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Sample records for carbon metabolism unveils

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

    Science.gov (United States)

    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 and thus have not been obvious targets as candidates for crop improvement. We test this functional conservatio...

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

    Directory of Open Access Journals (Sweden)

    Nengyi Zhang

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

  3. Unveiling the Metabolic Changes on Muscle Cell Metabolism Underlying p-Phenylenediamine Toxicity

    Science.gov (United States)

    Marín de Mas, Igor; Marín, Silvia; Pachón, Gisela; Rodríguez-Prados, Juan C.; Vizán, Pedro; Centelles, Josep J.; Tauler, Romà; Azqueta, Amaya; Selivanov, Vitaly; López de Ceraín, Adela; Cascante, Marta

    2017-01-01

    Rhabdomyolysis is a disorder characterized by acute damage of the sarcolemma of the skeletal muscle leading to release of potentially toxic muscle cell components into the circulation, most notably creatine phosphokinase (CK) and myoglobulin, and is frequently accompanied by myoglobinuria. In the present work, we evaluated the toxicity of p-phenylenediamine (PPD), a main component of hair dyes which is reported to induce rhabdomyolysis. We studied the metabolic effect of this compound in vivo with Wistar rats and in vitro with C2C12 muscle cells. To this aim we have combined multi-omic experimental measurements with computational approaches using model-driven methods. The integrative study presented here has unveiled the metabolic disorders associated to PPD exposure that may underlay the aberrant metabolism observed in rhabdomyolys disease. Animals treated with lower doses of PPD (10 and 20 mg/kg) showed depressed activity and myoglobinuria after 10 h of treatment. We measured the serum levels of aspartate aminotransferase (AST), alanine aminotransferase (ALT), and creatine kinase (CK) in rats after 24, 48, and 72 h of PPD exposure. At all times, treatment with PPD at higher doses (40 and 60 mg/kg) showed an increase of AST and ALT, and also an increase of lactate dehydrogenase (LDH) and CK after 24 h. Blood packed cell volume and hemoglobin levels, as well as organs weight at 48 and 72 h, were also measured. No significant differences were observed in these parameters under any condition. PPD induce cell cycle arrest in S phase and apoptosis (40% or early apoptotic cells) on mus musculus mouse C2C12 cells after 24 h of treatment. Incubation of mus musculus mouse C2C12 cells with [1,2-13C2]-glucose during 24 h, subsequent quantification of 13C isotopologues distribution in key metabolites of glucose metabolic network and a computational fluxomic analysis using in-house developed software (Isodyn) showed that PPD is inhibiting glycolysis, non-oxidative pentose

  4. -Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis.

    Science.gov (United States)

    Undabarrena, Agustina; Ugalde, Juan A; Seeger, Michael; Cámara, Beatriz

    2017-01-01

    Streptomyces sp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria (S. aureus and L. monocytogenes). Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs) for secondary metabolites, where among them, 81% have low similarities with known BGCs. In addition, a genomic search in Streptomyces sp. H-KF8 unveiled the presence of a wide variety of genetic determinants related to heavy metal resistance (49 genes), oxidative stress (69 genes) and antibiotic resistance (97 genes). This study revealed that the marine-derived Streptomyces sp. H-KF8 bacterium has the capability to tolerate a diverse set of heavy metals such as copper, cobalt, mercury, chromate and nickel; as well as the highly toxic tellurite, a feature first time described for Streptomyces. In addition, Streptomyces sp. H-KF8 possesses a major resistance towards oxidative stress, in comparison to the soil reference strain Streptomyces violaceoruber A3(2). Moreover, Streptomyces sp. H-KF8 showed resistance to 88% of the antibiotics tested, indicating overall, a strong response to several abiotic stressors. The combination of these biological traits confirms the metabolic versatility of Streptomyces sp. H-KF8, a genetically well-prepared microorganism with the ability to confront the dynamics of the fjord-unique marine environment.

  5. Unveiling the oxidative metabolism of Rhipicephalus microplus (Acari: Ixodidae) experimentally exposed to entomopathogenic fungi.

    Science.gov (United States)

    Tunholi-Alves, Vinícius Menezes; Tunholi Alves, Victor Menezes; da Silva, Jairo Pinheiro; Nora Castro, Rosane; Salgueiro, Fernanda Barbosa; Perinotto, Wendell Marcelo de Souza; Gôlo, Patrícia Silva; Camargo, Mariana Guedes; Angelo, Isabele da Costa; Bittencourt, Vânia Rita Elias Pinheiro

    2016-10-01

    Rhipicephalus microplus is an important tick in tropical regions due to the high economic losses caused by its parasitism. Metarhizium anisopliae and Beauveria bassiana are well-known entomopathogenic fungi that can afflict R. microplus ticks. The development of new targets and strategies to control this parasite can be driven by studies of this tick's physiology. Recently, it was reported that when exposed to adverse physiological conditions, ticks can activate fermentative pathways, indicating transition from aerobic to anaerobic metabolism. Nevertheless, the precise mechanism by which entomopathogenic fungi influence R. microplus metabolism has not been clarified, limiting understanding of the tick-fungus association. Thus, the present study aimed to evaluate the effect of infection of ticks by M. anisopliae and B. bassiana on the amount of selected carboxylic acids present in the hemolymph, enabling increased understanding of changes previously reported. The results showed preservation in the concentrations of oxalic, lactic, and pyruvic acids in the hemolymph 24 and 48 h after dropping from cattle; while there were variations in the concentration of these carboxylic acids after infection of female ticks to M. anisopliae and B. bassiana. Significant increases were observed in the concentration of oxalic and lactic acids and significant reduction of pyruvic acid for both observation times (24 and 48 h) after infection by entomopathogenic fungi. These results indicate that B. bassiana and M. anisopliae infection alters the basal metabolism of R. microplus females, resulting in the activation of fermentative pathways.

  6. Distinctive Metabolism of Flavonoid between Cultivated and Semiwild Soybean Unveiled through Metabolomics Approach.

    Science.gov (United States)

    Yun, Dae-Yong; Kang, Young-Gyu; Yun, Bohyun; Kim, Eun-Hee; Kim, Myoyeon; Park, Jun Seong; Lee, John Hwan; Hong, Young-Shick

    2016-07-27

    Soybeans are an important crop for agriculture and food, resulting in an increase in the range of its application. Recently, soybean leaves have been used not only for food products but also in the beauty industry. To provide useful and global metabolite information on the development of soy-based products, we investigated the metabolic evolution and cultivar-dependent metabolite variation in the leaves of cultivated (Glycine max) and semiwild (G. gracilis) soybean, through a (1)H NMR-based metabolomics approach, as they grew from V (vegetative) 1 to R (reproductive) 7 growth stages. The levels of primary metabolites, such as sucrose, amino acids, organic acids, and fatty acids, were decreased both in the G. gracilis and G. max leaves. However, the secondary metabolites, such as pinitol, rutin, and polyphenols, were increased while synthesis of glucose was elevated as the leaves grew. When metabolite variations between G. gracilis and G. max are compared, it was noteworthy that rutin and its precursor, quercetin-3-O-glucoside, were found only in G. gracilis but not in G. max. Furthermore, levels of pinitol, proline, β-alanine, and acetic acid, a metabolite related to adaptation toward environmental stress, were different between the two soybean cultivars. These results highlight their distinct metabolism for adaptation to environmental conditions and their intrinsic metabolic phenotype. This study therefore provides important information on the cultivar-dependent metabolites of soybean leaves for better understanding of plant physiology toward the development of soy-based products.

  7. (Carbon monoxide metabolism by photosynthetic bacteria)

    Energy Technology Data Exchange (ETDEWEB)

    1989-01-01

    Research continued on the metabolism of carbon monoxide by Rhodospirillum rubrum. This report discusses progress on the activity, induction, inhibition, and spectroscopic analysis of the enzyme Carbon Monoxide Dehydrogenase. (CBS)

  8. A conditional mutant of the fatty acid synthase unveils unexpected cross talks in mycobacterial lipid metabolism.

    Science.gov (United States)

    Cabruja, Matías; Mondino, Sonia; Tsai, Yi Ting; Lara, Julia; Gramajo, Hugo; Gago, Gabriela

    2017-02-01

    Unlike most bacteria, mycobacteria rely on the multi-domain enzyme eukaryote-like fatty acid synthase I (FAS I) to make fatty acids de novo. These metabolites are precursors of the biosynthesis of most of the lipids present both in the complex mycobacteria cell wall and in the storage lipids inside the cell. In order to study the role of the type I FAS system in Mycobacterium lipid metabolism in vivo, we constructed a conditional mutant in the fas-acpS operon of Mycobacterium smegmatis and analysed in detail the impact of reduced de novo fatty acid biosynthesis on the global architecture of the cell envelope. As expected, the mutant exhibited growth defect in the non-permissive condition that correlated well with the lower expression of fas-acpS and the concomitant reduction of FAS I, confirming that FAS I is essential for survival. The reduction observed in FAS I provoked an accumulation of its substrates, acetyl-CoA and malonyl-CoA, and a strong reduction of C12 to C18 acyl-CoAs, but not of long-chain acyl-CoAs (C19 to C24). The most intriguing result was the ability of the mutant to keep synthesizing mycolic acids when fatty acid biosynthesis was impaired. A detailed comparative lipidomic analysis showed that although reduced FAS I levels had a strong impact on fatty acid and phospholipid biosynthesis, mycolic acids were still being synthesized in the mutant, although with a different relative species distribution. However, when triacylglycerol degradation was inhibited, mycolic acid biosynthesis was significantly reduced, suggesting that storage lipids could be an intracellular reservoir of fatty acids for the biosynthesis of complex lipids in mycobacteria. Understanding the interaction between FAS I and the metabolic pathways that rely on FAS I products is a key step to better understand how lipid homeostasis is regulated in this microorganism and how this regulation could play a role during infection in pathogenic mycobacteria.

  9. Heme oxygenase-1/carbon monoxide: from metabolism to molecular therapy.

    Science.gov (United States)

    Ryter, Stefan W; Choi, Augustine M K

    2009-09-01

    Heme oxygenase-1 (HO-1), a ubiquitous inducible stress-response protein, serves a major metabolic function in heme turnover. HO activity cleaves heme to form biliverdin-IXalpha, carbon monoxide (CO), and iron. Genetic experiments have revealed a central role for HO-1 in tissue homeostasis, protection against oxidative stress, and in the pathogenesis of disease. Four decades of research have witnessed not only progress in elucidating the molecular mechanisms underlying the regulation and function of this illustrious enzyme, but also have opened remarkable translational applications for HO-1 and its reaction products. CO, once regarded as a metabolic waste, can act as an endogenous mediator of cellular signaling and vascular function. Exogenous application of CO by inhalation or pharmacologic delivery can confer cytoprotection in preclinical models of lung/vascular injury and disease, based on anti-apoptotic, anti-inflammatory, and anti-proliferative properties. The bile pigments, biliverdin and bilirubin, end products of heme degradation, have also shown potential as therapeutics in vascular disease based on anti-inflammatory and anti-proliferative activities. Further translational and clinical trials research will unveil whether the HO-1 system or any of its reaction products can be successfully applied as molecular medicine in human disease.

  10. Unveiling carbon dimers and their chains as precursor of graphene growth on Ru(0001)

    Science.gov (United States)

    Gao, Min; Zhang, Yan-Fang; Huang, Li; Pan, Yi; Wang, Yeliang; Ding, Feng; Lin, Yuan; Du, Shi-Xuan; Gao, Hong-Jun

    2016-09-01

    Carbon precursor that forms on the catalyst surface by the dissociation of feedstock gas plays an important role in the controllable growth of graphene on metal substrates. However, the configuration about the precursor has so far remained elusive. Here, we report the direct observation of uniformly structured precursor units and their chain formation at the nucleation stage of graphene growing on Ru(0001) substrate by using scanning tunneling microscopy. Combining this experimental information with density function theory calculations, the atomic-resolved structures of carbon precursor are characterized as adsorbed CH2 segments on the substrate. The dissociated carbon feedstock molecules or radicals further react to form nonplanar -[C2H4]- chains adsorbed on hexagonal-close-packed hollow sites of the Ru(0001) substrate before incorporating into the graphene island. These findings reveal that CH2 and nonplanar -[C2H4]- segments act as precursors in graphene growth and are helpful to improve the quality and the domain size of desired graphene by precursor or feedstock control.

  11. Photosynthetic carbon monoxide metabolism by sugarcane leaves

    Energy Technology Data Exchange (ETDEWEB)

    Kortschak, H.P.; Nickell, L.G.

    1973-01-01

    The photosynthetic carbon monoxide metabolism by sugarcane was studied to determine whether substantial quantities of CO are removed from the air by fields in Hawaii. Leaves metabolized low CO concentrations photosynthetically, with sucrose as an end product. Rates of uptake were of the order of 10/sup -4/ power mg/d sq m/hr. This was to low to be significant in removing CO from the atmosphere.

  12. Unveiling Stability Criteria of DNA-Carbon Nanotubes Constructs by Scanning Tunneling Microscopy and Computational Modeling

    Directory of Open Access Journals (Sweden)

    Svetlana Kilina

    2011-01-01

    Full Text Available We present a combined approach that relies on computational simulations and scanning tunneling microscopy (STM measurements to reveal morphological properties and stability criteria of carbon nanotube-DNA (CNT-DNA constructs. Application of STM allows direct observation of very stable CNT-DNA hybrid structures with the well-defined DNA wrapping angle of 63.4° and a coiling period of 3.3 nm. Using force field simulations, we determine how the DNA-CNT binding energy depends on the sequence and binding geometry of a single strand DNA. This dependence allows us to quantitatively characterize the stability of a hybrid structure with an optimal π-stacking between DNA nucleotides and the tube surface and better interpret STM data. Our simulations clearly demonstrate the existence of a very stable DNA binding geometry for (6,5 CNT as evidenced by the presence of a well-defined minimum in the binding energy as a function of an angle between DNA strand and the nanotube chiral vector. This novel approach demonstrates the feasibility of CNT-DNA geometry studies with subnanometer resolution and paves the way towards complete characterization of the structural and electronic properties of drug-delivering systems based on DNA-CNT hybrids as a function of DNA sequence and a nanotube chirality.

  13. Phenotypic bistability in Escherichia coli's central carbon metabolism

    NARCIS (Netherlands)

    Kotte, Oliver; Volkmer, Benjamin; Radzikowski, Jakub L.; Heinemann, Matthias

    2014-01-01

    Fluctuations in intracellular molecule abundance can lead to distinct, coexisting phenotypes in isogenic populations. Although metabolism continuously adapts to unpredictable environmental changes, and although bistability was found in certain substrate-uptake pathways, central carbon metabolism is

  14. 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...

  15. [Carbon monoxide metabolism by photosynthetic bacteria]. Progress report

    Energy Technology Data Exchange (ETDEWEB)

    1989-12-31

    Research continued on the metabolism of carbon monoxide by Rhodospirillum rubrum. This report discusses progress on the activity, induction, inhibition, and spectroscopic analysis of the enzyme Carbon Monoxide Dehydrogenase. (CBS)

  16. ­Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis

    Directory of Open Access Journals (Sweden)

    Agustina Undabarrena

    2017-02-01

    Full Text Available Streptomyces sp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria (S. aureus and L. monocytogenes. Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs for secondary metabolites, where among them, 81% have low similarities with known BGCs. In addition, a genomic search in Streptomyces sp. H-KF8 unveiled the presence of a wide variety of genetic determinants related to heavy metal resistance (49 genes, oxidative stress (69 genes and antibiotic resistance (97 genes. This study revealed that the marine-derived Streptomyces sp. H-KF8 bacterium has the capability to tolerate a diverse set of heavy metals such as copper, cobalt, mercury, chromate and nickel; as well as the highly toxic tellurite, a feature first time described for Streptomyces. In addition, Streptomyces sp. H-KF8 possesses a major resistance towards oxidative stress, in comparison to the soil reference strain Streptomyces violaceoruber A3(2. Moreover, Streptomyces sp. H-KF8 showed resistance to 88% of the antibiotics tested, indicating overall, a strong response to several abiotic stressors. The combination of these biological traits confirms the metabolic versatility of Streptomyces sp. H-KF8, a genetically well-prepared microorganism with the ability to confront the dynamics of the fjord-unique marine environment.

  17. ­Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis

    Science.gov (United States)

    Undabarrena, Agustina; Ugalde, Juan A.; Seeger, Michael

    2017-01-01

    Streptomyces sp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria (S. aureus and L. monocytogenes). Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs) for secondary metabolites, where among them, 81% have low similarities with known BGCs. In addition, a genomic search in Streptomyces sp. H-KF8 unveiled the presence of a wide variety of genetic determinants related to heavy metal resistance (49 genes), oxidative stress (69 genes) and antibiotic resistance (97 genes). This study revealed that the marine-derived Streptomyces sp. H-KF8 bacterium has the capability to tolerate a diverse set of heavy metals such as copper, cobalt, mercury, chromate and nickel; as well as the highly toxic tellurite, a feature first time described for Streptomyces. In addition, Streptomyces sp. H-KF8 possesses a major resistance towards oxidative stress, in comparison to the soil reference strain Streptomyces violaceoruber A3(2). Moreover, Streptomyces sp. H-KF8 showed resistance to 88% of the antibiotics tested, indicating overall, a strong response to several abiotic stressors. The combination of these biological traits confirms the metabolic versatility of Streptomyces sp. H-KF8, a genetically well-prepared microorganism with the ability to confront the dynamics of the fjord-unique marine environment. PMID:28229018

  18. Lord Shiva Statue Unveiled

    CERN Multimedia

    2004-01-01

    On 18 June, CERN unveiled an unusual new landmark, a 2m tall statue of the Indian deity Lord Shiva.It was unveiled by the Director General, Dr Robert Aymar, His Excellency Mr K. M. Chandrasekhar, Ambassador (WTO-Geneva) and Dr Anil Kakodkar, Chairman of the Atomic Energy Commission and Secretary, Dept of Atomic Energy, India. (18/06/2004)

  19. Engineering Plant One-Carbon Metabolism

    Energy Technology Data Exchange (ETDEWEB)

    David Rhodes

    2005-02-09

    Primary and secondary metabolism intersect in the one-carbon (C1) area. Primary metabolism supplies most of the C1 units and competes with secondary metabolism for their use. This competition is potentially severe because secondary products such as lignin, alkaloids, and glycine betaine (GlyBet) require massive amounts of C1 units. Towards the goal of understanding how C1 metabolism is regulated at the metabolic and gene levels so as to successfully engineer C1 supply to match demand, we have: (1) cloned complete suites of C1 genes from maize and tobacco, and incorporated them into DNA arrays; (2) prepared antisense constructs and mutants engineered with alterations in C1 unit supply and demand; and (3) have quantified the impacts of these alterations on gene expression (using DNA arrays), and on metabolic fluxes (by combining isotope labeling, MS, NMR and computer modeling). Metabolic flux analysis and modeling in tobacco engineered for GlyBet synthesis by expressing choline oxidizing enzymes in either the chloroplast or cytosol, has shown that the choline biosynthesis network is rigid, and tends to resist large changes in C1 demand. A major constraint on engineering enhanced flux to GlyBet in tobacco is a low capacity of choline transport across the chloroplast envelope. Maize and sorghum mutants defective in GlyBet synthesis show greatly reduced flux of C1 units into choline in comparison to GlyBet-accumulating wildtypes, but this is not associated with altered expression of any of the C1 genes. Control of C1 flux to choline in tobacco, maize and sorghum appears to reside primarily at the level of N-methylation of phosphoethanolamine. A candidate signal for the control of this flux is the pool size of phosphocholine which down-regulates and feedback inhibits phosphoethanolamine N-methyltransferase. Methionine S-methyltransferase (MMT) catalyzes the synthesis of S-methylmethionine (SMM) from methionine (Met) and S-adenosylmethionine (AdoMet). SMM can be

  20. Engineering Plant One-Carbon Metabolism

    Energy Technology Data Exchange (ETDEWEB)

    David Rhodes

    2005-02-09

    Primary and secondary metabolism intersect in the one-carbon (C1) area. Primary metabolism supplies most of the C1 units and competes with secondary metabolism for their use. This competition is potentially severe because secondary products such as lignin, alkaloids, and glycine betaine (GlyBet) require massive amounts of C1 units. Towards the goal of understanding how C1 metabolism is regulated at the metabolic and gene levels so as to successfully engineer C1 supply to match demand, we have: (1) cloned complete suites of C1 genes from maize and tobacco, and incorporated them into DNA arrays; (2) prepared antisense constructs and mutants engineered with alterations in C1 unit supply and demand; and (3) have quantified the impacts of these alterations on gene expression (using DNA arrays), and on metabolic fluxes (by combining isotope labeling, MS, NMR and computer modeling). Metabolic flux analysis and modeling in tobacco engineered for GlyBet synthesis by expressing choline oxidizing enzymes in either the chloroplast or cytosol, has shown that the choline biosynthesis network is rigid, and tends to resist large changes in C1 demand. A major constraint on engineering enhanced flux to GlyBet in tobacco is a low capacity of choline transport across the chloroplast envelope. Maize and sorghum mutants defective in GlyBet synthesis show greatly reduced flux of C1 units into choline in comparison to GlyBet-accumulating wildtypes, but this is not associated with altered expression of any of the C1 genes. Control of C1 flux to choline in tobacco, maize and sorghum appears to reside primarily at the level of N-methylation of phosphoethanolamine. A candidate signal for the control of this flux is the pool size of phosphocholine which down-regulates and feedback inhibits phosphoethanolamine N-methyltransferase. Methionine S-methyltransferase (MMT) catalyzes the synthesis of S-methylmethionine (SMM) from methionine (Met) and S-adenosylmethionine (AdoMet). SMM can be

  1. Molecular Basis of Microbial One-Carbon Metabolism

    Energy Technology Data Exchange (ETDEWEB)

    None

    2002-07-12

    The Gordon Research Conference (GRC) on Molecular Basis of Microbial One-Carbon Metabolism was held at Connecticut College, New London, Connecticut. Emphasis was placed on current unpublished research and discussion of the future target areas in this field.

  2. One Carbon Metabolism, Fetal Growth and Long Term Consequences

    OpenAIRE

    2013-01-01

    One carbon metabolism, or methyl transfer, is critical for metabolism in all cells, is involved in the synthesis of purines, pyrimidines, in the methylation of numerous substrates, proteins, DNA and RNA, and in the expression of a number of genes. Serine is the primary endogenous methyl donor to the one carbon pool. Perturbations in methyl transfer due to nutrient and hormonal changes can have profound effect on cell function, growth and proliferation. It is postulated that at critical stages...

  3. Unveiling Microbial Carbon Cycling Processes in Key U.S. Soils using ''Omics''

    Energy Technology Data Exchange (ETDEWEB)

    Myrold, David D. [Oregon State Univ., Corvallis, OR (United States); Bottomely, Peter J. [Oregon State Univ., Corvallis, OR (United States); Jumpponen, Ari [Kansas State Univ., Manhattan, KS (United States); Rice, Charles W. [Kansas State Univ., Manhattan, KS (United States); Zeglin, Lydia H. [Kansas State Univ., Manhattan, KS (United States); David, Maude M. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Jansson, Janet K. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Prestat, Emmanuel [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Hettich, Robert L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2014-09-17

    biology approach, considering the complex soil microbial community as a functioning system and using state-of-the-art metatranscriptomic, metaproteomic, and metabolomic approaches. These omics tools were refined, applied to field experiments, and confirmed with controlled laboratory studies. Our experiments were designed to specifically identify microbial community members and processes that are instrumental players in processing of C in the prairie soils and how these processes are impacted by wetting and drying events. This project addresses a key ecosystem in the United States that current climate models predict will be subjected to dramatic changes in rainfall patterns as a result of global warming. Currently Mollisols, such as those of the tallgrass prairie, are thought to sequester more C than is released into the atmosphere, but it is not known what changes in rainfall patterns will have on future C fluxes. Through an analysis of the molecular response of the soil microbial community to shifts in precipitation cycles that are accompanied by phenologically driven changes in quality of plant C rhizodeposits, we gained deeper insight into how the metabolism of microbes has adapted to different precipitation regimes and the impact of this adaption on the fate of C deposited into soil. In doing so, we addressed key questions about the microbial cycling of C in soils that have been identified by the DOE.

  4. Carbon isotopic fractionation in heterotrophic microbial metabolism

    Science.gov (United States)

    Blair, N.; Leu, A.; Munoz, E.; Olsen, J.; Kwong, E.; Des Marais, D.

    1985-01-01

    Differences in the natural-abundance carbon stable isotopic compositions between products from aerobic cultures of Escherichia coli K-12 were measured. Respired CO2 was 3.4 percent depleted in C-13 relative to the glucose used as the carbon source, whereas the acetate was 12.3 percent enriched in C-13. The acetate C-13 enrichment was solely in the carboxyl group. Even though the total cellular carbon was only 0.6 percent depleted in C-13, intracellular components exhibited a significant isotopic heterogeneity. The protein and lipid fractions were -1.1 and -2.7 percent, respectively. Aspartic and glutamic acids were -1.6 and +2.7 percent, respectively, yet citrate was isotopically identical to the glucose. Probable sites of carbon isotopic fractionation include the enzyme, phosphotransacetylase, and the Krebs cycle.

  5. Central carbon metabolism in the progression of mammary carcinoma

    Science.gov (United States)

    Richardson, Adam D.; Yang, Chen; Osterman, Andrei

    2007-01-01

    There is a growing belief that the metabolic program of breast tumor cells could be a therapeutic target. Yet, without detailed information on central carbon metabolism in breast tumors it is impossible to know which metabolic pathways to target, and how their inhibition might influence different stages of breast tumor progression. Here we perform the first comprehensive profiling of central metabolism in the MCF10 model of mammary carcinoma, where the steps of breast tumor progression (transformation, tumorigenicity and metastasis) can all be examined in the context of the same genetic background. The metabolism of [U-13C]-glucose by a series of progressively more aggressive MCF10 cell lines was tracked by 2D NMR and mass spectrometry. From this analysis the flux of carbon through distinct metabolic reactions was quantified by isotopomer modeling. The results indicate widespread changes to central metabolism upon cellular transformation including increased carbon flux through the pentose phosphate pathway (PPP), the TCA cycle, as well as increased synthesis of glutamate, glutathione and fatty acids (including elongation and desaturation). The de novo synthesis of glycine increased upon transformation as well as at each subsequent step of breast tumor cell progression. Interestingly, the major metabolic shift in metastatic cells is a large increase in the de novo synthesis of proline. This work provides the first comprehensive view of changes to central metabolism as a result of breast tumor progression. Electronic supplementary material The online version of this article (doi:10.1007/s10549-007-9732-3) contains supplementary material, which is available to authorized users. PMID:17879159

  6. Games Uniforms Unveiled

    Institute of Scientific and Technical Information of China (English)

    Linda

    2008-01-01

    The uniforms for Beijing Olympics’ workers, technical staff and volunteers have been unveiled to mark the 200-day countdown to the Games. The uniforms feature the key element of the clouds of promise and will be in three colors:red for Beijing Olympic Games Committee staff, blue

  7. Intracellular Acetyl Unit Transport in Fungal Carbon Metabolism

    NARCIS (Netherlands)

    Strijbis, K.; Distel, B.

    2010-01-01

    Acetyl coenzyme A (acetyl-CoA) is a central metabolite in carbon and energy metabolism. Because of its amphiphilic nature and bulkiness, acetyl-CoA cannot readily traverse biological membranes. In fungi, two systems for acetyl unit transport have been identified: a shuttle dependent on the carrier c

  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 in...

  9. Computer Modeling of Carbon Metabolism Enables Biofuel Engineering (Fact Sheet)

    Energy Technology Data Exchange (ETDEWEB)

    2011-09-01

    In an effort to reduce the cost of biofuels, the National Renewable Energy Laboratory (NREL) has merged biochemistry with modern computing and mathematics. The result is a model of carbon metabolism that will help researchers understand and engineer the process of photosynthesis for optimal biofuel production.

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

    DEFF Research Database (Denmark)

    Jensen, Peter Ruhdal; Michelsen, Ole

    1992-01-01

    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...

  11. Unified Index Unveiled

    Institute of Scientific and Technical Information of China (English)

    RENWEI

    2005-01-01

    China unveiled a unified stock index to track both markets in Shanghai and Shenzhen in April, a move likely to open a floodgate for more trading derivatives such as index futures. The new index, with 300 component companies traded on Shanghai and Shenzhen stock exchanges, will be the first of its kind on the mainland. The index members will be the largest 300 stocks - 180 from Shanghai and 120 from Shenzhen - in terms of market capitalization,

  12. The Central Carbon and Energy Metabolism of Marine Diatoms

    Directory of Open Access Journals (Sweden)

    Adriano Nunes-Nesi

    2013-05-01

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

  13. Methionine, homocysteine, one carbon metabolism and fetal growth.

    Science.gov (United States)

    Kalhan, Satish C; Marczewski, Susan E

    2012-06-01

    Methionine and folate are the key components of one carbon metabolism, providing the methyl groups for numerous methyl transferase reactions via the ubiquitous methyl donor, s-adenosyl methionine. Methionine metabolism is responsive to nutrient intake, is regulated by several hormones and requires a number of vitamins (B12, pyridoxine, riboflavin) as co-factors. The critical relationship between perturbations in the mother's methionine metabolism and its impact on fetal growth and development is now becoming evident. The relation of folate intake to fetal teratogenesis has been known for some time. Studies in human pregnancy show a continuous decrease in plasma homocysteine, and an increase in plasma choline concentrations with advancing gestation. A higher rate of transsulfuration of methionine in early gestation and of transmethylation in the 3rd trimester was seen in healthy pregnant women. How these processes are impacted by nutritional, hormonal and other influences in human pregnancy and their effect on fetal growth has not been examined. Isocaloric protein restriction in pregnant rats, resulted in fetal growth restriction and metabolic reprogramming. Isocaloric protein restriction in the non-pregnant rat, resulted in differential expression of a number of genes in the liver, a 50% increase in whole body serine biosynthesis and high rate of transmethylation, suggesting high methylation demands. These responses were associated with a significant decrease in intracellular taurine levels in the liver suggesting a role of cellular osmolarity in the observed metabolic responses. These unique changes in methionine and one carbon metabolism in response to physiological, nutritional and hormonal influences make these processes critical for cellular and organ function and growth.

  14. Lord Shiva Statue Unveiled

    CERN Multimedia

    2004-01-01

    On 18 June, CERN unveiled an unusual new landmark, a 2m tall statue of the Indian deity Lord Shiva. The Director-General and Dr. Kakodkar watch as Mr.Chandrasekhar signs the Guest Book. The statue is a gift from India, celebrating CERN's long association with India which started in the 1960's and continues strongly today. It was unveiled by the Director General, Dr Robert Aymar, His Excellency Mr K. M. Chandrasekhar, Ambassador (WTO-Geneva) and Dr Anil Kakodkar, Chairman of the Atomic Energy Commission and Secretary, Dept of Atomic Energy, India. In the Hindu religion, this form of the dancing Lord Shiva is known as the Nataraj and symbolises Shakti, or life force. As a plaque alongside the statue explains, the belief is that Lord Shiva danced the Universe into existence, motivates it, and will eventually extinguish it. Carl Sagan drew the metaphor between the cosmic dance of the Nataraj and the modern study of the 'cosmic dance' of subatomic particles. The statue was made in India. The original sculpture was...

  15. Correlations between carbon metabolism and virulence in bacteria.

    Science.gov (United States)

    Poncet, Sandrine; Milohanic, Eliane; Mazé, Alain; Nait Abdallah, Jamila; Aké, Francine; Larribe, Mireille; Deghmane, Ala-Eddine; Taha, Muhamed-Kheir; Dozot, Marie; De Bolle, Xavier; Letesson, Jean Jacques; Deutscher, Josef

    2009-01-01

    Bacteria have developed several mechanisms which allow the preferred utilization of the most efficiently metabolizable carbohydrates when these organisms are exposed to a mixture of carbon sources. Interestingly, the same or similar mechanisms are used by some pathogens to control various steps of their infection process. The efficient metabolism of a carbon source might serve as signal for proper fitness. Alternatively, the presence of a specific carbon source might indicate to bacterial cells that they thrive in infection-related organs, tissues or cells and that specific virulence genes should be turned on or switched off. Frequently, virulence gene regulators are affected by changes in carbon source availability. For example, expression of the gene encoding the Streptococcus pyogenes virulence regulator Mga is controlled by the classical carbon catabolite repression (CCR) mechanism operative in Firmicutes. The activity of PrfA, the major virulence regulator in Listeria monocytogenes, seems to be controlled by the phosphorylation state of phosphotransferase system(PTS) components. In Vibrio cholerae synthesis of HapR, which regulates the expression of genes required for motility, is controlled via the Crp/cAMP CCR mechanism, whereas synthesis of Salmonella enterica HilE, which represses genes in a pathogenicity island, is regulated by the carbohydrate-responsive, PTS-controlled Mlc.

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

    Directory of Open Access Journals (Sweden)

    Sayed-Rzgar Hosseini

    2015-08-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-08-19

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

  18. Carbon monoxide expedites metabolic exhaustion to inhibit tumor growth.

    Science.gov (United States)

    Wegiel, Barbara; Gallo, David; Csizmadia, Eva; Harris, Clair; Belcher, John; Vercellotti, Gregory M; Penacho, Nuno; Seth, Pankaj; Sukhatme, Vikas; Ahmed, Asif; Pandolfi, Pier Paolo; Helczynski, Leszek; Bjartell, Anders; Persson, Jenny Liao; Otterbein, Leo E

    2013-12-01

    One classical feature of cancer cells is their metabolic acquisition of a highly glycolytic phenotype. Carbon monoxide (CO), one of the products of the cytoprotective molecule heme oxygenase-1 (HO-1) in cancer cells, has been implicated in carcinogenesis and therapeutic resistance. However, the functional contributions of CO and HO-1 to these processes are poorly defined. In human prostate cancers, we found that HO-1 was nuclear localized in malignant cells, with low enzymatic activity in moderately differentiated tumors correlating with relatively worse clinical outcomes. Exposure to CO sensitized prostate cancer cells but not normal cells to chemotherapy, with growth arrest and apoptosis induced in vivo in part through mitotic catastrophe. CO targeted mitochondria activity in cancer cells as evidenced by higher oxygen consumption, free radical generation, and mitochondrial collapse. Collectively, our findings indicated that CO transiently induces an anti-Warburg effect by rapidly fueling cancer cell bioenergetics, ultimately resulting in metabolic exhaustion.

  19. Carbohydrate metabolism and carbon fixation in Roseobacter denitrificans OCh114.

    Directory of Open Access Journals (Sweden)

    Kuo-Hsiang Tang

    Full Text Available The Roseobacter clade of aerobic marine proteobacteria, which compose 10-25% of the total marine bacterial community, has been reported to fix CO(2, although it has not been determined what pathway is involved. In this study, we report the first metabolic studies on carbohydrate utilization, CO(2 assimilation, and amino acid biosynthesis in the phototrophic Roseobacter clade bacterium Roseobacter denitrificans OCh114. We develop a new minimal medium containing defined carbon source(s, in which the requirements of yeast extract reported previously for the growth of R. denitrificans can be replaced by vitamin B(12 (cyanocobalamin. Tracer experiments were carried out in R. denitrificans grown in a newly developed minimal medium containing isotopically labeled pyruvate, glucose or bicarbonate as a single carbon source or in combination. Through measurements of (13C-isotopomer labeling patterns in protein-derived amino acids, gene expression profiles, and enzymatic activity assays, we report that: (1 R. denitrificans uses the anaplerotic pathways mainly via the malic enzyme to fix 10-15% of protein carbon from CO(2; (2 R. denitrificans employs the Entner-Doudoroff (ED pathway for carbohydrate metabolism and the non-oxidative pentose phosphate pathway for the biosynthesis of histidine, ATP, and coenzymes; (3 the Embden-Meyerhof-Parnas (EMP, glycolysis pathway is not active and the enzymatic activity of 6-phosphofructokinase (PFK cannot be detected in R. denitrificans; and (4 isoleucine can be synthesized from both threonine-dependent (20% total flux and citramalate-dependent (80% total flux pathways using pyruvate as the sole carbon source.

  20. New insights into Escherichia coli metabolism: carbon scavenging, acetate metabolism and carbon recycling responses during growth on glycerol

    Directory of Open Access Journals (Sweden)

    Martínez-Gómez Karla

    2012-07-01

    Full Text Available Abstract Background Glycerol has enhanced its biotechnological importance since it is a byproduct of biodiesel synthesis. A study of Escherichia coli physiology during growth on glycerol was performed combining transcriptional-proteomic analysis as well as kinetic and stoichiometric evaluations in the strain JM101 and certain derivatives with important inactivated genes. Results Transcriptional and proteomic analysis of metabolic central genes of strain JM101 growing on glycerol, revealed important changes not only in the synthesis of MglB, LamB and MalE proteins, but also in the overexpression of carbon scavenging genes: lamB, malE, mglB, mglC, galP and glk and some members of the RpoS regulon (pfkA, pfkB, fbaA, fbaB, pgi, poxB, acs, actP and acnA. Inactivation of rpoS had an important effect on stoichiometric parameters and growth adaptation on glycerol. The observed overexpression of poxB, pta, acs genes, glyoxylate shunt genes (aceA, aceB, glcB and glcC and actP, suggested a possible carbon flux deviation into the PoxB, Acs and glyoxylate shunt. In this scenario acetate synthesized from pyruvate with PoxB was apparently reutilized via Acs and the glyoxylate shunt enzymes. In agreement, no acetate was detected when growing on glycerol, this strain was also capable of glycerol and acetate coutilization when growing in mineral media and derivatives carrying inactivated poxB or pckA genes, accumulated acetate. Tryptophanase A (TnaA was synthesized at high levels and indole was produced by this enzyme, in strain JM101 growing on glycerol. Additionally, in the isogenic derivative with the inactivated tnaA gene, no indole was detected and acetate and lactate were accumulated. A high efficiency aromatic compounds production capability was detected in JM101 carrying pJLBaroGfbrtktA, when growing on glycerol, as compared to glucose. Conclusions The overexpression of several carbon scavenging, acetate metabolism genes and the absence of acetate

  1. 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.

  2. [Carbon sources metabolic characteristics of airborne microbial communities in constructed wetlands].

    Science.gov (United States)

    Song, Zhi-Wen; Wang, Lin; Xu, Ai-Ling; Wu, Deng-Deng; Xia, Yan

    2015-02-01

    Using BIOLOG-GN plates, this article describes the carbon sources metabolic characteristics of airborne microbial communities in a free surface-flow constructed wetland in different seasons and clarify the correlation between airborne microbial metabolic functions and environmental factors. The average well color development (AWCD), carbon metabolic profiles and McIntosh values of airborne microbial communities in different seasons were quite different. Analysis of the variations showed that AWCD in spring and summer differed significantly from that in autumn and winter (P metabolic community, carbohydrates metabolic community, polymers metabolic community and carboxylic acids metabolic community respectively. Principal component analysis showed that the carbon metabolic characteristics of airborne microbial community in autumn were similar to those in winter but different from those in spring and summer. The characteristics of carbon metabolism revealed differences between summer and spring, autumn, or winter. These differences were mainly caused by amines or amides while the differences between spring and autumn or winter were mainly caused by carboxylic acids. Environmental factors, including changes in wind speed, temperature, and humidity acted to influence the carbon sources metabolic properties of airborne microbial community. The dominant environmental factors that acted to influence the carbon sources metabolic properties of airborne microbial community varied between different seasons.

  3. Influence of carbon and nitrogen sources on growth, nitrogenase activity, and carbon metabolism of Gluconacetobacter diazotrophicus.

    Science.gov (United States)

    Tejera, Noel A; Ortega, Eduardo; Rodés, Rosa; Lluch, Carmen

    2004-09-01

    The effects of different carbon and nitrogen sources on the growth, nitrogenase activity, and carbon metabolism of Gluconacetobacter diazotrophicus were investigated. The amino acids asparagine, aspartic acid, and glutamic acid affected microbial growth and nitrogenase activity. Several enzymatic activities involved in the tricarboxylic acid cycle were affected by the carbon source used. In addition, glucose and gluconate significantly increased the oxygen consumption (respiration rate) of whole cells of G. diazotrophicus grown under aerobic conditions. Enzymes responsible for direct oxidation of glucose and gluconate were especially active in cells grown with sucrose and gluconate. The presence of amino acids in the apoplastic and symplastic sap of sugarcane stems suggests that these compounds might be of importance in the regulation of growth and nitrogenase activity during the symbiotic association. The information obtained from the plant-bacterium association together with the results of other biochemical studies could contribute to the development of biotechnological applications of G. diazotrophicus.

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

    Science.gov (United States)

    2012-10-22

    glycolysis and the  citric   acid   cycle  and monitored the effect on RpoS degradation  in vivo. Nutrient  upshifts trigger RpoS degradation  independently...Yuan  et  al.,  2009). We  successfully combined the simplified nitrogen assimilation model with simplified models of glycolysis and the  TCA  cycle  to...TCA  cycle  (where carbon and nitrogen metabolism directly intersect). Our  investigation  yielded  significant  advances  in  the  understanding  of  E

  5. Export and Metabolism of Carbon in Urban Watersheds: Climate Implications

    Science.gov (United States)

    Smith, R. M.; Kaushal, S.

    2014-12-01

    Rivers export and transform globally-significant quantities of carbon from watersheds to coastal ecosystems. Urbanization and climate change influence these fluxes by altering the hydrologic regime, water temperature, and anthropogenic sources of organic matter. Here, we quantify export and metabolism of carbon in highly urbanized, coastal watersheds, and evaluate the importance of physical drivers linked to climate and land use. Using a combination of discrete-samples, continuous water quality sensors, lab experiments, and modeling, we quantified rates of DOC, DIC, and CO2 export as well as changes in DOC quality and in-stream metabolism in four highly developed watersheds of the Chesapeake Bay over three years. Annual DOC and DIC exports from the four watersheds varied from 9 to 23 and 19 to 59 Kg ha-1yr-1 respectively. The range of daily CO2 concentrations was 0.01 to 2.6mg L-1, equivalent to between 0.37 and 53% of daily DOC export across all streams and dates. All sites were net-heterotrophic for the majority of the year (NEP0) during spring and early summer. There was a significant (P<0.05) relationship between gross primary production and ecosystem respiration, suggesting that autotrophic respiration is an important fraction of ER, and labile algal biomass may influence oxygen demand downstream. Our results suggest that urban watersheds can export significant amounts of DOC, DIC, and CO2 to coastal zones. The influence of urbanization on coastal water quality and greenhouse gases may be exacerbated by climate change as temperatures and storm frequency continue to rise.

  6. No Association of SNPs in One-Carbon Metabolism Genes with Prostate Cancer Risk

    OpenAIRE

    Stevens, Victoria L.; Rodriguez, Carmen; Sun, Juzhong; Talbot, Jeffrey T.; Thun, Michael J.; Calle, Eugenia E.

    2008-01-01

    One-carbon metabolism mediates the inter-conversion of folates for the synthesis of precursors used in DNA synthesis, repair and methylation. Inadequate folate nutrition or compromised metabolism can disrupt these processes and facilitate carcinogenesis. In this study, we investigated associations of 39 candidate SNPs in nine one-carbon metabolism genes with risk of prostate cancer using 1,144 cases and 1,144 controls from the Cancer Prevention Study-II Nutrition Cohort. None of these SNPs we...

  7. One carbon metabolism in anaerobic bacteria: Regulation of carbon and electron flow during organic acid production

    Energy Technology Data Exchange (ETDEWEB)

    Zeikus, J.G.; Jain, M.

    1993-12-31

    The project deals with understanding the fundamental biochemical mechanisms that physiologically control and regulate carbon and electron flow in anaerobic chemosynthetic bacteria that couple metabolism of single carbon compounds and hydrogen to the production of organic acids (formic, acetic, butyric, and succinic) or methane. The authors compare the regulation of carbon dioxide and hydrogen metabolism by fermentation, enzyme, and electron carrier analysis using Butyribacterium methylotrophicum, Anaeroblospirillum succiniciproducens, Methanosarcina barkeri, and a newly isolated tri-culture composed of a syntrophic butyrate degrader strain IB, Methanosarcina mazei and Methanobacterium formicicum as model systems. To understand the regulation of hydrogen metabolism during butyrate production or acetate degradation, hydrogenase activity in B. methylotrophicum or M. barkeri is measured in relation to growth substrate and pH; hydrogenase is purified and characterized to investigate number of hydrogenases; their localization and functions; and, their sequences are determined. To understand the mechanism for catabolic CO{sub 2} fixation to succinate the PEP carboxykinase enzyme and gene of A. succiniciproducens are purified and characterized. Genetically engineered strains of Escherichia coli containing the phosphoenolpyruvate (PEP) carboxykinase gene are examined for their ability to produce succinate in high yield. To understand the mechanism of fatty acid degradation by syntrophic acetogens during mixed culture methanogenesis formate and hydrogen production are characterized by radio tracer studies. It is intended that these studies provide strategies to improve anaerobic fermentations used for the production of organic acids or methane and, new basic understanding on catabolic CO{sub 2} fixation mechanisms and on the function of hydrogenase in anaerobic bacteria.

  8. One carbon metabolism in pregnancy: Impact on maternal, fetal and neonatal health.

    Science.gov (United States)

    Kalhan, Satish C

    2016-11-01

    One carbon metabolism or methyl transfer, a crucial component of metabolism in all cells and tissues, supports the critical function of synthesis of purines, thymidylate and methylation via multiple methyl transferases driven by the ubiquitous methyl donor s-adenosylmethionine. Serine is the primary methyl donor to the one carbon pool. Intracellular folates and methionine metabolism are the critical components of one carbon transfer. Methionine metabolism requires vitamin B12, B6 as cofactors and is modulated by endocrine signals and is responsive to nutrient intake. Perturbations in one carbon transfer can have profound effects on cell proliferation, growth and function. Epidemiological studies in humans and experimental model have established a strong relationship between impaired fetal growth and the immediate and long term consequences to the health of the offspring. It is speculated that during development, maternal environmental and nutrient influences by their effects on one carbon transfer can impact the health of the mother, impair growth and reprogram metabolism of the fetus, and cause long term morbidity in the offspring. The potential for such effects is underscored by the unique responses in methionine metabolism in the human mother during pregnancy, the absence of transsulfuration activity in the fetus, ontogeny of methionine metabolism in the placenta and the unique metabolism of serine and glycine in the fetus. Dietary protein restriction in animals and marginal protein intake in humans causes characteristic changes in one carbon metabolism. The impact of perturbations in one carbon metabolism on the health of the mother during pregnancy, on fetal growth and the neonate are discussed and their possible mechanism explored.

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

    Science.gov (United States)

    Luciano-Mateo, Fedra; Hernández-Aguilera, Anna; Cabre, Noemi; Camps, Jordi; Fernández-Arroyo, Salvador; Lopez-Miranda, Jose; Menendez, Javier A.; Joven, Jorge

    2017-01-01

    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. PMID:28208582

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

    Directory of Open Access Journals (Sweden)

    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.

  11. Studies on carbon metabolism in wild type and mutants of Aspergillus nidulans

    NARCIS (Netherlands)

    Uitzetter, J.H.A.A.

    1982-01-01

    This thesis deals with carbon metabolism in the lower eukaryote Aspergillus nidulans. This fungus is an attractive organism as a model to study genetics in relation to metabolism in lower eukaryotes.In chapter I the present state of affairs in this field is summarized for A. nidulans and some of the

  12. Effect of sulfonamides as carbonic anhydrase VA and VB inhibitors on mitochondrial metabolic energy conversion.

    Science.gov (United States)

    Arechederra, Robert L; Waheed, Abdul; Sly, William S; Supuran, Claudiu T; Minteer, Shelley D

    2013-03-15

    Obesity is quickly becoming an increasing problem in the developed world. One of the major fundamental causes of obesity and diabetes is mitochondria dysfunction due to faulty metabolic pathways which alter the metabolic substrate flux resulting in the development of these diseases. This paper examines the role of mitochondrial carbonic anhydrase (CA) isozymes in the metabolism of pyruvate, acetate, and succinate when specific isozyme inhibitors are present. Using a sensitive electrochemical approach of wired mitochondria to analytically measure metabolic energy conversion, we determine the resulting metabolic difference after addition of an inhibitory compound. We found that certain sulfonamide analogues displayed broad spectrum inhibition of metabolism, where others only had significant effect on some metabolic pathways. Pyruvate metabolism always displayed the most dramatically affected metabolism by the sulfonamides followed by fatty acid metabolism, and then finally succinate metabolism. This allows for the possibility of using designed sulfonamide analogues to target specific mitochondrial CA isozymes in order to subtly shift metabolism and glucogenesis flux to treat obesity and diabetes.

  13. Disequilibrium δ18O values in microbial carbonates as a tracer of metabolic production of dissolved inorganic carbon

    Science.gov (United States)

    Thaler, Caroline; Millo, Christian; Ader, Magali; Chaduteau, Carine; Guyot, François; Ménez, Bénédicte

    2017-02-01

    Carbon and oxygen stable isotope compositions of carbonates are widely used to retrieve paleoenvironmental information. However, bias may exist in such reconstructions as carbonate precipitation is often associated with biological activity. Several skeleton-forming eukaryotes have been shown to precipitate carbonates with significant offsets from isotopic equilibrium with water. Although poorly understood, the origin of these biologically-induced isotopic shifts in biogenic carbonates, commonly referred to as "vital effects", could be related to metabolic effects that may not be restricted to mineralizing eukaryotes. The aim of our study was to determine whether microbially-mediated carbonate precipitation can also produce offsets from equilibrium for oxygen isotopes. We present here δ18O values of calcium carbonates formed by the activity of Sporosarcina pasteurii, a carbonatogenic bacterium whose ureolytic activity produces ammonia (thus increasing pH) and dissolved inorganic carbon (DIC) that precipitates as solid carbonates in the presence of Ca2+. We show that the 1000 lnαCaCO3-H2O values for these bacterially-precipitated carbonates are up to 24.7‰ smaller than those expected for precipitation at isotopic equilibrium. A similar experiment run in the presence of carbonic anhydrase (an enzyme able to accelerate oxygen isotope equilibration between DIC and water) resulted in δ18O values of microbial carbonates in line with values expected at isotopic equilibrium with water. These results demonstrate for the first time that bacteria can induce calcium carbonate precipitation in strong oxygen isotope disequilibrium with water, similarly to what is observed for eukaryotes. This disequilibrium effect can be unambiguously ascribed to oxygen isotope disequilibrium between DIC and water inherited from the oxygen isotope composition of the ureolytically produced CO2, probably combined with a kinetic isotope effect during CO2 hydration/hydroxylation. The fact that

  14. Microbial heterotrophic metabolic rates constrain the microbial carbon pump

    Digital Repository Service at National Institute of Oceanography (India)

    Robinson, C; Ramaiah, N.

    addition incubations are poised to discern the complex interactions between metabolic rate, community structure, and organic and inorganic nutrient availability. In a changing global environment, it is important to understand how increasing sea surface...

  15. Integration of Carbon, Nitrogen, and Oxygen Metabolism in Escherichia coli--Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Rabinowitz, Joshua D; Wingreen, Ned s; Rabitz, Herschel A; Xu, Yifan

    2012-10-22

    A key challenge for living systems is balancing utilization of multiple elemental nutrients, such as carbon, nitrogen, and oxygen, whose availability is subject to environmental fluctuations. As growth can be limited by the scarcity of any one nutrient, the rate at which each nutrient is assimilated must be sensitive not only to its own availability, but also to that of other nutrients. Remarkably, across diverse nutrient conditions, E. coli grows nearly optimally, balancing effectively the conversion of carbon into energy versus biomass. To investigate the link between the metabolism of different nutrients, we quantified metabolic responses to nutrient perturbations using LC-MS based metabolomics and built differential equation models that bridge multiple nutrient systems. We discovered that the carbonaceous substrate of nitrogen assimilation, -ketoglutarate, directly inhibits glucose uptake and that the upstream glycolytic metabolite, fructose-1,6-bisphosphate, ultrasensitively regulates anaplerosis to allow rapid adaptation to changing carbon availability. We also showed that NADH controls the metabolic response to changing oxygen levels. Our findings support a general mechanism for nutrient integration: limitation for a nutrient other than carbon leads to build-up of the most closely related product of carbon metabolism, which in turn feedback inhibits further carbon uptake.

  16. Carbon Metabolism, Uptake Kinetics, and Export: how Watershed Form Influences Carbon Mobilization and In-Stream Transformations in Headwater Catchments

    Science.gov (United States)

    Seybold, E. C.; McGlynn, B. L.

    2014-12-01

    Previous research has demonstrated the highly dynamic nature of hydrologic connectivity, and the vertical and spatial expansion of the active watershed area during wet periods. While activation of variable DOM and solute sources during expansion and contraction periods has been well documented in a number of systems, changes in nutrient loading to streams have rarely been linked explicitly to in-stream function. To this end, we investigated the linkages between terrestrial mobilization of DOC and DIC, in-stream biogeochemical cycling, and downstream transport across scales in two geomorphically contrasting watersheds located in Tenderfoot Creek Experimental Forest, Montana. We deployed a network of in-situ high frequency sensors with a focus on CO2, dissolved oxygen, fluorescent DOM, nitrate, and a suite of supporting chemical constituents every 30 minutes beginning with the onset of snowmelt and through summer baseflow recession. Our results suggest that DOM and DIC fluxes, as well as ecosystem processes such as metabolism, were coupled to watershed scale carbon accumulation and mobilization. In both watersheds, metabolism tracked the temporal trends of DOM loading from the terrestrial landscape, indicating that the streams are actively transforming allochthonous organic materials during transport. Headwater stream reaches in the watershed with more hydrologically connected riparian source areas exhibited elevated metabolism, carbon uptake, and carbon export as compared to streams in the watershed with less riparian connectivity, suggesting that the degree of riparian connectivity may explain spatial variation in metabolism and in-stream carbon cycling within and across stream networks. Ultimately, this study highlights the tight coupling between terrestrial uplands and in-stream ecosystem processes in headwater catchments, and identifies spatio-temporal variation in hydrologic connectivity as a key driver of in-stream metabolic variation. We posit that the

  17. Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Ülgen Kutlu Ö

    2007-03-01

    Full Text Available Abstract Background Control effective flux (CEF of a reaction is the weighted sum of all fluxes through that reaction, derived from elementary flux modes (EFM of a metabolic network. Change in CEFs under different environmental conditions has earlier been proven to be correlated with the corresponding changes in the transcriptome. Here we use this to investigate the degree of transcriptional regulation of fluxes in the metabolism of Saccharomyces cerevisiae. We do this by quantifying correlations between changes in CEFs and changes in transcript levels for shifts in carbon source, i.e. between the fermentative carbon source glucose and nonfermentative carbon sources like ethanol, acetate, and lactate. The CEF analysis is based on a simple stoichiometric model that includes reactions of the central carbon metabolism and the amino acid metabolism. Results The effect of the carbon shift on the metabolic fluxes was investigated for both batch and chemostat cultures. For growth on glucose in batch (respiro-fermentative cultures, EFMs with no by-product formation were removed from the analysis of the CEFs, whereas those including any by-products (ethanol, glycerol, acetate, succinate were omitted in the analysis of growth on glucose in chemostat (respiratory cultures. This resulted in improved correlations between CEF changes and transcript levels. A regression correlation coefficient of 0.60 was obtained between CEF changes and gene expression changes in the central carbon metabolism for the analysis of 5 different perturbations. Out of 45 data points there were no more than 6 data points deviating from the correlation. Additionally, up- or down-regulation of at least 75% of the genes were in qualitative agreement with the CEF changes for all perturbations studied. Conclusion The analysis indicates that changes in carbon source are associated with a high degree of hierarchical regulation of metabolic fluxes in the central carbon metabolism as the

  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. Network environ perspective for urban metabolism and carbon emissions: a case study of Vienna, Austria.

    Science.gov (United States)

    Chen, Shaoqing; Chen, Bin

    2012-04-17

    Cities are considered major contributors to global warming, where carbon emissions are highly embedded in the overall urban metabolism. To examine urban metabolic processes and emission trajectories we developed a carbon flux model based on Network Environ Analysis (NEA). The mutual interactions and control situation within the urban ecosystem of Vienna were examined, and the system-level properties of the city's carbon metabolism were assessed. Regulatory strategies to minimize carbon emissions were identified through the tracking of the possible pathways that affect these emission trajectories. Our findings suggest that indirect flows have a strong bearing on the mutual and control relationships between urban sectors. The metabolism of a city is considered self-mutualistic and sustainable only when the local and distal environments are embraced. Energy production and construction were found to be two factors with a major impact on carbon emissions, and whose regulation is only effective via ad-hoc pathways. In comparison with the original life-cycle tracking, the application of NEA was better at revealing details from a mechanistic aspect, which is crucial for informed sustainable urban management.

  20. Regulation of secondary metabolism by the carbon-nitrogen status in tobacco: nitrate inhibits large sectors of phenylpropanoid metabolism.

    Science.gov (United States)

    Fritz, Christina; Palacios-Rojas, Natalia; Feil, Regina; Stitt, Mark

    2006-05-01

    Interactions between nitrogen and carbon metabolism modulate many aspects of the metabolism, physiology and development of plants. This paper investigates the contribution of nitrate and nitrogen metabolism to the regulation of phenylpropanoid and nicotine synthesis. Wild-type tobacco was grown on 12 or 0.2 mm nitrate and compared with a nitrate reductase-deficient mutant [Nia30(145)] growing on 12 mm nitrate. Nitrate-deficient wild-type plants accumulate high levels of a range of phenylpropanoids including chlorogenic acid, contain high levels of rutin, are highly lignified, but contain less nicotine than nitrogen-replete wild-type tobacco. Nia30(145) resembles nitrate-deficient wild-type plants with respect to the levels of amino acids, but accumulates large amounts of nitrate. The levels of phenylpropanoids, rutin and lignin resemble those in nitrogen-replete wild-type plants, whereas the level of nicotine resembles that in nitrate-deficient wild-type plants. Expression arrays and real time RT-PCR revealed that a set of genes required for phenylpropanoid metabolism including PAL, 4CL and HQT are induced in nitrogen-deficient wild-type plants but not in Nia30(145). It is concluded that nitrogen deficiency leads to a marked shift from the nitrogen-containing alkaloid nicotine to carbon-rich phenylpropanoids. The stimulation of phenylpropanoid metabolism is triggered by changes of nitrate, rather than downstream nitrogen metabolites, and is mediated by induction of a set of enzymes in the early steps of the phenylpropanoid biosynthetic pathway.

  1. Targeting One-Carbon Metabolism in Breast Cancer

    Science.gov (United States)

    2014-04-01

    gene and association studies with diabetes and diabetic nephropathy . Mol Genet Metab 82, 321–328. Elenbaas, B. (2001). Human breast cancer cells... Diabetic Nephropathy , and Increased GFPT2 mRNA Levels. Journal of Clinical Endocrinology & Metabolism 89, 748–755. 48 Zhang, W.C., Shyh-Chang, N...Twist (HMLE-Twist-ER) following treatment with hydroxytamoxifen (OHT) (Mani et al., 2008; Taube et al., 2010). Over a 15-day treatment with OHT, the

  2. Oxygen and carbon metabolism of Zostera muelleri across a depth gradient - Implications for resilience and blue carbon

    Science.gov (United States)

    Ferguson, Angus J. P.; Gruber, Renee; Potts, Jaimie; Wright, Aaron; Welsh, David T.; Scanes, Peter

    2017-03-01

    There is growing interest in the role that seagrasses play as 'blue carbon' stores or sinks, and their potential to offset rising CO2 levels in the atmosphere. This study measured primary aspects of the carbon balance (biomass, community metabolism, dissolved organic carbon [DOC] fluxes, seston trapping) across the depth gradient in a Zostera muelleri meadow during the seasonal biomass minimum and maximum. Over the annual estimation, the meadow was neither a sink nor source of carbon, with inputs of seston (∼58% of total inputs) balanced by exports of wrack and DOC. The carbon sink represented by wrack export depends on the nature of the environment where the wrack accumulates; if it reaches subtidal sediments it will largely be remineralised over the annual cycle, whereas between 14 and 26% of the wrack may be preserved if the material is exported to terrestrial environments. The fate of DOC exuded by seagrasses is unknown due to a lack of knowledge about its composition and lability; however, a number of lines of evidence suggest that a large fraction of DOC is mineralised. The net community metabolism (NCM) of the meadow was balanced, indicating that photosynthetic O2 production balanced community respiration and/or the reoxidation of reduced compounds (sulphur and iron) in the rhizosphere. We suggest that a balanced NCM may be the preferred state for Zostera spp. and may limit their occurrence in environments where plants cannot balance the respiratory demand exerted by seston inputs. There was a close coupling between metabolism and biomass, which in turn is forced by antecedent light over the preceding 120 days (the time integration window for antecedent light that best predicted biomass). Increased metabolism with depth and seasonal variation in light is accompanied by a decrease in the above ground:below ground biomass ratio (AGB:BGB). This trend is suggested to be a morphological adaptation that balances the competing requirements of maintaining a

  3. 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, sulfur, phosphorous, an

  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 pre

  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 pre

  6. 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

    -P and glucose-C alone or in combination (0.01 and 0.3 mg L(-1), respectively) was added to 1.0 mu m filtered lake water and incubated in darkness at 20 degrees C. Additions of glucose (C) and phosphorus (P) alone did not lead to changes in the rates of bacterial metabolic processes, whereas bacterial...... respiration and bacterial production responded positively to C + P enrichment for most of the lakes sampled. Bacterial growth efficiency showed a wide range (2.5-28.7%) and low mean value (12%). These variations were not correlated with the DOC concentration. Our results show that heterotrophic bacterial...

  7. Role of inorganic carbon in lactic acid bacteria metabolism

    OpenAIRE

    Arsène-Ploetze, Florence; Bringel, Françoise

    2004-01-01

    International audience; Capnophiles are bacteria stimulated by bicarbonate and CO$_2$, the two major forms of inorganic carbon (IC) in physiological neutral liquids. Capnophiles are often pathogenic heterotrophs found in IC-rich ecological niches such as human cavities. Like capnophiles, the growth of lactic acid bacteria (LAB) such as Lactobacillus plantarum and Enterococcus faecalis is stimulated by IC. CO$_2$ or HCO$^{-}_3$ are substrates in carbamoyl phosphate (CP) synthesis and other car...

  8. Molecular and Metabolic Mechanisms of Carbon Sequestration in Marine Thrombolites

    Science.gov (United States)

    Mobberley, Jennifer

    2013-01-01

    The overall goal of my dissertation project has been to examine the molecular processes underlying carbon sequestration in lithifying microbial ecosystems, known as thrombolitic mats, and assess their feasibility for use in bioregenerative life support systems. The results of my research and education efforts funded by the Graduate Student Researchers Program can be summarized in four peer-reviewed research publication, one educational publication, two papers in preparation, and six research presentations at local and national science meetings (see below for specific details).

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

    Directory of Open Access Journals (Sweden)

    Nobuyuki Okahashi

    2014-05-01

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

  10. Coevolution trumps pleiotropy: carbon assimilation traits are independent of metabolic network structure in budding yeast.

    Science.gov (United States)

    Opulente, Dana A; Morales, Christopher M; Carey, Lucas B; Rest, Joshua S

    2013-01-01

    Phenotypic traits may be gained and lost together because of pleiotropy, the involvement of common genes and networks, or because of simultaneous selection for multiple traits across environments (multiple-trait coevolution). However, the extent to which network pleiotropy versus environmental coevolution shapes shared responses has not been addressed. To test these alternatives, we took advantage of the fact that the genus Saccharomyces has variation in habitat usage and diversity in the carbon sources that a given strain can metabolize. We examined patterns of gain and loss in carbon utilization traits across 488 strains of Saccharomyces to investigate whether the structure of metabolic pathways or selection pressure from common environments may have caused carbon utilization traits to be gained and lost together. While most carbon sources were gained and lost independently of each other, we found four clusters that exhibit non-random patterns of gain and loss across strains. Contrary to the network pleiotropy hypothesis, we did not find that these patterns are explained by the structure of metabolic pathways or shared enzymes. Consistent with the hypothesis that common environments shape suites of phenotypes, we found that the environment a strain was isolated from partially predicts the carbon sources it can assimilate.

  11. Coevolution trumps pleiotropy: carbon assimilation traits are independent of metabolic network structure in budding yeast.

    Directory of Open Access Journals (Sweden)

    Dana A Opulente

    Full Text Available Phenotypic traits may be gained and lost together because of pleiotropy, the involvement of common genes and networks, or because of simultaneous selection for multiple traits across environments (multiple-trait coevolution. However, the extent to which network pleiotropy versus environmental coevolution shapes shared responses has not been addressed. To test these alternatives, we took advantage of the fact that the genus Saccharomyces has variation in habitat usage and diversity in the carbon sources that a given strain can metabolize. We examined patterns of gain and loss in carbon utilization traits across 488 strains of Saccharomyces to investigate whether the structure of metabolic pathways or selection pressure from common environments may have caused carbon utilization traits to be gained and lost together. While most carbon sources were gained and lost independently of each other, we found four clusters that exhibit non-random patterns of gain and loss across strains. Contrary to the network pleiotropy hypothesis, we did not find that these patterns are explained by the structure of metabolic pathways or shared enzymes. Consistent with the hypothesis that common environments shape suites of phenotypes, we found that the environment a strain was isolated from partially predicts the carbon sources it can assimilate.

  12. France: the programme of festivities is unveiled

    CERN Document Server

    2004-01-01

    The programme of events to be held in the local French area in honour of CERN's fiftieth anniversary was unveiled in the CMS hall on 26 April at a ceremony attended by many local authority representatives.

  13. Georges Charpak street sign unveiled

    CERN Multimedia

    Paola Catapano

    2011-01-01

    While it might not be the only French street named in honour of the late Georges Charpak, who passed away in September 2010 at the age of 87, the street chosen by the mayor of Saint-Genis-Pouilly is certainly the only one located directly opposite the CERN "campus". The road overlooks buildings on the CERN Meyrin site, where Georges Charpak spent most of his career as a physicist, conducting the research that won him the Nobel Prize in Physics in 1992.   From left to right: Sigurd Lettow, Dominique Charpak and the mayor of Saint-Genis-Pouilly. The unveiling took place on 17 October and was organised by the mayor of Saint-Genis-Pouilly. George Charpak’s wife, Dominique, and Sigurd Lettow, CERN Director of Administration and General Infrastructure, attended what was an intimate and touching ceremony. The mayor’s speech at the event praised Georges’ commitment to scientific education. The highlight of the event, however, was a witty and humorous ...

  14. Proteomic Analysis of One-carbon Metabolism-related Marker in Liver of Rat Offspring.

    Science.gov (United States)

    You, Young-Ah; Lee, Ji Hye; Kwon, Eun Jin; Yoo, Jae Young; Kwon, Woo-Sung; Pang, Myung-Geol; Kim, Young Ju

    2015-11-01

    Maternal food intake has a significant effect on the fetal environment, and an inadequate maternal diet may result in intrauterine growth restriction. Intrauterine growth restriction newborn rat pups nursed by normal diet-fed dams exhibited rapid catch-up growth, which plays a critical role in the risk for metabolic and cardiovascular disease in later life. Specifically, one-carbon metabolism in the liver plays a critical role in placental and fetal growth. Impaired functioning of one-carbon metabolism is associated with increased homocysteine levels. In this study, we applied a comprehensive proteomic approach to identify differential expression of proteins related to one-carbon metabolism in the livers of rat offspring as an effect of maternal food restriction during gestation. Data are available via ProteomeXchange with identifier PXD002578. We determined that betaine-homocysteine S-methyltransferase 1, methylenetetrahydrofolate dehydrogenase 1, and ATP synthase subunit beta mitochondrial (ATP5B) expression levels were significantly reduced in the livers of rat offspring exposed to maternal food restriction during gestation compared with in the offspring of rats fed a normal diet (p normal diet during lactation. However, in female offspring only expression levels of methylenetetrahydrofolate dehydrogenase 1 were negatively correlated with homocysteine concentration. This study shows that maternal food restriction during late gestation and normal diet during lactation lead to increased homocysteine concentration through disturbance of one-carbon metabolism in the livers of male offspring. This suggests that male offspring have an increased gender-specific susceptibility to disease in later life through fetal programming.

  15. Histone Methylation Dynamics and Gene Regulation Occur through the Sensing of One-Carbon Metabolism.

    Science.gov (United States)

    Mentch, Samantha J; Mehrmohamadi, Mahya; Huang, Lei; Liu, Xiaojing; Gupta, Diwakar; Mattocks, Dwight; Gómez Padilla, Paola; Ables, Gene; Bamman, Marcas M; Thalacker-Mercer, Anna E; Nichenametla, Sailendra N; Locasale, Jason W

    2015-11-01

    S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) link one-carbon metabolism to methylation status. However, it is unknown whether regulation of SAM and SAH by nutrient availability can be directly sensed to alter the kinetics of key histone methylation marks. We provide evidence that the status of methionine metabolism is sufficient to determine levels of histone methylation by modulating SAM and SAH. This dynamic interaction led to rapid changes in H3K4me3, altered gene transcription, provided feedback regulation to one-carbon metabolism, and could be fully recovered upon restoration of methionine. Modulation of methionine in diet led to changes in metabolism and histone methylation in the liver. In humans, methionine variability in fasting serum was commensurate with concentrations needed for these dynamics and could be partly explained by diet. Together these findings demonstrate that flux through methionine metabolism and the sensing of methionine availability may allow direct communication to the chromatin state in cells.

  16. A metagenomic window into carbon metabolism at 3 km depth in Precambrian continental crust.

    Science.gov (United States)

    Magnabosco, Cara; Ryan, Kathleen; Lau, Maggie C Y; Kuloyo, Olukayode; Sherwood Lollar, Barbara; Kieft, Thomas L; van Heerden, Esta; Onstott, Tullis C

    2016-03-01

    Subsurface microbial communities comprise a significant fraction of the global prokaryotic biomass; however, the carbon metabolisms that support the deep biosphere have been relatively unexplored. In order to determine the predominant carbon metabolisms within a 3-km deep fracture fluid system accessed via the Tau Tona gold mine (Witwatersrand Basin, South Africa), metagenomic and thermodynamic analyses were combined. Within our system of study, the energy-conserving reductive acetyl-CoA (Wood-Ljungdahl) pathway was found to be the most abundant carbon fixation pathway identified in the metagenome. Carbon monoxide dehydrogenase genes that have the potential to participate in (1) both autotrophic and heterotrophic metabolisms through the reversible oxidization of CO and subsequent transfer of electrons for sulfate reduction, (2) direct utilization of H2 and (3) methanogenesis were identified. The most abundant members of the metagenome belonged to Euryarchaeota (22%) and Firmicutes (57%)-by far, the highest relative abundance of Euryarchaeota yet reported from deep fracture fluids in South Africa and one of only five Firmicutes-dominated deep fracture fluids identified in the region. Importantly, by combining the metagenomics data and thermodynamic modeling of this study with previously published isotopic and community composition data from the South African subsurface, we are able to demonstrate that Firmicutes-dominated communities are associated with a particular hydrogeologic environment, specifically the older, more saline and more reducing waters.

  17. 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...... to baseline ventilation, whereas CMR(glu) increased. CONCLUSION: In patients with acute bacterial meningitis, we found variable levels of CBF and cerebrovascular CO(2) reactivity, a low a-v DO(2), low cerebral metabolic rates of oxygen and glucose, and a cerebral lactate efflux. In these patients...

  18. 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

  19. Nutritional Manipulation of One-Carbon Metabolism: Effects on Arsenic Methylation and Toxicity

    Directory of Open Access Journals (Sweden)

    Megan N. Hall

    2012-01-01

    Full Text Available Exposure to arsenic (As through drinking water is a substantial problem worldwide. The methylation of As, a reactive metalloid, generates monomethyl- (MMA and dimethyl-arsenical (DMA species. The biochemical pathway that catalyzes these reactions, one-carbon metabolism, is regulated by folate and other micronutrients. Arsenic methylation exerts a critical influence on both its urinary elimination and chemical reactivity. Mice having the As methyltransferase null genotype show reduced urinary As excretion, increased As retention, and severe systemic toxicity. The most toxic As metabolite in vitro is MMAIII, an intermediate in the generation of DMAV, a much less toxic metabolite. These findings have raised the question of whether As methylation is a detoxification or bioactivation pathway. Results of population-based studies suggest that complete methylation of inorganic As to DMA is associated with reduced risk for As-induced health outcomes, and that nutrients involved in one-carbon metabolism, such as folate, can facilitate As methylation and elimination.

  20. Carbon metabolism of enterobacterial human pathogens growing in epithelial colorectal adenocarcinoma (Caco-2 cells.

    Directory of Open Access Journals (Sweden)

    Andreas Götz

    Full Text Available Analysis of the genome sequences of the major human bacterial pathogens has provided a large amount of information concerning their metabolic potential. However, our knowledge of the actual metabolic pathways and metabolite fluxes occurring in these pathogens under infection conditions is still limited. In this study, we analysed the intracellular carbon metabolism of enteroinvasive Escherichia coli (EIEC HN280 and EIEC 4608-58 and Salmonella enterica Serovar Typhimurium (Stm 14028 replicating in epithelial colorectal adenocarcinoma cells (Caco-2. To this aim, we supplied [U-(13C(6]glucose to Caco-2 cells infected with the bacterial strains or mutants thereof impaired in the uptake of glucose, mannose and/or glucose 6-phosphate. The (13C-isotopologue patterns of protein-derived amino acids from the bacteria and the host cells were then determined by mass spectrometry. The data showed that EIEC HN280 growing in the cytosol of the host cells, as well as Stm 14028 replicating in the Salmonella-containing vacuole (SCV utilised glucose, but not glucose 6-phosphate, other phosphorylated carbohydrates, gluconate or fatty acids as major carbon substrates. EIEC 4608-58 used C(3-compound(s in addition to glucose as carbon source. The labelling patterns reflected strain-dependent carbon flux via glycolysis and/or the Entner-Doudoroff pathway, the pentose phosphate pathway, the TCA cycle and anapleurotic reactions between PEP and oxaloacetate. Mutants of all three strains impaired in the uptake of glucose switched to C(3-substrate(s accompanied by an increased uptake of amino acids (and possibly also other anabolic monomers from the host cell. Surprisingly, the metabolism of the host cells, as judged by the efficiency of (13C-incorporation into host cell amino acids, was not significantly affected by the infection with either of these intracellular pathogens.

  1. 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 INTRODUCTION: 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. METHODS: 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. RESULTS: 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. CONCLUSIONS: 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.

  2. Zinc disrupts central carbon metabolism and capsule biosynthesis in Streptococcus pyogenes.

    Science.gov (United States)

    Ong, Cheryl-lynn Y; Walker, Mark J; McEwan, Alastair G

    2015-06-01

    Neutrophils release free zinc to eliminate the phagocytosed bacterial pathogen Streptococcus pyogenes (Group A Streptococcus; GAS). In this study, we investigated the mechanisms underpinning zinc toxicity towards this human pathogen, responsible for diseases ranging from pharyngitis and impetigo, to severe invasive infections. Using the globally-disseminated M1T1 GAS strain, we demonstrate that zinc stress impairs glucose metabolism through the inhibition of the glycolytic enzymes phosphofructokinase and glyceraldehyde-3-phosphate dehydrogenase. In the presence of zinc, a metabolic shift to the tagatose-6-phosphate pathway allows conversion of D-galactose to dihydroxyacetone phosphate and glyceraldehyde phosphate, partially bypassing impaired glycolytic enzymes to generate pyruvate. Additionally, zinc inhibition of phosphoglucomutase results in decreased capsule biosynthesis. These data indicate that zinc exerts it toxicity via mechanisms that inhibit both GAS central carbon metabolism and virulence pathways.

  3. Growth-related Metabolism of the Carbon Storage Poly-3-hydroxybutyrate in Legionella pneumophila.

    Science.gov (United States)

    Gillmaier, Nadine; Schunder, Eva; Kutzner, Erika; Tlapák, Hana; Rydzewski, Kerstin; Herrmann, Vroni; Stämmler, Maren; Lasch, Peter; Eisenreich, Wolfgang; Heuner, Klaus

    2016-03-18

    Legionella pneumophila, the causative agent of Legionnaires disease, has a biphasic life cycle with a switch from a replicative to a transmissive phenotype. During the replicative phase, the bacteria grow within host cells in Legionella-containing vacuoles. During the transmissive phenotype and the postexponential (PE) growth phase, the pathogens express virulence factors, become flagellated, and leave the Legionella-containing vacuoles. Using (13)C labeling experiments, we now show that, under in vitro conditions, serine is mainly metabolized during the replicative phase for the biosynthesis of some amino acids and for energy generation. During the PE phase, these carbon fluxes are reduced, and glucose also serves as an additional carbon substrate to feed the biosynthesis of poly-3-hydroxybuyrate (PHB), an essential carbon source for transmissive L. pneumophila. Whole-cell FTIR analysis and comparative isotopologue profiling further reveal that a putative 3-ketothiolase (Lpp1788) and a PHB polymerase (Lpp0650), but not enzymes of the crotonyl-CoA pathway (Lpp0931-0933) are involved in PHB metabolism during the PE phase. However, the data also reflect that additional bypassing reactions for PHB synthesis exist in agreement with in vivo competition assays using Acanthamoeba castellannii or human macrophage-like U937 cells as host cells. The data suggest that substrate usage and PHB metabolism are coordinated during the life cycle of the pathogen.

  4. Life-history strategies and carbon metabolism gene dosage in the Nakaseomyces yeasts.

    Science.gov (United States)

    Legrand, Judith; Bolotin-Fukuhara, Monique; Bourgais, Aurélie; Fairhead, Cécile; Sicard, Delphine

    2016-03-01

    The Nakaseomyces clade consists of a group of six hemiascomyceteous yeasts (Candida glabrata, Nakaseomyces delphensis, C. nivarensis, C. bracarensis, C. castelli, N. bacillisporus), phylogenetically close to the yeast Saccharomyces cerevisiae, their representative being the well-known pathogenic yeast C. glabrata. Four species had been previously examined for their carbon assimilation properties and found to have similar properties to S. cerevisiae (repression of respiration in high glucose-i.e. Crabtree positivity-and being a facultative anaerobe). We examined here the complete set of the six species for their carbon metabolic gene content. We also measured different metabolic and life-history traits (glucose consumption rate, population growth rate, carrying capacity, cell size, cell and biomass yield). We observed deviations from the glycolytic gene redundancy observed in S. cerevisiae presumed to be an important property for the Crabtree positivity, especially for the two species C. castelli and N. bacillisporus which frequently have only one gene copy, but different life strategies. Therefore, we show that the decrease in carbon metabolic gene copy cannot be simply associated with a reduction of glucose consumption rate and can be counterbalanced by other beneficial genetic variations.

  5. Soil carbon dioxide emissions controlled by an extracellular oxidative metabolism identifiable by its isotope signature

    Science.gov (United States)

    Kéraval, Benoit; Lehours, Anne Catherine; Colombet, Jonathan; Amblard, Christian; Alvarez, Gaël; Fontaine, Sébastien

    2016-11-01

    Soil heterotrophic respiration is a major determinant of the carbon (C) cycle and its interactions with climate. Given the complexity of the respiratory machinery, it is traditionally considered that oxidation of organic C into carbon dioxide (CO2) strictly results from intracellular metabolic processes. Here we show that C mineralization can operate in soils deprived of all observable cellular forms. Moreover, the process responsible for CO2 emissions in sterilized soils induced a strong C isotope fractionation (up to 50 ‰) incompatible with respiration of cellular origin. The supply of 13C glucose in sterilized soil led to the release of 13CO2 suggesting the presence of respiratory-like metabolism (glycolysis, decarboxylation reaction, chain of electron transfer) carried out by soil-stabilized enzymes, and by soil mineral and metal catalysts. These findings indicate that CO2 emissions from soils can have two origins: (1) from the well-known respiration of soil heterotrophic microorganisms and (2) from an extracellular oxidative metabolism (EXOMET) or, at least, catabolism. These two metabolisms should be considered separately when studying effects of environmental factors on the C cycle because the likelihood is that they do not obey the same laws and they respond differently to abiotic factors.

  6. 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 (...

  7. BENTHIC METABOLISM ON A SHELTERED ROCKY SHORE: ROLE OF THE CANOPY IN THE CARBON BUDGET(1).

    Science.gov (United States)

    Golléty, Claire; Migné, Aline; Davoult, Dominique

    2008-10-01

    While the importance of canopy-forming algae in structuring ecosystems is recognized, their role in the carbon budget is still not well understood. To our knowledge, no measurements of rocky shores primary production and respiration under emersion periods have been carried out in situ. A benthic chamber coupled to a CO2 -infrared gas analyzer was used to measure gross primary production and respiration on the Ascophyllum nodosum (L.) Le Jol. zone of a sheltered rocky shore in Brittany, France. Over a year of monthly measurements on the zone with and without the A. nodosum canopy showed fairly high production and respiration values for the global community as well as carbon fluxes due to the canopy that largely dominated the benthic metabolism of the zone. The strong canopy respiration relative to the primary production also suggested a high metabolic activity by microscopic heterotrophs on the surface of the alga. Both the canopy and the understory annual primary production and respiration were under the control of light and temperature seasonal variations. Finally, the range of the amount of carbon produced on the A. nodosum zone during diurnal emersions was estimated. Additional measures accounting for the day-night cycles and seasonal light variations over an entire tidal cycle are, however, necessary to establish an annual carbon budget. Such measures using the benthic chamber together with complementary techniques would allow a better understanding of the functioning of sheltered rocky shores.

  8. Epiphyte dynamics and carbon metabolism in a nutrient enriched Mediterranean seagrass ( Posidonia oceanica ) ecosystem

    Science.gov (United States)

    Apostolaki, Eugenia T.; Holmer, Marianne; Marbà, Núria; Karakassis, Ioannis

    2011-08-01

    The study aimed at examining the relationship between epiphyte dynamics and carbon metabolism in seagrass ecosystems under nutrient enrichment. Temporal variability of epiphytes and factors controlling their dynamics (i.e. environmental conditions, substratum availability, substratum stability and herbivore pressure) were assessed in a fish farm impacted and an unaffected Mediterranean seagrass ( Posidonia oceanica) meadow in the Aegean Sea (Greece). The factors controlling epiphyte dynamics responded differently to nutrient enrichment and partly interacted, rendering their cumulative effect on epiphyte load difficult to elucidate. Yet epiphytes accumulated on seagrass leaves near to the fish farm throughout the year, contributing 2 times more in above-ground biomass at cages than the control station. Reduction in substratum availability (i.e. decrease in leaf biomass) and increase in herbivore pressure affected epiphyte load, albeit their effects were not strong enough to counterbalance the effect of nutrient input from fish farm effluents. Moderate yet continuous nutrient input possibly stimulated epiphyte growth in excess of herbivory, shifting the control of epiphytes from top-down to bottom-up. Epiphyte accumulation affected carbon metabolism in the seagrass ecosystem by contributing to enhanced dissolved organic carbon (DOC) release, but seagrass loss was so acute that increased epiphyte cover could not counterbalance the decrease in community carbon production which was mainly driven by seagrass decline.

  9. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  11. 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

  12. 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

  13. Metabolism

    Science.gov (United States)

    ... Are More Common in People With Type 1 Diabetes Metabolic Syndrome Your Child's Weight Healthy Eating Endocrine System Blood Test: Basic Metabolic Panel (BMP) Activity: Endocrine System Growth Disorders Diabetes Center Thyroid Disorders Your Endocrine System Movie: Endocrine ...

  14. Metabolism

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

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

  15. Vitamin B12: one carbon metabolism, fetal growth and programming for chronic disease.

    Science.gov (United States)

    Rush, E C; Katre, P; Yajnik, C S

    2014-01-01

    This review brings together human and animal studies and reviews that examine the possible role of maternal vitamin B12 (B12) on fetal growth and its programming for susceptibility to chronic disease. A selective literature review was undertaken to identify studies and reviews that investigate these issues, particularly in the context of a vegetarian diet that may be low in B12 and protein and high in carbohydrate. Evidence is accumulating that maternal B12 status influences fetal growth and development. Low maternal vitamin B12 status and protein intake are associated with increased risk of neural tube defect, low lean mass and excess adiposity, increased insulin resistance, impaired neurodevelopment and altered risk of cancer in the offspring. Vitamin B12 is a key nutrient associated with one carbon metabolic pathways related to substrate metabolism, synthesis and stability of nucleic acids and methylation of DNA which regulates gene expression. Understanding of factors regulating maternal-fetal one carbon metabolism and its role in fetal programming of non communicable diseases could help design effective interventions, starting with maternal nutrition before conception.

  16. Recent advances in engineering the central carbon metabolism of industrially important bacteria

    Directory of Open Access Journals (Sweden)

    Papagianni Maria

    2012-04-01

    Full Text Available Abstract This paper gives an overview of the recent advances in engineering the central carbon metabolism of the industrially important bacteria Escherichia coli, Bacillus subtilis, Corynobacterium glutamicum, Streptomyces spp., Lactococcus lactis and other lactic acid bacteria. All of them are established producers of important classes of products, e.g. proteins, amino acids, organic acids, antibiotics, high-value metabolites for the food industry and also, promising producers of a large number of industrially or therapeutically important chemicals. Optimization of existing or introduction of new cellular processes in these microorganisms is often achieved through manipulation of targets that reside at major points of central metabolic pathways, such as glycolysis, gluconeogenesis, the pentose phosphate pathway and the tricarboxylic acid cycle with the glyoxylate shunt. Based on the huge progress made in recent years in biochemical, genetic and regulatory studies, new fascinating engineering approaches aim at ensuring an optimal carbon and energy flow within central metabolism in order to achieve optimized metabolite production.

  17. Inorganic carbon turnover caused by digestion of carbonate sands and metabolic activity of holothurians

    Science.gov (United States)

    Schneider, Kenneth; Silverman, Jacob; Kravitz, Ben; Rivlin, Tanya; Schneider-Mor, Aya; Barbosa, Sergio; Byrne, Maria; Caldeira, Ken

    2013-11-01

    Recent measurements have shown that holothurians (sea cucumbers) may play an important role in the cycling of CaCO3 in tropical coral reef systems through ingestion and processing of carbonate sediment. In this report, we present estimates of inorganic carbon turnover rates determined from laboratory incubations of Holothuria atra, Holothuria leucospilota and Stichopus herrmanni. The pH values of the gut lumen ranged from 7.0 to 7.6 when digestive tracts were filled with sediment compared with 6.1-6.7 in animals with empty digestive tracts. Empty gut volume estimates for H. atra and S. herrmanni were 36 ± 4 mL and 151 ± 14 mL, respectively. Based on these measurements and the density and porosity of carbonate sediments of coral reefs, it is estimated that these species process 19 ± 2 kg and 80 ± 7 kg CaCO3 sand yr-1 per individual, respectively. The annual CaCO3 dissolution rates per H. atra and S. herrmanni individual are estimated to be 6.5 ± 1.9 g and 9.6 ± 1.4 g, respectively, suggesting that 0.05 ± 0.02% and 0.1 ± 0.02% of the CaCO3 processed through their gut annually is dissolved. During incubations the CaCO3 dissolution of the fecal casts was 0.07 ± 0.01%, 0.04 ± 0.01% and 0.21 ± 0.05% for H. atra, H. leucospilota and S. herrmanni, respectively. The CaCO3 saturation state in the incubation seawater decreased markedly due to a greater increase in dissolved inorganic carbon (DIC) relative to total alkalinity (AT) as a result of respiration by the animals. Our results support the hypothesis that deposit feeders such as sea cucumbers play an important ecological role in the coral reef CaCO3 cycle.

  18. Airbus Unveils A380 "Superjumbo" Jet

    Institute of Scientific and Technical Information of China (English)

    Stefan Lovgren; 贾庆文

    2005-01-01

    @@ The new Airbus 380 "superjumbo"jet, unveiled in Toulouse1, France,will carry 555 passengers (when configured2 for three classes of seating). Its wingspan3 stretches nearly the length of a football field-50 feet (15 meters) wider than any commercial plane in the air today.

  19. Modulation of Central Carbon Metabolism by Acetylation of Isocitrate Lyase in Mycobacterium tuberculosis

    Science.gov (United States)

    Bi, Jing; Wang, Yihong; Yu, Heguo; Qian, Xiaoyan; Wang, Honghai; Liu, Jun; Zhang, Xuelian

    2017-01-01

    Several enzymes involved in central carbon metabolism such as isocitrate lyase and phosphoenolpyruvate carboxykinase are key determinants of pathogenesis of Mycobacterium tuberculosis (M. tb). In this study, we found that lysine acetylation plays an important role in the modulation of central carbon metabolism in M. tb. Mutant of M. tb defective in sirtuin deacetylase exhibited improved growth in fatty acid-containing media. Global analysis of lysine acetylome of M. tb identified three acetylated lysine residues (K322, K331, and K392) of isocitrate lyase (ICL1). Using a genetically encoding system, we demonstrated that acetylation of K392 increased the enzyme activity of ICL1, whereas acetylation of K322 decreased its activity. Antibodies that specifically recognized acetyllysine at 392 and 322 of ICL1 were used to monitor the levels of ICL1 acetylation in M. tb cultures. The physiological significance of ICL1 acetylation was demonstrated by the observation that M. tb altered the levels of acetylated K392 in response to changes of carbon sources, and that acetylation of K392 affected the abundance of ICL1 protein. Our study has uncovered another regulatory mechanism of ICL1. PMID:28322251

  20. 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).

  1. MapMaker and PathTracer for tracking carbon in genome-scale metabolic models.

    Science.gov (United States)

    Tervo, Christopher J; Reed, Jennifer L

    2016-05-01

    Constraint-based reconstruction and analysis (COBRA) modeling results can be difficult to interpret given the large numbers of reactions in genome-scale models. While paths in metabolic networks can be found, existing methods are not easily combined with constraint-based approaches. To address this limitation, two tools (MapMaker and PathTracer) were developed to find paths (including cycles) between metabolites, where each step transfers carbon from reactant to product. MapMaker predicts carbon transfer maps (CTMs) between metabolites using only information on molecular formulae and reaction stoichiometry, effectively determining which reactants and products share carbon atoms. MapMaker correctly assigned CTMs for over 97% of the 2,251 reactions in an Escherichia coli metabolic model (iJO1366). Using CTMs as inputs, PathTracer finds paths between two metabolites. PathTracer was applied to iJO1366 to investigate the importance of using CTMs and COBRA constraints when enumerating paths, to find active and high flux paths in flux balance analysis (FBA) solutions, to identify paths for putrescine utilization, and to elucidate a potential CO2 fixation pathway in E. coli. These results illustrate how MapMaker and PathTracer can be used in combination with constraint-based models to identify feasible, active, and high flux paths between metabolites.

  2. A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea

    Science.gov (United States)

    Kono, Takunari; Mehrotra, Sandhya; Endo, Chikako; Kizu, Natsuko; Matusda, Mami; Kimura, Hiroyuki; Mizohata, Eiichi; Inoue, Tsuyoshi; Hasunuma, Tomohisa; Yokota, Akiho; Matsumura, Hiroyoshi; Ashida, Hiroki

    2017-01-01

    Two enzymes are considered to be unique to the photosynthetic Calvin–Benson cycle: ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), responsible for CO2 fixation, and phosphoribulokinase (PRK). Some archaea possess bona fide RuBisCOs, despite not being photosynthetic organisms, but are thought to lack PRK. Here we demonstrate the existence in methanogenic archaea of a carbon metabolic pathway involving RuBisCO and PRK, which we term ‘reductive hexulose-phosphate' (RHP) pathway. These archaea possess both RuBisCO and a catalytically active PRK whose crystal structure resembles that of photosynthetic bacterial PRK. Capillary electrophoresis-mass spectrometric analysis of metabolites reveals that the RHP pathway, which differs from the Calvin–Benson cycle only in a few steps, is active in vivo. Our work highlights evolutionary and functional links between RuBisCO-mediated carbon metabolic pathways in methanogenic archaea and photosynthetic organisms. Whether the RHP pathway allows for autotrophy (that is, growth exclusively with CO2 as carbon source) remains unknown. PMID:28082747

  3. 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

  4. Inorganic Carbon Turnover caused by Digestion of Carbonate Sands and Metabolic Activity of Holothurians

    Energy Technology Data Exchange (ETDEWEB)

    Schneider, Kenneth; Silverman, Jacob; Kravitz, Benjamin S.; Rivlin, Tanya; Schneider-Mor, Aya; Barbosa, Sergio; Byrne, Maria; Caldeira, Ken

    2013-11-20

    Recent measurements have shown that holothurians (sea cucumbers) play an important role in the cycling of CaCO3 in tropical coral reef systems through ingestion and processing of carbonate sediment. In this study inorganic additional aspects of carbon turnover were determined in laboratory incubations of Holothuria atra, H. leucospilota and Stichopus herrmanni from One Tree Reef, Great Barrier Reef. The pH values of the gut lumen ranged from 6.1 to 6.7 in animals with empty digestive tracts as opposed to 7.0 to 7.6 when digestive tracts were filled with sediment. Empty gut volume estimates for H. atra and S. herrmanni were 36 ± 4 mL and 151 ± 14 mL, respectively. Based on these measurements it is estimated that these species process 19 ± 2kg and 80 ± 7kg CaCO3 sand yr-1 per individual, respectively. The annual dissolution rates of H. atra and S. herrmanni of 6.5±1.9g and 9.6±1.4g, respectively, suggest that 0.05±0.02% and 0.1±0.02% of the CaCO3 processed through their gut annually is dissolved. During the incubations the CaCO3 dissolution was 0.07±0.01%, 0.04±0.01% and 0.21±0.05% of the fecal casts for H. atra, H. leucospilota and S. herrmanni, respectively. The CaCO3 saturation state for both aragonite and calcite minerals during laboratory incubations decreased markedly due to a greater increase in dissolved inorganic carbon (DIC) relative to total alkalinity (AT) as a result of respiration by the animals. Our results support the hypothesis that deposit feeders such as sea cucumbers play an important ecological role in the coral reef CaCO3 cycle.

  5. An ancient riboswitch class in bacteria regulates purine biosynthesis and one-carbon metabolism.

    Science.gov (United States)

    Kim, Peter B; Nelson, James W; Breaker, Ronald R

    2015-01-22

    Over 30 years ago, ZTP (5-aminoimidazole-4-carboxamide riboside 5'-triphosphate), a modified purine biosynthetic intermediate, was proposed to signal 10-formyl-tetrahydrofolate (10f-THF) deficiency in bacteria. However, the mechanisms by which this putative alarmone or its precursor ZMP (5-aminoimidazole-4-carboxamide ribonucleotide, also known as AICAR) brings about any metabolic changes remain unexplained. Herein, we report the existence of a widespread riboswitch class that is most commonly associated with genes related to de novo purine biosynthesis and one-carbon metabolism. Biochemical data confirm that members of this riboswitch class selectively bind ZMP and ZTP with nanomolar affinity while strongly rejecting numerous natural analogs. Indeed, increases in the ZMP/ZTP pool, caused by folate stress in bacterial cells, trigger changes in the expression of a reporter gene fused to representative ZTP riboswitches in vivo. The wide distribution of this riboswitch class suggests that ZMP/ZTP signaling is important for species in numerous bacterial lineages.

  6. 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...... intake can affect OCM metabolites in plasma. Finally, we explored whether a fish oil supplement can induce epigenetic changes and whether these are related to MetS features. Methods: In two cross-sectional studies using the 3G-cohort, we investigated associations between plasma OCM metabolites, s...

  7. Toward microtesla MRI of hyperpolarized carbon-13 for real-time metabolic imaging

    CERN Document Server

    Zotev, V S; Savukov, I M; Matlashov, A N; Gómez, J J; Espy, M A

    2009-01-01

    Hyperpolarization of carbon-13 is a promising technique that has enabled MR angiography, perfusion mapping, and real-time metabolic imaging of C-13 labeled organic substances with unprecedented signal-to-noise levels. Because the hyperpolarization is performed outside an MRI scanner (using a special NMR-style hyperpolarizer), high magnetic fields of conventional MRI systems offer little advantage in terms of achievable C-13 polarization. Here we propose an ultimate low-field MRI scanner for imaging hyperpolarized C-13. It uses only microtesla-range magnetic fields and employs SQUID (superconducting quantum interference device) sensors for broadband reception of MRI signals. We present the first images acquired by SQUID-based microtesla MRI with dynamic nuclear polarization (Overhauser enhancement). We also report the first NMR spectra of C-13 at microtesla fields, including spectra of metabolically relevant sodium pyruvate, bicarbonate, and alanine. Our results demonstrate feasibility and potential of the pro...

  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. Untangling metabolic and spatial interactions of stress tolerance in plants. 1. Patterns of carbon metabolism within leaves.

    Science.gov (United States)

    Biel, Karl Y; Fomina, Irina R; Nazarova, Galina N; Soukhovolsky, Vladislav G; Khlebopros, Rem G; Nishio, John N

    2010-09-01

    The localization of the key photoreductive and oxidative processes and some stress-protective reactions within leaves of mesophytic C(3) plants were investigated. The role of light in determining the profile of Rubisco, glutamate oxaloacetate transaminase, catalase, fumarase, and cytochrome-c-oxidase across spinach leaves was examined by exposing leaves to illumination on either the adaxial or abaxial leaf surfaces. Oxygen evolution in fresh paradermal leaf sections and CO(2) gas exchange in whole leaves under adaxial or abaxial illumination was also examined. The results showed that the palisade mesophyll is responsible for the midday depression of photosynthesis in spinach leaves. The photosynthetic apparatus was more sensitive to the light environment than the respiratory apparatus. Additionally, examination of the paradermal leaf sections by optical microscopy allowed us to describe two new types of parenchyma in spinach-pirum mesophyll and pillow spongy mesophyll. A hypothesis that oxaloacetate may protect the upper leaf tissue from the destructive influence of active oxygen is presented. The application of mathematical modeling shows that the pattern of enzymatic distribution across leaves abides by the principle of maximal ecological utility. Light regulation of carbon metabolism across leaves is discussed.

  10. 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

  11. A vector library for silencing central carbon metabolism genes with antisense RNAs in Escherichia coli.

    Science.gov (United States)

    Nakashima, Nobutaka; Ohno, Satoshi; Yoshikawa, Katsunori; Shimizu, Hiroshi; Tamura, Tomohiro

    2014-01-01

    We describe here the construction of a series of 71 vectors to silence central carbon metabolism genes in Escherichia coli. The vectors inducibly express antisense RNAs called paired-terminus antisense RNAs, which have a higher silencing efficacy than ordinary antisense RNAs. By measuring mRNA amounts, measuring activities of target proteins, or observing specific phenotypes, it was confirmed that all the vectors were able to silence the expression of target genes efficiently. Using this vector set, each of the central carbon metabolism genes was silenced individually, and the accumulation of metabolites was investigated. We were able to obtain accurate information on ways to increase the production of pyruvate, an industrially valuable compound, from the silencing results. Furthermore, the experimental results of pyruvate accumulation were compared to in silico predictions, and both sets of results were consistent. Compared to the gene disruption approach, the silencing approach has an advantage in that any E. coli strain can be used and multiple gene silencing is easily possible in any combination.

  12. Early pregnancy B vitamin status, one carbon metabolism, pregnancy outcome and child development.

    Science.gov (United States)

    Solé-Navais, Pol; Cavallé-Busquets, Pere; Fernandez-Ballart, Joan D; Murphy, Michelle M

    2016-07-01

    Periconception supplementation with folic acid is recommended until 12 gestational weeks to prevent neural tube defects. Doses of folic acid contained in supplements and timing and length of use during pregnancy vary. The effects of status in periconception and pregnancy folate, cobalamin, betaine and their interactions on one carbon metabolism (1C), as well as the global effect of 1C on foetal growth and pregnancy outcome, are reviewed. Results from prospective studies are reviewed. Cessation of folic acid supplement use after the first trimester is associated with a sharp drop in plasma folate status and enhanced conversion of betaine to dimethylglycine. Dimethylglycine production is also higher in mothers with low folate status than in those with normal-high folate status. The effects of high doses of folic acid on one carbon metabolism in mothers with low early pregnancy cobalamin status and on foetal growth are also reviewed. Several studies report that moderately elevated early pregnancy fasting plasma total homocysteine (tHcy) is inversely associated with birth weight and a predictor of intrauterine growth retardation. There is also evidence for increased risk of preterm birth when maternal folate status is low.

  13. Expression of human dopamine receptor in potato (Solanum tuberosum results in altered tuber carbon metabolism

    Directory of Open Access Journals (Sweden)

    Świędrych Anna

    2005-02-01

    Full Text Available Abstract Background Even though the catecholamines (dopamine, norepinephrine and epinephrine have been detected in plants their role is poorly documented. Correlations between norepinephrine, soluble sugars and starch concentration have been recently reported for potato plants over-expressing tyrosine decarboxylase, the enzyme mediating the first step of catecholamine synthesis. More recently norepinephrine level was shown to significantly increase after osmotic stress, abscisic acid treatment and wounding. Therefore, it is possible that catecholamines might play a role in plant stress responses by modulating primary carbon metabolism, possibly by a mechanism similar to that in animal cells. Since to date no catecholamine receptor has been identified in plants we transformed potato plants with a cDNA encoding human dopamine receptor (HD1. Results Tuber analysis of transgenic plants revealed changes in the activities of key enzymes mediating sucrose to starch conversion (ADP-glucose phosphorylase and sucrose synthase and sucrose synthesis (sucrose phosphate synthase leading to altered content of both soluble sugars and starch. Surprisingly the catecholamine level measured in transgenic plants was significantly increased; the reason for this is as yet unknown. However the presence of the receptor affected a broader range of enzyme activities than those affected by the massive accumulation of norepinephrine reported for plants over-expressing tyrosine decarboxylase. Therefore, it is suggested that the presence of the exogenous receptor activates catecholamine cAMP signalling in plants. Conclusions Our data support the possible involvement of catecholamines in regulating plant carbon metabolism via cAMP signalling pathway.

  14. Carbon Uptake and the Metabolism and Transport of Lipids in an Arbuscular Mycorrhiza1

    Science.gov (United States)

    Pfeffer, Philip E.; Douds, David D.; Bécard, Guillaume; Shachar-Hill, Yair

    1999-01-01

    Both the plant and the fungus benefit nutritionally in the arbuscular mycorrhizal symbiosis: The host plant enjoys enhanced mineral uptake and the fungus receives fixed carbon. In this exchange the uptake, metabolism, and translocation of carbon by the fungal partner are poorly understood. We therefore analyzed the fate of isotopically labeled substrates in an arbuscular mycorrhiza (in vitro cultures of Ri T-DNA-transformed carrot [Daucus carota] roots colonized by Glomus intraradices) using nuclear magnetic resonance spectroscopy. Labeling patterns observed in lipids and carbohydrates after substrates were supplied to the mycorrhizal roots or the extraradical mycelium indicated that: (a) 13C-labeled glucose and fructose (but not mannitol or succinate) are effectively taken up by the fungus within the root and are metabolized to yield labeled carbohydrates and lipids; (b) the extraradical mycelium does not use exogenous sugars for catabolism, storage, or transfer to the host; (c) the fungus converts sugars taken up in the root compartment into lipids that are then translocated to the extraradical mycelium (there being little or no lipid synthesis in the external mycelium); and (d) hexose in fungal tissue undergoes substantially higher fluxes through an oxidative pentose phosphate pathway than does hexose in the host plant. PMID:10364411

  15. 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.

  16. Lanthanum carbonate versus sevelamer hydrochloride: improvement of metabolic acidosis and hyperkalemia in hemodialysis patients.

    Science.gov (United States)

    Filiopoulos, Vassilis; Koutis, Ioannis; Trompouki, Sofia; Hadjiyannakos, Dimitrios; Lazarou, Dimitrios; Vlassopoulos, Dimosthenis

    2011-02-01

    Sevelamer hydrochloride (SH) has been reported to aggravate metabolic acidosis and hyperkalemia. This study was performed to evaluate acid-base status and serum potassium changes after replacing SH with lanthanum carbonate (LC) in hemodialysis patients. SH was prescribed for 24 weeks in 14 stable hemodialysis patients and replaced by LC in a similar treatment schedule. Laboratory tests, including indices of acid-base status, nutrition, bone/mineral metabolism, and dialysis adequacy, were performed monthly during the study. Dialysate bicarbonate, potassium and calcium concentrations remained constant. Serum bicarbonate and pH rose, and serum potassium dropped significantly under LC. Alkaline phosphatase also decreased significantly under LC. No significant differences were observed in the other studied parameters between the two treatment periods. Control of serum phosphate was similar under both phosphate-binders and no differences were observed in calcium, Ca × P product, CRP, or lipid levels. Dialysis adequacy was constantly kept within K/DOQI target-range. Although full compliance to treatment was reported, three patients on LC complained of gastrointestinal upset and/or a metallic taste, and four had difficulty chewing the LC tablet. LC improves metabolic acidosis and hyperkalemia in hemodialysis patients previously under SH. Although both medications are well-tolerated, the gastrointestinal side-effects appear to occur more frequently with LC; a fact that, together with difficulties in chewing the tablet, may result in decreased compliance.

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

    Science.gov (United States)

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

    2014-10-10

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

  18. Cash boost to Great British science unveiled

    CERN Multimedia

    2002-01-01

    "Trade and Industry Secretary, Patricia Hewitt today unveiled new plans for the DTI's record science budget over the next three years, to keep Britain at the forefront of world science. The plans include funding to develop life saving new health techniques, to seek alternative energy sources, to help our rural economy, to develop the computers of tomorrow and boost business with the next generation of leading edge technologies" (1 page).

  19. 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.

  20. Nitrogen-induced metabolic changes and molecular determinants of carbon allocation in Dunaliella tertiolecta.

    Science.gov (United States)

    Tan, Kenneth Wei Min; Lin, Huixin; Shen, Hui; Lee, Yuan Kun

    2016-11-16

    Certain species of microalgae are natural accumulators of lipids, while others are more inclined to store starch. However, what governs the preference to store lipids or starch is not well understood. In this study, the microalga Dunaliella tertiolecta was used as a model to study the global gene expression profile regulating starch accumulation in microalgae. D. tertiolecta, when depleted of nitrogen, produced only 1% of dry cell weight (DCW) in neutral lipids, while starch was rapidly accumulated up to 46% DCW. The increased in starch content was accompanied by a coordinated overexpression of genes shunting carbon towards starch synthesis, a response not seen in the oleaginous microalgae Nannochloropsis oceanica, Chlamydomonas reinhardtii or Chlorella vulgaris. Genes in the central carbon metabolism pathways, particularly those of the tricarboxylic acid cycle, were also simultaneously upregulated, indicating a robust interchange of carbon skeletons for anabolic and catabolic processes. In contrast, fatty acid and triacylglycerol synthesis genes were downregulated or unchanged, suggesting that lipids are not a preferred form of storage in these cells. This study reveals the transcriptomic influence behind storage reserve allocation in D. tertiolecta and provides valuable insights into the possible manipulation of genes for engineering microorganisms to synthesize products of interest.

  1. The activated sludge metabolic characteristics changing sole carbon source from readily biodegradable acetate to toxic phenol.

    Science.gov (United States)

    Wu, Changyong; Zhou, Yuexi; Song, Jiamei

    2016-01-01

    A sequencing batch reactor was used to investigate the effect of carbon sources on the metabolism of activated sludge. Acetate and phenol, with the chemical oxygen demand (COD) of 330-350 mg L(-1), was used as the carbon source in Periods I and II, respectively. Acetate decreased in the initial 120 min with the intracellular storage materials (XSTO), extracellular polymeric substances (EPS), and the soluble microbial products (SMP) accumulating to 131.0 mg L(-1), 347.5 mg L(-1), and 35.5 mg L(-1), respectively. Then, XSTO and EPS decreased to 124.5 mg L(-1) and 340.0 mg L(-1), respectively, in the following 120 min. When acetate was replaced by phenol, it could not be used at the beginning due to its toxicity. The XSTO decreased from 142 mg L(-1) to 54.6 mg L(-1) during the aeration period. The EPS had a significant increase, with the highest value of 618.1 mg L(-1), which then decreased to 245.6 mg L(-1) at 240 min. The phenol was gradually degraded with the acclimation and it can be fully degraded 18 d later. Meanwhile, the usage ratio of the internal carbon source decreased. The effluent SMP in Period II was 1.7 times that in Period I.

  2. Metabolism

    Science.gov (United States)

    ... a particular food provides to the body. A chocolate bar has more calories than an apple, so ... acid phenylalanine, needed for normal growth and protein production). Inborn errors of metabolism can sometimes lead to ...

  3. Real-time detection of central carbon metabolism in living Escherichia coli and its response to perturbations.

    Science.gov (United States)

    Meier, Sebastian; Jensen, Pernille R; Duus, Jens Ø

    2011-10-03

    The direct tracking of cellular reactions in vivo has been facilitated with recent technologies that strongly enhance NMR signals in substrates of interest. This methodology can be used to assay intracellular reactions that occur within seconds to few minutes, as the NMR signal enhancement typically fades on this time scale. Here, we show that the enhancement of (13)C nuclear spin polarization in deuterated glucose allows to directly follow the flux of glucose signal through rather extended reaction networks of central carbon metabolism in living Escherichia coli. Alterations in central carbon metabolism depending on the growth phase or upon chemical perturbations are visualized with minimal data processing by instantaneous observation of cellular reactions.

  4. Targeted proteome analysis of single-gene deletion strains of Saccharomyces cerevisiae lacking enzymes in the central carbon metabolism

    Science.gov (United States)

    Kinoshita, Syohei; Nishino, Shunsuke; Tomita, Atsumi; Shimizu, Hiroshi

    2017-01-01

    Central carbon metabolism is controlled by modulating the protein abundance profiles of enzymes that maintain the essential systems in living organisms. In this study, metabolic adaptation mechanisms in the model organism Saccharomyces cerevisiae were investigated by direct determination of enzyme abundance levels in 30 wild type and mutant strains. We performed a targeted proteome analysis using S. cerevisiae strains that lack genes encoding the enzymes responsible for central carbon metabolism. Our analysis revealed that at least 30% of the observed variations in enzyme abundance levels could be explained by global regulatory mechanisms. A enzyme-enzyme co-abundance analysis revealed that the abundances of enzyme proteins involved in the trehalose metabolism and glycolysis changed in a coordinated manner under the control of the transcription factors for global regulation. The remaining variations were derived from local mechanisms such as a mutant-specific increase in the abundances of remote enzymes. The proteome data also suggested that, although the functional compensation of the deficient enzyme was attained by using more resources for protein biosynthesis, available resources for the biosynthesis of the enzymes responsible for central metabolism were not abundant in S. cerevisiae cells. These results showed that global and local regulation of enzyme abundance levels shape central carbon metabolism in S. cerevisiae by using a limited resource for protein biosynthesis. PMID:28241048

  5. Pyridoxine (Vitamin B6) and the Glutathione Peroxidase System; a Link between One-Carbon Metabolism and Antioxidation

    Science.gov (United States)

    Dalto, Danyel Bueno; Matte, Jean-Jacques

    2017-01-01

    Vitamin B6 (B6) has a central role in the metabolism of amino acids, which includes important interactions with endogenous redox reactions through its effects on the glutathione peroxidase (GPX) system. In fact, B6-dependent enzymes catalyse most reactions of the transsulfuration pathway, driving homocysteine to cysteine and further into GPX proteins. Considering that mammals metabolize sulfur- and seleno-amino acids similarly, B6 plays an important role in the fate of sulfur-homocysteine and its seleno counterpart between transsulfuration and one-carbon metabolism, especially under oxidative stress conditions. This is particularly important in reproduction because ovarian metabolism may generate an excess of reactive oxygen species (ROS) during the peri-estrus period, which may impair ovulatory functions and early embryo development. Later in gestation, placentation raises embryo oxygen tension and may induce a higher expression of ROS markers and eventually embryo losses. Interestingly, the metabolic accumulation of ROS up-regulates the flow of one-carbon units to transsulfuration and down-regulates remethylation. However, in embryos, the transsulfuration pathway is not functional, making the understanding of the interplay between these two pathways particularly crucial. In this review, the importance of the maternal metabolic status of B6 for the flow of one-carbon units towards both maternal and embryonic GPX systems is discussed. Additionally, B6 effects on GPX activity and gene expression in dams, as well as embryo development, are presented in a pig model under different oxidative stress conditions. PMID:28245568

  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. Association of aberrations in one-carbon metabolism with molecular phenotype and grade of breast cancer.

    Science.gov (United States)

    Naushad, Shaik Mohammad; Pavani, Addepalli; Rupasree, Yedluri; Divyya, Shree; Deepti, Sripurna; Digumarti, Raghunadha Rao; Gottumukkala, Suryanarayana Raju; Prayaga, Aruna; Kutala, Vijay Kumar

    2012-10-01

    We have earlier demonstrated the role of aberrant one-carbon metabolism in the etiology of breast cancer. In the current study, we examine the clinical utility of these factors in predicting the subtype of breast cancer and as indicators of disease progression. Polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) and PCR-amplified fragment length polymorphism (AFLP) approaches were used for genetic analysis. Plasma folate and homocysteine were measured using Axsym folate kit and reverse phase HPLC, respectively. Multiple linear regression models were used to test the predictability of disease progression. Luminal A subtype was associated with late age of onset, higher body mass index and lack of family history of breast cancer. Thymidylate synthase (TYMS) 5'-UTR 28 bp tandem repeat (OR: 2.09, 95% CI: 1.05-4.16) and methylene tetrahydrofolate reductase (MTHFR) C677T (OR: 4.10, 95% CI: 1.40-11.95) were strongly associated with Luminal B. Reduced folate carrier (RFC1) G80A (OR: 2.92, 95% CI: 1.22-6.97) and methionine synthase (MTR) A2756G (OR: 4.71, 95% CI: 1.66-13.31) polymorphisms were associated with LuminA-HH subtype while MTHFR C677T showed association with HER-enriched (OR: 30.41, 95% CI: 6.47-142.91). Cytosolic serine hydroxymethyltransferase (cSHMT) conferred protection against basal-like breast cancer (OR: 0.47, 95% CI: 0.22-0.98). HER-enriched and basal-like subtypes showed positive association with familial breast cancer and inverse association with plasma folate. Hyperhomocysteinemia was observed in Luminal B and basal-like subtypes. Multiple linear regression models of aberrant one-carbon metabolism were found to be moderate predictors of breast cancer grade (area under the receiver operating characteristic curve, C = 0.72, 95% CI: 0.58-0.87, P = 0.008). To conclude, aberrations in one-carbon metabolism predict the subtype of breast cancer and disease progression.

  8. Essential roles of four-carbon backbone chemicals in the control of metabolism

    Institute of Scientific and Technical Information of China (English)

    Sabrina; Chriett; Luciano; Pirola

    2015-01-01

    The increasing incidence of obesity worldwide and its related cardiometabolic complications is an urgent public health problem. While weight gain results from a negative balance between the energy expenditure and calorie intake, recent research has demonstrated that several small organic molecules containing a four-carbon backbone can modulate this balance by favoring energy expenditure, and alleviating endoplasmic reticulum stress and oxidative stress. Such small molecules include the bacterially produced short chain fatty acid butyric acid, its chemically produced derivative 4-phenylbutyric acid, the main ketone body D-β-hydroxybutyrate- synthesized by the liver- and the recently discovered myokine β-aminoisobutyric acid. Conversely, another butyraterelated molecule, α-hydroxybutyrate, has been found to be an early predictor of insulin resistance and glucose intolerance. In this minireview, we summarize recent advances in the understanding of the mechanism of action of these molecules, and discuss their use as therapeutics to improve metabolic homeostasis or their detection as early biomarkers of incipient insulin resistance.

  9. 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.

  10. Seed priming improves chilling tolerance in chickpea by modulating germination metabolism, trehalose accumulation and carbon assimilation.

    Science.gov (United States)

    Farooq, Muhammad; Hussain, Mubshar; Nawaz, Ahmad; Lee, Dong-Jin; Alghamdi, Salem S; Siddique, Kadambot H M

    2017-02-01

    Chilling stress is one of the major abiotic stresses affecting chickpea productivity worldwide. This study evaluated the potential role of seed priming in improving resistance to chilling stress in chickpea (cv. Punjab, 2008). The priming treatments involved soaking seeds of chickpea cultivar Punjab 2008 in either water for 8 h (on-farm priming), aerated water (hydropriming) for 18 h, or CaCl2 solution (ψs -1.25 MPa; osmopriming) for 18 h. Primed and untreated seeds were grown either at 18/15 °C (control) or 13/10 °C (chilling stress). Chilling stress suppressed the growth of chickpea while seed priming mitigated the adverse effects of chilling stress by improving stand establishment, growth, water relations, photosynthesis, α-amylase activity, sugar metabolism, antioxidant enzyme activity, membrane stability, and leaf accumulation of proline, nitrogen, potassium and soluble phenolics. Seed priming also improved the performance of chickpea under optimal (control) conditions. The overall order of improvement in resistance to chilling by using seed priming was osmopriming > hydropriming > on-farm priming. Osmopriming improved seedling dry weight, specific leaf area, leaf CO2 net assimilation rate, maximal photochemical efficiency of PSII, α-amylase activity, trehalose content and leaf relative water content by 10, 22, 17, 20, 73, 48 and 7%, respectively, relative to the non-primed control under chilling stress. Under optimal temperature conditions, the corresponding values were 30, 32, 16, 10, 83, 75 and 5%, respectively. Sugar metabolism, especially trehalose content, was strongly linked with stand establishment, photosynthesis, antioxidant potential (under chilling stress) and plant biomass. Overall, seed priming improved chickpea performance under both optimal temperature conditions and chilling stress through better germination metabolism and the accumulation of trehalose, which protected from oxidative damage and helped to maintain carbon

  11. Effects of oxidative stress on fatty acid- and one-carbon-metabolism in psychiatric and cardiovascular disease comorbidity

    NARCIS (Netherlands)

    Assies, J.; Mocking, R.J.; Lok, A.; Ruhe, H.G.; Pouwer, F.; Schene, A.H.

    2014-01-01

    OBJECTIVE: Cardiovascular disease (CVD) is the leading cause of death in severe psychiatric disorders (depression, schizophrenia). Here, we provide evidence of how the effects of oxidative stress on fatty acid (FA) and one-carbon (1-C) cycle metabolism, which may initially represent adaptive respons

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

    Directory of Open Access Journals (Sweden)

    Bin Rui

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

  13. Effects of oxidative stress on fatty acid- and one-carbon-metabolism in psychiatric and cardiovascular disease comorbidity

    NARCIS (Netherlands)

    Assies, J.; Mocking, R. J. T.; Lok, A.; Ruhe, H. G.; Pouwer, F.; Schene, A. H.

    2014-01-01

    Objective: Cardiovascular disease (CVD) is the leading cause of death in severe psychiatric disorders (depression, schizophrenia). Here, we provide evidence of how the effects of oxidative stress on fatty acid (FA) and one-carbon (1-C) cycle metabolism, which may initially represent adaptive respons

  14. METABOLISM

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    Objective: To determine the allele frequencies of genetic variants 373 Ala→Pro and 451 Arg→Gln of cholesteryl ester transfer protein (CETP) and to explore their potential impacts on serum lipid metabolism. Methods: The genotypes in CETP codon 373 and 451 in 91 German healthy students and 409 an-

  15. 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.

  16. Unveiling neutrino mixing and leptonic CP violation

    Energy Technology Data Exchange (ETDEWEB)

    Mena, Olga; /Fermilab

    2005-01-01

    We review the present understanding of neutrino masses and mixings, discussing what are the unknowns in the three family oscillation scenario. Despite the anticipated success coming from the planned long baseline neutrino experiments in unraveling the leptonic mixing sector, there are two important unknowns which may remain obscure: the mixing angle {theta}{sub 13} and the CP-phase {delta}. The measurement of these two parameters has led us to consider the combination of superbeams and neutrino factories as the key to unveil the neutrino oscillation picture.

  17. Primitive Form of Bony Fish Unveiled

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    @@ With over 50,000 species,Osteichthyans, or bony fish, accounts for 98% of the present-day vertebrates. Bony fish falls into two groups: actinopterygians, meaning ray-finned bony fish, and sarcopterygians,meaning lobe-finned bony fish. The huge morphotype difference of the two catagories cast doubts on research into the origin and evolution of bony fish. The recent discovery of a primitive fish species by CAS researchers and their overseas colleagues provides a missing link between the two lineages, unveiling unique features for understanding primitive bony vertebrates.

  18. 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.

  19. 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.

  20. Oxygen-18 incorporation into malic acid during nocturnal carbon dioxide fixation in crassulacean acid metabolism plants: a new approach to estimating in vivo carbonic anhydrase activity

    Energy Technology Data Exchange (ETDEWEB)

    Holtum, J.A.M.; Summons, R.; Roeske, C.A.; Comins, H.N.; O' Leary, M.H.

    1984-01-01

    Crassulacean acid metabolism (CAM) plants fix carbon dioxide at night by the carboxylation of phosphoenolpyruvate. If CO2 fixation is conducted with TC YO2, then in the absence of carbonic anhydrase, the malate formed by dark CO2 fixation should also contain high levels of carbon-13 and oxygen-18. Conversely, if carbonic anhydrase is present and highly active, oxygen exchange between CO2 and cellular H2O will occur more rapidly than carboxylation, and the ( TC) malate formed will contain little or no oxygen-18 above the natural abundance level. The presence of oxygen-18 in these molecules can be detected either by nuclear magnetic resonance or by mass spectrometry. Studies of phosphoenolpyruvate carboxylase in the presence and absence of carbonic anhydrase in vitro confirm the validity of the method. When CAM plants are studied by this method, we find that most species show incorporation of a significant amount of oxygen-18. Comparison of these results with results of isotope fractionation and gas exchange studies permits calculation of the in vivo activity of carbonic anhydrase toward HCO3 compared with that of phosphoenolpyruvate carboxylase. The ratio (carbonic anhydrase activity/phosphoenolpyruvate carboxylase activity) is species dependent and varies from a low of about 7 for Ananas comosus to values near 20 for Hoya carnosa and Bryophyllum pinnatum, 40 for Kalanchoee daigremontiana, and 100 or greater for Bryophyllum tubiflorum, Kalanchoee serrata, and Kalanchoae tomentosa. Carbonic anhydrase activity increases relative to phosphoenolpyruvate carboxylase activity at higher temperature. 37 references, 2 figures, 8 tables.

  1. Association between in vivo alcohol metabolism and genetic variation in pathways that metabolize the carbon skeleton of ethanol and NADH reoxidation in the Alcohol Challenge Twin Study

    Science.gov (United States)

    Lind, Penelope A; Macgregor, Stuart; Heath, Andrew C; Madden, Pamela AF; Montgomery, Grant W; Martin, Nicholas G; Whitfield, John B

    2013-01-01

    Background Variation in alcohol metabolism affects the duration of intoxication and alcohol use. While the majority of genetic association studies investigating variation in alcohol metabolism have focused on polymorphisms in alcohol or aldehyde dehydrogenases, we have now tested for association with genes in alternative metabolic pathways that catalyze the carbon skeleton of ethanol and NADH reoxidation. Methods 950 single nucleotide polymorphisms (SNPs) spanning 14 genes (ACN9, ACSS1, ACSS2, ALDH1A1, CAT, CYP2E1, GOT1, GOT2, MDH1, MDH2, SLC25A10, SLC25A11, SLC25A12, SLC25A13) were genotyped in 352 young adults who participated in an alcohol challenge study. Traits tested were blood and breath alcohol concentration, peak alcohol concentration and rates of alcohol absorption and elimination. Allelic association was tested using quantitative univariate and multivariate methods. Results A CYP2E1 promoter SNP (rs4838767, minor allele frequency 0.008) exceeded the threshold for study-wide significance (4.01 × 10−5) for two early blood alcohol concentration (BAC), eight breath alcohol concentration (BrAC) measures and the peak BrAC. For each phenotype the minor C-allele was related to a lower alcohol concentration, most strongly for the fourth BrAC (P = 2.07 × 10−7) explaining ~8% of the phenotypic variance. We also observed suggestive patterns of association with variants in ALDH1A1 and on chromosome 17 near SLC25A11 for aspects of blood and breath alcohol metabolism. A SNP upstream of GOT1 (rs2490286) reached study-wide significance for multivariate BAC metabolism (P = 0.000040). Conclusions Overall, we did not find strong evidence that variation in genes coding for proteins that further metabolize the carbon backbone of acetaldehyde, or contribute to mechanisms for regenerating NAD from NADH, affects alcohol metabolism in our European-descent subjects. However, based on the breath alcohol data, variation in the promoter of CYP2E1 may play a role in pre

  2. Betaine supplementation prevents fatty liver induced by a high-fat diet: effects on one-carbon metabolism.

    Science.gov (United States)

    Deminice, Rafael; da Silva, Robin P; Lamarre, Simon G; Kelly, Karen B; Jacobs, René L; Brosnan, Margaret E; Brosnan, John T

    2015-04-01

    The purpose of this study was to examine the effects of betaine supplementation on the regulation of one-carbon metabolism and liver lipid accumulation induced by a high-fat diet in rats. Rats were fed one of three different liquid diets: control diet, high-fat diet and high-fat diet supplemented with betaine. The control and high-fat liquid diets contained, respectively, 35 and 71 % of energy derived from fat. Betaine supplementation involved the addition of 1 % (g/L) to the diet. After three weeks on the high-fat diet the rats had increased total liver fat concentration, liver triglycerides, liver TBARS and plasma TNF-α. The high-fat diet decreased the hepatic S-adenosylmethionine concentration and the S-adenosylmethionine/S-adenosylhomocysteine ratio compared to the control as well as altering the expression of genes involved in one-carbon metabolism. Betaine supplementation substantially increased the hepatic S-adenosylmethionine concentration (~fourfold) and prevented fatty liver and hepatic injury induced by the high-fat diet. It was accompanied by the normalization of the gene expression of BHMT, GNMT and MGAT, which code for key enzymes of one-carbon metabolism related to liver fat accumulation. In conclusion, the regulation of the expression of MGAT by betaine supplementation provides an additional and novel mechanism by which betaine supplementation regulates lipid metabolism and prevents accumulation of fat in the liver.

  3. 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.

  4. A Candidate Gene Study of Folate-Associated One Carbon Metabolism Genes and Colorectal Cancer Risk

    Science.gov (United States)

    Levine, A. Joan; Figueiredo, Jane C.; Lee, Won; Conti, David V.; Kennedy, Kathleen; Duggan, David J; Poynter, Jenny N.; Campbell, Peter T.; Newcomb, Polly; Martinez, Maria Elena; Hopper, John L.; Le Marchand, Loic; Baron, John A.; Limburg, Paul J.; Ulrich, Cornelia M.; Haile, Robert W.

    2010-01-01

    Background Folate-associated one carbon metabolism (FOCM) may play an important role in colorectal carcinogenesis. Variation in FOCM genes may explain some of the underlying risk of colorectal cancer. Methods This study utilized data from 1,805 population-based colorectal cancer cases and 2,878 matched sibling controls from the Colon Cancer Family Registry (C-CFR). We used a comprehensive tagSNP approach to select 395 tagSNPs in 15 genes involved in folate and vitamin B12 metabolism. Genotyping was performed using the Illumina GoldenGate or Sequenom platforms. Risk factor and dietary data were collected using self-completed questionnaires. MSI status was determined using standard techniques and tumor subsite was obtained from pathology reports. The association between SNPs and colorectal cancer was assessed using conditional logistic regression with sibships as the matching factor and assuming a log additive or co-dominant model. Results In the log additive model, two linked (r2=0.99) tagSNPs in the DHFR gene (rs1677693 and rs1643659) were associated with a significant decrease in CRC risk after correction for multiple testing (OR=0.87; 95% CI=0.71 – 0.94; P=0.029 and OR=0.87 95% CI=0.71 – 0.95, P=0.034 for rs1677693 and rs1643659 respectively. These two linked (r2=0.99) tagSNPs and one tagSNP in the MTR gene (rs4659744) were significantly associated with reduced CRC risk only among individuals not using multivitamin supplements. Conclusions Overall, we found only moderate evidence that genetic variation in 15 folate pathway genes may affect CRC risk except in non multivitamin users. Impact This study suggests that multivitamin supplement use may modify the association between folate pathway genes and CRC risk in a post folic acid supplemented population. PMID:20615890

  5. Long-term monitoring reveals carbon-nitrogen metabolism key to microcystin production in eutrophic lakes

    Directory of Open Access Journals (Sweden)

    Lucas J Beversdorf

    2015-05-01

    Full Text Available The environmental drivers contributing to cyanobacterial dominance in aquatic systems have been extensively studied. However, understanding of toxic versus non-toxic cyanobacterial population dynamics and the mechanisms regulating cyanotoxin production remain elusive, both physiologically and ecologically. One reason is the disconnect between laboratory and field-based studies. Here, we combined three years of temporal data, including microcystin (MC concentrations, 16 years of long-term ecological research, and 10 years of molecular data to investigate the potential factors leading to the selection of toxic Microcystis and MC production. Our analysis revealed that nitrogen (N speciation and inorganic carbon (C availability might be important drivers of Microcystis population dynamics and that an imbalance in cellular C: N ratios may trigger MC production. More specifically, precipitous declines in ammonium concentrations lead to a transitional period of N stress, even in the presence of high nitrate concentrations, that we call the toxic phase. Following the toxic phase, temperature and cyanobacterial abundance remained elevated but MC concentrations drastically declined. Increases in ammonium due to lake turnover may have led to down regulation of MC synthesis or a shift in the community from toxic to non-toxic species. While total phosphorus (P to total N ratios were relatively low over the time-series, MC concentrations were highest when total N to total P ratios were also highest. Similarly, high C: N ratios were also strongly correlated to the toxic phase. We propose a metabolic model that corroborates molecular studies and reflects our ecological observations that C and N metabolism may regulate MC production physiologically and ecologically. In particular, we hypothesize that an imbalance between 2-oxoglutarate and ammonium in the cell regulates MC synthesis in the environment.

  6. Effect of Mitochondrial Dysfunction on Carbon Metabolism and Gene Expression in Flower Tissues of Arabidopsis thaliana

    Institute of Scientific and Technical Information of China (English)

    Maria V.Busi; Maria E.Gomez-Lobato; Sebastian P.Rius; Valeria R.Turowski; Paula Casati; Eduardo J.Zabaleta; Diego F.Gomez-Casati; Alejandro Araya

    2011-01-01

    We characterized the transcriptomic response of transgenic plants carrying a mitochondrial dysfunction induced by the expression of the unedited form of the ATP synthase subunit 9.The u-ATP9 transgene driven by A9 and APETALA3 promoters induce mitochondrial dysfunction revealed by a decrease jn both oxygen uptake and adenine nucleotides(ATP,ADP)levels without changes in the ATP/ADP ratio.Furthermore,we measured an increase in ROS accumulation and a decrease in glutathione and ascorbate levels with a concomitant oxidative stress response.The transcriptome analysis of young Arabidopsis flowers,validated by Qrt-PCR and enzymatic or functional tests,showed dramatic changes in u-ATP9 plants.Both lines display a modification in the expression of various genes involved in carbon,lipid,and cell wall metabolism,suggesting that an important metabolic readjustment occurs in plants with a mitochondrial dysfunction.Interestingly,transcript levels involved in mitochondrial respiration,protein synthesis,and degradation are affected.Moreover,the Ievels of several mRNAs encoding for transcription factors and DNA binding proteins were also changed.Some of them are involved in stress and hormone responses,suggesting that several signaling pathways overlap.Indeed,the transcriptome data revealed that the mitochondrial dysfunction dramatically alters the expression of genes involved in signaling pathways,including those related to ethylene,absicic acid,and auxin signal transduction.Our data suggest that the mitochondrial dysfunction model used in this report may be usefuI to uncover the retrograde signaling mechanism between the nucleus and mitochondria in plant cells.

  7. Dynamic proteomic analysis reveals a switch between central carbon metabolism and alcoholic fermentation in rice filling grains.

    Science.gov (United States)

    Xu, Sheng Bao; Li, Tang; Deng, Zhu Yun; Chong, Kang; Xue, Yongbiao; Wang, Tai

    2008-10-01

    Accumulation of reserve materials in filling grains involves the coordination of different metabolic and cellular processes, and understanding the molecular mechanisms underlying the interconnections remains a major challenge for proteomics. Rice (Oryza sativa) is an excellent model for studying grain filling because of its importance as a staple food and the available genome sequence database. Our observations showed that embryo differentiation and endosperm cellularization in developing rice seeds were completed approximately 6 d after flowering (DAF); thereafter, the immature seeds mainly underwent cell enlargement and reached the size of mature seeds at 12 DAF. Grain filling began at 6 DAF and lasted until 20 DAF. Dynamic proteomic analyses revealed 396 protein spots differentially expressed throughout eight sequential developmental stages from 6 to 20 DAF and determined 345 identities. These proteins were involved in different cellular and metabolic processes with a prominently functional skew toward metabolism (45%) and protein synthesis/destination (20%). Expression analyses of protein groups associated with different functional categories/subcategories showed that substantially up-regulated proteins were involved in starch synthesis and alcoholic fermentation, whereas the down-regulated proteins in the process were involved in central carbon metabolism and most of the other functional categories/subcategories such as cell growth/division, protein synthesis, proteolysis, and signal transduction. The coordinated changes were consistent with the transition from cell growth and differentiation to starch synthesis and clearly indicated that a switch from central carbon metabolism to alcoholic fermentation may be important for starch synthesis and accumulation in the developmental process.

  8. Vision changes after spaceflight are related to alterations in folate- and vitamin B-12-dependent one-carbon metabolism.

    Science.gov (United States)

    Zwart, Sara R; Gibson, C Robert; Mader, Thomas H; Ericson, Karen; Ploutz-Snyder, Robert; Heer, Martina; Smith, Scott M

    2012-03-01

    Approximately 20% (7 of 38) of astronauts on International Space Station (ISS) missions have developed measurable ophthalmic changes after flight. This study was conducted to determine if the folate- and vitamin B-12-dependent 1-carbon metabolic pathway is altered in these individuals. Since 2006, we have conducted experiments on the ISS to evaluate nutritional status and related biochemical indices of astronauts before, during, and after flight. Data were modeled to evaluate differences between individuals with ophthalmic changes (n = 5) and those without them (n = 15), all of whom were on ISS missions of 48-215 d. We also determined whether mean preflight serum concentrations of the 1-carbon metabolites and changes in measured cycloplegic refraction after flight were associated. Serum homocysteine (Hcy), cystathionine, 2-methylcitric acid (2MCA), and methylmalonic acid concentrations were 25-45% higher (P refraction (P < 0.05), and preflight serum concentrations of 2MCA tended to be associated (P = 0.06) with ophthalmic changes. The biochemical differences observed in crewmembers with vision issues strongly suggest that their folate- and vitamin B-12-dependent 1-carbon transfer metabolism was affected before and during flight. The consistent differences in markers of 1-carbon metabolism between those who did and those who did not develop changes in vision suggest that polymorphisms in enzymes of this pathway may interact with microgravity to cause these pathophysiologic changes.

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

    Directory of Open Access Journals (Sweden)

    Jiménez-Zurdo José I

    2010-03-01

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

  10. Anaerobic hydrocarbon and fatty acid metabolism by syntrophic bacteria and their impact on carbon steel corrosion

    Directory of Open Access Journals (Sweden)

    Christopher Neil Lyles

    2014-04-01

    Full Text Available The microbial metabolism of hydrocarbons is increasingly associated with the corrosion of carbon steel in sulfate-rich marine waters. However, how such transformations influence metal biocorrosion in the absence of an electron acceptor is not fully recognized. We grew a marine alkane-utilizing, sulfate-reducing bacterium, Desulfoglaeba alkanexedens, with either sulfate or Methanospirillum hungatei as electron acceptors, and tested the ability of the cultures to catalyze metal corrosion. Axenically, D. alkanexedens had a higher instantaneous corrosion rate and produced more pits in carbon steel coupons than when the same organism was grown in syntrophic co-culture with the methanogen. Since anaerobic hydrocarbon biodegradation pathways converge on fatty acid intermediates, the corrosive ability of a known fatty acid-oxidizing syntrophic bacterium, Syntrophus aciditrophicus was compared when grown in pure culture or in co-culture with a H2-utilizing sulfate-reducing bacterium (Desulfovibrio sp., strain G11 or a methanogen (M. hungatei. The instantaneous corrosion rates in the cultures were not substantially different, but the syntrophic, sulfate-reducing co-culture produced more pits in coupons than other combinations of microorganisms. Lactate-grown cultures of strain G11 had higher instantaneous corrosion rates and coupon pitting compared to the same organism cultured with hydrogen as an electron donor. Thus, if sulfate is available as an electron acceptor, the same microbial assemblages produce sulfide and low molecular weight organic acids that exacerbated biocorrosion. Despite these trends, a surprisingly high degree of variation was encountered with the corrosion assessments. Differences in biomass, initial substrate concentration, rates of microbial activity or the degree of end product formation did not account for the variations. We are forced to ascribe such differences to the metallurgical properties of the coupons.

  11. Anaerobic hydrocarbon and fatty acid metabolism by syntrophic bacteria and their impact on carbon steel corrosion.

    Science.gov (United States)

    Lyles, Christopher N; Le, Huynh M; Beasley, William Howard; McInerney, Michael J; Suflita, Joseph M

    2014-01-01

    The microbial metabolism of hydrocarbons is increasingly associated with the corrosion of carbon steel in sulfate-rich marine waters. However, how such transformations influence metal biocorrosion in the absence of an electron acceptor is not fully recognized. We grew a marine alkane-utilizing, sulfate-reducing bacterium, Desulfoglaeba alkanexedens, with either sulfate or Methanospirillum hungatei as electron acceptors, and tested the ability of the cultures to catalyze metal corrosion. Axenically, D. alkanexedens had a higher instantaneous corrosion rate and produced more pits in carbon steel coupons than when the same organism was grown in syntrophic co-culture with the methanogen. Since anaerobic hydrocarbon biodegradation pathways converge on fatty acid intermediates, the corrosive ability of a known fatty acid-oxidizing syntrophic bacterium, Syntrophus aciditrophicus was compared when grown in pure culture or in co-culture with a H2-utilizing sulfate-reducing bacterium (Desulfovibrio sp., strain G11) or a methanogen (M. hungatei). The instantaneous corrosion rates in the cultures were not substantially different, but the syntrophic, sulfate-reducing co-culture produced more pits in coupons than other combinations of microorganisms. Lactate-grown cultures of strain G11 had higher instantaneous corrosion rates and coupon pitting compared to the same organism cultured with hydrogen as an electron donor. Thus, if sulfate is available as an electron acceptor, the same microbial assemblages produce sulfide and low molecular weight organic acids that exacerbated biocorrosion. Despite these trends, a surprisingly high degree of variation was encountered with the corrosion assessments. Differences in biomass, initial substrate concentration, rates of microbial activity or the degree of end product formation did not account for the variations. We are forced to ascribe such differences to the metallurgical properties of the coupons.

  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. 2004 Molecular Basis of Microbial One-Carbon Metabolism Gordon Conference - August 1-6, 2004

    Energy Technology Data Exchange (ETDEWEB)

    Joseph A. Krzycki

    2005-09-15

    The Gordon Research Conference (GRC) on 2004 Molecular Basis of Microbial One-Carbon Metabolism Gordon Conference - August 1-6, 2004 was held at Mount Holyoke College, South Hadley, MA from August 1-6, 2004. The Conference was well-attended with 117 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students. In designing the formal speakers program, emphasis was placed on current unpublished research and discussion of the future target areas in this field. There was a conscious effort to stimulate lively discussion about the key issues in the field today. Time for formal presentations was limited in the interest of group discussions. In order that more scientists could communicate their most recent results, poster presentation time was scheduled. Attached is a copy of the formal schedule and speaker program and the poster program. In addition to these formal interactions, 'free time' was scheduled to allow informal discussions. Such discussions are fostering new collaborations and joint efforts in the field.

  14. [Use of genes of carbon metabolism enzymes as molecular markers of Chlorobi Phylum representatives].

    Science.gov (United States)

    Turova, T P; Kovaleva, O L; Gorlenko, V M; Ivanovskiĭ, R N

    2014-01-01

    This work examined the feasibility of using certain genes of carbon metabolism enzymes as molecular markers adequate for studying phylogeny and ecology of green sulfur bacteria (GSB) of the Chlorobi phylum. Primers designed to amplify the genes of ATP citrate lyase (aclB) and citrate synthase (gltA) revealed the respective genes in the genomes of all of the newly studied GSB strains. The phylogenetic trees constructed based on nucleotide sequences of these genes and amino acid sequences of the conceptually translated proteins were on the whole congruent with the 16S rRNA gene tree, with the single exception of GltA of Chloroherpeton thalassium, which formed a separate branch beyond the cluster comprised by other representatives of the Chlorobi phylum. Thus, the aclB genes but not gltA genes proved to be suitable for the design of primers specific to all Chlorobi representatives. Therefore, it was the aclB gene that was further used asa molecular marker to detect GSB in enrichment cultures and environmental samples. AclB phylotypes of GSB were revealed in all of the samples studied, with the exception of environmental samples from soda lakes. The identification of the revealed phylotypes was in agreement with the identification based on the FMO protein gene (fmo), is a well-known Chlorobi-specific molecular marker.

  15. Environmental regulation of carbon isotope composition and crassulacean acid metabolism in three plant communities along a water availability gradient

    OpenAIRE

    2010-01-01

    Expression of crassulacean acid metabolism (CAM) is characterized by extreme variability within and between taxa and its sensitivity to environmental variation. In this study, we determined seasonal fluctuations in CAM photosynthesis with measurements of nocturnal tissue acidification and carbon isotopic composition (δ13C) of bulk tissue and extracted sugars in three plant communities along a precipitation gradient (500, 700, and 1,000 mm year−1) on the Yucatan Peninsula. We also related the ...

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

    Science.gov (United States)

    Wallenius, Janne; Maaheimo, Hannu; Eerikäinen, Tero

    2016-11-01

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

  17. 13C-MFA delineates the photomixotrophic metabolism of Synechocystis sp. PCC 6803 under light- and carbon-sufficient conditions.

    Science.gov (United States)

    You, Le; Berla, Bert; He, Lian; Pakrasi, Himadri B; Tang, Yinjie J

    2014-05-01

    The central carbon metabolism of cyanobacteria is under debate. For over 50 years, the lack of α-ketoglutarate dehydrogenase has led to the belief that cyanobacteria have an incomplete TCA cycle. Recent in vitro enzymatic experiments suggest that this cycle may in fact be closed. The current study employed (13) C isotopomers to delineate pathways in the cyanobacterium Synechocystis sp. PCC 6803. By tracing the incorporation of supplemented glutamate into the downstream metabolites in the TCA cycle, we observed a direct in vivo transformation of α-ketoglutarate to succinate. Additionally, isotopic tracing of glyoxylate did not show a functional glyoxylate shunt and glyoxylate was used for glycine synthesis. The photomixotrophic carbon metabolism was then profiled with (13) C-MFA under light and carbon-sufficient conditions. We observed that: (i) the in vivo flux through the TCA cycle reactions (α-ketoglutarate → succinate) was minimal (<2%); (ii) the flux ratio of CO2 fixation was six times higher than that of glucose utilization; (iii) the relative flux through the oxidative pentose phosphate pathway was low (<2%); (iv) high flux through malic enzyme served as a main route for pyruvate synthesis. Our results improve the understanding of the versatile metabolism in cyanobacteria and shed light on their application for photo-biorefineries.

  18. 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.

  19. Choline and methionine differentially alter methyl carbon metabolism in bovine neonatal hepatocytes

    Science.gov (United States)

    Chandler, Tawny L.

    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

  20. 13C-metabolic flux ratio and novel carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose

    Directory of Open Access Journals (Sweden)

    Saloheimo Markku

    2009-10-01

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

  1. Reconstruction of central carbon metabolism in Sulfolobus solfataricus using a two-dimensional gel electrophoresis map, stable isotope labelling and DNA microarray analysis

    NARCIS (Netherlands)

    Snijders, B.P.L.; Walther, J.; Peter, S.; Kinnman, I.; Vos, de M.J.G.; Werken, van de H.J.G.; Brouns, S.J.J.; Oost, van der J.; Wright, P.C.

    2006-01-01

    In the last decade, an increasing number of sequenced archaeal genomes have become available, opening up the possibility for functional genomic analyses. Here, we reconstructed the central carbon metabolism in the hyperthermophilic crenarchaeon Sulfolobus solfataricus (glycolysis, gluconeogenesis an

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

    Directory of Open Access Journals (Sweden)

    Hammami Ines

    2012-07-01

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

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

    Science.gov (United States)

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

    2016-08-01

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

  4. 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.

  5. Metabolic engineering of Escherichia coli for the production of putrescine: a four carbon diamine.

    Science.gov (United States)

    Qian, Zhi-Gang; Xia, Xiao-Xia; Lee, Sang Yup

    2009-11-01

    A four carbon linear chain diamine, putrescine (1,4-diaminobutane), is an important platform chemical having a wide range of applications in chemical industry. Biotechnological production of putrescine from renewable feedstock is a promising alternative to the chemical synthesis that originates from non-renewable petroleum. Here we report development of a metabolically engineered strain of Escherichia coli that produces putrescine at high titer in glucose mineral salts medium. First, a base strain was constructed by inactivating the putrescine degradation and utilization pathways, and deleting the ornithine carbamoyltransferase chain I gene argI to make more precursors available for putrescine synthesis. Next, ornithine decarboxylase, which converts ornithine to putrescine, was amplified by a combination of plasmid-based and chromosome-based overexpression of the coding genes under the strong tac or trc promoter. Furthermore, the ornithine biosynthetic genes (argC-E) were overexpressed from the trc promoter, which replaced the native promoter in the genome, to increase the ornithine pool. Finally, strain performance was further improved by the deletion of the stress responsive RNA polymerase sigma factor RpoS, a well-known global transcription regulator that controls the expression of ca. 10% of the E. coli genes. The final engineered E. coli strain was able to produce 1.68 g L(-1) of putrescine with a yield of 0.168 g g(-1) glucose. Furthermore, high cell density cultivation allowed production of 24.2 g L(-1) of putrescine with a productivity of 0.75 g L(-1) h(-1). The strategy reported here should be useful for the bio-based production of putrescine from renewable resources, and also for the development of strains capable of producing other diamines, which are important as nitrogen-containing platform chemicals.

  6. Chemistry union unveils names of four new elements

    Science.gov (United States)

    Johnston, Hamish

    2016-07-01

    The periodic table could soon be graced by four new symbols - Nh, Mc, Ts and Og - after the International Union of Pure and Applied Chemistry (IUPAC) unveiled its proposed names for the four most recently discovered elements.

  7. Phosphate binders and metabolic acidosis in patients undergoing maintenance hemodialysis—sevelamer hydrochloride, calcium carbonate, and bixalomer.

    Science.gov (United States)

    Sanai, Toru; Tada, Hideo; Ono, Takashi; Fukumitsu, Toma

    2015-01-01

    The serum bicarbonate (HCO3(-)) levels are decreased in chronic hemodialysis (HD) patients treated with sevelamer hydrochloride (SH). We assessed the effects of bixalomer on the chronic metabolic acidosis in these patients. We examined 12 of the 122 consecutive Japanese patients with end-stage renal disease on HD, who orally ingested a dose of SH (≥2250 mg), and an arterial blood gas analysis and biochemical analysis were performed before HD. Patients whose serum HCO3(-) levels were under 18 mmol/L were changed from SH to the same dose of bixalomer. A total of 12 patients were treated with a large amount of SH. Metabolic acidosis (a serum HCO3(-) level under 18 mmol/L) was found in eight patients. These patients were also treated with or without small dose of calcium carbonate (1.2 ± 1.1 g). The dose of SH was changed to that of bixalomer. After 1 month, the serum HCO3(-) levels increased from 16.3 ± 1.4 to 19.6 ± 1.7 mmol/L (P Metabolic acidosis was not observed in four patients (serum HCO3(-) level: 20.3 ± 0.7 mmol/L) likely because they were taking 3 g of calcium carbonate with SH. In the present study, the development of chronic metabolic acidosis was induced by HCl containing phosphate binders, such as SH, and partially ameliorated by calcium carbonate, then subsequently improved after changing the treatment to bixalomer.

  8. Growth and metabolism of Saccharomyces cerevisiae in chemostat cultures under carbon-, nitrogen-, or carbon- and nitrogen-limiting conditions.

    OpenAIRE

    Larsson, C; von Stockar, U.; Marison, I; Gustafsson, L.

    1993-01-01

    Aerobic chemostat cultures of Saccharomyces cerevisiae were performed under carbon-, nitrogen-, and dual carbon- and nitrogen-limiting conditions. The glucose concentration was kept constant, whereas the ammonium concentration was varied among different experiments and different dilution rates. It was found that both glucose and ammonium were consumed at the maximal possible rate, i.e., the feed rate, over a range of medium C/N ratios and dilution rates. To a small extent, this was due to a c...

  9. 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...

  10. Stable isotope probing and Raman spectroscopy for monitoring carbon flow in a food chain and revealing metabolic pathway.

    Science.gov (United States)

    Li, Mengqiu; Huang, Wei E; Gibson, Christopher M; Fowler, Patrick W; Jousset, Alexandre

    2013-02-05

    Accurately measuring carbon flows is a challenge for understanding processes such as diverse intracellular metabolic pathways and predator-prey interactions. Combined with stable isotope probing (SIP), single-cell Raman spectroscopy was demonstrated for the first time to link the food chain from carbon substrate to bacterial prey up to predators at the single-cell level in a quantitative and nondestructive manner. Escherichia coli OP50 with different (13)C content, which were grown in a mixture of (12)C- and fully carbon-labeled (13)C-glucose (99%) as a sole carbon source, were fed to the nematode. The (13)C signal in Caenorhabditis elegans was proportional to the (13)C content in E. coli. Two Raman spectral biomarkers (Raman bands for phenylalanine at 1001 cm(-1) and thymine at 747 cm(-1) Raman bands), were used to quantify the (13)C content in E. coli and C. elegans over a range of 1.1-99%. The phenylalanine Raman band was a suitable biomarker for prokaryotic cells and thymine Raman band for eukaryotic cells. A biochemical mechanism accounting for the Raman red shifts of phenylalanine and thymine in response to (13)C-labeling is proposed in this study and is supported by quantum chemical calculation. This study offers new insights of carbon flow via the food chain and provides a research tool for microbial ecology and investigation of biochemical pathways.

  11. 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 H2 and H5 emitted net GHGs -152.20kg CO2 eq. and -140.32kg CO2 eq., respectively, in comparison with 420.88kg CO2 eq. of scenario H1 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.

  12. 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.

  13. 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.

    2014-01-01

    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−1day−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. PMID:25954055

  14. Use of Position-Specific 13C Isotopomers to Examine Central Carbon Metabolism in the Thermophile 'Thermoflexus hugenholtzii'

    Science.gov (United States)

    Thomas, S.; Tamadonfar, K. O.; Dijkstra, P.; Dodsworth, J. A.; Hedlund, B. P.

    2013-12-01

    'Thermoflexus hugenholtzii' is a member of a newly discovered class of Chloroflexi. It is the dominant microorganism in certain hot springs; however, very little is known about its physiology, and it is unable to grow on defined media. In order to examine central carbon metabolism in 'T. hugenholtzii', the genome was annotated for genes encoding enzymes for central carbon metabolism, revealing complete pathways for glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway (PPP). Isotope experiments were conducted to test predicted activities by adding position-specific carbon-13 (13C)-labeled metabolites of glucose, pyruvate, acetate, TCA metabolites, and amino acids and measuring the production of 13CO2 during exponential growth. Use of these metabolites demonstrated broad heterotrophic activity of 'T. hugenholtzii,' despite its inability to grow on defined media. Use of glucose-U demonstrated an active glycolytic pathway and pyruvate-1 demonstrated the functioning of the pyruvate oxidation pathway after glycolysis. Use of the TCA cycle intermediates citrate and succinate demonstrated an active TCA cycle. Production of CO2 from alanine and cysteine demonstrated oxidation of amino acids. However, lack of activity on glucose-1 failed to reveal an active PPP suggesting 'T. hugenholtzii' may rely on exogenous sources of pentoses for nucleic acid biosynthesis.

  15. 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...

  16. Autism and Folate-dependent One-carbon Metabolism: Serendipity and Critical Branch-point Decisions in Science.

    Science.gov (United States)

    James, S Jill

    2013-11-01

    Folate-dependent one-carbon metabolism is present in every cell of the body. It represents a central systems biology hub that reverberates into countless other pathways with more specialized roles in specialized cell types throughout the body. I have spent 25 years of research on this core biochemical pathway with several unanticipated iterations that led me from Down syndrome to congenital heart defects to leukemia and finally to autism about 12 years ago. Figure 1 provides an overview of the three interdependent pathways involved in folate-dependent methionine "transmethylation" and "transsulfuration." Methionine is necessary for the synthesis of S-adenosylmethionine (SAM), the major methyl donor for all cellular methylation reactions. It is also the major precursor for cysteine, the rate-limiting amino acid for glutathione synthesis linking transmethylation and transsulfuration pathways. Methionine levels can be negatively affected by genetic and environmental factors that reduce folate availability and/or oxidative inhibition of the methionine synthase enzyme. Because these three metabolic pathways are mutually interdependent, genetic or environmental perturbation of folate or methionine metabolism will indirectly impact glutathione synthesis, and conversely, alterations in glutathione synthesis will alter flux through pathways of folate and methionine metabolism. This interdependency translates into broader impact on essential cellular functions.

  17. Does use of oral contraceptives enhance the toxicity of carbon disulfide through interactions with pyridoxine and tryptophan metabolism?

    Science.gov (United States)

    Calabrese, E J

    1980-01-01

    It is proposed that oral contraceptive (OC) users are at increased risk to experiencing adverse psychological disorders (e.g. irritability, depression) from exposures to elevated levels of carbon disulfide (CS2). This theory is based on studies indicating that both OCs and CS2 induce either a vitamin B6 deficiency and/or enhance its requirement. Since disruptions of B6 metabolism are thought to explain, at least in part, the adverse psychological effects of OCs and CS2, it is speculated that joint exposure to these substances may result in an exaggerated disruption of B6 metabolism with the development of CS2 induced adverse psychological effects occurring at exposure levels below those normally associated with adverse effects.

  18. The role of flexibility and optimality in the prediction of intracellular fluxes of microbial central carbon metabolism.

    Science.gov (United States)

    Tarlak, Fatih; Sadıkoğlu, Hasan; Çakır, Tunahan

    2014-07-29

    Prediction of intracellular metabolic fluxes based on optimal biomass assumption is a well-known computational approach. While there has been a significant emphasis on the optimality, cellular flexibility, the co-occurrence of suboptimal flux distributions in a microbial population, has hardly been considered in the related computational methods. We have implemented a flexibility-incorporated optimization framework to calculate intracellular fluxes based on a few extracellular measurement constraints. Taking into account slightly suboptimal flux distributions together with a dual-optimality framework (maximization of the growth rate followed by the minimization of the total enzyme amount) we were able to show the positive effect of incorporating flexibility and minimal enzyme consumption on the better prediction of intracellular fluxes of central carbon metabolism of two microorganisms: E. coli and S. cerevisiae.

  19. Inter-Strain Differences in Liver Injury and One-Carbon Metabolism in Alcohol-Fed Mice

    Science.gov (United States)

    Tsuchiya, Masato; Ji, Cheng; Kosyk, Oksana; Shymonyak, Svitlana; Melnyk, Stepan; Kono, Hiroshi; Tryndyak, Volodymyr; Muskhelishvili, Levan; Pogribny, Igor P.; Kaplowitz, Neil; Rusyn, Ivan

    2012-01-01

    Alcoholic liver injury is a major public health issue worldwide. Even though the major mechanisms of this disease have been established over the past decades, little is known about genetic susceptibility factors that may predispose individuals who abuse alcoholic beverages to liver damage and subsequent pathological conditions. We hypothesized that a panel of genetically diverse mouse strains may be used to examine the role of ER stress and one-carbon metabolism in the mechanism of inter-individual variability in alcoholic liver injury. We administered alcohol (up to 27 mg/kg/d) in high fat diet using intragastric intubation model for 28 days to male mice from 14 inbred strains (129S1/SvImJ, AKR/J, BALB/cJ, BALB/cByJ, BTBR T+tf/J, C3H/HeJ, C57BL/10J, DBA/2J, FVB/NJ, KK/HIJ, MOLF/EiJ, NZW/LacJ, PWD/PhJ, and WSB/EiJ). Profound inter-strain differences (more than 3-fold) in alcohol-induced steatohepatitis were observed among the strains in spite of consistently high levels of urine alcohol that was monitored throughout the study. We found that endoplasmic reticulum stress genes were induced only in strains with the highest liver injury. Liver glutathione and methyl donor levels were affected in all strains, albeit to a different degree. Most pronounced effects that were closely associated with the degree of liver injury were hyperhomocysteinemia and strain-dependent differences in expression patterns of one-carbon metabolism-related genes. Conclusion Our data demonstrate that strain differences in alcohol-induced liver injury and steatosis are striking and independent of alcohol exposure and the most severely affected strains exhibit major differences in the expression of ER stress markers and genes of one-carbon metabolism. PMID:22307928

  20. 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

  1. Untangling the role of one-carbon metabolism in colorectal cancer risk: a comprehensive Bayesian network analysis

    Science.gov (United States)

    Myte, Robin; Gylling, Björn; Häggström, Jenny; Schneede, Jörn; Magne Ueland, Per; Hallmans, Göran; Johansson, Ingegerd; Palmqvist, Richard; Van Guelpen, Bethany

    2017-01-01

    The role of one-carbon metabolism (1CM), particularly folate, in colorectal cancer (CRC) development has been extensively studied, but with inconclusive results. Given the complexity of 1CM, the conventional approach, investigating components individually, may be insufficient. We used a machine learning-based Bayesian network approach to study, simultaneously, 14 circulating one-carbon metabolites, 17 related single nucleotide polymorphisms (SNPs), and several environmental factors in relation to CRC risk in 613 cases and 1190 controls from the prospective Northern Sweden Health and Disease Study. The estimated networks corresponded largely to known biochemical relationships. Plasma concentrations of folate (direct), vitamin B6 (pyridoxal 5-phosphate) (inverse), and vitamin B2 (riboflavin) (inverse) had the strongest independent associations with CRC risk. Our study demonstrates the importance of incorporating B-vitamins in future studies of 1CM and CRC development, and the usefulness of Bayesian network learning for investigating complex biological systems in relation to disease. PMID:28233834

  2. Microbial community structure and functional metabolic diversity are associated with organic carbon availability in an agricultural soil

    Institute of Scientific and Technical Information of China (English)

    LI Juan; LI Yan-ting; YANG Xiang-dong; ZHANG Jian-jun; LIN Zhi-an; ZHAO Bing-qiang

    2015-01-01

    Exploration of soil environmental characteristics governing soil microbial community structure and activity may improve our understanding of biogeochemical processes and soil quality. The impact of soil environmental characteristics especialy organic carbon availability after 15-yr different organic and inorganic fertilizer inputs on soil bacterial community structure and functional metabolic diversity of soil microbial communities were evaluated in a 15-yr fertilizer experiment in Chang-ping County, Beijing, China. The experiment was a wheat-maize rotation system which was established in 1991 including four different fertilizer treatments. These treatments included: a non-amended control (CK), a commonly used application rate of inorganic fertilizer treatment (NPK); a commonly used application rate of inorganic fertilizer with swine manure in-corporated treatment (NPKM), and a commonly used application rate of inorganic fertilizer with maize straw incorporated treatment (NPKS). Denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA gene was used to determine the bacterial community structure and single carbon source utilization proifles were determined to characterize the microbial community functional metabolic diversity of different fertilizer treatments using Biolog Eco plates. The results indicated that long-term fertilized treatments signiifcantly increased soil bacterial community structure compared to CK. The use of inorganic fertilizer with organic amendments incorporated for long term (NPKM, NPKS) signiifcantly promoted soil bacterial structure than the application of inorganic fertilizer only (NPK), and NPKM treatment was the most important driver for in-creases in the soil microbial community richness (S) and structural diversity (H). Overal utilization of carbon sources by soil microbial communities (average wel color development, AWCD) and microbial substrate utilization diversity and evenness indices (H’ and E) indicated that long

  3. Myocardial blood flow and metabolism in patients with hypertrophic cardiomyopathy. A study with carbon-11 acetate and positron emission tomography

    Energy Technology Data Exchange (ETDEWEB)

    Ishiwata, Sugao; Maruno, Hirotaka; Nishiyama, Shinichiro; Seki, Akira [Toranomon Hospital, Tokyo (Japan); Senda, Michio; Toyama, Hinako

    1997-03-01

    The underlying pathophysiology of hypertrophic cardiomyopathy (HCM) is still unclear. Positron emission tomography is a suitable and promising technique for the detection of possible metabolic consequences of the disease. To assess regional myocardial blood flow and metabolism, 19 asymptomatic or only mildly symptomatic patients with HCM and 10 normal control subjects were studied using carbon-11 acetate and fluorine-18-labelled deoxyglucose (FDG) as tracers of myocardial blood flow (Ao), oxygen consumption (k), and exogenous glucose utilization. In the patients, regional Ao in the hypertrophied septum and apex (H) was similar to that in the nonhypertrophied free wall (N) (91.3{+-}3.9% vs 92.9{+-}3.1%; p=NS). However, the k values were significantly lower in H than in N (0.044{+-}0.012 vs 0.060{+-}0.016/min, p<0.0001). The k value in N and normal control subjects (0.062{+-}0.013) was similar. Postprandial FDG uptake was lower in H than in N (70{+-}16 vs 91{+-}7%; p<0.0001) in 16 patients and slightly higher in 3 patients. Fasting FDG study showed increased FDG uptake in H in 3 out of 13 patients, suggesting a disorder of the myocardial microvascular circulation. A relative decrease in hypertrophied septal and apical oxidative metabolism and glucose utilization without any corresponding perfusion defect could reflect abnormal regional aerobic metabolism in the disproportionately thickened myocardium in patients with HCM. This suggests that a primary myocardial metabolic defect might be present in patients with HCM. (author)

  4. 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

  5. Plastidial metabolite transporters integrate photorespiration with carbon, nitrogen, and sulfur metabolism.

    Science.gov (United States)

    Eisenhut, Marion; Hocken, Nadine; Weber, Andreas P M

    2015-07-01

    Plant photorespiration is an essential prerequisite for oxygenic photosynthesis. This metabolic repair pathway bestrides four compartments, which poses the requirement for several metabolites transporters for pathway function. However, in contrast to the well-studied enzymatic steps of the core photorespiratory cycle, only few photorespiratory translocators have been identified to date. In this review, we give an overview of established and unknown plastidic transport proteins involved in photorespiration and intertwined nitrogen and sulfur metabolism, respectively. Furthermore, we discuss the evolutionary origin of the dicarboxylate translocators and the recently identified glycolate glycerate translocator.

  6. L-Lactic acid production from glycerol coupled with acetic acid metabolism by Enterococcus faecalis without carbon loss.

    Science.gov (United States)

    Murakami, Nao; Oba, Mana; Iwamoto, Mariko; Tashiro, Yukihiro; Noguchi, Takuya; Bonkohara, Kaori; Abdel-Rahman, Mohamed Ali; Zendo, Takeshi; Shimoda, Mitsuya; Sakai, Kenji; Sonomoto, Kenji

    2016-01-01

    Glycerol is a by-product in the biodiesel production process and considered as one of the prospective carbon sources for microbial fermentation including lactic acid fermentation, which has received considerable interest due to its potential application. Enterococcus faecalis isolated in our laboratory produced optically pure L-lactic acid from glycerol in the presence of acetic acid. Gas chromatography-mass spectrometry analysis using [1, 2-(13)C2] acetic acid proved that the E. faecalis strain QU 11 was capable of converting acetic acid to ethanol during lactic acid fermentation of glycerol. This indicated that strain QU 11 restored the redox balance by oxidizing excess NADH though acetic acid metabolism, during ethanol production, which resulted in lactic acid production from glycerol. The effects of pH control and substrate concentration on lactic acid fermentation were also investigated. Glycerol and acetic acid concentrations of 30 g/L and 10 g/L, respectively, were expected to be appropriate for lactic acid fermentation of glycerol by strain QU 11 at a pH of 6.5. Furthermore, fed-batch fermentation with 30 g/L glycerol and 10 g/L acetic acid wholly exhibited the best performance including lactic acid production (55.3 g/L), lactic acid yield (0.991 mol-lactic acid/mol-glycerol), total yield [1.08 mol-(lactic acid and ethanol)]/mol-(glycerol and acetic acid)], and total carbon yield [1.06 C-mol-(lactic acid and ethanol)/C-mol-(glycerol and acetic acid)] of lactic acid and ethanol. In summary, the strain QU 11 successfully produced lactic acid from glycerol with acetic acid metabolism, and an efficient fermentation system was established without carbon loss.

  7. Toward 'omic scale metabolite profiling: a dual separation-mass spectrometry approach for coverage of lipid and central carbon metabolism.

    Science.gov (United States)

    Ivanisevic, Julijana; Zhu, Zheng-Jiang; Plate, Lars; Tautenhahn, Ralf; Chen, Stephen; O'Brien, Peter J; Johnson, Caroline H; Marletta, Michael A; Patti, Gary J; Siuzdak, Gary

    2013-07-16

    Although the objective of any 'omic science is broad measurement of its constituents, such coverage has been challenging in metabolomics because the metabolome is comprised of a chemically diverse set of small molecules with variable physical properties. While extensive studies have been performed to identify metabolite isolation and separation methods, these strategies introduce bias toward lipophilic or water-soluble metabolites depending on whether reversed-phase (RP) or hydrophilic interaction liquid chromatography (HILIC) is used, respectively. Here we extend our consideration of metabolome isolation and separation procedures to integrate RPLC/MS and HILIC/MS profiling. An aminopropyl-based HILIC/MS method was optimized on the basis of mobile-phase additives and pH, followed by evaluation of reproducibility. When applied to the untargeted study of perturbed bacterial metabolomes, the HILIC method enabled the accurate assessment of key, dysregulated metabolites in central carbon pathways (e.g., amino acids, organic acids, phosphorylated sugars, energy currency metabolites), which could not be retained by RPLC. To demonstrate the value of the integrative approach, bacterial cells, human plasma, and cancer cells were analyzed by combined RPLC/HILIC separation coupled to ESI positive/negative MS detection. The combined approach resulted in the observation of metabolites associated with lipid and central carbon metabolism from a single biological extract, using 80% organic solvent (ACN:MeOH:H2O 2:2:1). It enabled the detection of more than 30,000 features from each sample type, with the highest number of uniquely detected features by RPLC in ESI positive mode and by HILIC in ESI negative mode. Therefore, we conclude that when time and sample are limited, the maximum amount of biological information related to lipid and central carbon metabolism can be acquired by combining RPLC ESI positive and HILIC ESI negative mode analysis.

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

    DEFF Research Database (Denmark)

    Machado, Daniel; Herrgard, Markus; Rocha, Isabel

    2015-01-01

    Modeling cellular metabolism is fundamental for many biotechnological applications, including drug discovery and rational cell factory design. Central carbon metabolism (CCM) is particularly important as it provides the energy and precursors for other biological processes. However, the complex...... coli with allosteric interactions obtained from relevant databases. This model is used to integrate multi-omics datasets and analyze the coordinated changes in enzyme, metabolite, and flux levels between multiple experimental conditions. We observe cases where allosteric interactions have a major...

  9. Oral facial clefts and gene polymorphisms in metabolism of folate/one-carbon and vitamin A

    DEFF Research Database (Denmark)

    Boyles, Abee L; Wilcox, Allen J; Taylor, Jack A;

    2009-01-01

    An increased risk of facial clefts has been observed among mothers with lower intake of folic acid or vitamin A around conception. We hypothesized that the risk of clefts may be further moderated by genes involved in metabolizing folate or vitamin A. We included 425 case-parent triads in which th...

  10. Carbon catabolite repression and global control of the carbohydrate metabolism in Lactococcus lactis.

    NARCIS (Netherlands)

    Luesink, E.J.

    1998-01-01

    In view of the economic importance of fermented dairy products considerable scientific attention has been given to various steps of fermentation processes, including the L-lactate formation of lactic acid bacteria (de Vos, 1996). In particular, the carbohydrate metabolism of L. lactis has been the s

  11. Metabolic engineering of carbon and redox flow in the production of small organic acids.

    Science.gov (United States)

    Thakker, Chandresh; Martínez, Irene; Li, Wei; San, Ka-Yiu; Bennett, George N

    2015-03-01

    The review describes efforts toward metabolic engineering of production of organic acids. One aspect of the strategy involves the generation of an appropriate amount and type of reduced cofactor needed for the designed pathway. The ability to capture reducing power in the proper form, NADH or NADPH for the biosynthetic reactions leading to the organic acid, requires specific attention in designing the host and also depends on the feedstock used and cell energetic requirements for efficient metabolism during production. Recent work on the formation and commercial uses of a number of small mono- and diacids is discussed with redox differences, major biosynthetic precursors and engineering strategies outlined. Specific attention is given to those acids that are used in balancing cell redox or providing reduction equivalents for the cell, such as formate, which can be used in conjunction with metabolic engineering of other products to improve yields. Since a number of widely studied acids derived from oxaloacetate as an important precursor, several of these acids are covered with the general strategies and particular components summarized, including succinate, fumarate and malate. Since malate and fumarate are less reduced than succinate, the availability of reduction equivalents and level of aerobiosis are important parameters in optimizing production of these compounds in various hosts. Several other more oxidized acids are also discussed as in some cases, they may be desired products or their formation is minimized to afford higher yields of more reduced products. The placement and connections among acids in the typical central metabolic network are presented along with the use of a number of specific non-native enzymes to enhance routes to high production, where available alternative pathways and strategies are discussed. While many organic acids are derived from a few precursors within central metabolism, each organic acid has its own special requirements for high

  12. Modeling Central Carbon Metabolic Processes in Soil Microbial Communities: Comparing Measured With Modeled

    Science.gov (United States)

    Dijkstra, P.; Fairbanks, D.; Miller, E.; Salpas, E.; Hagerty, S.

    2013-12-01

    Understanding the mechanisms regulating C cycling is hindered by our inability to directly observe and measure the biochemical processes of glycolysis, pentose phosphate pathway, and TCA cycle in intact and complex microbial communities. Position-specific 13C labeled metabolic tracer probing is proposed as a new way to study microbial community energy production, biosynthesis, C use efficiency (the proportion of substrate incorporated into microbial biomass), and enables the quantification of C fluxes through the central C metabolic network processes (Dijkstra et al 2011a,b). We determined the 13CO2 production from U-13C, 1-13C, 2-13C, 3-13C, 4-13C, 5-13C, and 6-13C labeled glucose and 1-13C and 2,3-13C pyruvate in parallel incubations in three soils along an elevation gradient. Qualitative and quantitative interpretation of the results indicate a high pentose phosphate pathway activity in soils. Agreement between modeled and measured CO2 production rates for the six C-atoms of 13C-labeled glucose indicate that the metabolic model used is appropriate for soil community processes, but that improvements can be made. These labeling and modeling techniques may improve our ability to analyze the biochemistry and (eco)physiology of intact microbial communities. Dijkstra, P., Blankinship, J.C., Selmants, P.C., Hart, S.C., Koch, G.W., Schwartz, E., Hungate, B.A., 2011a. Probing C flux patterns of soil microbial metabolic networks using parallel position-specific tracer labeling. Soil Biology & Biochemistry 43, 126-132. Dijkstra, P., Dalder, J.J., Selmants, P.C., Hart, S.C., Koch, G.W., Schwartz, E., Hungate, B.A., 2011b. Modeling soil metabolic processes using isotopologue pairs of position-specific 13C-labeled glucose and pyruvate. Soil Biology & Biochemistry 43, 1848-1857.

  13. 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 ...

  14. 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.

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

    Directory of Open Access Journals (Sweden)

    Olga Revelles

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

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

    Science.gov (United States)

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

    2013-01-01

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

  17. Proofpoint unveils the industry's most advanced anti-spam laboratory

    CERN Multimedia

    2003-01-01

    "Proofpoint, Inc., the leader in large enterprise anti-spam solutions, today unveiled its Anti-Spam Laboratory, the world's most advanced center for spam research and analysis, and the first to be based on advanced Machine Learning science" (1 page).

  18. Unveiling Reality of the Mind: Cultural Arbitrary of Consumerism

    Science.gov (United States)

    Choi, Su-Jin

    2012-01-01

    This paper discusses the cultural arbitrary of consumerism by focusing on a personal realm. That is, I discuss what consumerism appeals to and how it flourishes in relation to our minds. I argue that we need to unveil reality of the mind, be aware of ourselves in relation to the perpetuation of consumerism, in order to critically intervene in the…

  19. Carbon and nitrogen tracers of land use effects on net ecosystem metabolism in mangrove estuaries, southwest Florida

    Science.gov (United States)

    Dvorak, Matthew; Mora, Germán; Graniero, Lauren; Surge, Donna

    2016-11-01

    Four estuaries in southwest Florida with different land-use characteristics in their watersheds were chosen to investigate the effects of anthropogenic land use on estuarine biogeochemical cycling. We compared C:N ratios, concentrations of dissolved inorganic carbon (DIC), chlorophyll-a (chl-a) and particulate organic carbon (POC), stable isotope ratios of DIC (δ13CDIC) and POC (δ13CPOC), and nitrogen isotope ratios of particulate organic nitrogen (δ15NPON) among these estuaries. Values of δ13CDIC ranged from -14.1 to +0.9‰. The more negative values occurred upstream, resulting from DIC inputs derived from both the degradation of organic carbon and dissolution of carbonates. Upstream DIC concentrations were as high as 8066 μmol L-1, suggesting high respiration rates. Further, a comparison of DIC values to a conservative mixing model indicates net heterotrophic metabolic state in all four estuaries. Supporting this interpretation, low δ13CPOC values suggest that terrestrial plants were the main source of POC in the upstream sampling points. However, C:N ratios ranged from 7.2 to 13.4, and were consistent with the decomposition of both terrestrial and aquatic sources. Chl-a concentrations were variable and typically below 20 μg L-1, indicating moderate to low levels of autotrophy in all estuaries. Elevated chl-a concentrations indicative of increased primary productivity occurred at intermediate salinities, and were possibly caused by the mixing front at mid-estuary locations. There were no apparent differences in δ15NPON among estuaries, suggesting that the N sources to these estuaries are comparable. The combined results show no differences between near-natural and anthropogenically influenced estuaries, indicating a minimal effect of anthropogenic activities on the parameters measured, possibly as a result of the filtering capacity of the extensive surrounding mangrove vegetation.

  20. Metabolism of carbon-14-labeled benzene and toluene in avocado fruit

    Energy Technology Data Exchange (ETDEWEB)

    Jansen, E.F.; Olson, A.C.

    1969-01-01

    The method of exposing avocado fruit to /sup 14/C labeled benzene or toluene was as follows. Fuerte variety avocado fruit was used. It was exposed to the vapor of the hydrocarbons which were circulated in a container. Three mature preclimacteric fruit were used in each experiment. The nonvolatile metabolites from both hydrocarbons were separated into classes of compounds by their solution in water, separation of lipids, and passage of the aqueous solution through ion exchange columns. The results indicate that in avocados the relatively inert hydrocarbons benzene and toluene are metabolized to a series of compounds, toluene to a greater extent than benzene. Both are metabolized to a small but significant extent to CO/sub 2/. 7 references, 2 tables.

  1. Calcium and Vitamin D Metabolism in Submariners. Carbon Dioxide, Sunlight, and Absorption Considerations

    Science.gov (United States)

    1986-01-15

    synthe- sis, and melatonin production by the pineal gland . Less obvious and explainable^are findings by several investigators of increased 30 yard...hypercapnia--’ ’ and- in the persistent renal response in the post-exposure period. Poyart ’ studied the bone CO? content in rats and found...calcium-pnosphorus metabolism in hypokinetic rats . Aviat. Space. Environ. Med. 55: 534-537. 47. Will, M.R. 1973. Intestinal absorption of calcium

  2. Dynamics of dissolved inorganic carbon and aquatic metabolism in the Tana River basin, Kenya

    NARCIS (Netherlands)

    Tamooh, F.; Borges, A.V.; Meysman, F.J.R.; Van Den Meersche, K.; Dehairs, F.; Merckx, R.; Bouillon, S.

    2013-01-01

    A basin-wide study was conducted in the Tana River basin (Kenya) in February 2008 (dry season), September–November 2009 (wet season) and June–July 2010 (end of the wet season) to assess the dynamics and sources of dissolved inorganic carbon (DIC) as well as to quantify CO2 fluxes, community respirat

  3. Effects of dissolved carbon dioxide on energy metabolism and stress responses in European seabass (Dicentrarchus labrax)

    NARCIS (Netherlands)

    Santos, G.A.; Schrama, J.W.; Capelle, J.; Rombout, J.H.W.M.; Verreth, J.A.J.

    2013-01-01

    Elevated carbon dioxide concentrations reduce feed intake and growth in several fish species and induce stress responses. In this study, the effects of moderately elevated CO2 levels on performance, energy partitioning, swimming activity and stress response in European seabass were assessed. Europea

  4. Polyol synthesis in Aspergillus niger : influence of oxygen availability, carbon and nitrogen sources on the metabolism

    DEFF Research Database (Denmark)

    Diano, Audrey; Bekker-Jensen, S; Dynesen, Jens Østergaard

    2006-01-01

    Polyol production has been studied in Aspergillus niger under different conditions. Fermentations have been run using high concentration of glucose or xylose as carbon source and ammonium or nitrate as nitrogen source. The growth of biomass, as freely dispersed hyphae, led to an increase of medium...

  5. LIDAR-based urban metabolism approach to neighbourhood scale energy and carbon emissions modelling

    Energy Technology Data Exchange (ETDEWEB)

    Christen, A. [British Columbia Univ., Vancouver, BC (Canada). Dept. of Geography; Coops, N. [British Columbia Univ., Vancouver, BC (Canada). Dept. of Forest Sciences; Canada Research Chairs, Ottawa, ON (Canada); Kellet, R. [British Columbia Univ., Vancouver, BC (Canada). School of Architecture and Landscape Architecture

    2010-07-01

    A remote sensing technology was used to model neighbourhood scale energy and carbon emissions in a case study set in Vancouver, British Columbia (BC). The study was used to compile and aggregate atmospheric carbon flux, urban form, and energy and emissions data in a replicable neighbourhood-scale approach. The study illustrated methods of integrating diverse emission and uptake processes on a range of scales and resolutions, and benchmarked comparisons of modelled estimates with measured energy consumption data obtained over a 2-year period from a research tower located in the study area. The study evaluated carbon imports, carbon exports and sequestration, and relevant emissions processes. Fossil fuel emissions produced in the neighbourhood were also estimated. The study demonstrated that remote sensing technologies such as LIDAR and multispectral satellite imagery can be an effective means of generating and extracting urban form and land cover data at fine scales. Data from the study were used to develop several emissions reduction and energy conservation scenarios. 6 refs.

  6. Dynamic Metabolic Flux Analysis Demonstrated on Cultures Where the Limiting Substrate Is Changed from Carbon to Nitrogen and Vice Versa

    Directory of Open Access Journals (Sweden)

    Gaspard Lequeux

    2010-01-01

    Full Text Available The main requirement for metabolic flux analysis (MFA is that the cells are in a pseudo-steady state, that there is no accumulation or depletion of intracellular metabolites. In the past, the applications of MFA were limited to the analysis of continuous cultures. This contribution introduces the concept of dynamic MFA and extends MFA so that it is applicable to transient cultures. Time series of concentration measurements are transformed into flux values. This transformation involves differentiation, which typically increases the noisiness of the data. Therefore, a noise-reducing step is needed. In this work, polynomial smoothing was used. As a test case, dynamic MFA is applied on Escherichia coli cultivations shifting from carbon limitation to nitrogen limitation and vice versa. After switching the limiting substrate from N to C, a lag phase was observed accompanied with an increase in maintenance energy requirement. This lag phase did not occur in the C- to N-limitation case.

  7. The Effect of Different Nitrogen Form on Key Enzyme Activity of Sugarbeet (Vulgaris L.) Carbon and Nitrogen Metabolism

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    This article analyses the effect of the proportion of the different nitrogen forms on key enzyme activity of carbon and nitrogen metabolism under the condition of nutritional water while Tian Yan-7 was used as experimental material. The result showed that nitrate reductase(NR) activity in the leaves gradually enhanced with the increase of NO-3. No matter in root or leaves ,glutamina synthetase (GS) activity first enhanced with increasing NH4+ when NH4+ was lower than that of NO-3 ,and GS activity was the highest when NH4+and NO3-was equal ,then GS activity declined with NH4+ increasing further. In the anaphase of growth ,synthetic activity in root of sucrose synthetase(SS) in the mixed NH4+ and NO3- was obviously highr than or NO3- alone. Both of the root and sugar yields were the highest when the proportion of NH4+ and NO3- was 1: 1.

  8. Soybeans grown in the Chernobyl area produce fertile seeds that have increased heavy metal resistance and modified carbon metabolism.

    Directory of Open Access Journals (Sweden)

    Katarína Klubicová

    Full Text Available Plants grow and reproduce in the radioactive Chernobyl area, however there has been no comprehensive characterization of these activities. Herein we report that life in this radioactive environment has led to alteration of the developing soybean seed proteome in a specific way that resulted in the production of fertile seeds with low levels of oil and β-conglycinin seed storage proteins. Soybean seeds were harvested at four, five, and six weeks after flowering, and at maturity from plants grown in either non-radioactive or radioactive plots in the Chernobyl area. The abundance of 211 proteins was determined. The results confirmed previous data indicating that alterations in the proteome include adaptation to heavy metal stress and mobilization of seed storage proteins. The results also suggest that there have been adjustments to carbon metabolism in the cytoplasm and plastids, increased activity of the tricarboxylic acid cycle, and decreased condensation of malonyl-acyl carrier protein during fatty acid biosynthesis.

  9. Low contribution of internal metabolism to carbon dioxide emissions along lotic and lentic environments of a Mediterranean fluvial network

    Science.gov (United States)

    Gómez-Gener, Lluís.; Schiller, Daniel; Marcé, Rafael; Arroita, Maite; Casas-Ruiz, Joan Pere; Staehr, Peter Anton; Acuña, Vicenç; Sabater, Sergi; Obrador, Biel

    2016-12-01

    Inland waters are significant sources of carbon dioxide (CO2) to the atmosphere. CO2 supersaturation and subsequent CO2 emissions from inland waters can be driven by internal metabolism, external inputs of dissolved inorganic carbon (DIC) derived from the catchment, and other processes (e.g., internal geochemical reactions of calcite precipitation or photochemical mineralization of organic solutes). However, the sensitivity of the magnitude and sources of CO2 emissions to fluvial network hydromorphological alterations is still poorly understood. Here we investigated both the magnitude and sources of CO2 emissions from lotic (i.e., running waters) and lentic (i.e., stagnant waters associated to small dams) waterbodies of a Mediterranean fluvial network by computing segment-scale mass balances of CO2. Our results showed that sources other than internal metabolism sustained most (82%) of the CO2 emissions from the studied fluvial network. The magnitude and sources of CO2 emissions in lotic waterbodies were highly dependent on hydrology, with higher emissions dominated by DIC inputs derived from the catchment during high flows and lower emissions partially fueled by CO2 produced biologically within the river during low flows. In contrast, CO2 emissions in lentic waterbodies were low, relatively stable over the time and the space, and dominated by DIC inputs from the catchment regardless of the different hydrological situations. Overall, our results stress the sensitivity of fluvial networks to human activities and climate change and particularly highlight the role of hydromorphological conditions on modulating the magnitude and sources of CO2 emissions from fluvial networks.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-08-17

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

  11. "PH Value" Design Show Unveils the Shanghai Dream%"PH Value" Design Show Unveils the Shanghai Dream

    Institute of Scientific and Technical Information of China (English)

    Wanzy Wang

    2012-01-01

    "PH Value" Design Show, organized by China National Textile and Apparel Council (CNTAC), undertaken by the Sub- Council of Textile Industry, CCPIT (CCPIT-TEX), China Knitting industry Association, and China National Garment Association (CNGA), will be held from October 22rid to 23rd in Shanghai, unveiling the charming mysteries of "Shanghai Dream".

  12. ESA Unveils Its New Comet Chaser.

    Science.gov (United States)

    1999-07-01

    The objective is to study one of these primordial objects at close quarters by placing a lander on its surface and chasing, with an orbiter, the comet for millions of kilometres through space. Comets - among the oldest (4.6 billion years!) and last altered objects in the solar system - are regarded as the building blocks from which the planets formed. Thus the Rosetta's discoveries will allow the scientists to learn more about birth and evolution of the planets and about the origin of life on the Earth. The final design of the Rosetta orbiter will be revealed for the first time at the Royal Society in London on 1 July when a 1:4 scale model will be unveiled by ESA's Director of Science, Prof.. Roger Bonnet. (The full size version of the spacecraft is 32 metres across, so large that it would stretch the entire width of a football pitch. Almost 90 of this is accounted for by the giant solar panels which are needed to provide electrical power in the dark depths of the Solar System). "Rosetta is a mission of major scientific importance," said Prof. Bonnet. "It will build on the discoveries made by Giotto and confirm ESA's leading role in the exploration of the Solar System and the Universe as a whole." The timing of this event has been chosen to coincide with the London meeting of the Rosetta Science Working Team and the second Earth flyby of the now non-operational Giotto spacecraft. In addition, the opening of the British Museum's 'Cracking Codes' Exhibition, for which the Rosetta Stone is the centrepiece, is set to take place on 10 July. The Rosetta mission. Rosetta is the third Cornerstone in ESA's 'Horizon 2000' long-term scientific programme. It will be launched by Ariane 5 rocket from Kourou spaceport in French Guiana in January 2003. In order to gain sufficient speed to reach the distant comet, Rosetta will require gravity assists from the Earth (twice) and Mars. After swinging around Mars in May 2005, Rosetta will return to Earth's vicinity in October 2005 and

  13. Metabolism of hydrophobic carbon sources and regulation of it in n-alkane-assimilating yeast Yarrowia lipolytica.

    Science.gov (United States)

    Fukuda, Ryouichi

    2013-01-01

    A potent ability to assimilate hydrophobic compounds, including n-alkanes and fatty acids as carbon sources, is one of important characteristics of the yeast Yarrowia lipolytica, and has been studied for both basic microbiological interest and biotechnological applications. This review summarizes recent progress on the metabolism of n-alkanes and its transcriptional control in response to n-alkanes and to fatty acids in Y. lipolytica. In the metabolism of n-alkanes, cytochromes P450ALK catalyze their initial hydroxylation to fatty alcohols, which are subsequently converted to fatty acids and utilized. The transcription of ALK1, encoding a predominant cytochrome P450ALK, is regulated in response to n-alkanes by two basic helix-loop-helix transcription activators, Yas1p and Yas2p, and Opi1-family transcription repressor Yas3p. Transcription of the genes involved in fatty acid utilization and peroxisome biogenesis is controlled by Ctf1-family Zn2Cys6 type transcription factor Por1p in response to fatty acids in Y. lipolytica.

  14. 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.

  15. Overexpressing of OsAMT1-3, a High Affinity Ammonium Transporter Gene, Modifies Rice Growth and Carbon-Nitrogen Metabolic Status

    Directory of Open Access Journals (Sweden)

    Aili Bao

    2015-04-01

    Full Text Available AMT1-3 encodes the high affinity NH4+ transporter in rice roots and is predominantly expressed under nitrogen starvation. In order to evaluate the effect of AMT1-3 gene on rice growth, nitrogen absorption and metabolism, we generated AMT1-3-overexpressing plants and analyzed the growth phenotype, yield, carbon and nitrogen metabolic status, and gene expression profiles. Although AMT1-3 mRNA accumulated in transgenic plants, these plants displayed significant decreases in growth when compared to the wild-type plants. The nitrogen uptake assay using a 15N tracer revealed poor nitrogen uptake ability in AMT1-3-overexpressing plants. We found significant decreases in AMT1-3-overexpressing plant leaf carbon and nitrogen content accompanied with a higher leaf C/N ratio. Significant changes in soluble proteins and carbohydrates were also observed in AMT1-3-overexpressing plants. In addition, metabolite profile analysis demonstrated significant changes in individual sugars, organic acids and free amino acids. Gene expression analysis revealed distinct expression patterns of genes that participate in carbon and nitrogen metabolism. Additionally, the correlation between the metabolites and gene expression patterns was consistent in AMT1-3-overexpressing plants under both low and high nitrogen growth conditions. Therefore, we hypothesized that the carbon and nitrogen metabolic imbalance caused by AMT1-3 overexpressing attributed to the poor growth and yield of transgenic plants.

  16. Promoter methylation of E-cadherin, p16, and RAR-beta(2) genes in breast tumors and dietary intake of nutrients important in one-carbon metabolism

    Science.gov (United States)

    Aberrant DNA methylation plays a critical role in carcinogenesis, and the availability of dietary factors involved in 1-carbon metabolism may contribute to aberrant DNA methylation. We investigated the association of intake of folate, vitamins B(2), B(6), B(12), and methionine with promoter methylat...

  17. 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 ...

  18. Overexpressing of OsAMT1-3, a High Affinity Ammonium Transporter Gene, Modifies Rice Growth and Carbon-Nitrogen Metabolic Status.

    Science.gov (United States)

    Bao, Aili; Liang, Zhijun; Zhao, Zhuqing; Cai, Hongmei

    2015-04-23

    AMT1-3 encodes the high affinity NH₄⁺ transporter in rice roots and is predominantly expressed under nitrogen starvation. In order to evaluate the effect of AMT1-3 gene on rice growth, nitrogen absorption and metabolism, we generated AMT1-3-overexpressing plants and analyzed the growth phenotype, yield, carbon and nitrogen metabolic status, and gene expression profiles. Although AMT1-3 mRNA accumulated in transgenic plants, these plants displayed significant decreases in growth when compared to the wild-type plants. The nitrogen uptake assay using a 15N tracer revealed poor nitrogen uptake ability in AMT1-3-overexpressing plants. We found significant decreases in AMT1-3-overexpressing plant leaf carbon and nitrogen content accompanied with a higher leaf C/N ratio. Significant changes in soluble proteins and carbohydrates were also observed in AMT1-3-overexpressing plants. In addition, metabolite profile analysis demonstrated significant changes in individual sugars, organic acids and free amino acids. Gene expression analysis revealed distinct expression patterns of genes that participate in carbon and nitrogen metabolism. Additionally, the correlation between the metabolites and gene expression patterns was consistent in AMT1-3-overexpressing plants under both low and high nitrogen growth conditions. Therefore, we hypothesized that the carbon and nitrogen metabolic imbalance caused by AMT1-3 overexpressing attributed to the poor growth and yield of transgenic plants.

  19. Changes in photosynthetic carbon metabolism in senescent leaves of chickpea, Cicer arietinum L.

    OpenAIRE

    Chandrashekhar V. Murumkar; Prakash D Chavan

    2014-01-01

    Photosynthetic processes in mature and senescent leaves of chickpea (Cicer arietinum L.) have been compared. With age, leaf photosynthetic pigments viz. chlorophyll a, chlorophyll b and carotenoids, and rate of 14°C fixation were considerably affected. Analysis of δ13C, and short term photosynthetic products showed no major change in the path of photosynthetic carbon fixation. Study of long term photosynthetic 14C assimilation revealed that in old senescent leaves, 14C incorporation into orga...

  20. Effects of COD to Phosphorus Ratios on the Metabolism of PAOs in Enhanced Biological Phosphorus Removal with Different Carbon Sources

    Institute of Scientific and Technical Information of China (English)

    Tao Jiang; Junguo He; Xiaonan Yang; Jianzheng Li

    2015-01-01

    To elucidate the phosphorus removal and metabolism under various COD/P ratio, a sludge highly enriched in PAOs was used to investigate the impacts of COD/P in batch tests under different carbon supply conditions. Acetate, propionate and a mixture of acetate and propionate at a ratio of 3 ∶ 1 ( COD basis) was used as carbon sources with the COD/P of 20, 15,10 and 5�0 gCOD/gP, respectively. The minimum COD/P ratios for complete P removal were found to be 8�24 gCOD/gP for acetate, 11�40 gCOD/gP for propionate and 9�10 gCOD/gP for the 3 ∶ 1 mixture of acetate and propionate. Converted to a mass basis, all three cases had a very similar ratio of 7�7 gVFA/gP, which represented a useful guide for operation of EBPR plants to identify possible shortages inVFAs. The trend in PHV accumulation during the anaerobic period along with the decrease of COD/P ratios suggested that, PAOs may use the TCA pathway for anaerobic VFA uptake to maintain the required NADH production with reduced glycogen degradation. During the aerobic phase, the glycogen pool was reduced but remained enough compared to the requirement for anaerobic VFA uptake, and the synthesis and degradation of glycogen was not the inhibition factor of PAOs.

  1. Analysis of metabolic alterations in Arabidopsis following changes in the carbon dioxide and oxygen partial pressures

    Institute of Scientific and Technical Information of China (English)

    Alexandra Florian; Stefan Timm; Zoran Nikoloski; Takayuki Tohge; Hermann Bauwe; Wagner LArajo; Alisdair RFernie

    2014-01-01

    As sessile organisms, plants are subject to a multitude of environmental variations including several which directly affect their interaction with the atmosphere. Given the indiscriminant nature of Rubisco, the relative rates of photosynthesis and photorespiration are known to be responsive to changes in gas composition. However, compre-hensive profiling methods have not yet been applied in order to characterize the wider consequences of these changes on primary metabolism in general. Moreover, although transcrip-tional profiling has revealed that a subset of photorespiratory enzymes are co-expressed, whether transcriptional responses play a role in short-term responses to atmospheric composi-tional changes remains unknown. To address these questions, plants Arabidopsis thaliana (Arabidopsis) ecotype Columbia (Col-O) grown under normal air conditions were transferred to different CO2 and O2 concentrations and characterized at the physiological, molecular, and metabolic levels fol owing this transition. The results reveal alterations in the components, which are directly involved in, or supporting, photorespiration, including transcripts and metabolite levels. The results further highlight that the majority of the regulation of these pathways is not mediated at the level of transcription and that the photorespiratory pathway is essential also in conditions in which flux through the pathway is minimized, yet suggest that flux through this pathway is not mediated at the level of transcription.

  2. Sensitivity of chemical reaction networks: a structural approach. 1. Examples and the carbon metabolic network.

    Science.gov (United States)

    Mochizuki, Atsushi; Fiedler, Bernold

    2015-02-21

    In biological cells, chemical reaction pathways lead to complex network systems like metabolic networks. One experimental approach to the dynamics of such systems examines their "sensitivity": each enzyme mediating a reaction in the system is increased/decreased or knocked out separately, and the responses in the concentrations of chemicals or their fluxes are observed. In this study, we present a mathematical method, named structural sensitivity analysis, to determine the sensitivity of reaction systems from information on the network alone. We investigate how the sensitivity responses of chemicals in a reaction network depend on the structure of the network, and on the position of the perturbed reaction in the network. We establish and prove some general rules which relate the sensitivity response to the structure of the underlying network. We describe a hierarchical pattern in the flux response which is governed by branchings in the network. We apply our method to several hypothetical and real life chemical reaction networks, including the metabolic network of the Escherichia coli TCA cycle.

  3. In vivo carbon-13 nuclear magnetic resonance studies of heart metabolism.

    Science.gov (United States)

    Neurohr, K J; Barrett, E J; Shulman, R G

    1983-03-01

    Guinea pig heart metabolism was studied in vivo by 13C NMR at 20.18 MHz. High-quality proton-decoupled 13C NMR spectra with excellent signal-to-noise ratios and resolution could be obtained in 6 min. Natural-abundance spectra showed resonances that could be assigned to fatty acids, but glycogen was not seen. During intravenous infusion of D-[1-13C]glucose and insulin, the time course of myocardial glycogen synthesis was followed serially for up to 4 hr. Anoxia resulted in degradation of the labeled glycogen within 6 min and appearance of 13C label in lactic acid. Infusion of sodium [2-13C]acetate resulted in incorporation of label into the C-4, C-2, and C-3 positions of glutamate and glutamine, reflecting "scrambling" of the label expected from tricarboxylic acid cycle activity. Examination of the 31P NMR spectrum of the guinea pig heart in vivo demonstrated no change in the high-energy phosphates during the time periods of the 13C NMR experiments. Our studies indicate that 13C NMR is a unique non-destructive tool for the study of heart metabolism in vivo.

  4. Changes in photosynthetic carbon metabolism in senescent leaves of chickpea, Cicer arietinum L.

    Directory of Open Access Journals (Sweden)

    Chandrashekhar V. Murumkar

    2014-01-01

    Full Text Available Photosynthetic processes in mature and senescent leaves of chickpea (Cicer arietinum L. have been compared. With age, leaf photosynthetic pigments viz. chlorophyll a, chlorophyll b and carotenoids, and rate of 14°C fixation were considerably affected. Analysis of δ13C, and short term photosynthetic products showed no major change in the path of photosynthetic carbon fixation. Study of long term photosynthetic 14C assimilation revealed that in old senescent leaves, 14C incorporation into organic acid and sugar fractions was enhanced.

  5. Escherichia coli carbon source metabolism affects longevity of its predator Caenorhabditis elegans.

    Science.gov (United States)

    Brokate-Llanos, Ana María; Garzón, Andrés; Muñoz, Manuel J

    2014-01-01

    Nutrition is probably the most determinant factor affecting aging. Microorganisms of the intestinal flora lay in the interface between available nutrients and nutrients that are finally absorbed by multicellular organisms. They participate in the processing and transformation of these nutrients in a symbiotic or commensalistic relationship. In addition, they can also be pathogens. Alive Escherichia coli OP50 are usually used to culture the bacteriovorus nematode Caenorhabditis elegans. Here, we report a beneficial effect of low concentration of saccharides on the longevity of C. elegans. This effect is only observed when the bacterium can metabolize the sugar, suggesting that physiological changes in the bacterium feeding on the saccharides are the cause of this beneficial effect.

  6. Iron and carbon metabolism by a mineral-oxidizing Alicyclobacillus-like bacterium.

    Science.gov (United States)

    Yahya, Adibah; Hallberg, Kevin B; Johnson, D Barrie

    2008-04-01

    A novel iron-oxidizing, moderately thermophilic, acidophilic bacterium (strain "GSM") was isolated from mineral spoil taken from a gold mine in Montana. Biomolecular analysis showed that it was most closely related to Alicyclobacillus tolerans, although the two bacteria differed in some key respects, including the absence (in strain GSM) of varpi-alicyclic fatty acids and in their chromosomal base compositions. Isolate GSM was able to grow in oxygen-free media using ferric iron as terminal electron acceptor confirming that it was a facultative anaerobe, a trait not previously described in Alicyclobacillus spp.. The acidophile used both organic and inorganic sources of energy and carbon, although growth and iron oxidation by isolate GSM was uncoupled in media that contained both fructose and ferrous iron. Fructose utilization suppressed iron oxidation, and oxidation of ferrous iron occurred only when fructose was depleted. In contrast, fructose catabolism was suppressed when bacteria were harvested while actively oxidizing iron, suggesting that both ferrous iron- and fructose-oxidation are inducible in this acidophile. Isolate GSM accelerated the oxidative dissolution of pyrite in liquid media either free of, or amended with, organic carbon, although redox potentials were significantly different in these media. The potential of this isolate for commercial mineral processing is discussed.

  7. Universe unveiled the cosmos in my bubble bath

    CERN Document Server

    Vishveshwara, C V

    2015-01-01

    The bubbles were swirling all around me, massaging my body. As I luxuriated in this fantastic bath, I gasped realizing that those bubbles carried with them miniature galaxies bringing the entire Cosmos into my bathtub... Alfie is back. And so are George and other characters from the author’s previous book Einstein’s Enigma or Black Holes in My Bubble Bath. While the present book, Universe Unveiled - The Cosmos in My Bubble Bath, is completely independent, its storyline can be considered a sequel to the previous one. The scientific content spanning ancient world models to the most recent mysteries of cosmology is presented in an entirely nontechnical and descriptive style through the discussions between Alfie, the enlightened learner, and George, professor of astrophysics. Fantasies, based on these discussions that cover the scientific facts, are created by the magical bubble baths taken by Alfie. Universe Unveiled blends accurate science with philosophy, drama, humour, and fantasy to create an exciting co...

  8. Unveiling spatial correlations in biophotonic architecture of transparent insect wings

    CERN Document Server

    Kumar, Pramod; Singh, Dhirendra P; Mandal, Sudip; Singh, Kamal P

    2014-01-01

    We probe the natural complex structures in the transparent insect wings by a simple, non-invasive, real time optical technique using both monochromatic and broadband femtosecond lasers. A stable, reproducible and novel diffraction pattern is observed unveiling long range spatial correlations and structural-symmetry at various length scales for a large variety of wings. While matching the sensitivity of SEM for such microstructures, it is highly efficient for extracting long range structural organization with potentially broad applicability.

  9. The Model of France Pavilion for 2010 Unveiled

    Institute of Scientific and Technical Information of China (English)

    Audrey GUO

    2009-01-01

    @@ Amodel of the France Pavilion for the Expo 2010 was unveiled at Beijing's Ullens Center of Contemporary Art on February 20, 2009. H.E.Mr. Herve LADSOUS, the ambassador of France, Jose Freches, president of COFRES and Jacques Ferrier, the designer of the pavilion, attended the conference and presented the progress of the construction of the model and the plan before the World Expo 2010 in Shanghai.

  10. Metabolic Profiling with Gas Chromatography-Mass Spectrometry and Capillary Electrophoresis-Mass Spectrometry Reveals the Carbon-Nitrogen Status of Tobacco Leaves Across Different Planting Areas.

    Science.gov (United States)

    Zhao, Jieyu; Zhao, Yanni; Hu, Chunxiu; Zhao, Chunxia; Zhang, Junjie; Li, Lili; Zeng, Jun; Peng, Xiaojun; Lu, Xin; Xu, Guowang

    2016-02-05

    The interaction between carbon (C) and nitrogen (N) metabolism can reflect plant growth status and environmental factors. Little is known regarding the connections between C-N metabolism and growing regions under field conditions. To comprehensively investigate the relationship in mature tobacco leaves, we established metabolomics approaches based on gas chromatography-mass spectrometry (GC-MS) and capillary electrophoresis-time-of-flight-mass spectrometry (CE-TOF-MS). Approximately 240 polar metabolites were determined. Multivariate statistical analysis revealed that the growing region greatly influenced the metabolic profiles of tobacco leaves. A metabolic correlation network and related pathway maps were used to reveal the global overview of the alteration of C-N metabolism across three typical regions. In Yunnan, sugars and tricarboxylic acid (TCA) cycle intermediates were closely correlated with amino acid pools. Henan tobacco leaves showed positive correlation between the pentose phosphate pathway (PPP) intermediates and C-rich secondary metabolism. In Guizhou, the proline and asparagine had significant links with TCA cycle intermediates and urea cycle, and antioxidant accumulation was observed in response to drought. These results demonstrate that combined analytical approaches have great potential to detect polar metabolites and provide information on C-N metabolism related to planting regional characteristics.

  11. METABOLIC ENGINEERING TO DEVELOP A PATHWAY FOR THE SELECTIVE CLEAVAGE OF CARBON-NITROGEN BONDS

    Energy Technology Data Exchange (ETDEWEB)

    John J. Kilbane II

    2004-10-01

    The objective of the project is to develop biochemical pathways for the selective cleavage of C-N bonds in molecules found in petroleum. The initial phase of the project was focused on the isolation or development of an enzyme capable of cleaving the C-N bond in aromatic amides, specifically 2-aminobiphenyl. The objective of the second phase of the research will be to construct a biochemical pathway for the selective removal of nitrogen from carbazole by combining the carA genes from Sphingomonas sp. GTIN11 with the gene(s) encoding an appropriate deaminase. The objective of the final phase of the project will be to develop derivative C-N bond cleaving enzymes that have broader substrate ranges and to demonstrate the use of such strains to selectively remove nitrogen from petroleum. During the first year of the project (October, 2002-September, 2003) enrichment culture experiments resulted in the isolation of microbial cultures that utilize aromatic amides as sole nitrogen sources, several amidase genes were cloned and were included in directed evolution experiments to obtain derivatives that can cleave C-N bonds in aromatic amides, and the carA genes from Sphingomonas sp. GTIN11, and Pseudomonas resinovorans CA10 were cloned in vectors capable of replicating in Escherichia coli. During the second year of the project (October, 2003-September, 2004) enrichment culture experiments succeeded in isolating a mixed bacterial culture that can utilize 2-aminobiphenyl as a sole nitrogen source, directed evolution experiments were focused on the aniline dioxygenase enzyme that is capable of deaminating aniline, and expression vectors were constructed to enable the expression of genes encoding C-N bond cleaving enzymes in Rhodococcus hosts. The construction of a new metabolic pathway to selectively remove nitrogen from carbazole and other molecules typically found in petroleum should lead to the development of a process to improve oil refinery efficiency by reducing the

  12. The Stable Level of Glutamine synthetase 2 Plays an Important Role in Rice Growth and in Carbon-Nitrogen Metabolic Balance.

    Science.gov (United States)

    Bao, Aili; Zhao, Zhuqing; Ding, Guangda; Shi, Lei; Xu, Fangsen; Cai, Hongmei

    2015-06-04

    Glutamine synthetase 2 (GS2) is a key enzyme involved in the ammonium metabolism in plant leaves. In our previous study, we obtained GS2-cosuppressed plants, which displayed a normal growth phenotype at the seedling stage, while at the tillering stage they showed a chlorosis phenotype. In this study, to investigate the chlorosis mechanism, we systematically analyzed the plant growth, carbon-nitrogen metabolism and gene expressions between the GS2-cosuppressed rice and wild-type plants. The results revealed that the GS2-cosuppressed plants exhibited a poor plant growth phenotype and a poor nitrogen transport ability, which led to nitrogen accumulation and a decline in the carbon/nitrogen ratio in the stems. Interestingly, there was a higher concentration of soluble proteins and a lower concentration of carbohydrates in the GS2-cosuppressed plants at the seedling stage, while a contrasting result was displayed at the tillering stage. The analysis of the metabolic profile showed a significant increase of sugars and organic acids. Additionally, gene expression patterns were different in root and leaf of GS2-cosuppressed plants between the seedling and tillering stage. These results indicated the important role of a stable level of GS2 transcription during normal rice development and the importance of the carbon-nitrogen metabolic balance in rice growth.

  13. Exploring the Altered Dynamics of Mammalian Central Carbon Metabolic Pathway in Cancer Cells: A Classical Control Theoretic Approach.

    Directory of Open Access Journals (Sweden)

    Debjyoti Paul

    Full Text Available In contrast with normal cells, most of the cancer cells depend on aerobic glycolysis for energy production in the form of adenosine triphosphate (ATP bypassing mitochondrial oxidative phosphorylation. Moreover, compared to normal cells, cancer cells exhibit higher consumption of glucose with higher production of lactate. Again, higher rate of glycolysis provides the necessary glycolytic intermediary precursors for DNA, protein and lipid synthesis to maintain high active proliferation of the tumor cells. In this scenario, classical control theory based approach may be useful to explore the altered dynamics of the cancer cells. Since the dynamics of the cancer cells is different from that of the normal cells, understanding their dynamics may lead to development of novel therapeutic strategies.We have developed a model based on the state space equations of classical control theory along with an order reduction technique to mimic the actual dynamic behavior of mammalian central carbon metabolic (CCM pathway in normal cells. Here, we have modified Michaelis Menten kinetic equation to incorporate feedback mechanism along with perturbations and cross talks associated with a metabolic pathway. Furthermore, we have perturbed the proposed model to reduce the mitochondrial oxidative phosphorylation. Thereafter, we have connected proportional-integral (PI controller(s with the model for tuning it to behave like the CCM pathway of a cancer cell. This methodology allows one to track the altered dynamics mediated by different enzymes.The proposed model successfully mimics all the probable dynamics of the CCM pathway in normal cells. Moreover, experimental results demonstrate that in cancer cells, a coordination among enzymes catalyzing pentose phosphate pathway and intermediate glycolytic enzymes along with switching of pyruvate kinase (M2 isoform plays an important role to maintain their altered dynamics.

  14. Alcohol-induced One-carbon Metabolism Impairment Promotes Dysfunction of DNA Base Excision Repair in Adult Brain*

    Science.gov (United States)

    Fowler, Anna-Kate; Hewetson, Aveline; Agrawal, Rajiv G.; Dagda, Marisela; Dagda, Raul; Moaddel, Ruin; Balbo, Silvia; Sanghvi, Mitesh; Chen, Yukun; Hogue, Ryan J.; Bergeson, Susan E.; Henderson, George I.; Kruman, Inna I.

    2012-01-01

    The brain is one of the major targets of chronic alcohol abuse. Yet the fundamental mechanisms underlying alcohol-mediated brain damage remain unclear. The products of alcohol metabolism cause DNA damage, which in conditions of DNA repair dysfunction leads to genomic instability and neural death. We propose that one-carbon metabolism (OCM) impairment associated with long term chronic ethanol intake is a key factor in ethanol-induced neurotoxicity, because OCM provides cells with DNA precursors for DNA repair and methyl groups for DNA methylation, both critical for genomic stability. Using histological (immunohistochemistry and stereological counting) and biochemical assays, we show that 3-week chronic exposure of adult mice to 5% ethanol (Lieber-Decarli diet) results in increased DNA damage, reduced DNA repair, and neuronal death in the brain. These were concomitant with compromised OCM, as evidenced by elevated homocysteine, a marker of OCM dysfunction. We conclude that OCM dysfunction plays a causal role in alcohol-induced genomic instability in the brain because OCM status determines the alcohol effect on DNA damage/repair and genomic stability. Short ethanol exposure, which did not disturb OCM, also did not affect the response to DNA damage, whereas additional OCM disturbance induced by deficiency in a key OCM enzyme, methylenetetrahydrofolate reductase (MTHFR) in Mthfr+/− mice, exaggerated the ethanol effect on DNA repair. Thus, the impact of long term ethanol exposure on DNA repair and genomic stability in the brain results from OCM dysfunction, and MTHFR mutations such as Mthfr 677C→T, common in human population, may exaggerate the adverse effects of ethanol on the brain. PMID:23118224

  15. Carbon and nitrogen metabolism in barley plants exposed to UV-B radiation

    Energy Technology Data Exchange (ETDEWEB)

    Ghisi, R.; Trentin, A.R.; Masi, A.; Ferretti, M. [Dipartimento di Biotecnologie Agrarie, Legnaro, Padova (Italy)

    2002-10-01

    The effect of UV-B radiation on FW, leaf and stem length, photosynthetic O{sub 2} evolution, levels of carbohydrates and nitrates, and extractable activities of some of the enzymes involved in C and N metabolism was evaluated in barley (Hordeum vulgare L. cv. Express) seedlings during the 9 days following transfer to an UV-B enriched environment. The results show that under our experimental conditions UV-B radiation scarcely affects the photosynthetic competence of barley leaves, expressed as RuBP carboxylase (EC 4.1.1.39) activity, O{sub 2} evolution rate and chlorophyll content. Nevertheless, this treatment induced significant alterations of the enzyme activity of nitrate reductase (EC 1.6.6.1) and glutamine synthetase (EC 6.3.1.2), although only after a few days of treatment. The effects were not confined to the exposed tissue, but were detectable also at the root level. In fact, nitrate reductase decreased in response to UV-B in both leaf and root tissue, whereas glutamine synthetase was affected only in the root. In contrast, nitrate content was not influenced by the treatment, neither in root nor in leaf tissue, whilst leaf sucrose diminished in exposed plants only on the last day of treatment. (au)

  16. Metabolic Engineering to Develop a Pathway for the Selective Cleavage of Carbon-Nitrogen Bonds

    Energy Technology Data Exchange (ETDEWEB)

    John J. Kilbane II

    2005-10-01

    The objective of the project is to develop a biochemical pathway for the selective cleavage of C-N bonds in molecules found in petroleum. Specifically a novel biochemical pathway will be developed for the selective cleavage of C-N bonds in carbazole. The cleavage of the first C-N bond in carbazole is accomplished by the enzyme carbazole dioxygenase, that catalyzes the conversion of carbazole to 2-aminobiphenyl-2,3-diol. The genes encoding carbazole dioxygenase were cloned from Sphingomonas sp. GTIN11 and from Pseudomonas resinovorans CA10. The selective cleavage of the second C-N bond has been challenging, and efforts to overcome that challenge have been the focus of recent research in this project. Enrichment culture experiments succeeded in isolating bacterial cultures that can metabolize 2-aminobiphenyl, but no enzyme capable of selectively cleaving the C-N bond in 2-aminobiphenyl has been identified. Aniline is very similar to the structure of 2-aminobiphenyl and aniline dioxygenase catalyzes the conversion of aniline to catechol and ammonia. For the remainder of the project the emphasis of research will be to simultaneously express the genes for carbazole dioxygenase and for aniline dioxygenase in the same bacterial host and then to select for derivative cultures capable of using carbazole as the sole source of nitrogen.

  17. Patterns of Carbon Partitioning in Leaves of Crassulacean Acid Metabolism Species during Deacidification.

    Science.gov (United States)

    Christopher, J. T.; Holtum, JAM.

    1996-09-01

    Carbohydrates stored during deacidification in the light were examined in 11 Crassulacean acid metabolism (CAM) species from widely separated taxa grown under uniform conditions. The hypothesis that NAD(P) malic enzyme CAM species store chloroplastic starch and glucans, and phosphoenolpyruvate carboxykinase species store extrachloroplastic sugars or polymers was disproved. Of the six malic enzyme species examined, Kalanchoe tubiflora, Kalanchoe pinnata, Kalanchoe daigremontiana, and Vanilla planifolia stored mainly starch. Sansevieria hahnii stored sucrose and Agave guadalajarana did not store starch, glucose, fructose, or sucrose. Of the five phosphoenolpyruvate carboxykinase species investigated, Ananus comosus stored extrachloroplastic carbohydrate, but Stapelia gigantea, Hoya carnosa, and Portea petropolitana stored starch, whereas Aloe vera stored both starch and glucose. Within families, the major decarboxylase was common for all species examined, whereas storage carbohydrate could differ both between and within genera. In the Bromeliaceae, A. comosus stored mainly fructose, but P. petropolitana stored starch. In the genus Aloe, A. vera stored starch and glucose, but A. arborescens is known to store a galactomannan polymer. We postulate that the observed variation in carbohydrate partitioning between CAM species is the result of two principal components: (a) constraints imposed by the CAM syndrome itself, and (b) diversity in biochemistry resulting from different evolutionary histories.

  18. Carbonate extraction process for the metabolic, isozymic and proteomic profiling of rose-scented geranium (Pelargonium sp.), a hyper-acidic plant.

    Science.gov (United States)

    Sangwan, Rajender Singh; Sangwan, Neelam Singh; Sharma, Pankaj Kumar; Chaurasiya, Narayan Das; Mishra, Siddhartha Kumar; Tyagi, Bali Ram; Srivastava, Avdhesh Kumar

    2008-01-01

    Rose-scented geranium (Pelargonium sp.) is a valuable monoterpene-yielding plant. It has been well characterised phytochemically through the isolation of >270 secondary metabolites, however, there is hardly any biochemical or metabolic information concerning this plant. Initial attempts to investigate its metabolism failed to produce any enzyme activity in the tissue extracts prepared in routine extraction buffers owing to the intrinsic properties of the tissue matrix. It was recognised that cellular hyper-acidity (cell sap pH approximately 3.0) gave rise to very low protein levels in the extracts, thus prohibiting detection of activities of even primary metabolic enzymes that are usually abundantly present in plants. Tissue extraction in Tris solution without pH adjustment (as used for studies involving citrus and banana) led to little or no improvement. Therefore, a novel approach using sodium carbonate solution as an efficient extraction system for enzymes and proteins from the plant was studied. Functionality of the carbonate extraction has been demonstrated through its effectiveness, a several-fold superior performance, in yielding protein, monitoring primary metabolism and secondary metabolic enzymes, and isozymic and polypeptide profiling. The process may also be helpful in the reliable analysis of other acidic plant tissues.

  19. Systems-level analysis of nitrogen starvation-induced modifications of carbon metabolism in a Chlamydomonas reinhardtii starchless mutant.

    Science.gov (United States)

    Blaby, Ian K; Glaesener, Anne G; Mettler, Tabea; Fitz-Gibbon, Sorel T; Gallaher, Sean D; Liu, Bensheng; Boyle, Nanette R; Kropat, Janette; Stitt, Mark; Johnson, Shannon; Benning, Christoph; Pellegrini, Matteo; Casero, David; Merchant, Sabeeha S

    2013-11-01

    To understand the molecular basis underlying increased triacylglycerol (TAG) accumulation in starchless (sta) Chlamydomonas reinhardtii mutants, we undertook comparative time-course transcriptomics of strains CC-4348 (sta6 mutant), CC-4349, a cell wall-deficient (cw) strain purported to represent the parental STA6 strain, and three independent STA6 strains generated by complementation of sta6 (CC-4565/STA6-C2, CC-4566/STA6-C4, and CC-4567/STA6-C6) in the context of N deprivation. Despite N starvation-induced dramatic remodeling of the transcriptome, there were relatively few differences (5 × 10(2)) observed between sta6 and STA6, the most dramatic of which were increased abundance of transcripts encoding key regulated or rate-limiting steps in central carbon metabolism, specifically isocitrate lyase, malate synthase, transaldolase, fructose bisphosphatase and phosphoenolpyruvate carboxykinase (encoded by ICL1, MAS1, TAL1, FBP1, and PCK1 respectively), suggestive of increased carbon movement toward hexose-phosphate in sta6 by upregulation of the glyoxylate pathway and gluconeogenesis. Enzyme assays validated the increase in isocitrate lyase and malate synthase activities. Targeted metabolite analysis indicated increased succinate, malate, and Glc-6-P and decreased Fru-1,6-bisphosphate, illustrating the effect of these changes. Comparisons of independent data sets in multiple strains allowed the delineation of a sequence of events in the global N starvation response in C. reinhardtii, starting within minutes with the upregulation of alternative N assimilation routes and carbohydrate synthesis and subsequently a more gradual upregulation of genes encoding enzymes of TAG synthesis. Finally, genome resequencing analysis indicated that (1) the deletion in sta6 extends into the neighboring gene encoding respiratory burst oxidase, and (2) a commonly used STA6 strain (CC-4349) as well as the sequenced reference (CC-503) are not congenic with respect to sta6 (CC-4348

  20. Fungi, bacteria and soil pH: the oxalate-carbonate pathway as a model for metabolic interaction.

    Science.gov (United States)

    Martin, Gaëtan; Guggiari, Matteo; Bravo, Daniel; Zopfi, Jakob; Cailleau, Guillaume; Aragno, Michel; Job, Daniel; Verrecchia, Eric; Junier, Pilar

    2012-11-01

    The oxalate-carbonate pathway involves the oxidation of calcium oxalate to low-magnesium calcite and represents a potential long-term terrestrial sink for atmospheric CO(2). In this pathway, bacterial oxalate degradation is associated with a strong local alkalinization and subsequent carbonate precipitation. In order to test whether this process occurs in soil, the role of bacteria, fungi and calcium oxalate amendments was studied using microcosms. In a model system with sterile soil amended with laboratory cultures of oxalotrophic bacteria and fungi, the addition of calcium oxalate induced a distinct pH shift and led to the final precipitation of calcite. However, the simultaneous presence of bacteria and fungi was essential to drive this pH shift. Growth of both oxalotrophic bacteria and fungi was confirmed by qPCR on the frc (oxalotrophic bacteria) and 16S rRNA genes, and the quantification of ergosterol (active fungal biomass) respectively. The experiment was replicated in microcosms with non-sterilized soil. In this case, the bacterial and fungal contribution to oxalate degradation was evaluated by treatments with specific biocides (cycloheximide and bronopol). Results showed that the autochthonous microflora oxidized calcium oxalate and induced a significant soil alkalinization. Moreover, data confirmed the results from the model soil showing that bacteria are essentially responsible for the pH shift, but require the presence of fungi for their oxalotrophic activity. The combined results highlight that the interaction between bacteria and fungi is essential to drive metabolic processes in complex environments such as soil.

  1. METABOLIC ENGINEERING TO DEVELOP A PATHWAY FOR THE SELECTIVE CLEAVAGE OF CARBON-NITROGEN BONDS

    Energy Technology Data Exchange (ETDEWEB)

    John J. Kilbane III

    2003-12-01

    pathway. The construction of a new metabolic pathway to selectively remove nitrogen from carbazole and other molecules typically found in petroleum should lead to the development of a process to improve oil refinery efficiency by reducing the poisoning, by nitrogen, of catalysts used in the hydrotreating and catalytic cracking of petroleum.

  2. Visualizing Single Cell Biology: Nanosims Studies of Carbon and Nitrogen Metabolism in Diazotrophic Cyanobacteria

    Science.gov (United States)

    Pett-Ridge, J.; Finzi, J. A.; Capone, D. G.; Popa, R.; Nealson, K. H.; Ng, W.; Spormann, A. M.; Hutcheon, I. D.; Weber, P. K.

    2007-12-01

    , inter-species transfers (with Rhizobium epibionts), and within-cell depth profiles. Spatial enrichment patterns were correlated with morphological features evidenced in TEM images of microtomed filaments. These features indicate how 15N and 13C "hotspots" are dispersed throughout individual cells in different species, and may indicate isolated locations of increased N2 fixation, sites of amino acid/protein synthesis, or cyanophycin storage granules. This combination of Nano-Secondary Ion Mass Spectrometry (NanoSIMS) analysis and high resolution microscopy allows isotopic analysis to be linked to morphological features and holds great promise for fine-scale studies of bacteria metabolism.

  3. Effect of Carbon Monoxide Donor CORM-2 on Vitamin D3 Metabolism

    Directory of Open Access Journals (Sweden)

    Martina Feger

    2013-11-01

    Full Text Available Background/Aims: Carbon monoxide (CO interferes with cytochrome-dependent cellular functions and acts as gaseous transmitter. CO is released from CO-releasing molecules (CORM including tricarbonyl-dichlororuthenium (II dimer (CORM-2, molecules considered for the treatment of several disorders including vascular dysfunction, inflammation, tissue ischemia and organ rejection. Cytochrome P450-sensitive function include formation of 1,25-dihydroxyvitamin D3 (1,25(OH2D3 by renal 25-hydroxyvitamin D3 1-alpha-hydroxylase (Cyp27b1. The enzyme is regulated by PTH, FGF23 and klotho. 1,25(OH2D3 regulates Ca2+ and phosphate transport as well as klotho expression. The present study explored, whether CORM-2 influences 1,25(OH2D3 formation and klotho expression. Methods: Mice were treated with intravenous CORM-2 (20 mg/kg body weight. Plasma 1,25(OH2D3 and FGF23 concentrations were determined by ELISA, phosphate, calcium and creatinine concentrations by colorimetric methods, transcript levels by quantitative RT-PCR and protein expression by western blotting. Fgf23 mRNA transcript levels were further determined in rat osteosarcoma UMR106 cells without or with prior treatment for 24 hours with 20 µM CORM-2. Results: CORM-2 injection within 24 hours significantly increased FGF23 plasma levels and decreased 1,25(OH2D3 plasma levels, renal Cyp27b1 gene expression as well as renal klotho protein abundance and transcript levels. Moreover, treatment of UMR106 cells with CORM-2 significantly increased Fgf23 transcript levels. Conclusion: CO-releasing molecule CORM-2 enhances FGF23 expression and release and decreases klotho expression and 1,25(OH2D3 synthesis.

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

    Directory of Open Access Journals (Sweden)

    Usui Yuki

    2012-06-01

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

  5. The Carbon Storage Regulator (Csr) System Exerts a Nutrient-Specific Control over Central Metabolism in Escherichia coli Strain Nissle 1917

    OpenAIRE

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

    2013-01-01

    The role of the post-transcriptional carbon storage regulator (Csr) system in nutrient utilization and in the control of the central metabolism in E. coli reference commensal strain Nissle 1917 was investigated. Analysis of the growth capabilities of mutants altered for various components of the Csr system (csrA51, csrB, csrC and csrD mutations) showed that only the protein CsrA - the key component of the system - exerts a marked role in carbon nutrition. Attenuation of CsrA activity in the c...

  6. Characterization of Discrete Phosphopantetheinyl Transferases in Streptomyces tsukubaensis L19 Unveils a Complicate Phosphopantetheinylation Network

    Science.gov (United States)

    Wang, Yue-Yue; Zhang, Xiao-Sheng; Luo, Hong-Dou; Ren, Ni-Ni; Jiang, Xin-Hang; Jiang, Hui; Li, Yong-Quan

    2016-01-01

    Phosphopantetheinyl transferases (PPTases) play essential roles in both primary metabolisms and secondary metabolisms via post-translational modification of acyl carrier proteins (ACPs) and peptidyl carrier proteins (PCPs). In this study, an industrial FK506 producing strain Streptomyces tsukubaensis L19, together with Streptomyces avermitilis, was identified to contain the highest number (five) of discrete PPTases known among any species thus far examined. Characterization of the five PPTases in S. tsukubaensis L19 unveiled that stw ACP, an ACP in a type II PKS, was phosphopantetheinylated by three PPTases FKPPT1, FKPPT3, and FKACPS; sts FAS ACP, the ACP in fatty acid synthase (FAS), was phosphopantetheinylated by three PPTases FKPPT2, FKPPT3, and FKACPS; TcsA-ACP, an ACP involved in FK506 biosynthesis, was phosphopantetheinylated by two PPTases FKPPT3 and FKACPS; FkbP-PCP, an PCP involved in FK506 biosynthesis, was phosphopantetheinylated by all of these five PPTases FKPPT1-4 and FKACPS. Our results here indicate that the functions of these PPTases complement each other for ACPs/PCPs substrates, suggesting a complicate phosphopantetheinylation network in S. tsukubaensis L19. Engineering of these PPTases in S. tsukubaensis L19 resulted in a mutant strain that can improve FK506 production. PMID:27052100

  7. Optimizing the distribution of resources between enzymes of carbon metabolism can dramatically increase photosynthetic rate: a numerical simulation using an evolutionary algorithm.

    Science.gov (United States)

    Zhu, Xin-Guang; de Sturler, Eric; Long, Stephen P

    2007-10-01

    The distribution of resources between enzymes of photosynthetic carbon metabolism might be assumed to have been optimized by natural selection. However, natural selection for survival and fecundity does not necessarily select for maximal photosynthetic productivity. Further, the concentration of a key substrate, atmospheric CO(2), has changed more over the past 100 years than the past 25 million years, with the likelihood that natural selection has had inadequate time to reoptimize resource partitioning for this change. Could photosynthetic rate be increased by altered partitioning of resources among the enzymes of carbon metabolism? This question is addressed using an "evolutionary" algorithm to progressively search for multiple alterations in partitioning that increase photosynthetic rate. To do this, we extended existing metabolic models of C(3) photosynthesis by including the photorespiratory pathway (PCOP) and metabolism to starch and sucrose to develop a complete dynamic model of photosynthetic carbon metabolism. The model consists of linked differential equations, each representing the change of concentration of one metabolite. Initial concentrations of metabolites and maximal activities of enzymes were extracted from the literature. The dynamics of CO(2) fixation and metabolite concentrations were realistically simulated by numerical integration, such that the model could mimic well-established physiological phenomena. For example, a realistic steady-state rate of CO(2) uptake was attained and then reattained after perturbing O(2) concentration. Using an evolutionary algorithm, partitioning of a fixed total amount of protein-nitrogen between enzymes was allowed to vary. The individual with the higher light-saturated photosynthetic rate was selected and used to seed the next generation. After 1,500 generations, photosynthesis was increased substantially. This suggests that the "typical" partitioning in C(3) leaves might be suboptimal for maximizing the light

  8. Dynamics of dissolved inorganic carbon and aquatic metabolism in the Tana River Basin, Kenya

    Directory of Open Access Journals (Sweden)

    F. Tamooh

    2013-03-01

    Full Text Available A basin-wide study was conducted in the Tana River Basin (Kenya, in February 2008 (dry season, September–November 2009 (wet season, and June–July 2010 (end of the wet season to assess the dynamics and sources of dissolved inorganic carbon (DIC as well as to quantify CO2 fluxes, community respiration (R, and primary production (P. Samples were collected along the altitudinal gradient (from 3600 m to 8 m in several headwater streams, reservoirs (Kamburu and Masinga, and main Tana River. DIC concentrations ranged from 0.2 mmol L–1 to 4.8 mmol L–1 but with exceptionally high values (3.5 ± 1.6 mmol L–1 in Nyambene Hills tributaries. The wide range of δ13CDIC values (−15.0‰ to −2.4‰ indicate variable sources of DIC with headwater streams recording higher signatures compared to main Tana River. With few exceptions, the entire riverine network was supersaturated in CO2, implying the system is a net source of CO2 to the atmosphere. pCO2 values were generally higher in the lower main Tana River compared to headwater tributaries, opposite to the pattern typically observed in other river networks. This was attributed to high suspended sediment in the main Tana River fuelling in-stream community respiration and net heterotrophy. This was particularly evident during 2009 wet season campaign (median pCO2 of 1432 ppm compared to 2010 end of wet season (1002 ppm and 2008 dry season (579 ppm. First-order estimates show in-stream community respiration was responsible for the bulk of total CO2 evasion (59% to 89% in main Tana River while in tributaries respiration accounted for 4% to 52% of total CO2 evasion, suggesting CO2evasion in tributaries was sustained by processes than respiration, such as CO2-oversaturated groundwater input. While sediment loads increase downstream and thus light availability decreases in the water column, both chlorophyll a (0.2 μg L–1 to 9.6 μg L–1 and primary production (0.004 μmol L–1 h–1 to 7.38 μmol L

  9. 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.

    Science.gov (United States)

    Gérin, Stéphanie; Leprince, Pierre; Sluse, Francis E; Franck, Fabrice; Mathy, Grégory

    2016-01-01

    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 of the

  10. 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

  11. Abnormally activated one-carbon metabolic pathway is associated with mtDNA hypermethylation and mitochondrial malfunction in the oocytes of polycystic gilt ovaries

    OpenAIRE

    Longfei Jia; Juan Li; Bin He; Yimin Jia; Yingjie Niu; Chenfei Wang; Ruqian Zhao

    2016-01-01

    Polycystic ovarian syndrome (PCOS) is associated with hyperhomocysteinemia and polycystic ovaries (PCO) usually produce oocytes of poor quality. However, the intracellular mechanism linking hyperhomocysteinemia and oocyte quality remains elusive. In this study, the quality of the oocytes isolated from healthy and polycystic gilt ovaries was evaluated in vitro in association with one-carbon metabolism, mitochondrial DNA (mtDNA) methylation, and mitochondrial function. PCO oocytes demonstrated ...

  12. The CCAAT box-binding factor stimulates ammonium assimilation in Saccharomyces cerevisiae, defining a new cross-pathway regulation between nitrogen and carbon metabolisms.

    Science.gov (United States)

    Dang, V D; Bohn, C; Bolotin-Fukuhara, M; Daignan-Fornier, B

    1996-04-01

    In Saccharomyces cerevisiae, carbon and nitrogen metabolisms are connected via the incorporation of ammonia into glutamate; this reaction is catalyzed by the NADP-dependent glutamate dehydrogenase (NADP-GDH) encoded by the GDH1 gene. In this report, we show that the GDH1 gene requires the CCAAT box-binding activator (HAP complex) for optimal expression. This conclusion is based on several lines of evidence: (1) overexpression of GDH1 can correct the growth defect of hap2 and hap3 mutants on ammonium sulfate as a nitrogen source, (ii) Northern (RNA) blot analysis shows that the steady-state level of GDH1 mRNA is strongly lowered in a hap2 mutant, (iii) expression of a GDH1-lacZ fusion is drastically reduced in hap mutants, (iv) NADP-GDH activity is several times lower in the hap mutants compared with that in the isogenic wild-type strain, and finally, (v) site-directed mutagenesis of two consensual HAP binding sites in the GDH1 promoter strongly reduces expression of GDH1 and makes it HAP independent. Expression of GDH1 is also regulated by the carbon source, i.e., expression is higher on lactate than on ethanol, glycerol, or galactose, with the lowest expression being found on glucose. Finally, we show that a hap2 mutation does not affect expression of other genes involved in nitrogen metabolism (GDH2, GLN1, and GLN3 encoding, respectively, the NAD-GDH, glutamine synthetase, and a general activator of several nitrogen catabolic genes). The HAP complex is known to regulate expression of several genes involved in carbon metabolism; its role in the control of GDH1 gene expression, therefore, provides evidence for a cross-pathway regulation between carbon and nitrogen metabolisms.

  13. Abnormally activated one-carbon metabolic pathway is associated with mtDNA hypermethylation and mitochondrial malfunction in the oocytes of polycystic gilt ovaries.

    Science.gov (United States)

    Jia, Longfei; Li, Juan; He, Bin; Jia, Yimin; Niu, Yingjie; Wang, Chenfei; Zhao, Ruqian

    2016-01-13

    Polycystic ovarian syndrome (PCOS) is associated with hyperhomocysteinemia and polycystic ovaries (PCO) usually produce oocytes of poor quality. However, the intracellular mechanism linking hyperhomocysteinemia and oocyte quality remains elusive. In this study, the quality of the oocytes isolated from healthy and polycystic gilt ovaries was evaluated in vitro in association with one-carbon metabolism, mitochondrial DNA (mtDNA) methylation, and mitochondrial function. PCO oocytes demonstrated impaired polar body extrusion, and significantly decreased cleavage and blastocyst rates. The mitochondrial distribution was disrupted in PCO oocytes, together with decreased mitochondrial membrane potential and deformed mitochondrial structure. The mtDNA copy number and the expression of mtDNA-encoded genes were significantly lower in PCO oocytes. Homocysteine concentration in follicular fluid was significantly higher in PCO group, which was associated with significantly up-regulated one-carbon metabolic enzymes betaine homocysteine methyltransferase (BHMT), glycine N-methyltransferase (GNMT) and the DNA methyltransferase DNMT1. Moreover, mtDNA sequences coding for 12S, 16S rRNA and ND4, as well as the D-loop region were significantly hypermethylated in PCO oocytes. These results indicate that an abnormal activation of one-carbon metabolism and hypermethylation of mtDNA may contribute, largely, to the mitochondrial malfunction and decreased quality of PCO-derived oocytes in gilts.

  14. The PGC-1α/ERRα Axis Represses One-Carbon Metabolism and Promotes Sensitivity to Anti-folate Therapy in Breast Cancer

    Directory of Open Access Journals (Sweden)

    Étienne Audet-Walsh

    2016-02-01

    Full Text Available Reprogramming of cellular metabolism plays a central role in fueling malignant transformation, and AMPK and the PGC-1α/ERRα axis are key regulators of this process. The intersection of gene-expression and binding-event datasets for breast cancer cells shows that activation of AMPK significantly increases the expression of PGC-1α/ERRα and promotes the binding of ERRα to its cognate sites. Unexpectedly, the data also reveal that ERRα, in concert with PGC-1α, negatively regulates the expression of several one-carbon metabolism genes, resulting in substantial perturbations in purine biosynthesis. This PGC-1α/ERRα-mediated repression of one-carbon metabolism promotes the sensitivity of breast cancer cells and tumors to the anti-folate drug methotrexate. These data implicate the PGC-1α/ERRα axis as a core regulatory node of folate cycle metabolism and further suggest that activators of AMPK could be used to modulate this pathway in cancer.

  15. Transcriptional control of monolignol biosynthesis in Pinus taeda: factors affecting monolignol ratios and carbon allocation in phenylpropanoid metabolism

    Science.gov (United States)

    Anterola, Aldwin M.; Jeon, Jae-Heung; Davin, Laurence B.; Lewis, Norman G.

    2002-01-01

    Transcriptional profiling of the phenylpropanoid pathway in Pinus taeda cell suspension cultures was carried out using quantitative real time PCR analyses of all known genes involved in the biosynthesis of the two monolignols, p-coumaryl and coniferyl alcohols (lignin/lignan precursors). When the cells were transferred to a medium containing 8% sucrose and 20 mm potassium iodide, the monolignol/phenylpropanoid pathway was induced, and transcript levels for phenylalanine ammonia lyase, cinnamate 4-hydroxylase, p-coumarate 3-hydroxylase, 4-coumarate:CoA ligase, caffeoyl-CoA O-methyltransferase, cinnamoyl-CoA reductase, and cinnamyl alcohol dehydrogenase were coordinately up-regulated. Provision of increasing levels of exogenously supplied Phe to saturating levels (40 mm) to the induction medium resulted in further up-regulation of their transcript levels in the P. taeda cell cultures; this in turn was accompanied by considerable increases in both p-coumaryl and coniferyl alcohol formation and excretion. By contrast, transcript levels for both cinnamate 4-hydroxylase and p-coumarate 3-hydroxylase were only slightly up-regulated. These data, when considered together with metabolic profiling results and genetic manipulation of various plant species, reveal that carbon allocation to the pathway and its differential distribution into the two monolignols is controlled by Phe supply and differential modulation of cinnamate 4-hydroxylase and p-coumarate 3-hydroxylase activities, respectively. The coordinated up-regulation of phenylalanine ammonia lyase, 4-coumarate:CoA ligase, caffeoyl-CoA O-methyltransferase, cinnamoyl-CoA reductase and cinnamyl alcohol dehydrogenase in the presence of increasing concentrations of Phe also indicates that these steps are not truly rate-limiting, because they are modulated according to metabolic demand. Finally, the transcript profile of a putative acid/ester O-methyltransferase, proposed as an alternative catalyst for O-methylation leading

  16. Environmental regulation of carbon isotope composition and crassulacean acid metabolism in three plant communities along a water availability gradient.

    Science.gov (United States)

    Ricalde, M Fernanda; Andrade, José Luis; Durán, Rafael; Dupuy, Juan Manuel; Simá, J Luis; Us-Santamaría, Roberth; Santiago, Louis S

    2010-12-01

    Expression of crassulacean acid metabolism (CAM) is characterized by extreme variability within and between taxa and its sensitivity to environmental variation. In this study, we determined seasonal fluctuations in CAM photosynthesis with measurements of nocturnal tissue acidification and carbon isotopic composition (δ(13)C) of bulk tissue and extracted sugars in three plant communities along a precipitation gradient (500, 700, and 1,000 mm year(-1)) on the Yucatan Peninsula. We also related the degree of CAM to light habitat and relative abundance of species in the three sites. For all species, the greatest tissue acid accumulation occurred during the rainy season. In the 500 mm site, tissue acidification was greater for the species growing at 30% of daily total photon flux density (PFD) than species growing at 80% PFD. Whereas in the two wetter sites, the species growing at 80% total PFD had greater tissue acidification. All species had values of bulk tissue δ(13)C less negative than -20‰, indicating strong CAM activity. The bulk tissue δ(13)C values in plants from the 500 mm site were 2‰ less negative than in plants from the wetter sites, and the only species growing in the three communities, Acanthocereus tetragonus (Cactaceae), showed a significant negative relationship between both bulk tissue and sugar δ(13)C values and annual rainfall, consistent with greater CO(2) assimilation through the CAM pathway with decreasing water availability. Overall, variation in the use of CAM photosynthesis was related to water and light availability and CAM appeared to be more ecologically important in the tropical dry forests than in the coastal dune.

  17. The redox-sensing regulator Rex modulates central carbon metabolism, stress tolerance response and biofilm formation by Streptococcus mutans.

    Directory of Open Access Journals (Sweden)

    Jacob P Bitoun

    Full Text Available The Rex repressor has been implicated in regulation of central carbon and energy metabolism in gram-positive bacteria. We have previously shown that Streptococcus mutans, the primary causative agent of dental caries, alters its transcriptome upon Rex-deficiency and renders S. mutans to have increased susceptibility to oxidative stress, aberrations in glucan production, and poor biofilm formation. In this study, we showed that rex in S. mutans is co-transcribed as an operon with downstream guaA, encoding a putative glutamine amidotransferase. Electrophoretic mobility shift assays showed that recombinant Rex bound promoters of target genes avidly and specifically, including those down-regulated in response to Rex-deficiency, and that the ability of recombinant Rex to bind to selected promoters was modulated by NADH and NAD(+. Results suggest that Rex in S. mutans can function as an activator in response to intracellular NADH/NAD(+ level, although the exact binding site for activator Rex remains unclear. Consistent with a role in oxidative stress tolerance, hydrogen peroxide challenge assays showed that the Rex-deficient mutant, TW239, and the Rex/GuaA double mutant, JB314, were more susceptible to hydrogen peroxide killing than the wildtype, UA159. Relative to UA159, JB314 displayed major defects in biofilm formation, with a decrease of more than 50-fold in biomass after 48-hours. Collectively, these results further suggest that Rex in S. mutans regulates fermentation pathways, oxidative stress tolerance, and biofilm formation in response to intracellular NADH/NAD(+ level. Current effort is being directed to further investigation of the role of GuaA in S. mutans cellular physiology.

  18. Putting a Price On Carbon

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    The Australian Government unveils its new climate change plan amid controversy The Australian Government made public its long awaited new climate change plan on July 10. Based on the plan,the government will collect a carbon tax from Australia’s major

  19. Analysis of the metabolic utilization of carbon sources and potential functional diversity of the bacterial community in lab-scale horizontal subsurface-flow constructed wetlands.

    Science.gov (United States)

    Deng, Huanhuan; Ge, Liyun; Xu, Tan; Zhang, Minghua; Wang, Xuedong; Zhang, Yalei; Peng, Hong

    2011-01-01

    Microorganisms are an integral part of the biogeochemical processes in wetlands. To improve the performance of constructed wetlands, it is very important to know the metabolic properties and functional diversity of the microbial communities. The purpose of this study is to analyze the metabolic properties and functional diversity of the microbial community in a horizontal subsurface-flow constructed wetland (CW) in a laboratory study through the sole-carbon-source utilization profiles using Biolog-ECO microplates. The technique has advantages over traditional cell culture techniques, such as molecular-level techniques-RNA amplification, which are time-consuming, expensive, and only applicable to the small number of species that may be cultured. This CW was designed to treat rural eutrophic water in China, using the plant L. This study showed that the metabolic activities of upper front substrate microorganisms (UF) were greater than those of the lower back substrate microorganisms (LB) in the CW. Integrated areas under average well color development (AWCD) curves of substrate microorganisms in the UF were 131.9, 4.8, and 99.3% higher than in the lower front part (LF), the upper back part (UB), and the LB part of the CW, respectively. Principal components analysis showed significant differences in both community structure and metabolic utilization of carbon sources between substrate microorganisms from different sampling sites. Carbon source utilization of polymers, carbohydrates, carboxylic acids, and amino acids was higher in UF than in LF, but that of amines and phenolic compounds was very similar in UF and LF. The richness, evenness, and diversity of upper substrate microbial communities were significantly higher than those of lower substrate. The LF substrate microbial communities had lower evenness than the other sampling plots, and the lowest richness of substrate microbial community was found in the LB part of the CW.

  20. 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.

  1. Exposure to Glycolytic Carbon Sources Reveals a Novel Layer of Regulation for the MalT Regulon

    Directory of Open Access Journals (Sweden)

    Sylvia A. Reimann

    2011-01-01

    Full Text Available Bacteria adapt to changing environments by means of tightly coordinated regulatory circuits. The use of synthetic lethality, a genetic phenomenon in which the combination of two nonlethal mutations causes cell death, facilitates identification and study of such circuitry. In this study, we show that the E. coli ompR malTcon double mutant exhibits a synthetic lethal phenotype that is environmentally conditional. MalTcon, the constitutively active form of the maltose system regulator MalT, causes elevated expression of the outer membrane porin LamB, which leads to death in the absence of the osmoregulator OmpR. However, the presence and metabolism of glycolytic carbon sources, such as sorbitol, promotes viability and unveils a novel layer of regulation within the complex circuitry that controls maltose transport and metabolism.

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

    Science.gov (United States)

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

    2015-01-01

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

  3. 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 (Penzymes 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.

  4. 致病菌碳源代谢与毒力调控的关联性%Correlation between carbon metabolism and virulence regulation in pathogen

    Institute of Scientific and Technical Information of China (English)

    周妍妍; 阚飙

    2012-01-01

    在自然环境中,细菌需要应对生长环境的不断变化.细菌发展了一些机制以适应这些环境的变化.其中,对可用碳源的适应性机制是其中的重要方面.碳源是细菌对复杂环境作出适应反应的信号之一,某种特定碳源的出现也许使细菌感受到正处于感染相关的机体组织或细胞中,从而促使毒力基因表达.本文简述了细菌对可用碳源的适应性机制,并就致病菌碳源代谢与毒力调控的关联性进行了综述.这些致病菌主要包括了硬壁菌门的链球菌、单增李斯特菌、产气夹膜杆菌;变形菌门的牛种布鲁氏杆菌、脑膜炎奈瑟氏菌、鼠伤寒沙门氏菌、霍乱弧菌、根瘤菌;以及放线茵门的结核分枝杆菌,它们的碳源代谢通过多种途径,如HprK/P及PTS蛋白、CRP-cAMP、ABC转运系统、双组分系统等,影响其毒力表达.%In the natural environment, bacterium develop some mechanisms, especially the mechanism of carbon metabolism for adapting to changes in growth conditions. Since the carbon source serve as signal for environment fitness, the presence of some specific carbon source makes bacteria realizing that they have gained access to the infection-related host and then turning on or switching off expression of the specific virulence genes. In the review, we will briefly summarize the mechanisms used for responding to carbon source availability, and review the resent progress about the relation between carbon metabolism and virulence regulation in pathogen. The pathogens mentioned here mainly include the Streptococcus, Listeria monocytogenes, Clostridium perfringens in Firmicutes, Brucella abortus, Neisseria meningitidis, Salmonella Typhimurium, Vibrio chol-erae, Agrobacterium tumefaciens in Proteobacteria, and Mycobacterium tuberculosis in Actinobacteria . The virulence regulation could be affected by carbon metabolism through HprK/P, PTS proteins, CRP-cAMP, ATP-binding cassette transporters, two

  5. Bromine-76 and carbon-11 labelled NNC 13-8199, metabolically stable benzodiazepine receptor agonists as radioligands for positron emission tomography (PET)

    Energy Technology Data Exchange (ETDEWEB)

    Foged, C. [Karolinska Institutet, Department of Clinical Neuroscience, Psychiatry Section, Karolinska Hospital, Stockholm (Sweden)]|[Novo Nordisk A/S, Health Care Discovery and Development, Maaloev (Denmark); Halldin, C.; Pauli, S.; Suhara, T.; Swahn, C.G.; Karlsson, P.; Farde, L. [Karolinska Institutet, Department of Clinical Neuroscience, Psychiatry Section, Karolinska Hospital, Stockholm (Sweden); Loc`h, C.; Maziere, B.; Maziere, M. [Service Hospitalier Frederic Joliot, CEA, Orsay (France); Hansen, H.C. [Novo Nordisk A/S, Health Care Discovery and Development, Maaloev (Denmark)

    1997-10-01

    NNC 13-8241 has recently been labelled with iodine-123 and developed as a metabolically stable benzodiazepine receptor ligand for single-photon emission computed tomography (SPECT) in monkeys and man. NNC 13-8199 is a bromo-analogue of NNC 13-8241. This partial agonist binds selectively and with subnanomolar affinity to the benzodiazepine receptors. We prepared {sup 76}Br labelled NNC 13-8199 from the trimethyltin precursor by the chloramine-T method. Carbon-11 labelled NNC 13-8199 was synthesised by N-alkylation of the nitrogen of the amide group with [{sup 11}C]methyl iodide. Positron emission tomography (PET) examination with the two radioligands in monkeys demonstrated a high uptake of radioactivity in the occipital, temporal and frontal cortex. In the study with [{sup 76}Br]NNC 13-8199, the monkey brain uptake continued to increase until the time of displacement with flumazenil at 215 min after injection. For both radioligands the radioactivity in the cortical brain regions was markedly reduced after displacement with flumazenil. More than 98% of the radioactivity in monkey plasma represented unchanged radioligand 40 min after injection. The low degree of metabolism indicates that NNC 13-8199 is metabolically much more stable than hitherto developed PET radioligands for imaging of benzodiazepine receptors in the primate brain. [{sup 76}Br]NNC 13-8199 has potential as a radioligand in human PET studies using models where a slow metabolism is an advantage. (orig.) With 8 figs., 28 refs.

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

    Directory of Open Access Journals (Sweden)

    Fabien Coze

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

  7. The threonine degradation pathway of the Trypanosoma brucei procyclic form: the main carbon source for lipid biosynthesis is under metabolic control.

    Science.gov (United States)

    Millerioux, Yoann; Ebikeme, Charles; Biran, Marc; Morand, Pauline; Bouyssou, Guillaume; Vincent, Isabel M; Mazet, Muriel; Riviere, Loïc; Franconi, Jean-Michel; Burchmore, Richard J S; Moreau, Patrick; Barrett, Michael P; Bringaud, Frédéric

    2013-10-01

    The Trypanosoma brucei procyclic form resides within the digestive tract of its insect vector, where it exploits amino acids as carbon sources. Threonine is the amino acid most rapidly consumed by this parasite, however its role is poorly understood. Here, we show that the procyclic trypanosomes grown in rich medium only use glucose and threonine for lipid biosynthesis, with threonine's contribution being ∼ 2.5 times higher than that of glucose. A combination of reverse genetics and NMR analysis of excreted end-products from threonine and glucose metabolism, shows that acetate, which feeds lipid biosynthesis, is also produced primarily from threonine. Interestingly, the first enzymatic step of the threonine degradation pathway, threonine dehydrogenase (TDH, EC 1.1.1.103), is under metabolic control and plays a key role in the rate of catabolism. Indeed, a trypanosome mutant deleted for the phosphoenolpyruvate decarboxylase gene (PEPCK, EC 4.1.1.49) shows a 1.7-fold and twofold decrease of TDH protein level and activity, respectively, associated with a 1.8-fold reduction in threonine-derived acetate production. We conclude that TDH expression is under control and can be downregulated in response to metabolic perturbations, such as in the PEPCK mutant in which the glycolytic metabolic flux was redirected towards acetate production.

  8. A Functional Screen for Myc-Responsive Genes Reveals Serine Hydroxymethyltransferase, a Major Source of the One-Carbon Unit for Cell Metabolism

    Science.gov (United States)

    Nikiforov, Mikhail A.; Chandriani, Sanjay; O'Connell, Brenda; Petrenko, Oleksi; Kotenko, Iulia; Beavis, Andrew; Sedivy, John M.; Cole, Michael D.

    2002-01-01

    A cDNA library enriched with Myc-responsive cDNAs but depleted of myc cDNAs was used in a functional screen for growth enhancement in c-myc-null cells. A cDNA clone for mitochondrial serine hydroxymethyltransferase (mSHMT) that was capable of partial complementation of the growth defects of c-myc-null cells was identified. Expression analysis and chromatin immunoprecipitation demonstrated that mSHMT is a direct Myc target gene. Furthermore, a separate gene encoding the cytoplasmic isoform of the same enzyme is also a direct target of Myc regulation. SHMT enzymes are the major source of the one-carbon unit required for folate metabolism and for the biosynthesis of nucleotides and amino acids. Our data establish a novel functional link between Myc and the regulation of cellular metabolism. PMID:12138190

  9. Reimagining Field Education in Social Work: The Promise Unveiled

    Directory of Open Access Journals (Sweden)

    Purnima George

    2013-11-01

    Full Text Available The current wave of neo-liberalism in Canada has driven our universities to retreat from their responsibilities as public institutions, accountable to their communities. In this paper we present a case study of field education in Canada and discuss the implications of the neoliberal academy on social work field education. On the basis of our experience as faculty consultants of BSW and MSW students, and coming from a school of social work that embraces an anti-oppression perspective as its guiding philosophy, we undertake a reconceptualization exercise in which we re-imagine field education. We politicize field education as a site with transformative possibilities. We describe the principles and processes that inform our reconceptualization and offer an example of how this might be realized in practice. This paper contributes towards developing new knowledge that unveils the promise of transformative change through a re-imagination of field education.

  10. Unveiling the physics of the Thomson jumping ring

    Science.gov (United States)

    Ladera, Celso L.; Donoso, Guillermo

    2015-04-01

    We present a new theoretical model and validating experiments that unveil the rich physics behind the flight of the conductive ring in the Thomson experiment—physics that is hard to see because of the rapid motion. The electrodynamics of the flying ring exhibits interesting features, e.g., varying mutual inductance between the ring and the electromagnet. The dependences of the ring electrodynamics upon time and position as the ring travels upward are conveniently separated and determined to obtain a comprehensive view of the ring motion. We introduce a low-cost jumping ring setup that incorporates pickup coils connected in opposition, allowing us to scrutinize the ring electrodynamics and confirm our theoretical model with good accuracy. This work is within the reach of senior students of science or engineering, and it can be implemented either as a teaching laboratory experiment or as an open-ended project.

  11. Unveiling the Massive Stars in the Galactic Center

    CERN Document Server

    Dong, Hui; Morris, Mark R; Wang, Daniel Q; Cotera, Angela

    2013-01-01

    We present our recent efforts to unveil and understand the origin of massive stars outside the three massive star clusters in the Galactic Center. From our HST/NICMOS survey of the Galactic Center, we have identified 180 Paschen-alpha emitting sources, most of which should be evolved massive stars with strong optically thin stellar winds. Recently, we obtained Gemini GNIRS/NIFS H- and K-band spectra of eight massive stars near the Arches cluster. From their radial velocities, ages and masses, we suggest that in our sample, two stars are previous members of the Arches cluster, while other two stars embedded in the H1/H2 HII regions formed in-situ.

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

    Directory of Open Access Journals (Sweden)

    James L Falter

    Full Text Available 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.

  13. 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.

  14. The CCAAT box-binding factor stimulates ammonium assimilation in Saccharomyces cerevisiae, defining a new cross-pathway regulation between nitrogen and carbon metabolisms.

    OpenAIRE

    Dang, V D; Bohn, C.; Bolotin-Fukuhara, M; Daignan-Fornier, B.

    1996-01-01

    In Saccharomyces cerevisiae, carbon and nitrogen metabolisms are connected via the incorporation of ammonia into glutamate; this reaction is catalyzed by the NADP-dependent glutamate dehydrogenase (NADP-GDH) encoded by the GDH1 gene. In this report, we show that the GDH1 gene requires the CCAAT box-binding activator (HAP complex) for optimal expression. This conclusion is based on several lines of evidence: (1) overexpression of GDH1 can correct the growth defect of hap2 and hap3 mutants on a...

  15. Systems biology approach reveals that overflow metabolism of acetate in Escherichia coli is triggered by carbon catabolite repression of acetyl-CoA synthetase

    Directory of Open Access Journals (Sweden)

    Nahku Ranno

    2010-12-01

    Full Text Available Abstract Background The biotechnology industry has extensively exploited Escherichia coli for producing recombinant proteins, biofuels etc. However, high growth rate aerobic E. coli cultivations are accompanied by acetate excretion i.e. overflow metabolism which is harmful as it inhibits growth, diverts valuable carbon from biomass formation and is detrimental for target product synthesis. Although overflow metabolism has been studied for decades, its regulation mechanisms still remain unclear. Results In the current work, growth rate dependent acetate overflow metabolism of E. coli was continuously monitored using advanced continuous cultivation methods (A-stat and D-stat. The first step in acetate overflow switch (at μ = 0.27 ± 0.02 h-1 is the repression of acetyl-CoA synthethase (Acs activity triggered by carbon catabolite repression resulting in decreased assimilation of acetate produced by phosphotransacetylase (Pta, and disruption of the PTA-ACS node. This was indicated by acetate synthesis pathways PTA-ACKA and POXB component expression down-regulation before the overflow switch at μ = 0.27 ± 0.02 h-1 with concurrent 5-fold stronger repression of acetate-consuming Acs. This in turn suggests insufficient Acs activity for consuming all the acetate produced by Pta, leading to disruption of the acetate cycling process in PTA-ACS node where constant acetyl phosphate or acetate regeneration is essential for E. coli chemotaxis, proteolysis, pathogenesis etc. regulation. In addition, two-substrate A-stat and D-stat experiments showed that acetate consumption capability of E. coli decreased drastically, just as Acs expression, before the start of overflow metabolism. The second step in overflow switch is the sharp decline in cAMP production at μ = 0.45 h-1 leading to total Acs inhibition and fast accumulation of acetate. Conclusion This study is an example of how a systems biology approach allowed to propose a new regulation mechanism for

  16. Metabolic flux analysis of Escherichia coli creB and arcA mutants reveals shared control of carbon catabolism under microaerobic growth conditions.

    Science.gov (United States)

    Nikel, Pablo I; Zhu, Jiangfeng; San, Ka-Yiu; Méndez, Beatriz S; Bennett, George N

    2009-09-01

    Escherichia coli has several elaborate sensing mechanisms for response to availability of oxygen and other electron acceptors, as well as the carbon source in the surrounding environment. Among them, the CreBC and ArcAB two-component signal transduction systems are responsible for regulation of carbon source utilization and redox control in response to oxygen availability, respectively. We assessed the role of CreBC and ArcAB in regulating the central carbon metabolism of E. coli under microaerobic conditions by means of (13)C-labeling experiments in chemostat cultures of a wild-type strain, DeltacreB and DeltaarcA single mutants, and a DeltacreB DeltaarcA double mutant. Continuous cultures were conducted at D = 0.1 h(-1) under carbon-limited conditions with restricted oxygen supply. Although all experimental strains metabolized glucose mainly through the Embden-Meyerhof-Parnas pathway, mutant strains had significantly lower fluxes in both the oxidative and the nonoxidative pentose phosphate pathways. Significant differences were also found at the pyruvate branching point. Both pyruvate-formate lyase and the pyruvate dehydrogenase complex contributed to acetyl-coenzyme A synthesis from pyruvate, and their activity seemed to be modulated by both ArcAB and CreBC. Strains carrying the creB deletion showed a higher biomass yield on glucose compared to the wild-type strain and its DeltaarcA derivative, which also correlated with higher fluxes from building blocks to biomass. Glyoxylate shunt and lactate dehydrogenase were active mainly in the DeltaarcA strain. Finally, it was observed that the tricarboxylic acid cycle reactions operated in a rather cyclic fashion under our experimental conditions, with reduced activity in the mutant strains.

  17. Effects of oxidative stress on fatty acid- and one-carbon-metabolism in psychiatric and cardiovascular disease comorbidity

    DEFF Research Database (Denmark)

    Assies, Johanna; Mocking, Roel J T; Lok, Christianne A;

    2014-01-01

    membrane peroxidizability and fluidity, eicosanoid synthesis, neuroprotection and epigenetics. CONCLUSION: While oxidative-stress-induced alterations in FA and 1-C metabolism may initially enhance oxidative stress resistance, persisting chronically, they may cause damage possibly underlying (co...

  18. Sinorhizobium meliloti mutants lacking phosphotransferase system enzyme HPr or EIIA are altered in diverse processes, including carbon metabolism, cobalt requirements, and succinoglycan production.

    Science.gov (United States)

    Pinedo, Catalina Arango; Bringhurst, Ryan M; Gage, Daniel J

    2008-04-01

    Sinorhizobium meliloti is a member of the Alphaproteobacteria that fixes nitrogen when it is in a symbiotic relationship. Genes for an incomplete phosphotransferase system (PTS) have been found in the genome of S. meliloti. The genes present code for Hpr and ManX (an EIIA(Man)-type enzyme). HPr and EIIA regulate carbon utilization in other bacteria. hpr and manX in-frame deletion mutants exhibited altered carbon metabolism and other phenotypes. Loss of HPr resulted in partial relief of succinate-mediated catabolite repression, extreme sensitivity to cobalt limitation, rapid die-off during stationary phase, and altered succinoglycan production. Loss of ManX decreased expression of melA-agp and lac, the operons needed for utilization of alpha- and beta-galactosides, slowed growth on diverse carbon sources, and enhanced accumulation of high-molecular-weight succinoglycan. A strain with both hpr and manX deletions exhibited phenotypes similar to those of the strain with a single hpr deletion. Despite these strong phenotypes, deletion mutants exhibited wild-type nodulation and nitrogen fixation when they were inoculated onto Medicago sativa. The results show that HPr and ManX (EIIA(Man)) are involved in more than carbon regulation in S. meliloti and suggest that the phenotypes observed occur due to activity of HPr or one of its phosphorylated forms.

  19. Comparison of end-tidal carbon dioxide and arterial blood bicarbonate levels in patients with metabolic acidosis referred to emergency medicine

    Science.gov (United States)

    Taghizadieh, Ali; Pouraghaei, Mahboub; Moharamzadeh, Payman; Ala, Alireza; Rahmani, Farzad; Basiri Sofiani, Karim

    2016-01-01

    Introduction: The routine and gold standard method to diagnose of acid – base disturbance is arterial blood gas (ABG) sampling. Capnography could be used to measure the end-tidal carbon dioxide (ETCO2) levels and ETco2 has a close correlation with the PaCo2. The aim of this study was comparison the ETco2 and arterial blood bicarbonate levels in patients with metabolic acidosis. Methods: In a descriptive-analytical study that performed in Emergency Department of Emam Reza Medical Research and Training Hospital of Tabriz on patients with metabolic acidosis, ETco2 level and blood bicarbonate levels in 262 patients were evaluated. Results: Mean of ETco2 and Hco3 levels in patients with metabolic acidosis were 22.29 ± 4.15 and 12.78 ± 3.83, respectively. In all patients, the significant direct linear relationship was found between ETco2 with Hco3 (r = 0.553, P < 0.001). We had 4 groups of patients with metabolic acidosis, also there is a significant direct linear relationship between the ETCo2 and the Hco3 level of arterial blood in patients with renal failure (P < 0.001 and r = 0.551), sepsis (P < 0.001 and r = 0.431), drug toxicity (P < 0.001 and r = 0.856), and ketoacidosis (DKA) (P < 0.001 and r = 0.559). Conclusion: According to the results of this study, capnography can be used for primary diagnosis of metabolic acidosis in spontaneously breathing patients who referred to the emergency wards, however, the ABG must be considered as the gold standard tool for diagnosis and guiding the treatment. PMID:27777693

  20. Analysis of carbon and nitrogen co-metabolism in yeast by ultrahigh-resolution mass spectrometry applying {sup 13}C- and {sup 15}N-labeled substrates simultaneously

    Energy Technology Data Exchange (ETDEWEB)

    Blank, Lars M. [TU Dortmund University, Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, Dortmund (Germany); RWTH Aachen University, Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, Aachen (Germany); Desphande, Rahul R. [TU Dortmund University, Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, Dortmund (Germany); Michigan State University, Department of Plant Biology, East Lansing, MI (United States); Schmid, Andreas [TU Dortmund University, Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, Dortmund (Germany); Hayen, Heiko [Leibniz-Institut fuer Analytische Wissenschaften-ISAS-e.V, Dortmund (Germany); University of Wuppertal, Department of Food Chemistry, Wuppertal (Germany)

    2012-06-15

    Alternative metabolic pathways inside a cell can be deduced using stable isotopically labeled substrates. One prerequisite is accurate measurement of the labeling pattern of targeted metabolites. Experiments are generally limited to the use of single-element isotopes, mainly {sup 13}C. Here, we demonstrate the application of direct infusion nanospray, ultrahigh-resolution Fourier transform ion cyclotron resonance-mass spectrometry (FTICR-MS) for metabolic studies using differently labeled elemental isotopes simultaneously - i.e., {sup 13}C and {sup 15}N - in amino acids of a total protein hydrolysate. The optimized strategy for the analysis of metabolism by a hybrid linear ion trap-FTICR-MS comprises the collection of multiple adjacent selected ion monitoring scans. By limiting both the width of the mass range and the number of ions entering the ICR cell with automated gain control, sensitive measurements of isotopologue distribution were possible without compromising mass accuracy and isotope intensity mapping. The required mass-resolving power of more than 60,000 is only achievable on a routine basis by FTICR and Orbitrap mass spectrometers. Evaluation of the method was carried out by comparison of the experimental data to the natural isotope abundances of selected amino acids and by comparison to GC/MS results obtained from a labeling experiment with {sup 13}C-labeled glucose. The developed method was used to shed light on the complexity of the yeast Saccharomyces cerevisiae carbon-nitrogen co-metabolism by administering both {sup 13}C-labeled glucose and {sup 15}N-labeled alanine. The results indicate that not only glutamate but also alanine acts as an amino donor during alanine and valine synthesis. Metabolic studies using FTICR-MS can exploit new possibilities by the use of multiple-labeled elemental isotopes. (orig.)

  1. Compound specific isotopic fractionation patterns suggest different carbon metabolisms among Chloroflexus-like bacteria in hot spring microbial mats

    NARCIS (Netherlands)

    Sinninghe Damsté, J.S.; Meer, M.T.J. van der; Schouten, S.; Leeuw, J.W. de; Ward, D.M.

    2003-01-01

    Stable carbon isotope fractionations between dissolved inorganic carbon and lipid biomarkers suggest photoautotrophy by Chloroflexus-like organisms in sulfidic and nonsulfidic Yellowstone hot springs. Where co-occurring, cyanobacteria appear to cross-feed Chloroflexus-like organisms supporting photo

  2. Identification of glucose kinase-dependent and -independent pathways for carbon control of primary metabolism, development and antibiotic production in Streptomyces coelicolor by quantitative proteomics.

    Science.gov (United States)

    Gubbens, Jacob; Janus, Marleen; Florea, Bogdan I; Overkleeft, Herman S; van Wezel, Gilles P

    2012-12-01

    Members of the soil-dwelling prokaryotic genus Streptomyces are indispensable for the recycling of complex polysaccharides, and produce a wide range of natural products. Nutrient availability is a major determinant for the switch to development and antibiotic production in streptomycetes. Carbon catabolite repression (CCR), a main signalling pathway underlying this phenomenon, was so far considered fully dependent on the glycolytic enzyme glucose kinase (Glk). Here we provide evidence of a novel Glk-independent pathway in Streptomyces coelicolor, using advanced proteomics that allowed the comparison of the expression of some 2000 proteins, including virtually all enzymes for central metabolism. While CCR and inducer exclusion of enzymes for primary and secondary metabolism and precursor supply for natural products is mostly mediated via Glk, enzymes for the urea cycle, as well as for biosynthesis of the γ-butyrolactone Scb1 and the responsive cryptic polyketide Cpk are subject to Glk-independent CCR. Deletion of glkA led to strong downregulation of biosynthetic proteins for prodigionins and calcium-dependent antibiotic (CDA) in mannitol-grown cultures. Repression of bldB, bldN, and its target bldM may explain the poor development of S. coelicolor on solid-grown cultures containing glucose. A new model for carbon catabolite repression in streptomycetes is presented.

  3. Global RNA Fold and Molecular Recognition for a pfl Riboswitch Bound to ZMP, a Master Regulator of One-Carbon Metabolism.

    Science.gov (United States)

    Ren, Aiming; Rajashankar, Kanagalaghatta R; Patel, Dinshaw J

    2015-08-04

    ZTP, the pyrophosphorylated analog of ZMP (5-amino-4-imidazole carboxamide ribose-5'-monophosphate), was identified as an alarmone that senses 10-formyl-tetrahydroflate deficiency in bacteria. Recently, a pfl riboswitch was identified that selectively binds ZMP and regulates genes associated with purine biosynthesis and one-carbon metabolism. We report on the structure of the ZMP-bound Thermosinus carboxydivorans pfl riboswitch sensing domain, thereby defining the pseudoknot-based tertiary RNA fold, the binding-pocket architecture, and principles underlying ligand recognition specificity. Molecular recognition involves shape complementarity, with the ZMP 5-amino and carboxamide groups paired with the Watson-Crick edge of an invariant uracil, and the imidazole ring sandwiched between guanines, while the sugar hydroxyls form intermolecular hydrogen bond contacts. The burial of the ZMP base and ribose moieties, together with unanticipated coordination of the carboxamide by Mg(2+), contrasts with exposure of the 5'-phosphate to solvent. Our studies highlight the principles underlying RNA-based recognition of ZMP, a master regulator of one-carbon metabolism.

  4. Progress on photosynthetic carbon metabolism types in marine macroalgae%大型海藻光合碳代谢类型的研究进展

    Institute of Scientific and Technical Information of China (English)

    芦笛

    2013-01-01

    As a part of marine algae, marine macroalgae, whose edible and medicinal values are widely applied, participate in global CO2 and O2 turnover through photosynthesis. Therefore, when viewed from ecology as well as economics, the process of photosynthetic CO2 fixation and metabolism in marine macroalgae is of great significance. Up to the present, metabonomics and enzymology researches on photosynthetic carbon metabolism in marine macroalgae have proved the existence of the PEPCK-or PEPC-type C4 pathway as well as the CAM pathway in addition to the C3 pathway, although the integrality of the pathways is still unknown. Moreover, the results of photosynthetic gas exchange indicate that the photosynthetic carbon metabolism pathway in macroalgae performs the C4-like type on the whole. This situation resembles some terrestrial C3 plants with additional C4 pathway. Therefore, researches on photosynthetic carbon metabolism pathways in macroalgae remain to be explored in depth in the future.%作为海洋藻类的一部分,大型海藻通过光合作用参与了海洋对全球CO2和O2的周转,其食用和药用价值也得到了广泛应用。因此无论从生态还是经济角度来看,研究大型海藻通过光合作用对CO2进行固定和代谢的过程都具有重要意义。到目前为止,世界上对大型海藻光合碳代谢途径的研究从代谢组学和酶学角度证明了大型海藻体内除了C3途径外,还同时存在不能确定完整与否的PEPCK或PEPC类型的C4途径或CAM途径;光合气体交换的结果显示其光合碳代谢途径从整体上表现出类似C4(C4-like)类型。这种情况与一些体内存在C4途径的陆生C3植物相似。因此大型海藻光合碳代谢途径仍然有待深入研究。

  5. Carbon-Isotope Composition of Biochemical Fractions and the Regulation of Carbon Balance in Leaves of the C3-Crassulacean Acid Metabolism Intermediate Clusia minor L. Growing in Trinidad.

    Science.gov (United States)

    Borland, A. M.; Griffiths, H.; Broadmeadow, MSJ.; Fordham, M. C.; Maxwell, C.

    1994-10-01

    Carbon-isotope ratios ([delta]13Cs) were measured for various bio-chemical fractions quantitatively extracted from naturally exposed and shaded leaves of the C3-Crassulacean acid metabolism (CAM) intermediate Clusia minor, sampled at dawn and dusk on days during the wet and dry seasons in Trinidad. As the activity of CAM increased in response to decreased availability of water and higher photon flux density, organic acids and soluble sugars were enriched in 13C by approximately 3.5 to 4%[per mille (thousand) sign] compared to plants sampled during the wet season. The induction of CAM was accompanied by a doubling in size of the reserve carbohydrate pools. Moreover, stoichiometric measurements indicated that degradation of both chloroplastic reserves and soluble sugars were necessary to supply phosphoenolpyruvate for the synthesis of organic acids at night. Results also suggest that two pools of soluble sugars exist in leaves of C. minor that perform CAM, one a vacuolar pool enriched in 13C and the second a transport pool depleted in 13C. Estimates of carbon-isotope discrimination expressed during CAM, derived from the trafficking among inorganic carbon, organic acids, and carbohydrate pools overnight, ranged from 0.9 to 3.1%[per mille (thousand) sign]. The [delta]13C of structural material did not change significantly between wet and dry seasons, indicating that most of the carbon used in growth was derived from C3 carboxylation.

  6. Up-regulation of carbon metabolism-related glyoxylate cycle and toxin production in Beauveria bassiana JEF-007 during infection of bean bug, Riptortus pedestris (Hemiptera: Alydidae).

    Science.gov (United States)

    Yang, Yi-Ting; Lee, Se Jin; Nai, Yu-Shin; Kim, Sihyeon; Kim, Jae Su

    2016-10-01

    Beauveria bassiana (Bb) is used as an environment-friendly biopesticide. However, the molecular mechanisms of Bb-host interactions are not well understood. Herein, RNA isolated from B. bassiana (Bb JEF-007) and Riptortus pedestris (Hemiptera: Alydidae) infected with this strain were firstly subjected to high-throughput next generation sequencing (NGS) to analyze and compare transcriptomes. Due to lack of fungal and host genome information, fungal transcriptome was processed to partially exclude non-infection specific genes and host-flora. Differentially Expressed Gene (DEG) analysis showed that 2381 genes were up-regulated and 2303 genes were down-regulated upon infection. Most DEGs were classified into the categories of single-organism, cellular and metabolism processes by Gene Ontology analysis. Most DEGs were involved in metabolic pathways based on Kyoto Encyclopedia of Genes and Genomes pathway mapping. Carbon metabolism-related enzymes in the glyoxylate cycle were significantly up-regulated, suggesting a possible role for them in Bb growth in the host. Additionally, transcript levels of several fungal genes were dramatically increased after infection, such as cytotoxic lectin-like protein, bacterial-like toxin, proteins related to cell wall formation, hyphal growth, nutrient uptake, and halogenated compound synthesis. This work provides insight into how entomopathogenic B. bassiana grows in agriculturally harmful bean bug at 6 d post infection.

  7. Relationships among folate, alcohol consumption, gene variants in one-carbon metabolism and p16 INK4a methylation and expression in healthy breast tissues

    Science.gov (United States)

    Llanos, Adana A.; Dumitrescu, Ramona G.; Brasky, Theodore M.; Liu, Zhenhua; Mason, Joel B.; Marian, Catalin; Makambi, Kepher H.; Spear, Scott L.; Kallakury, Bhaskar V.S.; Freudenheim, Jo L.; Shields, Peter G.

    2015-01-01

    p16 INK4a is a tumor suppressor gene, frequently hypermethylated in breast cancer; this epigenetic silencing of p16 INK4a occurs early in carcinogenesis. The risk factors and functional consequences of p16 INK4a methylation are unknown. Alcohol consumption, a breast cancer risk factor, impedes folate metabolism and may thereby alter gene methylation since folate plays a pivotal role in DNA methylation. In a cross-sectional study of 138 women with no history of breast cancer who underwent reduction mammoplasty, we studied breast cancer risk factors, plasma and breast folate concentrations, variation in one-carbon metabolism genes, p16 INK4a promoter methylation and P16 protein expression. Logistic regression was used to estimate multivariable-adjusted odds ratios (OR) and 95% confidence intervals (CI). p16 INK4a methylation was negatively correlated with P16 expression (r = −0.28; P = 0.002). Alcohol consumption was associated with lower breast folate (P = 0.03), higher p16 INK4a promoter methylation (P = 0.007) and less P16 expression (P = 0.002). Higher breast folate concentrations were associated with lower p16 INK4a promoter methylation (P = 0.06). Genetic variation in MTRR (rs1801394) and MTHFD1 (rs1950902) was associated with higher p16 INK4a promoter methylation (OR = 2.66, 95% CI: 1.11–6.42 and OR = 2.72, 95% CI: 1.12–6.66, respectively), whereas variation in TYMS (rs502396) was associated with less P16 protein expression (OR = 0.22, 95% CI: 0.05–0.99). Given that this is the first study to indicate that alcohol consumption, breast folate and variation in one-carbon metabolism genes are associated with p16 INK4a promoter methylation and P16 protein expression in healthy tissues; these findings require replication. PMID:25344837

  8. Characterization of phosphofructokinase activity in Mycobacterium tuberculosis reveals that a functional glycolytic carbon flow is necessary to limit the accumulation of toxic metabolic intermediates under hypoxia.

    Directory of Open Access Journals (Sweden)

    Wai Yee Phong

    Full Text Available Metabolic versatility has been increasingly recognized as a major virulence mechanism that enables Mycobacterium tuberculosis to persist in many microenvironments encountered in its host. Glucose is one of the most abundant carbon sources that is exploited by many pathogenic bacteria in the human host. M. tuberculosis has an intact glycolytic pathway that is highly conserved in all clinical isolates sequenced to date suggesting that glucose may represent a non-negligible source of carbon and energy for this pathogen in vivo. Fructose-6-phosphate phosphorylation represents the key-committing step in glycolysis and is catalyzed by a phosphofructokinase (PFK activity. Two genes, pfkA and pfkB have been annotated to encode putative PFK in M. tuberculosis. Here, we show that PFKA is the sole PFK enzyme in M. tuberculosis with no functional redundancy with PFKB. PFKA is required for growth on glucose as sole carbon source. In co-metabolism experiments, we report that disruption of the glycolytic pathway at the PFK step results in intracellular accumulation of sugar-phosphates that correlated with significant impairment of the cell viability. Concomitantly, we found that the presence of glucose is highly toxic for the long-term survival of hypoxic non-replicating mycobacteria, suggesting that accumulation of glucose-derived toxic metabolites does occur in the absence of sustained aerobic respiration. The culture medium traditionally used to study the physiology of hypoxic mycobacteria is supplemented with glucose. In this medium, M. tuberculosis can survive for only 7-10 days in a true non-replicating state before death is observed. By omitting glucose in the medium this period could be extended for up to at least 40 days without significant viability loss. Therefore, our study suggests that glycolysis leads to accumulation of glucose-derived toxic metabolites that limits long-term survival of hypoxic mycobacteria. Such toxic effect is exacerbated when

  9. Characterization of phosphofructokinase activity in Mycobacterium tuberculosis reveals that a functional glycolytic carbon flow is necessary to limit the accumulation of toxic metabolic intermediates under hypoxia.

    Science.gov (United States)

    Phong, Wai Yee; Lin, Wenwei; Rao, Srinivasa P S; Dick, Thomas; Alonso, Sylvie; Pethe, Kevin

    2013-01-01

    Metabolic versatility has been increasingly recognized as a major virulence mechanism that enables Mycobacterium tuberculosis to persist in many microenvironments encountered in its host. Glucose is one of the most abundant carbon sources that is exploited by many pathogenic bacteria in the human host. M. tuberculosis has an intact glycolytic pathway that is highly conserved in all clinical isolates sequenced to date suggesting that glucose may represent a non-negligible source of carbon and energy for this pathogen in vivo. Fructose-6-phosphate phosphorylation represents the key-committing step in glycolysis and is catalyzed by a phosphofructokinase (PFK) activity. Two genes, pfkA and pfkB have been annotated to encode putative PFK in M. tuberculosis. Here, we show that PFKA is the sole PFK enzyme in M. tuberculosis with no functional redundancy with PFKB. PFKA is required for growth on glucose as sole carbon source. In co-metabolism experiments, we report that disruption of the glycolytic pathway at the PFK step results in intracellular accumulation of sugar-phosphates that correlated with significant impairment of the cell viability. Concomitantly, we found that the presence of glucose is highly toxic for the long-term survival of hypoxic non-replicating mycobacteria, suggesting that accumulation of glucose-derived toxic metabolites does occur in the absence of sustained aerobic respiration. The culture medium traditionally used to study the physiology of hypoxic mycobacteria is supplemented with glucose. In this medium, M. tuberculosis can survive for only 7-10 days in a true non-replicating state before death is observed. By omitting glucose in the medium this period could be extended for up to at least 40 days without significant viability loss. Therefore, our study suggests that glycolysis leads to accumulation of glucose-derived toxic metabolites that limits long-term survival of hypoxic mycobacteria. Such toxic effect is exacerbated when the glycolytic

  10. Fructose Alters Intermediary Metabolism of Glucose in Human Adipocytes and Diverts Glucose to Serine Oxidation in the One-Carbon Cycle Energy Producing Pathway.

    Science.gov (United States)

    Varma, Vijayalakshmi; Boros, László G; Nolen, Greg T; Chang, Ching-Wei; Wabitsch, Martin; Beger, Richard D; Kaput, Jim

    2015-06-16

    Increased consumption of sugar and fructose as sweeteners has resulted in the utilization of fructose as an alternative metabolic fuel that may compete with glucose and alter its metabolism. To explore this, human Simpson-Golabi-Behmel Syndrome (SGBS) preadipocytes were differentiated to adipocytes in the presence of 0, 1, 2.5, 5 or 10 mM of fructose added to a medium containing 5 mM of glucose representing the normal blood glucose concentration. Targeted tracer [1,2-13C2]-d-glucose fate association approach was employed to examine the influence of fructose on the intermediary metabolism of glucose. Increasing concentrations of fructose robustly increased the oxidation of [1,2-13C2]-d-glucose to 13CO2 (p < 0.000001). However, glucose-derived 13CO2 negatively correlated with 13C labeled glutamate, 13C palmitate, and M+1 labeled lactate. These are strong markers of limited tricarboxylic acid (TCA) cycle, fatty acid synthesis, pentose cycle fluxes, substrate turnover and NAD+/NADP+ or ATP production from glucose via complete oxidation, indicating diminished mitochondrial energy metabolism. Contrarily, a positive correlation was observed between glucose-derived 13CO2 formed and 13C oleate and doses of fructose which indicate the elongation and desaturation of palmitate to oleate for storage. Collectively, these results suggest that fructose preferentially drives glucose through serine oxidation glycine cleavage (SOGC pathway) one-carbon cycle for NAD+/NADP+ production that is utilized in fructose-induced lipogenesis and storage in adipocytes.

  11. Fructose Alters Intermediary Metabolism of Glucose in Human Adipocytes and Diverts Glucose to Serine Oxidation in the One–Carbon Cycle Energy Producing Pathway

    Directory of Open Access Journals (Sweden)

    Vijayalakshmi Varma

    2015-06-01

    Full Text Available Increased consumption of sugar and fructose as sweeteners has resulted in the utilization of fructose as an alternative metabolic fuel that may compete with glucose and alter its metabolism. To explore this, human Simpson-Golabi-Behmel Syndrome (SGBS preadipocytes were differentiated to adipocytes in the presence of 0, 1, 2.5, 5 or 10 mM of fructose added to a medium containing 5 mM of glucose representing the normal blood glucose concentration. Targeted tracer [1,2-13C2]-d-glucose fate association approach was employed to examine the influence of fructose on the intermediary metabolism of glucose. Increasing concentrations of fructose robustly increased the oxidation of [1,2-13C2]-d-glucose to 13CO2 (p < 0.000001. However, glucose-derived 13CO2 negatively correlated with 13C labeled glutamate, 13C palmitate, and M+1 labeled lactate. These are strong markers of limited tricarboxylic acid (TCA cycle, fatty acid synthesis, pentose cycle fluxes, substrate turnover and NAD+/NADP+ or ATP production from glucose via complete oxidation, indicating diminished mitochondrial energy metabolism. Contrarily, a positive correlation was observed between glucose-derived 13CO2 formed and 13C oleate and doses of fructose which indicate the elongation and desaturation of palmitate to oleate for storage. Collectively, these results suggest that fructose preferentially drives glucose through serine oxidation glycine cleavage (SOGC pathway one-carbon cycle for NAD+/NADP+ production that is utilized in fructose-induced lipogenesis and storage in adipocytes.

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

    Science.gov (United States)

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

    2014-05-01

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

  13. Action of gibberellins on growth and metabolism of Arabidopsis plants associated with high concentration of carbon dioxide.

    Science.gov (United States)

    Ribeiro, Dimas M; Araújo, Wagner L; Fernie, Alisdair R; Schippers, Jos H M; Mueller-Roeber, Bernd

    2012-12-01

    Although the positive effect of elevated CO(2) concentration [CO(2)] on plant growth is well known, it remains unclear whether global climate change will positively or negatively affect crop yields. In particular, relatively little is known about the role of hormone pathways in controlling the growth responses to elevated [CO(2)]. Here, we studied the impact of elevated [CO(2)] on plant biomass and metabolism in Arabidopsis (Arabidopsis thaliana) in relation to the availability of gibberellins (GAs). Inhibition of growth by the GA biosynthesis inhibitor paclobutrazol (PAC) at ambient [CO(2)] (350 µmol CO(2) mol(-1)) was reverted by elevated [CO(2)] (750 µmol CO(2) mol(-1)). Thus, we investigated the metabolic adjustment and modulation of gene expression in response to changes in growth of plants imposed by varying the GA regime in ambient and elevated [CO(2)]. In the presence of PAC (low-GA regime), the activities of enzymes involved in photosynthesis and inorganic nitrogen assimilation were markedly increased at elevated [CO(2)], whereas the activities of enzymes of organic acid metabolism were decreased. Under ambient [CO(2)], nitrate, amino acids, and protein accumulated upon PAC treatment; however, this was not the case when plants were grown at elevated [CO(2)]. These results suggest that only under ambient [CO(2)] is GA required for the integration of carbohydrate and nitrogen metabolism underlying optimal biomass determination. Our results have implications concerning the action of the Green Revolution genes in future environmental conditions.

  14. Traditional Islamic cities unveiled: the quest for urban design regularity

    Directory of Open Access Journals (Sweden)

    Jorge Correia

    2015-08-01

    Full Text Available Traditional Islamic cities have generally gathered orientalized gazes and perspectives, picking up from misconceptions and stereotypes that during the second half af the 19th century andwere perpectuated by colonialism. More recent scholarship has shed light on the urban organizationand composition of such tissues; most of them confined to old quarters or historical centres ofthriving contemporary cities within the Arab-Muslim world. In fact, one of the most striking featureshas been the unveiling of layered urban assemblages where exterior agents have somehowlaunched or interrupted an apparent islamicized continuum. Primarly, this paper wishes to search forexternal political factors that have designed regularly geometrized patterns in medium-sized Arabtowns. For that, two case studies from different geographies - Maghreb and the Near East - will bemorphologically analysed through updated urban surveys. Whereas Nablus (Palestine ows the urbanmatrix of its old town to its Roman past, in Azemmour’s medina (Morocco it is still possible to trackthe thin European early-modern colonial stratum. However, both cases show how regularity patternschallenge Western concepts of geometrical design to embrace levels of rationality related to tradionalIslamic urban forms, societal configurations and built environment. Urban morphology becomes afundamental tool for articulating the history with me processes of sedimentation and evolution in orderto read current urban prints and dynamics. Thus, the paper will also interpret alternative logics ofrational urban display in Azemmour and Nablus, linked to ways of living within the Islamic sphere.

  15. NuSTAR catches the unveiling nucleus of NGC 1068

    CERN Document Server

    Marinucci, A; Matt, G; Alexander, D M; Balokovic, M; Bauer, F E; Brandt, W N; Gandhi, P; Guainazzi, M; Harrison, F A; Iwasawa, K; Koss, M; Madsen, K K; Nicastro, F; Puccetti, S; Ricci, C; Stern, D; Walton, D J

    2015-01-01

    We present a NuSTAR and XMM-Newton monitoring campaign in 2014/2015 of the Compton-thick Seyfert 2 galaxy, NGC 1068. During the August 2014 observation, we detect with NuSTAR a flux excess above 20 keV ($32\\pm6 \\%$) with respect to the December 2012 observation and to a later observation performed in February 2015. We do not detect any spectral variation below 10 keV in the XMM-Newton data. The transient excess can be explained by a temporary decrease of the column density of the obscuring material along the line of sight (from N$_{\\rm H}\\simeq10^{25}$ cm$^{-2}$ to N$_{\\rm H}=6.7\\pm1.0\\times10^{24}$ cm$^{-2}$), which allows us for the first time to unveil the direct nuclear radiation of the buried AGN in NGC 1068 and to infer an intrinsic 2-10 keV luminosity L$_{\\rm X}=7^{+7}_{-4} \\times 10^{43}$ erg s$^{-1}$.

  16. Unveiling the physics of the Thomson jumping ring

    CERN Document Server

    Ladera, Celso L

    2014-01-01

    We present a new model, and the validating experiments, that unveil the rich physics behind the flight of a conductive ring in the Thomson experiment, a physics veiled by the fast thrust that impels the ring. We uncover interesting features of the electro-dynamics of the flying ring, e.g. the varying mutual inductance between ring and the thrusting electromagnet, or how to measure the ring proper magnetic field in the presence of the larger field of the electromagnet. We succeed in separating the position and time dependences of the ring variables as it travels upward in a diverging magnetic field, obtaining a comprehensive view of the ring motion. We introduce a low-cost jumping ring set-up that incorporates simple innovative devices, e.g. a couple of pick-up coils connected in opposition that allows us to scrutinize the ring electro-dynamics, and to confirm the predictions of our theoretical model with good accuracy. This work is within the reach of senior students of science or engineering, and it can be e...

  17. Hidden temporal order unveiled in stock market volatility variance

    Directory of Open Access Journals (Sweden)

    Y. Shapira

    2011-06-01

    Full Text Available When analyzed by standard statistical methods, the time series of the daily return of financial indices appear to behave as Markov random series with no apparent temporal order or memory. This empirical result seems to be counter intuitive since investor are influenced by both short and long term past market behaviors. Consequently much effort has been devoted to unveil hidden temporal order in the market dynamics. Here we show that temporal order is hidden in the series of the variance of the stocks volatility. First we show that the correlation between the variances of the daily returns and means of segments of these time series is very large and thus cannot be the output of random series, unless it has some temporal order in it. Next we show that while the temporal order does not show in the series of the daily return, rather in the variation of the corresponding volatility series. More specifically, we found that the behavior of the shuffled time series is equivalent to that of a random time series, while that of the original time series have large deviations from the expected random behavior, which is the result of temporal structure. We found the same generic behavior in 10 different stock markets from 7 different countries. We also present analysis of specially constructed sequences in order to better understand the origin of the observed temporal order in the market sequences. Each sequence was constructed from segments with equal number of elements taken from algebraic distributions of three different slopes.

  18. Microevolution Analysis of Bacillus coahuilensis Unveils Differences in Phosphorus Acquisition Strategies and Their Regulation.

    Science.gov (United States)

    Gómez-Lunar, Zulema; Hernández-González, Ismael; Rodríguez-Torres, María-Dolores; Souza, Valeria; Olmedo-Álvarez, Gabriela

    2016-01-01

    Bacterial genomes undergo numerous events of gene losses and gains that generate genome variability among strains of the same species (microevolution). Our aim was to compare the genomes and relevant phenotypes of three Bacillus coahuilensis strains from two oligotrophic hydrological systems in the Cuatro Ciénegas Basin (México), to unveil the environmental challenges that this species cope with, and the microevolutionary differences in these genotypes. Since the strains were isolated from a low P environment, we placed emphasis on the search of different phosphorus acquisition strategies. The three B. coahuilensis strains exhibited similar numbers of coding DNA sequences, of which 82% (2,893) constituted the core genome, and 18% corresponded to accessory genes. Most of the genes in this last group were associated with mobile genetic elements (MGEs) or were annotated as hypothetical proteins. Ten percent of the pangenome consisted of strain-specific genes. Alignment of the three B. coahuilensis genomes indicated a high level of synteny and revealed the presence of several genomic islands. Unexpectedly, one of these islands contained genes that encode the 2-keto-3-deoxymannooctulosonic acid (Kdo) biosynthesis enzymes, a feature associated to cell walls of Gram-negative bacteria. Some microevolutionary changes were clearly associated with MGEs. Our analysis revealed inconsistencies between phenotype and genotype, which we suggest result from the impossibility to map regulatory features to genome analysis. Experimental results revealed variability in the types and numbers of auxotrophies between the strains that could not consistently be explained by in silico metabolic models. Several intraspecific differences in preferences for carbohydrate and phosphorus utilization were observed. Regarding phosphorus recycling, scavenging, and storage, variations were found between the three genomes. The three strains exhibited differences regarding alkaline phosphatase that

  19. Microevolution analysis of Bacillus coahuilensis unveils differences in phosphorus acquisition strategies and their regulation

    Directory of Open Access Journals (Sweden)

    Zulema eGómez-Lunar

    2016-02-01

    Full Text Available Bacterial genomes undergo numerous events of gene losses and gains that generate genome variability among strains of the same species (microevolution. Our aim was to compare the genomes and relevant phenotypes of three Bacillus coahuilensis strains from two oligotrophic hydrological systems in the Cuatro Ciénegas Basin (México, to unveil the environmental challenges that this species cope with, and the microevolutionary differences in these genotypes. Since the strains were isolated from a low P environment, we placed emphasis on the search of different phosphorus acquisition strategies. The three B. coahuilensis strains exhibited similar numbers of coding DNA sequences, of which 82% (2, 893 constituted the core genome, and 18% corresponded to accessory genes. Most of the genes in this last group were associated with mobile genetic elements or were annotated as hypothetical proteins. Ten percent of the pangenome consisted of strain-specific genes. Alignment of the three B. coahuilensis genomes indicated a high level of synteny and revealed the presence of several genomic islands. Unexpectedly, one of these islands contained genes that encode the 2-keto-3-deoxymannooctulosonic acid (Kdo biosynthesis enzymes, a feature associated to cell walls of Gram-negative bacteria. Some microevolutionary changes were clearly associated with mobile genetic elements. Our analysis revealed inconsistencies between phenotype and genotype, which we suggest result from the impossibility to map regulatory features to genome analysis. Experimental results revealed variability in the types and numbers of auxotrophies between the strains that could not consistently be explained by in silico metabolic models. Several intraspecific differences in preferences for carbohydrate and phosphorus utilization were observed. Regarding phosphorus recycling, scavenging, and storage, variations were found between the three genomes. The three strains exhibited differences regarding

  20. Microevolution Analysis of Bacillus coahuilensis Unveils Differences in Phosphorus Acquisition Strategies and Their Regulation

    Science.gov (United States)

    Gómez-Lunar, Zulema; Hernández-González, Ismael; Rodríguez-Torres, María-Dolores; Souza, Valeria; Olmedo-Álvarez, Gabriela

    2016-01-01

    Bacterial genomes undergo numerous events of gene losses and gains that generate genome variability among strains of the same species (microevolution). Our aim was to compare the genomes and relevant phenotypes of three Bacillus coahuilensis strains from two oligotrophic hydrological systems in the Cuatro Ciénegas Basin (México), to unveil the environmental challenges that this species cope with, and the microevolutionary differences in these genotypes. Since the strains were isolated from a low P environment, we placed emphasis on the search of different phosphorus acquisition strategies. The three B. coahuilensis strains exhibited similar numbers of coding DNA sequences, of which 82% (2,893) constituted the core genome, and 18% corresponded to accessory genes. Most of the genes in this last group were associated with mobile genetic elements (MGEs) or were annotated as hypothetical proteins. Ten percent of the pangenome consisted of strain-specific genes. Alignment of the three B. coahuilensis genomes indicated a high level of synteny and revealed the presence of several genomic islands. Unexpectedly, one of these islands contained genes that encode the 2-keto-3-deoxymannooctulosonic acid (Kdo) biosynthesis enzymes, a feature associated to cell walls of Gram-negative bacteria. Some microevolutionary changes were clearly associated with MGEs. Our analysis revealed inconsistencies between phenotype and genotype, which we suggest result from the impossibility to map regulatory features to genome analysis. Experimental results revealed variability in the types and numbers of auxotrophies between the strains that could not consistently be explained by in silico metabolic models. Several intraspecific differences in preferences for carbohydrate and phosphorus utilization were observed. Regarding phosphorus recycling, scavenging, and storage, variations were found between the three genomes. The three strains exhibited differences regarding alkaline phosphatase that

  1. Vision Changes after Space Flight Are Related to Alterations in Folate-Dependent One-Carbon Metabolism

    Science.gov (United States)

    Smith, Scott M.; Gibson, C. Robert; Mader, Thomas H.; Ericson, Karen; Ploutz-Snyder, Robert; Heer, Martina; Zwart, Sara R.

    2011-01-01

    About 20% of astronauts on International Space Station missions have developed measurable ophthalmic changes after flight. This study was conducted to determine whether the folate-dependent 1-carbon pathway is altered in these individuals. Data were modeled to evaluate differences between individuals with ophthalmic changes (n=5) and those without them (n=15). We also correlated mean preflight serum concentrations of the 1-carbon metabolites with changes in measured refraction after flight. Serum homocysteine (HCy), cystathionine, 2-methylcitric acid, and methylmalonic acid concentrations were 25%-45% higher (Prefraction, and preflight serum concentrations of 2-methylcitric acid tended to be associated (P=0.06) with ophthalmic changes. The biochemical differences observed in those with vision issues strongly suggests impairment of the folate-dependent 1-carbon transfer pathway. Impairment of this pathway, by polymorphisms, diet or other means, may interact with components of the microgravity environment to influence these pathophysiologic changes. This study was funded by the NASA Human Research Program.

  2. Carbon Metabolism of Soil microorganisms at Low Temperatures: Position-Specific 13C Labeled Glucose Reveals the Story

    Science.gov (United States)

    Apostel, C.; Bore, E. K.; Halicki, S.; Kuzyakov, Y.; Dippold, M.

    2015-12-01

    Metabolic pathway activities at low temperature are not well understood, despite the fact that the processes are relevant for many soils globally and seasonally. To analyze soil metabolism at low temperature, isotopomeres of position-specifically 13C labeled glucose were applied at three temperature levels; +5, -5 -20 oC. In additon, one sterilization treatment with sodium azide at +5 oC was also performed. Soils were incubated for 1, 3 and 10 days while soil samples at -20 oC were additionally sampled after 30 days. The 13C from individual molecule position in respired CO2 was quantifed. Incorporation of 13C in bulk soil, extractable microbial biomass by chloroform fumigation extraction (CFE) and cell membranes of different microbial communities classified by 13C phospholipid fatty acid analysis (PLFA) was carried out. Our 13CO2 data showed a dominance of C-1 respiration at +5 °C for treatments with and without sodium azide, but total respiration for sodium azide inhibited treatments increased by 14%. In contrast, at -5 and -20 oC metabolic behavior showed intermingling of preferential respiration of the glucose C-4 and C-1 positions. Therefore, at +5 °C, pentose phosphate pathway activity is a dominant metabolic pathway used by microorganisms to metabolize glucose. The respiration increase due to NaN3 inhibition was attributed to endoenzymes released from dead organisms that are stabilized at the soil matrix and have access to suitable substrate and co-factors to permit their funtions. Our PLFA analysis showed that incorporation of glucose 13C was higher in Gram negative bacteria than other microbial groups as they are most competitive for LMWOS. Only a limited amount of microbial groups maintained their glucose utilizing activity at -5 and -20 °C and they strongly shifted towards a metabolization of glucose via both glycolysis and pentose phosphate pathways indicating both growth and cellular maintenance. This study revealed a remarkable microbial acitivity

  3. Insilico Analysis unveils Putative Metabolic Pathways and Essential Genes within Leishmania donovani ‘Orfeome’

    Directory of Open Access Journals (Sweden)

    Nithin eRavooru

    2014-08-01

    Full Text Available Leishmaniasis is a parasitic disease caused by the protozoan Leishmania, which is active in two broad forms namely, Visceral Leishmaniasis (VL or Kala Azar and Cutaneous Leishmaniasis (CL. The disease is most prevalent in the tropical regions and poses a threat to more than 70 countries across the globe. In the Indian subcontinent, about 200 million people are estimated to be at risk of developing VL and this area harbours an estimated 67% of the global VL disease burden. The state of Bihar alone has captured almost 50% of the total cases in the Indian region. While no vaccination exists, several pentavalent antimonials and drugs like Paromomycin, Amphotericin, Miltefosine etc., are used in the treatment of Leishmaniasis. However, due to low efficacy of these drugs and the resistance developed by the bug to these medications, there is an urgent need to look into species specific targets. The proteome information available suggests that among the 7960 proteins, a staggering 65% of it remains to be annotated with clarity.Hence, in the present study, we have demonstrated a protocol to integrate the seqeunce and functional information from various databases, such as GO, PFAM, KEGG, String DB, COG and DEG, to assign putative functions to many of the hypothetical seqeucences present in this proteome. These crucial information related to pathways and essential genes show promise for exploring the design strategies towards developing drugs, to tackle this notorious parasitic disease.

  4. Peculiarities of One-Carbon Metabolism in the Strict Carnivorous Cat and the Role in Feline Hepatic Lipidosis

    Directory of Open Access Journals (Sweden)

    Marica Bakovic

    2013-07-01

    Full Text Available Research in various species has indicated that diets deficient in labile methyl groups (methionine, choline, betaine, folate produce fatty liver and links to steatosis and metabolic syndrome, but also provides evidence of the importance of labile methyl group balance to maintain normal liver function. Cats, being obligate carnivores, rely on nutrients in animal tissues and have, due to evolutionary pressure, developed several physiological and metabolic adaptations, including a number of peculiarities in protein and fat metabolism. This has led to specific and unique nutritional requirements. Adult cats require more dietary protein than omnivorous species, maintain a consistently high rate of protein oxidation and gluconeogenesis and are unable to adapt to reduced protein intake. Furthermore, cats have a higher requirement for essential amino acids and essential fatty acids. Hastened use coupled with an inability to conserve certain amino acids, including methionine, cysteine, taurine and arginine, necessitates a higher dietary intake for cats compared to most other species. Cats also seemingly require higher amounts of several B-vitamins compared to other species and are predisposed to depletion during prolonged inappetance. This carnivorous uniqueness makes cats more susceptible to hepatic lipidosis.

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

    Directory of Open Access Journals (Sweden)

    Meza Eugenio

    2012-09-01

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

  6. Effect of Nitrogen and Potassium Nutrition on Carbon and Nitrogen Metabolism at Late Growing Stage and Grain Yield Formation in Spring Maize

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Study on the relationship between grain yield formation and metabolism of carbon and nitrogen as influenced by N and K nutrition level during maturation was carried out through field experiments and biochemistry analyses. The results confirmed that it was necessary to maintain a higher photosynthetic capacity of leaves and abundant N supplies for root at late growing stages. The soluble protein content, RuBPC and PEPC activities in leaves, harvest index(HI) and harvest index of nitrogen (HIN)increased obviously with appropriate N and K application rate, which accelerated C and N translocation from vegetative parts to grain, enhanced photosynthetic capacity of leaves and abundant(but not excessive)N supply for root during late growing period.

  7. Single-operator multiparameter metabolic analyzer (SOMMA) for total carbon dioxide (C{sub T}) with coulometric detection. Operator`s manual

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, K.M.

    1992-01-01

    This manual contains the presently known information about using the SOMMA (Single-Operator Multiparameter Metabolic Analyzer) -Coulometer system for total carbon dioxide (C{sub T}) analysis of seawater samples. Being Version 1.0, it is preliminary and will be revised as new information is obtained from SOMMA users. As part of a US Department of Energy (DOE) program to conduct a global survey of CO{sub 2} in the ocean in conjunction with the World Ocean Circulation Experiment (WOCE) Hydrographic Program and Joint Global Ocean Flux Study, C{sub T} measurements are being made with SOMMA systems by several US and foreign laboratories. The purpose of the manual and future versions is to improve the accuracy and precision of seawater analysis through better documentation of methods and to facilitate communication of new operating procedures.

  8. Called to respond: The potential of unveiling hiddens

    Directory of Open Access Journals (Sweden)

    Alison L Black

    2014-12-01

    Full Text Available Interested in exploring how personal stories and aesthetic modes of representing experiences can nudge open academic and educational spaces, this article/collection of particles seeks to document our encounters of being affected and called to respond to things the other has written and represented. As a way of engaging with questions about what research and research data might be and become, our attention has been drawn to stories and images from our lives that we have not shaken off – and to how, as we have opened these to the other, making once private moments public, our hiddens have morphed tenderly into a shared knowing and being. As we have acted on the call we have felt to respond we have found ourselves entering spaces of collaboration, communion, contemplation, and conversation – spaces illuminated by what we have not been able to – and cannot – set aside. Using visual and poetic materials we explore heartfelt and heartbroken aspects of our educational worlds and lives, to be present with each other and our (reemerging personal and professional meanings. We see the shared body (of work, of writing, of image that develops from the taking of brave steps and the risky slipping off of academic masks and language, as a manifestation of the trusted and nurturing spaces that can be generated through collaborative opportunities to gather together. These steps towards unveiling hiddens are producing in us and of us a friendship, fluency, and fluidity as we write new ways of becoming. In turn, we hope the uncovering and revealing of our dialogue in the public gathering of this journal might supports readers’ telling of their own life stories through what calls them to respond.

  9. Characterization of a NADH-dependent glutamate dehydrogenase mutant of Arabidopsis demonstrates the key role of this enzyme in root carbon and nitrogen metabolism.

    Science.gov (United States)

    Fontaine, Jean-Xavier; Tercé-Laforgue, Thérèse; Armengaud, Patrick; Clément, Gilles; Renou, Jean-Pierre; Pelletier, Sandra; Catterou, Manuella; Azzopardi, Marianne; Gibon, Yves; Lea, Peter J; Hirel, Bertrand; Dubois, Frédéric

    2012-10-01

    The role of NADH-dependent glutamate dehydrogenase (GDH) was investigated by studying the physiological impact of a complete lack of enzyme activity in an Arabidopsis thaliana plant deficient in three genes encoding the enzyme. This study was conducted following the discovery that a third GDH gene is expressed in the mitochondria of the root companion cells, where all three active GDH enzyme proteins were shown to be present. A gdh1-2-3 triple mutant was constructed and exhibited major differences from the wild type in gene transcription and metabolite concentrations, and these differences appeared to originate in the roots. By placing the gdh triple mutant under continuous darkness for several days and comparing it to the wild type, the evidence strongly suggested that the main physiological function of NADH-GDH is to provide 2-oxoglutarate for the tricarboxylic acid cycle. The differences in key metabolites of the tricarboxylic acid cycle in the triple mutant versus the wild type indicated that, through metabolic processes operating mainly in roots, there was a strong impact on amino acid accumulation, in particular alanine, γ-aminobutyrate, and aspartate in both roots and leaves. These results are discussed in relation to the possible signaling and physiological functions of the enzyme at the interface of carbon and nitrogen metabolism.

  10. Comparative Analysis of Genomics and Proteomics in the New Isolated Bacillus thuringiensis X022 Revealed the Metabolic Regulation Mechanism of Carbon Flux Following Cu(2+) Treatment.

    Science.gov (United States)

    Quan, Meifang; Xie, Junyan; Liu, Xuemei; Li, Yang; Rang, Jie; Zhang, Tong; Zhou, Fengjuan; Xia, Liqiu; Hu, Shengbiao; Sun, Yunjun; Ding, Xuezhi

    2016-01-01

    Bacillus thuringiensis (Bt) X022 is a novel strain isolated from soil in China, and showed strong insecticidal activity against several Lepidopteran pests. In this work, we performed whole genome sequencing of this Bt strain using the next-generation sequencing technology, and further conducted a comparative analysis with the proteomics data of the specific spore-release period based on LC-MS/MS approach. The Bt X022 genome consisted of one circular chromosomal DNA and seven plasmids, which were further functionally annotated using the RAST server. Comparative analysis of insecticidal substances showed that X022 contained genes coding for three Cry proteins (Cry1Ac, Cry1Ia and Cry2Ab) and a vegetative insecticidal protein (Vip3A). However, three insecticidal crystal proteins (ICPs) (Cry1Ca, Cry1Ac and Cry1Da) were detected by proteomics in the spore-release period. Moreover, a putative biosynthetic gene cluster and the metabolic pathway for poly-β-hydroxybutyrate in Bt X022 were deduced based on the comparative analysis of genomic and proteomic data, which revealed the metabolic regulation mechanism of carbon flux correlated with increased production of ICPs caused by Cu(2+.) Hence, these results provided a deeper understanding of the genetic background and protein expression profile of Bt X022. This study established a foundation for directed genetic modification and further application of this new isolated Bt strain.

  11. Comparative analysis of genomics and proteomics in the new isolated Bacillus thuringiensis X022 revealed the metabolic regulation mechanism of carbon flux following Cu2+ treatment

    Directory of Open Access Journals (Sweden)

    Meifang eQuan

    2016-05-01

    Full Text Available Bacillus thuringiensis (Bt X022, which showed strong insecticidal activity against several Lepidopteran pests, is a novel strain isolated from soil in China. In this work, we performed whole genome sequencing of this Bt strain using the next-generation sequencing technology, and further conducted a comparative analysis with the proteomics data of the specific spore-release period based on LC-MS/MS approach. The Bt X022 genome consisted of one circular chromosomal DNA and seven plasmids, which were further functionally annotated using the RAST server. Comparative analysis of insecticidal substances showed that X022 contained genes coding for three Cry proteins (Cry1Ac, Cry1Ia and Cry2Ab and a vegetative insecticidal protein (Vip3A. However, three insecticidal crystal proteins (ICPs (Cry1Ca, Cry1Ac and Cry1Da were detected by proteomics in the spore-release period. Moreover, a putative biosynthetic gene cluster and the metabolic pathway for poly-β-hydroxybutyrate in Bt X022 were deduced based on the comparative analysis of genomic and proteomic data, which revealed the metabolic regulation mechanism of carbon flux correlated with increased production of ICPs caused by Cu2+ . Hence, these results provided a deeper understanding of the genetic background and protein expression profile of Bt X022. This study established a foundation for directed genetic modification and further application of this new isolated Bt strain.

  12. Comparative Analysis of Genomics and Proteomics in the New Isolated Bacillus thuringiensis X022 Revealed the Metabolic Regulation Mechanism of Carbon Flux Following Cu2+ Treatment

    Science.gov (United States)

    Quan, Meifang; Xie, Junyan; Liu, Xuemei; Li, Yang; Rang, Jie; Zhang, Tong; Zhou, Fengjuan; Xia, Liqiu; Hu, Shengbiao; Sun, Yunjun; Ding, Xuezhi

    2016-01-01

    Bacillus thuringiensis (Bt) X022 is a novel strain isolated from soil in China, and showed strong insecticidal activity against several Lepidopteran pests. In this work, we performed whole genome sequencing of this Bt strain using the next-generation sequencing technology, and further conducted a comparative analysis with the proteomics data of the specific spore-release period based on LC-MS/MS approach. The Bt X022 genome consisted of one circular chromosomal DNA and seven plasmids, which were further functionally annotated using the RAST server. Comparative analysis of insecticidal substances showed that X022 contained genes coding for three Cry proteins (Cry1Ac, Cry1Ia and Cry2Ab) and a vegetative insecticidal protein (Vip3A). However, three insecticidal crystal proteins (ICPs) (Cry1Ca, Cry1Ac and Cry1Da) were detected by proteomics in the spore-release period. Moreover, a putative biosynthetic gene cluster and the metabolic pathway for poly-β-hydroxybutyrate in Bt X022 were deduced based on the comparative analysis of genomic and proteomic data, which revealed the metabolic regulation mechanism of carbon flux correlated with increased production of ICPs caused by Cu2+. Hence, these results provided a deeper understanding of the genetic background and protein expression profile of Bt X022. This study established a foundation for directed genetic modification and further application of this new isolated Bt strain. PMID:27303381

  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. Potential Links between Impaired One-Carbon Metabolism Due to Polymorphisms, Inadequate B-Vitamin Status, and the Development of Alzheimer’s Disease

    Science.gov (United States)

    Troesch, Barbara; Weber, Peter; Mohajeri, M. Hasan

    2016-01-01

    Alzheimer’s disease (AD) is the major cause of dementia and no preventive or effective treatment has been established to date. The etiology of AD is poorly understood, but genetic and environmental factors seem to play a role in its onset and progression. In particular, factors affecting the one-carbon metabolism (OCM) are thought to be important and elevated homocysteine (Hcy) levels, indicating impaired OCM, have been associated with AD. We aimed at evaluating the role of polymorphisms of key OCM enzymes in the etiology of AD, particularly when intakes of relevant B-vitamins are inadequate. Our review indicates that a range of compensatory mechanisms exist to maintain a metabolic balance. However, these become overwhelmed if the activity of more than one enzyme is reduced due to genetic factors or insufficient folate, riboflavin, vitamin B6 and/or vitamin B12 levels. Consequences include increased Hcy levels and reduced capacity to synthetize, methylate and repair DNA, and/or modulated neurotransmission. This seems to favor the development of hallmarks of AD particularly when combined with increased oxidative stress e.g., in apolipoprotein E (ApoE) ε4 carriers. However, as these effects can be compensated at least partially by adequate intakes of B-vitamins, achieving optimal B-vitamin status for the general population should be a public health priority. PMID:27973419

  15. Hepatic methionine homeostasis is conserved in C57BL/6N mice on high-fat diet despite major changes in hepatic one-carbon metabolism.

    Directory of Open Access Journals (Sweden)

    Christoph Dahlhoff

    Full Text Available Obesity is an underlying risk factor in the development of cardiovascular disease, dyslipidemia and non-alcoholic fatty liver disease (NAFLD. Increased hepatic lipid accumulation is a hallmark in the progression of NAFLD and impairments in liver phosphatidylcholine (PC metabolism may be central to the pathogenesis. Hepatic PC biosynthesis, which is linked to the one-carbon (C1 metabolism by phosphatidylethanolamine N-methyltransferase, is known to be important for hepatic lipid export by VLDL particles. Here, we assessed the influence of a high-fat (HF diet and NAFLD status in mice on hepatic methyl-group expenditure and C1-metabolism by analyzing changes in gene expression, protein levels, metabolite concentrations, and nuclear epigenetic processes. In livers from HF diet induced obese mice a significant downregulation of cystathionine β-synthase (CBS and an increased betaine-homocysteine methyltransferase (BHMT expression were observed. Experiments in vitro, using hepatoma cells stimulated with peroxisome proliferator activated receptor alpha (PPARα agonist WY14,643, revealed a significantly reduced Cbs mRNA expression. Moreover, metabolite measurements identified decreased hepatic cystathionine and L-α-amino-n-butyrate concentrations as part of the transsulfuration pathway and reduced hepatic betaine concentrations, but no metabolite changes in the methionine cycle in HF diet fed mice compared to controls. Furthermore, we detected diminished hepatic gene expression of de novo DNA methyltransferase 3b but no effects on hepatic global genomic DNA methylation or hepatic DNA methylation in the Cbs promoter region upon HF diet. Our data suggest that HF diet induces a PPARα-mediated downregulation of key enzymes in the hepatic transsulfuration pathway and upregulates BHMT expression in mice to accommodate to enhanced dietary fat processing while preserving the essential amino acid methionine.

  16. CO 2 -fixing one-carbon metabolism in a cellulose-degrading bacterium Clostridium thermocellum

    Energy Technology Data Exchange (ETDEWEB)

    Xiong, Wei; Lin, Paul P.; Magnusson, Lauren; Warner, Lisa; Liao, James C.; Maness, Pin-Ching; Chou, Katherine J.

    2016-10-28

    Clostridium thermocellum can ferment cellulosic biomass to formate and other end products, including CO2. This organism lacks formate dehydrogenase (Fdh), which catalyzes the reduction of CO2 to formate. However, feeding the bacterium 13C-bicarbonate and cellobiose followed by NMR analysis showed the production of 13C-formate in C. thermocellum culture, indicating the presence of an uncharacterized pathway capable of converting CO2 to formate. Combining genomic and experimental data, we demonstrated that the conversion of CO2 to formate serves as a CO2 entry point into the reductive one-carbon (C1) metabolism, and internalizes CO2 via two biochemical reactions: the reversed pyruvate:ferredoxin oxidoreductase (rPFOR), which incorporates CO2 using acetyl-CoA as a substrate and generates pyruvate, and pyruvate-formate lyase (PFL) converting pyruvate to formate and acetyl-CoA. We analyzed the labeling patterns of proteinogenic amino acids in individual deletions of all five putative PFOR mutants and in a PFL deletion mutant. We identified two enzymes acting as rPFOR, confirmed the dual activities of rPFOR and PFL crucial for CO2 uptake, and provided physical evidence of a distinct in vivo 'rPFOR-PFL shunt' to reduce CO2 to formate while circumventing the lack of Fdh. Such a pathway precedes CO2 fixation via the reductive C1 metabolic pathway in C. thermocellum. These findings demonstrated the metabolic versatility of C. thermocellum, which is thought of as primarily a cellulosic heterotroph but is shown here to be endowed with the ability to fix CO2 as well.

  17. Acetylome analysis reveals the involvement of lysine acetylation in photosynthesis and carbon metabolism in the model cyanobacterium Synechocystis sp. PCC 6803.

    Science.gov (United States)

    Mo, Ran; Yang, Mingkun; Chen, Zhuo; Cheng, Zhongyi; Yi, Xingling; Li, Chongyang; He, Chenliu; Xiong, Qian; Chen, Hui; Wang, Qiang; Ge, Feng

    2015-02-06

    Cyanobacteria are the oldest known life form inhabiting Earth and the only prokaryotes capable of performing oxygenic photosynthesis. Synechocystis sp. PCC 6803 (Synechocystis) is a model cyanobacterium used extensively in research on photosynthesis and environmental adaptation. Posttranslational protein modification by lysine acetylation plays a critical regulatory role in both eukaryotes and prokaryotes; however, its extent and function in cyanobacteria remain unexplored. Herein, we performed a global acetylome analysis on Synechocystis through peptide prefractionation, antibody enrichment, and high accuracy LC-MS/MS analysis; identified 776 acetylation sites on 513 acetylated proteins; and functionally categorized them into an interaction map showing their involvement in various biological processes. Consistent with previous reports, a large fraction of the acetylation sites are present on proteins involved in cellular metabolism. Interestingly, for the first time, many proteins involved in photosynthesis, including the subunits of phycocyanin (CpcA, CpcB, CpcC, and CpcG) and allophycocyanin (ApcA, ApcB, ApcD, ApcE, and ApcF), were found to be lysine acetylated, suggesting that lysine acetylation may play regulatory roles in the photosynthesis process. Six identified acetylated proteins associated with photosynthesis and carbon metabolism were further validated by immunoprecipitation and Western blotting. Our data provide the first global survey of lysine acetylation in cyanobacteria and reveal previously unappreciated roles of lysine acetylation in the regulation of photosynthesis. The provided data set may serve as an important resource for the functional analysis of lysine acetylation in cyanobacteria and facilitate the elucidation of the entire metabolic networks and photosynthesis process in this model cyanobacterium.

  18. 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.

    2010-01-01

    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

  19. 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, S.J.; Vollset, S.E.; Hustad, S.; Midttun, O.; Meyer, K.; Fredriksen, A.; Ueland, P.M.; Jenab, M.; Slimani, N.; Ferrari, P.; Agudo, A.; Sala, N.; Capella, G.; Giudice, G. Del; Palli, D.; Boeing, H.; Weikert, C.; Bueno-De-Mesquita, H.B.; Buchner, F.L.; Carneiro, F.; Berrino, F.; Vineis, P.; Tumino, R.; Panico, S.; Berglund, G.; Manjer, J.; Stenling, R.; Hallmans, G.; Martinez, C.; Arrizola, L.; Barricarte, A.; Navarro, C.; Rodriguez, L.; Bingham, S.; Linseisen, J.; Kaaks, R.; Overvad, K.; Tjonneland, A.; Peeters, P.H.M.; Numans, M.E.; Clavel-Chapelon, F.; Boutron-Ruault, M.C.; Morois, S.; Trichopoulou, A.; Lund, E.; Plebani, M.; Riboli, E.; Gonzalez, C.A.

    2010-01-01

    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

  20. Subcellular compartmentation of sugar signalling: Links among carbon cellular status, route of sucrolysis, sink-source allocation, and metabolic partitioning

    Directory of Open Access Journals (Sweden)

    Axel eTiessen

    2013-01-01

    Full Text Available Recent findings suggest that both subcellular compartmentation and route of sucrolysis are important for plant development, growth, and yield. Signalling effects are dependent on the tissue, cell type and stage of development. Downstream effects also depend on the amount and localisation of hexoses and disaccharides. All enzymes of sucrose metabolism (e.g. invertase, hexokinase, fructokinase, sucrose synthase, and sucrose 6-phosphate synthase are not produced from single genes, but from paralogue families in plant genomes. Each paralogue has unique expression across plant organs and developmental stages. Multiple isoforms can be targeted to different cellular compartments (e.g. plastids, mitochondria, nuclei, and cytosol. Many of the key enzymes are regulated by post-transcriptional modifications and associate in multimeric protein complexes. Some isoforms have regulatory functions, either in addition to or in replacement of their catalytic activity. This explains why some isozymes are not redundant, but also complicates elucidation of their specific involvement in sugar signalling. The subcellular compartmentation of sucrose metabolism forces refinement of some of the paradigms of sugar signalling during physiological processes. For example, the catalytic and signalling functions of diverse paralogues needs to be more carefully analysed in the context of post-genomic biology. It is important to note that it is the differential localization of both the sugars themselves as well as the sugar-metabolizing enzymes that ultimately led to sugar signalling. We conclude that a combination of subcellular complexity and gene duplication/subfunctionalization gave rise to sugar signalling as a regulatory mechanism in plant cells.

  1. Targeted mutagenesis of mitochondrial carbonic anhydrases VA and VB implicates both enzymes in ammonia detoxification and glucose metabolism

    OpenAIRE

    Shah, Gul N.; Rubbelke, Timothy S.; Hendin, Joshua; Nguyen, Hien; Waheed, Abdul; Shoemaker, James D.; Sly, William S.

    2013-01-01

    Prior studies with carbonic anhydrase (CA) inhibitors implicated mitochondrial CA in ureagenesis and gluconeogenesis. Subsequent studies identified two mitochondrial CAs. To distinguish the contribution of each enzyme, we studied the effects of targeted disruption of the murine CA genes, called Car5A and Car5B. The Car5A mutation had several deleterious consequences. Car5A null mice were smaller than wild-type littermates and bred poorly. However, on sodium–potassium citrate-supplemented wate...

  2. Utilization of carbon 13-labelled stable isotopes for studying drug toxicity on cellular metabolism; Utilisation d`isotopes stables marques au carbone 13 pour etudier la toxicite de drogues au niveau du metabolisme cellulaire

    Energy Technology Data Exchange (ETDEWEB)

    Herve, M.; Wietzerbin, J.; Tran-Dinh, S. [CEA Centre d`Etudes de Saclay, 91 - Gif-sur-Yvette (France). Dept. de Biologie Cellulaire et Moleculaire

    1994-12-31

    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.

  3. Metabolic and physiochemical responses to a whole-lake experimental increase in dissolved organic carbon in a north-temperate lake

    Science.gov (United States)

    Zwart, Jacob A.; Craig, Nicola; Kelly, Patrick T.; Sebestyen, Stephen D.; Solomon, Christopher T.; Weidel, Brian C.; Jones, Stuart E.

    2016-01-01

    Over the last several decades, many lakes globally have increased in dissolved organic carbon (DOC), calling into question how lake functions may respond to increasing DOC. Unfortunately, our basis for making predictions is limited to spatial surveys, modeling, and laboratory experiments, which may not accurately capture important whole-ecosystem processes. In this article, we present data on metabolic and physiochemical responses of a multiyear experimental whole-lake increase in DOC concentration. Unexpectedly, we observed an increase in pelagic gross primary production, likely due to a small increase in phosphorus as well as a surprising lack of change in epilimnetic light climate. We also speculate on the importance of lake size modifying the relationship between light climate and elevated DOC. A larger increase in ecosystem respiration resulted in an increased heterotrophy for the treatment basin. The magnitude of the increase in heterotrophy was extremely close to the excess DOC load to the treatment basin, indicating that changes in heterotrophy may be predictable if allochthonous carbon loads are well-constrained. Elevated DOC concentration also reduced thermocline and mixed layer depth and reduced whole-lake temperature. Results from this experiment were quantitatively different, and sometimes even in the opposite direction, from expectations based on cross-system surveys and bottle experiments, emphasizing the importance of whole-ecosystem experiments in understanding ecosystem response to environmental change.

  4. Elucidation of rice rhizosphere metagenome in relation to methane and nitrogen metabolism under elevated carbon dioxide and temperature using whole genome metagenomic approach.

    Science.gov (United States)

    Bhattacharyya, P; Roy, K S; Das, M; Ray, S; Balachandar, D; Karthikeyan, S; Nayak, A K; Mohapatra, T

    2016-01-15

    Carbon (C) and nitrogen (N) mineralization is one of the key processes of biogeochemical cycling in terrestrial ecosystem in general and rice ecology in particular. Rice rhizosphere is a rich niche of microbial diversity influenced by change in atmospheric temperature and concentration of carbon dioxide (CO2). Structural changes in microbial communities in rhizosphere influence the nutrient cycling. In the present study, the bacterial diversity and population dynamics were studied under ambient CO2 (a-CO2) and elevated CO2+temperature (e-CO2T) in lowland rice rhizosphere using whole genome metagenomic approach. The whole genome metagenomic sequence data of lowland rice exhibited the dominance of bacterial communities including Proteobacteria, Firmicutes, Acidobacteria, Actinobacteria and Planctomycetes. Interestingly, four genera related to methane production namely, Methanobacterium, Methanosphaera, Methanothermus and Methanothermococcus were absent in a-CO2 but noticed under e-CO2T. The acetoclastic pathway was found as the predominant pathway for methanogenesis, whereas, the serine pathway was found as the principal metabolic pathway for CH4 oxidation in lowland rice. The abundances of reads of enzymes in the acetoclastic methanogenesis pathway and serine pathways of methanotrophy were much higher in e-CO2T (328 and 182, respectively) as compared with a-CO2 (118 and 98, respectively). Rice rhizosphere showed higher structural diversities and functional activities in relation to N metabolism involving nitrogen fixation, assimilatory and dissimilatory nitrate reduction and denitrification under e-CO2T than that of a-CO2. Among the three pathways of N metabolism, dissimilarity pathways were predominant in lowland rice rhizosphere and more so under e-CO2T. Consequently, under e-CO2T, CH4 emission, microbial biomass nitrogen (MBN) and dehydrogenase activities were 45%, 20% and 35% higher than a-CO2, respectively. Holistically, a high bacterial diversity and

  5. New insights on transcriptional responses of genes involved in carbon central metabolism, respiration and fermentation to low ATP levels in Escherichia coli.

    Science.gov (United States)

    Soria, Sandra; de Anda, Ramón; Flores, Noemí; Romero-Garcia, Susana; Gosset, Guillermo; Bolívar, Francisco; Báez-Viveros, José Luis

    2013-04-01

    Adenosine-5-triphosphate (ATP) plays a fundamental role in many cellular processes such as transport, central carbon metabolism, biosynthetic reactions, macromolecular synthesis, signal transduction and cellular division. In addition, the intracellular [ATP]/[ADP] ratio in Escherichia coli plays an important role in controlling the specific rates of growth (µ), glucose consumption (qGlc ) and oxygen uptake (qO2), as well as the transcriptome pattern in the cell, as was recently reported. In the current study, the energetic level (expressed as [ATP]/[ADP] ratio) was substantially reduced in E. coli strains by either over-expressing the F1 -ATPase activity (JMAGD(+)) or inactivating ATP synthase (JMat(-)). The physiological characterization of the wild-type JM101 strain and its derivative JMAGD(+) and JMatp(-) strains was conducted in bioreactors containing minimal medium with glucose. The inactivation of the atp operon and F1 -ATPase overexpression significantly diminished the energetic level and cAMP concentration in derivative strains. Relative transcription levels of 105 genes involved in glucose transport, glycolysis, tricarboxylic acid (TCA) cycle, fermentation, respiration, transcriptional regulators, transcription and genes involved in stress were determined by using qPCR. Interestingly, in the JMAGD(+) and JMatp(-) strains, having a reduced energetic level, many transcripts of glycolysis, TCA cycle and respiratory genes were down-regulated when compared to wild type JM101. The transcriptional responses, detected in the strains with reduced energetic level show down-regulation of genes involved in central carbon metabolism and respiration, these results are apposite to the observed trends of increased metabolic fluxes in glucose consumption, glycolysis, acetate synthesis, TCA cycle and respiration. Regulation mediated by CRP-cAMP complex may explain some observed transcriptional responses of TCA cycle genes, since cAMP concentration and crp transcript level

  6. Effects of lanthanum carbonate versus calcium carbonate on vascular stiffness and bone mineral metabolism in hemodialysis patients with type 2 diabetes mellitus: a randomized controlled trial

    Directory of Open Access Journals (Sweden)

    Wada K

    2015-08-01

    Full Text Available Kentaro Wada,1 Yuko Wada,2 Haruhito Adam Uchida,3 Shuichi Tsuruoka4 1Division of Nephrology and Dialysis, Department of Internal Medicine, Nippon Kokan Fukuyama Hospital, Hiroshima, 2Department of Internal Medicine, Central Hospital, Hiroshima, 3Department of Chronic Kidney Disease and Cardiovascular Disease, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 4Division of Nephrology, Department of Internal Medicine, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan Background: Vascular calcification contributes to cardiovascular disease in hemodialysis (HD patients with diabetes. The randomized controlled trial reported here compared the effects of lanthanum carbonate (LC and calcium carbonate (CC on vascular stiffness assessed using brachial-ankle pulse wave velocity (ba-PWV, intima-media thickness (IMT, bone mineral density (BMD, and serum markers of chronic kidney disease – mineral and bone disorder in such patients. Methods: Ba-PWV, IMT, BMD, and the biomarkers osteocalcin (OC and bone alkaline phosphatase (BAP were examined in 43 type 2 diabetes HD patients treated with LC (n=21 or CC (n=22 for 2 years. Results: Forty-one patients completed the study (19, LC; 22, CC. The mean ba-PWV significantly increased only in the CC group (median: 2,280.5 to 2,402.5 cm/s, P<0.05, after 24-month treatment; it remained unchanged in the LC group (median: 1,830.5 to 2,018.3 cm/s. However, the difference between the groups did not reach statistical significance. Changes in IMT and BMD were not different between the two groups. Changes in serum phosphorus, corrected calcium, and intact parathyroid hormone levels were similar between the groups. The incidence of fracture was 0% (0/19 in the LC group, and 13.6% (3/22 in the CC group (P=0.2478. The OC/BAP ratio increased significantly in the LC group (median: 0.83 to 2.47, compared with in the CC group (median: 0.77 to 1.40 (P=0.036. Conclusion: From

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

    Science.gov (United States)

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

    2013-10-01

    The accelerated decline in Arctic sea ice combined with an ongoing trend toward a more dynamic atmosphere is modifying carbon cycling in the Arctic Ocean. A critical issue is to understand how net community production (NCP; the balance between gross primary production and community respiration) responds to changes and modulates air-sea CO2 fluxes. Using data collected as part of the ArcticNet-Malina 2009 expedition in southeastern Beaufort Sea (Arctic Ocean), we synthesize information on sea ice, wind, river, water column properties, metabolism of the planktonic food web, organic carbon fluxes and pools, as well as air-sea CO2 exchange, with the aim of identifying indices of ecosystem response to environmental changes. Data were analyzed to develop a non-steady-state carbon budget and an assessment of NCP against air-sea CO2 fluxes. The mean atmospheric forcing was a mild upwelling-favorable wind (~5 km h-1) blowing from the N-E and a decaying ice cover (600 mg C m-2d-1) over the shelf prior to our survey, (2) freshwater dilution by river runoff and ice melt, and (3) the presence of cold surface waters offshore. Only the Mackenzie River delta and localized shelf areas directly affected by upwelling were identified as substantial sources of CO2 to the atmosphere (>10mmol C m-2d-1). Although generally Arctic shelf-basin system; (2) the Mackenzie Shelf acts as a weak sink for atmospheric CO2, implying that PP exceeds the respiration of terrigenous and marine organic matter in the surface layer; and (3) shelf break upwelling can transfer CO2 to the atmosphere, but massive outgassing can be attenuated if nutrients brought also by upwelling support diatom production. Our study underscores that cross-shelf exchange of waters, nutrients and particles is a key mechanism that needs to be properly monitored as the Arctic transits to a new state.

  8. Labile pyrogenic dissolved organic carbon in major Siberian Arctic rivers: Implications for wildfire-stream metabolic linkages

    Science.gov (United States)

    Myers-Pigg, Allison N.; Louchouarn, Patrick; Amon, Rainer M. W.; Prokushkin, Anatoly; Pierce, Kayce; Rubtsov, Alexey

    2015-01-01

    burning produces a spectrum of thermally altered materials that releases pyrogenic carbon (PyC) to terrestrial, atmospheric, and aquatic systems. Most studies focus on the refractory end of the PyC spectrum, derived from middle- to high-temperature combustion. Low-temperature PyC is produced during wildfires and has been found to be particularly labile and water soluble. Here we find that in each of the major Siberian watersheds, low-temperature fire-derived biomarkers are present in detectable concentrations during all flow regimes of the 2004-2006 sampling period, confirming that PyC is an intrinsic component of the dissolved organic carbon (DOC) pool mobilized by hydrologic events. Gymnosperm combustion, from the southern portions of these watersheds, is the primary source of this Py-DOC input. Using first-order degradation rates and transit times of water through these rivers, about half of the total estimated flux of this material may be remineralized during transport from fire source to river mouth (20-40 days), demonstrating the input of a labile source of PyC to these watersheds.

  9. A theoretical framework for whole-plant carbon assimilation efficiency based on metabolic scaling theory: a test case using Picea seedlings.

    Science.gov (United States)

    Wang, Zhiqiang; Ji, Mingfei; Deng, Jianming; Milne, Richard I; Ran, Jinzhi; Zhang, Qiang; Fan, Zhexuan; Zhang, Xiaowei; Li, Jiangtao; Huang, Heng; Cheng, Dongliang; Niklas, Karl J

    2015-06-01

    Simultaneous and accurate measurements of whole-plant instantaneous carbon-use efficiency (ICUE) and annual total carbon-use efficiency (TCUE) are difficult to make, especially for trees. One usually estimates ICUE based on the net photosynthetic rate or the assumed proportional relationship between growth efficiency and ICUE. However, thus far, protocols for easily estimating annual TCUE remain problematic. Here, we present a theoretical framework (based on the metabolic scaling theory) to predict whole-plant annual TCUE by directly measuring instantaneous net photosynthetic and respiratory rates. This framework makes four predictions, which were evaluated empirically using seedlings of nine Picea taxa: (i) the flux rates of CO(2) and energy will scale isometrically as a function of plant size, (ii) whole-plant net and gross photosynthetic rates and the net primary productivity will scale isometrically with respect to total leaf mass, (iii) these scaling relationships will be independent of ambient temperature and humidity fluctuations (as measured within an experimental chamber) regardless of the instantaneous net photosynthetic rate or dark respiratory rate, or overall growth rate and (iv) TCUE will scale isometrically with respect to instantaneous efficiency of carbon use (i.e., the latter can be used to predict the former) across diverse species. These predictions were experimentally verified. We also found that the ranking of the nine taxa based on net photosynthetic rates differed from ranking based on either ICUE or TCUE. In addition, the absolute values of ICUE and TCUE significantly differed among the nine taxa, with both ICUE and temperature-corrected ICUE being highest for Picea abies and lowest for Picea schrenkiana. Nevertheless, the data are consistent with the predictions of our general theoretical framework, which can be used to access annual carbon-use efficiency of different species at the level of an individual plant based on simple, direct

  10. Foliar photochemical processes and carbon metabolism under favourable and adverse winter conditions in a Mediterranean mixed forest, Catalonia (Spain)

    Science.gov (United States)

    Sperlich, D.; Chang, C. T.; Peñuelas, J.; Gracia, C.; Sabaté, S.

    2014-06-01

    Evergreen trees in the Mediterranean region must cope with a wide range of environmental stresses from summer drought to winter cold. The mildness of Mediterranean winters can periodically lead to favourable environmental conditions above the threshold for a positive carbon balance, benefitting evergreen woody species more than deciduous ones. The comparatively lower solar energy input in winter decreases the foliar light saturation point. This leads to a higher susceptibility to photoinhibitory stress especially when chilly (change persisted for several weeks after the cold period despite the recovery of the temperature to the conditions previous to the frost event. The responses of Vc, max and Jmax were highly species-specific, where Q. ilex exhibited the highest and P. halepensis the lowest reductions. In contrast, the optimal fluorometric quantum yield of photosystem II (Fv/Fm) was significantly lower in A. unedo after the cold period. The leaf position played an important role in Q. ilex showing a comparatively stronger winter effect on sunlit leaves. Our results generally agreed with the previous classifications of photoinhibition-avoiding (P. halepensis) and photoinhibition-tolerant (Q. ilex) species on the basis of their susceptibility to dynamic photoinhibition, whereas A. unedo was the least tolerant to photoinhibition, which was chronic in this species. Q. ilex and P. halepensis seem to follow contrasting photoprotective strategies which are, however, equally successful under the prevailing conditions exhibiting an adaptive advantage over A. unedo in our study site. These results show that our understanding of the dynamics of interspecific competition in Mediterranean ecosystems requires consideration of the physiological behaviour during winter which may have important implications for long-term carbon budgets and growth trends.

  11. Determination of energy metabolites in cancer cells by porous graphitic carbon liquid chromatography electrospray ionization mass spectrometry for the assessment of energy metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Szoboszlai, Norbert, E-mail: szobosz@chem.elte.hu [Laboratory of Environmental Chemistry and Bioanalytics, Department of Analytical Chemistry, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter stny 1/A, H-1117 Budapest (Hungary); Guo, Xinghua [Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9, 8010 Graz (Austria); Ozohanics, Olivér [Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Pusztaszeri u. 59-67, H-1025 Budapest (Hungary); Oláh, Júlia [1st Institute of Pathology and Experimental Cancer Research, Semmelweis University, H-1085 Budapest (Hungary); Gömöry, Ágnes [Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Pusztaszeri u. 59-67, H-1025 Budapest (Hungary); Mihucz, Victor G. [Laboratory of Environmental Chemistry and Bioanalytics, Department of Analytical Chemistry, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter stny 1/A, H-1117 Budapest (Hungary); Jeney, András [1st Institute of Pathology and Experimental Cancer Research, Semmelweis University, H-1085 Budapest (Hungary); Vékey, Károly [Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Pusztaszeri u. 59-67, H-1025 Budapest (Hungary)

    2014-03-01

    Graphical abstract: - Highlights: • All types of sugar metabolites can be investigated in one run on graphitic stationary phase. • Method development for acidic metabolites of energy metabolism using a single LC–MS run. • Study of 15 acidic energy metabolites on a PGC column using common eluents. • Lactate, acidic amino acid, organic acid and sugar phosphate determination in a single run. • Metabolism of U-{sup 13}C glucose and 1-{sup 13}C acetate in ZR-75-1 cells studied. - Abstract: A high performance liquid chromatography (HPLC) tandem mass spectrometric (MS/MS) method has been developed for the simultaneous determination of fifteen glucose, or acetate derived metabolites isolated from tumor cells. Glycolytic and tricarboxylic acid (TCA) cycle metabolites as well as acidic amino acids were separated on a HPLC porous graphitic carbon (PGC) column and simultaneously determined by means of triple quadrupole MS/MS using multiple reaction monitoring (MRM). Target compounds were eluted within 10 min with 8% v/v formic acid as an electronic modifier added to a 4:1 v/v methanol water mobile phase. The calibration is linear in the 1–100 μM concentration range for each analyte. The limit of detection ranges between 0.39 and 2.78 μM for the analytes concerned. To test the PGC–HPLC–MS/MS method in metabolomic studies, ZR-75.1 human mammary adenocarcinoma cells were labeled with U-{sup 13}C glucose or 1-{sup 13}C acetate. Applying the MRM mode, the incorporation of {sup 13}C into metabolites, isolated from the tumor cells, and derived from glucose or acetate, could be properly identified.

  12. Gene promoter methylation in colorectal cancer and healthy adjacent mucosa specimens: correlation with physiological and pathological characteristics, and with biomarkers of one-carbon metabolism.

    Science.gov (United States)

    Coppedè, Fabio; Migheli, Francesca; Lopomo, Angela; Failli, Alessandra; Legitimo, Annalisa; Consolini, Rita; Fontanini, Gabriella; Sensi, Elisa; Servadio, Adele; Seccia, Massimo; Zocco, Giuseppe; Chiarugi, Massimo; Spisni, Roberto; Migliore, Lucia

    2014-04-01

    We evaluated the promoter methylation levels of the APC, MGMT, hMLH1, RASSF1A and CDKN2A genes in 107 colorectal cancer (CRC) samples and 80 healthy adjacent tissues. We searched for correlation with both physical and pathological features, polymorphisms of folate metabolism pathway genes (MTHFR, MTRR, MTR, RFC1, TYMS, and DNMT3B), and data on circulating folate, vitamin B12 and homocysteine, which were available in a subgroup of the CRC patients. An increased number of methylated samples were found in CRC respect to adjacent healthy tissues, with the exception of APC, which was also frequently methylated in healthy colonic mucosa. Statistically significant associations were found between RASSF1A promoter methylation and tumor stage, and between hMLH1 promoter methylation and tumor location. Increasing age positively correlated with both hMLH1 and MGMT methylation levels in CRC tissues, and with APC methylation levels in the adjacent healthy mucosa. Concerning gender, females showed higher hMLH1 promoter methylation levels with respect to males. In CRC samples, the MTR 2756AG genotype correlated with higher methylation levels of RASSF1A, and the TYMS 1494 6bp ins/del polymorphism correlated with the methylation levels of both APC and hMLH1. In adjacent healthy tissues, MTR 2756AG and TYMS 1494 6bp del/del genotypes correlated with APC and MGMT promoter methylation, respectively. Low folate levels were associated with hMLH1 hypermethylation. Present results support the hypothesis that DNA methylation in CRC depends from both physiological and environmental factors, with one-carbon metabolism largely involved in this process.

  13. Partitioning between primary and secondary metabolism of carbon allocated to roots in four maize genotypes under water deficit and its effects on productivity

    Institute of Scientific and Technical Information of China (English)

    Alyne; Oliveira; Lavinsky; Paulo; César; Magalh?es; Roniel; Geraldo; ávila; Mariana; Melo; Diniz; Thiago; Corrêa; de; Souza

    2015-01-01

    Plants may respond to drought by altering biomass allocation to shoots and roots or by changing the metabolic activities in these organs. To determine how drought changes the partitioning of carbon allocated to growth and secondary metabolism in maize roots and how it affects photosynthesis(A) and productivity in maize, we evaluated leaf gas exchange, yield componentes, root morphology, and primary and secondary metabolites including total soluble sugars(TSS), starch(S), phenolics(PHE), and lignin(LIG). Data were collected from pot-grown plants of four maize genotypes: BRS 1010 and 2B710(sensitive genotypes) and DKB390 and BRS1055(tolerant genotypes) under two soil water tensions: field capacity(FC,-18 kP a) and water deficit(WD,-138 kP a). WD was applied at the pre-flowering stage for 12 days and then the water supply was restored and maintained at optimum levels until the end of the cycle. For genotype BRS 1055 under FC, the greatest A did not result in greater grain biomass(DGB) because the accumulated photoassimilates had already filled the cells, and thus the excessive TSS synthesized in leaves was allocated to roots in large amounts. However, the sharp decrease in A caused by WD imposition in this genotype did not affect the influx pressure of leaf TSS, which was due largely to conversion of primary metabolites to PHE compounds to increase the length of fine roots. In leaves of DKB390 under WD, both S and TSS were reduced, whereas PHE were increased to prevent excessive water loss and xylem cavitation. Under WD, both BRS1010 and2B710 genotypes displayed reduced allocation of biomass to shoots and roots and LIG content in leaves, as well as lower A and DGB values. In BRS1010 this response was coupled to S decrease in leaves and TSS increase in roots, whereas in 2B710 there was a concomitant S increase in roots.

  14. Partitioning between primary and secondary metabolism of carbon allocated to roots in four maize genotypes under water deficit and its effects on productivity

    Institute of Scientific and Technical Information of China (English)

    Alyne Oliveira Lavinsky; Paulo César Magalhães; Roniel Geraldo Ávila; Mariana Melo Diniz; Thiago Corrêa de Souza

    2015-01-01

    Plants may respond to drought by altering biomass allocation to shoots and roots or by changing the metabolic activities in these organs. To determine how drought changes the partitioning of carbon allocated to growth and secondary metabolism in maize roots and how it affects photosynthesis (A) and productivity in maize, we evaluated leaf gas exchange, yield componentes, root morphology, and primary and secondary metabolites including total soluble sugars (TSS), starch (S), phenolics (PHE), and lignin (LIG). Data were collected from pot-grown plants of four maize genotypes:BRS 1010 and 2B710 (sensitive genotypes) and DKB390 and BRS1055 (tolerant genotypes) under two soil water tensions:field capacity (FC,−18 kPa) and water deficit (WD,−138 kPa). WD was applied at the pre-flowering stage for 12 days and then the water supply was restored and maintained at optimum levels until the end of the cycle. For genotype BRS 1055 under FC, the greatest A did not result in greater grain biomass (DGB) because the accumulated photoassimilates had already filled the cells, and thus the excessive TSS synthesized in leaves was allocated to roots in large amounts. However, the sharp decrease in A caused by WD imposition in this genotype did not affect the influx pressure of leaf TSS, which was due largely to conversion of primary metabolites to PHE compounds to increase the length of fine roots. In leaves of DKB390 under WD, both S and TSS were reduced, whereas PHE were increased to prevent excessive water loss and xylem cavitation. Under WD, both BRS1010 and 2B710 genotypes displayed reduced allocation of biomass to shoots and roots and LIG content in leaves, as well as lower A and DGB values. In BRS1010 this response was coupled to S decrease in leaves and TSS increase in roots, whereas in 2B710 there was a concomitant S increase in roots.

  15. Partitioning between primary and secondary metabolism of carbon allocated to roots in four maize genotypes under water deficit and its effects on productivity

    Directory of Open Access Journals (Sweden)

    Alyne Oliveira Lavinsky

    2015-10-01

    Full Text Available Plants may respond to drought by altering biomass allocation to shoots and roots or by changing the metabolic activities in these organs. To determine how drought changes the partitioning of carbon allocated to growth and secondary metabolism in maize roots and how it affects photosynthesis (A and productivity in maize, we evaluated leaf gas exchange, yield componentes, root morphology, and primary and secondary metabolites including total soluble sugars (TSS, starch (S, phenolics (PHE, and lignin (LIG. Data were collected from pot-grown plants of four maize genotypes: BRS 1010 and 2B710 (sensitive genotypes and DKB390 and BRS1055 (tolerant genotypes under two soil water tensions: field capacity (FC, − 18 kPa and water deficit (WD, − 138 kPa. WD was applied at the pre-flowering stage for 12 days and then the water supply was restored and maintained at optimum levels until the end of the cycle. For genotype BRS 1055 under FC, the greatest A did not result in greater grain biomass (DGB because the accumulated photoassimilates had already filled the cells, and thus the excessive TSS synthesized in leaves was allocated to roots in large amounts. However, the sharp decrease in A caused by WD imposition in this genotype did not affect the influx pressure of leaf TSS, which was due largely to conversion of primary metabolites to PHE compounds to increase the length of fine roots. In leaves of DKB390 under WD, both S and TSS were reduced, whereas PHE were increased to prevent excessive water loss and xylem cavitation. Under WD, both BRS1010 and 2B710 genotypes displayed reduced allocation of biomass to shoots and roots and LIG content in leaves, as well as lower A and DGB values. In BRS1010 this response was coupled to S decrease in leaves and TSS increase in roots, whereas in 2B710 there was a concomitant S increase in roots.

  16. Establishing research strategies, methodologies and technologies to link genomics and proteomics to seagrass productivity, community metabolism and ecosystem carbon fluxes

    Directory of Open Access Journals (Sweden)

    Silvia eMazzuca

    2013-03-01

    Full Text Available A complete understanding of the mechanistic basis of marine ecosystem functioning is only possible through integrative and interdisciplinary research. This enables the prediction of change and possibly the mitigation of the consequences of anthropogenic impacts. One major aim of the COST Action ES0609 Seagrasses productivity. From genes to ecosystem management, is the calibration and synthesis of various methods and the development of innovative techniques and protocols for studying seagrass ecosystems.During ten days, twenty researchers representing a range of disciplines (molecular biology, physiology, botany, ecology, oceanography, underwater acoustics gathered at the marine station of STARESO (Corsica to study together the nearby Posidonia oceanica meadow. The Station de Recherches Sous-marine et Océanographiques (STARESO is located in an oligotrophic area classified as "pristine site" where environmental disturbances caused by anthropogenic pressure are exceptionally low. The healthy P. oceanica meadow, that grows in front of the lab, colonizes the sea bottom from the surface to 37 m depth. During the study, genomic and proteomic approaches were integrated with ecophysiological and physical approaches with the aim of understanding changes in seagrass productivity and metabolism at different depths and along daily cycles. In this paper we report details on the approaches utilized and we forecast the potential of the data that will come from this synergistic approach not only for P. oceanica but for seagrasses in general.

  17. Establishing research strategies, methodologies and technologies to link genomics and proteomics to seagrass productivity, community metabolism, and ecosystem carbon fluxes.

    Science.gov (United States)

    Mazzuca, Silvia; Björk, M; Beer, S; Felisberto, P; Gobert, S; Procaccini, G; Runcie, J; Silva, J; Borges, A V; Brunet, C; Buapet, P; Champenois, W; Costa, M M; D'Esposito, D; Gullström, M; Lejeune, P; Lepoint, G; Olivé, I; Rasmusson, L M; Richir, J; Ruocco, M; Serra, I A; Spadafora, A; Santos, Rui

    2013-01-01

    A complete understanding of the mechanistic basis of marine ecosystem functioning is only possible through integrative and interdisciplinary research. This enables the prediction of change and possibly the mitigation of the consequences of anthropogenic impacts. One major aim of the European Cooperation in Science and Technology (COST) Action ES0609 "Seagrasses productivity. From genes to ecosystem management," is the calibration and synthesis of various methods and the development of innovative techniques and protocols for studying seagrass ecosystems. During 10 days, 20 researchers representing a range of disciplines (molecular biology, physiology, botany, ecology, oceanography, and underwater acoustics) gathered at The Station de Recherches Sous-marines et Océanographiques (STARESO, Corsica) to study together the nearby Posidonia oceanica meadow. STARESO is located in an oligotrophic area classified as "pristine site" where environmental disturbances caused by anthropogenic pressure are exceptionally low. The healthy P. oceanica meadow, which grows in front of the research station, colonizes the sea bottom from the surface to 37 m depth. During the study, genomic and proteomic approaches were integrated with ecophysiological and physical approaches with the aim of understanding changes in seagrass productivity and metabolism at different depths and along daily cycles. In this paper we report details on the approaches utilized and we forecast the potential of the data that will come from this synergistic approach not only for P. oceanica but for seagrasses in general.

  18. Metabolic engineering of Escherichia coli for the production of 1,3-diaminopropane, a three carbon diamine.

    Science.gov (United States)

    Chae, Tong Un; Kim, Won Jun; Choi, Sol; Park, Si Jae; Lee, Sang Yup

    2015-08-11

    Bio-based production of chemicals from renewable resources is becoming increasingly important for sustainable chemical industry. In this study, Escherichia coli was metabolically engineered to produce 1,3-diaminopropane (1,3-DAP), a monomer for engineering plastics. Comparing heterologous C4 and C5 pathways for 1,3-DAP production by genome-scale in silico flux analysis revealed that the C4 pathway employing Acinetobacter baumannii dat and ddc genes, encoding 2-ketoglutarate 4-aminotransferase and L-2,4-diaminobutanoate decarboxylase, respectively, was the more efficient pathway. In a strain that has feedback resistant aspartokinases, the ppc and aspC genes were overexpressed to increase flux towards 1,3-DAP synthesis. Also, studies on 128 synthetic small RNAs applied in gene knock-down revealed that knocking out pfkA increases 1,3-DAP production. Overexpression of ppc and aspC genes in the pfkA deleted strain resulted in production titers of 1.39 and 1.35 g l(-1) of 1,3-DAP, respectively. Fed-batch fermentation of the final engineered E. coli strain allowed production of 13 g l(-1) of 1,3-DAP in a glucose minimal medium.

  19. Nasa Unveils Cosmic Images Book in Braille for Blind Readers

    Science.gov (United States)

    2008-01-01

    BALTIMORE - At a Tuesday ceremony at the National Federation of the Blind, NASA unveiled a new book that brings majestic images taken by its Great Observatories to the fingertips of the blind. "Touch the Invisible Sky" is a 60-page book with color images of nebulae, stars, galaxies and some of the telescopes that captured the original pictures. Each image is embossed with lines, bumps and other textures. These raised patterns translate colors, shapes and other intricate details of the cosmic objects, allowing visually impaired people to experience them. Braille and large-print descriptions accompany each of the book's 28 photographs, making the book's design accessible to readers of all visual abilities. Sample page Sample page The book contains spectacular images from the Hubble Space Telescope, Chandra X-ray Observatory, Spitzer Space Telescope and powerful ground-based telescopes. The celestial objects are presented as they appear through visible-light telescopes and different spectral regions invisible to the naked eye, from radio to infrared, visible, ultraviolet and X-ray light. The book introduces the concept of light and the spectrum and explains how the different observatories complement each others' findings. Readers take a cosmic journey beginning with images of the sun, and travel out into the galaxy to visit relics of exploding and dying stars, as well as the Whirlpool galaxy and colliding Antennae galaxies. People Who Read This Also Read... Chandra Data Reveal Rapidly Whirling Black Holes Jet Power and Black Hole Assortment Revealed in New Chandra Image Action Replay of Powerful Stellar Explosion Black Holes Are The Rhythm at The Heart of Galaxies "Touch the Invisible Sky" was written by astronomy educator and accessibility specialist Noreen Grice of You Can Do Astronomy LLC and the Museum of Science, Boston, with authors Simon Steel, an astronomer with the Harvard-Smithsonian Center for Astrophysics in Cambridge, Mass., and Doris Daou, an astronomer

  20. 基于氧化还原酶活性时变研究巴利阿里假单胞菌中心碳代谢%Analysis of Central Carbon Metabolism in Pseudomonas balearica Based on Key Oxidoreductases Detecting

    Institute of Scientific and Technical Information of China (English)

    温卫卫; 周小芬; 王世珍; 方柏山

    2013-01-01

    Assaying the central carbon metabolism (CCM) through the enzyme's level may be one effective method to reveal the interaction between the adaptability of marine bacteria and the extreme environmental conditions. Marine bacteria may have different CCM with terrestrial bacteria as they have different growth environment. So it is valuable to research the related key oxidoreductases, which is important to uncover the CCM of marine bacteria. The response of central carbon metabolism of marine bacteria to incubation time was investigated based on key oxidoreductases detecting, while traditional metabolic analysis was carried out by 13C metabolic flux analysis. For example,Pseudomonas balearica isolated from sediment of China's offshore was investigated. Besides growth kinetics,the central carbon metabolism of P. balearica was uncovered by a comprehensive analysis of six key oxidoreductases, glu-cose-6-phosphate dehydrogenase, pyruvate dehydrogenase, 2-ketoglutarate dehydrogenase, malate dehydrogenase, malic enzyme and isocitrate dehydrogenase. The changing regularity of key oxidoreductases activities of central carbon metabolism in P. balearica was revealed on protein level. A new technique for the study of microbial central carbon metabolism and the excavation of new enzyme preparations from marine microbial was provided.%以分离自中国北部湾沉积物的海洋菌株巴利阿里假单胞菌(Pseudomonas balearica)为例,在考察其生长动力学的同时,监测了其中心碳代谢(CCM)中6种关键氧化还原酶,葡萄糖-6-磷酸脱氢酶、丙酮酸脱氢酶、2-酮戊二酸脱氢酶、苹果酸脱氢酶、苹果酸酶及异柠檬酸脱氢酶的酶活性时变,从酶蛋白表达水平揭示了海洋生长条件下巴利阿里假单胞菌CCM中关键氧化还原酶的酶活性变化的规律,为研究微生物CCM和发掘海洋微生物新型酶制剂提供一种新思路.

  1. Genome sequencing of Sulfolobus sp. A20 from Costa Rica and comparative analyses of the putative pathways of carbon, nitrogen and sulfur metabolism in various Sulfolobus strains

    Directory of Open Access Journals (Sweden)

    Xin Dai

    2016-11-01

    Full Text Available The genome of Sulfolobus sp. A20 isolated from a hot spring in Costa Rica was sequenced. This circular genome of the strain is 2,688,317 bp in size and 34.8% in G+C content, and contains 2,591 open reading frames (ORFs. Strain A20 shares ~95.6% identity at the 16S rRNA gene sequence level and less than 30% DNA-DNA hybridization (DDH values with the most closely related known Sulfolobus species (i.e., S. islandicus and S. solfataricus, suggesting that it represents a novel Sulfolobus species. Comparison of the genome of strain A20 with those of the type strains of S. solfataricus, S. acidocaldarius, S. islandicus and S. tokodaii, which were isolated from geographically separated areas, identified 1,801 genes conserved among all Sulfolobus species analyzed (core genes. Comparative genome analyses show that central carbon metabolism in Sulfolobus is highly conserved, and enzymes involved in the Entner-Doudoroff pathway, the tricarboxylic acid cycle and the CO2 fixation pathways are predominantly encoded by the core genes. All Sulfolobus species encode genes required for the conversion of ammonium into glutamate/glutamine. Some Sulfolobus strains have gained the ability to utilize additional nitrogen source such as nitrate (i.e. S. islandicus strain REY15A, LAL14/1, M14.25 and M16.27 or urea (i.e. S. islandicus HEV10/4, S. tokodaii strain7 and S. metallicus DSM 6482. The strategies for sulfur metabolism are most diverse and least understood. S. tokodaii encodes sulfur oxygenase/reductase (SOR, whereas both S. islandicus and S. solfataricus contain genes for sulfur reductase (SRE. However, neither SOR nor SRE genes exist in the genome of strain A20, raising the possibility that an unknown pathway for the utilization of elemental sulfur may be present in the strain. The ability of Sulfolobus to utilize nitrate or sulfur is encoded by a gene cluster flanked by IS elements or their remnants. These clusters appear to have become fixed at a specific

  2. Genome Sequencing of Sulfolobus sp. A20 from Costa Rica and Comparative Analyses of the Putative Pathways of Carbon, Nitrogen, and Sulfur Metabolism in Various Sulfolobus Strains.

    Science.gov (United States)

    Dai, Xin; Wang, Haina; Zhang, Zhenfeng; Li, Kuan; Zhang, Xiaoling; Mora-López, Marielos; Jiang, Chengying; Liu, Chang; Wang, Li; Zhu, Yaxin; Hernández-Ascencio, Walter; Dong, Zhiyang; Huang, Li

    2016-01-01

    The genome of Sulfolobus sp. A20 isolated from a hot spring in Costa Rica was sequenced. This circular genome of the strain is 2,688,317 bp in size and 34.8% in G+C content, and contains 2591 open reading frames (ORFs). Strain A20 shares ~95.6% identity at the 16S rRNA gene sequence level and Sulfolobus species (i.e., Sulfolobus islandicus and Sulfolobus solfataricus), suggesting that it represents a novel Sulfolobus species. Comparison of the genome of strain A20 with those of the type strains of S. solfataricus, Sulfolobus acidocaldarius, S. islandicus, and Sulfolobus tokodaii, which were isolated from geographically separated areas, identified 1801 genes conserved among all Sulfolobus species analyzed (core genes). Comparative genome analyses show that central carbon metabolism in Sulfolobus is highly conserved, and enzymes involved in the Entner-Doudoroff pathway, the tricarboxylic acid cycle and the CO2 fixation pathways are predominantly encoded by the core genes. All Sulfolobus species encode genes required for the conversion of ammonium into glutamate/glutamine. Some Sulfolobus strains have gained the ability to utilize additional nitrogen source such as nitrate (i.e., S. islandicus strain REY15A, LAL14/1, M14.25, and M16.27) or urea (i.e., S. islandicus HEV10/4, S. tokodaii strain7, and S. metallicus DSM 6482). The strategies for sulfur metabolism are most diverse and least understood. S. tokodaii encodes sulfur oxygenase/reductase (SOR), whereas both S. islandicus and S. solfataricus contain genes for sulfur reductase (SRE). However, neither SOR nor SRE genes exist in the genome of strain A20, raising the possibility that an unknown pathway for the utilization of elemental sulfur may be present in the strain. The ability of Sulfolobus to utilize nitrate or sulfur is encoded by a gene cluster flanked by IS elements or their remnants. These clusters appear to have become fixed at a specific genomic site in some strains and lost in other strains during the

  3. Systems-Level Analysis of Nitrogen Starvation–Induced Modifications of Carbon Metabolism in a Chlamydomonas reinhardtii Starchless Mutant[W

    Science.gov (United States)

    Blaby, Ian K.; Glaesener, Anne G.; Mettler, Tabea; Fitz-Gibbon, Sorel T.; Gallaher, Sean D.; Liu, Bensheng; Boyle, Nanette R.; Kropat, Janette; Stitt, Mark; Johnson, Shannon; Benning, Christoph; Pellegrini, Matteo; Casero, David; Merchant, Sabeeha S.

    2013-01-01

    To understand the molecular basis underlying increased triacylglycerol (TAG) accumulation in starchless (sta) Chlamydomonas reinhardtii mutants, we undertook comparative time-course transcriptomics of strains CC-4348 (sta6 mutant), CC-4349, a cell wall–deficient (cw) strain purported to represent the parental STA6 strain, and three independent STA6 strains generated by complementation of sta6 (CC-4565/STA6-C2, CC-4566/STA6-C4, and CC-4567/STA6-C6) in the context of N deprivation. Despite N starvation–induced dramatic remodeling of the transcriptome, there were relatively few differences (5 × 102) observed between sta6 and STA6, the most dramatic of which were increased abundance of transcripts encoding key regulated or rate-limiting steps in central carbon metabolism, specifically isocitrate lyase, malate synthase, transaldolase, fructose bisphosphatase and phosphoenolpyruvate carboxykinase (encoded by ICL1, MAS1, TAL1, FBP1, and PCK1 respectively), suggestive of increased carbon movement toward hexose-phosphate in sta6 by upregulation of the glyoxylate pathway and gluconeogenesis. Enzyme assays validated the increase in isocitrate lyase and malate synthase activities. Targeted metabolite analysis indicated increased succinate, malate, and Glc-6-P and decreased Fru-1,6-bisphosphate, illustrating the effect of these changes. Comparisons of independent data sets in multiple strains allowed the delineation of a sequence of events in the global N starvation response in C. reinhardtii, starting within minutes with the upregulation of alternative N assimilation routes and carbohydrate synthesis and subsequently a more gradual upregulation of genes encoding enzymes of TAG synthesis. Finally, genome resequencing analysis indicated that (1) the deletion in sta6 extends into the neighboring gene encoding respiratory burst oxidase, and (2) a commonly used STA6 strain (CC-4349) as well as the sequenced reference (CC-503) are not congenic with respect to sta6 (CC-4348

  4. Polymorphisms in genes related to one-carbon metabolism are not related to pancreatic cancer in PanScan and PanC4

    Science.gov (United States)

    Leenders, Max; Bhattacharjee, Samsiddhi; Vineis, Paolo; Stevens, Victoria; Bueno-de-Mesquita, H. Bas; Shu, Xiao-Ou; Amundadottir, Laufey; Gross, Myron; Tobias, Geoffrey S.; Wactawski-Wende, Jean; Arslan, Alan A.; Duell, Eric J.; Fuchs, Charles S.; Gallinger, Steven; Hartge, Patricia; Hoover, Robert N.; Holly, Elizabeth A.; Jacobs, Eric J.; Klein, Alison P.; Kooperberg, Charles; LaCroix, Andrea; Li, Donghui; Mandelson, Margaret T.; Olson, Sara H.; Petersen, Gloria; Risch, Harvey A.; Yu, Kai; Wolpin, Brian M.; Zheng, Wei; Agalliu, Ilir; Albanes, Demetrius; Boutron-Ruault, Marie-Christine; Bracci, Paige M.; Buring, Julie E.; Canzian, Federico; Chang, Kenneth; Chanock, Stephen J.; Cotterchio, Michelle; Gaziano, J. Michael; Giovanucci, Edward L.; Goggins, Michael; Hallmans, Göran; Hankinson, Susan E.; Hoffman-Bolton, Judith A.; Hunter, David J.; Hutchinson, Amy; Jacobs, Kevin B.; Jenab, Mazda; Khaw, Kay-Tee; Kraft, Peter; Krogh, Vittorio; Kurtz, Robert C.; McWilliams, Robert R.; Mendelsohn, Julie B.; Patel, Alpa V.; Rabe, Kari G.; Riboli, Elio; Tjønneland, Anne; Trichopoulos, Dimitrios; Virtamo, Jarmo; Visvanathan, Kala; Elena, Joanne W.; Yu, Herbert; Zeleniuch-Jacquotte, Anne; Stolzenberg-Solomon, Rachael Z.

    2014-01-01

    Purpose The evidence of a relation between folate intake and one-carbon metabolism (OCM) with pancreatic cancer (PanCa) is inconsistent. In this study, the association between genes and single-nucleotide polymorphisms (SNPs) related to OCM and PanCa was assessed. Methods Using biochemical knowledge of the OCM pathway, we identified thirty-seven genes and 834 SNPs to examine in association with PanCa. Our study included 1,408 cases and 1,463 controls nested within twelve cohorts (PanScan). The ten SNPs and five genes with lowest p values (<0.02) were followed up in 2,323 cases and 2,340 controls from eight case-control studies (PanC4) that participated in PanScan2. The correlation of SNPs with metabolite levels was assessed for 649 controls from the European Prospective Investigation into Cancer and Nutrition. Results When both stages were combined, we observed suggestive associations with PanCa for rs10887710 (MAT1A) (OR 1.13, 95%CI 1.04-1.23), rs1552462 (SYT9) (OR 1.27, 95%CI 1.02-1.59), and rs7074891 (CUBN) (OR 1.91, 95%CI 1.12-3.26). After correcting for multiple comparisons, no significant associations were observed in either the first or second stage. The three suggested SNPs showed no correlations with one-carbon biomarkers. Conclusions This is the largest genetic study to date to examine the relation between germline variations in OCM-related genes polymorphisms and the risk of PanCa. Suggestive evidence for an association between polymorphisms and PanCa was observed among the cohort-nested studies, but this did not replicate in the case-control studies. Our results do not strongly support the hypothesis that genes related to OCM play a role in pancreatic carcinogenesis. PMID:23334854

  5. Foliar photochemical processes and carbon metabolism under favourable and adverse winter conditions in a Mediterranean mixed forest, Catalonia (Spain

    Directory of Open Access Journals (Sweden)

    D. Sperlich

    2014-06-01

    Full Text Available Evergreen trees in the Mediterranean region must cope with a wide range of environmental stresses from summer drought to winter cold. The mildness of Mediterranean winters can periodically lead to favourable environmental conditions above the threshold for a positive carbon balance, benefitting evergreen woody species more than deciduous ones. The comparatively lower solar energy input in winter decreases the foliar light saturation point. This leads to a higher susceptibility to photoinhibitory stress especially when chilly (Quercus ilex L., Pinus halepensis Mill., and Arbutus unedo L. during a period of mild winter conditions and their responses to a sudden cold period. The state of the photosynthetic machinery in both periods was thus tested by estimating the foliar photosynthetic potential with CO2 response curves in parallel with chlorophyll fluorescence measurements. The studied evergreen tree species benefited strongly from mild winter conditions by exhibiting extraordinarily high photosynthetic potentials similar to those under spring conditions. A sudden period of frost, however, negatively affected the photosynthetic apparatus, leading to significant decreases in key physiological parameters such as the maximum carboxylation velocity (Vc, max, the maximum photosynthetic electron transport rate (Jmax, and the optimal fluorometric quantum yield of photosystem II (Fv/Fm. This change persisted for several weeks after the cold period despite the recovery of the temperature to the conditions previous to the frost event. The responses of Vc, max and Jmax were highly species-specific, where Q. ilex exhibited the highest and P. halepensis the lowest reductions. In contrast, the optimal fluorometric quantum yield of photosystem II (Fv/Fm was significantly lower in A. unedo after the cold period. The leaf position played an important role in Q. ilex showing a comparatively stronger winter effect on sunlit leaves. Our results generally agreed with

  6. The arogenate dehydratase gene family: towards understanding differential regulation of carbon flux through phenylalanine into primary versus secondary metabolic pathways.

    Science.gov (United States)

    Corea, Oliver R A; Bedgar, Diana L; Davin, Laurence B; Lewis, Norman G

    2012-10-01

    Phe is formed from arogenate in planta through the action of arogenate dehydratase (ADT), and there are six ADT isoenzymes in the "model" vascular plant species Arabidopsis thaliana. This raised the possibility that specific ADTs may be differentially regulated so as to control Phe biosynthesis for protein synthesis vs its much more massive deployment for phenylpropanoid metabolism. In our previous reverse genetics study using 25 single/multiple ADT knockout (KO) lines, a subset of these knockouts was differentially reduced in their lignin contents. In the current investigation, it was hypothesized that Phe pool sizes might correlate well with reduction in lignin contents in the affected KO lines. The free amino acid contents of these KO lines were thus comprehensively analyzed in stem, leaf and root tissues, over a growth/developmental time course from 3 to 8 weeks until senescence. The data obtained were then compared to, and contrasted with, the differential extent of lignin deposition occurring in the various lines. Relative changes in pool sizes were also analyzed by performing a pairwise confirmatory factor analysis for Phe:Tyr, Phe:Trp and Tyr:Trp, following determination of the deviation from the mean for Phe, Tyr and Trp in each plant line. It was found that the Phe pool sizes measured were differentially reduced only in lignin-deficient lines, and in tissues and at time points where lignin biosynthesis was constitutively highly active (in wild type lines) under the growth conditions employed. In contrast, this trend was not evident across all ADT KO lines, possibly due to maintenance of Phe pools by non-targeted isoenzymes, or by feedback mechanisms known to be in place.

  7. Carbon Dioxide Impacts in the Deep-Sea: Is Maintaining a Metabolically Required CO2 Efflux Rate Challenging?

    Science.gov (United States)

    Peltzer, E. T.; Hofmann, A. F.; Brewer, P. G.

    2011-12-01

    Increasing ocean acidification from fossil fuel CO2 invasion, from temperature driven changes in respiration, and from possible leakage from sub-seabed geologic CO2 disposal has aroused concern over the impacts of elevated CO2 concentrations on marine life. Here we describe the rate problem for animals who must export CO2 at about the same rate at which O2 is consumed. We analyze the basic properties controlling CO2 export within the diffusive boundary of marine animals in a changing ocean in order to compare the challenges posed by O2 uptake under stress with the equivalent problem of CO2 expulsion. The problem is more complex than that for a non-reactive gas since, as with gas exchange of CO2 at the air-sea interface, the influence of the ensemble of reactions within the CO2 - HCO3- - CO3= acid-base system needs to be considered. These reactions appear as an enhancement factor which significantly facilitates CO2 efflux compared to O2 intake at equal temperature, pressure and flow rate under typical oceanic concentrations. Possibly as an adaptation to this chemical advantage marine animals typically can respond to external CO2 stress simply by metabolic adjustment. This is energetically more favorable than having to resort to mechanically increasing flow over their surface to thin the boundary layer as is required to alleviate O2 stress. Regionally as with O2 the combination of T, P, and pH/pCO2 creates a zone of maximum CO2 stress at around 1000 m depth. But the net result is that the combination of an increase in T combined with declining O2 poses a greater respiratory challenge to marine life than does increasing CO2. The relationships developed here allow a more accurate prediction of the impacts on marine life from the combined effects of changing T, O2, and CO2 than can be estimated from single variable studies.

  8. 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)

    Guo, Li-Jin; Lin, Shan; 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 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.

  9. DOE unveils 20-year priority list for developing 28 research facilities

    CERN Multimedia

    Dawson, J

    2004-01-01

    "With a level of fanfare that signaled a significant commitment by the Bush administration to basic science research, Secretary of Energy Spencer Abraham used a packed National Press Club luncheon on 10 November to unveil the Department of Energy's priority list for developing 28 major science facilities over the next two decades" (1 page)

  10. Effect of Ethanol Accumulation on Porcine Interferon-α Production by Pichia pastoris and Activities of Key Enzymes in Carbon Metabolism.

    Science.gov (United States)

    Ding, Jian; Gao, Minjie; Hou, Guoli; Liang, Kexue

    2015-08-01

    In production of porcine interferon α (pIFN-α) by Pichia pastoris, improper glycerol feeding strategy leads to ethanol accumulation in the last stage of growth phase. In the present study, taking two runs with low ethanol accumulation under 2 g/L as control group, effects of long-term (>4 h) and instantaneous high ethanol concentration (>10 g/L) on pIFN-α production, and activities of key enzymes in carbon metabolism were discussed. As a result, compared with control group, pIFN-α expression level was decreased about 4~12 folds under long-term high ethanol concentration, from the level above 3 g/L to the level under 1 g/L; pIFN-α expression level was decreased about 8 folds under instantaneous high ethanol concentration, reaching to the low level of 0.42 g/L. The low production of pIFN-α was caused by the severe inhibitory effect of ethanol on these enzymes.

  11. Effects of soil type, fertilization and drought on carbon allocation to root growth and partitioning between secondary metabolism and ectomycorrhizae of Betula papyrifera.

    Science.gov (United States)

    Kleczewski, Nathan M; Herms, Daniel A; Bonello, Pierluigi

    2010-07-01

    Paper birch (Betula papyrifera Marsh) seedlings were grown in a greenhouse in either subsoil or topsoil in factorial combination with two fertilization and drought regimes to investigate how different soil environments and nutrient availability drive belowground partitioning between growth, secondary metabolism and ectomycorrhizal (EM) associations, and impact drought tolerance of paper birch. Root and total seedling dry biomass, starch, soluble sugars, soluble phenolics, lignin and EM abundance were quantified. In unfertilized topsoil, total plant biomass and root biomass were approximately nine times higher than in unfertilized subsoil, but the root weight ratios did not differ between soils. Root soluble phenolics and lignin were higher in unfertilized subsoil than in unfertilized topsoil, whereas EM abundance was significantly higher in unfertilized topsoil than in unfertilized subsoil. In topsoil, fertilization decreased root biomass and EM abundance and increased root phenolics and lignin. In contrast, fertilization of subsoil increased root biomass but decreased root phenolics and lignin, while EM abundance was unaffected. In both soil types, fertilization reduced root weight ratios. Across soil types, EM abundance was negatively correlated with root soluble sugars, root phenolics and lignin, but this was driven mainly by the responses in the topsoil treatment. Our results show that soil fertility mediates carbon tradeoffs among defense, growth and EM associations.

  12. Rain-Shelter Cultivation Modifies Carbon Allocation in the Polyphenolic and Volatile Metabolism of Vitis vinifera L. Chardonnay Grapes

    Science.gov (United States)

    Han, Mei-Mei; Yang, Xiao-Fan; Li, Zheng; Wang, Jun; Pan, Qiu-Hong

    2016-01-01

    This study investigated the effect of rain-shelter cultivation on the biosynthesis of flavonoids and volatiles in grapes, with an aim of determining whether rain-shelter application could help to improve the sensory attributes and quality of grapes. Vitis vinifera L. Chardonnay grapes, grown in the Huaizhuo basin region of northern China, were selected within two consecutive years. A rain-shelter roof was constructed using a colorless polyethylene (PE) film with a light transmittance of 80%. Results showed that rain-shelter treatment did not affect the accumulation of soluble solids during grape maturation. However, the allocation of assimilated carbon in phenolic and volatile biosynthetic pathways varied significantly, leading to alterations in polyphenolic and volatile profiles. The rain-shelter cultivation enhanced the concentration of flavan-3-ols via the flavonoid-3’5’-hydroxylase (F3’5’H) pathway, but reduced the level of flavonols and flavan-3-ols via the flavonoid-3’-hydroxylase (F3’H) pathway. In addition, the rain-shelter cultivation significantly enhanced the synthesis of fatty acid-derived volatiles, isoprene-derived terpenoids and amino acid-derived branched-chain aliphatics, but led to a decrease in the accumulation of isoprene-derived norisoprenoids and amino acid-derived benzenoids. Principal component analysis revealed some key compounds that differentiated the grapes cultivated under open-field and rain-shelter conditions. Moreover, the effect of the rain-shelter application on the accumulation of these compounds appeared to be vintage dependent. The alteration of their profiles caused by the rain-shelter treatment was significant in the vintage that received higher rainfall, which usually took place in the first rapid growth and veraison phases. PMID:27218245

  13. Targeted mutagenesis of mitochondrial carbonic anhydrases VA and VB implicates both enzymes in ammonia detoxification and glucose metabolism.

    Science.gov (United States)

    Shah, Gul N; Rubbelke, Timothy S; Hendin, Joshua; Nguyen, Hien; Waheed, Abdul; Shoemaker, James D; Sly, William S

    2013-04-30

    Prior studies with carbonic anhydrase (CA) inhibitors implicated mitochondrial CA in ureagenesis and gluconeogenesis. Subsequent studies identified two mitochondrial CAs. To distinguish the contribution of each enzyme, we studied the effects of targeted disruption of the murine CA genes, called Car5A and Car5B. The Car5A mutation had several deleterious consequences. Car5A null mice were smaller than wild-type littermates and bred poorly. However, on sodium-potassium citrate-supplemented water, they produced offspring in expected numbers. Their blood ammonia concentrations were markedly elevated, but their fasting blood sugars were normal. By contrast, Car5B null mice showed normal growth and normal blood ammonia levels. They too had normal fasting blood sugars. Car5A/B double-knockout (DKO) mice showed additional abnormalities. Impaired growth was more severe than for Car5A null mice. Hyperammonemia was even greater as well. Although fertile, DKO animals were produced in less-than-predicted numbers even when supplemented with sodium-potassium citrate in their drinking water. Survival after weaning was also reduced, especially for males. In addition, fasting blood glucose levels for DKO mice were significantly lower than for controls (153 ± 33 vs. 230 ± 24 mg/dL). The enhanced hyperammonemia and lower fasting blood sugar, which are both seen in the DKO mice, indicate that both Car5A and Car5B contribute to both ammonia detoxification (ureagenesis) and regulation of fasting blood sugar (gluconeogenesis). Car5A, which is expressed mainly in liver, clearly has the predominant role in ammonia detoxification. The contribution of Car5B to ureagenesis and gluconeogenesis was evident only on a Car5A null background.

  14. Rain-Shelter Cultivation Modifies Carbon Allocation in the Polyphenolic and Volatile Metabolism of Vitis vinifera L. Chardonnay Grapes.

    Directory of Open Access Journals (Sweden)

    Yuan Gao

    Full Text Available This study investigated the effect of rain-shelter cultivation on the biosynthesis of flavonoids and volatiles in grapes, with an aim of determining whether rain-shelter application could help to improve the sensory attributes and quality of grapes. Vitis vinifera L. Chardonnay grapes, grown in the Huaizhuo basin region of northern China, were selected within two consecutive years. A rain-shelter roof was constructed using a colorless polyethylene (PE film with a light transmittance of 80%. Results showed that rain-shelter treatment did not affect the accumulation of soluble solids during grape maturation. However, the allocation of assimilated carbon in phenolic and volatile biosynthetic pathways varied significantly, leading to alterations in polyphenolic and volatile profiles. The rain-shelter cultivation enhanced the concentration of flavan-3-ols via the flavonoid-3'5'-hydroxylase (F3'5'H pathway, but reduced the level of flavonols and flavan-3-ols via the flavonoid-3'-hydroxylase (F3'H pathway. In addition, the rain-shelter cultivation significantly enhanced the synthesis of fatty acid-derived volatiles, isoprene-derived terpenoids and amino acid-derived branched-chain aliphatics, but led to a decrease in the accumulation of isoprene-derived norisoprenoids and amino acid-derived benzenoids. Principal component analysis revealed some key compounds that differentiated the grapes cultivated under open-field and rain-shelter conditions. Moreover, the effect of the rain-shelter application on the accumulation of these compounds appeared to be vintage dependent. The alteration of their profiles caused by the rain-shelter treatment was significant in the vintage that received higher rainfall, which usually took place in the first rapid growth and veraison phases.

  15. 碳源对EBPR代谢过程及微生物特性的影响%Influence of Carbon Source on EBPR Metabolism and Microorganism Communities

    Institute of Scientific and Technical Information of China (English)

    吴昌永; 彭永臻; 万春黎; 李晓玲; 袁志国

    2009-01-01

    A SBR was used in this study for investigating the influence of carbon source on EBPR metabolism and microorganism communities when feeding with acetate and propionate. The SBR was operated with a cycle time of 8 h and each cycle consisted of 4 min feeding, 2 h anaerobic period, 5 h aerobic period, 35 min setting, 15 min decanting and 6 min waiting. The COD of influent was kept at 300 mg/L during the experiment. Acetate and propionate were used as the sole carbon source for operation of 60 days, respectively. The phosphorus release/ COD consumption in the end of anaerobic phase were 0.35 and 0.27 when acetate and propionate were used as the carbon source, respectively. The PHA composition was different when different carbon source was dosed. PHB accounted for 92.6% in the end of anaerobic phase but the value for PHV was only 7.4% when acetate was selected as the carbon source. No PH2MV was detected during this process. The compositions of PHA were PHB (10.2%), PHV (35.8%) and PH2MV (54.0%) in the end of anaerobic cycle when propionate was used as the sole carbon source. There was variation of microorganism communities during this process for the results of DGGE combined with SEM micrographs and PHA staining. Coccus morphotype PAOs were accumulated in acetate-fed phase and rod morphotype PAOs were accumulated in propionate-fed stage. Different PAOs were accumulated and the metabolic pathways were different when different carbon sources were used, but good EBPR could be achieved during all these conditions.%采用SBR反应器,研究了乙酸和丙酸分别作为唯一进水碳源时对EBPR过程物质转化及代表性微生物变化特性的影响,并对不同碳源可能导致不同的微生物代谢过程进行了讨论.SBR的运行模式为:厌氧2 h,好氧5 h,每天运行3个周期,乙酸和丙酸进水的COD均为300 mg/L,系统先用乙酸作为碳源运行60 d,随后以丙酸作为碳源运行60 d.结果表明,在采用乙酸作为碳源时,厌氧结束

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

    Directory of Open Access Journals (Sweden)

    A. Forest

    2013-10-01

    Full Text Available The accelerated decline in Arctic sea ice combined with an ongoing trend toward a more dynamic atmosphere is modifying carbon cycling in the Arctic Ocean. A critical issue is to understand how net community production (NCP; the balance between gross primary production and community respiration responds to changes and modulates air–sea CO2 fluxes. Using data collected as part of the ArcticNet-Malina 2009 expedition in southeastern Beaufort Sea (Arctic Ocean, we synthesize information on sea ice, wind, river, water column properties, metabolism of the planktonic food web, organic carbon fluxes and pools, as well as air–sea CO2 exchange, with the aim of identifying indices of ecosystem response to environmental changes. Data were analyzed to develop a non-steady-state carbon budget and an assessment of NCP against air–sea CO2 fluxes. The mean atmospheric forcing was a mild upwelling-favorable wind (~5 km h−1 blowing from the N-E and a decaying ice cover (2 with a mean uptake rate of −2.0 ± 3.3 mmol C m−2d−1. We attribute this discrepancy to: (1 elevated PP rates (>600 mg C m−2d−1 over the shelf prior to our survey, (2 freshwater dilution by river runoff and ice melt, and (3 the presence of cold surface waters offshore. Only the Mackenzie River delta and localized shelf areas directly affected by upwelling were identified as substantial sources of CO2 to the atmosphere (>10mmol C m−2d−1. Although generally −2d−1, daily PP rates cumulated to a total PP of ~437.6 × 103 t C, which was roughly twice higher than the organic carbon delivery by river inputs (~241.2 × 103 t C. Subsurface PP represented 37.4% of total PP for the whole area and as much as ~72.0% seaward of the shelf break. In the upper 100 m, bacteria dominated (54% total community respiration (~250 mg C m−2d−1, whereas protozoans, metazoans, and benthos, contributed to 24%, 10%, and 12%, respectively. The range of production-to-biomass ratios of bacteria was

  17. Effect of Carbon and Nitrogen Availability on Metabolism of Amino Acids in Germinating Spores of Arbuscular Mycorrhizal Fungi

    Institute of Scientific and Technical Information of China (English)

    JIN Hai-Ru; JIANG Dong-Hua; ZHANG Ping-Hua

    2011-01-01

    The effects of carbon (C) and nitrogen (N) sources on N utilization and biosynthesis of amino acids were examined in the germinating spores of the arbuscular mycorrhizal (AM) fungus Glomus intraradices Schenck & Smith after exposure to various N substrates,CO2,glucose,and/or root exudates.The N uptake and de novo biosynthesis of amino acids were analyzed using stable isotopic labeling with mass spectrometric detection.High-performance liquid chromatography-based analysis was used to measure amino acid levels.In the absence of exogenous N sources and in the presence of 25 mL L-1 CO2,the germinating AM fungal spores utilized internal N storage as well as C skeletons derived from the degradation of storage lipids to biosynthesize the free amino acids,in which serine and glycine were produced predominantly.The concentrations of internal amino acids increased gradually as the germination time increased from 0 to 1 or 2 weeks.However,asparagine and glutamine declined to the low levels; both degraded to provide the biosynthesis of other amino acids with C and N donors.The availability of exogenous inorganic N (ammonium and nitrate) and organic N (urea,arginine,and glutamine) to the AM fungal spores using only CO2 for germination generated more than 5 times more internal free amino acids than those in the absence of exogenous N.A supply of exogenous nitrate to the AM fungal spores with only CO2 gave rise to more than 10 times more asparagine than that without exogenous N.In contrast,the extra supply of exogenous glucose to the AM fungal spores generated a significant enhancement in the uptake of exogenous N sources,with more than 3 times more free amino acids being produced than those supplied with only exogenous CO2.Meanwhile,arginine was the most abundant free amino acid produced and it was incorporated into the proteins of AM fungal spores to serve as an N storage compound.

  18. Unveiling the pentagonal nature of perfectly aligned single-and double-strand Si nano-ribbons on Ag(110)

    Science.gov (United States)

    Cerdá, Jorge I.; Sławińska, Jagoda; Le Lay, Guy; Marele, Antonela C.; Gómez-Rodríguez, José M.; Dávila, María E.

    2016-10-01

    Carbon and silicon pentagonal low-dimensional structures attract a great interest as they may lead to new exotic phenomena such as topologically protected phases or increased spin-orbit effects. However, no pure pentagonal phase has yet been realized for any of them. Here we unveil through extensive density functional theory calculations and scanning tunnelling microscope simulations, confronted to key experimental facts, the hidden pentagonal nature of single- and double-strand chiral Si nano-ribbons perfectly aligned on Ag(110) surfaces whose structure has remained elusive for over a decade. Our study reveals an unprecedented one-dimensional Si atomic arrangement solely comprising almost perfect alternating pentagons residing in the missing row troughs of the reconstructed surface. We additionally characterize the precursor structure of the nano-ribbons, which consists of a Si cluster (nano-dot) occupying a silver di-vacancy in a quasi-hexagonal configuration. The system thus materializes a paradigmatic shift from a silicene-like packing to a pentagonal one.

  19. Unveiling the pentagonal nature of perfectly aligned single-and double-strand Si nano-ribbons on Ag(110)

    Science.gov (United States)

    Cerdá, Jorge I.; Sławińska, Jagoda; Le Lay, Guy; Marele, Antonela C.; Gómez-Rodríguez, José M.; Dávila, María E.

    2016-01-01

    Carbon and silicon pentagonal low-dimensional structures attract a great interest as they may lead to new exotic phenomena such as topologically protected phases or increased spin–orbit effects. However, no pure pentagonal phase has yet been realized for any of them. Here we unveil through extensive density functional theory calculations and scanning tunnelling microscope simulations, confronted to key experimental facts, the hidden pentagonal nature of single- and double-strand chiral Si nano-ribbons perfectly aligned on Ag(110) surfaces whose structure has remained elusive for over a decade. Our study reveals an unprecedented one-dimensional Si atomic arrangement solely comprising almost perfect alternating pentagons residing in the missing row troughs of the reconstructed surface. We additionally characterize the precursor structure of the nano-ribbons, which consists of a Si cluster (nano-dot) occupying a silver di-vacancy in a quasi-hexagonal configuration. The system thus materializes a paradigmatic shift from a silicene-like packing to a pentagonal one. PMID:27708263

  20. The CcpA regulon of Streptococcus suis reveals novel insights into the regulation of the streptococcal central carbon metabolism by binding of CcpA to two distinct binding motifs.

    Science.gov (United States)

    Willenborg, Jörg; de Greeff, Astrid; Jarek, Michael; Valentin-Weigand, Peter; Goethe, Ralph

    2014-04-01

    Streptococcus suis (S. suis) is a neglected zoonotic streptococcus causing fatal diseases in humans and in pigs. The transcriptional regulator CcpA (catabolite control protein A) is involved in the metabolic adaptation to different carbohydrate sources and virulence of S. suis and other pathogenic streptococci. In this study, we determined the DNA binding characteristics of CcpA and identified the CcpA regulon during growth of S. suis. Electrophoretic mobility shift analyses showed promiscuous DNA binding of CcpA to cognate cre sites in vitro. In contrast, sequencing of immunoprecipitated chromatin revealed two specific consensus motifs, a pseudo-palindromic cre motif (WWGAAARCGYTTTCWW) and a novel cre2 motif (TTTTYHWDHHWWTTTY), within the regulatory elements of the genes directly controlled by CcpA. Via these elements CcpA regulates expression of genes involved in carbohydrate uptake and conversion, and in addition in important metabolic pathways of the central carbon metabolism, like glycolysis, mixed-acid fermentation, and the fragmentary TCA cycle. Furthermore, our analyses provide evidence that CcpA regulates the genes of the central carbon metabolism by binding either the pseudo-palindromic cre motif or the cre2 motif in a HPr(Ser)∼P independent conformation.

  1. Open-air fumigation of winter barley with sulphur dioxide: Effects on growth of the flag leaf and enzymes of photosynthetic carbon metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Montiel-Canobra, P.O.; Bradbeer, J.W. (King' s Coll. London (UK)); Darrall, N.M. (National Power Technology and Environmental Centre, Leatherhead (UK))

    1991-01-01

    The effects SO{sub 2} on flag leaf growth and on a number of enzymes of photosynthetic carbon metabolism in leaves of winter barley (Hordeum vulgare L. cv. Igri) were investigated. Plant material was obtained from an open-air fumigation experiment operated at Littlehampton, West Sussex, U.K., throughout two growing seasons (1985-1986 and 1986-1987). In 1985-1986 samples were compared from an ambient plot and the highest SO{sub 2} treatment plot. In 1986-1987 samples from the ambient SO{sub 2} plot and the two highest treatments were sampled. The flag leaf was studied in particular because of its considerable contribution to grain filling. Significant reduction in flag leaf dry weight and flag leaf area were found in the highest SO{sub 2} treatment in both seasons. In 1986-1987, delays in flag leaf emergence and senescence in both the 0.028 and 0.038 microliter l{sup {minus}1} SO{sub 2} treatments were observed. Leaf extracts were used to assay the following enzymes: stromal phosphoribulokinase and NADP-dependent glyceraldehyde-phosphate dehydrogenase, phosphoglycerate kinase and cytosolic fructose-1,6-bisphosphatase. No effects of SO{sub 2} were detected on the total activity of any of the stromal enzymes, or on the activation status of NADP-dependent glyceraldehyde-phosphate dehydrogenase. Significant reductions in the post-anthesis activity of cytosolic fructose-1,6-bisphosphatase were recorded for the highest SO{sub 2} treatment (0.038 microliter l{sup {minus}1}) and provided a preliminary indication that these levels of SO{sub 2} could affect the flow of fixed carbon in leaves and could thereby affect the availability of photoassimilate for export from source leaves. Both the reduction in size of the flag leaf and decreased levels of activity of cytosolic fructose-1,6-bisphosphatase may have important implications for the process of grain filling. 7 figs., 42 refs., 1 tab.

  2. Association of seven functional polymorphisms of one-carbon metabolic pathway with total plasma homocysteine levels and susceptibility to Parkinson's disease among South Indians.

    Science.gov (United States)

    Kumudini, Nadella; Uma, Addepally; Naushad, Shaik Mohammad; Mridula, Rukmini; Borgohain, Rupam; Kutala, Vijay Kumar

    2014-05-07

    This study from South India was performed to ascertain the impact of seven functional polymorphisms of one-carbon metabolic pathway on total plasma homocysteine levels and susceptibility to PD. A total of 151 cases of Parkinson's disease and 416 healthy controls were analyzed for fasting plasma homocysteine levels by reverse phase HPLC. PCR-RFLP approaches were used to analyze glutamate carboxypeptidase II (GCPII) 1561 C>T, reduced folate carrier 1 (RFC1) 80 G>A, cytosolic serine hydroxymethyl transferase (cSHMT) 1420 C>T, methylene tetrahydrofolate reductase (MTHFR) 677 C>T, methionine synthase (MTR) 2756 A>G and methionine synthase reductase (MTRR) 66 A>G polymorphisms. PCR-AFLP was used for the analysis of thymidylate synthase (TYMS) 5'-UTR 28bp tandem repeat. PD cases exhibited elevated plasma homocysteine levels compared to controls (men: 28.8 ± 6.9 vs. 16.4 ± 8.8 μmol/L; women: 25.4 ± 5.3 vs. 11.2 ± 5.1μmol/L). Homocysteine levels showed positive correlation with male gender (r=0.39, pG (r=0.31, pT polymorphism. MTRR 66 A>G polymorphism showed independent risk for PD (OR: 3.42, 95% CI: 2.35-4.98) whereas cSHMT 1420 C>T conferred protection against PD (OR: 0.11, 95% CI: 0.07-0.17). Multifactor dimensionality reduction analysis showed synergistic interactions between MTHFR 677 C>T and MTRR 66 A>G, whereas cSHMT 1420 C>T exhibited counteracting interactions in altering susceptibility to PD. To conclude, PD cases exhibited hyperhomocysteinemia and MTRR 66 A>G and cSHMT 1420 C>T gene variants were shown to modulate PD risk by altering the homocysteine levels.

  3. Tumor cell metabolism

    Science.gov (United States)

    Romero-Garcia, Susana; Lopez-Gonzalez, Jose Sullivan; B´ez-Viveros, José Luis; Aguilar-Cazares, Dolores

    2011-01-01

    Cancer is a genetic disease that is caused by mutations in oncogenes, tumor suppressor genes and stability genes. The fact that the metabolism of tumor cells is altered has been known for many years. However, the mechanisms and consequences of metabolic reprogramming have just begun to be understood. In this review, an integral view of tumor cell metabolism is presented, showing how metabolic pathways are reprogrammed to satisfy tumor cell proliferation and survival requirements. In tumor cells, glycolysis is strongly enhanced to fulfill the high ATP demands of these cells; glucose carbons are the main building blocks in fatty acid and nucleotide biosynthesis. Glutaminolysis is also increased to satisfy NADPH regeneration, whereas glutamine carbons replenish the Krebs cycle, which produces metabolites that are constantly used for macromolecular biosynthesis. A characteristic feature of the tumor microenvironment is acidosis, which results from the local increase in lactic acid production by tumor cells. This phenomenon is attributed to the carbons from glutamine and glucose, which are also used for lactic acid production. Lactic acidosis also directs the metabolic reprogramming of tumor cells and serves as an additional selective pressure. Finally, we also discuss the role of mitochondria in supporting tumor cell metabolism. PMID:22057267

  4. Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III-reducer Rhodoferax ferrireducens

    Directory of Open Access Journals (Sweden)

    Daugherty Sean

    2009-09-01

    Full Text Available Abstract Background Rhodoferax ferrireducens is a metabolically versatile, Fe(III-reducing, subsurface microorganism that is likely to play an important role in the carbon and metal cycles in the subsurface. It also has the unique ability to convert sugars to electricity, oxidizing the sugars to carbon dioxide with quantitative electron transfer to graphite electrodes in microbial fuel cells. In order to expand our limited knowledge about R. ferrireducens, the complete genome sequence of this organism was further annotated and then the physiology of R. ferrireducens was investigated with a constraint-based, genome-scale in silico metabolic model and laboratory studies. Results The iterative modeling and experimental approach unveiled exciting, previously unknown physiological features, including an expanded range of substrates that support growth, such as cellobiose and citrate, and provided additional insights into important features such as the stoichiometry of the electron transport chain and the ability to grow via fumarate dismutation. Further analysis explained why R. ferrireducens is unable to grow via photosynthesis or fermentation of sugars like other members of this genus and uncovered novel genes for benzoate metabolism. The genome also revealed that R. ferrireducens is well-adapted for growth in the subsurface because it appears to be capable of dealing with a number of environmental insults, including heavy metals, aromatic compounds, nutrient limitation and oxidative stress. Conclusion This study demonstrates that combining genome-scale modeling with the annotation of a new genome sequence can guide experimental studies and accelerate the understanding of the physiology of under-studied yet environmentally relevant microorganisms.

  5. 2012 Molecular Basis of Microbial One-Carbon Metabolism Gordon Research Conferences and Gordon Research Seminar, August 4-10,2012

    Energy Technology Data Exchange (ETDEWEB)

    Hanson, Thomas

    2012-08-10

    The 2012 Gordon Conference will present and discuss cutting-edge research in the field of microbial metabolism of C1 compounds. The conference will feature the roles and application of C1 metabolism in natural and synthetic systems at scales from molecules to ecosystems. The conference will stress molecular aspects of the unique metabolism exhibited by autotrophic bacteria, methanogens, methylotrophs, aerobic and anaerobic methanotrophs, and acetogens.

  6. An analytical framework and indicator system of urban carbon-based energy metabolism%城市碳基能源代谢分析框架及核算体系

    Institute of Scientific and Technical Information of China (English)

    张丽君; 秦耀辰; 张金萍; 鲁丰先

    2013-01-01

    城市碳基能源代谢是当前应对全球气候变化与资源耗竭研究的重要突破口.针对碳排放研究在城市尺度核算的薄弱环节,以及城市代谢研究在社会经济子系统碳基能源转移分析上的缺陷,文章基于碳足迹与城市代谢阐释城市碳基能源代谢的内涵,界定其核算范畴与边界,构建城市复合生态系统碳基能源四种范畴不同代谢过程的核算方法体系.以北京市为案例,阐明三种核算方法的特点.研究认为,城市碳基能源代谢是对城市社会经济发展过程中资源利用与环境协调发展量度的一组低碳生态城市指标体系;不同碳基能源代谢核算方法各具特色,应根据数据可得性与研究目标针对性进行选择,以增加研究结果之间的规范性与可比性;不同范畴界定下的碳基能源代谢核算可以根据生产、消费及共担责任原则处理碳减排的责任问题;中国的城市碳基能源代谢实质是一种城市区域碳基能源代谢,三种核算方法从不同视角与层面揭示城市碳基能源代谢特点,三者结合能全面分析产业与能源结构调整、居民生活方式变化对低碳生态城市发展的作用路径与规律;城市部门结构(产业、居民)与技术结构变化的碳基能源代谢响应是进一步研究的重点.%It is crucial to assess carbon-based energy use and related carbon emissions to assign responsibility for emissions reductions.Previous studies have scantly documented urban carbon emissions and addressed carbon-based energy transfer in socio-economic subsystems.Therefore,this study aims to build a framework and indicator system of urban carbon-based energy metabolism to standardize the accounting methods on fossil-energy related carbon emissions.The framework explains the connotation of urban carbon-based energy metabolism and defines its accounting scope and boundary based on "carbon footprint" and "urban metabolism".The indicator system

  7. Metabolic acidosis

    Science.gov (United States)

    Acidosis - metabolic ... Metabolic acidosis occurs when the body produces too much acid. It can also occur when the kidneys are not ... the body. There are several types of metabolic acidosis. Diabetic acidosis develops when acidic substances, known as ...

  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.

  9. The crystal structures of the tryparedoxin-tryparedoxin peroxidase couple unveil the structural determinants of Leishmania detoxification pathway.

    Directory of Open Access Journals (Sweden)

    Annarita Fiorillo

    Full Text Available Leishmaniasis is a neglected disease caused by Leishmania, an intracellular protozoan parasite which possesses a unique thiol metabolism based on trypanothione. Trypanothione is used as a source of electrons by the tryparedoxin/tryparedoxin peroxidase system (TXN/TXNPx to reduce the hydroperoxides produced by macrophages during infection. This detoxification pathway is not only unique to the parasite but is also essential for its survival; therefore, it constitutes a most attractive drug target. Several forms of TXNPx, with very high sequence identity to one another, have been found in Leishmania strains, one of which has been used as a component of a potential anti-leishmanial polyprotein vaccine. The structures of cytosolic TXN and TXNPx from L. major (LmTXN and LmTXNPx offer a unique opportunity to study peroxide reduction in Leishmania parasites at a molecular level, and may provide new tools for multienzyme inhibition-based drug discovery. Structural analyses bring out key structural features to elucidate LmTXN and LmTXNPx function. LmTXN displays an unusual N-terminal α-helix which allows the formation of a stable domain-swapped dimer. In LmTXNPx, crystallized in reducing condition, both the locally unfolded (LU and fully folded (FF conformations, typical of the oxidized and reduced protein respectively, are populated. The structural analysis presented here points to a high flexibility of the loop that includes the peroxidatic cysteine which facilitates Cys52 to form an inter-chain disulfide bond with the resolving cysteine (Cys173, thereby preventing over-oxidation which would inactivate the enzyme. Analysis of the electrostatic surface potentials of both LmTXN and LmTXNPx unveils the structural elements at the basis of functionally relevant interaction between the two proteins. Finally, the structural analysis of TXNPx allows us to identify the position of the epitopes that make the protein antigenic and therefore potentially suitable

  10. Complex-disease networks of trait-associated single-nucleotide polymorphisms (SNPs) unveiled by information theory

    Science.gov (United States)

    Li, Haiquan; Lee, Younghee; Chen, James L; Rebman, Ellen; Li, Jianrong

    2012-01-01

    Objective Thousands of complex-disease single-nucleotide polymorphisms (SNPs) have been discovered in genome-wide association studies (GWAS). However, these intragenic SNPs have not been collectively mined to unveil the genetic architecture between complex clinical traits. The authors hypothesize that biological annotations of host genes of trait-associated SNPs may reveal the biomolecular modularity across complex-disease traits and offer insights for drug repositioning. Methods Trait-to-polymorphism (SNPs) associations confirmed in GWAS were used. A novel method to quantify trait–trait similarity anchored in Gene Ontology annotations of human proteins and information theory was developed. The results were then validated with the shortest paths of physical protein interactions between biologically similar traits. Results A network was constructed consisting of 280 significant intertrait similarities among 177 disease traits, which covered 1438 well-validated disease-associated SNPs. Thirty-nine percent of intertrait connections were confirmed by curators, and the following additional studies demonstrated the validity of a proportion of the remainder. On a phenotypic trait level, higher Gene Ontology similarity between proteins correlated with smaller ‘shortest distance’ in protein interaction networks of complexly inherited diseases (Spearman p<2.2×10−16). Further, ‘cancer traits’ were similar to one another, as were ‘metabolic syndrome traits’ (Fisher's exact test p=0.001 and 3.5×10−7, respectively). Conclusion An imputed disease network by information-anchored functional similarity from GWAS trait-associated SNPs is reported. It is also demonstrated that small shortest paths of protein interactions correlate with complex-disease function. Taken together, these findings provide the framework for investigating drug targets with unbiased functional biomolecular networks rather than worn-out single-gene and subjective canonical pathway approaches

  11. Effect of Nitrogen on Carbon Metabolism of Tobacco%不同供氮水平对烤烟叶片碳代谢的影响

    Institute of Scientific and Technical Information of China (English)

    张欢欢; 梁晓红; 熊德中

    2013-01-01

    At varied nitrogen levels ,a pot experiment was conducted to study the effect of nitrogen on the contents of chlorophyll ,invertase ,soluble sugar ,reducing sugar and starch ,as well as the quality of the tobacco leaves for flue-curing .The results showed that the invertase and amylase activities at the mid- and late-tobacco growth stages increased with appropriate application of potassium , which also benefited the transition of nitrogen to carbon metabolism at the right time period .After 30 and 55 ds of transplantation , the contents of total soluble sugar , reducing sugar and starch in the tobacco leaves decreased with increasing potassium fertilization at the early stage of tobacco .They increased with the increased application of potassium at the mid- and late-stages after 75 ds of the transplanting ,suggesting the application of potassium would be better for carbon accumulation at the late ,not the early stage of tobacco growth .When nitrogen supply was insufficient , the growth of tobacco was slow , the photosynthetic pigments low ,and the leaf color yellowish .When excess nitrogen was present ,the tobacco grew vigorously and delayed the normal leaf-falling .Under the experimental conditions ,the optimal levels of nitrogen for the paddy field soil (available nitrogen 184.31 mg ・ kg - 1 ) ,the yellow mud field soil (available nitrogen 127.27 mg ・ kg - 1 ) , and the tidal field soil (available nitrogen 105.45 mg ・ kg - 1 ) were 0.90 g ・ pot - 1 ,1.35 - 1.90 g ・ pot - 1 ,and 1.90 g ・ pot - 1 ,respectively ,which resulted in the highest yield and the most balanced and desirable quality for the tobacco .%采用盆栽试验,研究不同供氮水平对烤烟叶片中光合色素含量及蔗糖转化酶、可溶性糖、还原糖、淀粉含量和烟叶干物质累积的影响。结果表明:施用适量氮肥提高烤烟中后期烟叶蔗糖转化酶和淀粉酶活性,促进烟叶碳代谢。在烤烟移栽后30、55 d ,烟叶可溶性糖、

  12. Influence of net ecosystem metabolism in transferring riverine organic carbon to atmospheric CO2 in a tropical coastal lagoon (Chilka Lake, India)

    Digital Repository Service at National Institute of Oceanography (India)

    Gupta, G.V.M.; Sarma, V.V.S.S.; Robin, R.S.; Raman, A.V.; JaiKumar, M.; Rakesh, M.; Subramanian, B.R.

    was studied twice during May 2005 (premonsoon) and August 2005 (monsoon). It exchanges waters with the sea (Bay of Bengal) and several rivers open into the lake. The lake showed contrasting levels of dissolved inorganic carbon (DIC) and organic carbon (DOC...

  13. Formate metabolism in fetal and neonatal sheep

    OpenAIRE

    2015-01-01

    By virtue of its role in nucleotide synthesis, as well as the provision of methyl groups for vital methylation reactions, one-carbon metabolism plays a crucial role in growth and development. Formate, a critical albeit neglected component of one-carbon metabolism, occurs extracellularly and may provide insights into cellular events. We examined formate metabolism in chronically cannulated fetal sheep (gestation days 119–121, equivalent to mid-third trimester in humans) and in their mothers as...

  14. Nodule-enhanced expression of a sucrose phosphate synthase gene member (MsSPSA) has a role in carbon and nitrogen metabolism in the nodules of alfalfa (Medicago sativa L.).

    Science.gov (United States)

    Aleman, Lorenzo; Ortega, Jose Luis; Martinez-Grimes, Martha; Seger, Mark; Holguin, Francisco Omar; Uribe, Diana J; Garcia-Ibilcieta, David; Sengupta-Gopalan, Champa

    2010-01-01

    Sucrose phosphate synthase (SPS) catalyzes the first step in the synthesis of sucrose in photosynthetic tissues. We characterized the expression of three different isoforms of SPS belonging to two different SPS gene families in alfalfa (Medicago sativa L.), a previously identified SPS (MsSPSA) and two novel isoforms belonging to class B (MsSPSB and MsSPSB3). While MsSPSA showed nodule-enhanced expression, both MsSPSB genes exhibited leaf-enhanced expression. Alfalfa leaf and nodule SPS enzymes showed differences in chromatographic and electrophoretic migration and differences in V (max) and allosteric regulation. The root nodules in legume plants are a strong sink for photosynthates with its need for ATP, reducing power and carbon skeletons for dinitrogen fixation and ammonia assimilation. The expression of genes encoding SPS and other key enzymes in sucrose metabolism, sucrose phosphate phosphatase and sucrose synthase, was analyzed in the leaves and nodules of plants inoculated with Sinorhizobium meliloti. Based on the expression pattern of these genes, the properties of the SPS isoforms and the concentration of starch and soluble sugars in nodules induced by a wild type and a nitrogen fixation deficient strain, we propose that SPS has an important role in the control of carbon flux into different metabolic pathways in the symbiotic nodules.

  15. Effect of Manganese on the Carbon-nitrogen Metabolism of Medicago sativa Seedlings%锰胁迫对紫花苜蓿幼苗碳、氮代谢的影响

    Institute of Scientific and Technical Information of China (English)

    吴旭红; 张超; 马云祥; 何旻琦

    2016-01-01

    采用沙培法,以常规锰浓度为对照,研究不同锰营养状况对苜蓿早期光合碳同化与氮代谢的影响,结果表明:锰素缺乏(T1处理:5%CK;T2处理:20%CK),苜蓿叶片1,5-二磷酸核酮糖羧化酶积累量减少,光合色素含量下降,硝酸还原酶和谷氨酰胺合成酶活性降低。锰重度过量(T4处理:20倍 CK),苜蓿幼苗碳氮代谢运转受阻,可溶性蛋白、氨基酸总量和羧肽酶活性大幅下降。5倍常规浓度的中度锰过量处理,则促进了碳素同化、氨基酸的合成和可溶性蛋白的积累。综合分析表明,中度锰过量有助于苜蓿苗期的光合碳同化和蛋白质代谢。%Alfalfa was cultivated with sand culture method,and general Mn concentration was used as control,a series of experiments were designed to explore the function and effect of Manganese on the car-bon-nitrogen metabolism of Medicago sativa seedlings.The results showed that when the manganese was deficient(T1:5%CK;T2:20%CK),the accumulation amount of Rubisco reduced,the content of photo-synthetic pigment decreased,and the activities of NR and GS declined.On the other hand,when the Man-ganese was overfeeding seriously(T4:20 times of control),the carbon-nitrogen metabolism would be in-hibited,the soluble protein,total amino acids and the activity of Rubisco decreased greatly.However,un-der light stress which were 5 times of general Mn concentration,it would be benefit to the Medicago sati-va seedlings on the protein metabolism and photosynthesis.In conclusion,a proper overfeeding of Manga-nese would promote the carbon-nitrogen metabolism and protein metabolism in Medicago sativa seed-lings.

  16. Emotions unveiled

    OpenAIRE

    Knaus, Kordula

    2015-01-01

    Članek preučuje romantične komedije in romance, katerih zgodba vključuje prizore, v katerih vodilni igralci obiščejo operno predstavo. Analiza obiskov opernih predstav v filmih Moonstruck (1987), Pretty Woman (1990) in Little Women (1994) bo odgovorila na vprašanje o smislu in funkciji opere v zvrsti romance in postavila te ugotovitve v širše razprave o pomenu zvočnega filmskega traku za romantične komedije in za konvencije zadevnega žanra.

  17. Data analysis unveils a new stylized fact in foreign currency markets

    Science.gov (United States)

    Nacher, J. C.; Ochiai, T.

    2012-09-01

    The search for stylized facts (i.e., simplified empirical facts) is of capital importance in econophysics because the stylized facts constitute the experimental empirical body on which theories and models should be tested. At the moment they are too few and this is an important limitation to the progress in the field. In this work, we unveil a new stylized fact, which consists of resistance effect and breaking-acceleration effect that implicitly requires a long memory feature in price movement. By analyzing a vast amount of historical data, we demonstrate that the financial market tends to exceed a past (historical) extreme price less often than expected by a classic short-memory model (e.g., Black-Scholes model). We call it resistance effect. However, when the market does it, we predict that the average volatility at that time point will be much higher (accelerates more). It means, in average, volatility accelerates more when the price breaks the highest (lowest) value. We refer to this as breaking-acceleration effect. These observed empirical facts are actually an effect which may arise from technical trading and psychological effects. Taken together, these results indicate that, beyond the predictive capability of this unveiled stylized fact, traditional short-memory models do not faithfully capture the market dynamics.

  18. Fructose Alters Intermediary Metabolism of Glucose in Human Adipocytes and Diverts Glucose to Serine Oxidation in the One–Carbon Cycle Energy Producing Pathway

    OpenAIRE

    Vijayalakshmi Varma; Boros, László G; Nolen, Greg T.; Ching-Wei Chang; Martin Wabitsch; Beger, Richard D.; Jim Kaput

    2015-01-01

    Increased consumption of sugar and fructose as sweeteners has resulted in the utilization of fructose as an alternative metabolic fuel that may compete with glucose and alter its metabolism. To explore this, human Simpson-Golabi-Behmel Syndrome (SGBS) preadipocytes were differentiated to adipocytes in the presence of 0, 1, 2.5, 5 or 10 mM of fructose added to a medium containing 5 mM of glucose representing the normal blood glucose concentration. Targeted tracer [1,2-13C2]-d-glucose fate asso...

  19. Metabolic Syndrome

    Science.gov (United States)

    Metabolic syndrome is a group of conditions that put you at risk for heart disease and diabetes. These ... doctors agree on the definition or cause of metabolic syndrome. The cause might be insulin resistance. Insulin is ...

  20. Metabolic Panel

    Science.gov (United States)

    ... basic metabolic panel (BMP) and comprehensive metabolic panel (CMP). The BMP checks your blood sugar, calcium, and ... as creatinine to check your kidney function. The CMP includes all of those tests, as well as ...

  1. Metabolic Disorders

    Science.gov (United States)

    ... as your liver, muscles, and body fat. A metabolic disorder occurs when abnormal chemical reactions in your body ... that produce the energy. You can develop a metabolic disorder when some organs, such as your liver or ...

  2. Flux-P: Automating Metabolic Flux Analysis

    OpenAIRE

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

    2012-01-01

    Quantitative knowledge of intracellular fluxes in metabolic networks is invaluable for inferring metabolic system behavior and the design principles of biological systems. However, intracellular reaction rates can not often be calculated directly but have to be estimated; for instance, via 13C-based metabolic flux analysis, a model-based interpretation of stable carbon isotope patterns in intermediates of metabolism. Existing software such as FiatFlux, OpenFLUX or 13CFLUX supports experts in ...

  3. Characterization of the Pivotal Carbon Metabolism of Streptococcus suis Serotype 2 under ex Vivo and Chemically Defined in Vitro Conditions by Isotopologue Profiling*

    Science.gov (United States)

    Willenborg, Jörg; Huber, Claudia; Koczula, Anna; Lange, Birgit; Eisenreich, Wolfgang; Valentin-Weigand, Peter; Goethe, Ralph

    2015-01-01

    Streptococcus suis is a neglected zoonotic pathogen that has to adapt to the nutritional requirements in the different host niches encountered during infection and establishment of invasive diseases. To dissect the central metabolic activity of S. suis under different conditions of nutrient availability, we performed labeling experiments starting from [13C]glucose specimens and analyzed the resulting isotopologue patterns in amino acids of S. suis grown under in vitro and ex vivo conditions. In combination with classical growth experiments, we found that S. suis is auxotrophic for Arg, Gln/Glu, His, Leu, and Trp in chemically defined medium. De novo biosynthesis was shown for Ala, Asp, Ser, and Thr at high rates and for Gly, Lys, Phe, Tyr, and Val at moderate or low rates, respectively. Glucose degradation occurred mainly by glycolysis and to a minor extent by the pentose phosphate pathway. Furthermore, the exclusive formation of oxaloacetate by phosphoenolpyruvate (PEP) carboxylation became evident from the patterns in de novo synthesized amino acids. Labeling experiments with S. suis grown ex vivo in blood or cerebrospinal fluid reflected the metabolic adaptation to these host niches with different nutrient availability; however, similar key metabolic activities were identified under these conditions. This points at the robustness of the core metabolic pathways in S. suis during the infection process. The crucial role of PEP carboxylation for growth of S. suis in the host was supported by experiments with a PEP carboxylase-deficient mutant strain in blood and cerebrospinal fluid. PMID:25575595

  4. Characterization of the pivotal carbon metabolism of Streptococcus suis serotype 2 under ex vivo and chemically defined in vitro conditions by isotopologue profiling.

    Science.gov (United States)

    Willenborg, Jörg; Huber, Claudia; Koczula, Anna; Lange, Birgit; Eisenreich, Wolfgang; Valentin-Weigand, Peter; Goethe, Ralph

    2015-02-27

    Streptococcus suis is a neglected zoonotic pathogen that has to adapt to the nutritional requirements in the different host niches encountered during infection and establishment of invasive diseases. To dissect the central metabolic activity of S. suis under different conditions of nutrient availability, we performed labeling experiments starting from [(13)C]glucose specimens and analyzed the resulting isotopologue patterns in amino acids of S. suis grown under in vitro and ex vivo conditions. In combination with classical growth experiments, we found that S. suis is auxotrophic for Arg, Gln/Glu, His, Leu, and Trp in chemically defined medium. De novo biosynthesis was shown for Ala, Asp, Ser, and Thr at high rates and for Gly, Lys, Phe, Tyr, and Val at moderate or low rates, respectively. Glucose degradation occurred mainly by glycolysis and to a minor extent by the pentose phosphate pathway. Furthermore, the exclusive formation of oxaloacetate by phosphoenolpyruvate (PEP) carboxylation became evident from the patterns in de novo synthesized amino acids. Labeling experiments with S. suis grown ex vivo in blood or cerebrospinal fluid reflected the metabolic adaptation to these host niches with different nutrient availability; however, similar key metabolic activities were identified under these conditions. This points at the robustness of the core metabolic pathways in S. suis during the infection process. The crucial role of PEP carboxylation for growth of S. suis in the host was supported by experiments with a PEP carboxylase-deficient mutant strain in blood and cerebrospinal fluid.

  5. [Metabolic syndrome].

    Science.gov (United States)

    Mitsuishi, Masanori; Miyashita, Kazutoshi; Itoh, Hiroshi

    2009-02-01

    Metabolic syndrome, which is consisted of hypertension, dyslipidemia and impaired glucose tolerance, is one of the most significant lifestyle-related disorders that lead to cardiovascular diseases. Among many upstream factors that are related to metabolic syndrome, obesity, especially visceral obesity, plays an essential role in its pathogenesis. In recent studies, possible mechanisms which connect obesity to metabolic syndrome have been elucidated, such as inflammation, abnormal secretion of adipokines and mitochondrial dysfunction. In this review, we focus on the relationship between obesity and metabolic syndrome; and illustrate how visceral obesity contributes to, and how the treatments for obesity act on metabolic syndrome.

  6. Metabolic pathway visualization in living yeast by DNP-NMR.

    Science.gov (United States)

    Meier, Sebastian; Karlsson, Magnus; Jensen, Pernille R; Lerche, Mathilde H; Duus, Jens Ø

    2011-10-01

    Central carbon metabolism of living Saccharomyces cerevisiae is visualized by DNP-NMR. Experiments are conducted as real time assays that detect metabolic bottlenecks, pathway use, reversibility of reactions and reaction mechanisms in vivo with subsecond time resolution.

  7. Advances in Carbon Metabolism in Mycoplasma Pneumoniae%肺炎支原体碳源代谢的研究进展

    Institute of Scientific and Technical Information of China (English)

    曹阳; 张树明

    2014-01-01

    Mycoplasma pneumoniae as small genome, its metabolic network includes 129 enzyme catalytic completed 189, so its synthesis and catabolism of ability is poor, mainly from the outside world to absorb nutrients. They need to grow in in vitro culture medium contains 19 kinds of essential nutrients.Through the recent years, the research results show that MP metabolic processes, met-abolic processes play a key role in a variety of functions and the role of the enzyme metabolites.%肺炎支原体(M. pneumonia,Mp)由于基因组小,其代谢网络包括了由129个酶催化完成的189个反应,因此其合成和分解代谢的能力差,生长所需的营养成分主要从外界摄取,在体外培养时培养基中包含了19种基本营养物质。本文通过近年来,对MP代谢过程的研究结果表明,代谢过程中起到关键作用的酶具有多种功能以及代谢产物的作用。

  8. Diversity of carbon source metabolism of microbial community in farmland soils in an arsenic mining area%砷矿区农田土壤微生物群落碳源代谢多样性

    Institute of Scientific and Technical Information of China (English)

    华建峰; 林先贵; 蒋倩; 张华勇; 陈茜; 殷云龙

    2013-01-01

    By using Biolog technique, this paper studied the diversity of carbon source metabolism of microbial community in three farmland soils with different levels of arsenic ( As) in an As mining area, and the relationships between the diversity of the carbon source metabolism and the main soil chemical properties. The total N (TN) , total P (TP) , total K (TK) , organic matter (OM) , total Cu, and total Zn contents in the three soils were in the order of medium level As > high level As > low level As. The average well color development (AWCD), Shannon index (H'), Simpson index (D) , and Mclntosh index (U) of soil microbes were significantly higher in the soils with medium and high levels As than in the soil with low level As. The principal component analysis and the fingerprints of the physiological carbon metabolism of the microbial community in the three soils demonstrated that the microbes in the soils with medium and high levels As had a significantly higher (P<0.05) utilization rate in carbohydrates and amino acids than the microbes in the soil with low level As. The correlation analysis showed that the AWCD, H', D, and U were significantly positively correlated with the contents of soil TN, TP, OM, total As, total Cu, total Pb, and total Zn (P<0.05) , and the canonical correspondence analysis revealed that soil TP, OM, total Pb, total Zn, TN, and pH rather than soil total As were the main soil chemical properties affecting the carbon source metabolism of soil microbial community. It was considered that soil nutrients could be the main factors affecting the community structure and functions of soil microbes in long-term contaminated soils.%采用Biolog方法研究了砷(As)矿区农田土壤微生物碳源利用多样性及其与土壤化学性质的关系.结果表明:3种土壤的N、P、K、有机质(OM)、Cu和Zn全量依次为中As>高As>低As土壤.中As和高As土壤微生物平均吸光度以及多样性指数(H'、D、U)显著高于低As土壤.主成

  9. Unveiling the Proton Spin Decomposition at a Future Electron-Ion Collider

    CERN Document Server

    Aschenauer, Elke C; Stratmann, M

    2015-01-01

    We present a detailed assessment of how well a future Electron-Ion Collider could constrain helicity parton distributions in the nucleon and, therefore, unveil the role of the intrinsic spin of quarks and gluons in the proton's spin budget. Any remaining deficit in this decomposition will provide the best indirect constraint on the contribution due to the total orbital angular momenta of quarks and gluons. Specifically, all our studies are performed in the context of global QCD analyses based on realistic pseudo-data and in the light of the most recent data obtained from polarized proton-proton collisions at BNL-RHIC that have provided evidence for a significant gluon polarization in the accessible, albeit limited range of momentum fractions. We also present projections on what can be achieved on the gluon's helicity distribution by the end of BNL-RHIC operations. All estimates of current and projected uncertainties are performed with the robust Lagrange multiplier technique.

  10. Intrinsic flexibility of the zeolitic imidazolate framework ZIF-7 unveiled by CO₂ adsorption and Hg intrusion.

    Science.gov (United States)

    Pera-Titus, Marc

    2014-06-06

    ZIF-7, built as an assembly of Zn(II) centers and benzimidazolate ligands, shows prominent S-shaped isotherms upon CO2 adsorption that can be attributed to sorbate-induced gate-opening phenomena involving a narrow-to-large pore phase transition. This peculiar sorption pattern can be captured via the formulation of thermodynamic isotherms, providing a direct enthalpic and entropic view of the gate-opening process. Relying on such an approach, an energy barrier with preferential enthalpic nature for CO2 adsorption/desorption in the gate-opening region could be unveiled. Moreover, the elastic energy involved during the gate-opening process was revisited to 1.4-2.8 kJ mol(-1) of solid in the temperature range 273-323 K, matching the value measured by isostatic compression of a ZIF-7_lp sample filled with DMF and showing a dominant entropic contribution.

  11. Unveiling the dominant gas heating mechanism in local LIRGs and ULIRGs

    CERN Document Server

    Perez-Torres, Miguel A; Romero-Canizales, Cristina; Colina, Luis; Bondi, Marco; Giroletti, Marcello; Torrelles, Jose Maria; Polatidis, Antonis

    2008-01-01

    We show preliminary results from a sample of Luminous and Ultra-Luminous Infrared Galaxies (LIRGs and ULIRGs, respectively) in the local universe, obtained from observations using the Very Large Array (VLA), the Multi-Element Radio Link Interferometer Network (MERLIN), and the European VLBI Network (EVN). The main goal of our high-resolution, high-sensitivity radio observations is to unveil the dominant gas heating mechanism in the central regions of local (U)LIRGs. The main tracer of recent star-formation in (U)LIRGs is the explosion of core-collapse supernovae (CCSNe), which are the endproducts of the explosion of massive stars and yield bright radio events. Therefore, our observations will not only allow us to answer the question of the dominant heating mechanism in (U)LIRGs, but will yield also the CCSN rate and the star-formation rate (SFR) for the galaxies of the sample.

  12. Unveiling Magnetic Dipole Radiation in Phase-Reversal Leaky-Wave Antennas

    CERN Document Server

    Gupta, Shulabh; Caloz, Christophe

    2014-01-01

    The radiation principle of travelling-wave type phase-reversal antennas is explained in details, unveiling the presence of magnetic-dipole radiation in addition to well-known electric dipole radiation. It is point out that such magnetic dipole radiation is specific to the case of traveling-wave phase-reversal antennas whereas only electric-dipole radiation exists in resonant-type phase-reversal antennas. It is shown that a phase-reversal travelling-wave antenna alternately operates as an array of magnetic dipoles and an array of electric-dipoles during a time-harmonic period. This radiation mechanism is confirmed through both full-wave and experimental results.

  13. Poly(urethane–carbonate)s from Carbon Dioxide

    KAUST Repository

    Chen, Zuliang

    2017-03-09

    A one-pot, two-step protocol for the direct synthesis of polyurethanes containing few carbonate linkages through polycondensation of diamines, dihalides, and CO2 in the presence of Cs2CO3 and tetrabutylammonium bromide is described. The conditions were optimized by studying the polycondensation of CO2 with 1,6-hexanediamine and 1,4-dibromobutane as model monomers. Then, various diamines and dihalides were tested under optimal conditions. Miscellaneous samples of such carbonate-containing polyurethanes exhibiting molar masses from 6000 to 22 000 g/mol (GPC) and yields higher than 85% were obtained. The thermal properties of such polyurethanes were unveiled by differential scanning calorimetry (DSC) and thermal gravimetric analysis (TGA): they were found very similar to those of traditional polyurethanes obtained by diisocyanates + diols polycondensation.

  14. Nucleotide Metabolism

    DEFF Research Database (Denmark)

    Martinussen, Jan; Willemoës, M.; Kilstrup, Mogens

    2011-01-01

    Metabolic pathways are connected through their utilization of nucleotides as supplier of energy, allosteric effectors, and their role in activation of intermediates. Therefore, any attempt to exploit a given living organism in a biotechnological process will have an impact on nucleotide metabolism....... The aim of this article is to provide knowledge of nucleotide metabolism and its regulation to facilitate interpretation of data arising from genetics, proteomics, and transcriptomics in connection with biotechnological processes and beyond....

  15. Replicating DNA by cell factories: roles of central carbon metabolism and transcription in the control of DNA replication in microbes, and implications for understanding this process in human cells.

    Science.gov (United States)

    Barańska, Sylwia; Glinkowska, Monika; Herman-Antosiewicz, Anna; Maciąg-Dorszyńska, Monika; Nowicki, Dariusz; Szalewska-Pałasz, Agnieszka; Węgrzyn, Alicja; Węgrzyn, Grzegorz

    2013-05-29

    Precise regulation of DNA replication is necessary to ensure the inheritance of genetic features by daughter cells after each cell division. Therefore, determining how the regulatory processes operate to control DNA replication is crucial to our understanding and application to biotechnological processes. Contrary to early concepts of DNA replication, it appears that this process is operated by large, stationary nucleoprotein complexes, called replication factories, rather than by single enzymes trafficking along template molecules. Recent discoveries indicated that in bacterial cells two processes, central carbon metabolism (CCM) and transcription, significantly and specifically influence the control of DNA replication of various replicons. The impact of these discoveries on our understanding of the regulation of DNA synthesis is discussed in this review. It appears that CCM may influence DNA replication by either action of specific metabolites or moonlighting activities of some enzymes involved in this metabolic pathway. The role of transcription in the control of DNA replication may arise from either topological changes in nucleic acids which accompany RNA synthesis or direct interactions between replication and transcription machineries. Due to intriguing similarities between some prokaryotic and eukaryotic regulatory systems, possible implications of studies on regulation of microbial DNA replication on understanding such a process occurring in human cells are discussed.

  16. Algae metabolism and organic carbon in sediments determining arsenic mobilisation in ground- and surface water. A field study in Doñana National Park, Spain.

    Science.gov (United States)

    Kohfahl, Claus; Navarro, Daniel Sánchez-Rodas; Mendoza, Jorge Armando; Vadillo, Iñaki; Giménez-Forcada, Elena

    2016-02-15

    A study has been performed to explore the origin, spatiotemporal behaviour and mobilisation mechanism of the elevated arsenic (As) concentrations found in ground water and drinking ponds of the Doñana National Park, Southern Spain. At a larger scale, 13 piezometers and surface water samples of about 50 artificial drinking ponds and freshwater lagoons throughout the National Park were collected and analysed for major ions, metals and trace elements. At a smaller scale, 5 locations were equipped with piezometers and groundwater was sampled up to 4 times for ambient parameters, major ions, metals, trace elements and iron (Fe) speciation. As was analysed for inorganic and organic speciation. Undisturbed sediment samples were analysed for physical parameters, mineralogy, geochemistry as well as As species. Sediment analyses yielded total As between 0.1 and 18 mg/kg and are not correlated with As concentration in water. Results of the surface- and groundwater sampling revealed elevated concentration of As up to 302 μg/L within a restricted area of the National Park. Results of groundwater sampling reveals strong correlation of As with Fe(2+) pointing to As mobilisation due to reductive dissolution of hydroferric oxides (HFO) in areas of locally elevated amounts of organic matter within the sediments. High As concentrations in surface water ponds are correlated with elevated alkalinity and pH attributed to algae metabolism, leading to As desorption from HFO. The algae metabolism is responsible for the presence of methylated arsenic species in surface water, in contrast to ground water in which only inorganic As species was found. Temporal variations in surface water and groundwater are also related to changes in pH and alkalinity as a result of enhanced algae metabolism in surface water or related to changes in the redox level in the case of groundwater.

  17. Kinetic and metabolic isotope effects in coral skeletal carbon isotopes: A re-evaluation using experimental coral bleaching as a case study

    Science.gov (United States)

    Schoepf, Verena; Levas, Stephen J.; Rodrigues, Lisa J.; McBride, Michael O.; Aschaffenburg, Matthew D.; Matsui, Yohei; Warner, Mark E.; Hughes, Adam D.; Grottoli, Andréa G.

    2014-12-01

    Coral skeletal δ13C can be a paleo-climate proxy for light levels (i.e., cloud cover and seasonality) and for photosynthesis to respiration (P/R) ratios. The usefulness of coral δ13C as a proxy depends on metabolic isotope effects (related to changes in photosynthesis) being the dominant influence on skeletal δ13C. However, it is also influenced by kinetic isotope effects (related to calcification rate) which can overpower metabolic isotope effects and thus compromise the use of coral skeletal δ13C as a proxy. Heikoop et al. (2000) proposed a simple data correction to remove kinetic isotope effects from coral skeletal δ13C, as well as an equation to calculate P/R ratios from coral isotopes. However, despite having been used by other researchers, the data correction has never been directly tested, and isotope-based P/R ratios have never been compared to P/R ratios measured using respirometry. Experimental coral bleaching represents a unique environmental scenario to test this because bleaching produces large physiological responses that influence both metabolic and kinetic isotope effects in corals. Here, we tested the δ13C correction and the P/R calculation using three Pacific and three Caribbean coral species from controlled temperature-induced bleaching experiments where both the stable isotopes and the physiological variables that cause isotopic fractionation (i.e., photosynthesis, respiration, and calcification) were simultaneously measured. We show for the first time that the data correction proposed by Heikoop et al. (2000) does not effectively remove kinetic effects in the coral species studied here, and did not improve the metabolic signal of bleached and non-bleached corals. In addition, isotope-based P/R ratios were in poor agreement with measured P/R ratios, even when the data correction was applied. This suggests that additional factors influence δ13C and δ18O, which are not accounted for by the data correction. We therefore recommend that the

  18. The effects of folate intake on DNA and single-carbon pathway metabolism in the fruit fly Drosophila melanogaster compared to mammals.

    Science.gov (United States)

    Blatch, Sydella A; Stabler, Sally P; Harrison, Jon F

    2015-11-01

    Mechanisms of vitamin function in non-mammals are poorly understood, despite being essential for development. Folate and cobalamin are B-vitamin cofactors with overlapping roles in transferring various single-carbon units. In mammals, one or both is needed for nucleotide synthesis, DNA methylation, amino acid conversions and other reactions. However, there has been little investigation of the response to folate or cobalamin in insects. Here, we manipulated folate intake and potentially cobalamin levels in the fruit fly Drosophila melanogaster with chemically-defined diets, an antibiotic to reduce bacterially-derived vitamins, and the folate-interfering pharmaceutical methotrexate, to see if single-carbon metabolites and DNA synthesis rates would be affected. We found that similar to mammals with low folate intake, fruit fly larvae had significantly slower growth and DNA synthesis rates. But changes to single carbon-metabolites did not mirror that of mammals with abnormal folate or given MTX. Five of the nine metabolites measured were not significantly affected (methionine, serine, glycine, methylglycine, and dimethylglycine) and three (cystathionine, methylgycine, and methylmalonic acid) were only decreased in larvae consuming methotrexate. Metabolites expected to be elevated if flies used cobalamin from microbial symbionts were not affected by dietary sulfaquinoxaline. Our data support the role of folate in nucleotide synthesis in D. melanogaster and that microbial symbionts provide functioning folates. We could not confirm how folate intake affects single carbon pathway metabolites, nor whether Drososphila use microbially-derived cobalamin. Further work should explore which cofactors are used in fruit flies in these important and potentially novel pathways.

  19. Carbonylation and Loss-of-Function Analyses of SBPase Reveal Its Metabolic Interface Role in Oxidative Stress, Carbon Assimilation, and Multiple Aspects of Growth and Development in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    Xun-Liang Liu; Hai-Dong Yu; Yuan Guan; Ji-Kai Li; Fang-Qing Guo

    2012-01-01

    Sedoheptulose-1,7-bisphosphatase (SBPase) is a Calvin cycle enzyme and functions in photosynthetic carbon fixation.We found that SBPase was rapidly carbonylated in response to methyl viologen (MV) treatments in detached leaves of Arabidopsis plants.In vitro activity analysis of the purified recombinant SBPase showed that SBPase was carbonylated by hydroxyl radicals,which led to enzyme inactivation in an H2O2 dose-dependent manner.To determine the conformity with carbonylation-caused loss in enzymatic activity in response to stresses,we isolated a loss-of-function mutant sbp,which is deficient in SBPase-dependent carbon assimilation and starch biosynthesis,sbp mutant exhibited a severe growth retardation phenotype,especially for the developmental defects in leaves and flowers where SBPASE is highly expressed.The mutation of SBPASE caused growth retardation mainly through inhibition of cell division and expansion,which can be partially rescued by exogenous application of sucrose.Our findings demonstrate that ROS-induced oxidative damage to SBPase affects growth,development,and chloroplast biogenesis in Arabidopsis through inhibiting carbon assimilation efficiency.The data presented here provide a case study that such inactivation of SBPase caused by carbonyl modification may be a kind of adaptation for plants to restrict the operation of the reductive pentose phosphate pathway under stress conditions.

  20. Methionine and Choline Supply during the Periparturient Period Alter Plasma Amino Acid and One-Carbon Metabolism Profiles to Various Extents: Potential Role in Hepatic Metabolism and Antioxidant Status

    Directory of Open Access Journals (Sweden)

    Zheng Zhou

    2016-12-01

    Full Text Available The objective of this study was to profile plasma amino acids (AA and derivatives of their metabolism during the periparturient period in response to supplemental rumen-protected methionine (MET or rumen-protected choline (CHOL. Forty cows were fed from −21 through 30 days around parturition in a 2 × 2 factorial design a diet containing MET or CHOL. MET supply led to greater circulating methionine and proportion of methionine in the essential AA pool, total AA, and total sulfur-containing compounds. Lysine in total AA also was greater in these cows, indicating a better overall AA profile. Sulfur-containing compounds (cystathionine, cystine, homocystine, and taurine were greater in MET-fed cows, indicating an enriched sulfur-containing compound pool due to enhanced transsulfuration activity. Circulating essential AA and total AA concentrations were greater in cows supplied MET due to greater lysine, arginine, tryptophan, threonine, proline, asparagine, alanine, and citrulline. In contrast, CHOL supply had no effect on essential AA or total AA, and only tryptophan and cystine were greater. Plasma 3-methylhistidine concentration was lower in response to CHOL supply, suggesting less tissue protein mobilization in these cows. Overall, the data revealed that enhanced periparturient supply of MET has positive effects on plasma AA profiles and overall antioxidant status.

  1. 不同酸化条件对菜豆幼苗碳氮代谢酶系活性的影响%Effects of Acid on Enzyme Activity of Carbon-Nitrogen Metabolic in Kidney Bean Seedling

    Institute of Scientific and Technical Information of China (English)

    孙海燕; 郭伟

    2013-01-01

    Four different pH (pH 7, 6, 5, 4) nutrient solutions were applied to simulate the environment of germination and growth for kidney bean (Phaseolus vulgari L.). Seed germination, seedling growth characteristics, antioxidase enzyme activities of root and leaf and carbon-nitrogen metabolism enzyme activities and product levels of leaf were studied with decreasing pH in order to explain the response mechanism of carbon-nitrogen metabolism to acidification stress for kidney bean. The results showed that germinating potential and germination rate decreased, seedling and root dry weight reduced, and glutamine synthetase (GS) activity decreased and sucrose phosphate synthase (SPS) activity increased which increased the contents of sucrose, fructose and total soluble sugar, decreased the contents of superoxide anion free radical (O-·2) and malondialdehyde (MDA) of root, and increased the contents of O-·2 and MDA of leaf with decreasing pH. However, the change trend of antioxidase in root was the same as that in leaf, namely, the activity of superoxide dismutase (SOD) and catalase (CAT) increased, peroxidase (POD) activity decreased. Carbon metabolism was increased, however, nitrogen metabolism was inhibited under acidification stress, increased O-·2 content and reduced POD activity of leaf resulted in the increase of membrane lipid peroxidation.%采用4个不同pH值(pH 7,6,5,4)培养液模拟菜豆萌发和幼苗生长环境,研究了酸化条件下菜豆种子萌发和幼苗生长特性、幼苗根系和幼叶的抗氧化酶系活性以及叶片的碳氮代谢的主要酶系活性和产物水平,以期明确菜豆的碳氮代谢对酸化胁迫的响应机制.结果表明:随着pH的降低,菜豆发芽势和发芽率降低,幼苗和根系干物质量减少;谷氨酰胺合成酶活性降低,蔗糖磷酸合成酶活性增强,从而增加了蔗糖、果糖和总可溶性糖含量;根系的超氧阴离子自由基(O2-)和丙二醛(MDA)含量降低,叶片的O2-和MDA含

  2. Metabolic acidosis.

    Science.gov (United States)

    Lim, Salim

    2007-01-01

    Acute metabolic acidosis is frequently encountered in critically ill patients. Metabolic acidosis can occur as a result of either the accumulation of endogenous acids that consumes bicarbonate (high anion gap metabolic acidosis) or loss of bicarbonate from the gastrointestinal tract or the kidney (hyperchloremic or normal anion gap metabolic acidosis). The cause of high anion gap metabolic acidosis includes lactic acidosis, ketoacidosis, renal failure and intoxication with ethylene glycol, methanol, salicylate and less commonly with pyroglutamic acid (5-oxoproline), propylene glycole or djenkol bean (gjenkolism). The most common causes of hyperchloremic metabolic acidosis are gastrointestinal bicarbonate loss, renal tubular acidosis, drugs-induced hyperkalemia, early renal failure and administration of acids. The appropriate treatment of acute metabolic acidosis, in particular organic form of acidosis such as lactic acidosis, has been very controversial. The only effective treatment for organic acidosis is cessation of acid production via improvement of tissue oxygenation. Treatment of acute organic acidosis with sodium bicarbonate failed to reduce the morbidity and mortality despite improvement in acid-base parameters. Further studies are required to determine the optimal treatment strategies for acute metabolic acidosis.

  3. Bile acid signaling in metabolic disease and drug therapy.

    Science.gov (United States)

    Li, Tiangang; Chiang, John Y L

    2014-10-01

    Bile acids are the end products of cholesterol catabolism. Hepatic bile acid synthesis accounts for a major fraction of daily cholesterol turnover in humans. Biliary secretion of bile acids generates bile flow and facilitates hepatobiliary secretion of lipids, lipophilic metabolites, and xenobiotics. In the intestine, bile acids are essential for the absorption, transport, and metabolism of dietary fats and lipid-soluble vitamins. Extensive research in the last 2 decades has unveiled new functions of bile acids as signaling molecules and metabolic integrators. The bile acid-activated nuclear receptors farnesoid X receptor, pregnane X receptor, constitutive androstane receptor, vitamin D receptor, and G protein-coupled bile acid receptor play critical roles in the regulation of lipid, glucose, and energy metabolism, inflammation, and drug metabolism and detoxification. Bile acid synthesis exhibits a strong diurnal rhythm, which is entrained by fasting and refeeding as well as nutrient status and plays an important role for maintaining metabolic homeostasis. Recent research revealed an interaction of liver bile acids and gut microbiota in the regulation of liver metabolism. Circadian disturbance and altered gut microbiota contribute to the pathogenesis of liver diseases, inflammatory bowel diseases, nonalcoholic fatty liver disease, diabetes, and obesity. Bile acids and their derivatives are potential therapeutic agents for treating metabolic diseases of the liver.

  4. Determination of Krebs cycle metabolic carbon exchange in vivo and its use to estimate the individual contributions of gluconeogenesis and glycogenolysis to overall glucose output in man

    Energy Technology Data Exchange (ETDEWEB)

    Consoli, A.; Kennedy, F.; Miles, J.; Gerich, J.

    1987-11-01

    Current isotopic approaches underestimate gluconeogenesis in vivo because of Krebs cycle carbon exchange and the inability to measure intramitochondrial precursor specific activity. We therefore applied a new isotopic approach that theoretically overcomes these limitations and permits quantification of Krebs cycle carbon exchange and the individual contributions of gluconeogenesis and glycogenolysis to overall glucose outputex. (6-3H)Glucose was infused to measure overall glucose output; (2-14C)acetate was infused to trace phosphoenolpyruvate gluconeogenesis and to calculate Krebs cycle carbon exchange as proposed by Katz. Plasma (14C)3-OH-butyrate specific activity was used to estimate intramitochondrial acetyl coenzyme A (CoA) specific activity, and finally the ratio between plasma glucose 14C-specific activity and the calculated intracellular phosphoenolpyruvate 14C-specific activity was used to determine the relative contributions of gluconeogenesis and glycogenolysis to overall glucose output. Using this approach, acetyl CoA was found to enter the Krebs cycle at twice (postabsorptive subjects) and three times (2 1/2-d fasted subjects) the rate of pyruvate, respectively. Gluconeogenesis in postabsorptive subjects (3.36 +/- 0.20 mumol/kg per min) accounted for 28 +/- 2% of overall glucose output and increased twofold in subjects fasted for 2 1/2-d (P less than 0.01), accounting for greater than 97% of overall glucose output. Glycogenolysis in postabsorptive subjects averaged 8.96 +/- 0.40 mumol/kg per min and decreased to 0.34 +/- 0.08 mumol/kg per min (P less than 0.01) after a 2 1/2-d fast. Since these results agree well with previously reported values for gluconeogenesis and glycogenolysis based on determinations of splanchnic substrate balance and glycogen content of serial liver biopsies.

  5. Urban metabolism: a review of research methodologies.

    Science.gov (United States)

    Zhang, Yan

    2013-07-01

    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.

  6. Gerber Technology Unveils New YuniquePLMTM Brand Identity Expressing Commitment to Stimulate the Apparel, Footwear and Soft Goods PLM Landscape

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Gerber Technology, a business unit of Gerber Scientific, Inc. (NYSE:GRB) and a world leader in automated CAD/CAM and PLM solutions for the apparel and flexible materials industry, today unveiled its new PLM brand

  7. Metabolic encephalopathies.

    Science.gov (United States)

    Angel, Michael J; Young, G Bryan

    2011-11-01

    Kinnier Wilson coined the term metabolic encephalopathy to describe a clinical state of global cerebral dysfunction induced by systemic stress that can vary in clinical presentation from mild executive dysfunction to deep coma with decerebrate posturing; the causes are numerous. Some mechanisms by which cerebral dysfunction occurs in metabolic encephalopathies include focal or global cerebral edema, alterations in transmitter function, the accumulation of uncleared toxic metabolites, postcapillary venule vasogenic edema, and energy failure. This article focuses on common causes of metabolic encephalopathy, and reviews common causes, clinical presentations and, where relevant, management.

  8. 北京2008年奥运会吉祥物亮相%Beijing Unveils Mascots for 2008 Olympics

    Institute of Scientific and Technical Information of China (English)

    肖德林

    2005-01-01

    @@ After years of fierce lobbying2 and months of secrecy, Beijing unveiled five mascots for the 2008 Olympics on Nov. 11, opening a marketing blitz that is expected to reap record profits.3 In an elaborate, nationally televised gala4 at a Beijing sports arena5 to mark the 1,000-day countdown6 until the Games, senior Chinese leaders introduced the mascots-Beibei, Jingjing, Huanhuan, Yingying and Nini- which, put together, translates to "Beijing welcomes you!"

  9. Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks

    OpenAIRE

    2016-01-01

    Alternative splicing is regulated by multiple RNA-binding proteins and influences the expression of most eukaryotic genes. However, the role of this process in human disease, and particularly in cancer, is only starting to be unveiled. We systematically analyzed mutation, copy number, and gene expression patterns of 1348 RNA-binding protein (RBP) genes in 11 solid tumor types, together with alternative splicing changes in these tumors and the enrichment of binding motifs in the alternatively ...

  10. Metabolic neuropathies

    Science.gov (United States)

    ... as porphyria Severe infection throughout the body ( sepsis ) Thyroid disease Vitamin deficiencies (including vitamins B12 , B6 , E , and B1 ) Some metabolic disorders are passed down through families (inherited), while others ...

  11. Metabolic Syndrome

    Science.gov (United States)

    ... hypertension, hypertriglyceridemia, insulin resistance syndrome, low HDL cholesterol, Metabolic Syndrome, overweight, syndrome x, type 2 diabetes Family Health, Kids and Teens, Men, Women January 2005 Copyright © American Academy of Family PhysiciansThis ...

  12. Metabolic syndrome

    Directory of Open Access Journals (Sweden)

    Gogia Atul

    2006-02-01

    Full Text Available The Metabolic syndrome is a widely prevalent and multi-factorial disorder. The syndrome has been given several names, including- the metabolic syndrome, the insulin resistance syndrome, the plurimetabolic syndrome, and the deadly quartet. With the formulation of NCEP/ATP III guidelines, some uniformity and standardization has occurred in the definition of metabolic syndrome and has been very useful for epidemiological purposes. The mechanisms underlying the metabolic syndrome are not fully known; however resistance to insulin stimulated glucose uptake seems to modify biochemical responses in a way that predisposes to metabolic risk factors. The clinical relevance of the metabolic syndrome is related to its role in the development of cardiovascular disease. Management of the metabolic syndrome involves patient-education and intervention at various levels. Weight reduction is one of the main stays of treatment. In this article we comprehensively discuss this syndrome- the epidemiology, pathogenesis, clinical relevance and management. The need to do a comprehensive review of this particular syndrome has arisen in view of the ever increasing incidence of this entitiy. Soon, metabolic syndrome will overtake cigarette smoking as the number one risk factor for heart disease among the US population. Hardly any issue of any primary care medical journal can be opened without encountering an article on type 2 diabetes, dyslipidemia or hypertension. It is rare to see type 2 diabetes, dyslipidemia, obesity or hypertension in isolation. Insulin resistance and resulting hyperinsulinemia have been implicated in the development of glucose intolerance (and progression to type 2 diabetes, hypertriglyceridemia, hypertension, polycystic ovary yndrome, hypercoagulability and vascular inflammation, as well as the eventual development of atherosclerotic cardiovascular disease manifested as myocardial infarction, stroke and myriad end organ diseases. Conversely

  13. Lipid Metabolism

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    2008393 Effects of angiotensin Ⅱ type 1 receptor blocker on triglyceride metabolism in the liver: experiment with Zucker fatty rats. RAN Jianmin(冉建民), et al. Dept Endocrinol, Guangzhou Red Cross Hosp, 4th Hosp Med Coll, Jinan Univ, Guangzhou 510220. Natl Med J China 2008;88(22):1557-1561. Objective To investigate the effects of angiotensin receptor blocker (ARB) on triglyceride (TG) metabolism and mechanism thereof.

  14. The Role of Genetic Polymorphisms as Related to One-Carbon Metabolism, Vitamin B6, and Gene–Nutrient Interactions in Maintaining Genomic Stability and Cell Viability in Chinese Breast Cancer Patients

    Directory of Open Access Journals (Sweden)

    Xiayu Wu

    2016-06-01

    Full Text Available Folate-mediated one-carbon metabolism (FMOCM is linked to DNA synthesis, methylation, and cell proliferation. Vitamin B6 (B6 is a cofactor, and genetic polymorphisms of related key enzymes, such as serine hydroxymethyltransferase (SHMT, methionine synthase reductase (MTRR, and methionine synthase (MS, in FMOCM may govern the bioavailability of metabolites and play important roles in the maintenance of genomic stability and cell viability (GSACV. To evaluate the influences of B6, genetic polymorphisms of these enzymes, and gene–nutrient interactions on GSACV, we utilized the cytokinesis-block micronucleus assay (CBMN and PCR-restriction fragment length polymorphism (PCR-RFLP techniques in the lymphocytes from female breast cancer cases and controls. GSACV showed a significantly positive correlation with B6 concentration, and 48 nmol/L of B6 was the most suitable concentration for maintaining GSACV in vitro. The GSACV indexes showed significantly different sensitivity to B6 deficiency between cases and controls; the B6 effect on the GSACV variance contribution of each index was significantly higher than that of genetic polymorphisms and the sample state (tumor state. SHMT C1420T mutations may reduce breast cancer susceptibility, whereas MTRR A66G and MS A2756G mutations may increase breast cancer susceptibility. The role of SHMT, MS, and MTRR genotype polymorphisms in GSACV is reduced compared with that of B6. The results appear to suggest that the long-term lack of B6 under these conditions may increase genetic damage and cell injury and that individuals with various genotypes have different sensitivities to B6 deficiency. FMOCM metabolic enzyme gene polymorphism may be related to breast cancer susceptibility to a certain extent due to the effect of other factors such as stress, hormones, cancer therapies, psychological conditions, and diet. Adequate B6 intake may be good for maintaining genome health and preventing breast cancer.

  15. C/sub 4/ photosynthesis in Euphorbia degeneri and E. remyi: a comparison of photosynthetic carbon metabolism in leaves, callus cultures and regenerated plants

    Energy Technology Data Exchange (ETDEWEB)

    Ruzin, S.E.

    1984-04-01

    Based on analysis of /sup 14/CO/sub 2/ fixation kinetics and assays of enzymes related to C/sub 4/ metabolism (NAD-ME, NADP-ME, NAD-MDH, NADP-MDH, AST, ALT), leaves and regenerated plants of Euphorbia degeneri exhibit a modified NADP-ME-type photosynthesis. Apparently, both aspartate and malate are used for transport of CO/sub 2/ to bundle sheath cells. Callus grown on either non-shoot-forming or shoot-forming media fixes CO/sub 2/ into RPP-cycle intermediates and sucrose, as well as malate and aspartate. /sup 14/CO/sub 2/ pulse/chase kinetics show no significant loss of label from C/sub 4/ acids throughout a one minute chase. Analysis of PEPCase revealed the presence of 2 isoenzymes in both leaf and regenerated plant tissues (K/sub m/ (PEP) = 0.080 and 0.550) but only one isoenzyme in callus (K/sub m/ = 0.100). It appears that C/sub 4/ photosynthesis does not occur in callus derived from this C/sub 4/ dicot but is regenerated concomitant with shoot regeneration, and ..beta..-carboxylation of PEP in callus, mediated by the low K/sub m/ isoenzyme of PEPCase, produces C/sub 4/ acids that are not involved in the CO/sub 2/ shuttle mechanism characteristic of C/sub 4/ photosynthesis. 161 references, 19 figures, 12 tables.

  16. Whole Genome Comparison of Thermus sp. NMX2.A1 Reveals Principle Carbon Metabolism Differences with Closest Relation Thermus scotoductus SA-01

    Directory of Open Access Journals (Sweden)

    Walter J. Müller

    2016-09-01

    Full Text Available Genome sequencing of the yellow-pigmented, thermophilic bacterium Thermus sp. NMX2.A1 resulted in a 2.29 Mb draft genome that encodes for 2312 proteins. The genetic relationship between various strains from the genus Thermus was assessed based on phylogenomic analyses using a concatenated set of conserved proteins. The resulting phylogenetic tree illustrated that Thermus sp. NMX2 A.1 clusters together with Thermus scotoductus SA-01, despite being isolated from vastly different geographical locations. The close evolutionary relationship and metabolic parallels between the two strains has previously been recognized; however, neither strain’s genome data were available at that point in time. Genomic comparison of the Thermus sp. NMX2.A1 and T. scotoductus SA-01, as well as other closely related Thermus strains, revealed a high degree of synteny at both the genomic and proteomic level, with processes such as denitrification and natural cell competence appearing to be conserved. However, despite this high level of similarity, analysis revealed a complete, putative Calvin–Benson–Bassham (CBB cycle in NMX2.A1 that is absent in SA-01. Analysis of horizontally transferred gene islands provide evidence that NMX2 selected these genes due to pressure from its HCO3- rich environment, which is in stark contrast to that of the deep subsurface isolated SA-01.

  17. 硝酸钙胁迫对水培嫁接茄子氮碳同化的影响%Effects of calcium nitrate stress on nitrogen and carbon metabolism in hy- droponically-grown grafted eggplant seedlings

    Institute of Scientific and Technical Information of China (English)

    魏国平; 朱月林; 唐于银; 杨立飞; 张晓青

    2011-01-01

    为了研究Ca( NO3)2胁迫下茄子嫁接苗氮碳同化的生理响应以探讨嫁接茄子的耐盐生理机制,以日本引进的设施栽培专用耐盐砧木品种Torvum Vigor为砧木,栽培品种苏崎茄为接穗,用营养液栽培,对80 mmol/LCa(NO3)2胁迫下茄子嫁接苗和未嫁接苗叶片氮同化和碳同化进行了比较.结果显示:Ca(NO3)2胁迫下,茄子嫁接苗株高和生物量积累均显著高于未嫁接苗;茄子嫁接苗和未嫁接苗叶片NO3 -和NH4+含量呈先增加后下降趋势,而嫁接苗在胁迫后期均显著高于未嫁接苗;嫁接苗叶片硝酸还原酶(NR)活性在胁迫9d后显著高于未嫁接苗;可溶性蛋白含量在胁迫期间均显著高于未嫁接苗;嫁接苗和未嫁接苗叶片谷氨酰胺合成酶(GS)活性呈先上升后下降趋势,而嫁接苗GS活性在胁迫后期显著高于未嫁接苗;嫁接苗叶片可溶性糖含量呈先增加后下降趋势,而未嫁接苗叶片可溶性糖含量呈显著下降趋势,且嫁接苗在胁迫期间均显著高于未嫁接苗;嫁接苗淀粉含量显著高于未嫁接苗,而α、β淀粉酶活性均显著低于未嫁接苗.Ca( NO3)2胁迫下,茄子嫁接苗氮同化和碳同化效率较高,胁迫下仍能保持较好的能量储存和生理代谢机制,进而表现出对Ca(NO3)2胁迫有较强适应性.%To investigate the salt tolerance mechanism of grafted eggplant, and response of its nitrogen and carbon metabolism system under stress by excess of Ca( NO3) 2, using a Japanese salt tolerant eggplant cultivar Torvum Vigor ( Solarium torvum Swartz) as rootstock and cultivar Suqiqie (Solarum melongena L ) as scion, grafting was made to compare the changes of nitrogen metabolism and carbon metabolism in leaves of hydroponically-grown grafted and non-grafted eggplant seedlings under 80 mmol/L Ca( NO3 )2 stress. Under stress by excess of Ca( NO3 )2, the plant height and biomass accumulation of grafted eggplant seedlings were significantly higher than those of non

  18. Computer-Based Attention-Demanding Testing Unveils Severe Neglect in Apparently Intact Patients

    Science.gov (United States)

    Bonato, M.; Priftis, K.; Umiltà, C.; Zorzi, M.

    2013-01-01

    We tested a group of ten post-acute right-hemisphere damaged patients. Patients had no neglect according to paper-and-pencil cancellation tasks. They were administered computer-based single- and dual-tasks, requiring to orally name the position of appearance (e.g. left vs. right) of briefly-presented lateralized targets. Patients omitted a consistent number of contralesional targets (≈ 40%) under the single-task condition. When required to perform a concurrent task which recruited additional attentional resources (dual-tasks), patients’ awareness for contralesional hemispace was severely affected, with less than one third of contralesional targets detected (≈ 70% of omissions). In contrast, performance for ipsilesional (right-sided) targets was close to ceiling, showing that the deficit unveiled by computer-based testing selectively affected the contralesional hemispace. We conclude that computer-based, attention-demanding tasks are strikingly more sensitive than cancellation tasks in detecting neglect, because they are relatively immune to compensatory strategies that are often deployed by post-acute patients. PMID:22713418

  19. Unveiling the geography of historical patents in the United States from 1836 to 1975.

    Science.gov (United States)

    Petralia, Sergio; Balland, Pierre-Alexandre; Rigby, David L

    2016-08-30

    It is clear that technology is a key driver of economic growth. Much less clear is where new technologies are produced and how the geography of U.S. invention has changed over the last two hundred years. Patent data report the geography, history, and technological characteristics of invention. However, those data have only recently become available in digital form and at the present time there exists no comprehensive dataset on the geography of knowledge production in the United States prior to 1975. The database presented in this paper unveils the geography of historical patents granted by the United States Patent and Trademark Office (USPTO) from 1836 to 1975. This historical dataset, HistPat, is constructed using digitalized records of original patent documents that are publicly available. We describe a methodological procedure that allows recovery of geographical information on patents from the digital records. HistPat can be used in different disciplines ranging from geography, economics, history, network science, and science and technology studies. Additionally, it is easily merged with post-1975 USPTO digital patent data to extend it until today.

  20. A strategy to unveil transient sources of ultra-high-energy cosmic rays

    Directory of Open Access Journals (Sweden)

    Takami Hajime

    2013-06-01

    Full Text Available Transient generation of ultra-high-energy cosmic rays (UHECRs has been motivated from promising candidates of UHECR sources such as gamma-ray bursts, flares of active galactic nuclei, and newly born neutron stars and magnetars. Here we propose a strategy to unveil transient sources of UHECRs from UHECR experiments. We demonstrate that the rate of UHECR bursts and/or flares is related to the apparent number density of UHECR sources, which is the number density estimated on the assumption of steady sources, and the time-profile spread of the bursts produced by cosmic magnetic fields. The apparent number density strongly depends on UHECR energies under a given rate of the bursts, which becomes observational evidence of transient sources. It is saturated at the number density of host galaxies of UHECR sources. We also derive constraints on the UHECR burst rate and/or energy budget of UHECRs per source as a function of the apparent source number density by using models of cosmic magnetic fields. In order to obtain a precise constraint of the UHECR burst rate, high event statistics above ∼ 1020 eV for evaluating the apparent source number density at the highest energies and better knowledge on cosmic magnetic fields by future observations and/or simulations to better estimate the time-profile spread of UHECR bursts are required. The estimated rate allows us to constrain transient UHECR sources by being compared with the occurrence rates of known energetic transient phenomena.

  1. Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing.

    Science.gov (United States)

    Galand, Pierre E; Casamayor, Emilio O; Kirchman, David L; Potvin, Marianne; Lovejoy, Connie

    2009-07-01

    The Arctic Ocean plays a critical role in controlling nutrient budgets between the Pacific and Atlantic Ocean. Archaea are key players in the nitrogen cycle and in cycling nutrients, but their community composition has been little studied in the Arctic Ocean. Here, we characterize archaeal assemblages from surface and deep Arctic water masses using massively parallel tag sequencing of the V6 region of the 16S rRNA gene. This approach gave a very high coverage of the natural communities, allowing a precise description of archaeal assemblages. This first taxonomic description of archaeal communities by tag sequencing reported so far shows that it is possible to assign an identity below phylum level to most (95%) of the archaeal V6 tags, and shows that tag sequencing is a powerful tool for resolving the diversity and distribution of specific microbes in the environment. Marine group I Crenarchaeota was overall the most abundant group in the Arctic Ocean and comprised between 27% and 63% of all tags. Group III Euryarchaeota were more abundant in deep-water masses and represented the largest archaeal group in the deep Atlantic layer of the central Arctic Ocean. Coastal surface waters, in turn, harbored more group II Euryarchaeota. Moreover, group II sequences that dominated surface waters were different from the group II sequences detected in deep waters, suggesting functional differences in closely related groups. Our results unveiled for the first time an archaeal community dominated by group III Euryarchaeota and show biogeographical traits for marine Arctic Archaea.

  2. Unveiling the gas and dust disk structure in HD 163296 using ALMA observations

    CERN Document Server

    de Gregorio-Monsalvo, I; Dent, W; Pinte, C; López, C; Klaassen, P; Hales, A; Cortés, P; Rawlings, M G; Tachihara, K; Testi, L; Takahashi, S; Chapillon, E; Mathews, G; Juhasz, A; Akiyama, E; Higuchi, A E; Saito, M; Nyman, L - Å; Phillips, N; Rodń, J; Corder, S; Van Kempen, T

    2013-01-01

    Aims: The aim of this work is to study the structure of the protoplanetary disk surrounding the Herbig Ae star HD 163296. Methods: We have used high-resolution and high-sensitivity ALMA observations of the CO(3-2) emission line and the continuum at 850 microns, as well as the 3- dimensional radiative transfer code MCFOST to model the data presented in this work. Results: The CO(3-2) emission unveils for the first time at sub-millimeter frequencies the vertical structure details of a gaseous disk in Keplerian rotation, showing the back- and the front-side of a flared disk. Continuum emission at 850 microns reveals a compact dust disk with a 240 AU outer radius and a surface brightness profile that shows a very steep decline at radius larger than 125 AU. The gaseous disk is more than two times larger than the dust disk, with a similar critical radius but with a shallower radial profile. Radiative transfer models of the continuum data confirms the need for a sharp outer edge to the dust disk. The models for the ...

  3. Unveiling the structural basis for translational ambiguity tolerance in a human fungal pathogen.

    Science.gov (United States)

    Rocha, Rita; Pereira, Pedro José Barbosa; Santos, Manuel A S; Macedo-Ribeiro, Sandra

    2011-08-23

    In a restricted group of opportunistic fungal pathogens the universal leucine CUG codon is translated both as serine (97%) and leucine (3%), challenging the concept that translational ambiguity has a negative impact in living organisms. To elucidate the molecular mechanisms underlying the in vivo tolerance to a nonconserved genetic code alteration, we have undertaken an extensive structural analysis of proteins containing CUG-encoded residues and solved the crystal structures of the two natural isoforms of Candida albicans seryl-tRNA synthetase. We show that codon reassignment resulted in a nonrandom genome-wide CUG redistribution tailored to minimize protein misfolding events induced by the large-scale leucine-to-serine replacement within the CTG clade. Leucine or serine incorporation at the CUG position in C. albicans seryl-tRNA synthetase induces only local structural changes and, although both isoforms display tRNA serylation activity, the leucine-containing isoform is more active. Similarly, codon ambiguity is predicted to shape the function of C. albicans proteins containing CUG-encoded residues in functionally relevant positions, some of which have a key role in signaling cascades associated with morphological changes and pathogenesis. This study provides a first detailed analysis on natural reassignment of codon identity, unveiling a highly dynamic evolutionary pattern of thousands of fungal CUG codons to confer an optimized balance between protein structural robustness and functional plasticity.

  4. Unveiling the in Vivo Protein Corona of Circulating Leukocyte-like Carriers.

    Science.gov (United States)

    Corbo, Claudia; Molinaro, Roberto; Taraballi, Francesca; Toledano Furman, Naama E; Hartman, Kelly A; Sherman, Michael B; De Rosa, Enrica; Kirui, Dickson K; Salvatore, Francesco; Tasciotti, Ennio

    2017-03-10

    Understanding interactions occurring at the interface between nanoparticles and biological components is an urgent challenge in nanomedicine due to their effect on the biological fate of nanoparticles. After the systemic injection of nanoparticles, a protein corona constructed by blood components surrounds the carrier's surface and modulates its pharmacokinetics and biodistribution. Biomimicry-based approaches in nanotechnology attempt to imitate what happens in nature in order to transfer specific natural functionalities to synthetic nanoparticles. Several biomimetic formulations have been developed, showing superior in vivo features as a result of their cell-like identity. We have recently designed biomimetic liposomes, called leukosomes, which recapitulate the ability of leukocytes to target inflamed endothelium and escape clearance by the immune system. To gain insight into the properties of leukosomes, we decided to investigate their protein corona in vivo. So far, most information about the protein corona has been obtained using in vitro experiments, which have been shown to minimally reproduce in vivo phenomena. Here we directly show a time-dependent quantitative and qualitative analysis of the protein corona adsorbed in vivo on leukosomes and control liposomes. We observed that leukosomes absorb fewer proteins than liposomes, and we identified a group of proteins specifically adsorbed on leukosomes. Moreover, we hypothesize that the presence of macrophage receptors on leukosomes' surface neutralizes their protein corona-meditated uptake by immune cells. This work unveils the protein corona of a biomimetic carrier and is one of the few studies on the corona performed in vivo.

  5. Codon-triplet context unveils unique features of the Candida albicans protein coding genome

    Directory of Open Access Journals (Sweden)

    Oliveira José L

    2007-11-01

    Full Text Available Abstract Background The evolutionary forces that determine the arrangement of synonymous codons within open reading frames and fine tune mRNA translation efficiency are not yet understood. In order to tackle this question we have carried out a large scale study of codon-triplet contexts in 11 fungal species to unravel associations or relationships between codons present at the ribosome A-, P- and E-sites during each decoding cycle. Results Our analysis unveiled high bias within the context of codon-triplets, in particular strong preference for triplets of identical codons. We have also identified a surprisingly large number of codon-triplet combinations that vanished from fungal ORFeomes. Candida albicans exacerbated these features, showed an unbalanced tRNA population for decoding its pool of codons and used near-cognate decoding for a large set of codons, suggesting that unique evolutionary forces shaped the evolution of its ORFeome. Conclusion We have developed bioinformatics tools for large-scale analysis of codon-triplet contexts. These algorithms identified codon-triplets context biases, allowed for large scale comparative codon-triplet analysis, and identified rules governing codon-triplet context. They could also detect alterations to the standard genetic code.

  6. Unveiling Gargantua: A new search strategy for the most massive central cluster black holes

    CERN Document Server

    Brockamp, Michael; Britzen, Silke; Zensus, Anton

    2016-01-01

    We aim to unveil the most massive central cluster black holes in the universe. We present a new search strategy which is based on a black hole mass gain sensitive 'calorimeter' and which links the innermost stellar density profile of a galaxy to the adiabatic growth of its central SMBH. In a first step we convert observationally inferred feedback powers into SMBH growth rates by using reasonable energy conversion efficiency parameters, $\\epsilon$. In the main part of this paper we use these black hole growth rates, sorted in logarithmically increasing steps encompassing our whole parameter space, to conduct $N$-Body computations of brightest cluster galaxies with the newly developed MUESLI software. For the initial setup of galaxies we use core-Sersic models in order to account for SMBH scouring. We find that adiabatically driven core re-growth is significant at the highest accretion rates. As a result, the most massive black holes should be located in BCGs with less pronounced cores when compared to the pred...

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

    NARCIS (Netherlands)

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

    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' ar

  8. From an equilibrium based MOF adsorbent to a kinetic selective carbon molecular sieve for paraffin/iso-paraffin separation.

    Science.gov (United States)

    Li, Baiyan; Belmabkhout, Youssef; Zhang, Yiming; Bhatt, Prashant M; He, Hongming; Zhang, Daliang; Han, Yu; Eddaoudi, Mohamed; Perman, Jason A; Ma, Shengqian

    2016-11-24

    We unveil a unique kinetic driven separation material for selectively removing linear paraffins from iso-paraffins via a molecular sieving mechanism. Subsequent carbonization and thermal treatment of CD-MOF-2, the cyclodextrin metal-organic framework, afforded a carbon molecular sieve with a uniform and reduced pore size of ca. 5.0 Å, and it exhibited highly selective kinetic separation of n-butane and n-pentane from iso-butane and iso-pentane, respectively.

  9. Metabolic Syndrome (For Parents)

    Science.gov (United States)

    ... Old Feeding Your 1- to 2-Year-Old Metabolic Syndrome KidsHealth > For Parents > Metabolic Syndrome A A A ... this is a condition called metabolic syndrome . About Metabolic Syndrome Not to be confused with metabolic disease (which ...

  10. Metabolic Syndrome (For Parents)

    Science.gov (United States)

    ... Old Feeding Your 1- to 2-Year-Old Metabolic Syndrome KidsHealth > For Parents > Metabolic Syndrome Print A A ... this is a condition called metabolic syndrome . About Metabolic Syndrome Not to be confused with metabolic disease (which ...

  11. Metabolic and enzymatic changes associated with carbon mobilization, utilization and replenishment triggered in grain amaranth (Amaranthus cruentus in response to partial defoliation by mechanical injury or insect herbivory

    Directory of Open Access Journals (Sweden)

    Castrillón-Arbeláez Paula

    2012-09-01

    Full Text Available Abstract Background Amaranthus cruentus and A. hypochondriacus are crop plants grown for grain production in subtropical countries. Recently, the generation of large-scale transcriptomic data opened the possibility to study representative genes of primary metabolism to gain a better understanding of the biochemical mechanisms underlying tolerance to defoliation in these species. A multi-level approach was followed involving gene expression analysis, enzyme activity and metabolite measurements. Results Defoliation by insect herbivory (HD or mechanical damage (MD led to a rapid and transient reduction of non-structural carbohydrates (NSC in all tissues examined. This correlated with a short-term induction of foliar sucrolytic activity, differential gene expression of a vacuolar invertase and its inhibitor, and induction of a sucrose transporter gene. Leaf starch in defoliated plants correlated negatively with amylolytic activity and expression of a β-amylase-1 gene and positively with a soluble starch synthase gene. Fatty-acid accumulation in roots coincided with a high expression of a phosphoenolpyruvate/phosphate transporter gene. In all tissues there was a long-term replenishment of most metabolite pools, which allowed damaged plants to maintain unaltered growth and grain yield. Promoter analysis of ADP-glucose pyrophosphorylase and vacuolar invertase genes indicated the presence of cis-regulatory elements that supported their responsiveness to defoliation. HD and MD had differential effects on transcripts, enzyme activities and metabolites. However, the correlation between transcript abundance and enzymatic activities was very limited. A better correlation was found between enzymes, metabolite levels and growth and reproductive parameters. Conclusions It is concluded that a rapid reduction of NSC reserves in leaves, stems and roots followed by their long-term recovery underlies tolerance to defoliation in grain amaranth. This requires the

  12. METABOLIC ENGINEERING OF RAFFINOSE-FAMILY OLIGOSACCHARIDES IN THE PHLOEM REVEALS ALTERATIONS IN CARBON PARTITIONING AND ENHANCES RESISTANCE TO GREEN PEACH APHID

    Directory of Open Access Journals (Sweden)

    Te eCao

    2013-07-01

    Full Text Available Many plants employ energized loading strategies to accumulate osmotically-active solutes into the phloem of source organs to accentuate the hydrostatic pressure gradients that drive the flow of water, nutrients and signals from source to sinks. Proton-coupled symport of sugars from the apoplasm into the phloem symplasm is the best studied phloem-loading mechanism. As an alternative, numerous species use a polymer trapping mechanism to load through symplasm: sucrose enters the phloem through specialized plasmodesmata and is converted to raffinose-family oligosaccharides (RFOs which accumulate because of their larger size. In this study, metabolic engineering was used to generate RFOs at the inception of the translocation stream of Arabidopsis thaliana, which loads from the apoplasm and transports predominantly sucrose, and the fate of the sugars throughout the plant determined. Three genes, GALACTINOL SYNTHASE, RAFFINOSE SYNTHASE and STACHYOSE SYNTHASE, were expressed from promoters specific to the companion cells of minor veins. Two transgenic lines homozygous for all three genes (GRS63 and GRS47 were selected for further analysis. Three-week-old plants of both lines had RFO levels approaching 50% of total soluble sugar. RFOs were also identified in exudates from excised leaves of transgenic plants whereas levels were negligible in exudates from wild type (WT leaves. Differences in starch accumulation between WT and GRS63 and GRS47 lines were not observed. Similarly, there were no differences in vegetative growth between WT and engineered plants, but the latter flowered slightly earlier. Finally, since the sugar composition of the translocation stream appeared altered, we tested for an impact on green peach aphid (Myzus persicae Sulzer feeding. When given a choice between WT and transgenic plants, green peach aphids preferred settling on the WT plants. Furthermore, green peach aphid fecundity was lower on the transgenic plants compared to the WT

  13. Radioactive Chernobyl environment has produced high-oil flax seeds that show proteome alterations related to carbon metabolism during seed development.

    Science.gov (United States)

    Klubicová, Katarína; Danchenko, Maksym; Skultety, Ludovit; Berezhna, Valentyna V; Rashydov, Namik M; Hajduch, Martin

    2013-11-01

    Starting in 2007, we have grown soybean (Glycine max [L.] Merr. variety Soniachna) and flax (Linum usitatissimum, L. variety Kyivskyi) in the radio-contaminated Chernobyl area and analyzed the seed proteomes. In the second-generation flax seeds, we detected a 12% increase in oil content. To characterize the bases for this increase, seed development has been studied. Flax seeds were harvested in biological triplicate at 2, 4, and 6 weeks after flowering and at maturity from plants grown in nonradioactive and radio-contaminated plots in the Chernobyl area for two generations. Quantitative proteomic analyses based on 2-D gel electrophoresis (2-DE) allowed us to establish developmental profiles for 199 2-DE spots in both plots, out of which 79 were reliably identified by tandem mass spectrometry. The data suggest a statistically significant increased abundance of proteins associated with pyruvate biosynthesis via cytoplasmic glycolysis, L-malate decarboxylation, isocitrate dehydrogenation, and ethanol oxidation to acetaldehyde in early stages of seed development. This was followed by statistically significant increased abundance of ketoacyl-[acylcarrier protein] synthase I related to condensation of malonyl-ACP with elongating fatty acid chains. On the basis of these and previous data, we propose a preliminary model for plant adaptation to growth in a radio-contaminated environment. One aspect of the model suggests that changes in carbon assimilation and fatty acid biosynthesis are an integral part of plant adaptation.

  14. Context-dependent metabolic networks

    CERN Document Server

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

    2016-01-01

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

  15. Metabolism of hyperthermophiles.

    Science.gov (United States)

    Schönheit, P; Schäfer, T

    1995-01-01

    Hyperthermophiles are characterized by a temperature optimum for growth between 80 and 110°C. They are considered to represent the most ancient phenotype of living organisms and thus their metabolic design might reflect the situation at an early stage of evolution. Their modes of metabolism are diverse and include chemolithoautotrophic and chemoorganoheterotrophic. No extant phototrophic hyperthermophiles are known. Lithotrophic energy metabolism is mostly anaerobic or microaerophilic and based on the oxidation of H2 or S coupled to the reduction of S, SO inf4 (sup2-) , CO2 and NO inf3 (sup-) but rarely to O2. the substrates are derived from volcanic activities in hyperthermophilic habitats. The lithotrophic energy metabolism of hyperthermophiles appears to be similar to that of mesophiles. Autotrophic CO2 fixation proceeds via the reductive citric acid cycle, considered to be one of the first metabolic cycles, and via the reductive acetyl-CoA/carbon monoxide dehydrogenase pathway. The Calvin cycle has not been found in hyperthermophiles (or any Archaea). Organotrophic metabolism mainly involves peptides and sugars as substrates, which are either oxidized to CO2 by external electron acceptors or fermented to acetate and other products. Sugar catabolism in hyperthermophiles involves non-phosphorylated versions of the Entner-Doudoroff pathway and modified versions of the Embden-Meyerhof pathway. The 'classical' Embden-Meyerhof pathway is present in hyperthermophilic Bacteria (Thermotoga) but not in Archaea. All hyperthermophiles (and Archaea) tested so far utilize pyruvate:ferredoxin oxidoreductase for acetyl-CoA formation from pyruvate. Acetyl-CoA oxidation in anaerobic sulphur-reducing and aerobic hyperthermophiles proceeds via the citric acid cycle; in the hyperthermophilic sulphate-reducer Archaeoglobus an oxidative acetyl-CoA/carbon monoxide dehydrogenase pathway is operative. Acetate formation from acetyl-CoA in Archaea, including hyperthermophiles, is

  16. Generation and Evaluation of a Genome-Scale Metabolic Network Model of Synechococcus elongatus PCC7942

    Directory of Open Access Journals (Sweden)

    Julián Triana

    2014-08-01

    Full Text Available The reconstruction of genome-scale metabolic models and their applications represent a great advantage of systems biology. Through their use as metabolic flux simulation models, production of industrially-interesting metabolites can be predicted. Due to the growing number of studies of metabolic models driven by the increasing genomic sequencing projects, it is important to conceptualize steps of reconstruction and analysis. We have focused our work in the cyanobacterium Synechococcus elongatus PCC7942, for which several analyses and insights are unveiled. A comprehensive approach has been used, which can be of interest to lead the process of manual curation and genome-scale metabolic analysis. The final model, iSyf715 includes 851 reactions and 838 metabolites. A biomass equation, which encompasses elementary building blocks to allow cell growth, is also included. The applicability of the model is finally demonstrated by simulating autotrophic growth conditions of Synechococcus elongatus PCC7942.

  17. Generation and Evaluation of a Genome-Scale Metabolic Network Model of Synechococcus elongatus PCC7942

    Science.gov (United States)

    Triana, Julián; Montagud†, Arnau; Siurana, Maria; Fuente, David; Urchueguía, Arantxa; Gamermann, Daniel; Torres, Javier; Tena, Jose; de Córdoba, Pedro Fernández; Urchueguía, Javier F.

    2014-01-01

    The reconstruction of genome-scale metabolic models and their applications represent a great advantage of systems biology. Through their use as metabolic flux simulation models, production of industrially-interesting metabolites can be predicted. Due to the growing number of studies of metabolic models driven by the increasing genomic sequencing projects, it is important to conceptualize steps of reconstruction and analysis. We have focused our work in the cyanobacterium Synechococcus elongatus PCC7942, for which several analyses and insights are unveiled. A comprehensive approach has been used, which can be of interest to lead the process of manual curation and genome-scale metabolic analysis. The final model, iSyf715 includes 851 reactions and 838 metabolites. A biomass equation, which encompasses elementary building blocks to allow cell growth, is also included. The applicability of the model is finally demonstrated by simulating autotrophic growth conditions of Synechococcus elongatus PCC7942. PMID:25141288

  18. Fructose-bisphophate aldolase exhibits functional roles between carbon metabolism and the hrp system in rice pathogen Xanthomonas oryzae pv. oryzicola.

    Science.gov (United States)

    Guo, Wei; Zou, Li-fang; Li, Yu-rong; Cui, Yi-ping; Ji, Zhi-yuan; Cai, Lu-lu; Zou, Hua-song; Hutchins, William C; Yang, Ching-hong; Chen, Gong-you

    2012-01-01

    Fructose-bisphophate aldolase (FbaB), is an enzyme in glycolysis and gluconeogenesis in living organisms. The mutagenesis in a unique fbaB gene of Xanthomonas oryzae pv. oryzicola, the causal agent of rice bacterial leaf streak, led the pathogen not only unable to use pyruvate and malate for growth and delayed its growth when fructose was used as the sole carbon source, but also reduced extracellular polysaccharide (EPS) production and impaired bacterial virulence and growth in rice. Intriguingly, the fbaB promoter contains an imperfect PIP-box (plant-inducible promoter) (TTCGT-N(9)-TTCGT). The expression of fbaB was negatively regulated by a key hrp regulatory HrpG and HrpX cascade. Base substitution in the PIP-box altered the regulation of fbaB with the cascade. Furthermore, the expression of fbaB in X. oryzae pv. oryzicola RS105 strain was inducible in planta rather than in a nutrient-rich medium. Except other hrp-hrc-hpa genes, the expression of hrpG and hrpX was repressed and the transcripts of hrcC, hrpE and hpa3 were enhanced when fbaB was deleted. The mutation in hrcC, hrpE or hpa3 reduced the ability of the pathogen to acquire pyruvate and malate. In addition, bacterial virulence and growth in planta and EPS production in RΔfbaB mutant were completely restored to the wild-type level by the presence of fbaB in trans. This is the first report to demonstrate that carbohydrates, assimilated by X. oryzae pv. oryzicola, play critical roles in coordinating hrp gene expression through a yet unknown regulator.

  19. Effects of different nitrogen level on carbon-nitrogen metabolic balance in kidney bean (Phaseolus vulgari L .)%不同供氮水平对芸豆碳氮代谢平衡的影响

    Institute of Scientific and Technical Information of China (English)

    孙海燕; 郭伟

    2013-01-01

    采用盆栽土壤基施0、15、30 kg·hm-2三个氮素水平试验,研究了芸豆荚果形成后不同氮素水平下叶片和荚果的碳、氮代谢主要酶活性以及抗氧化酶系活性的变化。结果表明,芸豆荚果形成后,随着土壤供氮水平的增加,荚果的磷酸烯醇式丙酮酸羧化酶活性、多酚氧化酶活性、超氧化物歧化酶和过氧化氢酶活性逐渐增强;叶片的蔗糖合成酶活性、蔗糖磷酸合成酶活性、硝酸还原酶和磷酸烯醇式丙酮酸羧化酶活性大于同一供氮水平荚果的活性;且荚果的总可溶性糖和可溶性蛋白含量高于叶片;叶片的磷酸烯醇式丙酮酸羧化酶的活性与荚果的蔗糖磷酸合成酶和硝酸还原酶活性呈显著相关性。由此可以得出,源器官是芸豆植株的代谢活跃中心,而库器官成为植株的生长中心,且后者的碳、氮代谢过程主要受前者的调控。%Three base nitrogen fertilizer levels ,including 0 ,1 .5 kg·hm-2 and 3 .0 kg·hm-2 ,were adopted in a pot experiment to study the changes of enzyme system of carbon-nitrogen metabolism in leaves and pods of kidney bean ( Phaseolus vulgari L .) .The results showed that ,after the formation of pods ,the activity of phosphoenolpyruvate car-boxylase (PEP ) ,polyphenol oxidase (PPO ) , superoxide dismutase (SOD ) and catalase (CAT ) in pods gradually in-creased with the increase of nitrogen .Under the same nitrogen level ,the activity of sucrose synthase (SS ) ,sucrose phos-phate synthase (SPS ) ,nitrate reductase (NR) and PEP in leaves was greater than that in pods ,while the content of total soluble sugar and protein in pods was higher than that in leaves .The activity of PEP in leaves was correlated significantly with the activity of SPS and NR in pods .It could be concluded that ,in the plants of kidney bean ,the source organ was the active center of metabolism ,while the sink organ was the growth center ,and the carbon

  20. 大豆异黄酮联合碳酸钙调节去势大鼠骨代谢的研究%STUDY OF SOYBEAN ISOFLAVONES AND CALCIUM CARBONATE ON BONE METABOLISM IN OVARIECTOMIZED RATS

    Institute of Scientific and Technical Information of China (English)

    谭剑斌; 赵敏; 周轶琳; 陈瑞仪; 王凤岩; 胡帅尔

    2012-01-01

    [Objective] To observe the regulating effects of combining soybean isoflavones and calcium carbonate on bone metabolism in ovariectomized rats. [Methods] 60 female SD rats were divided randomly into sham, ovariectomized control group, calcium carbonate group, and three dosage groups, each group had 10 rats. Low, middle and high dosage groups were lavaged the test materials every day for 3 months { soybean isoflavones 4.8, 9.7, 29.0mg/kg BW, and calcium carbonate 25.5, 50.9, 152.8mg/kg BW) , and calcium carbonate group was given calcium carbonate (152.8mg/kg BW) in the same way. Body weight was recorded every week. At the end of the experiment, rats' serum AKP and serum calcium were measured, and femur were taken out to determine the bone density (middle and distal end point) and bone calcium content [Results] The femur bone density (distal side) of low and middle dosage groups were significantly higher than ovariectomized control group (P< 0.05), and bone calcium of low and high dosage groups were significantly higher than ovariectomized control group (P < 0.05). [Conclusion] Combining soybean isoflavones and calcium might increase bone density and bone calcium in o-variectomized rats.%[目的]观察大豆异黄酮联合碳酸钙对去势大鼠骨代谢的调节作用.[方法]将60只雌性SD大鼠随机分为6组,分别为假手术组、3个剂量组、碳酸钙组和去卵巢对照组,每组10只.假手术组单纯开腹,其余5组切除双例卵巢.低、中、高剂量组分别灌胃给予受试物(大豆异黄酮4.8、9.7、29.omg/kg BW,碳酸钙25.5、50.9、152.8mg/kg BW),碳酸钙组灌胃给予碳酸钙152.8 mg/kg BW,实验共3个月.每周记录一次体重.实验结束后测定大鼠血清碱性磷酸酶(AKP)和血清钙,取股骨检测股骨中点和远心端骨密度和骨钙含量.[结果]低、中剂量组大鼠股骨远心点骨密度与去卵巢对照组比较显著增加(P<0.05),低、高剂量组大鼠股骨骨钙含量与去卵巢

  1. AMPK Activation Affects Glutamate Metabolism in Astrocytes

    DEFF Research Database (Denmark)

    Voss, Caroline Marie; Pajęcka, Kamilla; Stridh, Malin H

    2015-01-01

    on glutamate metabolism in astrocytes was studied using primary cultures of these cells from mouse cerebral cortex during incubation in media containing 2.5 mM glucose and 100 µM [U-(13)C]glutamate. The metabolism of glutamate including a detailed analysis of its metabolic pathways involving the tricarboxylic...... acid (TCA) cycle was studied using high-performance liquid chromatography analysis supplemented with gas chromatography-mass spectrometry technology. It was found that AMPK activation had profound effects on the pathways involved in glutamate metabolism since the entrance of the glutamate carbon...... affected by a reduction of the flux of glutamate derived carbon through the malic enzyme and pyruvate carboxylase catalyzed reactions. Finally, it was found that in the presence of glutamate as an additional substrate, glucose metabolism monitored by the use of tritiated deoxyglucose was unaffected by AMPK...

  2. Wukong Sharpens Its Eyes and Unveils the Nature of Dark Matter

    Science.gov (United States)

    Cong, Kun-Lin

    2016-07-01

    Dark matter does not emit light or reflect electromagnetic radiation, but its existence can be inferred from the effects of measurements such as gravity and mass. Unveiling the nature of dark matter is one of the biggest mysteries of modern science. Exploration of dark matter could give scientists a clearer understanding of the past and future of galaxies and the universe. Chinese scientists have been engaged actively in dark matter research in recent years, and made some significant achievements in theoretical studies, numerical simulations, and experimental investigation. The Dark Matter Particles Explorer Satellite (DAMPE) was launched by LM launch vehicle on 17th December 2015. It was constructed as a scientific satellite that has four major parts - a plastic scintillator array detector, a silicon array detector, a BGO calorimeter and a neutron detector - together comprising about 76,000 minor detectors. The main scientific purpose of DAMPE is to investigate dark matter particle from deep space, via high resolution observation of gamma-rays and electrons spectra, and its space distribution. It will also help scientists study the transportation and acceleration of cosmic rays in the galaxy by measuring the energy spectra of heavy ions. DAMPE was dubbed Wukong after the Monkey King character from the Chinese classic legend Journey to the West. "Wu" means becoming aware of through the senses, and "Kong" refers to the space. The figurative meaning of "Wukong" is to know and comprehend the nature of the space. DAMPE is the most sensitive and accurate detectors designed for dark matter with the highest performance among the similar explorers. It will find the evidence that can certify the existence of dark matter.

  3. Unveiling the AGN in IC 883: discovery of a parsec-scale radio jet

    Science.gov (United States)

    Romero-Cañizales, C.; Alberdi, A.; Ricci, C.; Arévalo, P.; Pérez-Torres, M. Á.; Conway, J. E.; Beswick, R. J.; Bondi, M.; Muxlow, T. W. B.; Argo, M. K.; Bauer, F. E.; Efstathiou, A.; Herrero-Illana, R.; Mattila, S.; Ryder, S. D.

    2017-01-01

    IC 883 is a luminous infrared galaxy (LIRG) classified as a starburst-active galactic nucleus (AGN) composite. In a previous study we detected a low-luminosity AGN (LLAGN) radio candidate. Here we report on our radio follow-up at three frequencies which provides direct and unequivocal evidence of the AGN activity in IC 883. Our analysis of archival X-ray data, together with the detection of a transient radio source with luminosity typical of bright supernovae, give further evidence of the ongoing star formation activity, which dominates the energetics of the system. At sub-parsec scales, the radio nucleus has a core-jet morphology with the jet being a newly ejected component showing a subluminal proper motion of 0.6-1 c. The AGN contributes less than two per cent of the total IR luminosity of the system. The corresponding Eddington factor is ˜10-3, suggesting this is a low-accretion rate engine, as often found in LLAGNs. However, its high bolometric luminosity (˜1044 erg s-1) agrees better with a normal AGN. This apparent discrepancy may just be an indication of the transition nature of the nucleus from a system dominated by star-formation, to an AGN-dominated system. The nucleus has a strongly inverted spectrum and a turnover at ˜4.4 GHz, thus qualifying as a candidate for the least luminous (L5.0 GHz ˜ 6.3 × 1028 erg s-1 Hz-1) and one of the youngest (˜3 × 103 yr) gigahertz-peaked spectrum (GPS) sources. If the GPS origin for the IC 883 nucleus is confirmed, then advanced mergers in the LIRG category are potentially key environments to unveil the evolution of GPS sources into more powerful radio galaxies.

  4. Distance to the scaling law: a useful approach for unveiling relationships between crime and urban metrics.

    Directory of Open Access Journals (Sweden)

    Luiz G A Alves

    Full Text Available We report on a quantitative analysis of relationships between the number of homicides, population size and ten other urban metrics. By using data from Brazilian cities, we show that well-defined average scaling laws with the population size emerge when investigating the relations between population and number of homicides as well as population and urban metrics. We also show that the fluctuations around the scaling laws are log-normally distributed, which enabled us to model these scaling laws by a stochastic-like equation driven by a multiplicative and log-normally distributed noise. Because of the scaling laws, we argue that it is better to employ logarithms in order to describe the number of homicides in function of the urban metrics via regression analysis. In addition to the regression analysis, we propose an approach to correlate crime and urban metrics via the evaluation of the distance between the actual value of the number of homicides (as well as the value of the urban metrics and the value that is expected by the scaling law with the population size. This approach has proved to be robust and useful for unveiling relationships/behaviors that were not properly carried out by the regression analysis, such as [Formula: see text] the non-explanatory potential of the elderly population when the number of homicides is much above or much below the scaling law, [Formula: see text] the fact that unemployment has explanatory potential only when the number of homicides is considerably larger than the expected by the power law, and [Formula: see text] a gender difference in number of homicides, where cities with female population below the scaling law are characterized by a number of homicides above the power law.

  5. A new 4D trajectory-based approach unveils abnormal LV revolution dynamics in hypertrophic cardiomyopathy.

    Directory of Open Access Journals (Sweden)

    Andrea Madeo

    these methods. Left ventricle deformation in patients affected by hypertrophic cardiomyopathy compared to healthy subjects may be assessed by modern shape analysis better than by traditional 3D Speckle Tracking Echocardiography global parameters. Hypertrophic cardiomyopathy pathophysiology was unveiled in a new manner whereby also diastolic phase abnormalities are evident which is more difficult to investigate by traditional ecocardiographic techniques.

  6. Metabolic syndrome

    Institute of Scientific and Technical Information of China (English)

    Charles Shaeffer

    2004-01-01

    @@ The emergence of cardiac disease as the number one world-wide cause of death justifies efforts to identify individuals at higher risk for preventive therapy. The metabolic syndrome, originally described by Reaven, 1 has been associated with higher cardiovascular disease risk. 2 Type Ⅱ diabetes is also a frequent sequela. 3

  7. Secondary psychosis induced by metabolic disorders

    Directory of Open Access Journals (Sweden)

    Olivier eBonnot

    2015-05-01

    Full Text Available Metabolic disorders are not well recognized by psychiatrists as a possible source of secondary psychoses. Inborn errors of metabolism (IEMs are not frequent. Although, their prompt diagnosis may lead to suitable treatments. IEMs are well known to paediatricians, in particular for their most serious forms, having an early expression most of the time. Recent years discoveries have unveiled later expression forms, and sometimes, very discreet first physical signs. There is a growing body of evidence that supports the hypothesis that IEMs can manifest as atypical psychiatric symptoms, even in the absence of clear neurological symptoms. In the present review, we propose a detailed overview at schizophrenia-like and autism-like symptoms that can lead practitioners to bear in mind an IEM. Other psychiatric manifestations are also found, as behavioral., cognitive, learning and mood disorders. However, they are less frequent. Ensuring an accurate IEM diagnosis, in front of these psychiatric symptoms should be a priority, in order to grant suitable and valuable treatment for these pathologies.

  8. Biolog-Eco解析黄山风景区空气微生物碳代谢多样性特征%Analysis of Carbon Metabolism Diversity Characters of Air Microbes in Huangshan Scenic Spot Using Biolog-Eco Method

    Institute of Scientific and Technical Information of China (English)

    凌琪; 包金梅; 李瑞; 陶勇; 鲍立宁; 毛钦焱

    2012-01-01

    采用Biolog生态微平板分析黄山风景区6个景区空气样品的微生物碳代谢群落结构,旨在了解不同景区空气微生物碳代谢功能群落结构的特点与差异.结果表明:6个景区AWCD值变化趋势不同,空气微生物在碳源利用能力、微生物丰度等方面存在差异,可能与海拔、气象、游客集中与流动等因素有关;6个景区空气微生物对6类31种碳源的利用程度存在差异,但总体对羧酸类和碳水化合物类的利用程度较高,对其它化合物类的利用程度较低;主成分分析显示,6个景区空气微生物代谢基质主成分1的贡献度为58.7%,主成分2为28.5%;主成分1荷载0.55以上的基质有25种,主成分2只有7种.Biolog生态微平板技术能够客观、正确表征空气微生物碳代谢多样性的特征,是研究空气微生物群落功能多样性的较理想方法之一.%The community structure of the air microbes in Huangshan Scenic Spot was measured by the Biolog Eco plate to study the characters and differences of the carbon catabolic diversity of air microbes in different spots. The results showed the change patterns of the AWCD ( average well color development) in six scenic spots were different,mainly demonstrating in how the air microbes made use of the carbon sources and the abundance of the microbes. It may attribute to the height, the climate and the number of tourists, et al. Though the degree to which the air microbes in six scenic spots made use of 31 carbon sources of 6 types was different,in general, they made more use of the carboxylic acids and carbohydrates while making less use of other compounds. The PC A (principal component analysis) showed the contribution of the PCI of the air microbes metabolism substrates in six scenic spots was 58.7% ,PC2 was 28.5% ,and there were 25 types of substrates in PCI over 0. 55 of load, only 7 in PC2. The technology of the Biolog Eco plate is one of the effective approaches to study the

  9. Metabolic Syndrome

    Directory of Open Access Journals (Sweden)

    Sevil Ikinci

    2010-10-01

    Full Text Available Metabolic Syndrome is a combination of risk factors including common etiopathogenesis. These risk factors play different roles in occurence of atherosclerotic diseases, type 2 diabetes, and cancers. Although a compromise can not be achieved on differential diagnosis for MS, the existence of any three criterias enable to diagnose MS. These are abdominal obesity, dislipidemia (hypertrigliceridemia, hypercholesterolemia, and reduced high density lipoprotein hypertension, and elevated fasting blood glucose. According to the results of Metabolic Syndrome Research (METSAR, the overall prevalence of MS in Turkey is 34%; in females 40%, and in males it is 28%. As a result of “Western” diet, and increased frequency of obesity, MS is observed in children and in adolescents both in the world and in Turkey. Resulting in chronic diseases, it is thought that the syndrome can be prevented by healthy lifestyle behaviours. [TAF Prev Med Bull 2010; 9(5.000: 535-540

  10. What is Metabolic Syndrome?

    Science.gov (United States)

    ... from the NHLBI on Twitter. What Is Metabolic Syndrome? Metabolic syndrome is the name for a group of ... that may play a role in causing metabolic syndrome. Outlook Metabolic syndrome is becoming more common due to a ...

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

    Science.gov (United States)

    Angermayr, S Andreas; Gorchs Rovira, Aleix; Hellingwerf, Klaas J

    2015-06-01

    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 CO(2), light, and water directly. Such cyanobacterial 'cell factories' are constructed to produce biofuels, bioplastics, and commodity chemicals. Efforts of metabolic engineers and synthetic biologists allow the modification of the intermediary metabolism at various branching points, expanding the product range. The new biosynthesis routes 'tap' the metabolism ever more efficiently, particularly through the engineering of driving forces and utilization of cofactors generated during the light reactions of photosynthesis, resulting in higher product titers. High rates of carbon rechanneling ultimately allow an almost-complete allocation of fixed carbon to product above biomass.

  12. 苹果酸-乳酸发酵过程酒酒球菌碳源代谢分析研究进展%Research Progress on Carbon Metabolism in Malolactic Fermentation by Oenococcus oeni

    Institute of Scientific and Technical Information of China (English)

    康毅; 刘树文

    2012-01-01

    The metabolism of carbon sources and the generation of products and by-products during malolactic fermentation (MLF) in wine by Oenococcus oeni have a great impact on sensory quality of wine. O. oeni participates in the metabolism of glucose, malic acid, and citric acid and the formation of products during MLF, which finally affects the overall sensory quality of wine. Environmental conditions are also important factors influencing the growth of O. oeni in MLF. Malic acid, citric acid and pH influence on the growth of O. oeni. SO2 can inhibit the activity of ATPase and high content of ethanol may increase the fluidity of cell membrane, thus impeding the growth of O. oeni during MLF. Moreover, dissolved oxygen is unfavorable to bacterial growth, but favorable to the multiplication of other harmful microorganisms such as acetic acid bacteria and the increase in concentration of by-products such as diacetyl and acetic acids, thus leading to low quality of wine. In this paper, the metabolisms of malic acid, citric acid and glucose as well as the generation mechanisms and affecting factors of lactic acid, acetic acid, diacetyl and acetoin are reviewed.%葡萄酒苹果酸一乳酸发酵(malolactic fermentation,MLF)中碳源物质的利用及其产物、副产物的形成对葡萄酒感官品质有很大影响。其中,酒酒球菌参与的葡萄糖代谢、有机酸代谢及相关产物的形成和流向对葡萄酒MLF影响重大,决定着葡萄酒的最终品质。环境条件也是影响酒酒球菌生长的重要因素。苹果酸、柠檬酸和pH值三者在一定范围内相互作用,影响酒酒球菌生长。SO2:会抑制酒酒球菌细胞ATP酶活性,高含量乙醇能增加细胞膜流动性,这些都会阻碍酒酒球菌生长,而溶解氧不仅不利于酒酒球菌生长,还会使醋酸菌等有害微生物大量繁殖,乙酸、双乙酰等不良产物含量上升,使葡萄酒败坏。本文就葡萄酒MLF过程中酒酒球菌的苹

  13. Nuclear Reactor Simulations for Unveiling Diversion Scenarios: capabilities of the antineutrino probe

    Energy Technology Data Exchange (ETDEWEB)

    Bui, V.M.; Fallot, M.; Giot, L.; Guillon, B.; Martino, J.; Yermia, F. [SUBATECH - CNRS-IN2P3 - Univ. of Nantes - EMN, Nantes (France); Nuttin, A. [LPSC - CNRS-IN2P3/UJF/INPG, Grenoble (France)

    2009-06-15

    After many years of fundamental research, physicists have a good understanding of the neutrinos detection techniques. It is now possible to apply neutrino physics as a new tool to monitor nuclear power plants. We already know that modest size detectors are achievable to fulfill that task such as the SONGS 1 and the future Nucifer detectors. In parallel, sophisticated simulations of reactors and their associated antineutrino flux and energy spectrum have been developed to predict the neutrino signature of the fuel burnup and of a diversion. Taking advantage of the tremendous quantity of information available nowadays in nuclear databases, the total {beta} spectrum of a reactor is built by adding the contributions of all the {beta} branches involved in the decay of all fission products (FP). A package called MCNP Utility for Reactor Evolution (MURE) computes the fuel and FP inventories by simulating the neutronics and time evolution of a reactor core. MURE, initially developed by CNRS/IN2P3/LPSC Grenoble and IPN Orsay to study Generation IV reactors, is a precision code written in C++ which automates the preparation and computation of successive MCNP calculations either for precision burnup or thermal-hydraulics purpose. MURE will be soon available at NEA. The only user-defined inputs driving the time evolution of the isotopic composition of the core are the initial fuel composition, the refueling scheme, and the thermal power. The evolution of the antineutrino flux and energy spectrum with the fuel burnup, as well as the effect of neutron capture on various nuclei are taken into account. Nonproliferation scenarios and burnup monitoring with antineutrinos have been studied using these tools for PWR and Candu reactors. A full core simulation of an N4-PWR will be presented in a first part. Gross unveiling diversion scenarios using a PWR have been simulated in order to test the ability of the antineutrino probe. A channel of a Heavy Water Reactor (Candu 600) loaded with

  14. Insights into glycogen metabolism in Lactobacillus acidophilus: impact on carbohydrate metabolism, stress tolerance and gut retention.

    Science.gov (United States)

    Goh, Yong Jun; Klaenhammer, Todd R

    2014-11-20

    In prokaryotic species equipped with glycogen metabolism machinery, the co-regulation of glycogen biosynthesis and degradation has been associated with the synthesis of energy storage compounds and various crucial physiological functions, including global cellular processes such as carbon and nitrogen metabolism, energy sensing and production, stress response and cell-cell communication. In addition, the glycogen metabolic pathway was proposed to serve as a carbon capacitor that regulates downstream carbon fluxes, and in some microorganisms the ability to synthesize intracellular glycogen has been implicated in host persistence. Among lactobacilli, complete glycogen metabolic pathway genes are present only in select species predominantly associated with mammalian hosts or natural environments. This observation highlights the potential involvement of glycogen biosynthesis in probiotic activities and persistence of intestinal lactobacilli in the human gastrointestinal tract. In this review, we summarize recent findings on (i) the presence and potential ecological distribution of glycogen metabolic pathways among lactobacilli, (ii) influence of carbon substrates and growth phases on glycogen metabolic gene expression and glycogen accumulation in L. acidophilus, and (iii) the involvement of glycogen metabolism on growth, sugar utilization and bile tolerance. Our present in vivo studies established the significance of glycogen biosynthesis on the competitive retention of L. acidophilus in the mouse intestinal tract, demonstrating for the first time that the ability to synthesize intracellular glycogen contributes to gut fitness and retention among probiotic microorganisms.

  15. Unveiling topographical changes using LiDAR mapping capability: case study of Belaga in Sarawak, East-Malaysia

    Science.gov (United States)

    Ganendra, T. R.; Khan, N. M.; Razak, W. J.; Kouame, Y.; Mobarakeh, E. T.

    2016-06-01

    The use of Light Detection and Ranging (LiDAR) remote sensing technology to scan and map landscapes has proven to be one of the most popular techniques to accurately map topography. Thus, LiDAR technology is the ultimate method of unveiling the surface feature under dense vegetation, and, this paper intends to emphasize the diverse techniques that can be utilized to elucidate topographical changes over the study area, using multi-temporal airborne full waveform LiDAR datasets collected in 2012 and 2014. Full waveform LiDAR data offers access to an almost unlimited number of returns per shot, which enables the user to explore in detail topographical changes, such as vegetation growth measurement. The study also found out topography changes at the study area due to earthwork activities contributing to soil consolidation, soil erosion and runoff, requiring cautious monitoring. The implications of this study not only concurs with numerous investigations undertaken by prominent researchers to improve decision making, but also corroborates once again that investigations employing multi-temporal LiDAR data to unveil topography changes in vegetated terrains, produce more detailed and accurate results than most other remote sensing data.

  16. 河南省不同地区烤烟碳氮代谢与衰老启动关系的分析%Analysis on the Relationship between Carbon and Nitrogen Metabolism of Tobacco and the Beginning of Senescence inDifferent Regions of Henan

    Institute of Scientific and Technical Information of China (English)

    杜铮; 魏庆华; 刘卫群

    2011-01-01

    Taking NC89 as materials,this article investigated the variation trends of the key materials and the key enzymes in carbon and nitrogen metabolism, and the variation trends of the secondary metabolites. In order to explain the beginning of senescence and its effect on the secondary metabolites,the intensity and the degree of coordination of carbon and nitrogen metabolism during different periods at both regions were analyzed. The results showed that the accumulation of sucrose was due to its low strength of carbon metabolism. Because of the restriction of free ammonia, glutamine synthetase(GS) activity was simillar in both regions. In the tobacco growth process,tobaccos in Baofeng had stronger carbon metabolism than Queshan. At 98 days after transplanting,tocbaccos in Baofeng had accumulated 160% sucrose than Queshan, which accelerated the secondary metabolism process of Baofeng and accumulated more secondary metabolites.%以烤烟NC89为材料,研究了河南宝丰和确山两地区碳氮代谢关键物质和关键酶的变化趋势,以及次生代谢物质的变化,分析了两地区不同时期碳氮代谢的强度和协调程度.结果表明,确山地区烤烟较低的碳代谢引起蔗糖的积累.由于游离氨的限制,两地区谷氨酰胺合成酶的活性变化趋势基本一致.烟叶生长发育过程中,宝丰烟叶碳代谢比确山高;移栽后98 d,宝丰烤烟积累的蔗糖比确山烤烟高160%,加速了宝丰烤烟进入次生代谢的进程,积累了较多的次生代谢物.

  17. The Relationship between Growth-Inequality-Poverty Triangle and Environmental Degradation: Unveiling the Reality

    Directory of Open Access Journals (Sweden)

    Syeda Anam Hassan

    2015-06-01

    Full Text Available It is important to recognize that increase in well-being is no longer dependent on further economic growth, but on economic and social well-being, which means that the decline in carbon dioxide emission without reducing real wellbeing and growth. The aim of this study is to investigate the main driving forces affecting short and long-run carbon emissions pattern due to changes in growth, inequality and poverty triangle in Pakistan over the period 1980 – 2011 by using multivariate cointegration approach. This study uses five different models i.e., each model have an important policy implication in the context of Pakistan. The results indicate that, on the short run, there is a significant negative relationship between economic growth & carbon emissions and economic growth & poverty while there is a positive relationship between i economic growth & income inequality; and ii poverty & income inequality. On the long-run, there is a significant positive relationship between GDP & income inequality, carbon dioxide emissions & income inequality, and poverty & income inequality in Pakistan. On the other side, there is a negative relationship between carbon emissions & economic growth, carbon emissions & income inequality, and economic growth & income inequality. The results of environmental Kuznets curve (EKC hypothesis show an inverted U-shaped trajectory in relation to economic growth in Pakistan. This study contributes to the debate on the existence and policy relevance of the EKC for Pakistan. The conclusion ensures the sustainability of an urgent need to look beyond the EKC by adopting courageous policy measures of environmental preservation in Pakistan irrespective of the country's level of income. For reduction of CO2 emission, environmental progressive management policies, economic transport system regulations, and low emit fuel consumption by industries are the need of the world.

  18. Central Carbon Metabolic Pathways in Streptomyces

    NARCIS (Netherlands)

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

    2011-01-01

    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 surpr

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1989-02-07

    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.

  20. Glutamine synthetase in Medicago truncatula, unveiling new secrets of a very old enzyme

    Directory of Open Access Journals (Sweden)

    Ana Rita Seabra

    2015-07-01

    Full Text Available Glutamine Synthetase (GS catalyses the first step at which nitrogen is brought into cellular metabolism and is also involved in the reassimilation of ammonium released by a number of metabolic pathways. Due to its unique position in plant nitrogen metabolism, GS plays essential roles in all aspects of plant development, from germination to senescence, and is a key component of nitrogen use efficiency (NUE and plant yield. Understanding the mechanisms regulating GS activity is therefore of utmost importance and a great effort has been dedicated to understand how GS is regulated in different plant species. The present review summarizes exciting recent developments concerning the structure and regulation of glutamine synthetase isoenzymes, using the model legume Medicago truncatula. These include the understanding of the structural determinants of both the cytosolic and plastid located isoenzymes, the existence of a seed-specific GS gene unique to M. truncatula and closely related species and the discovery that GS isoenzymes are regulated by nitric oxide at the post-translational level. The data is discussed and integrated with the potential roles of the distinct GS isoenzymes within the whole plant context.

  1. Glutamine synthetase in Medicago truncatula, unveiling new secrets of a very old enzyme.

    Science.gov (United States)

    Seabra, Ana R; Carvalho, Helena G

    2015-01-01

    Glutamine synthetase (GS) catalyzes the first step at which nitrogen is brought into cellular metabolism and is also involved in the reassimilation of ammonium released by a number of metabolic pathways. Due to its unique position in plant nitrogen metabolism, GS plays essential roles in all aspects of plant development, from germination to senescence, and is a key component of nitrogen use efficiency (NUE) and plant yield. Understanding the mechanisms regulating GS activity is therefore of utmost importance and a great effort has been dedicated to understand how GS is regulated in different plant species. The present review summarizes exciting recent developments concerning the structure and regulation of GS isoenzymes, using the model legume Medicago truncatula. These include the understanding of the structural determinants of both the cytosolic and plastid located isoenzymes, the existence of a seed-specific GS gene unique to M. truncatula and closely related species and the discovery that GS isoenzymes are regulated by nitric oxide at the post-translational level. The data is discussed and integrated with the potential roles of the distinct GS isoenzymes within the whole plant context.

  2. Efficient preparation of carbamates by Rh-catalysed oxidative carbonylation: unveiling the role of the oxidant.

    Science.gov (United States)

    Iturmendi, Amaia; Iglesias, Manuel; Munárriz, Julen; Polo, Victor; Pérez-Torrente, Jesús J; Oro, Luis A

    2016-12-22

    The synthesis of a wide variety of carbamates from amines, alcohols and carbon monoxide has been achieved by means of a Rh-catalysed oxidative carbonylation reaction that uses Oxone as a stoichiometric oxidant. In-depth studies on the reaction mechanism shed light on the intimate role of Oxone in the catalytic cycle.

  3. Gr and hp-1 tomato mutants unveil unprecedented interactions between arbuscular mycorrhizal symbiosis and fruit ripening

    Science.gov (United States)

    The roots of plants interact with soil mycorrhizal fungi to facilitate soil nutrient acquisition by the plant and carbon transfer to the fungus. Here we use tomato fruit ripening mutations to demonstrate that this root interaction communicates with and supports genetic mechanisms associated with th...

  4. Carbon Carbon Composites: An Overview .

    Directory of Open Access Journals (Sweden)

    G. Rohini Devi

    1993-10-01

    Full Text Available Carbon carbon composites are a new class of engineering materials that are ceramic in nature but exhibit brittle to pseudoplastic behaviour. Carbon-carbon is a unique all-carbon composite with carbon fibre embeded in carbon matrix and is known as an inverse composite. Due to their excellent thermo-structural properties, carbon-carbon composites are used in specialised application like re-entry nose-tips, leading edges, rocket nozzles, and aircraft brake discs apart from several industrial and biomedical applications. The multidirectional carbon-carbon product technology is versatile and offers design flexibility. This paper describes the multidirectional preform and carbon-carbon process technology and research and development activities within the country. Carbon-carbon product experience at DRDL has also been discussed. Development of carbon-carbon brake discs process technology using the liquid impregnation process is described. Further the test results on material characterisation, thermal, mechanical and tribological properties are presented.

  5. Metabolic heterogeneity in human lung tumors

    Science.gov (United States)

    Hensley, Christopher T.; Faubert, Brandon; Yuan, Qing; Lev-Cohain, Naama; Jin, Eunsook; Kim, Jiyeon; Jiang, Lei; Ko, Bookyung; Skelton, Rachael; Loudat, Laurin; Wodzak, Michelle; Klimko, Claire; McMillan, Elizabeth; Butt, Yasmeen; Ni, Min; Oliver, Dwight; Torrealba, Jose; Malloy, Craig R.; Kernstine, Kemp; Lenkinski, Robert E.; DeBerardinis, Ralph J.

    2015-01-01

    SUMMARY Non-small cell lung cancer (NSCLC) is heterogeneous in the genetic and environmental parameters that influence cell metabolism in culture. Here, we assessed the impact of these factors on human NSCLC metabolism in vivo using intra-operative 13C-glucose infusions in nine NSCLC patients to compare metabolism between tumors and benign lung. While enhanced glycolysis and glucose oxidation were common among these tumors, we observed evidence for oxidation of multiple nutrients in each of them, including lactate as a potential carbon source. Moreover, metabolically heterogeneous regions were identified within and between tumors, and surprisingly, our data suggested potential contributions of non-glucose nutrients in well-perfused tumor areas. Our findings not only demonstrate the heterogeneity in tumor metabolism in vivo but also highlight the strong influence of the microenvironment on this feature. PMID:26853473

  6. Unveiling Their Worlds: The Use of Dialogue as a Health-Promotion Tool for HIV/AIDS Education in a Poor Community in Kenya

    Science.gov (United States)

    Kiragu, Susan; McLaughlin, Colleen

    2011-01-01

    Three decades since the onset of HIV/AIDS, 33.2 million people worldwide are infected and prevalence in Kenya is on the rise. This paper contributes to discussions about HIV/AIDS education and draws on the health promotion approach and the emancipatory theory of Paulo Freire. Freire argued that through dialogue people unveil their world. The…

  7. IEEE Milestone at CERN - W Cleon Anderson (right), president of the Institute of Electrical and Electronics Engineers, unveils the Milestone plaque at CERN, together with Georges Charpak

    CERN Multimedia

    Maximilien Brice

    2005-01-01

    At a ceremony on 26 September at CERN, W Cleon Anderson, president of the Institute of Electrical and Electronics Engineers (IEEE), formally dedicated a "Milestone" plaque in recognition of the invention of electronic particle detectors at CERN. The plaque was unveiled by Anderson and Georges Charpak, the Nobel-prize winning inventor of wire-chamber technology at CERN.

  8. Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism

    DEFF Research Database (Denmark)

    Buescher, Joerg Martin; Liebermeister, Wolfram; Jules, Matthieu

    2012-01-01

    Adaptation of cells to environmental changes requires dynamic interactions between metabolic and regulatory networks, but studies typically address only one or a few layers of regulation. For nutritional shifts between two preferred carbon sources of Bacillus subtilis, we combined statistical...

  9. Targeted metagenomics unveils the molecular basis for adaptive evolution of enzymes to their environment

    Science.gov (United States)

    Suenaga, Hikaru

    2015-01-01

    Microorganisms have a wonderful ability to adapt rapidly to new or altered environmental conditions. Enzymes are the basis of metabolism in all living organisms and, therefore, enzyme adaptation plays a crucial role in the adaptation of microorganisms. Comparisons of homology and parallel beneficial mutations in an enzyme family provide valuable hints of how an enzyme adapted to an ecological system; consequently, a series of enzyme collections is required to investigate enzyme evolution. Targeted metagenomics is a promising tool for the construction of enzyme pools and for studying the adaptive evolution of enzymes. This perspective article presents a summary of targeted metagenomic approaches useful for this purpose. PMID:26441940

  10. Targeted metagenomics unveils the molecular basis for adaptive evolution of enzymes to their environment

    Directory of Open Access Journals (Sweden)

    Hikaru eSuenaga

    2015-09-01

    Full Text Available Microorganisms have a wonderful ability to adapt rapidly to new or altered environmental conditions. Enzymes are the basis of metabolism in all living organisms and therefore enzyme adaptation plays a crucial role in the adaptation of microorganisms. Comparisons of homology and parallel beneficial mutations in an enzyme family provide valuable hints of how an enzyme adapted to an ecological system; consequently, a series of enzyme collections is required to investigate enzyme evolution. Targeted metagenomics is a promising tool for the construction of enzyme pools and for studying the adaptive evolution of enzymes. This perspective article presents a summary of targeted metagenomic approaches useful for this purpose.

  11. A possible FRB/GRB connection: towards a multi-wavelength campaign to unveil the nature of Fast Radio Bursts

    CERN Document Server

    Zhang, Bing

    2013-01-01

    The physical nature of Fast Radio Bursts (FRBs), a new type of cosmological transients discovered recently, is not known. It has been suggested that FRBs can be produced when a spinning supra-massive neutron star loses centrifugal support and collapses to a black hole. Here we suggest that such implosions can happen in supra-massive neutron stars shortly (hundreds to thousands of seconds) after their births, and an observational signature of such implosions may have been observed in the X-ray afterglows of some long and short gamma-ray bursts (GRBs). Within this picture, a small fraction of FRBs would be physically connected to GRBs. We discuss possible multi-wavelength electromagnetic signals and gravitational wave signals that might be associated with FRBs, and propose an observational campaign to unveil the physical nature of FRBs. In particular, we strongly encourage a rapid radio follow-up observation of GRBs starting from 100 s after GRB triggers.

  12. An integrative approach unveils FOSL1 as an oncogene vulnerability in KRAS-driven lung and pancreatic cancer

    DEFF Research Database (Denmark)

    Vallejo, Adrian; Perurena, Naiara; Guruceaga, Elisabet

    2017-01-01

    KRAS mutated tumours represent a large fraction of human cancers, but the vast majority remains refractory to current clinical therapies. Thus, a deeper understanding of the molecular mechanisms triggered by KRAS oncogene may yield alternative therapeutic strategies. Here we report the identifica......, combination of AURKA and MEK inhibitors induces a deleterious effect on mutant KRAS cells. Our findings unveil KRAS downstream effectors that provide opportunities to treat KRAS-driven cancers.......KRAS mutated tumours represent a large fraction of human cancers, but the vast majority remains refractory to current clinical therapies. Thus, a deeper understanding of the molecular mechanisms triggered by KRAS oncogene may yield alternative therapeutic strategies. Here we report...... the identification of a common transcriptional signature across mutant KRAS cancers of distinct tissue origin that includes the transcription factor FOSL1. High FOSL1 expression identifies mutant KRAS lung and pancreatic cancer patients with the worst survival outcome. Furthermore, FOSL1 genetic inhibition...

  13. Complex mitonuclear interactions and metabolic costs of mating in male seed beetles.

    Science.gov (United States)

    Immonen, E; Rönn, J; Watson, C; Berger, D; Arnqvist, G

    2016-02-01

    The lack of evolutionary response to selection on mitochondrial genes through males predicts the evolution of nuclear genetic influence on male-specific mitochondrial function, for example by gene duplication and evolution of sex-specific expression of paralogs involved in metabolic pathways. Intergenomic epistasis may therefore be a prevalent feature of the genetic architecture of male-specific organismal function. Here, we assess the role of mitonuclear genetic variation for male metabolic phenotypes [metabolic rate and respiratory quotient (RQ)] associated with ejaculate renewal, in the seed beetle Callosobruchus maculatus, by assaying lines with crossed combinations of distinct mitochondrial haplotypes and nuclear lineages. We found a significant increase in metabolic rate following mating relative to virgin males. Moreover, processes associated with ejaculate renewal showed variation in metabolic rate that was affected by mitonuclear interactions. Mitochondrial haplotype influenced mating-related changes in RQ, but this pattern varied over time. Mitonuclear genotype and the energy spent during ejaculate production affected the weight of the ejaculate, but the strength of this effect varied across mitochondrial haplotypes showing that the genetic architecture of male-specific reproductive function is complex. Our findings unveil hitherto underappreciated metabolic costs of mating and ejaculate renewal, and provide the first empirical demonstration of mitonuclear epistasis on male reproductive metabolic processes.

  14. Carbohydrate Metabolism Disorders

    Science.gov (United States)

    ... you eat. Food is made up of proteins, carbohydrates, and fats. Chemicals in your digestive system (enzymes) ... metabolic disorder, something goes wrong with this process. Carbohydrate metabolism disorders are a group of metabolic disorders. ...

  15. 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...... coupled to mass spectrometry revealed a distinct metabolic phenotype for nodules that reflected the global changes in metabolism inferred from transcriptome analysis. Udgivelsesdato: 2004-Aug...

  16. Database of normal human cerebral blood flow, cerebral blood volume, cerebral oxygen extraction fraction and cerebral metabolic rate of oxygen measured by positron emission tomography with {sup 15}O-labelled carbon dioxide or water, carbon monoxide and oxygen: a multicentre study in Japan

    Energy Technology Data Exchange (ETDEWEB)

    Ito, Hiroshi [Department of Radiology and Nuclear Medicine, Akita Research Institute of Brain and Blood Vessels, Akita (Japan); Department of Nuclear Medicine and Radiology, Division of Brain Sciences, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-Machi, 980-8575, Aoba-Ku, Sendai (Japan); Kanno, Iwao [Department of Radiology and Nuclear Medicine, Akita Research Institute of Brain and Blood Vessels, Akita (Japan); Kato, Chietsugu [Department of Nuclear Medicine, Hokkaido University School of Medicine, Sapporo (Japan); Sasaki, Toshiaki [Cyclotoron Research Center, Iwate Medical University, Morioka (Japan); Ishii, Kenji [Positron Medical Center, Tokyo Metropolitan Institute of Gerontology, Tokyo (Japan); Ouchi, Yasuomi [Positron Medical Center, Hamamatsu Medical Center, Hamakita (Japan); Iida, Akihiko [Nagoya City Rehabilitation Center, Nagoya (Japan); Okazawa, Hidehiko [PET Unit, Research Institute, Shiga Medical Center, Moriyama (Japan); Hayashida, Kohei [Department of Radiology, National Cardiovascular Center, Suita, Osaka (Japan); Tsuyuguchi, Naohiro [