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Sample records for regulating assimilative enzyme

  1. Ectomycorrhizal fungi enhance nitrogen and phosphorus nutrition of Nothofagus dombeyi under drought conditions by regulating assimilative enzyme activities.

    Science.gov (United States)

    Alvarez, Maricel; Huygens, Dries; Olivares, Erick; Saavedra, Isabel; Alberdi, Miren; Valenzuela, Eduardo

    2009-08-01

    Drought stress conditions (DC) reduce plant growth and nutrition, restraining the sustainable reestablishment of Nothofagus dombeyi in temperate south Chilean forest ecosystems. Ectomycorrhizal symbioses have been documented to enhance plant nitrogen (N) and phosphorus (P) uptake under drought, but the regulation of involved assimilative enzymes remains unclear. We studied 1-year-old N. dombeyi (Mirb.) Oerst. plants in association with the ectomycorrhizal fungi Pisolithus tinctorius (Pers.) Coker & Couch. and Descolea antartica Sing. In greenhouse experiments, shoot and root dry weights, mycorrhizal colonization, foliar N and P concentrations, and root enzyme activities [glutamate synthase (glutamine oxoglutarate aminotransferase (GOGAT), EC 1.4.1.13-14), glutamine synthetase (GS, EC 6.3.1.2), glutamate dehydrogenase (GDH, EC 1.4.1.2-4), nitrate reductase (NR, EC 1.6.6.1), and acid phosphomonoesterase (PME, EC 3.1.3.1-2)] were determined as a function of soil-water content. Inoculation of N. dombeyi with P. tinctorius and D. antartica significantly stimulated plant growth and increased plant foliar N and P concentrations, especially under DC. Ectomycorrhizal inoculation increased the activity of all studied enzymes relative to non-mycorrhizal plants under drought. We speculate that GDH is a key enzyme involved in the enhancement of ectomycorrhizal carbon (C) availability by fuelling the tricarboxylic acid (TCA) cycle under conditions of drought-induced carbon deficit. All studied assimilative enzymes of the ectomycorrhizal associations, involved in C, N, and P transfers, are closely interlinked and interdependent. The up-regulation of assimilative enzyme activities by ectomycorrhizal fungal root colonizers acts as a functional mechanism to increase seedling endurance to drought. We insist upon incorporating ectomycorrhizal inoculation in existing Chilean afforestation programs.

  2. The Enzymes of the Ammonia Assimilation in Pseudomonas aeruginosa

    NARCIS (Netherlands)

    Janssen, Dick B.; Camp, Huub J.M. op den; Leenen, Pieter J.M.; Drift, Chris van der

    1980-01-01

    Glutamine synthetase from Pseudomonas aeruginosa is regulated by repression/derepression of enzyme synthesis and by adenylylation/deadenylylation control. High levels of deadenylylated biosynthetically active glutamine synthetase were observed in cultures growing with limiting amounts of nitrogen

  3. How exogenous nitric oxide regulates nitrogen assimilation in wheat seedlings under different nitrogen sources and levels.

    Science.gov (United States)

    Balotf, Sadegh; Islam, Shahidul; Kavoosi, Gholamreza; Kholdebarin, Bahman; Juhasz, Angela; Ma, Wujun

    2018-01-01

    Nitrogen (N) is one of the most important nutrients for plants and nitric oxide (NO) as a signaling plant growth regulator involved in nitrogen assimilation. Understanding the influence of exogenous NO on nitrogen metabolism at the gene expression and enzyme activity levels under different sources of nitrogen is vitally important for increasing nitrogen use efficiency (NUE). This study investigated the expression of key genes and enzymes in relation to nitrogen assimilation in two Australian wheat cultivars, a popular high NUE cv. Spitfire and a normal NUE cv. Westonia, under different combinations of nitrogen and sodium nitroprusside (SNP) as the NO donor. Application of NO increased the gene expressions and activities of nitrogen assimilation pathway enzymes in both cultivars at low levels of nitrogen. At high nitrogen supplies, the expressions and activities of N assimilation genes increased in response to exogenous NO only in cv. Spitfire but not in cv. Westonia. Exogenous NO caused an increase in leaf NO content at low N supplies in both cultivars, while under high nitrogen treatments, cv. Spitfire showed an increase under ammonium nitrate (NH4NO3) treatment but cv. Westonia was not affected. N assimilation gene expression and enzyme activity showed a clear relationship between exogenous NO, N concentration and N forms in primary plant nitrogen assimilation. Results reveal the possible role of NO and different nitrogen sources on nitrogen assimilation in Triticum aestivum plants.

  4. Nitrogen assimilation system in maize is regulated by developmental and tissue-specific mechanisms

    KAUST Repository

    Plett, Darren

    2016-08-10

    Key message: We found metabolites, enzyme activities and enzyme transcript abundances vary significantly across the maize lifecycle, but weak correlation exists between the three groups. We identified putative genes regulating nitrate assimilation. Abstract: Progress in improving nitrogen (N) use efficiency (NUE) of crop plants has been hampered by the complexity of the N uptake and utilisation systems. To understand this complexity we measured the activities of seven enzymes and ten metabolites related to N metabolism in the leaf and root tissues of Gaspe Flint maize plants grown in 0.5 or 2.5 mM NO3 − throughout the lifecycle. The amino acids had remarkably similar profiles across the lifecycle except for transient responses, which only appeared in the leaves for aspartate or in the roots for asparagine, serine and glycine. The activities of the enzymes for N assimilation were also coordinated to a certain degree, most noticeably with a peak in root activity late in the lifecycle, but with wide variation in the activity levels over the course of development. We analysed the transcriptional data for gene sets encoding the measured enzymes and found that, unlike the enzyme activities, transcript levels of the corresponding genes did not exhibit the same coordination across the lifecycle and were only weakly correlated with the levels of various amino acids or individual enzyme activities. We identified gene sets which were correlated with the enzyme activity profiles, including seven genes located within previously known quantitative trait loci for enzyme activities and hypothesise that these genes are important for the regulation of enzyme activities. This work provides insights into the complexity of the N assimilation system throughout development and identifies candidate regulatory genes, which warrant further investigation in efforts to improve NUE in crop plants. © 2016, Springer Science+Business Media Dordrecht.

  5. Nitrogen assimilation system in maize is regulated by developmental and tissue-specific mechanisms

    KAUST Repository

    Plett, Darren; Holtham, Luke; Baumann, Ute; Kalashyan, Elena; Francis, Karen; Enju, Akiko; Toubia, John; Roessner, Ute; Bacic, Antony; Rafalski, Antoni; Dhugga, Kanwarpal S.; Tester, Mark A.; Garnett, Trevor; Kaiser, Brent N.

    2016-01-01

    Key message: We found metabolites, enzyme activities and enzyme transcript abundances vary significantly across the maize lifecycle, but weak correlation exists between the three groups. We identified putative genes regulating nitrate assimilation. Abstract: Progress in improving nitrogen (N) use efficiency (NUE) of crop plants has been hampered by the complexity of the N uptake and utilisation systems. To understand this complexity we measured the activities of seven enzymes and ten metabolites related to N metabolism in the leaf and root tissues of Gaspe Flint maize plants grown in 0.5 or 2.5 mM NO3 − throughout the lifecycle. The amino acids had remarkably similar profiles across the lifecycle except for transient responses, which only appeared in the leaves for aspartate or in the roots for asparagine, serine and glycine. The activities of the enzymes for N assimilation were also coordinated to a certain degree, most noticeably with a peak in root activity late in the lifecycle, but with wide variation in the activity levels over the course of development. We analysed the transcriptional data for gene sets encoding the measured enzymes and found that, unlike the enzyme activities, transcript levels of the corresponding genes did not exhibit the same coordination across the lifecycle and were only weakly correlated with the levels of various amino acids or individual enzyme activities. We identified gene sets which were correlated with the enzyme activity profiles, including seven genes located within previously known quantitative trait loci for enzyme activities and hypothesise that these genes are important for the regulation of enzyme activities. This work provides insights into the complexity of the N assimilation system throughout development and identifies candidate regulatory genes, which warrant further investigation in efforts to improve NUE in crop plants. © 2016, Springer Science+Business Media Dordrecht.

  6. Flux balance analysis of ammonia assimilation network in E. coli predicts preferred regulation point.

    Science.gov (United States)

    Wang, Lu; Lai, Luhua; Ouyang, Qi; Tang, Chao

    2011-01-25

    Nitrogen assimilation is a critical biological process for the synthesis of biomolecules in Escherichia coli. The central ammonium assimilation network in E. coli converts carbon skeleton α-ketoglutarate and ammonium into glutamate and glutamine, which further serve as nitrogen donors for nitrogen metabolism in the cell. This reaction network involves three enzymes: glutamate dehydrogenase (GDH), glutamine synthetase (GS) and glutamate synthase (GOGAT). In minimal media, E. coli tries to maintain an optimal growth rate by regulating the activity of the enzymes to match the availability of the external ammonia. The molecular mechanism and the strategy of the regulation in this network have been the research topics for many investigators. In this paper, we develop a flux balance model for the nitrogen metabolism, taking into account of the cellular composition and biosynthetic requirements for nitrogen. The model agrees well with known experimental results. Specifically, it reproduces all the (15)N isotope labeling experiments in the wild type and the two mutant (ΔGDH and ΔGOGAT) strains of E. coli. Furthermore, the predicted catalytic activities of GDH, GS and GOGAT in different ammonium concentrations and growth rates for the wild type, ΔGDH and ΔGOGAT strains agree well with the enzyme concentrations obtained from western blots. Based on this flux balance model, we show that GS is the preferred regulation point among the three enzymes in the nitrogen assimilation network. Our analysis reveals the pattern of regulation in this central and highly regulated network, thus providing insights into the regulation strategy adopted by the bacteria. Our model and methods may also be useful in future investigations in this and other networks.

  7. Flux balance analysis of ammonia assimilation network in E. coli predicts preferred regulation point.

    Directory of Open Access Journals (Sweden)

    Lu Wang

    Full Text Available Nitrogen assimilation is a critical biological process for the synthesis of biomolecules in Escherichia coli. The central ammonium assimilation network in E. coli converts carbon skeleton α-ketoglutarate and ammonium into glutamate and glutamine, which further serve as nitrogen donors for nitrogen metabolism in the cell. This reaction network involves three enzymes: glutamate dehydrogenase (GDH, glutamine synthetase (GS and glutamate synthase (GOGAT. In minimal media, E. coli tries to maintain an optimal growth rate by regulating the activity of the enzymes to match the availability of the external ammonia. The molecular mechanism and the strategy of the regulation in this network have been the research topics for many investigators. In this paper, we develop a flux balance model for the nitrogen metabolism, taking into account of the cellular composition and biosynthetic requirements for nitrogen. The model agrees well with known experimental results. Specifically, it reproduces all the (15N isotope labeling experiments in the wild type and the two mutant (ΔGDH and ΔGOGAT strains of E. coli. Furthermore, the predicted catalytic activities of GDH, GS and GOGAT in different ammonium concentrations and growth rates for the wild type, ΔGDH and ΔGOGAT strains agree well with the enzyme concentrations obtained from western blots. Based on this flux balance model, we show that GS is the preferred regulation point among the three enzymes in the nitrogen assimilation network. Our analysis reveals the pattern of regulation in this central and highly regulated network, thus providing insights into the regulation strategy adopted by the bacteria. Our model and methods may also be useful in future investigations in this and other networks.

  8. Allosteric regulation of epigenetic modifying enzymes.

    Science.gov (United States)

    Zucconi, Beth E; Cole, Philip A

    2017-08-01

    Epigenetic enzymes including histone modifying enzymes are key regulators of gene expression in normal and disease processes. Many drug development strategies to target histone modifying enzymes have focused on ligands that bind to enzyme active sites, but allosteric pockets offer potentially attractive opportunities for therapeutic development. Recent biochemical studies have revealed roles for small molecule and peptide ligands binding outside of the active sites in modulating the catalytic activities of histone modifying enzymes. Here we highlight several examples of allosteric regulation of epigenetic enzymes and discuss the biological significance of these findings. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Lanthanum (III) regulates the nitrogen assimilation in soybean seedlings under ultraviolet-B radiation.

    Science.gov (United States)

    Huang, Guangrong; Wang, Lihong; Zhou, Qing

    2013-01-01

    Ultraviolet-B (UV-B, 280-320 nm) radiation has seriously affected the growth of plants. Finding the technology/method to alleviate the damage of UV-B radiation has become a frontal topic in the field of environmental science. The pretreatment with rare earth elements (REEs) is an effective method, but the regulation mechanism of REEs is unknown. Here, the regulation effects of lanthanum (La(III)) on nitrogen assimilation in soybean seedlings (Glycine max L.) under ultraviolet-B radiation were investigated to elucidate the regulation mechanism of REEs on plants under UV-B radiation. UV-B radiation led to the inhibition in the activities of the key enzymes (nitrate reductase, glutamine synthetase, glutamate synthase) in the nitrogen assimilation, the decrease in the contents of nitrate and soluble proteins, as well as the increase in the content of amino acid in soybean seedlings. The change degree of UV-B radiation at the high level (0.45 W m(-2)) was higher than that of UV-B radiation at the low level (0.15 W m(-2)). The pretreatment with 20 mg L(-1) La(III) could alleviate the effects of UV-B radiation on the activities of nitrate reductase, glutamine synthetase, glutamate synthase, and glutamate dehydrogenase, promoting amino acid conversion and protein synthesis in soybean seedlings. The regulation effect of La(III) under UV-B radiation at the low level was better than that of UV-B radiation at the high level. The results indicated that the pretreatment with 20 mg L(-1) La(III) could alleviate the inhibition of UV-B radiation on nitrogen assimilation in soybean seedlings.

  10. Brassinosteroid-induced CO{sub 2} assimilation is associated with increased stability of redox-sensitive photosynthetic enzymes in the chloroplasts in cucumber plants

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Yu Ping; Cheng, Fei; Zhou, Yan Hong; Xia, Xiao Jian; Mao, Wei Hua; Shi, Kai [Department of Horticulture, Zijingang Campus, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058 (China); Chen, Zhi Xiang [Department of Horticulture, Zijingang Campus, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058 (China); Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907-2054 (United States); Yu, Jing Quan, E-mail: jqyu@zju.edu.cn [Department of Horticulture, Zijingang Campus, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058 (China); Key Laboratory of Horticultural Plants Growth, Development and Quality Improvement, Ministry of Agriculture of China, Yuhangtang Road 866, Hangzhou 310058 (China)

    2012-09-28

    Highlights: Black-Right-Pointing-Pointer Activity of certain Calvin cycle enzymes and CO{sub 2} assimilation are induced by BRs. Black-Right-Pointing-Pointer BRs upregulate the activity of the ascorbate-glutathione cycle in the chloroplasts. Black-Right-Pointing-Pointer BRs increase the chloroplast thiol reduction state. Black-Right-Pointing-Pointer A BR-induced reducing environment increases the stability of photosynthetic enzymes. -- Abstract: Brassinosteroids (BRs) play important roles in plant growth, development, photosynthesis and stress tolerance; however, the mechanism underlying BR-enhanced photosynthesis is currently unclear. Here, we provide evidence that an increase in the BR level increased the quantum yield of PSII, activities of Rubisco activase (RCA) and fructose-1,6-bisphosphatase (FBPase), and CO{sub 2} assimilation. BRs upregulated the transcript levels of genes and activity of enzymes involved in the ascorbate-glutathione cycle in the chloroplasts, leading to an increased ratio of reduced (GSH) to oxidized (GSSG) glutathione in the chloroplasts. An increased GSH/GSSG ratio protected RCA from proteolytic digestion and increased the stability of redox-sensitive enzymes in the chloroplasts. These results strongly suggest that BRs are capable of regulating the glutathione redox state in the chloroplasts through the activation of the ascorbate-glutathione cycle. The resulting increase in the chloroplast thiol reduction state promotes CO{sub 2} assimilation, at least in part, by enhancing the stability and activity of redox-sensitive photosynthetic enzymes through post-translational modifications.

  11. Brassinosteroid-induced CO2 assimilation is associated with increased stability of redox-sensitive photosynthetic enzymes in the chloroplasts in cucumber plants

    International Nuclear Information System (INIS)

    Jiang, Yu Ping; Cheng, Fei; Zhou, Yan Hong; Xia, Xiao Jian; Mao, Wei Hua; Shi, Kai; Chen, Zhi Xiang; Yu, Jing Quan

    2012-01-01

    Highlights: ► Activity of certain Calvin cycle enzymes and CO 2 assimilation are induced by BRs. ► BRs upregulate the activity of the ascorbate–glutathione cycle in the chloroplasts. ► BRs increase the chloroplast thiol reduction state. ► A BR-induced reducing environment increases the stability of photosynthetic enzymes. -- Abstract: Brassinosteroids (BRs) play important roles in plant growth, development, photosynthesis and stress tolerance; however, the mechanism underlying BR-enhanced photosynthesis is currently unclear. Here, we provide evidence that an increase in the BR level increased the quantum yield of PSII, activities of Rubisco activase (RCA) and fructose-1,6-bisphosphatase (FBPase), and CO 2 assimilation. BRs upregulated the transcript levels of genes and activity of enzymes involved in the ascorbate–glutathione cycle in the chloroplasts, leading to an increased ratio of reduced (GSH) to oxidized (GSSG) glutathione in the chloroplasts. An increased GSH/GSSG ratio protected RCA from proteolytic digestion and increased the stability of redox-sensitive enzymes in the chloroplasts. These results strongly suggest that BRs are capable of regulating the glutathione redox state in the chloroplasts through the activation of the ascorbate–glutathione cycle. The resulting increase in the chloroplast thiol reduction state promotes CO 2 assimilation, at least in part, by enhancing the stability and activity of redox-sensitive photosynthetic enzymes through post-translational modifications.

  12. Modulation of intestinal sulfur assimilation metabolism regulates iron homeostasis

    Science.gov (United States)

    Hudson, Benjamin H.; Hale, Andrew T.; Irving, Ryan P.; Li, Shenglan; York, John D.

    2018-01-01

    Sulfur assimilation is an evolutionarily conserved pathway that plays an essential role in cellular and metabolic processes, including sulfation, amino acid biosynthesis, and organismal development. We report that loss of a key enzymatic component of the pathway, bisphosphate 3′-nucleotidase (Bpnt1), in mice, both whole animal and intestine-specific, leads to iron-deficiency anemia. Analysis of mutant enterocytes demonstrates that modulation of their substrate 3′-phosphoadenosine 5′-phosphate (PAP) influences levels of key iron homeostasis factors involved in dietary iron reduction, import and transport, that in part mimic those reported for the loss of hypoxic-induced transcription factor, HIF-2α. Our studies define a genetic basis for iron-deficiency anemia, a molecular approach for rescuing loss of nucleotidase function, and an unanticipated link between nucleotide hydrolysis in the sulfur assimilation pathway and iron homeostasis. PMID:29507250

  13. Regulation of assimilate partitioning by daylength and spectral quality

    Energy Technology Data Exchange (ETDEWEB)

    Britz, S.J. [USDA-Climate Stress Lab., Beltsville, MD (United States)

    1994-12-31

    Photosynthesis is the process by which plants utilize light energy to assimilate and transform carbon dioxide into products that support growth and development. The preceding review provides an excellent summary of photosynthetic mechanisms and diurnal patterns of carbon metabolism with emphasis on the importance of gradual changes in photosynthetically-active radiation at dawn and dusk. In addition to these direct effects of irradiance, there are indirect effects of light period duration and spectral quality on carbohydrate metabolism and assimilate partitioning. Both daylength and spectral quality trigger developmental phenomena such as flowering (e.g., photoperiodism) and shade avoidance responses, but their effects on partitioning of photoassimilates in leaves are less well known. Moreover, the adaptive significance to the plants of such effects is sometimes not clear.

  14. Integration of Genome Scale Metabolic Networks and Gene Regulation of Metabolic Enzymes With Physiologically Based Pharmacokinetics.

    Science.gov (United States)

    Maldonado, Elaina M; Leoncikas, Vytautas; Fisher, Ciarán P; Moore, J Bernadette; Plant, Nick J; Kierzek, Andrzej M

    2017-11-01

    The scope of physiologically based pharmacokinetic (PBPK) modeling can be expanded by assimilation of the mechanistic models of intracellular processes from systems biology field. The genome scale metabolic networks (GSMNs) represent a whole set of metabolic enzymes expressed in human tissues. Dynamic models of the gene regulation of key drug metabolism enzymes are available. Here, we introduce GSMNs and review ongoing work on integration of PBPK, GSMNs, and metabolic gene regulation. We demonstrate example models. © 2017 The Authors CPT: Pharmacometrics & Systems Pharmacology published by Wiley Periodicals, Inc. on behalf of American Society for Clinical Pharmacology and Therapeutics.

  15. A thermodynamic and theoretical view for enzyme regulation.

    Science.gov (United States)

    Zhao, Qinyi

    2015-01-01

    Precise regulation is fundamental to the proper functioning of enzymes in a cell. Current opinions about this, such as allosteric regulation and dynamic contribution to enzyme regulation, are experimental models and substantially empirical. Here we proposed a theoretical and thermodynamic model of enzyme regulation. The main idea is that enzyme regulation is processed via the regulation of abundance of active conformation in the reaction buffer. The theoretical foundation, experimental evidence, and experimental criteria to test our model are discussed and reviewed. We conclude that basic principles of enzyme regulation are laws of protein thermodynamics and it can be analyzed using the concept of distribution curve of active conformations of enzymes.

  16. Peroxidase enzymes regulate collagen extracellular matrix biosynthesis.

    Science.gov (United States)

    DeNichilo, Mark O; Panagopoulos, Vasilios; Rayner, Timothy E; Borowicz, Romana A; Greenwood, John E; Evdokiou, Andreas

    2015-05-01

    Myeloperoxidase and eosinophil peroxidase are heme-containing enzymes often physically associated with fibrotic tissue and cancer in various organs, without any direct involvement in promoting fibroblast recruitment and extracellular matrix (ECM) biosynthesis at these sites. We report herein novel findings that show peroxidase enzymes possess a well-conserved profibrogenic capacity to stimulate the migration of fibroblastic cells and promote their ability to secrete collagenous proteins to generate a functional ECM both in vitro and in vivo. Mechanistic studies conducted using cultured fibroblasts show that these cells are capable of rapidly binding and internalizing both myeloperoxidase and eosinophil peroxidase. Peroxidase enzymes stimulate collagen biosynthesis at a post-translational level in a prolyl 4-hydroxylase-dependent manner that does not require ascorbic acid. This response was blocked by the irreversible myeloperoxidase inhibitor 4-amino-benzoic acid hydrazide, indicating peroxidase catalytic activity is essential for collagen biosynthesis. These results suggest that peroxidase enzymes, such as myeloperoxidase and eosinophil peroxidase, may play a fundamental role in regulating the recruitment of fibroblast and the biosynthesis of collagen ECM at sites of normal tissue repair and fibrosis, with enormous implications for many disease states where infiltrating inflammatory cells deposit peroxidases. Copyright © 2015 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

  17. Stress-induced cytokinin synthesis increases drought tolerance through the coordinated regulation of carbon and nitrogen assimilation in rice.

    Science.gov (United States)

    Reguera, Maria; Peleg, Zvi; Abdel-Tawab, Yasser M; Tumimbang, Ellen B; Delatorre, Carla A; Blumwald, Eduardo

    2013-12-01

    The effects of water deficit on carbon and nitrogen metabolism were investigated in flag leaves of wild-type and transgenic rice (Oryza sativa japonica 'Kitaake') plants expressing ISOPENTENYLTRANSFERASE (IPT; encoding the enzyme that mediates the rate-limiting step in cytokinin synthesis) under the control of P(SARK), a maturation- and stress-induced promoter. While the wild-type plants displayed inhibition of photosynthesis and nitrogen assimilation during water stress, neither carbon nor nitrogen assimilation was affected by stress in the transgenic P(SARK)::IPT plants. In the transgenic plants, photosynthesis was maintained at control levels during stress and the flag leaf showed increased sucrose (Suc) phosphate synthase activity and reduced Suc synthase and invertase activities, leading to increased Suc contents. The sustained carbon assimilation in the transgenic P(SARK)::IPT plants was well correlated with enhanced nitrate content, higher nitrate reductase activity, and sustained ammonium contents, indicating that the stress-induced cytokinin synthesis in the transgenic plants played a role in maintaining nitrate acquisition. Protein contents decreased and free amino acids increased in wild-type plants during stress, while protein content was preserved in the transgenic plants. Our results indicate that the stress-induced cytokinin synthesis in the transgenic plants promoted sink strengthening through a cytokinin-dependent coordinated regulation of carbon and nitrogen metabolism that facilitates an enhanced tolerance of the transgenic plants to water deficit.

  18. TetR Family Transcriptional Regulator PccD Negatively Controls Propionyl Coenzyme A Assimilation in Saccharopolyspora erythraea.

    Science.gov (United States)

    Xu, Zhen; Wang, Miaomiao; Ye, Bang-Ce

    2017-10-15

    Propanol stimulates erythromycin biosynthesis by increasing the supply of propionyl coenzyme A (propionyl-CoA), a starter unit of erythromycin production in Saccharopolyspora erythraea Propionyl-CoA is assimilated via propionyl-CoA carboxylase to methylmalonyl-CoA, an extender unit of erythromycin. We found that the addition of n -propanol or propionate caused a 4- to 16-fold increase in the transcriptional levels of the SACE_3398-3400 locus encoding propionyl-CoA carboxylase, a key enzyme in propionate metabolism. The regulator PccD was proved to be directly involved in the transcription regulation of the SACE_3398-3400 locus by EMSA and DNase I footprint analysis. The transcriptional levels of SACE_3398-3400 were upregulated 15- to 37-fold in the pccD gene deletion strain (Δ pccD ) and downregulated 3-fold in the pccD overexpression strain (WT/pIB- pccD ), indicating that PccD was a negative transcriptional regulator of SACE_3398-3400. The Δ pccD strain has a higher growth rate than that of the wild-type strain (WT) on Evans medium with propionate as the sole carbon source, whereas the growth of the WT/pIB- pccD strain was repressed. As a possible metabolite of propionate metabolism, methylmalonic acid was identified as an effector molecule of PccD and repressed its regulatory activity. A higher level of erythromycin in the Δ pccD strain was observed compared with that in the wild-type strain. Our study reveals a regulatory mechanism in propionate metabolism and suggests new possibilities for designing metabolic engineering to increase erythromycin yield. IMPORTANCE Our work has identified the novel regulator PccD that controls the expression of the gene for propionyl-CoA carboxylase, a key enzyme in propionyl-CoA assimilation in S. erythraea PccD represses the generation of methylmalonyl-CoA through carboxylation of propionyl-CoA and reveals an effect on biosynthesis of erythromycin. This finding provides novel insight into propionyl-CoA assimilation, and

  19. Multiple complexes of nitrogen assimilatory enzymes in spinach chloroplasts: possible mechanisms for the regulation of enzyme function.

    Directory of Open Access Journals (Sweden)

    Yoko Kimata-Ariga

    Full Text Available Assimilation of nitrogen is an essential biological process for plant growth and productivity. Here we show that three chloroplast enzymes involved in nitrogen assimilation, glutamate synthase (GOGAT, nitrite reductase (NiR and glutamine synthetase (GS, separately assemble into distinct protein complexes in spinach chloroplasts, as analyzed by western blots under blue native electrophoresis (BN-PAGE. GOGAT and NiR were present not only as monomers, but also as novel complexes with a discrete size (730 kDa and multiple sizes (>120 kDa, respectively, in the stromal fraction of chloroplasts. These complexes showed the same mobility as each monomer on two-dimensional (2D SDS-PAGE after BN-PAGE. The 730 kDa complex containing GOGAT dissociated into monomers, and multiple complexes of NiR reversibly converted into monomers, in response to the changes in the pH of the stromal solvent. On the other hand, the bands detected by anti-GS antibody were present not only in stroma as a conventional decameric holoenzyme complex of 420 kDa, but also in thylakoids as a novel complex of 560 kDa. The polypeptide in the 560 kDa complex showed slower mobility than that of the 420 kDa complex on the 2D SDS-PAGE, implying the assembly of distinct GS isoforms or a post-translational modification of the same GS protein. The function of these multiple complexes was evaluated by in-gel GS activity under native conditions and by the binding ability of NiR and GOGAT with their physiological electron donor, ferredoxin. The results indicate that these multiplicities in size and localization of the three nitrogen assimilatory enzymes may be involved in the physiological regulation of their enzyme function, in a similar way as recently described cases of carbon assimilatory enzymes.

  20. Promiscuous activities of heterologous enzymes lead to unintended metabolic rerouting in Saccharomyces cerevisiae engineered to assimilate various sugars from renewable biomass.

    Science.gov (United States)

    Yun, Eun Ju; Oh, Eun Joong; Liu, Jing-Jing; Yu, Sora; Kim, Dong Hyun; Kwak, Suryang; Kim, Kyoung Heon; Jin, Yong-Su

    2018-01-01

    Understanding the global metabolic network, significantly perturbed upon promiscuous activities of foreign enzymes and different carbon sources, is crucial for systematic optimization of metabolic engineering of yeast Saccharomyces cerevisiae . Here, we studied the effects of promiscuous activities of overexpressed enzymes encoded by foreign genes on rerouting of metabolic fluxes of an engineered yeast capable of assimilating sugars from renewable biomass by profiling intracellular and extracellular metabolites. Unbiased metabolite profiling of the engineered S. cerevisiae strain EJ4 revealed promiscuous enzymatic activities of xylose reductase and xylitol dehydrogenase on galactose and galactitol, respectively, resulting in accumulation of galactitol and tagatose during galactose fermentation. Moreover, during glucose fermentation, a trisaccharide consisting of glucose accumulated outside of the cells probably owing to the promiscuous and transglycosylation activity of β-glucosidase expressed for hydrolyzing cellobiose. Meanwhile, higher accumulation of fatty acids and secondary metabolites was observed during xylose and cellobiose fermentations, respectively. The heterologous enzymes functionally expressed in S. cerevisiae showed promiscuous activities that led to unintended metabolic rerouting in strain EJ4. Such metabolic rerouting could result in a low yield and productivity of a final product due to the formation of unexpected metabolites. Furthermore, the global metabolic network can be significantly regulated by carbon sources, thus yielding different patterns of metabolite production. This metabolomic study can provide useful information for yeast strain improvement and systematic optimization of yeast metabolism to manufacture bio-based products.

  1. Salinity and Salicylic Acid Interactions in Affecting Nitrogen Assimilation, Enzyme Activity, Ions Content and Translocation Rate of Maize Plants

    International Nuclear Information System (INIS)

    Khodary, S.E.A.; Moussa, H.R.

    2002-01-01

    This study was carried out to establish the relationship between nitrogen metabolism, enzyme activity, ions concentration as well as the translocation rate (TR) of carbohydrates and salicylic acid (SA) in salt-stressed maize (Zea mays L). Salicylic acid plus salinity treatment highly significantly increased: nucleic acids (DNA and RNA), protein content, phosphoenolpyruvate carboxylase (PEPCase) and nitrate reductase (NR) and inhibited nucleases (DNase and RNase) activities compared with Na CI-treated plants. In addition, the ionic levels of potassium (K), phosphorus (P), nitrate (NO 3 ) and the translocation rate of the labelled photo assimilates have also been stimulated while sodium (Na) ions content was decreased. It is concluded that, salinazid maize plants might show an enhancement in their growth pattern upon salicylic acid application

  2. FY 2000 report on the promotion projects by Research Institute of Innovative Technology for the Earth. Proceedings of the international seminar (Reports on photosynthetic CO2-assimilating enzymes by the international workshops); 2000 nendo chikyu kankyo sangyo gijutsu kaihatsu suishin jigyo kokusai seminar jigyo shiryo. Kogosei CO2 kotei koso kokusai workshop hokokusho

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2001-03-01

    Described herein are the reports on photosynthetic CO2-assimilating enzymes, presented to the international symposium. These enzymes are important for assimilating CO2 in air, maintaining the environments and production of foods. For genes and proteins, the topics include diversification and function evolution of the RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) in the natural environments, in particular in microorganisms. For activity regulation of PEPC, the topics include three-dimensional structures of PEPC and phosphorylation mechanisms and activity regulation therefor. For activity regulation of RuBisCO, the topics include post-translational activity of the enzymes (e.g., methylated enzyme); molecular regulation mechanisms involved in the biosynthesis and decomposition of RuBisCO; and activity regulation mechanisms in the chloroplast. For leaf photosynthesis and RuBisCO, the topics include importance of enzymes and involved in-vivo reaction steps for leaf photosynthesis CO2 assimilation reactions. For function of PEPC, the topics include the biochemically and molecular biologically necessary and sufficient conditions for the C4 mechanism as the special photosynthesis mechanism. For transgenic approaches, the topics include procedure for allowing the RuBisCO gene of a dissimilar organism to function in the tobacco chloroplast, and introduction of enzymes involved in the C4 photosynthesis pathway in C3 plants. (NEDO)

  3. Stress-Induced Cytokinin Synthesis Increases Drought Tolerance through the Coordinated Regulation of Carbon and Nitrogen Assimilation in Rice1[C][W][OPEN

    Science.gov (United States)

    Reguera, Maria; Peleg, Zvi; Abdel-Tawab, Yasser M.; Tumimbang, Ellen B.; Delatorre, Carla A.; Blumwald, Eduardo

    2013-01-01

    The effects of water deficit on carbon and nitrogen metabolism were investigated in flag leaves of wild-type and transgenic rice (Oryza sativa japonica ‘Kitaake’) plants expressing ISOPENTENYLTRANSFERASE (IPT; encoding the enzyme that mediates the rate-limiting step in cytokinin synthesis) under the control of PSARK, a maturation- and stress-induced promoter. While the wild-type plants displayed inhibition of photosynthesis and nitrogen assimilation during water stress, neither carbon nor nitrogen assimilation was affected by stress in the transgenic PSARK::IPT plants. In the transgenic plants, photosynthesis was maintained at control levels during stress and the flag leaf showed increased sucrose (Suc) phosphate synthase activity and reduced Suc synthase and invertase activities, leading to increased Suc contents. The sustained carbon assimilation in the transgenic PSARK::IPT plants was well correlated with enhanced nitrate content, higher nitrate reductase activity, and sustained ammonium contents, indicating that the stress-induced cytokinin synthesis in the transgenic plants played a role in maintaining nitrate acquisition. Protein contents decreased and free amino acids increased in wild-type plants during stress, while protein content was preserved in the transgenic plants. Our results indicate that the stress-induced cytokinin synthesis in the transgenic plants promoted sink strengthening through a cytokinin-dependent coordinated regulation of carbon and nitrogen metabolism that facilitates an enhanced tolerance of the transgenic plants to water deficit. PMID:24101772

  4. Mitochondrial uncoupling proteins regulate angiotensin-converting enzyme expression

    DEFF Research Database (Denmark)

    Dhamrait, Sukhbir S.; Maubaret, Cecilia; Pedersen-bjergaard, Ulrik

    2016-01-01

    Uncoupling proteins (UCPs) regulate mitochondrial function, and thus cellular metabolism. Angiotensin-converting enzyme (ACE) is the central component of endocrine and local tissue renin–angiotensin systems (RAS), which also regulate diverse aspects of whole-body metabolism and mitochondrial...... amongst UCP3-55C (rather than T) and UCP2 I (rather than D) allele carriers. RNA interference against UCP2 in human umbilical vein endothelial cells reduced UCP2 mRNA sixfold (P 

  5. Mitochondrial uncoupling proteins regulate angiotensin-converting enzyme expression

    DEFF Research Database (Denmark)

    Dhamrait, Sukhbir S.; Maubaret, Cecilia; Pedersen-Bjergaard, Ulrik

    2016-01-01

    Uncoupling proteins (UCPs) regulate mitochondrial function, and thus cellular metabolism. Angiotensin-converting enzyme (ACE) is the central component of endocrine and local tissue renin-angiotensin systems (RAS), which also regulate diverse aspects of whole-body metabolism and mitochondrial...... amongst UCP3-55C (rather than T) and UCP2 I (rather than D) allele carriers. RNA interference against UCP2 in human umbilical vein endothelial cells reduced UCP2 mRNA sixfold (P 

  6. Structure, inhibition, and regulation of essential lipid A enzymes.

    Science.gov (United States)

    Zhou, Pei; Zhao, Jinshi

    2017-11-01

    The Raetz pathway of lipid A biosynthesis plays a vital role in the survival and fitness of Gram-negative bacteria. Research efforts in the past three decades have identified individual enzymes of the pathway and have provided a mechanistic understanding of the action and regulation of these enzymes at the molecular level. This article reviews the discovery, biochemical and structural characterization, and regulation of the essential lipid A enzymes, as well as continued efforts to develop novel antibiotics against Gram-negative pathogens by targeting lipid A biosynthesis. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Regulation of assimilate import into sink organs: Update on molecular drivers of sink strength

    Directory of Open Access Journals (Sweden)

    Saadia eBihmidine

    2013-06-01

    Full Text Available Recent developments have altered our view of molecular mechanisms that determine sink strength, defined here as the capacity of non-photosynthetic structures to compete for import of photoassimilates. We review new findings from diverse systems, including stems, seeds, flowers, and fruits. An important advance has been the identification of new transporters and facilitators with major roles in the accumulation and equilibration of sugars at a cellular level. Exactly where each exerts its effect varies among systems. Sugarcane and sweet sorghum stems, for example, both accumulate high levels of sucrose, but may do so via different paths. The distinction is central to strategies for targeted manipulation of sink strength using transporter genes, and shows the importance of system-specific analyses. Another major advance has been the identification of deep hypoxia as a feature of normal grain development. This means that molecular drivers of sink strength in endosperm operate in very low oxygen levels, and under metabolic conditions quite different than previously assumed. Successful enhancement of sink strength has nonetheless been achieved in grains by up-regulating genes for starch biosynthesis. Additionally, our understanding of sink strength is enhanced by awareness of the dual roles played by invertases (INV, not only in sucrose metabolism, but also in production of the hexose sugar signals that regulate cell-cycle and cell-division programs. These contributions of INV to cell expansion and division prove to be vital for establishment of young sinks ranging from flowers to fruit. Since INV genes are themselves sugar-responsive feast genes, they can mediate a feed-forward enhancement of sink strength when assimilates are abundant. Greater overall productivity and yield have thus been attained in key instances, indicating that even broader enhancements may be achievable as we discover the detailed molecular mechanisms that drive sink strength

  8. Modeling cutinase enzyme regulation in polyethylene terepthalate plastic biodegradation

    International Nuclear Information System (INIS)

    Apri, M.; Silmi, M.; Heryanto, T. E.; Moeis, M. R.

    2016-01-01

    PET (Polyethylene terephthalate) is a plastic material that is commonly used in our daily life. The high production of PET and others plastics that can be up to three hundred million tons per year, is not matched by its degradation rate and hence leads to environmental pollution. To overcome this problem, we develop a biodegradation system. This system utilizes LC Cutinase enzyme produced by engineered escherichia coli bacteria to degrade PET. To make the system works efficaciously, it is important to understand the mechanism underlying its enzyme regulation. Therefore, we construct a mathematical model to describe the regulation of LC Cutinase production. The stability of the model is analyzed. We show that the designated biodegradation system can give an oscillatory behavior that is very important to control the amount of inclusion body (the miss-folded proteins that reduce the efficiency of the biodegradation system).

  9. Modeling cutinase enzyme regulation in polyethylene terepthalate plastic biodegradation

    Science.gov (United States)

    Apri, M.; Silmi, M.; Heryanto, T. E.; Moeis, M. R.

    2016-04-01

    PET (Polyethylene terephthalate) is a plastic material that is commonly used in our daily life. The high production of PET and others plastics that can be up to three hundred million tons per year, is not matched by its degradation rate and hence leads to environmental pollution. To overcome this problem, we develop a biodegradation system. This system utilizes LC Cutinase enzyme produced by engineered escherichia coli bacteria to degrade PET. To make the system works efficaciously, it is important to understand the mechanism underlying its enzyme regulation. Therefore, we construct a mathematical model to describe the regulation of LC Cutinase production. The stability of the model is analyzed. We show that the designated biodegradation system can give an oscillatory behavior that is very important to control the amount of inclusion body (the miss-folded proteins that reduce the efficiency of the biodegradation system).

  10. Modeling cutinase enzyme regulation in polyethylene terepthalate plastic biodegradation

    Energy Technology Data Exchange (ETDEWEB)

    Apri, M., E-mail: m.apri@math.itb.ac.id; Silmi, M. [Department of Mathematics, Institut Teknologi Bandung, Jalan Ganeca 10 Bandung, 40132 (Indonesia); Heryanto, T. E.; Moeis, M. R. [School of Life Sciences and Technology, Institut Teknologi Bandung, Jalan Ganeca 10 Bandung, 40132 (Indonesia)

    2016-04-06

    PET (Polyethylene terephthalate) is a plastic material that is commonly used in our daily life. The high production of PET and others plastics that can be up to three hundred million tons per year, is not matched by its degradation rate and hence leads to environmental pollution. To overcome this problem, we develop a biodegradation system. This system utilizes LC Cutinase enzyme produced by engineered escherichia coli bacteria to degrade PET. To make the system works efficaciously, it is important to understand the mechanism underlying its enzyme regulation. Therefore, we construct a mathematical model to describe the regulation of LC Cutinase production. The stability of the model is analyzed. We show that the designated biodegradation system can give an oscillatory behavior that is very important to control the amount of inclusion body (the miss-folded proteins that reduce the efficiency of the biodegradation system).

  11. The Crc global regulator inhibits the Pseudomonas putida pWW0 toluene/xylene assimilation pathway by repressing the translation of regulatory and structural genes.

    Science.gov (United States)

    Moreno, Renata; Fonseca, Pilar; Rojo, Fernando

    2010-08-06

    In Pseudomonas putida, the expression of the pWW0 plasmid genes for the toluene/xylene assimilation pathway (the TOL pathway) is subject to complex regulation in response to environmental and physiological signals. This includes strong inhibition via catabolite repression, elicited by the carbon sources that the cells prefer to hydrocarbons. The Crc protein, a global regulator that controls carbon flow in pseudomonads, has an important role in this inhibition. Crc is a translational repressor that regulates the TOL genes, but how it does this has remained unknown. This study reports that Crc binds to sites located at the translation initiation regions of the mRNAs coding for XylR and XylS, two specific transcription activators of the TOL genes. Unexpectedly, eight additional Crc binding sites were found overlapping the translation initiation sites of genes coding for several enzymes of the pathway, all encoded within two polycistronic mRNAs. Evidence is provided supporting the idea that these sites are functional. This implies that Crc can differentially modulate the expression of particular genes within polycistronic mRNAs. It is proposed that Crc controls TOL genes in two ways. First, Crc inhibits the translation of the XylR and XylS regulators, thereby reducing the transcription of all TOL pathway genes. Second, Crc inhibits the translation of specific structural genes of the pathway, acting mainly on proteins involved in the first steps of toluene assimilation. This ensures a rapid inhibitory response that reduces the expression of the toluene/xylene degradation proteins when preferred carbon sources become available.

  12. The Endosome-associated Deubiquitinating Enzyme USP8 Regulates BACE1 Enzyme Ubiquitination and Degradation.

    Science.gov (United States)

    Yeates, Eniola Funmilayo Aduke; Tesco, Giuseppina

    2016-07-22

    The β-site amyloid precursor protein-cleaving enzyme (BACE1) is the rate-limiting enzyme in the production of amyloid-β, the toxic peptide that accumulates in the brain of subjects affected by Alzheimer disease. Our previous studies have shown that BACE1 is degraded via the lysosomal pathway and that that depletion of the trafficking molecule Golgi-localized γ-ear-containing ARF-binding protein 3 (GGA3) results in increased BACE1 levels and activity because of impaired lysosomal degradation. We also determined that GGA3 regulation of BACE1 levels requires its ability to bind ubiquitin. Accordingly, we reported that BACE1 is ubiquitinated at lysine 501 and that lack of ubiquitination at lysine 501 produces BACE1 stabilization. Ubiquitin conjugation is a reversible process mediated by deubiquitinating enzymes. The ubiquitin-specific peptidase 8 (USP8), an endosome-associated deubiquitinating enzyme, regulates the ubiquitination, trafficking, and lysosomal degradation of several plasma membrane proteins. Here, we report that RNAi-mediated depletion of USP8 reduced levels of both ectopically expressed and endogenous BACE1 in H4 human neuroglioma cells. Moreover, USP8 depletion increased BACE1 ubiquitination, promoted BACE1 accumulation in the early endosomes and late endosomes/lysosomes, and decreased levels of BACE1 in the recycling endosomes. We also found that decreased BACE1 protein levels were accompanied by a decrease in BACE1-mediated amyloid precursor protein cleavage and amyloid-β levels. Our findings demonstrate that USP8 plays a key role in the trafficking and degradation of BACE1 by deubiquitinating lysine 501. These studies suggest that therapies able to accelerate BACE1 degradation (e.g. by increasing BACE1 ubiquitination) may represent a potential treatment for Alzheimer disease. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  13. The Endosome-associated Deubiquitinating Enzyme USP8 Regulates BACE1 Enzyme Ubiquitination and Degradation*

    Science.gov (United States)

    Yeates, Eniola Funmilayo Aduke; Tesco, Giuseppina

    2016-01-01

    The β-site amyloid precursor protein-cleaving enzyme (BACE1) is the rate-limiting enzyme in the production of amyloid-β, the toxic peptide that accumulates in the brain of subjects affected by Alzheimer disease. Our previous studies have shown that BACE1 is degraded via the lysosomal pathway and that that depletion of the trafficking molecule Golgi-localized γ-ear-containing ARF-binding protein 3 (GGA3) results in increased BACE1 levels and activity because of impaired lysosomal degradation. We also determined that GGA3 regulation of BACE1 levels requires its ability to bind ubiquitin. Accordingly, we reported that BACE1 is ubiquitinated at lysine 501 and that lack of ubiquitination at lysine 501 produces BACE1 stabilization. Ubiquitin conjugation is a reversible process mediated by deubiquitinating enzymes. The ubiquitin-specific peptidase 8 (USP8), an endosome-associated deubiquitinating enzyme, regulates the ubiquitination, trafficking, and lysosomal degradation of several plasma membrane proteins. Here, we report that RNAi-mediated depletion of USP8 reduced levels of both ectopically expressed and endogenous BACE1 in H4 human neuroglioma cells. Moreover, USP8 depletion increased BACE1 ubiquitination, promoted BACE1 accumulation in the early endosomes and late endosomes/lysosomes, and decreased levels of BACE1 in the recycling endosomes. We also found that decreased BACE1 protein levels were accompanied by a decrease in BACE1-mediated amyloid precursor protein cleavage and amyloid-β levels. Our findings demonstrate that USP8 plays a key role in the trafficking and degradation of BACE1 by deubiquitinating lysine 501. These studies suggest that therapies able to accelerate BACE1 degradation (e.g. by increasing BACE1 ubiquitination) may represent a potential treatment for Alzheimer disease. PMID:27302062

  14. Prolyl hydroxylase domain enzymes: important regulators of cancer metabolism

    Directory of Open Access Journals (Sweden)

    Yang M

    2014-08-01

    Full Text Available Ming Yang,1 Huizhong Su,1 Tomoyoshi Soga,2 Kamil R Kranc,3 Patrick J Pollard1 1Cancer Biology and Metabolism Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK; 2Institute for Advanced Biosciences, Keio University, Mizukami, Tsuruoka, Yamagata, Japan; 3MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK Abstract: The hypoxia-inducible factor (HIF prolyl hydroxylase domain enzymes (PHDs regulate the stability of HIF protein by post-translational hydroxylation of two conserved prolyl residues in its α subunit in an oxygen-dependent manner. Trans-4-prolyl hydroxylation of HIFα under normal oxygen (O2 availability enables its association with the von Hippel-Lindau (VHL tumor suppressor pVHL E3 ligase complex, leading to the degradation of HIFα via the ubiquitin-proteasome pathway. Due to the obligatory requirement of molecular O2 as a co-substrate, the activity of PHDs is inhibited under hypoxic conditions, resulting in stabilized HIFα, which dimerizes with HIFβ and, together with transcriptional co-activators CBP/p300, activates the transcription of its target genes. As a key molecular regulator of adaptive response to hypoxia, HIF plays important roles in multiple cellular processes and its overexpression has been detected in various cancers. The HIF1α isoform in particular has a strong impact on cellular metabolism, most notably by promoting anaerobic, whilst inhibiting O2-dependent, metabolism of glucose. The PHD enzymes also seem to have HIF-independent functions and are subject to regulation by factors other than O2, such as by metabolic status, oxidative stress, and abnormal levels of endogenous metabolites (oncometabolites that have been observed in some types of cancers. In this review, we aim to summarize current understandings of the function and regulation of PHDs in cancer with an emphasis on their roles in metabolism. Keywords: prolyl hydroxylase domain (PHD

  15. Regulation of sucrose metabolism in higher plants: localization and regulation of activity of key enzymes

    Science.gov (United States)

    Winter, H.; Huber, S. C.; Brown, C. S. (Principal Investigator)

    2000-01-01

    Sucrose (Suc) plays a central role in plant growth and development. It is a major end product of photosynthesis and functions as a primary transport sugar and in some cases as a direct or indirect regulator of gene expression. Research during the last 2 decades has identified the pathways involved and which enzymes contribute to the control of flux. Availability of metabolites for Suc synthesis and 'demand' for products of sucrose degradation are important factors, but this review specifically focuses on the biosynthetic enzyme sucrose-phosphate synthase (SPS), and the degradative enzymes, sucrose synthase (SuSy), and the invertases. Recent progress has included the cloning of genes encoding these enzymes and the elucidation of posttranslational regulatory mechanisms. Protein phosphorylation is emerging as an important mechanism controlling SPS activity in response to various environmental and endogenous signals. In terms of Suc degradation, invertase-catalyzed hydrolysis generally has been associated with cell expansion, whereas SuSy-catalyzed metabolism has been linked with biosynthetic processes (e.g., cell wall or storage products). Recent results indicate that SuSy may be localized in multiple cellular compartments: (1) as a soluble enzyme in the cytosol (as traditionally assumed); (2) associated with the plasma membrane; and (3) associated with the actin cytoskeleton. Phosphorylation of SuSy has been shown to occur and may be one of the factors controlling localization of the enzyme. The purpose of this review is to summarize some of the recent developments relating to regulation of activity and localization of key enzymes involved in sucrose metabolism in plants.

  16. Transcriptional regulation of the xylanolytic enzyme system of Aspergillus

    NARCIS (Netherlands)

    Peij, van N.N.M.E.

    1999-01-01

    Filamentous fungi, such as Aspergillus niger , produce high levels of polysaccharide degrading enzymes and are frequently used as production organisms for industrial enzyme preparations. The application of these polysaccharidases as xylanases and cellulases comprises

  17. Enzyme

    Science.gov (United States)

    Enzymes are complex proteins that cause a specific chemical change in all parts of the body. For ... use them. Blood clotting is another example of enzymes at work. Enzymes are needed for all body ...

  18. Co-regulation of histone-modifying enzymes in cancer.

    Directory of Open Access Journals (Sweden)

    Abul B M M K Islam

    Full Text Available Cancer is characterized by aberrant patterns of expression of multiple genes. These major shifts in gene expression are believed to be due to not only genetic but also epigenetic changes. The epigenetic changes are communicated through chemical modifications, including histone modifications. However, it is unclear whether the binding of histone-modifying proteins to genomic regions and the placing of histone modifications efficiently discriminates corresponding genes from the rest of the genes in the human genome. We performed gene expression analysis of histone demethylases (HDMs and histone methyltransferases (HMTs, their target genes and genes with relevant histone modifications in normal and tumor tissues. Surprisingly, this analysis revealed the existence of correlations in the expression levels of different HDMs and HMTs. The observed HDM/HMT gene expression signature was specific to particular normal and cancer cell types and highly correlated with target gene expression and the expression of genes with histone modifications. Notably, we observed that trimethylation at lysine 4 and lysine 27 separated preferentially expressed and underexpressed genes, which was strikingly different in cancer cells compared to normal cells. We conclude that changes in coordinated regulation of enzymes executing histone modifications may underlie global epigenetic changes occurring in cancer.

  19. Enzymatic characterization and gene identification of aconitate isomerase, an enzyme involved in assimilation of trans-aconitic acid, from Pseudomonas sp. WU-0701.

    Science.gov (United States)

    Yuhara, Kahori; Yonehara, Hiromi; Hattori, Takasumi; Kobayashi, Keiichi; Kirimura, Kohtaro

    2015-11-01

    trans-Aconitic acid is an unsaturated organic acid that is present in some plants such as soybean and wheat; however, it remains unclear how trans-aconitic acid is degraded and/or assimilated by living cells in nature. From soil, we isolated Pseudomonas sp. WU-0701 assimilating trans-aconitic acid as a sole carbon source. In the cell-free extract of Pseudomonas sp. WU-0701, aconitate isomerase (AI; EC 5.3.3.7) activity was detected. Therefore, it seems likely that strain Pseudomonas sp. WU-0701 converts trans-aconitic acid to cis-aconitic acid with AI, and assimilates this via the tricarboxylic acid cycle. For the characterization of AI from Pseudomonas sp. WU-0701, we performed purification, determination of enzymatic properties and gene identification of AI. The molecular mass of AI purified from cell-free extract was estimated to be ~ 25 kDa by both SDS/PAGE and gel filtration analyses, indicating that AI is a monomeric enzyme. The optimal pH and temperature of purified AI for the reaction were 6.0 °C and 37 °C, respectively. The gene ais encoding AI was cloned on the basis of the N-terminal amino acid sequence of the protein, and Southern blot analysis revealed that only one copy of ais is located on the bacterial genome. The gene ais contains an ORF of 786 bp, encoding a polypeptide of 262 amino acids, including the N-terminal 22 amino acids as a putative periplasm-targeting signal peptide. It is noteworthy that the amino acid sequence of AI shows 90% and 74% identity with molybdenum ABC transporter substrate-binding proteins of Pseudomonas psychrotolerans and Xanthomonas albilineans, respectively. This is the first report on purification to homogeneity, characterization and gene identification of AI. The nucleotide sequence of ais described in this article is available in the DDBJ/EMBL/GenBank nucleotide sequence databases under the Accession No. LC010980. © 2015 FEBS.

  20. Angiotensin Converting Enzyme Regulates Cell Proliferation and Migration.

    Directory of Open Access Journals (Sweden)

    Erika Costa de Alvarenga

    Full Text Available The angiotensin-I converting enzyme (ACE plays a central role in the renin-angiotensin system, acting by converting the hormone angiotensin-I to the active peptide angiotensin-II (Ang-II. More recently, ACE was shown to act as a receptor for Ang-II, and its expression level was demonstrated to be higher in melanoma cells compared to their normal counterparts. However, the function that ACE plays as an Ang-II receptor in melanoma cells has not been defined yet.Therefore, our aim was to examine the role of ACE in tumor cell proliferation and migration.We found that upon binding to ACE, Ang-II internalizes with a faster onset compared to the binding of Ang-II to its classical AT1 receptor. We also found that the complex Ang-II/ACE translocates to the nucleus, through a clathrin-mediated process, triggering a transient nuclear Ca2+ signal. In silico studies revealed a possible interaction site between ACE and phospholipase C (PLC, and experimental results in CHO cells, demonstrated that the β3 isoform of PLC is the one involved in the Ca2+ signals induced by Ang-II/ACE interaction. Further studies in melanoma cells (TM-5 showed that Ang-II induced cell proliferation through ACE activation, an event that could be inhibited either by ACE inhibitor (Lisinopril or by the silencing of ACE. In addition, we found that stimulation of ACE by Ang-II caused the melanoma cells to migrate, at least in part due to decreased vinculin expression, a focal adhesion structural protein.ACE activation regulates melanoma cell proliferation and migration.

  1. DUB3 Deubiquitylating Enzymes Regulate Hippo Pathway Activity by Regulating the Stability of ITCH, LATS and AMOT Proteins

    DEFF Research Database (Denmark)

    Nguyen, Thanh Hung; Kugler, Jan-Michael; Cohen, Stephen Michael

    2017-01-01

    /TAZ, is regulated by ubiquitin mediated protein turnover and several ubiquitin ligase complexes have been implicated in human cancer. However, little is known about the deubiquitylating enzymes that counteract these ubiquitin ligases in regulation of the Hippo pathway. Here we identify the DUB3 family...... deubiquitylating enzymes as regulators of Hippo pathway activity. We provide evidence that DUB3 proteins regulate YAP/TAZ activity by controlling the stability of the E3 ligase ITCH, the LATS kinases and the AMOT family proteins. As a novel Hippo pathway regulator, DUB3 has the potential to act a tumor suppressor...

  2. Structural biology of starch-degrading enzymes and their regulation

    DEFF Research Database (Denmark)

    Møller, Marie Sofie; Svensson, Birte

    2016-01-01

    disproportionating enzyme and a self-stabilised conformation of amylose accommodated in the active site of plant α-glucosidase. Important inhibitor complexes include a flavonol glycoside, montbretin A, binding at the active site of human pancreatic α-amylase and barley limit dextrinase inhibitor binding...

  3. Methanol Metabolism in Yeasts : Regulation of the Synthesis of Catabolic Enzymes

    NARCIS (Netherlands)

    Egli, Th.; Dijken, J.P. van; Veenhuis, M.; Harder, W.; Fiechter, A.

    1980-01-01

    The regulation of the synthesis of four dissimilatory enzymes involved in methanol metabolism, namely alcohol oxidase, formaldehyde dehydrogenase, formate dehydrogenase and catalase was investigated in the yeasts Hansenula polymorpha and Kloeckera sp. 2201. Enzyme profiles in cell-free extracts of

  4. Carbon: Nitrogen Interaction Regulates Expression of Genes Involved in N-Uptake and Assimilation in Brassica juncea L.

    Directory of Open Access Journals (Sweden)

    Parul Goel

    Full Text Available In plants, several cellular and metabolic pathways interact with each other to regulate processes that are vital for their growth and development. Carbon (C and Nitrogen (N are two main nutrients for plants and coordination of C and N pathways is an important factor for maintaining plant growth and development. In the present work, influence of nitrogen and sucrose (C source on growth parameters and expression of genes involved in nitrogen transport and assimilatory pathways was studied in B. juncea seedlings. For this, B. juncea seedlings were treated with four combinations of C and N source viz., N source alone (-Suc+N, C source alone (+Suc-N, with N and C source (+Suc+N or without N and C source (-Suc-N. Cotyledon size and shoot length were found to be increased in seedlings, when nitrogen alone was present in the medium. Distinct expression pattern of genes in both, root and shoot tissues was observed in response to exogenously supplied N and C. The presence or depletion of nitrogen alone in the medium leads to severe up- or down-regulation of key genes involved in N-uptake and transport (BjNRT1.1, BjNRT1.8 in root tissue and genes involved in nitrate reduction (BjNR1 and BjNR2 in shoot tissue. Moreover, expression of several genes, like BjAMT1.2, BjAMT2 and BjPK in root and two genes BjAMT2 and BjGS1.1 in shoot were found to be regulated only when C source was present in the medium. Majority of genes were found to respond in root and shoot tissues, when both C and N source were present in the medium, thus reflecting their importance as a signal in regulating expression of genes involved in N-uptake and assimilation. The present work provides insight into the regulation of genes of N-uptake and assimilatory pathway in B. juncea by interaction of both carbon and nitrogen.

  5. Carbon: Nitrogen Interaction Regulates Expression of Genes Involved in N-Uptake and Assimilation in Brassica juncea L.

    Science.gov (United States)

    Goel, Parul; Bhuria, Monika; Kaushal, Mamta

    2016-01-01

    In plants, several cellular and metabolic pathways interact with each other to regulate processes that are vital for their growth and development. Carbon (C) and Nitrogen (N) are two main nutrients for plants and coordination of C and N pathways is an important factor for maintaining plant growth and development. In the present work, influence of nitrogen and sucrose (C source) on growth parameters and expression of genes involved in nitrogen transport and assimilatory pathways was studied in B. juncea seedlings. For this, B. juncea seedlings were treated with four combinations of C and N source viz., N source alone (-Suc+N), C source alone (+Suc-N), with N and C source (+Suc+N) or without N and C source (-Suc-N). Cotyledon size and shoot length were found to be increased in seedlings, when nitrogen alone was present in the medium. Distinct expression pattern of genes in both, root and shoot tissues was observed in response to exogenously supplied N and C. The presence or depletion of nitrogen alone in the medium leads to severe up- or down-regulation of key genes involved in N-uptake and transport (BjNRT1.1, BjNRT1.8) in root tissue and genes involved in nitrate reduction (BjNR1 and BjNR2) in shoot tissue. Moreover, expression of several genes, like BjAMT1.2, BjAMT2 and BjPK in root and two genes BjAMT2 and BjGS1.1 in shoot were found to be regulated only when C source was present in the medium. Majority of genes were found to respond in root and shoot tissues, when both C and N source were present in the medium, thus reflecting their importance as a signal in regulating expression of genes involved in N-uptake and assimilation. The present work provides insight into the regulation of genes of N-uptake and assimilatory pathway in B. juncea by interaction of both carbon and nitrogen. PMID:27637072

  6. Light-regulation of enzyme activity in anacystis nidulans (Richt.).

    Science.gov (United States)

    Duggan, J X; Anderson, L E

    1975-01-01

    The effect of light on the levels of activity of six enzymes which are light-modulated in higher plants was examined in the photosynthetic procaryot Anacystis nidulans. Ribulose-5-phosphate kinase (EC 2.7.1.19) was found to be light-activated in vivo and dithiothreitol-activated in vitro while glucose-6-phosphate dehydrogenase (EC 1.1.1.49) was light-inactivated and dithiothreitol-inactivated. The enzymes fructose-1,6-diphosphate phosphatase (EC 3.1.3.11), sedoheptulose-1,7-diphosphate phosphatase, NAD- and NADP-linked glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12; EC 1.2.1.13) were not affected by light treatment of the intact algae, but sedoheptulose-diphosphate phosphatase and the glyceraldehyde-3-phosphate dehydrogenases were dithiothreitol-activated in crude extracts. Light apparently controls the activity of the reductive and oxidative pentose phosphate pathway in this photosynthetic procaryot as in higher plants, through a process which probably involves reductive modulation of enzyme activity.

  7. Cholesterol Assimilation by Lactobacillus Probiotic Bacteria: An In Vitro Investigation

    Directory of Open Access Journals (Sweden)

    Catherine Tomaro-Duchesneau

    2014-01-01

    Full Text Available Excess cholesterol is associated with cardiovascular diseases (CVD, an important cause of mortality worldwide. Current CVD therapeutic measures, lifestyle and dietary interventions, and pharmaceutical agents for regulating cholesterol levels are inadequate. Probiotic bacteria have demonstrated potential to lower cholesterol levels by different mechanisms, including bile salt hydrolase activity, production of compounds that inhibit enzymes such as 3-hydroxy-3-methylglutaryl coenzyme A, and cholesterol assimilation. This work investigates 11 Lactobacillus strains for cholesterol assimilation. Probiotic strains for investigation were selected from the literature: Lactobacillus reuteri NCIMB 11951, L. reuteri NCIMB 701359, L. reuteri NCIMB 702655, L. reuteri NCIMB 701089, L. reuteri NCIMB 702656, Lactobacillus fermentum NCIMB 5221, L. fermentum NCIMB 8829, L. fermentum NCIMB 2797, Lactobacillus rhamnosus ATCC 53103 GG, Lactobacillus acidophilus ATCC 314, and Lactobacillus plantarum ATCC 14917. Cholesterol assimilation was investigated in culture media and under simulated intestinal conditions. The best cholesterol assimilator was L. plantarum ATCC 14917 (15.18 ± 0.55 mg/1010 cfu in MRS broth. L. reuteri NCIMB 701089 assimilated over 67% (2254.70 ± 63.33 mg/1010 cfu of cholesterol, the most of all the strains, under intestinal conditions. This work demonstrates that probiotic bacteria can assimilate cholesterol under intestinal conditions, with L. reuteri NCIMB 701089 showing great potential as a CVD therapeutic.

  8. Thiamin diphosphate-dependent enzymes: from enzymology to metabolic regulation, drug design and disease models.

    Science.gov (United States)

    Bunik, Victoria I; Tylicki, Adam; Lukashev, Nikolay V

    2013-12-01

    Bringing a knowledge of enzymology into research in vivo and in situ is of great importance in understanding systems biology and metabolic regulation. The central metabolic significance of thiamin (vitamin B1 ) and its diphosphorylated derivative (thiamin diphosphate; ThDP), and the fundamental differences in the ThDP-dependent enzymes of metabolic networks in mammals versus plants, fungi and bacteria, or in health versus disease, suggest that these enzymes are promising targets for biotechnological and medical applications. Here, the in vivo action of known regulators of ThDP-dependent enzymes, such as synthetic structural analogs of the enzyme substrates and thiamin, is analyzed in light of the enzymological data accumulated during half a century of research. Mimicking the enzyme-specific catalytic intermediates, the phosphonate analogs of 2-oxo acids selectively inhibit particular ThDP-dependent enzymes. Because of their selectivity, use of these compounds in cellular and animal models of ThDP-dependent enzyme malfunctions improves the validity of the model and its predictive power when compared with the nonselective and enzymatically less characterized oxythiamin and pyrithiamin. In vitro studies of the interaction of thiamin analogs and their biological derivatives with potential in vivo targets are necessary to identify and attenuate the analog selectivity. For both the substrate and thiamin synthetic analogs, in vitro reactivities with potential targets are highly relevant in vivo. However, effective concentrations in vivo are often higher than in vitro studies would suggest. The significance of specific inihibition of the ThDP-dependent enzymes for the development of herbicides, antibiotics, anticancer and neuroprotective strategies is discussed. © 2013 FEBS.

  9. Light-dark regulation of sulfate assimilation in Lemna minor L. in the presence of o-acetyl-l-serine

    International Nuclear Information System (INIS)

    Brunold, C.; Neuenschwander, U.

    1989-01-01

    The effect of light removal and addition of O-acetyl-l-serine (OAS) on sulfate assimilation in Lemna minor L. was analyzed by measuring the extractable activity of adenosine 5'-phosphosulfate sulfotransferase (APSSTase) and the in vivo incorporation of 35 SO 4 2- . After removal of light APSSTase activity decreased to 10% within 24 h in the absence and to 50% in the presence of OAS. Within 24 h total 35 SO 4 2- uptake decreased to 60% without and increased to 130% with OAS compared to light controls. The incorporation of 35 S into cysteine increased 2 times without and 15 times with OAS, labelling of glutathione decreased to 65% and increased to 140%, the one of the protein fraction decreased to 30% and to 20% of the light control in the absence and presence of OAS. Our results indicate that OAS has a regulatory function on the assimilation of sulfate and that protein synthesis is inhibited in the dark

  10. Phosphorylation of linker histones regulates ATP-dependent chromatin remodeling enzymes.

    NARCIS (Netherlands)

    Horn, P.J.; Carruthers, L.M.; Logie, C.; Hill, D.A.; Solomon, M.J.; Wade, P.A.; Imbalzano, A.N.; Hansen, J.; Peterson, C.L.

    2002-01-01

    Members of the ATP-dependent family of chromatin remodeling enzymes play key roles in the regulation of transcription, development, DNA repair and cell cycle control. We find that the remodeling activities of the ySWI/SNF, hSWI/SNF, xMi-2 and xACF complexes are nearly abolished by incorporation of

  11. Regulation of hydantoin-hydrolyzing enzyme expression in Agrobacterium tumefaciens strain RU-AE01.

    Science.gov (United States)

    Jiwaji, Meesbah; Dorrington, Rosemary Ann

    2009-10-01

    Optically pure D-: amino acids, like D-: hydroxyphenylglycine, are used in the semi-synthetic production of pharmaceuticals. They are synthesized industrially via the biocatalytic hydrolysis of p-hydroxyphenylhydantoin using enzymes derived from Agrobacterium tumefaciens strains. The reaction proceeds via a three-step pathway: (a) the ring-opening cleavage of the hydantoin ring by a D-: hydantoinase (encoded by hyuH), (b) conversion of the resultant D-: N-carbamylamino acid to the corresponding amino acid by a D-: N-carbamoylase (encoded by hyuC), and (c) chemical or enzymatic racemization of the un-reacted hydantoin substrate. While the structure and biochemical properties of these enzymes are well understood, little is known about their origin, their function, and their regulation in the native host. We investigated the mechanisms involved in the regulation of expression of the hydantoinase and N-carbamoylase enzyme activity in A. tumefaciens strain RU-AE01. We present evidence for a complex regulatory network that responds to the growth status of the cells, the presence of inducer, and nitrogen catabolite repression. Deletion analysis and site-directed mutagenesis were used to identify regulatory elements involved in transcriptional regulation of hyuH and hyuC expression. Finally, a comparison between the hyu gene clusters in several Agrobacterium strains provides insight into the function of D-: selective hydantoin-hydrolyzing enzyme systems in Agrobacterium species.

  12. Regulation of antioxidant enzyme activities in male and female rat macrophages by sex steroids

    Directory of Open Access Journals (Sweden)

    Azevedo R.B.

    2001-01-01

    Full Text Available Human and animal immune functions present sex dimorphism that seems to be mainly regulated by sex hormones. In the present study, the activities of the antioxidant enzymes total superoxide dismutase (SOD, catalase (CAT, and glutathione peroxidase (GSH-Px were measured in intraperitoneal resident macrophages from adult male and female rats. In addition to comparing males and females, we also examined the regulation of these enzyme activities in macrophages by sex steroids. GSH-Px activity did not differ between male and female macrophages. However, both total SOD and CAT activities were markedly higher in females than in males (83 and 180%. Removal of the gonads in both males and females (comparison between castrated groups increased the difference in SOD activity from 83 to 138% and reduced the difference in CAT activity from 180 to 86%. Castration and testosterone administration did not significantly modify the activities of the antioxidant enzymes in male macrophages. Ovariectomy did not affect SOD or GSH-Px activity but markedly reduced (48% CAT activity. This latter change was fully reversed by estrogen administration, whereas progesterone had a smaller effect. These results led us to conclude that differences in the SOD and CAT activities may partially explain some of the differences in immune function reported for males and females. Also, estrogen is a potent regulator of CAT in macrophages and therefore this enzyme activity in macrophages may vary considerably during the menstrual cycle.

  13. Proteolytic regulation of metabolic enzymes by E3 ubiquitin ligase complexes: lessons from yeast.

    Science.gov (United States)

    Nakatsukasa, Kunio; Okumura, Fumihiko; Kamura, Takumi

    2015-01-01

    Eukaryotic organisms use diverse mechanisms to control metabolic rates in response to changes in the internal and/or external environment. Fine metabolic control is a highly responsive, energy-saving process that is mediated by allosteric inhibition/activation and/or reversible modification of preexisting metabolic enzymes. In contrast, coarse metabolic control is a relatively long-term and expensive process that involves modulating the level of metabolic enzymes. Coarse metabolic control can be achieved through the degradation of metabolic enzymes by the ubiquitin-proteasome system (UPS), in which substrates are specifically ubiquitinated by an E3 ubiquitin ligase and targeted for proteasomal degradation. Here, we review select multi-protein E3 ligase complexes that directly regulate metabolic enzymes in Saccharomyces cerevisiae. The first part of the review focuses on the endoplasmic reticulum (ER) membrane-associated Hrd1 and Doa10 E3 ligase complexes. In addition to their primary roles in the ER-associated degradation pathway that eliminates misfolded proteins, recent quantitative proteomic analyses identified native substrates of Hrd1 and Doa10 in the sterol synthesis pathway. The second part focuses on the SCF (Skp1-Cul1-F-box protein) complex, an abundant prototypical multi-protein E3 ligase complex. While the best-known roles of the SCF complex are in the regulation of the cell cycle and transcription, accumulating evidence indicates that the SCF complex also modulates carbon metabolism pathways. The increasing number of metabolic enzymes whose stability is directly regulated by the UPS underscores the importance of the proteolytic regulation of metabolic processes for the acclimation of cells to environmental changes.

  14. The effect of some growth regulators on enzyme systems in irradiated barley grain using disinfestation doses

    International Nuclear Information System (INIS)

    Bachman, S.

    1973-01-01

    Disinfestation doses of 20 to 100 krad may cause changes in the biological systems of barley grain and, therefore, may influence undesirably the technological quality of malted grain. The effect of some growth regulators on irradiated grain has been investigated. The experiments have been carried out on brewery barley var. Visa Breuns. Following growth-regulators were used: gibberellic acid (Polish preparation ''Gibrescol''), kinetin (6-furfurylo-aminopurin), CCC (2-chloroethyl trimethyl ammonium chloride), and betaine hydrochloride. By treating the irradiated barley with solutions of growth regulators it was possible to diminish the loss of enzyme activity. A ''regenerating'' effect of growth substances, mainly gibberellic acid and betain hydrochloride in 10 -4 M solutions, was observed. Amylolytic activity decreased immediately after irradiation but in samples treated with growth regulators it was higher than in those without regulators. The results may have a practical importance since gibberellic acid has just been introduced into the brewery industry. (F.J.)

  15. Proteomic analyses for profiling regulated proteins/enzymes by Fucus vesiculosus fucoidan in B16 melanoma cells: A combination of enzyme kinetics functional study.

    Science.gov (United States)

    Wang, Zhi-Jiang; Zheng, Li; Yang, Jun-Mo; Kang, Yani; Park, Yong-Doo

    2018-06-01

    Fucoidans are complex sulfated polysaccharides that have a wide range of biological activities. Previously, we reported the various effects of Fucus vesiculosus fucoidan on tyrosinase and B16 melanoma cells. In this study, to identify fucoidan-targeted proteins in B16 melanoma cells, we performed a proteomics study and integrated enzyme kinetics. We detected 19 candidate proteins dysregulated by fucoidan treatment. Among the probed proteins, the enzyme kinetics of two candidate enzymes, namely lactate dehydrogenase (LDH) as an upregulated protein and superoxide dismutase (SOD) as a downregulated enzyme, were determined. The enzyme kinetics results showed that Fucus vesiculosus fucoidan significantly inhibited LDH catalytic function while it did not affect SOD activity even at a high dose, while only slightly decreased activity (up to 10%) at a low dose. Based on our previous and present observations, fucoidan could inhibit B16 melanoma cells growth via regulating proteins/enzymes expression levels such as LDH and SOD known as cell survival biomarkers. Interestingly, both expression level and enzyme catalytic activity of LDH were regulated by fucoidan, which could directly induce the apoptotic effect on B16 melanoma cells along with SOD downregulation. This study highlights how combining proteomics with enzyme kinetics can yield valuable insights into fucoidan targets. Copyright © 2018 Elsevier B.V. All rights reserved.

  16. Progranulin acts as a shared chaperone and regulates multiple lysosomal enzymes

    Directory of Open Access Journals (Sweden)

    Jinlong Jian

    2017-09-01

    Full Text Available Multifunctional factor progranulin (PGRN plays an important role in lysosomes, and its mutations and insufficiency are associated with lysosomal storage diseases, including neuronal ceroid lipofuscinosis and Gaucher disease (GD. The first breakthrough in understanding the molecular mechanisms of PGRN as regulator of lysosomal storage diseases came unexpectedly while investigating the role of PGRN in inflammation. Challenged PGRN null mice displayed typical features of GD. In addition, GRN gene variants were identified in GD patients and the serum levels of PGRN were significantly lower in GD patients. PGRN directly binds to and functions as a chaperone of the lysosomal enzyme β-glucocerebrosidase (GCaase, whose mutations cause GD. In addition, its C-terminus containing granulin E domain, termed Pcgin (PGRN C-terminus for GCase Interaction, is required for the association between PGRN and GCase. The concept that PGRN acts as a chaperone of lysosomal enzymes was further supported and extended by a recent article showing that PGRN acts as a chaperone molecule of lysosomal enzyme cathepsin D (CSTD, and the association between PGRN and CSTD is also mediated by PGRN's C-terminal granulin E domain. Collectively, these reports suggest that PGRN may act as a shared chaperone and regulates multiple lysosomal enzymes.

  17. Regulation of Nox enzymes expression in vascular pathophysiology: Focusing on transcription factors and epigenetic mechanisms

    Directory of Open Access Journals (Sweden)

    Simona-Adriana Manea

    2015-08-01

    Full Text Available NADPH oxidases (Nox represent a family of hetero-oligomeric enzymes whose exclusive biological function is the generation of reactive oxygen species (ROS. Nox-derived ROS are essential modulators of signal transduction pathways that control key physiological activities such as cell growth, proliferation, migration, differentiation, and apoptosis, immune responses, and biochemical pathways. Enhanced formation of Nox-derived ROS, which is generally associated with the up-regulation of different Nox subtypes, has been established in various pathologies, namely cardiovascular diseases, diabetes, obesity, cancer, and neurodegeneration. The detrimental effects of Nox-derived ROS are related to alterations in cell signalling and/or direct irreversible oxidative damage of nucleic acids, proteins, carbohydrates, and lipids. Thus, understanding of transcriptional regulation mechanisms of Nox enzymes have been extensively investigated in an attempt to find ways to counteract the excessive formation of Nox-derived ROS in various pathological states. Despite the numerous existing data, the molecular pathways responsible for Nox up-regulation are not completely understood. This review article summarizes some of the recent advances and concepts related to the regulation of Nox expression in the vascular pathophysiology. It highlights the role of transcription factors and epigenetic mechanisms in this process. Identification of the signalling molecules involved in Nox up-regulation, which is associated with the onset and development of cardiovascular dysfunction may contribute to the development of novel strategies for the treatment of cardiovascular diseases.

  18. Direct Ionic Regulation of the Activity of Myo-Inositol Biosynthesis Enzymes in Mozambique Tilapia.

    Directory of Open Access Journals (Sweden)

    Fernando D Villarreal

    Full Text Available Myo-inositol (Ins is a major compatible osmolyte in many cells, including those of Mozambique tilapia (Oreochromis mossambicus. Ins biosynthesis is highly up-regulated in tilapia and other euryhaline fish exposed to hyperosmotic stress. In this study, enzymatic regulation of two enzymes of Ins biosynthesis, Ins phosphate synthase (MIPS and inositol monophosphatase (IMPase, by direct ionic effects is analyzed. Specific MIPS and IMPase isoforms from Mozambique tilapia (MIPS-160 and IMPase 1 were selected based on experimental, phylogenetic, and structural evidence supporting their role for Ins biosynthesis during hyperosmotic stress. Recombinant tilapia IMPase 1 and MIPS-160 activity was assayed in vitro at ionic conditions that mimic changes in the intracellular milieu during hyperosmotic stress. The in vitro activities of MIPS-160 and IMPase 1 are highest at alkaline pH of 8.8. IMPase 1 catalytic efficiency is strongly increased during hyperosmolality (particularly for the substrate D-Ins-3-phosphate, Ins-3P, mainly as a result of [Na+] elevation. Furthermore, the substrate-specificity of IMPase 1 towards D-Ins-1-phosphate (Ins-1P is lower than towards Ins-3P. Because MIPS catalysis results in Ins-3P this results represents additional evidence for IMPase 1 being the isoform that mediates Ins biosynthesis in tilapia. Our data collectively demonstrate that the Ins biosynthesis enzymes are activated under ionic conditions that cells are exposed to during hypertonicity, resulting in Ins accumulation, which, in turn, results in restoration of intracellular ion homeostasis. We propose that the unique and direct ionic regulation of the activities of Ins biosynthesis enzymes represents an efficient biochemical feedback loop for regulation of intracellular physiological ion homeostasis during hyperosmotic stress.

  19. Direct Ionic Regulation of the Activity of Myo-Inositol Biosynthesis Enzymes in Mozambique Tilapia.

    Science.gov (United States)

    Villarreal, Fernando D; Kültz, Dietmar

    2015-01-01

    Myo-inositol (Ins) is a major compatible osmolyte in many cells, including those of Mozambique tilapia (Oreochromis mossambicus). Ins biosynthesis is highly up-regulated in tilapia and other euryhaline fish exposed to hyperosmotic stress. In this study, enzymatic regulation of two enzymes of Ins biosynthesis, Ins phosphate synthase (MIPS) and inositol monophosphatase (IMPase), by direct ionic effects is analyzed. Specific MIPS and IMPase isoforms from Mozambique tilapia (MIPS-160 and IMPase 1) were selected based on experimental, phylogenetic, and structural evidence supporting their role for Ins biosynthesis during hyperosmotic stress. Recombinant tilapia IMPase 1 and MIPS-160 activity was assayed in vitro at ionic conditions that mimic changes in the intracellular milieu during hyperosmotic stress. The in vitro activities of MIPS-160 and IMPase 1 are highest at alkaline pH of 8.8. IMPase 1 catalytic efficiency is strongly increased during hyperosmolality (particularly for the substrate D-Ins-3-phosphate, Ins-3P), mainly as a result of [Na+] elevation. Furthermore, the substrate-specificity of IMPase 1 towards D-Ins-1-phosphate (Ins-1P) is lower than towards Ins-3P. Because MIPS catalysis results in Ins-3P this results represents additional evidence for IMPase 1 being the isoform that mediates Ins biosynthesis in tilapia. Our data collectively demonstrate that the Ins biosynthesis enzymes are activated under ionic conditions that cells are exposed to during hypertonicity, resulting in Ins accumulation, which, in turn, results in restoration of intracellular ion homeostasis. We propose that the unique and direct ionic regulation of the activities of Ins biosynthesis enzymes represents an efficient biochemical feedback loop for regulation of intracellular physiological ion homeostasis during hyperosmotic stress.

  20. Structure, function and regulation of the enzymes in the starch biosynthetic pathway.

    Energy Technology Data Exchange (ETDEWEB)

    Geiger, Jim

    2013-11-30

    Starch is the major reserve polysaccharide in nature and accounts for the majority of the caloric intact of humans. It is also gaining importance as a renewable and biodegradable industrial material. There is burgeoning interest in increasing the amount and altering the properties of the plant starches by plant genetic modification. A rational approach to this effort will require a detailed, atomic-level understanding of the enzymatic processes that produce the starch granule. The starch granule is a complex particle made up of alternating layers of crystalline and amorphous lamellae. It consists of two types of polymer, amylose, a polymer of relatively long chains of α-1,4-linked glucans that contain virtually no branches, and amylopectin, which is highly branched and contains much shorter chains. This complex structure is synthesized by the coordinate activities of the starch synthases (SS), which elongate the polysaccharide chain by addition of glucose units via α-1,4 linkages using ADP- glucose as a donor, and branching enzymes (BE), which branch the polysaccharide chain by cleavage of α₋1,4 linkages and subsequent re-attachment via α₋1,6 linkages. Several isoforms of both starch synthase (SS) and branching enzyme (BE) are found in plants, including SSI, SSII, SSIII and granule- bound SS (GBSS), and SBEI, SBEIIa and SBEIIb. These isoforms have different activities and substrate and product specificities and play different roles in creating the granule and determining the properties of the resulting starch. The overarching goal of this proposal is to begin to understand the regulation and specificities of these enzymes at the atomic level. High-resolution X-ray structures of these enzymes bound to substrates and products will be determined to visualize the molecular interactions responsible for the properties of the enzymes. Hypotheses regarding these issues will then be tested using mutagenesis and enzyme assays. To date, we have determined the

  1. The Role of Redox-Regulating Enzymes in Inoperable Breast Cancers Treated with Neoadjuvant Chemotherapy

    Directory of Open Access Journals (Sweden)

    Nelli Roininen

    2017-01-01

    Full Text Available Although validated predictive factors for breast cancer chemoresistance are scarce, there is emerging evidence that the induction of certain redox-regulating enzymes may contribute to a poor chemotherapy effect. We investigated the possible association between chemoresistance and cellular redox state regulation in patients undergoing neoadjuvant chemotherapy (NACT for breast cancer. In total, 53 women with primarily inoperable or inflammatory breast cancer who were treated with NACT were included in the study. Pre-NACT core needle biopsies and postoperative tumor samples were immunohistochemically stained for nuclear factor erythroid 2-related factor 2 (Nrf2, Kelch-like ECH-associated protein 1 (Keap1, thioredoxin (Trx, and peroxiredoxin I (Prx I. The expression of all studied markers increased during NACT. Higher pre-NACT nuclear Prx I expression predicted smaller size of a resected tumor (p=0.00052; r=−0.550, and higher pre-NACT cytoplasmic Prx I expression predicted a lower amount of evacuated nodal metastasis (p=0.0024; r=−0.472. Pre-NACT nuclear Trx expression and pre-NACT nuclear Keap1 expression had only a minor prognostic significance as separate factors, but when they were combined, low expression for both antibodies before NACT predicted dismal disease-free survival (log-rank p=0.0030. Our results suggest that redox-regulating enzymes may serve as potential prognostic factors in primarily inoperable breast cancer patients.

  2. Genetic variants of methyl metabolizing enzymes and epigenetic regulators: Associations with promoter CpG island hypermethylation in colorectal cancer

    NARCIS (Netherlands)

    Vogel, S. de; Wouters, K.A.D.; Gottschalk, R.W.H.; Schooten, F.J. van; Goeij, A.F.P.M. de; Bruïne, A.P. de; Goldbohm, R.A.; Brandt, P.A. van den; Weijenberg, M.P.; Engeland, M. van

    2009-01-01

    Aberrant DNA methylation affects carcinogenesis of colorectal cancer. Folate metabolizing enzymes may influence the bioavailability of methyl groups, whereas DNA and histone methyltransferases are involved in epigenetic regulation of gene expression. We studied associations of genetic variants of

  3. Peroxiredoxin II is an antioxidant enzyme that negatively regulates collagen-stimulated platelet function.

    Science.gov (United States)

    Jang, Ji Yong; Wang, Su Bin; Min, Ji Hyun; Chae, Yun Hee; Baek, Jin Young; Yu, Dae-Yeul; Chang, Tong-Shin

    2015-05-01

    Collagen-induced platelet signaling is mediated by binding to the primary receptor glycoprotein VI (GPVI). Reactive oxygen species produced in response to collagen have been found to be responsible for the propagation of GPVI signaling pathways in platelets. Therefore, it has been suggested that antioxidant enzymes could down-regulate GPVI-stimulated platelet activation. Although the antioxidant enzyme peroxiredoxin II (PrxII) has emerged as having a role in negatively regulating signaling through various receptors by eliminating H2O2 generated upon receptor stimulation, the function of PrxII in collagen-stimulated platelets is not known. We tested the hypothesis that PrxII negatively regulates collagen-stimulated platelet activation. We analyzed PrxII-deficient murine platelets. PrxII deficiency enhanced GPVI-mediated platelet activation through the defective elimination of H2O2 and the impaired protection of SH2 domain-containing tyrosine phosphatase 2 (SHP-2) against oxidative inactivation, which resulted in increased tyrosine phosphorylation of key components for the GPVI signaling cascade, including Syk, Btk, and phospholipase Cγ2. Interestingly, PrxII-mediated antioxidative protection of SHP-2 appeared to occur in the lipid rafts. PrxII-deficient platelets exhibited increased adhesion and aggregation upon collagen stimulation. Furthermore, in vivo experiments demonstrated that PrxII deficiency facilitated platelet-dependent thrombus formation in injured carotid arteries. This study reveals that PrxII functions as a protective antioxidant enzyme against collagen-stimulated platelet activation and platelet-dependent thrombosis. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  4. Dicarbonyl stress and glyoxalase enzyme system regulation in human skeletal muscle.

    Science.gov (United States)

    Mey, Jacob T; Blackburn, Brian K; Miranda, Edwin R; Chaves, Alec B; Briller, Joan; Bonini, Marcelo G; Haus, Jacob M

    2018-02-01

    Skeletal muscle insulin resistance is a hallmark of Type 2 diabetes (T2DM) and may be exacerbated by protein modifications by methylglyoxal (MG), known as dicarbonyl stress. The glyoxalase enzyme system composed of glyoxalase 1/2 (GLO1/GLO2) is the natural defense against dicarbonyl stress, yet its protein expression, activity, and regulation remain largely unexplored in skeletal muscle. Therefore, this study investigated dicarbonyl stress and the glyoxalase enzyme system in the skeletal muscle of subjects with T2DM (age: 56 ± 5 yr.; BMI: 32 ± 2 kg/m 2 ) compared with lean healthy control subjects (LHC; age: 27 ± 1 yr.; BMI: 22 ± 1 kg/m 2 ). Skeletal muscle biopsies obtained from the vastus lateralis at basal and insulin-stimulated states of the hyperinsulinemic (40 mU·m -2 ·min -1 )-euglycemic (5 mM) clamp were analyzed for proteins related to dicarbonyl stress and glyoxalase biology. At baseline, T2DM had increased carbonyl stress and lower GLO1 protein expression (-78.8%), which inversely correlated with BMI, percent body fat, and HOMA-IR, while positively correlating with clamp-derived glucose disposal rates. T2DM also had lower NRF2 protein expression (-31.6%), which is a positive regulator of GLO1, while Keap1 protein expression, a negative regulator of GLO1, was elevated (207%). Additionally, insulin stimulation during the clamp had a differential effect on NRF2, Keap1, and MG-modified protein expression. These data suggest that dicarbonyl stress and the glyoxalase enzyme system are dysregulated in T2DM skeletal muscle and may underlie skeletal muscle insulin resistance. Whether these phenotypic differences contribute to the development of T2DM warrants further investigation.

  5. Regulação da absorção e assimilação do nitrogênio nas plantas Regulation of nitrogen absortion and assimilation in plants

    Directory of Open Access Journals (Sweden)

    Christian Bredemeier

    2000-04-01

    groups are trying to identify bottlenecks on nitrogen metabolism processes. The main limitations referred are: a Carriers affinity for nitrate and amonium, b Carbohydrate supply to roots, c Phloem aminoacids level concentration, d Nitrate reductase (NR, glutamine synthetase (GS and glutamate synthase (GOGAT enzyme activity, e N source (NO3- ou NH4+ supplied, and f Site of assimilation (root or shoot. These studies are showing that N metabolism is multi-regulated and integrated to plant general metabolism. The identification of specific metabolic steps that limit plant productivity is very complex. Cloning specific N carriers may help breeding programs in order to get more nitrogen efficient plants.

  6. Regulators of nonsulfur purple phototrophic bacteria and the interactive control of CO2 assimilation, nitrogen fixation, hydrogen metabolism and energy generation.

    Science.gov (United States)

    Dubbs, James M; Tabita, F Robert

    2004-06-01

    For the metabolically diverse nonsulfur purple phototrophic bacteria, maintaining redox homeostasis requires balancing the activities of energy supplying and energy-utilizing pathways, often in the face of drastic changes in environmental conditions. These organisms, members of the class Alphaproteobacteria, primarily use CO2 as an electron sink to achieve redox homeostasis. After noting the consequences of inactivating the capacity for CO2 reduction through the Calvin-Benson-Bassham (CBB) pathway, it was shown that the molecular control of many additional important biological processes catalyzed by nonsulfur purple bacteria is linked to expression of the CBB genes. Several regulator proteins are involved, with the two component Reg/Prr regulatory system playing a major role in maintaining redox poise in these organisms. Reg/Prr was shown to be a global regulator involved in the coordinate control of a number of metabolic processes including CO2 assimilation, nitrogen fixation, hydrogen metabolism and energy-generation pathways. Accumulating evidence suggests that the Reg/Prr system senses the oxidation/reduction state of the cell by monitoring a signal associated with electron transport. The response regulator RegA/PrrA activates or represses gene expression through direct interaction with target gene promoters where it often works in concert with other regulators that can be either global or specific. For the key CO2 reduction pathway, which clearly triggers whether other redox balancing mechanisms are employed, the ability to activate or inactivate the specific regulator CbbR is of paramount importance. From these studies, it is apparent that a detailed understanding of how diverse regulatory elements integrate and control metabolism will eventually be achieved.

  7. The effects of space flight on some rat liver enzymes regulating carbohydrate and lipid metabolism

    Science.gov (United States)

    Abraham, S.; Lin, C. Y.; Klein, H. P.; Volkmann, C.

    1981-01-01

    The effects of space flight conditions on the activities of certain enzymes regulating carbohydrate and lipid metabolism in rat liver are investigated in an attempt to account for the losses in body weight observed during space flight despite preflight caloric consumption. Liver samples were analyzed for the activities of 32 cytosolic and microsomal enzymes as well as hepatic glycogen and individual fatty acid levels for ground control rats and rats flown on board the Cosmos 936 biosatellite under normal space flight conditions and in centrifuges which were sacrificed upon recovery or 25 days after recovery. Significant decreases in the activities of glycogen phosphorylase, alpha-glycerol phosphate acyl transferase, diglyceride acyl transferase, aconitase and 6-phosphogluconate dehydrogenase and an increase in palmitoyl CoA desaturase are found in the flight stationary relative to the flight contrifuged rats upon recovery, with all enzymes showing alterations returning to normal values 25 days postflight. The flight stationary group is also observed to be characterized by more than twice the amount of liver glycogen of the flight centrifuged group as well as a significant increase in the ratio of palmitic to palmitoleic acid. Results thus indicate metabolic changes which may be involved in the mechanism of weight loss during weightlessness, and demonstrate the equivalence of centrifugation during space flight to terrestrial gravity.

  8. PPARγ transcriptionally regulates the expression of insulin-degrading enzyme in primary neurons

    International Nuclear Information System (INIS)

    Du, Jing; Zhang, Lang; Liu, Shubo; Zhang, Chi; Huang, Xiuqing; Li, Jian; Zhao, Nanming; Wang, Zhao

    2009-01-01

    Insulin-degrading enzyme (IDE) is a protease that has been demonstrated to play a key role in degrading both Aβ and insulin and deficient in IDE function is associated with Alzheimer's disease (AD) and type 2 diabetes mellitus (DM2) pathology. However, little is known about the cellular and molecular regulation of IDE expression. Here we show IDE levels are markedly decreased in DM2 patients and positively correlated with the peroxisome proliferator-activated receptor γ (PPARγ) levels. Further studies show that PPARγ plays an important role in regulating IDE expression in rat primary neurons through binding to a functional peroxisome proliferator-response element (PPRE) in IDE promoter and promoting IDE gene transcription. Finally, we demonstrate that PPARγ participates in the insulin-induced IDE expression in neurons. These results suggest that PPARγ transcriptionally induces IDE expression which provides a novel mechanism for the use of PPARγ agonists in both DM2 and AD therapies.

  9. Nitric oxide mitigates salt stress by regulating levels of osmolytes and antioxidant enzymes in chickpea

    Directory of Open Access Journals (Sweden)

    Parvaiz eAhmad

    2016-03-01

    Full Text Available This work was designed to evaluate whether external application of nitric oxide (NO in the form of its donor S-nitroso-N-acetylpenicillamine (SNAP could mitigate the deleterious effects of NaCl stress on chickpea (Cicer arietinum L. plants. SNAP (50 μM was applied to chickpea plants grown under non-saline and saline conditions (50 and 100 mM NaCl. Salt stress negatively affected growth and biomass yield, leaf relative water content (LRWC and chlorophyll content of chickpea plants. High salinity increased electrolyte leakage, carotenoid content and the levels of osmolytes (proline, glycine betaine, soluble proteins and soluble sugars, hydrogen peroxide (H2O2 and malondialdehyde (MDA, as well as the activities of antioxidant enzymes, such as superoxide dismutase (SOD, catalase (CAT, ascorbate peroxidase (APX, and glutathione reductase (GR in chickpea plants. Expression of the representative SOD, CAT and APX genes examined was also up-regulated in chickpea plants by salt stress. On the other hand, exogenous application of NO to salinized plants enhanced the growth parameters, LRWC, photosynthetic pigment production and levels of osmolytes, as well as the activities of examined antioxidant enzymes which is correlated with up-regulation of the examined SOD, CAT and APX genes, in comparison with plants treated with NaCl only. Furthermore, electrolyte leakage, H2O2 and MDA contents showed decline in salt-stressed plants supplemented with NO as compared with those in NaCl-treated plants alone. Thus, the exogenous application of NO protected chickpea plants against salt-induced oxidative damage by enhancing the biosynthesis of antioxidant enzymes, thereby improving plant growth under saline stress. Taken together, our results demonstrate that NO has capability to mitigate the adverse effects of high salinity on chickpea plants by improving LRWC, photosynthetic pigment biosyntheses, osmolyte accumulation and antioxidative defense system.

  10. Nitrogen Assimilation in Escherichia coli: Putting Molecular Data into a Systems Perspective

    Science.gov (United States)

    van Heeswijk, Wally C.; Westerhoff, Hans V.

    2013-01-01

    SUMMARY We present a comprehensive overview of the hierarchical network of intracellular processes revolving around central nitrogen metabolism in Escherichia coli. The hierarchy intertwines transport, metabolism, signaling leading to posttranslational modification, and transcription. The protein components of the network include an ammonium transporter (AmtB), a glutamine transporter (GlnHPQ), two ammonium assimilation pathways (glutamine synthetase [GS]-glutamate synthase [glutamine 2-oxoglutarate amidotransferase {GOGAT}] and glutamate dehydrogenase [GDH]), the two bifunctional enzymes adenylyl transferase/adenylyl-removing enzyme (ATase) and uridylyl transferase/uridylyl-removing enzyme (UTase), the two trimeric signal transduction proteins (GlnB and GlnK), the two-component regulatory system composed of the histidine protein kinase nitrogen regulator II (NRII) and the response nitrogen regulator I (NRI), three global transcriptional regulators called nitrogen assimilation control (Nac) protein, leucine-responsive regulatory protein (Lrp), and cyclic AMP (cAMP) receptor protein (Crp), the glutaminases, and the nitrogen-phosphotransferase system. First, the structural and molecular knowledge on these proteins is reviewed. Thereafter, the activities of the components as they engage together in transport, metabolism, signal transduction, and transcription and their regulation are discussed. Next, old and new molecular data and physiological data are put into a common perspective on integral cellular functioning, especially with the aim of resolving counterintuitive or paradoxical processes featured in nitrogen assimilation. Finally, we articulate what still remains to be discovered and what general lessons can be learned from the vast amounts of data that are available now. PMID:24296575

  11. Sodium nitroprusside may modulate Escherichia coli antioxidant enzyme expression by interacting with the ferric uptake regulator.

    Science.gov (United States)

    Bertrand, R; Danielson, D; Gong, V; Olynik, B; Eze, M O

    2012-01-01

    Efforts to explore possible relationships between nitric oxide (NO) and antioxidant enzymes in an Escherichia coli model have uncovered a possible interaction between sodium nitroprusside (SNP), a potent, NO-donating drug, and the ferric uptake regulator (Fur), an iron(II)--dependent regulator of antioxidant and iron acquisition proteins present in Gram-negative bacteria. The enzymatic profiles of superoxide dismutase and hydroperoxidase during logarithmic phase of growth were studied via non-denaturing polyacrylamide gel electrophoresis and activity staining specific to each enzyme. Though NO is known to induce transcription of the manganese-bearing isozyme of SOD (MnSOD), treatment with SNP paradoxically suppressed MnSOD expression and greatly enhanced the activity of the iron-containing equivalent (FeSOD). Fur, one of six global regulators of MnSOD transcription, is uniquely capable of suppressing MnSOD while enhancing FeSOD expression through distinct mechanisms. We thus hypothesize that Fur is complacent in causing this behaviour and that the iron(II) component of SNP is activating Fur. E. coli was also treated with the SNP structural analogues, potassium ferricyanide (PFi) and potassium ferrocyanide (PFo). Remarkably, the ferrous PFo was capable of mimicking the SNP-related pattern, whereas the ferric PFi was not. As Fur depends upon ferrous iron for activation, we submit this observation of redox-specificity as preliminary supporting evidence for the hypothesized Fur-SNP interaction. Iron is an essential metal that the human innate immune system sequesters to prevent its use by invading pathogens. As NO is known to inhibit iron-bound Fur, and as activated Fur regulates iron uptake through feedback inhibition, we speculate that the administration of this drug may disrupt this strategic management of iron in favour of residing Gram-negative species by providing a source of iron in an otherwise iron-scarce environment capable of encouraging its own uptake

  12. Regulation of phase I and phase II steroid metabolism enzymes by PPARα activators

    International Nuclear Information System (INIS)

    Fan Liqun; You Li; Brown-Borg, Holly; Brown, Sherri; Edwards, Robert J.; Corton, J. Christopher

    2004-01-01

    Peroxisome proliferators (PP) are a large class of structurally diverse chemicals that mediate their effects in the liver mainly through the peroxisome proliferator-activated receptor α (PPARα). Exposure to some PP results in alterations of steroid levels that may be mechanistically linked to adverse effects in reproductive organs. We hypothesized that changes in steroid levels after PP exposure are due to alterations in the levels of P450 enzymes that hydroxylate testosterone and estrogen. In testosterone hydroxylase assays, exposure to the PP, WY-14,643 (WY), gemfibrozil or di-n-butyl phthalate (DBP) led to compound-specific increases in 6β and 16β-testosterone and androstenedione hydroxylase activities and decreases in 16α, 2α-hydroxylase activities by all three PP. The decreases in 16α and 2α-testosterone hydroxylase activity can be attributed to a 2α and 16α- testosterone hydroxylase, CYP2C11, which we previously showed was dramatically down-regulated in these same tissues (Corton et al., 1998; Mol. Pharmacol. 54, 463-473). To explain the increases in 6β- and 16β-testosterone hydroxylase activities, we examined the expression of P450 family members known to carry out these functions. Alterations in the 6β-testosterone hydroxylases CYP3A1, CYP3A2 and the 16β-testosterone hydroxylase, CYP2B1 were observed after exposure to some PP. The male-specific estrogen sulfotransferase was down-regulated in rat liver after exposure to all PP. The mouse 6β-testosterone hydroxylase, Cyp3a11 was down-regulated by WY in wild-type but not PPARα-null mice. In contrast, DEHP increased Cyp3a11 in both wild-type and PPARα-null mice. These studies demonstrate that PP alter the expression and activity of a number of enzymes which regulate levels of sex steroids. The changes in these enzymes may help explain why exposure to some PP leads to adverse effects in endocrine tissues that produce or are the targets of sex hormones

  13. The Natural Antimicrobial Enzyme Lysozyme is Up-Regulated in Gastrointestinal Inflammatory Conditions

    Directory of Open Access Journals (Sweden)

    Carlos A. Rubio

    2014-01-01

    Full Text Available The cells that line the mucosa of the human gastrointestinal tract (GI, that is, oral cavity, oesophagus, stomach, small intestine, large intestine, and rectum are constantly challenged by adverse micro-environmental factors, such as different pH, enzymes, and bacterial flora. With exception of the oral cavity, these microenvironments also contain remnant cocktails of secreted enzymes and bacteria from upper organs along the tract. The density of the GI bacteria varies, from 103/mL near the gastric outlet, to 1010/mL at the ileocecal valve, to 1011 to 1012/mL in the colon. The total microbial population (ca. 1014 exceeds the total number of cells in the tract. It is, therefore, remarkable that despite the prima facie inauspicious mixture of harmful secretions and bacteria, the normal GI mucosa retains a healthy state of cell renewal. To counteract the hostile microenvironment, the GI epithelia react by speeding cell exfoliation (the GI mucosa has a turnover time of two to three days, by increasing peristalsis, by eliminating bacteria through secretion of plasma cell-immunoglobulins and by increasing production of natural antibacterial compounds, such as defensin-5 and lysozyme. Only recently, lysozyme was found up-regulated in Barrett’s oesophagitis, chronic gastritis, gluten-induced atrophic duodenitis (coeliac disease, collagenous colitis, lymphocytic colitis, and Crohn’s colitis. This up-regulation is a response directed to the special types of bacteria recently detected in these diseases. The aim of lysozyme up-regulation is to protect individual mucosal segments to chronic inflammation. The molecular mechanisms connected to the crosstalk between the intraluminal bacterial flora and the production of lysozyme released by the GI mucosae, are discussed. Bacterial resistance continues to exhaust our supply of commercial antibiotics. The potential use of lysozyme to treat infectious diseases is receiving much attention.

  14. Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

    Science.gov (United States)

    Esser, Dominik; Rauch, Bernadette

    2014-01-01

    SUMMARY The metabolism of Archaea, the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya. However, this metabolic complexity in Archaea is accompanied by the absence of many “classical” pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of “new,” unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea. In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya. Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented. PMID:24600042

  15. Nucleophosmin/B23 regulates ubiquitin dynamics in nucleoli by recruiting deubiquitylating enzyme USP36.

    Science.gov (United States)

    Endo, Akinori; Kitamura, Naomi; Komada, Masayuki

    2009-10-09

    The nucleolus is a subnuclear compartment with multiple cellular functions, including ribosome biogenesis. USP36 is a deubiquitylating enzyme that localizes to nucleoli and plays an essential role in regulating the structure and function of the organelle. However, how the localization of USP36 is regulated remains unknown. Here, we identified a short stretch of basic amino acids (RGKEKKIKKFKREKRR) that resides in the C-terminal region of USP36 and serves as a nucleolar localization signal for the protein. We found that this motif interacts with a central acidic region of nucleophosmin/B23, a major nucleolar protein involved in various nucleolar functions. Knockdown of nucleophosmin/B23 resulted in a significant reduction in the amount of USP36 in nucleoli, without affecting the cellular USP36 level. This was associated with elevated ubiquitylation levels of fibrillarin, a USP36 substrate protein in nucleoli. We conclude that nucleophosmin/B23 recruits USP36 to nucleoli, thereby serving as a platform for the regulation of nucleolar protein functions through ubiquitylation/deubiquitylation.

  16. Chemically Regulated ROS Generation from Gold Nanoparticles for Enzyme-Free Electrochemiluminescent Immunosensing.

    Science.gov (United States)

    Higashi, Yui; Mazumder, Joyotu; Yoshikawa, Hiroyuki; Saito, Masato; Tamiya, Eiichi

    2018-04-17

    In the present work, we report on an enzyme-free electrochemiluminescent (ECL) immunosensing scheme utilizing the catalytic generation of reactive oxygen species (ROS) from gold nanoparticles (AuNPs) (diameter ≥5 nm) dispersed in aqueous solutions of trishydroxymethylaminomethane (Tris). First, to examine this catalytic pathway in detail, the effects of various factors such as the AuNP size and concentration, dispersant type and concentration, and dissolved oxygen were investigated using the electrochemiluminescence (ECL) of luminol. It was found that the catalytic generation of ROS from AuNPs can be regulated chemically by altering conditions such as the type, concentration, and pH of the solution that the AuNPs are dispersed in. Under the best conditions studied in this work, the AuNPs displayed high catalytic activity toward ROS generation, with an estimated apparent turnover number per AuNP of 0.1 s -1 , comparable to those of several common peroxide-producing enzymes. Following these studies, this phenomenon was applied to develop a one-step enzyme-free ECL immunosensor based on sandwiching the target analyte using antibody-conjugated magnetic beads (MB) and AuNPs. Using IgA as a model analyte, the developed immunosensor was able to detect the target in the range of 1 ng/mL to 10 μg/mL, with the lower detection limit being comparable to those of commercial assays for the same target. Altering the antibodies used to modify the MB and AuNPs could further improve the detection limit as well as expand the applicability of this immunoassay to the detection of other analytes.

  17. The regulation and catalytic mechanism of the NADP-malic enzyme from tobacco leaves

    Directory of Open Access Journals (Sweden)

    VERONIKA DOUBNEROVÁ

    2009-08-01

    Full Text Available The non-photosynthetic NADP-malic enzyme EC 1.1.1.40 (NADP-ME, which catalyzes the oxidative decarboxylation of L-malate and NADP+ to produce pyruvate and NADPH, respectively, and which could be involved in plant defense responses, was isolated from Nicotiana tabacum L. leaves. The mechanism of the enzyme reaction was studied by the initial rate method and was found to be an ordered sequential one. Regulation possibilities of purified cytosolic NADP-ME by cell metabolites were tested. Intermediates of the citric acid cycle (a-ketoglutarate, succinate, fumarate, metabolites of glycolysis (pyruvate, phosphoenolpyruvate, glucose-6-phosphate, compounds connected with lipogenesis (coenzyme A, acetyl-CoA, palmitoyl-CoA and some amino acids (glutamate, glutamine, aspartate did not significantly affect the NADP-ME activity from tobacco leaves. In contrast, macroergic compounds (GTP, ATP and ADP were strong inhibitors of NADP-ME; the type of inhibition and the inhibition constants were determined in the presence of the most effective cofactors (Mn2+ or Mg2+, required by NADP-ME. Predominantly non-competitive type of inhibitions of NADP-ME with respect to NADP+ and mixed type to L-malate were found.

  18. Glycolysis is governed by growth regime and simple enzyme regulation in adherent MDCK cells.

    Science.gov (United States)

    Rehberg, Markus; Ritter, Joachim B; Reichl, Udo

    2014-10-01

    Due to its vital importance in the supply of cellular pathways with energy and precursors, glycolysis has been studied for several decades regarding its capacity and regulation. For a systems-level understanding of the Madin-Darby canine kidney (MDCK) cell metabolism, we couple a segregated cell growth model published earlier with a structured model of glycolysis, which is based on relatively simple kinetics for enzymatic reactions of glycolysis, to explain the pathway dynamics under various cultivation conditions. The structured model takes into account in vitro enzyme activities, and links glycolysis with pentose phosphate pathway and glycogenesis. Using a single parameterization, metabolite pool dynamics during cell cultivation, glucose limitation and glucose pulse experiments can be consistently reproduced by considering the cultivation history of the cells. Growth phase-dependent glucose uptake together with cell-specific volume changes generate high intracellular metabolite pools and flux rates to satisfy the cellular demand during growth. Under glucose limitation, the coordinated control of glycolytic enzymes re-adjusts the glycolytic flux to prevent the depletion of glycolytic intermediates. Finally, the model's predictive power supports the design of more efficient bioprocesses.

  19. Genetic manipulation of a metabolic enzyme and a transcriptional regulator increasing succinate excretion from unicellular cyanobacterium

    Directory of Open Access Journals (Sweden)

    Takashi eOsanai

    2015-10-01

    Full Text Available Succinate is a building block compound that the U.S. Department of Energy has declared as important in biorefineries, and it is widely used as a commodity chemical. Here, we identified the two genes increasing succinate production of the unicellular cyanobacterium Synechocystis sp. PCC 6803. Succinate was excreted under dark, anaerobic conditions, and its production level increased by knocking out ackA, which encodes an acetate kinase, and by overexpressing sigE, which encodes an RNA polymerase sigma factor. Glycogen catabolism and organic acid biosynthesis were enhanced in the mutant lacking ackA and overexpressing sigE, leading to an increase in succinate production reaching 5 times of the wild-type levels. Our genetic and metabolomic analyses thus demonstrated the effect of genetic manipulation of a metabolic enzyme and a transcriptional regulator on succinate excretion from this cyanobacterium with the data based on metabolomic technique.

  20. Molecular evolution of nitrogen assimilatory enzymes in marine prasinophytes.

    Science.gov (United States)

    Ghoshroy, Sohini; Robertson, Deborah L

    2015-01-01

    Nitrogen assimilation is a highly regulated process requiring metabolic coordination of enzymes and pathways in the cytosol, chloroplast, and mitochondria. Previous studies of prasinophyte genomes revealed that genes encoding nitrate and ammonium transporters have a complex evolutionary history involving both vertical and horizontal transmission. Here we examine the evolutionary history of well-conserved nitrogen-assimilating enzymes to determine if a similar complex history is observed. Phylogenetic analyses suggest that genes encoding glutamine synthetase (GS) III in the prasinophytes evolved by horizontal gene transfer from a member of the heterokonts. In contrast, genes encoding GSIIE, a canonical vascular plant and green algal enzyme, were found in the Micromonas genomes but have been lost from Ostreococcus. Phylogenetic analyses placed the Micromonas GSIIs in a larger chlorophyte/vascular plant clade; a similar topology was observed for ferredoxin-dependent nitrite reductase (Fd-NiR), indicating the genes encoding GSII and Fd-NiR in these prasinophytes evolved via vertical transmission. Our results show that genes encoding the nitrogen-assimilating enzymes in Micromonas and Ostreococcus have been differentially lost and as well as recruited from different evolutionary lineages, suggesting that the regulation of nitrogen assimilation in prasinophytes will differ from other green algae.

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

    Science.gov (United States)

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

    2017-09-01

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

  2. Regulation of behavioral circadian rhythms and clock protein PER1 by the deubiquitinating enzyme USP2

    Directory of Open Access Journals (Sweden)

    Yaoming Yang

    2012-06-01

    Endogenous 24-hour rhythms are generated by circadian clocks located in most tissues. The molecular clock mechanism is based on feedback loops involving clock genes and their protein products. Post-translational modifications, including ubiquitination, are important for regulating the clock feedback mechanism. Previous work has focused on the role of ubiquitin ligases in the clock mechanism. Here we show a role for the rhythmically-expressed deubiquitinating enzyme ubiquitin specific peptidase 2 (USP2 in clock function. Mice with a deletion of the Usp2 gene (Usp2 KO display a longer free-running period of locomotor activity rhythms and altered responses of the clock to light. This was associated with altered expression of clock genes in synchronized Usp2 KO mouse embryonic fibroblasts and increased levels of clock protein PERIOD1 (PER1. USP2 can be coimmunoprecipitated with several clock proteins but directly interacts specifically with PER1 and deubiquitinates it. Interestingly, this deubiquitination does not alter PER1 stability. Taken together, our results identify USP2 as a new core component of the clock machinery and demonstrate a role for deubiquitination in the regulation of the circadian clock, both at the level of the core pacemaker and its response to external cues.

  3. Unusual Growth Phase and Oxygen Tension Regulation of Oxidative Stress Protection Enzymes, Catalase and Superoxide Dismutase, in the Phytopathogen Xanthomonas oryzae pv. oryzae

    OpenAIRE

    Chamnongpol, S.; Mongkolsuk, S.; Vattanaviboon, P.; Fuangthong, M.

    1995-01-01

    The enzymes catalase and superoxide dismutase play major roles in protecting phytopathogenic bacteria from oxidative stress. In Xanthomonas species, these enzymes are regulated by both growth phase and oxygen tension. The highest enzyme levels were detected within 1 h of growth. Continued growth resulted in a decline of both enzyme activities. High oxygen tension was an inducing signal for both enzyme activities. An 80,000-Da monofunctional catalase and a manganese superoxide dismutase were t...

  4. Co-ordinate regulation of sterol biosynthesis enzyme activity during accumulation of sterols in developing rape and tobacco seed.

    Science.gov (United States)

    Harker, Mark; Hellyer, Amanda; Clayton, John C; Duvoix, Annelyse; Lanot, Alexandra; Safford, Richard

    2003-02-01

    The activities of 3-hydroxy-3-methylglutaryl-coenzyme A reductase, sterol methyl transferase 1 and sterol acyltransferase, key enzymes involved in phytosterol biosynthesis were shown to be co-ordinately regulated during oilseed rape ( Brassica napus L.) and tobacco ( Nicotiana tabacum L.) seed development. In both plants, enzyme activities were low during the initial stages of seed development, increasing towards mid-maturation where they remained stable for a time, before declining rapidly as the oilseeds reached maturity. During seed development, the level of total sterols increased 12-fold in tobacco and 9-fold in rape, primarily due to an increase in steryl ester production. In both seed tissues, stages of maximum enzyme activity coincided with periods of high rates of sterol production, indicating developmental regulation of the enzymes to be responsible for the increases in the sterol content observed during seed development. Consistent with previous studies the data presented suggest that sterol biosynthesis is regulated by two key steps, although there may be others. The first is the regulation of carbon flux into the isoprenoid pathway to cycloartenol. The second is the flux from cycloartenol to Delta(5)-end-product sterols. The implications of the results in terms of enhancing seed sterol levels by genetic modification are also discussed.

  5. Angiotensin converting enzyme (ACE and ACE2 bind integrins and ACE2 regulates integrin signalling.

    Directory of Open Access Journals (Sweden)

    Nicola E Clarke

    Full Text Available The angiotensin converting enzymes (ACEs are the key catalytic components of the renin-angiotensin system, mediating precise regulation of blood pressure by counterbalancing the effects of each other. Inhibition of ACE has been shown to improve pathology in cardiovascular disease, whilst ACE2 is cardioprotective in the failing heart. However, the mechanisms by which ACE2 mediates its cardioprotective functions have yet to be fully elucidated. Here we demonstrate that both ACE and ACE2 bind integrin subunits, in an RGD-independent manner, and that they can act as cell adhesion substrates. We show that cellular expression of ACE2 enhanced cell adhesion. Furthermore, we present evidence that soluble ACE2 (sACE2 is capable of suppressing integrin signalling mediated by FAK. In addition, sACE2 increases the expression of Akt, thereby lowering the proportion of the signalling molecule phosphorylated Akt. These results suggest that ACE2 plays a role in cell-cell interactions, possibly acting to fine-tune integrin signalling. Hence the expression and cleavage of ACE2 at the plasma membrane may influence cell-extracellular matrix interactions and the signalling that mediates cell survival and proliferation. As such, ectodomain shedding of ACE2 may play a role in the process of pathological cardiac remodelling.

  6. Interaction of Sulfate Assimilation with Carbon and Nitrogen Metabolism in Lemna minor1

    Science.gov (United States)

    Kopriva, Stanislav; Suter, Marianne; von Ballmoos, Peter; Hesse, Holger; Krähenbühl, Urs; Rennenberg, Heinz; Brunold, Christian

    2002-01-01

    Cysteine synthesis from sulfide and O-acetyl-l-serine (OAS) is a reaction interconnecting sulfate, nitrogen, and carbon assimilation. Using Lemna minor, we analyzed the effects of omission of CO2 from the atmosphere and simultaneous application of alternative carbon sources on adenosine 5′-phosphosulfate reductase (APR) and nitrate reductase (NR), the key enzymes of sulfate and nitrate assimilation, respectively. Incubation in air without CO2 led to severe decrease in APR and NR activities and mRNA levels, but ribulose-1,5-bisphosphate carboxylase/oxygenase was not considerably affected. Simultaneous addition of sucrose (Suc) prevented the reduction in enzyme activities, but not in mRNA levels. OAS, a known regulator of sulfate assimilation, could also attenuate the effect of missing CO2 on APR, but did not affect NR. When the plants were subjected to normal air after a 24-h pretreatment in air without CO2, APR and NR activities and mRNA levels recovered within the next 24 h. The addition of Suc and glucose in air without CO2 also recovered both enzyme activities, with OAS again influenced only APR. 35SO42− feeding showed that treatment in air without CO2 severely inhibited sulfate uptake and the flux through sulfate assimilation. After a resupply of normal air or the addition of Suc, incorporation of 35S into proteins and glutathione greatly increased. OAS treatment resulted in high labeling of cysteine; the incorporation of 35S in proteins and glutathione was much less increased compared with treatment with normal air or Suc. These results corroborate the tight interconnection of sulfate, nitrate, and carbon assimilation. PMID:12428005

  7. The importance of cytosolic glutamine synthetase in nitrogen assimilation and recycling

    Energy Technology Data Exchange (ETDEWEB)

    Bernard, S.M.; Habash, D.Z.

    2009-07-02

    Glutamine synthetase assimilates ammonium into amino acids, thus it is a key enzyme for nitrogen metabolism. The cytosolic isoenzymes of glutamine synthetase assimilate ammonium derived from primary nitrogen uptake and from various internal nitrogen recycling pathways. In this way, cytosolic glutamine synthetase is crucial for the remobilization of protein-derived nitrogen. Cytosolic glutamine synthetase is encoded by a small family of genes that are well conserved across plant species. Members of the cytosolic glutamine synthetase gene family are regulated in response to plant nitrogen status, as well as to environmental cues, such as nitrogen availability and biotic/abiotic stresses. The complex regulation of cytosolic glutamine synthetase at the transcriptional to post-translational levels is key to the establishment of a specific physiological role for each isoenzyme. The diverse physiological roles of cytosolic glutamine synthetase isoenzymes are important in relation to current agricultural and ecological issues.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2001-07-01

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

  9. Synthesis and study on biological activity of nitrogen-containing heterocyclic compounds – regulators of enzymes of nucleic acid biosynthesis

    Directory of Open Access Journals (Sweden)

    Alexeeva I. V.

    2013-07-01

    Full Text Available Results of investigations on the development of new regulators of functional activity of nucleic acid biosynthesis enzymes based on polycyclic nitrogen-containing heterosystems are summarized. Computer design and molecular docking in the catalytic site of target enzyme (T7pol allowed to perform the directed optimization of basic structures. Several series of compounds were obtained and efficient inhibitors of herpes family (simple herpes virus type 2, Epstein-Barr virus, influenza A and hepatitis C viruses were identified, as well as compounds with potent antitumor, antibacterial and antifungal activity. It was established that the use of model test systems based on enzymes participating in nucleic acids synthesis is a promising approach to the primary screening of potential inhibitors in vitro.

  10. Ferredoxin-thioredoxin reductase: a catalytically active dithiol group links photoreduced ferredoxin to thioredoxin functional in photosynthetic enzyme regulation

    International Nuclear Information System (INIS)

    Droux, M.; Miginiac-Maslow, M.; Jacquot, J.P.; Gadal, P.; Crawford, N.A.; Kosower, N.S.; Buchanan, B.B.

    1987-01-01

    The mechanism by which the ferredoxin-thioredoxin system activates the target enzyme, NADP-malate dehydrogenase, was investigated by analyzing the sulfhydryl status of individual protein components with [ 14 C]iodoacetate and monobromobimane. The data indicate that ferredoxin-thioredoxin reductase (FTR)--an iron-sulfur enzyme present in oxygenic photosynthetic organisms--is the first member of a thiol chain that links light to enzyme regulation. FTR possesses a catalytically active dithiol group localized on the 13 kDa (similar) subunit, that occurs in all species investigated and accepts reducing equivalents from photoreduced ferredoxin and transfers them stoichiometrically to the disulfide form of thioredoxin m. The reduced thioredoxin m, in turn, reduces NADP-malate dehydrogenase, thereby converting it from an inactive (S-S) to an active (SH) form. The means by which FTR is able to combine electrons (from photoreduced ferredoxin) with protons (from the medium) to reduce its active disulfide group remains to be determined

  11. Regulation of SIRT 1 mediated NAD dependent deacetylation: A novel role for the multifunctional enzyme CD38

    International Nuclear Information System (INIS)

    Aksoy, Pinar; Escande, Carlos; White, Thomas A.; Thompson, Michael; Soares, Sandra; Benech, Juan Claudio; Chini, Eduardo N.

    2006-01-01

    The SIRT 1 enzyme is a NAD dependent deacetylase implicated in ageing, cell protection, and energy metabolism in mammalian cells. How the endogenous activity of SIRT 1 is modulated is not known. The enzyme CD38 is a multifunctional enzyme capable of synthesis of the second messenger, cADPR, NAADP, and ADPR. However, the major enzymatic activity of CD38 is the hydrolysis of NAD. Of particular interest is the fact that CD38 is present on the inner nuclear membrane. Here, we investigate the modulation of the SIRT 1 activity by CD38. We propose that by modulating availability of NAD to the SIRT1 enzyme, CD38 may regulate SIRT1 enzymatic activity. We observed that in CD38 knockout mice, tissue levels of NAD are significantly increased. We also observed that incubation of purified recombinant SIRT1 enzyme with CD38 or nuclear extracts of wild-type mice led to a significant inhibition of its activity. In contrast, incubation of SIRT1 with cellular extract from CD38 knockout mice was without effect. Furthermore, the endogenous activity of SIRT1 was several time higher in nuclear extracts from CD38 knockout mice when compared to wild-type nuclear extracts. Finally, the in vivo deacetylation of the SIRT1 substrate P53 is increased in CD38 knockout mice tissue. Our data support the novel concept that nuclear CD38 is a major regulator of cellular/nuclear NAD level, and SIRT1 activity. These findings have strong implications for understanding the basic mechanisms that modulate intracellular NAD levels, energy homeostasis, as well as ageing and cellular protection modulated by the SIRT enzymes

  12. Transforming Growth Factor β/Activin Signaling Functions as a Sugar-Sensing Feedback Loop to Regulate Digestive Enzyme Expression

    Directory of Open Access Journals (Sweden)

    Wen-bin Alfred Chng

    2014-10-01

    Full Text Available Summary: Organisms need to assess their nutritional state and adapt their digestive capacity to the demands for various nutrients. Modulation of digestive enzyme production represents a rational step to regulate nutriment uptake. However, the role of digestion in nutrient homeostasis has been largely neglected. In this study, we analyzed the mechanism underlying glucose repression of digestive enzymes in the adult Drosophila midgut. We demonstrate that glucose represses the expression of many carbohydrases and lipases. Our data reveal that the consumption of nutritious sugars stimulates the secretion of the transforming growth factor β (TGF-β ligand, Dawdle, from the fat body. Dawdle then acts via circulation to activate TGF-β/Activin signaling in the midgut, culminating in the repression of digestive enzymes that are highly expressed during starvation. Thus, our study not only identifies a mechanism that couples sugar sensing with digestive enzyme expression but points to an important role of TGF-β/Activin signaling in sugar metabolism. : Organisms modulate their digestive processes to reflect their nutritional state. In this study, Chng et al. demonstrate that the TGF-β/Activin pathway functions as a carbohydrate-sensing mechanism in the adult Drosophila midgut to regulate digestive enzyme expression. They show that the TGF-β ligand, Dawdle, and the canonical TGF-β/Activin signaling are essential to couple carbohydrate sensing with digestive enzyme expression. Thus, their study highlights an unexpected function of TGF-β/Activin signaling that is beyond their established roles in development and immunity.

  13. Regulation-Structured Dynamic Metabolic Model Provides a Potential Mechanism for Delayed Enzyme Response in Denitrification Process

    Energy Technology Data Exchange (ETDEWEB)

    Song, Hyun-Seob; Thomas, Dennis G.; Stegen, James C.; Li, Minjing; Liu, Chongxuan; Song, Xuehang; Chen, Xingyuan; Fredrickson, Jim K.; Zachara, John M.; Scheibe, Timothy D.

    2017-09-29

    In a recent study of denitrification dynamics in hyporheic zone sediments, we observed a significant time lag (up to several days) in enzymatic response to the changes in substrate concentration. To explore an underlying mechanism and understand the interactive dynamics between enzymes and nutrients, we developed a trait-based model that associates a community’s traits with functional enzymes, instead of typically used species guilds (or functional guilds). This enzyme-based formulation allows to collectively describe biogeochemical functions of microbial communities without directly parameterizing the dynamics of species guilds, therefore being scalable to complex communities. As a key component of modeling, we accounted for microbial regulation occurring through transcriptional and translational processes, the dynamics of which was parameterized based on the temporal profiles of enzyme concentrations measured using a new signature peptide-based method. The simulation results using the resulting model showed several days of a time lag in enzymatic responses as observed in experiments. Further, the model showed that the delayed enzymatic reactions could be primarily controlled by transcriptional responses and that the dynamics of transcripts and enzymes are closely correlated. The developed model can serve as a useful tool for predicting biogeochemical processes in natural environments, either independently or through integration with hydrologic flow simulators.

  14. Acetyl-CoA carboxylase in Reuber hepatoma cells: variation in enzyme activity, insulin regulation, and cellular lipid content.

    Science.gov (United States)

    Bianchi, A; Evans, J L; Nordlund, A C; Watts, T D; Witters, L A

    1992-01-01

    Reuber hepatoma cells are useful cultured lines for the study of insulin action, lipid and lipoprotein metabolism, and the regulation of acetyl-CoA carboxylase (ACC), the rate-limiting enzyme of fatty acid biosynthesis. During investigations in different clonal lines of these cells, we have uncovered marked intercellular variability in the activity, enzyme content, and insulin regulation of ACC paralleled by differences in cellular neutral lipid (triglyceride) content. Two contrasting clonal lines, Fao and H356A-1, have been studied in detail. Several features distinguish these two lines, including differences in ACC activity and enzyme kinetics, the content of the two major hepatic ACC isozymes (Mr 280,000 and 265,000 Da) and their heteroisozymic complex, the extent of ACC phosphorylation, and the ability of ACC to be activated on stimulation by insulin and insulinomimetic agonists. As studied by Nile Red staining and fluorescence-activated cell sorting, these two lines also display marked differences in neutral lipid content, which correlates with both basal levels of ACC activity and inhibition of ACC by the fatty acid analog, 5-(tetradecyloxy)-2-furoic acid (TOFA). These results emphasize the importance of characterization of any particular clonal line of Reuber cells for studies of enzyme regulation, substrate metabolism, and hormone action. With respect to ACC, studies in contrasting clonal lines of Reuber cells could provide valuable clues to understanding both the complex mechanisms of intracellular ACC regulation in the absence and presence of hormones and its regulatory role(s) in overall hepatic lipid metabolism.

  15. Expression and Regulation of Drug Transporters and Metabolizing Enzymes in the Human Gastrointestinal Tract.

    Science.gov (United States)

    Drozdzik, M; Oswald, S

    2016-01-01

    Orally administered drugs must pass through the intestinal wall and then through the liver before reaching systemic circulation. During this process drugs are subjected to different processes that may determine the therapeutic value. The intestinal barrier with active drug metabolizing enzymes and drug transporters in enterocytes plays an important role in the determination of drug bioavailability. Accumulating information demonstrates variable distribution of drug metabolizing enzymes and transporters along the human gastrointestinal tract (GI), that creates specific barrier characteristics in different segments of the GI. In this review, expression of drug metabolizing enzymes and transporters in the healthy and diseased human GI as well as their regulatory aspects: genetic, miRNA, DNA methylation are outlined. The knowledge of unique interplay between drug metabolizing enzymes and transporters in specific segments of the GI tract allows more precise definition of drug release sites within the GI in order to assure more complete bioavailability and prediction of drug interactions.

  16. A functional screen implicates microRNA-138-dependent regulation of the depalmitoylation enzyme APT1 in dendritic spine morphogenesis

    DEFF Research Database (Denmark)

    Siegel, Gabriele; Obernosterer, Gregor; Fiore, Roberto

    2009-01-01

    of acyl protein thioesterase 1 (APT1), an enzyme regulating the palmitoylation status of proteins that are known to function at the synapse, including the alpha(13) subunits of G proteins (Galpha(13)). RNA-interference-mediated knockdown of APT1 and the expression of membrane-localized Galpha(13) both...... suppress spine enlargement caused by inhibition of miR-138, suggesting that APT1-regulated depalmitoylation of Galpha(13) might be an important downstream event of miR-138 function. Our results uncover a previously unknown miRNA-dependent mechanism in neurons and demonstrate a previously unrecognized...

  17. Investigation on the Metabolic Regulation of pgi gene knockout Escherichia coli by Enzyme Activities and Intracellular Metabolite Concentrations

    Directory of Open Access Journals (Sweden)

    Nor ‘Aini, A. R.

    2006-01-01

    Full Text Available An integrated analysis of the cell growth characteristics, enzyme activities, intracellular metabolite concentrations was made to investigate the metabolic regulation of pgi gene knockout Escherichia coli based on batch culture and continuous culture which was performed at the dilution rate of 0.2h-1. The enzymatic study identified that pathways of pentose phosphate, ED pathway and glyoxylate shunt were all active in pgi mutant. The glycolysis enzymes i.e glyceraldehyde-3-phosphate dehydrogenase, fructose diphosphatase, pyruvate kinase, triose phosphate isomerase were down regulated implying that the inactivation of pgi gene reduced the carbon flux through glycolytic pathway. Meanwhile, the pentose phosphate pathway was active as a major route for intermediary carbohydrate metabolism instead of glycolysis. The pentose phosphate pathway generates most of the major reducing co-factor NADPH as shown by the increased of NADPH/NADP+ ratio in the mutant when compared with the parent strain. The fermentative enzymes such as acetate kinase and lactate dehydrogenase were down regulated in the mutant. Knockout of pgi gene results in the significant increase in the intracellular concentration of glucose-6-phosphate and decrease in the concentration of oxaloacetate. The slow growth rate of the mutant was assumed to be affected by the accumulation of glucose-6-phosphate and imbalance of NADPH reoxidation.

  18. Effect of salt-stresses on the hormonal regulation of growth, photosynthesis and distribution of 14C - assimilates in bean plants

    International Nuclear Information System (INIS)

    Starck, Z.; Karwowska, R.

    1978-01-01

    The experiments were carried out to study the effect of salt-stresses and ABA on the growth photosynthesis and translocation of assimilates in bean plants. It was planned to reduce the content of GA 3 and cytokinins and increase ABA content in salinized plants. The results show that salt-stress (NaCl and concentrated nutrient solution), reduces all the investigated processes in a different degree. NaCl-stress retarded most seriously growth of apical part and blades in contrast to 7-times concentrated nutrient solution decreasing mainly the rate of root and blade growth. Photosynthesis and 14 C-translocation of 14 C-assimilates were retarded more seriously by NaCl than by 7-times concentrated nutrient solution. In the case of seriously stressed plants GA 3 and cytokinins (more effectively) reversed the negative effect of stress conditions both on the photosynthesis and on the 14 C-translocation. On the basis of the obtained results, it seems that changes in the rate of investigated processes in salinized plants are due to hormonal disturbances which cause directly or indirectly retardation of photosynthesis and translocation of assimilates. (author)

  19. Effect of salt-stresses on the hormonal regulation of growth, photosynthesis and distribution of 14C-assimilates in bean plants

    Directory of Open Access Journals (Sweden)

    Z. Starck

    2015-01-01

    Full Text Available The experiments were carried out to study the effect of salt-stresses and ABA on the growth, photosynthesis and translocation of assimilates in bean plants. It was planed to reduce the content of GA3 and cytokinins and increase ABA content in salinized plants. The results show that salt-stress (NaCl and concentrated nutrient solution, reduce all the investigated processes in a different degree. NaCl-stress retarded most seriously growth of apical part and blades in contrast to 7-times concentrated nutrient solution decreasing mainly the rate of root and blade growth. Photosynthesis and 14C-translocation of 14C-assimilates were retarded more seriously by NaCl than by 7-times concentrated nutrient. solution. In the case of seriously stressed plants GA3 and cytokinins (more effectively reversed the ,negative effect of stress conditions both on the photosynthesis and on the 14C-tramslocation. On the basis of the obtained results, it seemes that changes in the rate of investigated processes in salinized plants are due to hormonal disturbances which cause directly or indirectly retardation of photosynthesis and trans-location of assimilates.

  20. The relative importance of kinetic mechanisms and variable enzyme abundances for the regulation of hepatic glucose metabolism--insights from mathematical modeling.

    Science.gov (United States)

    Bulik, Sascha; Holzhütter, Hermann-Georg; Berndt, Nikolaus

    2016-03-02

    Adaptation of the cellular metabolism to varying external conditions is brought about by regulated changes in the activity of enzymes and transporters. Hormone-dependent reversible enzyme phosphorylation and concentration changes of reactants and allosteric effectors are the major types of rapid kinetic enzyme regulation, whereas on longer time scales changes in protein abundance may also become operative. Here, we used a comprehensive mathematical model of the hepatic glucose metabolism of rat hepatocytes to decipher the relative importance of different regulatory modes and their mutual interdependencies in the hepatic control of plasma glucose homeostasis. Model simulations reveal significant differences in the capability of liver metabolism to counteract variations of plasma glucose in different physiological settings (starvation, ad libitum nutrient supply, diabetes). Changes in enzyme abundances adjust the metabolic output to the anticipated physiological demand but may turn into a regulatory disadvantage if sudden unexpected changes of the external conditions occur. Allosteric and hormonal control of enzyme activities allow the liver to assume a broad range of metabolic states and may even fully reverse flux changes resulting from changes of enzyme abundances alone. Metabolic control analysis reveals that control of the hepatic glucose metabolism is mainly exerted by enzymes alone, which are differently controlled by alterations in enzyme abundance, reversible phosphorylation, and allosteric effects. In hepatic glucose metabolism, regulation of enzyme activities by changes of reactants, allosteric effects, and reversible phosphorylation is equally important as changes in protein abundance of key regulatory enzymes.

  1. The space of enzyme regulation in HeLa cells can be inferred from its intracellular metabolome

    Science.gov (United States)

    Diener, Christian; Muñoz-Gonzalez, Felipe; Encarnación, Sergio; Resendis-Antonio, Osbaldo

    2016-01-01

    During the transition from a healthy state to a cancerous one, cells alter their metabolism to increase proliferation. The underlying metabolic alterations may be caused by a variety of different regulatory events on the transcriptional or post-transcriptional level whose identification contributes to the rational design of therapeutic targets. We present a mechanistic strategy capable of inferring enzymatic regulation from intracellular metabolome measurements that is independent of the actual mechanism of regulation. Here, enzyme activities are expressed by the space of all feasible kinetic constants (k-cone) such that the alteration between two phenotypes is given by their corresponding kinetic spaces. Deriving an expression for the transformation of the healthy to the cancer k-cone we identified putative regulated enzymes between the HeLa and HaCaT cell lines. We show that only a few enzymatic activities change between those two cell lines and that this regulation does not depend on gene transcription but is instead post-transcriptional. Here, we identify phosphofructokinase as the major driver of proliferation in HeLa cells and suggest an optional regulatory program, associated with oxidative stress, that affects the activity of the pentose phosphate pathway. PMID:27335086

  2. Extracellular enzyme kinetics scale with resource availability

    Science.gov (United States)

    Sinsabaugh, Robert L.; Belnap, Jayne; Findlay, Stuart G.; Follstad Shah, Jennifer J.; Hill, Brian H.; Kuehn, Kevin A.; Kuske, Cheryl; Litvak, Marcy E.; Martinez, Noelle G.; Moorhead, Daryl L.; Warnock, Daniel D.

    2014-01-01

    Microbial community metabolism relies on external digestion, mediated by extracellular enzymes that break down complex organic matter into molecules small enough for cells to assimilate. We analyzed the kinetics of 40 extracellular enzymes that mediate the degradation and assimilation of carbon, nitrogen and phosphorus by diverse aquatic and terrestrial microbial communities (1160 cases). Regression analyses were conducted by habitat (aquatic and terrestrial), enzyme class (hydrolases and oxidoreductases) and assay methodology (low affinity and high affinity substrates) to relate potential reaction rates to substrate availability. Across enzyme classes and habitats, the scaling relationships between apparent Vmax and apparent Km followed similar power laws with exponents of 0.44 to 0.67. These exponents, called elasticities, were not statistically distinct from a central value of 0.50, which occurs when the Km of an enzyme equals substrate concentration, a condition optimal for maintenance of steady state. We also conducted an ecosystem scale analysis of ten extracellular hydrolase activities in relation to soil and sediment organic carbon (2,000–5,000 cases/enzyme) that yielded elasticities near 1.0 (0.9 ± 0.2, n = 36). At the metabolomic scale, the elasticity of extracellular enzymatic reactions is the proportionality constant that connects the C:N:P stoichiometries of organic matter and ecoenzymatic activities. At the ecosystem scale, the elasticity of extracellular enzymatic reactions shows that organic matter ultimately limits effective enzyme binding sites. Our findings suggest that one mechanism by which microbial communities maintain homeostasis is regulating extracellular enzyme expression to optimize the short-term responsiveness of substrate acquisition. The analyses also show that, like elemental stoichiometry, the fundamental attributes of enzymatic reactions can be extrapolated from biochemical to community and ecosystem scales.

  3. The regulation and catalytic mechanism of the NADP-malic enzyme from tobacco leaves

    Czech Academy of Sciences Publication Activity Database

    Doubnerová, V.; Potůčková, L.; Müller, Karel; Ryšlavá, H.

    2009-01-01

    Roč. 14, 8-9 (2009), s. 893-906 ISSN 0352-5139 Institutional research plan: CEZ:AV0Z50380511 Keywords : NADP-malic enzyme * macroergic compounds * Nicotiana tabacum L. Subject RIV: ED - Physiology Impact factor: 0.820, year: 2009

  4. Astrocyte-neuron crosstalk regulates the expression and subcellular localization of carbohydrate metabolism enzymes.

    Science.gov (United States)

    Mamczur, Piotr; Borsuk, Borys; Paszko, Jadwiga; Sas, Zuzanna; Mozrzymas, Jerzy; Wiśniewski, Jacek R; Gizak, Agnieszka; Rakus, Dariusz

    2015-02-01

    Astrocytes releasing glucose- and/or glycogen-derived lactate and glutamine play a crucial role in shaping neuronal function and plasticity. Little is known, however, how metabolic functions of astrocytes, e.g., their ability to degrade glucosyl units, are affected by the presence of neurons. To address this issue we carried out experiments which demonstrated that co-culturing of rat hippocampal astrocytes with neurons significantly elevates the level of mRNA and protein for crucial enzymes of glycolysis (phosphofructokinase, aldolase, and pyruvate kinase), glycogen metabolism (glycogen synthase and glycogen phosphorylase), and glutamine synthetase in astrocytes. Simultaneously, the decrease of the capability of neurons to metabolize glucose and glutamine is observed. We provide evidence that neurons alter the expression of astrocytic enzymes by secretion of as yet unknown molecule(s) into the extracellular fluid. Moreover, our data demonstrate that almost all studied enzymes may localize in astrocytic nuclei and this localization is affected by the co-culturing with neurons which also reduces proliferative activity of astrocytes. Our results provide the first experimental evidence that the astrocyte-neuron crosstalk substantially affects the expression of basal metabolic enzymes in the both types of cells and influences their subcellular localization in astrocytes. © 2014 Wiley Periodicals, Inc.

  5. Regional Ocean Data Assimilation

    KAUST Repository

    Edwards, Christopher A.; Moore, Andrew M.; Hoteit, Ibrahim; Cornuelle, Bruce D.

    2015-01-01

    This article reviews the past 15 years of developments in regional ocean data assimilation. A variety of scientific, management, and safety-related objectives motivate marine scientists to characterize many ocean environments, including coastal

  6. Oxidative stress and redox state-regulating enzymes have prognostic relevance in diffuse large B-cell lymphoma

    Directory of Open Access Journals (Sweden)

    Peroja Pekka

    2012-03-01

    Full Text Available Abstract Background Oxidative stress and redox-regulating enzymes may have roles both in lymphomagenesis and resistance to lymphoma therapy. Previous studies from the pre-rituximab era suggest that antioxidant enzyme expression is related to prognosis in diffuse large B-cell lymphoma (DLBCL, although these results cannot be extrapolated to patient populations undergoing modern treatment modalities. In this study we assessed expression of the oxidative stress markers 8-hydroxydeoxyguanosine (8-OHdG and nitrotyrosine and the antioxidant enzymes thioredoxin (Trx, manganese superoxide dismutase (MnSOD and glutamate-cysteine ligase (GCL via immunohistochemistry in 106 patients with DLBCL. All patients were treated with CHOP-like therapy combined with rituximab. Immunostaining results were correlated with progression-free survival, disease-specific survival and traditional prognostic factors of DLBCL. Results Strong 8-OHdG immunostaining intensity was associated with extranodal involvement (p = 0.00002, a high International Prognostic Index (p = 0.002 and strong Trx (p = 0.011 and GCL (p = 0.0003 expression. Strong Trx staining intensity was associated with poor progression-free survival (p = 0.046 and poor disease-specific survival (p = 0.015. Strong GCL immunostaining intensity predicted poor progression-free survival (p = 0.049. Patients with either strong Trx or strong nitrotyrosine expression showed significantly poorer progression-free survival (p = 0.003 and disease-specific survival (p = 0.031 compared with the other patients. Conclusions The redox state-regulating enzymes GCL and Trx are promising markers in the evaluation of DLBCL prognosis in the era of modern immunochemotherapy.

  7. The effects of space flight on some rat liver enzymes regulating carbohydrate and lipid metabolism

    Science.gov (United States)

    Abraham, S.; Lin, C. Y.; Klein, H. P.; Volkmann, C.

    We have examined, in the livers of rats carried aboard the Cosmos 936 biosatellite, the activities of about 30 enzymes concerned with carbohydrate and lipid metabolism. In addition to the enzyme studies, the levels of glycogen and of the individual fatty acids in hepatic lipids were determined. Livers from flight and ground control rats at recovery (R0) and 25 days after recovery (R25) were used for these analyses. For all parameters measured, the most meaningful comparisons are those made between flight stationary (FS) and flight centrifuged (FC) animals at R0. When these two groups of flight rats were compared at R0, statistically significant decreases in the activity levels of glycogen phosphorylase, α-glycerol phosphate acyl transferase, diglyceride acyl transferase, aconitase and 6-phosphogluconate dehydrogenase and an increase in the palmitoyl CoA desaturase were noted in the weightless group (FS). The significance of these findings was strengthened by the fact that all enzyme activities showing alterations at R0 returned to normal 25 days postflight. When liver glycogen and total fatty acids of the two sets of flight animals were determined, significant differences that could be attributed to reduced gravity were observed. The weightless group (FS) at R0 contained, on the average, more than twice the amount of glycogen than did the centrifuged controls (FC) and a remarkable shift in the ratio of palmitate to palmitoleate was noted. These metabolic alterations, both in enzyme levels and in hepatic constituents, appear to be characteristic of the weightless condition. Our data seem to justify the conclusion that centrifugation during flight is equivalent to terrestrial gravity.

  8. Direct interaction of beta-amyloid with Na,K-ATPase as a putative regulator of the enzyme function

    Science.gov (United States)

    Petrushanko, Irina Yu.; Mitkevich, Vladimir A.; Anashkina, Anastasia A.; Adzhubei, Alexei A.; Burnysheva, Ksenia M.; Lakunina, Valentina A.; Kamanina, Yulia V.; Dergousova, Elena A.; Lopina, Olga D.; Ogunshola, Omolara O.; Bogdanova, Anna Yu.; Makarov, Alexander A.

    2016-06-01

    By maintaining the Na+ and K+ transmembrane gradient mammalian Na,K-ATPase acts as a key regulator of neuronal electrotonic properties. Na,K-ATPase has an important role in synaptic transmission and memory formation. Accumulation of beta-amyloid (Aβ) at the early stages of Alzheimer’s disease is accompanied by reduction of Na,K-ATPase functional activity. The molecular mechanism behind this phenomenon is not known. Here we show that the monomeric Aβ(1-42) forms a tight (Kd of 3 μM), enthalpy-driven equimolar complex with α1β1 Na,K-ATPase. The complex formation results in dose-dependent inhibition of the enzyme hydrolytic activity. The binding site of Aβ(1-42) is localized in the “gap” between the alpha- and beta-subunits of Na,K-ATPase, disrupting the enzyme functionality by preventing the subunits from shifting towards each other. Interaction of Na,K-ATPase with exogenous Aβ(1-42) leads to a pronounced decrease of the enzyme transport and hydrolytic activity and Src-kinase activation in neuroblastoma cells SH-SY5Y. This interaction allows regulation of Na,K-ATPase activity by short-term increase of the Aβ(1-42) level. However prolonged increase of Aβ(1-42) level under pathological conditions could lead to chronical inhibition of Na,K-ATPase and disruption of neuronal function. Taken together, our data suggest the role of beta-amyloid as a novel physiological regulator of Na,K-ATPase.

  9. Controlled sumoylation of the mevalonate pathway enzyme HMGS-1 regulates metabolism during aging

    NARCIS (Netherlands)

    Sapir, Amir; Tsur, Assaf; Koorman, Thijs; Ching, Kaitlin; Mishra, Prashant; Bardenheier, Annabelle; Podolsky, Lisa; Bening-Abu-Shach, Ulrike; Boxem, Mike; Chou, Tsui-Fen; Broday, Limor; Sternberg, Paul W

    2014-01-01

    Many metabolic pathways are critically regulated during development and aging but little is known about the molecular mechanisms underlying this regulation. One key metabolic cascade in eukaryotes is the mevalonate pathway. It catalyzes the synthesis of sterol and nonsterol isoprenoids, such as

  10. Purification, kinetic behavior, and regulation of NAD(P)+ malic enzyme of tumor mitochondria.

    Science.gov (United States)

    Moreadith, R W; Lehninger, A L

    1984-05-25

    The purification and kinetic characterization of an NAD(P)+-malic enzyme from 22aH mouse hepatoma mitochondria are described. The enzyme was purified 328-fold with a final yield of 51% and specific activity of 38.1 units/mg of protein by employing DEAE-cellulose chromatography and an ATP affinity column. Sephadex G-200 chromatography yielded a native Mr = 240,000. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a major subunit with Mr = 61,000, suggesting a tetrameric structure, and also showed that the preparation contained less than 10% polypeptide impurities. Use of the ATP affinity column required the presence of MnCl2 and fumarate (an allosteric activator) in the elution buffers. In the absence of fumarate, the Michaelis constants for malate, NAD+, and NADP+ were 3.6 mM, 55 microM, and 72 microM, respectively; in the presence of fumarate (2 mM), the constants were 0.34 mM, 9 microM, and 13 microM, respectively. ATP was shown to be an allosteric inhibitor, competitive with malate. However, the inhibition by ATP displayed hyperbolic competitive kinetics with a KI (ATP) of 80 microM (minus fumarate) and 0.5 mM (plus 2 mM fumarate). The allosteric properties of the enzyme are integrated into a rationale for its specific role in the pathways of malate and glutamate oxidation in tumor mitochondria.

  11. [Regulation of thermal stability of enzymes by changing the composition of media. Native and modified alpha-chymotrypsin].

    Science.gov (United States)

    Levitskiĭ, V Iu; Melik-Nubarov, N S; Slepnev, V I; Shikshnis, V A; Mozhaev, V V

    1990-01-01

    Stabilizing effect of denaturing salts on irreversible thermoinactivation of native and modified alpha-chymotrypsin at elevated temperatures is observed. The effect is caused by a shift of conformational equilibrium, at the primary step of reversible unfolding in the course of thermoinactivation, to a more unfolded form which is not able to refold "incorrectly". The stability of alpha-chymotrypsin is regulated within a wide range by medium alteration: the stabilizing effects are similar to those achieved by multipoint attachment of the enzyme to a support or by hydrophilization of protein by covalent modification.

  12. Land Surface Data Assimilation

    Science.gov (United States)

    Houser, P. R.

    2012-12-01

    Information about land surface water, energy and carbon conditions is of critical importance to real-world applications such as agricultural production, water resource management, flood prediction, water supply, weather and climate forecasting, and environmental preservation. While ground-based observational networks are improving, the only practical way to observe these land surface states on continental to global scales is via satellites. Remote sensing can make spatially comprehensive measurements of various components of the terrestrial system, but it cannot provide information on the entire system (e.g. evaporation), and the observations represent only an instant in time. Land surface process models may be used to predict temporal and spatial terrestrial dynamics, but these predictions are often poor, due to model initialization, parameter and forcing, and physics errors. Therefore, an attractive prospect is to combine the strengths of land surface models and observations (and minimize the weaknesses) to provide a superior terrestrial state estimate. This is the goal of land surface data assimilation. Data Assimilation combines observations into a dynamical model, using the model's equations to provide time continuity and coupling between the estimated fields. Land surface data assimilation aims to utilize both our land surface process knowledge, as embodied in a land surface model, and information that can be gained from observations. Both model predictions and observations are imperfect and we wish to use both synergistically to obtain a more accurate result. Moreover, both contain different kinds of information, that when used together, provide an accuracy level that cannot be obtained individually. Model biases can be mitigated using a complementary calibration and parameterization process. Limited point measurements are often used to calibrate the model(s) and validate the assimilation results. This presentation will provide a brief background on land

  13. Ferredoxin-thioredoxin reductase: a catalytically active dithiol group links photoreduced ferredoxin to thioredoxin functional in photosynthetic enzyme regulation

    Energy Technology Data Exchange (ETDEWEB)

    Droux, M.; Miginiac-Maslow, M.; Jacquot, J.P.; Gadal, P.; Crawford, N.A.; Kosower, N.S.; Buchanan, B.B.

    1987-07-01

    The mechanism by which the ferredoxin-thioredoxin system activates the target enzyme, NADP-malate dehydrogenase, was investigated by analyzing the sulfhydryl status of individual protein components with (/sup 14/C)iodoacetate and monobromobimane. The data indicate that ferredoxin-thioredoxin reductase (FTR)--an iron-sulfur enzyme present in oxygenic photosynthetic organisms--is the first member of a thiol chain that links light to enzyme regulation. FTR possesses a catalytically active dithiol group localized on the 13 kDa (similar) subunit, that occurs in all species investigated and accepts reducing equivalents from photoreduced ferredoxin and transfers them stoichiometrically to the disulfide form of thioredoxin m. The reduced thioredoxin m, in turn, reduces NADP-malate dehydrogenase, thereby converting it from an inactive (S-S) to an active (SH) form. The means by which FTR is able to combine electrons (from photoreduced ferredoxin) with protons (from the medium) to reduce its active disulfide group remains to be determined.

  14. Regulation of 11 beta-hydroxysteroid dehydrogenase enzymes in the rat kidney by estradiol.

    Science.gov (United States)

    Gomez-Sanchez, Elise P; Ganjam, Venkataseshu; Chen, Yuan Jian; Liu, Ying; Zhou, Ming Yi; Toroslu, Cigdem; Romero, Damian G; Hughson, Michael D; de Rodriguez, Angela; Gomez-Sanchez, Celso E

    2003-08-01

    The 11beta-hydroxysteroid dehydrogenase (11betaHSD) type 1 (11betaHSD1) enzyme is an NADP+-dependent oxidoreductase, usually reductase, of major glucocorticoids. The NAD+-dependent type 2 (11betaHSD2) enzyme is an oxidase that inactivates cortisol and corticosterone, conferring extrinsic specificity of the mineralocorticoid receptor for aldosterone. We reported that addition of a reducing agent to renal homogenates results in the monomerization of 11betaHSD2 dimers and a significant increase in NAD+-dependent corticosterone conversion. Estrogenic effects on expression, dimerization, and activity of the kidney 11betaHSD1 and -2 enzymes are described herein. Renal 11betaHSD1 mRNA and protein expressions were decreased to very low levels by estradiol (E2) treatment of both intact and castrated male rats; testosterone had no effect. NADP+-dependent enzymatic activity of renal homogenates from E2-treated rats measured under nonreducing conditions was less than that of homogenates from intact animals. Addition of 10 mM DTT to aliquots from these same homogenates abrogated the difference in NADP+-dependent activity between E2-treated and control rats. In contrast, 11betaHSD2 mRNA and protein expressions were significantly increased by E2 treatment. There was a marked increase in the number of juxtamedullary proximal tubules stained by the antibody against 11betaHSD2 after the administration of E2. Notwithstanding, neither the total corticosterone and 11-dehydrocorticosterone excreted in the urine nor their ratio differed between E2- and vehicle-treated rats. NAD+-dependent enzymatic activity in the absence or presence of a reducing agent demonstrated that the increase in 11betaHSD2 protein was not associated with an increase in in vitro activity unless the dimers were reduced to monomers.

  15. Iron Sulfur and Molybdenum Cofactor Enzymes Regulate the Drosophila Life Cycle by Controlling Cell Metabolism

    Science.gov (United States)

    Marelja, Zvonimir; Leimkühler, Silke; Missirlis, Fanis

    2018-01-01

    Iron sulfur (Fe-S) clusters and the molybdenum cofactor (Moco) are present at enzyme sites, where the active metal facilitates electron transfer. Such enzyme systems are soluble in the mitochondrial matrix, cytosol and nucleus, or embedded in the inner mitochondrial membrane, but virtually absent from the cell secretory pathway. They are of ancient evolutionary origin supporting respiration, DNA replication, transcription, translation, the biosynthesis of steroids, heme, catabolism of purines, hydroxylation of xenobiotics, and cellular sulfur metabolism. Here, Fe-S cluster and Moco biosynthesis in Drosophila melanogaster is reviewed and the multiple biochemical and physiological functions of known Fe-S and Moco enzymes are described. We show that RNA interference of Mocs3 disrupts Moco biosynthesis and the circadian clock. Fe-S-dependent mitochondrial respiration is discussed in the context of germ line and somatic development, stem cell differentiation and aging. The subcellular compartmentalization of the Fe-S and Moco assembly machinery components and their connections to iron sensing mechanisms and intermediary metabolism are emphasized. A biochemically active Fe-S core complex of heterologously expressed fly Nfs1, Isd11, IscU, and human frataxin is presented. Based on the recent demonstration that copper displaces the Fe-S cluster of yeast and human ferredoxin, an explanation for why high dietary copper leads to cytoplasmic iron deficiency in flies is proposed. Another proposal that exosomes contribute to the transport of xanthine dehydrogenase from peripheral tissues to the eye pigment cells is put forward, where the Vps16a subunit of the HOPS complex may have a specialized role in concentrating this enzyme within pigment granules. Finally, we formulate a hypothesis that (i) mitochondrial superoxide mobilizes iron from the Fe-S clusters in aconitase and succinate dehydrogenase; (ii) increased iron transiently displaces manganese on superoxide dismutase, which

  16. Iron Sulfur and Molybdenum Cofactor Enzymes Regulate the Drosophila Life Cycle by Controlling Cell Metabolism

    Directory of Open Access Journals (Sweden)

    Zvonimir Marelja

    2018-02-01

    Full Text Available Iron sulfur (Fe-S clusters and the molybdenum cofactor (Moco are present at enzyme sites, where the active metal facilitates electron transfer. Such enzyme systems are soluble in the mitochondrial matrix, cytosol and nucleus, or embedded in the inner mitochondrial membrane, but virtually absent from the cell secretory pathway. They are of ancient evolutionary origin supporting respiration, DNA replication, transcription, translation, the biosynthesis of steroids, heme, catabolism of purines, hydroxylation of xenobiotics, and cellular sulfur metabolism. Here, Fe-S cluster and Moco biosynthesis in Drosophila melanogaster is reviewed and the multiple biochemical and physiological functions of known Fe-S and Moco enzymes are described. We show that RNA interference of Mocs3 disrupts Moco biosynthesis and the circadian clock. Fe-S-dependent mitochondrial respiration is discussed in the context of germ line and somatic development, stem cell differentiation and aging. The subcellular compartmentalization of the Fe-S and Moco assembly machinery components and their connections to iron sensing mechanisms and intermediary metabolism are emphasized. A biochemically active Fe-S core complex of heterologously expressed fly Nfs1, Isd11, IscU, and human frataxin is presented. Based on the recent demonstration that copper displaces the Fe-S cluster of yeast and human ferredoxin, an explanation for why high dietary copper leads to cytoplasmic iron deficiency in flies is proposed. Another proposal that exosomes contribute to the transport of xanthine dehydrogenase from peripheral tissues to the eye pigment cells is put forward, where the Vps16a subunit of the HOPS complex may have a specialized role in concentrating this enzyme within pigment granules. Finally, we formulate a hypothesis that (i mitochondrial superoxide mobilizes iron from the Fe-S clusters in aconitase and succinate dehydrogenase; (ii increased iron transiently displaces manganese on superoxide

  17. The N domain of somatic angiotensin-converting enzyme negatively regulates ectodomain shedding and catalytic activity

    OpenAIRE

    Woodman, Zenda L.; Schwager, Sylva L. U.; Redelinghuys, Pierre; Carmona, Adriana K.; Ehlers, Mario R. W.; Sturrock, Edward D.

    2005-01-01

    sACE (somatic angiotensin-converting enzyme) consists of two homologous, N and C domains, whereas the testis isoenzyme [tACE (testis ACE)] consists of a single C domain. Both isoenzymes are shed from the cell surface by a sheddase activity, although sACE is shed much less efficiently than tACE. We hypothesize that the N domain of sACE plays a regulatory role, by occluding a recognition motif on the C domain required for ectodomain shedding and by influencing the catalytic efficiency. To test ...

  18. Structure and functional regulation of RipA, a mycobacterial enzyme essential for daughter cell separation.

    Science.gov (United States)

    Ruggiero, Alessia; Marasco, Daniela; Squeglia, Flavia; Soldini, Silvia; Pedone, Emilia; Pedone, Carlo; Berisio, Rita

    2010-09-08

    Cell separation depends on cell-wall hydrolases that cleave the peptidoglycan layer connecting daughter cells. In Mycobacterium tuberculosis, this process is governed by the predicted endopeptidase RipA. In the absence of this enzyme, the bacterium is unable to divide and exhibits an abnormal phenotype. We here report the crystal structure of a relevant portion of RipA, containing its catalytic-domain and an extra-domain of hitherto unknown function. The structure clearly demonstrates that RipA is produced as a zymogen, which needs to be activated to achieve cell-division. Bacterial cell-wall degradation assays and proteolysis experiments strongly suggest that activation occurs via proteolytic processing of a fully solvent exposed loop identified in the crystal structure. Indeed, proteolytic cleavage at this loop produces an activated form, consisting of the sole catalytic domain. Our work provides the first evidence of self-inhibition in cell-disconnecting enzymes and opens a field for the design of novel antitubercular therapeutics. Copyright © 2010 Elsevier Ltd. All rights reserved.

  19. Chlorophyll-derived fatty acids regulate expression of lipid metabolizing enzymes in liver - a nutritional opportunity

    Directory of Open Access Journals (Sweden)

    Wolfrum Christian

    2001-01-01

    Full Text Available Nutritional values of fatty acid classes are normally discussed on the basis of their saturated, monounsaturated and polyunsaturated structures with implicit understanding that they are straight-chain. Here we focus on chlorophyll-derived phytanic and pristanic acids that are minor isoprenoid branched-chain lipid constituents in food, but of unknown nutritional value. After describing the enzyme machinery that degrades these nutrient fatty acids in the peroxisome, we show by the criteria of a mouse model and of a human cell culture model that they induce with high potency expression of enzymes responsible for beta-oxidation of straight-chain fatty acids in the peroxisome. We summarize present mechanistic knowledge on fatty acid signaling to the nucleus, which involves protein/protein contacts between peroxisome proliferator activated receptor (PPAR and fatty acid binding protein (FABP. In this signaling event the branched-chain fatty acids are the most effective ones. Finally, on the basis of this nutrient-gene interaction we discuss nutritional opportunities and therapeutic aspects of the chlorophyll-derived fatty acids.

  20. Structure, function, and regulation of enzymes involved in amino acid metabolism of bacteria and archaea.

    Science.gov (United States)

    Tomita, Takeo

    2017-11-01

    Amino acids are essential components in all organisms because they are building blocks of proteins. They are also produced industrially and used for various purposes. For example, L-glutamate is used as the component of "umami" taste and lysine has been used as livestock feed. Recently, many kinds of amino acids have attracted attention as biological regulators and are used for a healthy life. Thus, to clarify the mechanism of how amino acids are biosynthesized and how they work as biological regulators will lead to further effective utilization of them. Here, I review the leucine-induced-allosteric activation of glutamate dehydrogenase (GDH) from Thermus thermophilus and the relationship with the allosteric regulation of GDH from mammals. Next, I describe structural insights into the efficient production of L-glutamate by GDH from an excellent L-glutamate producer, Corynebacterium glutamicum. Finally, I review the structural biology of lysine biosynthesis of thermophilic bacterium and archaea.

  1. Surface binding sites (SBSs), mechanism and regulation of enzymes degrading amylopectin and α-limit dextrins

    DEFF Research Database (Denmark)

    Møller, Marie Sofie; Cockburn, Darrell; Nielsen, Jonas W.

    2013-01-01

    into barley seed α-amylase 1 (AMY1) and limit dextrinase (LD) includes i. kinetics of bi-exponential amylopectin hydrolysis by AMY1, one reaction having low Km (8 μg/mL) and high kcat (57 s-1) and the other high Km (97 μg/mL) and low kcat (23 s-1). β-Cyclodextrin (β-CD) inhibits the first reaction by binding...... to an SBS (SBS2) on domain C with Kd = 70 μM, which for the SBS2 Y380A mutant increases to 1.4 mM. SBS2 thus has a role in the fast, high-affinity component of amylopectin degradation. ii. The N-terminal domain of LD, the debranching enzyme in germinating seeds, shows distant structural similarity...

  2. Mitochondrial uncoupling proteins regulate angiotensin-converting enzyme expression: crosstalk between cellular and endocrine metabolic regulators suggested by RNA interference and genetic studies.

    Science.gov (United States)

    Dhamrait, Sukhbir S; Maubaret, Cecilia; Pedersen-Bjergaard, Ulrik; Brull, David J; Gohlke, Peter; Payne, John R; World, Michael; Thorsteinsson, Birger; Humphries, Steve E; Montgomery, Hugh E

    2016-07-01

    Uncoupling proteins (UCPs) regulate mitochondrial function, and thus cellular metabolism. Angiotensin-converting enzyme (ACE) is the central component of endocrine and local tissue renin-angiotensin systems (RAS), which also regulate diverse aspects of whole-body metabolism and mitochondrial function (partly through altering mitochondrial UCP expression). We show that ACE expression also appears to be regulated by mitochondrial UCPs. In genetic analysis of two unrelated populations (healthy young UK men and Scandinavian diabetic patients) serum ACE (sACE) activity was significantly higher amongst UCP3-55C (rather than T) and UCP2 I (rather than D) allele carriers. RNA interference against UCP2 in human umbilical vein endothelial cells reduced UCP2 mRNA sixfold (P sACE suggests a novel means of crosstalk between (and mutual regulation of) cellular and endocrine metabolism. This might partly explain the reduced risk of developing diabetes and metabolic syndrome with RAS antagonists and offer insight into the origins of cardiovascular disease in which UCPs and ACE both play a role. © 2016 The Authors. BioEssays published by WILEY Periodicals, Inc.

  3. Mitochondrial uncoupling proteins regulate angiotensin‐converting enzyme expression: crosstalk between cellular and endocrine metabolic regulators suggested by RNA interference and genetic studies

    Science.gov (United States)

    Maubaret, Cecilia; Pedersen‐Bjergaard, Ulrik; Brull, David J.; Gohlke, Peter; Payne, John R.; World, Michael; Thorsteinsson, Birger; Humphries, Steve E.; Montgomery, Hugh E.

    2015-01-01

    Uncoupling proteins (UCPs) regulate mitochondrial function, and thus cellular metabolism. Angiotensin‐converting enzyme (ACE) is the central component of endocrine and local tissue renin–angiotensin systems (RAS), which also regulate diverse aspects of whole‐body metabolism and mitochondrial function (partly through altering mitochondrial UCP expression). We show that ACE expression also appears to be regulated by mitochondrial UCPs. In genetic analysis of two unrelated populations (healthy young UK men and Scandinavian diabetic patients) serum ACE (sACE) activity was significantly higher amongst UCP3‐55C (rather than T) and UCP2 I (rather than D) allele carriers. RNA interference against UCP2 in human umbilical vein endothelial cells reduced UCP2 mRNA sixfold (P sACE suggests a novel means of crosstalk between (and mutual regulation of) cellular and endocrine metabolism. This might partly explain the reduced risk of developing diabetes and metabolic syndrome with RAS antagonists and offer insight into the origins of cardiovascular disease in which UCPs and ACE both play a role. PMID:27347560

  4. Regulation of behavioral circadian rhythms and clock protein PER1 by the deubiquitinating enzyme USP2

    DEFF Research Database (Denmark)

    Yang, Yaoming; Duguay, David; Bédard, Nathalie

    2012-01-01

    Endogenous 24-hour rhythms are generated by circadian clocks located in most tissues. The molecular clock mechanism is based on feedback loops involving clock genes and their protein products. Post-translational modifications, including ubiquitination, are important for regulating the clock...

  5. The AMPK enzyme-complex: From the regulation of cellular energy homeostasis to a possible new molecular target in the management of chronic inflammatory disorders

    NARCIS (Netherlands)

    Antonioli, Luca; Colucci, Rocchina; Pellegrini, Carolina; Giustarini, Giulio; Sacco, Deborah; Tirotta, Erika; Caputi, Valentina; Marsilio, Ilaria; Giron, Maria Cecilia; Németh, Zoltán H; Blandizzi, Corrado; Fornai, Matteo

    2016-01-01

    Introduction: Adenosine monophosphate-activated protein kinase (AMPK), known as an enzymatic complex that regulates the energetic metabolism, is emerging as a pivotal enzyme and enzymatic pathway involved in the regulation of immune homeostatic networks. It is also involved in the molecular

  6. Protein Kinase D Enzymes as Regulators of EMT and Cancer Cell Invasion

    Directory of Open Access Journals (Sweden)

    Nisha Durand

    2016-02-01

    Full Text Available The Protein Kinase D (PKD isoforms PKD1, PKD2, and PKD3 are effectors of the novel Protein Kinase Cs (nPKCs and diacylglycerol (DAG. PKDs impact diverse biological processes like protein transport, cell migration, proliferation, epithelial to mesenchymal transition (EMT and apoptosis. PKDs however, have distinct effects on these functions. While PKD1 blocks EMT and cell migration, PKD2 and PKD3 tend to drive both processes. Given the importance of EMT and cell migration to the initiation and progression of various malignancies, abnormal expression of PKDs has been reported in multiple types of cancers, including breast, pancreatic and prostate cancer. In this review, we discuss how EMT and cell migration are regulated by PKD isoforms and the significance of this regulation in the context of cancer development.

  7. Antidiabetic activity of Ganoderma lucidum polysaccharides F31 down-regulated hepatic glucose regulatory enzymes in diabetic mice.

    Science.gov (United States)

    Xiao, Chun; Wu, Qingping; Zhang, Jumei; Xie, Yizhen; Cai, Wen; Tan, Jianbin

    2017-01-20

    Ganoderma lucidum (Lin Zhi) has been used to treat diabetes in Chinese folk for centuries. Our laboratory previously demonstrated that Ganoderma lucidum polysaccharides (GLPs) had hypoglycemic effects in diabetic mice. Our aim was to identify the main bioactives in GLPs and corresponding mechanism of action. Four polysaccharide-enriched fraction were isolated from GLPs and the antidiabetic activities were evaluated by type 2 diabetic mice. Fasting serum glucose (FSG), fasting serum insulin (FSI) and epididymal fat/BW ratio were measured at the end of the experiment. In liver, the mRNA levels of hepatic glucose regulatory enzymes were determined by quantitative polymerase chain reaction (qPCR) and the protein levels of phospho-AMP-activated protein kinase (p-AMPK)/AMPK were determined by western blotting test. In epididymal fat tissue, the mRNA and protein levels GLUT4, resistin, fatty acid synthase (FAS) and acetyl-CoA carboxylase (ACC1) were determined by qPCR and immuno-histochemistry. The structure of polysaccharide F31 was obtained from GPC, FTIR NMR and GC-MS spectroscopy, RESULTS: F31 significantly decreased FSG (P<0.05), FSI and epididymal fat/BW ratio (P<0.01). In liver, F31 decreased the mRNA levels of hepatic glucose regulatory enzymes, and up-regulated the ratio of phospho-AMP-activated protein kinase (p-AMPK)/AMPK. In epididymal fat tissue, F31 increased the mRNA levels of GLUT4 but decreased fatty acid synthase (FAS), acetyl-CoA carboxylase (ACC1) and resistin. Immuno-histochemistry results revealed F31 increased the protein levels of GLUT4 and decreased resistin. Data suggested that the main bioactives in GLPs was F31, which was determined to be a β-heteropolysaccharide with the weight-average molecular weight of 15.9kDa. The possible action mechanism of F31 may be associated with down-regulation of the hepatic glucose regulated enzyme mRNA levels via AMPK activation, improvement of insulin resistance and decrease of epididymal fat/BW ratio. These

  8. Displacement data assimilation

    Energy Technology Data Exchange (ETDEWEB)

    Rosenthal, W. Steven [Pacific Northwest Laboratory, Richland, WA 99354 (United States); Venkataramani, Shankar [Department of Mathematics and Program in Applied Mathematics, University of Arizona, Tucson, AZ 85721 (United States); Mariano, Arthur J. [Rosenstiel School of Marine & Atmospheric Science, University of Miami, Miami, FL 33149 (United States); Restrepo, Juan M., E-mail: restrepo@math.oregonstate.edu [Department of Mathematics, Oregon State University, Corvallis, OR 97331 (United States)

    2017-02-01

    We show that modifying a Bayesian data assimilation scheme by incorporating kinematically-consistent displacement corrections produces a scheme that is demonstrably better at estimating partially observed state vectors in a setting where feature information is important. While the displacement transformation is generic, here we implement it within an ensemble Kalman Filter framework and demonstrate its effectiveness in tracking stochastically perturbed vortices.

  9. Tet Enzymes Regulate Telomere Maintenance and Chromosomal Stability of Mouse ESCs

    Directory of Open Access Journals (Sweden)

    Jiao Yang

    2016-05-01

    Full Text Available Ten-eleven translocation (Tet family proteins convert 5-methylcytosine to 5-hydroxymethylcytosine. We show that mouse embryonic stem cells (ESCs depleted of Tet1 and/or Tet2 by RNAi exhibit short telomeres and chromosomal instability, concomitant with reduced telomere recombination. Tet1 and Tet2 double-knockout ESCs also display short telomeres but to a lesser extent. Notably, Tet1/2/3 triple-knockout ESCs show heterogeneous telomere lengths and increased frequency of telomere loss and chromosomal fusion. Mechanistically, Tets depletion or deficiency increases Dnmt3b and decreases 5hmC levels, resulting in elevated methylation levels at sub-telomeres. Consistently, knockdown of Dnmt3b or addition of 2i (MAPK and GSK3β inhibitors, which also inhibits Dnmt3b, reduces telomere shortening, partially rescuing Tet1/2 deficiency. Interestingly, Tet1/2 double or Tet1/2/3 triple knockout in ESCs consistently upregulates Zscan4, which may counteract telomere shortening. Together, Tet enzymes play important roles in telomere maintenance and chromosomal stability of ESCs by modulating sub-telomeric methylation levels.

  10. Altered drug metabolism during pregnancy: hormonal regulation of drug-metabolizing enzymes.

    Science.gov (United States)

    Jeong, Hyunyoung

    2010-06-01

    Medication use during pregnancy is prevalent, but pharmacokinetic information of most drugs used during pregnancy is lacking in spite of known effects of pregnancy on drug disposition. Accurate pharmacokinetic information is essential for optimal drug therapy in mother and fetus. Thus, understanding how pregnancy influences drug disposition is important for better prediction of pharmacokinetic changes of drugs in pregnant women. Pregnancy is known to affect hepatic drug metabolism, but the underlying mechanisms remain unknown. Physiological changes accompanying pregnancy are probably responsible for the reported alteration in drug metabolism during pregnancy. These include elevated concentrations of various hormones such as estrogen, progesterone, placental growth hormones and prolactin. This review covers how these hormones influence expression of drug-metabolizing enzymes (DMEs), thus potentially responsible for altered drug metabolism during pregnancy. The reader will gain a greater understanding of the altered drug metabolism in pregnant women and the regulatory effects of pregnancy hormones on expression of DMEs. In-depth studies in hormonal regulatory mechanisms as well as confirmatory studies in pregnant women are warranted for systematic understanding and prediction of the changes in hepatic drug metabolism during pregnancy.

  11. Epigenetic regulation of somatic angiotensin-converting enzyme by DNA methylation and histone acetylation.

    Science.gov (United States)

    Rivière, Guillaume; Lienhard, Daniel; Andrieu, Thomas; Vieau, Didier; Frey, Brigitte M; Frey, Felix J

    2011-04-01

    Somatic angiotensin-converting enzyme (sACE) is crucial in cardiovascular homeostasis and displays a tissue-specific profile. Epigenetic patterns modulate genes expression and their alterations were implied in pathologies including hypertension. However, the influence of DNA methylation and chromatin condensation state on the expression of sACE is unknown. We examined whether such epigenetic mechanisms could participate in the control of sACE expression in vitro and in vivo. We identified two CpG islands in the human ace-1 gene 3 kb proximal promoter region. Their methylation abolished the luciferase activity of ace-1 promoter/reporter constructs transfected into human liver (HepG2), colon (HT29), microvascular endothelial (HMEC-1) and lung (SUT) cell lines (p sACE mRNA expression cell-type specifically (p sACE mRNA expression in the lungs and liver (p = 0.05), but not in the kidney. In conclusion, the expression level of somatic ACE is modulated by CpG-methylation and histone deacetylases inhibition. The basal methylation pattern of the promoter of the ace-1 gene is cell-type specific and correlates to sACE transcription. DNMT inhibition is associated with altered methylation of the ace-1 promoter and a cell-type and tissue-specific increase of sACE mRNA levels. This study indicates a strong influence of epigenetic mechanisms on sACE expression.

  12. Deubiquitylating enzyme USP9x regulates hippo pathway activity by controlling angiomotin protein turnover

    DEFF Research Database (Denmark)

    Nguyen, Thanh Hung; Andrejeva, Diana; Gupta, Rajat

    2016-01-01

    /TAZ activity. We demonstrate that USPx regulates ubiquitin-mediated turnover of the YAP inhibitor, Angiomotin. USP9x acts to deubiquitylate Angiomotin at lysine 496, resulting in stabilization of Angiomotin and lower YAP/TAZ activity. USP9x mRNA levels were reduced in several cancers. Clinically, USP9x m......RNA levels were reduced in several cancers with low USPx expression correlating with poor prognosis in renal clear cell carcinoma. Our data indicate that USP9x may be a useful biomarker for renal clear cell carcinoma....

  13. Nicotine affects rat Leydig cell function in vivo and vitro via down-regulating some key steroidogenic enzyme expressions.

    Science.gov (United States)

    Guo, Xiaoling; Wang, Huang; Wu, Xiaolong; Chen, Xianwu; Chen, Yong; Guo, Jingjing; Li, Xiaoheng; Lian, Qingquan; Ge, Ren-Shan

    2017-12-01

    Nicotine is consumed largely as a component of cigarettes and has a potential effect on pubertal development of Leydig cells in males. To investigate its effects, 49-day-old male Sprague Dawley rats received intraperitoneal injections of nicotine (0.5 or 1 mg/kg/day) for 2 weeks and immature Leydig cells were isolated from the testes of 35-day-old rats and treated with nicotine (0.05-50 μM). Serum hormones, Leydig cell number and related gene expression levels after in vivo treatment were determined and medium androgen levels were measured and cell cycle, apoptosis, mitochondrial membrane potential (△Ψm), and reactive oxygen species (ROS) of Leydig cells after in vitro treatment were measured. In vivo exposure to nicotine lowered serum luteinizing hormone, follicle stimulating hormone, and testosterone levels and reduced Leydig cell number and gene expression levels. Nicotine in vitro inhibited androgen production in Leydig cells by downregulating the expression levels of P450 cholesterol side cleavage enzyme, 3β-hydroxysteroid dehydrogenase 1, and steroidogenic factor 1 at different concentration ranges. In conclusion, nicotine disrupts Leydig cell steroidogenesis during puberty possibly via down-regulating some key steroidogenic enzyme expressions. Copyright © 2017. Published by Elsevier Ltd.

  14. The N domain of somatic angiotensin-converting enzyme negatively regulates ectodomain shedding and catalytic activity.

    Science.gov (United States)

    Woodman, Zenda L; Schwager, Sylva L U; Redelinghuys, Pierre; Carmona, Adriana K; Ehlers, Mario R W; Sturrock, Edward D

    2005-08-01

    sACE (somatic angiotensin-converting enzyme) consists of two homologous, N and C domains, whereas the testis isoenzyme [tACE (testis ACE)] consists of a single C domain. Both isoenzymes are shed from the cell surface by a sheddase activity, although sACE is shed much less efficiently than tACE. We hypothesize that the N domain of sACE plays a regulatory role, by occluding a recognition motif on the C domain required for ectodomain shedding and by influencing the catalytic efficiency. To test this, we constructed two mutants: CNdom-ACE and CCdom-ACE. CNdom-ACE was shed less efficiently than sACE, whereas CCdom-ACE was shed as efficiently as tACE. Notably, cleavage occurred both within the stalk and the interdomain bridge in both mutants, suggesting that a sheddase recognition motif resides within the C domain and is capable of directly cleaving at both positions. Analysis of the catalytic properties of the mutants and comparison with sACE and tACE revealed that the k(cat) for sACE and CNdom-ACE was less than or equal to the sum of the kcat values for tACE and the N-domain, suggesting negative co-operativity, whereas the kcat value for the CCdom-ACE suggested positive co-operativity between the two domains. Taken together, the results provide support for (i) the existence of a sheddase recognition motif in the C domain and (ii) molecular flexibility of the N and C domains in sACE, resulting in occlusion of the C-domain recognition motif by the N domain as well as close contact of the two domains during hydrolysis of peptide substrates.

  15. Green tea diet decreases PCB 126-induced oxidative stress in mice by up-regulating antioxidant enzymes.

    Science.gov (United States)

    Newsome, Bradley J; Petriello, Michael C; Han, Sung Gu; Murphy, Margaret O; Eske, Katryn E; Sunkara, Manjula; Morris, Andrew J; Hennig, Bernhard

    2014-02-01

    Superfund chemicals such as polychlorinated biphenyls pose a serious human health risk due to their environmental persistence and link to multiple diseases. Selective bioactive food components such as flavonoids have been shown to ameliorate PCB toxicity, but primarily in an in vitro setting. Here, we show that mice fed a green tea-enriched diet and subsequently exposed to environmentally relevant doses of coplanar PCB exhibit decreased overall oxidative stress primarily due to the up-regulation of a battery of antioxidant enzymes. C57BL/6 mice were fed a low-fat diet supplemented with green tea extract (GTE) for 12 weeks and exposed to 5 μmol PCB 126/kg mouse weight (1.63 mg/kg-day) on weeks 10, 11 and 12 (total body burden: 4.9 mg/kg). F2-isoprostane and its metabolites, established markers of in vivo oxidative stress, measured in plasma via HPLC-MS/MS exhibited fivefold decreased levels in mice supplemented with GTE and subsequently exposed to PCB compared to animals on a control diet exposed to PCB. Livers were collected and harvested for both messenger RNA and protein analyses, and it was determined that many genes transcriptionally controlled by aryl hydrocarbon receptor and nuclear factor (erythroid-derived 2)-like 2 proteins were up-regulated in PCB-exposed mice fed the green tea-supplemented diet. An increased induction of genes such as SOD1, GSR, NQO1 and GST, key antioxidant enzymes, in these mice (green tea plus PCB) may explain the observed decrease in overall oxidative stress. A diet supplemented with green tea allows for an efficient antioxidant response in the presence of PCB 126, which supports the emerging paradigm that healthful nutrition may be able to bolster and buffer a physiological system against the toxicities of environmental pollutants. Copyright © 2014 Elsevier Inc. All rights reserved.

  16. Regulating inflammation through the anti-inflammatory enzyme platelet-activating factor-acetylhydrolase

    Directory of Open Access Journals (Sweden)

    Hugo C Castro Faria Neto

    2005-03-01

    Full Text Available Platelet-activating factor (PAF is one of the most potent lipid mediators involved in inflammatory events. The acetyl group at the sn-2 position of its glycerol backbone is essential for its biological activity. Deacetylation induces the formation of the inactive metabolite lyso-PAF. This deacetylation reaction is catalyzed by PAF-acetylhydrolase (PAF-AH, a calcium independent phospholipase A2 that also degrades a family of PAF-like oxidized phospholipids with short sn-2 residues. Biochemical and enzymological evaluations revealed that at least three types of PAF-AH exist in mammals, namely the intracellular types I and II and a plasma type. Many observations indicate that plasma PAF AH terminates signals by PAF and oxidized PAF-like lipids and thereby regulates inflammatory responses. In this review, we will focus on the potential of PAF-AH as a modulator of diseases of dysregulated inflammation.

  17. Regulations of enzymes in animals: effects of developmental processes, cancer, and radiation. Final report. [Analysis of enzymes in human cancer tissue

    Energy Technology Data Exchange (ETDEWEB)

    Knox, W.E.

    1978-09-01

    Low grade tumors of various origins are chemically very different. High grade tumors, whatever their origin, are chemically very similar to one another and to embryonic tissues. Analyses of human tumor tissues and sera from cancer patients were conducted for two new groups of enzymes expected to be informative about the physiological state of the tissue. The enzymes measured in tumors and sera were chosen because they were characteristic of fetal tissues and high grade neoplasms in rats, and could, therefore, be expected to exist in human cancers (and fetuses) and to predominate more in those of higher grade malignancies. Results indicated that the classification of enzymes (or isozymes) as fetal or adult types in the rat could be extended to man. Human cancers do contain most of the enzymes expected, and lack others, as expected. Analyses of the same enzymes in sera gave less clear results. It was recognized at the outset that no simple proportionality existed between tissue and serum levels. The tendency existed in cancer patients to have in serum elevated amounts of those enzymes characteristic of undifferentiated tissues. The abnormalities in a specific patient are conditioned by his physiological state, by the grade of his tumor, and by the mass of tumor present. The tumor mass had a very significant effect, so that monitoring this tumor burden by chemical means should be quite possible. The latest work focused on particular enzymes that have not previously been measured in cancer patients. These studies concentrated on pyrroline-5-carboxylate (P-5-C) reductase and its inhibition and on lysosomal glucosidases and phosphatases. Both groups are relatively high in fetal and neoplastic tissues.

  18. Regulation of drug-metabolizing enzymes in infectious and inflammatory disease: implications for biologics-small molecule drug interactions.

    Science.gov (United States)

    Mallick, Pankajini; Taneja, Guncha; Moorthy, Bhagavatula; Ghose, Romi

    2017-06-01

    Drug-metabolizing enzymes (DMEs) are primarily down-regulated during infectious and inflammatory diseases, leading to disruption in the metabolism of small molecule drugs (smds), which are increasingly being prescribed therapeutically in combination with biologics for a number of chronic diseases. The biologics may exert pro- or anti-inflammatory effect, which may in turn affect the expression/activity of DMEs. Thus, patients with infectious/inflammatory diseases undergoing biologic/smd treatment can have complex changes in DMEs due to combined effects of the disease and treatment. Areas covered: We will discuss clinical biologics-SMD interaction and regulation of DMEs during infection and inflammatory diseases. Mechanistic studies will be discussed and consequences on biologic-small molecule combination therapy on disease outcome due to changes in drug metabolism will be highlighted. Expert opinion: The involvement of immunomodulatory mediators in biologic-SMDs is well known. Regulatory guidelines recommend appropriate in vitro or in vivo assessments for possible interactions. The role of cytokines in biologic-SMDs has been documented. However, the mechanisms of drug-drug interactions is much more complex, and is probably multi-factorial. Studies aimed at understanding the mechanism by which biologics effect the DMEs during inflammation/infection are clinically important.

  19. Respiration and nitrogen assimilation: targeting mitochondria-associated metabolism as a means to enhance nitrogen use efficiency.

    Science.gov (United States)

    Foyer, Christine H; Noctor, Graham; Hodges, Michael

    2011-02-01

    Considerable advances in our understanding of the control of mitochondrial metabolism and its interactions with nitrogen metabolism and associated carbon/nitrogen interactions have occurred in recent years, particularly highlighting important roles in cellular redox homeostasis. The tricarboxylic acid (TCA) cycle is a central metabolic hub for the interacting pathways of respiration, nitrogen assimilation, and photorespiration, with components that show considerable flexibility in relation to adaptations to the different functions of mitochondria in photosynthetic and non-photosynthetic cells. By comparison, the operation of the oxidative pentose phosphate pathway appears to represent a significant limitation to nitrogen assimilation in non-photosynthetic tissues. Valuable new insights have been gained concerning the roles of the different enzymes involved in the production of 2-oxoglutarate (2-OG) for ammonia assimilation, yielding an improved understanding of the crucial role of cellular energy balance as a broker of co-ordinate regulation. Taken together with new information on the mechanisms that co-ordinate the expression of genes involved in organellar functions, including energy metabolism, and the potential for exploiting the existing flexibility for NAD(P)H utilization in the respiratory electron transport chain to drive nitrogen assimilation, the evidence that mitochondrial metabolism and machinery are potential novel targets for the enhancement of nitrogen use efficiency (NUE) is explored.

  20. High performance mass spectrometry based proteomics reveals enzyme and signaling pathway regulation in neutrophils during the early stage of surgical trauma

    DEFF Research Database (Denmark)

    Arshid, Samina; Tahir, Muhammad; Fontes, Belchor

    2017-01-01

    and surgical trauma rats in this study. Extracted proteins were analyzed using nano liquid chromatography coupled to tandem mass spectrometry. A total of 2924 rat neutrophil proteins were identified in our analysis, of which 393 were found differentially regulated between control and trauma groups. By using...... functional pathways analysis of the 190 proteins up-regulated in surgical trauma we found proteins related to transcription initiation and protein biosynthesis. On the other hand, among the 203 proteins down-regulated in surgical trauma we found enrichment for proteins of the immune response, proteasome...... degradation and actin cytoskeleton. Overall, enzyme prediction analysis revealed that regulated enzymes are directly involved in neutrophil apoptosis, directional migration and chemotaxis. Our observations were then confirmed by in silico protein-protein interaction analysis. Collectively, our results reveal...

  1. Coactivator PGC-1α regulates the fasting inducible xenobiotic-metabolizing enzyme CYP2A5 in mouse primary hepatocytes

    International Nuclear Information System (INIS)

    Arpiainen, Satu; Jaervenpaeae, Sanna-Mari; Manninen, Aki; Viitala, Pirkko; Lang, Matti A.; Pelkonen, Olavi; Hakkola, Jukka

    2008-01-01

    The nutritional state of organisms and energy balance related diseases such as diabetes regulate the metabolism of xenobiotics such as drugs, toxins and carcinogens. However, the mechanisms behind this regulation are mostly unknown. The xenobiotic-metabolizing cytochrome P450 (CYP) 2A5 enzyme has been shown to be induced by fasting and by glucagon and cyclic AMP (cAMP), which mediate numerous fasting responses. Peroxisome proliferator-activated receptor γ coactivator (PGC)-1α triggers many of the important hepatic fasting effects in response to elevated cAMP levels. In the present study, we were able to show that cAMP causes a coordinated induction of PGC-1α and CYP2A5 mRNAs in murine primary hepatocytes. Furthermore, the elevation of the PGC-1α expression level by adenovirus mediated gene transfer increased CYP2A5 transcription. Co-transfection of Cyp2a5 5' promoter constructs with the PGC-1α expression vector demonstrated that PGC-1α is able to activate Cyp2a5 transcription through the hepatocyte nuclear factor (HNF)-4α response element in the proximal promoter of the Cyp2a5 gene. Chromatin immunoprecipitation assays showed that PGC-1α binds, together with HNF-4α, to the same region at the Cyp2a5 proximal promoter. In conclusion, PGC-1α mediates the expression of CYP2A5 induced by cAMP in mouse hepatocytes through coactivation of transcription factor HNF-4α. This strongly suggests that PGC-1α is the major factor mediating the fasting response of CYP2A5

  2. A Cyanide-Induced 3-Cyanoalanine Nitrilase in the Cyanide-Assimilating Bacterium Pseudomonas pseudoalcaligenes Strain CECT 5344.

    Science.gov (United States)

    Acera, Felipe; Carmona, María Isabel; Castillo, Francisco; Quesada, Alberto; Blasco, Rafael

    2017-05-01

    Pseudomonas pseudoalcaligenes CECT 5344 is a bacterium able to assimilate cyanide as a sole nitrogen source. Under this growth condition, a 3-cyanoalanine nitrilase enzymatic activity was induced. This activity was encoded by nit4 , one of the four nitrilase genes detected in the genome of this bacterium, and its expression in Escherichia coli enabled the recombinant strain to fully assimilate 3-cyanoalanine. P. pseudoalcaligenes CECT 5344 showed a weak growth level with 3-cyanoalanine as the N source, unless KCN was also added. Moreover, a nit4 knockout mutant of P. pseudoalcaligenes CECT 5344 became severely impaired in its ability to grow with 3-cyanoalanine and cyanide as nitrogen sources. The native enzyme expressed in E. coli was purified up to electrophoretic homogeneity and biochemically characterized. Nit4 seems to be specific for 3-cyanoalanine, and the amount of ammonium derived from the enzymatic activity doubled in the presence of exogenously added asparaginase activity, which demonstrated that the Nit4 enzyme had both 3-cyanoalanine nitrilase and hydratase activities. The nit4 gene is located downstream of the cyanide resistance transcriptional unit containing cio1 genes, whose expression levels are under the positive control of cyanide. Real-time PCR experiments revealed that nit4 expression was also positively regulated by cyanide in both minimal and LB media. These results suggest that this gene cluster including cio1 and nit4 could be involved both in cyanide resistance and in its assimilation by P. pseudoalcaligenes CECT 5344. IMPORTANCE Cyanide is a highly toxic molecule present in some industrial wastes due to its application in several manufacturing processes, such as gold mining and the electroplating industry. The biodegradation of cyanide from contaminated wastes could be an attractive alternative to physicochemical treatment. P. pseudoalcaligenes CECT 5344 is a bacterial strain able to assimilate cyanide under alkaline conditions, thus

  3. Spatial Assimilation in Denmark?

    DEFF Research Database (Denmark)

    Andersen, Hans Skifter

    2010-01-01

    market and discrimination, which limits the housing possibilities for ethnic minorities. Another explanation could be that immigrants for different reasons choose to settle in so-called ethnic enclaves where they can find an ethnic social network, which can support them in their new country....... In traditional research literature about immigration it has been shown that for many immigrants living in enclaves has been a temporary situation. The 'spatial assimilation theory' says that this situation ends when the family has become more integrated in the new society and then moves to other parts...

  4. Regional Ocean Data Assimilation

    KAUST Repository

    Edwards, Christopher A.

    2015-01-03

    This article reviews the past 15 years of developments in regional ocean data assimilation. A variety of scientific, management, and safety-related objectives motivate marine scientists to characterize many ocean environments, including coastal regions. As in weather prediction, the accurate representation of physical, chemical, and/or biological properties in the ocean is challenging. Models and observations alone provide imperfect representations of the ocean state, but together they can offer improved estimates. Variational and sequential methods are among the most widely used in regional ocean systems, and there have been exciting recent advances in ensemble and four-dimensional variational approaches. These techniques are increasingly being tested and adapted for biogeochemical applications.

  5. Silicon Mitigates Salinity Stress by Regulating the Physiology, Antioxidant Enzyme Activities, and Protein Expression in Capsicum annuum 'Bugwang'.

    Science.gov (United States)

    Manivannan, Abinaya; Soundararajan, Prabhakaran; Muneer, Sowbiya; Ko, Chung Ho; Jeong, Byoung Ryong

    2016-01-01

    Silicon- (Si-) induced salinity stress resistance was demonstrated at physiological and proteomic levels in Capsicum annuum for the first time. Seedlings of C. annuum were hydroponically treated with NaCl (50 mM) with or without Si (1.8 mM) for 15 days. The results illustrated that saline conditions significantly reduced plant growth and biomass and photosynthetic parameters and increased the electrolyte leakage potential, lipid peroxidation, and hydrogen peroxide level. However, supplementation of Si allowed the plants to recover from salinity stress by improving their physiology and photosynthesis. During salinity stress, Si prevented oxidative damage by increasing the activities of antioxidant enzymes. Furthermore, Si supplementation recovered the nutrient imbalance that had occurred during salinity stress. Additionally, proteomic analysis by two-dimensional gel electrophoresis (2DE) followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) revealed that Si treatment upregulated the accumulation of proteins involved in several metabolic processes, particularly those associated with nucleotide binding and transferase activity. Moreover, Si modulated the expression of vital proteins involved in ubiquitin-mediated nucleosome pathway and carbohydrate metabolism. Overall, the results illustrate that Si application induced resistance against salinity stress in C. annuum by regulating the physiology, antioxidant metabolism, and protein expression.

  6. Silicon Mitigates Salinity Stress by Regulating the Physiology, Antioxidant Enzyme Activities, and Protein Expression in Capsicum annuum ‘Bugwang'

    Science.gov (United States)

    Manivannan, Abinaya; Soundararajan, Prabhakaran; Muneer, Sowbiya; Ko, Chung Ho

    2016-01-01

    Silicon- (Si-) induced salinity stress resistance was demonstrated at physiological and proteomic levels in Capsicum annuum for the first time. Seedlings of C. annuum were hydroponically treated with NaCl (50 mM) with or without Si (1.8 mM) for 15 days. The results illustrated that saline conditions significantly reduced plant growth and biomass and photosynthetic parameters and increased the electrolyte leakage potential, lipid peroxidation, and hydrogen peroxide level. However, supplementation of Si allowed the plants to recover from salinity stress by improving their physiology and photosynthesis. During salinity stress, Si prevented oxidative damage by increasing the activities of antioxidant enzymes. Furthermore, Si supplementation recovered the nutrient imbalance that had occurred during salinity stress. Additionally, proteomic analysis by two-dimensional gel electrophoresis (2DE) followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) revealed that Si treatment upregulated the accumulation of proteins involved in several metabolic processes, particularly those associated with nucleotide binding and transferase activity. Moreover, Si modulated the expression of vital proteins involved in ubiquitin-mediated nucleosome pathway and carbohydrate metabolism. Overall, the results illustrate that Si application induced resistance against salinity stress in C. annuum by regulating the physiology, antioxidant metabolism, and protein expression. PMID:27088085

  7. Positive regulation of prostate cancer cell growth by lipid droplet forming and processing enzymes DGAT1 and ABHD5.

    Science.gov (United States)

    Mitra, Ranjana; Le, Thuc T; Gorjala, Priyatham; Goodman, Oscar B

    2017-09-06

    Neoplastic cells proliferate rapidly and obtain requisite building blocks by reprogramming metabolic pathways that favor growth. Previously, we observed that prostate cancer cells uptake and store lipids in the form of lipid droplets, providing building blocks for membrane synthesis, to facilitate proliferation and growth. Mechanisms of lipid uptake, lipid droplet dynamics and their contribution to cancer growth have yet to be defined. This work is focused on elucidating the prostate cancer-specific modifications in lipid storage pathways so that these modified gene products can be identified and therapeutically targeted. To identify genes that promote lipid droplet formation and storage, the expression profiles of candidate genes were assessed and compared between peripheral blood mononuclear cells and prostate cancer cells. Subsequently, differentially expressed genes were inhibited and growth assays performed to elucidate their role in the growth of the cancer cells. Cell cycle, apoptosis and autophagy assays were performed to ascertain the mechanism of growth inhibition. Our results indicate that DGAT1, ABHD5, ACAT1 and ATGL are overexpressed in prostate cancer cells compared to PBMCs and of these overexpressed genes, DGAT1 and ABHD5 aid in the growth of the prostate cancer cells. Blocking the expression of both DGAT1 and ABHD5 results in inhibition of growth, cell cycle block and cell death. DGAT1 siRNA treatment inhibits lipid droplet formation and leads to autophagy where as ABHD5 siRNA treatment promotes accumulation of lipid droplets and leads to apoptosis. Both the siRNA treatments reduce AMPK phosphorylation, a key regulator of lipid metabolism. While DGAT1 siRNA reduces phosphorylation of ACC, the rate limiting enzyme in de novo fat synthesis and triggers phosphorylation of raptor and ULK-1 inducing autophagy and cell death, ABHD5 siRNA decreases P70S6 phosphorylation, leading to PARP cleavage, apoptosis and cell death. Interestingly, DGAT-1 is involved

  8. Transcriptional regulation of genes encoding ABA metabolism enzymes during the fruit development and dehydration stress of pear 'Gold Nijisseiki'.

    Science.gov (United States)

    Dai, Shengjie; Li, Ping; Chen, Pei; Li, Qian; Pei, Yuelin; He, Suihuan; Sun, Yufei; Wang, Ya; Kai, Wenbin; Zhao, Bo; Liao, Yalan; Leng, Ping

    2014-09-01

    To investigate the contribution of abscisic acid (ABA) in pear 'Gold Nijisseiki' during fruit ripening and under dehydration stress, two cDNAs (PpNCED1 and PpNCED2) which encode 9-cis-epoxycarotenoid dioxygenase (NCED) (a key enzyme in ABA biosynthesis), two cDNAs (PpCYP707A1 and PpCYP707A2) which encode 8'-hydroxylase (a key enzyme in the oxidative catabolism of ABA), one cDNA (PpACS3) which encodes 1-aminocyclopropane-1-carboxylic acid (ACC), and one cDNA (PpACO1) which encodes ACC oxidase involved in ethylene biosynthesis were cloned from 'Gold Nijisseiki' fruit. In the pulp, peel and seed, expressions of PpNCED1 and PpNCED2 rose in two stages which corresponded with the increase of ABA levels. The expression of PpCYP707A1 dramatically declined after 60-90 days after full bloom (DAFB) in contrast to the changes of ABA levels during this period, while PpCYP707A2 stayed low during the whole development of fruit. Application of exogenous ABA at 100 DAFB increased the soluble sugar content and the ethylene release but significantly decreased the titratable acid and chlorophyll contents in fruits. When fruits harvested at 100 DAFB were stored in the laboratory (25 °C, 50% relative humidity), the ABA content and the expressions of PpNCED1/2 and PpCYP707A1 in the pulp, peel and seed increased significantly, while ethylene reached its highest value after the maximum peak of ABA accompanied with the expressions of PpACS3 and PpACO1. In sum the endogenous ABA may play an important role in the fruit ripening and dehydration of pear 'Gold Nijisseiki' and the ABA level was regulated mainly by the dynamics of PpNCED1, PpNCED2 and PpCYP707A1 at the transcriptional level. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  9. Transgenic plants that exhibit enhanced nitrogen assimilation

    Science.gov (United States)

    Coruzzi, Gloria M.; Brears, Timothy

    1999-01-01

    The present invention relates to a method for producing plants with improved agronomic and nutritional traits. Such traits include enhanced nitrogen assimilatory and utilization capacities, faster and more vigorous growth, greater vegetative and reproductive yields, and enriched or altered nitrogen content in vegetative and reproductive parts. More particularly, the invention relates to the engineering of plants modified to have altered expression of key enzymes in the nitrogen assimilation and utilization pathways. In one embodiment of the present invention, the desired altered expression is accomplished by engineering the plant for ectopic overexpression of one of more the native or modified nitrogen assimilatory enzymes. The invention also has a number of other embodiments, all of which are disclosed herein.

  10. Lead nitrate-induced development of hypercholesterolemia in rats: sterol-independent gene regulation of hepatic enzymes responsible for cholesterol homeostasis.

    Science.gov (United States)

    Kojima, Misaki; Masui, Toshimitsu; Nemoto, Kiyomitsu; Degawa, Masakuni

    2004-12-01

    Changes in the gene expressions of hepatic enzymes responsible for cholesterol homeostasis were examined during the process of lead nitrate (LN)-induced development of hypercholesterolemia in male rats. Total cholesterol levels in the liver and serum were significantly increased at 3-72 h and 12-72 h, respectively, after LN-treatment (100 micromol/kg, i.v.). Despite the development of hypercholesterolemia, the genes for hepatic 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) and other enzymes (FPPS, farnesyl diphosphate synthase; SQS, squalene synthase; CYP51, lanosterol 14alpha-demethylase) responsible for cholesterol biosynthesis were activated at 3-24 h and 12-18 h, respectively. On the other hand, the gene expression of cholesterol 7alpha-hydroxylase (CYP7A1), a catabolic enzyme of cholesterol, was remarkably suppressed at 3-72 h. The gene expression levels of cytokines interleukin-1beta (IL-1beta) and TNF-alpha, which activate the HMGR gene and suppress the CYP7A1 gene, were significantly increased at 1-3 h and 3-24 h, respectively. Furthermore, gene activation of SREBP-2, a gene activator of several cholesterogenic enzymes, occurred before the gene activations of FPPS, SQS and CYP51. This is the first report demonstrating sterol-independent gene regulation of hepatic enzymes responsible for cholesterol homeostasis in LN-treated male rats. The mechanisms for the altered-gene expressions of hepatic enzymes in LN-treated rats are discussed.

  11. An ethanolic extract of Artemisia dracunculus L. regulates gene expression of ubiquitin-proteasome system enzymes in skeletal muscle: potential role in the treatment of sarcopenic obesity.

    Science.gov (United States)

    Kirk-Ballard, Heather; Kilroy, Gail; Day, Britton C; Wang, Zhong Q; Ribnicky, David M; Cefalu, William T; Floyd, Z Elizabeth

    2014-01-01

    Obesity is linked to insulin resistance, a primary component of metabolic syndrome and type 2 diabetes. The problem of obesity-related insulin resistance is compounded when age-related skeletal muscle loss, called sarcopenia, occurs with obesity. Skeletal muscle loss results from elevated levels of protein degradation and prevention of obesity-related sarcopenic muscle loss will depend on strategies that target pathways involved in protein degradation. An extract from Artemisia dracunculus, termed PMI 5011, improves insulin signaling and increases skeletal muscle myofiber size in a rodent model of obesity-related insulin resistance. The aim of this study was to examine the effect of PMI 5011 on the ubiquitin-proteasome system, a central regulator of muscle protein degradation. Gastrocnemius and vastus lateralis skeletal muscle was obtained from KK-A(y) obese diabetic mice fed a control or 1% (w/w) PMI 5011-supplemented diet. Regulation of genes encoding enzymes of the ubiquitin-proteasome system was determined using real-time quantitative reverse transcriptase polymerase chain reaction. Although MuRF-1 ubiquitin ligase gene expression is consistently down-regulated in skeletal muscle, atrogin-1, Fbxo40, and Traf6 expression is differentially regulated by PMI 5011. Genes encoding other enzymes of the ubiquitin-proteasome system ranging from ubiquitin to ubiquitin-specific proteases are also regulated by PMI 5011. Additionally, expression of the gene encoding the microtubule-associated protein-1 light chain 3 (LC3), a ubiquitin-like protein pivotal to autophagy-mediated protein degradation, is down-regulated by PMI 5011 in the vastus lateralis. PMI 5011 alters the gene expression of ubiquitin-proteasome system enzymes that are essential regulators of skeletal muscle mass. This suggests that PMI 5011 has therapeutic potential in the treatment of obesity-linked sarcopenia by regulating ubiquitin-proteasome-mediated protein degradation. Copyright © 2014 Elsevier Inc

  12. Regulation of nitrogen uptake and assimilation: Effects of nitrogen source and root-zone and aerial environment on growth and productivity of soybean

    Science.gov (United States)

    Raper, C. David, Jr.

    1994-01-01

    The interdependence of root and shoot growth produces a functional equilibrium as described in quantitative terms by numerous authors. It was noted that bean seedlings grown in a constant environment tended to have a constant distribution pattern of dry matter between roots and leaves characteristic of the set of environmental conditions. Disturbing equilibrium resulted in a change in relative growth of roots and leaves until the original ratio was restored. To define a physiological basis for regulation of nitrogen uptake within the balance between root and shoot activities, the authors combined a partioning scheme and a utilization priority assumption in which: (1) all carbon enters the plant through photosynthesis in leaves and all nitrogen enters the plant through active uptake by roots, (2) nitrogen uptake by roots and secretion into the xylem for transport to the shoots are active processes, (3) availability of exogenous nitrogen determines concentration of soluble carbohydrates within the roots, (4) leaves are a source and a sink for carbohydrates, and (5) the requirement for nitrogen by leaf growth is proportionally greater during initiation and early expansion than during later expansion.

  13. Schisandra chinensis regulates drug metabolizing enzymes and drug transporters via activation of Nrf2-mediated signaling pathway

    Directory of Open Access Journals (Sweden)

    He JL

    2014-12-01

    Full Text Available Jin-Lian He,1 Zhi-Wei Zhou,2,3 Juan-Juan Yin,2 Chang-Qiang He,1 Shu-Feng Zhou,2,3 Yang Yu1 1College of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, People’s Republic of China; 2Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, USA; 3Guizhou Provincial Key Laboratory for Regenerative Medicine, Stem Cell and Tissue Engineering Research Center and Sino-US Joint Laboratory for Medical Sciences, Guiyang Medical University, Guiyang, Guizhou, People’s Republic of China Abstract: Drug metabolizing enzymes (DMEs and drug transporters are regulated via epigenetic, transcriptional, posttranscriptional, and translational and posttranslational modifications. Phase I and II DMEs and drug transporters play an important role in the disposition and detoxification of a large number of endogenous and exogenous compounds. The nuclear factor (erythroid-derived 2-like 2 (Nrf2 is a critical regulator of a variety of important cytoprotective genes that are involved in disposition and detoxification of xenobiotics. Schisandra chinensis (SC is a commonly used traditional Chinese herbal medicine that has been primarily used to protect the liver because of its potent antioxidative and anti-inflammatory activities. SC can modulate some DMEs and drug transporters, but the underlying mechanisms are unclear. In this study, we aimed to explore the role of Nrf2 in the regulatory effect of SC extract (SCE on selected DMEs and drug transporters in human hepatocellular liver carcinoma cell line (HepG2 cells. The results showed that SCE, schisandrin A, and schisandrin B significantly increased the expression of NAD(PH: Nicotinamide Adenine Dinucleotide Phosphate-oxidase or:quinone oxidoreductase 1, heme oxygenase-1, glutamate–cysteine ligase, and glutathione S-transferase A4 at both transcriptional and posttranscriptional levels. Incubation of HepG2 cells with SCE resulted in a significant

  14. Specific phosphopeptide binding regulates a conformational change in the PI 3-kinase SH2 domain associated with enzyme activation.

    Science.gov (United States)

    Shoelson, S E; Sivaraja, M; Williams, K P; Hu, P; Schlessinger, J; Weiss, M A

    1993-01-01

    SH2 (src-homology 2) domains define a newly recognized binding motif that mediates the physical association of target phosphotyrosyl proteins with downstream effector enzymes. An example of such phosphoprotein-effector coupling is provided by the association of phosphatidylinositol 3-kinase (PI 3-kinase) with specific phosphorylation sites within the PDGF receptor, the c-Src/polyoma virus middle T antigen complex and the insulin receptor substrate IRS-1. Notably, phosphoprotein association with the SH2 domains of p85 also stimulates an increase in catalytic activity of the PI 3-kinase p110 subunit, which can be mimicked by phosphopeptides corresponding to targeted phosphoprotein phosphorylation sites. To investigate how phosphoprotein binding to the p85 SH2 domain stimulates p110 catalytic activation, we have examined the differential effects of phosphotyrosine and PDGF receptor-, IRS-1- and c-Src-derived phosphopeptides on the conformation of an isolated SH2 domain of PI 3-kinase. Although phosphotyrosine and both activating and non-activating phosphopeptides bind to the SH2 domain, activating phosphopeptides bind with higher affinity and induce a qualitatively distinct conformational change as monitored by CD and NMR spectroscopy. Amide proton exchange and protease protection assays further show that high affinity, specific phosphopeptide binding induces non-local dynamic SH2 domain stabilization. Based on these findings we propose that specific phosphoprotein binding to the p85 subunit induces a change in SH2 domain structure which is transmitted to the p110 subunit and regulates enzymatic activity by an allosteric mechanism. Images PMID:8382612

  15. Assimilate unloading from maize (Zea mays L.) pedicel tissues

    International Nuclear Information System (INIS)

    Porter, G.A.; Knievel, D.P.; Shannon, J.C.

    1987-01-01

    Sugar and 14 C-assimilate release from the pedicel tissue of attached maize (Zea mays L.) kernels was studied following treatment with solute concentrations of up to 800 millimolal. Exposure and collection times ranged from 3 to 6 hours. Sugar and 14 C-assimilate unloading and collection in agar traps was reduced by 25 and 43%, respectively, following exposure to 800 millimolal mannitol. Inhibition of unloading was not specific to mannitol, since similar concentrations of glucose, fructose, or equimolar glucose plus fructose resulted in comparable inhibition. Ethylene glycol, a rapidly permeating solute which should not greatly influence cell turgor, did not inhibit 14 C-assimilate unloading. Based on these results, they suggest that inhibition of unloading by high concentrations of sugar or mannitol was due to reduced pedicel cell turgor. Changes in pedicel cell turgor may play a role in the regulation of assimilate transfer within the maize kernel

  16. Nonlinear data assimilation

    CERN Document Server

    Van Leeuwen, Peter Jan; Reich, Sebastian

    2015-01-01

    This book contains two review articles on nonlinear data assimilation that deal with closely related topics but were written and can be read independently. Both contributions focus on so-called particle filters. The first contribution by Jan van Leeuwen focuses on the potential of proposal densities. It discusses the issues with present-day particle filters and explorers new ideas for proposal densities to solve them, converging to particle filters that work well in systems of any dimension, closing the contribution with a high-dimensional example. The second contribution by Cheng and Reich discusses a unified framework for ensemble-transform particle filters. This allows one to bridge successful ensemble Kalman filters with fully nonlinear particle filters, and allows a proper introduction of localization in particle filters, which has been lacking up to now.

  17. Transcriptomic analyses of nitrogen assimilation processes in a Chinese strain of Aureococcus anophagefferens

    Directory of Open Access Journals (Sweden)

    Li-Na Chen

    2015-09-01

    Full Text Available Aureococcus anophagefferens is a harmful alga that dominates plankton communities during brown tides in North America, Africa, and Asia. In order to figure out the processes of nitrogen assimilation in a Chinese strain of A. anophagefferens, RNA-seq technology was used to examine transcriptomic differences in A. anophagefferens that was grown on urea, nitrate, or a mixture of urea and nitrate, and that was under N-replete, limited and recovery conditions. We noted that transcripts upregulated by nitrate and N-limitation included those encoding proteins involved in amino acid, nucleotide and aminosugar transport, degradation of amides and cyanates, and nitrate assimilation pathway. The data suggest that A. anophagefferens possesses an ability to utilize a variety of dissolved organic nitrogen. Moreover, transcripts for synthesis of proteins, glutamate-derived amino acids, spermines and sterols were upregulated by urea. Transcripts encoding key enzymes that are involved in the ornithine–urea cycle (OUC and TCA cycle were differentially regulated by urea and nitrogen concentration, which suggests that the OUC may be linked to the TCA cycle and involved in reallocation of intracellular carbon and nitrogen. These genes regulated by urea may be crucial for the rapid proliferation of A. anophagefferens when urea is provided as the N source. Here, we provide the experimental procedures and analytical processes in detail. The data set is deposited in GEO with the accession number GSE60576.

  18. Emerging roles of the nucleolus in regulating the DNA damage response: the noncanonical DNA repair enzyme APE1/Ref-1 as a paradigmatical example.

    Science.gov (United States)

    Antoniali, Giulia; Lirussi, Lisa; Poletto, Mattia; Tell, Gianluca

    2014-02-01

    An emerging concept in DNA repair mechanisms is the evidence that some key enzymes, besides their role in the maintenance of genome stability, display also unexpected noncanonical functions associated with RNA metabolism in specific subcellular districts (e.g., nucleoli). During the evolution of these key enzymes, the acquisition of unfolded domains significantly amplified the possibility to interact with different partners and substrates, possibly explaining their phylogenetic gain of functions. After nucleolar stress or DNA damage, many DNA repair proteins can freely relocalize from nucleoli to the nucleoplasm. This process may represent a surveillance mechanism to monitor the synthesis and correct assembly of ribosomal units affecting cell cycle progression or inducing p53-mediated apoptosis or senescence. A paradigm for this kind of regulation is represented by some enzymes of the DNA base excision repair (BER) pathway, such as apurinic/apyrimidinic endonuclease 1 (APE1). In this review, the role of the nucleolus and the noncanonical functions of the APE1 protein are discussed in light of their possible implications in human pathologies. A productive cross-talk between DNA repair enzymes and proteins involved in RNA metabolism seems reasonable as the nucleolus is emerging as a dynamic functional hub that coordinates cell growth arrest and DNA repair mechanisms. These findings will drive further analyses on other BER proteins and might imply that nucleic acid processing enzymes are more versatile than originally thought having evolved DNA-targeted functions after a previous life in the early RNA world.

  19. Nitrogen-source preference in blueberry (Vaccinium sp.): Enhanced shoot nitrogen assimilation in response to direct supply of nitrate.

    Science.gov (United States)

    Alt, Douglas S; Doyle, John W; Malladi, Anish

    2017-09-01

    Blueberry (Vaccinium sp.) is thought to display a preference for the ammonium (NH 4 + ) form over the nitrate (NO 3 - ) form of inorganic nitrogen (N). This N-source preference has been associated with a generally low capacity to assimilate the NO 3 - form of N, especially within the shoot tissues. Nitrate assimilation is mediated by nitrate reductase (NR), a rate limiting enzyme that converts NO 3 - to nitrite (NO 2 - ). We investigated potential limitations of NO 3 - assimilation in two blueberry species, rabbiteye (Vaccinium ashei) and southern highbush (Vaccinium corymbosum) by supplying NO 3 - to the roots, leaf surface, or through the cut stem. Both species displayed relatively low but similar root uptake rates for both forms of inorganic N. Nitrate uptake through the roots transiently increased NR activity by up to 3.3-fold and root NR gene expression by up to 4-fold. However, supplying NO 3 - to the roots did not increase its transport in the xylem, nor did it increase NR activity in the leaves, indicating that the acquired N was largely assimilated or stored within the roots. Foliar application of NO 3 - increased leaf NR activity by up to 3.5-fold, but did not alter NO 3 - metabolism-related gene expression, suggesting that blueberries are capable of post translational regulation of NR activity in the shoots. Additionally, supplying NO 3 - to the cut ends of stems resulted in around a 5-fold increase in NR activity, a 10-fold increase in NR transcript accumulation, and up to a 195-fold increase in transcript accumulation of NITRITE REDUCTASE (NiR1) which codes for the enzyme catalyzing the conversion of NO 2 - to NH 4 + . These data indicate that blueberry shoots are capable of assimilating NO 3 - when it is directly supplied to these tissues. Together, these data suggest that limitations in the uptake and translocation of NO 3 - to the shoots may limit overall NO 3 - assimilation capacity in blueberry. Copyright © 2017 Elsevier GmbH. All rights reserved.

  20. A Rhodium(III) Complex as an Inhibitor of Neural Precursor Cell Expressed, Developmentally Down-Regulated 8-Activating Enzyme with in Vivo Activity against Inflammatory Bowel Disease.

    Science.gov (United States)

    Zhong, Hai-Jing; Wang, Wanhe; Kang, Tian-Shu; Yan, Hui; Yang, Yali; Xu, Lipeng; Wang, Yuqiang; Ma, Dik-Lung; Leung, Chung-Hang

    2017-01-12

    We report herein the identification of the rhodium(III) complex [Rh(phq) 2 (MOPIP)] + (1) as a potent and selective ATP-competitive neural precursor cell expressed, developmentally down-regulated 8 (NEDD8)-activating enzyme (NAE) inhibitor. Structure-activity relationship analysis indicated that the overall organometallic design of complex 1 was important for anti-inflammatory activity. Complex 1 showed promising anti-inflammatory activity in vivo for the potential treatment of inflammatory bowel disease.

  1. CHD8, A Novel Beta-Catenin Associated Chromatin Remodeling Enzyme, Regulates Androgen Receptor Mediated Gene Transcription

    National Research Council Canada - National Science Library

    Bochar, Daniel A

    2008-01-01

    .... To better understand the function of beta-catenin in AR mediated transcription, we have identified a novel chromatin remodeling enzyme, CHD8, that can associate with beta-catenin and functions in AR...

  2. Are changes in sulfate assimilation pathway needed for evolution of C4 photosynthesis?

    Directory of Open Access Journals (Sweden)

    Silke Christine Weckopp

    2015-01-01

    Full Text Available C4 photosynthesis characteristically features a cell-specific localization of enzymes involved in CO2 assimilation in bundle sheath cells or mesophyll cells. Interestingly, enzymes of sulfur assimilation are also specifically present in bundle sheath cells of maize and many other C4 species. This localization, however, could not be confirmed in C4 species of the genus Flaveria. It was, therefore, concluded that the bundle sheath localization of sulfate assimilation occurs only in C4 monocots. However, recently the sulfate assimilation pathway was found coordinately enriched in bundle sheath cells of Arabidopsis, opening new questions about the significance of such cell-specific localization of the pathway. In addition, next generation sequencing revealed expression gradients of many genes from C3 to C4 species and mathematical modelling proposed a sequence of adaptations during the evolutionary path from C3 to C4. Indeed, such gradient, with higher expression of genes for sulfate reduction in C4 species, has been observed within the genus Flaveria. These new tools provide the basis for reexamining the intriguing question of compartmentalization of sulfur assimilation. Therefore, this review summarizes the findings on spatial separation of sulfur assimilation in C4 plants and Arabidopsis, assesses the information on sulfur assimilation provided by the recent transcriptomics data and discusses their possible impact on understanding this interesting feature of plant sulfur metabolism to find out whether changes in sulfate assimilation are part of a general evolutionary trajectory towards C4 photosynthesis.

  3. Translocation of labelled assimilates, ion uptake and nucleic acids contents in zea mays plants as influenced by application of the herbicide dual and the bioregulaators GA3 and kinetin

    International Nuclear Information System (INIS)

    Hassanein, R.AA.; Khodary, S.E.A.; Abdel-Aziz, S.M.

    2001-01-01

    Maize seedlings, grown hydroponic for one month, were undertaken o investigate the effect of dual (metolachlor), bio regulators (GA 3 and kinetin) and their interaction with dual on translocation rate of assimilates, nucleic acids content. ion uptake and the activities of protease and nitrate reductase enzymes. Dual at all concentrations decreased the rate of assimilates translocation and nucleic acids levels. Also reduction in the ability of the treated plants to absorb ions from the growth medium as well as the activities of nitrate reductase and protease enzymes were retarded upon dual application. The results also revealed that treatment with either GA 3 or kinetin in combination with dual, reversed the adverse action of the herbicide on zea mays plants

  4. Global Data Assimilation System (GDAS)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Global Data Assimilation System (GDAS) is the system used by the Global Forecast System (GFS) model to place observations into a gridded model space for the...

  5. Data assimilation in hydrological modelling

    DEFF Research Database (Denmark)

    Drecourt, Jean-Philippe

    Data assimilation is an invaluable tool in hydrological modelling as it allows to efficiently combine scarce data with a numerical model to obtain improved model predictions. In addition, data assimilation also provides an uncertainty analysis of the predictions made by the hydrological model....... In this thesis, the Kalman filter is used for data assimilation with a focus on groundwater modelling. However the developed techniques are general and can be applied also in other modelling domains. Modelling involves conceptualization of the processes of Nature. Data assimilation provides a way to deal...... with model non-linearities and biased errors. A literature review analyzes the most popular techniques and their application in hydrological modelling. Since bias is an important problem in groundwater modelling, two bias aware Kalman filters have been implemented and compared using an artificial test case...

  6. Data Assimilation in Marine Models

    DEFF Research Database (Denmark)

    Frydendall, Jan

    maximum likelihood framework. These issues are discussed in paper B. The third part of the thesis falls a bit out of the above context is work published in papers C, F. In the first paper, a simple data assimilation scheme was investigated to examine the potential benefits of incorporating a data......This thesis consists of six research papers published or submitted for publication in the period 2006-2009 together with a summary report. The main topics of this thesis are nonlinear data assimilation techniques and estimation in dynamical models. The focus has been on the nonlinear filtering...... techniques for large scale geophysical numerical models and making them feasible to work with in the data assimilation framework. The filtering techniques investigated are all Monte Carlo simulation based. Some very nice features that can be exploited in the Monte Carlo based data assimilation framework from...

  7. Effective Assimilation of Global Precipitation

    Science.gov (United States)

    Lien, G.; Kalnay, E.; Miyoshi, T.; Huffman, G. J.

    2012-12-01

    Assimilating precipitation observations by modifying the moisture and sometimes temperature profiles has been shown successful in forcing the model precipitation to be close to the observed precipitation, but only while the assimilation is taking place. After the forecast start, the model tends to "forget" the assimilation changes and lose their extra skill after few forecast hours. This suggests that this approach is not an efficient way to modify the potential vorticity field, since this is the variable that the model would remember. In this study, the ensemble Kalman filter (EnKF) method is used to effectively change the potential vorticity field by allowing ensemble members with better precipitation to receive higher weights. In addition to using an EnKF, two other changes in the precipitation assimilation process are proposed to solve the problems related to the highly non-Gaussian nature of the precipitation variable: a) transform precipitation into a Gaussian distribution based on its climatological distribution, and b) only assimilate precipitation at the location where some ensemble members have positive precipitation. The idea is first tested by the observing system simulation experiments (OSSEs) using SPEEDY, a simplified but realistic general circulation model. When the global precipitation is assimilated in addition to conventional rawinsonde observations, both the analyses and the medium range forecasts are significantly improved as compared to only having rawinsonde observations. The improvement is much reduced when only modifying the moisture field with the same approach, which shows the importance of the error covariance between precipitation and all other model variables. The effect of precipitation assimilation is larger in the Southern Hemisphere than that in the Northern Hemisphere because the Northern Hemisphere analyses are already accurate as a result of denser rawinsonde stations. Assimilation of precipitation using a more comprehensive

  8. Ser/Thr Phosphorylation Regulates the Fatty Acyl-AMP Ligase Activity of FadD32, an Essential Enzyme in Mycolic Acid Biosynthesis*

    Science.gov (United States)

    Le, Nguyen-Hung; Molle, Virginie; Eynard, Nathalie; Miras, Mathieu; Stella, Alexandre; Bardou, Fabienne; Galandrin, Ségolène; Guillet, Valérie; André-Leroux, Gwenaëlle; Bellinzoni, Marco; Alzari, Pedro; Mourey, Lionel; Burlet-Schiltz, Odile; Daffé, Mamadou; Marrakchi, Hedia

    2016-01-01

    Mycolic acids are essential components of the mycobacterial cell envelope, and their biosynthetic pathway is a well known source of antituberculous drug targets. Among the promising new targets in the pathway, FadD32 is an essential enzyme required for the activation of the long meromycolic chain of mycolic acids and is essential for mycobacterial growth. Following the in-depth biochemical, biophysical, and structural characterization of FadD32, we investigated its putative regulation via post-translational modifications. Comparison of the fatty acyl-AMP ligase activity between phosphorylated and dephosphorylated FadD32 isoforms showed that the native protein is phosphorylated by serine/threonine protein kinases and that this phosphorylation induced a significant loss of activity. Mass spectrometry analysis of the native protein confirmed the post-translational modifications and identified Thr-552 as the phosphosite. Phosphoablative and phosphomimetic FadD32 mutant proteins confirmed both the position and the importance of the modification and its correlation with the negative regulation of FadD32 activity. Investigation of the mycolic acid condensation reaction catalyzed by Pks13, involving FadD32 as a partner, showed that FadD32 phosphorylation also impacts the condensation activity. Altogether, our results bring to light FadD32 phosphorylation by serine/threonine protein kinases and its correlation with the enzyme-negative regulation, thus shedding a new horizon on the mycolic acid biosynthesis modulation and possible inhibition strategies for this promising drug target. PMID:27590338

  9. Removal of the effect of ammonium on the regulation of nitrogenase enzyme in Rhodobacter capsulatus DSM1710 for improved hydrogen production

    Energy Technology Data Exchange (ETDEWEB)

    Pekgoez, Guelsah; Guenduez, Ufuk [Middle East Technical Univ. (Turkey). Dept. of Biology; Eroglu, Inci [Middle East Technical Univ. (Turkey). Dept. of Chemical Engineering; Rakhely, Gabor [Szeged Univ. (Hungary). Dept. of Biotechnology

    2010-07-01

    Photofermentative biohydrogen production by purple non-sulfur (PNS) bacteria is a renewable and clean way of producing hydrogen. Hydrogen production by PNS bacteria, Rhodobacter capsulatus, is mediated mainly by nitrogenases, which primarily fix molecular nitrogen to ammonium and produce hydrogen as byproduct. The reaction catalyzed by nitrogenases requires a lot of energy. Hence, there is a complex regulation on nitrogenase enzyme complex, consequently, on hydrogen production. Whenever ammonium, which is the end product of nitrogen fixation reaction, is found in the environment, hydrogen production stops. GlnB and GlnK proteins are the critical regulatory proteins in ammonium dependent regulation of the nitrogenase gene expression. In this study, the aim is to release the ammonium regulation on nitrogenase enzyme by inactivating glnB and glnK genes. For this purpose, relevant recombinant vectors were constructed; R.capsulatus glnB- strain was obtained. The double R.capsulatus glnB{sup -}glnK{sup -} strain, able to produce hydrogen independent of ammonium concentration of the environment is to be obtained. (orig.)

  10. The TMAO-Producing Enzyme Flavin-Containing Monooxygenase 3 Regulates Obesity and the Beiging of White Adipose Tissue

    Directory of Open Access Journals (Sweden)

    Rebecca C. Schugar

    2017-06-01

    Full Text Available Emerging evidence suggests that microbes resident in the human intestine represent a key environmental factor contributing to obesity-associated disorders. Here, we demonstrate that the gut microbiota-initiated trimethylamine N-oxide (TMAO-generating pathway is linked to obesity and energy metabolism. In multiple clinical cohorts, systemic levels of TMAO were observed to strongly associate with type 2 diabetes. In addition, circulating TMAO levels were associated with obesity traits in the different inbred strains represented in the Hybrid Mouse Diversity Panel. Further, antisense oligonucleotide-mediated knockdown or genetic deletion of the TMAO-producing enzyme flavin-containing monooxygenase 3 (FMO3 conferred protection against obesity in mice. Complimentary mouse and human studies indicate a negative regulatory role for FMO3 in the beiging of white adipose tissue. Collectively, our studies reveal a link between the TMAO-producing enzyme FMO3 and obesity and the beiging of white adipose tissue.

  11. Structural basis of the interaction of MbtH-like proteins, putative regulators of nonribosomal peptide biosynthesis, with adenylating enzymes.

    Science.gov (United States)

    Herbst, Dominik A; Boll, Björn; Zocher, Georg; Stehle, Thilo; Heide, Lutz

    2013-01-18

    The biosynthesis of nonribosomally formed peptides (NRPs), which include important antibiotics such as vancomycin, requires the activation of amino acids through adenylate formation. The biosynthetic gene clusters of NRPs frequently contain genes for small, so-called MbtH-like proteins. Recently, it was discovered that these MbtH-like proteins are required for some of the adenylation reactions in NRP biosynthesis, but the mechanism of their interaction with the adenylating enzymes has remained unknown. In this study, we determined the structure of SlgN1, a 3-methylaspartate-adenylating enzyme involved in the biosynthesis of the hybrid polyketide/NRP antibiotic streptolydigin. SlgN1 contains an MbtH-like domain at its N terminus, and our analysis defines the parameters required for an interaction between MbtH-like domains and an adenylating enzyme. Highly conserved tryptophan residues of the MbtH-like domain critically contribute to this interaction. Trp-25 and Trp-35 form a cleft on the surface of the MbtH-like domain, which accommodates the alanine side chain of Ala-433 of the adenylating domain. Mutation of Ala-433 to glutamate abolished the activity of SlgN1. Mutation of Ser-23 of the MbtH-like domain to tyrosine resulted in strongly reduced activity. However, the activity of this S23Y mutant could be completely restored by addition of the intact MbtH-like protein CloY from another organism. This suggests that the interface found in the structure of SlgN1 is the genuine interface between MbtH-like proteins and adenylating enzymes.

  12. A conserved degron containing an amphipathic helix regulates the cholesterol-mediated turnover of human squalene monooxygenase, a rate-limiting enzyme in cholesterol synthesis.

    Science.gov (United States)

    Chua, Ngee Kiat; Howe, Vicky; Jatana, Nidhi; Thukral, Lipi; Brown, Andrew J

    2017-12-08

    Cholesterol biosynthesis in the endoplasmic reticulum (ER) is tightly controlled by multiple mechanisms to regulate cellular cholesterol levels. Squalene monooxygenase (SM) is the second rate-limiting enzyme in cholesterol biosynthesis and is regulated both transcriptionally and post-translationally. SM undergoes cholesterol-dependent proteasomal degradation when cholesterol is in excess. The first 100 amino acids of SM (designated SM N100) are necessary for this degradative process and represent the shortest cholesterol-regulated degron identified to date. However, the fundamental intrinsic characteristics of this degron remain unknown. In this study, we performed a series of deletions, point mutations, and domain swaps to identify a 12-residue region (residues Gln-62-Leu-73), required for SM cholesterol-mediated turnover. Molecular dynamics and circular dichroism revealed an amphipathic helix within this 12-residue region. Moreover, 70% of the variation in cholesterol regulation was dependent on the hydrophobicity of this region. Of note, the earliest known Doa10 yeast degron, Deg1, also contains an amphipathic helix and exhibits 42% amino acid similarity with SM N100. Mutating SM residues Phe-35/Ser-37/Leu-65/Ile-69 into alanine, based on the key residues in Deg1, blunted SM cholesterol-mediated turnover. Taken together, our results support a model whereby the amphipathic helix in SM N100 attaches reversibly to the ER membrane depending on cholesterol levels; with excess, the helix is ejected and unravels, exposing a hydrophobic patch, which then serves as a degradation signal. Our findings shed new light on the regulation of a key cholesterol synthesis enzyme, highlighting the conservation of critical degron features from yeast to humans. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  13. Silicon improves seed germination and alleviates drought stress in lentil crops by regulating osmolytes, hydrolytic enzymes and antioxidant defense system.

    Science.gov (United States)

    Biju, Sajitha; Fuentes, Sigfredo; Gupta, Dorin

    2017-10-01

    Silicon (Si) has been widely reported to have beneficial effect on mitigating drought stress in plants. However, the effect of Si on seed germination under drought conditions is still poorly understood. This research was carried out to ascertain the role of Si to abate polyethylene glycol-6000 mediated drought stress on seed germination and seedling growth of lentil. Results showed that drought stress significantly decreased the seed germination traits and increased the concentration of osmolytes (proline, glycine betaine and soluble sugars), reactive oxygen species (hydrogen peroxide and superoxide anion) and lipid peroxides in lentil seedlings. The activities of hydrolytic enzymes and antioxidant enzymes increased significantly under osmotic stress. The application of Si significantly enhanced the plants ability to withstand drought stress conditions through increased Si content, improved antioxidants, hydrolytic enzymes activity, decreased concentration of osmolytes and reactive oxygen species. Multivariate data analysis showed statistically significant correlations among the drought-tolerance traits, whereas cluster analysis categorised the genotypes into distinct groups based on their drought-tolerance levels and improvements in expression of traits due to Si application. Thus, these results showed that Si supplementation of lentil was effective in alleviating the detrimental effects of drought stress on seed germination and increased seedling vigour. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  14. Recent insights into Protein Phosphatase 2A structure and regulation: the reasons why PP2A is no longer considered as a lazy passive housekeeping enzyme

    Directory of Open Access Journals (Sweden)

    Martin, M.

    2010-01-01

    Full Text Available Although intracellular signal transduction is often portrayed as a protein kinase "domino effect", the counterbalancing function of phosphatases, and thus the control of phosphatase activity, is equally relevant to proper regulation of cellular function. Protein Phosphatase 2A (PP2A is a widely expressed family of protein phosphatases made of a core dimer, composed of a catalytic (C subunit and a structural (A subunit, in association with a third variable regulatory (B subunit. Although viewed as a constitutive housekeeping enzyme in the past, PP2A is a highly regulated phosphatase and is emerging as an important regulator of multiple cellular processes involving protein phosphorylation. The regulation of PP2A is mainly accomplished by the identity of the regulatory B-type subunit, which determines substrate specificity, subcellular localization and catalytic activity of the PP2A holoenzyme. In agreement with this, recent findings on the structure and post-translational modifications of PP2A emphasize the importance of PP2A holoenzyme composition in its regulation and pleiotropic activities.

  15. Data Assimilation for Applied Meteorology

    Science.gov (United States)

    Haupt, S. E.

    2012-12-01

    Although atmospheric models provide a best estimate of the future state of the atmosphere, due to sensitivity to initial condition, it is difficult to predict the precise future state. For applied problems, however, users often depend on having accurate knowledge of that future state. To improve prediction of a particular realization of an evolving flow field requires knowledge of the current state of that field and assimilation of local observations into the model. This talk will consider how dynamic assimilation can help address the concerns of users of atmospheric forecasts. First, we will look at the value of assimilation for the renewable energy industry. If the industry decision makers can have confidence in the wind and solar power forecasts, they can build their power allocations around the expected renewable resource, saving money for the ratepayers as well as reducing carbon emissions. We will assess the value to that industry of assimilating local real-time observations into the model forecasts and the value that is provided. The value of the forecasts with assimilation is important on both short (several hour) to medium range (within two days). A second application will be atmospheric transport and dispersion problems. In particular, we will look at assimilation of concentration data into a prediction model. An interesting aspect of this problem is that the dynamics are a one-way coupled system, with the fluid dynamic equations affecting the concentration equation, but not vice versa. So when the observations are of the concentration, one must infer the fluid dynamics. This one-way coupled system presents a challenge: one must first infer the changes in the flow field from observations of the contaminant, then assimilate that to recover both the advecting flow and information on the subgrid processes that provide the mixing. To accomplish such assimilation requires a robust method to match the observed contaminant field to that modeled. One approach is

  16. Enzyme-regulated the changes of pH values for assembling a colorimetric and multistage interconnection logic network with multiple readouts

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Yanyan; Ran, Xiang; Lin, Youhui [Laboratory of Chemical Biology, Division of Biological Inorganic Chemistry, State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022 (China); Graduate School of University of Chinese Academy of Sciences, Beijing 100039 (China); Ren, Jinsong, E-mail: jren@ciac.ac.cn [Laboratory of Chemical Biology, Division of Biological Inorganic Chemistry, State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022 (China); Qu, Xiaogang [Laboratory of Chemical Biology, Division of Biological Inorganic Chemistry, State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022 (China)

    2015-04-22

    Highlights: • A colorimetric and multistage biological network has been developed. • This system was on the basis of the enzyme-regulated changes of pH values. • This enzyme-based system could assemble large biological circuit. • Two signal transducers (DNA/AuNPs and acid–base indicators) were used. • The compositions of samples could be detected through visual output signals. - Abstract: Based on enzymatic reactions-triggered changes of pH values and biocomputing, a novel and multistage interconnection biological network with multiple easy-detectable signal outputs has been developed. Compared with traditional chemical computing, the enzyme-based biological system could overcome the interference between reactions or the incompatibility of individual computing gates and offer a unique opportunity to assemble multicomponent/multifunctional logic circuitries. Our system included four enzyme inputs: β-galactosidase (β-gal), glucose oxidase (GOx), esterase (Est) and urease (Ur). With the assistance of two signal transducers (gold nanoparticles and acid–base indicators) or pH meter, the outputs of the biological network could be conveniently read by the naked eyes. In contrast to current methods, the approach present here could realize cost-effective, label-free and colorimetric logic operations without complicated instrument. By designing a series of Boolean logic operations, we could logically make judgment of the compositions of the samples on the basis of visual output signals. Our work offered a promising paradigm for future biological computing technology and might be highly useful in future intelligent diagnostics, prodrug activation, smart drug delivery, process control, and electronic applications.

  17. Enzyme-regulated the changes of pH values for assembling a colorimetric and multistage interconnection logic network with multiple readouts

    International Nuclear Information System (INIS)

    Huang, Yanyan; Ran, Xiang; Lin, Youhui; Ren, Jinsong; Qu, Xiaogang

    2015-01-01

    Highlights: • A colorimetric and multistage biological network has been developed. • This system was on the basis of the enzyme-regulated changes of pH values. • This enzyme-based system could assemble large biological circuit. • Two signal transducers (DNA/AuNPs and acid–base indicators) were used. • The compositions of samples could be detected through visual output signals. - Abstract: Based on enzymatic reactions-triggered changes of pH values and biocomputing, a novel and multistage interconnection biological network with multiple easy-detectable signal outputs has been developed. Compared with traditional chemical computing, the enzyme-based biological system could overcome the interference between reactions or the incompatibility of individual computing gates and offer a unique opportunity to assemble multicomponent/multifunctional logic circuitries. Our system included four enzyme inputs: β-galactosidase (β-gal), glucose oxidase (GOx), esterase (Est) and urease (Ur). With the assistance of two signal transducers (gold nanoparticles and acid–base indicators) or pH meter, the outputs of the biological network could be conveniently read by the naked eyes. In contrast to current methods, the approach present here could realize cost-effective, label-free and colorimetric logic operations without complicated instrument. By designing a series of Boolean logic operations, we could logically make judgment of the compositions of the samples on the basis of visual output signals. Our work offered a promising paradigm for future biological computing technology and might be highly useful in future intelligent diagnostics, prodrug activation, smart drug delivery, process control, and electronic applications

  18. Uteroplacental insufficiency down regulates insulin receptor and affects expression of key enzymes of long-chain fatty acid (LCFA metabolism in skeletal muscle at birth

    Directory of Open Access Journals (Sweden)

    Puglianiello Antonella

    2008-05-01

    Full Text Available Abstract Background Epidemiological studies have revealed a relationship between early growth restriction and the subsequent development of insulin resistance and type 2 diabetes. Ligation of the uterine arteries in rats mimics uteroplacental insufficiency and serves as a model of intrauterine growth restriction (IUGR and subsequent developmental programming of impaired glucose tolerance, hyperinsulinemia and adiposity in the offspring. The objective of this study was to investigate the effects of uterine artery ligation on the skeletal muscle expression of insulin receptor and key enzymes of LCFA metabolism. Methods Bilateral uterine artery ligation was performed on day 19 of gestation in Sprague-Dawley pregnant rats. Muscle of the posterior limb was dissected at birth and processed by real-time RT-PCR to analyze the expression of insulin receptor, ACCα, ACCβ (acetyl-CoA carboxylase alpha and beta subunits, ACS (acyl-CoA synthase, AMPK (AMP-activated protein kinase, alpha2 catalytic subunit, CPT1B (carnitine palmitoyltransferase-1 beta subunit, MCD (malonyl-CoA decarboxylase in 14 sham and 8 IUGR pups. Muscle tissue was treated with lysis buffer and Western immunoblotting was performed to assay the protein content of insulin receptor and ACC. Results A significant down regulation of insulin receptor protein (p Conclusion Our data suggest that uteroplacental insufficiency may affect skeletal muscle metabolism down regulating insulin receptor and reducing the expression of key enzymes involved in LCFA formation and oxidation.

  19. Effects of 200 Gy 60Co-γ Radiation on the Regulation of Antioxidant Enzymes, Hsp70 Genes, and Serum Molecules of Plutella xylostella (Linnaeus).

    Science.gov (United States)

    Li, Xiaoxue; Luo, Lingyan; Karthi, Sengodan; Zhang, Ke; Luo, Jianjun; Hu, Qiongbo; Weng, Qunfang

    2018-04-26

    The diamondback moth, Plutella xylostella (Linnaeus), is one of the notorious pests causing substantial loses to many cruciferous vegetables across the nations. The effects of 60 Co-γ radiation on physiology of P. xylostella were investigated and the results displayed that 200 Gy irradiation significantly alters the antioxidant enzyme regulation in six-day-old male pupae of P. xylostella . First, in our research, we detected Oxidase system and stress response mechanism of irradiated pupae, the results displayed that 200 Gy irradiation significantly alters the antioxidant enzyme regulation in six-day-old male pupae of P. xylostella . The levels of superoxide dismutase (SOD) and catalase (CAT) were increased significantly in contrast the level of peroxidase (POD) and glutathione S-transferase (GST) were decreased in 12⁻24 h post-treatment. The heat shock proteins (Hsps) gene expression level was significant increasing, maximum > 2-folds upregulation of genes were observed in peak. However, they also had a trend of gradual recovery with development. Second, we detected the testis lactate dehydrogenase (LDH) and acid phosphatase (ACP) activity found that in male adults testis they increased significantly than control during its development. Thus the present research investigation highlights that the 60 Co-γ radiation treatments alters the physiological development of diamondback moth. The results showed that 200 Gy dosage resulted in stress damage to the body and reproductive system of the diamondback moth.

  20. Effects of 200 Gy 60Co-γ Radiation on the Regulation of Antioxidant Enzymes, Hsp70 Genes, and Serum Molecules of Plutella xylostella (Linnaeus

    Directory of Open Access Journals (Sweden)

    Xiaoxue Li

    2018-04-01

    Full Text Available The diamondback moth, Plutella xylostella (Linnaeus, is one of the notorious pests causing substantial loses to many cruciferous vegetables across the nations. The effects of 60Co-γ radiation on physiology of P. xylostella were investigated and the results displayed that 200 Gy irradiation significantly alters the antioxidant enzyme regulation in six-day-old male pupae of P. xylostella. First, in our research, we detected Oxidase system and stress response mechanism of irradiated pupae, the results displayed that 200 Gy irradiation significantly alters the antioxidant enzyme regulation in six-day-old male pupae of P. xylostella. The levels of superoxide dismutase (SOD and catalase (CAT were increased significantly in contrast the level of peroxidase (POD and glutathione S-transferase (GST were decreased in 12–24 h post-treatment. The heat shock proteins (Hsps gene expression level was significant increasing, maximum > 2-folds upregulation of genes were observed in peak. However, they also had a trend of gradual recovery with development. Second, we detected the testis lactate dehydrogenase (LDH and acid phosphatase (ACP activity found that in male adults testis they increased significantly than control during its development. Thus the present research investigation highlights that the 60Co-γ radiation treatments alters the physiological development of diamondback moth. The results showed that 200 Gy dosage resulted in stress damage to the body and reproductive system of the diamondback moth.

  1. The human ubiquitin-conjugating enzyme Cdc34 controls cellular proliferation through regulation of p27Kip1 protein levels

    International Nuclear Information System (INIS)

    Butz, Nicole; Ruetz, Stephan; Natt, Francois; Hall, Jonathan; Weiler, Jan; Mestan, Juergen; Ducarre, Monique; Grossenbacher, Rita; Hauser, Patrick; Kempf, Dominique; Hofmann, Francesco

    2005-01-01

    Ubiquitin-mediated degradation of the cyclin-dependent kinase inhibitor p27 Kip1 was shown to be required for the activation of key cyclin-dependent kinases, thereby triggering the onset of DNA replication and cell cycle progression. Although the SCF Skp2 ubiquitin ligase has been reported to mediate p27 Kip1 degradation, the nature of the human ubiquitin-conjugating enzyme involved in this process has not yet been determined at the cellular level. Here, we show that antisense oligonucleotides targeting the human ubiquitin-conjugating enzyme Cdc34 downregulate its expression, inhibit the degradation of p27 Kip1 , and prevent cellular proliferation. Elevation of p27 Kip1 protein level is found to be the sole requirement for the inhibition of cellular proliferation induced upon downregulation of Cdc34. Indeed, reducing the expression of p27 Kip1 with a specific antisense oligonucleotide is sufficient to reverse the anti-proliferative phenotype elicited by the Cdc34 antisense. Furthermore, downregulation of Cdc34 is found to specifically increase the abundance of the SCF Skp2 ubiquitin ligase substrate p27 Kip1 , but has no concomitant effect on the level of IkBα and β-catenin, which are known substrates of a closely related SCF ligase

  2. The tomato Fni3 lysine-63-specific ubiquitin-conjugating enzyme and suv ubiquitin E2 variant positively regulate plant immunity.

    Science.gov (United States)

    Mural, Ravi V; Liu, Yao; Rosebrock, Tracy R; Brady, Jennifer J; Hamera, Sadia; Connor, Richard A; Martin, Gregory B; Zeng, Lirong

    2013-09-01

    The activation of an immune response in tomato (Solanum lycopersicum) against Pseudomonas syringae relies on the recognition of E3 ligase-deficient forms of AvrPtoB by the host protein kinase, Fen. To investigate the mechanisms by which Fen-mediated immunity is regulated, we characterize in this study a Fen-interacting protein, Fni3, and its cofactor, S. lycoperiscum Uev (Suv). Fni3 encodes a homolog of the Ubc13-type ubiquitin-conjugating enzyme that catalyzes exclusively Lys-63-linked ubiquitination, whereas Suv is a ubiquitin-conjugating enzyme variant. The C-terminal region of Fen was necessary for interaction with Fni3, and this interaction was required for cell death triggered by overexpression of Fen in Nicotiana benthamiana leaves. Fni3 was shown to be an active E2 enzyme, but Suv displayed no ubiquitin-conjugating activity; Fni3 and Suv together directed Lys-63-linked ubiquitination. Decreased expression of Fni3, another tomato Ubc13 homolog, Sl-Ubc13-2, or Suv in N. benthamiana leaves diminished cell death associated with Fen-mediated immunity and cell death elicited by several other resistance (R) proteins and their cognate effectors. We also discovered that coexpression of Fen and other R proteins/effectors with a Fni3 mutant that is compromised for ubiquitin-conjugating activity diminished the cell death. These results suggest that Fni3/Sl-Ubc13-2 and Suv regulate the immune response mediated by Fen and other R proteins through Lys-63-linked ubiquitination.

  3. The Tomato Fni3 Lysine-63–Specific Ubiquitin-Conjugating Enzyme and Suv Ubiquitin E2 Variant Positively Regulate Plant Immunity[C][W

    Science.gov (United States)

    Mural, Ravi V.; Liu, Yao; Rosebrock, Tracy R.; Brady, Jennifer J.; Hamera, Sadia; Connor, Richard A.; Martin, Gregory B.; Zeng, Lirong

    2013-01-01

    The activation of an immune response in tomato (Solanum lycopersicum) against Pseudomonas syringae relies on the recognition of E3 ligase–deficient forms of AvrPtoB by the host protein kinase, Fen. To investigate the mechanisms by which Fen-mediated immunity is regulated, we characterize in this study a Fen-interacting protein, Fni3, and its cofactor, S. lycoperiscum Uev (Suv). Fni3 encodes a homolog of the Ubc13-type ubiquitin-conjugating enzyme that catalyzes exclusively Lys-63–linked ubiquitination, whereas Suv is a ubiquitin-conjugating enzyme variant. The C-terminal region of Fen was necessary for interaction with Fni3, and this interaction was required for cell death triggered by overexpression of Fen in Nicotiana benthamiana leaves. Fni3 was shown to be an active E2 enzyme, but Suv displayed no ubiquitin-conjugating activity; Fni3 and Suv together directed Lys-63–linked ubiquitination. Decreased expression of Fni3, another tomato Ubc13 homolog, Sl-Ubc13-2, or Suv in N. benthamiana leaves diminished cell death associated with Fen-mediated immunity and cell death elicited by several other resistance (R) proteins and their cognate effectors. We also discovered that coexpression of Fen and other R proteins/effectors with a Fni3 mutant that is compromised for ubiquitin-conjugating activity diminished the cell death. These results suggest that Fni3/Sl-Ubc13-2 and Suv regulate the immune response mediated by Fen and other R proteins through Lys-63–linked ubiquitination. PMID:24076975

  4. A phospho-sugar binding domain homologous to NagB enzymes regulates the activity of the central glycolytic genes repressor.

    Science.gov (United States)

    Doan, Thierry; Martin, Laetitia; Zorrilla, Silvia; Chaix, Denis; Aymerich, Stéphane; Labesse, Gilles; Declerck, Nathalie

    2008-06-01

    CggR belongs to the SorC family of bacterial transcriptional regulators which control the expression of genes and operons involved in carbohydrate catabolism. CggR was first identified in Bacillus subtilis where it represses the gapA operon encoding the five enzymes that catalyze the central part of glycolysis. Here we present a structure/function study demonstrating that the C-terminal region of CggR regulates the DNA binding activity of this repressor in response to binding of a phosphorylated sugar. Molecular modeling of CggR revealed a winged-helix DNA-binding motif followed by a C-terminal domain presenting weak but significant homology with glucosamine-6-phosphate deaminases from the NagB family. In silico ligand screening suggested that the CggR C-terminal domain would bind preferentially bi-phosphorylated compounds, in agreement with previous studies that proposed fructuose-1,6-biphosphate (FBP) as the inducer metabolite. In vitro, FBP was the only sugar compound capable of interfering with CggR cooperative binding to DNA. FBP was also found to protect CggR against trypsin degradation at two arginine residues predicted to reside in a mobile loop forming the active site lid of the NagB enzymes. Replacement of residues predicted to interact with FBP led to mutant CggR with altered repressor activity in vivo but retaining their structural integrity and DNA binding activity in vitro. Interestingly, some of the mutant repressors responded with different specificity towards mono- and di-phospho-fructosides. Based on these results, we propose that the activity of the CggR-like repressors is controlled by a phospho-sugar binding (PSB) domain presenting structural and functional homology with NagB enzymes. (c) 2008 Wiley-Liss, Inc.

  5. Manganese-induced regulations in growth, yield formation, quality characters, rice aroma and enzyme involved in 2-acetyl-1-pyrroline biosynthesis in fragrant rice.

    Science.gov (United States)

    Li, Meijuan; Ashraf, Umair; Tian, Hua; Mo, Zhaowen; Pan, Shenggang; Anjum, Shakeel Ahmad; Duan, Meiyang; Tang, Xiangru

    2016-06-01

    Micro-nutrient application is essential for normal plant growth while a little is known about manganese (Mn)-induced regulations in morpho-physiological attributes, aroma formation and enzyme involved in 2-acetyl-1-pyrroline (2-AP) biosynthesis in aromatic rice. Present study aimed to examine the influence of four levels of Mn i.e., Mn1 (100 mg MnSO4 pot(-1)), Mn2 (150 mg MnSO4 pot(-1)), Mn3 (200 mg MnSO4 pot(-1)), and Mn4 (250 mg MnSO4 pot(-1)) on the growth, yield formation, quality characters, rice aroma and enzyme involved in 2-acetyl-1-pyrroline biosynthesis in two fragrant rice cultivars i.e., Meixiangzhan and Nongxiang 18. Pots without Mn application were served as control (Ck). Each pot contained 15 kg of soil. Effects on agronomic characters, quality attributes, 2-AP contents and enzymes involved in 2-AP biosynthesis have been studied in early and late season rice. Results depicted that Mn improved rice growth, yield and related characters, and some quality attributes significantly. It further up-regulated proline, pyrroline-5-carboxylic acid (P5C) (precursors of 2-AP), soluble proteins and activities of proline dehydrogenase (ProDH), Δ(1) pyrroline-5-carboxylic acid synthetase (P5CS) ornithine aminotransferase (OAT) that led to enhanced 2-AP production in rice grains. Moreover, higher Mn levels resulted in increased grain Mn contents in both rice cultivars. Along with growth and yield improvement, Mn application significantly improved rice aromatic contents. Overall, Nongxiang 18 accumulated more 2-AP contents than Meixiangzhan in both seasons under Mn application. This study further explored the importance of Mn in rice aroma formation and signifies that micro-nutrients can play significant roles in rice aroma synthesis; however, intensive studies at molecular levels are still needed to understand the exact mechanisms of Mn to improve rice aroma formation. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  6. Redox regulation of antioxidant enzymes: post-translational modulation of catalase and glutathione peroxidase activity by resveratrol in diabetic rat liver.

    Science.gov (United States)

    Sadi, Gökhan; Bozan, Davut; Yildiz, Huseyin Bekir

    2014-08-01

    Resveratrol is a strong antioxidant that exhibits blood glucose-lowering effects, which might contribute to its usefulness in preventing complications associated with diabetes. The present study aimed to investigate resveratrol effects on catalase (CAT) and glutathione peroxidase (GPx) gene and protein expression, their phosphorylation states and activities in rat liver of STZ-induced diabetes. Diabetes increased the levels of total protein phosphorylation and p-CAT, while mRNA expression, protein levels, and activity were reduced. Although diabetes induced transcriptional repression over GPx, it did not affect the protein levels and activity. When resveratrol was administered to diabetic rats, an increase in activity was associated with an increase in p-GPx levels. Decrease in Sirtuin1 (SIRT1) and nuclear factor erythroid 2-related factor (Nrf2) and increase in nuclear factor kappa B (NFκB) gene expression in diabetes were associated with a decrease in CAT and GPx mRNA expression. A possible compensatory mechanism for reduced gene expression of antioxidant enzymes is proved to be nuclear translocation of redox-sensitive Nrf2 and NFκB in diabetes which is confirmed by the increase in nuclear and decrease in cytoplasmic protein levels of Nrf2 and NFκB. Taken together, these findings revealed that an increase in the oxidized state in diabetes intricately modified the cellular phosphorylation status and regulation of antioxidant enzymes. Gene regulation of antioxidant enzymes was accompanied by nuclear translocation of Nrf2 and NFκB. Resveratrol administration also activated a coordinated cytoprotective response against diabetes-induced changes in liver tissues.

  7. Pancreatic Enzymes

    Science.gov (United States)

    ... Contact Us DONATE NOW GENERAL DONATION PURPLESTRIDE Pancreatic enzymes Home Facing Pancreatic Cancer Living with Pancreatic Cancer ... and see a registered dietitian. What are pancreatic enzymes? Pancreatic enzymes help break down fats, proteins and ...

  8. Yinchenhao Decoction Ameliorates Alpha-Naphthylisothiocyanate Induced Intrahepatic Cholestasis in Rats by Regulating Phase II Metabolic Enzymes and Transporters

    Directory of Open Access Journals (Sweden)

    Ya-Xiong Yi

    2018-05-01

    Full Text Available Yinchenhao Decoction (YCHD, a famous traditional Chinese formula, has been used for treating cholestasis for 1000s of years. The cholagogic effect of YCHD has been widely reported, but its pharmacodynamic material and underlying therapeutic mechanism remain unclear. By using ultra-high-performance liquid chromatography (UHPLC-quadrupole time-of-flight mass spectrometry, 11 original active components and eight phase II metabolites were detected in rats after oral administration of YCHD, including three new phase II metabolites. And it indicated that phase II metabolism was one of the major metabolic pathway for most active components in YCHD, which was similar to the metabolism process of bilirubin. It arouses our curiosity that whether the metabolism process of YCHD has any relationship with its cholagogic effects. So, a new method for simultaneous quantitation of eight active components and four phase II metabolites of rhein, emodin, genipin, and capillarisin has been developed and applied for their pharmacokinetic study in both normal and alpha-naphthylisothiocyanate (ANIT-induced intrahepatic cholestasis rats. The results indicated the pharmacokinetic behaviors of most components of YCHD were inhibited, which was hypothesized to be related to different levels of metabolic enzymes and transporters in rat liver. So dynamic changes of intrahepatic enzyme expression in cholestasis and YCHD treated rats have been monitored by an UHPLC-tandem mass spectrometry method. The results showed expression levels of UDP-glucuronosyltransferase 1-1 (UGT1A1, organic anion-transporting polypeptide 1A4 (OATP1A4, multidrug resistance-associated protein 2 (MRP2, multidrug resistance protein 1, sodium-dependent taurocholate cotransporter, and organic anion-transporting polypeptide 1A2 were significantly inhibited in cholestasis rats, which would account for reducing the drug absorption and the metabolic process of YCHD in cholestatic rats. A high dose (12 g/kg of

  9. Regulation of oxidative enzyme activity and eukaryotic elongation factor 2 in human skeletal muscle: influence of gender and exercise

    DEFF Research Database (Denmark)

    Roepstorff, Carsten; Schjerling, P.; Vistisen, Bodil

    2005-01-01

    AIM: To investigate gender-related differences in the responses of oxidative enzymes and eukaryotic elongation factor-2 (eEF2) to exercise. METHODS: The influence of exercise (90 min, 60%VO(2peak)) on citrate synthase (CS) and beta-hydroxyacyl-CoA dehydrogenase (HAD) activity and mRNA content...... expression and phosphorylation were unaffected by training status (NS). CONCLUSION: Basal transcriptional, translational, and/or post-translational control of CS and HAD seems to be gender-dependent. Also, gender differences in translation and/or post-translational protein modification of CS occur during...... not differ between females and males (NS). In females only, CS activity was enhanced (P differ between UT and ET but, nevertheless, CS activity was 56% higher in ET than in UT volunteers (P

  10. Dynamics of starch granule biogenesis - the role of redox-regulated enzymes and low-affinity carbohydrate-binding modules

    DEFF Research Database (Denmark)

    Blennow, A.; Svensson, Birte

    2010-01-01

    The deposition and degradation of starch in plants is subject to extensive post-translational regulation. To permit degradation of B-type crystallites present in tuberous and leaf starch these starch types are phosphorylated by glucan, water dikinase (GWD). At the level of post-translational redo...

  11. Differential regulation of c-di-GMP metabolic enzymes by environmental signals modulates biofilm formation in Yersinia pestis

    Directory of Open Access Journals (Sweden)

    Gai-Xian eRen

    2016-06-01

    Full Text Available Cyclic diguanylate (c-di-GMP is essential for Yersinia pestis biofilm formation, which is important for flea-borne blockage-dependent plague transmission. Two diguanylate cyclases (DGCs, HmsT and HmsD and one phosphodiesterase (PDE, HmsP are responsible for the synthesis and degradation of c-di-GMP in Y. pestis. Here, we systematically analyzed the effect of various environmental signals on regulation of the biofilm phenotype, the c-di-GMP levels, and expression of HmsT, HmsD and HmsP in Y. pestis. Biofilm formation was higher in the presence of nonlethal high concentration of CaCl2, MgCl2, CuSO4, sucrose, sodium dodecyl sulfonate, or dithiothreitol, and was lower in the presence of FeCl2 or NaCl. In addition, we found that HmsD plays a major role in biofilm formation in acidic or redox environments. These environmental signals differentially regulated expression of HmsT, HmsP and HmsD, resulting in changes in the intracellular levels of c-di-GMP in Y. pestis. Our results suggest that bacteria can sense various environmental signals, and differentially regulates their DGCs and PDEs to coordinately regulate and adapt metabolism of c-di-GMP and biofilm formation to changing environments.

  12. A functional screen implicates microRNA-138-dependent regulation of the depalmitoylation enzyme APT1 in dendritic spine morphogenesis

    NARCIS (Netherlands)

    Siegel, Gabriele; Obernosterer, Gregor; Fiore, Roberto; Oehmen, Martin; Bicker, Silvia; Christensen, Mette; Khudayberdiev, Sharof; Leuschner, Philipp F; Busch, Clara J L; Kane, Christina; Hübel, Katja; Dekker, Frank; Hedberg, Christian; Rengarajan, Balamurugan; Drepper, Carsten; Waldmann, Herbert; Kauppinen, Sakari; Greenberg, Michael E; Draguhn, Andreas; Rehmsmeier, Marc; Martinez, Javier; Schratt, Gerhard M; Dekker, Frank

    The microRNA pathway has been implicated in the regulation of synaptic protein synthesis and ultimately in dendritic spine morphogenesis, a phenomenon associated with long-lasting forms of memory. However, the particular microRNAs (miRNAs) involved are largely unknown. Here we identify specific

  13. SPIN1, negatively regulated by miR-148/152, enhances Adriamycin resistance via upregulating drug metabolizing enzymes and transporter in breast cancer.

    Science.gov (United States)

    Chen, Xu; Wang, Ya-Wen; Gao, Peng

    2018-05-09

    Spindlin1 (SPIN1), a protein highly expressed in several human cancers, has been correlated with tumorigenesis and development. Alterations of drug metabolizing enzymes and drug transporters are major determinants of chemoresistance in tumor cells. However, whether the metabolizing enzymes and transporters are under the control of SPIN1 in breast cancer chemoresistance has not yet been defined. SPIN1 expression in breast cancer cells and tissues was detected by quantitative real-time PCR (qRT-PCR) and immunohistochemistry. Chemosensitivity assays in vitro and in vivo were performed to determine the effect of SPIN1 on Adriamycin resistance. Downstream effectors of SPIN1 were screened by microarray and confirmed by qRT-PCR and Western blot. Luciferase assay and Western blot were used to identify miRNAs regulating SPIN1. We showed that SPIN1 was significantly elevated in drug-resistant breast cancer cell lines and tissues, compared with the chemosensitive ones. SPIN1 enhanced Adriamycin resistance of breast cancer cells in vitro, and downregulation of SPIN1 by miRNA could decrease Adriamycin resistance in vivo. Mechanistically, drug metabolizing enzymes and transporter CYP2C8, UGT2B4, UGT2B17 and ABCB4 were proven to be downstream effectors of SPIN1. Notably, SPIN1 was identified as a direct target of the miR-148/152 family (miR-148a-3p, miR-148b-3p and miR-152-3p). As expected, miR-148a-3p, miR-148b-3p or miR-152-3p could increase Adriamycin sensitivity in breast cancer cells in vitro. Moreover, high expression of SPIN1 or low expression of the miR-148/152 family predicted poorer survival in breast cancer patients. Our results establish that SPIN1, negatively regulated by the miR-148/152 family, enhances Adriamycin resistance in breast cancer via upregulating the expression of drug metabolizing enzymes and drug transporter.

  14. Zonation of heme synthesis enzymes in mouse liver and their regulation by β-catenin and Ha-ras.

    Science.gov (United States)

    Braeuning, Albert; Schwarz, Michael

    2010-11-01

    Cytochrome P450 (CYP) hemoproteins play an important role in hepatic biotransformation. Recently, β-catenin and Ha-ras signaling have been identified as players controlling transcription of various CYP genes in mouse liver. The aim of the present study was to analyze the role of β-catenin and Ha-ras in the regulation of heme synthesis. Heme synthesis-related gene expression was analyzed in normal liver, in transgenic mice expressing activated β-catenin or Ha-ras, and in hepatomas. Regulation of the aminolevulinate dehydratase promoter was studied in vitro. Elevated expression of mRNAs and proteins involved in heme biosynthesis was linked to β-catenin activation in perivenous hepatocytes, in transgenic hepatocytes, and in hepatocellular tumors. Stimulation of the aminolevulinate dehydratase promoter by β-catenin was independent of the β-catenin/T-cell-specific transcription factor dimer. By contrast, activation of Ha-ras repressed heme synthesis-related gene expression. The present data suggest that β-catenin enhances the expression of both CYPs and heme synthesis-related genes, thus coordinating the availability of CYP apoprotein and its prosthetic group heme. The reciprocal regulation of heme synthesis by β-catenin and Ha-ras-dependent signaling supports our previous hypothesis that antagonistic action of these pathways plays a major role in the control of zonal gene expression in healthy mouse liver and aberrant expression patterns in hepatocellular tumors.

  15. Cofactor Editing by the G-protein Metallochaperone Domain Regulates the Radical B12 Enzyme IcmF.

    Science.gov (United States)

    Li, Zhu; Kitanishi, Kenichi; Twahir, Umar T; Cracan, Valentin; Chapman, Derrell; Warncke, Kurt; Banerjee, Ruma

    2017-03-10

    IcmF is a 5'-deoxyadenosylcobalamin (AdoCbl)-dependent enzyme that catalyzes the carbon skeleton rearrangement of isobutyryl-CoA to butyryl-CoA. It is a bifunctional protein resulting from the fusion of a G-protein chaperone with GTPase activity and the cofactor- and substrate-binding mutase domains with isomerase activity. IcmF is prone to inactivation during catalytic turnover, thus setting up its dependence on a cofactor repair system. Herein, we demonstrate that the GTPase activity of IcmF powers the ejection of the inactive cob(II)alamin cofactor and requires the presence of an acceptor protein, adenosyltransferase, for receiving it. Adenosyltransferase in turn converts cob(II)alamin to AdoCbl in the presence of ATP and a reductant. The repaired cofactor is then reloaded onto IcmF in a GTPase-gated step. The mechanistic details of cofactor loading and offloading from the AdoCbl-dependent IcmF are distinct from those of the better characterized and homologous methylmalonyl-CoA mutase/G-protein chaperone system. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  16. Pathophysiological response to hypoxia - from the molecular mechanisms of malady to drug discovery: epigenetic regulation of the hypoxic response via hypoxia-inducible factor and histone modifying enzymes.

    Science.gov (United States)

    Mimura, Imari; Tanaka, Tetsuhiro; Wada, Youichiro; Kodama, Tatsuhiko; Nangaku, Masaomi

    2011-01-01

    The hypoxia response regulated primarily by hypoxia-inducible factor (HIF) influences metabolism, cell survival, and angiogenesis to maintain biological homeostasis. In addition to the traditional transcriptional regulation by HIF, recent studies have shown that epigenetic modulation such as histone methylation, acetylation, and DNA methylation could change the regulation of the response to hypoxia. Eukaryotic chromatin is known to be modified by multiple post-translational histone methylation and demethylation, which result in the chromatin conformation change to adapt to hypoxic stimuli. Interestingly, some of the histone demethylase enzymes, which have the Jumonji domain-containing family, require oxygen to function and are induced by hypoxia in an HIF-1-dependent manner. Recent studies have demonstrated that histone modifiers play important roles in the hypoxic environment such as that in cancer cells and that they may become new therapeutic targets for cancer patients. It may lead to finding a new therapy for cancer to clarify a new epigenetic mechanism by HIF and histone demethylase such as JMJD1A (KDM3A) under hypoxia.

  17. SIRT3 and SIRT5 regulate the enzyme activity and cardiolipin binding of very long-chain acyl-CoA dehydrogenase.

    Directory of Open Access Journals (Sweden)

    Yuxun Zhang

    Full Text Available SIRT3 and SIRT5 have been shown to regulate mitochondrial fatty acid oxidation but the molecular mechanisms behind the regulation are lacking. Here, we demonstrate that SIRT3 and SIRT5 both target human very long-chain acyl-CoA dehydrogenase (VLCAD, a key fatty acid oxidation enzyme. SIRT3 deacetylates and SIRT5 desuccinylates K299 which serves to stabilize the essential FAD cofactor in the active site. Further, we show that VLCAD binds strongly to cardiolipin and isolated mitochondrial membranes via a domain near the C-terminus containing lysines K482, K492, and K507. Acetylation or succinylation of these residues eliminates binding of VLCAD to cardiolipin. SIRT3 deacetylates K507 while SIRT5 desuccinylates K482, K492, and K507. Sirtuin deacylation of recombinant VLCAD rescues membrane binding. Endogenous VLCAD from SIRT3 and SIRT5 knockout mouse liver shows reduced binding to cardiolipin. Thus, SIRT3 and SIRT5 promote fatty acid oxidation by converging upon VLCAD to promote its activity and membrane localization. Regulation of cardiolipin binding by reversible lysine acylation is a novel mechanism that is predicted to extrapolate to other metabolic proteins that localize to the inner mitochondrial membrane.

  18. Integrative modelling of pH-dependent enzyme activity and transcriptomic regulation of the acetone–butanol–ethanol fermentation of Clostridium acetobutylicum in continuous culture

    Science.gov (United States)

    Millat, Thomas; Janssen, Holger; Bahl, Hubert; Fischer, Ralf-Jörg; Wolkenhauer, Olaf

    2013-01-01

    Summary In a continuous culture under phosphate limitation the metabolism of Clostridium acetobutylicum depends on the external pH level. By comparing seven steady-state conditions between pH 5.7 and pH 4.5 we show that the switch from acidogenesis to solventogenesis occurs between pH 5.3 and pH 5.0 with an intermediate state at pH 5.1. Here, an integrative study is presented investigating how a changing external pH level affects the clostridial acetone–butanol–ethanol (ABE) fermentation pathway. This is of particular interest as the biotechnological production of n-butanol as biofuel has recently returned into the focus of industrial applications. One prerequisite is the furthering of the knowledge of the factors determining the solvent production and their integrative regulations. We have mathematically analysed the influence of pH-dependent specific enzyme activities of branch points of the metabolism on the product formation. This kinetic regulation was compared with transcriptomic regulation regarding gene transcription and the proteomic profile. Furthermore, both regulatory mechanisms were combined yielding a detailed projection of their individual and joint effects on the product formation. The resulting model represents an important platform for future developments of industrial butanol production based on C. acetobutylicum. PMID:23332010

  19. Characterization of the gene encoding serine acetyltransferase, a regulated enzyme of cysteine biosynthesis from the protist parasites Entamoeba histolytica and Entamoeba dispar. Regulation and possible function of the cysteine biosynthetic pathway in Entamoeba.

    Science.gov (United States)

    Nozaki, T; Asai, T; Sanchez, L B; Kobayashi, S; Nakazawa, M; Takeuchi, T

    1999-11-05

    The enteric protist parasites Entamoeba histolytica and Entamoeba dispar possess a cysteine biosynthetic pathway, unlike their mammalian host, and are capable of de novo production of L-cysteine. We cloned and characterized cDNAs that encode the regulated enzyme serine acetyltransferase (SAT) in this pathway from these amoebae by genetic complementation of a cysteine-auxotrophic Escherichia coli strain with the amoebic cDNA libraries. The deduced amino acid sequences of the amoebic SATs exhibited, within the most conserved region, 36-52% identities with the bacterial and plant SATs. The amoebic SATs contain a unique insertion of eight amino acids, also found in the corresponding region of a plasmid-encoded SAT from Synechococcus sp., which showed the highest overall identities to the amoebic SATs. Phylogenetic reconstruction also revealed a close kinship of the amoebic SATs with cyanobacterial SATs. Biochemical characterization of the recombinant E. histolytica SAT revealed several enzymatic features that distinguished the amoebic enzyme from the bacterial and plant enzymes: 1) inhibition by L-cysteine in a competitive manner with L-serine; 2) inhibition by L-cystine; and 3) no association with cysteine synthase. Genetically engineered amoeba strains that overproduced cysteine synthase and SAT were created. The cysteine synthase-overproducing amoebae had a higher level of cysteine synthase activity and total thiol content and revealed increased resistance to hydrogen peroxide. These results indicate that the cysteine biosynthetic pathway plays an important role in antioxidative defense of these enteric parasites.

  20. Up-regulation of cytochrome P450 and phase II enzyme systems in rat precision-cut rat lung slices by the intact glucosinolates, glucoraphanin and glucoerucin.

    Science.gov (United States)

    Abdull Razis, Ahmad Faizal; Bagatta, Manuela; De Nicola, Gina Rosalinda; Iori, Renato; Ioannides, Costas

    2011-03-01

    It is believed that the chemopreventive activity of cruciferous vegetables in the lung and other tissues is exclusively the result of exposure to degradation products of glucosinolates, such as the isothiocyanates, and that the parent glucosinolates make no contribution. In the present study, evidence is presented for the first time that, in rat lung, the intact glucosinolates, glucoraphanin and glucoerucin, can modulate carcinogen-metabolising enzyme systems. The glucosinolates were isolated from cruciferous vegetables and incubated (1-25 μM) with precision-cut rat lung slices for 24h. Both glucosinolates, at concentrations as low as 1 μM, up-regulated the O-deethylation of ethoxyresorufin and the apoprotein levels of CYP1A1 and CYP1B1; supplementation of the incubation medium with myrosinase, the enzyme that converts glucosinolates to their corresponding isothiocyanates, abolished the rise in ethoxyresorufin O-deethylase activity. In contrast, neither glucosinolate, at the concentrations studied, influenced quinone reductase activity in the lung slices, but addition of myrosinase to the glucosinolate incubations led to a marked rise in activity. Glutathione S-transferase activity, monitored using 1-chloro-2,4-dinitrobenzene as the accepting substrate, was elevated in lung slices exposed to glucoraphanin. GSTα protein levels were increased by glucoraphanin and, to a much lesser extent, glucoerucin. It may be concluded that intact glucosinolates can modulate the activity of pulmonary carcinogen-metabolising enzyme systems, and can thus contribute to the documented chemopreventive activity of cruciferous vegetables in the lung. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  1. Assimilate partitioning during reproductive growth

    International Nuclear Information System (INIS)

    Finazzo, S.F.; Davenport, T.L.

    1987-01-01

    Leaves having various phyllotactic relationships to fruitlets were labeled for 1 hour with 10/sub r/Ci of 14 CO 2 . Fruitlets were also labeled. Fruitlets did fix 14 CO 2 . Translocation of radioactivity from the peel into the fruit occurred slowly and to a limited extent. No evidence of translocation out of the fruitlets was observed. Assimilate partitioning in avocado was strongly influenced by phyllotaxy. If a fruit and the labeled leaf had the same phyllotaxy then greater than 95% of the radiolabel was present in this fruit. When the fruit did not have the same phyllotaxy as the labeled leaf, the radiolabel distribution was skewed with 70% of the label going to a single adjacent position. Avocado fruitlets exhibit uniform labeling throughout a particular tissue. In avocado, assimilates preferentially move from leaves to fruits with the same phyllotaxy

  2. Dynamic regulation of auxin oxidase and conjugating enzymes AtDAO1 and GH3 modulates auxin homeostasis.

    Science.gov (United States)

    Mellor, Nathan; Band, Leah R; Pěnčík, Aleš; Novák, Ondřej; Rashed, Afaf; Holman, Tara; Wilson, Michael H; Voß, Ute; Bishopp, Anthony; King, John R; Ljung, Karin; Bennett, Malcolm J; Owen, Markus R

    2016-09-27

    The hormone auxin is a key regulator of plant growth and development, and great progress has been made understanding auxin transport and signaling. Here, we show that auxin metabolism and homeostasis are also regulated in a complex manner. The principal auxin degradation pathways in Arabidopsis include oxidation by Arabidopsis thaliana gene DIOXYGENASE FOR AUXIN OXIDATION 1/2 (AtDAO1/2) and conjugation by Gretchen Hagen3s (GH3s). Metabolic profiling of dao1-1 root tissues revealed a 50% decrease in the oxidation product 2-oxoindole-3-acetic acid (oxIAA) and increases in the conjugated forms indole-3-acetic acid aspartic acid (IAA-Asp) and indole-3-acetic acid glutamic acid (IAA-Glu) of 438- and 240-fold, respectively, whereas auxin remains close to the WT. By fitting parameter values to a mathematical model of these metabolic pathways, we show that, in addition to reduced oxidation, both auxin biosynthesis and conjugation are increased in dao1-1 Transcripts of AtDAO1 and GH3 genes increase in response to auxin over different timescales and concentration ranges. Including this regulation of AtDAO1 and GH3 in an extended model reveals that auxin oxidation is more important for auxin homoeostasis at lower hormone concentrations, whereas auxin conjugation is most significant at high auxin levels. Finally, embedding our homeostasis model in a multicellular simulation to assess the spatial effect of the dao1-1 mutant shows that auxin increases in outer root tissues in agreement with the dao1-1 mutant root hair phenotype. We conclude that auxin homeostasis is dependent on AtDAO1, acting in concert with GH3, to maintain auxin at optimal levels for plant growth and development.

  3. Castasterone confers copper stress tolerance by regulating antioxidant enzyme responses, antioxidants, and amino acid balance in B. juncea seedlings.

    Science.gov (United States)

    Yadav, Poonam; Kaur, Ravdeep; Kanwar, Mukesh Kumar; Sharma, Anket; Verma, Vinod; Sirhindi, Geetika; Bhardwaj, Renu

    2018-01-01

    The aim of the present study was to explore the effect of exogenous application of castasterone (CS) on physiologic and biochemical responses in Brassica juncea seedlings under copper (Cu) stress. Seeds were pre-soaked in different concentrations of CS and grown for 7 days under various levels of Cu. The exposure of B. juncea to higher levels of Cu led to decrease of morphologic parameters, with partial recovery of length and fresh weight in the CS pre-treated seedlings. Metal content was high in both roots and shoots under Cu exposure while the CS pre-treatment reduced the metal uptake. Accumulation of hydrogen peroxide (H 2 O 2 ) and superoxide anion radical (O 2 - ) were chosen as stress biomarker and higher levels of H 2 O 2 (88.89%) and O 2 - (62.11%) showed the oxidative stress in metal treated B. juncea seedlings, however, CS pre-treatment reduced ROS accumulation in Cu-exposed seedlings. The Cu exposures lead to enhance the plant's enzymatic and non-enzymatic antioxidant system. It was observed that enzymatic activities of ascorbate peroxidase (APOX), dehydroascorbate reductase (DHAR), and glutathione reductase (GR), glutathione perxoidase (GPOX) and gultrathione-s-transferase increased while activity of monodehydroascorbate reductase (MDHAR) decreased under Cu stress. The pre-treatment with CS positively affected the activities of enzymes. RT-PCR analysis showed that mRNA transcript levels were correlated with total enzymatic activity of DHAR, GR, GST and GSH. Increase in the gene expression of DHAR (1.85 folds), GR (3.24 folds), GST-1 (2.00 folds) and GSH-S (3.18 folds) was noticed with CS pre-treatment. Overall, the present study shows that Cu exposure induced severe oxidative stress in B. juncea plants and exogenous application of CS improved antioxidative defense system by modulating the ascorbate-glutathione cycle and amino acid metabolism. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Chloroplastic thioredoxin-f and thioredoxin-m1/4 play important roles in brassinosteroids-induced changes in CO2 assimilation and cellular redox homeostasis in tomato

    Science.gov (United States)

    Cheng, Fei; Zhou, Yan-Hong; Xia, Xiao-Jian; Shi, Kai; Zhou, Jie; Yu, Jing-Quan

    2014-01-01

    Chloroplast thioredoxins (TRXs) and glutathione function as redox messengers in the regulation of photosynthesis. In this work, the roles of chloroplast TRXs in brassinosteroids (BRs)-induced changes in cellular redox homeostasis and CO2 assimilation were studied in the leaves of tomato plants. BRs-deficient d ^im plants showed decreased transcripts of TRX-f, TRX-m2, TRX-m1/4, and TRX-x, while exogenous BRs significantly induced CO2 assimilation and the expression of TRX-f, TRX-m2, TRX-m1/4, and TRX-x. Virus-induced gene silencing (VIGS) of the chloroplast TRX-f, TRX-m2, TRX-m1/4, and TRX-y genes individually increased membrane lipid peroxidation and accumulation of 2-Cys peroxiredoxin dimers, and decreased the activities of the ascorbate–glutathione cycle enzymes and the ratio of reduced glutathione to oxidized glutathione (GSH/GSSG) in the leaves. Furthermore, partial silencing of TRX-f, TRX-m2, TRX-m1/4, and TRX-y resulted in decreased expression of genes involved in the Benson–Calvin cycle and decreased activity of the associated enzymes. Importantly, the BRs-induced increase in CO2 assimilation and the increased expression and activities of antioxidant- and photosynthesis-related genes and enzymes were compromised in the partially TRX-f- and TRX-m1/4-silenced plants. All of these results suggest that TRX-f and TRX-m1/4 are involved in the BRs-induced changes in CO2 assimilation and cellular redox homeostasis in tomato. PMID:24847092

  5. Alisol B 23-acetate protects against ANIT-induced hepatotoxity and cholestasis, due to FXR-mediated regulation of transporters and enzymes involved in bile acid homeostasis

    Energy Technology Data Exchange (ETDEWEB)

    Meng, Qiang; Chen, Xin-li; Wang, Chang-yuan; Liu, Qi; Sun, Hui-jun; Sun, Peng-yuan; Huo, Xiao-kui; Liu, Zhi-hao; Yao, Ji-hong; Liu, Ke-xin, E-mail: kexinliu@dlmedu.edu.cn

    2015-03-15

    Intrahepatic cholestasis is a clinical syndrome with systemic and intrahepatic accumulation of excessive toxic bile acids that ultimately cause hepatobiliary injury. Appropriate regulation of bile acids in hepatocytes is critically important for protection against liver injury. In the present study, we characterized the protective effect of alisol B 23-acetate (AB23A), a natural triterpenoid, on alpha-naphthylisothiocyanate (ANIT)-induced liver injury and intrahepatic cholestasis in mice and further elucidated the mechanisms in vivo and in vitro. AB23A treatment dose-dependently protected against liver injury induced by ANIT through reducing hepatic uptake and increasing efflux of bile acid via down-regulation of hepatic uptake transporters (Ntcp) and up-regulation of efflux transporter (Bsep, Mrp2 and Mdr2) expression. Furthermore, AB23A reduced bile acid synthesis through repressing Cyp7a1 and Cyp8b1, increased bile acid conjugation through inducing Bal, Baat and bile acid metabolism through an induction in gene expression of Sult2a1. We further demonstrate the involvement of farnesoid X receptor (FXR) in the hepatoprotective effect of AB23A. The changes in transporters and enzymes, as well as ameliorative liver histology in AB23A-treated mice were abrogated by FXR antagonist guggulsterone in vivo. In vitro evidences also directly demonstrated the effect of AB23A on FXR activation in a dose-dependent manner using luciferase reporter assay in HepG2 cells. In conclusion, AB23A produces protective effect against ANIT-induced hepatotoxity and cholestasis, due to FXR-mediated regulation of transporters and enzymes. - Highlights: • AB23A has at least three roles in protection against ANIT-induced liver injury. • AB23A decreases Ntcp, and increases Bsep, Mrp2 and Mdr2 expression. • AB23A represses Cyp7a1 and Cyp8b1 through inducing Shp and Fgf15 expression. • AB23A increases bile acid metabolism through inducing Sult2a1 expression. • FXR activation is involved

  6. Alisol B 23-acetate protects against ANIT-induced hepatotoxity and cholestasis, due to FXR-mediated regulation of transporters and enzymes involved in bile acid homeostasis

    International Nuclear Information System (INIS)

    Meng, Qiang; Chen, Xin-li; Wang, Chang-yuan; Liu, Qi; Sun, Hui-jun; Sun, Peng-yuan; Huo, Xiao-kui; Liu, Zhi-hao; Yao, Ji-hong; Liu, Ke-xin

    2015-01-01

    Intrahepatic cholestasis is a clinical syndrome with systemic and intrahepatic accumulation of excessive toxic bile acids that ultimately cause hepatobiliary injury. Appropriate regulation of bile acids in hepatocytes is critically important for protection against liver injury. In the present study, we characterized the protective effect of alisol B 23-acetate (AB23A), a natural triterpenoid, on alpha-naphthylisothiocyanate (ANIT)-induced liver injury and intrahepatic cholestasis in mice and further elucidated the mechanisms in vivo and in vitro. AB23A treatment dose-dependently protected against liver injury induced by ANIT through reducing hepatic uptake and increasing efflux of bile acid via down-regulation of hepatic uptake transporters (Ntcp) and up-regulation of efflux transporter (Bsep, Mrp2 and Mdr2) expression. Furthermore, AB23A reduced bile acid synthesis through repressing Cyp7a1 and Cyp8b1, increased bile acid conjugation through inducing Bal, Baat and bile acid metabolism through an induction in gene expression of Sult2a1. We further demonstrate the involvement of farnesoid X receptor (FXR) in the hepatoprotective effect of AB23A. The changes in transporters and enzymes, as well as ameliorative liver histology in AB23A-treated mice were abrogated by FXR antagonist guggulsterone in vivo. In vitro evidences also directly demonstrated the effect of AB23A on FXR activation in a dose-dependent manner using luciferase reporter assay in HepG2 cells. In conclusion, AB23A produces protective effect against ANIT-induced hepatotoxity and cholestasis, due to FXR-mediated regulation of transporters and enzymes. - Highlights: • AB23A has at least three roles in protection against ANIT-induced liver injury. • AB23A decreases Ntcp, and increases Bsep, Mrp2 and Mdr2 expression. • AB23A represses Cyp7a1 and Cyp8b1 through inducing Shp and Fgf15 expression. • AB23A increases bile acid metabolism through inducing Sult2a1 expression. • FXR activation is involved

  7. Some Brain Peptides Regulating the Secretion of Digestive Enzymes in the Indian Meal Moth, Plodia Interpunctella (Lepidoptera: Pyralidae

    Directory of Open Access Journals (Sweden)

    Sajjadian Seyede Minoo

    2014-07-01

    Full Text Available The Indian meal moth, Plodia interpunctella (Hübner (Lepidoptera: Pyralidae is a destructive polyphagous pest of many stored products. To interfere with the physiological processes, especially digestion, of the larval pest, more information on the regulatory mechanisms is needed. The brain extract from 1-day-old last instar larvae of P. interpunctella was examined. In the bioassays, the midguts were treated with the brain extract, and the carbohydrase and protease activities were measured. The brain extract showed increasing dose-dependent effects on α-amylase, α-glucosidase, β-glucosidase, α-galactosidase, β-galactosidase, and trypsin secretion in the larval midgut. The extract was further characterised and partially purified using high performance liquid chromatography (HPLC. Several peptides were determined in the brain extract regulating hydrolase activities in the larval midgut of the pest.

  8. Interleukin-1β regulates cell proliferation and activity of extracellular matrix remodelling enzymes in cultured primary pig heart cells

    International Nuclear Information System (INIS)

    Zitta, Karina; Brandt, Berenice; Wuensch, Annegret; Meybohm, Patrick; Bein, Berthold; Steinfath, Markus; Scholz, Jens; Albrecht, Martin

    2010-01-01

    Research highlights: → Levels of IL-1β are increased in the pig myocardium after infarction. → Cultured pig heart cells possess IL-1 receptors. → IL-1β increases cell proliferation of pig heart cells in-vitro. → IL-1β increases MMP-2 and MMP-9 activity in pig heart cells in-vitro. → IL-1β may be important for tissue remodelling events after myocardial infarction. -- Abstract: After myocardial infarction, elevated levels of interleukins (ILs) are found within the myocardial tissue and IL-1β is considered to play a major role in tissue remodelling events throughout the body. In the study presented, we have established a cell culture model of primary pig heart cells to evaluate the effects of different concentrations of IL-1β on cell proliferation as well as expression and activity of enzymes typically involved in tissue remodelling. Primary pig heart cell cultures were derived from three different animals and stimulated with recombinant pig IL-1β. RNA expression was detected by RT-PCR, protein levels were evaluated by Western blotting, activity of matrix metalloproteinases (MMPs) was quantified by gelatine zymography and cell proliferation was measured using colorimetric MTS assays. Pig heart cells express receptors for IL-1 and application of IL-1β resulted in a dose-dependent increase of cell proliferation (P < 0.05 vs. control; 100 ng/ml; 24 h). Gene expression of caspase-3 was increased by IL-1β (P < 0.05 vs. control; 100 ng/ml; 3 h), and pro-caspase-3 but not active caspase was detected in lysates of pig heart cells by Western blotting. MMP-2 gene expression as well as enzymatic activities of MMP-2 and MMP-9 were increased by IL-1β (P < 0.05 vs. control; 100 ng/ml; 3 h for gene expression, 48 and 72 h for enzymatic activities of MMP-2 and MMP-9, respectively). Our in vitro data suggest that IL-1β plays a major role in the events of tissue remodelling in the heart. Combined with our recently published in vivo data (Meybohm et al., PLoS One

  9. Interleukin-1{beta} regulates cell proliferation and activity of extracellular matrix remodelling enzymes in cultured primary pig heart cells

    Energy Technology Data Exchange (ETDEWEB)

    Zitta, Karina; Brandt, Berenice [Department of Anesthesiology and Intensive Care Medicine, University Hospital Schleswig-Holstein, Campus Kiel (Germany); Wuensch, Annegret [Institute of Molecular Animal Breeding and Biotechnology, Ludwig Maximilians University, Munich (Germany); Meybohm, Patrick; Bein, Berthold; Steinfath, Markus; Scholz, Jens [Department of Anesthesiology and Intensive Care Medicine, University Hospital Schleswig-Holstein, Campus Kiel (Germany); Albrecht, Martin, E-mail: Albrecht@anaesthesie.uni-kiel.de [Department of Anesthesiology and Intensive Care Medicine, University Hospital Schleswig-Holstein, Campus Kiel (Germany)

    2010-09-03

    Research highlights: {yields} Levels of IL-1{beta} are increased in the pig myocardium after infarction. {yields} Cultured pig heart cells possess IL-1 receptors. {yields} IL-1{beta} increases cell proliferation of pig heart cells in-vitro. {yields} IL-1{beta} increases MMP-2 and MMP-9 activity in pig heart cells in-vitro. {yields} IL-1{beta} may be important for tissue remodelling events after myocardial infarction. -- Abstract: After myocardial infarction, elevated levels of interleukins (ILs) are found within the myocardial tissue and IL-1{beta} is considered to play a major role in tissue remodelling events throughout the body. In the study presented, we have established a cell culture model of primary pig heart cells to evaluate the effects of different concentrations of IL-1{beta} on cell proliferation as well as expression and activity of enzymes typically involved in tissue remodelling. Primary pig heart cell cultures were derived from three different animals and stimulated with recombinant pig IL-1{beta}. RNA expression was detected by RT-PCR, protein levels were evaluated by Western blotting, activity of matrix metalloproteinases (MMPs) was quantified by gelatine zymography and cell proliferation was measured using colorimetric MTS assays. Pig heart cells express receptors for IL-1 and application of IL-1{beta} resulted in a dose-dependent increase of cell proliferation (P < 0.05 vs. control; 100 ng/ml; 24 h). Gene expression of caspase-3 was increased by IL-1{beta} (P < 0.05 vs. control; 100 ng/ml; 3 h), and pro-caspase-3 but not active caspase was detected in lysates of pig heart cells by Western blotting. MMP-2 gene expression as well as enzymatic activities of MMP-2 and MMP-9 were increased by IL-1{beta} (P < 0.05 vs. control; 100 ng/ml; 3 h for gene expression, 48 and 72 h for enzymatic activities of MMP-2 and MMP-9, respectively). Our in vitro data suggest that IL-1{beta} plays a major role in the events of tissue remodelling in the heart. Combined

  10. Expression of S1P metabolizing enzymes and receptors correlate with survival time and regulate cell migration in glioblastoma multiforme.

    Science.gov (United States)

    Bien-Möller, Sandra; Lange, Sandra; Holm, Tobias; Böhm, Andreas; Paland, Heiko; Küpper, Johannes; Herzog, Susann; Weitmann, Kerstin; Havemann, Christoph; Vogelgesang, Silke; Marx, Sascha; Hoffmann, Wolfgang; Schroeder, Henry W S; Rauch, Bernhard H

    2016-03-15

    A signaling molecule which is involved in proliferation and migration of malignant cells is the lipid mediator sphingosine-1-phosphate (S1P). There are hints for a potential role of S1P signaling in malignant brain tumors such as glioblastoma multiforme (GBM) which is characterized by a poor prognosis. Therefore, a comprehensive expression analysis of S1P receptors (S1P1-S1P5) and S1P metabolizing enzymes in human GBM (n = 117) compared to healthy brain (n = 10) was performed to evaluate their role for patient´s survival. Furthermore, influence of S1P receptor inhibition on proliferation and migration were studied in LN18 GBM cells. Compared to control brain, mRNA levels of S1P1, S1P2, S1P3 and S1P generating sphingosine kinase-1 were elevated in GBM. Kaplan-Meier analyses demonstrated an association between S1P1 and S1P2 with patient´s survival times. In vitro, an inhibitory effect of the SphK inhibitor SKI-II on viability of LN18 cells was shown. S1P itself had no effect on viability but stimulated LN18 migration which was blocked by inhibition of S1P1 and S1P2. The participation of S1P1 and S1P2 in LN18 migration was further supported by siRNA-mediated silencing of these receptors. Immunoblots and inhibition experiments suggest an involvement of the PI3-kinase/AKT1 pathway in the chemotactic effect of S1P in LN18 cells.In summary, our data argue for a role of S1P signaling in proliferation and migration of GBM cells. Individual components of the S1P pathway represent prognostic factors for patients with GBM. Perspectively, a selective modulation of S1P receptor subtypes could represent a therapeutic approach for GBM patients and requires further evaluation.

  11. Abundance and Diversity of CO2-Assimilating Bacteria and Algae Within Red Agricultural Soils Are Modulated by Changing Management Practice.

    Science.gov (United States)

    Yuan, Hongzhao; Ge, Tida; Chen, Xiangbi; Liu, Shoulong; Zhu, Zhenke; Wu, Xiaohong; Wei, Wenxue; Whiteley, Andrew Steven; Wu, Jinshui

    2015-11-01

    Elucidating the biodiversity of CO(2)-assimilating bacterial and algal communities in soils is important for obtaining a mechanistic view of terrestrial carbon sinks operating at global scales. "Red" acidic soils (Orthic Acrisols) cover large geographic areas and are subject to a range of management practices, which may alter the balance between carbon dioxide production and assimilation through changes in microbial CO(2)-assimilating populations. Here, we determined the abundance and diversity of CO(2)-assimilating bacteria and algae in acidic soils using quantitative PCR and terminal restriction fragment length polymorphism (T-RFLP) of the cbbL gene, which encodes the key CO(2) assimilation enzyme (ribulose-1,5-bisphosphate carboxylase/oxygenase) in the Calvin cycle. Within the framework of a long-term experiment (Taoyuan Agro-ecosystem, subtropical China), paddy rice fields were converted in 1995 to four alternative land management regimes: natural forest (NF), paddy rice (PR), maize crops (CL), and tea plantations (TP). In 2012 (17 years after land use transformation), we collected and analyzed the soils from fields under the original and converted land management regimes. Our results indicated that fields under the PR soil management system harbored the greatest abundance of cbbL copies (4.33 × 10(8) copies g(-1) soil). More than a decade after converting PR soils to natural, rotation, and perennial management systems, a decline in both the diversity and abundance of cbbL-harboring bacteria and algae was recorded. The lowest abundance of bacteria (0.98 × 10(8) copies g(-1) soil) and algae (0.23 × 10(6) copies g(-1) soil) was observed for TP soils. When converting PR soil management to alternative management systems (i.e., NF, CL, and TP), soil edaphic factors (soil organic carbon and total nitrogen content) were the major determinants of bacterial autotrophic cbbL gene diversity. In contrast, soil phosphorus concentration was the major regulator

  12. The AMPK enzyme-complex: from the regulation of cellular energy homeostasis to a possible new molecular target in the management of chronic inflammatory disorders.

    Science.gov (United States)

    Antonioli, Luca; Colucci, Rocchina; Pellegrini, Carolina; Giustarini, Giulio; Sacco, Deborah; Tirotta, Erika; Caputi, Valentina; Marsilio, Ilaria; Giron, Maria Cecilia; Németh, Zoltán H; Blandizzi, Corrado; Fornai, Matteo

    2016-01-01

    Adenosine monophosphate-activated protein kinase (AMPK), known as an enzymatic complex that regulates the energetic metabolism, is emerging as a pivotal enzyme and enzymatic pathway involved in the regulation of immune homeostatic networks. It is also involved in the molecular mechanisms underlying the pathophysiology of chronic inflammatory diseases. AMPK is expressed in several immune cell types including macrophages, lymphocytes, neutrophils and dendritic cells, and governs a broad array of cell functions, which include cytokine production, chemotaxis, cytotoxicity, apoptosis and proliferation. Based on its wide variety of immunoregulatory actions, the AMPK system has been targeted to reveal its impact on the course of immune-related diseases, such as atherosclerosis, psoriasis, joint inflammation and inflammatory bowel diseases. The identification of AMPK subunits responsible for specific anti-inflammatory actions and the understanding of the underlying molecular mechanisms will promote the generation of novel AMPK activators, endowed with improved pharmacodynamic and pharmacokinetic profiles. These new tools will aid us to utilize AMPK pathway activation in the management of acute and chronic inflammatory diseases, while minimizing potential adverse reactions related to the effects of AMPK on metabolic energy.

  13. Calcineurin regulates slow myosin, but not fast myosin or metabolic enzymes, during fast-to-slow transformation in rabbit skeletal muscle cell culture

    Science.gov (United States)

    Meißner, Joachim D; Gros, Gerolf; Scheibe, Renate J; Scholz, Michael; Kubis, Hans-Peter

    2001-01-01

    The addition of cyclosporin A (500 ng ml−1) - an inhibitor of the Ca2+-calmodulin-regulated serine/threonine phosphatase calcineurin - to primary cultures of rabbit skeletal muscle cells had no influence on the expression of fast myosin heavy chain (MHC) isoforms MHCIIa and MHCIId at the level of protein and mRNA, but reduced the expression of slow MHCI mRNA. In addition, no influence of cyclosporin A on the expression of citrate synthase (CS) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA was found. The level of enzyme activity of CS was also not affected. When the Ca2+ ionophore A23187 (4 × 10−7m) was added to the medium, a partial fast-to-slow transformation occurred. The level of MHCI mRNA increased, and the level of MHCIId mRNA decreased. Cotreatment with cyclosporin A was able to prevent the upregulation of MHCI at the level of mRNA as well as protein, but did not reverse the decrease in MHCIId expression. The expression of MHCIIa was also not influenced by cyclosporin A. Cyclosporin A was not able to prevent the upregulation of CS mRNA under Ca2+ ionophore treatment and failed to reduce the increased enzyme activity of CS. The expression of GAPDH mRNA was reduced under Ca2+ ionophore treatment and was not altered under cotreatment with cyclosporin A. When the myotubes in the primary muscle culture were electrostimulated at 1 Hz for 15 min periods followed by pauses of 30 min, a partial fast-to-slow transformation was induced. Again, cotreatment with cyclosporin A prevented the upregulation of MHCI at the level of mRNA and protein without affecting MHCIId expression. The nuclear translocation of the calcineurin-regulated transcription factor nuclear factor of activated thymocytes (NFATc1) during treatment with Ca2+ ionophore, and the prevention of the translocation in the presence of cyclosporin A, were demonstrated immunocytochemically in the myotubes of the primary culture. The effects of cyclosporin A demonstrate the involvement of

  14. Conditions for successful data assimilation

    Science.gov (United States)

    Morzfeld, M.; Chorin, A. J.

    2013-12-01

    Many applications in science and engineering require that the predictions of uncertain models be updated by information from a stream of noisy data. The model and the data jointly define a conditional probability density function (pdf), which contains all the information one has about the process of interest and various numerical methods can be used to study and approximate this pdf, e.g. the Kalman filter, variational methods or particle filters. Given a model and data, each of these algorithms will produce a result. We are interested in the conditions under which this result is reasonable, i.e. consistent with the real-life situation one is modeling. In particular, we show, using idealized models, that numerical data assimilation is feasible in principle only if a suitably defined effective dimension of the problem is not excessive. This effective dimension depends on the noise in the model and the data, and in physically reasonable problems it can be moderate even when the number of variables is huge. In particular, we find that the effective dimension being moderate induces a balance condition between the noises in the model and the data; this balance condition is often satisfied in realistic applications or else the noise levels are excessive and drown the underlying signal. We also study the effects of the effective dimension on particle filters in two instances, one in which the importance function is based on the model alone, and one in which it is based on both the model and the data. We have three main conclusions: (1) the stability (i.e., non-collapse of weights) in particle filtering depends on the effective dimension of the problem. Particle filters can work well if the effective dimension is moderate even if the true dimension is large (which we expect to happen often in practice). (2) A suitable choice of importance function is essential, or else particle filtering fails even when data assimilation is feasible in principle with a sequential algorithm

  15. Oxidation and Assimilation of Carbohydrates by Micrococcus sodonensis1

    Science.gov (United States)

    Perry, Jerome J.; Evans, James B.

    1966-01-01

    Perry, Jerome J. (North Carolina State University, Raleigh), and James B. Evans. Oxidation and assimilation of carbohydrates by Micrococcus sodonensis. J. Bacteriol. 91:33–38. 1966.—Micrococcus sodonensis is a biotin-requiring strict aerobe that cannot utilize carbohydrates as sole sources of carbon and energy. However, addition of mannose, glucose, sucrose, or maltose to a medium on which the organism can grow resulted in an increase in total growth. M. sodonensis oxidized these sugars without induction, thus indicating the presence of constitutive enzymes for their transport, activation, and metabolism. Under appropriate nonproliferating cell conditions, glucose was readily incorporated into essential constituents of the cell. When glucose-1-C14 and glucose-6-C14 were oxidized by nonproliferating cells, the label was found in both the protein and nucleic acid fractions of the cell. The respiratory quotients of cells oxidizing glucose in saline and in phosphate buffer indicated assimilation of sugar carbon in buffer and virtually no assimilation in saline. The ability of M. sodonensis to completely oxidize glucose and to grow on intermediates of glucose oxidation but not on glucose suggests that glucose may suppress or repress some reaction(s) necessary for growth, and that growth substrates either derepress or circumvent this block. PMID:5903100

  16. Regulation of adipose branched-chain amino acid catabolism enzyme expression and cross-adipose amino acid flux in human obesity

    Science.gov (United States)

    Lackey, Denise E.; Lynch, Christopher J.; Olson, Kristine C.; Mostaedi, Rouzbeh; Ali, Mohamed; Smith, William H.; Karpe, Fredrik; Humphreys, Sandy; Bedinger, Daniel H.; Dunn, Tamara N.; Thomas, Anthony P.; Oort, Pieter J.; Kieffer, Dorothy A.; Amin, Rajesh; Bettaieb, Ahmed; Haj, Fawaz G.; Permana, Paska; Anthony, Tracy G.

    2013-01-01

    Elevated blood branched-chain amino acids (BCAA) are often associated with insulin resistance and type 2 diabetes, which might result from a reduced cellular utilization and/or incomplete BCAA oxidation. White adipose tissue (WAT) has become appreciated as a potential player in whole body BCAA metabolism. We tested if expression of the mitochondrial BCAA oxidation checkpoint, branched-chain α-ketoacid dehydrogenase (BCKD) complex, is reduced in obese WAT and regulated by metabolic signals. WAT BCKD protein (E1α subunit) was significantly reduced by 35–50% in various obesity models (fa/fa rats, db/db mice, diet-induced obese mice), and BCKD component transcripts significantly lower in subcutaneous (SC) adipocytes from obese vs. lean Pima Indians. Treatment of 3T3-L1 adipocytes or mice with peroxisome proliferator-activated receptor-γ agonists increased WAT BCAA catabolism enzyme mRNAs, whereas the nonmetabolizable glucose analog 2-deoxy-d-glucose had the opposite effect. The results support the hypothesis that suboptimal insulin action and/or perturbed metabolic signals in WAT, as would be seen with insulin resistance/type 2 diabetes, could impair WAT BCAA utilization. However, cross-tissue flux studies comparing lean vs. insulin-sensitive or insulin-resistant obese subjects revealed an unexpected negligible uptake of BCAA from human abdominal SC WAT. This suggests that SC WAT may not be an important contributor to blood BCAA phenotypes associated with insulin resistance in the overnight-fasted state. mRNA abundances for BCAA catabolic enzymes were markedly reduced in omental (but not SC) WAT of obese persons with metabolic syndrome compared with weight-matched healthy obese subjects, raising the possibility that visceral WAT contributes to the BCAA metabolic phenotype of metabolically compromised individuals. PMID:23512805

  17. Ashanti pepper (Piper guineense Schumach et Thonn) attenuates carbohydrate hydrolyzing, blood pressure regulating and cholinergic enzymes in experimental type 2 diabetes rat model.

    Science.gov (United States)

    Adefegha, Stephen Adeniyi; Oboh, Ganiyu; Adefegha, Omowunmi Monisola

    2017-01-01

    Ashanti pepper (Piper guineense Schumach et Thonn) seed is well known in folkloric medicine in the management of type 2 diabetes (T2DM) with little or no scientific documentation for its action. This study investigated the effect of Ashanti pepper seed on some enzymes relevant to carbohydrate hydrolysis, blood regulation and the cholinergic system, as well as the blood glucose level, lipid profile, antioxidant parameters, and hepatic and renal function markers in T2DM rats. T2DM was induced by feeding rats with high-fat diet (HFD) for 14 days followed by a single intraperitoneal dose of 35 mg/kg body weight of streptozotocin (STZ). Three days after STZ induction, diabetic rats were placed on a dietary regimen containing 2%-4% Ashanti pepper. Reduced blood glucose level with decreased α-amylase, α-glucosidase and angiotensin I converting enzyme (ACE) activities were observed in Ashanti pepper seed and acarbose-treated rat groups when compared to that of the diabetic control rat group. Furthermore, the results revealed that inclusion of 2%-4% Ashanti pepper seed in diabetic rat fed group diets may ameliorate the lipid profile, antioxidant status, and hepatic and renal function in T2DM rats as much as in the acarbose-treated groups. In addition, a chromatographic profile of the seed revealed the presence of quercitrin (116.51 mg/g), capsaicin (113.94 mg/g), dihydrocapsaicin (88.29 mg/g) and isoquercitrin (74.89 mg/g). The results from this study clearly suggest that Ashanti pepper could serve as a promising source of phenolic compounds with great alternative therapeutic potentials in the management of T2DM.

  18. Up-regulation of glutathione-related genes, enzyme activities and transport proteins in human cervical cancer cells treated with doxorubicin.

    Science.gov (United States)

    Drozd, Ewa; Krzysztoń-Russjan, Jolanta; Marczewska, Jadwiga; Drozd, Janina; Bubko, Irena; Bielak, Magda; Lubelska, Katarzyna; Wiktorska, Katarzyna; Chilmonczyk, Zdzisław; Anuszewska, Elżbieta; Gruber-Bzura, Beata

    2016-10-01

    Doxorubicin (DOX), one of the most effective anticancer drugs, acts in a variety of ways including DNA damage, enzyme inhibition and generation of reactive oxygen species. Glutathione (GSH) and glutathione-related enzymes including: glutathione peroxidase (GPX), glutathione reductase (GSR) and glutathione S-transferases (GST) may play a role in adaptive detoxification processes in response to the oxidative stress, thus contributing to drug resistance phenotype. In this study, we investigated effects of DOX treatment on expression and activity of GSH-related enzymes and multidrug resistance-associated proteins in cultured human cervical cancer cells displaying different resistance against this drug (HeLa and KB-V1). Determination of expression level of genes encoding GST isoforms and MRP proteins (GCS, GPX, GSR, GSTA1-3, GSTM1, GSTP1, ABCC1-3, MGST1-3) was performed using StellARray™ Technology. Enzymatic activities of GPX and GSR were measured using biochemical methods. Expression of MRP1 was examined by immunofluorescence microscopy. This study showed that native expression levels of GSTM1 and GSTA3 were markedly higher in KB-V1 cells (2000-fold and 200-fold) compared to HeLa cells. Resistant cells have also shown significantly elevated expression of GSTA1 and GSTA2 genes (200-fold and 50-fold) as a result of DOX treatment. In HeLa cells, exposure to DOX increased expression of all genes: GSTM1 (7-fold) and GSTA1-3 (550-fold, 150-fold and 300-fold). Exposure to DOX led to the slight increase of GCS expression as well as GPX activity in KB-V1 cells, while in HeLa cells it did not. Expression of ABCC1 (MRP1) was not increased in any of the tested cell lines. Our results indicate that expression of GSTM1 and GSTA1-3 genes is up-regulated by DOX treatment and suggest that activity of these genes may be associated with drug resistance of the tested cells. At the same time, involvement of MRP1 in DOX resistance in the given experimental conditions is unlikely

  19. Cholesterol enhances amyloid {beta} deposition in mouse retina by modulating the activities of A{beta}-regulating enzymes in retinal pigment epithelial cells

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jiying [Department of Ophthalmology and Visual Science, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519 (Japan); Ohno-Matsui, Kyoko, E-mail: k.ohno.oph@tmd.ac.jp [Department of Ophthalmology and Visual Science, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519 (Japan); Morita, Ikuo [Section of Cellular Physiological Chemistry, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519 (Japan)

    2012-08-10

    Highlights: Black-Right-Pointing-Pointer Cholesterol-treated RPE produces more A{beta} than non-treated RPE. Black-Right-Pointing-Pointer Neprilysin expression and activity decreased in cholesterol-treated RPE. Black-Right-Pointing-Pointer {alpha}-Secretase expression and activity decreased in cholesterol-treated RPE. Black-Right-Pointing-Pointer Cholesterol-enriched diet induced subRPE deposits in aged mice. Black-Right-Pointing-Pointer A{beta} were present in cholesterol-enriched-diet-induced subRPE deposits in aged mice. -- Abstract: Subretinally-deposited amyloid {beta} (A{beta}) is a main contributor of developing age-related macular degeneration (AMD). However, the mechanism causing A{beta} deposition in AMD eyes is unknown. Hypercholesterolemia is a significant risk for developing AMD. Thus, we investigated the effects of cholesterol on A{beta} production in retinal pigment epithelial (RPE) cells in vitro and in the mouse retina in vivo. RPE cells isolated from senescent (12-month-old) C57BL/6 mice were treated with 10 {mu}g/ml cholesterol for 48 h. A{beta} amounts in culture supernatants were measured by ELISA. Activity and expression of enzymes and proteins that regulate A{beta} production were examined by activity assay and real time PCR. The retina of mice fed cholesterol-enriched diet was examined by transmission electron microscopy. Cholesterol significantly increased A{beta} production in cultured RPE cells. Activities of A{beta} degradation enzyme; neprilysin (NEP) and anti-amyloidogenic secretase; {alpha}-secretase were significantly decreased in cell lysates of cholesterol-treated RPE cells compared to non-treated cells, but there was no change in the activities of {beta}- or {gamma}-secretase. mRNA levels of NEP and {alpha}-secretase (ADAM10 and ADAM17) were significantly lower in cholesterol-treated RPE cells than non-treated cells. Senescent (12-month-old) mice fed cholesterol-enriched chow developed subRPE deposits containing A{beta}, whereas

  20. Furfural Inhibits Growth by Limiting Sulfur Assimilation in Ethanologenic Escherichia coli Strain LY180▿

    Science.gov (United States)

    Miller, Elliot N.; Jarboe, Laura R.; Turner, Peter C.; Pharkya, Priti; Yomano, Lorraine P.; York, Sean W.; Nunn, David; Shanmugam, K. T.; Ingram, Lonnie O.

    2009-01-01

    A wide variety of commercial products can be potentially made from monomeric sugars produced by the dilute acid hydrolysis of lignocellulosic biomass. However, this process is accompanied by side products such as furfural that hinder microbial growth and fermentation. To investigate the mechanism of furfural inhibition, mRNA microarrays of an ethanologenic strain of Escherichia coli (LY180) were compared immediately prior to and 15 min after a moderate furfural challenge. Expression of genes and regulators associated with the biosynthesis of cysteine and methionine was increased by furfural, consistent with a limitation of these critical metabolites. This was in contrast to a general stringent response and decreased expression of many other biosynthetic genes. Of the 20 amino acids individually tested as supplements (100 μM each), cysteine and methionine were the most effective in increasing furfural tolerance with serine (precursor of cysteine), histidine, and arginine of lesser benefit. Supplementation with other reduced sulfur sources such as d-cysteine and thiosulfate also increased furfural tolerance. In contrast, supplementation with taurine, a sulfur source that requires 3 molecules of NADPH for sulfur assimilation, was of no benefit. Furfural tolerance was also increased by inserting a plasmid encoding pntAB, a cytoplasmic NADH/NADPH transhydrogenase. Based on these results, a model is proposed for the inhibition of growth in which the reduction of furfural by YqhD, an enzyme with a low Km for NADPH, depletes NADPH sufficiently to limit the assimilation of sulfur into amino acids (cysteine and methionine) by CysIJ (sulfite reductase). PMID:19684179

  1. Global regulators ExpA (GacA) and KdgR modulate extracellular enzyme gene expression through the RsmA-rsmB system in Erwinia carotovora subsp. carotovora.

    Science.gov (United States)

    Hyytiäinen, H; Montesano, M; Palva, E T

    2001-08-01

    The production of the main virulence determinants, the extracellular plant cell wall-degrading enzymes, and hence virulence of Erwinia carotovora subsp. carotovora is controlled by a complex regulatory network. One of the global regulators, the response regulator ExpA, a GacA homolog, is required for transcriptional activation of the extracellular enzyme genes of this soft-rot pathogen. To elucidate the mechanism of ExpA control as well as interactions with other regulatory systems, we isolated second-site transposon mutants that would suppress the enzyme-negative phenotype of an expA (gacA) mutant. Inactivation of kdgR resulted in partial restoration of extracellular enzyme production and virulence to the expA mutant, suggesting an interaction between the two regulatory pathways. This interaction was mediated by the RsmA-rsmB system. Northern analysis was used to show that the regulatory rsmB RNA was under positive control of ExpA. Conversely, the expression of rsmA encoding a global repressor was under negative control of ExpA and positive control of KdgR. This study indicates a central role for the RsmA-rsmB regulatory system during pathogenesis, integrating signals from the ExpA (GacA) and KdgR global regulators of extracellular enzyme production in E. carotovora subsp. carotovora.

  2. Data Assimilation - Advances and Applications

    Energy Technology Data Exchange (ETDEWEB)

    Williams, Brian J. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2014-07-30

    This presentation provides an overview of data assimilation (model calibration) for complex computer experiments. Calibration refers to the process of probabilistically constraining uncertain physics/engineering model inputs to be consistent with observed experimental data. An initial probability distribution for these parameters is updated using the experimental information. Utilization of surrogate models and empirical adjustment for model form error in code calibration form the basis for the statistical methodology considered. The role of probabilistic code calibration in supporting code validation is discussed. Incorporation of model form uncertainty in rigorous uncertainty quantification (UQ) analyses is also addressed. Design criteria used within a batch sequential design algorithm are introduced for efficiently achieving predictive maturity and improved code calibration. Predictive maturity refers to obtaining stable predictive inference with calibrated computer codes. These approaches allow for augmentation of initial experiment designs for collecting new physical data. A standard framework for data assimilation is presented and techniques for updating the posterior distribution of the state variables based on particle filtering and the ensemble Kalman filter are introduced.

  3. Data assimilation with inequality constraints

    Science.gov (United States)

    Thacker, W. C.

    If values of variables in a numerical model are limited to specified ranges, these restrictions should be enforced when data are assimilated. The simplest option is to assimilate without regard for constraints and then to correct any violations without worrying about additional corrections implied by correlated errors. This paper addresses the incorporation of inequality constraints into the standard variational framework of optimal interpolation with emphasis on our limited knowledge of the underlying probability distributions. Simple examples involving only two or three variables are used to illustrate graphically how active constraints can be treated as error-free data when background errors obey a truncated multi-normal distribution. Using Lagrange multipliers, the formalism is expanded to encompass the active constraints. Two algorithms are presented, both relying on a solution ignoring the inequality constraints to discover violations to be enforced. While explicitly enforcing a subset can, via correlations, correct the others, pragmatism based on our poor knowledge of the underlying probability distributions suggests the expedient of enforcing them all explicitly to avoid the computationally expensive task of determining the minimum active set. If additional violations are encountered with these solutions, the process can be repeated. Simple examples are used to illustrate the algorithms and to examine the nature of the corrections implied by correlated errors.

  4. Robust Control of PEP Formation Rate in the Carbon Fixation Pathway of C4 Plants by a Bi-functional Enzyme

    Directory of Open Access Journals (Sweden)

    Hart Yuval

    2011-10-01

    Full Text Available Abstract Background C4 plants such as corn and sugarcane assimilate atmospheric CO2 into biomass by means of the C4 carbon fixation pathway. We asked how PEP formation rate, a key step in the carbon fixation pathway, might work at a precise rate, regulated by light, despite fluctuations in substrate and enzyme levels constituting and regulating this process. Results We present a putative mechanism for robustness in C4 carbon fixation, involving a key enzyme in the pathway, pyruvate orthophosphate dikinase (PPDK, which is regulated by a bifunctional enzyme, Regulatory Protein (RP. The robust mechanism is based on avidity of the bifunctional enzyme RP to its multimeric substrate PPDK, and on a product-inhibition feedback loop that couples the system output to the activity of the bifunctional regulator. The model provides an explanation for several unusual biochemical characteristics of the system and predicts that the system's output, phosphoenolpyruvate (PEP formation rate, is insensitive to fluctuations in enzyme levels (PPDK and RP, substrate levels (ATP and pyruvate and the catalytic rate of PPDK, while remaining sensitive to the system's input (light levels. Conclusions The presented PPDK mechanism is a new way to achieve robustness using product inhibition as a feedback loop on a bifunctional regulatory enzyme. This mechanism exhibits robustness to protein and metabolite levels as well as to catalytic rate changes. At the same time, the output of the system remains tuned to input levels.

  5. Enzyme Informatics

    Science.gov (United States)

    Alderson, Rosanna G.; Ferrari, Luna De; Mavridis, Lazaros; McDonagh, James L.; Mitchell, John B. O.; Nath, Neetika

    2012-01-01

    Over the last 50 years, sequencing, structural biology and bioinformatics have completely revolutionised biomolecular science, with millions of sequences and tens of thousands of three dimensional structures becoming available. The bioinformatics of enzymes is well served by, mostly free, online databases. BRENDA describes the chemistry, substrate specificity, kinetics, preparation and biological sources of enzymes, while KEGG is valuable for understanding enzymes and metabolic pathways. EzCatDB, SFLD and MACiE are key repositories for data on the chemical mechanisms by which enzymes operate. At the current rate of genome sequencing and manual annotation, human curation will never finish the functional annotation of the ever-expanding list of known enzymes. Hence there is an increasing need for automated annotation, though it is not yet widespread for enzyme data. In contrast, functional ontologies such as the Gene Ontology already profit from automation. Despite our growing understanding of enzyme structure and dynamics, we are only beginning to be able to design novel enzymes. One can now begin to trace the functional evolution of enzymes using phylogenetics. The ability of enzymes to perform secondary functions, albeit relatively inefficiently, gives clues as to how enzyme function evolves. Substrate promiscuity in enzymes is one example of imperfect specificity in protein-ligand interactions. Similarly, most drugs bind to more than one protein target. This may sometimes result in helpful polypharmacology as a drug modulates plural targets, but also often leads to adverse side-effects. Many cheminformatics approaches can be used to model the interactions between druglike molecules and proteins in silico. We can even use quantum chemical techniques like DFT and QM/MM to compute the structural and energetic course of enzyme catalysed chemical reaction mechanisms, including a full description of bond making and breaking. PMID:23116471

  6. 7 CFR 58.436 - Rennet, pepsin, other milk clotting enzymes and flavor enzymes.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Rennet, pepsin, other milk clotting enzymes and flavor enzymes. 58.436 Section 58.436 Agriculture Regulations of the Department of Agriculture (Continued... clotting enzymes and flavor enzymes. Enzyme preparations used in the manufacture of cheese shall be safe...

  7. Inverse Regulation of DHT Synthesis Enzymes 5α-Reductase Types 1 and 2 by the Androgen Receptor in Prostate Cancer.

    Science.gov (United States)

    Audet-Walsh, Étienne; Yee, Tracey; Tam, Ingrid S; Giguère, Vincent

    2017-04-01

    5α-Reductase types 1 and 2, encoded by SRD5A1 and SRD5A2, are the two enzymes that can catalyze the conversion of testosterone to dihydrotestosterone, the most potent androgen receptor (AR) agonist in prostate cells. 5α-Reductase type 2 is the predominant isoform expressed in the normal prostate. However, its expression decreases during prostate cancer (PCa) progression, whereas SRD5A1 increases, and the mechanism underlying this transcriptional regulatory switch is still unknown. Interrogation of SRD5A messenger RNA expression in three publicly available data sets confirmed that SRD5A1 is increased in primary and metastatic PCa compared with nontumoral prostate tissues, whereas SRD5A2 is decreased. Activation of AR, a major oncogenic driver of PCa, induced the expression of SRD5A1 from twofold to fourfold in three androgen-responsive PCa cell lines. In contrast, AR repressed SRD5A2 expression in this context. Chromatin-immunoprecipitation studies established that AR is recruited to both SRD5A1 and SRD5A2 genes following androgen stimulation but initiates transcriptional activation only at SRD5A1 as monitored by recruitment of RNA polymerase II and the presence of the H3K27Ac histone mark. Furthermore, we showed that the antiandrogens bicalutamide and enzalutamide block the AR-mediated regulation of both SRD5A1 and SRD5A2, highlighting an additional mechanism explaining their beneficial effects in patients. In summary, we identified an AR-dependent transcriptional regulation that explains the differential expression of 5α-reductase types 1 and 2 during PCa progression. Our work thus defines a mechanism by which androgens control their own synthesis via differential regulatory control of the expression of SRD5A1 and SRD5A2. Copyright © 2017 Endocrine Society.

  8. Anti-oxidative stress regulator NF-E2-related factor 2 mediates the adaptive induction of antioxidant and detoxifying enzymes by lipid peroxidation metabolite 4-hydroxynonenal

    Directory of Open Access Journals (Sweden)

    Huang Ying

    2012-11-01

    Full Text Available Abstract Background NF-E2-related factor 2 (NRF2 regulates a battery of antioxidative and phase II drug metabolizing/detoxifying genes through binding to the antioxidant response elements (ARE. NRF2-ARE signaling plays a central role in protecting cells from a wide spectrum of reactive toxic species including reactive oxygen/nitrogen species (RONS. 4-hydroxylnonenal (4-HNE is a major end product from lipid peroxidation of omega-6 polyunsaturated fatty acids (PUFA induced by oxidative stress, and it is highly reactive to nucleophilic sites in DNA and proteins, causing cytotoxicity and genotoxicity. In this study, we examined the role of NRF2 in regulating the 4-HNE induced gene expression of antioxidant and detoxifying enzymes. Results When HeLa cells were treated with 4-HNE, NRF2 rapidly transloated into the nucleus, as determined by the distribution of NRF2 tagged with the enhanced green fluorescent protein (EGFP and increased NRF2 protein in the nuclear fraction. Transcriptional activity of ARE-luciferase was significantly induced by 0.01-10 μM of 4-HNE in a dose-dependent manner, and the induction could be blocked by pretreatment with glutathione (GSH. 4-HNE induced transcriptional expression of glutathione S-transferase (GST A4, aldoketone reductase (AKR 1C1 and heme oxygenase-1 (HO-1, and the induction was attenuated by knocking down NRF2 using small interfering RNA. Conclusions NRF2 is critical in mediating 4-HNE induced expression of antioxidant and detoxifying genes. This may account for one of the major cellular defense mechanisms against reactive metabolites of lipids peroxidation induced by oxidative stress and protect cells from cytotoxicity.

  9. Aberrant expression of the S1P regulating enzymes, SPHK1 and SGPL1, contributes to a migratory phenotype in OSCC mediated through S1PR2.

    Science.gov (United States)

    Patmanathan, Sathya Narayanan; Johnson, Steven P; Lai, Sook Ling; Panja Bernam, Suthashini; Lopes, Victor; Wei, Wenbin; Ibrahim, Maha Hafez; Torta, Federico; Narayanaswamy, Pradeep; Wenk, Markus R; Herr, Deron R; Murray, Paul G; Yap, Lee Fah; Paterson, Ian C

    2016-05-10

    Oral squamous cell carcinoma (OSCC) is a lethal disease with a 5-year mortality rate of around 50%. Molecular targeted therapies are not in routine use and novel therapeutic targets are required. Our previous microarray data indicated sphingosine 1-phosphate (S1P) metabolism and signalling was deregulated in OSCC. In this study, we have investigated the contribution of S1P signalling to the pathogenesis of OSCC. We show that the expression of the two major enzymes that regulate S1P levels were altered in OSCC: SPHK1 was significantly upregulated in OSCC tissues compared to normal oral mucosa and low levels of SGPL1 mRNA correlated with a worse overall survival. In in vitro studies, S1P enhanced the migration/invasion of OSCC cells and attenuated cisplatin-induced death. We also demonstrate that S1P receptor expression is deregulated in primary OSCCs and that S1PR2 is over-expressed in a subset of tumours, which in part mediates S1P-induced migration of OSCC cells. Lastly, we demonstrate that FTY720 induced significantly more apoptosis in OSCC cells compared to non-malignant cells and that FTY720 acted synergistically with cisplatin to induce cell death. Taken together, our data show that S1P signalling promotes tumour aggressiveness in OSCC and identify S1P signalling as a potential therapeutic target.

  10. Covariance Function for Nearshore Wave Assimilation Systems

    Science.gov (United States)

    2018-01-30

    which is applicable for any spectral wave model. The four dimensional variational (4DVar) assimilation methods are based on the mathematical ...covariance can be modeled by a parameterized Gaussian function, for nearshore wave assimilation applications , the covariance function depends primarily on...SPECTRAL ACTION DENSITY, RESPECTIVELY. ............................ 5 FIGURE 2. TOP ROW: STATISTICAL ANALYSIS OF THE WAVE-FIELD PROPERTIES AT THE

  11. Data assimilation a mathematical introduction

    CERN Document Server

    Law, Kody; Zygalakis, Konstantinos

    2015-01-01

    This book provides a systematic treatment of the mathematical underpinnings of work in data assimilation, covering both theoretical and computational approaches. Specifically the authors develop a unified mathematical framework in which a Bayesian formulation of the problem provides the bedrock for the derivation, development and analysis of algorithms; the many examples used in the text, together with the algorithms which are introduced and discussed, are all illustrated by the MATLAB software detailed in the book and made freely available online. The book is organized into nine chapters: the first contains a brief introduction to the mathematical tools around which the material is organized; the next four are concerned with discrete time dynamical systems and discrete time data; the last four are concerned with continuous time dynamical systems and continuous time data and are organized analogously to the corresponding discrete time chapters. This book is aimed at mathematical researchers interested in a sy...

  12. Effective assimilation of global precipitation: simulation experiments

    Directory of Open Access Journals (Sweden)

    Guo-Yuan Lien

    2013-07-01

    Full Text Available Past attempts to assimilate precipitation by nudging or variational methods have succeeded in forcing the model precipitation to be close to the observed values. However, the model forecasts tend to lose their additional skill after a few forecast hours. In this study, a local ensemble transform Kalman filter (LETKF is used to effectively assimilate precipitation by allowing ensemble members with better precipitation to receive higher weights in the analysis. In addition, two other changes in the precipitation assimilation process are found to alleviate the problems related to the non-Gaussianity of the precipitation variable: (a transform the precipitation variable into a Gaussian distribution based on its climatological distribution (an approach that could also be used in the assimilation of other non-Gaussian observations and (b only assimilate precipitation at the location where at least some ensemble members have precipitation. Unlike many current approaches, both positive and zero rain observations are assimilated effectively. Observing system simulation experiments (OSSEs are conducted using the Simplified Parametrisations, primitivE-Equation DYnamics (SPEEDY model, a simplified but realistic general circulation model. When uniformly and globally distributed observations of precipitation are assimilated in addition to rawinsonde observations, both the analyses and the medium-range forecasts of all model variables, including precipitation, are significantly improved as compared to only assimilating rawinsonde observations. The effect of precipitation assimilation on the analyses is retained on the medium-range forecasts and is larger in the Southern Hemisphere (SH than that in the Northern Hemisphere (NH because the NH analyses are already made more accurate by the denser rawinsonde stations. These improvements are much reduced when only the moisture field is modified by the precipitation observations. Both the Gaussian transformation and

  13. Regulations of enzymes in animals: effects of developmental processes, cancer, and radiation. Comprehensive three-year progress report, 1 May 1972--30 April 1975

    International Nuclear Information System (INIS)

    Knox, W.E.

    1975-01-01

    Controls by genes and by adaptive phenomena of the patterns of enzymes in several rat tissues were extended by systematic investigations during development, in neoplasms, and after x-irradiation. Newly developed quantitative assays for tryptophan pyrrolase and phenylalanine hydroxylase were used to study the mechanism of degradation after induction of the former enzyme. Systematic investigation of the isoenzymic variants and of the quantitative pattern of enzymes in numerous rat tissues led to the discovery of new variants, the determination of the functional role of certain enzymes in specific tissues, and the identification of enzymes whose amount provides sensitive indicators fo neoplastic growth in rat liver and spleen. X-irradiation of young postnatal rats interfered with the development of some hepatic enzymes. This effect was distinct from that of tumor-bearing, and from abnormal hormonal or nutritional conditions. (U.S.)

  14. Expression and regulation of enzymes in the ceramide metabolic pathway in human retinal pigment epithelial cells and their relevance to retinal degeneration.

    Science.gov (United States)

    Zhu, DanHong; Sreekumar, Parameswaran G; Hinton, David R; Kannan, Ram

    2010-03-31

    Ceramide and its metabolic derivatives are important modulators of cellular apoptosis and proliferation. Dysregulation or imbalance of their metabolic pathways may promote the development of retinal degeneration. The aim of this study was to identify the expression and regulation of key enzymes of the ceramide pathway in retinal pigment epithelial (RPE) cells. RT-PCR was used to screen the enzymes involved in ceramide metabolism that are expressed in RPE. Over-expression of neutral sphingomyelinase-2 (SMPD3) or sphingosine kinase 1 (Sphk1) in ARPE-19 cells was achieved by transient transfection of SMPD3 or Sphk1 cDNA subcloned into an expression vector. The number of apoptotic or proliferating cells was determined using TUNEL and BrdU assays, respectively. Neutral sphingomyelinase-1, neutral sphingomyelinase-2, acidic ceramidase, ceramide kinase, SphK1 and Sphk2 were expressed in both ARPE-19 and early passage human fetal RPE (fRPE) cells, while alkaline ceramidase 2 was only expressed in fRPE cells. Over-expression of SMPD3 decreased RPE cell proliferation and increased cell apoptosis. The percentage of apoptotic cells increased proportionally with the amount of transfected SMPD3 DNA. Over-expression of SphK1 promoted cell proliferation and protected ARPE-19 cells from ceramide-induced apoptosis. The effect of C(2) ceramide on induction of apoptosis was evaluated in polarized vs. non-polarized RPE cultures; polarization of RPE was associated with much reduced apoptosis in response to ceramide. In conclusion, RPE cells possess the synthetic machinery for the production of ceramide, sphingosine, ceramide-1-phosphate (C1P), and sphingosine-1-phosphate (S1P). Over-expression of SMPD3 may increase cellular ceramide levels, leading to enhanced cell death and arrested cell proliferation. The selective induction of apoptosis in non-polarized RPE cultures by C(2) ceramide suggests that increased ceramide levels will preferentially affect non-polarized RPE, as are found in

  15. Duodenal-jejunal bypass surgery up-regulates the expression of the hepatic insulin signaling proteins and the key regulatory enzymes of intestinal gluconeogenesis in diabetic Goto-Kakizaki rats.

    Science.gov (United States)

    Sun, Dong; Wang, Kexin; Yan, Zhibo; Zhang, Guangyong; Liu, Shaozhuang; Liu, Fengjun; Hu, Chunxiao; Hu, Sanyuan

    2013-11-01

    Duodenal-jejunal bypass (DJB), which is not routinely applied in metabolic surgery, is an effective surgical procedure in terms of type 2 diabetes mellitus resolution. However, the underlying mechanisms are still undefined. Our aim was to investigate the diabetic improvement by DJB and to explore the changes in hepatic insulin signaling proteins and regulatory enzymes of gluconeogenesis after DJB in a non-obese diabetic rat model. Sixteen adult male Goto-Kakizaki rats were randomly divided into DJB and sham-operated groups. The body weight, food intake, hormone levels, and glucose metabolism were measured. The levels of protein expression and phosphorylation of insulin receptor-beta (IR-β) and insulin receptor substrate 2 (IRS-2) were evaluated in the liver. We also detected the expression of key regulatory enzymes of gluconeogenesis [phosphoenoylpyruvate carboxykinase-1 (PCK1), glucose-6-phosphatase-alpha (G6Pase-α)] in small intestine and liver. DJB induced significant diabetic improvement with higher postprandial glucagons-like peptide 1, peptide YY, and insulin levels, but without weight loss. The DJB group exhibited increased expression and phosphorylation of IR-β and IRS-2 in liver, up-regulated the expression of PCK1 and G6Pase-α in small intestine, and down-regulated the expression of these enzymes in liver. DJB is effective in up-regulating the expression of the key proteins in the hepatic insulin signaling pathway and the key regulatory enzymes of intestinal gluconeogenesis and down-regulating the expression of the key regulatory enzymes of hepatic gluconeogenesis without weight loss. Our study helps to reveal the potential role of hepatic insulin signaling pathway and intestinal gluconeogenesis in ameliorating insulin resistance after metabolic surgery.

  16. Skill Assessment in Ocean Biological Data Assimilation

    Science.gov (United States)

    Gregg, Watson W.; Friedrichs, Marjorie A. M.; Robinson, Allan R.; Rose, Kenneth A.; Schlitzer, Reiner; Thompson, Keith R.; Doney, Scott C.

    2008-01-01

    There is growing recognition that rigorous skill assessment is required to understand the ability of ocean biological models to represent ocean processes and distributions. Statistical analysis of model results with observations represents the most quantitative form of skill assessment, and this principle serves as well for data assimilation models. However, skill assessment for data assimilation requires special consideration. This is because there are three sets of information in the free-run model, data, and the assimilation model, which uses Data assimilation information from both the flee-run model and the data. Intercom parison of results among the three sets of information is important and useful for assessment, but is not conclusive since the three information sets are intertwined. An independent data set is necessary for an objective determination. Other useful measures of ocean biological data assimilation assessment include responses of unassimilated variables to the data assimilation, performance outside the prescribed region/time of interest, forecasting, and trend analysis. Examples of each approach from the literature are provided. A comprehensive list of ocean biological data assimilation and their applications of skill assessment, in both ecosystem/biogeochemical and fisheries efforts, is summarized.

  17. Methodological Developments in Geophysical Assimilation Modeling

    Science.gov (United States)

    Christakos, George

    2005-06-01

    This work presents recent methodological developments in geophysical assimilation research. We revisit the meaning of the term "solution" of a mathematical model representing a geophysical system, and we examine its operational formulations. We argue that an assimilation solution based on epistemic cognition (which assumes that the model describes incomplete knowledge about nature and focuses on conceptual mechanisms of scientific thinking) could lead to more realistic representations of the geophysical situation than a conventional ontologic assimilation solution (which assumes that the model describes nature as is and focuses on form manipulations). Conceptually, the two approaches are fundamentally different. Unlike the reasoning structure of conventional assimilation modeling that is based mainly on ad hoc technical schemes, the epistemic cognition approach is based on teleologic criteria and stochastic adaptation principles. In this way some key ideas are introduced that could open new areas of geophysical assimilation to detailed understanding in an integrated manner. A knowledge synthesis framework can provide the rational means for assimilating a variety of knowledge bases (general and site specific) that are relevant to the geophysical system of interest. Epistemic cognition-based assimilation techniques can produce a realistic representation of the geophysical system, provide a rigorous assessment of the uncertainty sources, and generate informative predictions across space-time. The mathematics of epistemic assimilation involves a powerful and versatile spatiotemporal random field theory that imposes no restriction on the shape of the probability distributions or the form of the predictors (non-Gaussian distributions, multiple-point statistics, and nonlinear models are automatically incorporated) and accounts rigorously for the uncertainty features of the geophysical system. In the epistemic cognition context the assimilation concept may be used to

  18. Dietary sodium deprivation evokes activation of brain regional neurons and down-regulation of angiotensin II type 1 receptor and angiotensin-convertion enzyme mRNA expression.

    Science.gov (United States)

    Lu, B; Yang, X J; Chen, K; Yang, D J; Yan, J Q

    2009-12-15

    Previous studies have indicated that the renin-angiotensin-aldosterone system (RAAS) is implicated in the induction of sodium appetite in rats and that different dietary sodium intakes influence the mRNA expression of central and peripheral RAAS components. To determine whether dietary sodium deprivation activates regional brain neurons related to sodium appetite, and changes their gene expression of RAAS components of rats, the present study examined the c-Fos expression after chronic exposure to low sodium diet, and determined the relationship between plasma and brain angiotensin I (ANG I), angiotensin II (ANG II) and aldosterone (ALD) levels and the sodium ingestive behavior variations, as well as the effects of prolonged dietary sodium deprivation on ANG II type 1 (AT1) and ANG II type 2 (AT2) receptors and angiotensin-convertion enzyme (ACE) mRNA levels in the involved brain regions using the method of real-time polymerase chain reaction (PCR). Results showed that the Fos immunoreactivity (Fos-ir) expression in forebrain areas such as subfornical organ (SFO), paraventricular hypothalamic nuclei (PVN), supraoptic nucleus (SON) and organum vasculosum laminae terminalis (OVLT) all increased significantly and that the levels of ANG I, ANG II and ALD also increased in plasma and forebrain in rats fed with low sodium diet. In contrast, AT1, ACE mRNA in PVN, SON and OVLT decreased significantly in dietary sodium depleted rats, while AT2 mRNA expression did not change in the examined areas. These results suggest that many brain areas are activated by increased levels of plasma and/or brain ANG II and ALD, which underlies the elevated preference for hypertonic salt solution after prolonged exposure to low sodium diet, and that the regional AT1 and ACE mRNA are down-regulated after dietary sodium deprivation, which may be mediated by increased ANG II in plasma and/or brain tissue.

  19. Quercetin treatment regulates the Na+,K+-ATPase activity, peripheral cholinergic enzymes, and oxidative stress in a rat model of demyelination.

    Science.gov (United States)

    Carvalho, Fabiano B; Gutierres, Jessié M; Beckmann, Diego; Santos, Rosmarini P; Thomé, Gustavo R; Baldissarelli, Jucimara; Stefanello, Naiara; Andrades, Amanda; Aiello, Graciane; Ripplinger, Angel; Lucio, Bruna M; Ineu, Rafael; Mazzanti, Alexandre; Morsch, Vera; Schetinger, Maria Rosa; Andrade, Cinthia M

    2018-07-01

    Quercetin is reported to exert a plethora of health benefits through many different mechanisms of action. This versatility and presence in the human diet has attracted the attention of the scientific community, resulting in a huge output of in vitro and in vivo (preclinical) studies. Therefore, we hypothesized that quercetin can protect Na + ,K + -ATPase activity in the central nervous system, reestablish the peripheral cholinesterases activities, and reduce oxidative stress during demyelination events in rats. In line with this expectation, our study aims to find out how quercetin acts on the Na + ,K + -ATPase activity in the central nervous system, peripheral cholinesterases, and stress oxidative markers in an experimental model of demyelinating disease. Wistar rats were divided into 4 groups: vehicle, quercetin, ethidium bromide (EB), and EB plus quercetin groups. The animals were treated once a day with vehicle (ethanol 20%) or quercetin 50 mg/kg for 7 (demyelination phase, by gavage) or 21 days (remyelination phase) after EB (0.1%, 10 μL) injection (intrapontine).The encephalon was removed, and the pons, hypothalamus, cerebral cortex, hippocampus, striatum, and cerebellum were dissected to verify the Na + ,K + -ATPase activity. Our results showed that quercetin protected against reduction in Na + ,K + -ATPase in the pons and cerebellum in the demyelination phase, and it increased the activity of this enzyme in the remyelination phase. During the demyelination, quercetin promoted the increase in acetylcholinesterase activity in whole blood and lymphocytes induced by EB, and it reduced the increase in acetylcholinesterase activity in lymphocytes in the remyelination phase. On day 7, EB increased the superoxide dismutase and decreased catalase activities, as well as increased the thiobarbituric acid-reactive substance levels. Taken together, these results indicated that quercetin regulates the Na + ,K + -ATPase activity, affects the alterations of redox state

  20. The Translesion Polymerase Pol η Is Required for Efficient Epstein-Barr Virus Infectivity and Is Regulated by the Viral Deubiquitinating Enzyme BPLF1.

    Science.gov (United States)

    Dyson, Ossie F; Pagano, Joseph S; Whitehurst, Christopher B

    2017-10-01

    lymphomas that develop in organ transplant recipients. Cellular DNA damage is a major determinant in the establishment of oncogenic processes and is well studied, but there are few studies of endogenous repair of viral DNA. This work evaluates how EBV's BPLF1 protein and its conserved deubiquitinating activity regulate the cellular DNA repair enzyme polymerase eta and recruit it to potential sites of viral damage and replication, resulting in enhanced production of infectious virus. These findings help to establish how EBV enlists and manipulates cellular DNA repair factors during the viral lytic cycle, contributing to efficient infectious virion production. Copyright © 2017 American Society for Microbiology.

  1. Data Assimilation with Optimal Maps

    Science.gov (United States)

    El Moselhy, T.; Marzouk, Y.

    2012-12-01

    Tarek El Moselhy and Youssef Marzouk Massachusetts Institute of Technology We present a new approach to Bayesian inference that entirely avoids Markov chain simulation and sequential importance resampling, by constructing a map that pushes forward the prior measure to the posterior measure. Existence and uniqueness of a suitable measure-preserving map is established by formulating the problem in the context of optimal transport theory. The map is written as a multivariate polynomial expansion and computed efficiently through the solution of a stochastic optimization problem. While our previous work [1] focused on static Bayesian inference problems, we now extend the map-based approach to sequential data assimilation, i.e., nonlinear filtering and smoothing. One scheme involves pushing forward a fixed reference measure to each filtered state distribution, while an alternative scheme computes maps that push forward the filtering distribution from one stage to the other. We compare the performance of these schemes and extend the former to problems of smoothing, using a map implementation of the forward-backward smoothing formula. Advantages of a map-based representation of the filtering and smoothing distributions include analytical expressions for posterior moments and the ability to generate arbitrary numbers of independent uniformly-weighted posterior samples without additional evaluations of the dynamical model. Perhaps the main advantage, however, is that the map approach inherently avoids issues of sample impoverishment, since it explicitly represents the posterior as the pushforward of a reference measure, rather than with a particular set of samples. The computational complexity of our algorithm is comparable to state-of-the-art particle filters. Moreover, the accuracy of the approach is controlled via the convergence criterion of the underlying optimization problem. We demonstrate the efficiency and accuracy of the map approach via data assimilation in

  2. Understanding Strategy of Nitrate and Urea Assimilation in a Chinese Strain of Aureococcus anophagefferens through RNA-Seq Analysis

    Science.gov (United States)

    Dong, Hong-Po; Huang, Kai-Xuan; Wang, Hua-Long; Lu, Song-Hui; Cen, Jing-Yi; Dong, Yue-Lei

    2014-01-01

    Aureococcus anophagefferens is a harmful alga that dominates plankton communities during brown tides in North America, Africa, and Asia. Here, RNA-seq technology was used to profile the transcriptome of a Chinese strain of A. anophagefferens that was grown on urea, nitrate, and a mixture of urea and nitrate, and that was under N-replete, limited and recovery conditions to understand the molecular mechanisms that underlie nitrate and urea utilization. The number of differentially expressed genes between urea-grown and mixture N-grown cells were much less than those between urea-grown and nitrate-grown cells. Compared with nitrate-grown cells, mixture N-grown cells contained much lower levels of transcripts encoding proteins that are involved in nitrate transport and assimilation. Together with profiles of nutrient changes in media, these results suggest that A. anophagefferens primarily feeds on urea instead of nitrate when urea and nitrate co-exist. Furthermore, we noted that transcripts upregulated by nitrate and N-limitation included those encoding proteins involved in amino acid and nucleotide transport, degradation of amides and cyanates, and nitrate assimilation pathway. The data suggest that A. anophagefferens possesses an ability to utilize a variety of dissolved organic nitrogen. Moreover, transcripts for synthesis of proteins, glutamate-derived amino acids, spermines and sterols were upregulated by urea. Transcripts encoding key enzymes that are involved in the ornithine-urea and TCA cycles were differentially regulated by urea and nitrogen concentration, which suggests that the OUC may be linked to the TCA cycle and involved in reallocation of intracellular carbon and nitrogen. These genes regulated by urea may be crucial for the rapid proliferation of A. anophagefferens when urea is provided as the N source. PMID:25338000

  3. Genotypic variation in sulphur assimilation and metabolism of onion (Allium cepa L.). II: Characterisation of ATP sulphurylase activity

    KAUST Repository

    Thomas, Ludivine

    2011-06-01

    To investigate the regulation of sulphur (S)-assimilation in onion further at the biochemical level, the pungent cultivar W202A and the milder cultivar Texas Grano 438 PVP (TG) have been grown in S-sufficient (S +; 4 meq S -1) or S-deficient (S -; 0.1 meq S -1) growth conditions, and tissues excised at the seedling stage (pre-bulbing; ca. 10-weeks-old) and at the mature stage (bulbing; ca. 16-weeks-old). S-supply negatively influenced adenosine-5′-phosphosulphate (APS) reductase (APR) enzyme activity in both cultivars at bulbing only, and a higher abundance of APR was observed in both cultivars at bulbing in response to low S-supply. In contrast, S-supply significantly influenced ATP sulphurylase (ATPS) activity in leaf tissues of W202A only, and only at bulbing, while an increase in abundance in response to high S-supply was observed for both cultivars at bulbing. To investigate the regulation of the ATPS enzyme activity and accumulation further, activity was shown to decrease significantly in roots at bulbing in the S-deficient treatment in both cultivars, a difference that was only supported by western analyses in W202A. Phylogenetic analysis revealed that AcATPS1 groups in a broad monocot clade with the closest sequences identified in Sorghum bicolour, Zea mays and Oryza sativa, but with some support for a divergence of AcATPS1. Detection of ATPS in leaf extracts after two dimensional gel electrophoresis (2-DE) revealed that the protein may undergo post-translational modification with a differential pattern of ATPS accumulation detected in both cultivars over the developmental progression from the seedling to the bulbing stage. Treatment of leaf extracts of W202A to dephosphorylate proteins resulted in the loss of immuno-recognised ATPS spots after 2-DE separation, although enzyme activity was not influenced. These results are discussed in terms of the tiers of control that operate at the biochemical level in the reductive S-assimilation pathway in a S

  4. Regulating and Combating Underground Banking

    NARCIS (Netherlands)

    Borgers, M.J.

    2009-01-01

    In combating and regulating underground banking, a choice can be made of roughly two models, the risk model and the assimilation model. The risk model comes down to a complete prohibition of underground banking combined with an active investigation and prosecution policy. In the assimilation model,

  5. The importance of peers: assimilation patterns among second-generation Turkish immigrants in Western Europe

    NARCIS (Netherlands)

    Ali, S.; Fokkema, C.M.

    2011-01-01

    The two dominant approaches to immigrant assimilation, segmented assimilation and "new" assimilation theories, have been successful at reporting and analyzing between-group differences in assimilation patterns. However, studies of assimilation generally do not address differences at the individual

  6. Assimilative and non-assimilative color spreading in the watercolor configuration

    Directory of Open Access Journals (Sweden)

    Eiji eKimura

    2014-09-01

    Full Text Available A colored line flanking a darker contour will appear to spread its color onto an area enclosed by the line (watercolor effect. The watercolor effect has been characterized as an assimilative effect, but non-assimilative color spreading has also been demonstrated in the same spatial configuration; e.g., when a black inner contour (IC is paired with a blue outer contour (OC, yellow color spreading can be observed. To elucidate visual mechanisms underlying these different color spreading effects, this study investigated the effects of luminance ratio between the double contours on the induced color by systematically manipulating the IC and OC luminances (Experiment 1 as well as the background luminance (Experiment 2. The results showed that the luminance conditions suitable for assimilative and non-assimilative color spreading were nearly opposite. When the Weber contrast of the IC to the background luminances (IC contrast was smaller than that of the OC (OC contrast, the induced color became similar to the IC color (assimilative spreading. In contrast, when the OC contrast was smaller than or equal to the IC contrast, the induced color became yellow (non-assimilative spreading. Extending these findings, Experiment 3 showed that bilateral color spreading, e.g., assimilative spreading on one side and non-assimilative spreading on the other side, can also be observed in the watercolor configuration. These results suggest that the assimilative and non-assimilative spreading were mediated by different visual mechanisms. The properties of the assimilative spreading are consistent with the model proposed to account for neon color spreading [Grossberg, S. & Mingolla, E. (1985 Percept. Psychophys., 38, 141-171] and extended for the watercolor effect [Pinna, B., & Grossberg, S. (2005 J. Opt. Soc. Am. A, 22, 2207-2221]. However, the present results suggest that additional mechanisms are needed to account for the non-assimilative color spreading.

  7. Assimilative and non-assimilative color spreading in the watercolor configuration.

    Science.gov (United States)

    Kimura, Eiji; Kuroki, Mikako

    2014-01-01

    A colored line flanking a darker contour will appear to spread its color onto an area enclosed by the line (watercolor effect). The watercolor effect has been characterized as an assimilative effect, but non-assimilative color spreading has also been demonstrated in the same spatial configuration; e.g., when a black inner contour (IC) is paired with a blue outer contour (OC), yellow color spreading can be observed. To elucidate visual mechanisms underlying these different color spreading effects, this study investigated the effects of luminance ratio between the double contours on the induced color by systematically manipulating the IC and the OC luminance (Experiment 1) as well as the background luminance (Experiment 2). The results showed that the luminance conditions suitable for assimilative and non-assimilative color spreading were nearly opposite. When the Weber contrast of the IC to the background luminance (IC contrast) was smaller in size than that of the OC (OC contrast), the induced color became similar to the IC color (assimilative spreading). In contrast, when the OC contrast was smaller than or equal to the IC contrast, the induced color became yellow (non-assimilative spreading). Extending these findings, Experiment 3 showed that bilateral color spreading, i.e., assimilative spreading on one side and non-assimilative spreading on the other side, can also be observed in the watercolor configuration. These results suggest that the assimilative and the non-assimilative spreading were mediated by different visual mechanisms. The properties of the assimilative spreading are consistent with the model proposed to account for neon color spreading (Grossberg and Mingolla, 1985) and extended for the watercolor effect (Pinna and Grossberg, 2005). However, the present results suggest that additional mechanisms are needed to account for the non-assimilative color spreading.

  8. Error Covariance Estimation of Mesoscale Data Assimilation

    National Research Council Canada - National Science Library

    Xu, Qin

    2005-01-01

    The goal of this project is to explore and develop new methods of error covariance estimation that will provide necessary statistical descriptions of prediction and observation errors for mesoscale data assimilation...

  9. ERP ASSIMILATION: AN END-USER APPROACH

    Directory of Open Access Journals (Sweden)

    Hurbean Luminita

    2013-07-01

    The paper discusses the ERP adoption based on the IT assimilation theory. The ERP lifecycle is associated with the IT assimilation steps. We propose a distribution of these steps along the lifecycle. Derived from the findings in the reviewed literature we will focus the cultural factors, in particular those related to the end-users (determined as a major impact factor in our previous study: Negovan et al., 2011. Our empirical study is centred on the end-users perspective and it tries to determine if and how their behaviour affects the achievement of the ERP assimilation steps. The paper reasons that organizations that understand the IT assimilation steps correlated to the ERP implementation critical factors are more likely to implement and use ERP successfully.

  10. Comparison between assimilated and non-assimilated experiments of the MACCii global reanalysis near surface ozone

    Science.gov (United States)

    Tsikerdekis, Athanasios; Katragou, Eleni; Zanis, Prodromos; Melas, Dimitrios; Eskes, Henk; Flemming, Johannes; Huijnen, Vincent; Inness, Antje; Kapsomenakis, Ioannis; Schultz, Martin; Stein, Olaf; Zerefos, Christos

    2014-05-01

    In this work we evaluate near surface ozone concentrations of the MACCii global reanalysis using measurements from the EMEP and AIRBASE database. The eight-year long reanalysis of atmospheric composition data covering the period 2003-2010 was constructed as part of the FP7-funded Monitoring Atmospheric Composition and Climate project by assimilating satellite data into a global model and data assimilation system (Inness et al., 2013). The study mainly focuses in the differences between the assimilated and the non-assimilated experiments and aims to identify and quantify any improvements achieved by adding data assimilation to the system. Results are analyzed in eight European sub-regions and region-specific Taylor plots illustrate the evaluation and the overall predictive skill of each experiment. The diurnal and annual cycles of near surface ozone are evaluated for both experiments. Furthermore ozone exposure indices for crop growth (AOT40), human health (SOMO35) and the number of days that 8-hour ozone averages exceeded 60ppb and 90ppb have been calculated for each station based on both observed and simulated data. Results indicate mostly improvement of the assimilated experiment with respect to the high near surface ozone concentrations, the diurnal cycle and range and the bias in comparison to the non-assimilated experiment. The limitations of the comparison between assimilated and non-assimilated experiments for near surface ozone are also discussed.

  11. Assimilation of Baba and Nyonya in Malaysia

    OpenAIRE

    Razaleigh Muhamat Kawangit

    2015-01-01

    This research set outs to explore the exact level of the social aspect of assimilation between Baba and Nyonya and their Malay counterparts in Malaysia. It was sure that assimilation in social aspect is a dilemma which Baba and Nyonya face when they interact with Malays as a dominant ethnic group. It suggests that when the process of interaction, their behavior changes in line with the identity of the Malays. This is because the majority influenced the minority in the Malaysian context. Whils...

  12. Computational methods for data evaluation and assimilation

    CERN Document Server

    Cacuci, Dan Gabriel

    2013-01-01

    Data evaluation and data combination require the use of a wide range of probability theory concepts and tools, from deductive statistics mainly concerning frequencies and sample tallies to inductive inference for assimilating non-frequency data and a priori knowledge. Computational Methods for Data Evaluation and Assimilation presents interdisciplinary methods for integrating experimental and computational information. This self-contained book shows how the methods can be applied in many scientific and engineering areas. After presenting the fundamentals underlying the evaluation of experiment

  13. Endogenous circadian regulation of carbon dioxide exchange in terrestrial ecosystems

    Science.gov (United States)

    Victor Resco de Dios; Michael L. Goulden; Kiona Ogle; Andrew D. Richardson; David Y. Hollinger; Eric A. Davidson; Josu G. Alday; Greg A. Barron-Gafford; Arnaud Carrara; Andrew S. Kowalski; Walt C. Oechel; Borja R. Reverter; Russell L. Scott; Ruth K. Varner; Ruben Diaz-Sierra; Jose M. Moreno

    2012-01-01

    It is often assumed that daytime patterns of ecosystem carbon assimilation are mostly driven by direct physiological responses to exogenous environmental cues. Under limited environmental variability, little variation in carbon assimilation should thus be expected unless endogenous plant controls on carbon assimilation, which regulate photosynthesis in time, are active...

  14. Temporal Reference, Attentional Modulation, and Crossmodal Assimilation

    Directory of Open Access Journals (Sweden)

    Yingqi Wan

    2018-06-01

    Full Text Available Crossmodal assimilation effect refers to the prominent phenomenon by which ensemble mean extracted from a sequence of task-irrelevant distractor events, such as auditory intervals, assimilates/biases the perception (such as visual interval of the subsequent task-relevant target events in another sensory modality. In current experiments, using visual Ternus display, we examined the roles of temporal reference, materialized as the time information accumulated before the onset of target event, as well as the attentional modulation in crossmodal temporal interaction. Specifically, we examined how the global time interval, the mean auditory inter-intervals and the last interval in the auditory sequence assimilate and bias the subsequent percept of visual Ternus motion (element motion vs. group motion. We demonstrated that both the ensemble (geometric mean and the last interval in the auditory sequence contribute to bias the percept of visual motion. Longer mean (or last interval elicited more reports of group motion, whereas the shorter mean (or last auditory intervals gave rise to more dominant percept of element motion. Importantly, observers have shown dynamic adaptation to the temporal reference of crossmodal assimilation: when the target visual Ternus stimuli were separated by a long gap interval after the preceding sound sequence, the assimilation effect by ensemble mean was reduced. Our findings suggested that crossmodal assimilation relies on a suitable temporal reference on adaptation level, and revealed a general temporal perceptual grouping principle underlying complex audio-visual interactions in everyday dynamic situations.

  15. A simple lightning assimilation technique for improving ...

    Science.gov (United States)

    Convective rainfall is often a large source of error in retrospective modeling applications. In particular, positive rainfall biases commonly exist during summer months due to overactive convective parameterizations. In this study, lightning assimilation was applied in the Kain-Fritsch (KF) convective scheme to improve retrospective simulations using the Weather Research and Forecasting (WRF) model. The assimilation method has a straightforward approach: force KF deep convection where lightning is observed and, optionally, suppress deep convection where lightning is absent. WRF simulations were made with and without lightning assimilation over the continental United States for July 2012, July 2013, and January 2013. The simulations were evaluated against NCEP stage-IV precipitation data and MADIS near-surface meteorological observations. In general, the use of lightning assimilation considerably improves the simulation of summertime rainfall. For example, the July 2012 monthly averaged bias of 6 h accumulated rainfall is reduced from 0.54 to 0.07 mm and the spatial correlation is increased from 0.21 to 0.43 when lightning assimilation is used. Statistical measures of near-surface meteorological variables also are improved. Consistent improvements also are seen for the July 2013 case. These results suggest that this lightning assimilation technique has the potential to substantially improve simulation of warm-season rainfall in retrospective WRF applications. The

  16. Data Assimilation: Making Sense of Earth Observation

    Directory of Open Access Journals (Sweden)

    William Albert Lahoz

    2014-05-01

    Full Text Available Climate change, air quality and environmental degradation are important societal challenges for the 21st Century. These challenges require an intelligent response from society, which in turn requires access to information about the Earth System. This information comes from observations and prior knowledge, the latter typically embodied in a model describing relationships between variables of the Earth System. Data assimilation provides an objective methodology to combine observational and model information to provide an estimate of the most likely state and its uncertainty for the whole Earth System. This approach adds value to the observations – by filling in the spatio-temporal gaps in observations; and to the model – by constraining it with the observations. In this review paper we motivate data assimilation as a methodology to fill in the gaps in observational information; illustrate the data assimilation approach with examples that span a broad range of features of the Earth System (atmosphere, including chemistry; ocean; land surface; and discuss the outlook for data assimilation, including the novel application of data assimilation ideas to observational information obtained using Citizen Science. Ultimately, a strong motivation of data assimilation is the many benefits it provides to users. These include: providing the initial state for weather and air quality forecasts; providing analyses and reanalyses for studying the Earth System; evaluating observations, instruments and models; assessing the relative value of elements of the Global Observing System (GOS; and assessing the added value of future additions to the GOS.

  17. Matrix Metalloproteinase Enzyme Family

    Directory of Open Access Journals (Sweden)

    Ozlem Goruroglu Ozturk

    2013-04-01

    Full Text Available Matrix metalloproteinases play an important role in many biological processes such as embriogenesis, tissue remodeling, wound healing, and angiogenesis, and in some pathological conditions such as atherosclerosis, arthritis and cancer. Currently, 24 genes have been identified in humans that encode different groups of matrix metalloproteinase enzymes. This review discuss the members of the matrix metalloproteinase family and their substrate specificity, structure, function and the regulation of their enzyme activity by tissue inhibitors. [Archives Medical Review Journal 2013; 22(2.000: 209-220

  18. Measuring the Enzyme Activity of Arabidopsis Deubiquitylating Enzymes.

    Science.gov (United States)

    Kalinowska, Kamila; Nagel, Marie-Kristin; Isono, Erika

    2016-01-01

    Deubiquitylating enzymes, or DUBs, are important regulators of ubiquitin homeostasis and substrate stability, though the molecular mechanisms of most of the DUBs in plants are not yet understood. As different ubiquitin chain types are implicated in different biological pathways, it is important to analyze the enzyme characteristic for studying a DUB. Quantitative analysis of DUB activity is also important to determine enzyme kinetics and the influence of DUB binding proteins on the enzyme activity. Here, we show methods to analyze DUB activity using immunodetection, Coomassie Brilliant Blue staining, and fluorescence measurement that can be useful for understanding the basic characteristic of DUBs.

  19. Human 3α-hydroxysteroid dehydrogenase type 3: structural clues of 5α-DHT reverse binding and enzyme down-regulation decreasing MCF7 cell growth.

    Science.gov (United States)

    Zhang, Bo; Hu, Xiao-Jian; Wang, Xiao-Qiang; Thériault, Jean-François; Zhu, Dao-Wei; Shang, Peng; Labrie, Fernand; Lin, Sheng-Xiang

    2016-04-15

    Human 3α-HSD3 (3α-hydroxysteroid dehydrogenase type 3) plays an essential role in the inactivation of the most potent androgen 5α-DHT (5α-dihydrotestosterone). The present study attempts to obtain the important structure of 3α-HSD3 in complex with 5α-DHT and to investigate the role of 3α-HSD3 in breast cancer cells. We report the crystal structure of human 3α-HSD3·NADP(+)·A-dione (5α-androstane-3,17-dione)/epi-ADT (epiandrosterone) complex, which was obtained by co-crystallization with 5α-DHT in the presence of NADP(+) Although 5α-DHT was introduced during the crystallization, oxidoreduction of 5α-DHT occurred. The locations of A-dione and epi-ADT were identified in the steroid-binding sites of two 3α-HSD3 molecules per crystal asymmetric unit. An overlay showed that A-dione and epi-ADT were oriented upside-down and flipped relative to each other, providing structural clues for 5α-DHT reverse binding in the enzyme with the generation of different products. Moreover, we report the crystal structure of the 3α-HSD3·NADP(+)·4-dione (4-androstene-3,17-dione) complex. When a specific siRNA (100 nM) was used to suppress 3α-HSD3 expression without interfering with 3α-HSD4, which shares a highly homologous active site, the 5α-DHT concentration increased, whereas MCF7 cell growth was suppressed. The present study provides structural clues for 5α-DHT reverse binding within 3α-HSD3, and demonstrates for the first time that down-regulation of 3α-HSD3 decreases MCF7 breast cancer cell growth. © 2016 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  20. Tomato UDP-Glucose Sterol Glycosyltransferases: A Family of Developmental and Stress Regulated Genes that Encode Cytosolic and Membrane-Associated Forms of the Enzyme

    Directory of Open Access Journals (Sweden)

    Karla Ramirez-Estrada

    2017-06-01

    Full Text Available Sterol glycosyltransferases (SGTs catalyze the glycosylation of the free hydroxyl group at C-3 position of sterols to produce sterol glycosides. Glycosylated sterols and free sterols are primarily located in cell membranes where in combination with other membrane-bound lipids play a key role in modulating their properties and functioning. In contrast to most plant species, those of the genus Solanum contain very high levels of glycosylated sterols, which in the case of tomato may account for more than 85% of the total sterol content. In this study, we report the identification and functional characterization of the four members of the tomato (Solanum lycopersicum cv. Micro-Tom SGT gene family. Expression of recombinant SlSGT proteins in E. coli cells and N. benthamiana leaves demonstrated the ability of the four enzymes to glycosylate different sterol species including cholesterol, brassicasterol, campesterol, stigmasterol, and β-sitosterol, which is consistent with the occurrence in their primary structure of the putative steroid-binding domain found in steroid UDP-glucuronosyltransferases and the UDP-sugar binding domain characteristic for a superfamily of nucleoside diphosphosugar glycosyltransferases. Subcellular localization studies based on fluorescence recovery after photobleaching and cell fractionation analyses revealed that the four tomato SGTs, like the Arabidopsis SGTs UGT80A2 and UGT80B1, localize into the cytosol and the PM, although there are clear differences in their relative distribution between these two cell fractions. The SlSGT genes have specialized but still largely overlapping expression patterns in different organs of tomato plants and throughout the different stages of fruit development and ripening. Moreover, they are differentially regulated in response to biotic and abiotic stress conditions. SlSGT4 expression increases markedly in response to osmotic, salt, and cold stress, as well as upon treatment with abscisic

  1. Selenium uptake, translocation, assimilation and metabolic fate in plants.

    Science.gov (United States)

    Sors, T G; Ellis, D R; Salt, D E

    2005-12-01

    The chemical and physical resemblance between selenium (Se) and sulfur (S) establishes that both these elements share common metabolic pathways in plants. The presence of isologous Se and S compounds indicates that these elements compete in biochemical processes that affect uptake, translocation and assimilation throughout plant development. Yet, minor but crucial differences in reactivity and other metabolic interactions infer that some biochemical processes involving Se may be excluded from those relating to S. This review examines the current understanding of physiological and biochemical relationships between S and Se metabolism by highlighting their similarities and differences in relation to uptake, transport and assimilation pathways as observed in Se hyperaccumulator and non-accumulator plant species. The exploitation of genetic resources used in bioengineering strategies of plants is illuminating the function of sulfate transporters and key enzymes of the S assimilatory pathway in relation to Se accumulation and final metabolic fate. These strategies are providing the basic framework by which to resolve questions relating to the essentiality of Se in plants and the mechanisms utilized by Se hyperaccumulators to circumvent toxicity. In addition, such approaches may assist in the future application of genetically engineered Se accumulating plants for environmental renewal and human health objectives.

  2. The effect of acetylcholine, LatA and FAA on phloem assimilates translocation of Raphanus sativus L

    International Nuclear Information System (INIS)

    Yang Chongjun; Zhang Ping

    2005-01-01

    The petiole phloem of Raphanus sativus L. is treated with the medicaments of acetylcholine (Ach, the expansionist material of protoplasm), latrunculin A (LatA, the dissolubility of microfilament) and FAA (the regularization of phloem). The effects of treatments are measured by the accumulated content of dissoluble sugar and starch in the leaves, and 14 C-labelled assimilates. The regulating role of three medicaments on the translocation of assimilates in the phloem of Raphanus sativus L are investigated. The results indicate that low Ach improves assimilates translocation while LatA and FAA inhibit it in petiole phloem of Raphanus sativus L.. (authors)

  3. Assimilation and subcellular partitioning of elements by grass shrimp collected along an impact gradient

    International Nuclear Information System (INIS)

    Seebaugh, David R.; Wallace, William G.

    2009-01-01

    Chronic exposure to polluted field conditions can impact metal bioavailability in prey and may influence metal transfer to predators. The present study investigated the assimilation of Cd, Hg and organic carbon by grass shrimp Palaemonetes pugio, collected along an impact gradient within the New York/New Jersey Harbor Estuary. Adult shrimp were collected from five Staten Island, New York study sites, fed 109 Cd- or 203 Hg-labeled amphipods or 14 C-labeled meals and analyzed for assimilation efficiencies (AE). Subsamples of amphipods and shrimp were subjected to subcellular fractionation to isolate metal associated with a compartment presumed to contain trophically available metal (TAM) (metal associated with heat-stable proteins [HSP - e.g., metallothionein-like proteins], heat-denatured proteins [HDP - e.g., enzymes] and organelles [ORG]). TAM- 109 Cd% and TAM- 203 Hg% in radiolabeled amphipods were ∼64% and ∼73%, respectively. Gradients in AE- 109 Cd% (∼54% to ∼75%) and AE- 203 Hg% (∼61% to ∼78%) were observed for grass shrimp, with the highest values exhibited by shrimp collected from sites within the heavily polluted Arthur Kill complex. Population differences in AE- 14 C% were not observed. Assimilated 109 Cd% partitioned to the TAM compartment in grass shrimp varied between ∼67% and ∼75%. 109 Cd bound to HSP in shrimp varied between ∼15% and ∼47%, while 109 Cd associated with metal-sensitive HDP was ∼17% to ∼44%. Percentages of assimilated 109 Cd bound to ORG were constant at ∼10%. Assimilated 203 Hg% associated with TAM in grass shrimp did not exhibit significant variation. Percentages of assimilated 203 Hg bound to HDP (∼47%) and ORG (∼11%) did not vary among populations and partitioning of 203 Hg to HSP was not observed. Using a simplified biokinetic model of metal accumulation from the diet, it is estimated that site-specific variability in Cd AE by shrimp and tissue Cd burdens in field-collected prey (polychaetes Nereis spp

  4. Properties of latent and thiol-activated rat hepatic 3-hydroxy-3-methylglutaryl-coenzyme A reductase and regulation of enzyme activity.

    Science.gov (United States)

    Dotan, I; Shechter, I

    1983-10-15

    The effect of the thiols glutathione (GSH), dithiothreitol (DTT), and dithioerythritol (DTE) on the conversion of an inactive, latent form (El) of rat liver 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMG-CoA reductase, EC 1.1.1.34) to a catalyticaly active form (Ea) is examined. Latent hepatic microsomal HMG-CoA reductase is activated to a similar degree of activation by DTT and DTE and to a lower extent by GSH. All three thiols affect both Km and Vmax values of the enzyme toward HMG-CoA and NADPH. Studies of the effect of DTT on the affinity binding of HMG-CoA reductase to agarose-hexane-HMG-CoA (AG-HMG-CoA) resin shows that thiols are necessary for the binding of the enzyme to the resin. Removal of DTT from AG-HMG-CoA-bound soluble Ea (active enzyme) does not cause dissociation of the enzyme from the resin at low salt concentrations. Substitution of DTT by NADPH does not promote binding of soluble El (latent enzyme) to AG-HMG-CoA. The enzymatic activity of Ea in the presence of DTT and GSH indicates that these thiols compete for the same binding site on the enzyme. Diethylene glycol disulfide (ESSE) and glutathione disulfide (GSSG) inhibit the activity of Ea. ESSE is more effective for the inhibition of Ea than GSSG, causing a higher degree of maximal inhibition and affecting the enzymatic activity at lower concentrations. A method is described for the rapid conversion of soluble purified Ea to El using gel-filtration chromatography on Bio-Gel P-4 columns. These combined results point to the importance of the thiol/disulfide ratio for the modulation of hepatic HMG-CoA reductase activity.

  5. Random-walk enzymes

    Science.gov (United States)

    Mak, Chi H.; Pham, Phuong; Afif, Samir A.; Goodman, Myron F.

    2015-09-01

    Enzymes that rely on random walk to search for substrate targets in a heterogeneously dispersed medium can leave behind complex spatial profiles of their catalyzed conversions. The catalytic signatures of these random-walk enzymes are the result of two coupled stochastic processes: scanning and catalysis. Here we develop analytical models to understand the conversion profiles produced by these enzymes, comparing an intrusive model, in which scanning and catalysis are tightly coupled, against a loosely coupled passive model. Diagrammatic theory and path-integral solutions of these models revealed clearly distinct predictions. Comparison to experimental data from catalyzed deaminations deposited on single-stranded DNA by the enzyme activation-induced deoxycytidine deaminase (AID) demonstrates that catalysis and diffusion are strongly intertwined, where the chemical conversions give rise to new stochastic trajectories that were absent if the substrate DNA was homogeneous. The C →U deamination profiles in both analytical predictions and experiments exhibit a strong contextual dependence, where the conversion rate of each target site is strongly contingent on the identities of other surrounding targets, with the intrusive model showing an excellent fit to the data. These methods can be applied to deduce sequence-dependent catalytic signatures of other DNA modification enzymes, with potential applications to cancer, gene regulation, and epigenetics.

  6. Closeout technical report for DOE award number DE-FG02-97ER62332 [Nitrogen budget under elevated CO{sub 2} levels: regulation by absorption and assimilation

    Energy Technology Data Exchange (ETDEWEB)

    BassiriRad, Hormoz; Gutschick, Vincent

    2001-10-01

    This entire project was conducted between 1995 and 1999, during which two postdocs and numerous undergraduate students received training in research. Furthermore, the funds from this grant contributed either totally or partially to the publication of 14 refereed journal articles. The focus of this research was to investigate plant nitrogen budget under elevated CO{sub 2} concentration. Of particular interest were the following: (1) Does elevated CO{sub 2} increase root carbohydrate availability? (2) Does such an enhancement increase kinetics of root nitrogen acquisition? (3) Does the effect on kinetics differ between NH{sub 4}{sup +} and NO{sub 3}{sup -}? (4) If there are interspecific differences in (1)-(3), could those variations lead to changes in community composition? This report shows that, although root carbohydrate availability often increases in response to elevated CO{sub 2}, such an increase is neither necessary nor directly related to changes in root N uptake kinetics . The data also show that, depending on species, the effects of elevated CO{sub 2} on root nitrogen uptake kinetics ranges from down regulation to no changes to up regulation. Furthermore, the effects on NH{sub 4}{sup +} are not always similar to the effects on NO{sub 3}{sup -}. Perhaps the most critical finding is the fact that in many instances a change in root N uptake kinetics alone does not provide a reliable prediction of plant N acquisition in response to elevated CO{sub 2}. It is shown that a better examination of whether plant N uptake responds to CO{sub 2} level and whether such a response can be scaled up to community level processes would require integration of knowledge of other root system characteristics. For example, it is well established that mycorrhizal fungi are important regulators of plant N uptake. The data suggest that, while elevated CO{sub 2} affects root N uptake capacity, this effect is highly dependent on the type and level of the mycorrhizal infection. Another

  7. Coupled assimilation for an intermediated coupled ENSO prediction model

    Science.gov (United States)

    Zheng, Fei; Zhu, Jiang

    2010-10-01

    The value of coupled assimilation is discussed using an intermediate coupled model in which the wind stress is the only atmospheric state which is slavery to model sea surface temperature (SST). In the coupled assimilation analysis, based on the coupled wind-ocean state covariance calculated from the coupled state ensemble, the ocean state is adjusted by assimilating wind data using the ensemble Kalman filter. As revealed by a series of assimilation experiments using simulated observations, the coupled assimilation of wind observations yields better results than the assimilation of SST observations. Specifically, the coupled assimilation of wind observations can help to improve the accuracy of the surface and subsurface currents because the correlation between the wind and ocean currents is stronger than that between SST and ocean currents in the equatorial Pacific. Thus, the coupled assimilation of wind data can decrease the initial condition errors in the surface/subsurface currents that can significantly contribute to SST forecast errors. The value of the coupled assimilation of wind observations is further demonstrated by comparing the prediction skills of three 12-year (1997-2008) hindcast experiments initialized by the ocean-only assimilation scheme that assimilates SST observations, the coupled assimilation scheme that assimilates wind observations, and a nudging scheme that nudges the observed wind stress data, respectively. The prediction skills of two assimilation schemes are significantly better than those of the nudging scheme. The prediction skills of assimilating wind observations are better than assimilating SST observations. Assimilating wind observations for the 2007/2008 La Niña event triggers better predictions, while assimilating SST observations fails to provide an early warning for that event.

  8. Model Uncertainty Quantification Methods In Data Assimilation

    Science.gov (United States)

    Pathiraja, S. D.; Marshall, L. A.; Sharma, A.; Moradkhani, H.

    2017-12-01

    Data Assimilation involves utilising observations to improve model predictions in a seamless and statistically optimal fashion. Its applications are wide-ranging; from improving weather forecasts to tracking targets such as in the Apollo 11 mission. The use of Data Assimilation methods in high dimensional complex geophysical systems is an active area of research, where there exists many opportunities to enhance existing methodologies. One of the central challenges is in model uncertainty quantification; the outcome of any Data Assimilation study is strongly dependent on the uncertainties assigned to both observations and models. I focus on developing improved model uncertainty quantification methods that are applicable to challenging real world scenarios. These include developing methods for cases where the system states are only partially observed, where there is little prior knowledge of the model errors, and where the model error statistics are likely to be highly non-Gaussian.

  9. Data assimilation the ensemble Kalman filter

    CERN Document Server

    Evensen, Geir

    2007-01-01

    Data Assimilation comprehensively covers data assimilation and inverse methods, including both traditional state estimation and parameter estimation. This text and reference focuses on various popular data assimilation methods, such as weak and strong constraint variational methods and ensemble filters and smoothers. It is demonstrated how the different methods can be derived from a common theoretical basis, as well as how they differ and/or are related to each other, and which properties characterize them, using several examples. Rather than emphasize a particular discipline such as oceanography or meteorology, it presents the mathematical framework and derivations in a way which is common for any discipline where dynamics is merged with measurements. The mathematics level is modest, although it requires knowledge of basic spatial statistics, Bayesian statistics, and calculus of variations. Readers will also appreciate the introduction to the mathematical methods used and detailed derivations, which should b...

  10. Lipolytic enzymes LipA and LipB from Bacillus subtilis differ in regulation of gene expression, biochemical properties, and three-dimensional structure

    NARCIS (Netherlands)

    Eggert, Thorsten; Pouderoyen, Gertie van; Dijkstra, Bauke W.; Jaeger, Karl-Erich

    2001-01-01

    Bacillus subtilis secretes the lipolytic enzymes LipA and LipB. We show here that they are differentially expressed depending on the composition of the growth medium: LipA is produced in rich and in minimal medium, whereas LipB is present only in rich medium. A comparison of biochemical

  11. Scalable and balanced dynamic hybrid data assimilation

    Science.gov (United States)

    Kauranne, Tuomo; Amour, Idrissa; Gunia, Martin; Kallio, Kari; Lepistö, Ahti; Koponen, Sampsa

    2017-04-01

    Scalability of complex weather forecasting suites is dependent on the technical tools available for implementing highly parallel computational kernels, but to an equally large extent also on the dependence patterns between various components of the suite, such as observation processing, data assimilation and the forecast model. Scalability is a particular challenge for 4D variational assimilation methods that necessarily couple the forecast model into the assimilation process and subject this combination to an inherently serial quasi-Newton minimization process. Ensemble based assimilation methods are naturally more parallel, but large models force ensemble sizes to be small and that results in poor assimilation accuracy, somewhat akin to shooting with a shotgun in a million-dimensional space. The Variational Ensemble Kalman Filter (VEnKF) is an ensemble method that can attain the accuracy of 4D variational data assimilation with a small ensemble size. It achieves this by processing a Gaussian approximation of the current error covariance distribution, instead of a set of ensemble members, analogously to the Extended Kalman Filter EKF. Ensemble members are re-sampled every time a new set of observations is processed from a new approximation of that Gaussian distribution which makes VEnKF a dynamic assimilation method. After this a smoothing step is applied that turns VEnKF into a dynamic Variational Ensemble Kalman Smoother VEnKS. In this smoothing step, the same process is iterated with frequent re-sampling of the ensemble but now using past iterations as surrogate observations until the end result is a smooth and balanced model trajectory. In principle, VEnKF could suffer from similar scalability issues as 4D-Var. However, this can be avoided by isolating the forecast model completely from the minimization process by implementing the latter as a wrapper code whose only link to the model is calling for many parallel and totally independent model runs, all of them

  12. Carbon assimilation in Eucalyptus urophylla grown under high atmospheric CO2 concentrations: A proteomics perspective.

    Science.gov (United States)

    Santos, Bruna Marques Dos; Balbuena, Tiago Santana

    2017-01-06

    Photosynthetic organisms may be drastically affected by the future climate projections of a considerable increase in CO 2 concentrations. Growth under a high concentration of CO 2 could stimulate carbon assimilation-especially in C3-type plants. We used a proteomics approach to test the hypothesis of an increase in the abundance of the enzymes involved in carbon assimilation in Eucalyptus urophylla plants grown under conditions of high atmospheric CO 2 . Our strategy allowed the profiling of all Calvin-Benson cycle enzymes and associated protein species. Among the 816 isolated proteins, those involved in carbon fixation were found to be the most abundant ones. An increase in the abundance of six key enzymes out of the eleven core enzymes involved in carbon fixation was detected in plants grown at a high CO 2 concentration. Proteome changes were corroborated by the detection of a decrease in the stomatal aperture and in the vascular bundle area in Eucalyptus urophylla plantlets grown in an environment of high atmospheric CO 2 . Our proteomics approach indicates a positive metabolic response regarding carbon fixation in a CO 2 -enriched atmosphere. The slight but significant increase in the abundance of the Calvin enzymes suggests that stomatal closure did not prevent an increase in the carbon assimilation rates. The sample enrichment strategy and data analysis used here enabled the identification of all enzymes and most protein isoforms involved in the Calvin-Benson-Bessham cycle in Eucalyptus urophylla. Upon growth in CO 2 -enriched chambers, Eucalyptus urophylla plantlets responded by reducing the vascular bundle area and stomatal aperture size and by increasing the abundance of six of the eleven core enzymes involved in carbon fixation. Our proteome approach provides an estimate on how a commercially important C3-type plant would respond to an increase in CO 2 concentrations. Additionally, confirmation at the protein level of the predicted genes involved in

  13. [The regulation of peroxisomal matrix enzymes (alcohol oxidase and catalase) formation by the product of the gene Mth1 in methylotrophic yeast Pichia methanolica].

    Science.gov (United States)

    Leonovich, O A; Kurales, Iu A; Dutova, T A; Isakova, E P; Deriabina, Iu I; Rabinovich, Ia M

    2009-01-01

    Two independent mutant strains of methylotrophic yeast Pichia methanolica (mth1 arg1 and mth2 arg4) from the initial line 616 (ade1 ade5) were investigated. The mutant strains possessed defects in genes MTH1 and MTH2 which resulted in the inability to assimilate methanol as a sole carbon source and the increased activity of alcohol oxidase (AO). The function of the AUG2 gene encoding one of the subunits of AO and CTA1, a probable homolog of peroxisomal catalase of Saccharomyces cereviseae, was investigated by analyses of the molecular forms of isoenzymes. It was shown that optimal conditions for the expression of the AUG2 gene on a medium supplemented with 3% of methanol leads to an increasing synthesis of peroxisomal catalase. The mutant mth1 possessed a dominant formation of AO isoform with electrophoretic mobility which is typical for isogenic form 9, the product of the AUG2 gene, and a decreased level of peroxisomal catalase. The restoration of growth of four spontaneous revertants of the mutant mth1 (Rmth1) on the methanol containing medium was accompanied by an increase in activity of AO isogenic form 9 and peroxisomal catalase. The obtained results confirmed the functional continuity of the structural gene AUG2 in mutant mth1. The correlation of activity of peroxisomal catalase and AO isogenic form 1 in different conditions evidenced the existence of common regulatory elements for genes AUG2 and CTA1 in methilotrophic yeast Pichia methanolica.

  14. Regulation of the expression of NADP-malic enzyme by UV-B, red and far-red light in maize seedlings

    Directory of Open Access Journals (Sweden)

    P. Casati

    1999-10-01

    Full Text Available The induction of nicotinamide adenine dinucleotide phosphate-malic enzyme (NADP-ME in etiolated maize (Zea mays seedlings by UV-B and UV-A radiation, and different levels of photosynthetically active radiation (PAR, 400-700 nm was investigated by measuring changes in activity, protein quantity and RNA levels as a function of intensity and duration of exposure to the different radiations. Under low levels of PAR, exposure to UV-B radiation but not UV-A radiation for 6 to 24 h caused a marked increase in the enzyme levels similar to that observed under high PAR in the absence of UV-B. UV-B treatment of green leaves following a 12-h dark period also caused an increase in NADP-ME expression. Exposure to UV-B radiation for only 5 min resulted in a rapid increase of the enzyme, followed by a more gradual rise with longer exposure up to 6 h. Low levels of red light for 5 min or 6 h were also effective in inducing NADP-ME activity equivalent to that obtained with UV-B radiation. A 5-min exposure to far-red light following UV-B or red light treatment reversed the induction of NADP-ME, and this effect could be eliminated by further treatment with UV-B or red light. These results indicate that physiological levels of UV-B radiation can have a positive effect on the induction of this photosynthetic enzyme. The reducing power and pyruvate generated by the activity of NADP-ME may be used for respiration, in cellular repair processes and as substrates for fatty acid synthesis required for membrane repair.

  15. Ammonia Assimilation in Zea mays L. Infected with a Vesicular-Arbuscular Mycorrhizal Fungus Glomus fasciculatum.

    Science.gov (United States)

    Cliquet, J. B.; Stewart, G. R.

    1993-03-01

    To investigate nitrogen assimilation and translocation in Zea mays L. colonized by the vesicular-arbuscular mycorrhizal (VAM) fungus Glomus fasciculatum (Thax. sensu Gerd.), we measured key enzyme activities, 15N incorporation into free amino acids, and 15N translocation from roots to shoots. Glutamine synthetase and nitrate reductase activities were increased in both roots and shoots compared with control plants, and glutamate dehydrogenase activity increased in roots only. In the presence of [15N]ammonium, glutamine amide was the most heavily labeled product. More label was incorporated into amino acids in VAM plants. The kinetics of 15N labeling and effects of methionine sulfoximine on distribution of 15N-labeled products were entirely consistent with the operation of the glutamate synthase cycle. No evidence was found for ammonium assimilation via glutamate dehydrogenase. 15N translocation from roots to shoots through the xylem was higher in VAM plants compared with control plants. These results establish that, in maize, VAM fungi increase ammonium assimilation, glutamine production, and xylem nitrogen translocation. Unlike some ectomycorrhizal fungi, VAM fungi do not appear to alter the pathway of ammonium assimilation in roots of their hosts.

  16. Fat metabolism is regulated by altered gene expression oflipogenic enzymes and regulatory factors in liver and adiposetissue but not in semimembranosus muscle of pigs during thefattening period

    DEFF Research Database (Denmark)

    Duran-Montge, P; Theil, Peter Kappel; Lauridsen, Charlotte

    2009-01-01

    It has been shown previously that lipid metabolism is regulated by fatty acids (FA) and that thyroid hormones are important regulators of energy metabolism. The effects of weight, dietary fat level and dietary FA profile on thyroid hormone levels and expression of lipogenic genes and tissue FA co...

  17. Differentiation between Trichophyton mentagrophytes and T. rubrum by sorbitol assimilation.

    OpenAIRE

    Rezusta, A; Rubio, M C; Alejandre, M C

    1991-01-01

    Trichophyton rubrum was easily differentiated from T. mentagrophytes by its ability to assimilate sorbitol with an API 20C AUX strip. One hundred percent of 36 T. rubrum strains and none of 147 T. mentagrophytes strains assimilated sorbitol.

  18. Assimilation of Doppler weather radar observations in a mesoscale ...

    Indian Academy of Sciences (India)

    Research (PSU–NCAR) mesoscale model (MM5) version 3.5.6. The variational data assimilation ... investigation of the direct assimilation of radar reflectivity data in 3DVAR system. The present ...... Results presented in this paper are based on.

  19. Data assimilation of CALIPSO aerosol observations

    Directory of Open Access Journals (Sweden)

    T. T. Sekiyama

    2010-01-01

    Full Text Available We have developed an advanced data assimilation system for a global aerosol model with a four-dimensional ensemble Kalman filter in which the Level 1B data from the Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO were successfully assimilated for the first time, to the best of the authors' knowledge. A one-month data assimilation cycle experiment for dust, sulfate, and sea-salt aerosols was performed in May 2007. The results were validated via two independent observations: 1 the ground-based lidar network in East Asia, managed by the National Institute for Environmental Studies of Japan, and 2 weather reports of aeolian dust events in Japan. Detailed four-dimensional structures of aerosol outflows from source regions over oceans and continents for various particle types and sizes were well reproduced. The intensity of dust emission at each grid point was also corrected by this data assimilation system. These results are valuable for the comprehensive analysis of aerosol behavior as well as aerosol forecasting.

  20. Development of a data assimilation algorithm

    DEFF Research Database (Denmark)

    Thomsen, Per Grove; Zlatev, Zahari

    2008-01-01

    It is important to incorporate all available observations when large-scale mathematical models arising in different fields of science and engineering are used to study various physical and chemical processes. Variational data assimilation techniques can be used in the attempts to utilize efficien......It is important to incorporate all available observations when large-scale mathematical models arising in different fields of science and engineering are used to study various physical and chemical processes. Variational data assimilation techniques can be used in the attempts to utilize...... assimilation technique is applied. Therefore, it is important to study the interplay between the three components of the variational data assimilation techniques as well as to apply powerful parallel computers in the computations. Some results obtained in the search for a good combination of numerical methods...... computers, Mathematics and Computers in Simulation, 65 (2004) 557–577, Z. Zlatev, Computer Treatment of Large Air Pollution Models, Kluwer Academic Publishers, Dordrecht, Boston, London, 1995]. The ideas are rather general and can easily be applied in connection with other mathematical models....

  1. Nitrogen assimilation in soybean nodules, 1

    International Nuclear Information System (INIS)

    Ohyama, Takuji; Kumazawa, Kikuo

    1980-01-01

    In order to elucidate the pathways to assimilate the ammonia produced by N 2 -fixation in soybean nodules, 15 N-labeled compounds were administered to intact nodules or nodule slices pretreated with various inhibitors of nitrogen assimilation. After exposure to 15 N 2 , 15 N-incorporation into various nitrogenous compounds was investigated in attached nodules injected with methionine sulfoximine (MSX) or azaserine (AS). MSX treatment increased the 15 N content of ammonia more than 6 times, however, depressed 15 N content of most of amides and amino acids. AS treatment enhanced 15 N content of amido-N of glutamine as well as ammonia, but decreased amino-N of glutamine and most of amino acids. Experiments with nodule slices pretreated with MSX or AS solution and then fed with 15 N-labeled ammonia or amido- 15 N of glutamine showed the same trends. Aminooxyacetate inhibited nitrogen flow from glutamic acid to other amino acids. These results strongly indicate that the ammonia produced by N 2 -fixation is assimilated by GS/GOGAT system to glutamic acid and then transaminated to various amino acids in situ. 15 N-incorporation patterns in nodule slices fed with 15 N-labeled ammonia, hydroxylamine, nitrite were similar, but nitrate seemed to be reduced in a definite compartment and assimilated similarly as in intact nodules fed with 15 N 2 (author)

  2. Data assimilation for air quality models

    DEFF Research Database (Denmark)

    Silver, Jeremy David

    2014-01-01

    -dimensional optimal interpolation procedure (OI), an Ensemble Kalman Filter (EnKF), and a three-dimensional variational scheme (3D-var). The three assimilation procedures are described and tested. A multi-faceted approach is taken for the verification, using independent measurements from surface air-quality...

  3. Data ingestion and assimilation in ionospheric models

    Czech Academy of Sciences Publication Activity Database

    Burešová, Dalia; Nava, B.; Galkin, I.; Angling, M.; Stankov, S. M.; Coisson, P.

    2009-01-01

    Roč. 52, 3/4 (2009), s. 235-253 ISSN 1593-5213 R&D Projects: GA ČR GA205/08/1356; GA MŠk OC 091 Institutional research plan: CEZ:AV0Z30420517 Keywords : ionosphere * models * data assimilation * data ingestion Subject RIV: DG - Athmosphere Sciences, Meteorology Impact factor: 0.548, year: 2009

  4. A study on assimilating potential vorticity data

    Science.gov (United States)

    Li, Yong; Ménard, Richard; Riishøjgaard, Lars Peter; Cohn, Stephen E.; Rood, Richard B.

    1998-08-01

    The correlation that exists between the potential vorticity (PV) field and the distribution of chemical tracers such as ozone suggests the possibility of using tracer observations as proxy PV data in atmospheric data assimilation systems. Especially in the stratosphere, there are plentiful tracer observations but a general lack of reliable wind observations, and the correlation is most pronounced. The issue investigated in this study is how model dynamics would respond to the assimilation of PV data. First, numerical experiments of identical-twin type were conducted with a simple univariate nuding algorithm and a global shallow water model based on PV and divergence (PV-D model). All model fields are successfully reconstructed through the insertion of complete PV data alone if an appropriate value for the nudging coefficient is used. A simple linear analysis suggests that slow modes are recovered rapidly, at a rate nearly independent of spatial scale. In a more realistic experiment, appropriately scaled total ozone data from the NIMBUS-7 TOMS instrument were assimilated as proxy PV data into the PV-D model over a 10-day period. The resulting model PV field matches the observed total ozone field relatively well on large spatial scales, and the PV, geopotential and divergence fields are dynamically consistent. These results indicate the potential usefulness that tracer observations, as proxy PV data, may offer in a data assimilation system.

  5. Cholesterol Assimilation by Lactobacillus Probiotic Bacteria: An In Vitro Investigation

    OpenAIRE

    Tomaro-Duchesneau, Catherine; Jones, Mitchell L.; Shah, Divya; Jain, Poonam; Saha, Shyamali; Prakash, Satya

    2014-01-01

    Excess cholesterol is associated with cardiovascular diseases (CVD), an important cause of mortality worldwide. Current CVD therapeutic measures, lifestyle and dietary interventions, and pharmaceutical agents for regulating cholesterol levels are inadequate. Probiotic bacteria have demonstrated potential to lower cholesterol levels by different mechanisms, including bile salt hydrolase activity, production of compounds that inhibit enzymes such as 3-hydroxy-3-methylglutaryl coenzyme A, and ch...

  6. Sterols regulate 3β-hydroxysterol Δ24-reductase (DHCR24) via dual sterol regulatory elements: cooperative induction of key enzymes in lipid synthesis by Sterol Regulatory Element Binding Proteins.

    Science.gov (United States)

    Zerenturk, Eser J; Sharpe, Laura J; Brown, Andrew J

    2012-10-01

    3β-Hydroxysterol Δ24-reductase (DHCR24) catalyzes a final step in cholesterol synthesis, and has been ascribed diverse functions, such as being anti-apoptotic and anti-inflammatory. How this enzyme is regulated transcriptionally by sterols is currently unclear. Some studies have suggested that its expression is regulated by Sterol Regulatory Element Binding Proteins (SREBPs) while another suggests it is through the Liver X Receptor (LXR). However, these transcription factors have opposing effects on cellular sterol levels, so it is likely that one predominates. Here we establish that sterol regulation of DHCR24 occurs predominantly through SREBP-2, and identify the particular region of the DHCR24 promoter to which SREBP-2 binds. We demonstrate that sterol regulation is mediated by two sterol regulatory elements (SREs) in the promoter of the gene, assisted by two nearby NF-Y binding sites. Moreover, we present evidence that the dual SREs work cooperatively to regulate DHCR24 expression by comparison to two known SREBP target genes, the LDL receptor with one SRE, and farnesyl-diphosphate farnesyltransferase 1, with two SREs. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. Empowering Geoscience with Improved Data Assimilation Using the Data Assimilation Research Testbed "Manhattan" Release.

    Science.gov (United States)

    Raeder, K.; Hoar, T. J.; Anderson, J. L.; Collins, N.; Hendricks, J.; Kershaw, H.; Ha, S.; Snyder, C.; Skamarock, W. C.; Mizzi, A. P.; Liu, H.; Liu, J.; Pedatella, N. M.; Karspeck, A. R.; Karol, S. I.; Bitz, C. M.; Zhang, Y.

    2017-12-01

    The capabilities of the Data Assimilation Research Testbed (DART) at NCAR have been significantly expanded with the recent "Manhattan" release. DART is an ensemble Kalman filter based suite of tools, which enables researchers to use data assimilation (DA) without first becoming DA experts. Highlights: significant improvement in efficient ensemble DA for very large models on thousands of processors, direct read and write of model state files in parallel, more control of the DA output for finer-grained analysis, new model interfaces which are useful to a variety of geophysical researchers, new observation forward operators and the ability to use precomputed forward operators from the forecast model. The new model interfaces and example applications include the following: MPAS-A; Model for Prediction Across Scales - Atmosphere is a global, nonhydrostatic, variable-resolution mesh atmospheric model, which facilitates multi-scale analysis and forecasting. The absence of distinct subdomains eliminates problems associated with subdomain boundaries. It demonstrates the ability to consistently produce higher-quality analyses than coarse, uniform meshes do. WRF-Chem; Weather Research and Forecasting + (MOZART) Chemistry model assimilates observations from FRAPPÉ (Front Range Air Pollution and Photochemistry Experiment). WACCM-X; Whole Atmosphere Community Climate Model with thermosphere and ionosphere eXtension assimilates observations of electron density to investigate sudden stratospheric warming. CESM (weakly) coupled assimilation; NCAR's Community Earth System Model is used for assimilation of atmospheric and oceanic observations into their respective components using coupled atmosphere+land+ocean+sea+ice forecasts. CESM2.0; Assimilation in the atmospheric component (CAM, WACCM) of the newly released version is supported. This version contains new and extensively updated components and software environment. CICE; Los Alamos sea ice model (in CESM) is used to assimilate

  8. Photoperiodism and Enzyme Activity

    Science.gov (United States)

    Queiroz, Orlando; Morel, Claudine

    1974-01-01

    Metabolic readjustments after a change from long days to short days appear, in Kalanchoe blossfeldiana, to be achieved through the operation of two main mechanisms: variation in enzyme capacity, and circadian rhythmicity. After a lag time, capacity in phosphoenolpyruvate carboxylase and capacity in aspartate aminotransferase increase exponentially and appear to be allometrically linked during 50 to 60 short days; then a sudden fall takes place in the activity of the former. Malic enzyme and alanine aminotransferase behave differently. Thus, the operation of the two sections of the pathway (before and after the malate step) give rise to a continuously changing functional compartmentation in the pathway. Circadian rhythmicity, on the other hand, produces time compartmentation through phase shifts and variation in amplitude, independently for each enzyme. These characteristics suggest that the operation of a so-called biological clock would be involved. We propose the hypothesis that feedback regulation would be more accurate and efficient when applied to an already oscillating, clock-controlled enzyme system. PMID:16658749

  9. An algorithm for variational data assimilation of contact concentration measurements for atmospheric chemistry models

    Science.gov (United States)

    Penenko, Alexey; Penenko, Vladimir

    2014-05-01

    Contact concentration measurement data assimilation problem is considered for convection-diffusion-reaction models originating from the atmospheric chemistry study. High dimensionality of models imposes strict requirements on the computational efficiency of the algorithms. Data assimilation is carried out within the variation approach on a single time step of the approximated model. A control function is introduced into the source term of the model to provide flexibility for data assimilation. This function is evaluated as the minimum of the target functional that connects its norm to a misfit between measured and model-simulated data. In the case mathematical model acts as a natural Tikhonov regularizer for the ill-posed measurement data inversion problem. This provides flow-dependent and physically-plausible structure of the resulting analysis and reduces a need to calculate model error covariance matrices that are sought within conventional approach to data assimilation. The advantage comes at the cost of the adjoint problem solution. This issue is solved within the frameworks of splitting-based realization of the basic convection-diffusion-reaction model. The model is split with respect to physical processes and spatial variables. A contact measurement data is assimilated on each one-dimensional convection-diffusion splitting stage. In this case a computationally-efficient direct scheme for both direct and adjoint problem solution can be constructed based on the matrix sweep method. Data assimilation (or regularization) parameter that regulates ratio between model and data in the resulting analysis is obtained with Morozov discrepancy principle. For the proper performance the algorithm takes measurement noise estimation. In the case of Gaussian errors the probability that the used Chi-squared-based estimate is the upper one acts as the assimilation parameter. A solution obtained can be used as the initial guess for data assimilation algorithms that assimilate

  10. Regulation

    International Nuclear Information System (INIS)

    Ballereau, P.

    1999-01-01

    The different regulations relative to nuclear energy since the first of January 1999 are given here. Two points deserve to be noticed: the decree of the third august 1999 authorizing the national Agency for the radioactive waste management to install and exploit on the commune of Bures (Meuse) an underground laboratory destined to study the deep geological formations where could be stored the radioactive waste. The second point is about the uranium residues and the waste notion. The judgment of the administrative tribunal of Limoges ( 9. july 1998) forbidding the exploitation of a storage installation of depleted uranium considered as final waste and qualifying it as an industrial waste storage facility has been annulled bu the Court of Appeal. It stipulated that, according to the law number 75663 of the 15. july 1965, no criteria below can be applied to depleted uranium: production residue (possibility of an ulterior enrichment), abandonment of a personal property or simple intention to do it ( future use aimed in the authorization request made in the Prefecture). This judgment has devoted the primacy of the waste notion on this one of final waste. (N.C.)

  11. Age- and brain region-dependent α-synuclein oligomerization is attributed to alterations in intrinsic enzymes regulating α-synuclein phosphorylation in aging monkey brains.

    Science.gov (United States)

    Chen, Min; Yang, Weiwei; Li, Xin; Li, Xuran; Wang, Peng; Yue, Feng; Yang, Hui; Chan, Piu; Yu, Shun

    2016-02-23

    We previously reported that the levels of α-syn oligomers, which play pivotal pathogenic roles in age-related Parkinson's disease (PD) and dementia with Lewy bodies, increase heterogeneously in the aging brain. Here, we show that exogenous α-syn incubated with brain extracts from older cynomolgus monkeys and in Lewy body pathology (LBP)-susceptible brain regions (striatum and hippocampus) forms higher amounts of phosphorylated and oligomeric α-syn than that in extracts from younger monkeys and LBP-insusceptible brain regions (cerebellum and occipital cortex). The increased α-syn phosphorylation and oligomerization in the brain extracts from older monkeys and in LBP-susceptible brain regions were associated with higher levels of polo-like kinase 2 (PLK2), an enzyme promoting α-syn phosphorylation, and lower activity of protein phosphatase 2A (PP2A), an enzyme inhibiting α-syn phosphorylation, in these brain extracts. Further, the extent of the age- and brain-dependent increase in α-syn phosphorylation and oligomerization was reduced by inhibition of PLK2 and activation of PP2A. Inversely, phosphorylated α-syn oligomers reduced the activity of PP2A and showed potent cytotoxicity. In addition, the activity of GCase and the levels of ceramide, a product of GCase shown to activate PP2A, were lower in brain extracts from older monkeys and in LBP-susceptible brain regions. Our results suggest a role for altered intrinsic metabolic enzymes in age- and brain region-dependent α-syn oligomerization in aging brains.

  12. Enzyme-regulated the changes of pH values for assembling a colorimetric and multistage interconnection logic network with multiple readouts.

    Science.gov (United States)

    Huang, Yanyan; Ran, Xiang; Lin, Youhui; Ren, Jinsong; Qu, Xiaogang

    2015-04-22

    Based on enzymatic reactions-triggered changes of pH values and biocomputing, a novel and multistage interconnection biological network with multiple easy-detectable signal outputs has been developed. Compared with traditional chemical computing, the enzyme-based biological system could overcome the interference between reactions or the incompatibility of individual computing gates and offer a unique opportunity to assemble multicomponent/multifunctional logic circuitries. Our system included four enzyme inputs: β-galactosidase (β-gal), glucose oxidase (GOx), esterase (Est) and urease (Ur). With the assistance of two signal transducers (gold nanoparticles and acid-base indicators) or pH meter, the outputs of the biological network could be conveniently read by the naked eyes. In contrast to current methods, the approach present here could realize cost-effective, label-free and colorimetric logic operations without complicated instrument. By designing a series of Boolean logic operations, we could logically make judgment of the compositions of the samples on the basis of visual output signals. Our work offered a promising paradigm for future biological computing technology and might be highly useful in future intelligent diagnostics, prodrug activation, smart drug delivery, process control, and electronic applications. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. DR2539 is a novel DtxR-like regulator of Mn/Fe ion homeostasis and antioxidant enzyme in Deinococcus radiodurans

    International Nuclear Information System (INIS)

    Chen, Huan; Wu, Rongrong; Xu, Guangzhi; Fang, Xu; Qiu, Xiaoli; Guo, Hongyin; Tian, Bing; Hua, Yuejin

    2010-01-01

    Transcriptional regulators of the diphtheria toxin repressor (DtxR) family control the expression of genes involved in the uptake of iron and manganese, which is not only necessitous nutrients but also was suggested to be essential for intracellular redox cycling of microorganisms. We identified a unique DtxR homologue (DR2539) with special characteristics from Deinococcus radiodurans, which is known for its extreme resistance to radiation and oxidants. The dr2539 mutant showed higher resistance to hydrogen peroxide than the wild-type strain R1. Intracellular catalase activity assay and semiquantitative PCR analysis demonstrated that this DtxR is a negative regulator of catalase (katE). Furthermore, quantitative real-time PCR, global transcription profile and inductively coupled plasma-mass spectrometry analysis showed that the DtxR is involved in the regulation of antioxidant system by maintaining the intracellular Mn/Fe ion homeostasis of D. radiodurans. However, unlike the other DtxR homologues, the DtxR of D. radiodurans acts as a negative regulator of a Mn transporter gene (dr2283) and as a positive regulator of Fe-dependent transporter genes (dr1219, drb0125) in D. radiodurans.

  14. DR2539 is a novel DtxR-like regulator of Mn/Fe ion homeostasis and antioxidant enzyme in Deinococcus radiodurans

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Huan [Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029 (China); Zhejiang Institute of Microbiology, Zhejiang Province, Hangzhou 310012 (China); Wu, Rongrong [Department of Cardiology, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310009 (China); Xu, Guangzhi [Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029 (China); Fang, Xu; Qiu, Xiaoli; Guo, Hongyin [Zhejiang Institute of Microbiology, Zhejiang Province, Hangzhou 310012 (China); Tian, Bing, E-mail: tianbing@zju.edu.cn [Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029 (China); Hua, Yuejin, E-mail: yjhua@zju.edu.cn [Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029 (China)

    2010-05-28

    Transcriptional regulators of the diphtheria toxin repressor (DtxR) family control the expression of genes involved in the uptake of iron and manganese, which is not only necessitous nutrients but also was suggested to be essential for intracellular redox cycling of microorganisms. We identified a unique DtxR homologue (DR2539) with special characteristics from Deinococcus radiodurans, which is known for its extreme resistance to radiation and oxidants. The dr2539 mutant showed higher resistance to hydrogen peroxide than the wild-type strain R1. Intracellular catalase activity assay and semiquantitative PCR analysis demonstrated that this DtxR is a negative regulator of catalase (katE). Furthermore, quantitative real-time PCR, global transcription profile and inductively coupled plasma-mass spectrometry analysis showed that the DtxR is involved in the regulation of antioxidant system by maintaining the intracellular Mn/Fe ion homeostasis of D. radiodurans. However, unlike the other DtxR homologues, the DtxR of D. radiodurans acts as a negative regulator of a Mn transporter gene (dr2283) and as a positive regulator of Fe-dependent transporter genes (dr1219, drb0125) in D. radiodurans.

  15. Distinct features of C/N balance regulation in Prochlorococcus sp. strain MIT9313.

    Science.gov (United States)

    Domínguez-Martín, María Agustina; López-Lozano, Antonio; Rangel-Zúñiga, Oriol Alberto; Díez, Jesús; García-Fernández, José Manuel

    2018-02-01

    The abundance and significant contribution to global primary production of the marine cyanobacterium Prochlorococcus have made it one of the main models in marine ecology. Several conditions known to cause strong effects on the regulation of N-related enzymes in other cyanobacteria lacked such effect in Prochlorococcus. Prochlorococcus sp. strain MIT9313 is one of the most early-branching strains among the members of this genus. In order to further understand the C/N control system in this cyanobacterium, we studied the effect of the absence of three key elements in the ocean, namely N, P and Fe, as well as the effect of inhibitors of the N assimilation or photosynthesis on the N metabolism of this strain. Furthermore, we focused our work in the effect of ageing, as the age of cultures has clear effects on the regulation of some enzymes in Prochlorococcus. To reach this goal, expression of the main three regulators involved in N assimilation in cyanobacteria, namely ntcA, glnB and pipX, as well as that of icd (encoding for isocitrate dehydrogenase) were analysed. Our results show that the control of the main proteins involved in the C/N balance in strain MIT9313 differs from other model Prochlorococcus strains. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  16. Assimilation of Gridded GRACE Terrestrial Water Storage Estimates in the North American Land Data Assimilation System

    Science.gov (United States)

    Kumar, Sujay V.; Zaitchik, Benjamin F.; Peters-Lidard, Christa D.; Rodell, Matthew; Reichle, Rolf; Li, Bailing; Jasinski, Michael; Mocko, David; Getirana, Augusto; De Lannoy, Gabrielle; hide

    2016-01-01

    The objective of the North American Land Data Assimilation System (NLDAS) is to provide best available estimates of near-surface meteorological conditions and soil hydrological status for the continental United States. To support the ongoing efforts to develop data assimilation (DA) capabilities for NLDAS, the results of Gravity Recovery and Climate Experiment (GRACE) DA implemented in a manner consistent with NLDAS development are presented. Following previous work, GRACE terrestrial water storage (TWS) anomaly estimates are assimilated into the NASA Catchment land surface model using an ensemble smoother. In contrast to many earlier GRACE DA studies, a gridded GRACE TWS product is assimilated, spatially distributed GRACE error estimates are accounted for, and the impact that GRACE scaling factors have on assimilation is evaluated. Comparisons with quality-controlled in situ observations indicate that GRACE DA has a positive impact on the simulation of unconfined groundwater variability across the majority of the eastern United States and on the simulation of surface and root zone soil moisture across the country. Smaller improvements are seen in the simulation of snow depth, and the impact of GRACE DA on simulated river discharge and evapotranspiration is regionally variable. The use of GRACE scaling factors during assimilation improved DA results in the western United States but led to small degradations in the eastern United States. The study also found comparable performance between the use of gridded and basin averaged GRACE observations in assimilation. Finally, the evaluations presented in the paper indicate that GRACE DA can be helpful in improving the representation of droughts.

  17. Data Assimilation in Integrated and Distributed Hydrological Models

    DEFF Research Database (Denmark)

    Zhang, Donghua

    processes and provide simulations in refined temporal and spatial resolutions. Recent developments in measurement and sensor technologies have significantly improved the coverage, quality, frequency and diversity of hydrological observations. Data assimilation provides a great potential in relation...... point of view, different assimilation methodologies and techniques have been developed or customized to better serve hydrological assimilation. From the application point of view, real data and real-world complex catchments are used with the focus of investigating the models’ improvements with data...... a variety of model uncertainty sources and scales. Next the groundwater head assimilation experiment was tested in a much more complex catchment with assimilation of biased real observations. In such cases, the bias-aware assimilation method significantly outperforms the standard assimilation method...

  18. Dark matter assimilation into the baryon asymmetry

    International Nuclear Information System (INIS)

    D'Eramo, Francesco; Fei, Lin; Thaler, Jesse

    2012-01-01

    Pure singlets are typically disfavored as dark matter candidates, since they generically have a thermal relic abundance larger than the observed value. In this paper, we propose a new dark matter mechanism called a ssimilation , which takes advantage of the baryon asymmetry of the universe to generate the correct relic abundance of singlet dark matter. Through assimilation, dark matter itself is efficiently destroyed, but dark matter number is stored in new quasi-stable heavy states which carry the baryon asymmetry. The subsequent annihilation and late-time decay of these heavy states yields (symmetric) dark matter as well as (asymmetric) standard model baryons. We study in detail the case of pure bino dark matter by augmenting the minimal supersymmetric standard model with vector-like chiral multiplets. In the parameter range where this mechanism is effective, the LHC can discover long-lived charged particles which were responsible for assimilating dark matter

  19. Data assimilation in integrated hydrological modelling

    DEFF Research Database (Denmark)

    Rasmussen, Jørn

    Integrated hydrological models are useful tools for water resource management and research, and advances in computational power and the advent of new observation types has resulted in the models generally becoming more complex and distributed. However, the models are often characterized by a high...... degree of parameterization which results in significant model uncertainty which cannot be reduced much due to observations often being scarce and often taking the form of point measurements. Data assimilation shows great promise for use in integrated hydrological models , as it allows for observations...... to be efficiently combined with models to improve model predictions, reduce uncertainty and estimate model parameters. In this thesis, a framework for assimilating multiple observation types and updating multiple components and parameters of a catchment scale integrated hydrological model is developed and tested...

  20. Probabilistic forecasting and Bayesian data assimilation

    CERN Document Server

    Reich, Sebastian

    2015-01-01

    In this book the authors describe the principles and methods behind probabilistic forecasting and Bayesian data assimilation. Instead of focusing on particular application areas, the authors adopt a general dynamical systems approach, with a profusion of low-dimensional, discrete-time numerical examples designed to build intuition about the subject. Part I explains the mathematical framework of ensemble-based probabilistic forecasting and uncertainty quantification. Part II is devoted to Bayesian filtering algorithms, from classical data assimilation algorithms such as the Kalman filter, variational techniques, and sequential Monte Carlo methods, through to more recent developments such as the ensemble Kalman filter and ensemble transform filters. The McKean approach to sequential filtering in combination with coupling of measures serves as a unifying mathematical framework throughout Part II. Assuming only some basic familiarity with probability, this book is an ideal introduction for graduate students in ap...

  1. Regulations of enzymes in animals: effects of developmental processes, cancer and radiation. Progress report IX, 1 May 1974--31 April 1975

    International Nuclear Information System (INIS)

    Knox, W.E.

    1975-01-01

    Investigations of the properties of variant forms of emnzymes in rat tissues were continued. Two glutamyltransferases, one which remains associated with glutamine synthetase and the other which can be separated from it, were purified. A new assay method forglutaminase activity was established which facilitated further characterization of the 3 isozymes and their concentration in normal and neoplastic tissues. Studies of arginase led to the demonstration of the role that the new variant of arginase plays in proline synthesis in mammary gland. An inhibitor of asparagine synthetase, which is absent from fetal liver and tumors, was discovered in adult rat liver. Peptidyl proline hydroxylase (an essential enzyme in collagen synthesis) was identified as one of the most sensitive indicators of neoplastic growth. The spectrum of experimental, transplantable rat tumors was extended to a series of salivary gland tumors and a radiation-induced lymphoma. (U.S.)

  2. Regulation of dCTP deaminase from Escherichia coli by nonallosteric dTTP binding to an inactive form of the enzyme

    DEFF Research Database (Denmark)

    Johansson, Eva; Thymark, Majbritt; Bynck, Julie H

    2007-01-01

    -maximal activity and the cooperativity of dCTP saturation. Likewise, increasing concentrations of dCTP increase the cooperativity of dTTP inhibition. Previous structural studies showed that the complexes of inactive mutant protein, E138A, with dUTP or dCTP bound, and wild-type enzyme with dUTP bound were all...... highly similar and characterized by having an ordered C-terminal. When comparing with a new structure in which dTTP is bound to the active site of E138A, the region between Val120 and His125 was found to be in a new conformation. This and the previous conformation were mutually exclusive within...

  3. Methyl jasmonate counteracts boron toxicity by preventing oxidative stress and regulating antioxidant enzyme activities and artemisinin biosynthesis in Artemisia annua L.

    Science.gov (United States)

    Aftab, Tariq; Khan, M Masroor A; Idrees, Mohd; Naeem, M; Moinuddin; Hashmi, Nadeem

    2011-07-01

    Boron is an essential plant micronutrient, but it is phytotoxic if present in excessive amounts in soil for certain plants such as Artemisia annua L. that contains artemisinin (an important antimalarial drug) in its areal parts. Artemisinin is a sesquiterpene lactone with an endoperoxide bridge. It is quite expensive compound because the only commercial source available is A. annua and the compound present in the plant is in very low concentration. Since A. annua is a major source of the antimalarial drug and B stress is a deadly threat to its cultivation, the present research was conducted to determine whether the exogenous application of methyl jasmonate (MeJA) could combat the ill effects of excessive B present in the soil. According to the results obtained, the B toxicity induced oxidative stress and reduced the stem height as well as fresh and dry masses of the plant remarkably. The excessive amounts of soil B also lowered the net photosynthetic rate, stomatal conductance, internal CO(2) concentration and total chlorophyll content in the leaves. In contrast, the foliar application of MeJA enhanced the growth and photosynthetic efficiency both in the stressed and non-stressed plants. The excessive B levels also increased the activities of antioxidant enzymes, such as catalase, peroxidase and superoxide dismutase. Endogenous H(2)O(2) and O(2)(-) levels were also high in the stressed plants. However, the MeJA application to the stressed plants reduced the amount of lipid peroxidation and stimulated the synthesis of antioxidant enzymes, enhancing the content and yield of artemisinin as well. Thus, it was concluded that MeJA might be utilized in mitigating the B toxicity and improving the content and yield of artemisinin in A. annua plant.

  4. Data assimilation techniques in modeling ocean processes

    Digital Repository Service at National Institute of Oceanography (India)

    Mahadevan, R.; Fernandes, A.A.; Naqvi, S.W.A.

    are usually called data analysis or assimilation. These homogeneous fields are prerequisites for various practical applications and theoretical studies. The fields produced by an analysi the one hand, they must be close to the observations.... The practical usefulness of variational methods for meteorological problems are pointed out very early by Sasaki (1955, 1958), but in spite of that these methods have not been fully utilized. Probably, the complex mathematical technicality of these methods...

  5. Improving operational flood forecasting through data assimilation

    Science.gov (United States)

    Rakovec, Oldrich; Weerts, Albrecht; Uijlenhoet, Remko; Hazenberg, Pieter; Torfs, Paul

    2010-05-01

    Accurate flood forecasts have been a challenging topic in hydrology for decades. Uncertainty in hydrological forecasts is due to errors in initial state (e.g. forcing errors in historical mode), errors in model structure and parameters and last but not least the errors in model forcings (weather forecasts) during the forecast mode. More accurate flood forecasts can be obtained through data assimilation by merging observations with model simulations. This enables to identify the sources of uncertainties in the flood forecasting system. Our aim is to assess the different sources of error that affect the initial state and to investigate how they propagate through hydrological models with different levels of spatial variation, starting from lumped models. The knowledge thus obtained can then be used in a data assimilation scheme to improve the flood forecasts. This study presents the first results of this framework and focuses on quantifying precipitation errors and its effect on discharge simulations within the Ourthe catchment (1600 km2), which is situated in the Belgian Ardennes and is one of the larger subbasins of the Meuse River. Inside the catchment, hourly rain gauge information from 10 different locations is available over a period of 15 years. Based on these time series, the bootstrap method has been applied to generate precipitation ensembles. These were then used to simulate the catchment's discharges at the outlet. The corresponding streamflow ensembles were further assimilated with observed river discharges to update the model states of lumped hydrological models (R-PDM, HBV) through Residual Resampling. This particle filtering technique is a sequential data assimilation method and takes no prior assumption of the probability density function for the model states, which in contrast to the Ensemble Kalman filter does not have to be Gaussian. Our further research will be aimed at quantifying and reducing the sources of uncertainty that affect the initial

  6. Stereoselective interactions of warfarin enantiomers with the pregnane X nuclear receptor in gene regulation of major drug-metabolizing cytochrome P450 enzymes

    Czech Academy of Sciences Publication Activity Database

    Rulcová, A.; Prokopová, I.; Krausová, L.; Bitman, M.; Vrzal, R.; Dvořák, Z.; Blahoš, Jaroslav; Pávek, P.

    2010-01-01

    Roč. 8, č. 12 (2010), s. 2708-2717 ISSN 1538-7933 R&D Projects: GA MŠk(CZ) LC06063 Institutional research plan: CEZ:AV0Z50520514 Keywords : CYP3A4 * gene regulation * warfarin Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.439, year: 2010

  7. Assimilation of ocean colour to improve the simulation and understanding of the North West European shelf-sea ecosystem

    Science.gov (United States)

    Ciavatta, Stefano; Brewin, Robert; Skakala, Jozef; Sursham, David; Ford, David

    2017-04-01

    Shelf-seas and coastal zones provide essential goods and services to humankind, such as fisheries, aquaculture, tourism and climate regulation. The understanding and management of these regions can be enhanced by merging ocean-colour observations and marine ecosystem simulations through data assimilation, which provides (sub)optimal estimates of key biogeochemical variables. Here we present a range of applications of ocean-colour data assimilation in the North West European shelf-sea. A reanalysis application illustrates that assimilation of error-characterized chlorophyll concentrations could provide a map of the shelf sea vulnerability to oxygen deficiency, as well as estimates of the shelf sea uptake of atmospheric carbon dioxide (CO2) in the last decade. The interannual variability of CO2 uptake and its uncertainty were related significantly to interannual fluctuations of the simulated primary production. However, the reanalysis also indicates that assimilation of total chlorophyll did not improve significantly the simulation of some other variables, e.g. nutrients. We show that the assimilation of alternative products derived from ocean colour (i.e. spectral diffuse attenuation coefficient and phytoplankton size classes) can overcome this limitation. In fact, these products can constrain a larger number of model variables, which define either the underwater light field or the structure of the lower trophic levels. Therefore, the assimilation of such ocean-colour products into marine ecosystem models is an advantageous novel approach to improve the understanding and simulation of shelf-sea environments.

  8. Comparison of Sequential and Variational Data Assimilation

    Science.gov (United States)

    Alvarado Montero, Rodolfo; Schwanenberg, Dirk; Weerts, Albrecht

    2017-04-01

    Data assimilation is a valuable tool to improve model state estimates by combining measured observations with model simulations. It has recently gained significant attention due to its potential in using remote sensing products to improve operational hydrological forecasts and for reanalysis purposes. This has been supported by the application of sequential techniques such as the Ensemble Kalman Filter which require no additional features within the modeling process, i.e. it can use arbitrary black-box models. Alternatively, variational techniques rely on optimization algorithms to minimize a pre-defined objective function. This function describes the trade-off between the amount of noise introduced into the system and the mismatch between simulated and observed variables. While sequential techniques have been commonly applied to hydrological processes, variational techniques are seldom used. In our believe, this is mainly attributed to the required computation of first order sensitivities by algorithmic differentiation techniques and related model enhancements, but also to lack of comparison between both techniques. We contribute to filling this gap and present the results from the assimilation of streamflow data in two basins located in Germany and Canada. The assimilation introduces noise to precipitation and temperature to produce better initial estimates of an HBV model. The results are computed for a hindcast period and assessed using lead time performance metrics. The study concludes with a discussion of the main features of each technique and their advantages/disadvantages in hydrological applications.

  9. Data assimilation and model evaluation experiment datasets

    Science.gov (United States)

    Lai, Chung-Cheng A.; Qian, Wen; Glenn, Scott M.

    1994-01-01

    The Institute for Naval Oceanography, in cooperation with Naval Research Laboratories and universities, executed the Data Assimilation and Model Evaluation Experiment (DAMEE) for the Gulf Stream region during fiscal years 1991-1993. Enormous effort has gone into the preparation of several high-quality and consistent datasets for model initialization and verification. This paper describes the preparation process, the temporal and spatial scopes, the contents, the structure, etc., of these datasets. The goal of DAMEE and the need of data for the four phases of experiment are briefly stated. The preparation of DAMEE datasets consisted of a series of processes: (1) collection of observational data; (2) analysis and interpretation; (3) interpolation using the Optimum Thermal Interpolation System package; (4) quality control and re-analysis; and (5) data archiving and software documentation. The data products from these processes included a time series of 3D fields of temperature and salinity, 2D fields of surface dynamic height and mixed-layer depth, analysis of the Gulf Stream and rings system, and bathythermograph profiles. To date, these are the most detailed and high-quality data for mesoscale ocean modeling, data assimilation, and forecasting research. Feedback from ocean modeling groups who tested this data was incorporated into its refinement. Suggestions for DAMEE data usages include (1) ocean modeling and data assimilation studies, (2) diagnosis and theoretical studies, and (3) comparisons with locally detailed observations.

  10. The translational repressor Crc controls the Pseudomonas putida benzoate and alkane catabolic pathways using a multi-tier regulation strategy.

    Science.gov (United States)

    Hernández-Arranz, Sofía; Moreno, Renata; Rojo, Fernando

    2013-01-01

    Metabolically versatile bacteria usually perceive aromatic compounds and hydrocarbons as non-preferred carbon sources, and their assimilation is inhibited if more preferable substrates are available. This is achieved via catabolite repression. In Pseudomonas putida, the expression of the genes allowing the assimilation of benzoate and n-alkanes is strongly inhibited by catabolite repression, a process controlled by the translational repressor Crc. Crc binds to and inhibits the translation of benR and alkS mRNAs, which encode the transcriptional activators that induce the expression of the benzoate and alkane degradation genes respectively. However, sequences similar to those recognized by Crc in benR and alkS mRNAs exist as well in the translation initiation regions of the mRNA of several structural genes of the benzoate and alkane pathways, which suggests that Crc may also regulate their translation. The present results show that some of these sites are functional, and that Crc inhibits the induction of both pathways by limiting not only the translation of their transcriptional activators, but also that of genes coding for the first enzyme in each pathway. Crc may also inhibit the translation of a gene involved in benzoate uptake. This multi-tier approach probably ensures the rapid regulation of pathway genes, minimizing the assimilation of non-preferred substrates when better options are available. A survey of possible Crc sites in the mRNAs of genes associated with other catabolic pathways suggested that targeting substrate uptake, pathway induction and/or pathway enzymes may be a common strategy to control the assimilation of non-preferred compounds. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

  11. NMR characterization of altered lignins extracted from tobacco plants down-regulated for lignification enzymes cinnamylalcohol dehydrogenase and cinnamoyl-CoA reductase

    OpenAIRE

    Ralph, John; Hatfield, Ronald D.; Piquemal, Joël; Yahiaoui, Nabila; Pean, Michel; Lapierre, Catherine; Boudet, Alain M.

    1998-01-01

    Homologous antisense constructs were used to down-regulate tobacco cinnamyl-alcohol dehydrogenase (CAD; EC 1.1.1.195) and cinnamoyl-CoA reductase (CCR; EC 1.2.1.44) activities in the lignin monomer biosynthetic pathway. CCR converts activated cinnamic acids (hydroxycinnamoyl–SCoAs) to cinnamaldehydes; cinnamaldehydes are then reduced to cinnamyl alcohols by CAD. The transformations caused the incorporation of nontraditional components into the extractable tobacco lignins, as evidenced by NMR....

  12. Pattern of growth and 14C-assimilates distributions in relation to photosynthesis in radish plants treated with growth substances

    Directory of Open Access Journals (Sweden)

    Z. Starck

    2015-01-01

    Full Text Available In a series of radish plants, with very thin hypocotyl and with a normal storage organ, the rates of photosynthesis, photorespiration and dark respiration did not differ. Therefore, the conclusion may be advanced, that translocation to the swollen hypocotyl is not determinated by the photosynthetic productivity, but rather the by storage capacity. To check it this is connected with an unbalanced hormonal content, plants were treated with lanoline paste, with IAA, GA3, zeatin and all three in mixture or with injections of GA3-water solution into the swollen hypocotyl. In young radish plants, with high rate of growth of aerial parts, treatment with the above mentioned substances stimulated 14CO2-assimilation and increased retention of assimilates in 14C-donors, probably owing to retardation of their senescence. It increased the competition for photosynthates between shoot and storage organ. In older plants, in the stage of accumulation of nutrients in the swollen hypocotyl, IAA +GA3+zeatin did not affect 14CO2-assimilation, but in plants treated with growth regulators separately, assimilation decreased; IAA and GA3 stimulated transport and accumulation of labelled substances in the swollen hypocotyl. On the basis of experimental data the conclusion may be advanced that responsiveness of the particular organs and processes to growth regulators depends on the stage of plant development. Phytohormone did not changed quantitatively the pattern of 14C-assimilates distribution. They stimulated processes with preference for particular stages of development.

  13. mTOR regulates the expression of DNA damage response enzymes in long-lived Snell dwarf, GHRKO, and PAPPA-KO mice.

    Science.gov (United States)

    Dominick, Graham; Bowman, Jacqueline; Li, Xinna; Miller, Richard A; Garcia, Gonzalo G

    2017-02-01

    Studies of the mTOR pathway have prompted speculation that diminished mTOR complex-1 (mTORC1) function may be involved in controlling the aging process. Our previous studies have shown diminished mTORC1 activity in tissues of three long-lived mutant mice: Snell dwarf mice, growth hormone receptor gene disrupted mice (GHRKO), and in this article, mice deficient in the pregnancy-associated protein-A (PAPPA-KO). The ways in which lower mTOR signals slow aging and age-related diseases are, however, not well characterized. Here, we show that Snell, GHKRO, and PAPPA-KO mice express high levels of two proteins involved in DNA repair, O-6-methylguanine-DNA methyltransferase (MGMT) and N-myc downstream-regulated gene 1 (NDRG1). Furthermore, we report that lowering mTOR enhances MGMT and NDRG1 protein expression via post-transcriptional mechanisms. We show that the CCR4-NOT complex, a post-transcriptional regulator of gene expression, is downstream of the mTORC1 pathway and may be responsible for the upregulation of MGMT and NDRG1 in all three varieties of long-lived mice. Our data thus suggest a novel link between DNA repair and mTOR signaling via post-transcriptional regulation involving specific alteration in the CCR4-NOT complex, whose modulation could control multiple aspects of the aging process. © 2016 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.

  14. Regulations of enzymes in animals: effects of developmental processes, cancer and radiation. Progress report XI, 1 May 1976--30 April 1977

    Energy Technology Data Exchange (ETDEWEB)

    Knox, W.E.

    1977-06-01

    Two outstandingly successful studies were among those outlined in the proposal last year. They are the first and last topics summarized in this progress report: the first evidence that the chemical composition of human tumors can probably be predicted on the basis of our previous studies in the rat, and the elucidation of the function of the arginine-proline pathway, its importance in fetal and tumor tissues, and its regulation. The variety of other studies are summarized under headings somewhat different from those used in the original proposal, in order to denote more clearly what was actually found, but all proposed topics have been studied to some extent.

  15. Regulations of enzymes in animals: effects of developmental processes, cancer and radiation. Progress report XI, 1 May 1976--30 April 1977

    International Nuclear Information System (INIS)

    Knox, W.E.

    1977-06-01

    Two outstandingly successful studies were among those outlined in the proposal last year. They are the first and last topics summarized in this progress report: the first evidence that the chemical composition of human tumors can probably be predicted on the basis of our previous studies in the rat, and the elucidation of the function of the arginine-proline pathway, its importance in fetal and tumor tissues, and its regulation. The variety of other studies are summarized under headings somewhat different from those used in the original proposal, in order to denote more clearly what was actually found, but all proposed topics have been studied to some extent

  16. The re-assimilation of ammonia produced by photorespiration and the nitrogen economy of C3 higher plants.

    Science.gov (United States)

    Keys, Alfred J

    2006-02-01

    Photorespiration involves the conversion of glycine to serine with the release of ammonia and CO(2). In C(3) terrestrial higher plants the flux through glycine and serine is so large that it results in the production of ammonia at a rate far exceeding that from reduction of new nitrogen entering the plant. The photorespiratory nitrogen cycle re-assimilates this ammonia using the enzymes glutamine synthetase and glutamine:2-oxoglutarateaminotransferase.

  17. Site-Directed Mutagenesis Study Revealed Three Important Residues in Hc-DAF-22, a Key Enzyme Regulating Diapause of Haemonchus contortus

    Directory of Open Access Journals (Sweden)

    Yan Huang

    2017-11-01

    Full Text Available Haemonchus contortus (H. contortus is one of the most important parasites of small ruminants, especially goats and sheep. The complex life cycle of this nematode is a main obstacle for the control and prevention of haemonchosis. So far, a special form of arrested development called diapause different from the dauer stage in Caenorhabditis elegans (C. elegans has been found in many parasitic nematodes. In our previous study, we have characterized a novel gene Hc-daf-22 from H. contortus sharing high homology with Ce-daf-22 and functional analysis showed this gene has similar biological function with Ce-daf-22. In this study, Hc-daf-22 mutants were constructed using site-directed mutagenesis, and carried out rescue experiments, RNA interference (RNAi experiments and in vitro enzyme activity analysis with the mutants to further explore the precise function site of Hc-DAF-22. The results showed that Hc-daf-22 mutants could be expressed in the rescued ok693 worms and the expression positions were mainly in the intestine which was identical with that of Hc-daf-22 rescued worms. Through lipid staining we found that Hc-daf-22 could rescue daf-22 mutant (ok693 from the fatty acid metabolism deficiency while Hc-daf-22 mutants failed. Brood size and body length analyses in rescue experiment along with body length and life span analyses in RNAi experiment elucidated that Hc-daf-22 resembled Ce-daf-22 in effecting the development and capacity of C. elegans and mutants impaired the function of Hc-daf-22. Together with the protease activity assay, this research revealed three important active resides 84C/299H/349H in Hc-DAF-22 by site-directed mutagenesis.

  18. Site-Directed Mutagenesis Study Revealed Three Important Residues in Hc-DAF-22, a Key Enzyme Regulating Diapause of Haemonchus contortus.

    Science.gov (United States)

    Huang, Yan; Zheng, Xiuping; Zhang, Hongli; Ding, Haojie; Guo, Xiaolu; Yang, Yi; Chen, Xueqiu; Zhou, Qianjin; Du, Aifang

    2017-01-01

    Haemonchus contortus ( H. contortus ) is one of the most important parasites of small ruminants, especially goats and sheep. The complex life cycle of this nematode is a main obstacle for the control and prevention of haemonchosis. So far, a special form of arrested development called diapause different from the dauer stage in Caenorhabditis elegans ( C. elegans ) has been found in many parasitic nematodes. In our previous study, we have characterized a novel gene Hc-daf-22 from H. contortus sharing high homology with Ce-daf-22 and functional analysis showed this gene has similar biological function with Ce-daf-22 . In this study, Hc-daf-22 mutants were constructed using site-directed mutagenesis, and carried out rescue experiments, RNA interference (RNAi) experiments and in vitro enzyme activity analysis with the mutants to further explore the precise function site of Hc-DAF-22. The results showed that Hc-daf-22 mutants could be expressed in the rescued ok693 worms and the expression positions were mainly in the intestine which was identical with that of Hc-daf-22 rescued worms. Through lipid staining we found that Hc-daf-22 could rescue daf-22 mutant ( ok693 ) from the fatty acid metabolism deficiency while Hc-daf-22 mutants failed. Brood size and body length analyses in rescue experiment along with body length and life span analyses in RNAi experiment elucidated that Hc-daf-22 resembled Ce-daf-22 in effecting the development and capacity of C. elegans and mutants impaired the function of Hc-daf-22 . Together with the protease activity assay, this research revealed three important active resides 84C/299H/349H in Hc-DAF-22 by site-directed mutagenesis.

  19. Light-induced Variation in Phenolic Compounds in Cabernet Sauvignon Grapes (Vitis vinifera L.) Involves Extensive Transcriptome Reprogramming of Biosynthetic Enzymes, Transcription Factors, and Phytohormonal Regulators.

    Science.gov (United States)

    Sun, Run-Ze; Cheng, Guo; Li, Qiang; He, Yan-Nan; Wang, Yu; Lan, Yi-Bin; Li, Si-Yu; Zhu, Yan-Rong; Song, Wen-Feng; Zhang, Xue; Cui, Xiao-Di; Chen, Wu; Wang, Jun

    2017-01-01

    Light environments have long been known to influence grape ( Vitis vinifera L.) berry development and biosynthesis of phenolic compounds, and ultimately affect wine quality. Here, the accumulation and compositional changes of hydroxycinnamic acids (HCAs) and flavonoids, as well as global gene expression were analyzed in Cabernet Sauvignon grape berries under sunlight exposure treatments at different phenological stages. Sunlight exposure did not consistently affect the accumulation of berry skin flavan-3-ol or anthocyanin among different seasons due to climatic variations, but increased HCA content significantly at véraison and harvest, and enhanced flavonol accumulation dramatically with its timing and severity degree trend. As in sunlight exposed berries, a highly significant correlation was observed between the expression of genes coding phenylalanine ammonia-lyase, 4-coumarate: CoA ligase, flavanone 3-hydroxylase and flavonol synthase family members and corresponding metabolite accumulation in the phenolic biosynthesis pathway, which may positively or negatively be regulated by MYB, bHLH, WRKY, AP2/EREBP, C2C2, NAC, and C2H2 transcription factors (TFs). Furthermore, some candidate genes required for auxin, ethylene and abscisic acid signal transductions were also identified which are probably involved in berry development and flavonoid biosynthesis in response to enhanced sunlight irradiation. Taken together, this study provides a valuable overview of the light-induced phenolic metabolism and transcriptome changes, especially the dynamic responses of TFs and signaling components of phytohormones, and contributes to the further understanding of sunlight-responsive phenolic biosynthesis regulation in grape berries.

  20. NMR characterization of altered lignins extracted from tobacco plants down-regulated for lignification enzymes cinnamylalcohol dehydrogenase and cinnamoyl-CoA reductase.

    Science.gov (United States)

    Ralph, J; Hatfield, R D; Piquemal, J; Yahiaoui, N; Pean, M; Lapierre, C; Boudet, A M

    1998-10-27

    Homologous antisense constructs were used to down-regulate tobacco cinnamyl-alcohol dehydrogenase (CAD; EC 1.1.1.195) and cinnamoyl-CoA reductase (CCR; EC 1.2.1.44) activities in the lignin monomer biosynthetic pathway. CCR converts activated cinnamic acids (hydroxycinnamoyl-SCoAs) to cinnamaldehydes; cinnamaldehydes are then reduced to cinnamyl alcohols by CAD. The transformations caused the incorporation of nontraditional components into the extractable tobacco lignins, as evidenced by NMR. Isolated lignin of antisense-CAD tobacco contained fewer coniferyl and sinapyl alcohol-derived units that were compensated for by elevated levels of benzaldehydes and cinnamaldehydes. Products from radical coupling of cinnamaldehydes, particularly sinapaldehyde, which were barely discernible in normal tobacco, were major components of the antisense-CAD tobacco lignin. Lignin content was reduced in antisense-CCR tobacco, which displayed a markedly reduced vigor. That lignin contained fewer coniferyl alcohol-derived units and significant levels of tyramine ferulate. Tyramine ferulate is a sink for the anticipated build-up of feruloyl-SCoA, and may be up-regulated in response to a deficit of coniferyl alcohol. Although it is not yet clear whether the modified lignins are true structural components of the cell wall, the findings provide further indications of the metabolic plasticity of plant lignification. An ability to produce lignin from alternative monomers would open new avenues for manipulation of lignin by genetic biotechnologies.

  1. Light-induced Variation in Phenolic Compounds in Cabernet Sauvignon Grapes (Vitis vinifera L.) Involves Extensive Transcriptome Reprogramming of Biosynthetic Enzymes, Transcription Factors, and Phytohormonal Regulators

    Science.gov (United States)

    Sun, Run-Ze; Cheng, Guo; Li, Qiang; He, Yan-Nan; Wang, Yu; Lan, Yi-Bin; Li, Si-Yu; Zhu, Yan-Rong; Song, Wen-Feng; Zhang, Xue; Cui, Xiao-Di; Chen, Wu; Wang, Jun

    2017-01-01

    Light environments have long been known to influence grape (Vitis vinifera L.) berry development and biosynthesis of phenolic compounds, and ultimately affect wine quality. Here, the accumulation and compositional changes of hydroxycinnamic acids (HCAs) and flavonoids, as well as global gene expression were analyzed in Cabernet Sauvignon grape berries under sunlight exposure treatments at different phenological stages. Sunlight exposure did not consistently affect the accumulation of berry skin flavan-3-ol or anthocyanin among different seasons due to climatic variations, but increased HCA content significantly at véraison and harvest, and enhanced flavonol accumulation dramatically with its timing and severity degree trend. As in sunlight exposed berries, a highly significant correlation was observed between the expression of genes coding phenylalanine ammonia-lyase, 4-coumarate: CoA ligase, flavanone 3-hydroxylase and flavonol synthase family members and corresponding metabolite accumulation in the phenolic biosynthesis pathway, which may positively or negatively be regulated by MYB, bHLH, WRKY, AP2/EREBP, C2C2, NAC, and C2H2 transcription factors (TFs). Furthermore, some candidate genes required for auxin, ethylene and abscisic acid signal transductions were also identified which are probably involved in berry development and flavonoid biosynthesis in response to enhanced sunlight irradiation. Taken together, this study provides a valuable overview of the light-induced phenolic metabolism and transcriptome changes, especially the dynamic responses of TFs and signaling components of phytohormones, and contributes to the further understanding of sunlight-responsive phenolic biosynthesis regulation in grape berries. PMID:28469625

  2. Enzyme detection by microfluidics

    DEFF Research Database (Denmark)

    2013-01-01

    Microfluidic-implemented methods of detecting an enzyme, in particular a DNA-modifying enzyme, are provided, as well as methods for detecting a cell, or a microorganism expressing said enzyme. The enzyme is detected by providing a nucleic acid substrate, which is specifically targeted...... by that enzyme...

  3. Spatial dependence of color assimilation by the watercolor effect.

    Science.gov (United States)

    Devinck, Frédéric; Delahunt, Peter B; Hardy, Joseph L; Spillmann, Lothar; Werner, John S

    2006-01-01

    Color assimilation with bichromatic contours was quantified for spatial extents ranging from von Bezold-type color assimilation to the watercolor effect. The magnitude and direction of assimilative hue change was measured as a function of the width of a rectangular stimulus. Assimilation was quantified by hue cancellation. Large hue shifts were required to null the color of stimuli < or = 9.3 min of arc in width, with an exponential decrease for stimuli increasing up to 7.4 deg. When stimuli were viewed through an achromatizing lens, the magnitude of the assimilation effect was reduced for narrow stimuli, but not for wide ones. These results demonstrate that chromatic aberration may account, in part, for color assimilation over small, but not large, surface areas.

  4. Accelerating assimilation development for new observing systems using EFSO

    Science.gov (United States)

    Lien, Guo-Yuan; Hotta, Daisuke; Kalnay, Eugenia; Miyoshi, Takemasa; Chen, Tse-Chun

    2018-03-01

    To successfully assimilate data from a new observing system, it is necessary to develop appropriate data selection strategies, assimilating only the generally useful data. This development work is usually done by trial and error using observing system experiments (OSEs), which are very time and resource consuming. This study proposes a new, efficient methodology to accelerate the development using ensemble forecast sensitivity to observations (EFSO). First, non-cycled assimilation of the new observation data is conducted to compute EFSO diagnostics for each observation within a large sample. Second, the average EFSO conditionally sampled in terms of various factors is computed. Third, potential data selection criteria are designed based on the non-cycled EFSO statistics, and tested in cycled OSEs to verify the actual assimilation impact. The usefulness of this method is demonstrated with the assimilation of satellite precipitation data. It is shown that the EFSO-based method can efficiently suggest data selection criteria that significantly improve the assimilation results.

  5. Benefits and Pitfalls of GRACE Terrestrial Water Storage Data Assimilation

    Science.gov (United States)

    Girotto, Manuela

    2018-01-01

    Satellite observations of terrestrial water storage (TWS) from the Gravity Recovery and Climate Experiment (GRACE) mission have a coarse resolution in time (monthly) and space (roughly 150,000 sq km at midlatitudes) and vertically integrate all water storage components over land, including soil moisture and groundwater. Nonetheless, data assimilation can be used to horizontally downscale and vertically partition GRACE-TWS observations. This presentation illustrates some of the benefits and drawbacks of assimilating TWS observations from GRACE into a land surface model over the continental United States and India. The assimilation scheme yields improved skill metrics for groundwater compared to the no-assimilation simulations. A smaller impact is seen for surface and root-zone soil moisture. Further, GRACE observes TWS depletion associated with anthropogenic groundwater extraction. Results from the assimilation emphasize the importance of representing anthropogenic processes in land surface modeling and data assimilation systems.

  6. Epigenetic-based combinatorial resveratrol and pterostilbene alters DNA damage response by affecting SIRT1 and DNMT enzyme expression, including SIRT1-dependent γ-H2AX and telomerase regulation in triple-negative breast cancer

    International Nuclear Information System (INIS)

    Kala, Rishabh; Shah, Harsh N.; Martin, Samantha L.; Tollefsbol, Trygve O.

    2015-01-01

    , the effects of this combination treatment was also explored on DNA methyltransferases (DNMTs) expression. Interestingly, the compounds resulted in a significant down-regulation of DNMT enzymes with no significant effects on DNMT enzyme expression in MCF10A control cells. Collectively, these results provide new insights into the epigenetic mechanisms of a novel combinatorial nutrient control strategy that exhibits synergy and may contribute to future recalcitrant TNBC prevention and/or therapy. The online version of this article (doi:10.1186/s12885-015-1693-z) contains supplementary material, which is available to authorized users

  7. Testbed model and data assimilation for ARM

    International Nuclear Information System (INIS)

    Louis, J.F.

    1992-01-01

    The objectives of this contract are to further develop and test the ALFA (AER Local Forecast and Assimilation) model originally designed at AER for local weather prediction and apply it to three distinct but related purposes in connection with the Atmospheric Radiation Measurement (ARM) program: (a) to provide a testbed that simulates a global climate model in order to facilitate the development and testing of new cloud parametrizations and radiation models; (b) to assimilate the ARM data continuously at the scale of a climate model, using the adjoint method, thus providing the initial conditions and verification data for testing parameumtions; (c) to study the sensitivity of a radiation scheme to cloud parameters, again using the adjoint method, thus demonstrating the usefulness of the testbed model. The data assimilation will use a variational technique that minimizes the difference between the model results and the observation during the analysis period. The adjoint model is used to compute the gradient of a measure of the model errors with respect to nudging terms that are added to the equations to force the model output closer to the data. The radiation scheme that will be included in the basic ALFA model makes use of a gen two-stream approximation, and is designed for vertically inhonogeneous, multiple-scattering atmospheres. The sensitivity of this model to the definition of cloud parameters will be studied. The adjoint technique will also be used to compute the sensitivities. This project is designed to provide the Science Team members with the appropriate tools and modeling environment for proper testing and tuning of new radiation models and cloud parametrization schemes

  8. Variational data assimilation using targetted random walks

    KAUST Repository

    Cotter, S. L.

    2011-02-15

    The variational approach to data assimilation is a widely used methodology for both online prediction and for reanalysis. In either of these scenarios, it can be important to assess uncertainties in the assimilated state. Ideally, it is desirable to have complete information concerning the Bayesian posterior distribution for unknown state given data. We show that complete computational probing of this posterior distribution is now within the reach in the offline situation. We introduce a Markov chain-Monte Carlo (MCMC) method which enables us to directly sample from the Bayesian posterior distribution on the unknown functions of interest given observations. Since we are aware that these methods are currently too computationally expensive to consider using in an online filtering scenario, we frame this in the context of offline reanalysis. Using a simple random walk-type MCMC method, we are able to characterize the posterior distribution using only evaluations of the forward model of the problem, and of the model and data mismatch. No adjoint model is required for the method we use; however, more sophisticated MCMC methods are available which exploit derivative information. For simplicity of exposition, we consider the problem of assimilating data, either Eulerian or Lagrangian, into a low Reynolds number flow in a two-dimensional periodic geometry. We will show that in many cases it is possible to recover the initial condition and model error (which we describe as unknown forcing to the model) from data, and that with increasing amounts of informative data, the uncertainty in our estimations reduces. © 2011 John Wiley & Sons, Ltd.

  9. Nitrogen uptake and assimilation by corn roots

    International Nuclear Information System (INIS)

    Yoneyama, Tadakatsu; Akiyama, Yoko; Kumazawa, Kikuo

    1977-01-01

    The site of nitrogen uptake in the apical root zone of corn was experimentally investigated. Two experiments were performed. The one is to see the assimilation of nitrate and ammonium and the effects of low temperature on it. The 4-day-old roots were treated with 15 N-labelled inorganic nitrogen of 20 ppm N in 5 x 10 -4 M CaSO 4 solution at 30 deg. C and 0 deg. C. The other is to see the nitrogen uptake at apical root zone and the utilization of newly absorbed nitrogen at the root top. The 4-day-old roots were transferred into 5 x 10 -4 M CaSO 4 solution containing 15 N-labelled ammonium nitrate of 40 ppm N. As a result, the effect of low temperature on the nitrogen uptake appeared to be more drastic in the case of nitrate than ammonium. The 15 N content of amino acids indicates that ammonium is assimilated into amino acids even at 0 deg. C, but nitrate is not. The ammonium nitrogen seemed to be absorbed at both cell dividing and elongating zones. On the other hand, nitrate nitrogen seemed to be strongly absorbed at cell elongating zone. The nitrogen in the apical part may be supplied not only by direct absorption but also by translocation from the basal part. The clear difference was found in the utilization of nitrate and ammonium nitrogen at the root top when the root was elongating. This may be due to the difference of assimilation products of inorganic nitrogen. Newly absorbed ammonium nitrogen is more utilizable for the growth of root top than nitrate nitrogen. (Iwakiri, K.)

  10. Selected soil enzymes: Examples of their potential roles in the ...

    African Journals Online (AJOL)

    SERVER

    2008-02-05

    Feb 5, 2008 ... Soil enzymes regulate ecosystem functioning and in particular play a key role in nutrient cycling. In ... A better understanding of the role of these soil enzyme- es activity ..... measure of any disruption caused by pesticides, trace.

  11. Data assimilation strategies for volcano geodesy

    Science.gov (United States)

    Zhan, Yan; Gregg, Patricia M.

    2017-09-01

    Ground deformation observed using near-real time geodetic methods, such as InSAR and GPS, can provide critical information about the evolution of a magma chamber prior to volcanic eruption. Rapid advancement in numerical modeling capabilities has resulted in a number of finite element models targeted at better understanding the connection between surface uplift associated with magma chamber pressurization and the potential for volcanic eruption. Robust model-data fusion techniques are necessary to take full advantage of the numerical models and the volcano monitoring observations currently available. In this study, we develop a 3D data assimilation framework using the Ensemble Kalman Filter (EnKF) approach in order to combine geodetic observations of surface deformation with geodynamic models to investigate volcanic unrest. The EnKF sequential assimilation method utilizes disparate data sets as they become available to update geodynamic models of magma reservoir evolution. While the EnKF has been widely applied in hydrologic and climate modeling, the adaptation for volcano monitoring is in its initial stages. As such, our investigation focuses on conducting a series of sensitivity tests to optimize the EnKF for volcano applications and on developing specific strategies for assimilation of geodetic data. Our numerical experiments illustrate that the EnKF is able to adapt well to the spatial limitations posed by GPS data and the temporal limitations of InSAR, and that specific strategies can be adopted to enhance EnKF performance to improve model forecasts. Specifically, our numerical experiments indicate that: (1) incorporating additional iterations of the EnKF analysis step is more efficient than increasing the number of ensemble members; (2) the accuracy of the EnKF results are not affected by initial parameter assumptions; (3) GPS observations near the center of uplift improve the quality of model forecasts; (4) occasionally shifting continuous GPS stations to

  12. Data assimilation approaches in the EURANOS project

    DEFF Research Database (Denmark)

    Kaiser, J.C.; Gering, F.; Astrup, Poul

    2010-01-01

    -nuclides in urban areas the results of demonstration exercises are presented here. With the data assimilation module of the RIMPUFF dispersion code, predictions of the gamma dose rate are corrected with simulated readings of fixed detector stations. Using the DA capabilities of the IAMM package for mapping...... the radioactive contamination in inhabited areas, predictions of a large scale deposition model have been combined with hypothetical measurements on a local scale. In both examples the accuracy of the model predictions has been improved and the uncertainties have been reduced. © EDP Sciences, 2010...

  13. Improving carbon model phenology using data assimilation

    Science.gov (United States)

    Exrayat, Jean-François; Smallman, T. Luke; Bloom, A. Anthony; Williams, Mathew

    2015-04-01

    Carbon cycle dynamics is significantly impacted by ecosystem phenology, leading to substantial seasonal and inter-annual variation in the global carbon balance. Representing inter-annual variability is key for predicting the response of the terrestrial ecosystem to climate change and disturbance. Existing terrestrial ecosystem models (TEMs) often struggle to accurately simulate observed inter-annual variability. TEMs often use different phenological models based on plant functional type (PFT) assumptions. Moreover, due to a high level of computational overhead in TEMs they are unable to take advantage of globally available datasets to calibrate their models. Here we describe the novel CARbon DAta MOdel fraMework (CARDAMOM) for data assimilation. CARDAMOM is used to calibrate the Data Assimilation Linked Ecosystem Carbon version 2 (DALEC2) model using Bayes' Theorem within a Metropolis Hastings - Markov Chain Monte Carlo (MH-MCMC). CARDAMOM provides a framework which combines knowledge from observations, such as remotely sensed LAI, and heuristic information in the form of Ecological and Dynamical Constraints (EDCs). The EDCs are representative of real world processes and constrain parameter interdependencies and constrain carbon dynamics. We used CARDAMOM to bring together globally spanning datasets of LAI and the DALEC2 and DALEC2-GSI models. These analyses allow us to investigate the sensitivity ecosystem processes to the representation of phenology. DALEC2 uses an analytically solved model of phenology which is invariant between years. In contrast DALEC2-GSI uses a growing season index (GSI) calculated as a function of temperature, vapour pressure deficit (VPD) and photoperiod to calculate bud-burst and leaf senescence, allowing the model to simulate inter-annual variability in response to climate. Neither model makes any PFT assumptions about the phenological controls of a given ecosystem, allowing the data alone to determine the impact of the meteorological

  14. Light-induced Variation in Phenolic Compounds in Cabernet Sauvignon Grapes (Vitis vinifera L. Involves Extensive Transcriptome Reprogramming of Biosynthetic Enzymes, Transcription Factors, and Phytohormonal Regulators

    Directory of Open Access Journals (Sweden)

    Jun Wang

    2017-04-01

    Full Text Available Light environments have long been known to influence grape (Vitis vinifera L. berry development and biosynthesis of phenolic compounds, and ultimately affect wine quality. Here, the accumulation and compositional changes of hydroxycinnamic acids (HCAs and flavonoids, as well as global gene expression were analyzed in Cabernet Sauvignon grape berries under sunlight exposure treatments at different phenological stages. Sunlight exposure did not consistently affect the accumulation of berry skin flavan-3-ol or anthocyanin among different seasons due to climatic variations, but increased HCA content significantly at véraison and harvest, and enhanced flavonol accumulation dramatically with its timing and severity degree trend. As in sunlight exposed berries, a highly significant correlation was observed between the expression of genes coding phenylalanine ammonia-lyase, 4-coumarate: CoA ligase, flavanone 3-hydroxylase and flavonol synthase family members and corresponding metabolite accumulation in the phenolic biosynthesis pathway, which may positively or negatively be regulated by MYB, bHLH, WRKY, AP2/EREBP, C2C2, NAC, and C2H2 transcription factors (TFs. Furthermore, some candidate genes required for auxin, ethylene and abscisic acid signal transductions were also identified which are probably involved in berry development and flavonoid biosynthesis in response to enhanced sunlight irradiation. Taken together, this study provides a valuable overview of the light-induced phenolic metabolism and transcriptome changes, especially the dynamic responses of TFs and signaling components of phytohormones, and contributes to the further understanding of sunlight-responsive phenolic biosynthesis regulation in grape berries.

  15. First assimilations of COSMIC radio occultation data into the Electron Density Assimilative Model (EDAM

    Directory of Open Access Journals (Sweden)

    M. J. Angling

    2008-02-01

    Full Text Available Ground based measurements of slant total electron content (TEC can be assimilated into ionospheric models to produce 3-D representations of ionospheric electron density. The Electron Density Assimilative Model (EDAM has been developed for this purpose. Previous tests using EDAM and ground based data have demonstrated that the information on the vertical structure of the ionosphere is limited in this type of data. The launch of the COSMIC satellite constellation provides the opportunity to use radio occultation data which has more vertical information. EDAM assimilations have been run for three time periods representing quiet, moderate and disturbed geomagnetic conditions. For each run, three data sets have been ingested – only ground based data, only COSMIC data and both ground based and COSMIC data. The results from this preliminary study show that both ground and space based data are capable of improving the representation of the vertical structure of the ionosphere. However, the analysis is limited by the incomplete deployment of the COSMIC constellation and the use of auto-scaled ionosonde data. The first of these can be addressed by repeating this type of study once full deployment has been achieved. The latter requires the manual scaling of ionosonde data; ideally an agreed data set would be scaled and made available to the community to facilitate comparative testing of assimilative models.

  16. Development of airborne remote sensing data assimilation system

    International Nuclear Information System (INIS)

    Gudu, B R; Bi, H Y; Wang, H Y; Qin, S X; Ma, J W

    2014-01-01

    In this paper, an airborne remote sensing data assimilation system for China Airborne Remote Sensing System is introduced. This data assimilation system is composed of a land surface model, data assimilation algorithms, observation data and fundamental parameters forcing the land surface model. In this data assimilation system, Variable Infiltration Capacity hydrologic model is selected as the land surface model, which also serves as the main framework of the system. Three-dimensional variation algorithm, four-dimensional variation algorithms, ensemble Kalman filter and Particle filter algorithms are integrated in this system. Observation data includes ground observations and remotely sensed data. The fundamental forcing parameters include soil parameters, vegetation parameters and the meteorological data

  17. Boundary Conditions, Data Assimilation, and Predictability in Coastal Ocean Models

    National Research Council Canada - National Science Library

    Samelson, Roger M; Allen, John S; Egbert, Gary D; Kindle, John C; Snyder, Chris

    2007-01-01

    ...: The specific objectives of this research are to determine the impact on coastal ocean circulation models of open ocean boundary conditions from Global Ocean Data Assimilation Experiment (GODAE...

  18. Assimilation of enterprise technology upgrades: a factor-based study

    Science.gov (United States)

    Claybaugh, Craig C.; Ramamurthy, Keshavamurthy; Haseman, William D.

    2017-02-01

    The purpose of this study is to gain a better understanding of the differences in the propensity of firms to initiate and commit to the assimilation of an enterprise technology upgrade. A research model is proposed that examines the influences that four technological and four organisational factors have on predicting assimilation of a technology upgrade. Results show that firms with a greater propensity to assimilate the new enterprise resource planning (ERP) version have a higher assessment of relative advantage, IS technical competence, and the strategic role of IS relative to those firms with a lower propensity to assimilate a new ERP version.

  19. DNA-Based Enzyme Reactors and Systems

    Directory of Open Access Journals (Sweden)

    Veikko Linko

    2016-07-01

    Full Text Available During recent years, the possibility to create custom biocompatible nanoshapes using DNA as a building material has rapidly emerged. Further, these rationally designed DNA structures could be exploited in positioning pivotal molecules, such as enzymes, with nanometer-level precision. This feature could be used in the fabrication of artificial biochemical machinery that is able to mimic the complex reactions found in living cells. Currently, DNA-enzyme hybrids can be used to control (multi-enzyme cascade reactions and to regulate the enzyme functions and the reaction pathways. Moreover, sophisticated DNA structures can be utilized in encapsulating active enzymes and delivering the molecular cargo into cells. In this review, we focus on the latest enzyme systems based on novel DNA nanostructures: enzyme reactors, regulatory devices and carriers that can find uses in various biotechnological and nanomedical applications.

  20. Elevated Liver Enzymes

    Science.gov (United States)

    Symptoms Elevated liver enzymes By Mayo Clinic Staff Elevated liver enzymes may indicate inflammation or damage to cells in the liver. Inflamed or ... than normal amounts of certain chemicals, including liver enzymes, into the bloodstream, which can result in elevated ...

  1. Asymmetrical Damage Partitioning in Bacteria: A Model for the Evolution of Stochasticity, Determinism, and Genetic Assimilation.

    Science.gov (United States)

    Chao, Lin; Rang, Camilla Ulla; Proenca, Audrey Menegaz; Chao, Jasper Ubirajara

    2016-01-01

    Non-genetic phenotypic variation is common in biological organisms. The variation is potentially beneficial if the environment is changing. If the benefit is large, selection can favor the evolution of genetic assimilation, the process by which the expression of a trait is transferred from environmental to genetic control. Genetic assimilation is an important evolutionary transition, but it is poorly understood because the fitness costs and benefits of variation are often unknown. Here we show that the partitioning of damage by a mother bacterium to its two daughters can evolve through genetic assimilation. Bacterial phenotypes are also highly variable. Because gene-regulating elements can have low copy numbers, the variation is attributed to stochastic sampling. Extant Escherichia coli partition asymmetrically and deterministically more damage to the old daughter, the one receiving the mother's old pole. By modeling in silico damage partitioning in a population, we show that deterministic asymmetry is advantageous because it increases fitness variance and hence the efficiency of natural selection. However, we find that symmetrical but stochastic partitioning can be similarly beneficial. To examine why bacteria evolved deterministic asymmetry, we modeled the effect of damage anchored to the mother's old pole. While anchored damage strengthens selection for asymmetry by creating additional fitness variance, it has the opposite effect on symmetry. The difference results because anchored damage reinforces the polarization of partitioning in asymmetric bacteria. In symmetric bacteria, it dilutes the polarization. Thus, stochasticity alone may have protected early bacteria from damage, but deterministic asymmetry has evolved to be equally important in extant bacteria. We estimate that 47% of damage partitioning is deterministic in E. coli. We suggest that the evolution of deterministic asymmetry from stochasticity offers an example of Waddington's genetic assimilation

  2. Asymmetrical Damage Partitioning in Bacteria: A Model for the Evolution of Stochasticity, Determinism, and Genetic Assimilation.

    Directory of Open Access Journals (Sweden)

    Lin Chao

    2016-01-01

    Full Text Available Non-genetic phenotypic variation is common in biological organisms. The variation is potentially beneficial if the environment is changing. If the benefit is large, selection can favor the evolution of genetic assimilation, the process by which the expression of a trait is transferred from environmental to genetic control. Genetic assimilation is an important evolutionary transition, but it is poorly understood because the fitness costs and benefits of variation are often unknown. Here we show that the partitioning of damage by a mother bacterium to its two daughters can evolve through genetic assimilation. Bacterial phenotypes are also highly variable. Because gene-regulating elements can have low copy numbers, the variation is attributed to stochastic sampling. Extant Escherichia coli partition asymmetrically and deterministically more damage to the old daughter, the one receiving the mother's old pole. By modeling in silico damage partitioning in a population, we show that deterministic asymmetry is advantageous because it increases fitness variance and hence the efficiency of natural selection. However, we find that symmetrical but stochastic partitioning can be similarly beneficial. To examine why bacteria evolved deterministic asymmetry, we modeled the effect of damage anchored to the mother's old pole. While anchored damage strengthens selection for asymmetry by creating additional fitness variance, it has the opposite effect on symmetry. The difference results because anchored damage reinforces the polarization of partitioning in asymmetric bacteria. In symmetric bacteria, it dilutes the polarization. Thus, stochasticity alone may have protected early bacteria from damage, but deterministic asymmetry has evolved to be equally important in extant bacteria. We estimate that 47% of damage partitioning is deterministic in E. coli. We suggest that the evolution of deterministic asymmetry from stochasticity offers an example of Waddington

  3. [Research advance in nitrogen metabolism of plant and its environmental regulation].

    Science.gov (United States)

    Xu, Zhenzhu; Zhou, Guangsheng

    2004-03-01

    Nitrogen metabolism is not only one of the basic processes of plant physiology, but also one of the important parts of global chemical cycle. Plant nitrogen assimilation directly takes part in the synthesis and conversion of amino acid through the reduction of nitrate. During this stage, some key enzymes, e.g., nitrate reductase (NR), glutamine synthetase (GS), glutamate dehydrogenase (GDH), glutamine synthase (GOGAT), aspargine synthetase (AS), and asparate aminotransferase (AspAT) participate these processes. The protein is assimilated in plant cell through amino acid, and becomes a part of plant organism through modifying, classifying, transporting and storing processes, etc. The nitrogen metabolism is associated with carbonic metabolism through key enzyme regulations and the conversion of products, which consists of basic life process. Among these amino acids in plant cell, glutamic acid (Glu), glutamine (Gln), aspartic acid (Asp) and asparagines (Asn), etc., play a key role, which regulates their conversion each other and their contents in the plant cell through regulating formation and activity of those key enzymes. Environmental factors also affect the conversion and recycle of the key amino acids through regulating gene expression of the key enzymes and their activities. Nitrate and light intensity positively regulate the gene transcription of NR, but ammonium ions and Glu, Gln do the negative way. Water deficit is a very serious constraint on N2 fixation rate and soybean (Glycine max Merr.) grain yield, in which, ureide accumulation and degradation under water deficit appear to be the key issues of feedback mechanism on nitrogen fixation. Water stress decreases NR activity, but increases proteinase activity, and thus, they regulate plant nitrogen metabolism, although there are some different effects among species and cultivars. Water stress also decreases plant tissue protein content, ratio of protein and amino acid, and reduces the absorption of amino

  4. Data assimilation and PWR primary measurement

    International Nuclear Information System (INIS)

    Mercier, Thibaud

    2015-01-01

    A Pressurized Water Reactor (PWR) Reactor Coolant System (RCS) is a highly complex physical process: heterogeneous power, flow and temperature distributions are difficult to be accurately measured, since instrumentations are limited in number, thus leading to the relevant safety and protection margins. EDF R and D is seeking to assess the potential benefits of applying Data Assimilation to a PWR's RCS (Reactor Coolant System) measurements, in order to improve the estimators for parameters of a reactor's operating setpoint, i.e. improving accuracy and reducing uncertainties and biases of measured RCS parameters. In this thesis, we define a 0D semi-empirical model for RCS, satisfying the description level usually chosen by plant operators, and construct a Monte-Carlo Method (inspired from Ensemble Methods) in order to use this model with Data Assimilation tools. We apply this method on simulated data in order to assess the reduction of uncertainties on key parameters: results are beyond expectations, however strong hypothesis are required, implying a careful preprocessing of input data. (author)

  5. Data Assimilation by delay-coordinate nudging

    Science.gov (United States)

    Pazo, Diego; Lopez, Juan Manuel; Carrassi, Alberto

    2016-04-01

    A new nudging method for data assimilation, delay-coordinate nudging, is presented. Delay-coordinate nudging makes explicit use of present and past observations in the formulation of the forcing driving the model evolution at each time-step. Numerical experiments with a low order chaotic system show that the new method systematically outperforms standard nudging in different model and observational scenarios, also when using an un-optimized formulation of the delay-nudging coefficients. A connection between the optimal delay and the dominant Lyapunov exponent of the dynamics is found based on heuristic arguments and is confirmed by the numerical results, providing a guideline for the practical implementation of the algorithm. Delay-coordinate nudging preserves the easiness of implementation, the intuitive functioning and the reduced computational cost of the standard nudging, making it a potential alternative especially in the field of seasonal-to-decadal predictions with large Earth system models that limit the use of more sophisticated data assimilation procedures.

  6. Turbulent viscosity optimized by data assimilation

    Directory of Open Access Journals (Sweden)

    Y. Leredde

    Full Text Available As an alternative approach to classical turbulence modelling using a first or second order closure, the data assimilation method of optimal control is applied to estimate a time and space-dependent turbulent viscosity in a three-dimensional oceanic circulation model. The optimal control method, described for a 3-D primitive equation model, involves the minimization of a cost function that quantifies the discrepancies between the simulations and the observations. An iterative algorithm is obtained via the adjoint model resolution. In a first experiment, a k + L model is used to simulate the one-dimensional development of inertial oscillations resulting from a wind stress at the sea surface and with the presence of a halocline. These results are used as synthetic observations to be assimilated. The turbulent viscosity is then recovered without the k + L closure, even with sparse and noisy observations. The problems of controllability and of the dimensions of the control are then discussed. A second experiment consists of a two-dimensional schematic simulation. A 2-D turbulent viscosity field is estimated from data on the initial and final states of a coastal upwelling event.

    Key words. Oceanography: general (numerical modelling · Oceanography: physical (turbulence · diffusion · and mixing processes

  7. Impact of Assimilation on Heavy Rainfall Simulations Using WRF Model: Sensitivity of Assimilation Results to Background Error Statistics

    Science.gov (United States)

    Rakesh, V.; Kantharao, B.

    2017-03-01

    Data assimilation is considered as one of the effective tools for improving forecast skill of mesoscale models. However, for optimum utilization and effective assimilation of observations, many factors need to be taken into account while designing data assimilation methodology. One of the critical components that determines the amount and propagation observation information into the analysis, is model background error statistics (BES). The objective of this study is to quantify how BES in data assimilation impacts on simulation of heavy rainfall events over a southern state in India, Karnataka. Simulations of 40 heavy rainfall events were carried out using Weather Research and Forecasting Model with and without data assimilation. The assimilation experiments were conducted using global and regional BES while the experiment with no assimilation was used as the baseline for assessing the impact of data assimilation. The simulated rainfall is verified against high-resolution rain-gage observations over Karnataka. Statistical evaluation using several accuracy and skill measures shows that data assimilation has improved the heavy rainfall simulation. Our results showed that the experiment using regional BES outperformed the one which used global BES. Critical thermo-dynamic variables conducive for heavy rainfall like convective available potential energy simulated using regional BES is more realistic compared to global BES. It is pointed out that these results have important practical implications in design of forecast platforms while decision-making during extreme weather events

  8. Immune responses of mussel hemocyte subpopulations are differentially regulated by enzymes of the PI 3-K, PKC, and ERK kinase families.

    Science.gov (United States)

    García-García, Erick; Prado-Alvarez, Maria; Novoa, Beatriz; Figueras, Antonio; Rosales, Carlos

    2008-01-01

    Various hemocyte cell types have been described in invertebrates, but for most species a functional characterization of different hemocyte cell types is still lacking. In order to characterize some immunological properties of mussel (Mytilus galloprovincialis) hemocytes, cells were separated by flow cytometry and their capacity for phagocytosis, production of reactive oxygen species (ROS), and production of nitric oxide (NO), was examined. Phosphatidylinositol 3-kinase (PI 3-K), protein kinase C (PKC), and extracellular signal-regulated kinase (ERK) inhibitors were also used to biochemically characterize these cell responses. Four morphologically distinct subpopulations, designated R1-R4, were detected. R1, R2, and R3 cells presented different levels of phagocytosis towards zymosan, latex beads, and two bacteria species. Similarly, R1 to R3, but not R4, cells produced ROS, while all subpopulations produced NO, in response to zymosan. Internalization of all phagocytic targets was blocked by PI 3-K inhibition. In addition, internalization of latex particles, but not of bacteria, was partially blocked by PKC or ERK inhibition. Interestingly, phagocytosis of zymosan was impaired by PKC, or ERK inhibitors, only in R2 cells. Zymosan-induced ROS production was blocked by PI 3-K inhibition, but not by PKC, or ERK inhibition. In addition, zymosan-stimulated NO production was affected by PI 3-K inhibition in R1 and R2, but not in R3 or R4 cells. NO production in all cell types was unaffected by PKC inhibition, but ERK inhibition blocked it in R2 cells. These data reveal the existence of profound functional and biochemical differences in mussel hemocytes and indicate that M. galloprovincialis hemocytes are specialized cells fulfilling specific tasks in the context of host defense.

  9. Redox regulation of the Calvin-Benson cycle: something old, something new

    Directory of Open Access Journals (Sweden)

    Laure eMichelet

    2013-11-01

    Full Text Available Reversible redox post-translational modifications such as oxido-reduction of disulfide bonds, S-nitrosylation and S-glutathionylation, play a prominent role in the regulation of cell metabolism and signaling in all organisms. These modifications are mainly controlled by members of the thioredoxin and glutaredoxin families. Early studies in photosynthetic organisms have identified the Calvin-Benson cycle, the photosynthetic pathway responsible for carbon assimilation, as a redox regulated process. Indeed, 4 out of 11 enzymes of the cycle were shown to have a low activity in the dark and to be activated in the light through thioredoxin-dependent reduction of regulatory disulfide bonds. The underlying molecular mechanisms were extensively studied at the biochemical and structural level. Unexpectedly, recent biochemical and proteomic studies have suggested that all enzymes of the cycle and several associated regulatory proteins may undergo redox regulation through multiple redox post-translational modifications including glutathionylation and nitrosylation. The aim of this review is to detail the well-established mechanisms of redox regulation of Calvin-Benson cycle enzymes as well as the most recent reports indicating that this pathway is tightly controlled by multiple interconnected redox post-translational modifications. This redox control is likely allowing fine tuning of the Calvin-Benson cycle required for adaptation to varying environmental conditions, especially during responses to biotic and abiotic stresses.

  10. Shengjiang Xiexin Decoction Alters Pharmacokinetics of Irinotecan by Regulating Metabolic Enzymes and Transporters: A Multi-Target Therapy for Alleviating the Gastrointestinal Toxicity.

    Science.gov (United States)

    Guan, Huan-Yu; Li, Peng-Fei; Wang, Xiao-Ming; Yue, Jia-Jing; He, Yang; Luo, Xiao-Mei; Su, Mei-Feng; Liao, Shang-Gao; Shi, Yue

    2017-01-01

    Shengjiang Xiexin decoction (SXD), a classic traditional Chinese medical formula chronicled in Shang Han Lun , is used in modern clinical practice to decrease gastrointestinal toxicity induced by the chemotherapeutic drug irinotecan (CPT-11). In this study, the effect of SXD on the pharmacokinetics of CPT-11 and its active metabolites (SN-38 and SN-38G), and the underlying mechanisms were further examined. An ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method was developed and validated for the simultaneous quantification of CPT-11, SN-38, and SN-38G in the plasma, bile, liver, intestine, and intestinal contents of control and SXD-pre-treated rats after intravenous administration of CPT-11. SXD pretreatment increased the area under the curve (AUC) and the initial plasma concentration (C 0 ) of CPT-11 but decreased the plasma clearance (CL). The AUC and the maximum plasma concentration (C max ) of SN-38 decreased, whereas the C max of SN-38G increased. Compared with that of the control group, the biliary excretion of CPT-11, SN-38, and SN-38G was inhibited. The CPT-11, SN-38, and SN-38G concentrations in the liver, intestine, and intestinal contents were different between the two groups. Furthermore, the hepatic expression of multidrug resistance-associated protein-2 (Mrp-2), P-glycoprotein (P-gp), and carboxylesterase 2 (CES2) was significantly down-regulated by SXD, while the hepatic and jejunal uridine diphosphate (UDP)-glucuronosyltransferase 1A1 (UGT1A1) expression was elevated. The hydrolysis of CPT-11 to SN-38 by CES and the glucuronidation of SN-38 to SN-38G by UGT were affected by liver and jejunum S9 fractions from rats pre-treated with SXD. Therefore, this study demonstrated for the first time that SXD could alter the pharmacokinetics of CPT-11 and its metabolites to alleviate CPT-11-induced diarrhea. And the underlying mechanism of drug interaction between CPT-11 and SXD involves decreasing hepatic Mrp-2 and P

  11. Shengjiang Xiexin Decoction Alters Pharmacokinetics of Irinotecan by Regulating Metabolic Enzymes and Transporters: A Multi-Target Therapy for Alleviating the Gastrointestinal Toxicity

    Directory of Open Access Journals (Sweden)

    Huan-yu Guan

    2017-10-01

    Full Text Available Shengjiang Xiexin decoction (SXD, a classic traditional Chinese medical formula chronicled in Shang Han Lun, is used in modern clinical practice to decrease gastrointestinal toxicity induced by the chemotherapeutic drug irinotecan (CPT-11. In this study, the effect of SXD on the pharmacokinetics of CPT-11 and its active metabolites (SN-38 and SN-38G, and the underlying mechanisms were further examined. An ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS method was developed and validated for the simultaneous quantification of CPT-11, SN-38, and SN-38G in the plasma, bile, liver, intestine, and intestinal contents of control and SXD-pre-treated rats after intravenous administration of CPT-11. SXD pretreatment increased the area under the curve (AUC and the initial plasma concentration (C0 of CPT-11 but decreased the plasma clearance (CL. The AUC and the maximum plasma concentration (Cmax of SN-38 decreased, whereas the Cmax of SN-38G increased. Compared with that of the control group, the biliary excretion of CPT-11, SN-38, and SN-38G was inhibited. The CPT-11, SN-38, and SN-38G concentrations in the liver, intestine, and intestinal contents were different between the two groups. Furthermore, the hepatic expression of multidrug resistance-associated protein-2 (Mrp-2, P-glycoprotein (P-gp, and carboxylesterase 2 (CES2 was significantly down-regulated by SXD, while the hepatic and jejunal uridine diphosphate (UDP-glucuronosyltransferase 1A1 (UGT1A1 expression was elevated. The hydrolysis of CPT-11 to SN-38 by CES and the glucuronidation of SN-38 to SN-38G by UGT were affected by liver and jejunum S9 fractions from rats pre-treated with SXD. Therefore, this study demonstrated for the first time that SXD could alter the pharmacokinetics of CPT-11 and its metabolites to alleviate CPT-11-induced diarrhea. And the underlying mechanism of drug interaction between CPT-11 and SXD involves decreasing hepatic Mrp-2 and P

  12. Data assimilation in the decision support system RODOS

    DEFF Research Database (Denmark)

    Rojas-Palma, C.; Madsen, H.; Gering, F.

    2003-01-01

    . The process of combining model predictions and observations, usually referred to as data assimilation, is described in this article within the framework of the real time on-line decision support system (RODOS) for off-site nuclear emergency management in Europe. Data assimilation capabilities, based on Kalman...

  13. Assimilation as Attraction: Computing Distance, Similarity, and Locality in Phonology

    Science.gov (United States)

    Wayment, Adam

    2009-01-01

    This dissertation explores similarity effects in assimilation, proposing an Attraction Framework to analyze cases of parasitic harmony where a trigger-target pair only results in harmony if the trigger and target agree on other features. Attraction provides a natural model of these effects by relating the pressure for assimilation to the…

  14. The dynamic radiation environment assimilation model (DREAM)

    International Nuclear Information System (INIS)

    Reeves, Geoffrey D.; Koller, Josef; Tokar, Robert L.; Chen, Yue; Henderson, Michael G.; Friedel, Reiner H.

    2010-01-01

    The Dynamic Radiation Environment Assimilation Model (DREAM) is a 3-year effort sponsored by the US Department of Energy to provide global, retrospective, or real-time specification of the natural and potential nuclear radiation environments. The DREAM model uses Kalman filtering techniques that combine the strengths of new physical models of the radiation belts with electron observations from long-term satellite systems such as GPS and geosynchronous systems. DREAM includes a physics model for the production and long-term evolution of artificial radiation belts from high altitude nuclear explosions. DREAM has been validated against satellites in arbitrary orbits and consistently produces more accurate results than existing models. Tools for user-specific applications and graphical displays are in beta testing and a real-time version of DREAM has been in continuous operation since November 2009.

  15. Assimilating data into open ocean tidal models

    Science.gov (United States)

    Kivman, Gennady A.

    The problem of deriving tidal fields from observations by reason of incompleteness and imperfectness of every data set practically available has an infinitely large number of allowable solutions fitting the data within measurement errors and hence can be treated as ill-posed. Therefore, interpolating the data always relies on some a priori assumptions concerning the tides, which provide a rule of sampling or, in other words, a regularization of the ill-posed problem. Data assimilation procedures used in large scale tide modeling are viewed in a common mathematical framework as such regularizations. It is shown that they all (basis functions expansion, parameter estimation, nudging, objective analysis, general inversion, and extended general inversion), including those (objective analysis and general inversion) originally formulated in stochastic terms, may be considered as utilizations of one of the three general methods suggested by the theory of ill-posed problems. The problem of grid refinement critical for inverse methods and nudging is discussed.

  16. How Do Enzymes 'Meet' Nanoparticles and Nanomaterials?

    Science.gov (United States)

    Chen, Ming; Zeng, Guangming; Xu, Piao; Lai, Cui; Tang, Lin

    2017-11-01

    Enzymes are fundamental biological catalysts responsible for biological regulation and metabolism. The opportunity for enzymes to 'meet' nanoparticles and nanomaterials is rapidly increasing due to growing demands for applications in nanomaterial design, environmental monitoring, biochemical engineering, and biomedicine. Therefore, understanding the nature of nanomaterial-enzyme interactions is becoming important. Since 2014, enzymes have been used to modify, degrade, or make nanoparticles/nanomaterials, while numerous nanoparticles/nanomaterials have been used as materials for enzymatic immobilization and biosensors and as enzyme mimicry. Among the various nanoparticles and nanomaterials, metal nanoparticles and carbon nanomaterials have received extensive attention due to their fascinating properties. This review provides an overview about how enzymes meet nanoparticles and nanomaterials. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Assimilation of stratospheric ozone in the chemical transport model STRATAQ

    Directory of Open Access Journals (Sweden)

    B. Grassi

    2004-09-01

    Full Text Available We describe a sequential assimilation approach useful for assimilating tracer measurements into a three-dimensional chemical transport model (CTM of the stratosphere. The numerical code, developed largely according to Kha00, uses parameterizations and simplifications allowing assimilation of sparse observations and the simultaneous evaluation of analysis errors, with reasonable computational requirements. Assimilation parameters are set by using χ2 and OmF (Observation minus Forecast statistics. The CTM used here is a high resolution three-dimensional model. It includes a detailed chemical package and is driven by UKMO (United Kingdom Meteorological Office analyses. We illustrate the method using assimilation of Upper Atmosphere Research Satellite/Microwave Limb Sounder (UARS/MLS ozone observations for three weeks during the 1996 antarctic spring. The comparison of results from the simulations with TOMS (Total Ozone Mapping Spectrometer measurements shows improved total ozone fields due to assimilation of MLS observations. Moreover, the assimilation gives indications on a possible model weakness in reproducing polar ozone values during springtime.

  18. Statistical techniques to extract information during SMAP soil moisture assimilation

    Science.gov (United States)

    Kolassa, J.; Reichle, R. H.; Liu, Q.; Alemohammad, S. H.; Gentine, P.

    2017-12-01

    Statistical techniques permit the retrieval of soil moisture estimates in a model climatology while retaining the spatial and temporal signatures of the satellite observations. As a consequence, the need for bias correction prior to an assimilation of these estimates is reduced, which could result in a more effective use of the independent information provided by the satellite observations. In this study, a statistical neural network (NN) retrieval algorithm is calibrated using SMAP brightness temperature observations and modeled soil moisture estimates (similar to those used to calibrate the SMAP Level 4 DA system). Daily values of surface soil moisture are estimated using the NN and then assimilated into the NASA Catchment model. The skill of the assimilation estimates is assessed based on a comprehensive comparison to in situ measurements from the SMAP core and sparse network sites as well as the International Soil Moisture Network. The NN retrieval assimilation is found to significantly improve the model skill, particularly in areas where the model does not represent processes related to agricultural practices. Additionally, the NN method is compared to assimilation experiments using traditional bias correction techniques. The NN retrieval assimilation is found to more effectively use the independent information provided by SMAP resulting in larger model skill improvements than assimilation experiments using traditional bias correction techniques.

  19. On the role of perception in shaping phonological assimilation rules.

    Science.gov (United States)

    Hura, S L; Lindblom, B; Diehl, R L

    1992-01-01

    Assimilation of nasals to the place of articulation of following consonants is a common and natural process among the world's languages. Recent phonological theory attributes this naturalness to the postulated geometry of articulatory features and the notion of spreading (McCarthy, 1988). Others view assimilation as a result of perception (Ohala, 1990), or as perceptually tolerated articulatory simplification (Kohler, 1990). Kohler notes that certain consonant classes (such as nasals and stops) are more likely than other classes (such as fricatives) to undergo place assimilation to a following consonant. To explain this pattern, he proposes that assimilation tends not to occur when the members of a consonant class are relatively distinctive perceptually, such that their articulatory reduction would be particularly salient. This explanation, of course, presupposes that the stops and nasals which undergo place assimilation are less distinctive than fricatives, which tend not to assimilate. We report experimental results that confirm Kohler's perceptual assumption: In the context of a following word initial stop, fricatives were less confusable than nasals or unreleased stops. We conclude, in agreement with Ohala and Kohler, that perceptual factors are likely to shape phonological assimilation rules.

  20. Assimilation of stratospheric ozone in the chemical transport model STRATAQ

    Directory of Open Access Journals (Sweden)

    B. Grassi

    2004-09-01

    Full Text Available We describe a sequential assimilation approach useful for assimilating tracer measurements into a three-dimensional chemical transport model (CTM of the stratosphere. The numerical code, developed largely according to Kha00, uses parameterizations and simplifications allowing assimilation of sparse observations and the simultaneous evaluation of analysis errors, with reasonable computational requirements. Assimilation parameters are set by using χ2 and OmF (Observation minus Forecast statistics. The CTM used here is a high resolution three-dimensional model. It includes a detailed chemical package and is driven by UKMO (United Kingdom Meteorological Office analyses. We illustrate the method using assimilation of Upper Atmosphere Research Satellite/Microwave Limb Sounder (UARS/MLS ozone observations for three weeks during the 1996 antarctic spring. The comparison of results from the simulations with TOMS (Total Ozone Mapping Spectrometer measurements shows improved total ozone fields due to assimilation of MLS observations. Moreover, the assimilation gives indications on a possible model weakness in reproducing polar ozone values during springtime.

  1. SMOS brightness temperature assimilation into the Community Land Model

    Directory of Open Access Journals (Sweden)

    D. Rains

    2017-11-01

    Full Text Available SMOS (Soil Moisture and Ocean Salinity mission brightness temperatures at a single incident angle are assimilated into the Community Land Model (CLM across Australia to improve soil moisture simulations. Therefore, the data assimilation system DasPy is coupled to the local ensemble transform Kalman filter (LETKF as well as to the Community Microwave Emission Model (CMEM. Brightness temperature climatologies are precomputed to enable the assimilation of brightness temperature anomalies, making use of 6 years of SMOS data (2010–2015. Mean correlation R with in situ measurements increases moderately from 0.61 to 0.68 (11 % for upper soil layers if the root zone is included in the updates. A reduced improvement of 5 % is achieved if the assimilation is restricted to the upper soil layers. Root-zone simulations improve by 7 % when updating both the top layers and root zone, and by 4 % when only updating the top layers. Mean increments and increment standard deviations are compared for the experiments. The long-term assimilation impact is analysed by looking at a set of quantiles computed for soil moisture at each grid cell. Within hydrological monitoring systems, extreme dry or wet conditions are often defined via their relative occurrence, adding great importance to assimilation-induced quantile changes. Although still being limited now, longer L-band radiometer time series will become available and make model output improved by assimilating such data that are more usable for extreme event statistics.

  2. Chromatic assimilation unaffected by perceived depth of inducing light.

    Science.gov (United States)

    Shevell, Steven K; Cao, Dingcai

    2004-01-01

    Chromatic assimilation is a shift toward the color of nearby light. Several studies conclude that a neural process contributes to assimilation but the neural locus remains in question. Some studies posit a peripheral process, such as retinal receptive-field organization, while others claim the neural mechanism follows depth perception, figure/ground segregation, or perceptual grouping. The experiments here tested whether assimilation depends on a neural process that follows stereoscopic depth perception. By introducing binocular disparity, the test field judged in color was made to appear in a different depth plane than the light that induced assimilation. The chromaticity and spatial frequency of the inducing light, and the chromaticity of the test light, were varied. Chromatic assimilation was found with all inducing-light sizes and chromaticities, but the magnitude of assimilation did not depend on the perceived relative depth planes of the test and inducing fields. We found no evidence to support the view that chromatic assimilation depends on a neural process that follows binocular combination of the two eyes' signals.

  3. Assimilation of wheat starch in patients with chronic pancreatitis. Positive effect of enzyme replacement

    DEFF Research Database (Denmark)

    Nordgaard, I; Rumessen, J J; Gudmand-Høyer, E

    1992-01-01

    Pancreatic insufficiency due to chronic pancreatitis may lead to symptomatic malabsorption of both starch and fat. The absorption capacity of wheat starch has not been studied previously in patients with chronic pancreatitis, although this carbohydrate is a quantitatively important component of t...

  4. Horizontal transfer of a nitrate assimilation gene cluster and ecological transitions in fungi: a phylogenetic study.

    Directory of Open Access Journals (Sweden)

    Jason C Slot

    Full Text Available High affinity nitrate assimilation genes in fungi occur in a cluster (fHANT-AC that can be coordinately regulated. The clustered genes include nrt2, which codes for a high affinity nitrate transporter; euknr, which codes for nitrate reductase; and NAD(PH-nir, which codes for nitrite reductase. Homologs of genes in the fHANT-AC occur in other eukaryotes and prokaryotes, but they have only been found clustered in the oomycete Phytophthora (heterokonts. We performed independent and concatenated phylogenetic analyses of homologs of all three genes in the fHANT-AC. Phylogenetic analyses limited to fungal sequences suggest that the fHANT-AC has been transferred horizontally from a basidiomycete (mushrooms and smuts to an ancestor of the ascomycetous mold Trichoderma reesei. Phylogenetic analyses of sequences from diverse eukaryotes and eubacteria, and cluster structure, are consistent with a hypothesis that the fHANT-AC was assembled in a lineage leading to the oomycetes and was subsequently transferred to the Dikarya (Ascomycota+Basidiomycota, which is a derived fungal clade that includes the vast majority of terrestrial fungi. We propose that the acquisition of high affinity nitrate assimilation contributed to the success of Dikarya on land by allowing exploitation of nitrate in aerobic soils, and the subsequent transfer of a complete assimilation cluster improved the fitness of T. reesei in a new niche. Horizontal transmission of this cluster of functionally integrated genes supports the "selfish operon" hypothesis for maintenance of gene clusters.

  5. Application of Bred Vectors To Data Assimilation

    Science.gov (United States)

    Corazza, M.; Kalnay, E.; Patil, Dj

    We introduced a statistic, the BV-dimension, to measure the effective local finite-time dimensionality of the atmosphere. We show that this dimension is often quite low, and suggest that this finding has important implications for data assimilation and the accuracy of weather forecasting (Patil et al, 2001). The original database for this study was the forecasts of the NCEP global ensemble forecasting system. The initial differences between the control forecast and the per- turbed forecasts are called bred vectors. The control and perturbed initial conditions valid at time t=n(t are evolved using the forecast model until time t=(n+1) (t. The differences between the perturbed and the control forecasts are scaled down to their initial amplitude, and constitute the bred vectors valid at (n+1) (t. Their growth rate is typically about 1.5/day. The bred vectors are similar by construction to leading Lya- punov vectors except that they have small but finite amplitude, and they are valid at finite times. The original NCEP ensemble data set has 5 independent bred vectors. We define a local bred vector at each grid point by choosing the 5 by 5 grid points centered at the grid point (a region of about 1100km by 1100km), and using the north-south and east- west velocity components at 500mb pressure level to form a 50 dimensional column vector. Since we have k=5 global bred vectors, we also have k local bred vectors at each grid point. We estimate the effective dimensionality of the subspace spanned by the local bred vectors by performing a singular value decomposition (EOF analysis). The k local bred vector columns form a 50xk matrix M. The singular values s(i) of M measure the extent to which the k column unit vectors making up the matrix M point in the direction of v(i). We define the bred vector dimension as BVDIM={Sum[s(i)]}^2/{Sum[s(i)]^2} For example, if 4 out of the 5 vectors lie along v, and one lies along v, the BV- dimension would be BVDIM[sqrt(4), 1, 0

  6. Melatonin Improves the Photosynthetic Carbon Assimilation and Antioxidant Capacity in Wheat Exposed to Nano-ZnO Stress

    Directory of Open Access Journals (Sweden)

    Zhiyu Zuo

    2017-10-01

    Full Text Available The release of nanoparticles into the environment is inevitable, which has raised global environmental concern. Melatonin is involved in various stress responses in plants. The present study investigated the effects of melatonin on photosynthetic carbon (C assimilation and plant growth in nano-ZnO stressed plants. It was found that melatonin improved the photosynthetic C assimilation in nano-ZnO stressed wheat plants, mainly due to the enhanced photosynthetic energy transport efficiency, higher chlorophyll concentration and higher activities of Rubisco and ATPases. In addition, melatonin enhanced the activities of antioxidant enzymes to protect the photosynthetic electron transport system in wheat leaves against the oxidative burst caused by nano-ZnO stress. These results suggest that melatonin could improve the tolerance of wheat plants to nano-ZnO stress.

  7. Towards a Comprehensive Dynamic-chemistry Assimilation for Eos-Chem: Plans and Status in NASA's Data Assimilation Office

    Science.gov (United States)

    Pawson, Steven; Lin, Shian-Jiann; Rood, Richard B.; Stajner, Ivanka; Nebuda, Sharon; Nielsen, J. Eric; Douglass, Anne R.

    2000-01-01

    In order to support the EOS-Chem project, a comprehensive assimilation package for the coupled chemical-dynamical system is being developed by the Data Assimilation Office at NASA GSFC. This involves development of a coupled chemistry/meteorology model and of data assimilation techniques for trace species and meteorology. The model is being developed using the flux-form semi-Lagrangian dynamical core of Lin and Rood, the physical parameterizations from the NCAR Community Climate Model, and atmospheric chemistry modules from the Atmospheric Chemistry and Dynamics branch at NASA GSFC. To date the following results have been obtained: (i) multi-annual simulations with the dynamics-radiation model show the credibility of the package for atmospheric simulations; (ii) initial simulations including a limited number of middle atmospheric trace gases reveal the realistic nature of transport mechanisms, although there is still a need for some improvements. Samples of these results will be shown. A meteorological assimilation system is currently being constructed using the model; this will form the basis for the proposed meteorological/chemical assimilation package. The latter part of the presentation will focus on areas targeted for development in the near and far terms, with the objective of Providing a comprehensive assimilation package for the EOS-Chem science experiment. The first stage will target ozone assimilation. The plans also encompass a reanalysis (ReSTS) for the 1991-1995 period, which includes the Mt. Pinatubo eruption and the time when a large number of UARS observations were available. One of the most challenging aspects of future developments will be to couple theoretical advances in tracer assimilation with the practical considerations of a real environment and eventually a near-real-time assimilation system.

  8. Assimilate partitioning in avocado, Persea americana

    Energy Technology Data Exchange (ETDEWEB)

    Finazzo, S.; Davenport, T.L.

    1986-04-01

    Assimilate partitioning is being studied in avocado, Persea americana cv. Millborrow in relation to fruit set. Single leaves on girdled branches of 10 year old trees were radiolabeled for 1 hr with 13..mu..Ci of /sup 14/CO/sub 2/. The source leaves were sampled during the experiment to measure translocation rates. At harvest the sink tissues were dissected and the incorporated radioactivity was measured. The translocation of /sup 14/C-labelled compounds to other leaves was minimal. Incorporation of label into fruitlets varied with the tissue and the stage of development. Sink (fruitlets) nearest to the labelled leaf and sharing the same phyllotaxy incorporated the most /sup 14/C. Source leaves for single non-abscising fruitlets retained 3X more /sup 14/C-labelled compounds than did source leaves for 2 or more fruitlets at 31 hrs. post-labelling. Export of label decreased appreciably when fruitlets abscised. If fruitlets abscised within 4 days of labeling then the translocation pattern was similar to the pattern for single fruitlets. If the fruitlet abscised later, the translocation pattern was intermediate between the single and double fruitlet pattern.

  9. Efficient data assimilation algorithm for bathymetry application

    Science.gov (United States)

    Ghorbanidehno, H.; Lee, J. H.; Farthing, M.; Hesser, T.; Kitanidis, P. K.; Darve, E. F.

    2017-12-01

    Information on the evolving state of the nearshore zone bathymetry is crucial to shoreline management, recreational safety, and naval operations. The high cost and complex logistics of using ship-based surveys for bathymetry estimation have encouraged the use of remote sensing techniques. Data assimilation methods combine the remote sensing data and nearshore hydrodynamic models to estimate the unknown bathymetry and the corresponding uncertainties. In particular, several recent efforts have combined Kalman Filter-based techniques such as ensembled-based Kalman filters with indirect video-based observations to address the bathymetry inversion problem. However, these methods often suffer from ensemble collapse and uncertainty underestimation. Here, the Compressed State Kalman Filter (CSKF) method is used to estimate the bathymetry based on observed wave celerity. In order to demonstrate the accuracy and robustness of the CSKF method, we consider twin tests with synthetic observations of wave celerity, while the bathymetry profiles are chosen based on surveys taken by the U.S. Army Corps of Engineer Field Research Facility (FRF) in Duck, NC. The first test case is a bathymetry estimation problem for a spatially smooth and temporally constant bathymetry profile. The second test case is a bathymetry estimation problem for a temporally evolving bathymetry from a smooth to a non-smooth profile. For both problems, we compare the results of CSKF with those obtained by the local ensemble transform Kalman filter (LETKF), which is a popular ensemble-based Kalman filter method.

  10. Efficient Data Assimilation Algorithms for Bathymetry Applications

    Science.gov (United States)

    Ghorbanidehno, H.; Kokkinaki, A.; Lee, J. H.; Farthing, M.; Hesser, T.; Kitanidis, P. K.; Darve, E. F.

    2016-12-01

    Information on the evolving state of the nearshore zone bathymetry is crucial to shoreline management, recreational safety, and naval operations. The high cost and complex logistics of using ship-based surveys for bathymetry estimation have encouraged the use of remote sensing monitoring. Data assimilation methods combine monitoring data and models of nearshore dynamics to estimate the unknown bathymetry and the corresponding uncertainties. Existing applications have been limited to the basic Kalman Filter (KF) and the Ensemble Kalman Filter (EnKF). The former can only be applied to low-dimensional problems due to its computational cost; the latter often suffers from ensemble collapse and uncertainty underestimation. This work explores the use of different variants of the Kalman Filter for bathymetry applications. In particular, we compare the performance of the EnKF to the Unscented Kalman Filter and the Hierarchical Kalman Filter, both of which are KF variants for non-linear problems. The objective is to identify which method can better handle the nonlinearities of nearshore physics, while also having a reasonable computational cost. We present two applications; first, the bathymetry of a synthetic one-dimensional cross section normal to the shore is estimated from wave speed measurements. Second, real remote measurements with unknown error statistics are used and compared to in situ bathymetric survey data collected at the USACE Field Research Facility in Duck, NC. We evaluate the information content of different data sets and explore the impact of measurement error and nonlinearities.

  11. Assimilate partitioning in avocado, Persea americana

    International Nuclear Information System (INIS)

    Finazzo, S.; Davenport, T.L.

    1986-01-01

    Assimilate partitioning is being studied in avocado, Persea americana cv. Millborrow in relation to fruit set. Single leaves on girdled branches of 10 year old trees were radiolabeled for 1 hr with 13μCi of 14 CO 2 . The source leaves were sampled during the experiment to measure translocation rates. At harvest the sink tissues were dissected and the incorporated radioactivity was measured. The translocation of 14 C-labelled compounds to other leaves was minimal. Incorporation of label into fruitlets varied with the tissue and the stage of development. Sink (fruitlets) nearest to the labelled leaf and sharing the same phyllotaxy incorporated the most 14 C. Source leaves for single non-abscising fruitlets retained 3X more 14 C-labelled compounds than did source leaves for 2 or more fruitlets at 31 hrs. post-labelling. Export of label decreased appreciably when fruitlets abscised. If fruitlets abscised within 4 days of labeling then the translocation pattern was similar to the pattern for single fruitlets. If the fruitlet abscised later, the translocation pattern was intermediate between the single and double fruitlet pattern

  12. Enzyme inhibition by iminosugars

    DEFF Research Database (Denmark)

    López, Óscar; Qing, Feng-Ling; Pedersen, Christian Marcus

    2013-01-01

    Imino- and azasugar glycosidase inhibitors display pH dependant inhibition reflecting that both the inhibitor and the enzyme active site have groups that change protonation state with pH. With the enzyme having two acidic groups and the inhibitor one basic group, enzyme-inhibitor complexes...

  13. Develop a Hybrid Coordinate Ocean Model with Data Assimilation Capabilities

    National Research Council Canada - National Science Library

    Thacker, W. C

    2003-01-01

    .... The objectives of the research are as follows: (1) to develop a methodology for assimilating temperature and salinity profiles from XBT, CTD, and ARGO float data that accommodates the peculiarities of HYCOM's hybrid vertical coordinates, allowing...

  14. Regional Ocean Modeling System (ROMS): CNMI: Data Assimilating

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Regional Ocean Modeling System (ROMS) 3-day, 3-hourly data assimilating hindcast for the region surrounding the Commonwealth of the Northern Mariana Islands (CNMI)...

  15. A simple lightning assimilation technique for improving retrospective WRF simulations.

    Science.gov (United States)

    Convective rainfall is often a large source of error in retrospective modeling applications. In particular, positive rainfall biases commonly exist during summer months due to overactive convective parameterizations. In this study, lightning assimilation was applied in the Kain-F...

  16. Data assimilation in modeling ocean processes: A bibliographic study

    Digital Repository Service at National Institute of Oceanography (India)

    Mahadevan, R.; Fernandes, A.A.; Saran, A.K.

    An annotated bibliography on studies related to data assimilation in modeling ocean processes has been prepared. The bibliography listed here is not comprehensive and is not prepared from the original references. Information obtainable from...

  17. Air Quality Activities in the Global Modeling and Assimilation Office

    Science.gov (United States)

    Pawson, Steven

    2016-01-01

    GMAO's mission is to enhance the use of NASA's satellite observations in weather and climate modeling. This presentation will be discussing GMAO's mission, value of data assimilation, and some relevant (available) GMAO data products.

  18. UARS Correlative UKMO Daily Gridded Stratospheric Assimilated Data V001

    Data.gov (United States)

    National Aeronautics and Space Administration — The UARS Correlative assimilation data from the U.K. Meteorological Office (UKMO) consists of daily model runs at 12:00 GMT as a means of providing an independent...

  19. Regional Ocean Modeling System (ROMS): Samoa: Data Assimilating

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Regional Ocean Modeling System (ROMS) 3-day, 3-hourly data assimilating hindcast for the region surrounding the islands of Samoa at approximately 3-km resolution....

  20. Regional Ocean Modeling System (ROMS): Main Hawaiian Islands: Data Assimilating

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Regional Ocean Modeling System (ROMS) 3-day, 3-hourly data assimilating hindcast for the region surrounding the main Hawaiian islands at approximately 4-km...

  1. The Culure Assimilator: An Approach to Cross-Cultural Training

    Science.gov (United States)

    Fiedler, Fred E.; And Others

    1971-01-01

    Evaluates the cultural assimilator, a kind of training manual to help members of one culture understand and adjust to another culture. Describes those constructed for the Arab countries, Iran, Thailand, Central America, and Greece. (MB)

  2. Regional Ocean Modeling System (ROMS): Oahu: Data Assimilating

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Regional Ocean Modeling System (ROMS) 2-day, 3-hourly data assimilating hindcast for the region surrounding the island of Oahu at approximately 1-km resolution....

  3. Assimilation of Aircraft Observations in High-Resolution Mesoscale Modeling

    Directory of Open Access Journals (Sweden)

    Brian P. Reen

    2018-01-01

    Full Text Available Aircraft-based observations are a promising source of above-surface observations for assimilation into mesoscale model simulations. The Tropospheric Airborne Meteorological Data Reporting (TAMDAR observations have potential advantages over some other aircraft observations including the presence of water vapor observations. The impact of assimilating TAMDAR observations via observation nudging in 1 km horizontal grid spacing Weather Research and Forecasting model simulations is evaluated using five cases centered over California. Overall, the impact of assimilating the observations is mixed, with the layer with the greatest benefit being above the surface in the lowest 1000 m above ground level and the variable showing the most consistent benefit being temperature. Varying the nudging configuration demonstrates the sensitivity of the results to details of the assimilation, but does not clearly demonstrate the superiority of a specific configuration.

  4. Disconfirmed hedonic expectations produce perceptual contrast, not assimilation.

    Science.gov (United States)

    Zellner, Debra A; Strickhouser, Dinah; Tornow, Carina E

    2004-01-01

    In studies of hedonic ratings, contrast is the usual result when expectations about test stimuli are produced through the presentation of context stimuli, whereas assimilation is the usual result when expectations about test stimuli are produced through labeling, advertising, or the relaying of information to the subject about the test stimuli. Both procedures produce expectations that are subsequently violated, but the outcomes are different. The present studies demonstrate that both assimilation and contrast can occur even when expectations are produced by verbal labels and the degree of violation of the expectation is held constant. One factor determining whether assimilation or contrast occurs appears to be the certainty of the expectation. Expectations that convey certainty are produced by methods that lead to social influence on subjects' ratings, producing assimilation. When social influence is not a factor and subjects give judgments influenced only by the perceived hedonic value of the stimulus, contrast is the result.

  5. Satellite Sounder Data Assimilation for Improving Alaska Region Weather Forecast

    Science.gov (United States)

    Zhu, Jiang; Stevens, E.; Zavodsky, B. T.; Zhang, X.; Heinrichs, T.; Broderson, D.

    2014-01-01

    Data assimilation has been demonstrated very useful in improving both global and regional numerical weather prediction. Alaska has very coarser surface observation sites. On the other hand, it gets much more satellite overpass than lower 48 states. How to utilize satellite data to improve numerical prediction is one of hot topics among weather forecast community in Alaska. The Geographic Information Network of Alaska (GINA) at University of Alaska is conducting study on satellite data assimilation for WRF model. AIRS/CRIS sounder profile data are used to assimilate the initial condition for the customized regional WRF model (GINA-WRF model). Normalized standard deviation, RMSE, and correlation statistic analysis methods are applied to analyze one case of 48 hours forecasts and one month of 24-hour forecasts in order to evaluate the improvement of regional numerical model from Data assimilation. The final goal of the research is to provide improved real-time short-time forecast for Alaska regions.

  6. Multi-parametric variational data assimilation for hydrological forecasting

    Science.gov (United States)

    Alvarado-Montero, R.; Schwanenberg, D.; Krahe, P.; Helmke, P.; Klein, B.

    2017-12-01

    Ensemble forecasting is increasingly applied in flow forecasting systems to provide users with a better understanding of forecast uncertainty and consequently to take better-informed decisions. A common practice in probabilistic streamflow forecasting is to force deterministic hydrological model with an ensemble of numerical weather predictions. This approach aims at the representation of meteorological uncertainty but neglects uncertainty of the hydrological model as well as its initial conditions. Complementary approaches use probabilistic data assimilation techniques to receive a variety of initial states or represent model uncertainty by model pools instead of single deterministic models. This paper introduces a novel approach that extends a variational data assimilation based on Moving Horizon Estimation to enable the assimilation of observations into multi-parametric model pools. It results in a probabilistic estimate of initial model states that takes into account the parametric model uncertainty in the data assimilation. The assimilation technique is applied to the uppermost area of River Main in Germany. We use different parametric pools, each of them with five parameter sets, to assimilate streamflow data, as well as remotely sensed data from the H-SAF project. We assess the impact of the assimilation in the lead time performance of perfect forecasts (i.e. observed data as forcing variables) as well as deterministic and probabilistic forecasts from ECMWF. The multi-parametric assimilation shows an improvement of up to 23% for CRPS performance and approximately 20% in Brier Skill Scores with respect to the deterministic approach. It also improves the skill of the forecast in terms of rank histogram and produces a narrower ensemble spread.

  7. Ethnicity, assimilation and harassment in the labor market

    OpenAIRE

    Epstein, Gil S.; Gang, Ira N.

    2008-01-01

    We often observe minority ethnic groups at a disadvantage relative to the majority. Why is this and what can be done about it? Efforts made to assimilate, and time, are two elements working to bring the minority into line with the majority. A third element, the degree to which the majority welcomes the minority, also plays a role. We develop a simple theoretical model useful for examining the consequences for assimilation and harassment of growth in the minority population, time, and the role...

  8. Joint Center for Satellite Data Assimilation Overview and Research Activities

    Science.gov (United States)

    Auligne, T.

    2017-12-01

    In 2001 NOAA/NESDIS, NOAA/NWS, NOAA/OAR, and NASA, subsequently joined by the US Navy and Air Force, came together to form the Joint Center for Satellite Data Assimilation (JCSDA) for the common purpose of accelerating the use of satellite data in environmental numerical prediction modeling by developing, using, and anticipating advances in numerical modeling, satellite-based remote sensing, and data assimilation methods. The primary focus was to bring these advances together to improve operational numerical model-based forecasting, under the premise that these partners have common technical and logistical challenges assimilating satellite observations into their modeling enterprises that could be better addressed through cooperative action and/or common solutions. Over the last 15 years, the JCSDA has made and continues to make major contributions to operational assimilation of satellite data. The JCSDA is a multi-agency U.S. government-owned-and-operated organization that was conceived as a venue for the several agencies NOAA, NASA, USAF and USN to collaborate on advancing the development and operational use of satellite observations into numerical model-based environmental analysis and forecasting. The primary mission of the JCSDA is to "accelerate and improve the quantitative use of research and operational satellite data in weather, ocean, climate and environmental analysis and prediction systems." This mission is fulfilled through directed research targeting the following key science objectives: Improved radiative transfer modeling; new instrument assimilation; assimilation of humidity, clouds, and precipitation observations; assimilation of land surface observations; assimilation of ocean surface observations; atmospheric composition; and chemistry and aerosols. The goal of this presentation is to briefly introduce the JCSDA's mission and vision, and to describe recent research activities across various JCSDA partners.

  9. Diversity and abundance of nitrate assimilation genes in the northern South china sea.

    Science.gov (United States)

    Cai, Haiyuan; Jiao, Nianzhi

    2008-11-01

    Marine heterotrophic microorganisms that assimilate nitrate play an important role in nitrogen and carbon cycling in the water column. The nasA gene, encoding the nitrate assimilation enzyme, was selected as a functional marker to examine the nitrate assimilation community in the South China Sea (SCS). PCR amplification, restriction fragment length polymorphism (RFLP) screening, and phylogenetic analysis of nasA gene sequences were performed to characterize in situ nitrate assimilatory bacteria. Furthermore, the effects of nutrients and other environmental factors on the genetic heterogeneity of nasA fragments from the SCS were evaluated at the surface in three stations, and at two other depths in one of these stations. The diversity indices and rarefaction curves indicated that the nasA gene was more diverse in offshore waters than in the Pearl River estuary. The phylotype rank abundance curve showed an abundant and unique RFLP pattern in all five libraries, indicating that a high diversity but low abundance of nasA existed in the study areas. Phylogenetic analysis of environmental nasA gene sequences further revealed that the nasA gene fragments came from several common aquatic microbial groups, including the Proteobacteria, Cytophaga-Flavobacteria (CF), and Cyanobacteria. In addition to the direct PCR/sequence analysis of environmental samples, we also cultured a number of nitrate assimilatory bacteria isolated from the field. Comparison of nasA genes from these isolates and from the field samples indicated the existence of horizontal nasA gene transfer. Application of real-time quantitative PCR to these nasA genes revealed a great variation in their abundance at different investigation sites and water depths.

  10. Yeast identification: reassessment of assimilation tests as sole universal identifiers.

    Science.gov (United States)

    Spencer, J; Rawling, S; Stratford, M; Steels, H; Novodvorska, M; Archer, D B; Chandra, S

    2011-11-01

    To assess whether assimilation tests in isolation remain a valid method of identification of yeasts, when applied to a wide range of environmental and spoilage isolates. Seventy-one yeast strains were isolated from a soft drinks factory. These were identified using assimilation tests and by D1/D2 rDNA sequencing. When compared to sequencing, assimilation test identifications (MicroLog™) were 18·3% correct, a further 14·1% correct within the genus and 67·6% were incorrectly identified. The majority of the latter could be attributed to the rise in newly reported yeast species. Assimilation tests alone are unreliable as a universal means of yeast identification, because of numerous new species, variability of strains and increasing coincidence of assimilation profiles. Assimilation tests still have a useful role in the identification of common species, such as the majority of clinical isolates. It is probable, based on these results, that many yeast identifications reported in older literature are incorrect. This emphasizes the crucial need for accurate identification in present and future publications. © 2011 The Authors. Letters in Applied Microbiology © 2011 The Society for Applied Microbiology.

  11. IASI Radiance Data Assimilation in Local Ensemble Transform Kalman Filter

    Science.gov (United States)

    Cho, K.; Hyoung-Wook, C.; Jo, Y.

    2016-12-01

    Korea institute of Atmospheric Prediction Systems (KIAPS) is developing NWP model with data assimilation systems. Local Ensemble Transform Kalman Filter (LETKF) system, one of the data assimilation systems, has been developed for KIAPS Integrated Model (KIM) based on cubed-sphere grid and has successfully assimilated real data. LETKF data assimilation system has been extended to 4D- LETKF which considers time-evolving error covariance within assimilation window and IASI radiance data assimilation using KPOP (KIAPS package for observation processing) with RTTOV (Radiative Transfer for TOVS). The LETKF system is implementing semi operational prediction including conventional (sonde, aircraft) observation and AMSU-A (Advanced Microwave Sounding Unit-A) radiance data from April. Recently, the semi operational prediction system updated radiance observations including GPS-RO, AMV, IASI (Infrared Atmospheric Sounding Interferometer) data at July. A set of simulation of KIM with ne30np4 and 50 vertical levels (of top 0.3hPa) were carried out for short range forecast (10days) within semi operation prediction LETKF system with ensemble forecast 50 members. In order to only IASI impact, our experiments used only conventional and IAIS radiance data to same semi operational prediction set. We carried out sensitivity test for IAIS thinning method (3D and 4D). IASI observation number was increased by temporal (4D) thinning and the improvement of IASI radiance data impact on the forecast skill of model will expect.

  12. Curious Cases of the Enzymes.

    Science.gov (United States)

    Ulusu, Nuriye Nuray

    2015-07-01

    Life as we know it heavily relies on biological catalysis, in fact, in a very nonromantic version of it, life could be considered as a series of chemical reactions, regulated by the guarding principles of thermodynamics. In ancient times, a beating heart was a good sign of vitality, however, to me, it is actually the presence of active enzymes that counts… Though we do not usually pay attention, the history of enzymology is as old as humanity itself, and dates back to the ancient times. This paper is dedicated to these early moments of this remarkable science that touched our lives in the past and will make life a lot more efficient for humanity in the future. There was almost always a delicate, fundamentally essential relationship between mankind and the enzymes. Challenged by a very alien and hostile Nature full of predators, prehistoric men soon discovered the medicinal properties of the plants, through trial and error. In fact, they accidently discovered the enzyme inhibitors and thus, in crude terms, kindled a sparkling area of research. These plant-derivatives that acted as enzyme inhibitors helped prehistoric men in their pursuit of survival and protection from predators; in hunting and fishing… Later in history, while the underlying purposes of survival and increasing the quality of life stayed intact, the ways and means of enzymology experienced a massive transformation, as the 'trial and error' methodology of the ancients is now replaced with rational scientific theories.

  13. Involvement of adenosine monophosphate activated kinase in interleukin-6 regulation of steroidogenic acute regulatory protein and cholesterol side chain cleavage enzyme in the bovine zona fasciculata and zona reticularis.

    Science.gov (United States)

    De Silva, Matharage S I; Dayton, Adam W; Rhoten, Lance R; Mallett, John W; Reese, Jared C; Squires, Mathieu D; Dalley, Andrew P; Porter, James P; Judd, Allan M

    2018-06-01

    In bovine adrenal zona fasciculata (ZF) and NCI-H295R cells, interleukin-6 (IL-6) increases cortisol release, increases expression of steroidogenic acute regulatory protein (StAR), cholesterol side chain cleavage enzyme (P450scc), and steroidogenic factor 1 (SF-1) (increases steroidogenic proteins), and decreases the expression of adrenal hypoplasia congenita-like protein (DAX-1) (inhibits steroidogenic proteins). In contrast, IL-6 decreases bovine adrenal zona reticularis (ZR) androgen release, StAR, P450scc, and SF-1 expression, and increases DAX-1 expression. Adenosine monophosphate (AMP) activated kinase (AMPK) regulates steroidogenesis, but its role in IL-6 regulation of adrenal steroidogenesis is unknown. In the present study, an AMPK activator (AICAR) increased (P < 0.01) NCI-H295R StAR promoter activity, StAR and P450scc expression, and the phosphorylation of AMPK (PAMPK) and acetyl-CoA carboxylase (PACC) (indexes of AMPK activity). In ZR (decreased StAR, P450scc, SF-1, increased DAX-1) (P < 0.01) and ZF tissues (increased StAR, P450scc, SF-1, decreased DAX-1) (P < 0.01), AICAR modified StAR, P450scc, SF-1 and DAX-1 mRNAs/proteins similar to the effects of IL-6. The activity (increased PAMPK and PACC) (P < 0.01) of AMPK in the ZF and ZR was increased by AICAR and IL-6. In support of an AMPK role in IL-6 ZF and ZR effects, the AMPK inhibitor compound C blocked (P < 0.01) the effects of IL-6 on the expression of StAR, P450scc, SF-1, and DAX-1. Therefore, IL-6 modification of the expression of StAR and P450scc in the ZF and ZR may involve activation of AMPK and these changes may be related to changes in the expression of SF-1 and DAX-1. Copyright © 2018 Elsevier Inc. All rights reserved.

  14. Exploring synchronisation in nonlinear data assimilation

    Science.gov (United States)

    Rodrigues-Pinheiro, Flavia; van Leeuwen, Peter Jan

    2016-04-01

    Present-day data assimilation methods are based on linearizations and face serious problems in strongly nonlinear cases such as convection. A promising solution to this problem is a particle filter, which provides a representation of the model probability density function (pdf) by a discrete set of model states, or particles. The basic particle filter uses Bayes's theorem directly, but does not work in high-dimensional cases. The performance can be improved by considering the proposal density freedom. This allows one to change the model equations to bring the particles closer to the observations, resulting in very efficient update schemes at observation times, but extending these schemes between observation times is computationally expensive. Simple solutions like nudging have been shown to be not powerful enough. A potential solution might be synchronization, in which one tries to synchronise the model of a system with the true evolution of the system via the observations. In practice this means that an extra term is added to the model equations that hampers growth of instabilities on the synchronization manifold. Especially the delayed versions, where observations are allowed to influence the state in the past have shown some remarkable successes. Unfortunately, all efforts ignore errors in the observations, and as soon as these are introduced the performance degrades considerably. There is a close connection between time-delayed synchronization and a Kalman Smoother, which does allow for observational (and other) errors. In this presentation we will explore this connection to the full, with a view to extend synchronization to more realistic settings. Specifically performance of the spread of information from observed to unobserved variables is studied in detail. The results indicate that this extended synchronisation is a promising tool to steer the model states towards the observations efficiently. If time permits, we will show initial results of embedding the

  15. Biological data assimilation for parameter estimation of a phytoplankton functional type model for the western North Pacific

    Science.gov (United States)

    Hoshiba, Yasuhiro; Hirata, Takafumi; Shigemitsu, Masahito; Nakano, Hideyuki; Hashioka, Taketo; Masuda, Yoshio; Yamanaka, Yasuhiro

    2018-06-01

    Ecosystem models are used to understand ecosystem dynamics and ocean biogeochemical cycles and require optimum physiological parameters to best represent biological behaviours. These physiological parameters are often tuned up empirically, while ecosystem models have evolved to increase the number of physiological parameters. We developed a three-dimensional (3-D) lower-trophic-level marine ecosystem model known as the Nitrogen, Silicon and Iron regulated Marine Ecosystem Model (NSI-MEM) and employed biological data assimilation using a micro-genetic algorithm to estimate 23 physiological parameters for two phytoplankton functional types in the western North Pacific. The estimation of the parameters was based on a one-dimensional simulation that referenced satellite data for constraining the physiological parameters. The 3-D NSI-MEM optimized by the data assimilation improved the timing of a modelled plankton bloom in the subarctic and subtropical regions compared to the model without data assimilation. Furthermore, the model was able to improve not only surface concentrations of phytoplankton but also their subsurface maximum concentrations. Our results showed that surface data assimilation of physiological parameters from two contrasting observatory stations benefits the representation of vertical plankton distribution in the western North Pacific.

  16. Coordinate changes in photosynthesis, sugar accumulation and antioxidative enzymes improve the performance of Jatropha curcas plants under drought stress

    International Nuclear Information System (INIS)

    Silva, Evandro N.; Ribeiro, Rafael V.; Ferreira-Silva, Sérgio L.; Vieira, Suyanne A.; Ponte, Luiz F.A.; Silveira, Joaquim A.G.

    2012-01-01

    The aim of this study was to assess the relationships between photosynthesis, sugars and photo-oxidative protection mechanisms in Jatropha curcas under drought stress. Leaf CO 2 assimilation rate (P N ) and instantaneous carboxylation efficiency decreased progressively as the water deficit increased. The sucrose and reducing sugar concentrations were negatively and highly correlated with photosynthesis indicating a modulation by negative feedback mechanism. The alternative electron sinks (ETR s '/P N ), relative excess of light energy (EXC) and non-photochemical quenching were strongly increased by drought, indicating effective mechanisms of energy excess dissipation. The photochemistry data indicate partial preservation of photosystem II integrity and function even under severe drought. EXC was positively correlated with superoxide dismutase (SOD) and ascorbate peroxidase (APX) activities evidencing an effective role of these enzymes in the oxidative protection against excess of reactive oxygen species in chloroplasts. Leaf H 2 O 2 content and lipid peroxidation were inversely and highly correlated with catalase (CAT) activity indicating that drought-induced inhibition of this enzyme might have allowed oxidative damage. Our data suggest that drought triggers a coordinate down-regulation in photosynthesis through sucrose and reducing sugar accumulation and an energy excess dissipation at PSII level by non-photochemical mechanisms associate with enhancement in photorespiration, restricting photo-damages. In parallel, drought up-regulates SOD and APX activities avoiding accumulation of reactive oxygen species, while CAT activity is not able to avoid H 2 O 2 accumulation in drought-stressed J. curcas leaves. -- Highlights: ► Drought triggers a down-regulation in photosynthesis by sucrose and reducing sugar. ► Drought induces energy dissipation at PSII level and increase in photorespiration. ► Drought up-regulates SOD and APX activities avoiding accumulation of

  17. Enzymes for improved biomass conversion

    Science.gov (United States)

    Brunecky, Roman; Himmel, Michael E.

    2016-02-02

    Disclosed herein are enzymes and combinations of the enzymes useful for the hydrolysis of cellulose and the conversion of biomass. Methods of degrading cellulose and biomass using enzymes and cocktails of enzymes are also disclosed.

  18. Data Assimilation in Forest Inventory: First Empirical Results

    Directory of Open Access Journals (Sweden)

    Mattias Nyström

    2015-12-01

    Full Text Available Data assimilation techniques were used to estimate forest stand data in 2011 by sequentially combining remote sensing based estimates of forest variables with predictions from growth models. Estimates of stand data, based on canopy height models obtained from image matching of digital aerial images at six different time-points between 2003 and 2011, served as input to the data assimilation. The assimilation routines were built on the extended Kalman filter. The study was conducted in hemi-boreal forest at the Remningstorp test site in southern Sweden (lat. 13°37′ N; long. 58°28′ E. The assimilation results were compared with two other methods used in practice for estimation of forest variables: the first was to use only the most recent estimate obtained from remotely sensed data (2011 and the second was to forecast the first estimate (2003 to the endpoint (2011. All three approaches were validated using nine 40 m radius validation plots, which were carefully measured in the field. The results showed that the data assimilation approach provided better results than the two alternative methods. Data assimilation of remote sensing time series has been used previously for calibrating forest ecosystem models, but, to our knowledge, this is the first study with real data where data assimilation has been used for estimating forest inventory data. The study constitutes a starting point for the development of a framework useful for sequentially utilizing all types of remote sensing data in order to provide precise and up-to-date estimates of forest stand parameters.

  19. Immobilized enzymes and cells

    Energy Technology Data Exchange (ETDEWEB)

    Bucke, C; Wiseman, A

    1981-04-04

    This article reviews the current state of the art of enzyme and cell immobilization and suggests advances which might be made during the 1980's. Current uses of immobilized enzymes include the use of glucoamylase in the production of glucose syrups from starch and glucose isomerase in the production of high fructose corn syrup. Possibilities for future uses of immobilized enzymes and cells include the utilization of whey and the production of ethanol.

  20. Profiling the orphan enzymes

    Science.gov (United States)

    2014-01-01

    The emergence of Next Generation Sequencing generates an incredible amount of sequence and great potential for new enzyme discovery. Despite this huge amount of data and the profusion of bioinformatic methods for function prediction, a large part of known enzyme activities is still lacking an associated protein sequence. These particular activities are called “orphan enzymes”. The present review proposes an update of previous surveys on orphan enzymes by mining the current content of public databases. While the percentage of orphan enzyme activities has decreased from 38% to 22% in ten years, there are still more than 1,000 orphans among the 5,000 entries of the Enzyme Commission (EC) classification. Taking into account all the reactions present in metabolic databases, this proportion dramatically increases to reach nearly 50% of orphans and many of them are not associated to a known pathway. We extended our survey to “local orphan enzymes” that are activities which have no representative sequence in a given clade, but have at least one in organisms belonging to other clades. We observe an important bias in Archaea and find that in general more than 30% of the EC activities have incomplete sequence information in at least one superkingdom. To estimate if candidate proteins for local orphans could be retrieved by homology search, we applied a simple strategy based on the PRIAM software and noticed that candidates may be proposed for an important fraction of local orphan enzymes. Finally, by studying relation between protein domains and catalyzed activities, it appears that newly discovered enzymes are mostly associated with already known enzyme domains. Thus, the exploration of the promiscuity and the multifunctional aspect of known enzyme families may solve part of the orphan enzyme issue. We conclude this review with a presentation of recent initiatives in finding proteins for orphan enzymes and in extending the enzyme world by the discovery of new

  1. DART: New Research Using Ensemble Data Assimilation in Geophysical Models

    Science.gov (United States)

    Hoar, T. J.; Raeder, K.

    2015-12-01

    The Data Assimilation Research Testbed (DART) is a community facilityfor ensemble data assimilation developed and supported by the NationalCenter for Atmospheric Research. DART provides a comprehensive suite of software, documentation, and tutorials that can be used for ensemble data assimilation research, operations, and education. Scientists and software engineers at NCAR are available to support DART users who want to use existing DART products or develop their own applications. Current DART users range from university professors teaching data assimilation, to individual graduate students working with simple models, through national laboratories doing operational prediction with large state-of-the-art models. DART runs efficiently on many computational platforms ranging from laptops through thousands of cores on the newest supercomputers.This poster focuses on several recent research activities using DART with geophysical models.Using CAM/DART to understand whether OCO-2 Total Precipitable Water observations can be useful in numerical weather prediction.Impacts of the synergistic use of Infra-red CO retrievals (MOPITT, IASI) in CAM-CHEM/DART assimilations.Assimilation and Analysis of Observations of Amazonian Biomass Burning Emissions by MOPITT (aerosol optical depth), MODIS (carbon monoxide) and MISR (plume height).Long term evaluation of the chemical response of MOPITT-CO assimilation in CAM-CHEM/DART OSSEs for satellite planning and emission inversion capabilities.Improved forward observation operators for land models that have multiple land use/land cover segments in a single grid cell,Simulating mesoscale convective systems (MCSs) using a variable resolution, unstructured grid in the Model for Prediction Across Scales (MPAS) and DART.The mesoscale WRF+DART system generated an ensemble of year-long, real-time initializations of a convection allowing model over the United States.Constraining WACCM with observations in the tropical band (30S-30N) using DART

  2. Assimilation of Altimeter Data into a Quasigeostrophic Model of the Gulf Stream System. Part 2; Assimilation Results

    Science.gov (United States)

    Capotondi, Antonietta; Holland, William R.; Malanotte-Rizzoli, Paola

    1995-01-01

    The improvement in the climatological behavior of a numerical model as a consequence of the assimilation of surface data is investigated. The model used for this study is a quasigeostrophic (QG) model of the Gulf Stream region. The data that have been assimilated are maps of sea surface height that have been obtained as the superposition of sea surface height variability deduced from the Geosat altimeter measurements and a mean field constructed from historical hydrographic data. The method used for assimilating the data is the nudging technique. Nudging has been implemented in such a way as to achieve a high degree of convergence of the surface model fields toward the observations. Comparisons of the assimilation results with available in situ observations show a significant improvement in the degree of realism of the climatological model behavior, with respect to the model in which no data are assimilated. The remaining discrepancies in the model mean circulation seem to be mainly associated with deficiencies in the mean component of the surface data that are assimilated. On the other hand, the possibility of building into the model more realistic eddy characteristics through the assimilation of the surface eddy field proves very successful in driving components of the mean model circulation that are in relatively good agreement with the available observations. Comparisons with current meter time series during a time period partially overlapping the Geosat mission show that the model is able to 'correctly' extrapolate the instantaneous surface eddy signals to depths of approximately 1500 m. The correlation coefficient between current meter and model time series varies from values close to 0.7 in the top 1500 m to values as low as 0.1-0.2 in the deep ocean.

  3. An integrated GIS application system for soil moisture data assimilation

    Science.gov (United States)

    Wang, Di; Shen, Runping; Huang, Xiaolong; Shi, Chunxiang

    2014-11-01

    The gaps in knowledge and existing challenges in precisely describing the land surface process make it critical to represent the massive soil moisture data visually and mine the data for further research.This article introduces a comprehensive soil moisture assimilation data analysis system, which is instructed by tools of C#, IDL, ArcSDE, Visual Studio 2008 and SQL Server 2005. The system provides integrated service, management of efficient graphics visualization and analysis of land surface data assimilation. The system is not only able to improve the efficiency of data assimilation management, but also comprehensively integrate the data processing and analysis tools into GIS development environment. So analyzing the soil moisture assimilation data and accomplishing GIS spatial analysis can be realized in the same system. This system provides basic GIS map functions, massive data process and soil moisture products analysis etc. Besides,it takes full advantage of a spatial data engine called ArcSDE to effeciently manage, retrieve and store all kinds of data. In the system, characteristics of temporal and spatial pattern of soil moiture will be plotted. By analyzing the soil moisture impact factors, it is possible to acquire the correlation coefficients between soil moisture value and its every single impact factor. Daily and monthly comparative analysis of soil moisture products among observations, simulation results and assimilations can be made in this system to display the different trends of these products. Furthermore, soil moisture map production function is realized for business application.

  4. Development Of A Data Assimilation Capability For RAPID

    Science.gov (United States)

    Emery, C. M.; David, C. H.; Turmon, M.; Hobbs, J.; Allen, G. H.; Famiglietti, J. S.

    2017-12-01

    The global decline of in situ observations associated with the increasing ability to monitor surface water from space motivates the creation of data assimilation algorithms that merge computer models and space-based observations to produce consistent estimates of terrestrial hydrology that fill the spatiotemporal gaps in observations. RAPID is a routing model based on the Muskingum method that is capable of estimating river streamflow over large scales with a relatively short computing time. This model only requires limited inputs: a reach-based river network, and lateral surface and subsurface flow into the rivers. The relatively simple model physics imply that RAPID simulations could be significantly improved by including a data assimilation capability. Here we present the early developments of such data assimilation approach into RAPID. Given the linear and matrix-based structure of the model, we chose to apply a direct Kalman filter, hence allowing for the preservation of high computational speed. We correct the simulated streamflows by assimilating streamflow observations and our early results demonstrate the feasibility of the approach. Additionally, the use of in situ gauges at continental scales motivates the application of our new data assimilation scheme to altimetry measurements from existing (e.g. EnviSat, Jason 2) and upcoming satellite missions (e.g. SWOT), and ultimately apply the scheme globally.

  5. Kinetics of 15NH4+ assimilation in Zea mays

    International Nuclear Information System (INIS)

    Magalhaes, J.R.; Ju, G.C.; Rich, P.J.; Rhodes, D.

    1990-01-01

    Comparative studies of 15 NH 4 + assimilation were undertaken with a GDH1-null mutant of Zea mays and a related (but not strictly isogenic) GDH1-positive wild type from which this mutant was derived. The kinetics of 15 NH 4 + assimilation into free amino acids and total reduced nitrogen were monitored in both roots and shoots of 2-week-old seedlings supplied with 5 millimolar 99% ( 15 NH 4 ) 2 SO 4 via the aerated root medium in hydroponic culture over a 24-h period. The GDH1-null mutant, with a 10- to 15-fold lower total root GDH activity in comparison to the wild type, was found to exhibit a 40 to 50% lower rate of 15 NH 4 + assimilation into total reduced nitrogen. The lower rates of 15 NH 4 + assimilation in the mutant was associated with lower rates of labeling of several free amino acids (including glutamate, glutamine-amino N, aspartate, asparagine-amino N, and alanine) in both roots and shoots of the mutant in comparison to the wild type. Qualitatively, these labeling kinetics appear consistent with a reduced flux of 15 N via glutamate in the GDH1-null mutant. However, the responses of the two genotypes to the potent inhibitor of glutamine synthetase, methionine sulfoximine, and differences in morphology of the two genotypes (particularly a lower shoot:root ratio in the GDH1-null mutant) urge caution in concluding that GDH1 is solely responsible for these differences in ammonia assimilation rate

  6. Nitrogen assimilation in denitrifier Bacillus azotoformans LMG 9581T.

    Science.gov (United States)

    Sun, Yihua; De Vos, Paul; Willems, Anne

    2017-12-01

    Until recently, it has not been generally known that some bacteria can contain the gene inventory for both denitrification and dissimilatory nitrate (NO 3 - )/nitrite (NO 2 - ) reduction to ammonium (NH 4 + ) (DNRA). Detailed studies of these microorganisms could shed light on the differentiating environmental drivers of both processes without interference of organism-specific variation. Genome analysis of Bacillus azotoformans LMG 9581 T shows a remarkable redundancy of dissimilatory nitrogen reduction, with multiple copies of each denitrification gene as well as DNRA genes nrfAH, but a reduced capacity for nitrogen assimilation, with no nas operon nor amtB gene. Here, we explored nitrogen assimilation in detail using growth experiments in media with different organic and inorganic nitrogen sources at different concentrations. Monitoring of growth, NO 3 - NO 2 - , NH 4 + concentration and N 2 O production revealed that B. azotoformans LMG 9581 T could not grow with NH 4 + as sole nitrogen source and confirmed the hypothesis of reduced nitrogen assimilation pathways. However, NH 4 + could be assimilated and contributed up to 50% of biomass if yeast extract was also provided. NH 4 + also had a significant but concentration-dependent influence on growth rate. The mechanisms behind these observations remain to be resolved but hypotheses for this deficiency in nitrogen assimilation are discussed. In addition, in all growth conditions tested a denitrification phenotype was observed, with all supplied NO 3 - converted to nitrous oxide (N 2 O).

  7. Multiscale Data Assimilation for Large-Eddy Simulations

    Science.gov (United States)

    Li, Z.; Cheng, X.; Gustafson, W. I., Jr.; Xiao, H.; Vogelmann, A. M.; Endo, S.; Toto, T.

    2017-12-01

    Large-eddy simulation (LES) is a powerful tool for understanding atmospheric turbulence, boundary layer physics and cloud development, and there is a great need for developing data assimilation methodologies that can constrain LES models. The U.S. Department of Energy Atmospheric Radiation Measurement (ARM) User Facility has been developing the capability to routinely generate ensembles of LES. The LES ARM Symbiotic Simulation and Observation (LASSO) project (https://www.arm.gov/capabilities/modeling/lasso) is generating simulations for shallow convection days at the ARM Southern Great Plains site in Oklahoma. One of major objectives of LASSO is to develop the capability to observationally constrain LES using a hierarchy of ARM observations. We have implemented a multiscale data assimilation (MSDA) scheme, which allows data assimilation to be implemented separately for distinct spatial scales, so that the localized observations can be effectively assimilated to constrain the mesoscale fields in the LES area of about 15 km in width. The MSDA analysis is used to produce forcing data that drive LES. With such LES workflow we have examined 13 days with shallow convection selected from the period May-August 2016. We will describe the implementation of MSDA, present LES results, and address challenges and opportunities for applying data assimilation to LES studies.

  8. Assimilating uncertain, dynamic and intermittent streamflow observations in hydrological models

    Science.gov (United States)

    Mazzoleni, Maurizio; Alfonso, Leonardo; Chacon-Hurtado, Juan; Solomatine, Dimitri

    2015-09-01

    Catastrophic floods cause significant socio-economical losses. Non-structural measures, such as real-time flood forecasting, can potentially reduce flood risk. To this end, data assimilation methods have been used to improve flood forecasts by integrating static ground observations, and in some cases also remote sensing observations, within water models. Current hydrologic and hydraulic research works consider assimilation of observations coming from traditional, static sensors. At the same time, low-cost, mobile sensors and mobile communication devices are becoming also increasingly available. The main goal and innovation of this study is to demonstrate the usefulness of assimilating uncertain streamflow observations that are dynamic in space and intermittent in time in the context of two different semi-distributed hydrological model structures. The developed method is applied to the Brue basin, where the dynamic observations are imitated by the synthetic observations of discharge. The results of this study show how model structures and sensors locations affect in different ways the assimilation of streamflow observations. In addition, it proves how assimilation of such uncertain observations from dynamic sensors can provide model improvements similar to those of streamflow observations coming from a non-optimal network of static physical sensors. This can be a potential application of recent efforts to build citizen observatories of water, which can make the citizens an active part in information capturing, evaluation and communication, helping simultaneously to improvement of model-based flood forecasting.

  9. Assimilation of GNSS radio occultation observations in GRAPES

    Science.gov (United States)

    Liu, Y.; Xue, J.

    2014-07-01

    This paper reviews the development of the global navigation satellite system (GNSS) radio occultation (RO) observations assimilation in the Global/Regional Assimilation and PrEdiction System (GRAPES) of China Meteorological Administration, including the choice of data to assimilate, the data quality control, the observation operator, the tuning of observation error, and the results of the observation impact experiments. The results indicate that RO data have a significantly positive effect on analysis and forecast at all ranges in GRAPES not only in the Southern Hemisphere where conventional observations are lacking but also in the Northern Hemisphere where data are rich. It is noted that a relatively simple assimilation and forecast system in which only the conventional and RO observation are assimilated still has analysis and forecast skill even after nine months integration, and the analysis difference between both hemispheres is gradually reduced with height when compared with NCEP (National Centers for Enviromental Prediction) analysis. Finally, as a result of the new onboard payload of the Chinese FengYun-3 (FY-3) satellites, the research status of the RO of FY-3 satellites is also presented.

  10. Assimilating the Future for Better Forecasts and Earlier Warnings

    Science.gov (United States)

    Du, H.; Wheatcroft, E.; Smith, L. A.

    2016-12-01

    Multi-model ensembles have become popular tools to account for some of the uncertainty due to model inadequacy in weather and climate simulation-based predictions. The current multi-model forecasts focus on combining single model ensemble forecasts by means of statistical post-processing. Assuming each model is developed independently or with different primary target variables, each is likely to contain different dynamical strengths and weaknesses. Using statistical post-processing, such information is only carried by the simulations under a single model ensemble: no advantage is taken to influence simulations under the other models. A novel methodology, named Multi-model Cross Pollination in Time, is proposed for multi-model ensemble scheme with the aim of integrating the dynamical information regarding the future from each individual model operationally. The proposed approach generates model states in time via applying data assimilation scheme(s) to yield truly "multi-model trajectories". It is demonstrated to outperform traditional statistical post-processing in the 40-dimensional Lorenz96 flow. Data assimilation approaches are originally designed to improve state estimation from the past to the current time. The aim of this talk is to introduce a framework that uses data assimilation to improve model forecasts at future time (not to argue for any one particular data assimilation scheme). Illustration of applying data assimilation "in the future" to provide early warning of future high-impact events is also presented.

  11. The role of nickel in urea assimilation by algae.

    Science.gov (United States)

    Rees, T A; Bekheet, I A

    1982-12-01

    Nickel is required for urease synthesis by Phaeodactylum tricornutum and Tetraselmis subcordiformis and for growth on urea by Phaeodactylum. There is no requirement for nickel for urea amidolyase synthesis by Chlorella fusca var. vacuolata. Neither copper nor palladium can substitute for nickel but cobalt partially restored urease activity in Phaeodactylum. The addition of nickel to nickel-deficient cultures of Phaeodactylum or Tetraselmis resulted in a rapid increase of urease activity to 7-30 times the normal level; this increase was not inhibited by cycloheximide. It is concluded that nickel-deficient cells over-produce a non-functional urease protein and that either nickel or the functional urease enzyme participates in the regulation of the production of urease protein.

  12. Artificial Enzymes, "Chemzymes"

    DEFF Research Database (Denmark)

    Bjerre, Jeannette; Rousseau, Cyril Andre Raphaël; Pedersen, Lavinia Georgeta M

    2008-01-01

    Enzymes have fascinated scientists since their discovery and, over some decades, one aim in organic chemistry has been the creation of molecules that mimic the active sites of enzymes and promote catalysis. Nevertheless, even today, there are relatively few examples of enzyme models that successf......Enzymes have fascinated scientists since their discovery and, over some decades, one aim in organic chemistry has been the creation of molecules that mimic the active sites of enzymes and promote catalysis. Nevertheless, even today, there are relatively few examples of enzyme models...... that successfully perform Michaelis-Menten catalysis under enzymatic conditions (i.e., aqueous medium, neutral pH, ambient temperature) and for those that do, very high rate accelerations are seldomly seen. This review will provide a brief summary of the recent developments in artificial enzymes, so called...... "Chemzymes", based on cyclodextrins and other molecules. Only the chemzymes that have shown enzyme-like activity that has been quantified by different methods will be mentioned. This review will summarize the work done in the field of artificial glycosidases, oxidases, epoxidases, and esterases, as well...

  13. Magnetically responsive enzyme powders

    Energy Technology Data Exchange (ETDEWEB)

    Pospiskova, Kristyna, E-mail: kristyna.pospiskova@upol.cz [Regional Centre of Advanced Technologies and Materials, Palacky University, Slechtitelu 11, 783 71 Olomouc (Czech Republic); Safarik, Ivo, E-mail: ivosaf@yahoo.com [Regional Centre of Advanced Technologies and Materials, Palacky University, Slechtitelu 11, 783 71 Olomouc (Czech Republic); Department of Nanobiotechnology, Institute of Nanobiology and Structural Biology of GCRC, Na Sadkach 7, 370 05 Ceske Budejovice (Czech Republic)

    2015-04-15

    Powdered enzymes were transformed into their insoluble magnetic derivatives retaining their catalytic activity. Enzyme powders (e.g., trypsin and lipase) were suspended in various liquid media not allowing their solubilization (e.g., saturated ammonium sulfate and highly concentrated polyethylene glycol solutions, ethanol, methanol, 2-propanol) and subsequently cross-linked with glutaraldehyde. Magnetic modification was successfully performed at low temperature in a freezer (−20 °C) using magnetic iron oxides nano- and microparticles prepared by microwave-assisted synthesis from ferrous sulfate. Magnetized cross-linked enzyme powders were stable at least for two months in water suspension without leakage of fixed magnetic particles. Operational stability of magnetically responsive enzymes during eight repeated reaction cycles was generally without loss of enzyme activity. Separation of magnetically modified cross-linked powdered enzymes from reaction mixtures was significantly simplified due to their magnetic properties. - Highlights: • Cross-linked enzyme powders were prepared in various liquid media. • Insoluble enzymes were magnetized using iron oxides particles. • Magnetic iron oxides particles were prepared by microwave-assisted synthesis. • Magnetic modification was performed under low (freezing) temperature. • Cross-linked powdered trypsin and lipase can be used repeatedly for reaction.

  14. Targeted enzyme prodrug therapies.

    Science.gov (United States)

    Schellmann, N; Deckert, P M; Bachran, D; Fuchs, H; Bachran, C

    2010-09-01

    The cure of cancer is still a formidable challenge in medical science. Long-known modalities including surgery, chemotherapy and radiotherapy are successful in a number of cases; however, invasive, metastasized and inaccessible tumors still pose an unresolved and ongoing problem. Targeted therapies designed to locate, detect and specifically kill tumor cells have been developed in the past three decades as an alternative to treat troublesome cancers. Most of these therapies are either based on antibody-dependent cellular cytotoxicity, targeted delivery of cytotoxic drugs or tumor site-specific activation of prodrugs. The latter is a two-step procedure. In the first step, a selected enzyme is accumulated in the tumor by guiding the enzyme or its gene to the neoplastic cells. In the second step, a harmless prodrug is applied and specifically converted by this enzyme into a cytotoxic drug only at the tumor site. A number of targeting systems, enzymes and prodrugs were investigated and improved since the concept was first envisioned in 1974. This review presents a concise overview on the history and latest developments in targeted therapies for cancer treatment. We cover the relevant technologies such as antibody-directed enzyme prodrug therapy (ADEPT), gene-directed enzyme prodrug therapy (GDEPT) as well as related therapies such as clostridial- (CDEPT) and polymer-directed enzyme prodrug therapy (PDEPT) with emphasis on prodrug-converting enzymes, prodrugs and drugs.

  15. Enzymes in Fermented Fish.

    Science.gov (United States)

    Giyatmi; Irianto, H E

    Fermented fish products are very popular particularly in Southeast Asian countries. These products have unique characteristics, especially in terms of aroma, flavor, and texture developing during fermentation process. Proteolytic enzymes have a main role in hydrolyzing protein into simpler compounds. Fermentation process of fish relies both on naturally occurring enzymes (in the muscle or the intestinal tract) as well as bacteria. Fermented fish products processed using the whole fish show a different characteristic compared to those prepared from headed and gutted fish. Endogenous enzymes like trypsin, chymotrypsin, elastase, and aminopeptidase are the most involved in the fermentation process. Muscle tissue enzymes like cathepsins, peptidases, transaminases, amidases, amino acid decarboxylases, glutamic dehydrogenases, and related enzymes may also play a role in fish fermentation. Due to the decreased bacterial number during fermentation, contribution of microbial enzymes to proteolysis may be expected prior to salting of fish. Commercial enzymes are supplemented during processing for specific purposes, such as quality improvement and process acceleration. In the case of fish sauce, efforts to accelerate fermentation process and to improve product quality have been studied by addition of enzymes such as papain, bromelain, trypsin, pepsin, and chymotrypsin. © 2017 Elsevier Inc. All rights reserved.

  16. Storm surge model based on variational data assimilation method

    Directory of Open Access Journals (Sweden)

    Shi-li Huang

    2010-06-01

    Full Text Available By combining computation and observation information, the variational data assimilation method has the ability to eliminate errors caused by the uncertainty of parameters in practical forecasting. It was applied to a storm surge model based on unstructured grids with high spatial resolution meant for improving the forecasting accuracy of the storm surge. By controlling the wind stress drag coefficient, the variation-based model was developed and validated through data assimilation tests in an actual storm surge induced by a typhoon. In the data assimilation tests, the model accurately identified the wind stress drag coefficient and obtained results close to the true state. Then, the actual storm surge induced by Typhoon 0515 was forecast by the developed model, and the results demonstrate its efficiency in practical application.

  17. a Thtee-Dimensional Variational Assimilation Scheme for Satellite Aod

    Science.gov (United States)

    Liang, Y.; Zang, Z.; You, W.

    2018-04-01

    A three-dimensional variational data assimilation scheme is designed for satellite AOD based on the IMPROVE (Interagency Monitoring of Protected Visual Environments) equation. The observation operator that simulates AOD from the control variables is established by the IMPROVE equation. All of the 16 control variables in the assimilation scheme are the mass concentrations of aerosol species from the Model for Simulation Aerosol Interactions and Chemistry scheme, so as to take advantage of this scheme in providing comprehensive analyses of species concentrations and size distributions as well as be calculating efficiently. The assimilation scheme can save computational resources as the IMPROVE equation is a quadratic equation. A single-point observation experiment shows that the information from the single-point AOD is effectively spread horizontally and vertically.

  18. Data Assimilation in Hydrodynamic Models of Continental Shelf Seas

    DEFF Research Database (Denmark)

    Sørensen, Jacob Viborg Tornfeldt

    2004-01-01

    . Assimilation of sea surface temperature and parameter estimation in hydrodynamic models are also considered. The main focus has been on the development of robust and efficient techniques applicable in real operational settings. The applied assimilation techniques all use a Kalman filter approach. They consist....... The assimilation schemes used in this work are primarily based on two ensemble based schemes, the Ensemble Kalman Filter and the Reduced Rank Square Root Kalman Filter. In order to investigate the applicability of these and derived schemes, the sensitivity to filter parameters, nonlinearity and bias is examined...... in artificial tests. Approximate schemes, which are theoretically presented as using regularised Kalman gains, are introduced and successfully applied in artificial as well real case scenarios. Particularly, distant dependent and slowly time varying or constant Kalman gains are shown to possess good hindcast...

  19. The Impact of the Assimilation of Aquarius Sea Surface Salinity Data in the GEOS Ocean Data Assimilation System

    Science.gov (United States)

    Vernieres, Guillaume Rene Jean; Kovach, Robin M.; Keppenne, Christian L.; Akella, Santharam; Brucker, Ludovic; Dinnat, Emmanuel Phillippe

    2014-01-01

    Ocean salinity and temperature differences drive thermohaline circulations. These properties also play a key role in the ocean-atmosphere coupling. With the availability of L-band space-borne observations, it becomes possible to provide global scale sea surface salinity (SSS) distribution. This study analyzes globally the along-track (Level 2) Aquarius SSS retrievals obtained using both passive and active L-band observations. Aquarius alongtrack retrieved SSS are assimilated into the ocean data assimilation component of Version 5 of the Goddard Earth Observing System (GEOS-5) assimilation and forecast model. We present a methodology to correct the large biases and errors apparent in Version 2.0 of the Aquarius SSS retrieval algorithm and map the observed Aquarius SSS retrieval into the ocean models bulk salinity in the topmost layer. The impact of the assimilation of the corrected SSS on the salinity analysis is evaluated by comparisons with insitu salinity observations from Argo. The results show a significant reduction of the global biases and RMS of observations-minus-forecast differences at in-situ locations. The most striking results are found in the tropics and southern latitudes. Our results highlight the complementary role and problems that arise during the assimilation of salinity information from in-situ (Argo) and space-borne surface (SSS) observations

  20. Assimilation of satellite color observations in a coupled ocean GCM-ecosystem model

    Science.gov (United States)

    Sarmiento, Jorge L.

    1992-01-01

    Monthly average coastal zone color scanner (CZCS) estimates of chlorophyll concentration were assimilated into an ocean global circulation model(GCM) containing a simple model of the pelagic ecosystem. The assimilation was performed in the simplest possible manner, to allow the assessment of whether there were major problems with the ecosystem model or with the assimilation procedure. The current ecosystem model performed well in some regions, but failed in others to assimilate chlorophyll estimates without disrupting important ecosystem properties. This experiment gave insight into those properties of the ecosystem model that must be changed to allow data assimilation to be generally successful, while raising other important issues about the assimilation procedure.

  1. Biomass assimilation in coupled ecohydrodynamical model of the Mediterranean Sea

    Science.gov (United States)

    Crispi, G.; Bournaski, E.; Crise, A.

    2003-04-01

    Data assimilation has raised new interest in the last years in the context of the environmental sciences. The swift increment of the attention paid to it in oceanography is due to the coming age of operational services for the marine environment which is going to dramatically increase the demand for accurate, timely and reliable estimates of the space and time distribution both for physical and in a near future for biogeochemical fields. Data assimilation combines information derived from measurements with knowledge of the rules that govern the evolution of the system of interest through formalization and implementation in numerical models. The importance of ocean data assimilation has been recognized by several international programmes as JGOFS, GOOS and CLIVAR. This work presents an eco-hydrodynamic model of the Mediterranean Sea developed at the Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Trieste, Italy. It includes 3-D MOM-based hydrodynamics of the Mediterranean Sea, coupled with biochemical model of Nitrogen, Phytoplankton, Zooplankton, and Detritus (NPZD). Monthly mean wind forcings are adopted to force this MOM-NPZD model. For better prediction and analysis of N, P, Z and D distributions in the sea the model needs data assimilation from biomass observations on the sea surface. Chosen approach for evaluating performances of data assimilation techniques in coupled model is the definition of a twin experiment testbed where a reference run is carried out assuming its result as the truth. We define a sampling strategy to obtain different datasets to be incorporated in another ecological model in successive runs in order to appraise the potential of the data assimilation and sampling strategy. The runs carried out with different techniques and different spatio-temporal coverages are compared in order to evaluate the sensitivity to different coverage of dataset. The discussed alternative way is to assume the ecosystem at steady state and

  2. Ensemble streamflow assimilation with the National Water Model.

    Science.gov (United States)

    Rafieeinasab, A.; McCreight, J. L.; Noh, S.; Seo, D. J.; Gochis, D.

    2017-12-01

    Through case studies of flooding across the US, we compare the performance of the National Water Model (NWM) data assimilation (DA) scheme to that of a newly implemented ensemble Kalman filter approach. The NOAA National Water Model (NWM) is an operational implementation of the community WRF-Hydro modeling system. As of August 2016, the NWM forecasts of distributed hydrologic states and fluxes (including soil moisture, snowpack, ET, and ponded water) over the contiguous United States have been publicly disseminated by the National Center for Environmental Prediction (NCEP) . It also provides streamflow forecasts at more than 2.7 million river reaches up to 30 days in advance. The NWM employs a nudging scheme to assimilate more than 6,000 USGS streamflow observations and provide initial conditions for its forecasts. A problem with nudging is how the forecasts relax quickly to open-loop bias in the forecast. This has been partially addressed by an experimental bias correction approach which was found to have issues with phase errors during flooding events. In this work, we present an ensemble streamflow data assimilation approach combining new channel-only capabilities of the NWM and HydroDART (a coupling of the offline WRF-Hydro model and NCAR's Data Assimilation Research Testbed; DART). Our approach focuses on the single model state of discharge and incorporates error distributions on channel-influxes (overland and groundwater) in the assimilation via an ensemble Kalman filter (EnKF). In order to avoid filter degeneracy associated with a limited number of ensemble at large scale, DART's covariance inflation (Anderson, 2009) and localization capabilities are implemented and evaluated. The current NWM data assimilation scheme is compared to preliminary results from the EnKF application for several flooding case studies across the US.

  3. Assimilation of satellite altimeter data into an open ocean model

    Science.gov (United States)

    Vogeler, Armin; SchröTer, Jens

    1995-08-01

    Geosat sea surface height data are assimilated into an eddy-resolving quasi-geostrophic open ocean model using the adjoint technique. The method adjusts the initial conditions for all layers and is successful on the timescale of a few weeks. Time-varying values for the open boundaries are prescribed by a much larger quasi-geostrophic model of the Antarctic Circumpolar Current (ACC). Both models have the same resolution of approximately 20×20 km (1/3°×1/6°), have three layers, and include realistic bottom topography and coastlines. The open model box is embedded in the African sector of the ACC. For continuous assimilation of satellite data into the larger model the nudging technique is applied. These results are used for the adjoint optimization procedure as boundary conditions and as a first guess for the initial condition. For the open model box the difference between model and satellite sea surface height that remains after the nudging experiment amounts to a 19-cm root-mean-square error (rmse). By assimilation into the regional model this value can be reduced to a 6-cm rmse for an assimilation period of 20 days. Several experiments which attempt to improve the convergence of the iterative optimization method are reported. Scaling and regularization by smoothing have to be applied carefully. Especially during the first 10 iterations, the convergence can be improved considerably by low-pass filtering of the cost function gradient. The result of a perturbation experiment shows that for longer assimilation periods the influence of the boundary values becomes dominant and they should be determined inversely by data assimilation into the open ocean model.

  4. Assimilation scheme of the Mediterranean Forecasting System: operational implementation

    Directory of Open Access Journals (Sweden)

    E. Demirov

    Full Text Available This paper describes the operational implementation of the data assimilation scheme for the Mediterranean Forecasting System Pilot Project (MFSPP. The assimilation scheme, System for Ocean Forecast and Analysis (SOFA, is a reduced order Optimal Interpolation (OI scheme. The order reduction is achieved by projection of the state vector into vertical Empirical Orthogonal Functions (EOF. The data assimilated are Sea Level Anomaly (SLA and temperature profiles from Expandable Bathy Termographs (XBT. The data collection, quality control, assimilation and forecast procedures are all done in Near Real Time (NRT. The OI is used intermittently with an assimilation cycle of one week so that an analysis is produced once a week. The forecast is then done for ten days following the analysis day. The root mean square (RMS between the model forecast and the analysis (the forecast RMS is below 0.7°C in the surface layers and below 0.2°C in the layers deeper than 200 m for all the ten forecast days. The RMS between forecast and initial condition (persistence RMS is higher than forecast RMS after the first day. This means that the model improves forecast with respect to persistence. The calculation of the misfit between the forecast and the satellite data suggests that the model solution represents well the main space and time variability of the SLA except for a relatively short period of three – four weeks during the summer when the data show a fast transition between the cyclonic winter and anti-cyclonic summer regimes. This occurs in the surface layers that are not corrected by our assimilation scheme hypothesis. On the basis of the forecast skill scores analysis, conclusions are drawn about future improvements.

    Key words. Oceanography; general (marginal and semi-enclosed seas; numerical modeling; ocean prediction

  5. Assimilation scheme of the Mediterranean Forecasting System: operational implementation

    Directory of Open Access Journals (Sweden)

    E. Demirov

    2003-01-01

    Full Text Available This paper describes the operational implementation of the data assimilation scheme for the Mediterranean Forecasting System Pilot Project (MFSPP. The assimilation scheme, System for Ocean Forecast and Analysis (SOFA, is a reduced order Optimal Interpolation (OI scheme. The order reduction is achieved by projection of the state vector into vertical Empirical Orthogonal Functions (EOF. The data assimilated are Sea Level Anomaly (SLA and temperature profiles from Expandable Bathy Termographs (XBT. The data collection, quality control, assimilation and forecast procedures are all done in Near Real Time (NRT. The OI is used intermittently with an assimilation cycle of one week so that an analysis is produced once a week. The forecast is then done for ten days following the analysis day. The root mean square (RMS between the model forecast and the analysis (the forecast RMS is below 0.7°C in the surface layers and below 0.2°C in the layers deeper than 200 m for all the ten forecast days. The RMS between forecast and initial condition (persistence RMS is higher than forecast RMS after the first day. This means that the model improves forecast with respect to persistence. The calculation of the misfit between the forecast and the satellite data suggests that the model solution represents well the main space and time variability of the SLA except for a relatively short period of three – four weeks during the summer when the data show a fast transition between the cyclonic winter and anti-cyclonic summer regimes. This occurs in the surface layers that are not corrected by our assimilation scheme hypothesis. On the basis of the forecast skill scores analysis, conclusions are drawn about future improvements. Key words. Oceanography; general (marginal and semi-enclosed seas; numerical modeling; ocean prediction

  6. Assimilation of LAI time-series in crop production models

    Science.gov (United States)

    Kooistra, Lammert; Rijk, Bert; Nannes, Louis

    2014-05-01

    Agriculture is worldwide a large consumer of freshwater, nutrients and land. Spatial explicit agricultural management activities (e.g., fertilization, irrigation) could significantly improve efficiency in resource use. In previous studies and operational applications, remote sensing has shown to be a powerful method for spatio-temporal monitoring of actual crop status. As a next step, yield forecasting by assimilating remote sensing based plant variables in crop production models would improve agricultural decision support both at the farm and field level. In this study we investigated the potential of remote sensing based Leaf Area Index (LAI) time-series assimilated in the crop production model LINTUL to improve yield forecasting at field level. The effect of assimilation method and amount of assimilated observations was evaluated. The LINTUL-3 crop production model was calibrated and validated for a potato crop on two experimental fields in the south of the Netherlands. A range of data sources (e.g., in-situ soil moisture and weather sensors, destructive crop measurements) was used for calibration of the model for the experimental field in 2010. LAI from cropscan field radiometer measurements and actual LAI measured with the LAI-2000 instrument were used as input for the LAI time-series. The LAI time-series were assimilated in the LINTUL model and validated for a second experimental field on which potatoes were grown in 2011. Yield in 2011 was simulated with an R2 of 0.82 when compared with field measured yield. Furthermore, we analysed the potential of assimilation of LAI into the LINTUL-3 model through the 'updating' assimilation technique. The deviation between measured and simulated yield decreased from 9371 kg/ha to 8729 kg/ha when assimilating weekly LAI measurements in the LINTUL model over the season of 2011. LINTUL-3 furthermore shows the main growth reducing factors, which are useful for farm decision support. The combination of crop models and sensor

  7. Multivariate and multiscale data assimilation in terrestrial systems: a review.

    Science.gov (United States)

    Montzka, Carsten; Pauwels, Valentijn R N; Franssen, Harrie-Jan Hendricks; Han, Xujun; Vereecken, Harry

    2012-11-26

    More and more terrestrial observational networks are being established to monitor climatic, hydrological and land-use changes in different regions of the World. In these networks, time series of states and fluxes are recorded in an automated manner, often with a high temporal resolution. These data are important for the understanding of water, energy, and/or matter fluxes, as well as their biological and physical drivers and interactions with and within the terrestrial system. Similarly, the number and accuracy of variables, which can be observed by spaceborne sensors, are increasing. Data assimilation (DA) methods utilize these observations in terrestrial models in order to increase process knowledge as well as to improve forecasts for the system being studied. The widely implemented automation in observing environmental states and fluxes makes an operational computation more and more feasible, and it opens the perspective of short-time forecasts of the state of terrestrial systems. In this paper, we review the state of the art with respect to DA focusing on the joint assimilation of observational data precedents from different spatial scales and different data types. An introduction is given to different DA methods, such as the Ensemble Kalman Filter (EnKF), Particle Filter (PF) and variational methods (3/4D-VAR). In this review, we distinguish between four major DA approaches: (1) univariate single-scale DA (UVSS), which is the approach used in the majority of published DA applications, (2) univariate multiscale DA (UVMS) referring to a methodology which acknowledges that at least some of the assimilated data are measured at a different scale than the computational grid scale, (3) multivariate single-scale DA (MVSS) dealing with the assimilation of at least two different data types, and (4) combined multivariate multiscale DA (MVMS). Finally, we conclude with a discussion on the advantages and disadvantages of the assimilation of multiple data types in a

  8. Multivariate and Multiscale Data Assimilation in Terrestrial Systems: A Review

    Directory of Open Access Journals (Sweden)

    Harry Vereecken

    2012-11-01

    Full Text Available More and more terrestrial observational networks are being established to monitor climatic, hydrological and land-use changes in different regions of the World. In these networks, time series of states and fluxes are recorded in an automated manner, often with a high temporal resolution. These data are important for the understanding of water, energy, and/or matter fluxes, as well as their biological and physical drivers and interactions with and within the terrestrial system. Similarly, the number and accuracy of variables, which can be observed by spaceborne sensors, are increasing. Data assimilation (DA methods utilize these observations in terrestrial models in order to increase process knowledge as well as to improve forecasts for the system being studied. The widely implemented automation in observing environmental states and fluxes makes an operational computation more and more feasible, and it opens the perspective of short-time forecasts of the state of terrestrial systems. In this paper, we review the state of the art with respect to DA focusing on the joint assimilation of observational data precedents from different spatial scales and different data types. An introduction is given to different DA methods, such as the Ensemble Kalman Filter (EnKF, Particle Filter (PF and variational methods (3/4D-VAR. In this review, we distinguish between four major DA approaches: (1 univariate single-scale DA (UVSS, which is the approach used in the majority of published DA applications, (2 univariate multiscale DA (UVMS referring to a methodology which acknowledges that at least some of the assimilated data are measured at a different scale than the computational grid scale, (3 multivariate single-scale DA (MVSS dealing with the assimilation of at least two different data types, and (4 combined multivariate multiscale DA (MVMS. Finally, we conclude with a discussion on the advantages and disadvantages of the assimilation of multiple data types in a

  9. Reconstruction of Historical Weather by Assimilating Old Weather Diary Data

    Science.gov (United States)

    Neluwala, P.; Yoshimura, K.; Toride, K.; Hirano, J.; Ichino, M.; Okazaki, A.

    2017-12-01

    Climate can control not only human life style but also other living beings. It is important to investigate historical climate to understand the current and future climates. Information about daily weather can give a better understanding of past life on earth. Long-term weather influences crop calendar as well as the development of civilizations. Unfortunately, existing reconstructed daily weather data are limited to 1850s due to the availability of instrumental data. The climate data prior to that are derived from proxy materials (e.g., tree-ring width, ice core isotopes, etc.) which are either in annual or decadal scale. However, there are many historical documents which contain information about weather such as personal diaries. In Japan, around 20 diaries in average during the 16th - 19th centuries have been collected and converted into a digitized form. As such, diary data exist in many other countries. This study aims to reconstruct historical daily weather during the 18th and 19th centuries using personal daily diaries which have analogue weather descriptions such as `cloudy' or `sunny'. A recent study has shown the possibility of assimilating coarse weather data using idealized experiments. We further extend this study by assimilating modern weather descriptions similar to diary data in recent periods. The Global Spectral model (GSM) of National Centers for Environmental Prediction (NCEP) is used to reconstruct weather with the Local Ensemble Kalman filter (LETKF). Descriptive data are first converted to model variables such as total cloud cover (TCC), solar radiation and precipitation using empirical relationships. Those variables are then assimilated on a daily basis after adding random errors to consider the uncertainty of actual diary data. The assimilation of downward short wave solar radiation using weather descriptions improves RMSE from 64.3 w/m2 to 33.0 w/m2 and correlation coefficient (R) from 0.5 to 0.8 compared with the case without any

  10. SMAP Data Assimilation at NASA SPoRT

    Science.gov (United States)

    Blankenship, Clay B.; Case, Jonathan L.; Zavodsky, Bradley T.

    2016-01-01

    The NASA Short-Term Prediction Research and Transition (SPoRT) Center maintains a near-real- time run of the Noah Land Surface Model within the Land Information System (LIS) at 3-km resolution. Soil moisture products from this model are used by several NOAA/National Weather Service Weather Forecast Offices for flood and drought situational awareness. We have implemented assimilation of soil moisture retrievals from the Soil Moisture Ocean Salinity (SMOS) and Soil Moisture Active/ Passive (SMAP) satellites, and are now evaluating the SMAP assimilation. The SMAP-enhanced LIS product is planned for public release by October 2016.

  11. Assimilation of radar-based nowcast into HIRLAM NWP model

    DEFF Research Database (Denmark)

    Jensen, David Getreuer; Petersen, Claus; Rasmussen, Michael R.

    2015-01-01

    The present study introduces a nowcast scheme that assimilates radar extrapolation data (RED) into a nowcasting version of the high resolution limited area model (HIRLAM) numerical weather prediction (NWP) model covering the area of Denmark. The RED are based on the Co-TREC (tracking radar echoes...... by correlation) methodology and are generated from cleaned radar mosaics from the Danish weather radar network. The assimilation technique is a newly developed method that increases model precipitation by increasing low-level convergence and decreasing convergence aloft in order to increase the vertical velocity....... The level of improved predictability relies on the RED quality, which again relies on the type of event....

  12. Data assimilation in integrated hydrological modeling using ensemble Kalman filtering

    DEFF Research Database (Denmark)

    Rasmussen, Jørn; Madsen, H.; Jensen, Karsten Høgh

    2015-01-01

    Groundwater head and stream discharge is assimilated using the ensemble transform Kalman filter in an integrated hydrological model with the aim of studying the relationship between the filter performance and the ensemble size. In an attempt to reduce the required number of ensemble members...... and estimating parameters requires a much larger ensemble size than just assimilating groundwater head observations. However, the required ensemble size can be greatly reduced with the use of adaptive localization, which by far outperforms distance-based localization. The study is conducted using synthetic data...

  13. Effect of multi-effect triazole on absorption of phosphorus and nitrogen and distribution of 14CO2-assimilates in rape plant

    International Nuclear Information System (INIS)

    Xi Haifu; Ye Qingfu; Shen Huicong; Zhou Weijun

    1995-01-01

    By using tracer technique, the effects of Multi-Effect Triazole (MET) on uptake of 32 P, 15 N and distribution of 14 CO 2 -assimilates in rape plant were studied. The experimental results showed that the foliar spraying of MET with the concentration of 150 ppm in three leaves stage could significantly increase 32 P uptake by 75.34%∼101.08%, the utilization rate of base fertilizer 15 NH 4 HCO 3 by 9.10%. And the rate of photosynthesis increased by 7.44%∼31.40% in seedling stage, by 47.74% in initial flowering stage and by 47.93% in mature stage. The regulation effects of MET on distribution of 15 N absorbed and 14 CO 2 -assimilates were shown by increasing absorption of 15 N and assimilates in seeds of rape plant

  14. Coupled atmosphere and land-surface assimilation of surface observations with a single column model and ensemble data assimilation

    Science.gov (United States)

    Rostkier-Edelstein, Dorita; Hacker, Joshua P.; Snyder, Chris

    2014-05-01

    Numerical weather prediction and data assimilation models are composed of coupled atmosphere and land-surface (LS) components. If possible, the assimilation procedure should be coupled so that observed information in one module is used to correct fields in the coupled module. There have been some attempts in this direction using optimal interpolation, nudging and 2/3DVAR data assimilation techniques. Aside from satellite remote sensed observations, reference height in-situ observations of temperature and moisture have been used in these studies. Among other problems, difficulties in coupled atmosphere and LS assimilation arise as a result of the different time scales characteristic of each component and the unsteady correlation between these components under varying flow conditions. Ensemble data-assimilation techniques rely on flow dependent observations-model covariances. Provided that correlations and covariances between land and atmosphere can be adequately simulated and sampled, ensemble data assimilation should enable appropriate assimilation of observations simultaneously into the atmospheric and LS states. Our aim is to explore assimilation of reference height in-situ temperature and moisture observations into the coupled atmosphere-LS modules(simultaneously) in NCAR's WRF-ARW model using the NCAR's DART ensemble data-assimilation system. Observing system simulation experiments (OSSEs) are performed using the single column model (SCM) version of WRF. Numerical experiments during a warm season are centered on an atmospheric and soil column in the South Great Plains. Synthetic observations are derived from "truth" WRF-SCM runs for a given date,initialized and forced using North American Regional Reanalyses (NARR). WRF-SCM atmospheric and LS ensembles are created by mixing the atmospheric and soil NARR profile centered on a given date with that from another day (randomly chosen from the same season) with weights drawn from a logit-normal distribution. Three

  15. Hormonal and metabolic regulation of tomato fruit sink activity and yield under salinity

    DEFF Research Database (Denmark)

    Albacete, Alfonso; Cantero-Navarro, Elena; Balibrea, María E.

    2014-01-01

    Salinization of water and soil has a negative impact on tomato (Solanum lycopersicum L.) productivity by reducing growth of sink organs and by inducing senescence in source leaves. It has been hypothesized that yield stability implies the maintenance or increase of sink activity in the reproductive...... structures, thus contributing to the transport of assimilates from the source leaves through changes in sucrolytic enzymes and their regulation by phytohormones. In this study, classical and functional physiological approaches have been integrated to study the influence of metabolic and hormonal factors...... sucrolytic activities (mainly cwInv and sucrose synthase), sink strength, and fruit weight, whereas the ethylene-releasing compound ethephon had a negative effect in equivalent non-stressed fruits. Fruit yield was increased by both the constitutive expression of CIN1 in the fruits (up to 4-fold) or IPT...

  16. Hindcasting and Forecasting of Surface Flow Fields through Assimilating High Frequency Remotely Sensing Radar Data

    Directory of Open Access Journals (Sweden)

    Lei Ren

    2017-09-01

    Full Text Available In order to improve the forecasting ability of numerical models, a sequential data assimilation scheme, nudging, was applied to blend remotely sensing high-frequency (HF radar surface currents with results from a three-dimensional numerical, EFDC (Environmental Fluid Dynamics Code model. For the first time, this research presents the most appropriate nudging parameters, which were determined from sensitivity experiments. To examine the influence of data assimilation cycle lengths on forecasts and to extend forecasting improvements, the duration of data assimilation cycles was studied through assimilating linearly interpolated temporal radar data. Data assimilation nudging parameters have not been previously analyzed. Assimilation of HF radar measurements at each model computational timestep outperformed those assimilation models using longer data assimilation cycle lengths; root-mean-square error (RMSE values of both surface velocity components during a 12 h model forecasting period indicated that surface flow fields were significantly improved when implementing nudging assimilation at each model computational timestep. The Data Assimilation Skill Score (DASS technique was used to quantitatively evaluate forecast improvements. The averaged values of DASS over the data assimilation domain were 26% and 33% for east–west and north–south velocity components, respectively, over the half-day forecasting period. Correlation of Averaged Kinetic Energy (AKE was improved by more than 10% in the best data assimilation model. Time series of velocity components and surface flow fields were presented to illustrate the improvement resulting from data assimilation application over time.

  17. Induction of the Nitrate Assimilation nirA Operon and Protein-Protein Interactions in the Maturation of Nitrate and Nitrite Reductases in the Cyanobacterium Anabaena sp. Strain PCC 7120.

    Science.gov (United States)

    Frías, José E; Flores, Enrique

    2015-07-01

    Nitrate is widely used as a nitrogen source by cyanobacteria, in which the nitrate assimilation structural genes frequently constitute the so-called nirA operon. This operon contains the genes encoding nitrite reductase (nirA), a nitrate/nitrite transporter (frequently an ABC-type transporter; nrtABCD), and nitrate reductase (narB). In the model filamentous cyanobacterium Anabaena sp. strain PCC 7120, which can fix N2 in specialized cells termed heterocysts, the nirA operon is expressed at high levels only in media containing nitrate or nitrite and lacking ammonium, a preferred nitrogen source. Here we examined the genes downstream of the nirA operon in Anabaena and found that a small open reading frame of unknown function, alr0613, can be cotranscribed with the operon. The next gene in the genome, alr0614 (narM), showed an expression pattern similar to that of the nirA operon, implying correlated expression of narM and the operon. A mutant of narM with an insertion mutation failed to produce nitrate reductase activity, consistent with the idea that NarM is required for the maturation of NarB. Both narM and narB mutants were impaired in the nitrate-dependent induction of the nirA operon, suggesting that nitrite is an inducer of the operon in Anabaena. It has previously been shown that the nitrite reductase protein NirA requires NirB, a protein likely involved in protein-protein interactions, to attain maximum activity. Bacterial two-hybrid analysis confirmed possible NirA-NirB and NarB-NarM interactions, suggesting that the development of both nitrite reductase and nitrate reductase activities in cyanobacteria involves physical interaction of the corresponding enzymes with their cognate partners, NirB and NarM, respectively. Nitrate is an important source of nitrogen for many microorganisms that is utilized through the nitrate assimilation system, which includes nitrate/nitrite membrane transporters and the nitrate and nitrite reductases. Many cyanobacteria

  18. Effects of Model Chemistry and Data Biases on Stratospheric Ozone Assimilation

    National Research Council Canada - National Science Library

    Coy, L; Allen, D. R; Eckermann, S. D; McCormack, J. P; Stajner, I; Hogan, T. F

    2007-01-01

    .... In this study, O-F statistics from the Global Ozone Assimilation Testing System (GOATS) are used to examine how ozone assimilation products and their associated O-F statistics depend on input data biases and ozone photochemistry parameterizations (OPP...

  19. Sensitivity of Satellite Altimetry Data Assimilation on a Weapon Acoustic Preset Using MODAS

    National Research Council Canada - National Science Library

    Chu, Peter; Mancini, Steven; Gottshall, Eric; Cwalina, David; Barron, Charlie N

    2007-01-01

    ...) is analyzed with SSP derived from the modular ocean data assimilation system (MODAS). The MODAS fields differ in that one uses altimeter data assimilated from three satellites while the other uses no altimeter data...

  20. Sucrose assimilation and the role of sucrose transporters in plant ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-12-29

    Dec 29, 2008 ... African Journal of Biotechnology Vol. 7 (25), pp. ... Review. Sucrose assimilation and the role of sucrose transporters in plant wound response. Omodele ... Key words: Sucrose transporters, Plasma membrane, carbohydrate, sieve element, source-sink. ... pathogens (Paul et al., 2000) and results in a severe.

  1. Economic Assimilation and Outmigration of Immigrants in West-Germany

    NARCIS (Netherlands)

    Bellemare, C.

    2003-01-01

    By analyzing earnings of observed immigrants workers, the literature on the economic assimilation of immigrants has generally overlooked two potentially important selectivity issues.First, earnings of immigrant workers may di¿er substantially from those of non-workers.Second, earnings of immigrants

  2. Opinion Dynamics with Heterogeneous Interactions and Information Assimilation

    Science.gov (United States)

    Mir Tabatabaei, Seydeh Anahita

    2013-01-01

    In any modern society, individuals interact to form opinions on various topics, including economic, political, and social aspects. Opinions evolve as the result of the continuous exchange of information among individuals and of the assimilation of information distributed by media. The impact of individuals' opinions on each other forms a network,…

  3. Anterior Cingulate Cortex in Schema Assimilation and Expression

    Science.gov (United States)

    Wang, Szu-Han; Tse, Dorothy; Morris, Richard G. M.

    2012-01-01

    In humans and in animals, mental schemas can store information within an associative framework that enables rapid and efficient assimilation of new information. Using a hippocampal-dependent paired-associate task, we now report that the anterior cingulate cortex is part of a neocortical network of schema storage with NMDA receptor-mediated…

  4. Naming game with biased assimilation over adaptive networks

    Science.gov (United States)

    Fu, Guiyuan; Zhang, Weidong

    2018-01-01

    The dynamics of two-word naming game incorporating the influence of biased assimilation over adaptive network is investigated in this paper. Firstly an extended naming game with biased assimilation (NGBA) is proposed. The hearer in NGBA accepts the received information in a biased manner, where he may refuse to accept the conveyed word from the speaker with a predefined probability, if the conveyed word is different from his current memory. Secondly, the adaptive network is formulated by rewiring the links. Theoretical analysis is developed to show that the population in NGBA will eventually reach global consensus on either A or B. Numerical simulation results show that the larger strength of biased assimilation on both words, the slower convergence speed, while larger strength of biased assimilation on only one word can slightly accelerate the convergence; larger population size can make the rate of convergence slower to a large extent when it increases from a relatively small size, while such effect becomes minor when the population size is large; the behavior of adaptively reconnecting the existing links can greatly accelerate the rate of convergence especially on the sparse connected network.

  5. Volcanic Ash Data Assimilation System for Atmospheric Transport Model

    Science.gov (United States)

    Ishii, K.; Shimbori, T.; Sato, E.; Tokumoto, T.; Hayashi, Y.; Hashimoto, A.

    2017-12-01

    The Japan Meteorological Agency (JMA) has two operations for volcanic ash forecasts, which are Volcanic Ash Fall Forecast (VAFF) and Volcanic Ash Advisory (VAA). In these operations, the forecasts are calculated by atmospheric transport models including the advection process, the turbulent diffusion process, the gravitational fall process and the deposition process (wet/dry). The initial distribution of volcanic ash in the models is the most important but uncertain factor. In operations, the model of Suzuki (1983) with many empirical assumptions is adopted to the initial distribution. This adversely affects the reconstruction of actual eruption plumes.We are developing a volcanic ash data assimilation system using weather radars and meteorological satellite observation, in order to improve the initial distribution of the atmospheric transport models. Our data assimilation system is based on the three-dimensional variational data assimilation method (3D-Var). Analysis variables are ash concentration and size distribution parameters which are mutually independent. The radar observation is expected to provide three-dimensional parameters such as ash concentration and parameters of ash particle size distribution. On the other hand, the satellite observation is anticipated to provide two-dimensional parameters of ash clouds such as mass loading, top height and particle effective radius. In this study, we estimate the thickness of ash clouds using vertical wind shear of JMA numerical weather prediction, and apply for the volcanic ash data assimilation system.

  6. A reduced adjoint approach to variational data assimilation

    KAUST Repository

    Altaf, Muhammad; El Gharamti, Mohamad; Heemink, Arnold W.; Hoteit, Ibrahim

    2013-01-01

    The adjoint method has been used very often for variational data assimilation. The computational cost to run the adjoint model often exceeds several original model runs and the method needs significant programming efforts to implement the adjoint model code. The work proposed here is variational data assimilation based on proper orthogonal decomposition (POD) which avoids the implementation of the adjoint of the tangent linear approximation of the original nonlinear model. An ensemble of the forward model simulations is used to determine the approximation of the covariance matrix and only the dominant eigenvectors of this matrix are used to define a model subspace. The adjoint of the tangent linear model is replaced by the reduced adjoint based on this reduced space. Thus the adjoint model is run in reduced space with negligible computational cost. Once the gradient is obtained in reduced space it is projected back in full space and the minimization process is carried in full space. In the paper the reduced adjoint approach to variational data assimilation is introduced. The characteristics and performance of the method are illustrated with a number of data assimilation experiments in a ground water subsurface contaminant model. © 2012 Elsevier B.V.

  7. A reduced adjoint approach to variational data assimilation

    KAUST Repository

    Altaf, Muhammad

    2013-02-01

    The adjoint method has been used very often for variational data assimilation. The computational cost to run the adjoint model often exceeds several original model runs and the method needs significant programming efforts to implement the adjoint model code. The work proposed here is variational data assimilation based on proper orthogonal decomposition (POD) which avoids the implementation of the adjoint of the tangent linear approximation of the original nonlinear model. An ensemble of the forward model simulations is used to determine the approximation of the covariance matrix and only the dominant eigenvectors of this matrix are used to define a model subspace. The adjoint of the tangent linear model is replaced by the reduced adjoint based on this reduced space. Thus the adjoint model is run in reduced space with negligible computational cost. Once the gradient is obtained in reduced space it is projected back in full space and the minimization process is carried in full space. In the paper the reduced adjoint approach to variational data assimilation is introduced. The characteristics and performance of the method are illustrated with a number of data assimilation experiments in a ground water subsurface contaminant model. © 2012 Elsevier B.V.

  8. Probability Maps for the Visualization of Assimilation Ensemble Flow Data

    KAUST Repository

    Hollt, Thomas

    2015-05-25

    Ocean forecasts nowadays are created by running ensemble simulations in combination with data assimilation techniques. Most of these techniques resample the ensemble members after each assimilation cycle. This means that in a time series, after resampling, every member can follow up on any of the members before resampling. Tracking behavior over time, such as all possible paths of a particle in an ensemble vector field, becomes very difficult, as the number of combinations rises exponentially with the number of assimilation cycles. In general a single possible path is not of interest but only the probabilities that any point in space might be reached by a particle at some point in time. In this work we present an approach using probability-weighted piecewise particle trajectories to allow such a mapping interactively, instead of tracing quadrillions of individual particles. We achieve interactive rates by binning the domain and splitting up the tracing process into the individual assimilation cycles, so that particles that fall into the same bin after a cycle can be treated as a single particle with a larger probability as input for the next time step. As a result we loose the possibility to track individual particles, but can create probability maps for any desired seed at interactive rates.

  9. Music playlist generation by assimilating GMMs into SOMs

    NARCIS (Netherlands)

    Balkema, Wietse; van der Heijden, Ferdinand

    A method for music playlist generation, using assimilated Gaussian mixture models (GMMs) in self organizing maps (SOMs) is presented. Traditionally, the neurons in a SOM are represented by vectors, but in this paper we propose to use GMMs instead. To this end, we introduce a method to adapt a GMM

  10. Growth, assimilate partitioning and grain yield response of soybean ...

    African Journals Online (AJOL)

    This investigation tested variation in the growth components, assimilate partitioning and grain yield of soybean (Glycine max L. Merrrill) varieties established in CO2 enriched atmosphere when inoculated with mixtures of Arbuscular mycorrhizal fungi (AMF) species in the humid rainforest of Nigeria. A pot and a field ...

  11. Homophily and assimilation among sportactive adolescent substance users

    NARCIS (Netherlands)

    Pearson, M; Steglich, Ch.; Snijders, T.A.B.

    2006-01-01

    We analyse the co-evolution of social networks and substance use behaviour of adolescents and address the problem of separating the effects of homophily and assimilation. Adolescents who prefer friends with the same substance-use behaviour exhibit the homophily principle. Adolescents who adapt their

  12. Modelling Effluent Assimilative Capacity of Ikpoba River, Benin City ...

    African Journals Online (AJOL)

    The sheer display of reprehensible propensity on the part of public hospitals, abattoirs, breweries and city dwellers at large to discharge untreated waste, debris, scum and, in particular, municipal and industrial effluents into Ikpoba River has morphed into a situation whereby the assimilative capacity of the river has reached ...

  13. Satellite Data Assimilation within KIAPS-LETKF system

    Science.gov (United States)

    Jo, Y.; Lee, S., Sr.; Cho, K.

    2016-12-01

    Korea Institute of Atmospheric Prediction Systems (KIAPS) has been developing an ensemble data assimilation system using four-dimensional local ensemble transform kalman filter (LETKF; Hunt et al., 2007) within KIAPS Integrated Model (KIM), referred to as "KIAPS-LETKF". KIAPS-LETKF system was successfully evaluated with various Observing System Simulation Experiments (OSSEs) with NCAR Community Atmospheric Model - Spectral Element (Kang et al., 2013), which has fully unstructured quadrilateral meshes based on the cubed-sphere grid as the same grid system of KIM. Recently, assimilation of real observations has been conducted within the KIAPS-LETKF system with four-dimensional covariance functions over the 6-hr assimilation window. Then, conventional (e.g., sonde, aircraft, and surface) and satellite (e.g., AMSU-A, IASI, GPS-RO, and AMV) observations have been provided by the KIAPS Package for Observation Processing (KPOP). Wind speed prediction was found most beneficial due to ingestion of AMV and for the temperature prediction the improvement in assimilation is mostly due to ingestion of AMSU-A and IASI. However, some degradation in the simulation of the GPS-RO is presented in the upper stratosphere, even though GPS-RO leads positive impacts on the analysis and forecasts. We plan to test the bias correction method and several vertical localization strategies for radiance observations to improve analysis and forecast impacts.

  14. Assimilation of Long-Range Lightning Data over the Pacific

    Science.gov (United States)

    2011-09-30

    convective rainfall analyses over the Pacific, and (iii) to improve marine prediction of cyclogenesis of both tropical and extratropical cyclones through...data over the North Pacific Ocean, refine the relationships between lightning and storm hydrometeor characteristics, and assimilate lightning...unresolved storm -scale areas of deep convection over the data-sparse open oceans. Diabatic heating sources, especially latent heat release in deep

  15. Abscisic acid and assimilate partitioning during seed development

    NARCIS (Netherlands)

    Bruijn, de S.M.

    1993-01-01

    This thesis describes the influence of abscisic acid (ABA) on the transport of assimilates to seeds and the deposition of reserves in seeds. It is well-known from literature that ABA accumulates in seeds during development, and that ABA concentrations in seeds correlate rather well with

  16. A Generic Software Framework for Data Assimilation and Model Calibration

    NARCIS (Netherlands)

    Van Velzen, N.

    2010-01-01

    The accuracy of dynamic simulation models can be increased by using observations in conjunction with a data assimilation or model calibration algorithm. However, implementing such algorithms usually increases the complexity of the model software significantly. By using concepts from object oriented

  17. Educational Attainments of Immigrant Offspring: Success or Segmented Assimilation?

    Science.gov (United States)

    Boyd, Monica

    2002-01-01

    Examined the educational attainments of adult offspring of immigrants age 20-64 years, analyzing data from Canada's 1996 Survey of Labour and Income Dynamics. Contrary to second generation decline and segmented underclass assimilation found in the United States, Canadian adult visible-minority immigrant offspring did not have lower educational…

  18. Global assimilation of X Project Loon stratospheric balloon observations

    Science.gov (United States)

    Coy, L.; Schoeberl, M. R.; Pawson, S.; Candido, S.; Carver, R. W.

    2017-12-01

    Project Loon has an overall goal of providing worldwide internet coverage using a network of long-duration super-pressure balloons. Beginning in 2013, Loon has launched over 1600 balloons from multiple tropical and middle latitude locations. These GPS tracked balloon trajectories provide lower stratospheric wind information over the oceans and remote land areas where traditional radiosonde soundings are sparse, thus providing unique coverage of lower stratospheric winds. To fully investigate these Loon winds we: 1) compare the Loon winds to winds produced by a global data assimilation system (DAS: NASA GEOS) and 2) assimilate the Loon winds into the same comprehensive DAS. Results show that in middle latitudes the Loon winds and DAS winds agree well and assimilating the Loon winds have only a small impact on short-term forecasting of the Loon winds, however, in the tropics the loon winds and DAS winds often disagree substantially (8 m/s or more in magnitude) and in these cases assimilating the loon winds significantly improves the forecast of the loon winds. By highlighting cases where the Loon and DAS winds differ, these results can lead to improved understanding of stratospheric winds, especially in the tropics.

  19. Enzymic lactose hydrolysis

    Energy Technology Data Exchange (ETDEWEB)

    Miller, J J; Brand, J C

    1980-01-01

    Acid or enzymic hydrolysis can be used to hydrolyze lactose. Advantages of both are compared and details of enzymic hydrolysis using yeast or fungal enzymes given. The new scheme outlined involves recycling lactase. Because lactose and lactase react to ultrafiltration (UF) membranes differently separation is possible. Milk or milk products are ultrafiltered to separate a concentrate from a lactose-rich permeate which is treated with lactase in a reactor until hydrolysis reaches a required level. The lactase can be removed by UF as it does not permeate the membrane, and it is recycled back to the reactor. Permeate from the second UF stage may or may not be recombined with the concentrate from the first stage to produce a low lactose product (analysis of a typical low-lactose dried whole milk is given). Batch or continuous processes are explained and a batch process without enzyme recovery is discussed. (Refs. 4).

  20. Indicators: Sediment Enzymes

    Science.gov (United States)

    Sediment enzymes are proteins that are produced by microorganisms living in the sediment or soil. They are indicators of key ecosystem processes and can help determine which nutrients are affecting the biological community of a waterbody.

  1. Enzyme Vs. Extremozyme -32 ...

    Indian Academy of Sciences (India)

    Enzymes are biocatalytic protein molecules that enhance the rates of ... to physical forces (hydrogen bonds, hydrophobic 1, electrostatic and Van der ... conformation. In 1995 ... surface against 14.7% in Klenow poll (some of the hydrophobic.

  2. Lidar data assimilation for improved analyses of volcanic aerosol events

    Science.gov (United States)

    Lange, Anne Caroline; Elbern, Hendrik

    2014-05-01

    Observations of hazardous events with release of aerosols are hardly analyzable by today's data assimilation algorithms, without producing an attenuating bias. Skillful forecasts of unexpected aerosol events are essential for human health and to prevent an exposure of infirm persons and aircraft with possibly catastrophic outcome. Typical cases include mineral dust outbreaks, mostly from large desert regions, wild fires, and sea salt uplifts, while the focus aims for volcanic eruptions. In general, numerical chemistry and aerosol transport models cannot simulate such events without manual adjustments. The concept of data assimilation is able to correct the analysis, as long it is operationally implemented in the model system. Though, the tangent-linear approximation, which describes a substantial precondition for today's cutting edge data assimilation algorithms, is not valid during unexpected aerosol events. As part of the European COPERNICUS (earth observation) project MACC II and the national ESKP (Earth System Knowledge Platform) initiative, we developed a module that enables the assimilation of aerosol lidar observations, even during unforeseeable incidences of extreme emissions of particulate matter. Thereby, the influence of the background information has to be reduced adequately. Advanced lidar instruments comprise on the one hand the aspect of radiative transfer within the atmosphere and on the other hand they can deliver a detailed quantification of the detected aerosols. For the assimilation of maximal exploited lidar data, an appropriate lidar observation operator is constructed, compatible with the EURAD-IM (European Air Pollution and Dispersion - Inverse Model) system. The observation operator is able to map the modeled chemical and physical state on lidar attenuated backscatter, transmission, aerosol optical depth, as well as on the extinction and backscatter coefficients. Further, it has the ability to process the observed discrepancies with lidar

  3. Data Assimilation to Extract Soil Moisture Information from SMAP Observations

    Directory of Open Access Journals (Sweden)

    Jana Kolassa

    2017-11-01

    Full Text Available This study compares different methods to extract soil moisture information through the assimilation of Soil Moisture Active Passive (SMAP observations. Neural network (NN and physically-based SMAP soil moisture retrievals were assimilated into the National Aeronautics and Space Administration (NASA Catchment model over the contiguous United States for April 2015 to March 2017. By construction, the NN retrievals are consistent with the global climatology of the Catchment model soil moisture. Assimilating the NN retrievals without further bias correction improved the surface and root zone correlations against in situ measurements from 14 SMAP core validation sites (CVS by 0.12 and 0.16, respectively, over the model-only skill, and reduced the surface and root zone unbiased root-mean-square error (ubRMSE by 0.005 m 3 m − 3 and 0.001 m 3 m − 3 , respectively. The assimilation reduced the average absolute surface bias against the CVS measurements by 0.009 m 3 m − 3 , but increased the root zone bias by 0.014 m 3 m − 3 . Assimilating the NN retrievals after a localized bias correction yielded slightly lower surface correlation and ubRMSE improvements, but generally the skill differences were small. The assimilation of the physically-based SMAP Level-2 passive soil moisture retrievals using a global bias correction yielded similar skill improvements, as did the direct assimilation of locally bias-corrected SMAP brightness temperatures within the SMAP Level-4 soil moisture algorithm. The results show that global bias correction methods may be able to extract more independent information from SMAP observations compared to local bias correction methods, but without accurate quality control and observation error characterization they are also more vulnerable to adverse effects from retrieval errors related to uncertainties in the retrieval inputs and algorithm. Furthermore, the results show that using global bias correction approaches without a

  4. Improving Forecast Skill by Assimilation of AIRS Temperature Soundings

    Science.gov (United States)

    Susskind, Joel; Reale, Oreste

    2010-01-01

    AIRS was launched on EOS Aqua on May 4, 2002, together with AMSU-A and HSB, to form a next generation polar orbiting infrared and microwave atmospheric sounding system. The primary products of AIRS/AMSU-A are twice daily global fields of atmospheric temperature-humidity profiles, ozone profiles, sea/land surface skin temperature, and cloud related parameters including OLR. The AIRS Version 5 retrieval algorithm, is now being used operationally at the Goddard DISC in the routine generation of geophysical parameters derived from AIRS/AMSU data. A major innovation in Version 5 is the ability to generate case-by-case level-by-level error estimates delta T(p) for retrieved quantities and the use of these error estimates for Quality Control. We conducted a number of data assimilation experiments using the NASA GEOS-5 Data Assimilation System as a step toward finding an optimum balance of spatial coverage and sounding accuracy with regard to improving forecast skill. The model was run at a horizontal resolution of 0.5 deg. latitude X 0.67 deg longitude with 72 vertical levels. These experiments were run during four different seasons, each using a different year. The AIRS temperature profiles were presented to the GEOS-5 analysis as rawinsonde profiles, and the profile error estimates delta (p) were used as the uncertainty for each measurement in the data assimilation process. We compared forecasts analyses generated from the analyses done by assimilation of AIRS temperature profiles with three different sets of thresholds; Standard, Medium, and Tight. Assimilation of Quality Controlled AIRS temperature profiles significantly improve 5-7 day forecast skill compared to that obtained without the benefit of AIRS data in all of the cases studied. In addition, assimilation of Quality Controlled AIRS temperature soundings performs better than assimilation of AIRS observed radiances. Based on the experiments shown, Tight Quality Control of AIRS temperature profile performs best

  5. Overproduction of ligninolytic enzymes

    Science.gov (United States)

    Elisashvili, Vladimir; Kachlishvili, Eva; Torok, Tamas

    2014-06-17

    Methods, compositions, and systems for overproducing ligninolytic enzymes from the basidiomycetous fungus are described herein. As described, the method can include incubating a fungal strain of Cerrena unicolor IBB 303 in a fermentation system having growth medium which includes lignocellulosic material and then cultivating the fungal strain in the fermentation system under conditions wherein the fungus expresses the ligninolytic enzymes. In some cases, the lignocellulosic material is mandarin peel, ethanol production residue, walnut pericarp, wheat bran, wheat straw, or banana peel.

  6. Snow multivariable data assimilation for hydrological predictions in mountain areas

    Science.gov (United States)

    Piazzi, Gaia; Campo, Lorenzo; Gabellani, Simone; Rudari, Roberto; Castelli, Fabio; Cremonese, Edoardo; Morra di Cella, Umberto; Stevenin, Hervé; Ratto, Sara Maria

    2016-04-01

    The seasonal presence of snow on alpine catchments strongly impacts both surface energy balance and water resource. Thus, the knowledge of the snowpack dynamics is of critical importance for several applications, such as water resource management, floods prediction and hydroelectric power production. Several independent data sources provide information about snowpack state: ground-based measurements, satellite data and physical models. Although all these data types are reliable, each of them is affected by specific flaws and errors (respectively dependency on local conditions, sensor biases and limitations, initialization and poor quality forcing data). Moreover, there are physical factors that make an exhaustive reconstruction of snow dynamics complicated: snow intermittence in space and time, stratification and slow phenomena like metamorphism processes, uncertainty in snowfall evaluation, wind transportation, etc. Data Assimilation (DA) techniques provide an objective methodology to combine observational and modeled information to obtain the most likely estimate of snowpack state. Indeed, by combining all the available sources of information, the implementation of DA schemes can quantify and reduce the uncertainties of the estimations. This study presents SMASH (Snow Multidata Assimilation System for Hydrology), a multi-layer snow dynamic model, strengthened by a robust multivariable data assimilation algorithm. The model is physically based on mass and energy balances and can be used to reproduce the main physical processes occurring within the snowpack: accumulation, density dynamics, melting, sublimation, radiative balance, heat and mass exchanges. The model is driven by observed forcing meteorological data (air temperature, wind velocity, relative air humidity, precipitation and incident solar radiation) to provide a complete estimate of snowpack state. The implementation of an Ensemble Kalman Filter (EnKF) scheme enables to assimilate simultaneously ground

  7. Measurement of enzyme activity.

    Science.gov (United States)

    Harris, T K; Keshwani, M M

    2009-01-01

    To study and understand the nature of living cells, scientists have continually employed traditional biochemical techniques aimed to fractionate and characterize a designated network of macromolecular components required to carry out a particular cellular function. At the most rudimentary level, cellular functions ultimately entail rapid chemical transformations that otherwise would not occur in the physiological environment of the cell. The term enzyme is used to singularly designate a macromolecular gene product that specifically and greatly enhances the rate of a chemical transformation. Purification and characterization of individual and collective groups of enzymes has been and will remain essential toward advancement of the molecular biological sciences; and developing and utilizing enzyme reaction assays is central to this mission. First, basic kinetic principles are described for understanding chemical reaction rates and the catalytic effects of enzymes on such rates. Then, a number of methods are described for measuring enzyme-catalyzed reaction rates, which mainly differ with regard to techniques used to detect and quantify concentration changes of given reactants or products. Finally, short commentary is given toward formulation of reaction mixtures used to measure enzyme activity. Whereas a comprehensive treatment of enzymatic reaction assays is not within the scope of this chapter, the very core principles that are presented should enable new researchers to better understand the logic and utility of any given enzymatic assay that becomes of interest.

  8. Transcript profiling reveals rewiring of iron assimilation gene expression in Candida albicans and C. dubliniensis.

    LENUS (Irish Health Repository)

    Moran, Gary P

    2012-12-01

    Hyphal growth is repressed in Candida albicans and Candida dubliniensis by the transcription factor Nrg1. Transcript profiling of a C. dubliniensis NRG1 mutant identified a common group of 28 NRG1-repressed genes in both species, including the hypha-specific genes HWP1, ECE1 and the regulator of cell elongation UME6. Unexpectedly, C. dubliniensis NRG1 was required for wild-type levels of expression of 10 genes required for iron uptake including seven ferric reductases, SIT1, FTR1 and RBT5. However, at alkaline pH and during filamentous growth in 10% serum, most of these genes were highly induced in C. dubliniensis. Conversely, RBT5, PGA10, FRE10 and FRP1 did not exhibit induction during hyphal growth when NRG1 is downregulated, indicating that in C. dubliniensis NRG1 is also required for optimal expression of these genes in alkaline environments. In iron-depleted medium at pH 4.5, reduced growth of the NRG1 mutant relative to wild type was observed; however, growth was restored to wild-type levels or greater at pH 6.5, indicating that alkaline induction of iron assimilation gene expression could rescue this phenotype. These data indicate that transcriptional control of iron assimilation and pseudohypha formation has been separated in C. albicans, perhaps promoting growth in a wider range of niches.

  9. Impact of Bee Venom Enzymes on Diseases and Immune Responses.

    Science.gov (United States)

    Hossen, Md Sakib; Shapla, Ummay Mahfuza; Gan, Siew Hua; Khalil, Md Ibrahim

    2016-12-27

    Bee venom (BV) is used to treat many diseases and exhibits anti-inflammatory, anti-bacterial, antimutagenic, radioprotective, anti-nociceptive immunity promoting, hepatocyte protective and anti-cancer activity. According to the literature, BV contains several enzymes, including phospholipase A2 (PLA2), phospholipase B, hyaluronidase, acid phosphatase and α-glucosidase. Recent studies have also reported the detection of different classes of enzymes in BV, including esterases, proteases and peptidases, protease inhibitors and other important enzymes involved in carbohydrate metabolism. Nevertheless, the physiochemical properties and functions of each enzyme class and their mechanisms remain unclear. Various pharmacotherapeutic effects of some of the BV enzymes have been reported in several studies. At present, ongoing research aims to characterize each enzyme and elucidate their specific biological roles. This review gathers all the current knowledge on BV enzymes and their specific mechanisms in regulating various immune responses and physiological changes to provide a basis for future therapies for various diseases.

  10. Impact of Bee Venom Enzymes on Diseases and Immune Responses

    Directory of Open Access Journals (Sweden)

    Md. Sakib Hossen

    2016-12-01

    Full Text Available Bee venom (BV is used to treat many diseases and exhibits anti-inflammatory, anti-bacterial, antimutagenic, radioprotective, anti-nociceptive immunity promoting, hepatocyte protective and anti-cancer activity. According to the literature, BV contains several enzymes, including phospholipase A2 (PLA2, phospholipase B, hyaluronidase, acid phosphatase and α-glucosidase. Recent studies have also reported the detection of different classes of enzymes in BV, including esterases, proteases and peptidases, protease inhibitors and other important enzymes involved in carbohydrate metabolism. Nevertheless, the physiochemical properties and functions of each enzyme class and their mechanisms remain unclear. Various pharmacotherapeutic effects of some of the BV enzymes have been reported in several studies. At present, ongoing research aims to characterize each enzyme and elucidate their specific biological roles. This review gathers all the current knowledge on BV enzymes and their specific mechanisms in regulating various immune responses and physiological changes to provide a basis for future therapies for various diseases.

  11. Assimilation of diazotrophic nitrogen into pelagic food webs.

    Directory of Open Access Journals (Sweden)

    Ryan J Woodland

    Full Text Available The fate of diazotrophic nitrogen (N(D fixed by planktonic cyanobacteria in pelagic food webs remains unresolved, particularly for toxic cyanophytes that are selectively avoided by most herbivorous zooplankton. Current theory suggests that N(D fixed during cyanobacterial blooms can enter planktonic food webs contemporaneously with peak bloom biomass via direct grazing of zooplankton on cyanobacteria or via the uptake of bioavailable N(D (exuded from viable cyanobacterial cells by palatable phytoplankton or microbial consortia. Alternatively, N(D can enter planktonic food webs post-bloom following the remineralization of bloom detritus. Although the relative contribution of these processes to planktonic nutrient cycles is unknown, we hypothesized that assimilation of bioavailable N(D (e.g., nitrate, ammonium by palatable phytoplankton and subsequent grazing by zooplankton (either during or after the cyanobacterial bloom would be the primary pathway by which N(D was incorporated into the planktonic food web. Instead, in situ stable isotope measurements and grazing experiments clearly documented that the assimilation of N(D by zooplankton outpaced assimilation by palatable phytoplankton during a bloom of toxic Nodularia spumigena Mertens. We identified two distinct temporal phases in the trophic transfer of N(D from N. spumigena to the plankton community. The first phase was a highly dynamic transfer of N(D to zooplankton with rates that covaried with bloom biomass while bypassing other phytoplankton taxa; a trophic transfer that we infer was routed through bloom-associated bacteria. The second phase was a slowly accelerating assimilation of the dissolved-N(D pool by phytoplankton that was decoupled from contemporaneous variability in N. spumigena concentrations. These findings provide empirical evidence that N(D can be assimilated and transferred rapidly throughout natural plankton communities and yield insights into the specific processes

  12. Assimilation of SMOS Retrievals in the Land Information System

    Science.gov (United States)

    Blankenship, Clay B.; Case, Jonathan L.; Zavodsky, Bradley T.; Crosson, William L.

    2016-01-01

    The Soil Moisture and Ocean Salinity (SMOS) satellite provides retrievals of soil moisture in the upper 5 cm with a 30-50 km resolution and a mission accuracy requirement of 0.04 cm(sub 3 cm(sub -3). These observations can be used to improve land surface model soil moisture states through data assimilation. In this paper, SMOS soil moisture retrievals are assimilated into the Noah land surface model via an Ensemble Kalman Filter within the NASA Land Information System. Bias correction is implemented using Cumulative Distribution Function (CDF) matching, with points aggregated by either land cover or soil type to reduce sampling error in generating the CDFs. An experiment was run for the warm season of 2011 to test SMOS data assimilation and to compare assimilation methods. Verification of soil moisture analyses in the 0-10 cm upper layer and root zone (0-1 m) was conducted using in situ measurements from several observing networks in the central and southeastern United States. This experiment showed that SMOS data assimilation significantly increased the anomaly correlation of Noah soil moisture with station measurements from 0.45 to 0.57 in the 0-10 cm layer. Time series at specific stations demonstrate the ability of SMOS DA to increase the dynamic range of soil moisture in a manner consistent with station measurements. Among the bias correction methods, the correction based on soil type performed best at bias reduction but also reduced correlations. The vegetation-based correction did not produce any significant differences compared to using a simple uniform correction curve.

  13. Assimilation of diazotrophic nitrogen into pelagic food webs.

    Science.gov (United States)

    Woodland, Ryan J; Holland, Daryl P; Beardall, John; Smith, Jonathan; Scicluna, Todd; Cook, Perran L M

    2013-01-01

    The fate of diazotrophic nitrogen (N(D)) fixed by planktonic cyanobacteria in pelagic food webs remains unresolved, particularly for toxic cyanophytes that are selectively avoided by most herbivorous zooplankton. Current theory suggests that N(D) fixed during cyanobacterial blooms can enter planktonic food webs contemporaneously with peak bloom biomass via direct grazing of zooplankton on cyanobacteria or via the uptake of bioavailable N(D) (exuded from viable cyanobacterial cells) by palatable phytoplankton or microbial consortia. Alternatively, N(D) can enter planktonic food webs post-bloom following the remineralization of bloom detritus. Although the relative contribution of these processes to planktonic nutrient cycles is unknown, we hypothesized that assimilation of bioavailable N(D) (e.g., nitrate, ammonium) by palatable phytoplankton and subsequent grazing by zooplankton (either during or after the cyanobacterial bloom) would be the primary pathway by which N(D) was incorporated into the planktonic food web. Instead, in situ stable isotope measurements and grazing experiments clearly documented that the assimilation of N(D) by zooplankton outpaced assimilation by palatable phytoplankton during a bloom of toxic Nodularia spumigena Mertens. We identified two distinct temporal phases in the trophic transfer of N(D) from N. spumigena to the plankton community. The first phase was a highly dynamic transfer of N(D) to zooplankton with rates that covaried with bloom biomass while bypassing other phytoplankton taxa; a trophic transfer that we infer was routed through bloom-associated bacteria. The second phase was a slowly accelerating assimilation of the dissolved-N(D) pool by phytoplankton that was decoupled from contemporaneous variability in N. spumigena concentrations. These findings provide empirical evidence that N(D) can be assimilated and transferred rapidly throughout natural plankton communities and yield insights into the specific processes underlying

  14. A virtual reality catchment for data assimilation experiments

    Science.gov (United States)

    Schalge, Bernd; Rihani, Jehan; Haese, Barbara; Baroni, Gabriele; Erdal, Daniel; Neuweiler, Insa; Hendricks-Franssen, Harrie-Jan; Geppert, Gernot; Ament, Felix; Kollet, Stefan; Cirpka, Olaf; Saavedra, Pablo; Han, Xujun; Attinger, Sabine; Kunstmann, Harald; Vereecken, Harry; Simmer, Clemens

    2016-04-01

    Current data assimilation (DA) systems often lack the possibility to assimilate measurements across compartments to accurately estimate states and fluxes in subsurface-land surface-atmosphere systems (SLAS). In order to develop a new DA framework that is able to realize this cross-compartmental assimilation a comprehensive testing environment is needed. Therefore a virtual reality (VR) catchment is constructed with the Terrestrial System Modeling Platform (TerrSysMP). This catchment mimics the Neckar catchment in Germany. TerrSysMP employs the atmospheric model COSMO, the land surface model CLM and the hydrological model ParFlow coupled with the external coupler OASIS. We will show statistical tests to prove the plausibility of the VR. The VR is running in a fully-coupled mode (subsurface - land surface - atmosphere) which includes the interactions of subsurface dynamics with the atmosphere, such as the effects of soil moisture, which can influence near-surface temperatures, convection patterns or the surface heat fluxes. A reference high resolution run serves as the "truth" from which virtual observations are extracted with observation operators like virtual rain gauges, synoptic stations and satellite observations (amongst others). This effectively solves the otherwise often encountered data scarcity issues with respect to DA. Furthermore an ensemble of model runs at a reduced resolution is performed. This ensemble serves also for open loop runs to be compared with data assimilation experiments. The model runs with this ensemble served to identify sets of parameters that are especially sensitive to changes and have the largest impact on the system. These parameters were