecka-Mulik, Joanna; Boss, Lidia; Maciąg-Dorszyńska, Monika; Matias Rodrigues, João F; Gaffke, Lidia; Wosinski, Anna; Cech, Grzegorz M; Szalewska-Pałasz, Agnieszka; Węgrzyn, Grzegorz; Glinkowska, Monika

    2017-01-01

    To ensure faithful transmission of genetic material to progeny cells, DNA replication is tightly regulated, mainly at the initiation step. Escherichia coli cells regulate the frequency of initiation according to growth conditions. Results of the classical, as well as the latest studies, suggest that the DNA replication in E. coli starts at a predefined, constant cell volume per chromosome but the mechanisms coordinating DNA replication with cell growth are still not fully understood. Results of recent investigations have revealed a role of metabolic pathway proteins in the control of cell division and a direct link between metabolism and DNA replication has also been suggested both in Bacillus subtilis and E. coli cells. In this work we show that defects in the acetate overflow pathway suppress the temperature-sensitivity of a defective replication initiator-DnaA under acetogenic growth conditions. Transcriptomic and metabolic analyses imply that this suppression is correlated with pyruvate accumulation, resulting from alterations in the pyruvate dehydrogenase (PDH) activity. Consequently, deletion of genes encoding the pyruvate dehydrogenase subunits likewise resulted in suppression of the thermal-sensitive growth of the dnaA46 strain. We propose that the suppressor effect may be directly related to the PDH complex activity, providing a link between an enzyme of the central carbon metabolism and DNA replication.

  5. Comprehensive evaluation of one-carbon metabolism pathway gene variants and renal cell cancer risk.

    Directory of Open Access Journals (Sweden)

    Todd M Gibson

    Full Text Available Folate and one-carbon metabolism are linked to cancer risk through their integral role in DNA synthesis and methylation. Variation in one-carbon metabolism genes, particularly MTHFR, has been associated with risk of a number of cancers in epidemiologic studies, but little is known regarding renal cancer.Tag single nucleotide polymorphisms (SNPs selected to produce high genomic coverage of 13 gene regions of one-carbon metabolism (ALDH1L1, BHMT, CBS, FOLR1, MTHFR, MTR, MTRR, SHMT1, SLC19A1, TYMS and the closely associated glutathione synthesis pathway (CTH, GGH, GSS were genotyped for 777 renal cell carcinoma (RCC cases and 1,035 controls in the Central and Eastern European Renal Cancer case-control study. Associations of individual SNPs (n = 163 with RCC risk were calculated using unconditional logistic regression adjusted for age, sex and study center. Minimum p-value permutation (Min-P tests were used to identify gene regions associated with risk, and haplotypes were evaluated within these genes.The strongest associations with RCC risk were observed for SLC19A1 (P(min-P = 0.03 and MTHFR (P(min-P = 0.13. A haplotype consisting of four SNPs in SLC19A1 (rs12483553, rs2838950, rs2838951, and rs17004785 was associated with a 37% increased risk (p = 0.02, and exploratory stratified analysis suggested the association was only significant among those in the lowest tertile of vegetable intake.To our knowledge, this is the first study to comprehensively examine variation in one-carbon metabolism genes in relation to RCC risk. We identified a novel association with SLC19A1, which is important for transport of folate into cells. Replication in other populations is required to confirm these findings.

  6. Zooplankton biomass and metabolism through image analysis systems: from the development and testing of metabolic equations to the assessment of carbon fluxes

    OpenAIRE

    Garijo, Juan Carlos

    2016-01-01

    Programa de Doctorado en Oceanografía Zooplankton plays an important role in the biogeochemical cycles in the ocean. Due to their central position in the ocean’s food web, they recycle and redistribute energy and matter, not only at different levels of the trophic web, but also horizontally and vertically in the water column. Understanding the role of zooplankton in the biological pump and the ocean carbon cycle requires accurate estimates of community biomass and metabolism at large spati...

  7. The effect of selected metals on the central metabolic pathways in ...

    African Journals Online (AJOL)

    compounds, interfere with xenobiotic metabolic pathways, and may also affect glycolysis, the Krebs cycle, oxidative phosphorylation, protein amino acid metabolism as well as carbohydrate and lipid metabolism. Therefore, in this review, we discuss the two phases of the central metabolic pathways, as well as how metals ...

  8. Enhancing Carbon Fixation by Metabolic Engineering: A Model System of Complex Network Modulation

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Gregory Stephanopoulos

    2008-04-10

    In the first two years of this research we focused on the development of a DNA microarray for transcriptional studies in the photosynthetic organism Synechocystis and the elucidation of the metabolic pathway for biopolymer synthesis in this organism. In addition we also advanced the molecular biological tools for metabolic engineering of biopolymer synthesis in Synechocystis and initiated a series of physiological studies for the elucidation of the carbon fixing pathways and basic central carbon metabolism of these organisms. During the last two-year period we focused our attention on the continuation and completion of the last task, namely, the development of tools for basic investigations of the physiology of these cells through, primarily, the determination of their metabolic fluxes. The reason for this decision lies in the importance of fluxes as key indicators of physiology and the high level of information content they carry in terms of identifying rate limiting steps in a metabolic pathway. While flux determination is a well-advanced subject for heterotrophic organisms, for the case of autotrophic bacteria, like Synechocystis, some special challenges had to be overcome. These challenges stem mostly from the fact that if one uses {sup 13}C labeled CO{sub 2} for flux determination, the {sup 13}C label will mark, at steady state, all carbon atoms of all cellular metabolites, thus eliminating the necessary differentiation required for flux determination. This peculiarity of autotrophic organisms makes it imperative to carry out flux determination under transient conditions, something that had not been accomplished before. We are pleased to report that we have solved this problem and we are now able to determine fluxes in photosynthetic organisms from stable isotope labeling experiments followed by measurements of label enrichment in cellular metabolites using Gas Chromatography-Mass Spectrometry. We have conducted extensive simulations to test the method and

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

    Directory of Open Access Journals (Sweden)

    Christopher J Alteri

    2015-01-01

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

  10. Preferential Use of Central Metabolism In Vivo Reveals a Nutritional Basis for Polymicrobial Infection

    Science.gov (United States)

    Alteri, Christopher J.; Himpsl, Stephanie D.; Mobley, Harry L. T.

    2015-01-01

    The human genitourinary tract is a common anatomical niche for polymicrobial infection and a leading site for the development of bacteremia and sepsis. Most uncomplicated, community-acquired urinary tract infections (UTI) are caused by Escherichia coli, while another bacterium, Proteus mirabilis, is more often associated with complicated UTI. Here, we report that uropathogenic E. coli and P. mirabilis have divergent requirements for specific central pathways in vivo despite colonizing and occupying the same host environment. Using mutants of specific central metabolism enzymes, we determined glycolysis mutants lacking pgi, tpiA, pfkA, or pykA all have fitness defects in vivo for P. mirabilis but do not affect colonization of E. coli during UTI. Similarly, the oxidative pentose phosphate pathway is required only for P. mirabilis in vivo. In contrast, gluconeogenesis is required only for E. coli fitness in vivo. The remarkable difference in central pathway utilization between E. coli and P. mirabilis during experimental UTI was also observed for TCA cycle mutants in sdhB, fumC, and frdA. The distinct in vivo requirements between these pathogens suggest E. coli and P. mirabilis are not direct competitors within host urinary tract nutritional niche. In support of this, we found that co-infection with E. coli and P. mirabilis wild-type strains enhanced bacterial colonization and persistence of both pathogens during UTI. Our results reveal that complementary utilization of central carbon metabolism facilitates polymicrobial disease and suggests microbial activity in vivo alters the host urinary tract nutritional niche. PMID:25568946

  11. The effects of phosphorus limitation on carbon metabolism in diatoms.

    Science.gov (United States)

    Brembu, Tore; Mühlroth, Alice; Alipanah, Leila; Bones, Atle M

    2017-09-05

    Phosphorus is an essential element for life, serving as an integral component of nucleic acids, lipids and a diverse range of other metabolites. Concentrations of bioavailable phosphorus are low in many aquatic environments. Microalgae, including diatoms, apply physiological and molecular strategies such as phosphorus scavenging or recycling as well as adjusting cell growth in order to adapt to limiting phosphorus concentrations. Such strategies also involve adjustments of the carbon metabolism. Here, we review the effect of phosphorus limitation on carbon metabolism in diatoms. Two transcriptome studies are analysed in detail, supplemented by other transcriptome, proteome and metabolite data, to gain an overview of different pathways and their responses. Phosphorus, nitrogen and silicon limitation responses are compared, and similarities and differences discussed. We use the current knowledge to propose a suggestive model for the carbon flow in phosphorus-replete and phosphorus-limited diatom cells.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'. © 2017 The Authors.

  12. Central nervous system regulation of intestinal lipid and lipoprotein metabolism.

    Science.gov (United States)

    Farr, Sarah; Taher, Jennifer; Adeli, Khosrow

    2016-02-01

    In response to nutrient availability, the small intestine and brain closely communicate to modulate energy homeostasis and metabolism. The gut-brain axis involves complex nutrient sensing mechanisms and an integration of neuronal and hormonal signaling. This review summarizes recent evidence implicating the gut-brain axis in regulating lipoprotein metabolism, with potential implications for the dyslipidemia of insulin resistant states. The intestine and brain possess distinct mechanisms for sensing lipid availability, which triggers subsequent regulation of feeding, glucose homeostasis, and adipose tissue metabolism. More recently, central receptors, neuropeptides, and gut hormones that communicate with the brain have been shown to modulate hepatic and intestinal lipoprotein metabolism via parasympathetic and sympathetic signaling. Gut-derived glucagon-like peptides appear to be particularly important in modulating the intestinal secretion of chylomicron particles via a novel brain-gut axis. Dysregulation of these pathways may contribute to postprandial diabetic dyslipidemia. Emerging evidence implicates the central and enteric nervous systems in controlling many aspects of lipid and lipoprotein metabolism. Bidirectional communication between the gut and brain involving neuronal pathways and gut peptides is critical for regulating feeding and metabolism, and forms a neuroendocrine circuit to modulate dietary fat absorption and intestinal production of atherogenic chylomicron particles.

  13. Dynamic optimal metabolic control theory: a cybernetic approach for modelling of the central nitrogen metabolism of S. cerevisiae

    NARCIS (Netherlands)

    Riel, van N.A.W.; Giuseppin, M.L.F.; Verrips, C.T.

    2000-01-01

    The theory of dynamic optimal metabolic control (DOMC), as developed by Giuseppin and Van Riel (Metab. Eng., 2000), is applied to model the central nitrogen metabolism (CNM) in Saccharomyces cerevisiae. The CNM represents a typical system encountered in advanced metabolic engineering. The CNM is the

  14. Metabolic effects of Carbon Dioxide (CO 2 ) insufflation during ...

    African Journals Online (AJOL)

    Metabolic effects of Carbon Dioxide (CO 2 ) insufflation during laparoscopic surgery: changes in pH, arterial partial Pressure of Carbon Dioxide (PaCo 2 ) and End Tidal Carbon Dioxide (EtCO 2 ) ... Respiratory adjustments were done for EtCO2 levels above 60mmHg or SPO2 below 92% or adverse haemodynamic changes.

  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. Engineering microbial fatty acid metabolism for biofuels and biochemicals

    DEFF Research Database (Denmark)

    Marella, Eko Roy; Holkenbrink, Carina; Siewers, Verena

    2017-01-01

    microbial catalysis. This review summarizes the recent advances in the engineering of microbial metabolism for production of fatty acid-derived products. We highlight the efforts in engineering the central carbon metabolism, redox metabolism, controlling the chain length of the products, and obtaining...

  18. Reconstruction of the central carbon metabolism of Aspergillus niger

    DEFF Research Database (Denmark)

    David, Helga; Åkesson, Mats Fredrik; Nielsen, Jens

    2003-01-01

    database for annotation of genes identified in future genome sequencing projects on aspergilli. Based on the metabolic reconstruction, a stoichiometric model was set up that includes 284 metabolites and 335 reactions, of which 268 represent biochemical conversions and 67 represent transport processes...

  19. Proteins involved in flor yeast carbon metabolism under biofilm formation conditions.

    Science.gov (United States)

    Moreno-García, Jaime; García-Martínez, Teresa; Moreno, Juan; Mauricio, Juan Carlos

    2015-04-01

    A lack of sugars during the production of biologically aged wines after fermentation of grape must causes flor yeasts to metabolize other carbon molecules formed during fermentation (ethanol and glycerol, mainly). In this work, a proteome analysis involving OFFGEL fractionation prior to LC/MS detection was used to elucidate the carbon metabolism of a flor yeast strain under biofilm formation conditions (BFC). The results were compared with those obtained under non-biofilm formation conditions (NBFC). Proteins associated to processes such as non-fermentable carbon uptake, the glyoxylate and TCA cycles, cellular respiration and inositol metabolism were detected at higher concentrations under BFC than under the reference conditions (NBFC). This study constitutes the first attempt at identifying the flor yeast proteins responsible for the peculiar sensory profile of biologically aged wines. A better metabolic knowledge of flor yeasts might facilitate the development of effective strategies for improved production of these special wines. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Organic carbon balance and net ecosystem metabolism in Chesapeake Bay

    Science.gov (United States)

    Kemp, W.M.; Smith, E.M.; Marvin-DiPasquale, M.; Boynton, W.R.

    1997-01-01

    The major fluxes of organic carbon associated with physical transport and biological metabolism were compiled, analyzed and compared for the mainstem portion of Chesapeake Bay (USA). In addition, 5 independent methods were used to calculate the annual mean net ecosystem metabolism (NEM = production - respiration) for the integrated Bay. These methods, which employed biogeochemical models, nutrient mass-balances anti summation of individual organic carbon fluxes, yielded remarkably similar estimates, with a mean NEM of +50 g C m-2 yr-1 (?? SE = 751, which is approximately 8% of the estimated annual average gross primary production. These calculations suggest a strong cross-sectional pattern in NEM throughout the Bay, wherein net heterotrophic metabolism prevails in the pelagic zones of the main channel, while net autotrophy occurs in the littoral zones which flank the deeper central area. For computational purposes, the estuary was separated into 3 regions along the land-sea gradient: (1) the oligohaline Upper Bay (11% of total area); (2) the mesohaline Mid Bay (36% of area); and (3) the polyhaline Lower Bay (53% of area). A distinct regional trend in NEM was observed along this salinity gradient, with net here(atrophy (NEM = 87 g C m-2 yr-1) in the Upper Bay, balanced metabolism in the Mid Bay and net autotrophy (NEM = +92 g C m-2 yr-1) in the Lower Bay. As a consequence of overall net autotrophy, the ratio of dissolved inorganic nitrogen (DIN) to total organic nitrogen (TON) changed from DIN:TON = 5.1 for riverine inputs to DIN:TON = 0.04 for water exported to the ocean. A striking feature of this organic C mass-balance was the relative dominance of biologically mediated metabolic fluxes compared to physical transport fluxes. The overall ratio of physical TOC inputs (1) to biotic primary production (P) was 0.08 for the whole estuary, but varied dramatically from 2.3 in the Upper Bay to 0.03 in the Mid and Lower Bay regions. Similarly, ecosystem respiration was

  1. Metabolic adjustment upon repetitive substrate perturbations using dynamic

    NARCIS (Netherlands)

    Suarez Mendez, C.A.; Ras, C.; Wahl, S.A.

    2017-01-01

    Background: Natural and industrial environments are dynamic with respect to substrate availability and other conditions like temperature and pH. Especially, metabolism is strongly affected by changes in the extracellular space. Here we study the dynamic flux of central carbon metabolism and

  2. Nutrients in Energy and One-Carbon Metabolism: Learning from Metformin Users

    Directory of Open Access Journals (Sweden)

    Fedra Luciano-Mateo

    2017-02-01

    Full Text Available Metabolic vulnerability is associated with age-related diseases and concomitant co-morbidities, which include obesity, diabetes, atherosclerosis and cancer. Most of the health problems we face today come from excessive intake of nutrients and drugs mimicking dietary effects and dietary restriction are the most successful manipulations targeting age-related pathways. Phenotypic heterogeneity and individual response to metabolic stressors are closely related food intake. Understanding the complexity of the relationship between dietary provision and metabolic consequences in the long term might provide clinical strategies to improve healthspan. New aspects of metformin activity provide a link to many of the overlapping factors, especially the way in which organismal bioenergetics remodel one-carbon metabolism. Metformin not only inhibits mitochondrial complex 1, modulating the metabolic response to nutrient intake, but also alters one-carbon metabolic pathways. Here, we discuss findings on the mechanism(s of action of metformin with the potential for therapeutic interpretations.

  3. Nonstructural leaf carbohydrate dynamics of Pinus edulis during drought-induced tree mortality reveal role for carbon metabolism in mortality mechanism.

    Science.gov (United States)

    Adams, Henry D; Germino, Matthew J; Breshears, David D; Barron-Gafford, Greg A; Guardiola-Claramonte, Maite; Zou, Chris B; Huxman, Travis E

    2013-03-01

    Vegetation change is expected with global climate change, potentially altering ecosystem function and climate feedbacks. However, causes of plant mortality, which are central to vegetation change, are understudied, and physiological mechanisms remain unclear, particularly the roles of carbon metabolism and xylem function. We report analysis of foliar nonstructural carbohydrates (NSCs) and associated physiology from a previous experiment where earlier drought-induced mortality of Pinus edulis at elevated temperatures was associated with greater cumulative respiration. Here, we predicted faster NSC decline for warmed trees than for ambient-temperature trees. Foliar NSC in droughted trees declined by 30% through mortality and was lower than in watered controls. NSC decline resulted primarily from decreased sugar concentrations. Starch initially declined, and then increased above pre-drought concentrations before mortality. Although temperature did not affect NSC and sugar, starch concentrations ceased declining and increased earlier with higher temperatures. Reduced foliar NSC during lethal drought indicates a carbon metabolism role in mortality mechanism. Although carbohydrates were not completely exhausted at mortality, temperature differences in starch accumulation timing suggest that carbon metabolism changes are associated with time to death. Drought mortality appears to be related to temperature-dependent carbon dynamics concurrent with increasing hydraulic stress in P. edulis and potentially other similar species. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

  4. An integrative approach to energy, carbon, and redox metabolism in the cyanobacterium Synechocystis sp. PCC 6803

    Energy Technology Data Exchange (ETDEWEB)

    Overbeek, Ross; Fonstein, Veronika; Osterman, Andrei; Gerdes, Svetlana; Vassieva, Olga; Zagnitko, Olga; Rodionov, Dmitry

    2005-02-15

    covering energy, carbon, and redox metabolism in the Synechocystis sp. PCC 6803 and other cyanobacteria has been performed (Specific Aim 4). The main objectives for this year (adjusted to reflect a new, public domain, setting of the Project research team) were: Aim 1. To develop, test, and deploy a new open source system, the SEED, for integrating community-based annotation, and comparative analysis of all publicly available microbial genomes. Develop a comprehensive genomic database by integrating within SEED all publicly available complete and nearly complete genome sequences with special emphasis on genomes of cyanobacteria, phototrophic eukaryotes, and anoxygenic phototrophic bacteria--invaluable for comparative genomic studies of energy and carbon metabolism in Synechocystis sp. PCC 6803. Aim 2. To develop the SEED's biological content in the form of a collection of encoded Subsystems largely covering the conserved cellular machinery in prokaryotes (and central metabolic machinery in eukaryotes). Aim 3. To develop, utilizing core SEED technology, the CyanoSEED--a specialized WEB portal for community-based annotation, and comparative analysis of all publicly available cyanobacterial genomes. Encode the set of additional subsystems representing key metabolic transformations in cyanobacteria and other photoautotrophs. We envisioned this resource as complementary to other public access databases for comparative genomic analysis currently available to the cyanobacterial research community. Aim 4. Perform in-depth analysis of several subsystems covering energy, carbon, and redox metabolism in the Synechocystis sp. PCC 6803 and all other cyanobacteria with available genome sequences. Reveal inconsistencies and gaps in the current knowledge of these subsystems. Use functional and genome context analysis tools in CyanoSEED to predict, whenever possible, candidate genes for inferred functional roles. To disseminate freely these conjectures and predictions by publishing

  5. Transcriptional and metabolic effects of glucose on Streptococcus pneumoniae sugar metabolism

    Directory of Open Access Journals (Sweden)

    Laura ePaixão

    2015-10-01

    Full Text Available Streptococcus pneumoniae is a strictly fermentative human pathogen that relies on carbohydrate metabolism to generate energy for growth. The nasopharynx colonised by the bacterium is poor in free sugars, but mucosa lining glycans can provide a source of sugar. In blood and inflamed tissues glucose is the prevailing sugar. As a result during progression from colonisation to disease S. pneumoniae has to cope with a pronounced shift in carbohydrate nature and availability. Thus, we set out to assess the pneumococcal response to sugars found in glycans and the influence of glucose (Glc on this response at the transcriptional, physiological and metabolic levels. Galactose (Gal, N-acetylglucosamine (GlcNAc and mannose (Man affected the expression of 8 to 14% of the genes covering cellular functions including central carbon metabolism and virulence. The pattern of end-products as monitored by in vivo 13C-NMR is in good agreement with the fermentation profiles during growth, while the pools of phosphorylated metabolites are consistent with the type of fermentation observed (homolactic vs. mixed and regulation at the metabolic level. Furthermore, the accumulation of α-Gal6P and Man6P indicate metabolic bottlenecks in the metabolism of Gal and Man, respectively. Glc added to cells actively metabolizing other sugar(s was readily consumed and elicited a metabolic shift towards a homolactic profile. The transcriptional response to Glc was large (over 5% of the genome. In central carbon metabolism (most represented category, Glc exerted mostly negative regulation. The smallest response to Glc was observed on a sugar mix, suggesting that exposure to varied sugars improves the fitness of S. pneumoniae. The expression of virulence factors was negatively controlled by Glc in a sugar-dependent manner. Overall, our results shed new light on the link between carbohydrate metabolism, adaptation to host niches and virulence.

  6. Transcriptional and metabolic effects of glucose on Streptococcus pneumoniae sugar metabolism.

    Science.gov (United States)

    Paixão, Laura; Caldas, José; Kloosterman, Tomas G; Kuipers, Oscar P; Vinga, Susana; Neves, Ana R

    2015-01-01

    Streptococcus pneumoniae is a strictly fermentative human pathogen that relies on carbohydrate metabolism to generate energy for growth. The nasopharynx colonized by the bacterium is poor in free sugars, but mucosa lining glycans can provide a source of sugar. In blood and inflamed tissues glucose is the prevailing sugar. As a result during progression from colonization to disease S. pneumoniae has to cope with a pronounced shift in carbohydrate nature and availability. Thus, we set out to assess the pneumococcal response to sugars found in glycans and the influence of glucose (Glc) on this response at the transcriptional, physiological, and metabolic levels. Galactose (Gal), N-acetylglucosamine (GlcNAc), and mannose (Man) affected the expression of 8 to 14% of the genes covering cellular functions including central carbon metabolism and virulence. The pattern of end-products as monitored by in vivo (13)C-NMR is in good agreement with the fermentation profiles during growth, while the pools of phosphorylated metabolites are consistent with the type of fermentation observed (homolactic vs. mixed) and regulation at the metabolic level. Furthermore, the accumulation of α-Gal6P and Man6P indicate metabolic bottlenecks in the metabolism of Gal and Man, respectively. Glc added to cells actively metabolizing other sugar(s) was readily consumed and elicited a metabolic shift toward a homolactic profile. The transcriptional response to Glc was large (over 5% of the genome). In central carbon metabolism (most represented category), Glc exerted mostly negative regulation. The smallest response to Glc was observed on a sugar mix, suggesting that exposure to varied sugars improves the fitness of S. pneumoniae. The expression of virulence factors was negatively controlled by Glc in a sugar-dependent manner. Overall, our results shed new light on the link between carbohydrate metabolism, adaptation to host niches and virulence.

  7. A Natural Light/Dark Cycle Regulation of Carbon-Nitrogen Metabolism and Gene Expression in Rice Shoots.

    Science.gov (United States)

    Li, Haixing; Liang, Zhijun; Ding, Guangda; Shi, Lei; Xu, Fangsen; Cai, Hongmei

    2016-01-01

    Light and temperature are two particularly important environmental cues for plant survival. Carbon and nitrogen are two essential macronutrients required for plant growth and development, and cellular carbon and nitrogen metabolism must be tightly coordinated. In order to understand how the natural light/dark cycle regulates carbon and nitrogen metabolism in rice plants, we analyzed the photosynthesis, key carbon-nitrogen metabolites, and enzyme activities, and differentially expressed genes and miRNAs involved in the carbon and nitrogen metabolic pathway in rice shoots at the following times: 2:00, 6:00, 10:00, 14:00, 18:00, and 22:00. Our results indicated that more CO2 was fixed into carbohydrates by a high net photosynthetic rate, respiratory rate, and stomatal conductance in the daytime. Although high levels of the nitrate reductase activity, free ammonium and carbohydrates were exhibited in the daytime, the protein synthesis was not significantly facilitated by the light and temperature. In mRNA sequencing, the carbon and nitrogen metabolism-related differentially expressed genes were obtained, which could be divided into eight groups: photosynthesis, TCA cycle, sugar transport, sugar metabolism, nitrogen transport, nitrogen reduction, amino acid metabolism, and nitrogen regulation. Additionally, a total of 78,306 alternative splicing events have been identified, which primarily belong to alternative 5' donor sites, alternative 3' acceptor sites, intron retention, and exon skipping. In sRNA sequencing, four carbon and nitrogen metabolism-related miRNAs (osa-miR1440b, osa-miR2876-5p, osa-miR1877 and osa-miR5799) were determined to be regulated by natural light/dark cycle. The expression level analysis showed that the four carbon and nitrogen metabolism-related miRNAs negatively regulated their target genes. These results may provide a good strategy to study how natural light/dark cycle regulates carbon and nitrogen metabolism to ensure plant growth and

  8. A natural light/dark cycle regulation of carbon-nitrogen metabolism and gene expression in rice shoots

    Directory of Open Access Journals (Sweden)

    Haixing Li

    2016-08-01

    Full Text Available Light and temperature are two particularly important environmental cues for plant survival. Carbon and nitrogen are two essential macronutrients required for plant growth and development, and cellular carbon and nitrogen metabolism must be tightly coordinated. In order to understand how the natural light/dark cycle regulates carbon and nitrogen metabolism in rice plants, we analyzed the photosynthesis, key carbon-nitrogen metabolites and enzyme activities, and differentially expressed genes and miRNAs involved in the carbon and nitrogen metabolic pathway in rice shoots at the following times: 2:00, 6:00, 10:00, 14:00, 18:00 and 22:00. Our results indicated that more CO2 was fixed into carbohydrates by a high net photosynthetic rate, respiratory rate and stomatal conductance in the daytime. Although high levels of the nitrate reductase activity, free ammonium and carbohydrates were exhibited in the daytime, the protein synthesis was not significantly facilitated by the light and temperature. In mRNA sequencing, the carbon and nitrogen metabolism-related differentially expressed genes were obtained, which could be divided into eight groups: photosynthesis, TCA cycle, sugar transport, sugar metabolism, nitrogen transport, nitrogen reduction, amino acid metabolism and nitrogen regulation. Additionally, a total of 78,306 alternative splicing events have been identified, which primarily belong to alternative 5' donor sites, alternative 3' acceptor sites, intron retention and exon skipping. In sRNA sequencing, four carbon and nitrogen metabolism-related miRNAs (osa-miR1440b, osa-miR2876-5p, osa-miR1877 and osa-miR5799 were determined to be regulated by natural light/dark cycle. The expression level analysis showed that the four carbon and nitrogen metabolism-related miRNAs negatively regulated their target genes. These results may provide a good strategy to study how natural light/dark cycle regulates carbon and nitrogen metabolism to ensure plant

  9. Fermentation of Xylose Causes Inefficient Metabolic State Due to Carbon/Energy Starvation and Reduced Glycolytic Flux in Recombinant Industrial Saccharomyces cerevisiae

    Science.gov (United States)

    Matsushika, Akinori; Nagashima, Atsushi; Goshima, Tetsuya; Hoshino, Tamotsu

    2013-01-01

    In the present study, comprehensive, quantitative metabolome analysis was carried out on the recombinant glucose/xylose-cofermenting S. cerevisiae strain MA-R4 during fermentation with different carbon sources, including glucose, xylose, or glucose/xylose mixtures. Capillary electrophoresis time-of-flight mass spectrometry was used to determine the intracellular pools of metabolites from the central carbon pathways, energy metabolism pathways, and the levels of twenty amino acids. When xylose instead of glucose was metabolized by MA-R4, glycolytic metabolites including 3- phosphoglycerate, 2- phosphoglycerate, phosphoenolpyruvate, and pyruvate were dramatically reduced, while conversely, most pentose phosphate pathway metabolites such as sedoheptulose 7- phosphate and ribulose 5-phosphate were greatly increased. These results suggest that the low metabolic activity of glycolysis and the pool of pentose phosphate pathway intermediates are potential limiting factors in xylose utilization. It was further demonstrated that during xylose fermentation, about half of the twenty amino acids declined, and the adenylate/guanylate energy charge was impacted due to markedly decreased adenosine triphosphate/adenosine monophosphate and guanosine triphosphate/guanosine monophosphate ratios, implying that the fermentation of xylose leads to an inefficient metabolic state where the biosynthetic capabilities and energy balance are severely impaired. In addition, fermentation with xylose alone drastically increased the level of citrate in the tricarboxylic acid cycle and increased the aromatic amino acids tryptophan and tyrosine, strongly supporting the view that carbon starvation was induced. Interestingly, fermentation with xylose alone also increased the synthesis of the polyamine spermidine and its precursor S-adenosylmethionine. Thus, differences in carbon substrates, including glucose and xylose in the fermentation medium, strongly influenced the dynamic metabolism of MA-R4

  10. Lipids Reprogram Metabolism to Become a Major Carbon Source for Histone Acetylation

    DEFF Research Database (Denmark)

    McDonnell, Eoin; Crown, Scott B; Fox, Douglas B

    2016-01-01

    Cells integrate nutrient sensing and metabolism to coordinate proper cellular responses to a particular nutrient source. For example, glucose drives a gene expression program characterized by activating genes involved in its metabolism, in part by increasing glucose-derived histone acetylation....... Here, we find that lipid-derived acetyl-CoA is a major source of carbon for histone acetylation. Using (13)C-carbon tracing combined with acetyl-proteomics, we show that up to 90% of acetylation on certain histone lysines can be derived from fatty acid carbon, even in the presence of excess glucose...

  11. Central regulation of metabolism by protein tyrosine phosphatases

    Directory of Open Access Journals (Sweden)

    Ryan eTsou

    2013-01-01

    Full Text Available Protein tyrosine phosphatases (PTPs are important regulators of intracellular signaling pathways via the dephosphorylation of phosphotyrosyl residues on various receptor and non-receptor substrates. The phosphorylation state of central nervous system (CNS signaling components underlies the molecular mechanisms of a variety of physiological functions including the control of energy balance and glucose homeostasis. In this review, we summarize the current evidence implicating PTPs as central regulators of metabolism, specifically highlighting their interactions with the neuronal leptin and insulin signaling pathways. We discuss the role of a number of PTPs (PTP1B, SHP2, TCPTP, RPTPe, and PTEN, reviewing the findings from genetic mouse models and in vitro studies which highlight these phosphatases as key central regulators of energy homeostasis.

  12. Observability of plant metabolic networks is reflected in the correlation of metabolic profiles

    DEFF Research Database (Denmark)

    Schwahn, Kevin; Küken, Anika; Kliebenstein, Daniel James

    2016-01-01

    to obtain information about the entire system. Yet, the extent to which the data profiles reflect the role of components in the observability of the system remains unexplored. Here we first identify the sensor metabolites in the model plant Arabidopsis (Arabidopsis thaliana) by employing state...... with in silico generated metabolic profiles from a medium-size kinetic model of plant central carbon metabolism. Altogether, due to the small number of identified sensors, our study implies that targeted metabolite analyses may provide the vast majority of relevant information about plant metabolic systems....

  13. Carbon balance studies of glucose metabolism in rat cerebral cortical synaptosomes

    Energy Technology Data Exchange (ETDEWEB)

    Bauer, U; Brand, K

    1982-07-01

    Synaptosomes were isolated from rat cerebral cortex and incubated with (U-/sup 14/C)-, (1-/sup 14/C)- or (6-/sup 14/C)glucose. Glucose utilization and the metabolic partitioning of glucose carbon in products were determined by isotopic methods. From the data obtained a carbon balance was constructed, showing lactate to be the main product of glucose metabolism, followed by CO/sup 2/, amino acids and pyruvate. Measuring the release of /sup 14/CO/sup 2/ from glucose labelled in three different positions allowed the construction of a flow diagram of glucose carbon atoms in synaptosomes, which provides information about the contribution of the various pathways of glucose metabolism. Some 2% of glucose utilized was calculated to be degraded via the pentose phosphate pathway. Addition of chlorpromazine, imipramine or haloperidol at concentrations of 10(-5) M reduced glucose utilisation by 30% without changing the distribution pattern of radioactivity in the various products.

  14. Metabolite secretion in microorganisms: the theory of metabolic overflow put to the test

    DEFF Research Database (Denmark)

    Pinu, Farhana R.; Granucci, Ninna; Daniell, James

    2018-01-01

    Introduction Microbial cells secrete many metabolites during growth, including important intermediates of the central carbon metabolism. This has not been taken into account by researchers when modeling microbial metabolism for metabolic engineering and systems biology studies. Materials and Meth...

  15. Metabolic response of Candida albicans to phenylethyl alcohol under hyphae-inducing conditions.

    Science.gov (United States)

    Han, Ting-Li; Tumanov, Sergey; Cannon, Richard D; Villas-Boas, Silas G

    2013-01-01

    Phenylethyl alcohol was one of the first quorum sensing molecules (QSMs) identified in C. albicans. This extracellular signalling molecule inhibits the hyphal formation of C. albicans at high cell density. Little is known, however, about the underlying mechanisms by which this QSM regulates the morphological switches of C. albicans. Therefore, we have applied metabolomics and isotope labelling experiments to investigate the metabolic changes that occur in C. albicans in response to phenylethyl alcohol under defined hyphae-inducing conditions. Our results showed a global upregulation of central carbon metabolism when hyphal development was suppressed by phenylethyl alcohol. By comparing the metabolic changes in response to phenylethyl alcohol to our previous metabolomic studies, we were able to short-list 7 metabolic pathways from central carbon metabolism that appear to be associated with C. albicans morphogenesis. Furthermore, isotope-labelling data showed that phenylethyl alcohol is indeed taken up and catabolised by yeast cells. Isotope-labelled carbon atoms were found in the majority of amino acids as well as in lactate and glyoxylate. However, isotope-labelled carbon atoms from phenylethyl alcohol accumulated mainly in the pyridine ring of NAD(+)/NADH and NADP(-/)NADPH molecules, showing that these nucleotides were the main products of phenylethyl alcohol catabolism. Interestingly, two metabolic pathways where these nucleotides play an important role, nitrogen metabolism and nicotinate/nicotinamide metabolism, were also short-listed through our previous metabolomics works as metabolic pathways likely to be closely associated with C. albicans morphogenesis.

  16. [Carbon footprint of buildings in the urban agglomeration of central Liaoning, China].

    Science.gov (United States)

    Shi, Yu; Yun, Ying Xia; Liu, Chong; Chu, Ya Qi

    2017-06-18

    With the development of urbanization in China, buildings consumed lots of material and energy. How to estimate carbon emission of buildings is an important scientific problem. Carbon footprint of the central Liaoning agglomeration was studied with carbon footprint approach, geographic information system (GIS) and high-resolution remote sensing (HRRS) technology. The results showed that the construction carbon footprint coefficient of central Liaoning urban agglomeration was 269.16 kg·m -2 . The approach of interpreting total building area and spatial distribution with HRRS was effective, and the accuracy was 89%. The extraction approach was critical for total carbon footprint and spatial distribution estimation. The building area and total carbon footprint of central Liaoning urban agglomeration in descending order was Shenyang, Anshan, Fushun, Liao-yang, Yingkou, Tieling and Benxi. The annual average increment of footprint from 2011 to 2013 in descending order was Shenyang, Benxi, Fushun, Anshan, Tieling, Yingkou and Liaoyang. The accurate estimation of construction carbon footprint spatial and its distribution was of significance for the planning and optimization of carbon emission reduction.

  17. An Optimal Centralized Carbon Dioxide Repository for Florida, USA

    Directory of Open Access Journals (Sweden)

    Brandon Poiencot

    2011-03-01

    Full Text Available For over a decade, the United States Department of Energy, and engineers, geologists, and scientists from all over the world have investigated the potential for reducing atmospheric carbon emissions through carbon sequestration. Numerous reports exist analyzing the potential for sequestering carbon dioxide at various sites around the globe, but none have identified the potential for a statewide system in Florida, USA. In 2005, 83% of Florida’s electrical energy was produced by natural gas, coal, or oil (e.g., fossil fuels, from power plants spread across the state. In addition, only limited research has been completed on evaluating optimal pipeline transportation networks to centralized carbon dioxide repositories. This paper describes the feasibility and preliminary locations for an optimal centralized Florida-wide carbon sequestration repository. Linear programming optimization modeling is used to plan and route an idealized pipeline network to existing Florida power plants. Further analysis of the subsurface geology in these general locations will provide insight into the suitability of the subsurface conditions and the available capacity for carbon sequestration at selected possible repository sites. The identification of the most favorable site(s is also presented.

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

    Science.gov (United States)

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

    2013-12-01

    (13)C-metabolic flux analysis ((13)C-MFA) has become a key method for metabolic engineering and systems biology. In the most common methodology, fluxes are calculated by global isotopomer balancing and iterative fitting to stationary (13)C-labeling data. This approach requires a closed carbon balance, long-lasting metabolic steady state, and the detection of (13)C-patterns in a large number of metabolites. These restrictions mostly reduced the application of (13)C-MFA to the central carbon metabolism of well-studied model organisms grown in minimal media with a single carbon source. Here we introduce non-stationary (13)C-metabolic flux ratio analysis as a novel method for (13)C-MFA to allow estimating local, relative fluxes from ultra-short (13)C-labeling experiments and without the need for global isotopomer balancing. The approach relies on the acquisition of non-stationary (13)C-labeling data exclusively for metabolites in the proximity of a node of converging fluxes and a local parameter estimation with a system of ordinary differential equations. We developed a generalized workflow that takes into account reaction types and the availability of mass spectrometric data on molecular ions or fragments for data processing, modeling, parameter and error estimation. We demonstrated the approach by analyzing three key nodes of converging fluxes in central metabolism of Bacillus subtilis. We obtained flux estimates that are in agreement with published results obtained from steady state experiments, but reduced the duration of the necessary (13)C-labeling experiment to less than a minute. These results show that our strategy enables to formally estimate relative pathway fluxes on extremely short time scale, neglecting cellular carbon balancing. Hence this approach paves the road to targeted (13)C-MFA in dynamic systems with multiple carbon sources and towards rich media. © 2013 Wiley Periodicals, Inc.

  19. Overview of the physiological ecology of carbon metabolism in seagrasses.

    Science.gov (United States)

    Touchette; Burkholder

    2000-07-30

    carbon sink to source. Unlike terrestrial plants, SPS apparently is not light-activated, and is positively influenced by increasing temperature and salinity. This response may indicate an osmotic adjustment in marine angiosperms, analogous to increased SPS activity as a cryoprotectant response in terrestrial non-halophytic plants. Sucrose synthase (SS, involved in sucrose metabolism and degradation in sink tissues) of both above- and belowground tissues decreases with tissue age. In belowground tissues, SS activity increases under low oxygen availability and with increasing temperatures, likely indicating increased metabolic carbohydrate demand. Respiration in seagrasses is primarily influenced by temperature and, in belowground tissues, by oxygen availability. Aboveground tissues (involved in C assimilation and other energy-costly processes) generally have higher respiration rates than belowground (mostly storage) tissues. Respiration rates increase with increasing temperature (in excess of 40 degrees C) and increasing water-column nitrate enrichment (Z. marina), which may help to supply the energy and carbon needed to assimilate and reduce nitrate. Seagrasses translocate oxygen from photosynthesizing leaves to belowground tissues for aerobic respiration. During darkness or extended periods of low light, belowground tissues can sustain extended anerobiosis. Documented alternate fermentation pathways have yielded high alanine, a metabolic 'strategy' that would depress production of the more toxic product ethanol, while conserving carbon skeletons and assimilated nitrogen. In comparison to the wealth of information available for terrestrial plants, little is known about the physiological ecology of seagrasses in carbon acquisition and metabolism. Many aspects of their carbon metabolism - controls by interactive environmental factors; and the role of carbon metabolism in salt tolerance, growth under resource-limited conditions, and survival through periods of dormancy

  20. High-sensitivity C-reactive protein to detect metabolic syndrome in a centrally obese population: a cross-sectional analysis

    Directory of Open Access Journals (Sweden)

    den Engelsen Corine

    2012-03-01

    Full Text Available Abstract Background People with central obesity have an increased risk for developing the metabolic syndrome, type 2 diabetes and cardiovascular disease. However, a substantial part of obese individuals have no other cardiovascular risk factors, besides their obesity. High sensitivity C-reactive protein (hs-CRP, a marker of systemic inflammation and a predictor of type 2 diabetes and cardiovascular disease, is associated with the metabolic syndrome and its separate components. We evaluated the use of hs-CRP to discriminate between centrally obese people with and without the metabolic syndrome. Methods 1165 people with central obesity but without any previous diagnosis of hypertension, dyslipidemia, diabetes or cardiovascular disease, aged 20-70 years, underwent a physical examination and laboratory assays to determine the presence of the metabolic syndrome (NCEP ATP III criteria. Multivariable linear regression analyses were performed to assess which metabolic syndrome components were independently associated with hs-CRP. A ROC curve was drawn and the area under the curve was calculated to evaluate whether hs-CRP was capable to predict the presence of the metabolic syndrome. Results Median hs-CRP levels were significantly higher in individuals with central obesity with the metabolic syndrome (n = 417; 35.8% compared to individuals with central obesity without the metabolic syndrome (2.2 mg/L (IQR 1.2-4.0 versus 1.7 mg/L (IQR 1.0-3.4; p Conclusions Hs-CRP has limited capacity to predict the presence of the metabolic syndrome in a population with central obesity.

  1. Net Community Metabolism and Seawater Carbonate Chemistry Scale Non-intuitively with Coral Cover

    Directory of Open Access Journals (Sweden)

    Heather N. Page

    2017-05-01

    Full Text Available Coral cover and reef health have been declining globally as reefs face local and global stressors including higher temperature and ocean acidification (OA. Ocean warming and acidification will alter rates of benthic reef metabolism (i.e., primary production, respiration, calcification, and CaCO3 dissolution, but our understanding of community and ecosystem level responses is limited in terms of functional, spatial, and temporal scales. Furthermore, dramatic changes in coral cover and benthic metabolism could alter seawater carbonate chemistry on coral reefs, locally alleviating or exacerbating OA. This study examines how benthic metabolic rates scale with changing coral cover (0–100%, and the subsequent influence of these coral communities on seawater carbonate chemistry based on mesocosm experiments in Bermuda and Hawaii. In Bermuda, no significant differences in benthic metabolism or seawater carbonate chemistry were observed for low (40% and high (80% coral cover due to large variability within treatments. In contrast, significant differences were detected between treatments in Hawaii with benthic metabolic rates increasing with increasing coral cover. Observed increases in daily net community calcification and nighttime net respiration scaled proportionally with coral cover. This was not true for daytime net community organic carbon production rates, which increased the most between 0 and 20% coral cover and then less so between 20 and 100%. Consequently, diel variability in seawater carbonate chemistry increased with increasing coral cover, but absolute values of pH, Ωa, and pCO2 were not significantly different during daytime. To place the results of the mesocosm experiments into a broader context, in situ seawater carbon dioxide (CO2 at three reef sites in Bermuda and Hawaii were also evaluated; reefs with higher coral cover experienced a greater range of diel CO2 levels, complementing the mesocosm results. The results from this study

  2. Metabolic Syndrome in a Rural Nigerian Community: Is Central ...

    African Journals Online (AJOL)

    Alasia Datonye

    ABSTRACT. Background. Metabolic syndrome (MS) is primarily the consequence of excess central adiposity but can also result from low grade systemic inflammation inducing insulin resistance. There is a global increase in the prevalence of MS; it is on this background that evaluation of the prevalence of MS in a poor rural ...

  3. Engineering microorganisms to increase ethanol production by metabolic redirection

    Science.gov (United States)

    Deng, Yu; Olson, Daniel G.; van Dijken, Johannes Pieter; Shaw, IV, Arthur J.; Argyros, Aaron; Barrett, Trisha; Caiazza, Nicky; Herring, Christopher D.; Rogers, Stephen R.; Agbogbo, Frank

    2017-10-31

    The present invention provides for the manipulation of carbon flux in a recombinant host cell to increase the formation of desirable products. The invention relates to cellulose-digesting organisms that have been genetically modified to allow the production of ethanol at a high yield by redirecting carbon flux at key steps of central metabolism.

  4. Biosynthesis and metabolic fate of phenylalanine in conifers

    Directory of Open Access Journals (Sweden)

    María Belén Pascual

    2016-07-01

    Full Text Available The amino acid phenylalanine (Phe is a critical metabolic node that plays an essential role in the interconnection between primary and secondary metabolism in plants. Phe is used as a protein building block but it is also as a precursor for numerous plant compounds that are crucial for plant reproduction, growth, development and defense against different types of stresses. The metabolism of Phe plays a central role in the channeling of carbon from photosynthesis to the biosynthesis of phenylpropanoids. The study of this metabolic pathway is particularly relevant in trees, which divert large amounts of carbon into the biosynthesis of Phe-derived compounds, particularly lignin, an important constituent of wood. The trunks of trees are metabolic sinks that consume a considerable percentage of carbon and energy from photosynthesis, and carbon is finally immobilized in wood. This paper reviews recent advances in the biosynthesis and metabolic utilization of Phe in conifer trees. Two alternative routes have been identified: the ancient phenylpyruvate pathway that is present in microorganisms, and the arogenate pathway that possibly evolved later during plant evolution. Additionally, an efficient nitrogen recycling mechanism is required to maintain sustained growth during xylem formation. The relevance of phenylalanine metabolic pathways in wood formation, the biotic interactions and ultraviolet protection is discussed. The genetic manipulation and transcriptional regulation of the pathways are also outlined.

  5. Biosynthesis and Metabolic Fate of Phenylalanine in Conifers.

    Science.gov (United States)

    Pascual, María B; El-Azaz, Jorge; de la Torre, Fernando N; Cañas, Rafael A; Avila, Concepción; Cánovas, Francisco M

    2016-01-01

    The amino acid phenylalanine (Phe) is a critical metabolic node that plays an essential role in the interconnection between primary and secondary metabolism in plants. Phe is used as a protein building block but it is also as a precursor for numerous plant compounds that are crucial for plant reproduction, growth, development, and defense against different types of stresses. The metabolism of Phe plays a central role in the channeling of carbon from photosynthesis to the biosynthesis of phenylpropanoids. The study of this metabolic pathway is particularly relevant in trees, which divert large amounts of carbon into the biosynthesis of Phe-derived compounds, particularly lignin, an important constituent of wood. The trunks of trees are metabolic sinks that consume a considerable percentage of carbon and energy from photosynthesis, and carbon is finally immobilized in wood. This paper reviews recent advances in the biosynthesis and metabolic utilization of Phe in conifer trees. Two alternative routes have been identified: the ancient phenylpyruvate pathway that is present in microorganisms, and the arogenate pathway that possibly evolved later during plant evolution. Additionally, an efficient nitrogen recycling mechanism is required to maintain sustained growth during xylem formation. The relevance of phenylalanine metabolic pathways in wood formation, the biotic interactions, and ultraviolet protection is discussed. The genetic manipulation and transcriptional regulation of the pathways are also outlined.

  6. Chemical Constraints Governing the Origin of Metabolism: The Thermodynamic Landscape of Carbon Group Transformations

    Science.gov (United States)

    Weber, Arthur L.; Fonda, Mark (Technical Monitor)

    2001-01-01

    The thermodynamics of organic chemistry under mild aqueous conditions was examined in order to begin to understand its influence on the structure and operation of metabolism and its antecedents. Free energies were estimated for four types reactions of biochemical importance carbon-carbon bond cleavage and synthesis, hydrogen transfer between carbon groups, dehydration of alcohol groups, and aldo-keto isomerization. The energies were calculated for mainly aliphatic groups composed of carbon, hydrogen, and oxygen. The energy values showed that (1) when carbon-carbon bond cleavage involves two different types of functional groups, transfer of the shared electron-pair to the more reduced carbon group is energetically favored over transfer to the more oxidized carbon group, and (2) the energy of carbon-carbon bond transformation is strongly dependent on the type of functional group that donates the shared electron-pair during cleavage, and the group that accepts the shared electron-pair during synthesis, and (3) the energetics of C-C bond transformation is determined primarily by the half-reaction energies of the couples: carbonyl/carboxylic acid, carboxylic acid/carbon dioxide, alcohol/carbonyl, and hydrocarbon/alcohol. The energy of hydrogen-transfer between carbon groups was found to depend on the functional group class of both the hydrogen-donor and hydrogen-acceptor. From these and other observations we concluded that the chemistry of the origin of metabolism (and to a lesser degree modem metabolism) is strongly constrained by the (1) limited disproportionation energy of organic substrates that can be dissipated in a few irreversible reactions, (2) the energy-dominance of few half-reaction couples in carbon-carbon bond transformation that establishes whether a chemical reaction is energetically irreversible, reversible or unfeasible, and (3) the dependence of the transformation-energy on the oxidation state of carbon groups (functional group type) which is

  7. Biosynthesis and Metabolic Fate of Phenylalanine in Conifers

    OpenAIRE

    Pascual, María B.; El-Azaz, Jorge; de la Torre, Fernando N.; Cañas, Rafael A.; Avila, Concepción; Cánovas, Francisco M.

    2016-01-01

    The amino acid phenylalanine (Phe) is a critical metabolic node that plays an essential role in the interconnection between primary and secondary metabolism in plants. Phe is used as a protein building block but it is also as a precursor for numerous plant compounds that are crucial for plant reproduction, growth, development, and defense against different types of stresses. The metabolism of Phe plays a central role in the channeling of carbon from photosynthesis to the biosynthesis of pheny...

  8. Nitrogen, carbon, and sulfur metabolism in natural Thioploca samples

    DEFF Research Database (Denmark)

    Otte, S.; Kuenen, JG; Nielsen, LP

    1999-01-01

    Filamentous sulfur bacteria of the genus Thioploca occur as dense mats on the continental shelf off the coast of Chile and Peru. Since little is known about their nitrogen, sulfur, and carbon metabolism, this study was undertaken to investigate their (eco)physiology. Thioploca is able to store...

  9. Hydrogen production and metabolic flux analysis of metabolically engineered Escherichia coli strains

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Seohyoung; Seol, Eunhee; Park, Sunghoon [Department of Chemical and Biochemical Engineering, Pusan National University, Busan 609-735 (Korea); Oh, You-Kwan [Bioenergy Research Center, Korea Institute of Energy Research, Daejeon 305-543 (Korea); Wang, G.Y. [Department of Oceanography, University of Hawaii at Manoa Honolulu, HI 96822 (United States)

    2009-09-15

    Escherichia coli can produce H{sub 2} from glucose via formate hydrogen lyase (FHL). In order to improve the H{sub 2} production rate and yield, metabolically engineered E. coli strains, which included pathway alterations in their H{sub 2} production and central carbon metabolism, were developed and characterized by batch experiments and metabolic flux analysis. Deletion of hycA, a negative regulator for FHL, resulted in twofold increase of FHL activity. Deletion of two uptake hydrogenases (1 (hya) and hydrogenase 2 (hyb)) increased H{sub 2} production yield from 1.20 mol/mol glucose to 1.48 mol/mol glucose. Deletion of lactate dehydrogenase (ldhA) and fumarate reductase (frdAB) further improved the H{sub 2} yield; 1.80 mol/mol glucose under high H{sub 2} pressure or 2.11 mol/mol glucose under reduced H{sub 2} pressure. Several batch experiments at varying concentrations of glucose (2.5-10 g/L) and yeast extract (0.3 or 3.0 g/L) were conducted for the strain containing all these genetic alternations, and their carbon and energy balances were analyzed. The metabolic flux analysis revealed that deletion of ldhA and frdAB directed most of the carbons from glucose to the glycolytic pathway leading to H{sub 2} production by FHL, not to the pentose phosphate pathway. (author)

  10. Age, extent and carbon storage of the central Congo Basin peatland complex.

    Science.gov (United States)

    Dargie, Greta C; Lewis, Simon L; Lawson, Ian T; Mitchard, Edward T A; Page, Susan E; Bocko, Yannick E; Ifo, Suspense A

    2017-02-02

    Peatlands are carbon-rich ecosystems that cover just three per cent of Earth's land surface, but store one-third of soil carbon. Peat soils are formed by the build-up of partially decomposed organic matter under waterlogged anoxic conditions. Most peat is found in cool climatic regions where unimpeded decomposition is slower, but deposits are also found under some tropical swamp forests. Here we present field measurements from one of the world's most extensive regions of swamp forest, the Cuvette Centrale depression in the central Congo Basin. We find extensive peat deposits beneath the swamp forest vegetation (peat defined as material with an organic matter content of at least 65 per cent to a depth of at least 0.3 metres). Radiocarbon dates indicate that peat began accumulating from about 10,600 years ago, coincident with the onset of more humid conditions in central Africa at the beginning of the Holocene. The peatlands occupy large interfluvial basins, and seem to be largely rain-fed and ombrotrophic-like (of low nutrient status) systems. Although the peat layer is relatively shallow (with a maximum depth of 5.9 metres and a median depth of 2.0 metres), by combining in situ and remotely sensed data, we estimate the area of peat to be approximately 145,500 square kilometres (95 per cent confidence interval of 131,900-156,400 square kilometres), making the Cuvette Centrale the most extensive peatland complex in the tropics. This area is more than five times the maximum possible area reported for the Congo Basin in a recent synthesis of pantropical peat extent. We estimate that the peatlands store approximately 30.6 petagrams (30.6 × 10 15  grams) of carbon belowground (95 per cent confidence interval of 6.3-46.8 petagrams of carbon)-a quantity that is similar to the above-ground carbon stocks of the tropical forests of the entire Congo Basin. Our result for the Cuvette Centrale increases the best estimate of global tropical peatland carbon stocks by

  11. A Mathematical Model of Metabolism and Regulation Provides a Systems-Level View of How Escherichia coli Responds to Oxygen

    Directory of Open Access Journals (Sweden)

    Michael eEderer

    2014-03-01

    Full Text Available The efficient redesign of bacteria for biotechnological purposes, such as biofuel production, waste disposal or specific biocatalytic functions, requires a quantitative systems-level understanding of energy supply, carbon and redox metabolism. The measurement of transcript levels, metabolite concentrations and metabolic fluxes per se gives an incomplete picture. An appreciation of the interdependencies between the different measurement values is essential for systems-level understanding. Mathematical modeling has the potential to provide a coherent and quantitative description of the interplay between gene expression, metabolite concentrations and metabolic fluxes. Escherichia coli undergoes major adaptations in central metabolism when the availability of oxygen changes. Thus, an integrated description of the oxygen response provides a benchmark of our understanding of carbon, energy and redox metabolism. We present the first comprehensive model of the central metabolism of E. coli that describes steady-state metabolism at different levels of oxygen availability. Variables of the model are metabolite concentrations, gene expression levels, transcription factor activities, metabolic fluxes and biomass concentration. We analyze the model with respect to the production capabilities of central metabolism of E. coli. In particular, we predict how precursor and biomass concentration are affected by product formation.

  12. A Kinetic Modelling of Enzyme Inhibitions in the Central Metabolism of Yeast Cells

    Science.gov (United States)

    Kasbawati; Kalondeng, A.; Aris, N.; Erawaty, N.; Azis, M. I.

    2018-03-01

    Metabolic regulation plays an important role in the metabolic engineering of a cellular process. It is conducted to improve the productivity of a microbial process by identifying the important regulatory nodes of a metabolic pathway such as fermentation pathway. Regulation of enzymes involved in a particular pathway can be held to improve the productivity of the system. In the central metabolism of yeast cell, some enzymes are known as regulating enzymes that can be inhibited to increase the production of ethanol. In this research we study the kinetic modelling of the enzymes in the central pathway of yeast metabolism by taking into consideration the enzyme inhibition effects to the ethanol production. The existence of positive steady state solution and the stability of the system are also analysed to study the property and dynamical behaviour of the system. One stable steady state of the system is produced if some conditions are fulfilled. The conditions concern to the restriction of the maximum reactions of the enzymes in the pyruvate and acetaldehyde branch points. There exists a certain time of fermentation reaction at which a maximum and a minimum ethanol productions are attained after regulating the system. Optimal ethanol concentration is also produced for a certain initial concentration of inhibitor.

  13. One-carbon metabolism in acetogenic and sulfate-reducing bacteria

    NARCIS (Netherlands)

    Visser, M.

    2015-01-01

    ABSTRACT

    One-carbon metabolism in acetogenic and sulfate-reducing bacteria

    Life on earth is sustained by the constant cycling of six essential elements: oxygen, hydrogen, nitrogen,

  14. 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.

  15. Investigating the effect of carbon source on rabies virus glycoprotein production in Pichia pastoris by a transcriptomic approach.

    Science.gov (United States)

    Ben Azoun, Safa; Kallel, Héla

    2017-08-01

    Several factors affect protein expression in Pichia pastoris, one among them is the carbon source. In this work, we studied the effect of this factor on the expression level of rabies virus glycoprotein (RABV-G) in two recombinant clones harboring seven copies of the gene of interest. The expression was driven either by the constitutive glyceraldehyde-3-phosphate dehydrogenase (GAP) promoter or the inducible alcohol oxidase1 (AOX1) promoter. Clones were compared in terms of cell physiology and carbon source metabolism. The transcription levels of 16 key genes involved in the central metabolic pathway, the methanol catabolism, and the oxidative stress were investigated in both clones. Cell size, as a parameter reflecting cell physiological changes, was also monitored. Our results showed that when glucose was used as the sole carbon source, large cells were obtained. Transcript levels of the genes of the central metabolic pathway were also upregulated, whereas antioxidative gene transcript levels were low. By contrast, the use of methanol as a carbon source generated small cells and a shift in carbon metabolism toward the dissimilatory pathway by the upregulation of formaldehyde dehydrogenase gene and the downregulation of those of the central metabolic. These observations are in favor of the use of glucose to enhance the expression of RABV-G in P. pastoris. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  16. Carbon conversion and metabolic rate in two marine sponges

    NARCIS (Netherlands)

    Koopmans, M.; Van Rijswijk, P.; Martens, D.; Egorova-Zachernyuk, T.A.; Middelburg, J.J.; Wijffels, R.H.

    2011-01-01

    The carbon metabolism of two marine sponges, Haliclona oculata and Dysidea avara, has been studied using a 13C isotope pulse-chase approach. The sponges were fed 13C-labeled diatoms (Skeletonema costatum) for 8 h and they took up between 75 and 85%. At different times, sponges were sampled for total

  17. Double silencing of relevant genes suggests the existence of the direct link between DNA replication/repair and central carbon metabolism in human fibroblasts.

    Science.gov (United States)

    Wieczorek, Aneta; Fornalewicz, Karolina; Mocarski, Łukasz; Łyżeń, Robert; Węgrzyn, Grzegorz

    2018-04-15

    Genetic evidence for a link between DNA replication and glycolysis has been demonstrated a decade ago in Bacillus subtilis, where temperature-sensitive mutations in genes coding for replication proteins could be suppressed by mutations in genes of glycolytic enzymes. Then, a strong influence of dysfunctions of particular enzymes from the central carbon metabolism (CCM) on DNA replication and repair in Escherichia coli was reported. Therefore, we asked if such a link occurs only in bacteria or it is a more general phenomenon. Here, we demonstrate that effects of silencing (provoked by siRNA) of expression of genes coding for proteins involved in DNA replication and repair (primase, DNA polymerase ι, ligase IV, and topoisomerase IIIβ) on these processes (less efficient entry into the S phase of the cell cycle and decreased level of DNA synthesis) could be suppressed by silencing of specific genes of enzymes from CMM. Silencing of other pairs of replication/repair and CMM genes resulted in enhancement of the negative effects of lower expression levels of replication/repair genes. We suggest that these results may be proposed as a genetic evidence for the link between DNA replication/repair and CMM in human cells, indicating that it is a common biological phenomenon, occurring from bacteria to humans. Copyright © 2018 Elsevier B.V. All rights reserved.

  18. The metabolic response of Candida albicans to farnesol under hyphae-inducing conditions.

    Science.gov (United States)

    Han, Ting-Li; Cannon, Richard D; Villas-Bôas, Silas G

    2012-12-01

    Farnesol is a quorum-sensing molecule (QSM) produced, and sensed, by the polymorphic fungus, Candida albicans. This cell-to-cell communication molecule is known to suppress the hyphal formation of C. albicans at high cell density. Despite many studies investigating the signalling mechanisms by which QSMs influence the morphogenesis of C. albicans, the downstream metabolic effect of these signalling pathways in response to farnesol-mediated morphogenesis remains obscure. Here, we have used metabolomics to investigate the metabolic response of C. albicans upon exposure to farnesol under hyphae-inducing conditions. We have found a general up-regulation of central carbon metabolic pathways when hyphal formation was suppressed by farnesol evidenced by a considerably larger number of central carbon metabolic intermediates detected under this condition at an overall lower intracellular level. By combining the metabolic profiles from farnesol-exposed cells with previous metabolomics data for C. albicans undergoing morphogenesis, we have identified several metabolic pathways that are likely to be associated with the morphogenetic process of C. albicans, as well as metabolic pathways such as those involved in lipid metabolism that appeared to be specifically affected by farnesol. Therefore, our results provide important new insights into the metabolic role of farnesol in C. albicans metabolism. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

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

    Science.gov (United States)

    de Lorenzo, Víctor

    2014-03-01

    The standard representation of the Central Dogma (CD) of Molecular Biology conspicuously ignores metabolism. However, both the metabolites and the biochemical fluxes behind any biological phenomenon are encrypted in the DNA sequence. Metabolism constrains and even changes the information flow when the DNA-encoded instructions conflict with the homeostasis of the biochemical network. Inspection of adaptive virulence programs and emergence of xenobiotic-biodegradation pathways in environmental bacteria suggest that their main evolutionary drive is the expansion of their metabolic networks towards new chemical landscapes rather than perpetuation and spreading of their DNA sequences. Faulty enzymatic reactions on suboptimal substrates often produce reactive oxygen species (ROS), a process that fosters DNA diversification and ultimately couples catabolism of the new chemicals to growth. All this calls for a revision of the CD in which metabolism (rather than DNA) has the leading role. © 2014 WILEY Periodicals, Inc.

  20. Central Retinal Artery Occlusion in a Patient with Metabolic Syndrome X

    Directory of Open Access Journals (Sweden)

    Sonja Predrag Cekić

    2010-01-01

    Full Text Available Purpose: To report a case of central retinal artery occlusion (CRAO in a patient with metabolic syndrome X. Case Report: A 64 year-old-man presented with abrupt, painless, and severe loss of vision in his left eye. Indirect ophthalmoscopy disclosed signs compatible with CRAO and laboratory investigations revealed erythrocyte sedimentation rate of 74 mm/h, C-reactive protein (CRP level of 21 mg/l, hyperglycemia, hyperuricemia, hypertriglyceridemia and hypercholesterolemia. Fluorescein angiography and immunological studies excluded other systemic disorders. The patient met the full criteria of the National Cholesterol Education Program for metabolic syndrome X. Conclusion: In addition to different vascular complications such as stroke, and cardiovascular disease, metabolic syndrome X may be associated with retinal vascular occlusions.

  1. SNS Central Helium Liquefier spare Carbon Bed installation and commissioning

    Energy Technology Data Exchange (ETDEWEB)

    Degraff, Brian D. [ORNL; Howell, Matthew P. [ORNL; Kim, Sang-Ho [ORNL; Neustadt, Thomas S. [ORNL

    2017-07-01

    The Spallation Neutron Source (SNS) Central Helium Liquefier (CHL) at Oak Ridge National Laboratory (ORNL) has been without major operations downtime since operations were started back in 2006. This system utilizes a vessel filled with activated carbon as the final major component to remove oil vapor from the compressed helium circuit prior to insertion into the system's cryogenic cold box. The need for a spare carbon bed at SNS due to the variability of carbon media lifetime calculation to adsorption efficiency will be discussed. The fabrication, installation and commissioning of this spare carbon vessel will be presented. The novel plan for connecting the spare carbon vessel piping to the existing infrastructure will be presented.

  2. Sugar-starvation-induced changes of carbon metabolism in excised maize root tips

    International Nuclear Information System (INIS)

    Dieuaide-Noubhani, M.; Canioni, P.; Raymond, P.

    1997-01-01

    Excised maize (Zea mays L.) root tips were used to study the early metabolic effects of glucose (Glc) starvation. Root tips were prelabeled with [1-13C]Glc so that carbohydrates and metabolic intermediates were close to steady-state labeling, but lipids and proteins were scarcely labeled. They were then incubated in a sugar-deprived medium for carbon starvation. Changes in the level of soluble sugars, the respiratory quotient, and the 13C enrichment of intermediates, as measured by 13C and 1H nuclear magnetic resonance, were studied to detect changes in carbon fluxes through glycolysis and the tricarboxylic acid cycle. Labeling of glutamate carbons revealed two major changes in carbon input into the tricarboxylic acid cycle: (a) the phosphoenolpyruvate carboxylase flux stopped early after the start of Glc starvation, and (b) the contribution of glycolysis as the source of acetyl-coenzyme A for respiration decreased progressively, indicating an increasing contribution of the catabolism of protein amino acids, fatty acids, or both. The enrichment of glutamate carbons gave no evidence for proteolysis in the early steps of starvation, indicating that the catabolism of proteins was delayed compared with that of fatty acids. Labeling of carbohydrates showed that sucrose turnover continues during sugar starvation, but gave no indication for any significant flux through gluconeogenesis

  3. Genetic signatures in choline and 1-carbon metabolism are associated with the severity of hepatic steatosis

    Science.gov (United States)

    Corbin, Karen D.; Abdelmalek, Manal F.; Spencer, Melanie D.; da Costa, Kerry-Ann; Galanko, Joseph A.; Sha, Wei; Suzuki, Ayako; Guy, Cynthia D.; Cardona, Diana M.; Torquati, Alfonso; Diehl, Anna Mae; Zeisel, Steven H.

    2013-01-01

    Choline metabolism is important for very low-density lipoprotein secretion, making this nutritional pathway an important contributor to hepatic lipid balance. The purpose of this study was to assess whether the cumulative effects of multiple single nucleotide polymorphisms (SNPs) across genes of choline/1-carbon metabolism and functionally related pathways increase susceptibility to developing hepatic steatosis. In biopsy-characterized cases of nonalcoholic fatty liver disease and controls, we assessed 260 SNPs across 21 genes in choline/1-carbon metabolism. When SNPs were examined individually, using logistic regression, we only identified a single SNP (PNPLA3 rs738409) that was significantly associated with severity of hepatic steatosis after adjusting for confounders and multiple comparisons (P=0.02). However, when groupings of SNPs in similar metabolic pathways were defined using unsupervised hierarchical clustering, we identified groups of subjects with shared SNP signatures that were significantly correlated with steatosis burden (P=0.0002). The lowest and highest steatosis clusters could also be differentiated by ethnicity. However, unique SNP patterns defined steatosis burden irrespective of ethnicity. Our results suggest that analysis of SNP patterns in genes of choline/1-carbon metabolism may be useful for prediction of severity of steatosis in specific subsets of people, and the metabolic inefficiencies caused by these SNPs should be examined further.—Corbin, K. D., Abdelmalek, M. F., Spencer, M. D., da Costa, K.-A., Galanko, J. A., Sha, W., Suzuki, A., Guy, C. D., Cardona, D. M., Torquati, A., Diehl, A. M., Zeisel, S. H. Genetic signatures in choline and 1-carbon metabolism are associated with the severity of hepatic steatosis. PMID:23292069

  4. Leptin and the central nervous system control of glucose metabolism.

    Science.gov (United States)

    Morton, Gregory J; Schwartz, Michael W

    2011-04-01

    The regulation of body fat stores and blood glucose levels is critical for survival. This review highlights growing evidence that leptin action in the central nervous system plays a key role in both processes. Investigation into underlying mechanisms has begun to clarify the physiological role of leptin in the control of glucose metabolism and raises interesting new possibilities for the treatment of diabetes and related disorders.

  5. Preschool Weight and Body Mass Index in Relation to Central Obesity and Metabolic Syndrome in Adulthood

    DEFF Research Database (Denmark)

    Graversen, Lise; Sørensen, Thorkild I A; Petersen, Liselotte

    2014-01-01

    BACKGROUND: If preschool measures of body size routinely collected at preventive health examinations are associated with adult central obesity and metabolic syndrome, a focused use of these data for the identification of high risk children is possible. The aim of this study was to test the associ......BACKGROUND: If preschool measures of body size routinely collected at preventive health examinations are associated with adult central obesity and metabolic syndrome, a focused use of these data for the identification of high risk children is possible. The aim of this study was to test...... the associations between preschool weight and body mass index (BMI) and adult BMI, central obesity and metabolic alterations. METHODS: The Northern Finland Birth Cohort 1966 (NFBC1966) (N = 4111) is a population-based cohort. Preschool weight (age 5 months and 1 year) and BMI (age 2-5 years) were studied...... in relation to metabolic syndrome as well as BMI, waist circumference, lipoproteins, blood pressure, and fasting glucose at the age of 31 years. Linear regression models and generalized linear regression models with log link were used. RESULTS: Throughout preschool ages, weight and BMI were significantly...

  6. Integration of C1 and C2 Metabolism in Trees

    OpenAIRE

    Jardine, Kolby J.; Fernandes de Souza, Vinicius; Oikawa, Patty; Higuchi, Niro; Bill, Markus; Porras, Rachel; Niinemets, Ülo; Chambers, Jeffrey Q.

    2017-01-01

    C1 metabolism in plants is known to be involved in photorespiration, nitrogen and amino acid metabolism, as well as methylation and biosynthesis of metabolites and biopolymers. Although the flux of carbon through the C1 pathway is thought to be large, its intermediates are difficult to measure and relatively little is known about this potentially ubiquitous pathway. In this study, we evaluated the C1 pathway and its integration with the central metabolism using aqueous solutions of 13C-labele...

  7. Current views on the regulation of autotrophic carbon dioxide fixation via the Calvin cycle in bacteria

    NARCIS (Netherlands)

    Dijkhuizen, L.; Harder, W.

    1984-01-01

    The Calvin cycle of carbon dioxide fixation constitutes a biosynthetic pathway for the generation of (multi-carbon) intermediates of central metabolism from the one-carbon compound carbon dioxide. The product of this cycle can be used as a precursor for the synthesis of all components of cell

  8. Soil microbial community and its interaction with soil carbon and nitrogen dynamics following afforestation in central China.

    Science.gov (United States)

    Deng, Qi; Cheng, Xiaoli; Hui, Dafeng; Zhang, Qian; Li, Ming; Zhang, Quanfa

    2016-01-15

    Afforestation may alter soil microbial community structure and function, and further affect soil carbon (C) and nitrogen (N) dynamics. Here we investigated soil microbial carbon and nitrogen (MBC and MBN) and microbial community [e.g. bacteria (B), fungi (F)] derived from phospholipid fatty acids (PLFAs) analysis in afforested (implementing woodland and shrubland plantations) and adjacent croplands in central China. Relationships of microbial properties with biotic factors [litter, fine root, soil organic carbon (SOC), total nitrogen (TN) and inorganic N], abiotic factors (soil temperature, moisture and pH), and major biological processes [basal microbial respiration, microbial metabolic quotient (qCO2), net N mineralization and nitrification] were developed. Afforested soils had higher mean MBC, MBN and MBN:TN ratios than the croplands due to an increase in litter input, but had lower MBC:SOC ratio resulting from low-quality (higher C:N ratio) litter. Afforested soils also had higher F:B ratio, which was probably attributed to higher C:N ratios in litter and soil, and shifts of soil inorganic N forms, water, pH and disturbance. Alterations in soil microbial biomass and community structure following afforestation were associated with declines in basal microbial respiration, qCO2, net N mineralization and nitrification, which likely maintained higher soil carbon and nitrogen storage and stability. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. The relationship between microbial metabolic activity and biocorrosion of carbon steel.

    Science.gov (United States)

    Dzierzewicz, Z; Cwalina, B; Chodurek, E; Wilczok, T

    1997-12-01

    The effect of metabolic activity (expressed by generation time, rate of H2S production and the activity of hydrogenase and adenosine phosphosulphate (APS)-reductase enzymes) of the 8 wild strains of Desulfovibrio desulfuricans and of their resistance to metal ions (Hg2+, Cu2+, Mn2+, Zn2+, Ni2+, Cr3+) on the rate of corrosion of carbon steel was studied. The medium containing lactate as the carbon source and sulphate as the electron acceptor was used for bacterial metabolic activity examination and in corrosive assays. Bacterial growth inhibition by metal ions was investigated in the sulphate-free medium. The rate of H2S production was approximately directly proportional to the specific activities of the investigated enzymes. These activities were inversely proportional to the generation time. The rate of microbiologically induced corrosion (MIC) of carbon steel was directly proportional to bacterial resistance to metal ions (correlation coefficient r = 0.95). The correlation between the MIC rate and the activity of enzymes tested, although weaker, was also observed (r = 0.41 for APS-reductase; r = 0.69 for hydrogenase; critical value rc = 0.30, p = 0.05, n = 40).

  10. Metabolic cost of incubation in the Laysan albatross and Bonin petrel.

    Science.gov (United States)

    Grant, G S; Whittow, G C

    1983-01-01

    1. Oxygen consumption and carbon dioxide production were measured in resting and incubating Laysan albatrosses and Bonin petrels on Midway Atoll in the north central Pacific Ocean. 2. Incubation metabolism within the thermal neutral zone is less than or equal to resting metabolism in the albatross and petrel. 3. The respiratory quotients (0.64-0.72) during the long fasts indicate fat metabolism. 4. The estimated fractional water content of the albatross and petrel do not change during incubation fasts because water loss is balanced by metabolic water production.

  11. Effect of Carbon Monoxide on Active Oxygen Metabolism of Postharvest Jujube

    OpenAIRE

    Shaoying Zhang; Qin Li; Yulan Mao

    2014-01-01

    To prolong the shelf life postharvest jujube, the effect of carbon monoxide (CO) on senescence of postharvest jujube in relation to active oxygen metabolism was investigated. Jujubes were fumigated with CO gas at 5, 10, 20 or 40μmol/L for 1 h, and then stored for 30 days at room temperature. Changes in membrane permeability, malonaldehyde (MDA), H2O2, O2•− content, and activities of active oxygen metabolism associated enzymes including superoxide dismutase (SOD), catalase (CAT) and peroxidase...

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

    LENUS (Irish Health Repository)

    Healy, L A

    2012-02-01

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

  13. P-Ser-HPr-a link between carbon metabolism and the virulence of some pathogenic bacteria

    DEFF Research Database (Denmark)

    Mijakovic, Ivan

    2005-01-01

    HPr kinase/phosphorylase phosphorylates HPr, a phosphocarrier protein of the phosphoenolpyruvate:carbohydrate phosphotransferase system, at serine-46. P-Ser-HPr is the central regulator of carbon metabolism in Gram-positive bacteria, but also plays a role in virulence development of certain...... pathogens. In Listeria monocytogenes, several virulence genes, which depend on the transcription activator PrfA, are repressed by glucose, fructose, etc., in a catabolite repressor (CcpA)-independent mechanism. However, the catabolite co-repressor P-Ser-HPr was found to inhibit the activity of Prf...... is preceded by an operator site, which serves as target for the CcpA/P-Ser-HPr complex. Numerous Gram-negative pathogens also contain hprK, which is often organised in an operon with transcription regulators necessary for the development of virulence, indicating that in these organisms P-Ser-HPr also plays...

  14. Metformin regulates global DNA methylation via mitochondrial one-carbon metabolism.

    Science.gov (United States)

    Cuyàs, E; Fernández-Arroyo, S; Verdura, S; García, R Á-F; Stursa, J; Werner, L; Blanco-González, E; Montes-Bayón, M; Joven, J; Viollet, B; Neuzil, J; Menendez, J A

    2018-02-15

    The anti-diabetic biguanide metformin may exert health-promoting effects via metabolic regulation of the epigenome. Here we show that metformin promotes global DNA methylation in non-cancerous, cancer-prone and metastatic cancer cells by decreasing S-adenosylhomocysteine (SAH), a strong feedback inhibitor of S-adenosylmethionine (SAM)-dependent DNA methyltransferases, while promoting the accumulation of SAM, the universal methyl donor for cellular methylation. Using metformin and a mitochondria/complex I (mCI)-targeted analog of metformin (norMitoMet) in experimental pairs of wild-type and AMP-activated protein kinase (AMPK)-, serine hydroxymethyltransferase 2 (SHMT2)- and mCI-null cells, we provide evidence that metformin increases the SAM:SAH ratio-related methylation capacity by targeting the coupling between serine mitochondrial one-carbon flux and CI activity. By increasing the contribution of one-carbon units to the SAM from folate stores while decreasing SAH in response to AMPK-sensed energetic crisis, metformin can operate as a metabolo-epigenetic regulator capable of reprogramming one of the key conduits linking cellular metabolism to the DNA methylation machinery.

  15. Quantitative Tools for Dissection of Hydrogen-Producing Metabolic Networks-Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Rabinowitz, Joshua D.; Dismukes, G.Charles.; Rabitz, Herschel A.; Amador-Noguez, Daniel

    2012-10-19

    During this project we have pioneered the development of integrated experimental-computational technologies for the quantitative dissection of metabolism in hydrogen and biofuel producing microorganisms (i.e. C. acetobutylicum and various cyanobacteria species). The application of these new methodologies resulted in many significant advances in the understanding of the metabolic networks and metabolism of these organisms, and has provided new strategies to enhance their hydrogen or biofuel producing capabilities. As an example, using mass spectrometry, isotope tracers, and quantitative flux-modeling we mapped the metabolic network structure in C. acetobutylicum. This resulted in a comprehensive and quantitative understanding of central carbon metabolism that could not have been obtained using genomic data alone. We discovered that biofuel production in this bacterium, which only occurs during stationary phase, requires a global remodeling of central metabolism (involving large changes in metabolite concentrations and fluxes) that has the effect of redirecting resources (carbon and reducing power) from biomass production into solvent production. This new holistic, quantitative understanding of metabolism is now being used as the basis for metabolic engineering strategies to improve solvent production in this bacterium. In another example, making use of newly developed technologies for monitoring hydrogen and NAD(P)H levels in vivo, we dissected the metabolic pathways for photobiological hydrogen production by cyanobacteria Cyanothece sp. This investigation led to the identification of multiple targets for improving hydrogen production. Importantly, the quantitative tools and approaches that we have developed are broadly applicable and we are now using them to investigate other important biofuel producers, such as cellulolytic bacteria.

  16. Evaluating Soil Carbon Sequestration in Central Iowa

    Science.gov (United States)

    Doraiswamy, P. C.; Hunt, E. R.; McCarty, G. W.; Daughtry, C. S.; Izaurralde, C.

    2005-12-01

    The potential for reducing atmospheric carbon dioxide (CO2) concentration through landuse and management of agricultural systems is of great interest worldwide. Agricultural soils can be a source of CO2 when not properly managed but can also be a sink for sequestering CO2 through proper soil and crop management. The EPIC-CENTURY biogeochemical model was used to simulate the baseline level of soil carbon from soil survey data and project changes in soil organic carbon (SOC) under different tillage and crop management practices for corn and soybean crops. The study was conducted in central Iowa (50 km x 100 km) to simulate changes in soil carbon over the next 50 years. The simulations were conducted in two phases; initially a 25-year period (1971-1995) was simulated using conventional tillage practices since there was a transition in new management after 1995. In the second 25-year period (1996-2020), four different modeling scenarios were applied namely; conventional tillage, mulch tillage, no-tillage and no-tillage with a rye cover crop over the winter. The model simulation results showed potential gains in soil carbon in the top layers of the soil for conservation tillage. The simulations were made at a spatial resolution of 1.6 km x 1.6 km and mapped for the study area. There was a mean reduction in soil organic carbon of 0.095 T/ha per year over the 25-year period starting with 1996 for the conventional tillage practice. However, for management practices of mulch tillage, no tillage and no tillage with cover crop there was an increase in soil organic carbon of 0.12, 0.202 and 0.263 T/ha respectively over the same 25-year period. These results are in general similar to studies conducted in this region.

  17. Leishmania carbon metabolism in the macrophage phagolysosome- feast or famine?

    Science.gov (United States)

    McConville, Malcolm J; Saunders, Eleanor C; Kloehn, Joachim; Dagley, Michael J

    2015-01-01

    A number of medically important microbial pathogens target and proliferate within macrophages and other phagocytic cells in their mammalian hosts. While the majority of these pathogens replicate within the host cell cytosol or non-hydrolytic vacuolar compartments, a few, including protists belonging to the genus Leishmania, proliferate long-term within mature lysosome compartments.  How these parasites achieve this feat remains poorly defined. In this review, we highlight recent studies that suggest that Leishmania virulence is intimately linked to programmed changes in the growth rate and carbon metabolism of the obligate intra-macrophage stages. We propose that activation of a slow growth and a stringent metabolic response confers resistance to multiple stresses (oxidative, temperature, pH), as well as both nutrient limitation and nutrient excess within this niche. These studies highlight the importance of metabolic processes as key virulence determinants in Leishmania.

  18. Advances in Metabolic Engineering of Cyanobacteria for Photosynthetic Biochemical Production

    OpenAIRE

    Lai, Martin C.; Lan, Ethan I.

    2015-01-01

    Engineering cyanobacteria into photosynthetic microbial cell factories for the production of biochemicals and biofuels is a promising approach toward sustainability. Cyanobacteria naturally grow on light and carbon dioxide, bypassing the need of fermentable plant biomass and arable land. By tapping into the central metabolism and rerouting carbon flux towards desirable compound production, cyanobacteria are engineered to directly convert CO2 into various chemicals. This review discusses the d...

  19. Biomass carbon accumulation in aging Japanese cedar plantations in Xitou, central Taiwan.

    Science.gov (United States)

    Cheng, Chih-Hsin; Hung, Chih-Yu; Chen, Chiou-Peng; Pei, Chuang-Wun

    2013-12-01

    Japanese cedar (Chrytomeria japonica D. Don) is an important plantation species in Taiwan and represents 10% of total plantation area. It was first introduced in 1910 and widely planted in the northern and central mountainous areas of Taiwan. However, a change in forest management from exotic species to native species in 1980 had resulted in few new Japanese cedar plantations being established. Most Japanese cedar plantations are now between 30 and 50 years old and reaching their rotation period. It is of interest to know whether these plantations could be viable for future carbon sequestration through the accumulations of stand carbon stocks. Twelve even-aged Japanese cedar stands along a stand age gradient from 37 to 93 years were selected in Xitou of central Taiwan. The study aims were to investigate the basic stand characteristics and biomass carbon stock in current Japanese cedar stands, and determine the relationships among stand characteristics, tree biomass carbon, and stand age. Our results indicate that existing Japanese cedar plantations are still developing and their live tree biomass carbon continues to accumulate. At stands with a stand age of 90 years, tree density, canopy height, mean diameter at breast height, basal area, and live tree biomass carbon stocks reach to nearly 430 tree ha -1 , 27 m, 48 cm, 82 m 2 ha -1 and 300 Mg C ha -1 , respectively. Therefore, with no harvesting, current Japanese cedar plantations provide a carbon sink by storing carbon in tree biomass.

  20. 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

  1. One carbon metabolism in anaerobic bacteria: Regulation of carbon and electron flow during organic acid production: Progress report, February 1, 1987-February 1, 1988

    International Nuclear Information System (INIS)

    Zeikus, J.G.; Shen, Gwo-Jenn.

    1988-01-01

    These studies concern the fundamental biochemical mechanisms that control carbon and electron flow in anaerobic bacteria that conserve energy when coupling hydrogen consumption to the production of acetic, propionic, or butyric acids. Two acidogens, Propionispira arboris and Butyribacterium methylotrophicum were chosen as model systems to understand the function of oxidoreductases and electron carriers in the regulation of hydrogen metabolism and single carbon metabolism. In P. arboris, H 2 consumption was linked to the inhibition of CO 2 production and an increase in the propionate/acetate rate; whereas, H 2 consumption was linked to a stimulation of CO 2 consumption and an increase in the butyrate/acetate ratio in B. methylotrophicum. We report studies on the enzymes involved in the regulation of singe carbon metabolism, the enzyme activities and pathways responsible for conversion of multicarbon components to acetate and propionate or butyrate, and how low pH inhibits H 2 and acetic acid production in Sarcina ventriculi as a consequence of hydrogenase regulation. 9 refs

  2. Integration of Carbon, Nitrogen, and Oxygen Metabolism in Escherichia coli

    Science.gov (United States)

    2012-10-22

    optimally, balancing effectively the conversion of carbon into energy versus biomass . To investigate the link between the metabolism of different nutrients...diverse nutrient conditions, E. coli  grows nearly optimally, balancing effectively the  conversion  of carbon  into energy versus  biomass . Here we  show... enzymatic  connections, with kinetic parameters taken from the  literature or computationally  inferred  based on  the data  from Aim 1. As proposed  initially

  3. Framing REDD+ in India: Carbonizing and centralizing Indian forest governance?

    International Nuclear Information System (INIS)

    Vijge, Marjanneke J.; Gupta, Aarti

    2014-01-01

    Highlights: • We analyze whether India's REDD+ strategy induces carbonization and centralization. • REDD+ in India is framed as an opportunity for synergistic, decentralized governance. • Yet national safeguards are not as strong as asserted. • Controversial issues have so far been side-lined in India's REDD+ strategy. • Without investments, synergistic and decentralized REDD+ governance remains unlikely. - Abstract: This article analyzes the interaction of newly articulated climate governance goals with long-standing forest policies and practices in India. We focus on India's REDD+ (reducing emissions from deforestation and forest degradation and related forest activities) strategy, with a particular focus on the Green India Mission (GIM). The GIM calls for a doubling of the area for afforestation and reforestation in India in the next decade as a dominant climate mitigation strategy. We analyze how the GIM policy document frames carbon versus non-carbon benefits to be derived from forest-related activities; and how the GIM envisages division of authority (between national, regional and local levels) in its implementation. We are interested in assessing (a) whether the GIM promotes a “carbonization” of Indian forest governance, i.e. an increased focus on forest carbon at the expense of other ecosystem services; and (b) whether it promotes an increased centralization of forest governance in India through retaining or transferring authority and control over forest resources to national and state-level authorities, at the expense of local communities. We argue that the GIM frames the climate-forest interaction as an opportunity to synergistically enhance both carbon and non-carbon benefits to be derived from forests; while simultaneously promoting further decentralization of Indian forest governance. However, based on past experiences and developments to date, we conclude that without significant investments in community-based carbon and biodiversity

  4. Identification and functional verification of archaeal-type phosphoenolpyruvate carboxylase, a missing link in archaeal central carbohydrate metabolism.

    Science.gov (United States)

    Ettema, Thijs J G; Makarova, Kira S; Jellema, Gera L; Gierman, Hinco J; Koonin, Eugene V; Huynen, Martijn A; de Vos, Willem M; van der Oost, John

    2004-11-01

    Despite the fact that phosphoenolpyruvate carboxylase (PEPC) activity has been measured and in some cases even purified from some Archaea, the gene responsible for this activity has not been elucidated. Using sensitive sequence comparison methods, we detected a highly conserved, uncharacterized archaeal gene family that is distantly related to the catalytic core of the canonical PEPC. To verify the predicted function of this archaeal gene family, we cloned a representative from the hyperthermophilic acidophile Sulfolobus solfataricus and functionally produced the corresponding enzyme as a fusion with the Escherichia coli maltose-binding protein. The purified fusion protein indeed displayed highly thermostable PEPC activity. The structural and biochemical properties of the characterized archaeal-type PEPC (atPEPC) from S. solfataricus are in good agreement with previously reported biochemical analyses of other archaeal PEPC enzymes. The newly identified atPEPC, with its distinct properties, constitutes yet another example of the versatility of the enzymes of the central carbon metabolic pathways in the archaeal domain.

  5. Initial water deficit effects on Lupinus albus photosynthetic performance, carbon metabolism, and hormonal balance: metabolic reorganization prior to early stress responses

    Czech Academy of Sciences Publication Activity Database

    Pinheiro, C.; António, C.; Dobrev, Petre; Vaňková, Radomíra; Wilson, J. C.

    2011-01-01

    Roč. 62, č. 14 (2011), s. 4965-4974 ISSN 0022-0957 Institutional research plan: CEZ:AV0Z50380511 Keywords : Carbon metabolism * hormone balance * LC-MS Subject RIV: EF - Botanics Impact factor: 5.364, year: 2011

  6. Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism

    Science.gov (United States)

    Flamholz, Avi; Reznik, Ed; Liebermeister, Wolfram; Milo, Ron

    2014-01-01

    In metabolism research, thermodynamics is usually used to determine the directionality of a reaction or the feasibility of a pathway. However, the relationship between thermodynamic potentials and fluxes is not limited to questions of directionality: thermodynamics also affects the kinetics of reactions through the flux-force relationship, which states that the logarithm of the ratio between the forward and reverse fluxes is directly proportional to the change in Gibbs energy due to a reaction (ΔrG′). Accordingly, if an enzyme catalyzes a reaction with a ΔrG′ of -5.7 kJ/mol then the forward flux will be roughly ten times the reverse flux. As ΔrG′ approaches equilibrium (ΔrG′ = 0 kJ/mol), exponentially more enzyme counterproductively catalyzes the reverse reaction, reducing the net rate at which the reaction proceeds. Thus, the enzyme level required to achieve a given flux increases dramatically near equilibrium. Here, we develop a framework for quantifying the degree to which pathways suffer these thermodynamic limitations on flux. For each pathway, we calculate a single thermodynamically-derived metric (the Max-min Driving Force, MDF), which enables objective ranking of pathways by the degree to which their flux is constrained by low thermodynamic driving force. Our framework accounts for the effect of pH, ionic strength and metabolite concentration ranges and allows us to quantify how alterations to the pathway structure affect the pathway's thermodynamics. Applying this methodology to pathways of central metabolism sheds light on some of their features, including metabolic bypasses (e.g., fermentation pathways bypassing substrate-level phosphorylation), substrate channeling (e.g., of oxaloacetate from malate dehydrogenase to citrate synthase), and use of alternative cofactors (e.g., quinone as an electron acceptor instead of NAD). The methods presented here place another arrow in metabolic engineers' quiver, providing a simple means of evaluating

  7. 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.

  8. One carbon metabolism in SAR11 pelagic marine bacteria.

    Directory of Open Access Journals (Sweden)

    Jing Sun

    Full Text Available The SAR11 Alphaproteobacteria are the most abundant heterotrophs in the oceans and are believed to play a major role in mineralizing marine dissolved organic carbon. Their genomes are among the smallest known for free-living heterotrophic cells, raising questions about how they successfully utilize complex organic matter with a limited metabolic repertoire. Here we show that conserved genes in SAR11 subgroup Ia (Candidatus Pelagibacter ubique genomes encode pathways for the oxidation of a variety of one-carbon compounds and methyl functional groups from methylated compounds. These pathways were predicted to produce energy by tetrahydrofolate (THF-mediated oxidation, but not to support the net assimilation of biomass from C1 compounds. Measurements of cellular ATP content and the oxidation of (14C-labeled compounds to (14CO(2 indicated that methanol, formaldehyde, methylamine, and methyl groups from glycine betaine (GBT, trimethylamine (TMA, trimethylamine N-oxide (TMAO, and dimethylsulfoniopropionate (DMSP were oxidized by axenic cultures of the SAR11 strain Ca. P. ubique HTCC1062. Analyses of metagenomic data showed that genes for C1 metabolism occur at a high frequency in natural SAR11 populations. In short term incubations, natural communities of Sargasso Sea microbial plankton expressed a potential for the oxidation of (14C-labeled formate, formaldehyde, methanol and TMAO that was similar to cultured SAR11 cells and, like cultured SAR11 cells, incorporated a much larger percentage of pyruvate and glucose (27-35% than of C1 compounds (2-6% into biomass. Collectively, these genomic, cellular and environmental data show a surprising capacity for demethylation and C1 oxidation in SAR11 cultures and in natural microbial communities dominated by SAR11, and support the conclusion that C1 oxidation might be a significant conduit by which dissolved organic carbon is recycled to CO(2 in the upper ocean.

  9. Central and storage carbon metabolism of the brown alga Ectocarpus siliculosus: insights into the origin and evolution of storage carbohydrates in Eukaryotes.

    Science.gov (United States)

    Michel, Gurvan; Tonon, Thierry; Scornet, Delphine; Cock, J Mark; Kloareg, Bernard

    2010-10-01

    • Brown algae exhibit a unique carbon (C) storage metabolism. The photoassimilate D-fructose 6-phosphate is not used to produce sucrose but is converted into D-mannitol. These seaweeds also store C as β-1,3-glucan (laminarin), thus markedly departing from most living organisms, which use α-1,4-glucans (glycogen or starch). • Using a combination of bioinformatic and phylogenetic approaches, we identified the candidate genes for the enzymes involved in C storage in the genome of the brown alga Ectocarpus siliculosus and traced their evolutionary origins. • Ectocarpus possesses a complete set of enzymes for synthesis of mannitol, laminarin and trehalose. By contrast, the pathways for sucrose, starch and glycogen are completely absent. • The synthesis of β-1,3-glucans appears to be a very ancient eukaryotic pathway. Brown algae inherited the trehalose pathway from the red algal progenitor of phaeoplasts, while the mannitol pathway was acquired by lateral gene transfer from Actinobacteria. The starch metabolism of the red algal endosymbiont was entirely lost in the ancestor of Stramenopiles. In light of these novel findings we question the validity of the 'Chromalveolate hypothesis'.

  10. Rerouting of carbon flux in a glycogen mutant of cyanobacteria assessed via isotopically non-stationary 13 C 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.

  11. Carbon monoxide is not responsible for the cigarette smokeinduced changes in the pulmonary metabolism of arachidonic acid and prostaglandin E2

    International Nuclear Information System (INIS)

    Maennistoe, J.; Puustinen, T.; Uotila, P.

    1985-01-01

    Cigarette smoke is known to interfere with the pulmonary metabolism of arachidomic acid and prostaglandin E 2 (PGE 2 ). We investigated the possible role of carbon monoxide in these cigarette smoke-infuced alterations. 4 C-Arachidonic acid (50 nmol) was indused into the pulmonary circulation of isolated perfused hamster lungs and the radioactive metabolites in the perfusion effluent, as well as the distribution of incorporated radioactive arachidonic acid within the lung lipids, were analysed. Carbon monoxide, added into the ventilatory air, had no effect on the oxidative metabolism of arachidonic acid or on the distribution of radioactive arachidonic acid within the lung. In addition, carbon monoxide had no effect on the metabolism of PGE 2 following infusion of 100 nmol of 14 C-PGE 2 into the rat pulmonary circulation. The present study suggests that carbon monoxide is not responsible for the cigarette smoke-induced changes in the pulmonary metabolism of arachidonic acid and PGE 2 . (author)

  12. Carbon and nitrogen metabolism in arbuscular mycorrhizal maize plants under low-temperature stress

    DEFF Research Database (Denmark)

    Zhu, Xian-Can; Song, Feng-Bin; Liu, Fulai

    2015-01-01

    Effects of the arbuscular mycorrhizal (AM) fungus Glomus tortuosum on carbon (C) and nitrogen (N) metabolism of Zea mays L. grown under low-temperature stress was investigated. Maize plants inoculated or not inoculated with AM fungus were grown in a growth chamber at 258C for 4 weeks...... temperature regimes. AM symbiosis modulated C metabolic enzymes, thereby inducing an accumulation of soluble sugars, which may have contributed to an increased tolerance to low temperature, and therefore higher Pn in maize plants....

  13. Direct monitoring by carbon-13 nuclear magnetic resonance spectroscopy of the metabolism and metabolic rate of 13C-labeled compounds in vivo.

    Science.gov (United States)

    Iida, K; Hidoh, O; Fukami, J; Kajiwara, M

    1991-01-01

    Carbon-13 nuclear magnetic resonance spectroscopy has been used to observe the transformations of [1-13C]-D-glucose to [1,1'-13C2]-D-trehalose, and [3-13C]-L-alanine to [2-13C]-L-glutamic acid in the living body of Gryllodes sigillatus. [3-13C]-D-Alanine was not metabolized. The metabolic rate of [1-13C]-D-glucose was found to be altered by prior injection of boric acid.

  14. Partitioning of Intermediary Carbon Metabolism in Vesicular-Arbuscular Mycorrhizal Leek.

    Science.gov (United States)

    Shachar-Hill, Y.; Pfeffer, P. E.; Douds, D.; Osman, S. F.; Doner, L. W.; Ratcliffe, R. G.

    1995-05-01

    Vesicular-arbuscular mycorrhizal fungi are symbionts for a large variety of crop plants; however, the form in which they take up carbon from the host is not established. To trace the course of carbon metabolism, we have used nuclear magnetic resonance spectroscopy with [13C]glucose labeling in vivo and in extracts to examine leek (Allium porrum) roots colonized by Glomus etunicatum (and uncolonized controls) as well as germinating spores. These studies implicate glucose as a likely substrate for vesicular-arbuscular mycorrhizal fungi in the symbiotic state. Root feeding of 0.6 mM 1-[13C]glucose labeled only the fungal metabolites trehalose and glycogen. The time course of this labeling was dependent on the status of the host. Incubation with 50 mM 1-[13C]glucose caused labeling of sucrose (in addition to fungal metabolites) with twice as much labeling in uncolonized plants. There was no detectable scrambling of the label from C1 glucose to the C6 position of glucose moieties in trehalose or glycogen. Labeling of mannitol C1,6 in the colonized root tissue was much less than in axenically germinating spores. Thus, carbohydrate metabolism of host and fungus are significantly altered in the symbiotic state.

  15. The metabolism and dosimetry of carbon-14 labelled diethylenetriaminepentaacetic acid (DTPA)

    International Nuclear Information System (INIS)

    Crawley, F.E.H.; Haines, J.W.

    1978-01-01

    Male rats were given carbon-14 labelled Ca-DTPA either by intravenous injection or by pulmonary intubation. The elimination of the carbon-14 by excretion in urine, faeces and breath was followed, Chromatographic examination of the urine showed that no metabolic degradation of the 14 C-DTPA had occurred. The distribution of activity between lung, kidneys, bone, muscle and GI tract was also followed. The data obtained have been used to assess the radiation dose to man from an intake of 14 C-DTPA on the assumption that the behaviour of 14 C-DTPA in man is the same as in the rat. The results are discussed. (U K.)

  16. Chemical constraints governing the origin of metabolism: the thermodynamic landscape of carbon group transformations under mild aqueous conditions

    Science.gov (United States)

    Weber, Arthur L.

    2002-01-01

    The thermodynamics of organic chemistry under mild aqueous conditions was examined in order to begin to understand its influence on the structure and operation of metabolism and its antecedents. Free energies (deltaG) were estimated for four types of reactions of biochemical importance carbon-carbon bond cleavage and synthesis, hydrogen transfer between carbon groups, dehydration of alcohol groups, and aldo-keto isomerization. The energies were calculated for mainly aliphatic groups composed of carbon, hydrogen, and oxygen. The energy values showed (1) that generally when carbon-carbon bond cleavage involves groups from different functional group classes (i.e., carboxylic acids, carbonyl groups, alcohols, and hydrocarbons), the transfer of the shared electron-pair to the more reduced carbon group is energetically favored over transfer to the more oxidized carbon group, and (2) that the energy of carbon-carbon bond transformation is primarily determined by the functional group class of the group that changes oxidation state in the reaction (i.e., the functional group class of the group that donates the shared electron-pair during cleavage, or that accepts the incipient shared electron-pair during synthesis). In contrast, the energy of hydrogen transfer between carbon groups is determined by the functional group class of both the hydrogen-donor group and the hydrogen-acceptor group. From these and other observations we concluded that the chemistry involved in the origin of metabolism (and to a lesser degree modern metabolism) was strongly constrained by (1) the limited redox-based transformation energy of organic substrates that is readily dissipated in a few energetically favorable irreversible reactions; (2) the energy dominance of a few transformation half-reactions that determines whether carbon-carbon bond transformation (cleavage or synthesis) is energetically favorable (deltaG +3.5 kcal/mol); and (3) the dependence of carbon group transformation energy on the

  17. Natural selection drove metabolic specialization of the chromatophore in Paulinella chromatophora.

    Science.gov (United States)

    Valadez-Cano, Cecilio; Olivares-Hernández, Roberto; Resendis-Antonio, Osbaldo; DeLuna, Alexander; Delaye, Luis

    2017-04-14

    Genome degradation of host-restricted mutualistic endosymbionts has been attributed to inactivating mutations and genetic drift while genes coding for host-relevant functions are conserved by purifying selection. Unlike their free-living relatives, the metabolism of mutualistic endosymbionts and endosymbiont-originated organelles is specialized in the production of metabolites which are released to the host. This specialization suggests that natural selection crafted these metabolic adaptations. In this work, we analyzed the evolution of the metabolism of the chromatophore of Paulinella chromatophora by in silico modeling. We asked whether genome reduction is driven by metabolic engineering strategies resulted from the interaction with the host. As its widely known, the loss of enzyme coding genes leads to metabolic network restructuring sometimes improving the production rates. In this case, the production rate of reduced-carbon in the metabolism of the chromatophore. We reconstructed the metabolic networks of the chromatophore of P. chromatophora CCAC 0185 and a close free-living relative, the cyanobacterium Synechococcus sp. WH 5701. We found that the evolution of free-living to host-restricted lifestyle rendered a fragile metabolic network where >80% of genes in the chromatophore are essential for metabolic functionality. Despite the lack of experimental information, the metabolic reconstruction of the chromatophore suggests that the host provides several metabolites to the endosymbiont. By using these metabolites as intracellular conditions, in silico simulations of genome evolution by gene lose recover with 77% accuracy the actual metabolic gene content of the chromatophore. Also, the metabolic model of the chromatophore allowed us to predict by flux balance analysis a maximum rate of reduced-carbon released by the endosymbiont to the host. By inspecting the central metabolism of the chromatophore and the free-living cyanobacteria we found that by

  18. Ecosystem carbon stocks of mangroves across broad environmental gradients in West-Central Africa: Global and regional comparisons.

    Directory of Open Access Journals (Sweden)

    J Boone Kauffman

    Full Text Available Globally, it is recognized that blue carbon ecosystems, especially mangroves, often sequester large quantities of carbon and are of interest for inclusion in climate change mitigation strategies. While 19% of the world's mangroves are in Africa, they are among the least investigated of all blue carbon ecosystems. We quantified total ecosystem carbon stocks in 33 different mangrove stands along the Atlantic coast of West-Central Africa from Senegal to Southern Gabon spanning large gradients of latitude, soil properties, porewater salinity, and precipitation. Mangrove structure ranged from low and dense stands that were 35,000 trees ha-1 to tall and open stands >40m in height and 1,000 Mg C ha-1. The lowest carbon stocks were found in the low mangroves of the semiarid region of Senegal (463 Mg C ha-1 and in mangroves on coarse-textured soils in Gabon South (541 Mg C ha-1. At the scale of the entirety of West-Central Africa, total ecosystem carbon stocks were poorly correlated to aboveground ecosystem carbon pools, precipitation, latitude and soil salinity (r2 = ≤0.07 for all parameters. Based upon a sample of 158 sites from Africa, Asia and Latin America that were sampled in a similar manner to this study, the global mean of carbon stocks for mangroves is 885 Mg C ha-1. The ecosystem carbon stocks of mangroves for West-Central Africa are slightly lower than those of Latin America (940 Mg C ha-1 and Asia (1049 Mg C ha-1 but substantially higher than the default Intergovernmental Panel on Climate Change (IPCC values for mangroves (511 Mg C ha-1. This study provides an improved estimation of default estimates (Tier 1 values of mangroves for Asia, Latin America, and West Central Africa.

  19. Abscisic acid as a factor in regulation of photosynthetic carbon metabolism of pea seedlings

    Directory of Open Access Journals (Sweden)

    Maria Faltynowicz

    2014-01-01

    Full Text Available The influence of abscisic acid (ABA on carbon metabolism and the activity of ribulosebisphosphate (RuBP and phosphoenolpyruvate (PEP carboxylases in 8-day-old pea seedlings was investigated. It was endeavoured to correlate the changes observed in metabolic processes with the endogenous ABA level. In plants treated with ABA incorporation of labeled carbon into sucrose, glucose, fructose and sugar phosphates was depressed, while 14C incorporation into starch, ribulose and malic acid was enhanced. The activity of RuBP carboxylase was considerably lowered, whereas that of PEP carboxylase was slightly increased. It is considered that inhibition of photosynthesis due to the action of ABA is caused to a great extent by the obstruction of the C-3 pathway and reduced activity of RuBP carboxylase, whereas (β-carboxylation was not blocked.

  20. Partitioning of One-Carbon Units in Folate and Methionine Metabolism Is Essential for Neural Tube Closure

    Directory of Open Access Journals (Sweden)

    Kit-Yi Leung

    2017-11-01

    Full Text Available Summary: Abnormal folate one-carbon metabolism (FOCM is implicated in neural tube defects (NTDs, severe malformations of the nervous system. MTHFR mediates unidirectional transfer of methyl groups from the folate cycle to the methionine cycle and, therefore, represents a key nexus in partitioning one-carbon units between FOCM functional outputs. Methionine cycle inhibitors prevent neural tube closure in mouse embryos. Similarly, the inability to use glycine as a one-carbon donor to the folate cycle causes NTDs in glycine decarboxylase (Gldc-deficient embryos. However, analysis of Mthfr-null mouse embryos shows that neither S-adenosylmethionine abundance nor neural tube closure depend on one-carbon units derived from embryonic or maternal folate cycles. Mthfr deletion or methionine treatment prevents NTDs in Gldc-null embryos by retention of one-carbon units within the folate cycle. Overall, neural tube closure depends on the activity of both the methionine and folate cycles, but transfer of one-carbon units between the cycles is not necessary. : Leung at al. find that embryonic neural tube closure depends both on the supply of one-carbon units to the folate cycle from glycine cleavage and on the methionine cycle. In contrast, transfer of one-carbon units from the folate cycle to the methionine cycle by MTHFR is dispensable. Keywords: one-carbon metabolism, folic acid, neural tube defects, spina bifida, glycine cleavage system, non-ketotic hyperglycinemia, eye, Mthfr, Gldc

  1. High-throughput metabolic state analysis: The missing link in integrated functional genomics of yeasts

    DEFF Research Database (Denmark)

    Villas-Bôas, Silas Granato; Moxley, Joel. F; Åkesson, Mats Fredrik

    2005-01-01

    that achieve comparable throughput, effort and cost compared with DNA arrays. Our sample workup method enables simultaneous metabolite measurements throughout central carbon metabolism and amino acid biosynthesis, using a standard GC-MS platform that was optimized for this Purpose. As an implementation proof......-of-concept, we assayed metabolite levels in two yeast strains and two different environmental conditions in the context of metabolic pathway reconstruction. We demonstrate that these differential metabolite level data distinguish among sample types, such as typical metabolic fingerprinting or footprinting. More...

  2. Photosynthetic carbon metabolism in the submerged aquatic angiosperm Scirpus subterminalis

    Energy Technology Data Exchange (ETDEWEB)

    Beer, S; Wetzel, R G

    1981-01-01

    Scirpus subterminalis Torr., a submerged angiosperm abundant in many hardwater lakes of the Great Lakes region, was investigated for various photosynthetic carbon fixation properties in relation to available inorganic carbon and levels of carbon fixing enzymes. Photosynthetic experiments were CO/sub 2/ and HCO/sub 3//sup -/ were supplied at various concentrations showed that Scirpus was able to utilize HCO/sub 3//sup -/ at those concentrations close to natural conditions. However, when CO/sub 2/ concentrations were increased above ambient, photosynthetic rates increased markedly. It was concluded that the photosynthetic potential of this plant in many natural situations may be limited by inorganic carbon uptake in the light. Phosphoenolpyruvate carboxylase (PEPcase)/ribulose-1,5-bisphosphate carboxylase (ruBPcase) ratios of the leaves varied between 0.5 and 0.9 depending on substrate concentration during assay. The significance of PEP-mediated carbon fixation of Scirpus (basically a C/sub 3/ plant) in the dark was investigated. Malate accumulated in the leaves during the dark period of a 24-h cycle and malate levels decreased significantly during the following light period. The accumulation was not due to transport of malate from the roots. Carbon uptake rates in the dark by the leaves of Scirpus were lower than malate accumulation rates. Therefore, part of the malate was likely derived from respired CO/sub 2/. Carbon uptake rates in the light were much higher than malate turnover rates. It was estimated that carbon fixation via malate could contribute up to 12% to net photosynthetic rates. The ecological significance of this type of metabolism in submerged aquatics is discussed.

  3. Future forest aboveground carbon dynamics in the central United States: the importance of forest demographic processes

    Science.gov (United States)

    Wenchi Jin; Hong S. He; Frank R. Thompson; Wen J. Wang; Jacob S. Fraser; Stephen R. Shifley; Brice B. Hanberry; William D. Dijak

    2017-01-01

    The Central Hardwood Forest (CHF) in the United States is currently a major carbon sink, there are uncertainties in how long the current carbon sink will persist and if the CHF will eventually become a carbon source. We used a multi-model ensemble to investigate aboveground carbon density of the CHF from 2010 to 2300 under current climate. Simulations were done using...

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

    Directory of Open Access Journals (Sweden)

    Alexandra Stoianov

    2014-12-01

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

  5. Regulation of lipid metabolism by energy availability: a role for the central nervous system.

    Science.gov (United States)

    Nogueiras, R; López, M; Diéguez, C

    2010-03-01

    The central nervous system (CNS) is crucial in the regulation of energy homeostasis. Many neuroanatomical studies have shown that the white adipose tissue (WAT) is innervated by the sympathetic nervous system, which plays a critical role in adipocyte lipid metabolism. Therefore, there are currently numerous reports indicating that signals from the CNS control the amount of fat by modulating the storage or oxidation of fatty acids. Importantly, some CNS pathways regulate adipocyte metabolism independently of food intake, suggesting that some signals possess alternative mechanisms to regulate energy homeostasis. In this review, we mainly focus on how neuronal circuits within the hypothalamus, such as leptin- ghrelin-and resistin-responsive neurons, as well as melanocortins, neuropeptide Y, and the cannabinoid system exert their actions on lipid metabolism in peripheral tissues such as WAT, liver or muscle. Dissecting the complicated interactions between peripheral signals and neuronal circuits regulating lipid metabolism might open new avenues for the development of new therapies preventing and treating obesity and its associated cardiometabolic sequelae.

  6. Determinants of maternal pregnancy one-carbon metabolism and newborn human DNA methylation profiles

    NARCIS (Netherlands)

    N.H. van Mil (Nina); M.I. Bouwl-Both (Marieke I.); L. Stolk (Lisette); M.M.P.J. Verbiest (Michael); A. Hofman (Albert); V.W.V. Jaddoe (Vincent); F.C. Verhulst (Frank); P.H.C. Eilers (Paul); A.G. Uitterlinden (André); E.A.P. Steegers (Eric); H.W. Tiemeier (Henning); R.P.M. Steegers-Theunissen (Régine)

    2014-01-01

    textabstractMaternal one-carbon (1-C) metabolism provides methylgroups for fetal development and programing by DNA methylation as one of the underlying epigenetic mechanisms. We aimed to investigate maternal 1-C biomarkers, folic acid supplement use, and MTHFR C677T genotype as determinants of 1-C

  7. Nutrition, One-Carbon Metabolism and Neural Tube Defects: A Review

    Directory of Open Access Journals (Sweden)

    Kelei Li

    2016-11-01

    Full Text Available Neural tube defects (NTDs are a group of severe congenital malformations, induced by the combined effects of genes and the environment. The most valuable finding so far has been the protective effect of folic acid supplementation against NTDs. However, many women do not take folic acid supplements until they are pregnant, which is too late to prevent NTDs effectively. Long-term intake of folic acid–fortified food is a good choice to solve this problem, and mandatory folic acid fortification should be further promoted, especially in Europe, Asia and Africa. Vitamin B2, vitamin B-6, vitamin B-12, choline, betaine and n-3 polyunsaturated fatty acids (PUFAs can also reduce the NTD risk by interacting with the one-carbon metabolism pathway. This suggest that multivitamin B combined with choline, betaine and n-3 PUFAs supplementation may have a better protective effect against NTDs than folic acid alone. Genetic polymorphisms involved in one-carbon metabolism are associated with NTD risk, and gene screening for women of childbearing age prior to pregnancy may help prevent NTDs induced by the risk allele. In addition, the consumption of alcohol, tea and coffee, and low intakes of fruit and vegetable are also associated with the increased risk of NTDs, and should be avoided by women of childbearing age.

  8. Ecological network analysis for carbon metabolism of eco-industrial parks: a case study of a typical eco-industrial park in Beijing.

    Science.gov (United States)

    Lu, Yi; Chen, Bin; Feng, Kuishuang; Hubacek, Klaus

    2015-06-16

    Energy production and industrial processes are crucial economic sectors accounting for about 62% of greenhouse gas (GHG) emissions globally in 2012. Eco-industrial parks are practical attempts to mitigate GHG emissions through cooperation among businesses and the local community in order to reduce waste and pollution, efficiently share resources, and help with the pursuit of sustainable development. This work developed a framework based on ecological network analysis to trace carbon metabolic processes in eco-industrial parks and applied it to a typical eco-industrial park in Beijing. Our findings show that the entire metabolic system is dominated by supply of primary goods from the external environment and final demand. The more carbon flows through a sector, the more influence it would exert upon the whole system. External environment and energy providers are the most active and dominating part of the carbon metabolic system, which should be the first target to mitigate emissions by increasing efficiencies. The carbon metabolism of the eco-industrial park can be seen as an evolutionary system with high levels of efficiency, but this may come at the expense of larger levels of resilience. This work may provide a useful modeling framework for low-carbon design and management of industrial parks.

  9. Carbon dioxide emissions embodied in international trade in Central Europe between 1995 and 2008

    Directory of Open Access Journals (Sweden)

    Vlčková Jana

    2015-12-01

    Full Text Available Climate change and environmental policies are widely discussed, but much less is known about emissions embodied in goods traded internationally, and the distinction between emission producers and consumers. The carbon dioxide emissions embodied in international trade in Central European countries are subject to examination in this paper. As a result of industrial restructuring and environmental legislation, air pollution has improved significantly in Central European countries since the 1989 transition. On the other hand, economic growth has been accompanied by a rise in consumerism. Despite the increasing role of exports, the Visegrad group countries have become net importers of carbon dioxide emissions between 1995 and 2008. This seems to be the ‘standard trajectory’ of a country’s transition toward a more developed and consumption-oriented economy. The global patterns of carbon dioxide emissions embodied in manufacturing exports are also mapped, using network analysis and constructing ‘product space’. The analysis confirms that industrial re-structuring played an important role in lowering the production of carbon dioxide emissions in the Visegrad countries.

  10. The logics of metabolic regulation in bacteria challenges biosensor-based metabolic engineering

    Directory of Open Access Journals (Sweden)

    Matthieu Jules

    2017-12-01

    Full Text Available Synthetic Biology (SB aims at the rational design and engineering of novel biological functions and systems. By facilitating the engineering of living organisms, SB promises to facilitate the development of many new applications for health, biomanufacturing, and the environment. Over the last decade, SB promoted the construction of libraries of components enabling the fine-tuning of genetic circuits expression and the development of novel genome engineering methodologies for many organisms of interest. SB thus opened new perspectives in the field of metabolic engineering, which was until then mainly limited to (overproducing naturally synthesized metabolic compounds. To engineer efficient cell factories, it is key to precisely reroute cellular resources from the central carbon metabolism (CCM to the synthetic circuitry. This task is however difficult as there is still significant lack of knowledge regarding both the function of several metabolic components and the regulation of the CCM fluxes for many industrially important bacteria. Pyruvate is a pivotal metabolite at the heart of the CCM and a key precursor for the synthesis of several commodity compounds and fine chemicals. Numerous bacterial species can also use it as a carbon source when present in the environment but bacterial, pyruvate-specific uptake systems were to be discovered. This is an issue for metabolic engineering as one can imagine to make use of pyruvate transport systems to replenish synthetic metabolic pathways towards the synthesis of chemicals of interest. Here we describe a recent study (MBio 8(5: e00976-17, which identified and characterized a pyruvate transport system in the Gram-positive (G+ve bacterium Bacillus subtilis, a well-established biotechnological workhorse for the production of enzymes, fine chemicals and antibiotics. This study also revealed that the activity of the two-component system (TCS responsible for its induction is retro-inhibited by the level of

  11. Phylogeny, Morphology, and Metabolic and Invasive Capabilities of Epicellular Fish Coccidium Goussia janae

    Czech Academy of Sciences Publication Activity Database

    Dogga, S.K.; Bartošová-Sojková, Pavla; Lukeš, Julius; Soldati-Favre, D.

    2015-01-01

    Roč. 166, č. 6 (2015), s. 659-676 ISSN 1434-4610 R&D Projects: GA ČR GBP505/12/G112 Institutional support: RVO:60077344 Keywords : Apicomplexa * Coccidia * Goussia janae * phylogeny * ultrastructure * invasion * central carbon metabolism. Subject RIV: EG - Zoology Impact factor: 2.898, year: 2015

  12. Dissolved organic carbon in the INDEX area of the Central Indian Basin

    Digital Repository Service at National Institute of Oceanography (India)

    Sardessai, S.; De

    -Sea Research II 48 (2001) 3353–3361 Dissolved organic carbon in the INDEX area of the Central Indian Basin Sugandha Sardessai*, S.N. de Sousa National Institute of Oceanography, Dona-Paula, Goa 403 004, India Abstract Dissolved organic carbon (DOC..., 1996). While there is substantial information available on the DOC content of sea water throughout the Atlantic, Pacific and southern oceans, there are limited reports on contents and distribution of this organic fraction in the Indian Ocean (Menzel...

  13. Differential Metabolism of a Two-Carbon Substrate by Members of the Paracoccidioides Genus

    Directory of Open Access Journals (Sweden)

    Lilian C. Baeza

    2017-11-01

    Full Text Available The genus Paracoccidioides comprises known fungal pathogens of humans and can be isolated from different infection sites. Metabolic peculiarities in different members of the Paracoccidioides led us to perform proteomic studies in the presence of the two-carbon molecule acetate, which predominates in the nutrient-poor environment of the phagosome. To investigate the expression rates of proteins of different members of Paracoccidioides, including one isolate of P. lutzii (Pb01 and three isolates of P. brasiliensis (Pb03, Pb339, and PbEPM83, using sodium acetate as a carbon source, proteins were quantified using label-free and data-independent liquid chromatography-mass spectrometry. Protein profiles of the isolates were statistically analyzed, revealing proteins that were differentially expressed when the fungus was cultivated in a non-preferential carbon source rather than glucose. A total of 1,160, 1,211, 1,280, and 1,462 proteins were reproducibly identified and relatively quantified in P. lutzii and the P. brasiliensis isolates Pb03, Pb339, and PbEPM83, respectively. Notably, 526, 435, 744, and 747 proteins were differentially expressed among P. lutzii and the P. brasiliensis isolates Pb03, Pb339, and PbEPM83, respectively, with a fold-change equal to or higher than 1.5. This analysis revealed that reorganization of metabolism occurred through the induction of proteins related to gluconeogenesis, glyoxylic/glyoxylate cycle, response to stress, and degradation of amino acids in the four isolates. The following differences were observed among the isolates: higher increases in the expression levels of proteins belonging to the TCA and respiratory chain in PbEPM83 and Pb01; increase in ethanol production in Pb01; utilization of cell wall components for gluconeogenesis in Pb03 and PbEPM83; and increased β-oxidation and methylcitrate cycle proteins in Pb01and PbEPM83. Proteomic profiles indicated that the four isolates reorganized their metabolism

  14. Reprogramming One-Carbon Metabolic Pathways To Decouple l-Serine Catabolism from Cell Growth in Corynebacterium glutamicum.

    Science.gov (United States)

    Zhang, Yun; Shang, Xiuling; Lai, Shujuan; Zhang, Yu; Hu, Qitiao; Chai, Xin; Wang, Bo; Liu, Shuwen; Wen, Tingyi

    2018-02-16

    l-Serine, the principal one-carbon source for DNA biosynthesis, is difficult for microorganisms to accumulate due to the coupling of l-serine catabolism and microbial growth. Here, we reprogrammed the one-carbon unit metabolic pathways in Corynebacterium glutamicum to decouple l-serine catabolism from cell growth. In silico model-based simulation showed a negative influence on glyA-encoding serine hydroxymethyltransferase flux with l-serine productivity. Attenuation of glyA transcription resulted in increased l-serine accumulation, and a decrease in purine pools, poor growth and longer cell shapes. The gcvTHP-encoded glycine cleavage (Gcv) system from Escherichia coli was introduced into C. glutamicum, allowing glycine-derived 13 CH 2 to be assimilated into intracellular purine synthesis, which resulted in an increased amount of one-carbon units. Gcv introduction not only restored cell viability and morphology but also increased l-serine accumulation. Moreover, comparative proteomic analysis indicated that abundance changes of the enzymes involved in one-carbon unit cycles might be responsible for maintaining one-carbon unit homeostasis. Reprogramming of the one-carbon metabolic pathways allowed cells to reach a comparable growth rate to accumulate 13.21 g/L l-serine by fed-batch fermentation in minimal medium. This novel strategy provides new insights into the regulation of cellular properties and essential metabolite accumulation by introducing an extrinsic pathway.

  15. Connecting metabolism and reproduction: roles of central energy sensors and key molecular mediators.

    Science.gov (United States)

    Roa, Juan; Tena-Sempere, Manuel

    2014-11-01

    It is well established that pubertal activation of the reproductive axis and maintenance of fertility are critically dependent on the magnitude of body energy reserves and the metabolic state of the organism. Hence, conditions of impaired energy homeostasis often result in deregulation of puberty and reproduction, whereas gonadal dysfunction can be associated with the worsening of the metabolic profile and, eventually, changes in body weight. While much progress has taken place in our knowledge about the neuroendocrine mechanisms linking metabolism and reproduction, our understanding of how such dynamic interplay happens is still incomplete. As paradigmatic example, much has been learned in the last two decades on the reproductive roles of key metabolic hormones (such as leptin, insulin and ghrelin), their brain targets and the major transmitters and neuropeptides involved. Yet, the molecular mechanisms whereby metabolic information is translated and engages into the reproductive circuits remain largely unsolved. In this work, we will summarize recent developments in the characterization of the putative central roles of key cellular energy sensors, such as mTOR, in this phenomenon, and will relate these with other molecular mechanisms likely contributing to the brain coupling of energy balance and fertility. In doing so, we aim to provide an updated view of an area that, despite still underdeveloped, may be critically important to fully understand how reproduction and metabolism are tightly connected in health and disease. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  16. Organic carbon accumulation and reactivity in central Swedish lakes during the Holocene

    Science.gov (United States)

    Chmiel, H.; Kokic, J.; Niggemann, J.; Dittmar, T.; Sobek, S.

    2012-04-01

    Sedimentation and burial of particulate organic carbon (POC), received from terrestrial sources and from lake internal primary production, are responsible for the progressive accumulation and long-term storage of organic matter in lake basins. For lakes in the boreal zone of central Sweden it can be presumed, that the onset of POC accumulation occurred during the early Holocene (˜8000 BP.) after the retreat of the Scandinavian ice sheet. In this study we investigated carbon mass accumulation rates (CMARs), as well as sources and reactivity of deposited organic material, for seven lakes in central Sweden (60°N, 15°E), in order to obtain a detailed temporal resolution of carbon burial and preservation in boreal lakes. Sediment long-cores were sampled in March 2011 from the ice, and CMARs were calculated from water contents, dry bulk densities, carbon contents and radiocarbon (14C) ages of the depth profiles. To indicate the sources of the organic material and characterize its diagenetic state, we determined carbon-nitrogen ratios (C/N) as well as amounts and compositions of lignin phenols. The transitions from organic rich sediment layers to glacial till deposits were found to be in sediment depths of ˜3 m in each lake. POC contents were on average highest (25-34 wt. % C), in small lakes (≤ 0.07 km2) and lowest (10-18 wt. % C) in the larger lakes (≥ 165 km2). The CMARs over the Holocene showed significant variations and were on average lower in the early Holocene, compared to recent accumulation rates. C/N values and the composition of lignin phenols further provided indications of important changes in organic matter source and reactivity over the Holocene. In summary, our data suggest that boreal lake sediments were a significantly stronger sink for organic carbon during the last ~150 years than during earlier periods of the Holocene.

  17. Synthetic biology for engineering acetyl coenzyme a metabolism in yeast

    DEFF Research Database (Denmark)

    Nielsen, Jens

    2014-01-01

    The yeast Saccharomyces cerevisiae is a widely used cell factory for the production of fuels, chemicals, and pharmaceuticals. The use of this cell factory for cost-efficient production of novel fuels and chemicals requires high yields and low by-product production. Many industrially interesting...... chemicals are biosynthesized from acetyl coenzyme A (acetyl-CoA), which serves as a central precursor metabolite in yeast. To ensure high yields in production of these chemicals, it is necessary to engineer the central carbon metabolism so that ethanol production is minimized (or eliminated) and acetyl...

  18. Metabolism and risks from tritium and carbon-14 in the developing organism

    International Nuclear Information System (INIS)

    Gerber, G.B.; Kirchmann, R.; Hoek, J. van den

    1987-01-01

    In this review the risks are considered from tritium and carbon-14 to the developing organs of mammals. It mainly deals with H-3 but the conclusions are largely valid also for C-14. The metabolism and average tissue of THO as well as of organically bound tritium are discussed. Dosimetry of radiosensitive structures is also considered. 14 refs.; 2 figs.; 1 table

  19. Central melanin-concentrating hormone influences liver and adipose metabolism via specific hypothalamic nuclei and efferent autonomic/JNK1 pathways.

    Science.gov (United States)

    Imbernon, Monica; Beiroa, Daniel; Vázquez, María J; Morgan, Donald A; Veyrat-Durebex, Christelle; Porteiro, Begoña; Díaz-Arteaga, Adenis; Senra, Ana; Busquets, Silvia; Velásquez, Douglas A; Al-Massadi, Omar; Varela, Luis; Gándara, Marina; López-Soriano, Francisco-Javier; Gallego, Rosalía; Seoane, Luisa M; Argiles, Josep M; López, Miguel; Davis, Roger J; Sabio, Guadalupe; Rohner-Jeanrenaud, Françoise; Rahmouni, Kamal; Dieguez, Carlos; Nogueiras, Ruben

    2013-03-01

    Specific neuronal circuits modulate autonomic outflow to liver and white adipose tissue. Melanin-concentrating hormone (MCH)-deficient mice are hypophagic, lean, and do not develop hepatosteatosis when fed a high-fat diet. Herein, we sought to investigate the role of MCH, an orexigenic neuropeptide specifically expressed in the lateral hypothalamic area, on hepatic and adipocyte metabolism. Chronic central administration of MCH and adenoviral vectors increasing MCH signaling were performed in rats and mice. Vagal denervation was performed to assess its effect on liver metabolism. The peripheral effects on lipid metabolism were assessed by real-time polymerase chain reaction and Western blot. We showed that the activation of MCH receptors promotes nonalcoholic fatty liver disease through the parasympathetic nervous system, whereas it increases fat deposition in white adipose tissue via the suppression of sympathetic traffic. These metabolic actions are independent of parallel changes in food intake and energy expenditure. In the liver, MCH triggers lipid accumulation and lipid uptake, with c-Jun N-terminal kinase being an essential player, whereas in adipocytes MCH induces metabolic pathways that promote lipid storage and decreases lipid mobilization. Genetic activation of MCH receptors or infusion of MCH specifically in the lateral hypothalamic area modulated hepatic lipid metabolism, whereas the specific activation of this receptor in the arcuate nucleus affected adipocyte metabolism. Our findings show that central MCH directly controls hepatic and adipocyte metabolism through different pathways. Copyright © 2013 AGA Institute. Published by Elsevier Inc. All rights reserved.

  20. 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.

  1. Integrating tracer-based metabolomics data and metabolic fluxes in a linear fashion via Elementary Carbon Modes.

    Science.gov (United States)

    Pey, Jon; Rubio, Angel; Theodoropoulos, Constantinos; Cascante, Marta; Planes, Francisco J

    2012-07-01

    Constraints-based modeling is an emergent area in Systems Biology that includes an increasing set of methods for the analysis of metabolic networks. In order to refine its predictions, the development of novel methods integrating high-throughput experimental data is currently a key challenge in the field. In this paper, we present a novel set of constraints that integrate tracer-based metabolomics data from Isotope Labeling Experiments and metabolic fluxes in a linear fashion. These constraints are based on Elementary Carbon Modes (ECMs), a recently developed concept that generalizes Elementary Flux Modes at the carbon level. To illustrate the effect of our ECMs-based constraints, a Flux Variability Analysis approach was applied to a previously published metabolic network involving the main pathways in the metabolism of glucose. The addition of our ECMs-based constraints substantially reduced the under-determination resulting from a standard application of Flux Variability Analysis, which shows a clear progress over the state of the art. In addition, our approach is adjusted to deal with combinatorial explosion of ECMs in genome-scale metabolic networks. This extension was applied to infer the maximum biosynthetic capacity of non-essential amino acids in human metabolism. Finally, as linearity is the hallmark of our approach, its importance is discussed at a methodological, computational and theoretical level and illustrated with a practical application in the field of Isotope Labeling Experiments. Copyright © 2012 Elsevier Inc. All rights reserved.

  2. Effects of Laparoscopic Sleeve Gastrectomy on Central Obesity and Metabolic Syndrome in Indian Adults- A Prospective Study.

    Science.gov (United States)

    Sethi, Pulkit; Thillai, Manoj; Nain, Prabhdeep Singh; Ahuja, Ashish; Vayoth, Sudheer Othiyil; Khurana, Preetika

    2017-01-01

    Increasing incidence of obesity in Indian population has led to an exponential rise in the number of bariatric operations performed annually. Laparoscopic Sleeve Gastrectomy (LSG) has been proposed to cause rapid remission of Type 2 Diabetes Melitus (T2DM) and metabolic syndrome in a weight loss independent manner. To evaluate the effects of LSG on metabolic syndrome and central obesity in morbidly and severely obese Indian adults. Material and Methods: Study was conducted on 91 morbidly obese [Body Mass Index (BMI)>40 kg/m 2 ] and severely obese (BMI>35 kg/m 2 ) individuals who were suffering from diabetes, hypertension or dyslipidemia. The patients were followed up for six months and the trends of glycaemic control, mean blood pressure, lipid profile, weight loss parameters and changes in parameters of central obesity were studied. Weight loss was significant at three months postsurgery and was sustained through six months. There was significant improvement in glycaemic control leading to reduction in need for oral hypoglycaemic agents or insulin in majority of them and even discontinuation of these medications in few patients. Hypertension and dyslipidemia also showed an improving trend through six months postsurgery. There was a significant impact on reduction of central obesity in these patients as marked by significant reduction in waist to hip ratio. LSG produces sustainable weight loss with significant improvement in glycaemic status and control of metabolic syndrome in severe to morbidly obese patients. LSG is also efficacious in reducing central obesity in Indian population which is a major depressive ailment amongst obese individuals.

  3. The flexible feedstock concept in Industrial Biotechnology: Metabolic engineering of Escherichia coli, Corynebacterium glutamicum, Pseudomonas, Bacillus and yeast strains for access to alternative carbon sources.

    Science.gov (United States)

    Wendisch, Volker F; Brito, Luciana Fernandes; Gil Lopez, Marina; Hennig, Guido; Pfeifenschneider, Johannes; Sgobba, Elvira; Veldmann, Kareen H

    2016-09-20

    Most biotechnological processes are based on glucose that is either present in molasses or generated from starch by enzymatic hydrolysis. At the very high, million-ton scale production volumes, for instance for fermentative production of the biofuel ethanol or of commodity chemicals such as organic acids and amino acids, competing uses of carbon sources e.g. in human and animal nutrition have to be taken into account. Thus, the biotechnological production hosts E. coli, C. glutamicum, pseudomonads, bacilli and Baker's yeast used in these large scale processes have been engineered for efficient utilization of alternative carbon sources. This flexible feedstock concept is central to the use of non-glucose second and third generation feedstocks in the emerging bioeconomy. The metabolic engineering efforts to broaden the substrate scope of E. coli, C. glutamicum, pseudomonads, B. subtilis and yeasts to include non-native carbon sources will be reviewed. Strategies to enable simultaneous consumption of mixtures of native and non-native carbon sources present in biomass hydrolysates will be summarized and a perspective on how to further increase feedstock flexibility for the realization of biorefinery processes will be given. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Biomarkers related to one-carbon metabolism as potential risk factors for distal colorectal adenomas

    NARCIS (Netherlands)

    Vogel, S. de; Schneede, J.; Ueland, P.M.; Vollset, S.E.; Meyer, K.; Fredriksen, A.; Midttun, O.; Bjorge, T.; Kampman, E.; Bretthauer, M.; Hoff, G.

    2011-01-01

    BACKGROUND: Efficient one-carbon metabolism, which requires adequate supply of methyl group donors and B-vitamins, may protect against colorectal carcinogenesis. However, plasma folate and vitamins B2 and B12 have inconsistently been associated with colorectal cancer risk, and there have been no

  5. Biomarkers Related to One-Carbon Metabolism as Potential Risk Factors for Distal Colorectal Adenomas

    NARCIS (Netherlands)

    Vogel, de S.; Schneede, J.; Ueland, P.M.; Vollset, S.E.; Meyer, K.; Fredriksen, A.; Midttun, O.; Bjorge, T.; Kampman, E.; Bretthauer, M.; Hoff, G.

    2011-01-01

    Background: Efficient one-carbon metabolism, which requires adequate supply of methyl group donors and B-vitamins, may protect against colorectal carcinogenesis. However, plasma folate and vitamins B2 and B12 have inconsistently been associated with colorectal cancer risk, and there have been no

  6. International Workshop on Carbon Cycling and Coral Reef Metabolism; Sangosho no tanso junkan ni kansuru kokusai workshop hokokusho

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-10-16

    The paper described the International Workshop on Carbon Cycling and Coral Reef Metabolism which was held at Miyako-jima, Okinawa Pref. on October 17-24, 1995. In the workshop, researchers got together which are involved in marine chemistry, marine biology, coral ecology, and environmental science, and discussed the carbon cycling and metabolism of coral reef. Discussions were made on what the coral reef ecosystem is, and what the definition of a sink or a source for CO2 is. Also discussed were scales of how much time and space should be considered to make these issues clear. Further, it was proposed that it was necessary to investigate carbon balance of both the whole system and the components of the system and to keep track of mass transfer among neighboring components of the system. Seventeen presentations were given. The workshop obtained a definite consensus on carbon balance of the coral reef system. 123 refs., 39 figs., 9 tabs.

  7. Photosystem II excitation pressure and photosynthetic carbon metabolism in Chlorella vulgaris

    International Nuclear Information System (INIS)

    Savitch, L.V.; Maxwell, D.P.; Huner, N.P.A.

    1996-01-01

    Chlorella vulgaris grown at 5 degrees C/150 micromoles m -2 s -1 mimics cells grown under high irradiance (27 degrees C/2200 micromoles m -2 s -1 ). This has been rationalized through the suggestion that both populations of cells were exposed to comparable photosystem II (PSII) excitation pressures measured as the chlorophyll a fluorescence quenching parameter, 1 - qP (D.P. Maxwell, S. Falk, N.P.A. Huner [1995] Plant Physiol 107: 687-694). To assess the possible role(s) of feedback mechanisms on PSII excitation pressure, stromal and cytosolic carbon metabolism were examined. Sucrose phosphate synthase and fructose-1,6-bisphosphatase activities as well as the ratios of fructose-1,6-bisphosphate/fructose-6 phosphate and sucrose/starch indicated that cells grown at 27 degrees C/2200 micromoles m -2 s -1 appeared to exhibit a restriction in starch metabolism. In contrast, cells grown at 5 degrees C/150 micromoles-1 m -2 s -1 appeared to exhibit a restriction in the sucrose metabolism based on decreased cytosolic fructose-1,6-bisphosphatase and sucrose phosphate synthase activities as well as a low sucrose/starch ratio. These metabolic restrictions may feedback on photosynthetic electron transport and, thus, contribute to the observed PSII excitation pressure. We conclude that, although PSII excitation pressure may reflect redox regulation of photosynthetic acclimation to light and temperature in C. vulgaris, it cannot be considered the primary redox signal. Alternative metabolic sensing/signaling mechanisms are discussed

  8. Microarray and bioinformatic analyses suggest models for carbon metabolism in the autotroph Acidithiobacillus ferrooxidans

    Energy Technology Data Exchange (ETDEWEB)

    C. Appia-ayme; R. Quatrini; Y. Denis; F. Denizot; S. Silver; F. Roberto; F. Veloso; J. Valdes; J. P. Cardenas; M. Esparza; O. Orellana; E. Jedlicki; V. Bonnefoy; D. Holmes

    2006-09-01

    Acidithiobacillus ferrooxidans is a chemolithoautotrophic bacterium that uses iron or sulfur as an energy and electron source. Bioinformatic analysis was used to identify putative genes and potential metabolic pathways involved in CO2 fixation, 2P-glycolate detoxification, carboxysome formation and glycogen utilization in At. ferrooxidans. Microarray transcript profiling was carried out to compare the relative expression of the predicted genes of these pathways when the microorganism was grown in the presence of iron versus sulfur. Several gene expression patterns were confirmed by real-time PCR. Genes for each of the above predicted pathways were found to be organized into discrete clusters. Clusters exhibited differential gene expression depending on the presence of iron or sulfur in the medium. Concordance of gene expression within each cluster, suggested that they are operons Most notably, clusters of genes predicted to be involved in CO2 fixation, carboxysome formation, 2P-glycolate detoxification and glycogen biosynthesis were up-regulated in sulfur medium, whereas genes involved in glycogen utilization were preferentially expressed in iron medium. These results can be explained in terms of models of gene regulation that suggest how A. ferrooxidans can adjust its central carbon management to respond to changing environmental conditions.

  9. Ecophysiology of terminal carbon metabolizing bacteria in anoxic sedimentary environments

    International Nuclear Information System (INIS)

    Phelps, T.J.

    1985-01-01

    Chemical, radiotracer, and microbiological experiments were used to understand the transformation of simple carbon compounds by anaerobic bacteria in diverse aquatic sediments and laboratory cultures. The mildly acidic sediments of Knack Lake (pH 6.2), displayed low rates of organic decomposition, and methane formation occurred almost exclusively from acetate. Low pH inhibited methanogenesis and organic decomposition. Fall turnover in Lake Mendota sediments was associated with dramatic changes in environmental parameters including: elevated concentrations of sulfate and carbon metabolites, increased rates of sulfate reduction, decreased levels of methanogenesis, increased ratio (by viable counts) of sulfate reducing to methanogenic bacteria, and higher 14 CO 2 / 14 C 4 + 14 CO 2 gas ratios produced during the biodegradation of 14 C-carbon substrates (e.g., acetate and methanol). Hydrogen consumption by sulfate reducers in Lake Mendota sediments and in co-cultures of Desulfovibrio vulgaris and Methanosarcina barkeri led to an alteration in the carbon and electron flow pathway resulting in increased CO 2 , sulfide production, and decreased methanogenesis. These data agreed with the environmental observations in Lake Mendota that high sulfate concentrations resulted in higher ratios of CO 2 /CH 4 produced from the degradation of organic matter. A new glycine-metabolizing acetogenic species was isolated and characterized from Knaack Lake which further extended the known diversity of anaerobic bacteria in nature

  10. In Vivo Analysis of NH4+ Transport and Central Nitrogen Metabolism in Saccharomyces cerevisiae during Aerobic Nitrogen-Limited Growth

    Science.gov (United States)

    Maleki Seifar, R.; ten Pierick, A.; van Helmond, W.; Pieterse, M. M.; Heijnen, J. J.

    2016-01-01

    ABSTRACT Ammonium is the most common N source for yeast fermentations. Although its transport and assimilation mechanisms are well documented, there have been only a few attempts to measure the in vivo intracellular concentration of ammonium and assess its impact on gene expression. Using an isotope dilution mass spectrometry (IDMS)-based method, we were able to measure the intracellular ammonium concentration in N-limited aerobic chemostat cultivations using three different N sources (ammonium, urea, and glutamate) at the same growth rate (0.05 h−1). The experimental results suggest that, at this growth rate, a similar concentration of intracellular (IC) ammonium, about 3.6 mmol NH4+/literIC, is required to supply the reactions in the central N metabolism, independent of the N source. Based on the experimental results and different assumptions, the vacuolar and cytosolic ammonium concentrations were estimated. Furthermore, we identified a futile cycle caused by NH3 leakage into the extracellular space, which can cost up to 30% of the ATP production of the cell under N-limited conditions, and a futile redox cycle between Gdh1 and Gdh2 reactions. Finally, using shotgun proteomics with protein expression determined relative to a labeled reference, differences between the various environmental conditions were identified and correlated with previously identified N compound-sensing mechanisms. IMPORTANCE In our work, we studied central N metabolism using quantitative approaches. First, intracellular ammonium was measured under different N sources. The results suggest that Saccharomyces cerevisiae cells maintain a constant NH4+ concentration (around 3 mmol NH4+/literIC), independent of the applied nitrogen source. We hypothesize that this amount of intracellular ammonium is required to obtain sufficient thermodynamic driving force. Furthermore, our calculations based on thermodynamic analysis of the transport mechanisms of ammonium suggest that ammonium is not equally

  11. In vivo analysis of NH4+ transport and central N-metabolism of Saccharomyces cerevisiae under aerobic N-limited conditions.

    Science.gov (United States)

    Cueto-Rojas, H F; Maleki Seifar, R; Ten Pierick, A; van Helmond, W; Pieterse M, M; Heijnen, J J; Wahl, S A

    2016-09-16

    Ammonium is the most common N-source for yeast fermentations. Although, its transport and assimilation mechanisms are well documented, there have been only few attempts to measure the in vivo intracellular concentration of ammonium and assess its impact on gene expression. Using an isotope dilution mass spectrometry (IDMS)-based method we were able to measure the intracellular ammonium concentration in N-limited aerobic chemostat cultivations using three different N-sources (ammonium, urea and glutamate) at the same growth rate (0.05 h -1 ). The experimental results suggest that, at this growth rate, a similar concentration of intracellular ammonium, about 3.6 mmol NH 4 + /L IC , is required to supply the reactions in the central N-metabolism independent of the N-source. Based on the experimental results and different assumptions, the vacuolar and cytosolic ammonium concentrations were estimated. Furthermore, we identified a futile cycle caused by NH 3 leakage to the extracellular space, which can cost up to 30% of the ATP production of the cell under N-limited conditions, and a futile redox cycle between reactions Gdh1 and Gdh2. Finally, using shotgun proteomics with labeled reference-relative protein expression, differences between the various environmental conditions were identified and correlated with previously identified N-compound sensing mechanisms. In our work, we study central N-metabolism using quantitative approaches. First, intracellular ammonium was measured under different N-sources. The results suggest that Saccharomyces cerevisiae cells keep a constant NH 4 + concentration (around 3 mmol NH 4 + /L IC ), independent of the applied nitrogen source. We hypothesize that this amount of intracellular ammonium is required to obtain sufficient thermodynamic driving force.Furthermore, our calculations based on thermodynamic analysis of the transport mechanisms of ammonium suggest that ammonium is not equally distributed, indicating a high degree of

  12. 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.

  13. Investigation of the microbial metabolism of carbon dioxide and hydrogen in the kangaroo foregut by stable isotope probing.

    Science.gov (United States)

    Godwin, Scott; Kang, Alicia; Gulino, Lisa-Maree; Manefield, Mike; Gutierrez-Zamora, Maria-Luisa; Kienzle, Marco; Ouwerkerk, Diane; Dawson, Kerri; Klieve, Athol V

    2014-09-01

    Kangaroos ferment forage material in an enlarged forestomach analogous to the rumen, but in contrast to ruminants, they produce little or no methane. The objective of this study was to identify the dominant organisms and pathways involved in hydrogenotrophy in the kangaroo forestomach, with the broader aim of understanding how these processes are able to predominate over methanogenesis. Stable isotope analysis of fermentation end products and RNA stable isotope probing (RNA-SIP) were used to investigate the organisms and biochemical pathways involved in the metabolism of hydrogen and carbon dioxide in the kangaroo forestomach. Our results clearly demonstrate that the activity of bacterial reductive acetogens is a key factor in the reduced methane output of kangaroos. In in vitro fermentations, the microbial community of the kangaroo foregut produced very little methane, but produced a significantly greater proportion of acetate derived from carbon dioxide than the microbial community of the bovine rumen. A bacterial operational taxonomic unit closely related to the known reductive acetogen Blautia coccoides was found to be associated with carbon dioxide and hydrogen metabolism in the kangaroo foregut. Other bacterial taxa including members of the genera Prevotella, Oscillibacter and Streptococcus that have not previously been reported as containing hydrogenotrophic organisms were also significantly associated with metabolism of hydrogen and carbon dioxide in the kangaroo forestomach.

  14. Discontinuities Characteristics of the Upper Jurassic Arab-D Reservoir Equivalent Tight Carbonates Outcrops, Central Saudi Arabia

    Science.gov (United States)

    Abdlmutalib, Ammar; Abdullatif, Osman

    2017-04-01

    Jurassic carbonates represent an important part of the Mesozoic petroleum system in the Arabian Peninsula in terms of source rocks, reservoirs, and seals. Jurassic Outcrop equivalents are well exposed in central Saudi Arabia and which allow examining and measuring different scales of geological heterogeneities that are difficult to collect from the subsurface due to limitations of data and techniques. Identifying carbonates Discontinuities characteristics at outcrops might help to understand and predict their properties and behavior in the subsurface. The main objective of this study is to identify the lithofacies and the discontinuities properties of the upper Jurassic carbonates of the Arab D member and the Jubaila Formation (Arab-D reservoir) based on their outcrop equivalent strata in central Saudi Arabia. The sedimentologic analysis revealed several lithofacies types that vary in their thickness, abundances, cyclicity and vertical and lateral stacking patterns. The carbonates lithofacies included mudstone, wackestone, packstone, and grainstone. These lithofacies indicate deposition within tidal flat, skeletal banks and shallow to deep lagoonal paleoenvironmental settings. Field investigations of the outcrops revealed two types of discontinuities within Arab D Member and Upper Jubaila. These are depositional discontinuities and tectonic fractures and which all vary in their orientation, intensity, spacing, aperture and displacements. It seems that both regional and local controls have affected the fracture development within these carbonate rocks. On the regional scale, the fractures seem to be structurally controlled by the Central Arabian Graben System, which affected central Saudi Arabia. While, locally, at the outcrop scale, stratigraphic, depositional and diagenetic controls appear to have influenced the fracture development and intensity. The fracture sets and orientations identified on outcrops show similarity to those fracture sets revealed in the upper

  15. 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.

  16. Ordovas-Oxidized LDL is associated with metabolic syndrome traits independently of central obesity and insulin resistance

    Science.gov (United States)

    This study assesses whether oxidative stress, using oxidized LDL (ox-LDL) as a proxy, is associated with metabolic syndrome (MS), whether ox-LDL mediates the association between central obesity and MS, and whether insulin resistance mediates the association between ox-LDL and MS. We examined baselin...

  17. 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.

  18. Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications

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    Blake Robert

    2008-12-01

    Full Text Available Abstract Background Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining. It is a chemolithoautrophic, γ-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. It thrives at extremely low pH (pH 1–2 and fixes both carbon and nitrogen from the atmosphere. It solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemical cycling in acid environments. The lack of a well-developed system for genetic manipulation has prevented thorough exploration of its physiology. Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism. Results The genome of the type strain A. ferrooxidans ATCC 23270 was sequenced and annotated to identify general features and provide a framework for in silico metabolic reconstruction. Earlier models of iron and sulfur oxidation, biofilm formation, quorum sensing, inorganic ion uptake, and amino acid metabolism are confirmed and extended. Initial models are presented for central carbon metabolism, anaerobic metabolism (including sulfur reduction, hydrogen metabolism and nitrogen fixation, stress responses, DNA repair, and metal and toxic compound fluxes. Conclusion Bioinformatics analysis provides a valuable platform for gene discovery and functional prediction that helps explain the activity of A. ferrooxidans in industrial bioleaching and its role as a primary producer in acidic environments. An analysis of the genome of the type strain provides a coherent view of its gene content and metabolic potential.

  19. Comparable Enhanced Prothrombogenesis in Simple Central Obesity and Metabolic Syndrome

    Directory of Open Access Journals (Sweden)

    Noor Shafina Mohd Nor

    2018-01-01

    Full Text Available Objective. There is limited data comparing prothrombogenic or fibrinolysis biomarkers (tissue plasminogen activator (tPA and plasminogen activator inhibitor-1 (PAI-1 simultaneously in subjects with Metabolic Syndrome (MS, simple central obesity without MS (COB and normal controls (NC. We investigated the concentrations of fibrinolysis biomarkers in subjects with MS, COB and NC. Methods. A cross-sectional study involving 503 drug naive subjects (163 males, aged 30–65 years old (mean age ± SD = 47.4 ± 8.3 years divided into MS, COB and NC groups. COB was defined as central obesity (waist circumference (WC males ≥90 cm, females ≥80 cm in the absence of MS according to the International Diabetes Federation 2006. Fasting blood levels of tPA and PAI-1were analyzed. Results. MS and COB had significantly higher concentration of all biomarkers compared to NC. The MS group had significantly higher concentration of tPA and PAI-1 compared to COB. WC and HDL-c had significant correlation with all biomarkers (tPA p<0.001, PAI-1 p<0.001. Fasting plasma glucose and diastolic blood pressure were independent predictors after correcting for confounding factors. Conclusion. Central obesity with or without MS both demonstrated enhanced prothrombogenesis. This suggests that simple obesity possibly increases the risk of coronary artery disease in part, via increased susceptibility to thrombogenesis.

  20. Depositional facies mosaics and their time lines in Lower Ordovician carbonates of central Appalachians

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, C.T.; Goldhammer, R.K.; Hardie, L.A.

    1985-02-01

    A comparative sedimentology and facies stratigraphy study of the Lower Ordovician carbonate of the central Appalachians (Beekmantown Group and equivalents) has been carried out. Our approach used subfacies (rock record of subenvironments) as the basin units of section measurement. The authors differentiated related sets of subfacies into larger facies units (rock record of environments). Facies were then correlated from section to section using fossils and lithostratigraphy to make a 3-dimensional facies mosaic. Within this mosaic, time lines were constructed using onlap-offlap tongues and cyclic sequences. These time lines cut across facies boundaries. Using this approach, the authors have established that the lower 600 m of the Lower Ordovician carbonate sequence is made up of 4 main facies: (1) cyclic laminite facies composed of a package of shoaling-upward shelf lagoon-peritidal cycles, (2) thin-bedded grainstone facies deposited in a shelf lagoon, (3) Renalcis bioherm facies recording a shelf lagoon patch-reef environment, and (4) Epiphyton bioherm facies recording a shelf-edge reef system. The distribution of these facies along time lines across the strike of the central Appalachians is markedly zoned. Epiphyton bioherm facies dominate the eastern margin while cyclic laminite facies dominate the western margin, with thin-bedded grainstone and Renalcis bioherm facies making up the central belt. This zonation of facies is a typical shallow carbonate shelf system with fringing reefs along the eastern, seaward margin and tidal flats along the western, landward margin. Vertical distribution of these facies across strike records 3 major sea level changes during deposition of the lower 600 m of this extensive Lower Ordovician carbonate shelf.

  1. Growth versus metabolic tissue replacement in mouse tissues determined by stable carbon and nitrogen isotope analysis

    Science.gov (United States)

    Macavoy, S. E.; Jamil, T.; Macko, S. A.; Arneson, L. S.

    2003-12-01

    Stable isotope analysis is becoming an extensively used tool in animal ecology. The isotopes most commonly used for analysis in terrestrial systems are those of carbon and nitrogen, due to differential carbon fractionation in C3 and C4 plants, and the approximately 3‰ enrichment in 15N per trophic level. Although isotope signatures in animal tissues presumably reflect the local food web, analysis is often complicated by differential nutrient routing and fractionation by tissues, and by the possibility that large organisms are not in isotopic equilibrium with the foods available in their immediate environment. Additionally, the rate at which organisms incorporate the isotope signature of a food through both growth and metabolic tissue replacement is largely unknown. In this study we have assessed the rate of carbon and nitrogen isotopic turnover in liver, muscle and blood in mice following a diet change. By determining growth rates, we were able to determine the proportion of tissue turnover caused by growth versus that caused by metabolic tissue replacement. Growth was found to account for approximately 10% of observed tissue turnover in sexually mature mice (Mus musculus). Blood carbon was found to have the shortest half-life (16.9 days), followed by muscle (24.7 days). Liver carbon turnover was not as well described by the exponential decay equations as other tissues. However, substantial liver carbon turnover was observed by the 28th day after diet switch. Surprisingly, these tissues primarily reflect the carbon signature of the protein, rather than carbohydrate, source in their diet. The nitrogen signature in all tissues was enriched by 3 - 5‰ over their dietary protein source, depending on tissue type, and the isotopic turnover rates were comparable to those observed in carbon.

  2. Comprehensive and accurate tracking of carbon origin of LC-tandem mass spectrometry collisional fragments for 13C-MFA.

    Science.gov (United States)

    Kappelmann, Jannick; Klein, Bianca; Geilenkirchen, Petra; Noack, Stephan

    2017-03-01

    In recent years the benefit of measuring positionally resolved 13 C-labeling enrichment from tandem mass spectrometry (MS/MS) collisional fragments for improved precision of 13 C-Metabolic Flux Analysis ( 13 C-MFA) has become evident. However, the usage of positional labeling information for 13 C-MFA faces two challenges: (1) The mass spectrometric acquisition of a large number of potentially interfering mass transitions may hamper accuracy and sensitivity. (2) The positional identity of carbon atoms of product ions needs to be known. The present contribution addresses the latter challenge by deducing the maximal positional labeling information contained in LC-ESI-MS/MS spectra of product anions of central metabolism as well as product cations of amino acids. For this purpose, we draw on accurate mass spectrometry, selectively labeled standards, and published fragmentation pathways to structurally annotate all dominant mass peaks of a large collection of metabolites, some of which with a complete fragmentation pathway. Compiling all available information, we arrive at the most detailed map of carbon atom fate of LC-ESI-MS/MS collisional fragments yet, comprising 170 intense and structurally annotated product ions with unique carbon origin from 76 precursor ions of 72 metabolites. Our 13 C-data proof that heuristic fragmentation rules often fail to yield correct fragment structures and we expose common pitfalls in the structural annotation of product ions. We show that the positionally resolved 13 C-label information contained in the product ions that we structurally annotated allows to infer the entire isotopomer distribution of several central metabolism intermediates, which is experimentally demonstrated for malate using quadrupole-time-of-flight MS technology. Finally, the inclusion of the label information from a subset of these fragments improves flux precision in a Corynebacterium glutamicum model of the central carbon metabolism.

  3. Sulfosys (Sulfolobus Systems Biology): towards a silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation.

    NARCIS (Netherlands)

    Albers, S.V.; Birkeland, N.K.; Driessen, A.J.; Gertig, S.; Haferkamp, P.; Klenk, H.P.; Kouril, T.; Manica, A.; Pham, T.K.; Ruoff, P.; Schleper, C.; Schomburg, D.; Sharkey, K.J.; Siebers, B.; Sierocinski, P.; Steuer, R.; van der Oost, J.; Westerhoff, H.V.; Wieloch, P.; Wright, P.C.; Zaparty, M.

    2009-01-01

    SulfoSYS (Sulfolobus Systems Biology) focuses on the study of the CCM (central carbohydrate metabolism) of Sulfolobus solfataricus and its regulation under temperature variation at the systems level. In Archaea, carbohydrates are metabolized by modifications of the classical pathways known from

  4. Radio-metabolite analysis of carbon-11 biochemical partitioning to non-structural carbohydrates for integrated metabolism and transport studies.

    Science.gov (United States)

    Babst, Benjamin A; Karve, Abhijit A; Judt, Tatjana

    2013-06-01

    Metabolism and phloem transport of carbohydrates are interactive processes, yet each is often studied in isolation from the other. Carbon-11 ((11)C) has been successfully used to study transport and allocation processes dynamically over time. There is a need for techniques to determine metabolic partitioning of newly fixed carbon that are compatible with existing non-invasive (11)C-based methodologies for the study of phloem transport. In this report, we present methods using (11)C-labeled CO2 to trace carbon partitioning to the major non-structural carbohydrates in leaves-sucrose, glucose, fructose and starch. High-performance thin-layer chromatography (HPTLC) was adapted to provide multisample throughput, raising the possibility of measuring different tissues of the same individual plant, or for screening multiple plants. An additional advantage of HPTLC was that phosphor plate imaging of radioactivity had a much higher sensitivity and broader range of sensitivity than radio-HPLC detection, allowing measurement of (11)C partitioning to starch, which was previously not possible. Because of the high specific activity of (11)C and high sensitivity of detection, our method may have additional applications in the study of rapid metabolic responses to environmental changes that occur on a time scale of minutes. The use of this method in tandem with other (11)C assays for transport dynamics and whole-plant partitioning makes a powerful combination of tools to study carbohydrate metabolism and whole-plant transport as integrated processes.

  5. Sustainable yield of the Colle Quartara carbonate aquifer in the Southern Lepini Mountains (Central Italy

    Directory of Open Access Journals (Sweden)

    Giovanni Conte

    2016-10-01

    Full Text Available The present research is aimed to contribute to the groundwater resource sustainable management of a carbonate aquifer in a test area of the Lepini Mountains (Central Italy. This aquifer constitutes a major exploited groundwater body of central Apennines. At regional scale, the hydrogeological features of the Lepini hydrostructure are well known. The present study focuses on a portion of the Lepini Mountains where important tapping-works for drinking water supply are in activity (about 1.2 m3/s. New investigations were carried out including: meteo-climatic analysis, spring discharge and hydrometric time series processing, pumping test result interpretation. In addition, a detailed lithostratigraphical and structural survey of a portion of the Lepini hydrostructure at 1:10,000 scale was performed also examining the dense network of discontinuities affecting the carbonate aquifer. Extensional Plio-Pleistocene tectonic activity displaced the carbonate rock sequence under the Pontina Plain, where the carbonate aquifer is confined. The investigation results have allowed the reconstruction of the hydrogeological conceptual model of the studied portion of carbonate massif. Given the scale of the study and the results of the investigation, the carbonate aquifer can be treated as an equivalent porous medium, and the simplified numerical model of the aquifer was constructed with the code MODFLOW-2005. The numerical model, still now under continuous implementation, produced first results on the current withdrawal sustainability, allowing evaluation of possible alternative exploitation scenarios of the carbonate aquifer also considering the probably not significant flow exchanges with the Pontina Plain aquifer.

  6. Nutrient cycling and ecosystem metabolism in boreal streams of the Central Siberian Plateau

    Science.gov (United States)

    Diemer, L.; McDowell, W. H.; Prokushkin, A. S.

    2013-12-01

    Arctic boreal streams are undergoing considerable change in carbon and nutrient biogeochemistry due to degrading permafrost and increasing fire activity. Recent studies show that fire increases transport of inorganic solutes from the boreal landscape to arctic streams in some regions; couple this with expected greater labile dissolved organic carbon (DOC) from deepening active layers, enhanced biomass production, and increased annual precipitation and boreal streams may experience greater in-stream primary production and respiration in the coming century. Little is known about the spatial and temporal dynamics of inorganic nutrients in relation to C availability in headwater streams of a major Arctic region, the Central Siberian Plateau. Our preliminary data of Central Siberian headwater streams show NO3 and PO4 concentrations near or below detection limits (e.g. nine samples taken in spring from a small stream near the Russian settlement of Tura averaged 10 μg/L NO3-N and 9.7 μg/L PO4-P), and recent studies in Central Siberia suggest that bioavailable organic matter and inorganic nutrients such as NO3 will likely increase with climate warming. We examined the fate of nutrients in Central Siberian streams using Tracer for Spiraling Curve Characterization (TASCC) additions of NO3, NH4, and PO4 along with conservative tracer, NaCl, in spring at high and low discharges in streams underlain by continuous permafrost in Central Siberia. We also sampled two sites in spring every 2 hours overnight for 24 hours to document any diel patterns in DOC and inorganic nutrients. Our results thus far show that NO3 uptake length may be strongly correlated with DOC concentration (a function of fire activity). Preliminary results also show that despite high discharge and cold temperatures (4-8°C) in mid to late spring, there appears to be biological activity stimulating a diel signal for NO3 with maximum concentration corresponding to low light (11 PM). Investigating the primary

  7. Fasting ameliorates metabolism, immunity, and oxidative stress in carbon tetrachloride-intoxicated rats.

    Science.gov (United States)

    Sadek, Km; Saleh, Ea

    2014-12-01

    Fasting has been recently discovered to improve overall health, but its beneficial effects in the presence of hepatic insufficiency have not been proven. The influence of fasting on the metabolism, immunological aspects, and oxidative stress of 40 male carbon tetrachloride (CCl4)-intoxicated Wistar rats was investigated in the present study. The rats were divided into four groups, including a placebo group, CCl4-intoxicated rats, which were injected subcutaneously with 1.0 ml/kg of CCl4 solution, a fasting group, which was fasted 12 h/day for 30 days, and a fourth group, which was injected with CCl4 and fasted. The metabolism, immunity, and oxidative stress improved in CCl4-intoxicated rats fasted for 12 h/day for 30 days, as evidenced in significant increase (p fasting improved metabolism, immunity, and oxidative stress in CCl4-intoxicated rats. Thus, fasting during Ramadan is safe for patients with hepatic disorders, as the prophet Mohammed (S) said "Keep the fast, keep your health". © The Author(s) 2014.

  8. 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.

  9. Prevalence of metabolic syndrome in Central America: a cross-sectional population-based study

    Directory of Open Access Journals (Sweden)

    Roy A. Wong-McClure

    2015-09-01

    Full Text Available OBJECTIVE: To report the prevalence of metabolic syndrome (MetS as found by the Central American Diabetes Initiative (CAMDI study for five major Central American populations: Belize (national; Costa Rica (San José; Guatemala (Guatemala City; Honduras (Tegucigalpa; and Nicaragua (Managua. METHODS: Study data on 6 185 adults aged 20 years or older with anthropometric and laboratory determination of MetS from population-based surveys were analyzed. Overall, the survey response rate was 82.0%. MetS prevalence was determined according to criteria from the Adult Treatment Panel III of the National Cholesterol Education Program. The study's protocol was reviewed and approved by the bioethical committee of each country studied. RESULTS: The overall standardized prevalence of MetS in the Central American region was 30.3% (95% confidence interval (CI: 27.1-33.4. There was wide variability by gender and work conditions, with higher prevalence among females and unpaid workers. The standardized percentage of the population free of any component of MetS was lowest in Costa Rica (9.0%; CI: 6.5-11.4 and highest in Honduras (21.1%; CI: 16.4-25.9. CONCLUSIONS: Overall prevalence of MetS in Central America is high. Strengthening surveillance of chronic diseases and establishing effective programs for preventing cardiovascular diseases might reduce the risk of MetS in Central America.

  10. New Perspectives on Acetate and One-Carbon Metabolism in the Methanoarchaea

    Energy Technology Data Exchange (ETDEWEB)

    Ferry, James [Pennsylvania State Univ., University Park, PA (United States)

    2017-03-20

    Carbonic anhydrases catalyze the reversible hydration of carbon dioxide to bicarbonate. Although widespread in prokaryotes of the domains Bacteria and Archaea, few have been investigated and the physiological functions are largely unknown. Carbonic anhydrases are of biotechnological interest for carbon dioxide capture and sequestration at point sources. Prokaryotes encode three independently evolved classes. The alpha-class is restricted to a few pathogens and the other two are uniformly distributed in phylogenetically and physiologically diverse species. Although wide-spread in prokaryotes, only three gamma-class enzymes have been biochemically characterized and the physiological functions have not been investigated. The gamma-class is prominent in anaerobic acetate-utilizing methane-producing species of the genus Methanosarcina that encode three subclasses. Enzymes from two of the subclasses, Cam and CamH from Methanosarcina thermophila, have been characterized and found to utilize iron in the active site which is the first example of an iron-containing carbonic anhydrase. No representative of the third subclass has been isolated, although this subclass constitutes the great majority of the β-class. This grant application proposed to characterize gamma-class carbonic anhydrases from diverse anaerobic prokaryotes from the domains Bacteria and Archaea to broaden the understanding of this enzyme. In particular, the three subclasses present the genetically tractable acetate-utilizing methanogen Methanosarcina acetivorans will be investigated to extend studies of acetate and one-carbon metabolism in this species. A genetic approach will be taken to ascertain the physiological functions. It is also proposed to delve deeper into the mechanism of Cam from M. thermophila, the archetype of the gamma-class, via a high resolution neutron structure and kinetic analysis of site-specific amino acid replacement variants. In the course of the investigation, goals were added to

  11. (Carbon and hydrogen metabolism of green algae in light and dark)

    Energy Technology Data Exchange (ETDEWEB)

    1990-01-01

    The focus of this project was the elucidation of anaerobic metabolism in ecuaryotic green algae, chlamydomonas reinhardii. Chlamydomonas is a versatile organism that can grow under disparate conditions such as fresh water lakes and sewage ponds. The cell an photoassimilate CO{sub 2} aerobically and anaerobically, the latter after adaptation'' to a hydrogen metabolism. It can recall the knallgas or oxyhydrogen reaction and utilize hydrogen the simplest of all reducing agents for the dark assimilation of CO{sub 2} by the photosynthetic carbon reduction cycle. The dark reduction with hydrogen lies on the border line between autotrophic and heterotrophic carbon assimilation. Both autotrophic and heterotrophic bacteria are known in which molecular hydrogen can replace either inorganic or organic hydrogen donors. Here the dark reduction of CO{sub 2} acquires a particular importance since it occurs in the same cell that carries on photoreduction and photosynthesis. We will demonstrate here that the alga chloroplast possesses a respiratory capacity. It seems likely that Chlamydomonas may have retained the chloroplastic respiratory pathway because of the selective advantage provided to the algae under a wide range of environmental conditions that the cells experience in nature. The ability to cycle electrons and poise the reduction level of the photosynthetic apparatus under aerobic and microaerobic conditions could allow more efficient CO{sub 2} fixation and enhanced growth under unfavorable conditions or survival under more severe conditions.

  12. Arsenic methylation capacity in relation to nutrient intake and genetic polymorphisms in one-carbon metabolism.

    Science.gov (United States)

    Gamboa-Loira, Brenda; Hernández-Alcaraz, César; Gandolfi, A Jay; Cebrián, Mariano E; Burguete-García, Ana; García-Martínez, Angélica; López-Carrillo, Lizbeth

    2018-07-01

    Nutrients and genetic polymorphisms participating in one-carbon metabolism may explain interindividual differences in inorganic arsenic (iAs) methylation capacity, which in turn may account for variations in susceptibility to iAs-induced diseases. 1) To evaluate the association between polymorphisms in five one-carbon metabolism genes (FOLH1 c.223 T > C, MTHFD1 c.1958 G > A, MTHFR c.665 C > T, MTR c.2756 A > G, and MTRR c.66 A > G) and iAs methylation capacity; 2) To assess if previously reported associations between nutrient intake and iAs methylation capacity are modified by those polymorphisms. Women (n = 1027) exposed to iAs in Northern Mexico were interviewed. Blood and urine samples were collected. Nutrient dietary intake was estimated using a validated food frequency questionnaire. iAs methylation capacity was calculated from urinary iAs species (iAs, monomethylarsonic acid [MMA] and dimethylarsinic acid [DMA]) measured by high performance liquid chromatography (HPLC-ICP-MS). One polymorphism in each of the five genes evaluated was genotyped by allelic discrimination. Multivariable linear regression models were used to evaluate if genetic polymorphisms modified the associations between iAs methylation capacity parameters and nutrient intake. The median (min-max) concentration of total arsenic (TAs) was 20.2 (1.3-2776.0) µg/g creatinine in the study population. Significant interactions for iAs metabolism were only found with FOLH1 c.223 T > C polymorphism and vitamin B12 intake, so that CT and CC genotype carriers had significantly lower %iAs, and higher DMA/iAs with an increased vitamin B12 intake, as compared to carriers of wild-type TT. Differences in dietary nutrient intake and genetic variants in one-carbon metabolism may jointly influence iAs methylation capacity. Confirmation of these interactions in other populations is warranted. Copyright © 2018 Elsevier Inc. All rights reserved.

  13. Transcriptome-based analysis on carbon metabolism of Haematococcus pluvialis mutant under 15% CO2.

    Science.gov (United States)

    Li, Ke; Cheng, Jun; Lu, Hongxiang; Yang, Weijuan; Zhou, Junhu; Cen, Kefa

    2017-06-01

    To elucidate the mechanism underlying the enhanced growth rate in the Haematococcus pluvialis mutated with 60 Co-γ rays and domesticated with 15% CO 2 , transcriptome sequencing was conducted to clarify the carbon metabolic pathways of mutant cells. The CO 2 fixation rate of mutant cells increased to 2.57gL -1 d -1 under 15% CO 2 due to the enhanced photosynthesis, carbon fixation, glycolysis pathways. The upregulation of PetH, ATPF0A and PetJ related to photosynthetic electron transport, ATP synthase and NADPH generation promoted the photosynthesis. The upregulation of genes related to Calvin cycle and ppdK promoted carbon fixation in both C3 and C4 photosynthetic pathways. The reallocation of carbon was also enhanced under 15% CO 2 . The 19-, 14- and 3.5-fold upregulation of FBA, TPI and PK genes, respectively, remarkably promoted the glycolysis pathways. This accelerated the conversion of photosynthetic carbon to pyruvate, which was an essential precursor for astaxanthin and lipids biosynthesis. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Diminished metabolic responses to centrally-administered apelin-13 in diet-induced obese rats fed a high-fat diet.

    Science.gov (United States)

    Clarke, K J; Whitaker, K W; Reyes, T M

    2009-02-01

    The central administration of apelin, a recently identified adipokine, has been shown to affect food and water intake. The present study investigated whether body weight could affect an animal's response to apelin. The effects of centrally-administered apelin-13 on food and water intake, activity and metabolic rate were investigated in adult male diet-induced obese (DIO) rats fed either a high fat (32%) or control diet. Rats were administered i.c.v. apelin-13, 15-30 min prior to lights out, and food and water intake, activity and metabolic rate were assessed. Intracerebroventricular administration of apelin-13 decreased food and water intake and respiratory exchange ratio in DIO rats on the control diet, but had no effect in DIO rats on the high-fat diet. In an effort to identify potential central mechanisms explaining the observed physiological responses, the mRNA level of the apelin receptor, APJ, was examined in the hypothalamus. A high-fat diet induced an up-regulation of the expression of the receptor. Apelin induced a down-regulation of the receptor, but only in the DIO animals on the high-fat diet. In conclusion, we have demonstrated a diminished central nervous system response to apelin that is coincident with obesity.

  15. Effects of physical characteristics of carbon black on metabolic regulation in mice

    International Nuclear Information System (INIS)

    Chuang, Hsiao-Chi; Hsiao, Ta-Chih; Lee, Chii-Hong; Chun-Te Lin, Justin; Chuang, Kai-Jen; Feng, Po-Hao; Cheng, Tsun-Jen

    2018-01-01

    Potential adverse effects of human exposure to carbon black (CB) have been reported, but limited knowledge regarding CB-regulated metabolism is currently available. To evaluate how physical parameters of CB influence metabolism, we investigated CB and diesel exhaust particles (DEPs) and attempted to relate various physical parameters, including the hydrodynamic diameter, zeta potential, and particle number concentrations, to lung energy metabolism in female BALB/c mice. A body weight increase was arrested by 3 months of exposure to CB of smaller-size fractions, which was negatively correlated with pyruvate in plasma. There were no significant differences in cytotoxic lactate dehydrogenase (LDH) or total protein in bronchoalveolar lavage fluid (BALF) after 3 months of CB exposure. However, we observed alterations in acetyl CoA and the NADP/NADPH ratio in lung tissues with CB exposure. Additionally, the NADP/NADPH ratio was associated with the zeta potential of CB. Mild peribronchiovascular and interstitial inflammation and multinucleated giant cells (macrophages) with a transparent and rhomboid appearance and containing foreign bodies were observed in lung sections. We suggest that physical characteristics of CB, such as the zeta potential, may disrupt metabolism after pulmonary exposure. These results, therefore, provide the first evidence of a link between pulmonary exposure to CB and metabolism. - Highlights: • We evaluated how physical parameters of CB influence metabolism in mice lungs. • Body weight was arrested by exposure to CB in mice. • CB-induced peribronchiovascular and interstitial inflammation in the lungs. • Disruption in functions of acetyl CoA and NADP/NADPH was observed in lungs. • NADP/NADPH ratio was associated with the zeta potentials of CB.

  16. Noninvasive assessment of canine myocardial oxidative metabolism with carbon-11 acetate and positron emission tomography

    International Nuclear Information System (INIS)

    Brown, M.A.; Myears, D.W.; Bergmann, S.R.

    1988-01-01

    Noninvasive quantification of regional myocardial metabolism would be highly desirable to evaluate pathogenetic mechanisms of heart disease and their response to therapy. It was previously demonstrated that the metabolism of radiolabeled acetate, a readily utilized myocardial substrate predominantly metabolized to carbon dioxide (CO2) by way of the tricarboxylic acid cycle, provides a good index of oxidative metabolism in isolated perfused rabbit hearts because of tight coupling between the tricarboxylic acid cycle and oxidative phosphorylation. In the present study, in a prelude to human studies, the relation between myocardial clearance of carbon-11 (11C)-labeled acetate and myocardial oxygen consumption was characterized in eight intact dogs using positron emission tomography. Anesthetized dogs were studied during baseline conditions and again during either high or low work states induced pharmacologically. High myocardial extraction and rapid blood clearance of tracer yielded myocardial images of excellent quality. The turnover (clearance) of 11C radioactivity from the myocardium was biexponential with the mean half-time of the dominant rapid phase averaging 5.4 +/- 2.2, 2.8 +/- 1.3 and 11.1 +/- 1.3 min in control, high and low work load studies, respectively. No significant difference was found between the rate of clearance of 11C radioactivity from the myocardium measured noninvasively with positron emission tomography and the myocardial efflux of 11CO2 measured directly from the coronary sinus. The rate of clearance of the 11C radioactivity from the heart correlated closely with myocardial oxygen consumption (r = 0.90, p less than 0.001) as well as with the rate-pressure product (r = 0.95, p less than 0.001). Hence, the rate of oxidation of 11C-acetate can be determined noninvasively with positron emission tomography, providing a quantitative index of oxidative metabolism under diverse conditions

  17. SulfoSYS (Sulfolobus Systems Biology) : towards a silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation

    NARCIS (Netherlands)

    Albers, Sonja-Verena; Birkeland, Nils-Kare; Driessen, Arnold J. M.; Gertig, Susanne; Haferkamp, Patrick; Klenk, Hans-Peter; Kouril, Theresa; Manica, Andrea; Pham, Trong K.; Ruoff, Peter; Schleper, Christa; Schomburg, Dietmar; Sharkey, Kieran J.; Siebers, Bettina; Sierocinski, Pawel; Steuer, Ralf; van der Oost, John; Westerhoff, Hans V.; Wieloch, Patricia; Wright, Phillip C.; Zaparty, Melanie; Birkeland, Nils-Kåre

    SulfoSYS (Sulfolobus Systems Biology) focuses on the study of the CCM (central carbohydrate metabolism) of Sulfolobus solfataricus and its regulation under temperature variation at the systems level. in Archaea, carbohydrates are metabolized by modifications of the classical pathways known from

  18. SulfoSYS (Sulfolobus Systems Biology): towards a silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation

    NARCIS (Netherlands)

    Albers, S.V.; Birkeland, N.K.; Driessen, A.J.M.; Gertig, S.; Haferkamp, P.; Klenk, H.P.; Kouril, T.; Manica, A.; Pham, T.K.; Ruoff, P.; Schleper, C.; Schomburg, D.; Sharkey, K.; Siebers, B.; Sierocinski, P.; Steur, R.; Oost, van der J.; Westerhoff, H.V.; Wieloch, P.; Wright, P.C.; Zaparty, M.

    2009-01-01

    SulfoSYS (Sulfolobus Systems Biology) focuses on the study of the CCM (central carbohydrate metabolism) of Sulfolobus solfataricus and its regulation under temperature variation at the systems level. In Archaea, carbohydrates are metabolized by modifications of the classical pathways known from

  19. Charge-associated effects of fullerene derivatives on microbialstructural integrity and central metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Yinjie J.; Ashcroft, Jared M.; Chen, Ding; Min, Guangwei; Kim, Chul; Murkhejee, Bipasha; Larabell, Carolyn; Keasling, Jay D.; Chen,Fanqing Frank

    2007-01-23

    The effects of four types of fullerene compounds (C60,C60-OH, C60-COOH, C60-NH2) were examined on two model microorganisms(Escherichia coli W3110 and Shewanella oneidensis MR-1). Positivelycharged C60-NH2 at concentrations as low as 10 mg/L inhibited growth andreduced substrate uptake for both microorganisms. Scanning ElectronMicroscopy (SEM) revealed damage to cellular structures.Neutrally-charged C60 and C60-OH had mild negative effects on S.oneidensis MR-1, whereas the negatively-charged C60-COOH did not affecteither microorganism s growth. The effect of fullerene compounds onglobal metabolism was further investigated using [3-13C]L-lactateisotopic labeling, which tracks perturbations to metabolic reaction ratesin bacteria by examining the change in the isotopic labeling pattern inthe resulting metabolites (often amino acids).1-3 The 13C isotopomeranalysis from all fullerene-exposed cultures revealed no significantdifferences in isotopomer distributions from unstressed cells. Thisresult indicates that microbial central metabolism is robust toenvironmental stress inflicted by fullerene nanoparticles. In addition,although C60-NH2 compounds caused mechanical stress on the cell wall ormembrane, both S. oneidensis MR-1 and E. coli W3110 can efficientlyalleviate such stress by cell aggregation and precipitation of the toxicnanoparticles. The results presented here favor the hypothesis thatfullerenes cause more membrane stress4, 5, 6 than perturbation to energymetabolism7

  20. Bactericidal Antibiotics Induce Toxic Metabolic Perturbations that Lead to Cellular Damage

    Directory of Open Access Journals (Sweden)

    Peter Belenky

    2015-11-01

    Full Text Available Understanding how antibiotics impact bacterial metabolism may provide insight into their mechanisms of action and could lead to enhanced therapeutic methodologies. Here, we profiled the metabolome of Escherichia coli after treatment with three different classes of bactericidal antibiotics (β-lactams, aminoglycosides, quinolones. These treatments induced a similar set of metabolic changes after 30 min that then diverged into more distinct profiles at later time points. The most striking changes corresponded to elevated concentrations of central carbon metabolites, active breakdown of the nucleotide pool, reduced lipid levels, and evidence of an elevated redox state. We examined potential end-target consequences of these metabolic perturbations and found that antibiotic-treated cells exhibited cytotoxic changes indicative of oxidative stress, including higher levels of protein carbonylation, malondialdehyde adducts, nucleotide oxidation, and double-strand DNA breaks. This work shows that bactericidal antibiotics induce a complex set of metabolic changes that are correlated with the buildup of toxic metabolic by-products.

  1. Seagrass metabolism and carbon dynamics in a tropical coastal embayment.

    Science.gov (United States)

    Ganguly, Dipnarayan; Singh, Gurmeet; Ramachandran, Purvaja; Selvam, Arumughan Paneer; Banerjee, Kakolee; Ramachandran, Ramesh

    2017-10-01

    Net ecosystem metabolism and subsequent changes in environmental variables were studied seasonally in the seagrass-dominated Palk Bay, located along the southeast coast of India. The results showed that although the water column was typically net heterotrophic, the ecosystem as a whole displayed autotrophic characteristics. The mean net community production from the seagrass meadows was 99.31 ± 45.13 mM C m -2  d -1 , while the P/R ratio varied between 1.49 and 1.56. Oxygen produced through in situ photosynthesis, exhibited higher dependence over dissolved CO 2 and available light. Apportionment of carbon stores in biomass indicated that nearly three-fourths were available belowground compared to aboveground. However, the sediment horizon accumulated nearly 40 times more carbon than live biomass. The carbon storage capacities of the sediments and seagrass biomass were comparable with the global mean for seagrass meadows. The results of this study highlight the major role of seagrass meadows in modification of seawater chemistry. Though the seagrass meadows of Palk Bay are increasingly subject to human impacts, with coupled regulatory and management efforts focused on improved water quality and habitat conservation, these key coastal ecosystems will continue to be valuable for climate change mitigation, considering their vital role in C dynamics and interactions with the overlying water column.

  2. One-carbon metabolism, cognitive impairment and CSF measures of Alzheimer pathology: homocysteine and beyond.

    Science.gov (United States)

    Dayon, Loïc; Guiraud, Seu Ping; Corthésy, John; Da Silva, Laeticia; Migliavacca, Eugenia; Tautvydaitė, Domilė; Oikonomidi, Aikaterini; Moullet, Barbara; Henry, Hugues; Métairon, Sylviane; Marquis, Julien; Descombes, Patrick; Collino, Sebastiano; Martin, François-Pierre J; Montoliu, Ivan; Kussmann, Martin; Wojcik, Jérôme; Bowman, Gene L; Popp, Julius

    2017-06-17

    Hyperhomocysteinemia is a risk factor for cognitive decline and dementia, including Alzheimer disease (AD). Homocysteine (Hcy) is a sulfur-containing amino acid and metabolite of the methionine pathway. The interrelated methionine, purine, and thymidylate cycles constitute the one-carbon metabolism that plays a critical role in the synthesis of DNA, neurotransmitters, phospholipids, and myelin. In this study, we tested the hypothesis that one-carbon metabolites beyond Hcy are relevant to cognitive function and cerebrospinal fluid (CSF) measures of AD pathology in older adults. Cross-sectional analysis was performed on matched CSF and plasma collected from 120 older community-dwelling adults with (n = 72) or without (n = 48) cognitive impairment. Liquid chromatography-mass spectrometry was performed to quantify one-carbon metabolites and their cofactors. Least absolute shrinkage and selection operator (LASSO) regression was initially applied to clinical and biomarker measures that generate the highest diagnostic accuracy of a priori-defined cognitive impairment (Clinical Dementia Rating-based) and AD pathology (i.e., CSF tau phosphorylated at threonine 181 [p-tau181]/β-Amyloid 1-42 peptide chain [Aβ 1-42 ] >0.0779) to establish a reference benchmark. Two other LASSO-determined models were generated that included the one-carbon metabolites in CSF and then plasma. Correlations of CSF and plasma one-carbon metabolites with CSF amyloid and tau were explored. LASSO-determined models were stratified by apolipoprotein E (APOE) ε4 carrier status. The diagnostic accuracy of cognitive impairment for the reference model was 80.8% and included age, years of education, Aβ 1-42 , tau, and p-tau181. A model including CSF cystathionine, methionine, S-adenosyl-L-homocysteine (SAH), S-adenosylmethionine (SAM), serine, cysteine, and 5-methyltetrahydrofolate (5-MTHF) improved the diagnostic accuracy to 87.4%. A second model derived from plasma included cystathionine

  3. Understanding the interplay of carbon and nitrogen supply for ectoines production and metabolic overflow in high density cultures of Chromohalobacter salexigens.

    Science.gov (United States)

    Salar-García, María J; Bernal, Vicente; Pastor, José M; Salvador, Manuel; Argandoña, Montserrat; Nieto, Joaquín J; Vargas, Carmen; Cánovas, Manuel

    2017-02-08

    The halophilic bacterium Chromohalobacter salexigens has been proposed as promising cell factory for the production of the compatible solutes ectoine and hydroxyectoine. This bacterium has evolved metabolic adaptations to efficiently grow under high salt concentrations by accumulating ectoines as compatible solutes. However, metabolic overflow, which is a major drawback for the efficient conversion of biological feedstocks, occurs as a result of metabolic unbalances during growth and ectoines production. Optimal production of ectoines is conditioned by the interplay of carbon and nitrogen metabolisms. In this work, we set out to determine how nitrogen supply affects the production of ectoines. Chromohalobacter salexigens was challenged to grow in media with unbalanced carbon/nitrogen ratio. In C. salexigens, overflow metabolism and ectoines production are a function of medium composition. At low ammonium conditions, the growth rate decreased importantly, up to 80%. Shifts in overflow metabolism were observed when changing the C/N ratio in the culture medium. 13 C-NMR analysis of ectoines labelling revealed a high metabolic rigidity, with almost constant flux ratios in all conditions assayed. Unbalanced C/N ratio led to pyruvate accumulation, especially upon N-limitation. Analysis of an ect - mutant demonstrated the link between metabolic overflow and ectoine biosynthesis. Under non ectoine synthesizing conditions, glucose uptake and metabolic overflow decreased importantly. Finally, in fed-batch cultures, biomass yield was affected by the feeding scheme chosen. High growth (up to 42.4 g L -1 ) and volumetric ectoine yields (up to 4.21 g L -1 ) were obtained by minimizing metabolite overflow and nutrient accumulation in high density cultures in a low nitrogen fed-batch culture. Moreover, the yield coefficient calculated for the transformation of glucose into biomass was 30% higher in fed-batch than in the batch culture, demonstrating that the metabolic

  4. Robust metabolic responses to varied carbon sources in natural and laboratory strains of Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Wayne A Van Voorhies

    Full Text Available Understanding factors that regulate the metabolism and growth of an organism is of fundamental biologic interest. This study compared the influence of two different carbon substrates, dextrose and galactose, on the metabolic and growth rates of the yeast Saccharomyces cerevisiae. Yeast metabolic and growth rates varied widely depending on the metabolic substrate supplied. The metabolic and growth rates of a yeast strain maintained under long-term laboratory conditions was compared to strain isolated from natural condition when grown on different substrates. Previous studies had determined that there are numerous genetic differences between these two strains. However, the overall metabolic and growth rates of a wild isolate of yeast was very similar to that of a strain that had been maintained under laboratory conditions for many decades. This indicates that, at in least this case, metabolism and growth appear to be well buffered against genetic differences. Metabolic rate and cell number did not co-vary in a simple linear manner. When grown in either dextrose or galactose, both strains showed a growth pattern in which the number of cells continued to increase well after the metabolic rate began a sharp decline. Previous studied have reported that O₂ consumption in S. cerevisiae grown in reduced dextrose levels were elevated compared to higher levels. Low dextrose levels have been proposed to induce caloric restriction and increase life span in yeast. However, there was no evidence that reduced levels of dextrose increased metabolic rates, measured by either O₂ consumption or CO₂ production, in the strains used in this study.

  5. Metabolic Pathways Involved in Carbon Dioxide Enhanced Heat Tolerance in Bermudagrass

    Directory of Open Access Journals (Sweden)

    Jingjin Yu

    2017-09-01

    Full Text Available Global climate changes involve elevated temperature and CO2 concentration, imposing significant impact on plant growth of various plant species. Elevated temperature exacerbates heat damages, but elevated CO2 has positive effects on promoting plant growth and heat tolerance. The objective of this study was to identify metabolic pathways affected by elevated CO2 conferring the improvement of heat tolerance in a C4 perennial grass species, bermudagrass (Cynodon dactylon Pers.. Plants were planted under either ambient CO2 concentration (400 μmol⋅mol-1 or elevated CO2 concentration (800 μmol⋅mol-1 and subjected to ambient temperature (30/25°C, day/night or heat stress (45/40°C, day/night. Elevated CO2 concentration suppressed heat-induced damages and improved heat tolerance in bermudagrass. The enhanced heat tolerance under elevated CO2 was attributed to some important metabolic pathways during which proteins and metabolites were up-regulated, including light reaction (ATP synthase subunit and photosystem I reaction center subunit and carbon fixation [(glyceraldehyde-3-phosphate dehydrogenase, GAPDH, fructose-bisphosphate aldolase, phosphoglycerate kinase, sedoheptulose-1,7-bisphosphatase and sugars of photosynthesis, glycolysis (GAPDH, glucose, fructose, and galactose and TCA cycle (pyruvic acid, malic acid and malate dehydrogenase of respiration, amino acid metabolism (aspartic acid, methionine, threonine, isoleucine, lysine, valine, alanine, and isoleucine as well as the GABA shunt (GABA, glutamic acid, alanine, proline and 5-oxoproline. The up-regulation of those metabolic processes by elevated CO2 could at least partially contribute to the improvement of heat tolerance in perennial grass species.

  6. Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max Embryos

    Directory of Open Access Journals (Sweden)

    Ruth Grene

    2013-05-01

    Full Text Available Soybean (Glycine max seeds are an important source of seed storage compounds, including protein, oil, and sugar used for food, feed, chemical, and biofuel production. We assessed detailed temporal transcriptional and metabolic changes in developing soybean embryos to gain a systems biology view of developmental and metabolic changes and to identify potential targets for metabolic engineering. Two major developmental and metabolic transitions were captured enabling identification of potential metabolic engineering targets specific to seed filling and to desiccation. The first transition involved a switch between different types of metabolism in dividing and elongating cells. The second transition involved the onset of maturation and desiccation tolerance during seed filling and a switch from photoheterotrophic to heterotrophic metabolism. Clustering analyses of metabolite and transcript data revealed clusters of functionally related metabolites and transcripts active in these different developmental and metabolic programs. The gene clusters provide a resource to generate predictions about the associations and interactions of unknown regulators with their targets based on “guilt-by-association” relationships. The inferred regulators also represent potential targets for future metabolic engineering of relevant pathways and steps in central carbon and nitrogen metabolism in soybean embryos and drought and desiccation tolerance in plants.

  7. Reconnaissance survey for lightweight and carbon tetrachloride extractable hydrocarbons in the central and eastern basins of Lake Erie: September 1978

    Energy Technology Data Exchange (ETDEWEB)

    Zapotosky, J.E.; White, W.S.

    1980-10-01

    A reconnaissance survey of the central and eastern basins of Lake Erie (22,240 km/sup 2/) was conducted from September 17 to 27, 1978. The survey provided baseline information on natural gas and oil losses from geologic formations, prior to any potential development of natural gas resources beneath the United States portion of the Lake. Lightweight hydrocarbons indicative of natural gas (methane, ethane, propane, isobutane, and n-butane) are introduced into the waters of Lake Erie by escape from geologic formations and by biological/photochemical processes. The geochemical exploration technique of hydrocarbon sniffing provided enough data to reveal significant distribution patterns, approximate concentrations, and potential sources. Twelve sites with elevated lightweight hydrocarbon concentrations had a composition similar to natural gas. In one area of natural gas input, data analysis suggested a potential negative effect of natural gas on phytoplanktonic metabolism (i.e., ethylene concentration). Samples taken for liquid hydrocarbon analysis (carbon tetrachloride extractable hydrocarbons) correlated best with biologically derived lightweight hydrocarbons.

  8. A DIGE analysis of developing poplar leaves subjected to ozone reveals major changes in carbon metabolism.

    Science.gov (United States)

    Bohler, Sacha; Bagard, Matthieu; Oufir, Mouhssin; Planchon, Sébastien; Hoffmann, Lucien; Jolivet, Yves; Hausman, Jean-François; Dizengremel, Pierre; Renaut, Jenny

    2007-05-01

    Tropospheric ozone pollution is described as having major negative effects on plants, compromising plant survival. Carbon metabolism is especially affected. In the present work, the effects of chronic ozone exposure were evaluated at the proteomic level in developing leaves of young poplar plants exposed to 120 ppb of ozone for 35 days. Soluble proteins (excluding intrinsic membrane proteins) were extracted from leaves after 3, 14 and 35 days of ozone exposure, as well as 10 days after a recovery period. Proteins (pI 4 to 7) were analyzed by 2-D DIGE experiments, followed by MALDI-TOF-TOF identification. Additional observations were obtained on growth, lesion formation, and leaf pigments analysis. Although treated plants showed large necrotic spots and chlorosis in mature leaves, growth decreased only slightly and plant height was not affected. The number of abscised leaves was higher in treated plants, but new leaf formation was not affected. A decrease in chlorophylls and lutein contents was recorded. A large number of proteins involved in carbon metabolism were identified. In particular, proteins associated with the Calvin cycle and electron transport in the chloroplast were down-regulated. In contrast, proteins associated with glucose catabolism increased in response to ozone exposure. Other identified enzymes are associated with protein folding, nitrogen metabolism and oxidoreductase activity.

  9. Cyanobacterial carbon metabolism: Fluxome plasticity and oxygen dependence: Cyanobacterial Carbon Metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Wan, Ni [Washington Univ., St. Louis, MO (United States); DeLorenzo, Drew M. [Washington Univ., St. Louis, MO (United States); He, Lian [Washington Univ., St. Louis, MO (United States); You, Le [Washington Univ., St. Louis, MO (United States); Immethun, Cheryl M. [Washington Univ., St. Louis, MO (United States); Wang, George [Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Baidoo, Edward E. K. [Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Hollinshead, Whitney [Washington Univ., St. Louis, MO (United States); Keasling, Jay D. [Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States); Technical Univ. of Denmark, Lyngby (Denmark); Moon, Tae Seok [Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis Missouri 63130; Tang, Yinjie J. [Washington Univ., St. Louis, MO (United States)

    2017-03-30

    Synechocystis sp. strain PCC 6803 has been widely used as a photo-biorefinery chassis. Based on its genome annotation, this species contains a complete TCA cycle, an Embden-Meyerhof-Parnas pathway (EMPP), an oxidative pentose phosphate pathway (OPPP), and an Entner–Doudoroff pathway (EDP). To evaluate how Synechocystis 6803 catabolizes glucose under heterotrophic conditions, we performed 13C metabolic flux analysis, metabolite pool size analysis, gene knockouts, and heterologous expressions. The results revealed a cyclic mode of flux through the OPPP. Small, but non-zero, fluxes were observed through the TCA cycle and the malic shunt. Independent knockouts of 6-phosphogluconate dehydrogenase (gnd) and malic enzyme (me) corroborated these results, as neither mutant could grow under dark heterotrophic conditions. Our data also indicate that Synechocystis 6803 metabolism relies upon oxidative phosphorylation to generate ATP from NADPH under dark or insufficient light conditions. The pool sizes of intermediates in the TCA cycle, particularly acetyl-CoA, were found to be several fold lower in Synechocystis 6803 (compared to E. coli metabolite pool sizes), while its sugar phosphate intermediates were several-fold higher. Moreover, negligible flux was detected through the native, or heterologous, EDP in the wild type or Δgnd strains under heterotrophic conditions. Comparing photoautotrophic, photomixotrophic, and heterotrophic conditions, the Calvin cycle, OPPP, and EMPP in Synechocystis 6803 possess the ability to regulate their fluxes under various growth conditions (plastic), whereas its TCA cycle always maintains at low levels (rigid). This work also demonstrates how genetic profiles do not always reflect actual metabolic flux through native or heterologous pathways. Biotechnol. Bioeng. 2017;114: 1593–1602. © 2017 Wiley Periodicals, Inc.

  10. The investment in scent: time-resolved metabolic processes in developing volatile-producing Nigella sativa L. seeds.

    Directory of Open Access Journals (Sweden)

    Wentao Xue

    Full Text Available The interplay of processes in central and specialized metabolisms during seed development of Nigella sativa L. was studied by using a high-throughput metabolomics technology and network-based analysis. Two major metabolic shifts were identified during seed development: the first was characterized by the accumulation of storage lipids (estimated as total fatty acids and N-compounds, and the second by the biosynthesis of volatile organic compounds (VOCs and a 30% average decrease in total fatty acids. Network-based analysis identified coordinated metabolic processes during development and demonstrated the presence of five network communities. Enrichment analysis indicated that different compound classes, such as sugars, amino acids, and fatty acids, are largely separated and over-represented in certain communities. One community displayed several terpenoids and the central metabolites, shikimate derived amino acids, raffinose, xylitol and glycerol-3-phosphate. The latter are related to precursors of the mevalonate-independent pathway for VOC production in the plastid; also plastidial fatty acid 18∶3n-3 abundant in "green" seeds grouped with several major terpenes. The findings highlight the interplay between the components of central metabolism and the VOCs. The developmental regulation of Nigella seed metabolism during seed maturation suggests a substantial re-allocation of carbon from the breakdown of fatty acids and from N-compounds, probably towards the biosynthesis of VOCs.

  11. Central nervous system control of triglyceride metabolism

    NARCIS (Netherlands)

    Geerling, Johanna Janetta (Janine)

    2013-01-01

    This thesis describes the role of the brain in the regulation of peripheral triglyceride metabolism, in the context of the metabolic syndrome. Based on various pharmacological studies we described the role of two hormones, insulin and glucagon-like peptide-1, in the production and clearance of

  12. Krüppel-like factor 15: Regulator of BCAA metabolism and circadian protein rhythmicity.

    Science.gov (United States)

    Fan, Liyan; Hsieh, Paishiun N; Sweet, David R; Jain, Mukesh K

    2018-04-01

    Regulation of nutrient intake, utilization, and storage exhibits a circadian rhythmicity that allows organisms to anticipate and adequately respond to changes in the environment across day/night cycles. The branched-chain amino acids (BCAAs) leucine, isoleucine, and valine are important modulators of metabolism and metabolic health - for example, their catabolism yields carbon substrates for gluconeogenesis during periods of fasting. Krüppel-like factor 15 (KLF15) has recently emerged as a critical transcriptional regulator of BCAA metabolism, and the absence of this transcription factor contributes to severe pathologies such as Duchenne muscular dystrophy and heart failure. This review highlights KLF15's role as a central regulator of BCAA metabolism during periods of fasting, throughout day/night cycles, and in experimental models of muscle disease. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Reductive glutamine metabolism by IDH1 mediates lipogenesis under hypoxia

    Science.gov (United States)

    Metallo, Christian M.; Gameiro, Paulo A.; Bell, Eric L.; Mattaini, Katherine R.; Yang, Juanjuan; Hiller, Karsten; Jewell, Christopher M.; Johnson, Zachary R.; Irvine, Darrell J.; Guarente, Leonard; Kelleher, Joanne K.; Vander Heiden, Matthew G.; Iliopoulos, Othon; Stephanopoulos, Gregory

    2013-01-01

    Acetyl coenzyme A (AcCoA) is the central biosynthetic precursor for fatty acid synthesis and protein acetylation. In the conventional view of mammalian cell metabolism, AcCoA is primarily generated from glucose-derived pyruvate through the citrate shuttle and adenosine triphosphate citrate lyase (ACL) in the cytosol1-3. However, proliferating cells that exhibit aerobic glycolysis and those exposed to hypoxia convert glucose to lactate at near stoichiometric levels, directing glucose carbon away from the tricarboxylic acid cycle (TCA) and fatty acid synthesis4. Although glutamine is consumed at levels exceeding that required for nitrogen biosynthesis5, the regulation and utilization of glutamine metabolism in hypoxic cells is not well understood. Here we show that human cells employ reductive metabolism of alpha-ketoglutarate (αKG) to synthesize AcCoA for lipid synthesis. This isocitrate dehydrogenase 1 (IDH1) dependent pathway is active in most cell lines under normal culture conditions, but cells grown under hypoxia rely almost exclusively on the reductive carboxylation of glutamine-derived αKG for de novo lipogenesis. Furthermore, renal cell lines deficient in the von Hippel-Lindau (VHL) tumor suppressor protein preferentially utilize reductive glutamine metabolism for lipid biosynthesis even at normal oxygen levels. These results identify a critical role for oxygen in regulating carbon utilization in order to produce AcCoA and support lipid synthesis in mammalian cells. PMID:22101433

  14. Carbon Disulfide (CS2) Interference in Glucose Metabolism from Unconventional Oil and Gas Extraction and Processing Emissions.

    Science.gov (United States)

    Rich, Alisa L; Patel, Jay T; Al-Angari, Samiah S

    2016-01-01

    Carbon disulfide (CS2) has been historically associated with the manufacturing of rayon, cellophane, and carbon tetrachloride production. This study is one of the first to identify elevated atmospheric levels of CS2 above national background levels and its mechanisms to dysregulate normal glucose metabolism. Interference in glucose metabolism can indirectly cause other complications (diabetes, neurodegenerative disease, and retinopathy), which may be preventable if proper precautions are taken. Rich et al found CS2 and 12 associated sulfide compounds present in the atmosphere in residential areas where unconventional shale oil and gas extraction and processing operations were occurring. Ambient atmospheric concentrations of CS2 ranged from 0.7 parts per billion by volume (ppbv) to 103 ppbv over a continuous 24-hour monitoring period. One-hour ambient atmospheric concentrations ranged from 3.4 ppbv to 504.6 ppbv. Using the U.S. Environmental Protection Agency Urban Air Toxic Monitoring Program study as a baseline comparison for atmospheric CS2 concentrations found in this study, it was determined that CS2 atmospheric levels were consistently elevated in areas where unconventional oil and gas extraction and processing occurred. The mechanisms by which CS2 interferes in normal glucose metabolism by dysregulation of the tryptophan metabolism pathway are presented in this study. The literature review found an increased potential for alteration of normal glucose metabolism in viscose rayon occupational workers exposed to CS2. Occupational workers in the energy extraction industry exposed to CS2 and other sulfide compounds may have an increased potential for glucose metabolism interference, which has been an indicator for diabetogenic effect and other related health impacts. The recommendation of this study is for implementation of regular monitoring of blood glucose levels in CS2-exposed populations as a preventative health measure.

  15. A simple method for measuring fungal metabolic quotient and comparing carbon use efficiency of different isolates: Application to Mediterranean leaf litter fungi

    NARCIS (Netherlands)

    Pinzari, F.; Maggi, O.; Lunghini, D.; Di Lonardo, Paolo; Persiani, A. M.

    2017-01-01

    AbstractThe metabolic efficiency of different microbial groups in carbon source uses and single species storage efficiency is poorly characterised and not adequately represented in most biogeochemical models. It is proposed here a simple approach for an estimation of the metabolic quotient of fungal

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

    Science.gov (United States)

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

    2013-01-01

    The importance of hypothalamic insulin action to the regulation of hepatic glucose metabolism in the presence of a normal liver/brain insulin ratio (3:1) is unknown. Thus, we assessed the role of central insulin action in the response of the liver to normal physiologic hyperinsulinemia over 4 h. Using a pancreatic clamp, hepatic portal vein insulin delivery was increased three- or eightfold in the conscious dog. Insulin action was studied in the presence or absence of intracerebroventricularly mediated blockade of hypothalamic insulin action. Euglycemia was maintained, and glucagon was clamped at basal. Both the molecular and metabolic aspects of insulin action were assessed. Blockade of hypothalamic insulin signaling did not alter the insulin-mediated suppression of hepatic gluconeogenic gene transcription but blunted the induction of glucokinase gene transcription and completely blocked the inhibition of glycogen synthase kinase-3β gene transcription. Thus, central and peripheral insulin action combined to control some, but not other, hepatic enzyme programs. Nevertheless, inhibition of hypothalamic insulin action did not alter the effects of the hormone on hepatic glucose flux (production or uptake). These data indicate that brain insulin action is not a determinant of the rapid (<4 h) inhibition of hepatic glucose metabolism caused by normal physiologic hyperinsulinemia in this large animal model. PMID:23011594

  17. Prognosis of breast cancer is associated with one-carbon metabolism related nutrients among Korean women

    Directory of Open Access Journals (Sweden)

    Lee Yunhee

    2012-08-01

    Full Text Available Abstract Background The 5-year survival rate for breast cancer among Korean women has increased steadily; however, breast cancer remains the leading cause of cancer mortality among women. One-carbon metabolism, which requires an adequate supply of methyl group donors and B vitamins, may affect the prognosis of breast cancer. This aim of this study was to investigate the associations of dietary intake of vitamin B2, vitamin B6 and folate before diagnosis on the prognosis of breast cancer. Methods We assessed the dietary intake using a food frequency questionnaire with 980 women who were newly diagnosed and histopathologically confirmed to have primary breast cancer from hospitals in Korea, and 141 disease progression events occurred. Cox’s proportional hazard regression models were used to estimate the hazard ratio (HR and 95% confidence interval (95% CI adjusting for age, education, recruitment sites, TNM stage, hormone status, nuclear grade and total calorie. Results There was no significant association between any one-carbon metabolism related nutrients (vitamin B2, B6 and folate and the progression of breast cancer overall. However, one-carbon metabolism related nutrients were associated with disease progression in breast cancer patients stratified by subtypes. In ER + and/or PR + breast cancers, no association was observed; however, in ER–/PR– breast cancers, a high intake of vitamin B2 and folate statistically elevated the HR of breast cancer progression (HR = 2.28; 95% CI, 1.20-4.35, HR = 1.84; 95% CI, 1.02-3.32, respectively compared to a low intake. This positive association between the ER/PR status and progression of the disease was profound when the nutrient intakes were categorized in a combined score (Pinteraction = 0.018. In ER–/PR– breast cancers, high combined scores were associated with a significantly poor DFS compared to those belonging to the low score group (HR = 3.84; 95% CI, 1

  18. Increased iron availability resulting from increased CO2 enhances carbon and nitrogen metabolism in the economical marine red macroalga Pyropia haitanensis (Rhodophyta).

    Science.gov (United States)

    Chen, Binbin; Zou, Dinghui; Yang, Yufeng

    2017-04-01

    Ocean acidification caused by rising CO 2 is predicted to increase the concentrations of dissolved species of Fe(II) and Fe(III), leading to the enhanced photosynthetic carbon sequestration in some algal species. In this study, the carbon and nitrogen metabolism in responses to increased iron availability under two CO 2 levels (390 μL L -1 and 1000 μL L -1 ), were investigated in the maricultivated macroalga Pyropia haitanensis (Rhodophyta). The results showed that, elevated CO 2 increased soluble carbonhydrate (SC) contents, resulting from enhanced photosynthesis and photosynthetic pigment synthesis in this algae, but declined its soluble protein (SP) contents, resulting in increased ratio of SC/SP. This enhanced photosynthesis performance and carbon accumulation was more significant under iron enrichment condition in seawater, with higher iron uptake rate at high CO 2 level. As a key essential biogenic element for algae, Fe-replete functionally contributed to P. haitanensis photosynthesis. Increased SC fundamentally provided carbon skeletons for nitrogen assimilation. The significant increase of carbon and nitrogen assimilation finally contributed to enhanced growth in this alga. This was also intuitively reflected by respiration that provided energy for cellular metabolism and algal growth. We propose that, in the predicted scenario of rising atmospheric CO 2 , P. haitanensis is capable to adjust its physiology by increasing its carbon and nitrogen metabolism to acclimate the acidified seawater, at the background of global climate change and simultaneously increased iron concentration due to decreased pH levels. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Central Carbon Metabolic Pathways in Streptomyces

    NARCIS (Netherlands)

    van Keulen, Geertje; Siebring, Jeroen; Dijkhuizen, Lubbert; Dyson, Paul

    Streptomyces and other actinomycetes are fascinating soil bacteria of major economic importance. They produce 70% of antibiotics known to man and numerous other pharmaceuticals for treatment of, e.g. cancer, a range of infections, high cholesterol, or have immunosuppressive activity. It is not

  20. Imaging of karsts on buried carbonate platform in Central Luconia Province, Malaysia

    Science.gov (United States)

    Nur Fathiyah Jamaludin, Siti; Mubin, Mukhriz; Latiff, Abdul Halim Abdul

    2017-10-01

    Imaging of carbonate rocks in the subsurface through seismic method is always challenging due to its heterogeneity and fast velocity compared to the other rock types. Existence of karsts features on the carbonate rocks make it more complicated to interpret the reflectors. Utilization of modern interpretation software such as PETREL and GeoTeric® to image the karsts morphology make it possible to model the karst network within the buried carbonate platform used in this study. Using combination of different seismic attributes such as Variance, Conformance, Continuity, Amplitude, Frequency and Edge attributes, we are able to image the karsts features that are available in the proven gas-field in Central Luconia Province, Malaysia. The mentioned attributes are excellent in visualize and image the stratigraphic features based on the difference in their acoustic impedance as well as structural features, which include karst. 2D & 3D Karst Models were developed to give a better understanding on the characteristics of the identified karsts. From the models, it is found that the karsts are concentrated in the top part of the carbonate reservoir (epikarst) and the middle layer with some of them becomes extensive and create karst networks, either laterally or vertically. Most of the vertical network karst are related to the existence of faults that displaced all the horizons in the carbonate platform.

  1. Genome-wide meta-analysis of homocysteine and methionine metabolism identifies five one carbon metabolism loci and a novel association of ALDH1L1 with ischemic stroke

    Science.gov (United States)

    Circulating homocysteine levels (tHcy), a product of the folate one carbon metabolism pathway (FOCM) through the demethylation of methionine, are heritable and are associated with an increased risk of common diseases such as stroke, cardiovascular disease (CVD), cancer and dementia. The FOCM is the ...

  2. Central Asian supra-glacier snow melt enhanced by anthropogenic black carbon

    Science.gov (United States)

    Schmale, Julia; Flanner, Mark; Kang, Shichang; Sprenger, Michael; Farinotti, Daniel; Zhang, Qianggong; Guo, Junming; Li, Yang; Lawrence, Mark; Schwikowski, Margit

    2016-04-01

    In Central Asia, more than 60 % of the population depends on water stored in glaciers and mountain snow. Densely populated areas near lower-lying mountain ranges are particularly vulnerable and a recent study showed that the region might lose 50 % of its glacier mass by 2050. While temperature, precipitation and dynamic processes are key drivers of glacial change, deposition of light absorbing impurities such as mineral dust and black carbon can lead to accelerated melting through surface albedo reduction. Here, we discuss the origin of deposited mineral dust and black carbon and their impacts on albedo change and snow melt. 218 snow samples were taken on 4 glaciers, Abramov (Pamir), Suek, Glacier No. 354 and Golubin (Tien Shan), representing deposition between summer 2012 and 2014. They were analyzed for elemental carbon, mineral dust and iron among other parameters. We find the elemental carbon concentration to be at the higher end of the range reported for neighboring mountain ranges between 70 and 502 ng g-1 (interquartile range). To investigate the origin of the snow impurities, we used a Lagrangian particle dispersion model, LAGRANTO. Back trajectory ensembles of 40 members with varied starting points to capture the meteorological spread were released every 6 hours for the covered period at all sites. "Footprints" were calculated and combined with emission inventories to estimate the relative contribution of anthropogenic and natural BC to deposited aerosol on the glaciers. We find that more than 94 % of BC is of anthropogenic origin and the major source region is Central Asia followed by the Middle East. Further exploring the implications of mineral dust and BC deposition, we calculate the snow albedo reduction with the Snow-Ice-Aerosol-Radiative model (SNICAR). Even though mineral dust concentrations were up to a factor of 50 higher than BC concentrations, BC dominates the albedo reduction. Using these results we calculate the snow melt induced by

  3. Enhanced photosynthetic capacity increases nitrogen metabolism through the coordinated regulation of carbon and nitrogen assimilation in Arabidopsis thaliana.

    Science.gov (United States)

    Otori, Kumi; Tanabe, Noriaki; Maruyama, Toshiki; Sato, Shigeru; Yanagisawa, Shuichi; Tamoi, Masahiro; Shigeoka, Shigeru

    2017-09-01

    Plant growth and productivity depend on interactions between the metabolism of carbon and nitrogen. The sensing ability of internal carbon and nitrogen metabolites (the C/N balance) enables plants to regulate metabolism and development. In order to investigate the effects of an enhanced photosynthetic capacity on the metabolism of carbon and nitrogen in photosynthetically active tissus (source leaves), we herein generated transgenic Arabidopsis thaliana plants (ApFS) that expressed cyanobacterial fructose-1,6-/sedoheptulose-1,7-bisphosphatase in their chloroplasts. The phenotype of ApFS plants was indistinguishable from that of wild-type plants at the immature stage. However, as plants matured, the growth of ApFS plants was superior to that of wild-type plants. Starch levels were higher in ApFS plants than in wild-type plants at 2 and 5 weeks. Sucrose levels were also higher in ApFS plants than in wild-type plants, but only at 5 weeks. On the other hand, the contents of various free amino acids were lower in ApFS plants than in wild-type plants at 2 weeks, but were similar at 5 weeks. The total C/N ratio was the same in ApFS plants and wild-type plants, whereas nitrite levels increased in parallel with elevations in nitrate reductase activity at 5 weeks in ApFS plants. These results suggest that increases in the contents of photosynthetic intermediates at the early growth stage caused a temporary imbalance in the free-C/free-N ratio and, thus, the feedback inhibition of the expression of genes involved in the Calvin cycle and induction of the expression of those involved in nitrogen metabolism due to supply deficient free amino acids for maintenance of the C/N balance in source leaves of ApFS plants.

  4. Tumor microenvironment derived exosomes pleiotropically modulate cancer cell metabolism.

    Science.gov (United States)

    Zhao, Hongyun; Yang, Lifeng; Baddour, Joelle; Achreja, Abhinav; Bernard, Vincent; Moss, Tyler; Marini, Juan C; Tudawe, Thavisha; Seviour, Elena G; San Lucas, F Anthony; Alvarez, Hector; Gupta, Sonal; Maiti, Sourindra N; Cooper, Laurence; Peehl, Donna; Ram, Prahlad T; Maitra, Anirban; Nagrath, Deepak

    2016-02-27

    Cancer-associated fibroblasts (CAFs) are a major cellular component of tumor microenvironment in most solid cancers. Altered cellular metabolism is a hallmark of cancer, and much of the published literature has focused on neoplastic cell-autonomous processes for these adaptations. We demonstrate that exosomes secreted by patient-derived CAFs can strikingly reprogram the metabolic machinery following their uptake by cancer cells. We find that CAF-derived exosomes (CDEs) inhibit mitochondrial oxidative phosphorylation, thereby increasing glycolysis and glutamine-dependent reductive carboxylation in cancer cells. Through 13C-labeled isotope labeling experiments we elucidate that exosomes supply amino acids to nutrient-deprived cancer cells in a mechanism similar to macropinocytosis, albeit without the previously described dependence on oncogenic-Kras signaling. Using intra-exosomal metabolomics, we provide compelling evidence that CDEs contain intact metabolites, including amino acids, lipids, and TCA-cycle intermediates that are avidly utilized by cancer cells for central carbon metabolism and promoting tumor growth under nutrient deprivation or nutrient stressed conditions.

  5. A deuterium and carbon nuclear magnetic resonance spectroscopic investigation of blood flow and carbohydrate metabolism

    International Nuclear Information System (INIS)

    Bosch, C.S.E.

    1988-01-01

    The purpose of this study is the development and application of nuclear magnetic resonance (NMR) spectroscopic techniques for this study of whole tissue metabolism, tissue perfusion and blood flow. The feasibility of spin imaging deuterium-enriched tissue water is demonstrated in cat brain in vivo and in situ. The potential application of D 2 O administration to deuterium-flow-imaging is considered. NMR investigations of hepatic carbohydrate metabolism were performed in rat liver in vivo and in situ. A coaxial, double-surface-coil, double-resonance probe was developed for carbon detection while decoupling neighboring proton scalar interactions ( 13 C-[ 1 H]) in hepatic tissue within the living animal. Hormonal and substrate regulation of hepatic glucose and glycogen metabolism was investigated by monitoring the metabolic fate of an administered c-dose of [1- 13 C]glucose. Label flux was directed primarily into newly-synthesized 13 C-labeled glycogen. A multiple resonance ( 1 H, 13 C, 31 P) liver perfusion probe was designed for complimentary carbohydrate metabolic studies in rat liver in vitro. A description of the 13 C-[ 1 H]/ 31 P NMR perfusion probe is given. The surgical technique used for liver excision and peripheral life-support apparatus required to maintain hepatic function are also detailed

  6. Effects of Pheretima Guillelmi Cultivation Time on Microbial Community Diversity and Characteristics of Carbon Metabolism in Vegetable Soil

    Directory of Open Access Journals (Sweden)

    ZHENG Xian-qing

    2015-12-01

    Full Text Available In order to study the effect of different biological tillage time (Pheretima guillelmi on soil microbial community metabolic functions in different soil depths, we set a location test in vegetable field at Chongming Island in Shanghai to analyze the changes of soil microbial community and carbon utilization abilities (Average well- color development, AWCD by using biolog eco-plate method. The three-year results showed that: Bio-tillage significantly improved microbial community activity, and with the increase of tillage years, biological tillage could make the average AWCD 3 to 7 times higher. The Simpson index and Shannon index of the biological tillage treatments were significantly higher than that of the control. The cumulative increase of 0~5 cm soil layer was 49 and 6.28 respectively, and the cumulative increase of 5~20 cm soil layer was 31 and 2.55 respectively. Earthworm bio-tillage significantly increased the soil microbial metabolic ability of 6 kinds of carbon sources, and increased the carbohydrate metabolism activity. In this study, earthworm bio-tillage is an effective way to increase the microbial activity of microbial soil.

  7. Endothelial dysfunction in normal and prediabetic rats with metabolic syndrome exposed by oral gavage to carbon black nanoparticles

    DEFF Research Database (Denmark)

    Folkmann, Janne Kjærsgaard; Vesterdal, Lise Kristine; Sheykhzade, Majid

    2012-01-01

    Exposure to nanosized particles may increase the risk of cardiovascular diseases by endothelial dysfunction, particularly in susceptible subjects with metabolic syndrome. We investigated vasomotor dysfunction in aorta from obese and lean Zucker rats after oral exposure to nanosized carbon black (...

  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. Alzheimer-associated Aβ oligomers impact the central nervous system to induce peripheral metabolic deregulation

    Science.gov (United States)

    Clarke, Julia R; Lyra e Silva, Natalia M; Figueiredo, Claudia P; Frozza, Rudimar L; Ledo, Jose H; Beckman, Danielle; Katashima, Carlos K; Razolli, Daniela; Carvalho, Bruno M; Frazão, Renata; Silveira, Marina A; Ribeiro, Felipe C; Bomfim, Theresa R; Neves, Fernanda S; Klein, William L; Medeiros, Rodrigo; LaFerla, Frank M; Carvalheira, Jose B; Saad, Mario J; Munoz, Douglas P; Velloso, Licio A; Ferreira, Sergio T; De Felice, Fernanda G

    2015-01-01

    Alzheimer's disease (AD) is associated with peripheral metabolic disorders. Clinical/epidemiological data indicate increased risk of diabetes in AD patients. Here, we show that intracerebroventricular infusion of AD-associated Aβ oligomers (AβOs) in mice triggered peripheral glucose intolerance, a phenomenon further verified in two transgenic mouse models of AD. Systemically injected AβOs failed to induce glucose intolerance, suggesting AβOs target brain regions involved in peripheral metabolic control. Accordingly, we show that AβOs affected hypothalamic neurons in culture, inducing eukaryotic translation initiation factor 2α phosphorylation (eIF2α-P). AβOs further induced eIF2α-P and activated pro-inflammatory IKKβ/NF-κB signaling in the hypothalamus of mice and macaques. AβOs failed to trigger peripheral glucose intolerance in tumor necrosis factor-α (TNF-α) receptor 1 knockout mice. Pharmacological inhibition of brain inflammation and endoplasmic reticulum stress prevented glucose intolerance in mice, indicating that AβOs act via a central route to affect peripheral glucose homeostasis. While the hypothalamus has been largely ignored in the AD field, our findings indicate that AβOs affect this brain region and reveal novel shared molecular mechanisms between hypothalamic dysfunction in metabolic disorders and AD. PMID:25617315

  10. Constraint-based model of Shewanella oneidensis MR-1 metabolism: a tool for data analysis and hypothesis generation.

    Directory of Open Access Journals (Sweden)

    Grigoriy E Pinchuk

    2010-06-01

    Full Text Available Shewanellae are gram-negative facultatively anaerobic metal-reducing bacteria commonly found in chemically (i.e., redox stratified environments. Occupying such niches requires the ability to rapidly acclimate to changes in electron donor/acceptor type and availability; hence, the ability to compete and thrive in such environments must ultimately be reflected in the organization and utilization of electron transfer networks, as well as central and peripheral carbon metabolism. To understand how Shewanella oneidensis MR-1 utilizes its resources, the metabolic network was reconstructed. The resulting network consists of 774 reactions, 783 genes, and 634 unique metabolites and contains biosynthesis pathways for all cell constituents. Using constraint-based modeling, we investigated aerobic growth of S. oneidensis MR-1 on numerous carbon sources. To achieve this, we (i used experimental data to formulate a biomass equation and estimate cellular ATP requirements, (ii developed an approach to identify cycles (such as futile cycles and circulations, (iii classified how reaction usage affects cellular growth, (iv predicted cellular biomass yields on different carbon sources and compared model predictions to experimental measurements, and (v used experimental results to refine metabolic fluxes for growth on lactate. The results revealed that aerobic lactate-grown cells of S. oneidensis MR-1 used less efficient enzymes to couple electron transport to proton motive force generation, and possibly operated at least one futile cycle involving malic enzymes. Several examples are provided whereby model predictions were validated by experimental data, in particular the role of serine hydroxymethyltransferase and glycine cleavage system in the metabolism of one-carbon units, and growth on different sources of carbon and energy. This work illustrates how integration of computational and experimental efforts facilitates the understanding of microbial metabolism at a

  11. The metabolism and dosimetry of carbon-14 labelled compounds

    International Nuclear Information System (INIS)

    Crawley, F.E.H.

    1977-01-01

    The number of compounds labelled at high specific activity with carbon-14 has greatly increased over the last few years. There are limited biological data available to enable an assessment of the internal radiation dose and to identify the critical tissues after an intake of such compounds. The ICRP consider two Model Systems for deriving dose. Both Models assume a total elimination of the carbon-14 in the breath and only bone or whole body as critical tissues and are not representative of the majority of the compounds now available. A research programme has been established to study the rate of excretion and tissue distribution of selected carbon-14 labelled compounds in the rat after intravenous injection, pulmonary and gastric intubation and skin absorption. These metabolic data have been used to calculate the committed dose equivalent and maximum permissible annual intake (MPAI) for various tissues in man on the assumption that the experimental data obtained in the rat are true for man. To date potassium 14 C-cyanide and 14 C-methanol have been studied. The values for the MPAI's derived from the doses to individual tissues are more restrictive than values calculated from the whole body doses. The MPAI calculated from excretion data in terms of whole body dose is 31 mCi for 14 C-cyanide and 25 mCi for 14 C-methanol. However, the critical tissue for 14 C-cyanide is the stomach with an MPAI of 1.5 mCi based on a dose of 10.7 rem mCi -1 . This was an order of magnitude greater than the dose to any other region of the GI tract and 5 times that to the testis. The critical organs for 14 C-methanol are the testis (MPAI 2.5 mCi) for males and the ovaries (MPAI 6.2 mCi) for females

  12. Up-regulation of sucrose metabolizing enzymes in Oncidium goldiana grown under elevated carbon dioxide

    Energy Technology Data Exchange (ETDEWEB)

    Chang Run Li; Sun, W.Q.; Choy Sin Hew [National Univ. of Singapore. dept. of Biological Sciences (Singapore)

    2001-07-01

    Experiments were conducted in controlled growth chambers to evaluate how increase in CO{sub 2} concentration affected sucrose metabolizing enzymes, especially sucrose phosphate synthase (SPS; EC 2.4.1.14) and sucrose synthase (SS; EC 2.4.1.13), as well as carbon metabolism and partitioning in a tropical epiphytic orchid species (Oncidium goldiana). Response of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco; EC 4.1.1.39) to elevated CO{sub 2} was determined along with dry mass production, photosynthesis rate, chlorophyll content, total nitrogen and total soluble protein content. After 60 days of growth, there was a 80% and 150% increase in dry mass production in plants grown at 750 and 1100 {mu} l{sup -}1 CO{sub 2}, respectively, compared with those grown at ambient CO{sub 2} (about 370 {mu} l{sup -}1). A similar increase in photosynthesis rate was detected throughout the growth period when measured under growth CO{sub 2} conditions. Concomitantly, there was a decline in leaf Rubisco activity in plants in elevated CO{sub 2} after 10 days of growth. Over the growth period, leaf SPS and SS activities were up-regulated by an average of 20% and 40% for plants grown at 750 and 1100 {mu} l{sup -}1 CO{sub 2}, respectively. Leaf sucrose content and starch content were significantly higher throughout the growth period in plants grown at elevated CO{sub 2} than those at ambient CO{sub 2}. The partitioning of photosynthetically fixed carbon between sucrose and starch appeared to be unaffected by the 750 {mu} l{sup -}1 CO{sub 2} treatment, but it was favored into starch under the 1100 {mu} l{sup -}1 CO{sub 2} condition. The activities of SPS and SS in leaf extracts were closely associated with photosynthetic rates and with partitioning of carbon between starch and sucrose in leaves. The data are consistent with the hypothesis that the up-regulation of leaf SPS and SS might be an acclimation response to optimize the utilization and export of organic carbon with the

  13. Factors influencing organic-horizon carbon pools in mixed-species stands of central Maine, USA

    Science.gov (United States)

    Joshua J. Puhlick; Shawn Fraver; Ivan J. Fernandez; Aaron R. Weiskittel; Laura S. Kenefic; Randy Kolka; Marie-Cecile Gruselle

    2016-01-01

    The overall goal of this study was to evaluate the correlation of multiple abiotic and biotic factors with organic-horizon (O-horizon) carbon (C) content on the Penobscot Experimental Forest in central Maine, USA. O-horizon samples were collected and their associated depths were recorded from stands managed with a range of silvicultural and harvesting treatments (i.e...

  14. Single nucleotide polymorphisms of one-carbon metabolism and cancers of the esophagus, stomach, and liver in a Chinese population.

    Directory of Open Access Journals (Sweden)

    Shen-Chih Chang

    Full Text Available One-carbon metabolism (folate metabolism is considered important in carcinogenesis because of its involvement in DNA synthesis and biological methylation reactions. We investigated the associations of single nucleotide polymorphisms (SNPs in folate metabolic pathway and the risk of three GI cancers in a population-based case-control study in Taixing City, China, with 218 esophageal cancer cases, 206 stomach cancer cases, 204 liver cancer cases, and 415 healthy population controls. Study participants were interviewed with a standardized questionnaire, and blood samples were collected after the interviews. We genotyped SNPs of the MTHFR, MTR, MTRR, DNMT1, and ALDH2 genes, using PCR-RFLP, SNPlex, or TaqMan assays. To account for multiple comparisons and reduce the chances of false reports, we employed semi-Bayes (SB shrinkage analysis. After shrinkage and adjusting for potential confounding factors, we found positive associations between MTHFR rs1801133 and stomach cancer (any T versus C/C, SB odds-ratio [SBOR]: 1.79, 95% posterior limits: 1.18, 2.71 and liver cancer (SBOR: 1.51, 95% posterior limits: 0.98, 2.32. There was an inverse association between DNMT1 rs2228612 and esophageal cancer (any G versus A/A, SBOR: 0.60, 95% posterior limits: 0.39, 0.94. In addition, we detected potential heterogeneity across alcohol drinking status for ORs relating MTRR rs1801394 to esophageal (posterior homogeneity P = 0.005 and stomach cancer (posterior homogeneity P = 0.004, and ORs relating MTR rs1805087 to liver cancer (posterior homogeneity P = 0.021. Among non-alcohol drinkers, the variant allele (allele G of these two SNPs was inversely associated with the risk of these cancers; while a positive association was observed among ever-alcohol drinkers. Our results suggest that genetic polymorphisms related to one-carbon metabolism may be associated with cancers of the esophagus, stomach, and liver. Heterogeneity across alcohol consumption status of

  15. Isotopic labeling affects 1,25-dihydroxyvitamin D metabolism

    International Nuclear Information System (INIS)

    Halloran, B.P.; Bikle, D.D.; Castro, M.E.; Gee, E.

    1989-01-01

    Isotope substitution can change the biochemical properties of vitamin D. To determine the effect of substituting 3H for 1H on the metabolism of 1,25(OH)2D3, we measured the metabolic clearance rate and renal metabolism of unlabeled and 3H-labeled 1,25(OH)2D3. Substitution of 3H for 1H on carbons 26 and 27 [1,25(OH)2[26,27(n)-3H]D3] or on carbons 23 and 24 [1,25(OH)2[23,24(n)-3H]D3] reduced the in vivo metabolic clearance rate of 1,25(OH)2D3 by 36% and 37%, respectively, and reduced the in vitro renal catabolism of 1,25(OH)2D3 by 11% and 54%, respectively. Substitutions of 3H for 1H on carbons 23 and 24 as opposed to carbons 26 and 27 reduced conversion of [3H]1,25(OH)2D3 to [3H]1,24,25(OH)2D3 by 25% and to putative 24-oxo-1,23,25-dihydroxyvitamin D3 by 1600%. These results indicate that substitution of 3H for 1H on carbons 26 and 27 or on carbons 23 and 24 can reduce the metabolic clearance rate and in vitro metabolism of 1,25(OH)2D3 and quantitatively alter the pattern of metabolic products produced

  16. Contribution of carbon fixed by Rubisco and PEPC to phloem export in the Crassulacean acid metabolism plant Kalanchoe daigremontiana.

    Science.gov (United States)

    Wild, Birgit; Wanek, Wolfgang; Postl, Wolfgang; Richter, Andreas

    2010-03-01

    Crassulacean acid metabolism (CAM) plants exhibit a complex interplay between CO(2) fixation by phosphoenolpyruvate carboxylase (PEPC) and ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco), and carbon demand for CAM maintenance and growth. This study investigated the flux of carbon from PEPC and direct Rubisco fixation to different leaf carbon pools and to phloem sap over the diurnal cycle. Concentrations and carbon isotope compositions of starch, soluble sugars, and organic acids were determined in leaves and phloem exudates of Kalanchoë daigremontiana Hamet et Perr., and related to CO(2) fixation by PEPC and Rubisco. Three types of leaf carbon pools could be distinguished. (i) Starch and malate pools were dominant and showed a pattern of reciprocal mobilization and accumulation (85/54 and 13/48 mg C g(-1) DW, respective, at the beginning/end of phase I). The carbon isotope composition of these pools was compatible with predominant PEPC fixation (delta(13)C values of -13 and -11 per thousand for starch and malate compared to -11 per thousand of PEPC fixed carbon). (ii) Isotopic composition (-17 per thousand and -14 per thousand) and concentration of glucose and fructose (2 and 3 mg C g(-1) DW, respectively) were not affected by diurnal metabolism, suggesting a low turnover. (iii) Sucrose (1-3 mg C g(-1) DW), in contrast, exhibited large diurnal changes in delta(13)C values (from -17 per thousand in the evening to -12 per thousand in the morning), which were not matched by net changes in sucrose concentration. This suggests a high sucrose turnover, fed by nocturnal starch degradation and direct Rubisco fixation during the day. A detailed dissection of the carbon fixation and mobilization pattern in K. daigremontiana revealed that direct fixation of Rubisco during the light accounted for 30% of phloem sucrose, but only 15% of fixed carbon, indicating that carbon from direct Rubisco fixation was preferentially used for leaf export.

  17. Genome-wide meta-analysis of homocysteine and methionine metabolism identifies five one carbon metabolism loci and a novel association of ALDH1L1 with ischemic stroke.

    Directory of Open Access Journals (Sweden)

    Stephen R Williams

    2014-03-01

    Full Text Available Circulating homocysteine levels (tHcy, a product of the folate one carbon metabolism pathway (FOCM through the demethylation of methionine, are heritable and are associated with an increased risk of common diseases such as stroke, cardiovascular disease (CVD, cancer and dementia. The FOCM is the sole source of de novo methyl group synthesis, impacting many biological and epigenetic pathways. However, the genetic determinants of elevated tHcy (hyperhomocysteinemia, dysregulation of methionine metabolism and the underlying biological processes remain unclear. We conducted independent genome-wide association studies and a meta-analysis of methionine metabolism, characterized by post-methionine load test tHcy, in 2,710 participants from the Framingham Heart Study (FHS and 2,100 participants from the Vitamin Intervention for Stroke Prevention (VISP clinical trial, and then examined the association of the identified loci with incident stroke in FHS. Five genes in the FOCM pathway (GNMT [p = 1.60 × 10(-63], CBS [p = 3.15 × 10(-26], CPS1 [p = 9.10 × 10(-13], ALDH1L1 [p = 7.3 × 10(-13] and PSPH [p = 1.17 × 10(-16] were strongly associated with the difference between pre- and post-methionine load test tHcy levels (ΔPOST. Of these, one variant in the ALDH1L1 locus, rs2364368, was associated with incident ischemic stroke. Promoter analyses reveal genetic and epigenetic differences that may explain a direct effect on GNMT transcription and a downstream affect on methionine metabolism. Additionally, a genetic-score consisting of the five significant loci explains 13% of the variance of ΔPOST in FHS and 6% of the variance in VISP. Association between variants in FOCM genes with ΔPOST suggest novel mechanisms that lead to differences in methionine metabolism, and possibly the epigenome, impacting disease risk. These data emphasize the importance of a concerted effort to understand regulators of one carbon metabolism as potential therapeutic targets.

  18. The association between donor genetic variations in one-carbon metabolism pathway genes and hepatitis B recurrence after liver transplantation.

    Science.gov (United States)

    Lu, Di; Zhuo, Jianyong; Yang, Modan; Wang, Chao; Linhui, Pan; Xie, Haiyang; Xu, Xiao; Zheng, Shusen

    2018-04-05

    Hepatitis B recurrence adversely affects patients' survival after liver transplantation. This study aims to find association between donor gene variations of one carbon metabolism and post-transplant hepatitis B recurrence. This study enrolled 196 patients undergoing liver transplantation for HBV related end-stage liver diseases. We detected 11 single nucleotide polymorphisms (SNP) of 7 one-carbon metabolism pathway genes (including MTHFR, MTR, MTRR, ALDH1L1, GART, SHMT1 and CBS) in donor livers and analyzed their association with HBV reinfection after liver transplantation. Hepatitis B recurrence was observed in 19 of the 196 patients (9.7%) undergoing liver transplantation. Hepatitis B recurrence significantly affected post-transplant survival in the 196 patients (p = 0.018), and correlate with tumor recurrence in the subgroup of HCC patients (n = 99, p = 0.006). Among the 11 SNPs, donor liver mutation in rs1979277 (G > A) was adversely associated with post-transplant hepatitis B recurrence (p = 0.042). In the subgroup of HCC patients, survival analysis showed donor liver mutations in rs1801133 (G > A) and rs1979277 (G > A) were risk factors for hepatitis B recurrence (p B recurrence in non-HCC patients (n = 97, p > 0.05). Hepatitis B recurrence impaired post-transplant survival. Donor liver genetic variations in one-carbon metabolism pathway genes were significantly associated with post-transplant hepatitis B recurrence. Copyright © 2017. Published by Elsevier B.V.

  19. Constraint-Based Modeling Highlights Cell Energy, Redox Status and α-Ketoglutarate Availability as Metabolic Drivers for Anthocyanin Accumulation in Grape Cells Under Nitrogen Limitation

    Directory of Open Access Journals (Sweden)

    Eric Soubeyrand

    2018-05-01

    Full Text Available Anthocyanin biosynthesis is regulated by environmental factors (such as light, temperature, and water availability and nutrient status (such as carbon, nitrogen, and phosphate nutrition. Previous reports show that low nitrogen availability strongly enhances anthocyanin accumulation in non carbon-limited plant organs or cell suspensions. It has been hypothesized that high carbon-to-nitrogen ratio would lead to an energy excess in plant cells, and that an increase in flavonoid pathway metabolic fluxes would act as an “energy escape valve,” helping plant cells to cope with energy and carbon excess. However, this hypothesis has never been tested directly. To this end, we used the grapevine Vitis vinifera L. cultivar Gamay Teinturier (syn. Gamay Freaux or Freaux Tintorier, VIVC #4382 cell suspension line as a model system to study the regulation of anthocyanin accumulation in response to nitrogen supply. The cells were sub-cultured in the presence of either control (25 mM or low (5 mM nitrate concentration. Targeted metabolomics and enzyme activity determinations were used to parametrize a constraint-based model describing both the central carbon and nitrogen metabolisms and the flavonoid (phenylpropanoid pathway connected by the energy (ATP and reducing power equivalents (NADPH and NADH cofactors. The flux analysis (2 flux maps generated, for control and low nitrogen in culture medium clearly showed that in low nitrogen-fed cells all the metabolic fluxes of central metabolism were decreased, whereas fluxes that consume energy and reducing power, were either increased (upper part of glycolysis, shikimate, and flavonoid pathway or maintained (pentose phosphate pathway. Also, fluxes of flavanone 3β-hydroxylase, flavonol synthase, and anthocyanidin synthase were strongly increased, advocating for a regulation of the flavonoid pathway by alpha-ketoglutarate levels. These results strongly support the hypothesis of anthocyanin biosynthesis acting as

  20. Changes in bone sodium and carbonate in metabolic acidosis and alkalosis in the dog

    Science.gov (United States)

    Burnell, James M.

    1971-01-01

    Metabolic acidosis and alkalosis were produced in adult dogs over 5- to 10-day periods. Midtibial cortical bone was analyzed for calcium, sodium, phosphorus, and carbonate. In acidosis bone CO3/Ca decreased 9.5% and bone Na/Ca decreased 6.3%. In alkalosis bone CO3/Ca increased 3.1% and bone Na/Ca increased 3.0%. Previous attempts to account for changes in net acid balance by summation of extra- and intracellular acid-base changes have uniformly resulted in about 40-60% of acid gained or lost being “unaccounted for.” If it is assumed that changes in tibial cortex reflect changes in the entire skeletal system, changes in bone CO3= are sufficiently large to account for the “unaccounted for” acid change without postulating changes in cellular metabolic acid production. PMID:5540172

  1. Induction of a stringent metabolic response in intracellular stages of Leishmania mexicana leads to increased dependence on mitochondrial metabolism.

    Directory of Open Access Journals (Sweden)

    Eleanor C Saunders

    2014-01-01

    Full Text Available Leishmania parasites alternate between extracellular promastigote stages in the insect vector and an obligate intracellular amastigote stage that proliferates within the phagolysosomal compartment of macrophages in the mammalian host. Most enzymes involved in Leishmania central carbon metabolism are constitutively expressed and stage-specific changes in energy metabolism remain poorly defined. Using (13C-stable isotope resolved metabolomics and (2H2O labelling, we show that amastigote differentiation is associated with reduction in growth rate and induction of a distinct stringent metabolic state. This state is characterized by a global decrease in the uptake and utilization of glucose and amino acids, a reduced secretion of organic acids and increased fatty acid β-oxidation. Isotopomer analysis showed that catabolism of hexose and fatty acids provide C4 dicarboxylic acids (succinate/malate and acetyl-CoA for the synthesis of glutamate via a compartmentalized mitochondrial tricarboxylic acid (TCA cycle. In vitro cultivated and intracellular amastigotes are acutely sensitive to inhibitors of mitochondrial aconitase and glutamine synthetase, indicating that these anabolic pathways are essential for intracellular growth and virulence. Lesion-derived amastigotes exhibit a similar metabolism to in vitro differentiated amastigotes, indicating that this stringent response is coupled to differentiation signals rather than exogenous nutrient levels. Induction of a stringent metabolic response may facilitate amastigote survival in a nutrient-poor intracellular niche and underlie the increased dependence of this stage on hexose and mitochondrial metabolism.

  2. Transcriptome analysis of temporal regulation of carbon metabolism by CcpA in Bacillus subtilis reveals additional target genes

    NARCIS (Netherlands)

    Lulko, Andrzej T.; Buist, Girbe; Kok, Jan; Kuipers, Oscar P.

    2007-01-01

    The pleiotropic regulator of carbon metabolism in Grampositive bacteria, CcpA, regulates gene expression by binding to so-called cre elements, which are located either upstream or in promoter regions, or in open-reading frames. In this study we compared the transcriptomes of Bacillus subtilis 168

  3. Constraining the subsoil carbon source to cave-air CO2 and speleothem calcite in central Texas

    Science.gov (United States)

    Bergel, Shelly J.; Carlson, Peter E.; Larson, Toti E.; Wood, Chris T.; Johnson, Kathleen R.; Banner, Jay L.; Breecker, Daniel O.

    2017-11-01

    Canonical models for speleothem formation and the subsurface carbon cycle invoke soil respiration as the dominant carbon source. However, evidence from some karst regions suggests that belowground CO2 originates from a deeper, older source. We therefore investigated the carbon sources to central Texas caves. Drip-water chemistry of two caves in central Texas implies equilibration with calcite at CO2 concentrations (PCO2_sat) higher than the maximum CO2 concentrations observed in overlying soils. This observation suggests that CO2 is added to waters after they percolate through the soils, which requires a subsoil carbon source. We directly evaluate the carbon isotope composition of the subsoil carbon source using δ13C measurements on cave-air CO2, which we independently demonstrate has little to no contribution from host rock carbon. We do so using the oxidative ratio, OR, defined as the number of moles of O2 consumed per mole of CO2 produced during respiration. However, additional belowground processes that affect O2 and CO2 concentrations, such as gas-water exchange and/or diffusion, may also influence the measured oxidative ratio, yielding an apparent OR (ORapparent). Cave air in Natural Bridge South Cavern has ORapparent values (1.09 ± 0.06) indistinguishable from those expected for respiration alone (1.08 ± 0.06). Pore space gases from soils above the cave have lower values (ORapparent = 0.67 ± 0.05) consistent with respiration and gas transport by diffusion. The simplest explanation for these observations is that cave air in NB South is influenced by respiration in open-system bedrock fractures such that neither diffusion nor exchange with water influence the composition of the cave air. The radiocarbon activities of NB South cave-air CO2 suggest the subsoil carbon source is hundreds of years old. The calculated δ13C values of the subsoil carbon source are consistent with tree-sourced carbon (perhaps decomposing root matter), the δ13C values of which

  4. ANALISIS TOTAL PRODUCTIVE MAINTENANCE PADA LINE 8/CARBONATED SOFT DRINK PT COCA-COLA BOTTLING INDONESIA CENTRAL JAVA

    Directory of Open Access Journals (Sweden)

    Darminto Pujotomo

    2012-02-01

    Full Text Available PT. Coca-Cola Bottling Indonesia (CCBI Central Java merupakan salah satu perusahaan produsen minuman ringan yang terkemuka di Indonesia, dengan dua jenis kelompok produk yang dihasilkan yaitu minuman karbonasi/Carbonated Soft Drink (Coca-Cola, Sprite, dan Fanta dan non-karbonasi (Frestea dan Ades. Dalam usaha untuk mempertahankan mutu dan meningkatkan produktifitas, salah satu faktor yang harus diperhatikan adalah masalah perawatan fasilitas/mesin produksi.  Makalah ini membahas mengenai penyebab dan akibat yang ditimbulkan oleh breakdown mesin terjadi pada Line 8/Carbonated Soft Drink, khususnya pada conveyor, filler machine, dan bottle washer machine. Untuk mendapatkan mesin yang dapat terjaga keterandalannya dibutuhkan suatu konsep yang baik. Total Productive Maintenance (TPM merupakan sebuah konsep yang baik untuk merealisasikan hal tersebut. Konsep ini, selain melibatkan semua personil dalam perusahaan, juga bertujuan untuk merawat semua fasilitas produksi yang dimiliki perusahaan.Data yang digunakan merupakan data breakdown conveyor, filler machine, dan bottle washer machine dari ME Monthly Report PT.CCBI selama bulan Januari-Desember 2005 khususnya line 8. Selain itu makalah ini juga membahas performance maintenance PT. Coca-Cola Bottling Indonesia-Central Java, dengan memperhitungkan nilai Mean Time Beetwen Failure (MTBF, Mean Time To Repair (MTTR, serta Availability mesin, dengan menggunakan data record Line 8 selama bulan Mei 2006 sampai bulan Juli 2006. Sehingga nantinya akan diketahui informasi keadaan aktual dari perusahaan tentang sistem perawatannya, khususnya pada Line 8/Carbonated Soft Drink apakah baik atau buruk. Kata kunci : Total Production Maintenance, Conveyor, Filler Machine, Bottle Washer Machine, Performance Maintenance   PT. Coca-Cola Bottling Indonesia (CCBI-Central Java represent one of notable light beverage producer company in Indonesia, with two product group type yielded is carbonated beverage/Carbonated Soft

  5. Comparative genome analysis of central nitrogen metabolism and its control by GlnR in the class Bacilli

    Directory of Open Access Journals (Sweden)

    Kormelink Tom

    2012-05-01

    Full Text Available Abstract Background The assimilation of nitrogen in bacteria is achieved through only a few metabolic conversions between alpha-ketoglutarate, glutamate and glutamine. The enzymes that catalyze these conversions are glutamine synthetase, glutaminase, glutamate dehydrogenase and glutamine alpha-ketoglutarate aminotransferase. In low-GC Gram-positive bacteria the transcriptional control over the levels of the related enzymes is mediated by four regulators: GlnR, TnrA, GltC and CodY. We have analyzed the genomes of all species belonging to the taxonomic families Bacillaceae, Listeriaceae, Staphylococcaceae, Lactobacillaceae, Leuconostocaceae and Streptococcaceae to determine the diversity in central nitrogen metabolism and reconstructed the regulation by GlnR. Results Although we observed a substantial difference in the extent of central nitrogen metabolism in the various species, the basic GlnR regulon was remarkably constant and appeared not affected by the presence or absence of the other three main regulators. We found a conserved regulatory association of GlnR with glutamine synthetase (glnRA operon, and the transport of ammonium (amtB-glnK and glutamine/glutamate (i.e. via glnQHMP, glnPHQ, gltT, alsT. In addition less-conserved associations were found with, for instance, glutamate dehydrogenase in Streptococcaceae, purine catabolism and the reduction of nitrite in Bacillaceae, and aspartate/asparagine deamination in Lactobacillaceae. Conclusions Our analyses imply GlnR-mediated regulation in constraining the import of ammonia/amino-containing compounds and the production of intracellular ammonia under conditions of high nitrogen availability. Such a role fits with the intrinsic need for tight control of ammonia levels to limit futile cycling.

  6. Vision Issues and Space Flight: Evaluation of One-Carbon Metabolism Polymorphisms

    Science.gov (United States)

    Smith, Scott M.; Gregory, Jesse F.; Zeisel, Steven; Ueland, Per; Gibson, C. R.; Mader, Thomas; Kinchen, Jason; Ploutz-Snyder, Robert; Zwart, Sara R.

    2015-01-01

    Intermediates of the one-carbon metabolic pathway are altered in astronauts who experience vision-related issues during and after space flight. Serum concentrations of homocysteine, cystathionine, 2-methylcitric acid, and methylmalonic acid were higher in astronauts with ophthalmic changes than in those without (Zwart et al., J Nutr, 2012). These differences existed before, during, and after flight. Potential confounding factors did not explain the differences. Genetic polymorphisms could contribute to these differences, and could help explain why crewmembers on the same mission do not all have ophthalmic issues, despite the same environmental factors (e.g., microgravity, exercise, diet). A follow-up study was conducted to evaluate 5 polymorphisms of enzymes in the one-carbon pathway, and to evaluate how these relate to vision and other ophthalmic changes after flight. Preliminary evaluations of the genetic data indicate that all of the crewmembers with the MTRR GG genotype had vision issues to one degree or another. However, not everyone who had vision issues had this genetic polymorphism, so the situation is more complex than the involvement of this single polymorphism. Metabolomic and further data analyses are underway to clarify these findings, but the preliminary assessments are promising.

  7. A direct evidence for high carbon dioxide and radon-222 discharge in Central Nepal

    International Nuclear Information System (INIS)

    Perrier, F.; Byrdina, S.; Richon, P.; Bollinger, L.; Bureau, S.; Richon, P.; France-Lanord, Ch.; Rajaure, S.; Koirala, Bharat Prasad; Shrestha, Prithvi Lal; Gautam, Umesh Prasad; Tiwari, Dilli Ram; Sapkota, Soma Nath; Revil, A.; Revil, A.; Contraires, S.

    2009-01-01

    Gas discharges have been identified at the Syabru-Bensi hot springs, located at the front of the High Himalaya in Central Nepal, in the Main Central Thrust zone. The hot spring waters are characterized by a temperature reaching 61 C, high salinity, high alkalinity and δ 13 C varying from +0. 7 parts per thousand to +4. 8 parts per thousand. The gas is mainly dry carbon dioxide, with a δ 13 C of -0. 8 parts per thousand. The diffuse carbon dioxide flux, mapped by the accumulation chamber method, reached a value of 19000 g m -2 day -1 , which is comparable with values measured on active volcanoes. Similar values have been observed over a two-year time interval and the integral around the main gas discharge amounts to 0. 25 ± 0. 07 mol s -1 , or 350 ± 100 ton a -1 . The mean radon-222 concentration in spring water did not exceed 2. 5 Bq L -1 , exponentially decreasing with water temperature. In contrast, in gas bubbles collected in the water or in the dry gas discharges, the radon concentration varied from 16 000 to 41000 Bq m -3 . In the soil, radon concentration varied from 25000 to more than 50000 Bq m -3 . Radon flux, measured at more than fifty points, reached extreme values, larger than 2 Bq m -2 s -1 , correlated to the larger values of the carbon dioxide flux. Our direct observation confirms previous studies which indicated large degassing in the Himalaya. The proposed understanding is that carbon dioxide is released at mid-crustal depth by metamorphic reactions within the Indian basement, transported along pre-existing faults by meteoric hot water circulation, and degassed before reaching surface. This work, first, confirms that further studies should be undertaken to better constrain the carbon budget of the Himalaya, and, more generally, the contribution of mountain building to the global carbon balance. Furthermore, the evidenced gas discharges provide a unique natural laboratory for methodological studies, and appear particularly important to study as

  8. Dust, Elemental Carbon and Other Impurities on Central Asian Glaciers: Origin and Radiative Forcing

    Science.gov (United States)

    Schmale, J.; Flanner, M.; Kang, S.; Sprenger, M.; Zhang, Q.; Li, Y.; Guo, J.; Schwikowski, M.

    2015-12-01

    In Central Asia, more than 60 % of the population depends on water stored in glaciers and mountain snow. While temperature, precipitation and dynamic processes are key drivers of glacial change, deposition of light absorbing impurities such as mineral dust and black carbon can lead to accelerated melting through surface albedo reduction. Here, we discuss the origin of deposited mineral dust and black carbon and their impacts on albedo change and radiative forcing (RF). 218 snow samples were taken from 13 snow pits on 4 glaciers, Abramov (Pamir), Suek, Glacier No. 354 and Golubin (Tien Shan), representing deposition between summer 2012 and 2014. They were analyzed for elemental and organic carbon by a thermo-optical method, mineral dust by gravimetry, and iron by ICP-MS. Back trajectory ensembles were released every 6 hours with the Lagranto model for the covered period at all sites. Boundary layer "footprints" were calculated to estimate general source regions and combined with MODIS fire counts for potential fire contributions. Albedo reduction due to black carbon and mineral dust was calculated with the Snow-Ice-Aerosol-Radiative model (SNICAR), and surface spectral irradiances were derived from atmospheric radiative transfer calculations to determine the RF under clear-sky and all sky conditions using local radiation measurements. Dust contributions came from Central Asia, the Arabian Peninsula, the Sahara and partly the Taklimakan. Fire contributions were higher in 2014 and generally came from the West and North. We find that EC exerts roughly 3 times more RF than mineral dust in fresh and relatively fresh snow (~5 W/m2) and up to 6 times more in snow that experienced melting (> 10 W/m2) even though EC concentrations (average per snow pit from 90 to 700 ng/g) were up to two orders of magnitude lower than mineral dust (10 to 140 μg/g).

  9. Low oxygen affects photophysiology and the level of expression of two-carbon metabolism genes in the seagrass Zostera muelleri.

    Science.gov (United States)

    Kim, Mikael; Brodersen, Kasper Elgetti; Szabó, Milán; Larkum, Anthony W D; Raven, John A; Ralph, Peter J; Pernice, Mathieu

    2018-05-01

    Seagrasses are a diverse group of angiosperms that evolved to live in shallow coastal waters, an environment regularly subjected to changes in oxygen, carbon dioxide and irradiance. Zostera muelleri is the dominant species in south-eastern Australia, and is critical for healthy coastal ecosystems. Despite its ecological importance, little is known about the pathways of carbon fixation in Z. muelleri and their regulation in response to environmental changes. In this study, the response of Z. muelleri exposed to control and very low oxygen conditions was investigated by using (i) oxygen microsensors combined with a custom-made flow chamber to measure changes in photosynthesis and respiration, and (ii) reverse transcription quantitative real-time PCR to measure changes in expression levels of key genes involved in C 4 metabolism. We found that very low levels of oxygen (i) altered the photophysiology of Z. muelleri, a characteristic of C 3 mechanism of carbon assimilation, and (ii) decreased the expression levels of phosphoenolpyruvate carboxylase and carbonic anhydrase. These molecular-physiological results suggest that regulation of the photophysiology of Z. muelleri might involve a close integration between the C 3 and C 4 , or other CO 2 concentrating mechanisms metabolic pathways. Overall, this study highlights that the photophysiological response of Z. muelleri to changing oxygen in water is capable of rapid acclimation and the dynamic modulation of pathways should be considered when assessing seagrass primary production.

  10. Central nervous insulin resistance: a promising target in the treatment of metabolic and cognitive disorders?

    Science.gov (United States)

    Hallschmid, M; Schultes, B

    2009-11-01

    Research on functions and signalling pathways of insulin has traditionally focused on peripheral tissues such as muscle, fat and liver, while the brain was commonly believed to be insensitive to the effects of this hormone secreted by pancreatic beta cells. However, since the discovery some 30 years ago that insulin receptors are ubiquitously found in the central nervous system, an ever-growing research effort has conclusively shown that circulating insulin accesses the brain, which itself does not synthesise insulin, and exerts pivotal functions in central nervous networks. As an adiposity signal reflecting the amount of body fat, insulin provides direct negative feedback to hypothalamic nuclei that control whole-body energy and glucose homeostasis. Moreover, insulin affects distinct cognitive processes, e.g. by triggering the formation of psychological memory contents. Accordingly, metabolic and cognitive disorders such as obesity, type 2 diabetes mellitus and Alzheimer's disease are associated with resistance of central nervous structures to the effects of insulin, which may derive from genetic polymorphisms as well as from long-term exposure to excess amounts of circulating insulin due to peripheral insulin resistance. Thus, overcoming central nervous insulin resistance, e.g. by pharmacological interventions, appears to be an attractive strategy in the treatment and prevention of these disorders. Enhancement of central nervous insulin signalling by administration of intranasal insulin, insulin analogues and insulin sensitisers in basic research approaches has yielded encouraging results that bode well for the successful translation of these effects into future clinical practice.

  11. Starch as a source, starch as a sink: the bifunctional role of starch in carbon allocation.

    Science.gov (United States)

    MacNeill, Gregory J; Mehrpouyan, Sahar; Minow, Mark A A; Patterson, Jenelle A; Tetlow, Ian J; Emes, Michael J

    2017-07-20

    Starch commands a central role in the carbon budget of the majority of plants on earth, and its biological role changes during development and in response to the environment. Throughout the life of a plant, starch plays a dual role in carbon allocation, acting as both a source, releasing carbon reserves in leaves for growth and development, and as a sink, either as a dedicated starch store in its own right (in seeds and tubers), or as a temporary reserve of carbon contributing to sink strength, in organs such as flowers, fruits, and developing non-starchy seeds. The presence of starch in tissues and organs thus has a profound impact on the physiology of the growing plant as its synthesis and degradation governs the availability of free sugars, which in turn control various growth and developmental processes. This review attempts to summarize the large body of information currently available on starch metabolism and its relationship to wider aspects of carbon metabolism and plant nutrition. It highlights gaps in our knowledge and points to research areas that show promise for bioengineering and manipulation of starch metabolism in order to achieve more desirable phenotypes such as increased yield or plant biomass. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  12. NAD(+) metabolism: A therapeutic target for age-related metabolic disease

    NARCIS (Netherlands)

    Mouchiroud, Laurent; Houtkooper, Riekelt H.; Auwerx, Johan

    2013-01-01

    Abstract Nicotinamide adenine dinucleotide (NAD) is a central metabolic cofactor by virtue of its redox capacity, and as such regulates a wealth of metabolic transformations. However, the identification of the longevity protein silent regulator 2 (Sir2), the founding member of the sirtuin protein

  13. Assessment of changes in energy metabolism parameters provoked by carbon tetrachloride in Wistar rats and the protective effect of white grape juice

    Directory of Open Access Journals (Sweden)

    Tatiane Gabardo

    2015-01-01

    Full Text Available The objective of this study was to evaluate the effect of organic and conventional grape juices consumption on the behavior of rats and their neuroprotective effect on the activity of brain energy metabolism enzymes in different brain areas of adult rats on the experimental model of hepatic encephalopathy. Male Wistar rats (90-days-old were treated once a day with conventional or organic white grape juice by gavage for 14 days (7 μL/g. On the 15th day the rats received carbon tetrachloride (CCl4 in a single dose of 3.0 mL/kg. Cerebral cortex, hippocampus and cerebellum were dissected to measure the activity of creatine kinase (CK and pyruvate kinase (PK. No changes in feeding behavior were observed after the treatment with the grapes juices. However, there was an increase in grooming behavior in the open field test provoked by both juices. CCl4 inhibited CK activity in cerebral cortex and hippocampus of the rats and CCl4 also reduced PK activity in all brain structures studied. Furthermore, both white grape juices prevented the decrease in the activity of CK and PK. Therefore, we can suggest that organic and conventional white grape juices could restore the activity of enzymes with a central role in brain energy metabolism.

  14. Fungi contribute critical but spatially varying roles in nitrogen and carbon cycling in acid mine drainage

    Directory of Open Access Journals (Sweden)

    Annika C. Mosier

    2016-03-01

    Full Text Available The ecosystem roles of fungi have been extensively studied by targeting one organism and/or biological process at a time, but the full metabolic potential of fungi has rarely been captured in an environmental context. We hypothesized that fungal genome sequences could be assembled directly from the environment using metagenomics and that transcriptomics and proteomics could simultaneously reveal metabolic differentiation across habitats. We reconstructed the near-complete 27 Mbp genome of a filamentous fungus, Acidomyces richmondensis, and evaluated transcript and protein expression in floating and streamer biofilms from an acid mine drainage system. A. richmondensis transcripts involved in denitrification and in the degradation of complex carbon sources (including cellulose were up-regulated in floating biofilms, whereas central carbon metabolism and stress-related transcripts were significantly up-regulated in streamer biofilms. These findings suggest that the biofilm niches are distinguished by distinct carbon and nitrogen resource utilization, oxygen availability and environmental challenges. An isolated A. richmondensis strain from this environment was used to validate the metagenomics-derived genome and confirm nitrous oxide production at pH 1. Overall, our analyses defined mechanisms of fungal adaptation and identified a functional shift related to different roles in carbon and nitrogen turnover for the same species of fungi growing in closely located but distinct biofilm niches.

  15. Deforestation projections for carbon-rich peat swamp forests of Central Kalimantan, Indonesia.

    Science.gov (United States)

    Fuller, Douglas O; Hardiono, Martin; Meijaard, Erik

    2011-09-01

    We evaluated three spatially explicit land use and cover change (LUCC) models to project deforestation from 2005-2020 in the carbon-rich peat swamp forests (PSF) of Central Kalimantan, Indonesia. Such models are increasingly used to evaluate the impact of deforestation on carbon fluxes between the biosphere and the atmosphere. We considered both business-as-usual (BAU) and a forest protection scenario to evaluate each model's accuracy, sensitivity, and total projected deforestation and landscape-level fragmentation patterns. The three models, Dinamica EGO (DE), GEOMOD and the Land Change Modeler (LCM), projected similar total deforestation amounts by 2020 with a mean of 1.01 million ha (Mha) and standard deviation of 0.17 Mha. The inclusion of a 0.54 Mha strict protected area in the LCM simulations reduced projected loss to 0.77 Mha over 15 years. Calibrated parameterizations of the models using nearly identical input drivers produced very different landscape properties, as measured by the number of forest patches, mean patch area, contagion, and Euclidean nearest neighbor determined using Fragstats software. The average BAU outputs of the models suggests that Central Kalimantan may lose slightly less than half (45.1%) of its 2005 PSF by 2020 if measures are not taken to reduce deforestation there. The relatively small reduction of 0.24 Mha in deforestation found in the 0.54 Mha protection scenario suggests that these models can identify potential leakage effects in which deforestation is forced to occur elsewhere in response to a policy intervention.

  16. Convergent Metabolic Specialization through Distinct Evolutionary Paths in Pseudomonas aeruginosa

    DEFF Research Database (Denmark)

    La Rosa, Ruggero; Johansen, Helle Krogh; Molin, Søren

    2018-01-01

    fibrosis (CF) infection. In this work, we investigated how and through which trajectories evolution of Pseudomonas aeruginosa occurs when migrating from the environment to the airways of CF patients, and specifically, we determined reduction of growth rate and metabolic specialization as signatures...... of adaptive evolution. We show that central metabolic pathways of three distinct Pseudomonas aeruginosa lineages coevolving within the same environment become restructured at the cost of versatility during long-term colonization. Cell physiology changes from naive to adapted phenotypes resulted in (i......) alteration of growth potential that particularly converged to a slow-growth phenotype, (ii) alteration of nutritional requirements due to auxotrophy, (iii) tailored preference for carbon source assimilation from CF sputum, (iv) reduced arginine and pyruvate fermentation processes, and (v) increased oxygen...

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

    Directory of Open Access Journals (Sweden)

    Dorthe S Bille

    Full Text Available Two meta-analyses of genome-wide association studies (GWAS have suggested that four variants: rs2605100 in lysophospholipase-like 1 (LYPLAL1, rs10146997 in neuroxin 3 (NRXN3, rs545854 in methionine sulfoxide reductase A (MSRA, and rs987237 in transcription factor activating enhancer-binding protein 2 beta (TFAP2B associate with measures of central obesity. To elucidate potential underlying phenotypes we aimed to investigate whether these variants associated with: 1 quantitative metabolic traits, 2 anthropometric measures (waist circumference (WC, waist-hip ratio, and BMI, or 3 type 2 diabetes, and central and general overweight and obesity.The four variants were genotyped in Danish individuals using KASPar®. Quantitative metabolic traits were examined in a population-based sample (n = 6,038 and WC and BMI were furthermore analyzed in a combined study sample (n = 13,507. Case-control studies of diabetes and adiposity included 15,326 individuals. The major G-allele of LYPLAL1 rs2605100 associated with increased fasting serum triglyceride concentrations (per allele effect (β = 3%(1;5(95%CI, p(additive = 2.7×10(-3, an association driven by the male gender (p(interaction = 0.02. The same allele associated with increased fasting serum insulin concentrations (β = 3%(1;5, p(additive = 2.5×10(-3 and increased insulin resistance (HOMA-IR (β = 4%(1;6, p(additive = 1.5×10(-3. The minor G-allele of rs10146997 in NRXN3 associated with increased WC among women (β = 0.55cm (0.20;0.89, p(additive = 1.7×10(-3, p(interaction = 1.0×10(-3, but showed no associations with obesity related metabolic traits. The MSRA rs545854 and TFAP2B rs987237 showed nominal associations with central obesity; however, no underlying metabolic phenotypes became obvious, when investigating quantitative metabolic traits. None of the variants influenced the prevalence of type 2 diabetes.We demonstrate that several of the central

  18. Increasing galactose consumption by Saccharomyces cerevisiae through metabolic engineering of the GAL gene regulatory network

    DEFF Research Database (Denmark)

    Østergaard, Simon; Olsson, Lisbeth; Johnston, M.

    2000-01-01

    Increasing the flux through central carbon metabolism is difficult because of rigidity in regulatory structures, at both the genetic and the enzymatic levels. Here we describe metabolic engineering of a regulatory network to obtain a balanced increase in the activity of all the enzymes in the pat...... media. The improved galactose consumption of the gal mutants did not favor biomass formation, but rather caused excessive respiro-fermentative metabolism, with the ethanol production rate increasing linearly with glycolytic flux....... by eliminating three known negative regulators of the GAL system: Gale, Gal80, and Mig1. This led to a 41% increase in flux through the galactose utilization pathway compared with the wild-type strain. This is of significant interest within the field of biotechnology since galactose is present in many industrial...

  19. Metabolic activation of carbon tetrachloride by the cervico-vaginal epithelium in rodents

    International Nuclear Information System (INIS)

    Brittebo, E.B.; Brandt, I.

    1989-01-01

    The metabolism and binding of 14 C-labelled carbon tetrachloride (CCl 4 ) in the genital tract of female adult or juvenile NMRI-mice and Sprague-Dawly rats (mainly in the pro-oestrous/oestrous stage) and an adult New Zealand rabbit were studied. A marked irreversible binding of radioactivity in the squamous cervico-vaginal epithelium of mice given intravenous injections of 14 C-CCl 4 was revealed by autoradiography of solvent-extracted tissue. The localization of binding in the mouse genital tract incubated with 14 C-CCl 4 under air was similar to that observed in vivo. Bound radioactivity was also present in the cylindrical epithelium of the rabbit vagina incubated with 14 C-CCl 4 in vitro. For a comparison, no preferential binding of radiolabelled diethylstilbestrol or ethinylestradiol was observed in the mouse cervico-vaginal epithelium. The level of irreversible binding to PMSG-primed (pregnant mare's serum gonadotrophin) vaginal epithelial 100 x g supernatants of mice and rats incubated with 14 C-CCl 4 under air was low. Addition of the reducing agent dithionite to the incubations increased the binding in the vaginal epithelium 20-fold. In juvenile mice and rats injected with 14 C-CCl 4 , the levels of metabolites in the epithelium were low, whereas PMSG-primed juvenile rats contained a higher level of metabolites. The results show that the cervico-vaginal epithelium can metabolically activate CCl 4 to reactive metabolites and suggest that the metabolism is under endocrine control. (author)

  20. Pyruvate Kinase Triggers a Metabolic Feedback Loop that Controls Redox Metabolism in Respiring Cells

    NARCIS (Netherlands)

    Grüning, N.M.; Rinnerthaler, M.; Bluemlein, K.; Mulleder, M.; Wamelink, M.M.C.; Lehrach, H.; Jakobs, C.A.J.M.; Breitenbach, M.; Ralser, M.

    2011-01-01

    In proliferating cells, a transition from aerobic to anaerobic metabolism is known as the Warburg effect, whose reversal inhibits cancer cell proliferation. Studying its regulator pyruvate kinase (PYK) in yeast, we discovered that central metabolism is self-adapting to synchronize redox metabolism

  1. The Central Metabolism Regulator EIIAGlc Switches Salmonella from Growth Arrest to Acute Virulence through Activation of Virulence Factor Secretion

    Directory of Open Access Journals (Sweden)

    Alain Mazé

    2014-06-01

    Full Text Available The ability of Salmonella to cause disease depends on metabolic activities and virulence factors. Here, we show that a key metabolic protein, EIIAGlc, is absolutely essential for acute infection, but not for Salmonella survival, in a mouse typhoid fever model. Surprisingly, phosphorylation-dependent EIIAGlc functions, including carbohydrate transport and activation of adenylate cyclase for global regulation, do not explain this virulence phenotype. Instead, biochemical studies, in vitro secretion and translocation assays, and in vivo genetic epistasis experiments suggest that EIIAGlc binds to the type three secretion system 2 (TTSS-2 involved in systemic virulence, stabilizes its cytoplasmic part including the crucial TTSS-2 ATPase, and activates virulence factor secretion. This unexpected role of EIIAGlc reveals a striking direct link between central Salmonella metabolism and a crucial virulence mechanism.

  2. Carbon isotope geothermometry of graphite-bearing marbles from Central Dronning Maud Land, East Antarctica

    International Nuclear Information System (INIS)

    Wand, U.; Muehle, K.

    1988-01-01

    In order to estimate the peak metamorphic temperatures in high-grade regional metamorphic marbles from central Dronning Maud Land (East Antarctica), 13 C/ 12 C isotope ratios have been measured for coexisting carbonate and graphite pairs. The δ 13 C values of carbonates (calcite ± dolomite) and graphite vary from -0.1 to +4.6 permill (PDB) and from -3.3 to +1.7 permill, respectively. The isotopic fractionation between carbonate and graphite ranges from 2.9 to 4.0 permill and is similar to the Δ 13 C (carb-gr) values observed in other East Antarctic and non-Antarctic granulite-facies marbles. The metamorphic temperatures calculated using the equation of VALLEY and O'NEIL (1981) for calcite-graphite pairs are predominantly in the range 700 0 - 800 0 C (x n=5 ± s = 730 0 ± 30 0 C) and agree well with metamorphic temperatures derived from mineral chemical studies in this East Antarctic region. (author)

  3. Tumor microenvironment derived exosomes pleiotropically modulate cancer cell metabolism

    Science.gov (United States)

    Zhao, Hongyun; Yang, Lifeng; Baddour, Joelle; Achreja, Abhinav; Bernard, Vincent; Moss, Tyler; Marini, Juan C; Tudawe, Thavisha; Seviour, Elena G; San Lucas, F Anthony; Alvarez, Hector; Gupta, Sonal; Maiti, Sourindra N; Cooper, Laurence; Peehl, Donna; Ram, Prahlad T; Maitra, Anirban; Nagrath, Deepak

    2016-01-01

    Cancer-associated fibroblasts (CAFs) are a major cellular component of tumor microenvironment in most solid cancers. Altered cellular metabolism is a hallmark of cancer, and much of the published literature has focused on neoplastic cell-autonomous processes for these adaptations. We demonstrate that exosomes secreted by patient-derived CAFs can strikingly reprogram the metabolic machinery following their uptake by cancer cells. We find that CAF-derived exosomes (CDEs) inhibit mitochondrial oxidative phosphorylation, thereby increasing glycolysis and glutamine-dependent reductive carboxylation in cancer cells. Through 13C-labeled isotope labeling experiments we elucidate that exosomes supply amino acids to nutrient-deprived cancer cells in a mechanism similar to macropinocytosis, albeit without the previously described dependence on oncogenic-Kras signaling. Using intra-exosomal metabolomics, we provide compelling evidence that CDEs contain intact metabolites, including amino acids, lipids, and TCA-cycle intermediates that are avidly utilized by cancer cells for central carbon metabolism and promoting tumor growth under nutrient deprivation or nutrient stressed conditions. DOI: http://dx.doi.org/10.7554/eLife.10250.001 PMID:26920219

  4. Low black carbon concentration in agricultural soils of central and northern Ethiopia.

    Science.gov (United States)

    Yli-Halla, Markku; Rimhanen, Karoliina; Muurinen, Johanna; Kaseva, Janne; Kahiluoto, Helena

    2018-08-01

    Soil carbon (C) represents the largest terrestrial carbon stock and is key for soil productivity. Major fractions of soil C consist of organic C, carbonates and black C. The turnover rate of black C is lower than that of organic C, and black C abundance decreases the vulnerablility of soil C stock to decomposition under climate change. The aim of this study was to determine the distribution of soil C in different pools and impact of agricultural management on the abundance of different species. Soil C fractions were quantified in the topsoils (0-15cm) of 23 sites in the tropical highlands of Ethiopia. The sites in central Ethiopia represented paired plots of agroforestry and adjacent control plots where cereal crops were traditionally grown in clayey soils. In the sandy loam and loam soils of northern Ethiopia, the pairs represented restrained grazing with adjacent control plots with free grazing, and terracing with cereal-based cropping with adjacent control plots without terracing. Soil C contained in carbonates, organic matter and black C along with total C was determined. The total C median was 1.5% (range 0.3-3.6%). The median proportion of organic C was 85% (range 53-94%), 6% (0-41%) for carbonate C and 6% (4-21%) for black C. An increase was observed in the organic C and black C fractions attributable to agroforestry and restrained grazing. The very low concentration of the relatively stable black C fraction and the dominance of organic C in these Ethiopian soils suggest vulnerability to degradation and the necessity for cultivation practices maintaining the C stock. Copyright © 2018 Elsevier B.V. All rights reserved.

  5. Shell carbon isotope indicators of metabolic activity in the deep-sea mussel Bathymodiolus childressi

    Science.gov (United States)

    Riekenberg, P. M.; Carney, R. S.; Fry, B.

    2018-04-01

    The incorporation of metabolic carbon (Cm) into shells of mollusks has been used as an indicator of animal condition and availability of food resources in estuarine and freshwater settings. This study examines Cm in Bathymodiolus childressi, a marine cold seep mussel dependent on methanotrophic symbionts. As seeps develop, mature, and go quiescent, methane supply will vary and affect the amount of metabolic carbon deposited into the growing shell. B. childressi (n = 136) were live-collected from two seep sites over a 17 year period in the Northern Gulf of Mexico to investigate whether changes in Cm were detectable between sites and across years. Significant differences in Cm were observed between mussel populations at Brine Pool (15.4 ± 0.4%) and Bush Hill (10.3 ± 0.3%). Cm also changed significantly within each site across year (Bush Hill 1991: 12.2 ± 0.5%, 1992: 17.3 ± 0.8%) and decadal time scales (Brine Pool 1989: 15.5 ± 0.7%, 2006: 19.5 ± 0.7%). These findings agree with previous studies that found mussel condition was higher at Brine Pool and correlate well with a trophic mixing model that indicated significantly higher methane source utilization at the Brine Pool (65 ± 1.1%) than at Bush Hill (49 ± 1.6%). Further development of this method should allow for assessment of Cm in shell assemblages as an indicator of historical resource availability at both active and former cold seep sites.

  6. Micronutrients Involved in One-Carbon Metabolism and Risk of Breast Cancer Subtypes.

    Directory of Open Access Journals (Sweden)

    Ilaria Cancarini

    Full Text Available Vitamins involved in one-carbon metabolism are hypothesized to influence breast cancer (BC risk. However, epidemiologic studies that examined associations between B vitamin intake and BC risk have provided inconsistent results. We prospectively examined, in the Italian ORDET cohort, whether B vitamin consumption was associated with risk of BC and BC subtypes.After a mean follow-up of 16.5 years, 391 BCs were diagnosed among 10,786 cohort women. B vitamin intakes were estimated from food frequency questionnaires. Cox proportional hazard models adjusted for energy intake and confounders, estimated hazard ratios (HR with 95% confidence intervals (CIs for BC according to intake.RRs were 0.61 (95% CI 0.38-0.97 highest vs. lowest quartile; P trend 0.025 for thiamine; 0.48 (95% CI 0.32-0.71; P trend <0.001 for riboflavin; 0.59 (95% CI 0.39-0.90; P trend 0.008 for vitamin B6, and 0.65 (95% CI 0.44-0.95; P trend 0.021 for folate. As regards risk of BC subtypes, high riboflavin and folate were significantly associated with lower risk of estrogen receptor positive (ER+ and progesterone receptor positive (PR+ cancers, and high thiamine was associated with lower risk of ER-PR- cancers. High riboflavin was associated with lower risk of both HER2+ and HER2- cancers, high folate with lower risk of HER2- disease, and high thiamine with HER2+ disease.These findings support protective effects of thiamine and one-carbon metabolism vitamins (folate, riboflavin, and vitamin B6 against BC in general; while folate may also protect against ER+PR+ and HER2- disease; and thiamine against ER-PR-, and HER2+ disease.

  7. The post-transcriptional regulatory system CSR controls the balance of metabolic pools in upper glycolysis of Escherichia coli.

    Science.gov (United States)

    Morin, Manon; Ropers, Delphine; Letisse, Fabien; Laguerre, Sandrine; Portais, Jean-Charles; Cocaign-Bousquet, Muriel; Enjalbert, Brice

    2016-05-01

    Metabolic control in Escherichia coli is a complex process involving multilevel regulatory systems but the involvement of post-transcriptional regulation is uncertain. The post-transcriptional factor CsrA is stated as being the only regulator essential for the use of glycolytic substrates. A dozen enzymes in the central carbon metabolism (CCM) have been reported as potentially controlled by CsrA, but its impact on the CCM functioning has not been demonstrated. Here, a multiscale analysis was performed in a wild-type strain and its isogenic mutant attenuated for CsrA (including growth parameters, gene expression levels, metabolite pools, abundance of enzymes and fluxes). Data integration and regulation analysis showed a coordinated control of the expression of glycolytic enzymes. This also revealed the imbalance of metabolite pools in the csrA mutant upper glycolysis, before the phosphofructokinase PfkA step. This imbalance is associated with a glucose-phosphate stress. Restoring PfkA activity in the csrA mutant strain suppressed this stress and increased the mutant growth rate on glucose. Thus, the carbon storage regulator system is essential for the effective functioning of the upper glycolysis mainly through its control of PfkA. This work demonstrates the pivotal role of post-transcriptional regulation to shape the carbon metabolism. © 2016 John Wiley & Sons Ltd.

  8. Carbon and energy metabolism of atp mutants of Escherichia coli

    DEFF Research Database (Denmark)

    Jensen, Peter Ruhdal; Michelsen, Ole

    1992-01-01

    strain is not able to utilize the resulting proton motive force for ATP synthesis. Indeed, the ratio of ATP concentration to ADP concentration was decreased from 19 in the wild type to 7 in the atp mutant, and the membrane potential of the atp deletion strain was increased by 20%, confirming......The membrane-bound H+-ATPase plays a key role in free-energy transduction of biological systems. We report how the carbon and energy metabolism of Escherichia coli changes in response to deletion of the atp operon that encodes this enzyme. Compared with the isogenic wild-type strain, the growth...... rate and growth yield were decreased less than expected for a shift from oxidative phosphorylation to glycolysis alone as a source of ATP. Moreover, the respiration rate of a atp deletion strain was increased by 40% compared with the wild-type strain. This result is surprising, since the atp deletion...

  9. Integrative investigation of metabolic and transcriptomic data

    Directory of Open Access Journals (Sweden)

    Önsan Z İlsen

    2006-04-01

    Full Text Available Abstract Background New analysis methods are being developed to integrate data from transcriptome, proteome, interactome, metabolome, and other investigative approaches. At the same time, existing methods are being modified to serve the objectives of systems biology and permit the interpretation of the huge datasets currently being generated by high-throughput methods. Results Transcriptomic and metabolic data from chemostat fermentors were collected with the aim of investigating the relationship between these two data sets. The variation in transcriptome data in response to three physiological or genetic perturbations (medium composition, growth rate, and specific gene deletions was investigated using linear modelling, and open reading-frames (ORFs whose expression changed significantly in response to these perturbations were identified. Assuming that the metabolic profile is a function of the transcriptome profile, expression levels of the different ORFs were used to model the metabolic variables via Partial Least Squares (Projection to Latent Structures – PLS using PLS toolbox in Matlab. Conclusion The experimental design allowed the analyses to discriminate between the effects which the growth medium, dilution rate, and the deletion of specific genes had on the transcriptome and metabolite profiles. Metabolite data were modelled as a function of the transcriptome to determine their congruence. The genes that are involved in central carbon metabolism of yeast cells were found to be the ORFs with the most significant contribution to the model.

  10. Architecture and evolution of an Early Permian carbonate complex on a tectonically active island in east-central California

    Science.gov (United States)

    Stevens, Calvin H.; Magginetti, Robert T.; Stone, Paul

    2015-01-01

    The newly named Upland Valley Limestone represents a carbonate complex that developed on and adjacent to a tectonically active island in east-central California during a brief interval of Early Permian (late Artinskian) time. This lithologically unique, relatively thin limestone unit lies within a thick sequence of predominantly siliciclastic rocks and is characterized by its high concentration of crinoidal debris, pronounced lateral changes in thickness and lithofacies, and a largely endemic fusulinid fauna. Most outcrops represent a carbonate platform and debris derived from it and shed downslope, but another group of outcrops represents one or possibly more isolated carbonate buildups that developed offshore from the platform. Tectonic activity in the area occurred before, probably during, and after deposition of this short-lived carbonate complex.

  11. [Carbon emissions and low-carbon regulation countermeasures of land use change in the city and town concentrated area of central Liaoning Province, China].

    Science.gov (United States)

    Xi, Feng-ming; Liang, Wen-juan; Niu, Ming-fen; Wang, Jiao-yue

    2016-02-01

    Carbon emissions due to land use change have an important impact on global climate change. Adjustment of regional land use patterns has a great scientific significance to adaptation to a changing climate. Based on carbon emission/absorption parameters suitable for Liaoning Province, this paper estimated the carbon emission of land use change in the city and town concentrated area of central Liaoning Province. The results showed that the carbon emission and absorption were separately 308.51 Tg C and 11.64 Tg C from 1997 to 2010. It meant 3.8% of carbon emission. was offset by carbon absorption. Among the 296.87 Tg C net carbon emission of land use change, carbon emission of remaining land use type was 182.24 Tg C, accounting for 61.4% of the net carbon emission, while the carbon emission of land use transformation was 114.63 Tg C, occupying the rest 38.6% of net carbon emission. Through quantifying the mapping relationship between land use change and carbon emission, it was shown that during 1997-2004 the contributions of remaining construction land (40.9%) and cropland transform ation to construction land (40.6%) to carbon emission were larger, but the greater contributions to carbon absorption came from cropland transformation to forest land (38.6%) and remaining forest land (37.5%). During 2004-2010, the land use types for carbon emission and absorption were the same to the period of 1997-2004, but the contribution of remaining construction land to carbon emission increased to 80.6%, and the contribution of remaining forest land to carbon absorption increased to 71.7%. Based on the carbon emission intensity in different land use types, we put forward the low-carbon regulation countermeasures of land use in two aspects. In carbon emission reduction, we should strict control land transformation to construction land, increase the energy efficiency of construction land, and avoid excessive development of forest land and water. In carbon sink increase, we should

  12. The Effects of Legumes on Metabolic Features, Insulin Resistance and Hepatic Function Tests in Women with Central Obesity: A Randomized Controlled Trial

    OpenAIRE

    Mohammad Alizadeh; Rasool Gharaaghaji; Bahram Pourghassem Gargari

    2014-01-01

    Background: The effect of high-legume hypocaloric diet on metabolic features in women is unclear. This study provided an opportunity to find effects of high-legume diet on metabolic features in women who consumed high legumes at pre-study period. Methods: In this randomized controlled trial after 2 weeks of a run-in period on an isocaloric diet, 42 premenopausal women with central obesity were randomly assigned into two groups: (1) Hypocaloric diet enriched in legumes (HDEL) and (2) hypoc...

  13. Frozen in Time? Microbial strategies for survival and carbon metabolism over geologic time in a Pleistocene permafrost chronosequence

    Science.gov (United States)

    Mackelprang, R.; Douglas, T. A.; Waldrop, M. P.

    2014-12-01

    Permafrost soils have received tremendous interest due to their importance as a global carbon store with the potential to be thawed over the coming centuries. Instead of being 'frozen in time,' permafrost contains active microbes. Most metagenomic studies have focused on Holocene aged permafrost. Here, we target Pleistocene aged ice and carbon rich permafrost (Yedoma), which can differ in carbon content and stage of decay. Our aim was to understand how microbes in the permafrost transform organic matter over geologic time and to identify physiological and biochemical adaptations that enable long-term survival. We used next-generation sequencing to characterize microbial communities along a permafrost age gradient. Samples were collected from the Cold Regions Research and Engineering Laboratory (CRREL) Permafrost Tunnel near Fox, AK, which penetrates a hillside providing access to permafrost ranging in age from 12 to 40 kyr. DNA was extracted directly from unthawed samples. 16S rRNA amplicon (16S) and shotgun metagenome sequencing revealed significant age-driven differences. First, microbial diversity declines with permafrost age, likely due to long-term exposure to environmental stresses and a reduction in metabolic resources. Second, we observed taxonomic differences among ages, with an increasing abundance of Firmicutes (endospore-formers) in older samples, suggesting that dormancy is a common survival strategy in older permafrost. Ordination of 16S and metagenome data revealed age-based clustering. Genes differing significantly between age categories included those involved in lipopolysaccharide assembly, cold-response, and carbon processing. These data point to the physiological adaptations to long-term frozen conditions and to the metabolic processes utilized in ancient permafrost. In fact, a gene common in older samples is involved in cadaverine production, which could potentially explain the putrefied smell of Pleistocene aged permafrost. Coupled with soil

  14. An alternate metabolic hypothesis for a binary mixture of trichloroethylene and carbon tetrachloride: application of physiologically based pharmacokinetic (PBPK) modeling in rats.

    Science.gov (United States)

    Carbon tetrachloride (CC4) and trichloroethylene (TCE) are hepatotoxic volatile organic compounds (VOCs) and environmental contaminants. Previous physiologically based pharmacokinetic (PBPK) models describe the kinetics ofindividual chemical disposition and metabolic clearance fo...

  15. Possible role for abscisic acid in regulation of photosynthetic and photorespiratory carbon metabolism in barley leaves

    International Nuclear Information System (INIS)

    Popova, L.P.; Tsonev, T.D.; Vaklinova, S.G.

    1987-01-01

    The influence of abscisic acid (ABA) on carbon metabolism, rate of photorespiration, and the activity of the photorespiratory enzymes ribulose bisphosphate oxygenase and glycolate oxidase in 7-day-old barley seedlings (Hordeum vulgare L. var. Alfa) was investigated. Plants treated with ABA had enhanced incorporation of labeled carbon from 14 CO 2 into glycolic acid, glycine, and serine, while 14 C incorporation into 3-phosphoglyceric acid and sugarphosphate esters was depressed. Parallel with this effect, treated plants showed a rise in activity of RuBP oxygenase and glycolic acid oxidase. The rate of photorespiration was increased twofold by ABA treatment at IO -6 molar while the CO 2 -compensation point increased 46% and stomatal resistance increased more than twofold over control plants

  16. Mitochondrial Carriers Link the Catabolism of Hydroxyaromatic Compounds to the Central Metabolism in Candida parapsilosis

    Directory of Open Access Journals (Sweden)

    Igor Zeman

    2016-12-01

    Full Text Available The pathogenic yeast Candida parapsilosis metabolizes hydroxyderivatives of benzene and benzoic acid to compounds channeled into central metabolism, including the mitochondrially localized tricarboxylic acid cycle, via the 3-oxoadipate and gentisate pathways. The orchestration of both catabolic pathways with mitochondrial metabolism as well as their evolutionary origin is not fully understood. Our results show that the enzymes involved in these two pathways operate in the cytoplasm with the exception of the mitochondrially targeted 3-oxoadipate CoA-transferase (Osc1p and 3-oxoadipyl-CoA thiolase (Oct1p catalyzing the last two reactions of the 3-oxoadipate pathway. The cellular localization of the enzymes indicates that degradation of hydroxyaromatic compounds requires a shuttling of intermediates, cofactors, and products of the corresponding biochemical reactions between cytosol and mitochondria. Indeed, we found that yeast cells assimilating hydroxybenzoates increase the expression of genes SFC1, LEU5, YHM2, and MPC1 coding for succinate/fumarate carrier, coenzyme A carrier, oxoglutarate/citrate carrier, and the subunit of pyruvate carrier, respectively. A phylogenetic analysis uncovered distinct evolutionary trajectories for sparsely distributed gene clusters coding for enzymes of both pathways. Whereas the 3-oxoadipate pathway appears to have evolved by vertical descent combined with multiple losses, the gentisate pathway shows a striking pattern suggestive of horizontal gene transfer to the evolutionarily distant Mucorales.

  17. 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.

  18. Metabolism of carbon-14 labelled l-tryptophan, l-kynerenine and hydroxy-l-kynerenine in miners with scleroderma

    International Nuclear Information System (INIS)

    Hankes, L.V.; De Bruin, E.; Jansen, C.R.; Voster, L.; Schmaeler, M.

    1977-01-01

    Six South African white miners were studied with the 2-g l-tryptophan load test and tracer doses of L-tryptophan-7a-carbon-14, L-kynurenine-keto-carbon-14 and hydroxy-L-kynerenine-keto-carbon-14. The breath 14 CO 2 and 14 urinary metabolites were measured. When they were compared with a previous study of American women with scleroderma, similar 14 CO 2 and tryptophan metabolite excretion patterns were observed in the data from the miners. The labelled quinolinic acid excretion was more significantly elevated in the South African miners' urine than in the urine of the American women. The data from both studies suggest that some patients with scleroderma have an altered step in the tryptophan metabolic pathway after hydroxy-anthranilic acid. What relationship exists between the induction of pulmonary silicosis and the subsequent development of scleroderma, requires additional human studies

  19. Plant metabolic modeling: achieving new insight into metabolism and metabolic engineering.

    Science.gov (United States)

    Baghalian, Kambiz; Hajirezaei, Mohammad-Reza; Schreiber, Falk

    2014-10-01

    Models are used to represent aspects of the real world for specific purposes, and mathematical models have opened up new approaches in studying the behavior and complexity of biological systems. However, modeling is often time-consuming and requires significant computational resources for data development, data analysis, and simulation. Computational modeling has been successfully applied as an aid for metabolic engineering in microorganisms. But such model-based approaches have only recently been extended to plant metabolic engineering, mainly due to greater pathway complexity in plants and their highly compartmentalized cellular structure. Recent progress in plant systems biology and bioinformatics has begun to disentangle this complexity and facilitate the creation of efficient plant metabolic models. This review highlights several aspects of plant metabolic modeling in the context of understanding, predicting and modifying complex plant metabolism. We discuss opportunities for engineering photosynthetic carbon metabolism, sucrose synthesis, and the tricarboxylic acid cycle in leaves and oil synthesis in seeds and the application of metabolic modeling to the study of plant acclimation to the environment. The aim of the review is to offer a current perspective for plant biologists without requiring specialized knowledge of bioinformatics or systems biology. © 2014 American Society of Plant Biologists. All rights reserved.

  20. Metabolic engineering of Corynebacterium glutamicum aimed at alternative carbon sources and new products

    Directory of Open Access Journals (Sweden)

    Volker Fritz Wendisch

    2012-10-01

    Full Text Available Corynebacterium glutamicum is well known as the amino acid-producing workhorse of fermentation industry, being used for multi-million-ton scale production of glutamate and lysine for more than 60 years. However, it is only recently that extensive research has focused on engineering it beyond the scope of amino acids. Meanwhile, a variety of corynebacterial strains allows access to alternative carbon sources and/or allows production of a wide range of industrially relevant compounds. Some of these efforts set new standards in terms of titers and productivities achieved whereas others represent a proof-of-principle. These achievements manifest the position of C. glutamicum as an important industrial microorganism with capabilities far beyond the traditional amino acid production. In this review we focus on the state of the art of metabolic engineering of C. glutamicum for utilization of alternative carbon sources, (e.g. coming from wastes and unprocessed sources, and construction of C. glutamicum strains for production of new products such as diamines, organic acids and alcohols.

  1. Environmental dynamics and carbon accumulation rate of a tropical peatland in Central Sumatra, Indonesia

    Science.gov (United States)

    Hapsari, Kartika Anggi; Biagioni, Siria; Jennerjahn, Tim C.; Reimer, Peter Meyer; Saad, Asmadi; Achnopha, Yudhi; Sabiham, Supiandi; Behling, Hermann

    2017-08-01

    Tropical peatlands are important for the global carbon cycle as they store 18% of the total global peat carbon. As they are vulnerable to changes in temperature and precipitation, a rapidly changing environment endangers peatlands and their carbon storage potential. Understanding the mechanisms of peatland carbon accumulation from studying past developments may, therefore, help to assess the future role of tropical peatlands. Using a multi-proxy palaeoecological approach, a peat core taken from the Sungai Buluh peatland in Central Sumatra has been analyzed for its pollen and spore, macro charcoal and biogeochemical composition. The result suggests that peat and C accumulation rates were driven mainly by sea level change, river water level, climatic variability and anthropogenic activities. It is also suggested that peat C accumulation in Sungai Buluh is correlated to the abundance of Freycinetia, Myrtaceae, Calophyllum, Stemonuraceae, Ficus and Euphorbiaceae. Sungai Buluh has reasonable potential for being a future global tropical peat C sinks. However, considering the impact of rapid global climate change in addition to land-use change following rapid economic growth in Indonesia, such potential may be lost. Taking advantage of available palaeoecological records and advances made in Quaternary studies, some considerations for management practice such as identification of priority taxa and conservation sites are suggested.

  2. U-Th age evidence from carbonate veins for episodic crustal deformation of Central Anatolian Volcanic Province

    Science.gov (United States)

    Karabacak, Volkan; Uysal, I. Tonguç; Ünal-İmer, Ezgi; Mutlu, Halim; Zhao, Jian-xin

    2017-12-01

    Central Anatolia represents one of the most outstanding examples of intraplate deformation related to both continental collision and back-arc extension generating non-uniformly distributed stress fields. In this study, we provide direct field evidence of various stress directions and investigate carbonate-filled fracture systems in the Central Anatolian Volcanic Province using U/Th geochronology and isotope geochemistry for evaluating the episodes of latest volcanic activity under regional stress. Field data reveal two independent fracture systems in the region. Successive fracture development has been controlled by two different volcanic eruption centers (Hasandağ Composite Volcano and Acıgöl Caldera). Trace element, and stable (C and O) and radiogenic (Sr) isotope compositions of carbonate veins indicate different fluid migration pathways for two different fracture systems. The U/Th age data for carbonate veins of two independent fracture systems indicate that the crustal deformation intensified during 7 episodic periods in the last 150 ka. The NNE-trending first fracture system was formed as a result of strain cycles in a period from 149 ± 2.5, through 91 ± 1.5 to 83 ± 2.5 ka BP. Subsequent deformation events represented by the ENE-trending second fracture zone have been triggered during the period of 53 ± 3.5, 44 ± 0.6 and 34 ± 1 ka BP before the first fracture zone resumed the activity at about 4.7 ± 0.15 ka BP. Although further studies are needed to evaluate statistical significance of age correlations, the periods of carbonate precipitation inferred from U-Th age distributions in this study are comparable with the previous dating results of surrounding volcanic eruption events.

  3. Inter-relationships between single carbon units' metabolism and resting energy expenditure in weight-losing patients with small cell lung cancer. Effects of methionine supply and chemotherapy

    DEFF Research Database (Denmark)

    Sengeløv, H; Hansen, O P; Simonsen, L

    1994-01-01

    The one-carbon unit metabolism was investigated in 8 weight-losing patients with small cell carcinoma of the lung (SCLC). At diagnosis, 6 of the 8 patients had elevated formiminoglutamic acid (FIGLU) excretion after a histidine load, suggesting a lack of one-carbon units. In accordance...

  4. Analysis of the energy metabolism of urban socioeconomic sectors and the associated carbon footprints: Model development and a case study for Beijing

    International Nuclear Information System (INIS)

    Zhang, Yan; Zheng, Hongmei; Fath, Brian D.

    2014-01-01

    Cities consume 80% of the world's energy; therefore, analyzing urban energy metabolism and the resulting carbon footprint provides basic data for formulating target carbon emission reductions. While energy metabolism includes both direct and indirect consumptions among sectors, few researchers have studied indirect consumption due to a lack of data. In this study, we used input–output analysis to calculate the energy flows among directly linked sectors. Building on this, we used ecological network analysis to develop a model of urban energy flows and also account for energy consumption embodied by the flows among indirectly linked sectors (represented numerically as paths with a length of 2 or more). To illustrate the model, monetary input–output tables for Beijing from 2000 to 2010 were analyzed to determine the embodied energy consumption and associated carbon footprints of these sectors. This analysis reveals the environmental pressure based on the source (energy consumption) and sink (carbon footprint) values. Indirect consumption was Beijing's primary form, and the carbon footprint therefore resulted mainly from indirect consumption (both accounting for ca. 60% of the total, though with considerable variation among sectors). To reduce emissions, the utilization efficiency of indirect consumption must improve. - Highlights: • We quantified the embodied energy transfers among Beijing's socioeconomic sectors. • We calculated the sectors' intensity of energy consumption and carbon footprint. • The indirect energy consumption was higher than the direct for all sectors. • The high-indirect-consumption sectors are at the end of industrial supply chains. • High-indirect-consumption sectors can improve upstream products energy efficiency

  5. 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

  6. 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

  7. Inter-relationships between single carbon units' metabolism and resting energy expenditure in weight-losing patients with small cell lung cancer. Effects of methionine supply and chemotherapy

    DEFF Research Database (Denmark)

    Sengeløv, H; Hansen, O P; Simonsen, L

    1994-01-01

    The one-carbon unit metabolism was investigated in 8 weight-losing patients with small cell carcinoma of the lung (SCLC). At diagnosis, 6 of the 8 patients had elevated formiminoglutamic acid (FIGLU) excretion after a histidine load, suggesting a lack of one-carbon units. In accordance, a signifi...

  8. The metabolism of the Antartic crytoendolithic microbiota

    Science.gov (United States)

    Vestal, J. Robie

    1989-01-01

    The carbon metabolism of the cryptoendolithic microbiota in sandstones from the Ross Desert region of Antarctica was studied in situ and in vitro. Organic and inorganic compounds were metabolized by the microbiota, with bicarbonate being metabolized maximally in the light. There was a linear response of photosynthesis to light up to 200 to 300 micromole photons/sq m/s. The community photosynthetic response to temperature was a minimum at -5 C, two optima at +5 and +15 C and a maximum at +35 C. Photosynthetic metabolism occurred maximally in the presence of liquid water, but could occur in an environment of water vapor. Biomass of the cryptoendolithic microbiota was measured as the amount of lipid phosphate present. The in situ biomass ranged from 1.92 to 3.26 g carbon/sq m of rock and 2 orders of magnitude less than epilithic lichen microbiota from Antarctica in a location 7 degrees more north in latitude. With these data, it was possible to calculate primary production and carbon turnover in this simple microbiota. Production values ranged from 0.108 to 4.41 mg carbon/sq m/yr, while carbon turnover values ranged from 576 to 23,520 years. These values are the lowest and longest yet recorded for any ecosystem on Earth. If life did evolve on Mars to the level of prokaryotes or primitive eukaryotes, the possibility that the organisms retreated, to the protection of the inside of the rock so that metabolism could continue during planetary cooling, cannot be overlooked.

  9. Clinical utility of polymorphisms in one-carbon metabolism for breast cancer risk prediction

    Directory of Open Access Journals (Sweden)

    Shaik Mohammad Naushad

    2011-01-01

    Full Text Available This study addresses the issues in translating the laboratory derived data obtained during discovery phase of research to a clinical setting using a breast cancer model. Laboratory-based risk assessment indi-cated that a family history of breast cancer, reduced folate carrier 1 (RFC1 G80A, thymidylate synthase (TYMS 5’-UTR 28bp tandem repeat, methylene tetrahydrofolate reductase (MTHFR C677T and catecholamine-O-methyl transferase (COMT genetic polymorphisms in one-carbon metabolic pathway increase the risk for breast cancer. Glutamate carboxypeptidase II (GCPII C1561T and cytosolic serine hydroxymethyl transferase (cSHMT C1420T polymorphisms were found to decrease breast cancer risk. In order to test the clinical validity of this information in the risk prediction of breast cancer, data was stratified based on number of protective alleles into four categories and in each category sensitivity and 1-specificity values were obtained based on the distribution of number of risk alleles in cases and controls. Receiver operating characteristic (ROC curves were plotted and the area under ROC curve (C was used as a measure of discriminatory ability between cases and controls. In subjects without any protective allele, aberrations in one-carbon metabolism showed perfect prediction (C=0.93 while the predictability was lost in subjects with one protective allele (C=0.60. However, predictability increased steadily with increasing number of protective alleles (C=0.63 for 2 protective alleles and C=0.71 for 3 protective alleles. The cut-off point for discrimination was >4 alleles in all predictable combinations. Models of this kind can serve as valuable tools in translational re-search, especially in identifying high-risk individuals and reducing the disease risk either by life style modification or by medical intervention.

  10. Effect of Temperature on Precipitation Rate of Calcium Carbonate Produced through Microbial Metabolic Process of Bio Materials

    Directory of Open Access Journals (Sweden)

    Prima Yane Putri

    2016-09-01

    Full Text Available Concrete is the most widely used construction material in civil engineering. But plain concrete is a brittle material and has little resistance to cracking. The cracking in concrete promotes deterioration such as the corrosion of reinforcing rebar, therefore, repair in filling the crack is often carried out. Recently, repair methods using bio-based materials associated with microbial metabolic processes leading to precipitation of calcium carbonate have been intensively studied. In this study, influencing factors on the precipitation rate depending on the constituents of bio-based material comprising yeast, glucose and calcium acetate mixed in tris buffer solution was examined for improving the rate of initial reactions. In addition, effect of temperature change on the amount of calcium carbonate precipitation was also investigated. The precipitates were identified by X-ray diffraction. It was shown that the increase of temperature lead to a change on calcium carbonate precipitation and caused the pH decrease under 7.0.

  11. Systematically variable planktonic carbon metabolism along a land-to-lake gradient in a Great Lakes coastal zone.

    Science.gov (United States)

    Weinke, Anthony D; Kendall, Scott T; Kroll, Daniel J; Strickler, Eric A; Weinert, Maggie E; Holcomb, Thomas M; Defore, Angela A; Dila, Deborah K; Snider, Michael J; Gereaux, Leon C; Biddanda, Bopaiah A

    2014-11-01

    During the summers of 2002-2013, we measured rates of carbon metabolism in surface waters of six sites across a land-to-lake gradient from the upstream end of drowned river-mouth Muskegon Lake (ML) (freshwater estuary) to 19 km offshore in Lake Michigan (LM) (a Great Lake). Despite considerable inter-year variability, the average rates of gross production (GP), respiration (R) and net production (NP) across ML (604 ± 58, 222 ± 22 and 381 ± 52 µg C L -1 day -1 , respectively) decreased steeply in the furthest offshore LM site (22 ± 3, 55 ± 17 and -33 ± 15 µg C L -1 day -1 , respectively). Along this land-to-lake gradient, GP decreased by 96 ± 1%, whereas R only decreased by 75 ± 9%, variably influencing the carbon balance along this coastal zone. All ML sites were consistently net autotrophic (mean GP:R = 2.7), while the furthest offshore LM site was net heterotrophic (mean GP:R = 0.4). Our study suggests that pelagic waters of this Great Lakes coastal estuary are net carbon sinks that transition into net carbon sources offshore. Reactive and dynamic estuarine coastal zones everywhere may contribute similarly to regional and global carbon cycles.

  12. Modulation of snow reflectance and snowmelt from Central Asian glaciers by anthropogenic black carbon.

    Science.gov (United States)

    Schmale, Julia; Flanner, Mark; Kang, Shichang; Sprenger, Michael; Zhang, Qianggong; Guo, Junming; Li, Yang; Schwikowski, Margit; Farinotti, Daniel

    2017-01-12

    Deposited mineral dust and black carbon are known to reduce the albedo of snow and enhance melt. Here we estimate the contribution of anthropogenic black carbon (BC) to snowmelt in glacier accumulation zones of Central Asia based on in-situ measurements and modelling. Source apportionment suggests that more than 94% of the BC is emitted from mostly regional anthropogenic sources while the remaining contribution comes from natural biomass burning. Even though the annual deposition flux of mineral dust can be up to 20 times higher than that of BC, we find that anthropogenic BC causes the majority (60% on average) of snow darkening. This leads to summer snowmelt rate increases of up to 6.3% (7 cm a -1 ) on glaciers in three different mountain environments in Kyrgyzstan, based on albedo reduction and snowmelt models.

  13. Metabolic engineering of cyanobacteria for the synthesis of commodity products

    NARCIS (Netherlands)

    Angermayr, S.A.; Gorchs Rovira, A.; Hellingwerf, K.J.

    2015-01-01

    Through metabolic engineering cyanobacteria can be employed in biotechnology. Combining the capacity for oxygenic photosynthesis and carbon fixation with an engineered metabolic pathway allows carbon-based product formation from CO2, light, and water directly. Such cyanobacterial 'cell factories'

  14. Engineering strategy of yeast metabolism for higher alcohol production

    Directory of Open Access Journals (Sweden)

    Shimizu Hiroshi

    2011-09-01

    Full Text Available Abstract Background While Saccharomyces cerevisiae is a promising host for cost-effective biorefinary processes due to its tolerance to various stresses during fermentation, the metabolically engineered S. cerevisiae strains exhibited rather limited production of higher alcohols than that of Escherichia coli. Since the structure of the central metabolism of S. cerevisiae is distinct from that of E. coli, there might be a problem in the structure of the central metabolism of S. cerevisiae. In this study, the potential production of higher alcohols by S. cerevisiae is compared to that of E. coli by employing metabolic simulation techniques. Based on the simulation results, novel metabolic engineering strategies for improving higher alcohol production by S. cerevisiae were investigated by in silico modifications of the metabolic models of S. cerevisiae. Results The metabolic simulations confirmed that the high production of butanols and propanols by the metabolically engineered E. coli strains is derived from the flexible behavior of their central metabolism. Reducing this flexibility by gene deletion is an effective strategy to restrict the metabolic states for producing target alcohols. In contrast, the lower yield using S. cerevisiae originates from the structurally limited flexibility of its central metabolism in which gene deletions severely reduced cell growth. Conclusions The metabolic simulation demonstrated that the poor productivity of S. cerevisiae was improved by the introduction of E. coli genes to compensate the structural difference. This suggested that gene supplementation is a promising strategy for the metabolic engineering of S. cerevisiae to produce higher alcohols which should be the next challenge for the synthetic bioengineering of S. cerevisiae for the efficient production of higher alcohols.

  15. Long-range transported dissolved organic matter, ions and black carbon deposited on Central Asian snow covered glaciers

    Science.gov (United States)

    Schmale, Julia; Kang, Shichang; Peltier, Richard

    2014-05-01

    Ninety percent of the Central Asian population depend on water precipitated in the mountains stored in glaciers and snow cover. Accelerated melting of the snow and ice can be induced by the deposition of airborne impurities such as mineral dust, black carbon and co-emitted species leading to significant reductions of the surface albedo. However, Central Asia is a relatively understudied region and data on the source regions, chemical and microphysical characteristics as well as modelling studies of long-range transported air pollution and dust to the Tien Shan mountains is very scarce. We studied the atmospheric aerosol deposited most likely between summer 2012 and summer 2013on three different glaciers in the Kyrgyz Republic. Samples were taken from four snow pits on the glaciers Abramov (2 pits, 39.59 °N, 71.56 °E, 4390 m elevation, 240 cm deep, and 39.62°N, 71.52 °E, 4275 m elevation, 125 cm deep), Ak-Shiirak (41.80 °N, 78.18 °E, 4325 m elevation, 75 cm deep) and Suek (41.78 °N, 77.75 °E, 4341 m elevation, 200 cm deep). The latter two glaciers are located roughly within 6 and 38 km of an operating gold mine. The snow was analyzed for black carbon, ions, metals and organic carbon. We here focus on the results of inorganic ion measurements and organic carbon speciation based on analysis with an Aerodyne high-resolution time-of-flight aerosol spectrometer (HR-ToF-AMS) and potential pollution sources that can be deduced from the chemical information as well as back trajectories. Average contributions of snow impurities measured by the HR-ToF-AMS were dominated by organic carbon. Relative concentrations of organic carbon, sulfate, nitrate and ammonium in snow were 86 %, 3 %, 9 % and 2 % respectively for Abramov, 92 %, 1 %, 5 % and 1 % for Suek, and 95 %, 1 %, 3 % and 1 % for Ak-Shiirak. Generally, impurities on Suek and Ak-Shiirak were three and five times higher than on Abramov. Mass concentrations of organic carbon were on average 6 times higher in samples

  16. Effects of photoperiodism on the metabolism of carbon compounds and the migration of these products in tobacco

    International Nuclear Information System (INIS)

    Farineau, Jack

    1961-01-01

    This research thesis addressed the influence of photoperiodism on migrations. The author more particularly studied migrations of carbon-compound metabolism products by using a tobacco leaf in presence of "1"4CO_2, and which thus contained a high quantity of radioactive compounds. Some experiments were performed on short durations (few hours), and others on longer durations (15 days). As far as the first ones were concerned, the author studied the content of the petiole and of the terminal bud, and the first reactions of integration of carbon 14 compounds of the sap in the leaf. As far as the second type of experiments is concerned, the author measured the quantities of radioactive products migrating towards the terminal bud [fr

  17. Differential proteomic analysis reveals novel links between primary metabolism and antibiotic production in Amycolatopsis balhimycina

    DEFF Research Database (Denmark)

    Gallo, G.; Renzone, G.; Alduina, R.

    2010-01-01

    A differential proteomic analysis, based on 2-DE and MS procedures, was performed on Amycolatopsis balhimycina DSM5908, the actinomycete producing the vancomycin-like antibiotic balhimycin. A comparison of proteomic profiles before and during balhimycin production characterized differentially...... available over the World Wide Web as interactive web pages (http://www.unipa.it/ampuglia/Abal-proteome-maps). Functional clustering analysis revealed that differentially expressed proteins belong to functional groups involved in central carbon metabolism, amino acid metabolism and protein biosynthesis...... intermediates, were upregulated during antibiotic production. qRT-PCR analysis revealed that 8 out of 14 upregulated genes showed a positive correlation between changes at translational and transcriptional expression level. Furthermore, proteomic analysis of two nonproducing mutants, restricted to a sub...

  18. Urban metabolism: A review of research methodologies

    International Nuclear Information System (INIS)

    Zhang, Yan

    2013-01-01

    Urban metabolism analysis has become an important tool for the study of urban ecosystems. The problems of large metabolic throughput, low metabolic efficiency, and disordered metabolic processes are a major cause of unhealthy urban systems. In this paper, I summarize the international research on urban metabolism, and describe the progress that has been made in terms of research methodologies. I also review the methods used in accounting for and evaluating material and energy flows in urban metabolic processes, simulation of these flows using a network model, and practical applications of these methods. Based on this review of the literature, I propose directions for future research, and particularly the need to study the urban carbon metabolism because of the modern context of global climate change. Moreover, I recommend more research on the optimal regulation of urban metabolic systems. Highlights: •Urban metabolic processes can be analyzed by regarding cities as superorganisms. •Urban metabolism methods include accounting, assessment, modeling, and regulation. •Research methodologies have improved greatly since this field began in 1965. •Future research should focus on carbon metabolism and optimal regulation. -- The author reviews research progress in the field of urban metabolism, and based on her literature review, proposes directions for future research

  19. Central melanin-concentrating hormone influences liver and adipose metabolism via specific hypothalamic nuclei and efferent autonomic/JNK1 pathways.

    OpenAIRE

    Imbernon, Monica; Beiroa, Daniel; Vázquez, María J.; Morgan, Donald A.; Veyrat–Durebex, Christelle; Porteiro, Begoña; Díaz–Arteaga, Adenis; Senra, Ana; Busquets, Silvia; Velásquez, Douglas A.; Al–Massadi, Omar; Varela, Luis; Gándara, Marina; López–Soriano, Francisco–Javier; Gallego, Rosalía

    2013-01-01

    BACKGROUND AIMS Specific neuronal circuits modulate autonomic outflow to liver and white adipose tissue. Melanin concentrating hormone (MCH) deficient mice are hypophagic lean and do not develop hepatosteatosis when fed a high fat diet. Herein we sought to investigate the role of MCH an orexigenic neuropeptide specifically expressed in the lateral hypothalamic area on hepatic and adipocyte metabolism. METHODS Chronic central administration of MCH and adenoviral vectors increasing MCH sign...

  20. Metabolic bone disease and central retinal degeneration in a kitten due to nutritional inadequacy of an all-meat raw diet

    Directory of Open Access Journals (Sweden)

    Catherine Lenox

    2015-05-01

    Full Text Available A 5-month-old castrated male Sphynx kitten presented with left hindlimb lameness shortly after adoption. Prior to adoption, the breeder had fed the kitten an exclusively raw chicken diet. Radiographs revealed generalized osteopenia and a left tibia–fibula fracture. Ophthalmic examination revealed corneal vascularization and opacity in the right eye, and lesions suggestive of feline central retinal degeneration in the left eye. The patient’s diagnoses included metabolic bone disease and feline central retinal degeneration, which can result from taurine deficiency. The kitten’s nutritional diseases were managed with a complete and balanced canned diet designed for kitten growth and with taurine supplementation.

  1. Modeling the carbon isotope composition of bivalve shells (Invited)

    Science.gov (United States)

    Romanek, C.

    2010-12-01

    The stable carbon isotope composition of bivalve shells is a valuable archive of paleobiological and paleoenvironmental information. Previous work has shown that the carbon isotope composition of the shell is related to the carbon isotope composition of dissolved inorganic carbon (DIC) in the ambient water in which a bivalve lives, as well as metabolic carbon derived from bivalve respiration. The contribution of metabolic carbon varies among organisms, but it is generally thought to be relatively low (e.g., 90%) in the shells from terrestrial organisms. Because metabolic carbon contains significantly more C-12 than DIC, negative excursions from the expected environmental (DIC) signal are interpreted to reflect an increased contribution of metabolic carbon in the shell. This observation contrasts sharply with modeled carbon isotope compositions for shell layers deposited from the inner extrapallial fluid (EPF). Previous studies have shown that growth lines within the inner shell layer of bivalves are produced during periods of anaerobiosis when acidic metabolic byproducts (e.g., succinic acid) are neutralized (or buffered) by shell dissolution. This requires the pH of EPF to decrease below ambient levels (~7.5) until a state of undersaturation is achieved that promotes shell dissolution. This condition may occur when aquatic bivalves are subjected to external stressors originating from ecological (predation) or environmental (exposure to atm; low dissolved oxygen; contaminant release) pressures; normal physiological processes will restore the pH of EPF when the pressure is removed. As a consequence of this process, a temporal window should also exist in EPF at relatively low pH where shell carbonate is deposited at a reduced saturation state and precipitation rate. For example, EPF chemistry should remain slightly supersaturated with respect to aragonite given a drop of one pH unit (6.5), but under closed conditions, equilibrium carbon isotope fractionation

  2. Decoding the dynamics of cellular metabolism and the action of 3-bromopyruvate and 2-deoxyglucose using pulsed stable isotope-resolved metabolomics.

    Science.gov (United States)

    Pietzke, Matthias; Zasada, Christin; Mudrich, Susann; Kempa, Stefan

    2014-01-01

    Cellular metabolism is highly dynamic and continuously adjusts to the physiological program of the cell. The regulation of metabolism appears at all biological levels: (post-) transcriptional, (post-) translational, and allosteric. This regulatory information is expressed in the metabolome, but in a complex manner. To decode such complex information, new methods are needed in order to facilitate dynamic metabolic characterization at high resolution. Here, we describe pulsed stable isotope-resolved metabolomics (pSIRM) as a tool for the dynamic metabolic characterization of cellular metabolism. We have adapted gas chromatography-coupled mass spectrometric methods for metabolomic profiling and stable isotope-resolved metabolomics. In addition, we have improved robustness and reproducibility and implemented a strategy for the absolute quantification of metabolites. By way of examples, we have applied this methodology to characterize central carbon metabolism of a panel of cancer cell lines and to determine the mode of metabolic inhibition of glycolytic inhibitors in times ranging from minutes to hours. Using pSIRM, we observed that 2-deoxyglucose is a metabolic inhibitor, but does not directly act on the glycolytic cascade.

  3. Why devote an entire issue to the topic of how nutrients in one-carbon metabolism play roles in modern medicine?

    Science.gov (United States)

    The vitamins that serve as essential co-factors in one-carbon metabolism-B2, B6, B9 (folate), and B12-have had a long and storied history in the field of medicine over the past two centuries, as have related intermediary metabolites such as methionine, homocysteine, betaine and choline. The megalobl...

  4. Discharge modulates stream metabolism dependence on fine particulate organic carbon in a Mediterranean WWTP-influenced stream

    Science.gov (United States)

    Drummond, J. D.; Bernal, S.; Meredith, W.; Schumer, R.; Martí Roca, E.

    2017-12-01

    Waste water treatment plant (WWTP) effluents constitute point source inputs of fine sediment, nutrients, carbon, and microbes to stream ecosystems. A range of responses to these inputs may be observed in recipient streams, including increases in respiration rates, which augment CO2 emissions to the atmosphere. Yet, little is known about which fractions of organic carbon (OC) contribute the most to stream metabolism in WWTP-influenced streams. Fine particulate OC (POC) represents ca. 40% of the total mass of OC in river networks, and is generally more labile than dissolved OC. Therefore, POC inputs from WWTPs could contribute disproportionately to higher rates of heterotrophic metabolism by stream microbial communities. The aim of this study was to investigate the influence of POC inputs from a WWTP effluent on the metabolism of a Mediterranean stream over a wide range of hydrologic conditions. We hypothesized that POC inputs would have a positive effect on respiration rates, and that the response to POC availability would be larger during low flows when the dilution capacity of the recipient stream is negligible. We focused on the easily resuspended fine sediment near the sediment-water interface (top 3 cm), as this region is a known hot spot for biogeochemical processes. For one year, samples of resuspended sediment were collected bimonthly at 7 sites from 0 to 800 m downstream of the WWTP point source. We measured total POC, organic matter (OM) content (%), and the associated metabolic activity of the resuspended sediment using the resazurin-resorufin smart tracer system as a proxy for aerobic ecosystem respiration. Resuspended sediment showed no difference in total POC over the year, while the OM content increased with decreasing discharge. This result together with the decreasing trend of total POC observed downstream of the point source during autumn after a long dry period, suggests that the WWTP effluent was the main contributor to stream POC. Furthermore

  5. Nuclear receptors and metabolism: from feast to famine.

    Science.gov (United States)

    Hong, Suk-Hyun; Ahmadian, Maryam; Yu, Ruth T; Atkins, Annette R; Downes, Michael; Evans, Ronald M

    2014-05-01

    The ability to adapt to cycles of feast and famine is critical for survival. Communication between multiple metabolic organs must be integrated to properly metabolise nutrients. By controlling networks of genes in major metabolic organs, nuclear hormone receptors (NHRs) play central roles in regulating metabolism in a tissue-specific manner. NHRs also establish daily rhythmicity by controlling the expression of core clock genes both centrally and peripherally. Recent findings show that many of the metabolic effects of NHRs are mediated through certain members of the fibroblast growth factor (FGF) family. This review focuses on the roles of NHRs in critical metabolic organs, including adipose tissue, liver and muscle, during the fed and fasted states, as well as their roles in circadian metabolism and downstream regulation of FGFs.

  6. Dynamic optimal control of homeostasis: an integrative system approach for modeling of the central nitrogen metabolism in Saccharomyces cerevisiae.

    Science.gov (United States)

    van Riel, N A; Giuseppin, M L; Verrips, C T

    2000-01-01

    The theory of dynamic optimal metabolic control (DOMC), as developed by Giuseppin and Van Riel (Metab. Eng., 2000), is applied to model the central nitrogen metabolism (CNM) in Saccharomyces cerevisiae. The CNM represents a typical system encountered in advanced metabolic engineering. The CNM is the source of the cellular amino acids and proteins, including flavors and potentially valuable biomolecules; therefore, it is also of industrial interest. In the DOMC approach the cell is regarded as an optimally controlled system. Given the metabolic genotype, the cell faces a control problem to maintain an optimal flux distribution in a changing environment. The regulation is based on strategies and balances feedback control of homeostasis and feedforward regulation for adaptation. The DOMC approach is an integrative, holistic approach, not based on mechanistic descriptions and (therefore) not biased by the variation present in biochemical and molecular biological data. It is an effective tool to structure the rapidly increasing amount of data on the function of genes and pathways. The DOMC model is used successfully to predict the responses of pulses of ammonia and glutamine to nitrogen-limited continuous cultures of a wild-type strain and a glutamine synthetase-negative mutant. The simulation results are validated with experimental data.

  7. Carbon isotopic patterns of amino acids associated with various microbial metabolic pathways and physiological conditions

    Science.gov (United States)

    Wang, P. L.; Hsiao, K. T.; Lin, L. H.

    2017-12-01

    Amino acids represent one of the most important categories of biomolecule. Their abundance and isotopic patterns have been broadly used to address issues related to biochemical processes and elemental cycling in natural environments. Previous studies have shown that various carbon assimilative pathways of microorganisms (e.g. autotrophy, heterotrophy and acetotrophy) could be distinguished by carbon isotopic patterns of amino acids. However, the taxonomic and catabolic coverage are limited in previous examination. This study aims to uncover the carbon isotopic patterns of amino acids for microorganisms remaining uncharacterized but bearing biogeochemical and ecological significance in anoxic environments. To fulfill the purpose, two anaerobic strains were isolated from riverine wetland and mud volcano in Taiwan. One strain is a sulfate reducing bacterium (related to Desulfovibrio marrakechensis), which is capable of utilizing either H2 or lactate, and the other is a methanogen (related to Methanolobus profundi), which grows solely with methyl-group compounds. Carbon isotope analyses of amino acids were performed on cells grown in exponential and stationary phase. The isotopic patterns were similar for all examined cultures, showing successive 13C depletion along synthetic pathways. No significant difference was observed for the methanogen and lactate-utilizing sulfate reducer harvested in exponential and stationary phases. In contrast, the H2-utilizing sulfate reducer harvested in stationary phase depleted and enriched 13C in aspartic acid and glycine, respectively when compared with that harvested in exponential phase. Such variations might infer the change of carbon flux during synthesis of these two amino acids in the reverse TCA cycle. In addition, the discriminant function analysis for all available data from culture studies further attests the capability of using carbon isotope patterns of amino acids in identifying microbial metabolisms.

  8. Climate Change in Central and West Asia. Routes to a More Secure, Low-Carbon Future

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2010-11-15

    ADB's Central and West Asian countries are Afghanistan, Armenia, Azerbaijan, Georgia, Kazakhstan, the Kyrgyz Republic, Pakistan, Tajikistan, Turkmenistan, and Uzbekistan. Geoclimatic and environmental factors make this region highly vulnerable to the risks and hazards of climate change. For example, accelerated glacial melt has serious implications for agriculture, water supply, and energy generation - problems exacerbated by overexploitation of natural resources. Countries may find it difficult to shift to low-carbon growth, since many have abundant fossil fuel and tend to use energy inefficiently. ADB is responding to these climate hazards and low-carbon pathways with a comprehensive strategy that strengthens policies, governance, and capacity support; expands the use of clean and renewable energy; encourages sustainable transport and urban development; promotes development that will be more resilient to climate change, especially in water-dependent sectors; and manages land use and forests for carbon sequestration. ADB's support is helping its developing member countries face the challenges of climate change and, with partners, is providing innovative solutions, while continuing to work to reduce poverty.

  9. Pathways of carbon and energy metabolism of the epibiotic community associated with the deep-sea hydrothermal vent shrimp Rimicaris exoculata.

    Science.gov (United States)

    Hügler, Michael; Petersen, Jillian M; Dubilier, Nicole; Imhoff, Johannes F; Sievert, Stefan M

    2011-01-07

    The shrimp Rimicaris exoculata dominates the faunal biomass at many deep-sea hydrothermal vent sites at the Mid-Atlantic Ridge. In its enlarged gill chamber it harbors a specialized epibiotic bacterial community for which a nutritional role has been proposed. We analyzed specimens from the Snake Pit hydrothermal vent field on the Mid-Atlantic Ridge by complementing a 16S rRNA gene survey with the analysis of genes involved in carbon, sulfur and hydrogen metabolism. In addition to Epsilon- and Gammaproteobacteria, the epibiotic community unexpectedly also consists of Deltaproteobacteria of a single phylotype, closely related to the genus Desulfocapsa. The association of these phylogenetic groups with the shrimp was confirmed by fluorescence in situ hybridization. Based on functional gene analyses, we hypothesize that the Gamma- and Epsilonproteobacteria are capable of autotrophic growth by oxidizing reduced sulfur compounds, and that the Deltaproteobacteria are also involved in sulfur metabolism. In addition, the detection of proteobacterial hydrogenases indicates the potential for hydrogen oxidation in these communities. Interestingly, the frequency of these phylotypes in 16S rRNA gene clone libraries from the mouthparts differ from that of the inner lining of the gill chamber, indicating potential functional compartmentalization. Our data show the specific association of autotrophic bacteria with Rimicaris exoculata from the Snake Pit hydrothermal vent field, and suggest that autotrophic carbon fixation is contributing to the productivity of the epibiotic community with the reductive tricarboxylic acid cycle as one important carbon fixation pathway. This has not been considered in previous studies of carbon fixation and stable carbon isotope composition of the shrimp and its epibionts. Furthermore, the co-occurrence of sulfur-oxidizing and sulfur-reducing epibionts raises the possibility that both may be involved in the syntrophic exchange of sulfur compounds

  10. Carbon dioxide and methane emission dynamics in central London (UK)

    Science.gov (United States)

    Helfter, Carole; Nemitz, Eiko; Barlow, Janet F.; Wood, Curtis R.

    2013-04-01

    London, with a population of 8.2 million, is the largest city in Europe. It is heavily built-up (typically 8% vegetation cover within the central boroughs) and boasts some of the busiest arteries in Europe despite efforts to reduce traffic in the city centre with the introduction of a congestion charging scheme in 2007. We report on two substantial pollution monitoring efforts in the heart of London between October 2006 and present. Fluxes of carbon dioxide (CO2) and water (H2O) were measured continuously by eddy-covariance in central London from October 2006 until May 2008 from a 190 m telecommunication tower (BT tower; 51° 31' 17.4'' N 0° 8' 20.04'' W). The eddy-covariance system consisted of a Gill R3-50 ultrasonic anemometer operated at 20 Hz and a LI-COR 6262 infrared gas analyser. Air was sampled 0.3 m below the sensor head of the ultrasonic anemometer - which was itself mounted on a 3 m mast to the top of a 15 m lattice tower situated on the roof of the tower (instrument head at 190 m above street level) - and pulled down 45 m of 12.7 mm OD Teflon tubing. In addition, meteorological variables (temperature, relative humidity, pressure, precipitation, wind speed and direction) were also measured with a multi-sensor (Weather Transmitter WXT510, Vaisala). Eddy-covariance measurements at the BT tower location were reinstated in July 2011 and include methane (CH4), CO2 and H2O concentrations measured by a Picarro fast methane analyser (G2301-f). CO2 emissions were found to be mainly controlled by fossil fuel combustion (e.g. traffic, commercial and domestic heating). Diurnal averages of CO2 fluxes were found to be highly correlated to traffic. However changes in heating-related natural gas consumption and, to a lesser extent, photosynthetic activity in two large city centre green spaces (Hyde Park and Regent's Park) explained the seasonal variability. Annual estimates of net exchange of CO2 obtained by eddy-covariance agreed well with up-scaled data from the UK

  11. New features on the environmental regulation of metabolism revealed by modeling the cellular proteomic adaptations induced by light, carbon and inorganic nitrogen in Chlamydomonas reinhardtii

    Directory of Open Access Journals (Sweden)

    Stéphanie Gérin

    2016-08-01

    Full Text Available Microalgae are currently emerging to be very promising organisms for the production of biofuels and high-added value compounds. Understanding the influence of environmental alterations on their metabolism is a crucial issue. Light, carbon and nitrogen availability have been reported to induce important metabolic adaptations. So far, the influence of these variables has essentially been studied while varying only one or two environmental factors at the same time. The goal of the present work was to model the cellular proteomic adaptations of the green microalga Chlamydomonas reinhardtii upon the simultaneous changes of light intensity, carbon concentrations (CO2 and acetate and inorganic nitrogen concentrations (nitrate and ammonium in the culture medium. Statistical design of experiments (DOE enabled to define 32 culture conditions to be tested experimentally. Relative protein abundance was quantified by two dimensional differential in-gel electrophoresis (2D-DIGE. Additional assays for respiration, photosynthesis, and lipid and pigment concentrations were also carried out. A hierarchical clustering survey enabled to partition biological variables (proteins + assays into eight co-regulated clusters. In most cases, the biological variables partitioned in the same cluster had already been reported to participate to common biological functions (acetate assimilation, bioenergetic processes, light harvesting, Calvin cycle and protein metabolism. The environmental regulation within each cluster was further characterized by a series of multivariate methods including principal component analysis and multiple linear regressions. This metadata analysis enabled to highlight the existence of a clear regulatory pattern for every cluster and to mathematically simulate the effects of light, carbon and nitrogen. The influence of these environmental variables on cellular metabolism is described in details and thoroughly discussed. This work provides an overview

  12. Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting.

    Directory of Open Access Journals (Sweden)

    Alyaa M Abdel-Haleem

    2018-01-01

    Full Text Available Several antimalarial drugs exist, but differences between life cycle stages among malaria species pose challenges for developing more effective therapies. To understand the diversity among stages and species, we reconstructed genome-scale metabolic models (GeMMs of metabolism for five life cycle stages and five species of Plasmodium spanning the blood, transmission, and mosquito stages. The stage-specific models of Plasmodium falciparum uncovered stage-dependent changes in central carbon metabolism and predicted potential targets that could affect several life cycle stages. The species-specific models further highlight differences between experimental animal models and the human-infecting species. Comparisons between human- and rodent-infecting species revealed differences in thiamine (vitamin B1, choline, and pantothenate (vitamin B5 metabolism. Thus, we show that genome-scale analysis of multiple stages and species of Plasmodium can prioritize potential drug targets that could be both anti-malarials and transmission blocking agents, in addition to guiding translation from non-human experimental disease models.

  13. Anaerobic carbon monoxide metabolism by Pleomorphomonas carboxyditropha sp. nov., a new mesophilic hydrogenogenic carboxydotroph.

    Science.gov (United States)

    Esquivel-Elizondo, Sofia; Maldonado, Juan; Krajmalnik-Brown, Rosa

    2018-06-01

    Carbon monoxide (CO)-metabolism and phenotypic and phylogenetic characterization of a novel anaerobic, mesophilic and hydrogenogenic carboxydotroph are reported. Strain SVCO-16 was isolated from anaerobic sludge and grows autotrophically and mixotrophically with CO. The genes cooS and cooF, coding for a CO dehydrogenase complex, and genes similar to hycE2, encoding a CO-induced hydrogenase, were present in its genome. The isolate produces H2 and CO2 from CO, and acetate and formate from organic substrates. Based on the 16S rRNA sequence, it is an Alphaproteobacterium most closely related to the genus Pleomorphomonas (98.9%-99.2% sequence identity). Comparison with other previously characterized Pleomorphomonas showed that P. diazotrophica and P. oryzae do not metabolize CO, and P. diazotrophica does not grow anaerobically with organic substrates. Average nucleotide identity values between strain SVCO-16 and P. diazotrophica, P. oryzae or P. koreensis were 86.66 ± 0.21%. These values are below the boundary to define species (95%-96%). Digital DNA-DNA hybridization estimates between strain SVCO-16 and reference strains were also below the 70% threshold for species delineation: 29.1%-34.5%. Based on the differences in CO metabolism, genome analyses and cellular fatty acid composition, the isolate should be classified into the genus Pleomorphomonas as a representative of a novel species, Pleomorphomonas carboxyditropha. The type strain of Pleomorphomonas carboxyditropha is SVCO-16T (strain deposit numbers, DSM 106132T and TSD-119T).

  14. Prognostic value of gasometric parameters of carbon dioxide in resuscitation of septic patients. A bibliography review.

    Science.gov (United States)

    Lamsfus-Prieto, J Á; de Castro-Fernández, R; Hernández-García, A M; Marcano-Rodriguez, G

    2016-04-01

    The anaerobic metabolism is the cornerstone in physiopathology of septic shock. Nowadays we have both the central or mixed venous oxygen saturation and lactate levels to monitoring the metabolism in septic patients. Some studies have shown that normalization of systemic hemodynamic and oxygen metabolism variables not prevent progression to multiorgan damage and death. Recently has been proposed the venous-to-arterial carbon dioxide difference (ΔpvaCO2) as an alternative marker of tissue hypoperfusion, like Cardiac Index. High ΔpvaCO2 predicts adverse outcomes. Also has been proposed both, the ratio between the ΔpvaCO2 and arterial-to-venous oxygen content difference (ΔCavO2): ΔpvaCO2/ΔCavO2; and, the ratio between venous-to-arterial carbon dioxide difference (ΔCvaCO2) and ΔCavO2: ΔCvaCO2/ΔCavO2, as markers of anaerobic metabolism. Both of high ratios are related to high levels of lactate and worse prognosis. Therefore in patients with sepsis the combination of markers of resuscitation could be important to improve the outcomes. Copyright © 2015 Sociedad Española de Anestesiología, Reanimación y Terapéutica del Dolor. Publicado por Elsevier España, S.L.U. All rights reserved.

  15. Photochemical alteration of organic carbon draining permafrost soils shifts microbial metabolic pathways and stimulates respiration.

    Science.gov (United States)

    Ward, Collin P; Nalven, Sarah G; Crump, Byron C; Kling, George W; Cory, Rose M

    2017-10-03

    In sunlit waters, photochemical alteration of dissolved organic carbon (DOC) impacts the microbial respiration of DOC to CO 2 . This coupled photochemical and biological degradation of DOC is especially critical for carbon budgets in the Arctic, where thawing permafrost soils increase opportunities for DOC oxidation to CO 2 in surface waters, thereby reinforcing global warming. Here we show how and why sunlight exposure impacts microbial respiration of DOC draining permafrost soils. Sunlight significantly increases or decreases microbial respiration of DOC depending on whether photo-alteration produces or removes molecules that native microbial communities used prior to light exposure. Using high-resolution chemical and microbial approaches, we show that rates of DOC processing by microbes are likely governed by a combination of the abundance and lability of DOC exported from land to water and produced by photochemical processes, and the capacity and timescale that microbial communities have to adapt to metabolize photo-altered DOC.The role of dissolved organic carbon (DOC) photo-alteration in the microbial respiration of DOC to CO 2 is unclear. Here, the authors show that the impact of this mechanism depends on whether photo-alteration of DOC produces or removes molecules used by native microbial communities prior to light exposure.

  16. Carbon mineralization in surface and subsurface soils in a subtropical mixed forest in central China

    Science.gov (United States)

    Liu, F.; Tian, Q.

    2014-12-01

    About a half of soil carbon is stored in subsurface soil horizons, their dynamics have the potential to significantly affect carbon balancing in terrestrial ecosystems. However, the main factors regulating subsurface soil carbon mineralization are poorly understood. As affected by mountain humid monsoon, the subtropical mountains in central China has an annual precipitation of about 2000 mm, which causes strong leaching of ions and nutrition. The objectives of this study were to monitor subsurface soil carbon mineralization and to determine if it is affected by nutrient limitation. We collected soil samples (up to 1 m deep) at three locations in a small watershed with three soil layers (0-10 cm, 10-30 cm, below 30 cm). For the three layers, soil organic carbon (SOC) ranged from 35.8 to 94.4 mg g-1, total nitrogen ranged from 3.51 to 8.03 mg g-1, microbial biomass carbon (MBC) ranged from 170.6 to 718.4 μg g-1 soil. We measured carbon mineralization with the addition of N (100 μg N/g soil), P (50 μg P/g soil), and liable carbon (glucose labeled by 5 atom% 13C, at five levels: control, 10% MBC, 50% MBC, 100% MBC, 200% MBC). The addition of N and P had negligible effects on CO2 production in surface soil layers; in the deepest soil layer, the addition of N and P decreased CO2 production from 4.32 to 3.20 μg C g-1 soil carbon h-1. Glucose addition stimulated both surface and subsurface microbial mineralization of SOC, causing priming effects. With the increase of glucose addition rate from 10% to 200% MBC, the primed mineralization rate increased from 0.19 to 3.20 μg C g-1 soil carbon h-1 (fifth day of glucose addition). The magnitude of priming effect increased from 28% to 120% as soil layers go deep compare to the basal CO2 production (fifth day of 200% MBC glucose addition, basal CO2 production rate for the surface and the deepest soil was 11.17 and 2.88 μg C g-1 soil carbon h-1). These results suggested that the mineralization of subsurface carbon is more

  17. The prevalence of the metabolic syndrome did not increase in Mexico City between 1990-1992 and 1997-1999 despite more central obesity.

    Science.gov (United States)

    Lorenzo, Carlos; Williams, Ken; Gonzalez-Villalpando, Clicerio; Haffner, Steven M

    2005-10-01

    Trends in the metabolic syndrome might follow trends in obesity. We examined this hypothesis in the Mexico City Diabetes Study (MCDS), a study that showed rising trends in obesity, and the effect of the metabolic syndrome on the risk of coronary heart disease (CHD). Designed as a population-based study, the MCDS enrolled subjects in 1990-1992 (n = 2,282). Follow-up visits were held in 1993-1995 (n = 1,764) and 1997-1999 (n = 1,754). We used the revised metabolic syndrome definition of the National Cholesterol Education Program and the Framingham equations to estimate the 10-year CHD risk. In men, the age-adjusted prevalence of the metabolic syndrome was 38.9% in 1990-1992, 43.4% in 1993-1995, and 39.9% in 1997-1999; in women, the prevalences were 65.4, 65.7, and 59.9%, respectively. The prevalence did not change in men (P = 0.349) between 1990-1992 and 1997-1999, but decreased in women (P metabolic syndrome nor CHD risk has increased in Mexico City. Lower blood pressure and triglyceride values appear to have counteracted increases in central obesity and fasting glucose.

  18. Unique flexibility in energy metabolism allows mycobacteria to combat starvation and hypoxia.

    Directory of Open Access Journals (Sweden)

    Michael Berney

    Full Text Available Mycobacteria are a group of obligate aerobes that require oxygen for growth, but paradoxically have the ability to survive and metabolize under hypoxia. The mechanisms responsible for this metabolic plasticity are unknown. Here, we report on the adaptation of Mycobacterium smegmatis to slow growth rate and hypoxia using carbon-limited continuous culture. When M. smegmatis is switched from a 4.6 h to a 69 h doubling time at a constant oxygen saturation of 50%, the cells respond through the down regulation of respiratory chain components and the F1Fo-ATP synthase, consistent with the cells lower demand for energy at a reduced growth rate. This was paralleled by an up regulation of molecular machinery that allowed more efficient energy generation (i.e. Complex I and the use of alternative electron donors (e.g. hydrogenases and primary dehydrogenases to maintain the flow of reducing equivalents to the electron transport chain during conditions of severe energy limitation. A hydrogenase mutant showed a 40% reduction in growth yield highlighting the importance of this enzyme in adaptation to low energy supply. Slow growing cells at 50% oxygen saturation subjected to hypoxia (0.6% oxygen saturation responded by switching on oxygen scavenging cytochrome bd, proton-translocating cytochrome bc1-aa3 supercomplex, another putative hydrogenase, and by substituting NAD+-dependent enzymes with ferredoxin-dependent enzymes thus highlighting a new pattern of mycobacterial adaptation to hypoxia. The expression of ferredoxins and a hydrogenase provides a potential conduit for disposing of and transferring electrons in the absence of exogenous electron acceptors. The use of ferredoxin-dependent enzymes would allow the cell to maintain a high carbon flux through its central carbon metabolism independent of the NAD+/NADH ratio. These data demonstrate the remarkable metabolic plasticity of the mycobacterial cell and provide a new framework for understanding their

  19. Cerebral blood flow, oxidative metabolism and cerebrovascular carbon dioxide reactivity in patients with acute bacterial meningitis

    DEFF Research Database (Denmark)

    Møller, Kirsten; Strauss, Gitte Irene; Thomsen, Gerda

    2002-01-01

    BACKGROUND: The optimal arterial carbon dioxide tension (P(a)CO(2)) in patients with acute bacterial meningitis (ABM) is unknown and controversial. The objective of this study was to measure global cerebral blood flow (CBF), cerebrovascular CO(2) reactivity (CO(2)R), and cerebral metabolic rates...... and hyperventilation with single-photon emission computed tomography (SPECT) (14 patients) and/or the Kety-Schmidt technique (KS) (11 patients and all controls). In KS studies, CMR was measured by multiplying the arterial to jugular venous concentration difference (a-v D) by CBF. RESULTS: CBF did not differ...

  20. Utilization of carbon 13-labelled stable isotopes for studying drug toxicity on cellular metabolism

    International Nuclear Information System (INIS)

    Herve, M.; Wietzerbin, J.; Tran-Dinh, S.

    1994-01-01

    A new approach for studying the effects of two drugs, amphotericine B (AMB), an anti-fungal antibiotic, and 2-deoxy-D-glucose (DG), on the glucose metabolism in brewer yeast cells (Saccharomyces cerevisiae), is presented; AMB interacts with the membrane sterols, inducing formation of pores through which ions and small molecules can pass. DG may enter in the cytosol, where it is phosphoryled by hexokinase into deoxy-D-glucose 6-phosphate (DG6P) which disappears very slowly. DG slows down the glycolysis process and induces the formation of new substances. This paper shows the advantages of utilizing carbon 13-labelled substrates combined to the NMR-13C and NMR-1H techniques. 6 figs., 5 refs

  1. Towards a sustainable bio-based economy: Redirecting primary metabolism to new products with plant synthetic biology.

    Science.gov (United States)

    Shih, Patrick M

    2018-08-01

    Humans have domesticated many plant species as indispensable sources of food, materials, and medicines. The dawning era of synthetic biology represents a means to further refine, redesign, and engineer crops to meet various societal and industrial needs. Current and future endeavors will utilize plants as the foundation of a bio-based economy through the photosynthetic production of carbohydrate feedstocks for the microbial fermentation of biofuels and bioproducts, with the end goal of decreasing our dependence on petrochemicals. As our technological capabilities improve, metabolic engineering efforts may expand the utility of plants beyond sugar feedstocks through the direct production of target compounds, including pharmaceuticals, renewable fuels, and commodity chemicals. However, relatively little work has been done to fully realize the potential in redirecting central carbon metabolism in plants for the engineering of novel bioproducts. Although our ability to rationally engineer and manipulate plant metabolism is in its infancy, I highlight some of the opportunities and challenges in applying synthetic biology towards engineering plant primary metabolism. Copyright © 2018 Elsevier B.V. All rights reserved.

  2. Central nervous system complications after liver transplantation.

    Science.gov (United States)

    Kim, Jeong-Min; Jung, Keun-Hwa; Lee, Soon-Tae; Chu, Kon; Roh, Jae-Kyu

    2015-08-01

    We investigated the diversity of central nervous system complications after liver transplantation in terms of clinical manifestations and temporal course. Liver transplantation is a lifesaving option for end stage liver disease patients but post-transplantation neurologic complications can hamper recovery. Between 1 January 2001 and 31 December 2010, patients who had undergone liver transplantation at a single tertiary university hospital were included. We reviewed their medical records and brain imaging data and classified central nervous system complications into four categories including vascular, metabolic, infectious and neoplastic. The onset of central nervous system complications was grouped into five post-transplantation intervals including acute (within 1 month), early subacute (1-3 months), late subacute (3-12 months), chronic (1-3 years), and long-term (after 3 years). During follow-up, 65 of 791 patients (8.2%) experienced central nervous system complications, with 30 occurring within 1 month after transplantation. Vascular etiology was the most common (27 patients; 41.5%), followed by metabolic (23; 35.4%), infectious (nine patients; 13.8%), and neoplastic (six patients). Metabolic encephalopathy with altered consciousness was the most common etiology during the acute period, followed by vascular disorders. An initial focal neurologic deficit was detected in vascular and neoplastic complications, whereas metabolic and infectious etiologies presented with non-focal symptoms. Our study shows that the etiology of central nervous system complications after liver transplantation changes over time, and initial symptoms can help to predict etiology. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Mechanisms of carbon dioxide acquisition and CO2 sensing in marine diatoms: a gateway to carbon metabolism.

    Science.gov (United States)

    Matsuda, Yusuke; Hopkinson, Brian M; Nakajima, Kensuke; Dupont, Christopher L; Tsuji, Yoshinori

    2017-09-05

    discussed.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'. © 2017 The Author(s).

  4. Physical and Biological Controls on the Carbonate Chemistry of Coral Reef Waters: Effects of Metabolism, Wave Forcing, Sea Level, and Geomorphology

    Science.gov (United States)

    Falter, James L.; Lowe, Ryan J.; Zhang, Zhenlin; McCulloch, Malcolm

    2013-01-01

    We present a three-dimensional hydrodynamic-biogeochemical model of a wave-driven coral-reef lagoon system using the circulation model ROMS (Regional Ocean Modeling System) coupled with the wave transformation model SWAN (Simulating WAves Nearshore). Simulations were used to explore the sensitivity of water column carbonate chemistry across the reef system to variations in benthic reef metabolism, wave forcing, sea level, and system geomorphology. Our results show that changes in reef-water carbonate chemistry depend primarily on the ratio of benthic metabolism to the square root of the onshore wave energy flux as well as on the length and depth of the reef flat; however, they are only weakly dependent on channel geometry and the total frictional resistance of the reef system. Diurnal variations in pCO2, pH, and aragonite saturation state (Ωar) are primarily dependent on changes in net production and are relatively insensitive to changes in net calcification; however, net changes in pCO2, pH, and Ωar are more strongly influenced by net calcification when averaged over 24 hours. We also demonstrate that a relatively simple one-dimensional analytical model can provide a good description of the functional dependence of reef-water carbonate chemistry on benthic metabolism, wave forcing, sea level, reef flat morphology, and total system frictional resistance. Importantly, our results indicate that any long-term (weeks to months) net offsets in reef-water pCO2 relative to offshore values should be modest for reef systems with narrow and/or deep lagoons. Thus, the long-term evolution of water column pCO2 in many reef environments remains intimately connected to the regional-scale oceanography of offshore waters and hence directly influenced by rapid anthropogenically driven increases in pCO2. PMID:23326411

  5. Physical and biological controls on the carbonate chemistry of coral reef waters: effects of metabolism, wave forcing, sea level, and geomorphology.

    Science.gov (United States)

    Falter, James L; Lowe, Ryan J; Zhang, Zhenlin; McCulloch, Malcolm

    2013-01-01

    We present a three-dimensional hydrodynamic-biogeochemical model of a wave-driven coral-reef lagoon system using the circulation model ROMS (Regional Ocean Modeling System) coupled with the wave transformation model SWAN (Simulating WAves Nearshore). Simulations were used to explore the sensitivity of water column carbonate chemistry across the reef system to variations in benthic reef metabolism, wave forcing, sea level, and system geomorphology. Our results show that changes in reef-water carbonate chemistry depend primarily on the ratio of benthic metabolism to the square root of the onshore wave energy flux as well as on the length and depth of the reef flat; however, they are only weakly dependent on channel geometry and the total frictional resistance of the reef system. Diurnal variations in pCO(2), pH, and aragonite saturation state (Ω(ar)) are primarily dependent on changes in net production and are relatively insensitive to changes in net calcification; however, net changes in pCO(2), pH, and Ω(ar) are more strongly influenced by net calcification when averaged over 24 hours. We also demonstrate that a relatively simple one-dimensional analytical model can provide a good description of the functional dependence of reef-water carbonate chemistry on benthic metabolism, wave forcing, sea level, reef flat morphology, and total system frictional resistance. Importantly, our results indicate that any long-term (weeks to months) net offsets in reef-water pCO(2) relative to offshore values should be modest for reef systems with narrow and/or deep lagoons. Thus, the long-term evolution of water column pCO(2) in many reef environments remains intimately connected to the regional-scale oceanography of offshore waters and hence directly influenced by rapid anthropogenically driven increases in pCO(2).

  6. Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans

    Energy Technology Data Exchange (ETDEWEB)

    Khosravi, Claire; Battaglia, Evy; Kun, Roland S.; Dalhuijsen, Sacha; Visser, Jaap; Aguilar-Pontes, Maria V.; Zhou, Miamiao; Heyman, Heino M.; Kim, Young-Mo; Baker, Scott E.; de Vries, Ronald P.

    2018-03-22

    Background: Plant biomass is the most abundant carbon source for many fungal species. In the biobased industry fungi are used to produce lignocellulolytic enzymes to degrade agricultural waste biomass. Here we evaluated if it would be possible to create an Aspergillus nidulans strain that releases but does not metabolize hexoses from plant biomass. For this purpose, metabolic mutants were generated that were impaired in glycolysis, by using hexokinase (hxkA) and glucokinase (glkA) negative strains. To prevent repression of enzyme production due to the hexose accumulation, strains were generated that combined these mutations with a deletion in creA, the repressor involved in regulating preferential use of different carbon catabolic pathways. Results: Phenotypic analysis revealed reduced growth for the hxkA1 glkA4 mutant on wheat bran. However, hexoses did not accumulate during growth of the mutants on wheat bran, suggesting that glucose metabolism is re-routed towards alternative carbon catabolic pathways. The creAΔ4 mutation in combination with preventing initial phosphorylation in glycolysis resulted in better growth than the hxkA/glkA mutant and an increased expression of pentose catabolic and pentose phosphate pathway genes. This indicates that the reduced ability to use hexoses as carbon sources created a shift towards the pentose fraction of wheat bran as a major carbon source to support growth. Conclusion: Blocking the direct entry of hexoses to glycolysis activates alternative metabolic conversion of these sugars in A. nidulans during growth on plant biomass, but also upregulates conversion of other sugars, such as pentoses.

  7. Influence of plankton metabolism and mixing depth on CO2 dynamics in an Amazon floodplain lake.

    Science.gov (United States)

    Amaral, João Henrique F; Borges, Alberto V; Melack, John M; Sarmento, Hugo; Barbosa, Pedro M; Kasper, Daniele; de Melo, Michaela L; De Fex-Wolf, Daniela; da Silva, Jonismar S; Forsberg, Bruce R

    2018-07-15

    We investigated plankton metabolism and its influence on carbon dioxide (CO 2 ) dynamics in a central Amazon floodplain lake (Janauacá, 3°23' S, 60°18' W) from September 2015 to May 2016, including a period with exceptional drought. We made diel measurements of CO 2 emissions to the atmosphere with floating chambers and depth profiles of temperature and CO 2 partial pressure (pCO 2 ) at two sites with differing wind exposure and proximity to vegetated habitats. Dissolved oxygen (DO) concentrations were monitored continuously during day and night in clear and dark chambers with autonomous optical sensors to evaluate plankton metabolism. Overnight community respiration (CR), and gross primary production (GPP) rates were higher in clear chambers and positively correlated with chlorophyll-a (Chl-a). CO 2 air-water fluxes varied over 24-h periods with changes in thermal structure and metabolism. Most net daily CO 2 fluxes during low water and mid-rising water at the wind exposed site were into the lake as a result of high rates of photosynthesis. All other measurements indicated net daily release to the atmosphere. Average GPP rates (6.8gCm -2 d -1 ) were high compared with other studies in Amazon floodplain lakes. The growth of herbaceous plants on exposed sediment during an exceptional drought led to large carbon inputs when these areas were flooded, enhancing CR, pCO 2 , and CO 2 fluxes. During the period when the submerged herbaceous vegetation decayed phytoplankton abundance increased and photosynthetic uptake of CO 2 occurred. While planktonic metabolism was often autotrophic (GPP:CR>1), CO 2 out-gassing occurred during most periods investigated indicating other inputs of carbon such as sediments or soils and wetland plants. Copyright © 2018 Elsevier B.V. All rights reserved.

  8. Molecular evidence for the coordination of nitrogen and carbon metabolisms, revealed by a study on the transcriptional regulation of the agl3EFG operon that encodes a putative carbohydrate transporter in Streptomyces coelicolor.

    Science.gov (United States)

    Cen, Xu-Feng; Wang, Jing-Zhi; Zhao, Guo-Ping; Wang, Ying; Wang, Jin

    2016-03-18

    In the agl3EFGXYZ operon (SCO7167-SCO7162, abbreviated as agl3 operon) of Streptomyces coelicolor M145, agl3EFG genes encode a putative ABC-type carbohydrate transporter. The transcription of this operon has been proved to be repressed by Agl3R (SCO7168), a neighboring GntR-family regulator, and this repression can be released by growth on poor carbon sources. Here in this study, we prove that the transcription of agl3 operon is also directly repressed by GlnR, a central regulator governing the nitrogen metabolism in S. coelicolor. The electrophoretic mobility shift assay (EMSA) employing the agl3 promoter and mixtures of purified recombinant GlnR and Agl3R indicates that GlnR and Agl3R bind to different DNA sequences within the promoter region of agl3 operon, which is further confirmed by the DNase I footprinting assay. As Agl3R and GlnR have been demonstrated to sense the extracellular carbon and nitrogen supplies, respectively, it is hypothesized that the transcription of agl3 operon is stringently governed by the availabilities of extracellular carbon and nitrogen sources. Consistent with the hypothesis, the agl3 operon is further found to be derepressed only under the condition of poor carbon and rich nitrogen supplies, when both regulators are inactivated. It is believed that activation of the expression of agl3 operon may facilitate the absorption of extracellular carbohydrates to balance the ratio of intracellular carbon to nitrogen. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. Metabolite profile analysis reveals functional effects of 28-day vitamin B-6 restriction on one-carbon metabolism and tryptophan catabolic pathways in healthy men and women.

    Science.gov (United States)

    da Silva, Vanessa R; Rios-Avila, Luisa; Lamers, Yvonne; Ralat, Maria A; Midttun, Øivind; Quinlivan, Eoin P; Garrett, Timothy J; Coats, Bonnie; Shankar, Meena N; Percival, Susan S; Chi, Yueh-Yun; Muller, Keith E; Ueland, Per Magne; Stacpoole, Peter W; Gregory, Jesse F

    2013-11-01

    Suboptimal vitamin B-6 status, as reflected by low plasma pyridoxal 5'-phosphate (PLP) concentration, is associated with increased risk of vascular disease. PLP plays many roles, including in one-carbon metabolism for the acquisition and transfer of carbon units and in the transsulfuration pathway. PLP also serves as a coenzyme in the catabolism of tryptophan. We hypothesize that the pattern of these metabolites can provide information reflecting the functional impact of marginal vitamin B-6 deficiency. We report here the concentration of major constituents of one-carbon metabolic processes and the tryptophan catabolic pathway in plasma from 23 healthy men and women before and after a 28-d controlled dietary vitamin B-6 restriction (restriction yielded increased cystathionine (53% pre- and 76% postprandial; P restriction yielded lower kynurenic acid (22% pre- and 20% postprandial; P restriction and multilevel partial least squares-discriminant analysis supported this conclusion. Thus, plasma concentrations of creatine, cystathionine, kynurenic acid, and 3-hydroxykynurenine jointly reveal effects of vitamin B-6 restriction on the profiles of one-carbon and tryptophan metabolites and serve as biomarkers of functional effects of marginal vitamin B-6 deficiency.

  10. 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

  11. Administration of secretin for autism alters dopamine metabolism in the central nervous system.

    Science.gov (United States)

    Toda, Yoshihiro; Mori, Kenji; Hashimoto, Toshiaki; Miyazaki, Masahito; Nozaki, Satoshi; Watanabe, Yasuyoshi; Kuroda, Yasuhiro; Kagami, Shoji

    2006-03-01

    We evaluated the clinical effects of intravenously administered secretin in 12 children with autism (age range: 4-6 years, median age: 9 years, boy:girl=8:4). In addition, we investigated the association between improvement in symptoms and changes in the cerebrospinal fluid (CSF) homovanillic acid (HVA),5-hydroxyindole-3-acetic acid (5-HIAA), and 6R-5,6,7,8-tetrahydro-L-biopterin (BH(4)) levels after administration. After administration of secretin, the Autism Diagnostic Interview-Revised (ADI-R) score improved in 7 of the 12 children. However, the score deteriorated in 2 of the 12 children (in the item of 'restricted and repetitive, stereotyped interests and behaviors'). The HVA and BH(4) levels in CSF were increased in all children with improvement in the ADI-R score. In contrast, no patient without the elevation of the BH(4) level showed improvement in the score. These findings suggest that secretin activated metabolic turnover of dopamine in the central nervous system via BH(4), improving symptoms.

  12. The effect of zilpaterol hydrochloride supplementation on energy metabolism and nitrogen and carbon retention of steers fed at maintenance and fasting intake levels

    Science.gov (United States)

    An indirect calorimetry trial examined energy metabolism, apparent nutrient digestibility (appND), carbon retention (CR) and nitrogen retention (NR) of cattle supplemented with zilpaterol hydrochloride (Z). Beef steers (n=20; 463 ± 14 kg) blocked (n=5) by weight and source were individually fed and ...

  13. Dynamic Metabolic Footprinting Reveals the Key Components of Metabolic Network in Yeast Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Chumnanpuen, Pramote; Hansen, Michael Adsetts Edberg; Smedsgaard, Jørn

    2014-01-01

    relies on analysis at a single time point. Using direct infusion-mass spectrometry (DI-MS), we could observe the dynamic metabolic footprinting in yeast S. cerevisiae BY4709 (wild type) cultured on 3 different C-sources (glucose, glycerol, and ethanol) and sampled along 10 time points with 5 biological...... replicates. In order to analyze the dynamic mass spectrometry data, we developed the novel analysis methods that allow us to perform correlation analysis to identify metabolites that significantly correlate over time during growth on the different carbon sources. Both positive and negative electrospray...... reconstructed an interaction map that provides information of how different metabolic pathways have correlated patterns during growth on the different carbon sources....

  14. Effect of carbon/nitrogen ratio on carbohydrate metabolism and light energy dissipation mechanisms in Arabidopsis thaliana.

    Science.gov (United States)

    Huarancca Reyes, Thais; Scartazza, Andrea; Lu, Yu; Yamaguchi, Junji; Guglielminetti, Lorenzo

    2016-08-01

    Carbon (C) and nitrogen (N) nutrient sources are essential elements for metabolism, and their availability must be tightly coordinated for the optimal growth and development in plants. Plants are able to sense and respond to different C/N conditions via specific partitioning of C and N sources and the regulation of a complex cellular metabolic activity. We studied how the interaction between C and N signaling could affect carbohydrate metabolism, soluble sugar levels, photochemical efficiency of photosystem II (PSII) and the ability to drive the excess energy in Arabidopsis seedlings under moderated and disrupted C/N-nutrient conditions. Invertase and sucrose synthase activities were markedly affected by C/N-nutrient status depending on the phosphorylation status, suggesting that these enzymes may necessarily be modulated by their direct phosphorylation or phosphorylation of proteins that form complex with them in response to C/N stress. In addition, the enzymatic activity of these enzymes was also correlated with the amount of sugars, which not only act as substrate but also as signaling compounds. Analysis of chlorophyll fluorescence in plants under disrupted C/N condition suggested a reduction of electron transport rate at PSII level associated with a higher capacity for non-radiative energy dissipation in comparison with plants under moderated C/N condition. In conclusion, the tight coordination between C and N not only affects the carbohydrates metabolism and their concentration within plant tissues, but also the partitioning of the excitation energy at PSII level between radiative (electron transport) and non-radiative (heat) dissipation pathways. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  15. Carbon partitioning in Arabidopsis thaliana is a dynamic process controlled by the plants metabolic status and its circadian clock

    Science.gov (United States)

    Kölling, Katharina; Thalmann, Matthias; Müller, Antonia; Jenny, Camilla; Zeeman, Samuel C

    2015-01-01

    Abstract Plant growth involves the coordinated distribution of carbon resources both towards structural components and towards storage compounds that assure a steady carbon supply over the complete diurnal cycle. We used 14CO2 labelling to track assimilated carbon in both source and sink tissues. Source tissues exhibit large variations in carbon allocation throughout the light period. The most prominent change was detected in partitioning towards starch, being low in the morning and more than double later in the day. Export into sink tissues showed reciprocal changes. Fewer and smaller changes in carbon allocation occurred in sink tissues where, in most respects, carbon was partitioned similarly, whether the sink leaf assimilated it through photosynthesis or imported it from source leaves. Mutants deficient in the production or remobilization of leaf starch exhibited major alterations in carbon allocation. Low-starch mutants that suffer from carbon starvation at night allocated much more carbon into neutral sugars and had higher rates of export than the wild type, partly because of the reduced allocation into starch, but also because of reduced allocation into structural components. Moreover, mutants deficient in the plant’s circadian system showed considerable changes in their carbon partitioning pattern suggesting control by the circadian clock. This work focusses on the temporal changes in the allocation and transport of photoassimilates within Arabidopsis rosettes, helping to fill a gap in our understanding of plant growth. Using short pulses of 14C-labelled carbon dioxide, we quantified how much carbon is used for growth and how much is stored as starch for use at night. In source leaves, partitioning is surprisingly dynamic during the day, even though photosynthesis is relatively constant, while in sink leaves, utilisation is more constant. Furthermore, by analysing metabolic mutants and clock mutants, and by manipulating the growth conditions, we show that

  16. Metabolic Regulation of a Bacterial Cell System with Emphasis on Escherichia coli Metabolism

    Science.gov (United States)

    Shimizu, Kazuyuki

    2013-01-01

    It is quite important to understand the overall metabolic regulation mechanism of bacterial cells such as Escherichia coli from both science (such as biochemistry) and engineering (such as metabolic engineering) points of view. Here, an attempt was made to clarify the overall metabolic regulation mechanism by focusing on the roles of global regulators which detect the culture or growth condition and manipulate a set of metabolic pathways by modulating the related gene expressions. For this, it was considered how the cell responds to a variety of culture environments such as carbon (catabolite regulation), nitrogen, and phosphate limitations, as well as the effects of oxygen level, pH (acid shock), temperature (heat shock), and nutrient starvation. PMID:25937963

  17. 210Pb dating of sediments from the central and the northern Adriatic Sea: The deposition and preservation of sedimentary organic carbon

    International Nuclear Information System (INIS)

    Hamilton, T.; Fowler, S.; Miquel, J.C.; La Rosa, J.

    1996-04-01

    A central goal of the ELNA project is to assess the carbon assimilation capacity of the Northern Adriatic Sea. This requires fundamental quantitative information on budgets and sinks of organic carbon. Any change in carbon production in the water column should be reflected in the underlying sediments. Moreover, the fraction of particulate organic carbon reaching the sea floor which is subsequently preserved in the sediment will be strongly coupled to sediment accumulation and mixing. In this study a series of box cores were collected in order to characterize a hypothetical eutrophication gradient extending from the Po River outflow region in the north down to the shallow meso-Adriatic depression (Jabuka Pit). The main tasks assigned to IAEA-MEL were to provide 210 Pb derived sedimentation and dry-mass accumulation rates and to examine the possible correlations between sedimentary processes, the deposition and preservation of sedimentary organic carbon and pelagic primary productivity

  18. 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.

  19. Fatty acids in energy metabolism of the central nervous system.

    Science.gov (United States)

    Panov, Alexander; Orynbayeva, Zulfiya; Vavilin, Valentin; Lyakhovich, Vyacheslav

    2014-01-01

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

  20. Metabolite Profile Analysis Reveals Functional Effects of 28-Day Vitamin B-6 Restriction on One-Carbon Metabolism and Tryptophan Catabolic Pathways in Healthy Men and Women123

    Science.gov (United States)

    da Silva, Vanessa R.; Rios-Avila, Luisa; Lamers, Yvonne; Ralat, Maria A.; Midttun, Øivind; Quinlivan, Eoin P.; Garrett, Timothy J.; Coats, Bonnie; Shankar, Meena N.; Percival, Susan S.; Chi, Yueh-Yun; Muller, Keith E.; Ueland, Per Magne; Stacpoole, Peter W.; Gregory, Jesse F.

    2013-01-01

    Suboptimal vitamin B-6 status, as reflected by low plasma pyridoxal 5′-phosphate (PLP) concentration, is associated with increased risk of vascular disease. PLP plays many roles, including in one-carbon metabolism for the acquisition and transfer of carbon units and in the transsulfuration pathway. PLP also serves as a coenzyme in the catabolism of tryptophan. We hypothesize that the pattern of these metabolites can provide information reflecting the functional impact of marginal vitamin B-6 deficiency. We report here the concentration of major constituents of one-carbon metabolic processes and the tryptophan catabolic pathway in plasma from 23 healthy men and women before and after a 28-d controlled dietary vitamin B-6 restriction (restriction yielded increased cystathionine (53% pre- and 76% postprandial; P restriction yielded lower kynurenic acid (22% pre- and 20% postprandial; P restriction and multilevel partial least squares-discriminant analysis supported this conclusion. Thus, plasma concentrations of creatine, cystathionine, kynurenic acid, and 3-hydroxykynurenine jointly reveal effects of vitamin B-6 restriction on the profiles of one-carbon and tryptophan metabolites and serve as biomarkers of functional effects of marginal vitamin B-6 deficiency. PMID:23966327

  1. Substrate metabolism in isolated rat jejunal epithelium. Analysis using 14C-radioisotopes

    International Nuclear Information System (INIS)

    Mallet, R.T.

    1986-01-01

    The jejunal epithelium absorbs nutrients from the intestinal lumen and is therefore the initial site for metabolism of these compounds. The purpose of this investigation is to analyze substrate metabolism in a preparation of jejunal epithelium relatively free of other tissues. Novel radioisotopic labelling techniques allow quantitation of substrate metabolism in the TCA cycle, Embden-Meyerhof (glycolytic) pathway, and hexose monophosphate shunt. For example, ratios of 14 CO 2 production from pairs of 14 C-pyruvate, and 14 C-succinate radioisotopes (CO 2 ratios) indicate the probability of TCA cycle intermediate efflux to generate compounds other than CO 2 . With (2,3- 14 C)succinate as tracer, the ratio of 14 C in carbon 4 + 5 versus carbon 2 + 3 of citrate, the citrate labelling ratio, equals the probability of TCA intermediate flux to the acetyl CoA-derived portion of citrate versus flux to the oxaloacetate-derived portion. The principal metabolic substrates for the jejunal epithelium are glucose and glutamine. CO 2 ratios indicate that glutamine uptake and metabolism is partially Na + -independent, and is saturable, with a half-maximal rate at physiological plasma glutamine concentrations. Glucose metabolism in the jejunal epithelium proceeds almost entirely via the Embden-Meyerhof pathway. Conversion of substrates to multi-carbon products in this tissue allows partial conservation of reduced carbon for further utilization in other tissues. In summary, metabolic modeling based on 14 C labelling ratios is a potentially valuable technique for analysis of metabolic flux patterns in cell preparations

  2. A systematic analysis of TCA Escherichia coli mutants reveals suitable genetic backgrounds for enhanced hydrogen and ethanol production using glycerol as main carbon source.

    Science.gov (United States)

    Valle, Antonio; Cabrera, Gema; Muhamadali, Howbeer; Trivedi, Drupad K; Ratray, Nicholas J W; Goodacre, Royston; Cantero, Domingo; Bolivar, Jorge

    2015-09-01

    Biodiesel has emerged as an environmentally friendly alternative to fossil fuels; however, the low price of glycerol feed-stocks generated from the biodiesel industry has become a burden to this industry. A feasible alternative is the microbial biotransformation of waste glycerol to hydrogen and ethanol. Escherichia coli, a microorganism commonly used for metabolic engineering, is able to biotransform glycerol into these products. Nevertheless, the wild type strain yields can be improved by rewiring the carbon flux to the desired products by genetic engineering. Due to the importance of the central carbon metabolism in hydrogen and ethanol synthesis, E. coli single null mutant strains for enzymes of the TCA cycle and other related reactions were studied in this work. These strains were grown anaerobically in a glycerol-based medium and the concentrations of ethanol, glycerol, succinate and hydrogen were analysed by HPLC and GC. It was found that the reductive branch is the more relevant pathway for the aim of this work, with malate playing a central role. It was also found that the putative C4-transporter dcuD mutant improved the target product yields. These results will contribute to reveal novel metabolic engineering strategies for improving hydrogen and ethanol production by E. coli. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Commentary on: "An integrated metabolic atlas of clear cell renal cell carcinoma." Hakimi AA, Reznik E, Lee CH, Creighton CJ, Brannon AR, Luna A, Aksoy BA, Liu EM, Shen R, Lee W, Chen Y, Stirdivant SM, Russo P, Chen YB, Tickoo SK, Reuter VE, Cheng EH, Sander C, Hsieh JJ.: Cancer Cell. 2016 Jan 11;29(1):104-16.

    Science.gov (United States)

    Lee, Byron H

    2017-09-01

    Dysregulated metabolism is a hallmark of cancer, manifested through alterations in metabolites. We performed metabolomic profiling on 138 matched clear cell renal cell carcinoma (ccRCC)/normal tissue pairs and found that ccRCC is characterized by broad shifts in central carbon metabolism, one-carbon metabolism, and antioxidant response. Tumor progression and metastasis were associated with metabolite increases in glutathione and cysteine/methionine metabolism pathways. We develop an analytic pipeline and visualization tool (metabolograms) to bridge the gap between TCGA transcriptomic profiling and our metabolomic data, which enables us to assemble an integrated pathway-level metabolic atlas and to demonstrate discordance between transcriptome and metabolome. Lastly, expression profiling was performed on a high-glutathione cluster, which corresponds to a poor-survival subgroup in the ccRCC TCGA cohort. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. NIH Mouse Metabolic Phenotyping Centers: the power of centralized phenotyping.

    Science.gov (United States)

    Laughlin, Maren R; Lloyd, K C Kent; Cline, Gary W; Wasserman, David H

    2012-10-01

    The Mouse Metabolic Phenotyping Centers (MMPCs) were founded in 2001 by the National Institutes of Health (NIH) to advance biomedical research by providing the scientific community with standardized, high-quality phenotyping services for mouse models of diabetes, obesity, and their complications. The intent is to allow researchers to take optimum advantage of the many new mouse models produced in labs and in high-throughput public efforts. The six MMPCs are located at universities around the country and perform complex metabolic tests in intact mice and hormone and analyte assays in tissues on a fee-for-service basis. Testing is subsidized by the NIH in order to reduce the barriers for mouse researchers. Although data derived from these tests belong to the researcher submitting mice or tissues, these data are archived after publication in a public database run by the MMPC Coordinating and Bioinformatics Unit. It is hoped that data from experiments performed in many mouse models of metabolic diseases, using standard protocols, will be useful in understanding the nature of these complex disorders. The current areas of expertise include energy balance and body composition, insulin action and secretion, whole-body and tissue carbohydrate and lipid metabolism, cardiovascular and renal function, and metabolic pathway kinetics. In addition to providing services, the MMPC staff provides expertise and advice to researchers, and works to develop and refine test protocols to best meet the community's needs in light of current scientific developments. Test technology is disseminated by publications and through annual courses.

  5. 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

    constructed model to simulate disease behaviour on the flux level, and its potential to analyze cellular metabolic behaviour in silico. Conclusion The predictive power of the constructed model for the key flux distributions, especially central carbon metabolism and glutamate-glutamine cycle fluxes, and its application to hypoxia is promising. The resultant acceptable predictions strengthen the power of such stoichiometric models in the analysis of mammalian cell metabolism.

  6. alpha-Ketoglutarate application in hemodialysis patients improves amino acid metabolism.

    Science.gov (United States)

    Riedel, E; Nündel, M; Hampl, H

    1996-01-01

    In hemodialysis patients, free amino acids and alpha-ketoacids in plasma were determined by fluorescence HPLC to assess the effect of alpha-ketoglutarate administration in combination with the phosphate binder calcium carbonate on the amino acid metabolism. During 1 year of therapy in parallel to inorganic phosphate, urea in plasma decreased significantly, histidine, arginine and proline as well as branched chain alpha-ketoacids, in particular alpha-ketoisocaproate, a regulator of protein metabolism, increased. Thus, administration of alpha-ketoglutarate with calcium carbonate effectively improves amino acid metabolism in hemodialysis patients as it decreases hyperphosphatemia.

  7. Contrasting Inherent Optical Properties and Carbon Metabolism Between Five Northeastern (USA) Estuary-plume Systems

    Science.gov (United States)

    Vandemark, Doug; Salisbury, Joe; Hunt, Chris; McGillis, Wade R.

    2004-01-01

    We have recently developed the ability to rapidly assess Surface inherent optical properties (IOP), oxygen concentration and pCO2 in estuarine-plume systems using flow-through instrumentation. During the summer of 2004, several estuarine-plume systems were surveyed which include the Pleasant (ME), Penobscot (ME), Kennebec-Androscoggin (ME), Merrimack (NH-MA) and Hudson (NY). Continuous measurements of surface chlorophyll and colored dissolved organic carbon (CDOM) fluorescence, beam attenuation, temperature, salinity, oxygen and pC02 were taken at each system along a salinity gradient from fresh water to near oceanic endmembers. CTD and IOP profiles were also taken at predetermined surface salinity intervals. These were accompanied by discrete determinations of chlorophyll (HPLC and fluorometric), total suspended solids (TSS), dissolved organic carbon (DOC) and alkalinity. IOP data were calibrated using chlorophyll, DOC and TSS data to enable the retrieval of these constituents from IOP data. Considerable differences in the data sets were observed between systems. These ranged from the DOC-enriched, strongly heterotrophic Pleasant River System to the high-chlorophyll autotrophic Merrimack River System. Using pCO2 and oxygen saturation measurements as proxies for water column metabolism, distinct relationships were found between trophic status and inherent optical properties. The nature of these relationships varies between systems and is likely a function of watershed and estuarine attributes including carbon and nutrient loading, in-situ production and related autochthonous inputs of DOC and alkalinity. Our results suggest that IOP data may contain significant information about the trophic status of estuarine and plume systems.

  8. Tropical forest soil microbial communities couple iron and carbon biogeochemistry

    Energy Technology Data Exchange (ETDEWEB)

    Dubinsky, E.A.; Silver, W.L.; Firestone, M.K.

    2009-10-15

    We report that iron-reducing bacteria are primary mediators of anaerobic carbon oxidation in upland tropical soils spanning a rainfall gradient (3500 - 5000 mm yr-1) in northeast Puerto Rico. The abundant rainfall and high net primary productivity of these tropical forests provide optimal soil habitat for iron-reducing and iron-oxidizing bacteria. Spatially and temporally dynamic redox conditions make iron-transforming microbial communities central to the belowground carbon cycle in these wet tropical forests. The exceedingly high abundance of iron-reducing bacteria (up to 1.2 x 10{sup 9} cells per gram soil) indicated that they possess extensive metabolic capacity to catalyze the reduction of iron minerals. In soils from the higher rainfall sites, measured rates of ferric iron reduction could account for up to 44 % of organic carbon oxidation. Iron reducers appeared to compete with methanogens when labile carbon availability was limited. We found large numbers of bacteria that oxidize reduced iron at sites with high rates of iron reduction and large numbers of iron-reducers. the coexistence of large populations of ironreducing and iron-oxidizing bacteria is evidence for rapid iron cycling between its reduced and oxidized states, and suggests that mutualistic interactions among these bacteria ultimately fuel organic carbon oxidation and inhibit CH4 production in these upland tropical forests.

  9. Gene-diet-interactions in folate-mediated one-carbon metabolism modify colon cancer risk.

    Science.gov (United States)

    Liu, Amy Y; Scherer, Dominique; Poole, Elizabeth; Potter, John D; Curtin, Karen; Makar, Karen; Slattery, Martha L; Caan, Bette J; Ulrich, Cornelia M

    2013-04-01

    The importance of folate-mediated one-carbon metabolism (FOCM) in colorectal carcinogenesis is emphasized by observations that high dietary folate intake is associated with decreased risk of colon cancer (CC) and its precursors. Additionally, polymorphisms in FOCM-related genes have been repeatedly associated with risk, supporting a causal relationship between folate and colorectal carcinogenesis. We investigated ten candidate polymorphisms with defined or probable functional impact in eight FOCM-related genes (SHMT1, DHFR, DNMT1, MTHFD1, MTHFR, MTRR, TCN2, and TDG) in 1609 CC cases and 1974 controls for association with CC risk and for interaction with dietary factors. No polymorphism was statistically significantly associated with overall risk of CC. However, statistically significant interactions modifying CC risk were observed for DNMT1 I311V with dietary folate, methionine, vitamin B2 , and vitamin B12 intake and for MTRR I22M with dietary folate, a predefined one-carbon dietary pattern, and vitamin B6 intake. We observed statistically significant gene-diet interactions with five additional polymorphisms. Our results provide evidence that FOCM-related dietary intakes modify the association between CC risk and FOCM allelic variants. These findings add to observations showing that folate-related gene-nutrient interactions play an important role in modifying the risk of CC. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Transcriptomic Analysis Reveals Selective Metabolic Adaptation of Streptococcus suis to Porcine Blood and Cerebrospinal Fluid

    Directory of Open Access Journals (Sweden)

    Anna Koczula

    2017-02-01

    Full Text Available Streptococcus suis is a zoonotic pathogen that can cause severe pathologies such as septicemia and meningitis in its natural porcine host as well as in humans. Establishment of disease requires not only virulence of the infecting strain but also an appropriate metabolic activity of the pathogen in its host environment. However, it is yet largely unknown how the streptococcal metabolism adapts to the different host niches encountered during infection. Our previous isotopologue profiling studies on S. suis grown in porcine blood and cerebrospinal fluid (CSF revealed conserved activities of central carbon metabolism in both body fluids. On the other hand, they suggested differences in the de novo amino acid biosynthesis. This prompted us to further dissect S. suis adaptation to porcine blood and CSF by RNA deep sequencing (RNA-seq. In blood, the majority of differentially expressed genes were associated with transport of alternative carbohydrate sources and the carbohydrate metabolism (pentose phosphate pathway, glycogen metabolism. In CSF, predominantly genes involved in the biosynthesis of branched-chain and aromatic amino acids were differentially expressed. Especially, isoleucine biosynthesis seems to be of major importance for S. suis in CSF because several related biosynthetic genes were more highly expressed. In conclusion, our data revealed niche-specific metabolic gene activity which emphasizes a selective adaptation of S. suis to host environments.

  11. Stable carbon isotopes as an indicator for soil degradation in an alpine environment (Urseren Valley, Switzerland).

    Science.gov (United States)

    Schaub, Monika; Alewell, Christine

    2009-05-01

    Analyses of soil organic carbon (SOC) content and stable carbon isotope signatures (delta(13)C) of soils were assessed for their suitability to detect early stage soil erosion. We investigated the soils in the alpine Urseren Valley (southern central Switzerland) which are highly impacted by soil erosion. Hill slope transects from uplands (cambisols) to adjacent wetlands (histosols and histic to mollic gleysols) differing in their intensity of visible soil erosion, and reference wetlands without erosion influence were sampled. Carbon isotopic signature and SOC content of soil depth profiles were determined. A close correlation of delta(13)C and carbon content (r > 0.80) is found for upland soils not affected by soil erosion, indicating that depth profiles of delta(13)C of these upland soils mainly reflect decomposition of SOC. Long-term disturbance of an upland soil is indicated by decreasing correlation of delta(13)C and SOC (r soil erosion in hill slope transects from uplands to adjacent wetlands is documented as an intermediate delta(13)C value (-27.5 per thousand) for affected wetland soil horizons (0-12 cm) between upland (aerobic metabolism, relatively heavier delta(13)C of -26.6 per thousand) and wetland isotopic signatures (anaerobic metabolism, relatively lighter delta(13)C of -28.6 per thousand). Carbon isotopic signature and SOC content are found to be sensitive indicators of short- and long-term soil erosion processes. Copyright (c) 2009 John Wiley & Sons, Ltd.

  12. Spatial variation in microbial processes controlling carbon mineralization within soils and sediments

    Energy Technology Data Exchange (ETDEWEB)

    Fendorf, Scott [Stanford Univ., CA (United States); Kleber, Markus [Oregon State Univ., Corvallis, OR (United States); Nico, Peter [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2017-10-19

    Soils have a defining role in global carbon cycling, having one of the largest dynamic stocks of C on earth—3300 Pg of C are stored in soils, which is three-times the amount stored in the atmosphere and more than the terrestrial land plants. An important control on soil organic matter (SOM) quantities is the mineralization rate. It is well recognized that the rate and extent of SOM mineralization is affected by climatic factors and mineral-organic matter associations. What remained elusive is to what extent constraints on microbial metabolism induced by the respiratory pathway, and specifically the electron acceptor in respiration, control overall rates of carbon mineralization in soils. Therefore, physical factors limiting oxygen diffusion such as soil texture and aggregate size (soil structure) may therefore be central controls on C mineralization rates. The goal of our research was therefore to determine if variations in microbial metabolic rates induced by anaerobic microsites in soils are a major control on SOM mineralization rates and thus storage. We performed a combination of laboratory experiments and field investigations will be performed to fulfill our research objectives. We used laboratory studies to examine fundamental factors of respiratory constraints (i.e., electron acceptor) on organic matter mineralization rates. We ground our laboratory studies with both manipulation of field samples and in-field measurements. Selection of the field sites is guided by variation in soil texture and structure while having (other environmental/soil factors constant. Our laboratory studies defined redox gradients and variations in microbial metabolism operating at the aggregate-scale (cm-scale) within soils using a novel constructed diffusion reactor. We further examined micro-scale variation in terminal electron accepting processes and resulting C mineralization rates within re-packed soils. A major outcome of our research is the ability to quantitatively place

  13. Carbonate platform growth and demise offshore Central Vietnam

    DEFF Research Database (Denmark)

    Fyhn, Michael B.W.; Boldreel, Lars Ole; Nielsen, Lars H.

    2013-01-01

    Fault Zone, the Tuy Hoa Carbonate Platform fringes the continental margin between Da Nang and Nha Trang. Here, platform growth initiated during the Early Miocene and continued until Middle Miocene time when regional uplift led to subaerial exposure, termination of platform growth and karstification...... continues on isolated platforms hosting the Paracel Islands farther seawards. The onset of widespread carbonate deposition largely reflects the Early Miocene transgression of the area linked with early post-rift subsidence and the opening of the South China Sea. The mid-Neogene shift in carbonate deposition...

  14. Towards an understanding of the molecular regulation of carbon allocation in diatoms: the interaction of energy and carbon allocation.

    Science.gov (United States)

    Wagner, Heiko; Jakob, Torsten; Fanesi, Andrea; Wilhelm, Christian

    2017-09-05

    In microalgae, the photosynthesis-driven CO 2 assimilation delivers cell building blocks that are used in different biosynthetic pathways. Little is known about how the cell regulates the subsequent carbon allocation to, for example, cell growth or for storage. However, knowledge about these regulatory mechanisms is of high biotechnological and ecological importance. In diatoms, the situation becomes even more complex because, as a consequence of their secondary endosymbiotic origin, the compartmentation of the pathways for the primary metabolic routes is different from green algae. Therefore, the mechanisms to manipulate the carbon allocation pattern cannot be adopted from the green lineage. This review describes the general pathways of cellular energy distribution from light absorption towards the final allocation of carbon into macromolecules and summarizes the current knowledge of diatom-specific allocation patterns. We further describe the (limited) knowledge of regulatory mechanisms of carbon partitioning between lipids, carbohydrates and proteins in diatoms. We present solutions to overcome the problems that hinder the identification of regulatory elements of carbon metabolism.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'. © 2017 The Author(s).

  15. Mathematical modeling of cancer metabolism.

    Science.gov (United States)

    Medina, Miguel Ángel

    2018-04-01

    Systemic approaches are needed and useful for the study of the very complex issue of cancer. Modeling has a central position in these systemic approaches. Metabolic reprogramming is nowadays acknowledged as an essential hallmark of cancer. Mathematical modeling could contribute to a better understanding of cancer metabolic reprogramming and to identify new potential ways of therapeutic intervention. Herein, I review several alternative approaches to metabolic modeling and their current and future impact in oncology. Copyright © 2018 Elsevier B.V. All rights reserved.

  16. Static magnetic field treatment of seeds improves carbon and nitrogen metabolism under salinity stress in soybean.

    Science.gov (United States)

    Baghel, Lokesh; Kataria, Sunita; Guruprasad, Kadur Narayan

    2016-10-01

    The effectiveness of magnetopriming was assessed for alleviation of salt-induced adverse effects on soybean growth. Soybean seeds were pre-treated with static magnetic field (SMF) of 200 mT for 1 h to evaluate the effect of magnetopriming on growth, carbon and nitrogen metabolism, and yield of soybean plants under different salinity levels (0, 25, and 50 mM NaCl). The adverse effect of NaCl-induced salt stress was found on growth, yield, and various physiological attributes of soybeans. Results indicate that SMF pre-treatment significantly increased plant growth attributes, number of root nodules, nodules, fresh weight, biomass accumulation, and photosynthetic performance under both non-saline and saline conditions as compared to untreated seeds. Polyphasic chlorophyll a fluorescence (OJIP) transients from magnetically treated plants gave a higher fluorescence yield at J-I-P phase. Nitrate reductase activity, PIABS , photosynthetic pigments, and net rate of photosynthesis were also higher in plants that emerged from SMF pre-treated seeds as compared to untreated seeds. Leghemoglobin content and hemechrome content in root nodules were also increased by SMF pre-treatment. Thus pre-sowing exposure of seeds to SMF enhanced carbon and nitrogen metabolism and improved the yield of soybeans in terms of number of pods, number of seeds, and seed weight under saline as well as non-saline conditions. Consequently, SMF pre-treatment effectively mitigated adverse effects of NaCl on soybeans. It indicates that magnetopriming of dry soybean seeds can be effectively used as a pre-sowing treatment for alleviating salinity stress. Bioelectromagnetics. 37:455-470, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  17. Changes in the Phosphoproteome and Metabolome Link Early Signaling Events to Rearrangement of Photosynthesis and Central Metabolism in Salinity and Oxidative Stress Response in Arabidopsis.

    Science.gov (United States)

    Chen, Yanmei; Hoehenwarter, Wolfgang

    2015-12-01

    Salinity and oxidative stress are major factors affecting and limiting the productivity of agricultural crops. The molecular and biochemical processes governing the plant response to abiotic stress have often been researched in a reductionist manner. Here, we report a systemic approach combining metabolic labeling and phosphoproteomics to capture early signaling events with quantitative metabolome analysis and enzyme activity assays to determine the effects of salt and oxidative stress on plant physiology. K(+) and Na(+) transporters showed coordinated changes in their phosphorylation pattern, indicating the importance of dynamic ion homeostasis for adaptation to salt stress. Unique phosphorylation sites were found for Arabidopsis (Arabidopsis thaliana) SNF1 kinase homolog10 and 11, indicating their central roles in the stress-regulated responses. Seven Sucrose Non-fermenting1-Related Protein Kinase2 kinases showed varying levels of phosphorylation at multiple serine/threonine residues in their kinase domain upon stress, showing temporally distinct modulation of the various isoforms. Salinity and oxidative stress also lead to changes in protein phosphorylation of proteins central to photosynthesis, in particular the kinase State Transition Protein7 required for state transition and light-harvesting II complex proteins. Furthermore, stress-induced changes of the phosphorylation of enzymes of central metabolism were observed. The phosphorylation patterns of these proteins were concurrent with changes in enzyme activity. This was reflected by altered levels of metabolites, such as the sugars sucrose and fructose, glycolysis intermediates, and amino acids. Together, our study provides evidence for a link between early signaling in the salt and oxidative stress response that regulates the state transition of photosynthesis and the rearrangement of primary metabolism. © 2015 American Society of Plant Biologists. All Rights Reserved.

  18. 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

  19. Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting

    KAUST Repository

    Abdel-Haleem, Alyaa M.

    2018-01-04

    Several antimalarial drugs exist, but differences between life cycle stages among malaria species pose challenges for developing more effective therapies. To understand the diversity among stages and species, we reconstructed genome-scale models (GEMs) of metabolism for five life cycle stages and five species of Plasmodium spanning the blood, transmission, and mosquito stages. The stage-specific models of Plasmodium falciparum uncovered stage-dependent changes in central carbon metabolism and predicted potential targets that could affect several life cycle stages. The species-specific models further highlight differences between experimental animal models and the human-infecting species. Comparisons between human- and rodent-infecting species revealed differences in thiamine (vitamin B1), choline, and pantothenate (vitamin B5) metabolism. Thus, we show that genome-scale analysis of multiple stages and species of Plasmodium can prioritize potential drug targets that could be both anti-malarials and transmission blocking agents, in addition to guiding translation from non-human experimental disease models.

  20. Differential controls on soil carbon density and mineralization among contrasting forest types in a temperate forest ecosystem

    Science.gov (United States)

    You, Ye-Ming; Wang, Juan; Sun, Xiao-Lu; Tang, Zuo-Xin; Zhou, Zhi-Yong; Sun, Osbert Jianxin

    2016-01-01

    Understanding the controls on soil carbon dynamics is crucial for modeling responses of ecosystem carbon balance to global change, yet few studies provide explicit knowledge on the direct and indirect effects of forest stands on soil carbon via microbial processes. We investigated tree species, soil, and site factors in relation to soil carbon density and mineralization in a temperate forest of central China. We found that soil microbial biomass and community structure, extracellular enzyme activities, and most of the site factors studied varied significantly across contrasting forest types, and that the associations between activities of soil extracellular enzymes and microbial community structure appeared to be weak and inconsistent across forest types, implicating complex mechanisms in the microbial regulation of soil carbon metabolism in relation to tree species. Overall, variations in soil carbon density and mineralization are predominantly accounted for by shared effects of tree species, soil, microclimate, and microbial traits rather than the individual effects of the four categories of factors. Our findings point to differential controls on soil carbon density and mineralization among contrasting forest types and highlight the challenge to incorporate microbial processes for constraining soil carbon dynamics in global carbon cycle models. PMID:26925871

  1. Greenhouse gas footprint and the carbon flow associated with different solid waste management strategy for urban metabolism in Bangladesh.

    Science.gov (United States)

    Islam, K M Nazmul

    2017-02-15

    Greenhouse gas (GHG) emissions from municipal solid waste (MSW) and associated climate change consequences are gripping attention globally, while MSW management as a vital subsystem of urban metabolism significantly influences the urban carbon cycles. This study evaluates the GHG emissions and carbon flow of existing and proposed MSW management in Bangladesh through scenario analysis, including landfill with landfill gas (LFG) recovery, waste to energy (WtE), and material recovery facility (MRF). The analysis indicates that, scenario H 2 and H 5 emitted net GHGs -152.20kg CO 2 eq. and -140.32kg CO 2 eq., respectively, in comparison with 420.88kg CO 2 eq. of scenario H 1 for managing per ton of wastes during the reference year 2015. The annual horizontal carbon flux of the waste input was 319Gg and 158Gg during 2015 in Dhaka and Chittagong, respectively. An integrated strategy of managing the wastes in the urban areas of Bangladesh involving WtE incineration plant and LFG recovery to generate electricity as well as MRF could reverse back 209.46Gg carbon and 422.29Gg carbon to the Chittagong and Dhaka urban system, respectively. This study provides valuable insights for the MSW policy framework and revamp of existing MSW management practices with regards to reduction of GHGs emissions from the waste sector in Bangladesh. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Metabolism and disposition of ethylene carbonate in male Fischer 344 rats

    International Nuclear Information System (INIS)

    Hanley, T.R. Jr.; Schumann, A.M.; Langvardt, P.W.; Rusek, T.F.; Watanabe, P.G.

    1989-01-01

    Ethylene carbonate (EC) has a toxicity profile which resembles that of ethylene glycol (EG). To determine whether the toxicity of EC could be explained on the basis of its metabolism to EG, male Fischer 344 rats were given 200 mg/kg of uniformly labeled [ 14 C]EC in water by gavage and the disposition of the radiolabel was then followed for 72 hr. EC was rapidly metabolized, with approximately 57 and 27% of the administered dose eliminated in the expired air as 14CO2 and in the urine, respectively; the remainder was found in the carcass. Separation of the urinary metabolites using liquid chromatography revealed a single radioactive peak. This metabolite was unequivocally identified as ethylene glycol via gas chromatography-mass spectrometry with the aid of 13C enrichment of the EC dose. Measurement of whole blood levels of EC and EG in rats given 200 mg/kg of EC by gavage revealed blood levels of EG approximately 100-fold higher than the levels of EC in these same animals, with a half-life of EG in blood of 2 hr, indicating rapid conversion of EC to EG. In a separate group of animals administered an equimolar dose of [ 14 C]EG (141 mg/kg), approximately 37% of the dose was expired as 14 CO 2 and 42% was excreted in the urine as parent compound. When expressed on the basis of the ethanediol moiety, the disposition of EC was identical to that of EG. In view of the rapid and extensive biotransformation of EC to EG and the similarity of the existing (though limited) toxicity data base of EC compared to EG, utilization of the extensive EG systemic toxicity data base for assessing the safety of EC appears justified

  3. Respiration and nitrogen assimilation: targeting mitochondria-associated metabolism as a means to enhance nitrogen use efficiency.

    Science.gov (United States)

    Foyer, Christine H; Noctor, Graham; Hodges, Michael

    2011-02-01

    Considerable advances in our understanding of the control of mitochondrial metabolism and its interactions with nitrogen metabolism and associated carbon/nitrogen interactions have occurred in recent years, particularly highlighting important roles in cellular redox homeostasis. The tricarboxylic acid (TCA) cycle is a central metabolic hub for the interacting pathways of respiration, nitrogen assimilation, and photorespiration, with components that show considerable flexibility in relation to adaptations to the different functions of mitochondria in photosynthetic and non-photosynthetic cells. By comparison, the operation of the oxidative pentose phosphate pathway appears to represent a significant limitation to nitrogen assimilation in non-photosynthetic tissues. Valuable new insights have been gained concerning the roles of the different enzymes involved in the production of 2-oxoglutarate (2-OG) for ammonia assimilation, yielding an improved understanding of the crucial role of cellular energy balance as a broker of co-ordinate regulation. Taken together with new information on the mechanisms that co-ordinate the expression of genes involved in organellar functions, including energy metabolism, and the potential for exploiting the existing flexibility for NAD(P)H utilization in the respiratory electron transport chain to drive nitrogen assimilation, the evidence that mitochondrial metabolism and machinery are potential novel targets for the enhancement of nitrogen use efficiency (NUE) is explored.

  4. Ecological network analysis for a low-carbon and high-tech industrial park.

    Science.gov (United States)

    Lu, Yi; Su, Meirong; Liu, Gengyuan; Chen, Bin; Zhou, Shiyi; Jiang, Meiming

    2012-01-01

    Industrial sector is one of the indispensable contributors in global warming. Even if the occurrence of ecoindustrial parks (EIPs) seems to be a good improvement in saving ecological crises, there is still a lack of definitional clarity and in-depth researches on low-carbon industrial parks. In order to reveal the processes of carbon metabolism in a low-carbon high-tech industrial park, we selected Beijing Development Area (BDA) International Business Park in Beijing, China as case study, establishing a seven-compartment- model low-carbon metabolic network based on the methodology of Ecological Network Analysis (ENA). Integrating the Network Utility Analysis (NUA), Network Control Analysis (NCA), and system-wide indicators, we compartmentalized system sectors into ecological structure and analyzed dependence and control degree based on carbon metabolism. The results suggest that indirect flows reveal more mutuality and exploitation relation between system compartments and they are prone to positive sides for the stability of the whole system. The ecological structure develops well as an approximate pyramidal structure, and the carbon metabolism of BDA proves self-mutualistic and sustainable. Construction and waste management were found to be two active sectors impacting carbon metabolism, which was mainly regulated by internal and external environment.

  5. Application of central composite design to optimize the amount of carbon source and prebiotics for Bifidobacterium bifidum BB01

    Directory of Open Access Journals (Sweden)

    Shu Guowei

    2016-06-01

    Full Text Available The objective of the present study was to obtain the optimum proportion of the carbon source and prebiotics for Bifidobacterium bifidum BB01 by the central composite design (CCD. The effect of carbon source (lactose and two prebiotics (inulin and fructooligosaccharides on the BB01 were observed by measuring the OD600 value, pH value and the viable counts at 18h. The final optimized concentrations of carbon source and prebiotics were: lactose 1.6%, inulin 0.26%, and fructooligosaccharides 0.22%. The result indicates that the growth of B. bifidum BB01 shows an significant increase in the optimized culture medium (p < 0.05, the OD600 value reached 1.434 at 18h, which increased 6.58% compared to the control. And the viable counts of B. bifidum BB01 increased 24.36% and reached (2.17±0.06 ×109cfu/mL. The results show that the optimization of the carbon source and prebiotics using CCD in this study is workable and necessary.

  6. Respiratory compensation to a primary metabolic alkalosis in humans.

    Science.gov (United States)

    Feldman, Mark; Alvarez, Naiara M; Trevino, Michael; Weinstein, Gary L

    2012-11-01

    There is limited and disparate information about the extent of the respiratory compensation (hypoventilation) that occurs in response to a primary metabolic alkalosis in humans. Our aim was to examine the influence of the plasma bicarbonate concentration, the plasma base excess, and the arterial pH on the arterial carbon dioxide tension in 52 adult patients with primary metabolic alkalosis, mostly due to diuretic use or vomiting. Linear regression analysis was used to correlate degrees of alkalosis with arterial carbon dioxide tensions. In this alkalotic cohort, whose arterial plasma bicarbonate averaged 31.6 mEq/l, plasma base excess averaged 7.8 mEq/l, and pH averaged 7.48, both plasma bicarbonate and base excess correlated closely with arterial carbon dioxide tensions (r = 0.97 and 0.96, respectively; p respiratory compensation (hypoventilation) to primary metabolic alkalosis than has been reported in prior smaller studies.

  7. Photoperiod length paces the temporal orchestration of cell cycle and carbon-nitrogen metabolism in Crocosphaera watsonii.

    Science.gov (United States)

    Dron, Anthony; Rabouille, Sophie; Claquin, Pascal; Talec, Amélie; Raimbault, Virginie; Sciandra, Antoine

    2013-12-01

    We analysed the effect of photoperiod length (PPL) (16:8 and 8:16 h of light-dark regime, named long and short PPL, respectively) on the temporal orchestration of the two antagonistic, carbon and nitrogen acquisitions in the unicellular, diazotrophic cyanobacterium Crocosphaera watsonii strain WH8501 growing diazotrophically. Carbon and nitrogen metabolism were monitored at high frequency, and their patterns were compared with the cell cycle progression. The oxygen-sensitive N2 fixation process occurred mainly during the dark period, where photosynthesis cannot take place, inducing a light-dark cycle of cellular C : N ratio. Examination of circadian patterns in the cell cycle revealed that cell division occurred during the midlight period, (8 h and 4 h into the light in the long and short PPL conditions, respectively), thus timely separated from the energy-intensive diazotrophic process. Results consistently show a nearly 5 h time lag between the end of cell division and the onset of N2 fixation. Shorter PPLs affected DNA compaction of C. watsonii cells and also led to a decrease in the cell division rate. Therefore, PPL paces the growth of C. watsonii: a long PPL enhances cell division while a short PPL favours somatic growth (biomass production) with higher carbon and nitrogen cell contents. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

  8. Generation of nitric oxide from nitrite by carbonic anhydrase: a possible link between metabolic activity and vasodilation

    DEFF Research Database (Denmark)

    Aamand, Rasmus; Dalsgaard, Thomas; Jensen, Frank Bo

    2009-01-01

    In catalyzing the reversible hydration of CO2 to bicarbonate and protons, the ubiquitous enzyme carbonic anhydrase (CA) plays a crucial role in CO2 transport, in acid-base balance, and in linking local acidosis to O2 unloading from hemoglobin. Considering the structural similarity between...... bicarbonate and nitrite, we hypothesized that CA uses nitrite as a substrate to produce the potent vasodilator nitric oxide (NO) to increase local blood flow to metabolically active tissues. Here we show that CA readily reacts with nitrite to generate NO, particularly at low pH, and that the NO produced...

  9. Metabolic regulation in the facultative methylotroph arthrobacter P1

    NARCIS (Netherlands)

    1985-01-01

    Many microorganisms are able to utilize C1 compounds, i.e. compounds which do not contain carbon-carbon bonds, as carbon- and energy sources for growth. In order to synthesize cell constituents from these C1 compounds special metabolic pathways are employed by such organisms. Although a great deal

  10. Effect of metabolic alkalosis on respiratory function in patients with chronic obstructive lung disease.

    Science.gov (United States)

    Bear, R.; Goldstein, M.; Phillipson, E.; Ho, M.; Hammeke, M.; Feldman, R.; Handelsman, S.; Halperin, M.

    1977-01-01

    Eleven instances of a mixed acid-base disorder consisting of chronic respiratory acidosis and metabolic alkalosis were recognized in eight patients with chronic obstructive lung disease and carbon dioxide retention. Correction of the metabolic alkalosis led to substantial improvement in blood gas values and clinical symptoms. Patients with mixed chronic respiratory acidosis and metabolic alkalosis constitute a common subgroup of patients with chronic obstructive lung disease and carbon dioxide retention; these patients benefit from correction of the metabolic alkalosis. PMID:21028

  11. Linking carbon and nitrogen metabolism to depth distribution of submersed macrophytes using high ammonium dosing tests and a lake survey.

    Science.gov (United States)

    Yuan, Guixiang; Cao, Te; Fu, Hui; Ni, Leyi; Zhang, Xiaolin; Li, Wei; Song, Xin; Xie, Ping; Jeppesen, Erik

    2013-12-01

    Strategies of carbon (C) and nitrogen (N) utilisation are among the factors determining plant distribution. It has been argued that submersed macrophytes adapted to lower light environments are more efficient in maintaining C metabolic homeostasis due to their conservative C strategy and ability to balance C shortage. We studied how depth distributions of 12 submersed macrophytes in Lake Erhai, China, were linked to their C-N metabolic strategies when facing acute [Formula: see text] dosing.[Formula: see text] dosing changed C-N metabolism significantly by decreasing the soluble carbohydrate (SC) content and increasing the [Formula: see text]-N and free amino acid (FAA) content of plant tissues.The proportional changes in SC contents in the leaves and FAA contents in the stems induced by [Formula: see text] dosing were closely correlated (positive for SC and negative for FAA) with the colonising water depths of the plants in Lake Erhai, the plants adapted to lower light regimes being more efficient in maintaining SC and FAA homeostasis.These results indicate that conservative carbohydrate metabolism of submersed macrophytes allowed the plants to colonise greater water depths in eutrophic lakes, where low light availability in the water column diminishes carbohydrate production by the plants.

  12. 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

    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 13C MFA or 2S- 13C MFA, as well as provide for a substantially lower set of flux bounds......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...

  13. Central obesity is important but not essential component of the metabolic syndrome for predicting diabetes mellitus in a hypertensive family-based cohort. Results from the Stanford Asia-pacific program for hypertension and insulin resistance (SAPPHIRe) Taiwan follow-up study.

    Science.gov (United States)

    Lee, I-Te; Chiu, Yen-Feng; Hwu, Chii-Min; He, Chih-Tsueng; Chiang, Fu-Tien; Lin, Yu-Chun; Assimes, Themistocles; Curb, J David; Sheu, Wayne H-H

    2012-04-26

    Metabolic abnormalities have a cumulative effect on development of diabetes, but only central obesity has been defined as the essential criterion of metabolic syndrome (MetS) by the International Diabetes Federation. We hypothesized that central obesity contributes to a higher risk of new-onset diabetes than other metabolic abnormalities in the hypertensive families. Non-diabetic Chinese were enrolled and MetS components were assessed to establish baseline data in a hypertensive family-based cohort study. Based on medical records and glucose tolerance test (OGTT), the cumulative incidence of diabetes was analyzed in this five-year study by Cox regression models. Contribution of central obesity to development of new-onset diabetes was assessed in subjects with the same number of positive MetS components. Among the total of 595 subjects who completed the assessment, 125 (21.0%) developed diabetes. Incidence of diabetes increased in direct proportion to the number of positive MetS components (P ≪ 0.001). Although subjects with central obesity had a higher incidence of diabetes than those without (55.7 vs. 30.0 events/1000 person-years, P ≪ 0.001), the difference became non-significant after adjusting of the number of positive MetS components (hazard ratio = 0.72, 95%CI: 0.45-1.13). Furthermore, in all participants with three positive MetS components, there was no difference in the incidence of diabetes between subjects with and without central obesity (hazard ratio = 1.04, 95%CI: 0.50-2.16). In Chinese hypertensive families, the incidence of diabetes in subjects without central obesity was similar to that in subjects with central obesity when they also had the same number of positive MetS components. We suggest that central obesity is very important, but not the essential component of the metabolic syndrome for predicting of new-onset diabetes. ( NCT00260910, ClinicalTrials.gov).

  14. Metabolic responses of primary and transformed cells to intracellular Listeria monocytogenes.

    Directory of Open Access Journals (Sweden)

    Nadine Gillmaier

    Full Text Available The metabolic response of host cells, in particular of primary mammalian cells, to bacterial infections is poorly understood. Here, we compare the carbon metabolism of primary mouse macrophages and of established J774A.1 cells upon Listeria monocytogenes infection using (13C-labelled glucose or glutamine as carbon tracers. The (13C-profiles of protein-derived amino acids from labelled host cells and intracellular L. monocytogenes identified active metabolic pathways in the different cell types. In the primary cells, infection with live L. monocytogenes increased glycolytic activity and enhanced flux of pyruvate into the TCA cycle via pyruvate dehydrogenase and pyruvate carboxylase, while in J774A.1 cells the already high glycolytic and glutaminolytic activities hardly changed upon infection. The carbon metabolism of intracellular L. monocytogenes was similar in both host cells. Taken together, the data suggest that efficient listerial replication in the cytosol of the host cells mainly depends on the glycolytic activity of the hosts.

  15. Seasonal variations of dissolved organic carbon in precipitation over urban and forest sites in central Poland.

    Science.gov (United States)

    Siudek, Patrycja; Frankowski, Marcin; Siepak, Jerzy

    2015-07-01

    Spatial and temporal variability of carbon species in rainwater (bulk deposition) was studied for the first time at two sites located in urban area of Poznań City and protected woodland area (Jeziory), in central Poland, between April and December 2013. The mean concentration of total carbon (TC) for the first site was 5.86 mg L(-1), whereas for the second, 5.21 mg L(-1). Dissolved organic carbon (DOC) concentration accounted for, on average, 87 and 91 % of total carbon in precipitation at urban and non-urban sites, respectively. Significant changes in TC concentrations in rainwater were observed at both sites, indicating that atmospheric transformation, transport, and removal mechanisms of carbonaceous particles were affected by seasonal fluctuations in biogenic/anthropogenic emission and meteorological conditions (i.e., precipitation height and type, atmospheric transport). During the warm season, the DOC concentration in rainwater was mostly influenced by mixed natural and anthropogenic sources. In contrast, during the cold season, the DOC concentration significantly increased mainly as a result of anthropogenic activities, i.e., intensive coal combustion, domestic wood burning, high-temperature processes, etc. In addition, during the winter measurements, significant differences in mean DOC concentration (Kruskal-Wallis test, p urban and non-urban sites. These data imply that carbonaceous compounds are of crucial importance in atmospheric chemistry and should be considered as an important parameter while considering wet deposition, reactions with different substances, especially over polluted environments.

  16. Carbon and oxygen isotope compositions of the carbonate facies

    Indian Academy of Sciences (India)

    The Vindhyan sedimentary succession in central India spans a wide time bracket from the Paleopro- terozoic to the Neoproterozoic period.Chronostratigraphic significance of stable carbon and oxygen isotope ratios of the carbonate phase in Vindhyan sediments has been discussed in some recent studies.However,the ...

  17. Carbon and phosphorus regulating bacterial metabolism in oligotrophic boreal lakes

    DEFF Research Database (Denmark)

    Vidal, L. O.; Graneli, W.; Daniel, C. B.

    2011-01-01

    This study focused on how phosphorus and carbon control pelagic bacteria in lakes over a gradient of dissolved organic carbon (DOC from 6.7 to 29.5 mg C L(-1)) and phosphorus (P-tot from 5 to 19 mu g L(-1)). Five oligotrophic lakes in southern Sweden were sampled in late autumn. Phosphate...... carbon mineralization in this kind of system during autumn is conditioned by the combined availability of labile carbon and phosphorus, with the assimilated carbon mainly transformed to inorganic carbon in respiration, contributing to CO(2) supersaturation in these systems....

  18. DL-7-azatryptophan and citrulline metabolism in the cyanobacterium Anabaena sp. strain 1F

    International Nuclear Information System (INIS)

    Chen, C.H.; Van Baalen, C.; Tabita, F.R.

    1987-01-01

    An alternative route for the primary assimilation of ammonia proceeds via glutamine synthetase-carbamyl phosphate synthetase and its inherent glutaminase activity in Anabaena sp. strain 1F, a marine filamentous, heterocystous cyanobacterium. Evidence for the presence of this possible alternative route to glutamate was provided by the use of amino acid analogs as specific enzyme inhibitors, enzymological studies, and radioistopic labeling experiments. The amino acid pool patterns of continuous cultures of Anabaena sp. strain 1F were markedly influenced by the nitrogen source. A relatively high concentration of glutamate was maintained in the amino acid pools of all cultures irrespective of the nitrogen source, reflecting the central role of glutamate in nitrogen metabolism. The addition of 1.0 microM azaserine increased the intracellular pools of glutamate and glutamine. All attempts to detect any enzymatic activity for glutamate synthase by measuring the formation of L-[ 14 C]glutamate from 2-keto-[1- 14 C]glutarate and glutamine failed. The addition of 10 microM DL-7-azatryptophan caused a transient accumulation of intracellular citrulline and alanine which was not affected by the presence of chloramphenicol. The in vitro activity of carbamyl phosphate synthetase and glutaminase increased severalfold in the presence of azatryptophan. Results from radioisotopic labeling experiments with [ 14 C]bicarbonate and L-[1- 14 C]ornithine also indicated that citrulline was formed via carbamyl phosphate synthetase and ornithine transcarbamylase. In addition to its effects on nitrogen metabolism, azatryptophan also affected carbon metabolism by inhibiting photosynthetic carbon assimilation and photosynthetic oxygen evolution

  19. Prevalence of metabolic syndrome among Filipino-Americans: a cross-sectional study.

    Science.gov (United States)

    Dalusung-Angosta, Alona; Gutierrez, Antonio

    2013-11-01

    The aims of this study are a) to examine the prevalence of metabolic syndrome among Filipino-Americans, b) to compare the rate of metabolic syndrome between Filipino men and women, and c) to examine the prevalence of central adiposity. Filipino-Americans are the second largest Asian subgroup in the United States and their leading cause of death is coronary heart disease (CHD). This study utilized a descriptive correlational, cross-sectional design that included a convenience sample of 300 Filipino-Americans residing in Southern Nevada. Survey questionnaires were used to collect the sample's demographic data and presence of CHD risk factors. Waist circumference measurements were used to examine central adiposity. Metabolic syndrome and central adiposity are highly prevalent among Filipino-Americans residing in Southern Nevada. More men than women had the syndrome, but the rate of central adiposity was significantly higher in women than in men. Intensive lifestyle modifications and treatment are indicated to decrease the prevalence of metabolic syndrome and the risk of heart disease in this group. Published by Elsevier Inc.

  20. World-Economy Centrality and Carbon Dioxide Emissions: A New Look at the Position in the Capitalist World-System and Environmental Pollution

    Directory of Open Access Journals (Sweden)

    Paul Prew

    2015-08-01

    Full Text Available With the ever-growing concern of climate change, much attention has been paid to the factors driving carbon dioxide emissions. Previous research in the World-Systems perspective has identified a relationship between carbon dioxide emissions and position in the world-economy. This study intends to build on the previous research by developing a new, more parsimonious indicator of World-System position based on Immanuel Wallerstein’s theoretical concepts of incorporation and core-periphery processes. The new World-System indicator is derived from the centrality measure in network analysis based on import data from the International Monetary Fund’s Direction of Trade Statistics. Based on the theoretical concepts of core-periphery processes, carbon dioxide emissions are predicted to rise based on the predominance of energy-intensive, high-technology, core processes within the nation. The results tend to demonstrate a strong relationship between carbon dioxide emissions and position in the world-economy, and the new World-System position indicator is more strongly related with carbon dioxide emissions than Gross Domestic Product per capita.

  1. Metabolic Evidence of Diminished Lipid Oxidation in Women With Polycystic Ovary Syndrome

    Science.gov (United States)

    Whigham, Leah D.; Butz, Daniel E.; Dashti, Hesam; Tonelli, Marco; Johnson, LuAnn K.; Cook, Mark E.; Porter, Warren P.; Eghbalnia, Hamid R.; Markley, John L.; Lindheim, Steven R.; Schoeller, Dale A.; Abbott, David H.; Assadi-Porter, Fariba M.

    2014-01-01

    Polycystic ovary syndrome (PCOS), a common female endocrinopathy, is a complex metabolic syndrome of enhanced weight gain. The goal of this pilot study was to evaluate metabolic differences between normal (n=10) and PCOS (n=10) women via breath carbon isotope ratio, urinary nitrogen and nuclear magnetic resonance (NMR)-determined serum metabolites. Breath carbon stable isotopes measured by cavity ring down spectroscopy (CRDS) indicated diminished (pglucose tolerance test showed that a transient elevation in blood glucose levels decreased circulating levels of lipid, glucose and amino acid metabolic intermediates (acetone, 2-oxocaporate, 2-aminobutyrate, pyruvate, formate, and sarcosine) in PCOS women, whereas the 2 h glucose challenge led to increases in the same intermediates in normal women. These pilot data suggest that PCOS-related inflexibility in fasting-related switching between lipid and carbohydrate/protein utilization for carbon metabolism may contribute to enhanced weight gain. PMID:24765590

  2. Essential nutrient supplementation prevents heritable metabolic disease in multigenerational intrauterine growth-restricted rats

    Science.gov (United States)

    Goodspeed, Danielle; Seferovic, Maxim D.; Holland, William; Mcknight, Robert A.; Summers, Scott A.; Branch, D. Ware; Lane, Robert H.; Aagaard, Kjersti M.

    2015-01-01

    Intrauterine growth restriction (IUGR) confers heritable alterations in DNA methylation, rendering risk of adult metabolic syndrome (MetS). Because CpG methylation is coupled to intake of essential nutrients along the one-carbon pathway, we reasoned that essential nutrient supplementation (ENS) may abrogate IUGR-conferred multigenerational MetS. Pregnant Sprague-Dawley rats underwent bilateral uterine artery ligation causing IUGR in F1. Among the F2 generation, IUGR lineage rats were underweight at birth (6.7 vs. 8.0 g, P 30% elevated, P 5-fold less central fat mass, normal hepatic glucose efflux, and >70% reduced circulating triglycerides and very-LDLs compared with IUGR control-fed F2 offspring (P intrauterine growth-restricted rats. PMID:25395450

  3. Light-dark (12:12) cycle of carbon and nitrogen metabolism in Crocosphaera watsonii WH8501: relation to the cell cycle.

    Science.gov (United States)

    Dron, Anthony; Rabouille, Sophie; Claquin, Pascal; Le Roy, Bertrand; Talec, Amélie; Sciandra, Antoine

    2012-04-01

    This study provides with original data sets on the physiology of the unicellular diazotrophic cyanobacterium Crocosphaera watsonii WH8501, maintained in continuous culture in conditions of obligate diazotrophy. Cultures were exposed to a 12:12 light-dark regime, representative of what they experience in nature and where growth is expected to be balanced. Nitrogen and carbon metabolism were monitored at high frequency and their dynamics was compared with the cell cycle. Results reveal a daily cycle in the physiological and biochemical parameters, tightly constrained by the timely decoupled processes of N(2) fixation and carbon acquisition. The cell division rate increased concomitantly to carbon accumulation and peaked 6 h into the light. The carbon content reached a maximum at the end of the light phase. N(2) fixation occurred mostly during the dark period and peaked between 9 and 10 h into the night, while DNA synthesis, reflected by DNA fluorescence, increased until the end of the night. Consequently, cells in G1- and S-phases present a marked decrease in their C:N ratio. Nitrogen acquisition through N(2) fixation exceeded 1.3- to 3-fold the nitrogen requirements for growth, suggesting that important amounts of nitrogen are excreted even under conditions supposed to favour balanced, carbon and nitrogen acquisitions. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

  4. A state of the art of metabolic networks of unicellular microalgae and cyanobacteria for biofuel production.

    Science.gov (United States)

    Baroukh, Caroline; Muñoz-Tamayo, Rafael; Steyer, Jean-Philippe; Bernard, Olivier

    2015-07-01

    The most promising and yet challenging application of microalgae and cyanobacteria is the production of renewable energy: biodiesel from microalgae triacylglycerols and bioethanol from cyanobacteria carbohydrates. A thorough understanding of microalgal and cyanobacterial metabolism is necessary to master and optimize biofuel production yields. To this end, systems biology and metabolic modeling have proven to be very efficient tools if supported by an accurate knowledge of the metabolic network. However, unlike heterotrophic microorganisms that utilize the same substrate for energy and as carbon source, microalgae and cyanobacteria require light for energy and inorganic carbon (CO2 or bicarbonate) as carbon source. This double specificity, together with the complex mechanisms of light capture, makes the representation of metabolic network nonstandard. Here, we review the existing metabolic networks of photoautotrophic microalgae and cyanobacteria. We highlight how these networks have been useful for gaining insight on photoautotrophic metabolism. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  5. A bottom-up approach to urban metabolism: the perspective of BRIDGE

    Science.gov (United States)

    Chrysoulakis, N.; Borrego, C.; San Josè, R.; Grimmond, S. B.; Jones, M. B.; Magliulo, V.; Klostermann, J.; Santamouris, M.

    2011-12-01

    Urban metabolism considers a city as a system and usually distinguishes between energy and material flows as its components. "Metabolic" studies are usually top-down approaches that assess the inputs and outputs of food, water, energy, and pollutants from a city, or that compare the changing metabolic process of several cities. In contrast, bottom-up approaches are based on quantitative estimates of urban metabolism components at local to regional scales. Such approaches consider the urban metabolism as the 3D exchange and transformation of energy and matter between a city and its environment. The city is considered as a system and the physical flows between this system and its environment are quantitatively estimated. The transformation of landscapes from primarily agricultural and forest uses to urbanized landscapes can greatly modify energy and material exchanges and it is, therefore, an important aspect of an urban area. Here we focus on the exchanges and transformation of energy, water, carbon and pollutants. Recent advances in bio-physical sciences have led to new methods and models to estimate local scale energy, water, carbon and pollutant fluxes. However, there is often poor communication of new knowledge and its implications to end-users, such as planners, architects and engineers. The FP7 Project BRIDGE (SustainaBle uRban plannIng Decision support accountinG for urban mEtabolism) aims at bridging this gap and at illustrating the advantages of considering environmental issues in urban planning. BRIDGE does not perform a complete life cycle analysis or calculate whole system urban metabolism, but rather focuses on specific metabolism components (energy, water, carbon and pollutants). Its main goal is the development of a Decision Suport System (DSS) with the potential to select planning actions which better fit the goal of changing the metabolism of urban systems towards sustainability. BRIDGE evaluates how planning alternatives can modify the physical

  6. Combination therapy with lercanidipine and enalapril reduced central blood pressure augmentation in hypertensive patients with metabolic syndrome.

    Science.gov (United States)

    Ghiadoni, Lorenzo; Bruno, Rosa Maria; Cartoni, Giulia; Stea, Francesco; Magagna, Armando; Virdis, Agostino; Grassi, Davide; Ferri, Claudio; Taddei, Stefano

    2017-05-01

    Arterial stiffness and blood pressure (BP) augmentation are independent predictors of cardiovascular events. In a randomized, open, parallel group study we compared the effect on these parameters of combination therapy with an ACE-inhibitor plus calcium channel blocker or thiazide diuretic in 76 hypertensive patients with metabolic syndrome uncontrolled by ACE-inhibitor monotherapy. After 4weeks run-in with enalapril (ENA, 20mg), patients were randomized to a combination therapy with lercanidipine (LER, 10-20mg) or hydrochlorothiazide (HCT, 12.5-25mg) for 24weeks. Aortic stiffness (carotid to femoral pulse wave velocity, PWV), central BP values and augmentation (augmentation index, AIx) were measured by applanation tonometry. The two groups showed similar office and central BP after run-in. Office (ENA/LER: from 149.1±4.9/94.5±1.5 to 131.7±8.1/82.2±5.3; ENA/HCT: from 150.3±4.7/94.7±2.1 to 133.1±7.1/82.8±5.3mmHg) and central BP (ENA/LER 127.4±17.1/85.2±12.1 to 120.5±13.5/80.0±9.5mmHg; ENA/HCT 121.6±13.4/79.3±9.5mmHg) were similarly reduced after 24weeks. PWV was comparable after run-in and not differently reduced by the two treatments (ENA/LER from 8.6±1.5 to 8.1±1.3m/s, pmetabolic syndrome not controlled by ENA alone. These results indicate a positive effect of the combination of ENA/LER on central BP augmentation, suggesting a potential additive role for cardiovascular protection. Copyright © 2015 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    Scheen, A J

    2010-10-01

    Recent evidence suggests that the brain has a key role in the control of energy metabolism, body fat content and glucose metabolism. Neuronal systems, which regulate energy intake, energy expenditure, and endogenous glucose production, sense and respond to input from hormonal and nutrient-related signals that convey information regarding both body energy stores and current energy availability. In response to this input, adaptive changes occur that promote energy homeostasis and the maintenance of blood glucose levels in the normal range. Defects in this control system are implicated in the link between obesity and type 2 diabetes mellitus. The central nervous system may be considered the conductor of an orchestra involving many peripheral organs involved in these homeostatic processes. However, the brain is mainly a glucose-dependent organ, which can be damaged by both hypoglycaemia and hyperglycaemia. Hypoglycaemia unawareness is a major problem in clinical practice and is associated with an increased risk of coma. Stroke is another acute complication associated with diabetes mellitus, especially in elderly people, and the control of glucose level in this emergency situation remains challenging. The prognosis of stroke is worse in diabetic patients and both its prevention and management in at-risk patients should be improved. Finally, chronic diabetic encephalopathies, which may lead to cognitive dysfunction and even dementia, are also recognized. They may result from recurrent hypoglycaemia and/or from chronic hyperglycaemia leading to cerebral vascular damage. Functional imaging is of interest for exploring diabetes-associated cerebral abnormalities. Thus, the intimate relationship between the brain and diabetes is increasingly acknowledged in both research and clinical practice. Copyright © 2010 Elsevier Masson SAS. All rights reserved.

  8. Carbon isotope composition of intermediates of the starch-malate sequence and level of the crassulacean acid metabolism in leaves of Kalanchoe blossfeldiana Tom Thumb.

    Science.gov (United States)

    Deleens, E; Garnier-Dardart, J; Queiroz, O

    1979-09-01

    Isotype analyses were performed on biochemical fractions isolated from leaves of Kalanchoe blossfeldiana Tom Thumb. during aging under long days or short days. Irrespective of the age or photoperiodic conditions, the intermediates of the starch-malate sequence (starch, phosphorylated compounds and organic acids) have a level of (13)C higher than that of soluble sugars, cellulose and hemicellulose. In short days, the activity of the crassulacean acid metabolism pathway is predominant as compared to that of C3 pathway: leaves accumulate organic acids, rich in (13)C. In long days, the activity of the crassulacean acid metabolism pathway increases as the leaves age, remaining, however, relatively low as compared to that of C3 pathway: leaves accumulate soluble sugars, poor in (13)C. After photoperiodic change (long days→short days), isotopic modifications of starch and organic acids suggest evidence for a lag phase in the establishment of the crassulacean acid metabolism pathway specific to short days. The relative proportions of carbon from a C3-origin (RuBPC acitivity as strong discriminating step, isotope discrimination in vivo=20‰) or C4-origin (PEPC activity as weak discriminating step, isotope discrimination in vivo=4‰) present in the biochemical fractions were calculated from their δ(13)C values. Under long days, 30 to 70% versus 80 to 100% under short days, of the carbon of the intermediates linked to the starch-malate sequence, or CAM pathway (starch, phosphorylated compounds and organic acids), have a C4-origin. Products connected to the C3 pathway (free sugars, cellulose, hemicellulose) have 0 to 50% of their carbon, arising from reuptake of the C4 from malate, under long days versus 30 to 70% under short days.

  9. Bactericidal peptidoglycan recognition protein induces oxidative stress in Escherichia coli through a block in respiratory chain and increase in central carbon catabolism.

    Science.gov (United States)

    Kashyap, Des R; Kuzma, Marcin; Kowalczyk, Dominik A; Gupta, Dipika; Dziarski, Roman

    2017-09-01

    Mammalian Peptidoglycan Recognition Proteins (PGRPs) kill both Gram-positive and Gram-negative bacteria through simultaneous induction of oxidative, thiol and metal stress responses in bacteria. However, metabolic pathways through which PGRPs induce these bactericidal stress responses are unknown. We screened Keio collection of Escherichia coli deletion mutants and revealed that deleting genes for respiratory chain flavoproteins or for tricarboxylic acid (TCA) cycle resulted in increased resistance of E. coli to PGRP killing. PGRP-induced killing depended on the production of hydrogen peroxide, which required increased supply of NADH for respiratory chain oxidoreductases from central carbon catabolism (glycolysis and TCA cycle), and was controlled by cAMP-Crp. Bactericidal PGRP induced a rapid decrease in respiration, which suggested that the main source of increased production of hydrogen peroxide was a block in respiratory chain and diversion of electrons from NADH oxidoreductases to oxygen. CpxRA two-component system was a negative regulator of PGRP-induced oxidative stress. By contrast, PGRP-induced thiol stress (depletion of thiols) and metal stress (increase in intracellular free Zn 2+ through influx of extracellular Zn 2+ ) were mostly independent of oxidative stress. Thus, manipulating pathways that induce oxidative, thiol and metal stress in bacteria could be a useful strategy to design new approaches to antibacterial therapy. © 2017 John Wiley & Sons Ltd.

  10. Forming mechanism of the Ordovician karst carbonate reservoirs on the northern slope of central Tarim Basin

    Directory of Open Access Journals (Sweden)

    Heng Fu

    2017-07-01

    Full Text Available The Ordovician karst carbonate reservoirs on the northern slope of central Tarim Basin are important oil and gas exploration targets in the basin, but their dissolution mechanisms are in controversy. In this paper, based on the integrated study of sedimentation, sequence and reservoir, together with microscopic analysis and macroscopic seismic data analysis, the carbonate karst reservoirs in the study area were divided into three types: dissolved pore-cavity limestone reservoir, pore-cavity dolomite reservoir and fracture-cavity siliceous reservoir, and their forming mechanisms were discussed respectively. Some findings were obtained. First, dissolved pore-cavity limestone reservoirs are distributed in the upper Yingshan Fm and Yijianfang Fm of the Ordovician vertically, while pore-cavity dolomite reservoirs are mainly developed in the Penglai Fm and lower Yingshan Fm of the Ordovician with great thickness. Second, dissolved pore-cavity limestone reservoirs were formed by karstification on the third-order sequence boundary (lowstand tract, while pore-cavity dolomite reservoirs were formed by deep burial dolomitization controlled by karstification on the third-order sequence boundary, both of which are distributed in the highstand tract below the third-order sequence boundary. Third, siliceous reservoirs are developed under the control of faulting, as a result of reworking of deep hydrothermal fluids along faults to the limestone, and the siliceous reservoirs and their hydrothermal solution fracture-cavity systems are distributed near faults. It is further predicted that, in addition to the three types of reservoir above, platform-margin reef-flat reservoirs are developed in the Ordovician on the northern slope of central Tarim Basin.

  11. Intracerebroventricular ghrelin treatment affects lipid metabolism in liver of rainbow trout (Oncorhynchus mykiss).

    Science.gov (United States)

    Velasco, Cristina; Librán-Pérez, Marta; Otero-Rodiño, Cristina; López-Patiño, Marcos A; Míguez, Jesús M; Soengas, José L

    2016-03-01

    We aimed to elucidate in rainbow trout (Oncorhynchus mykiss) the effects of central ghrelin (GHRL) treatment on the regulation of liver lipid metabolism, and the possible modulatory effect of central GHRL treatment on the simultaneous effects of raised levels of oleate. Thus, we injected intracerebroventricularly (ICV) rainbow trout GHRL in the presence or absence of oleate and evaluated in liver variables related to lipid metabolism. Oleate treatment elicited in liver of rainbow trout decreased lipogenesis and increased oxidative capacity in agreement with previous studies. Moreover, as demonstrated for the first time in fish in the present study, GHRL also acts centrally modulating lipid metabolism in liver, resulting in increased potential for lipogenesis and decreased potential for fatty acid oxidation, i.e. the converse effects to those elicited by central oleate treatment. The simultaneous treatment of GHRL and oleate confirmed these counteractive effects. Thus, the nutrient sensing mechanisms present in hypothalamus, particularly those involved in sensing of fatty acid, are involved in the control of liver energy metabolism in fish, and this control is modulated by the central action of GHRL. These results give support to the notion of hypothalamus as an integrative place for the regulation of peripheral energy metabolism in fish. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. Short Term vs Long Term Environmental Reconstruction from Carbonated Deposits of the Limagne Area (Massif Central, France)

    Energy Technology Data Exchange (ETDEWEB)

    Barbecot, F.; Gibert, E.; Amokrane, Y.; Massault, M.; Noret, A. [Centre National de la Recherche Scientifique Interaction et Dynamique des Environnements de Surface, Universite Paris (France); Ghaleb, B. [Geotop, Universite du Quebec a Montreal, Montreal (Canada)

    2013-07-15

    A 80 cm sequence has been cored from carbonated travertine in the limagne area (French Massif Central, France) in order to document recent environmental fluctuations (0-100 a) of gaseous springs, in relation to the environmental and geochemical parameters that control the isotopic signatures of modern carbonate deposits. The chronology of these finely laminated deposits that are ideal for reconstructing hydrological conditions at very narrow time steps is determined through AMS-{sup 14}C and {sup 210}Pb/{sup 226}Ra radiometric methods. Preliminary results highlight a high enrichment in stable isotopes (eg up to +8 per mille vs VPDB for {delta}{sup 13}C), likely linked to both recharge temperature and degassing processes. Moreover, two general trends are superimposed: the first one, cyclic, may be correlated to the hydrologic annual/biannual budget while the second one, linear, implies a long term environmental trend. (author)

  13. Central composite design approach towards optimization of flamboyant pods derived steam activated carbon for its use as heterogeneous catalyst in transesterification of Hevea brasiliensis oil

    International Nuclear Information System (INIS)

    Dhawane, Sumit H.; Kumar, Tarkeshwar; Halder, Gopinath

    2015-01-01

    Highlights: • Activated carbon was prepared from novel precursor flamboyant pods (Delonix regia). • Activation process was optimized using central composite design approach. • Prepared activated carbon at optimized condition was used as support for KOH. • Carbon based heterogeneous catalyst was used in transesterification of HBO. • Effect of catalyst loading and alcohol ratio on biodiesel yield was studied. - Abstract: The present investigation emphasises the preparation of carbon based KOH impregnated heterogeneous catalyst from flamboyant pods (Delonix regia) for the production of biodiesel from novel feedstock Hevea brasiliensis oil (HBO). Initially, carbonized char was physically activated by superheated steam and the process was optimized to study the effects of activation time and temperature by central composite design approach (CCD) using response surface methodology (RSM). Activated carbon was impregnated with KOH at four different ratios. Biodiesel production process was carried out at constant temperature 60 °C, reaction time 1 h, and 5 g of carbon based catalyst at varying quantities of catalyst loading (0.5, 2, 3.5, 5 wt%) and methanol to oil ratio (5:1–20:1). The influence of parameters on the biodiesel yield at varied condition was studied. Maximum yield of 89.3% was obtained at methanol to oil ratio 15:1 and catalyst loading 3.5 wt% and corresponding yield at same process parameters was observed to be 88.7% implying the significant activity of catalyst in reutilization. Produced biodiesel was characterized following ASTM standards. The experimental analysis confirmed that the carbonaceous catalyst developed from flamboyant pods under optimized condition is capable of transesterifying HBO into biodiesel

  14. Uric acid in metabolic syndrome: From an innocent bystander to a central player

    Science.gov (United States)

    Kanbay, Mehmet; Jensen, Thomas; Solak, Yalcin; Le, Myphuong; Roncal-Jimenez, Carlos; Rivard, Chris; Lanaspa, Miguel A.; Nakagawa, Takahiko; Johnson, Richard J.

    2016-01-01

    Uric acid, once viewed as an inert metabolic end-product of purine metabolism, has been recently incriminated in a number of chronic disease states, including hypertension, metabolic syndrome, diabetes, non-alcoholic fatty liver disease, and chronic kidney disease. Several experimental and clinical studies support a role for uric acid as a contributory causal factor in these conditions. Here we discuss some of the major mechanisms linking uric acid to metabolic and cardiovascular diseases. At this time the key to understanding the importance of uric acid in these diseases will be the conduct of large clinical trials in which the effect of lowering uric acid on hard clinical outcomes is assessed. Elevated uric acid may turn out to be one of the more important remediable risk factors for metabolic and cardiovascular diseases. PMID:26703429

  15. Feasible metabolisms in high pH springs of the Philippines.

    Science.gov (United States)

    Cardace, Dawn; Meyer-Dombard, D'Arcy R; Woycheese, Kristin M; Arcilla, Carlo A

    2015-01-01

    A field campaign targeting high pH, H2-, and CH4-emitting serpentinite-associated springs in the Zambales and Palawan Ophiolites of the Philippines was conducted in 2012-2013, and enabled description of several springs sourced in altered pillow basalts, gabbros, and peridotites. We combine field observations of pH, temperature, conductivity, dissolved oxygen, and oxidation-reduction potential with analyses of major ions, dissolved inorganic carbon, dissolved organic carbon, and dissolved gas phases in order to model the activities of selected phases important to microbial metabolism, and to rank feasible metabolic reactions based on energy yield. We document changing geochemical inventories in these springs between sampling years, and examine how the environment supports or prevents the function of certain microbial metabolisms. In all, this geochemistry-based assessment of feasible metabolisms indicates methane cycling, hydrogen oxidation, some iron and sulfur metabolisms, and ammonia oxidation are feasible reactions in this continental site of serpentinization.

  16. Aerial and underwater carbon metabolism of a

    NARCIS (Netherlands)

    Clavier, J.; Chauvaud, L.; Carlier, A.; Amice, E.; van der Geest, M.; Labrosse, P.; Diagne, A.; Hily, H.

    2011-01-01

    Community respiration and primary production were measured in a dense intertidal Zostera noltii bed on the Banc d’Arguin, Mauritania (West Africa) under aerial and submerged conditions. Metabolism was studied in situ in dark and transparent benthic chambers. CO2 fluxes in the air were measured over

  17. Metabolic Evidence of Diminished Lipid Oxidation in Women With Polycystic Ovary Syndrome

    OpenAIRE

    Whigham, Leah D.; Butz, Daniel E.; Dashti, Hesam; Tonelli, Marco; Johnson, LuAnn K.; Cook, Mark E.; Porter, Warren P.; Eghbalnia, Hamid R.; Markley, John L.; Lindheim, Steven R.; Schoeller, Dale A.; Abbott, David H.; Assadi-Porter, Fariba M.

    2014-01-01

    Polycystic ovary syndrome (PCOS), a common female endocrinopathy, is a complex metabolic syndrome of enhanced weight gain. The goal of this pilot study was to evaluate metabolic differences between normal (n=10) and PCOS (n=10) women via breath carbon isotope ratio, urinary nitrogen and nuclear magnetic resonance (NMR)-determined serum metabolites. Breath carbon stable isotopes measured by cavity ring down spectroscopy (CRDS) indicated diminished (p

  18. Proteomic analysis of carbon concentrating chemolithotrophic bacteria Serratia sp. for sequestration of carbon dioxide.

    Science.gov (United States)

    Bharti, Randhir K; Srivastava, Shaili; Thakur, Indu Shekhar

    2014-01-01

    A chemolithotrophic bacterium enriched in the chemostat in presence of sodium bicarbonate as sole carbon source was identified as Serratia sp. by 16S rRNA sequencing. Carbon dioxide sequestering capacity of bacterium was detected by carbonic anhydrase enzyme and ribulose-1, 5- bisphosphate carboxylase/oxygenase (RuBisCO). The purified carbonic anhydrase showed molecular weight of 29 kDa. Molecular weight of RuBisCO was 550 kDa as determined by fast protein liquid chromatography (FPLC), however, sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) showed presence of two subunits whose molecular weights were 56 and 14 kDa. The Western blot analysis of the crude protein and purified sample cross reacted with RuBisCO large-subunit polypeptides antibodies showed strong band pattern at molecular weight around 56 kDa regions. Whole cell soluble proteins of Serratia sp. grown under autotrophic and heterotrophic conditions were resolved by two-dimensional gel electrophoresis and MALDI-TOF/MS for differential expression of proteins. In proteomic analysis of 63 protein spots, 48 spots were significantly up-regulated in the autotrophically grown cells; seven enzymes showed its utilization in autotrophic carbon fixation pathways and other metabolic activities of bacterium including lipid metabolisms indicated sequestration potency of carbon dioxide and production of biomaterials.

  19. Proteomic analysis of carbon concentrating chemolithotrophic bacteria Serratia sp. for sequestration of carbon dioxide.

    Directory of Open Access Journals (Sweden)

    Randhir K Bharti

    Full Text Available A chemolithotrophic bacterium enriched in the chemostat in presence of sodium bicarbonate as sole carbon source was identified as Serratia sp. by 16S rRNA sequencing. Carbon dioxide sequestering capacity of bacterium was detected by carbonic anhydrase enzyme and ribulose-1, 5- bisphosphate carboxylase/oxygenase (RuBisCO. The purified carbonic anhydrase showed molecular weight of 29 kDa. Molecular weight of RuBisCO was 550 kDa as determined by fast protein liquid chromatography (FPLC, however, sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE showed presence of two subunits whose molecular weights were 56 and 14 kDa. The Western blot analysis of the crude protein and purified sample cross reacted with RuBisCO large-subunit polypeptides antibodies showed strong band pattern at molecular weight around 56 kDa regions. Whole cell soluble proteins of Serratia sp. grown under autotrophic and heterotrophic conditions were resolved by two-dimensional gel electrophoresis and MALDI-TOF/MS for differential expression of proteins. In proteomic analysis of 63 protein spots, 48 spots were significantly up-regulated in the autotrophically grown cells; seven enzymes showed its utilization in autotrophic carbon fixation pathways and other metabolic activities of bacterium including lipid metabolisms indicated sequestration potency of carbon dioxide and production of biomaterials.

  20. Effects of Graphene Oxide and Oxidized Carbon Nanotubes on the Cellular Division, Microstructure, Uptake, Oxidative Stress, and Metabolic Profiles.

    Science.gov (United States)

    Hu, Xiangang; Ouyang, Shaohu; Mu, Li; An, Jing; Zhou, Qixing

    2015-09-15

    Nanomaterial oxides are common formations of nanomaterials in the natural environment. Herein, the nanotoxicology of typical graphene oxide (GO) and carboxyl single-walled carbon nanotubes (C-SWCNT) was compared. The results showed that cell division of Chlorella vulgaris was promoted at 24 h and then inhibited at 96 h after nanomaterial exposure. At 96 h, GO and C-SWCNT inhibited the rates of cell division by 0.08-15% and 0.8-28.3%, respectively. Both GO and C-SWCNT covered the cell surface, but the uptake percentage of C-SWCNT was 2-fold higher than that of GO. C-SWCNT induced stronger plasmolysis and mitochondrial membrane potential loss and decreased the cell viability to a greater extent than GO. Moreover, C-SWCNT-exposed cells exhibited more starch grains and lysosome formation and higher reactive oxygen species (ROS) levels than GO-exposed cells. Metabolomics analysis revealed significant differences in the metabolic profiles among the control, C-SWCNT and GO groups. The metabolisms of alkanes, lysine, octadecadienoic acid and valine was associated with ROS and could be considered as new biomarkers of ROS. The nanotoxicological mechanisms involved the inhibition of fatty acid, amino acid and small molecule acid metabolisms. These findings provide new insights into the effects of GO and C-SWCNT on cellular responses.

  1. Carbonate compensation depth: relation to carbonate solubility in ocean waters.

    Science.gov (United States)

    Ben-Yaakov, S; Ruth, E; Kaplan, I R

    1974-05-31

    In situ calcium carbonate saturometry measurements suggest that the intermediate water masses of the central Pacific Ocean are close to saturation with resppect to both calcite and local carbonate sediment. The carbonate compensation depth, located at about 3700 meters in this area, appears to represent a depth above which waters are essentially saturated with respect to calcite and below which waters deviate toward undersaturation with respect to calcite.

  2. Metabolic disturbances connecting obesity and depression

    Directory of Open Access Journals (Sweden)

    Cecile eHryhorczuk

    2013-10-01

    Full Text Available Obesity markedly increases the odds of developing depression. Depressed mood not only impairs motivation, quality of life and overall functioning but also increases the risks of obesity complications. Abdominal obesity is a better predictor of depression and anxiety risk than overall adipose mass. A growing amount of research suggests that metabolic abnormalities stemming from central obesity that lead to metabolic disease may also responsible for the increased incidence of depression in obesity. As reviewed here, a higher mass of dysfunctional adipose tissue is associated with several metabolic disturbances that are either directly or indirectly implicated in the control of emotions and mood. To better comprehend the development of depression in obesity, this review pulls together select findings addressing the link between adiposity, diet and negative emotional states and discusses the evidence that alterations in glucocorticoids, adipose-derived hormones and inflammatory signalling that are characteristic of central obesity may be involved.

  3. Variation of Enzyme Activities and Metabolite Levels in 24 Arabidopsis Accessions Growing in Carbon-Limited Conditions1[W

    Science.gov (United States)

    Cross, Joanna M.; von Korff, Maria; Altmann, Thomas; Bartzetko, Linda; Sulpice, Ronan; Gibon, Yves; Palacios, Natalia; Stitt, Mark

    2006-01-01

    Our understanding of the interaction of carbon (C) metabolism with nitrogen (N) metabolism and growth is based mainly on studies of responses to environmental treatments, and studies of mutants and transformants. Here, we investigate which metabolic parameters vary and which parameters change in a coordinated manner in 24 genetically diverse Arabidopsis (Arabidopsis thaliana) accessions, grown in C-limited conditions. The accessions were grown in short days, moderate light, and high nitrate, and analyzed for rosette biomass, levels of structural components (protein, chlorophyll), total phenols and major metabolic intermediates (sugars, starch, nitrate, amino acids), and the activities of seven representative enzymes from central C and N metabolism. The largest variation was found for plant weight, reducing sugars, starch at the end of the night, and several enzyme activities. High levels of one sugar correlated with high levels of other sugars and starch, and a trend to increased amino acids, slightly lower nitrate, and higher protein. The activities of enzymes at the interface of C and N metabolism correlated with each other, but were unrelated to carbohydrates, amino acid levels, and total protein. Rosette weight was unrelated or showed a weak negative trend to sugar and amino acid contents at the end of the day in most of the accessions, and was negatively correlated with starch at the end of the night. Rosette weight was positively correlated with several enzyme activities. We propose that growth is not related to the absolute levels of starch, sugars, and amino acids; instead, it is related to flux, which is indicated by the enzymatic capacity to use these central resources. PMID:17085515

  4. Xenoliths in Eocene lavas from Central Tibet record carbonated metasomatism of the lithosphere

    Science.gov (United States)

    Goussin, Fanny; Cordier, Carole; Boulvais, Philippe; Guillot, Stéphane; Roperch, Pierrick; Replumaz, Anne

    2017-04-01

    Cenozoic post-collisional volcanism of the Tibetan Plateau, emplaced on an accreted continental margin under compression, could bring important information regarding the edification of the Plateau. In this study, we combined petrography, whole rock geochemistry, stable isotopes and in situ mineral analysis to decipher the genesis of Eocene-Oligocene magmatic rocks from the Nangqian basin (35-38 Ma, [Spurlin et al., 2005; Xu et al., 2016]), located at the hinge between Central Tibet and the Eastern Indo-Asia Collision Zone. Our dataset includes potassic trachyandesites; amphibole-bearing potassic trachytes; and rare ultrapotassic (K2O/Na2O ≥ 4) mafic syenites. All samples have high REE abundances (La = 100 - 500 x primitive mantle). Fractionation of heavy REE (Gd/YbN > 3) indicates melting in the garnet stability field, and relative depletion in high-field strength elements (Nb, Ta) indicates a selective enrichment of the source by metasomatic fluids. This metasomatism event is also evidenced by the occurrence of re-equilibrated mantle xenocrysts of phlogopite (Mg# = 88 - 90 and Cr2O3 content = 0.9 - 1.82 wt%) in mafic syenites. Potassic trachyandesites have specific composition, with negative Zr-Hf anomaly and low Hf/Sm (0.2 - 0.4). Indeed, they include xenocrystic aggregates, composed of magmatic clinopyroxene, apatite and subordinate biotite and feldspar, with interstitial calcite and dolomite. δ18OV -SMOW (9.2 - 11.0 ) and δ13CV -PDB (-6.1 - -4.0 ) of these rocks indicate the presence of primary, mantle-derived carbonates. In situ analysis of the major and trace element compositions of the carbonates, clinopyroxenes and apatites further suggest that these aggregates represent cumulates of a carbonate-bearing magma. These xenoliths thus show that the lithospheric mantle was also metasomatized by CO2-rich fluids. Cenozoic carbonatites in China have been identified in Maoniuping in Western Sichuan (31.7 Ma), Lixian in the Western Qinlin (22-23 Ma), and

  5. 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.

  6. Effect of U and 137Cs chronic contamination on dopamine and serotonin metabolism in the central nervous system of the rat

    International Nuclear Information System (INIS)

    Houpert, P.; Lestaevel, P.; Amourette, C.; Dhieux, B.; Bussy, C.; Paquet, F.

    2004-01-01

    Following the Chernobyl accident, the most significant problem for the population of the former Soviet Union for the next 50-70 years will be chronic internal contamination by radionuclides. One of the few experiments carried out in this field reported that neurotransmitter metabolism in the central nervous system of the rat was disturbed after feeding with oats contaminated by 137 Cs for 1 month. The present study assessed the effect of chronic contamination by depleted U or 137 Cs on the metabolism of two neurotransmitters in cerebral areas of rats. Dopamine and serotonin were chosen because their metabolism has been shown to be disturbed after external irradiation, even at moderate doses. Dopamine, serotonin, and some of their catabolites were measured by high-pressure liquid chromatography coupled with an electrochemical detector in five cerebral structures of rats contaminated over a 1-month period by drinking water (40 mg U·L -1 or 6500 Bq 137 Cs·L -1 ). In the striatum, hippocampus, cerebral cortex, thalamus, and cerebellum, the dopamine, serotonin, and catabolite levels were not significantly different between the control rats and rats contaminated by U or 137 Cs. These results are not in accordance with those previously described. (author)

  7. [1-14C]Glycolate metabolism and serine biosynthesis in soybean plants

    International Nuclear Information System (INIS)

    Calmes, J.; Viala, G.; Latche, J.C.; Cavalie, G.

    1977-01-01

    [1- 14 C]Glycolate metabolism was examined in leafy shoots of soybean plants (Glycine max (L.) Merr., var. Adepta). Only small amounts of 14 C were incorporated into evolved carbon dioxide and glucidic compounds. Free and protein glycine was labelled but higher levels of radioactivity were found in free serine. Changes in the distribution of 14 C with time showed that metabolic conversion glycollate → glycine → serine occurred very early and serine biosynthesis was more important in the shoot than in the leaves. Carbon dioxide labelling was always slight compared to serine labelling. These data suggest strong relations between glycollate and nitrogen metabolism

  8. Genome-Scale Reconstruction of the Human Astrocyte Metabolic Network

    OpenAIRE

    Mart?n-Jim?nez, Cynthia A.; Salazar-Barreto, Diego; Barreto, George E.; Gonz?lez, Janneth

    2017-01-01

    Astrocytes are the most abundant cells of the central nervous system; they have a predominant role in maintaining brain metabolism. In this sense, abnormal metabolic states have been found in different neuropathological diseases. Determination of metabolic states of astrocytes is difficult to model using current experimental approaches given the high number of reactions and metabolites present. Thus, genome-scale metabolic networks derived from transcriptomic data can be used as a framework t...

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

    Science.gov (United States)

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

    2016-05-01

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

  10. Shikimic acid production in Escherichia coli: From classical metabolic engineering strategies to omics applied to improve its production

    Directory of Open Access Journals (Sweden)

    Juan Andrés Martínez

    2015-09-01

    Full Text Available Shikimic acid (SA is an intermediate of the SA pathway that is present in bacteria and plants. SA has gained great interest because it is a precursor in the synthesis of the drug oseltamivir phosphate (OSF, an efficient inhibitor of the neuraminidase enzyme of diverse seasonal influenza viruses, the avian influenza virus H5N1, and the human influenza virus H1N1. For the purposes of OSF production, SA is extracted from the pods of Chinese star anise plants (Illicium spp., yielding up to 17% of SA (dry basis content. The high demand for OSF necessary to manage a major influenza outbreak is not adequately met by industrial production using SA from plants sources. As the SA pathway is present in the model bacteria Escherichia coli, several intuitive metabolically engineered strains have been applied for its successful overproduction by biotechnological processes, resulting in strains producing up to 71 g/L of SA, with high conversion yields of up to 0.42 (mol SA/mol Glc, in both batch and fed-batch cultures using complex fermentation broths, including glucose as a carbon source and yeast extract. Global transcriptomic analyses have been performed in SA producing strains, resulting in the identification of possible key target genes for the design of a rational strain improvement strategy. Because possible target genes are involved in the transport, catabolism and interconversion of different carbon sources and metabolic intermediates outside the central carbon metabolism and SA pathways, as genes involved in diverse cellular stress responses, the development of rational cellular strain improvement strategies based on omics data constitutes a challenging task to improve SA production in currently overproducing engineered strains. In this review, we discuss the main metabolic engineering strategies that have been applied for the development of efficient SA producing strains, as the perspective of omics analysis has focused on further strain improvement

  11. Microbial Development and Metabolic Engineering | Bioenergy | NREL

    Science.gov (United States)

    Diversity Our genetically engineered microbes utilize a variety of feedstock including cellulose, xylan , syngas, simple sugars, organic acids, and carbon dioxide (CO2). We have modified the metabolic pathways

  12. DRUM: a new framework for metabolic modeling under non-balanced growth. Application to the carbon metabolism of unicellular microalgae.

    Science.gov (United States)

    Baroukh, Caroline; Muñoz-Tamayo, Rafael; Steyer, Jean-Philippe; Bernard, Olivier

    2014-01-01

    Metabolic modeling is a powerful tool to understand, predict and optimize bioprocesses, particularly when they imply intracellular molecules of interest. Unfortunately, the use of metabolic models for time varying metabolic fluxes is hampered by the lack of experimental data required to define and calibrate the kinetic reaction rates of the metabolic pathways. For this reason, metabolic models are often used under the balanced growth hypothesis. However, for some processes such as the photoautotrophic metabolism of microalgae, the balanced-growth assumption appears to be unreasonable because of the synchronization of their circadian cycle on the daily light. Yet, understanding microalgae metabolism is necessary to optimize the production yield of bioprocesses based on this microorganism, as for example production of third-generation biofuels. In this paper, we propose DRUM, a new dynamic metabolic modeling framework that handles the non-balanced growth condition and hence accumulation of intracellular metabolites. The first stage of the approach consists in splitting the metabolic network into sub-networks describing reactions which are spatially close, and which are assumed to satisfy balanced growth condition. The left metabolites interconnecting the sub-networks behave dynamically. Then, thanks to Elementary Flux Mode analysis, each sub-network is reduced to macroscopic reactions, for which simple kinetics are assumed. Finally, an Ordinary Differential Equation system is obtained to describe substrate consumption, biomass production, products excretion and accumulation of some internal metabolites. DRUM was applied to the accumulation of lipids and carbohydrates of the microalgae Tisochrysis lutea under day/night cycles. The resulting model describes accurately experimental data obtained in day/night conditions. It efficiently predicts the accumulation and consumption of lipids and carbohydrates.

  13. DRUM: a new framework for metabolic modeling under non-balanced growth. Application to the carbon metabolism of unicellular microalgae.

    Directory of Open Access Journals (Sweden)

    Caroline Baroukh

    Full Text Available Metabolic modeling is a powerful tool to understand, predict and optimize bioprocesses, particularly when they imply intracellular molecules of interest. Unfortunately, the use of metabolic models for time varying metabolic fluxes is hampered by the lack of experimental data required to define and calibrate the kinetic reaction rates of the metabolic pathways. For this reason, metabolic models are often used under the balanced growth hypothesis. However, for some processes such as the photoautotrophic metabolism of microalgae, the balanced-growth assumption appears to be unreasonable because of the synchronization of their circadian cycle on the daily light. Yet, understanding microalgae metabolism is necessary to optimize the production yield of bioprocesses based on this microorganism, as for example production of third-generation biofuels. In this paper, we propose DRUM, a new dynamic metabolic modeling framework that handles the non-balanced growth condition and hence accumulation of intracellular metabolites. The first stage of the approach consists in splitting the metabolic network into sub-networks describing reactions which are spatially close, and which are assumed to satisfy balanced growth condition. The left metabolites interconnecting the sub-networks behave dynamically. Then, thanks to Elementary Flux Mode analysis, each sub-network is reduced to macroscopic reactions, for which simple kinetics are assumed. Finally, an Ordinary Differential Equation system is obtained to describe substrate consumption, biomass production, products excretion and accumulation of some internal metabolites. DRUM was applied to the accumulation of lipids and carbohydrates of the microalgae Tisochrysis lutea under day/night cycles. The resulting model describes accurately experimental data obtained in day/night conditions. It efficiently predicts the accumulation and consumption of lipids and carbohydrates.

  14. Citrate metabolism and its complications in non-massive blood transfusions: association with decompensated metabolic alkalosis+respiratory acidosis and serum electrolyte levels.

    Science.gov (United States)

    Bıçakçı, Zafer; Olcay, Lale

    2014-06-01

    Metabolic alkalosis, which is a non-massive blood transfusion complication, is not reported in the literature although metabolic alkalosis dependent on citrate metabolism is reported to be a massive blood transfusion complication. The aim of this study was to investigate the effect of elevated carbon dioxide production due to citrate metabolism and serum electrolyte imbalance in patients who received frequent non-massive blood transfusions. Fifteen inpatients who were diagnosed with different conditions and who received frequent blood transfusions (10-30 ml/kg/day) were prospectively evaluated. Patients who had initial metabolic alkalosis (bicarbonate>26 mmol/l), who needed at least one intensive blood transfusion in one-to-three days for a period of at least 15 days, and whose total transfusion amount did not fit the massive blood transfusion definition (alkalosis+respiratory acidosis developed as a result of citrate metabolism. There was a positive correlation between cumulative amount of citrate and the use of fresh frozen plasma, venous blood pH, ionized calcium, serum-blood gas sodium and mortality, whereas there was a negative correlation between cumulative amount of citrate and serum calcium levels, serum phosphorus levels and amount of urine chloride. In non-massive, but frequent blood transfusions, elevated carbon dioxide production due to citrate metabolism causes intracellular acidosis. As a result of intracellular acidosis compensation, decompensated metabolic alkalosis+respiratory acidosis and electrolyte imbalance may develop. This situation may contribute to the increase in mortality. In conclusion, it should be noted that non-massive, but frequent blood transfusions may result in certain complications. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Mitochondrial Dysfunction in Metabolic Syndrome and Asthma

    Science.gov (United States)

    Mabalirajan, Ulaganathan; Ghosh, Balaram

    2013-01-01

    Though severe or refractory asthma merely affects less than 10% of asthma population, it consumes significant health resources and contributes significant morbidity and mortality. Severe asthma does not fell in the routine definition of asthma and requires alternative treatment strategies. It has been observed that asthma severity increases with higher body mass index. The obese-asthmatics, in general, have the features of metabolic syndrome and are progressively causing a significant burden for both developed and developing countries thanks to the westernization of the world. As most of the features of metabolic syndrome seem to be originated from central obesity, the underlying mechanisms for metabolic syndrome could help us to understand the pathobiology of obese-asthma condition. While mitochondrial dysfunction is the common factor for most of the risk factors of metabolic syndrome, such as central obesity, dyslipidemia, hypertension, insulin resistance, and type 2 diabetes, the involvement of mitochondria in obese-asthma pathogenesis seems to be important as mitochondrial dysfunction has recently been shown to be involved in airway epithelial injury and asthma pathogenesis. This review discusses current understanding of the overlapping features between metabolic syndrome and asthma in relation to mitochondrial structural and functional alterations with an aim to uncover mechanisms for obese-asthma. PMID:23840225

  16. Food Insecurity and Its Association With Central Obesity and Other Markers of Metabolic Syndrome Among Persons Aged 12 to 18 Years in the United States.

    Science.gov (United States)

    Holben, David H; Taylor, Christopher A

    2015-09-01

    Food insecurity is a preventable health threat and may precipitate central obesity and metabolic syndrome in children and adolescents in the United States. To examine (1) health by household food security status; and (2) differences and prevalence of central obesity among persons aged 12 to 18 years in the United States. The National Health and Nutrition Examination Survey was administered to a cross-sectional sample of persons aged 12 to 18 years in 1999 to 2006. Controlling for age, race/ethnicity, and sex differences in mean obesity and chronic disease factors across levels of food insecurity (analysis of covariance [Bonferroni post hoc] and ORs [logistic regression analyses]) were examined, as were differences in the rates of risk factors (χ(2) statistics). A total of 7435 participants were analyzed. Those from marginally food secure (n=751) and low-food secure (n=1206) (population size estimate, 26,714,182) households were significantly more likely than their high-food secure counterparts (n=4831) to be overweight (P=.036) (OR, 1.44), and those from marginally food secure households were 1.3-times more likely to be obese (P=.036). Nearly 25% of respondents from marginally food secure, low-food secure, and very low-food secure (n=647) households reported central obesity (P=.002), which was 1.4 to 1.5 times more likely than those from high-food secure households. Participants from high-food secure households had significantly higher mean high-density lipoprotein values (P=.019). Risk factors indicative of metabolic syndrome were present in 3.1%. Household food insecurity was associated with an increased likelihood of being overweight and having central obesity. Limitations included the use of cross-sectional data and some self-reported data and the inability to control for all moderating variables in obesity and overall health status.

  17. Lisosan G, a powder of grain, does not interfere with the drug metabolizing enzymes and has a protective role on carbon tetrachloride-induced hepatotoxicity.

    Science.gov (United States)

    Longo, Vincenzo; Chirulli, Vera; Gervasi, Pier Giovanni; Nencioni, Simona; Pellegrini, Michela

    2007-08-01

    Lisosan G is a powder of grain registered as an alimentary integrator. The treatment of rats for 4 days with 0.5 g Lisosan G/kg had no effect on various drug metabolizing enzymes. Experiments in vitro showed that Lisosan G had radical scavenger activity. A confirmation of the antioxidative property of Lisosan G was also confirmed when it was administered in vivo to carbon tetrachloride (CCl(4))-intoxicated rats. The toxicity caused by CCl(4)-treatment of rats was restored to the control levels when the rats were given Lisosan G for 4 days before CCl(4). Lisosan G thus does not interfere with drug metabolizing system but has antioxidant properties and protects against CCl(4)-induced hepatotoxicity.

  18. Controls on reef development and the terrigenous-carbonate interface on a shallow shelf, Nicaragua (Central America)

    Science.gov (United States)

    Roberts, H. H.; Murray, S. P.

    1983-06-01

    Marine geology and physical oceanographic data collected during two field projects (˜4 months) on the Caribbean shelf of Nicaragua indicate a surprising dominance of carbonate deposition and reef growth on a shelf that is receiving an abnormally large volume of terrigenous sediments. High rainfall rates (˜400 500 cm/year), coupled with a warm tropical climate, encourage rapid denudation of the country's central volcanic highland and transport of large volumes of terrigenous sediment and fresh water to the coast. Estimates suggest that three times more fresh water and fifteen times more sediment are introduced per unit length of coastline than on the east coast of the United States. Distribution of the terrigenous facies, development of carbonate sediment suites, and the location and quality of viable reefs are strongly controlled by the dynamic interaction near the coasts of highly turbid fresh to brackish water effluents from thirteen rivers with clear marine waters of the shelf. Oceanic water from the central Caribbean drift current intersects the shelf and moves slowely in a dominant northwest direction toward the Yucatan Channel. A sluggish secondary gyre moves to the south toward Costa Rica. In contrast, the turbid coastal water is deflected to the south in response to density gradients, surface water slopes, and momentum supplied by the steady northeast trade winds. A distinct two-layered flow is commonly present in the sediment-rich coastal boundary zone, which is typically 10 20 km wide. The low-salinity upper layer is frictionally uncoupled from the ambient shelf water and therefore can expand out of the normally coherent coastal boundary zone during periods of abnormal flooding or times when instability is introduced into the northeast trades. Reef distribution, abruptness of the terrigenous-carbonate interface, and general shelf morphology reflect the long-term dynamic structure of the shelf waters. A smooth-bottomed ramp of siliciclastic sands to

  19. Essential role of UCP1 modulating the central effects of thyroid hormones on energy balance

    Science.gov (United States)

    Alvarez-Crespo, Mayte; Csikasz, Robert I.; Martínez-Sánchez, Noelia; Diéguez, Carlos; Cannon, Barbara; Nedergaard, Jan; López, Miguel

    2016-01-01

    Objective Classically, metabolic effects of thyroid hormones (THs) have been considered to be peripherally mediated, i.e. different tissues in the body respond directly to thyroid hormones with an increased metabolism. An alternative view is that the metabolic effects are centrally regulated. We have examined here the degree to which prolonged, centrally infused triiodothyronine (T3) could in itself induce total body metabolic effects and the degree to which brown adipose tissue (BAT) thermogenesis was essential for such effects, by examining uncoupling protein 1 (UCP1) KO mice. Methods Wildtype and UPC1 KO mice were centrally-treated with T3 by using minipumps. Metabolic measurements were analyzed by indirect calorimetry and expression analysis by RT-PCR or western blot. BAT morphology and histology were studied by immunohistochemistry. Results We found that central T3-treatment led to reduced levels of hypothalamic AMP-activated protein kinase (AMPK) and elevated body temperature (0.7 °C). UCP1 was essential for the T3-induced increased rate of energy expenditure, which was only observable at thermoneutrality and notably only during the active phase, for the increased body weight loss, for the increased hypothalamic levels of neuropeptide Y (NPY) and agouti-related peptide (AgRP) and for the increased food intake induced by central T3-treatment. Prolonged central T3-treatment also led to recruitment of BAT and britening/beiging (“browning”) of inguinal white adipose tissue (iWAT). Conclusions We conclude that UCP1 is essential for mediation of the central effects of thyroid hormones on energy balance, and we suggest that similar UCP1-dependent effects may underlie central energy balance effects of other agents. PMID:27069867

  20. A comparative economic assessment of hydrogen production from large central versus smaller distributed plant in a carbon constrained world

    International Nuclear Information System (INIS)

    Nguyen, Y.V.; Ngo, Y.A.; Tinkler, M.J.; Cowan, N.

    2003-01-01

    This paper compares the economics of producing hydrogen at large central plants versus smaller distributed plants at user sites. The economics of two types of central plant, each at 100 million standard cubic feet per day of hydrogen, based on electrolysis and natural gas steam reforming technologies, will be discussed. The additional cost of controlling CO 2 emissions from the natural gas steam reforming plant will be included in the analysis in order to satisfy the need to live in a future carbon constrained world. The cost of delivery of hydrogen from the large central plant to the user sites in a large metropolitan area will be highlighted, and the delivered cost will be compared to the cost from on-site distributed generation plants. Five types of distributed generation plants, based on proton exchange membrane, alkaline electrolysis and advanced steam reforming, will be analysed and discussed. Two criteria were used to rank various hydrogen production options, the cost of production and the price of hydrogen to achieve an acceptable return of investment. (author)

  1. Cycling of modern autochthonous organic matter dominates carbon flow in lakes of north central Alaska

    Science.gov (United States)

    Bogard, M.; Striegl, R. G.; Holtgrieve, G. W.; Kuhn, C.; Dornblaser, M.; Butman, D. E.

    2017-12-01

    Boreal and subarctic regions of the world are warming faster than anywhere else on earth, and undergoing rapid climatic and hydrologic changes. Much of this landscape is underlain by organic carbon (OC)-rich permafrost, and it is hypothesized that climate-induced environmental changes could positively reinforce climatic shifts via an increased delivery of terrestrial OC to aquatic networks. Increased OC terrestrial OC export could potentially result in greater aquatic OC mineralization and greenhouse gas production. Currently, a lack of ecosystem-level data precludes our understanding of aquatic OC processing for the vast majority of this remote northern area. To address this knowledge gap, we quantified whole-lake metabolism, limnological-, and hydrological characteristics across multiple seasons in a diverse set of lakes in the Yukon River Basin (YRB), Alaska. Intense gross primary production (GPP) and autotrophic net ecosystem production (NEP = GPP - respiration [R]) was common across lakes in spring, followed by a spatially synchronous shift toward heterotrophy (NEP origin, suggesting shifts in NEP were fueled by the recently fixed, lake OC. By scaling our metabolic estimates to the entire YRB, we found mineralization of terrestrial OC in lakes likely accounts for < 1% of terrestrial net primary production on an annual scale. We conclude that flows of autochthonous OC drive C cycling in most YRB lakes, that ancient permafrost-OC currently contributes little to heterotrophic processes in YRB lakes, and that the lakes play little role in remineralizing terrestrial organic material at the whole-catchment scale.

  2. Corynebacterium glutamicum for Sustainable Bioproduction: From Metabolic Physiology to Systems Metabolic Engineering.

    Science.gov (United States)

    Becker, Judith; Gießelmann, Gideon; Hoffmann, Sarah Lisa; Wittmann, Christoph

    Since its discovery 60 years ago, Corynebacterium glutamicum has evolved into a workhorse for industrial biotechnology. Traditionally well known for its remarkable capacity to produce amino acids, this Gram-positive soil bacterium, has become a flexible, efficient production platform for various bulk and fine chemicals, materials, and biofuels. The central turnstile of all these achievements is our excellent understanding of its metabolism and physiology. This knowledge base, together with innovative systems metabolic engineering concepts, which integrate systems and synthetic biology into strain engineering, has upgraded C. glutamicum into one of the most successful industrial microorganisms in the world.

  3. 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.

    2006-01-01

    It has been proposed that during growth under anaerobic or oxygen-limited conditions Shewanella oneidensis MR-1 uses the serine-isocitrate lyase pathway common to many methylotrophic anaerobes, in which formaldehyde produced from pyruvate is condensed with glycine to form serine. The serine is then transformed through hydroxypyruvate and glycerate to enter central metabolism at phosphoglycerate. To examine its use of the serine-isocitrate lyase pathway under anaerobic conditions, we grew S. oneidensis MR-1 on [1-13C] lactate as the sole carbon source with either trimethylamine N-oxide (TMAO) or fumarate as an electron acceptor. Analysis of cellular metabolites indicates that a large percentage (>75 percent) of lactate was partially oxidized to either acetate or pyruvate. The 13C isotope distributions in amino acids and other key metabolites indicate that, under anaerobic conditions, a complete serine pathway is not present, and lactate is oxidized via a highly reversible serine degradation pathway. The labeling data also suggest significant activity in the anaplerotic (malic enzyme and phosphoenolpyruvatecarboxylase) and glyoxylate shunt (isocitrate lyase and malate synthase) reactions. Although the tricarboxylic acid (TCA) cycle is often observed to be incomplete in many other anaerobes (absence of 2-oxoglutaratede hydrogenase activity), isotopic labeling supports the existence of a complete TCA cycle in S. oneidensis MR-1 under TMAO reduction condition

  4. Understanding Regulation of Metabolism through Feasibility Analysis

    Science.gov (United States)

    Nikerel, Emrah; Berkhout, Jan; Hu, Fengyuan; Teusink, Bas; Reinders, Marcel J. T.; de Ridder, Dick

    2012-01-01

    Understanding cellular regulation of metabolism is a major challenge in systems biology. Thus far, the main assumption was that enzyme levels are key regulators in metabolic networks. However, regulation analysis recently showed that metabolism is rarely controlled via enzyme levels only, but through non-obvious combinations of hierarchical (gene and enzyme levels) and metabolic regulation (mass action and allosteric interaction). Quantitative analyses relating changes in metabolic fluxes to changes in transcript or protein levels have revealed a remarkable lack of understanding of the regulation of these networks. We study metabolic regulation via feasibility analysis (FA). Inspired by the constraint-based approach of Flux Balance Analysis, FA incorporates a model describing kinetic interactions between molecules. We enlarge the portfolio of objectives for the cell by defining three main physiologically relevant objectives for the cell: function, robustness and temporal responsiveness. We postulate that the cell assumes one or a combination of these objectives and search for enzyme levels necessary to achieve this. We call the subspace of feasible enzyme levels the feasible enzyme space. Once this space is constructed, we can study how different objectives may (if possible) be combined, or evaluate the conditions at which the cells are faced with a trade-off among those. We apply FA to the experimental scenario of long-term carbon limited chemostat cultivation of yeast cells, studying how metabolism evolves optimally. Cells employ a mixed strategy composed of increasing enzyme levels for glucose uptake and hexokinase and decreasing levels of the remaining enzymes. This trade-off renders the cells specialized in this low-carbon flux state to compete for the available glucose and get rid of over-overcapacity. Overall, we show that FA is a powerful tool for systems biologists to study regulation of metabolism, interpret experimental data and evaluate hypotheses. PMID

  5. Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions1

    Science.gov (United States)

    Zuñiga, Cristal; Li, Chien-Ting; Zielinski, Daniel C.; Guarnieri, Michael T.; Antoniewicz, Maciek R.; Zengler, Karsten

    2016-01-01

    The green microalga Chlorella vulgaris has been widely recognized as a promising candidate for biofuel production due to its ability to store high lipid content and its natural metabolic versatility. Compartmentalized genome-scale metabolic models constructed from genome sequences enable quantitative insight into the transport and metabolism of compounds within a target organism. These metabolic models have long been utilized to generate optimized design strategies for an improved production process. Here, we describe the reconstruction, validation, and application of a genome-scale metabolic model for C. vulgaris UTEX 395, iCZ843. The reconstruction represents the most comprehensive model for any eukaryotic photosynthetic organism to date, based on the genome size and number of genes in the reconstruction. The highly curated model accurately predicts phenotypes under photoautotrophic, heterotrophic, and mixotrophic conditions. The model was validated against experimental data and lays the foundation for model-driven strain design and medium alteration to improve yield. Calculated flux distributions under different trophic conditions show that a number of key pathways are affected by nitrogen starvation conditions, including central carbon metabolism and amino acid, nucleotide, and pigment biosynthetic pathways. Furthermore, model prediction of growth rates under various medium compositions and subsequent experimental validation showed an increased growth rate with the addition of tryptophan and methionine. PMID:27372244

  6. Redesign of the Human Metabolic Simulator

    Science.gov (United States)

    Duffield, Bruce; Jeng, Frank; Lange, Kevin

    2004-01-01

    The National Aeronautics and Space Administration (NASA) is currently building a Human Metabolic Simulator (HMS) at the Johnson Space Center as part of the Advanced Life Support Air Revitalization Technology Evaluation Facility (ARTEF). The purpose of ARTEF is to evaluate Environmental Control and Life Support System Technologies for Advanced Missions. The HMS is needed to reproduce the primary metabolic effects of human respiration on an enclosed atmosphere when humans cannot be present and the impact of human presence on the system is required. A HMS was designed, built and successfully operated in 2000 but larger crew size requirements and the expense of upgrade of the current system necessitate redesign. This paper addresses the redesign. Several concepts were considered, ranging from chemical oxidation of a hydrocarbon like ethanol or ethyl acetate to carbon dioxide and water, oxidation of an iron-containing compound, or by using a fuel cell. For reasons of cost, simplicity, safety and other factors, the concept chosen includes: a molecular sieve packaged as an industrial oxygen concentrator to remove oxygen from the atmosphere, with direct carbon dioxide, water and heat injection. The water injection is done via heating water to steam with a heat exchanger and thermal effects are handled by directly adding heat to the air stream with a second heat exchanger. Both heat exchangers are supplied by a hot oil loop. The amount of oxygen removal, carbon dioxide addition, water addition and heat addition were calculated using metabolic profiles for respiration and heat, calculated using a series of empirical equations developed for International Space Station (ISS). Sketches of the Human Metabolic Simulator and the hot oil bath loop used to supply heat to the heat exchangers are included

  7. Sedimentary Record of the Back-Arc Basins of South-Central Mexico: an Evolution from Extensional Basin to Carbonate Platform.

    Science.gov (United States)

    Sierra-Rojas, M. I.; Molina-Garza, R. S.; Lawton, T. F.

    2015-12-01

    The Lower Cretaceous depositional systems of southwestern Oaxaquia, in south-central Mexico, were controlled by tectonic processes related to the instauration of a continental arc and the accretion of the Guerrero arc to mainland Mexico. The Atzompa Formation refers to a succession of conglomerate, sandstone, siltstone, and limestone that crop out in southwestern Mexico with Early Cretaceous fauna and detrital zircon maximum depositional ages. The sedimentary record shows a transition from early fluvial/alluvial to shallow marine depositional environments. The first stage corresponds to juvenile fluvial/alluvial setting followed by a deep lacustrine depositional environment, suggesting the early stages of an extensional basin. The second stage is characterized by anabranched deposits of axial fluvial systems flowing to the NE-SE, showing deposition during a period of rapid subsidence. The third and final stage is made of tidal deposits followed, in turn, by abrupt marine flooding of the basin and development of a Barremian-Aptian carbonate ramp. We interpret the Tentzo basin as a response to crustal extension in a back-arc setting, with high rates of sedimentation in the early stages of the basin (3-4 mm/m.y), slower rates during the development of starved fluvial to tidal systems and carbonate ramps, and at the top of the Atzompa Formation an abrupt deepening of the basin due to flexural subsidence related to terrane docking and attendant thrusting to the west. These events were recorded in the back-arc region of a continental convergent margin (Zicapa arc) where syn-sedimentary magmatism is indicated by Early Cretaceous detrital and volcanic clasts from alluvial fan facies west of the basin. Finally, and as a response to the accretion of the Guerrero superterrane to Oaxaquia during the Aptian, a carbonate platform facing toward the Gulf of Mexico was established in central to eastern Oaxaquia.

  8. Folic acid, one-carbon metabolism & childhood cancer

    Directory of Open Access Journals (Sweden)

    Nirmalya Roy Moulik

    2017-01-01

    Full Text Available Folate has been studied in relation to many diseases, especially cancer. Although it has been postulated to exert a dual effect on development of cancer, its role remains to be clearly defined. Its effect on cancer is the result of gene-nutrient interaction between the genes in folate metabolic pathway and dietary folate availability; mutations in genes of folate metabolism have been shown to alter individual susceptibility to certain childhood cancers as well as response to cancer chemotherapy. Although mandatory fortification of food items with folate has been initiated in some countries, many countries are yet to adopt this due to concerns about undesired adverse effects of high folate levels on health, especially cancer. However, initial reports suggest that folate fortification has led to reduction in incidence of certain childhood cancers such as neuroblastoma, wilms tumour and leukaemias. Despite studies showing folate depletion during antifolate chemotherapy and higher toxicity of chemotherapy in folate-depleted individuals, folate supplementation during cancer chemotherapy is not routinely recommended. Studies investigating the precise effect of folate supplementation during chemotherapy on both short- and long-term outcomes of cancer are needed to arrive at a consensus guideline.

  9. Regulation of dual glycolytic pathways for fructose metabolism in heterofermentative Lactobacillus panis PM1.

    Science.gov (United States)

    Kang, Tae Sun; Korber, Darren R; Tanaka, Takuji

    2013-12-01

    Lactobacillus panis PM1 belongs to the group III heterofermentative lactobacilli that use the 6-phosphogluconate/phosphoketolase (6-PG/PK) pathway as their central metabolic pathway and are reportedly unable to grow on fructose as a sole carbon source. We isolated a variant PM1 strain capable of sporadic growth on fructose medium and observed its distinctive characteristics of fructose metabolism. The end product pattern was different from what is expected in typical group III lactobacilli using the 6-PG/PK pathway (i.e., more lactate, less acetate, and no mannitol). In addition, in silico analysis revealed the presence of genes encoding most of critical enzymes in the Embden-Meyerhof (EM) pathway. These observations indicated that fructose was metabolized via two pathways. Fructose metabolism in the PM1 strain was influenced by the activities of two enzymes, triosephosphate isomerase (TPI) and glucose 6-phosphate isomerase (PGI). A lack of TPI resulted in the intracellular accumulation of dihydroxyacetone phosphate (DHAP) in PM1, the toxicity of which caused early growth cessation during fructose fermentation. The activity of PGI was enhanced by the presence of glyceraldehyde 3-phosphate (GAP), which allowed additional fructose to enter into the 6-PG/PK pathway to avoid toxicity by DHAP. Exogenous TPI gene expression shifted fructose metabolism from heterolactic to homolactic fermentation, indicating that TPI enabled the PM1 strain to mainly use the EM pathway for fructose fermentation. These findings clearly demonstrate that the balance in the accumulation of GAP and DHAP determines the fate of fructose metabolism and the activity of TPI plays a critical role during fructose fermentation via the EM pathway in L. panis PM1.

  10. Organic Acids: The Pools of Fixed Carbon Involved in Redox Regulation and Energy Balance in Higher Plants

    Directory of Open Access Journals (Sweden)

    Abir U Igamberdiev

    2016-07-01

    Full Text Available Organic acids are synthesized in plants as a result of the incomplete oxidation of photosynthetic products and represent the stored pools of fixed carbon accumulated due to different transient times of conversion of carbon compounds in metabolic pathways. When redox level in the cell increases, e.g., in conditions of active photosynthesis, the tricarboxylic acid (TCA cycle in mitochondria is transformed to a partial cycle supplying citrate for the synthesis of 2-oxoglutarate and glutamate (citrate valve, while malate is accumulated and participates in the redox balance in different cell compartments (via malate valve. This results in malate and citrate frequently being the most accumulated acids in plants. However, the intensity of reactions linked to the conversion of these compounds can cause preferential accumulation of other organic acids, e.g., fumarate or isocitrate, in higher concentrations than malate and citrate. The secondary reactions, associated with the central metabolic pathways, in particularly with the TCA cycle, result in accumulation of other organic acids that are derived from the intermediates of the cycle. They form the additional pools of fixed carbon and stabilize the TCA cycle. Trans-aconitate is formed from citrate or cis-aconitate, accumulation of hydroxycitrate can be linked to metabolism of 2-oxoglutarate, while 4-hydroxy-2-oxoglutarate can be formed from pyruvate and glyoxylate. Glyoxylate, a product of either glycolate oxidase or isocitrate lyase, can be converted to oxalate. Malonate is accumulated at high concentrations in legume plants. Organic acids play a role in plants in providing redox equilibrium, supporting ionic gradients on membranes, and acidification of the extracellular medium.

  11. Sequential metabolic phases as a means to optimize cellular output in a constant environment.

    Science.gov (United States)

    Palinkas, Aljoscha; Bulik, Sascha; Bockmayr, Alexander; Holzhütter, Hermann-Georg

    2015-01-01

    Temporal changes of gene expression are a well-known regulatory feature of all cells, which is commonly perceived as a strategy to adapt the proteome to varying external conditions. However, temporal (rhythmic and non-rhythmic) changes of gene expression are also observed under virtually constant external conditions. Here we hypothesize that such changes are a means to render the synthesis of the metabolic output more efficient than under conditions of constant gene activities. In order to substantiate this hypothesis, we used a flux-balance model of the cellular metabolism. The total time span spent on the production of a given set of target metabolites was split into a series of shorter time intervals (metabolic phases) during which only selected groups of metabolic genes are active. The related flux distributions were calculated under the constraint that genes can be either active or inactive whereby the amount of protein related to an active gene is only controlled by the number of active genes: the lower the number of active genes the more protein can be allocated to the enzymes carrying non-zero fluxes. This concept of a predominantly protein-limited efficiency of gene expression clearly differs from other concepts resting on the assumption of an optimal gene regulation capable of allocating to all enzymes and transporters just that fraction of protein necessary to prevent rate limitation. Applying this concept to a simplified metabolic network of the central carbon metabolism with glucose or lactate as alternative substrates, we demonstrate that switching between optimally chosen stationary flux modes comprising different sets of active genes allows producing a demanded amount of target metabolites in a significantly shorter time than by a single optimal flux mode at fixed gene activities. Our model-based findings suggest that temporal expression of metabolic genes can be advantageous even under conditions of constant external substrate supply.

  12. Neuron-glia metabolic coupling and plasticity.

    Science.gov (United States)

    Magistretti, Pierre J

    2006-06-01

    The coupling between synaptic activity and glucose utilization (neurometabolic coupling) is a central physiological principle of brain function that has provided the basis for 2-deoxyglucose-based functional imaging with positron emission tomography (PET). Astrocytes play a central role in neurometabolic coupling, and the basic mechanism involves glutamate-stimulated aerobic glycolysis; the sodium-coupled reuptake of glutamate by astrocytes and the ensuing activation of the Na-K-ATPase triggers glucose uptake and processing via glycolysis, resulting in the release of lactate from astrocytes. Lactate can then contribute to the activity-dependent fuelling of the neuronal energy demands associated with synaptic transmission. An operational model, the 'astrocyte-neuron lactate shuttle', is supported experimentally by a large body of evidence, which provides a molecular and cellular basis for interpreting data obtained from functional brain imaging studies. In addition, this neuron-glia metabolic coupling undergoes plastic adaptations in parallel with adaptive mechanisms that characterize synaptic plasticity. Thus, distinct subregions of the hippocampus are metabolically active at different time points during spatial learning tasks, suggesting that a type of metabolic plasticity, involving by definition neuron-glia coupling, occurs during learning. In addition, marked variations in the expression of genes involved in glial glycogen metabolism are observed during the sleep-wake cycle, with in particular a marked induction of expression of the gene encoding for protein targeting to glycogen (PTG) following sleep deprivation. These data suggest that glial metabolic plasticity is likely to be concomitant with synaptic plasticity.

  13. Upstream-Downstream Joint Carbon Reduction Strategies Based on Low-Carbon Promotion

    Directory of Open Access Journals (Sweden)

    Xiqiang Xia

    2018-06-01

    Full Text Available A differential game model is established to analyze the impact of emissions reduction efforts and low-carbon product promotion on the reduction strategies of low-carbon product manufacturers (subsequently referred to as manufacturers and the retailers of such products in a dynamic environment. Based on this model, changes in emissions reduction efforts and promotional efforts are comparatively analyzed under three scenarios (retailers bearing the promotional cost, manufacturers bearing the promotional cost, and centralized decision-making. The results are as follows: (1 the trajectory of carbon emissions reduction per product unit is the highest when the supply chain is under centralized decision-making, followed by when manufacturers bear the promotional cost, and lastly when retailers bear the cost; (2 when manufacturers bear the promotional cost, the market demand, emissions reduction effort, and promotional effort are higher, although the unit retail price is higher than when retailers bear the promotional cost; and (3 under centralized decision-making, the unit retail price is the lowest; however, sales volume, the emissions reduction effort, and the promotional effort are all higher than those in the other scenarios.

  14. Homocysteine metabolism and risk of schizophrenia

    NARCIS (Netherlands)

    Muntjewerff, J.W.

    2006-01-01

    The one-carbon cycle hypothesis initiated research of schizophrenia risk in relation to sensitive markers of aberrant homocysteine metabolism, such as B-vitamin concentrations, plasma total homocysteine (tHcy) concentrations, and genetic determinants. We observed decreased plasma and elevated RBC

  15. Convergent Metabolic Specialization through Distinct Evolutionary Paths in Pseudomonas aeruginosa.

    Science.gov (United States)

    La Rosa, Ruggero; Johansen, Helle Krogh; Molin, Søren

    2018-04-10

    Evolution by natural selection under complex and dynamic environmental conditions occurs through intricate and often counterintuitive trajectories affecting many genes and metabolic solutions. To study short- and long-term evolution of bacteria in vivo , we used the natural model system of cystic fibrosis (CF) infection. In this work, we investigated how and through which trajectories evolution of Pseudomonas aeruginosa occurs when migrating from the environment to the airways of CF patients, and specifically, we determined reduction of growth rate and metabolic specialization as signatures of adaptive evolution. We show that central metabolic pathways of three distinct Pseudomonas aeruginosa lineages coevolving within the same environment become restructured at the cost of versatility during long-term colonization. Cell physiology changes from naive to adapted phenotypes resulted in (i) alteration of growth potential that particularly converged to a slow-growth phenotype, (ii) alteration of nutritional requirements due to auxotrophy, (iii) tailored preference for carbon source assimilation from CF sputum, (iv) reduced arginine and pyruvate fermentation processes, and (v) increased oxygen requirements. Interestingly, although convergence was evidenced at the phenotypic level of metabolic specialization, comparative genomics disclosed diverse mutational patterns underlying the different evolutionary trajectories. Therefore, distinct combinations of genetic and regulatory changes converge to common metabolic adaptive trajectories leading to within-host metabolic specialization. This study gives new insight into bacterial metabolic evolution during long-term colonization of a new environmental niche. IMPORTANCE Only a few examples of real-time evolutionary investigations in environments outside the laboratory are described in the scientific literature. Remembering that biological evolution, as it has progressed in nature, has not taken place in test tubes, it is not

  16. Central chemoreceptors and neural mechanisms of cardiorespiratory control

    Directory of Open Access Journals (Sweden)

    T.S. Moreira

    2011-09-01

    Full Text Available The arterial partial pressure (P CO2 of carbon dioxide is virtually constant because of the close match between the metabolic production of this gas and its excretion via breathing. Blood gas homeostasis does not rely solely on changes in lung ventilation, but also to a considerable extent on circulatory adjustments that regulate the transport of CO2 from its sites of production to the lungs. The neural mechanisms that coordinate circulatory and ventilatory changes to achieve blood gas homeostasis are the subject of this review. Emphasis will be placed on the control of sympathetic outflow by central chemoreceptors. High levels of CO2 exert an excitatory effect on sympathetic outflow that is mediated by specialized chemoreceptors such as the neurons located in the retrotrapezoid region. In addition, high CO2 causes an aversive awareness in conscious animals, activating wake-promoting pathways such as the noradrenergic neurons. These neuronal groups, which may also be directly activated by brain acidification, have projections that contribute to the CO2-induced rise in breathing and sympathetic outflow. However, since the level of activity of the retrotrapezoid nucleus is regulated by converging inputs from wake-promoting systems, behavior-specific inputs from higher centers and by chemical drive, the main focus of the present manuscript is to review the contribution of central chemoreceptors to the control of autonomic and respiratory mechanisms.

  17. Relationship Between Organophosphate Toxicity and Choline Metabolism

    Science.gov (United States)

    1986-06-06

    Results from studies on the actions of the organophosphates on the central nervus system have suggested that these compounds, through an action on...Grganophosphates alter the disposition and metabolism of choline and choline-containing compounds in the nervous system , the relationshi ý of these changes to...mechanisms regulating the metabolism of choline, as well as the specific interactions of the organophospha:es with biochemical systems , may differ

  18. Essential role of UCP1 modulating the central effects of thyroid hormones on energy balance

    Directory of Open Access Journals (Sweden)

    Mayte Alvarez-Crespo

    2016-04-01

    Full Text Available Objective: Classically, metabolic effects of thyroid hormones (THs have been considered to be peripherally mediated, i.e. different tissues in the body respond directly to thyroid hormones with an increased metabolism. An alternative view is that the metabolic effects are centrally regulated. We have examined here the degree to which prolonged, centrally infused triiodothyronine (T3 could in itself induce total body metabolic effects and the degree to which brown adipose tissue (BAT thermogenesis was essential for such effects, by examining uncoupling protein 1 (UCP1 KO mice. Methods: Wildtype and UPC1 KO mice were centrally-treated with T3 by using minipumps. Metabolic measurements were analyzed by indirect calorimetry and expression analysis by RT-PCR or western blot. BAT morphology and histology were studied by immunohistochemistry. Results: We found that central T3-treatment led to reduced levels of hypothalamic AMP-activated protein kinase (AMPK and elevated body temperature (0.7 °C. UCP1 was essential for the T3-induced increased rate of energy expenditure, which was only observable at thermoneutrality and notably only during the active phase, for the increased body weight loss, for the increased hypothalamic levels of neuropeptide Y (NPY and agouti-related peptide (AgRP and for the increased food intake induced by central T3-treatment. Prolonged central T3-treatment also led to recruitment of BAT and britening/beiging (“browning” of inguinal white adipose tissue (iWAT. Conclusions: We conclude that UCP1 is essential for mediation of the central effects of thyroid hormones on energy balance, and we suggest that similar UCP1-dependent effects may underlie central energy balance effects of other agents. Keywords: AMPK, Brown adipose tissue, Hypothalamus, Thyroid hormones, UCP1

  19. Adipose tissue remodeling: its role in energy metabolism and metabolic disorders

    Directory of Open Access Journals (Sweden)

    Sung Sik eChoe

    2016-04-01

    Full Text Available The adipose tissue is a central metabolic organ in the regulation of whole-body energy homeostasis. The white adipose tissue (WAT functions as a key energy reservoir for other organs, whereas the brown adipose tissue (BAT accumulates lipids for cold-induced adaptive thermogenesis. Adipose tissues secret various hormones, cytokines, and metabolites (termed as adipokines that control systemic energy balance by regulating appetitive signals from the central nerve system as well as metabolic activity in peripheral tissues. In response to changes in the nutritional status, the adipose tissue undergoes dynamic remodeling, including quantitative and qualitative alterations in adipose tissue resident cells. A growing body of evidence indicates that adipose tissue remodeling in obesity is closely associated with adipose tissue function. Changes in the number and size of the adipocytes affect the microenvironment of expanded fat tissues, accompanied by alterations in adipokine secretion, adipocyte death, local hypoxia, and fatty acid fluxes. Concurrently, stromal vascular cells in the adipose tissue, including immune cells, are involved in numerous adaptive processes, such as dead adipocyte clearance, adipogenesis, and angiogenesis, all of which are dysregulated in obese adipose tissue remodeling. Chronic over-nutrition triggers uncontrolled inflammatory responses, leading to systemic low-grade inflammation and metabolic disorders, such as insulin resistance. This review will discuss current mechanistic understandings of adipose tissue remodeling processes in adaptive energy homeostasis and pathological remodeling of adipose tissue in connection with immune response.

  20. Carbonate aquifers

    Science.gov (United States)

    Cunningham, Kevin J.; Sukop, Michael; Curran, H. Allen

    2012-01-01

    Only limited hydrogeological research has been conducted using ichnology in carbonate aquifer characterization. Regardless, important applications of ichnology to carbonate aquifer characterization include its use to distinguish and delineate depositional cycles, correlate mappable biogenically altered surfaces, identify zones of preferential groundwater flow and paleogroundwater flow, and better understand the origin of ichnofabric-related karst features. Three case studies, which include Pleistocene carbonate rocks of the Biscayne aquifer in southern Florida and Cretaceous carbonate strata of the Edwards–Trinity aquifer system in central Texas, demonstrate that (1) there can be a strong relation between ichnofabrics and groundwater flow in carbonate aquifers and (2) ichnology can offer a useful methodology for carbonate aquifer characterization. In these examples, zones of extremely permeable, ichnofabric-related macroporosity are mappable stratiform geobodies and as such can be represented in groundwater flow and transport simulations.

  1. Impact of folic acid intake during pregnancy on genomic imprinting of IGF2/H19 and 1-carbon metabolism.

    Science.gov (United States)

    Tserga, Aggeliki; Binder, Alexandra M; Michels, Karin B

    2017-12-01

    Folic acid is an essential component of 1-carbon metabolism, which generates methyl groups for DNA methylation. Disruption of genomic imprinting leads to biallelic expression which may affect disease susceptibility possibly reflected in high levels of S -adenosyl-homocysteine (SAH) and low levels of S -adenosyl-methionine (SAM). We investigated the association between folic acid supplementation during pregnancy and loss of imprinting (LOI) of IGF2 and H19 genes in placentas and cord blood of 90 mother-child dyads in association with the methylenetetrahydrofolate reductase ( MTHFR ) genotype. Pyrosequencing was used to evaluate deviation from monoallelic expression among 47 placentas heterozygous for H19 and 37 placentas and cord blood tissues heterozygous for IGF2 and H19 methylation levels of 48 placentas. We detected relaxation of imprinting (ROI) and LOI of H19 in placentas not associated with differences in methylation levels of the H19ICR. Placentas retained monoallelic allele-specific gene expression of IGF2 , but 32.4% of cord blood samples displayed LOI of IGF2 and 10.8% showed ROI. High SAH levels were significantly associated with low H19 methylation. An interesting positive association between SAM/SAH ratio and high H19 methylation levels was detected among infants with low B 12 levels. Our data suggest profound differences in regulation of imprinting in placenta and cord blood; a lack of correlation of the methylome, transcriptome, and proteome; and a complex regulatory feedback network between free methyl groups and genomic imprinting at birth.-Tserga, A., Binder, A. M., Michels, K. B. Impact of folic acid intake during pregnancy on genomic imprinting of IGF2/H19 and 1-carbon metabolism. © FASEB.

  2. Breaking Carbon Lock-in

    DEFF Research Database (Denmark)

    Driscoll, Patrick Arthur

    2014-01-01

    This central focus of this paper is to highlight the ways in which path dependencies and increasing returns (network effects) serve to reinforce carbon lock-in in large-scale road transportation infrastructure projects. Breaking carbon lock-in requires drastic changes in the way we plan future...

  3. The metabolic consequences of thyroxine replacement in adult hypopituitary patients

    DEFF Research Database (Denmark)

    Filipsson Nyström, Helena; Feldt-Rasmussen, Ulla; Kourides, Ione

    2012-01-01

    The metabolic consequences of thyroxine replacement in patients with central hypothyroidism (CH) need to be evaluated. The aim was to examine the outcome of thyroxine replacement in CH. Adult hypopituitary patients (n = 1595) with and without CH from KIMS (Pfizer International Metabolic Database...

  4. Choline and methionine differentially alter methyl carbon metabolism in bovine neonatal hepatocytes.

    Science.gov (United States)

    Chandler, Tawny L; White, Heather M

    2017-01-01

    Intersections in hepatic methyl group metabolism pathways highlights potential competition or compensation of methyl donors. The objective of this experiment was to examine the expression of genes related to methyl group transfer and lipid metabolism in response to increasing concentrations of choline chloride (CC) and DL-methionine (DLM) in primary neonatal hepatocytes that were or were not exposed to fatty acids (FA). Primary hepatocytes isolated from 4 neonatal Holstein calves were maintained as monolayer cultures for 24 h before treatment with CC (61, 128, 2028, and 4528 μmol/L) and DLM (16, 30, 100, 300 μmol/L), with or without a 1 mmol/L FA cocktail in a factorial arrangement. After 24 h of treatment, media was collected for quantification of reactive oxygen species (ROS) and very low-density lipoprotein (VLDL), and cell lysates were collected for quantification of gene expression. No interactions were detected between CC, DLM, or FA. Both CC and DLM decreased the expression of methionine adenosyltransferase 1A (MAT1A). Increasing CC did not alter betaine-homocysteine S-methyltranferase (BHMT) but did increase 5-methyltetrahydrofolate-homocysteine methyltransferase (MTR) and methylenetetrahydrofolate reductase (MTHFR) expression. Increasing DLM decreased expression of BHMT and MTR, but did not affect MTHFR. Expression of both phosphatidylethanolamine N-methyltransferase (PEMT) and microsomal triglyceride transfer protein (MTTP) were decreased by increasing CC and DLM, while carnitine palmitoyltransferase 1A (CPT1A) was unaffected by either. Treatment with FA decreased the expression of MAT1A, MTR, MTHFR and tended to decrease PEMT but did not affect BHMT and MTTP. Treatment with FA increased CPT1A expression. Increasing CC increased secretion of VLDL and decreased the accumulation of ROS in media. Within neonatal bovine hepatocytes, choline and methionine differentially regulate methyl carbon pathways and suggest that choline may play a critical role in

  5. Nitrogen Addition Exacerbates the Negative Effects of Low Temperature Stress on Carbon and Nitrogen Metabolism in Moss

    Directory of Open Access Journals (Sweden)

    Bin-Yang Liu

    2017-08-01

    Full Text Available Global environmental changes are leading to an increase in localized abnormally low temperatures and increasing nitrogen (N deposition is a phenomenon recognized worldwide. Both low temperature stress (LTS and excess N induce oxidative stress in plants, and excess N also reduces their resistance to LTS. Mosses are primitive plants that are generally more sensitive to alterations in environmental factors than vascular species. To study the combined effects of N deposition and LTS on carbon (C and N metabolism in moss, two moss species, Pogonatum cirratum subsp. fuscatum, and Hypnum plumaeforme, exposed to various concentrations of nitrate (KNO3 or ammonium (NH4Cl, were treated with or without LTS. C/N metabolism indices were then monitored, both immediately after the stress and after a short recovery period (10 days. LTS decreased the photosystem II (PSII performance index and inhibited non-cyclic photophosphorylation, ribulose-1,5-bisphosphate carboxylase, and glutamine synthetase activities, indicating damage to PSII and reductions in C/N assimilation in these mosses. LTS did not affect cyclic photophosphorylation, sucrose synthase, sucrose-phosphate synthase, and NADP-isocitrate dehydrogenase activities, suggesting a certain level of energy and C skeleton generation were maintained in the mosses to combat LTS; however, LTS inhibited the activity of glycolate oxidase. As predicted, N supply increased the sensitivity of the mosses to LTS, resulting in greater damage to PSII and a sharper decrease in C/N assimilation. After the recovery period, the performance of PSII and C/N metabolism, which were inhibited by LTS increased significantly, and were generally higher than those of control samples not exposed to LTS, suggesting overcompensation effects; however, N application reduced the extent of compensation effects. Both C and N metabolism exhibited stronger compensation effects in H. plumaeforme than in P. cirratum subsp. fuscatum. The

  6. NRG1-Fc improves metabolic health via dual hepatic and central action.

    Science.gov (United States)

    Zhang, Peng; Kuang, Henry; He, Yanlin; Idiga, Sharon O; Li, Siming; Chen, Zhimin; Yang, Zhao; Cai, Xing; Zhang, Kezhong; Potthoff, Matthew J; Xu, Yong; Lin, Jiandie D

    2018-03-08

    Neuregulins (NRGs) are emerging as an important family of signaling ligands that regulate glucose and lipid homeostasis. NRG1 lowers blood glucose levels in obese mice, whereas the brown fat-enriched secreted factor NRG4 protects mice from high-fat diet-induced insulin resistance and hepatic steatosis. However, the therapeutic potential of NRGs remains elusive, given the poor plasma half-life of the native ligands. Here, we engineered a fusion protein using human NRG1 and the Fc domain of human IgG1 (NRG1-Fc) that exhibited extended half-life in circulation and improved potency in receptor signaling. We evaluated its efficacy in improving metabolic parameters and dissected the mechanisms of action. NRG1-Fc treatment triggered potent AKT activation in the liver, lowered blood glucose, improved insulin sensitivity, and suppressed food intake in obese mice. NRG1-Fc acted as a potent secretagogue for the metabolic hormone FGF21; however, the latter was largely dispensable for its metabolic effects. NRG1-Fc directly targeted the hypothalamic POMC neurons to promote membrane depolarization and increase firing rate. Together, NRG1-Fc exhibits improved pharmacokinetic properties and exerts metabolic benefits through dual inhibition of hepatic gluconeogenesis and caloric intake.

  7. Comprehensive Mapping of Pluripotent Stem Cell Metabolism Using Dynamic Genome-Scale Network Modeling

    Directory of Open Access Journals (Sweden)

    Sriram Chandrasekaran

    2017-12-01

    Full Text Available Summary: Metabolism is an emerging stem cell hallmark tied to cell fate, pluripotency, and self-renewal, yet systems-level understanding of stem cell metabolism has been limited by the lack of genome-scale network models. Here, we develop a systems approach to integrate time-course metabolomics data with a computational model of metabolism to analyze the metabolic state of naive and primed murine pluripotent stem cells. Using this approach, we find that one-carbon metabolism involving phosphoglycerate dehydrogenase, folate synthesis, and nucleotide synthesis is a key pathway that differs between the two states, resulting in differential sensitivity to anti-folates. The model also predicts that the pluripotency factor Lin28 regulates this one-carbon metabolic pathway, which we validate using metabolomics data from Lin28-deficient cells. Moreover, we identify and validate metabolic reactions related to S-adenosyl-methionine production that can differentially impact histone methylation in naive and primed cells. Our network-based approach provides a framework for characterizing metabolic changes influencing pluripotency and cell fate. : Chandrasekaran et al. use computational modeling, metabolomics, and metabolic inhibitors to discover metabolic differences between various pluripotent stem cell states and infer their impact on stem cell fate decisions. Keywords: systems biology, stem cell biology, metabolism, genome-scale modeling, pluripotency, histone methylation, naive (ground state, primed state, cell fate, metabolic network

  8. Metabolism of chlorofluorocarbons and polybrominated compounds by Pseudomonas putida G786(pHG-2) via an engineered metabolic pathway.

    OpenAIRE

    Hur, H G; Sadowsky, M J; Wackett, L P

    1994-01-01

    The recombinant bacterium Pseudomonas putida G786(pHG-2) metabolizes pentachloroethane to glyoxylate and carbon dioxide, using cytochrome P-450CAM and toluene dioxygenase to catalyze consecutive reductive and oxidative dehalogenation reactions (L.P. Wackett, M.J. Sadowsky, L.N. Newman, H.-G. Hur, and S. Li, Nature [London] 368:627-629, 1994). The present study investigated metabolism of brominated and chlorofluorocarbon compounds by the recombinant strain. Under anaerobic conditions, P. putid...

  9. Energetic and metabolic transient response of Saccharomyces cerevisiae to benzoic acid.

    Science.gov (United States)

    Kresnowati, M T A P; van Winden, W A; van Gulik, W M; Heijnen, J J

    2008-11-01

    Saccharomyces cerevisiae is known to be able to adapt to the presence of the commonly used food preservative benzoic acid with a large energy expenditure. Some mechanisms for the adaptation process have been suggested, but its quantitative energetic and metabolic aspects have rarely been discussed. This study discusses use of the stimulus response approach to quantitatively study the energetic and metabolic aspects of the transient adaptation of S. cerevisiae to a shift in benzoic acid concentration, from 0 to 0.8 mM. The information obtained also serves as the basis for further utilization of benzoic acid as a tool for targeted perturbation of the energy system, which is important in studying the kinetics and regulation of central carbon metabolism in S. cerevisiae. Using this experimental set-up, we found significant fast-transient (< 3000 s) increases in O(2) consumption and CO(2) production rates, of approximately 50%, which reflect a high energy requirement for the adaptation process. We also found that with a longer exposure time to benzoic acid, S. cerevisiae decreases the cell membrane permeability for this weak acid by a factor of 10 and decreases the cell size to approximately 80% of the initial value. The intracellular metabolite profile in the new steady-state indicates increases in the glycolytic and tricarboxylic acid cycle fluxes, which are in agreement with the observed increases in specific glucose and O(2) uptake rates.

  10. Global changes in transcription orchestrate metabolic differentiation during symbiotic nitrogen fixation in Lotus japonicus

    DEFF Research Database (Denmark)

    Colebatch, Gillian; Desbrosses, Guilhem; Ott, Thomas

    2004-01-01

    Research on legume nodule metabolism has contributed greatly to our knowledge of primary carbon and nitrogen metabolism in plants in general, and in symbiotic nitrogen fixation in particular. However, most previous studies focused on one or a few genes/enzymes involved in selected metabolic...

  11. Global metabolic rewiring for improved CO2 fixation and chemical production in cyanobacteria

    Science.gov (United States)

    Kanno, Masahiro; Carroll, Austin L.; Atsumi, Shota

    2017-03-01

    Cyanobacteria have attracted much attention as hosts to recycle CO2 into valuable chemicals. Although cyanobacteria have been engineered to produce various compounds, production efficiencies are too low for commercialization. Here we engineer the carbon metabolism of Synechococcus elongatus PCC 7942 to improve glucose utilization, enhance CO2 fixation and increase chemical production. We introduce modifications in glycolytic pathways and the Calvin Benson cycle to increase carbon flux and redirect it towards carbon fixation. The engineered strain efficiently uses both CO2 and glucose, and produces 12.6 g l-1 of 2,3-butanediol with a rate of 1.1 g l-1 d-1 under continuous light conditions. Removal of native regulation enables carbon fixation and 2,3-butanediol production in the absence of light. This represents a significant step towards industrial viability and an excellent example of carbon metabolism plasticity.

  12. Feasible Metabolic Schema Associated with High pH Springs in the Philippines

    Directory of Open Access Journals (Sweden)

    DAWN eCARDACE

    2015-02-01

    Full Text Available A field campaign targeting high pH springs in the Zambales and Palawan Ophiolites of the Philippines was conducted in 2012-2013, and enabled description of several springs sourced in altered pillow basalts, gabbros, and peridotites. We combine field observations of pH, temperature, conductivity, dissolved oxygen, and oxidation-reduction potential with analyses of major ions, dissolved inorganic carbon, dissolved organic carbon, and dissolved gas phases in order to model the activities of selected phases important to microbial metabolism, and to evaluate feasible metabolic reactions based on energy yield. We document changing geochemical inventories in these springs, and examine how the environment supports or prevents the function of certain microbial metabolisms.

  13. Risk of Visual Impairment and Intracranial Hypertension After Space Flight: Evaluation of the Role of Polymorphism of Enzymes Involved in One-Carbon Metabolism

    Science.gov (United States)

    Smith, S. M.; Gregory, J. F.; Zeisel, G. H.; Gibson, C. R.; Mader, T. H.; Kinchen, J.; Ueland, P.; Ploutz-Snyder, R.; Heer, M.; Zwart, S. R.

    2016-01-01

    Data from the Nutritional Status Assessment protocol provided biochemical evidence that the one-carbon metabolic pathway may be altered in individuals experiencing vision-related issues during and after space flight (1, 2). Briefly, serum concentrations of homocysteine, cystathionine, 2-methylcitric acid, and methylmalonic acid were significantly (P<0.001) higher (25-45%) in astronauts with ophthalmic changes than in those without such changes (1). These differences existed before, during, and after flight. Serum folate was lower (P<0.01) during flight in individuals with ophthalmic changes. Preflight serum concentrations of cystathionine and 2-methylcitric acid, and mean in-flight serum folate, were significantly (P<0.05) correlated with postflight changes in refraction (1). A follow-up study was conducted to evaluate a small number of known polymorphisms of enzymes in the one-carbon pathway, and to evaluate how these relate to vision and other medical aspects of the eye. Specifically, we investigated 5 polymorphisms in MTRR, MTHFR, SHMT, and CBS genes and their association with ophthalmic changes after flight in 49 astronauts. The number of G alleles of MTRR 66 and C alleles of SHMT1 1420 both contributed to the odds of visual disturbances (3). Block regression showed that B-vitamin status at landing and genetics were significant predictors for many of the ophthalmic outcomes studied (3). In conclusion, we document an association between MTRR 66 and SHMT1 1420 polymorphisms and space flightinduced vision changes. These data document that individuals with an altered 1-carbon metabolic pathway may be predisposed to anatomic and/or physiologic changes that render them susceptible to ophthalmic damage during space flight.

  14. The NQO1 bioactivatable drug, β-lapachone, alters the redox state of NQO1+ pancreatic cancer cells, causing perturbation in central carbon metabolism.

    Science.gov (United States)

    Silvers, Molly A; Deja, Stanislaw; Singh, Naveen; Egnatchik, Robert A; Sudderth, Jessica; Luo, Xiuquan; Beg, Muhammad S; Burgess, Shawn C; DeBerardinis, Ralph J; Boothman, David A; Merritt, Matthew E

    2017-11-03

    Many cancer treatments, such as those for managing recalcitrant tumors like pancreatic ductal adenocarcinoma, cause off-target toxicities in normal, healthy tissue, highlighting the need for more tumor-selective chemotherapies. β-Lapachone is bioactivated by NAD(P)H:quinone oxidoreductase 1 (NQO1). This enzyme exhibits elevated expression in most solid cancers and therefore is a potential cancer-specific target. β-Lapachone's therapeutic efficacy partially stems from the drug's induction of a futile NQO1-mediated redox cycle that causes high levels of superoxide and then peroxide formation, which damages DNA and causes hyperactivation of poly(ADP-ribose) polymerase, resulting in extensive NAD + /ATP depletion. However, the effects of this drug on energy metabolism due to NAD + depletion were never described. The futile redox cycle rapidly consumes O 2 , rendering standard assays of Krebs cycle turnover unusable. In this study, a multimodal analysis, including metabolic imaging using hyperpolarized pyruvate, points to reduced oxidative flux due to NAD + depletion after β-lapachone treatment of NQO1+ human pancreatic cancer cells. NAD + -sensitive pathways, such as glycolysis, flux through lactate dehydrogenase, and the citric acid cycle (as inferred by flux through pyruvate dehydrogenase), were down-regulated by β-lapachone treatment. Changes in flux through these pathways should generate biomarkers useful for in vivo dose responses of β-lapachone treatment in humans, avoiding toxic side effects. Targeting the enzymes in these pathways for therapeutic treatment may have the potential to synergize with β-lapachone treatment, creating unique NQO1-selective combinatorial therapies for specific cancers. These findings warrant future studies of intermediary metabolism in patients treated with β-lapachone. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  15. Helicobacter pylori seropositivity's association with markers of iron, 1-carbon metabolism, and antioxidant status among US adults: a structural equations modeling approach.

    Directory of Open Access Journals (Sweden)

    May A Beydoun

    Full Text Available We tested a model in which Helicobacter pylori seropositivity (Hps predicted iron status, which in turn acted as a predictor for markers of 1-C metabolism that were then allowed to predict antioxidant status.National Health and Nutrition Examination Surveys (NHANES 1999-2000 cross-sectional data among adults aged 20-85 y were analyzed (n = 3,055. Markers of Hps, iron status (serum ferritin and transferrin saturation (TS; 1-C metabolism (serum folate (FOLserum, B-12, total homocysteine (tHcy, methylmalonic acid (MMA and antioxidant status (vitamins A and E were entered into a structural equations model (SEM.Predictors of Hps included older age, lower education and income, racial/ethnic groups (lowest among Non-Hispanic Whites, and lifetime cigarette smoking. SEM modeling indicated that Hps had a direct inverse relationship with iron status (combining serum ferritin and TS which in turn was positively related to 1-C metabolites (higher serum folate, B-12 or lower tHcy/MMA that were positively associated with antioxidant status (combining serum vitamins A and E. Another pathway that was found bypassed 1-C metabolites (Hps → Iron_st → Antiox. The sum of all indirect effects from Hps combining both pathways and the other indirect pathways in the model (Hps → Iron_st → OneCarbon; Hps →OneCarbon →Antiox was estimated at β = -0.006±0.003, p<0.05.In sum, of the total effect of H. pylori seropositivity on antioxidant status, two significant indirect pathways through Iron status and 1-Carbon metabolites were found. Randomized controlled trials should be conducted to uncover the concomitant causal effect of H. pylori eradication on improving iron status, folate, B-12 and antioxidant status among H. pylori seropositive individuals.

  16. Promotion of renewable energy to mitigate impact of heavy use of carbon energy on society and climate change in Central Sub-Saharan Africa remote areas.

    Science.gov (United States)

    Kenfack, Joseph; Bignom, Blaise

    2015-04-01

    Sub-Saharan Africa owns important renewable energy potential and is still heavily using carbon energy. This is having a negative impact on the climate and on the environment. Given the local cost of carbon energy, the purchase power of people, the availability and the reserve of carbon energy in the area, this resource is being heavily used. This practice is harmful to the climate and is also resulting on poor effort to promote renewable energy in remote areas. The important renewable energy potential is still suffering from poor development. The purpose of this paper is among other things aiming at showing the rate of carbon energy use and its potential impact on climate and environment. We will also ensure that the renewable energy resources of Central Sub-Saharan Africa are known and are subject to be used optimally to help mitigate climate change. After showing some negative impacts of carbon energy used in the area, the work also suggests actions to promote and sustain the development of renewable energy. Based on the knowledge of the Central African energy sector, this paper will identify actions for reduce access to carbon energy and improved access to sustainable, friendly, affordable energy services to users as well as a significant improvement of energy infrastructure and the promotion of energy efficiency. We will show all type of carbon energy used, the potential for solar, biomass and hydro while showing where available the level of development. After a swot analysis of the situation, identified obstacles for the promotion of clean energy will be targeted. Finally, suggestions will be made to help the region develop a vision aiming at developing good clean energy policy to increase the status of renewable energy and better contribute to fight against climate change. Cameroon case study will be examined as illustration. Analysis will be made from data collected in the field. |End Text|

  17. Volatile profiling reveals intracellular metabolic changes in Aspergillus parasiticus: veA regulates branched chain amino acid and ethanol metabolism

    Directory of Open Access Journals (Sweden)

    Roze Ludmila V

    2010-08-01

    Full Text Available Abstract Background Filamentous fungi in the genus Aspergillus produce a variety of natural products, including aflatoxin, the most potent naturally occurring carcinogen known. Aflatoxin biosynthesis, one of the most highly characterized secondary metabolic pathways, offers a model system to study secondary metabolism in eukaryotes. To control or customize biosynthesis of natural products we must understand how secondary metabolism integrates into the overall cellular metabolic network. By applying a metabolomics approach we analyzed volatile compounds synthesized by Aspergillus parasiticus in an attempt to define the association of secondary metabolism with other metabolic and cellular processes. Results Volatile compounds were examined using solid phase microextraction - gas chromatography/mass spectrometry. In the wild type strain Aspergillus parasiticus SU-1, the largest group of volatiles included compounds derived from catabolism of branched chain amino acids (leucine, isoleucine, and valine; we also identified alcohols, esters, aldehydes, and lipid-derived volatiles. The number and quantity of the volatiles produced depended on media composition, time of incubation, and light-dark status. A block in aflatoxin biosynthesis or disruption of the global regulator veA affected the volatile profile. In addition to its multiple functions in secondary metabolism and development, VeA negatively regulated catabolism of branched chain amino acids and synthesis of ethanol at the transcriptional level thus playing a role in controlling carbon flow within the cell. Finally, we demonstrated that volatiles generated by a veA disruption mutant are part of the complex regulatory machinery that mediates the effects of VeA on asexual conidiation and sclerotia formation. Conclusions 1 Volatile profiling provides a rapid, effective, and powerful approach to identify changes in intracellular metabolic networks in filamentous fungi. 2 VeA coordinates the

  18. Linking metabolomics data to underlying metabolic regulation

    Directory of Open Access Journals (Sweden)

    Thomas eNägele

    2014-11-01

    Full Text Available The comprehensive experimental analysis of a metabolic constitution plays a central role in approaches of organismal systems biology.Quantifying the impact of a changing environment on the homeostasis of cellular metabolism has been the focus of numerous studies applying various metabolomics techniques. It has been proven that approaches which integrate different analytical techniques, e.g. LC-MS, GC-MS, CE-MS and H-NMR, can provide a comprehensive picture of a certain metabolic homeostasis. Identification of metabolic compounds and quantification of metabolite levels represent the groundwork for the analysis of regulatory strategies in cellular metabolism. This significantly promotes our current understanding of the molecular organization and regulation of cells, tissues and whole organisms.Nevertheless, it is demanding to elicit the pertinent information which is contained in metabolomics data sets.Based on the central dogma of molecular biology, metabolite levels and their fluctuations are the result of a directed flux of information from gene activation over transcription to translation and posttranslational modification.Hence, metabolomics data represent the summed output of a metabolic system comprising various levels of molecular organization.As a consequence, the inverse assignment of metabolomics data to underlying regulatory processes should yield information which-if deciphered correctly-provides comprehensive insight into a metabolic system.Yet, the deduction of regulatory principles is complex not only due to the high number of metabolic compounds, but also because of a high level of cellular compartmentalization and differentiation.Motivated by the question how metabolomics approaches can provide a representative view on regulatory biochemical processes, this article intends to present and discuss current metabolomics applications, strategies of data analysis and their limitations with respect to the interpretability in context of

  19. Clumped Isotope Thermometry Reveals Variations in Soil Carbonate Seasonal Biases Over >4 km of Relief in the Semi-Arid Andes of Central Chile

    Science.gov (United States)

    Burgener, L. K.; Huntington, K. W.; Hoke, G. D.; Schauer, A. J.; Ringham, M. C.; Latorre Hidalgo, C.; Díaz, F.

    2015-12-01

    The application of carbonate clumped isotope thermometry to soil carbonates has the potential to shed new light on questions regarding terrestrial paleoclimate. In order to better utilize this paleoclimate tool, outstanding questions regarding seasonal biases in soil carbonate formation and the relationship between soil carbonate formation temperatures (T(Δ47)) and surface temperatures must be resolved. We address these questions by comparing C, O, and clumped isotope data from Holocene/modern soil carbonates to modern meteorological data. The data were collected along a 170 km transect with >4 km of relief in central Chile (~30°S). Previous studies have suggested that soil carbonates should record a warm season bias and form in isotopic equilibrium with soil water and soil CO2. We identify two discrete climate zones separated by the local winter snow line (~3200 m). Below this boundary, precipitation falls as rain and soil carbonate T(Δ47) values at depths >40 cm resemble summer soil temperatures; at higher elevations, precipitation falls as snow and T(Δ47) values resemble mean annual soil temperatures. Soil carbonates from the highest sample site (4700 m), which is devoid of vegetation and located near perennial snow fields, yield anomalous δ18O, δ13C, and T(Δ47) values, indicative of kinetic isotope effects that we attribute to cryogenic carbonate formation. Our results suggest that soil carbonates from depths temperature and precipitation, and should not be used as paleotemperature proxies. These findings (1) highlight the role of soil moisture in modulating soil carbonate formation and the resulting T(Δ47) values, (2) underscore the importance of understanding past soil moisture conditions when attempting to reconstruct paleotemperatures using carbonate clumped isotope thermometry, and (3) suggest that soil carbonates from high elevation or high latitude sites may form under non-equilibrium conditions.

  20. 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)

    Azizan, Kamalrul Azlan; Ressom, Habtom W; Mendoza, Eduardo R; Baharum, Syarul Nataqain

    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, 13 C 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

  1. 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

  2. 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

  3. Prevalence of metabolic syndrome and its association with depression in patients with schizophrenia

    Directory of Open Access Journals (Sweden)

    Suttajit S

    2013-07-01

    Full Text Available Sirijit Suttajit, Sutrak PilakantaDepartment of Psychiatry, Faculty of Medicine, Chiang Mai University, Chiang Mai, ThailandPurpose: To identify the point prevalence of metabolic syndrome in patients with schizophrenia and to evaluate the association between depressive symptoms and metabolic syndrome in patients with schizophrenia.Patients and methods: Metabolic syndrome was assessed based on an updated definition derived from the modified National Cholesterol Education Program Adult Treatment Panel III (NCEP-ATP III and the International Diabetes Federation criteria. The 17-item Hamilton Depression Rating Scale (HDRS-17 was used to measure depressive symptoms in 80 patients with schizophrenia. Odds ratios and 95% confidence intervals were calculated using logistic regression for the association between each depressive symptom and metabolic syndrome.Results: The point prevalence rates of metabolic syndrome according to the modified NCEP-ATP III and International Diabetes Federation criteria were 37% and 35%, respectively. The risk of having metabolic syndrome significantly increased in those who were widowed or separated, or had longer duration of illness. Central obesity was the metabolic feature with the highest odds ratios for metabolic syndrome at 19.3. Three out of 17 items of HDRS subscales were found to be significantly associated with metabolic syndrome, including depressed mood, middle insomnia, and retardation with the odds ratios of 3.0, 3.4, and 3.6, respectively.Conclusion: This study showed that the prevalence of metabolic syndrome in patients with schizophrenia was higher than the overall rate but was slightly lower than in the general population in the USA. Central obesity, measured by waist circumference, was found to be highly correlated with metabolic syndrome. Depressed mood, middle insomnia, and retardation were significantly associated with metabolic syndrome in patients with schizophrenia. Waist circumference and screening

  4. Metabolic engineering tools in model cyanobacteria.

    Science.gov (United States)

    Carroll, Austin L; Case, Anna E; Zhang, Angela; Atsumi, Shota

    2018-03-26

    Developing sustainable routes for producing chemicals and fuels is one of the most important challenges in metabolic engineering. Photoautotrophic hosts are particularly attractive because of their potential to utilize light as an energy source and CO 2 as a carbon substrate through photosynthesis. Cyanobacteria are unicellular organisms capable of photosynthesis and CO 2 fixation. While engineering in heterotrophs, such as Escherichia coli, has result in a plethora of tools for strain development and hosts capable of producing valuable chemicals efficiently, these techniques are not always directly transferable to cyanobacteria. However, recent efforts have led to an increase in the scope and scale of chemicals that cyanobacteria can produce. Adaptations of important metabolic engineering tools have also been optimized to function in photoautotrophic hosts, which include Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9, 13 C Metabolic Flux Analysis (MFA), and Genome-Scale Modeling (GSM). This review explores innovations in cyanobacterial metabolic engineering, and highlights how photoautotrophic metabolism has shaped their development. Copyright © 2018 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  5. Metabolism in anoxic permeable sediments is dominated by eukaryotic dark fermentation

    DEFF Research Database (Denmark)

    Bourke, Michael F.; Marriott, Philip J.; Glud, Ronnie N.

    2017-01-01

    Permeable sediments are common across continental shelves and are critical contributors to marine biogeochemical cycling. Organic matter in permeable sediments is dominated by microalgae, which as eukaryotes have different anaerobic metabolic pathways to prokaryotes such as bacteria and archaea....... Here we present analyses of flow-through reactor experiments showing that dissolved inorganic carbon is produced predominantly as a result of anaerobic eukaryotic metabolic activity. In our experiments, anaerobic production of dissolved inorganic carbon was consistently accompanied by large dissolved H....../hydrogenase pathway of fermentative eukaryotic H2 production, suggesting that pathway as the source of H2 and dissolved inorganic carbon production. Metabolomic analysis showed large increases in lipid production at the onset of anoxia, consistent with documented pathways of anoxic dark fermentation in microalgae...

  6. Carbonate microfacies of the San Juan Formation (Ordovician: Oepikodus evae and Oepikodus intermedius conodont zones), Niquivil, Central Precordillera, Province of San Juan (Argentina); Microfacies carbonáticas de la Formación San Juan (Ordovícico: zonas de conodontos Oepikodus evae y Oepikodus intermedius), Niquivil, Precordillera Central, Provincia de San Juan (Argentina)

    Energy Technology Data Exchange (ETDEWEB)

    Soria, T.; Beresi, M.; Mestre, A.; Heredia, S.; Rodríguez, M.C.

    2017-09-01

    This contribution presents the description and interpretation of carbonate microfacies of the San Juan Formation (Ordovician) at the Niquivil section, considering the stratigraphical interval between the Oepikodus evae and Oepikodus intermedius conodont zones. The distribution of the microfacies and the conodonts assemblages allow us to identify different sub-environments within the late Floian carbonate ramp of the Central Precordillera. Five microfacies were recognized from the base to the top: M1 Bioclastic mudstone-wackestone; M2 Bioclastic-peloidal wackestone; M3 Intra-bioclastic wackestone; M4 Intra-bioclastic packstone; M5 Peloidal grainstone. The vertical distribution of these microfacies indicates a shallowing trend of the carbonate ramp in the Niquivil section for this temporal interval, which suggests a middle ramp environment with low energy, without wave action, and that evolved towards the middle-inner ramp environment with more energy by wave action and development of tempestites. [Spanish] En la presente contribución se realiza la descripción e interpretación de las microfacies carbonáticas de la Formación San Juan (Ordovícico) en la sección de Niquivil, considerando el intervalo estratigráfico comprendido entre las zonas de conodontos Oepikodus evae y Oepikodus intermedius. El análisis de las microfacies y los conodontos asociados permiten el reconocimiento de diferentes subambientes carbonáticos dentro de la rampa carbonática desarrollada durante el Floiense tardío de la Precordillera Central. Se reconocieron cinco microfacies que, de base a techo, son: M1 Mudstone-Wackestone bioclástico; M2 Wackestone bioclástico-peloidal; M3 Wackestone intra-bioclástico; M4 Packstone intra-bioclástico; M5 Grainstone peloidal. La interpretación vertical de estas microfacies indica una tendencia hacia la somerización de la rampa carbonática en la sección de Niquivil para el lapso temporal estudiado. El que se correspondería con un ambiente de

  7. Adaptive remodeling of skeletal muscle energy metabolism in high-altitude hypoxia: Lessons from AltitudeOmics.

    Science.gov (United States)

    Chicco, Adam J; Le, Catherine H; Gnaiger, Erich; Dreyer, Hans C; Muyskens, Jonathan B; D'Alessandro, Angelo; Nemkov, Travis; Hocker, Austin D; Prenni, Jessica E; Wolfe, Lisa M; Sindt, Nathan M; Lovering, Andrew T; Subudhi, Andrew W; Roach, Robert C

    2018-05-04

    Metabolic responses to hypoxia play important roles in cell survival strategies and disease pathogenesis in humans. However, the homeostatic adjustments that balance changes in energy supply and demand to maintain organismal function under chronic low oxygen conditions remain incompletely understood, making it difficult to distinguish adaptive from maladaptive responses in hypoxia-related pathologies. We integrated metabolomic and proteomic profiling with mitochondrial respirometry and blood gas analyses to comprehensively define the physiological responses of skeletal muscle energy metabolism to 16 days of high-altitude hypoxia (5260 m) in healthy volunteers from the AltitudeOmics project. In contrast to the view that hypoxia down-regulates aerobic metabolism, results show that mitochondria play a central role in muscle hypoxia adaptation by supporting higher resting phosphorylation potential and enhancing the efficiency of long-chain acylcarnitine oxidation. This directs increases in muscle glucose toward pentose phosphate and one-carbon metabolism pathways that support cytosolic redox balance and help mitigate the effects of increased protein and purine nucleotide catabolism in hypoxia. Muscle accumulation of free amino acids favor these adjustments by coordinating cytosolic and mitochondrial pathways to rid the cell of excess nitrogen, but might ultimately limit muscle oxidative capacity in vivo Collectively, these studies illustrate how an integration of aerobic and anaerobic metabolism is required for physiological hypoxia adaptation in skeletal muscle, and highlight protein catabolism and allosteric regulation as unexpected orchestrators of metabolic remodeling in this context. These findings have important implications for the management of hypoxia-related diseases and other conditions associated with chronic catabolic stress. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

  8. Combining central venous-to-arterial partial pressure of carbon dioxide difference and central venous oxygen saturation to guide resuscitation in septic shock.

    Science.gov (United States)

    Du, Wei; Liu, Da-Wei; Wang, Xiao-Ting; Long, Yun; Chai, Wen-Zhao; Zhou, Xiang; Rui, Xi

    2013-12-01

    Central venous oxygen saturation (Scvo2) is a useful therapeutic target when treating septic shock. We hypothesized that combining Scvo2 and central venous-to-arterial partial pressure of carbon dioxide difference (△Pco2) may provide additional information about survival. We performed a retrospective analysis of 172 patients treated for septic shock. All patients were treated using goal-directed therapy to achieve Scvo2 ≥ 70%. After 6 hours of treatment, we divided patients into 4 groups based on Scvo2 (<70% or ≥ 70%) and △Pco2 (<6 mm Hg or ≥ 6 mm Hg). Overall, 28-day mortality was 35.5%. For patients in whom the Scvo2 target was not achieved at 6 hours, mortality was 50.0%, compared with 29.5% in those in whom Scvo2 exceeded 70% (P = .009). In patients with Scvo2 ≥ 70%, mortality was lower if △Pco2 was <6 mm Hg than if △Pco2 was ≥ 6 mm Hg (56.1% vs 16.1%, respectively; P < .001) and 6-hour lactate clearance was superior (0.01 ± 0.61 vs 0.21 ± 0.31, respectively; P = .016). The combination of Scvo2 and △Pco2 appears to predict outcome in critically ill patients resuscitated from septic shock better than Scvo2 alone. Patients who meet both targets appear to clear lactate more efficiently. © 2013.

  9. 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

  10. Interdisciplinary Pathways for Urban Metabolism Research

    Science.gov (United States)

    Newell, J. P.

    2011-12-01

    With its rapid rise as a metaphor to express coupled natural-human systems in cities, the concept of urban metabolism is evolving into a series of relatively distinct research frameworks amongst various disciplines, with varying definitions, theories, models, and emphases. In industrial ecology, housed primarily within the disciplinary domain of engineering, urban metabolism research has focused on quantifying material and energy flows into, within, and out of cities, using methodologies such as material flow analysis and life cycle assessment. In the field of urban ecology, which is strongly influenced by ecology and urban planning, research focus has been placed on understanding and modeling the complex patterns and processes of human-ecological systems within urban areas. Finally, in political ecology, closely aligned with human geography and anthropology, scholars theorize about the interwoven knots of social and natural processes, material flows, and spatial structures that form the urban metabolism. This paper offers three potential interdisciplinary urban metabolism research tracks that might integrate elements of these three "ecologies," thereby bridging engineering and the social and physical sciences. First, it presents the idea of infrastructure ecology, which explores the complex, emergent interdependencies between gray (water and wastewater, transportation, etc) and green (e.g. parks, greenways) infrastructure systems, as nested within a broader socio-economic context. For cities to be sustainable and resilient over time-space, the theory follows, these is a need to understand and redesign these infrastructure linkages. Second, there is the concept of an urban-scale carbon metabolism model which integrates consumption-based material flow analysis (including goods, water, and materials), with the carbon sink and source dynamics of the built environment (e.g. buildings, etc) and urban ecosystems. Finally, there is the political ecology of the material

  11. Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions.

    Science.gov (United States)

    Zuñiga, Cristal; Li, Chien-Ting; Huelsman, Tyler; Levering, Jennifer; Zielinski, Daniel C; McConnell, Brian O; Long, Christopher P; Knoshaug, Eric P; Guarnieri, Michael T; Antoniewicz, Maciek R; Betenbaugh, Michael J; Zengler, Karsten

    2016-09-01

    The green microalga Chlorella vulgaris has been widely recognized as a promising candidate for biofuel production due to its ability to store high lipid content and its natural metabolic versatility. Compartmentalized genome-scale metabolic models constructed from genome sequences enable quantitative insight into the transport and metabolism of compounds within a target organism. These metabolic models have long been utilized to generate optimized design strategies for an improved production process. Here, we describe the reconstruction, validation, and application of a genome-scale metabolic model for C. vulgaris UTEX 395, iCZ843. The reconstruction represents the most comprehensive model for any eukaryotic photosynthetic organism to date, based on the genome size and number of genes in the reconstruction. The highly curated model accurately predicts phenotypes under photoautotrophic, heterotrophic, and mixotrophic conditions. The model was validated against experimental data and lays the foundation for model-driven strain design and medium alteration to improve yield. Calculated flux distributions under different trophic conditions show that a number of key pathways are affected by nitrogen starvation conditions, including central carbon metabolism and amino acid, nucleotide, and pigment biosynthetic pathways. Furthermore, model prediction of growth rates under various medium compositions and subsequent experimental validation showed an increased growth rate with the addition of tryptophan and methionine. © 2016 American Society of Plant Biologists. All rights reserved.

  12. The effects of lead on the gaseous exchange and photosynthetic carbon metabolism of pea seedlings

    Directory of Open Access Journals (Sweden)

    Jerzy W. Poskuta

    2014-01-01

    Full Text Available Roots of whole 3 week-old pea seedlings (Pisum sativum L. var. "Bordi" were immersed for 24 h in solutions of lead chloride at Pb copcentrations of 200, 400, 800,12000 mg dm3. Accumulation of lead in roots was independent of the Pb concentration, whereas the accumulation of Pb in shoots was an almost linear function of the concentration of this element in the root medium. This treatment caused Pb concentration-dependent inhibition of apparent photosynthesis (APS, photorespiration (PR, 14CO2 uptake, stomatal opening and transpiration of shoots and also germination of seeds. The most sensitive to Pb contamination was CO2 exchange, then transpiration and to a lesser degree germination of seeds. Lead caused a considerable alteration of photosynthetic and photorespiratory carbon metabolism, restricted the 14C-labeling of: phosphoglycerate, ribose+ribulose, sucrose, glycolate and glycine+serine. Under conditions of C02 uptake limited by lead, an enhancement of the 14C-labeling of malate+citrate, alanine and glucose was observed.

  13. Estimating Carbon Stocks and Atmospheric Exchange of Depressional Marshes on the Central Florida Landscape

    Science.gov (United States)

    Benscoter, B.; McClellan, M. D.; Benavides, V.; Harshbarger, D.; Comas, X.

    2014-12-01

    Depressional marshes are ubiquitous throughout central and south Florida. Often distributed within a matrix of sandy pine flatwoods and hammocks, these wetlands have a seasonally variable water table, alternating between inundation and complete drydown. Though these landforms are typically small individually, they comprise a substantial component of the landscape and provide vital habitat for an array of flora and fauna. Given their fluctuating hydrology, conditions for soil and plant carbon (C) exchange mechanisms can vary greatly both spatially and temporally. In this study, we are developing a C budget for depressional marsh landforms by assessing ecosystem carbon exchange along an ecotone gradient and quantifying belowground C stocks using non-invasive geophysical methods (ground penetrating radar, GPR) at the Disney Wilderness Preserve (DWP) in Kissimmee, FL, USA. Using a series of closed chambers transecting the marsh from the center outward into the surrounding flatwoods, we are quantifying the effects of seasonal water table change on the magnitude of C exchange. Three dimensional GPR surveys were used to quantify peat layer thickness, and were constrained with direct core sampling to verify subsurface lithology and to assess peat C content. Using the relationship between landform surface area and belowground C volume, we assessed the cumulative C storage in depressional marshes across the DWP landscape. In conjunction with a nearby eddy covariance tower and seasonal hydrologic data, these response functions will help to evaluate the contribution of these small but widespread landscape features on regional C cycling.

  14. An Examination of the Carbon Isotope Effects Associated with Amino Acid Biosynthesis

    Science.gov (United States)

    Scott, James H.; O'Brien, Diane M.; Emerson, David; Sun, Henry; McDonald, Gene D.; Salgado, Antonio; Fogel, Marilyn L.

    2006-12-01

    Stable carbon isotope ratios (δ13C) were determined for alanine, proline, phenylalanine, valine, leucine, isoleucine, aspartate (aspartic acid and asparagine), glutamate (glutamic acid and glutamine), lysine, serine, glycine, and threonine from metabolically diverse microorganisms. The microorganisms examined included fermenting bacteria, organotrophic, chemolithotrophic, phototrophic, methylotrophic, methanogenic, acetogenic, acetotrophic, and naturally occurring cryptoendolithic communities from the Dry Valleys of Antarctica. Here we demonstrated that reactions involved in amino acid biosynthesis can be used to distinguish amino acids formed by life from those formed by nonbiological processes. The unique patterns of δ13C imprinted by life on amino acids produced a biological bias. We also showed that, by applying discriminant function analysis to the δ13C value of a pool of amino acids formed by biological activity, it was possible to identify key aspects of intermediary carbon metabolism in the microbial world. In fact, microorganisms examined in this study could be placed within one of three metabolic groups: (1) heterotrophs that grow by oxidizing compounds containing three or more carbon-to-carbon bonds (fermenters and organotrophs), (2) autotrophs that grow by taking up carbon dioxide (chemolitotrophs and phototrophs), and (3) acetoclastic microbes that grow by assimilation of formaldehyde or acetate (methylotrophs, methanogens, acetogens, and acetotrophs). Furthermore, we demonstrated that cryptoendolithic communities from Antarctica grouped most closely with the autotrophs, which indicates that the dominant metabolic pathways in these communities are likely those utilized for CO2 fixation. We propose that this technique can be used to determine the dominant metabolic types in a community and reveal the overall flow of carbon in a complex ecosystem.

  15. δ13C chemostratigraphy in the upper Tremadocian through lower Katian (Ordovician carbonate succession of the Siljan district, central Sweden

    Directory of Open Access Journals (Sweden)

    Oliver Lehnert

    2014-12-01

    Full Text Available Based on δ13C data from two drillcores recovered from the Siljan district, we present a first continuous carbon isotope record of the upper Tremadocian–lower Katian limestone succession of central Sweden. New names for some isotopic carbon excursions from the Cambrian–Ordovician boundary through the basal Darriwilian are introduced. The Mora 001 core from the western part of the Siljan impact structure ranges through the Lower–Middle Ordovician, whereas the Solberga 1 core from its eastern part ranges through the Middle–lower Upper Ordovician. Upper Tremadocian and Floian units are extremely condensed and include extensive stratigraphic gaps. Multiple hardgrounds, sometimes with minor karstic overprint, imply recurrent periods of erosion and/or non-deposition. Like in other parts of Sweden, the Dapingian and Darriwilian succession is characterized by a relatively complete sedimentary record and low sedimentation rates.

  16. Linking neuronal brain activity to the glucose metabolism.

    Science.gov (United States)

    Göbel, Britta; Oltmanns, Kerstin M; Chung, Matthias

    2013-08-29

    Energy homeostasis ensures the functionality of the entire organism. The human brain as a missing link in the global regulation of the complex whole body energy metabolism is subject to recent investigation. The goal of this study is to gain insight into the influence of neuronal brain activity on cerebral and peripheral energy metabolism. In particular, the tight link between brain energy supply and metabolic responses of the organism is of interest. We aim to identifying regulatory elements of the human brain in the whole body energy homeostasis. First, we introduce a general mathematical model describing the human whole body energy metabolism. It takes into account the two central roles of the brain in terms of energy metabolism. The brain is considered as energy consumer as well as regulatory instance. Secondly, we validate our mathematical model by experimental data. Cerebral high-energy phosphate content and peripheral glucose metabolism are measured in healthy men upon neuronal activation induced by transcranial direct current stimulation versus sham stimulation. By parameter estimation we identify model parameters that provide insight into underlying neurophysiological processes. Identified parameters reveal effects of neuronal activity on regulatory mechanisms of systemic glucose metabolism. Our examinations support the view that the brain increases its glucose supply upon neuronal activation. The results indicate that the brain supplies itself with energy according to its needs, and preeminence of cerebral energy supply is reflected. This mechanism ensures balanced cerebral energy homeostasis. The hypothesis of the central role of the brain in whole body energy homeostasis as active controller is supported.

  17. Carbon and oxygen stable isotope and trace element studies in speleothems and across the J-K boundary, Central Italy

    International Nuclear Information System (INIS)

    Kudielka, G.

    2001-07-01

    Carbon and Oxygen stable isotope ratios of carbonates decisively depend on fractionation during physicochemical processes. Therefore, they represent a powerful tool to derive information on past conditions under which the carbonates formed. Isotope ratio mass spectrometry (IRMS) offers a large range of applications. This thesis presents two projects based upon investigation of carbon and oxygen stable isotope ratios combined with trace element abundances (determined by instrumental neutron activation analysis, INAA) in carbonates. (1) Palaeoclimatic investigation on speleothems from central Italy. Four speleothems from Grotta Grande del Vento, central Italy, were analyzed for stable isotope ratios and trace element abundances, and age dated to obtain a chronologically reliable stable isotope profile. The speleothems were sampled by means of a dental drill to gain a stable isotope profile with a 0.5 mm resolution, trace element abundances have been performed by INAA every 0.5 cm, and the samples for age dating were picked according to remarkable features in the stable isotope trends and analyzed by TIMS. The record covers the period from 93 ka until the early holocene with a hiatus lasting from 75 ka until 65.0 ka. Speleothem growth during the last glacial indicates moderate conditions in the Frasassi region back then. Comparison with speleothems from Ireland, France and northern Italy reveal a north-south slope in d18O, indicating, that the rain over central Italy mainly originates from the North Atlantic. Depletion of moisture in d18O during its continental trajectory is due to rainout, which primarily extracts the heavy isotopes. The stable isotope record is in good agreement with the high-resolution speleothem record from Soreq Cave, Israel. Distinct isotopic events coincide between 85 ka and 80 ka, between ∼ 60 ka and 50 ka and from the last glacial to the early holocene. An offset has been existing between the two records at any time. The speleothems of

  18. Study on the correlation of serum lipid metabolism and central retinal artery hemodynamics with diabetic retinopathy

    Institute of Scientific and Technical Information of China (English)

    Ran-Yang Guo

    2016-01-01

    Objective:To explore the correlation of serum lipid metabolism and central retinal artery (CRA) hemodynamics with diabetic retinopathy (DR).Methods:A total of 120 patients with type 2 diabetes who were admitted in our hospital from May, 2015 to May, 2016 were included in the study and divided into NDR group (non-diabetic retinopathy), NPR group (non-proliferative retinopathy), and PR group (proliferative retinopathy) with 40 cases in each group according to DR clinical staging. Moreover, 50 healthy individuals who came for physical examinations were served as the control group. The full automatic biochemical analyzer was used to detect the levels of TG, TC, LDL-C, and HDL-C. The color Doppler flow imaging (CDFI) was used to detect EDV, PSV, RI, and PI of CRA and OA.Results:The levels of TG, TC, and LDL-C in NDG, NPR, and PR groups were gradually increased with the aggravation of retinopathy, HDL-C was reduced, the comparison among the three groups was statistically significant, and the comparison with the control group was statistically significant. EDV, PSV, and PI of CRA and OA in NDG, NPR, and PR groups were gradually increased with the aggravation of retinopathy, RI was reduced, the comparison among the three groups was statistically significant, and the comparison with the control group was statistically significant. Conclusions: The lipid metabolism disorder can promote the occurrence and development of DR. The change of CRA and OA hemodynamics is an important pathological basis for developing DR. Clinical detection of serum lipid level and monitoring of the changes of fundus artery hemocynamic parameters are of great significance in early detecting DR.

  19. The Crc/CrcZ-CrcY global regulatory system helps the integration of gluconeogenic and glycolytic metabolism in Pseudomonas putida.

    Science.gov (United States)

    La Rosa, Ruggero; Nogales, Juan; Rojo, Fernando

    2015-09-01

    In metabolically versatile bacteria, carbon catabolite repression (CCR) facilitates the preferential assimilation of the most efficient carbon sources, improving growth rates and fitness. In Pseudomonas putida, the Crc and Hfq proteins and the CrcZ and CrcY small RNAs, which are believed to antagonize Crc/Hfq, are key players in CCR. Unlike that seen in other bacterial species, succinate and glucose elicit weak CCR in this bacterium. In the present work, metabolic, transcriptomic and constraint-based metabolic flux analyses were combined to clarify whether P. putida prefers succinate or glucose, and to identify the role of the Crc protein in the metabolism of these compounds. When provided simultaneously, succinate was consumed faster than glucose, although both compounds were metabolized. CrcZ and CrcY levels were lower when both substrates were present than when only one was provided, suggesting a role for Crc in coordinating metabolism of these compounds. Flux distribution analysis suggested that, when both substrates are present, Crc works to organize a metabolism in which carbon compounds flow in opposite directions: from glucose to pyruvate, and from succinate to pyruvate. Thus, our results support that Crc not only favours the assimilation of preferred compounds, but balances carbon fluxes, optimizing metabolism and growth. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  20. Vitamins B2 and B6 and Genetic Polymorphisms Related to One-Carbon Metabolism as Risk Factors for Gastric Adenocarcinoma in the European Prospective Investigation into Cancer and Nutrition

    NARCIS (Netherlands)

    Eussen, Simone J. P. M.; Vollset, Stein Emil; Hustad, Steinar; Midttun, Oivind; Meyer, Klaus; Fredriksen, Ase; Ueland, Per Magne; Jenab, Mazda; Slimani, Nadia; Ferrari, Pietro; Agudo, Antonio; Sala, Nuria; Capella, Gabriel; Del Giudice, Giuseppe; Palli, Domenico; Boeing, Heiner; Weikert, Cornelia; Bueno-de-Mesquita, H. Bas; Buechner, Frederike L.; Carneiro, Fatima; Berrino, Franco; Vineis, Paolo; Tumino, Rosario; Panico, Salvatore; Berglund, Goran; Manjer, Jonas; Stenling, Roger; Hallmans, Goeran; Martinez, Carmen; Arrizola, Larraitz; Barricarte, Aurelio; Navarro, Carmen; Rodriguez, Laudina; Bingham, Sheila; Linseisen, Jakob; Kaaks, Rudolf; Overvad, Kim; Tjonneland, Anne; Peeters, Petra H. M.; Numans, Mattijs E.; Clavel-Chapelon, Francoise; Boutron-Ruault, Marie-Christine; Morois, Sophie; Trichopoulou, Antonia; Lund, Eiliv; Plebani, Mario; Riboli, Elio; Gonzalez, Carlos A.

    B vitamins and polymorphisms in genes coding for enzymes involved in one-carbon metabolism may affect DNA synthesis and methylation and thereby be implicated in carcinogenesis. Previous data on vitamins B2 and B6 and genetic polymorphisms other than those involving MTHFR as risk factors for gastric

  1. The Glycerate and Phosphorylated Pathways of Serine Synthesis in Plants: The Branches of Plant Glycolysis Linking Carbon and Nitrogen Metabolism.

    Science.gov (United States)

    Igamberdiev, Abir U; Kleczkowski, Leszek A

    2018-01-01

    Serine metabolism in plants has been studied mostly in relation to photorespiration where serine is formed from two molecules of glycine. However, two other pathways of serine formation operate in plants and represent the branches of glycolysis diverging at the level of 3-phosphoglyceric acid. One branch (the glycerate - serine pathway) is initiated in the cytosol and involves glycerate formation from 3-phosphoglycerate, while the other (the phosphorylated serine pathway) operates in plastids and forms phosphohydroxypyruvate as an intermediate. Serine formed in these pathways becomes a precursor of glycine, formate and glycolate accumulating in stress conditions. The pathways can be linked to GABA shunt via transamination reactions and via participation of the same reductase for both glyoxylate and succinic semialdehyde. In this review paper we present a hypothesis of the regulation of redox balance in stressed plant cells via participation of the reactions associated with glycerate and phosphorylated serine pathways. We consider these pathways as important processes linking carbon and nitrogen metabolism and maintaining cellular redox and energy levels in stress conditions.

  2. Metabolism of lipids in Epidermophyton floccosum

    Energy Technology Data Exchange (ETDEWEB)

    Chopra, A; Khuller, G K [Post-Graduate Inst. of Medical Education and Research, Chandigarh (India)

    1981-03-01

    Metabolism of major lipids in E. floccosum was studied with /sup 14/C-acetate as a precursor. Among the phosphatides, phosphatidylcholine exhibited the maximum rate of synthesis and degradation, followed by phosphatidylethanolamine and phosphatidylserine. These phospholipids appear to exist in two pools, one metabolically more active than the other. In neutral lipids, maximum uptake was observed in triglycerides, followed by free fatty acids, diglycerides and monoglycerides. However, on chase of the labelled lipids, a continuous synthesis of all neutral lipid fractions was observed suggesting a recycling of the labelled carbon.

  3. LCE: leaf carbon exchange data set for tropical, temperate, and boreal species of North and Central America.

    Science.gov (United States)

    Smith, Nicholas G; Dukes, Jeffrey S

    2017-11-01

    Leaf canopy carbon exchange processes, such as photosynthesis and respiration, are substantial components of the global carbon cycle. Climate models base their simulations of photosynthesis and respiration on an empirical understanding of the underlying biochemical processes, and the responses of those processes to environmental drivers. As such, data spanning large spatial scales are needed to evaluate and parameterize these models. Here, we present data on four important biochemical parameters defining leaf carbon exchange processes from 626 individuals of 98 species at 12 North and Central American sites spanning ~53° of latitude. The four parameters are the maximum rate of Rubisco carboxylation (V cmax ), the maximum rate of electron transport for the regeneration of Ribulose-1,5,-bisphosphate (J max ), the maximum rate of phosphoenolpyruvate carboxylase carboxylation (V pmax ), and leaf dark respiration (R d ). The raw net photosynthesis by intercellular CO 2 (A/C i ) data used to calculate V cmax , J max , and V pmax rates are also presented. Data were gathered on the same leaf of each individual (one leaf per individual), allowing for the examination of each parameter relative to others. Additionally, the data set contains a number of covariates for the plants measured. Covariate data include (1) leaf-level traits (leaf mass, leaf area, leaf nitrogen and carbon content, predawn leaf water potential), (2) plant-level traits (plant height for herbaceous individuals and diameter at breast height for trees), (3) soil moisture at the time of measurement, (4) air temperature from nearby weather stations for the day of measurement and each of the 90 d prior to measurement, and (5) climate data (growing season mean temperature, precipitation, photosynthetically active radiation, vapor pressure deficit, and aridity index). We hope that the data will be useful for obtaining greater understanding of the abiotic and biotic determinants of these important biochemical

  4. Plankton community respiration, net ecosystem metabolism, and oxygen dynamics on the Louisiana continental shelf: Implications for hypoxia

    Science.gov (United States)

    Murrell, Michael C.; Stanley, Roman S.; Lehrter, John C.; Hagy, James D.

    2013-01-01

    We conducted a multi-year study of the Louisiana continental shelf (LCS) to better understand the linkages between water column metabolism and the formation of hypoxia (dissolved oxygen Continental Shelf Research, 29: 1861-1872) to estimate net water column metabolism. There was consistent evidence of net heterotrophy, particularly in western transects, and in deeper waters (>40 m depth), indicating a net organic carbon deficit on the LCS. We offer a simple scale argument to suggest that riverine and inshore coastal waters may be significant sources of organic carbon to account for this deficit. This study provided unprecedented, continental shelf scale coverage of heterotrophic metabolism, which is useful for constraining models of oxygen, carbon, and nutrient dynamics along the LCS.

  5. Metabolic and physiological interdependencies in the Bathymodiolus azoricus symbiosis.

    Science.gov (United States)

    Ponnudurai, Ruby; Kleiner, Manuel; Sayavedra, Lizbeth; Petersen, Jillian M; Moche, Martin; Otto, Andreas; Becher, Dörte; Takeuchi, Takeshi; Satoh, Noriyuki; Dubilier, Nicole; Schweder, Thomas; Markert, Stephanie

    2017-02-01

    The hydrothermal vent mussel Bathymodiolus azoricus lives in an intimate symbiosis with two types of chemosynthetic Gammaproteobacteria in its gills: a sulfur oxidizer and a methane oxidizer. Despite numerous investigations over the last decades, the degree of interdependence between the three symbiotic partners, their individual metabolic contributions, as well as the mechanism of carbon transfer from the symbionts to the host are poorly understood. We used a combination of proteomics and genomics to investigate the physiology and metabolism of the individual symbiotic partners. Our study revealed that key metabolic functions are most likely accomplished jointly by B. azoricus and its symbionts: (1) CO 2 is pre-concentrated by the host for carbon fixation by the sulfur-oxidizing symbiont, and (2) the host replenishes essential biosynthetic TCA cycle intermediates for the sulfur-oxidizing symbiont. In return (3), the sulfur oxidizer may compensate for the host's putative deficiency in amino acid and cofactor biosynthesis. We also identified numerous 'symbiosis-specific' host proteins by comparing symbiont-containing and symbiont-free host tissues and symbiont fractions. These proteins included a large complement of host digestive enzymes in the gill that are likely involved in symbiont digestion and carbon transfer from the symbionts to the host.

  6. Regulation of glycogen metabolism by the CRE-1, RCO-1 and RCM-1 proteins in Neurospora crassa. The role of CRE-1 as the central transcriptional regulator.

    Science.gov (United States)

    Cupertino, Fernanda Barbosa; Virgilio, Stela; Freitas, Fernanda Zanolli; Candido, Thiago de Souza; Bertolini, Maria Célia

    2015-04-01

    The transcription factor CreA/Mig1/CRE-1 is a repressor protein that regulates the use of alternative carbon sources via a mechanism known as Carbon Catabolite Repression (CCR). In Saccharomyces cerevisiae, Mig1 recruits the complex Ssn6-Tup1, the Neurospora crassa RCM-1 and RCO-1 orthologous proteins, respectively, to bind to promoters of glucose-repressible genes. We have been studying the regulation of glycogen metabolism in N. crassa and the identification of the RCO-1 corepressor as a regulator led us to investigate the regulatory role of CRE-1 in this process. Glycogen content is misregulated in the rco-1(KO), rcm-1(RIP) and cre-1(KO) strains, and the glycogen synthase phosphorylation is decreased in all strains, showing that CRE-1, RCO-1 and RCM-1 proteins are involved in glycogen accumulation and in the regulation of GSN activity by phosphorylation. We also confirmed the regulatory role of CRE-1 in CCR and its nuclear localization under repressing condition in N. crassa. The expression of all glycogenic genes is misregulated in the cre-1(KO) strain, suggesting that CRE-1 also controls glycogen metabolism by regulating gene expression. The existence of a high number of the Aspergillus nidulans CreA motif (5'-SYGGRG-3') in the glycogenic gene promoters led us to analyze the binding of CRE-1 to some DNA motifs both in vitro by DNA gel shift and in vivo by ChIP-qPCR analysis. CRE-1 bound in vivo to all motifs analyzed demonstrating that it down-regulates glycogen metabolism by controlling gene expression and GSN phosphorylation. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. Impact of Hypoglycemia on Brain Metabolism During Diabetes.

    Science.gov (United States)

    Rehni, Ashish K; Dave, Kunjan R

    2018-04-10

    Diabetes is a metabolic disease afflicting millions of people worldwide. A substantial fraction of world's total healthcare expenditure is spent on treating diabetes. Hypoglycemia is a serious consequence of anti-diabetic drug therapy, because it induces metabolic alterations in the brain. Metabolic alterations are one of the central mechanisms mediating hypoglycemia-related functional changes in the brain. Acute, chronic, and/or recurrent hypoglycemia modulate multiple metabolic pathways, and exposure to hypoglycemia increases consumption of alternate respiratory substrates such as ketone bodies, glycogen, and monocarboxylates in the brain. The aim of this review is to discuss hypoglycemia-induced metabolic alterations in the brain in glucose counterregulation, uptake, utilization and metabolism, cellular respiration, amino acid and lipid metabolism, and the significance of other sources of energy. The present review summarizes information on hypoglycemia-induced metabolic changes in the brain of diabetic and non-diabetic subjects and the manner in which they may affect brain function.

  8. Optimization of a recompression supercritical carbon dioxide cycle for an innovative central receiver solar power plant

    International Nuclear Information System (INIS)

    Reyes-Belmonte, M.A.; Sebastián, A.; Romero, M.; González-Aguilar, J.

    2016-01-01

    Peculiar thermodynamic properties of carbon dioxide (CO 2 ) when it is held at or above its critical condition (stated as supercritical CO 2 or sCO 2 ) have attracted the attention of many researchers. Its excellent thermophysical properties at medium-to-moderate temperature range have made it to be considered as the alternative working fluid for next power plant generation. Among those applications, future nuclear reactors, solar concentrated thermal energy or waste energy recovery have been shown as the most promising ones. In this paper, a recompression sCO 2 cycle for a solar central particles receiver application has been optimized, observing net cycle efficiency close to 50%. However, small changes on cycle parameters such as working temperatures, recuperators efficiencies or mass flow distribution between low and high temperature recuperators were found to drastically modify system overall efficiency. In order to mitigate these uncertainties, an optimization analysis based on recuperators effectiveness definition was performed observing that cycle efficiency could lie among 40%–50% for medium-to-moderate temperature range of the studied application (630 °C–680 °C). Due to the lack of maturity of current sCO 2 technologies and no power production scale demonstrators, cycle boundary conditions based on the solar application and a detailed literature review were chosen. - Highlights: • Mathematical modelling description for recompression sCO 2 cycle. • Split fraction and recuperators effectiveness effect into sCO 2 cycle performance. • Optimization methodology of sCO 2 cycle for an innovative solar central receiver. • Power generation using particles central receiver.

  9. Carbonate microfacies of the San Juan Formation (Ordovician: Oepikodus evae and Oepikodus intermedius conodont zones), Niquivil, Central Precordillera, Province of San Juan (Argentina)

    International Nuclear Information System (INIS)

    Soria, T.; Beresi, M.; Mestre, A.; Heredia, S.; Rodríguez, M.C.

    2017-01-01

    This contribution presents the description and interpretation of carbonate microfacies of the San Juan Formation (Ordovician) at the Niquivil section, considering the stratigraphical interval between the Oepikodus evae and Oepikodus intermedius conodont zones. The distribution of the microfacies and the conodonts assemblages allow us to identify different sub-environments within the late Floian carbonate ramp of the Central Precordillera. Five microfacies were recognized from the base to the top: M1 Bioclastic mudstone-wackestone; M2 Bioclastic-peloidal wackestone; M3 Intra-bioclastic wackestone; M4 Intra-bioclastic packstone; M5 Peloidal grainstone. The vertical distribution of these microfacies indicates a shallowing trend of the carbonate ramp in the Niquivil section for this temporal interval, which suggests a middle ramp environment with low energy, without wave action, and that evolved towards the middle-inner ramp environment with more energy by wave action and development of tempestites. [es

  10. Transcriptome landscape of Lactococcus lactis reveals many novel RNAs including a small regulatory RNA involved in carbon uptake and metabolism.

    Science.gov (United States)

    van der Meulen, Sjoerd B; de Jong, Anne; Kok, Jan

    2016-01-01

    RNA sequencing has revolutionized genome-wide transcriptome analyses, and the identification of non-coding regulatory RNAs in bacteria has thus increased concurrently. Here we reveal the transcriptome map of the lactic acid bacterial paradigm Lactococcus lactis MG1363 by employing differential RNA sequencing (dRNA-seq) and a combination of manual and automated transcriptome mining. This resulted in a high-resolution genome annotation of L. lactis and the identification of 60 cis-encoded antisense RNAs (asRNAs), 186 trans-encoded putative regulatory RNAs (sRNAs) and 134 novel small ORFs. Based on the putative targets of asRNAs, a novel classification is proposed. Several transcription factor DNA binding motifs were identified in the promoter sequences of (a)sRNAs, providing insight in the interplay between lactococcal regulatory RNAs and transcription factors. The presence and lengths of 14 putative sRNAs were experimentally confirmed by differential Northern hybridization, including the abundant RNA 6S that is differentially expressed depending on the available carbon source. For another sRNA, LLMGnc_147, functional analysis revealed that it is involved in carbon uptake and metabolism. L. lactis contains 13% leaderless mRNAs (lmRNAs) that, from an analysis of overrepresentation in GO classes, seem predominantly involved in nucleotide metabolism and DNA/RNA binding. Moreover, an A-rich sequence motif immediately following the start codon was uncovered, which could provide novel insight in the translation of lmRNAs. Altogether, this first experimental genome-wide assessment of the transcriptome landscape of L. lactis and subsequent sRNA studies provide an extensive basis for the investigation of regulatory RNAs in L. lactis and related lactococcal species.

  11. Metabolic profiling of a mapping population exposes new insights in the regulation of seed metabolism and seed, fruit, and plant relations.

    Directory of Open Access Journals (Sweden)

    David Toubiana

    Full Text Available To investigate the regulation of seed metabolism and to estimate the degree of metabolic natural variability, metabolite profiling and network analysis were applied to a collection of 76 different homozygous tomato introgression lines (ILs grown in the field in two consecutive harvest seasons. Factorial ANOVA confirmed the presence of 30 metabolite quantitative trait loci (mQTL. Amino acid contents displayed a high degree of variability across the population, with similar patterns across the two seasons, while sugars exhibited significant seasonal fluctuations. Upon integration of data for tomato pericarp metabolite profiling, factorial ANOVA identified the main factor for metabolic polymorphism to be the genotypic background rather than the environment or the tissue. Analysis of the coefficient of variance indicated greater phenotypic plasticity in the ILs than in the M82 tomato cultivar. Broad-sense estimate of heritability suggested that the mode of inheritance of metabolite traits in the seed differed from that in the fruit. Correlation-based metabolic network analysis comparing metabolite data for the seed with that for the pericarp showed that the seed network displayed tighter interdependence of metabolic processes than the fruit. Amino acids in the seed metabolic network were shown to play a central hub-like role in the topology of the network, maintaining high interactions with other metabolite categories, i.e., sugars and organic acids. Network analysis identified six exceptionally highly co-regulated amino acids, Gly, Ser, Thr, Ile, Val, and Pro. The strong interdependence of this group was confirmed by the mQTL mapping. Taken together these results (i reflect the extensive redundancy of the regulation underlying seed metabolism, (ii demonstrate the tight co-ordination of seed metabolism with respect to fruit metabolism, and (iii emphasize the centrality of the amino acid module in the seed metabolic network. Finally, the study

  12. Proteomic evidences for rex regulation of metabolism in toxin-producing Bacillus cereus ATCC 14579.

    Directory of Open Access Journals (Sweden)

    Sabrina Laouami

    Full Text Available The facultative anaerobe, Bacillus cereus, causes diarrheal diseases in humans. Its ability to deal with oxygen availability is recognized to be critical for pathogenesis. The B. cereus genome comprises a gene encoding a protein with high similarities to the redox regulator, Rex, which is a central regulator of anaerobic metabolism in Bacillus subtilis and other Gram-positive bacteria. Here, we showed that B. cereus rex is monocistronic and down-regulated in the absence of oxygen. The protein encoded by rex is an authentic Rex transcriptional factor since its DNA binding activity depends on the NADH/NAD+ ratio. Rex deletion compromised the ability of B. cereus to cope with external oxidative stress under anaerobiosis while increasing B. cereus resistance against such stress under aerobiosis. The deletion of rex affects anaerobic fermentative and aerobic respiratory metabolism of B. cereus by decreasing and increasing, respectively, the carbon flux through the NADH-recycling lactate pathway. We compared both the cellular proteome and exoproteome of the wild-type and Δrex cells using a high throughput shotgun label-free quantitation approach and identified proteins that are under control of Rex-mediated regulation. Proteomics data have been deposited to the ProteomeXchange with identifier PXD000886. The data suggest that Rex regulates both the cross-talk between metabolic pathways that produce NADH and NADPH and toxinogenesis, especially in oxic conditions.

  13. Monitoring in situ biodegradation of hydrocarbons by using stable carbon isotopes

    International Nuclear Information System (INIS)

    Aggarwal, P.K.; Hinchee, R.E.

    1991-01-01

    Spilled or leaked nonhalogenated petroleum hydrocarbons in the soil can generally be metabolized by indigenous, aerobic bacteria. In situ biological degradation of hydrocarbons may be accelerated by supplying inorganic nutrients and/or oxygen. Approaches to monitoring and verifying enhanced in situ biodegradation have included measurements of changes over time in the (a) concentration of hydrocarbons, (b) temperature, (c) number of hydrocarbon-degrading microorganisms, (d) ratio of fast-degrading hydrocarbons (e.g., pristanes or phytanes), and (e) metabolic intermediates. Measurements of oxygen consumption over time and elevated carbon dioxide concentrations in soil gas also have been used as indicators of hydrocarbon degradation. An alternative approach that may help substantiate biodegradation is to measure stable carbon isotope ratios in soil gas CO 2 . Stable carbon isotope ratio analysis is inexpensive and commercially available at many laboratories. Carbon dioxide produced by hydrocarbon degradation may be distinguished from that produced by other processes based on the carbon isotopic compositions characteristic of the source material and/or fractionation accompanying microbial metabolism. Here the authors demonstrate the applicability of the stable isotope technique for monitoring enhanced. aerobic biodegradation of hydrocarbons using data from three locations in the United States

  14. Pathways and bioenergetics of anaerobic carbon monoxide fermentation

    NARCIS (Netherlands)

    Diender, Martijn; Stams, Fons; Machado de Sousa, Diana

    2015-01-01

    Carbon monoxide can act as a substrate for different modes of fermentative anaerobic metabolism. The trait of utilizing CO is spread among a diverse group of microorganisms, including members of bacteria as well as archaea. Over the last decade this metabolism has gained interest due to the

  15. Forest Restoration Carbon Analysis of Baseline Carbon Emissions and Removal in Tropical Rainforest at La Selva Central, Peru

    Energy Technology Data Exchange (ETDEWEB)

    Patrick Gonzalez; Benjamin Kroll; Carlos R. Vargas

    2006-01-10

    Conversion of tropical forest to agricultural land and pasture has reduced forest extent and the provision of ecosystem services, including watershed protection, biodiversity conservation, and carbon sequestration. Forest conservation and reforestation can restore those ecosystem services. We have assessed forest species patterns, quantified deforestation and reforestation rates, and projected future baseline carbon emissions and removal in Amazon tropical rainforest at La Selva Central, Peru. The research area is a 4800 km{sup 2} buffer zone around the Parque Nacional Yanachaga-Chemillen, Bosque de Proteccion San Matias-San Carlos, and the Reserva Comunal Yanesha. A planned project for the period 2006-2035 would conserve 4000 ha of forest in a proposed 7000 ha Area de Conservacion Municipale de Chontabamba and establish 5600 ha of natural regeneration and 1400 ha of native species plantations, laid out in fajas de enriquecimiento (contour plantings), to reforest 7000 ha of agricultural land. Forest inventories of seven sites covering 22.6 ha in primary forest and 17 sites covering 16.5 ha in secondary forest measured 17,073 trees of diameter {ge} 10 cm. The 24 sites host trees of 512 species, 267 genera, and 69 families. We could not identify the family of 7% of the trees or the scientific species of 21% of the trees. Species richness is 346 in primary forest and 257 in the secondary forest. In primary forest, 90% of aboveground biomass resides in old-growth species. Conversely, in secondary forest, 66% of aboveground biomass rests in successional species. The density of trees of diameter {ge} 10 cm is 366 trees ha{sup -1} in primary forest and 533 trees ha{sup -1} in secondary forest, although the average diameter is 24 {+-} 15 cm in primary forest and 17 {+-} 8 cm in secondary forest. Using Amazon forest biomass equations and wood densities for 117 species, aboveground biomass is 240 {+-} 30 t ha{sup -1} in the primary sites and 90 {+-} 10 t ha{sup -1} in the

  16. Acute nutritional ketosis: implications for exercise performance and metabolism

    Science.gov (United States)

    2014-01-01

    Ketone bodies acetoacetate (AcAc) and D-β-hydroxybutyrate (βHB) may provide an alternative carbon source to fuel exercise when delivered acutely in nutritional form. The metabolic actions of ketone bodies are based on sound evolutionary principles to prolong survival during caloric deprivation. By harnessing the potential of these metabolic actions during exercise, athletic performance could be influenced, providing a useful model for the application of ketosis in therapeutic conditions. This article examines the energetic implications of ketone body utilisation with particular reference to exercise metabolism and substrate energetics. PMID:25379174

  17. Neuroinflammatory basis of metabolic syndrome.

    Science.gov (United States)

    Purkayastha, Sudarshana; Cai, Dongsheng

    2013-10-05

    Inflammatory reaction is a fundamental defense mechanism against threat towards normal integrity and physiology. On the other hand, chronic diseases such as obesity, type 2 diabetes, hypertension and atherosclerosis, have been causally linked to chronic, low-grade inflammation in various metabolic tissues. Recent cross-disciplinary research has led to identification of hypothalamic inflammatory changes that are triggered by overnutrition, orchestrated by hypothalamic immune system, and sustained through metabolic syndrome-associated pathophysiology. While continuing research is actively trying to underpin the identity and mechanisms of these inflammatory stimuli and actions involved in metabolic syndrome disorders and related diseases, proinflammatory IκB kinase-β (IKKβ), the downstream nuclear transcription factor NF-κB and some related molecules in the hypothalamus were discovered to be pathogenically significant. This article is to summarize recent progresses in the field of neuroendocrine research addressing the central integrative role of neuroinflammation in metabolic syndrome components ranging from obesity, glucose intolerance to cardiovascular dysfunctions.

  18. ER Stress and Lipid Metabolism in Adipocytes

    Directory of Open Access Journals (Sweden)

    Beth S. Zha

    2012-01-01

    Full Text Available The role of endoplasmic reticulum (ER stress is a rapidly emerging field of interest in the pathogenesis of metabolic diseases. Recent studies have shown that chronic activation of ER stress is closely linked to dysregulation of lipid metabolism in several metabolically important cells including hepatocytes, macrophages, β-cells, and adipocytes. Adipocytes are one of the major cell types involved in the pathogenesis of the metabolic syndrome. Recent advances in dissecting the cellular and molecular mechanisms involved in the regulation of adipogenesis and lipid metabolism indicate that activation of ER stress plays a central role in regulating adipocyte function. In this paper, we discuss the current understanding of the potential role of ER stress in lipid metabolism in adipocytes. In addition, we touch upon the interaction of ER stress and autophagy as well as inflammation. Inhibition of ER stress has the potential of decreasing the pathology in adipose tissue that is seen with energy overbalance.

  19. Influence of wildfires on atmospheric composition and carbon uptake of forest ecosystems in Central Siberia: the establishing of a long-term post-fire monitoring system

    Science.gov (United States)

    Panov, Alexey; Chi, Xuguang; Winderlich, Jan; Prokushkin, Anatoly; Bryukhanov, Alexander; Korets, Mikhail; Ponomarev, Evgenii; Timokhina, Anastasya; Andreae, Meinrat O.; Heimann, Martin

    2014-05-01

    Calculations of direct emissions of greenhouse gases from boreal wildfires remain uncertain due to problems with emission factors, available carbon, and imprecise estimates of burned areas. Even more varied and sparse are accurate in situ calculations of temporal changes in boreal forest carbon dynamics following fire. Linking simultaneous instrumental atmospheric observations, GIS-based estimates of burned areas, and ecosystem carbon uptake calculations is vital to fill this knowledge gap. Since 2006 the Zotino Tall Tower Observatory (ZOTTO; www.zottoproject.org) a research platform for large-scale climatic observations is operational in Central Siberia (60°48'N, 89°21'E). The data of ongoing greenhouse gases measurements at the tower are used in atmospheric inversions studies to infer the distribution of carbon sinks and sources over central Northern Eurasia. We present our contribution to reducing uncertainties in estimates of fire influence on atmospheric composition and post-fire ecosystem carbon uptake deduced from the large-scale fires that happened in 2012 in the tall tower footprint area. The burned areas were estimated from Landsat ETM 5,8 satellite images, while fires were detected from Terra/Aqua MODIS satellite data. The magnitude of ecological change caused by fires ("burn severity") was measured and mapped with a Normalized Burn Ratio (NBR) index and further calibrated by a complementary field based Composite Burn Index (CBI). Measures of fire radiative power (FRP) index provided information on fire heat release intensity and on the amount and completeness of biomass combustion. Based on the analyzed GIS data, the system of study plots was established in the 5 dominating ecosystem types for a long-term post-fire monitoring. On the plots the comprehensive estimation of ecosystem parameters and carbon pools and their mapping was organized with a laser-based field instrumentation system. The work was supported financially by ISTC Project # 2757p

  20. The central nervous system

    International Nuclear Information System (INIS)

    Holmes, R.A.

    1984-01-01

    The first section presents a comprehensive evaluation of radionuclide imaging of the central nervous system and provides a comparison of the detection accuracies of radionuclide imaging (RNI) and XCT in certain lesions, realizing that the XCT results may vary when radiocontrast or newer generation XCT scanners are used. Although conventional radionuclide imaging of the central nervous system has experienced no significant changes over the last 7 years except for mild refinements, a new section has been added on positron emission tomography (PET). Most positron radiopharmaceuticals passively cross the intact blood-brain barrier, and their localization has catalyzed renewed interest in our ability to metabolically study and obtain images of the central nervous system. The section on radionuclide cisternography has been rewritten to reflect present day practice and the wider application of XCT in describing conditions affecting the ventricular system