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Sample records for model organism saccharomyces

  1. Saccharomyces cerevisiae as a model organism: a comparative study.

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    Hiren Karathia

    Full Text Available BACKGROUND: Model organisms are used for research because they provide a framework on which to develop and optimize methods that facilitate and standardize analysis. Such organisms should be representative of the living beings for which they are to serve as proxy. However, in practice, a model organism is often selected ad hoc, and without considering its representativeness, because a systematic and rational method to include this consideration in the selection process is still lacking. METHODOLOGY/PRINCIPAL FINDINGS: In this work we propose such a method and apply it in a pilot study of strengths and limitations of Saccharomyces cerevisiae as a model organism. The method relies on the functional classification of proteins into different biological pathways and processes and on full proteome comparisons between the putative model organism and other organisms for which we would like to extrapolate results. Here we compare S. cerevisiae to 704 other organisms from various phyla. For each organism, our results identify the pathways and processes for which S. cerevisiae is predicted to be a good model to extrapolate from. We find that animals in general and Homo sapiens in particular are some of the non-fungal organisms for which S. cerevisiae is likely to be a good model in which to study a significant fraction of common biological processes. We validate our approach by correctly predicting which organisms are phenotypically more distant from S. cerevisiae with respect to several different biological processes. CONCLUSIONS/SIGNIFICANCE: The method we propose could be used to choose appropriate substitute model organisms for the study of biological processes in other species that are harder to study. For example, one could identify appropriate models to study either pathologies in humans or specific biological processes in species with a long development time, such as plants.

  2. [Saccharomyces cerevisiae as a model organism for studying the carcinogenicity of non-ionizing electromagnetic fields and radiation].

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    Voĭchuk, S I

    2014-01-01

    Medical and biological aspects of the effects of non-ionizing electromagnetic (EM) fields and radiation on human health are the important issues that have arisen as a result of anthropogenic impact on the biosphere. Safe use of man-made sources of non-ionizing electromagnetic fields and radiation in a broad range of frequencies--static, radio-frequency and microwave--is a subject of discussions and speculations. The main problem is the lack of understanding of the mechanism(s) of reception of EMFs by living organisms. In this review we have analyzed the existing literature data regarding the effects of the electromagnetic radiation on the model eukaryotic organism--yeast Saccharomyces cerevisiae. An attempt was made to estimate the probability of induction of carcinogenesis in humans under the influence of magnetic fields and electromagnetic radiation of extremely low frequency, radio frequency and microwave ranges.

  3. Different reactive oxygen species lead to distinct changes of cellular metal ions in the eukaryotic model organism Saccharomyces cerevisiae.

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    Wu, Ming J; O'Doherty, Patrick J; Murphy, Patricia A; Lyons, Victoria; Christophersen, Melinda; Rogers, Peter J; Bailey, Trevor D; Higgins, Vincent J

    2011-01-01

    Elemental uptake and export of the cell are tightly regulated thereby maintaining the ionomic homeostasis. This equilibrium can be disrupted upon exposure to exogenous reactive oxygen species (ROS), leading to reduction or elevation of the intracellular metal ions. In this study, the ionomic composition in the eukaryotic model organism Saccharomyces cerevisiae was profiled using the inductively-coupled plasma optical emission spectrometer (ICP-OES) following the treatment with individual ROS, including hydrogen peroxide, cumen hydroperoxide, linoleic acid hydroperoxide (LAH), the superoxide-generating agent menadione, the thiol-oxidising agent diamide [diazine-dicarboxylic acid-bis(dimethylamide)], dimedone and peroxynitrite. The findings demonstrated that different ROS resulted in distinct changes in cellular metal ions. Aluminium (Al(3+)) level rose up to 50-fold after the diamide treatment. Cellular potassium (K(+)) in LAH-treated cells was 26-fold less compared to the non-treated controls. The diamide-induced Al(3+) accumulation was further validated by the enhanced Al(3+) uptake along the time course and diamide doses. Pre-incubation of yeast with individual elements including iron, copper, manganese and magnesium failed to block diamide-induced Al(3+) uptake, suggesting Al(3+)-specific transporters could be involved in Al(3+) uptake. Furthermore, LAH-induced potassium depletion was validated by a rescue experiment in which addition of potassium increased yeast growth in LAH-containing media by 26% compared to LAH alone. Taken together, the data, for the first time, demonstrated the linkage between ionomic profiles and individual oxidative conditions.

  4. Different Reactive Oxygen Species Lead to Distinct Changes of Cellular Metal Ions in the Eukaryotic Model Organism Saccharomyces cerevisiae

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    Peter J. Rogers

    2011-11-01

    Full Text Available Elemental uptake and export of the cell are tightly regulated thereby maintaining the ionomic homeostasis. This equilibrium can be disrupted upon exposure to exogenous reactive oxygen species (ROS, leading to reduction or elevation of the intracellular metal ions. In this study, the ionomic composition in the eukaryotic model organism Saccharomyces cerevisiae was profiled using the inductively-coupled plasma optical emission spectrometer (ICP-OES following the treatment with individual ROS, including hydrogen peroxide, cumen hydroperoxide, linoleic acid hydroperoxide (LAH, the superoxide-generating agent menadione, the thiol-oxidising agent diamide [diazine-dicarboxylic acid-bis(dimethylamide], dimedone and peroxynitrite. The findings demonstrated that different ROS resulted in distinct changes in cellular metal ions. Aluminium (Al3+ level rose up to 50-fold after the diamide treatment. Cellular potassium (K+ in LAH-treated cells was 26-fold less compared to the non-treated controls. The diamide-induced Al3+ accumulation was further validated by the enhanced Al3+ uptake along the time course and diamide doses. Pre-incubation of yeast with individual elements including iron, copper, manganese and magnesium failed to block diamide-induced Al3+ uptake, suggesting Al3+-specific transporters could be involved in Al3+ uptake. Furthermore, LAH-induced potassium depletion was validated by a rescue experiment in which addition of potassium increased yeast growth in LAH-containing media by 26% compared to LAH alone. Taken together, the data, for the first time, demonstrated the linkage between ionomic profiles and individual oxidative conditions.

  5. Investigating genotype-phenotype relationships in Saccharomyces cerevisiae metabolic network through stoichiometric modeling

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    Brochado, Ana Rita

    . This chapter aims at providing the reader with relevant state-of-the-art information concerning Systems Biology, Genome-Scale Metabolic Modeling and Metabolic Engineering. Particular attention is given to the yeast Saccharomyces cerevisiae, the eukaryotic model organism used thought the thesis....

  6. ORGANIC ACIDS CONCENTRATION IN WINE STOCKS AFTER Saccharomyces cerevisiae FERMENTATION

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    V. N. Bayraktar

    2013-04-01

    Full Text Available The biochemical constituents in wine stocks that influence the flavor and quality of wine are investigated in the paper. The tested parameters consist of volume fraction of ethanol, residual sugar, phenolic compounds, tartaric, malic, citric, lactic, acetic acids, titratable acidity and volatile acids. The wine stocks that were received from white and red grape varieties Tairov`s selection were tested. There was a correlation between titratable acidity and volatile acids in the wine stocks from white and red grape varieties. High correlation was also found between lactic and acetic acids, between volatile acids, acetic acid and sugar. It was determined that wine stocks with a high concentration of ethanol originated from those yeast strains of Saccharomyces cerevisiae, in a fermented grape must of high speed of enzyme activity. The taste of wine stocks correlated with the ratio of tartaric to malic acid. Analysis showed significant differences between the varieties of white and red wine stocks in concentrations of organic acids, phenolic compounds, residual sugar, and volume fraction of ethanol. Positive correlation was indicated for both studied groups for volatile acids and acetic acid, tartaric, malic, lactic acids and total sugar. Prospective yeast cultures with high productivity of alcohol (ethanol were selected for winemaking biotechnology.

  7. Organization of Replication of Ribosomal DNA in Saccharomyces cerevisiae

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    Linskens, Maarten H.K.; Huberman, Joel A.

    1988-01-01

    Using recently developed replicon mapping techniques, we have analyzed the replication of the ribosomal DNA in Saccharomyces cerevisiae. The results show that (i) the functional origin of replication colocalizes with an autonomously replicating sequence element previously mapped to the

  8. Global organization of protein complexome in the yeast Saccharomyces cerevisiae

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    Lee Sang

    2011-08-01

    Full Text Available Abstract Background Proteins in organisms, rather than act alone, usually form protein complexes to perform cellular functions. We analyze the topological network structure of protein complexes and their component proteins in the budding yeast in terms of the bipartite network and its projections, where the complexes and proteins are its two distinct components. Compared to conventional protein-protein interaction networks, the networks from the protein complexes show more homogeneous structures than those of the binary protein interactions, implying the formation of complexes that cause a relatively more uniform number of interaction partners. In addition, we suggest a new optimization method to determine the abundance and function of protein complexes, based on the information of their global organization. Estimating abundance and biological functions is of great importance for many researches, by providing a quantitative description of cell behaviors, instead of just a "catalogues" of the lists of protein interactions. Results With our new optimization method, we present genome-wide assignments of abundance and biological functions for complexes, as well as previously unknown abundance and functions of proteins, which can provide significant information for further investigations in proteomics. It is strongly supported by a number of biologically relevant examples, such as the relationship between the cytoskeleton proteins and signal transduction and the metabolic enzyme Eno2's involvement in the cell division process. Conclusions We believe that our methods and findings are applicable not only to the specific area of proteomics, but also to much broader areas of systems biology with the concept of optimization principle.

  9. Membrane trafficking in the yeast Saccharomyces cerevisiae model.

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    Feyder, Serge; De Craene, Johan-Owen; Bär, Séverine; Bertazzi, Dimitri L; Friant, Sylvie

    2015-01-09

    The yeast Saccharomyces cerevisiae is one of the best characterized eukaryotic models. The secretory pathway was the first trafficking pathway clearly understood mainly thanks to the work done in the laboratory of Randy Schekman in the 1980s. They have isolated yeast sec mutants unable to secrete an extracellular enzyme and these SEC genes were identified as encoding key effectors of the secretory machinery. For this work, the 2013 Nobel Prize in Physiology and Medicine has been awarded to Randy Schekman; the prize is shared with James Rothman and Thomas Südhof. Here, we present the different trafficking pathways of yeast S. cerevisiae. At the Golgi apparatus newly synthesized proteins are sorted between those transported to the plasma membrane (PM), or the external medium, via the exocytosis or secretory pathway (SEC), and those targeted to the vacuole either through endosomes (vacuolar protein sorting or VPS pathway) or directly (alkaline phosphatase or ALP pathway). Plasma membrane proteins can be internalized by endocytosis (END) and transported to endosomes where they are sorted between those targeted for vacuolar degradation and those redirected to the Golgi (recycling or RCY pathway). Studies in yeast S. cerevisiae allowed the identification of most of the known effectors, protein complexes, and trafficking pathways in eukaryotic cells, and most of them are conserved among eukaryotes.

  10. Membrane Trafficking in the Yeast Saccharomyces cerevisiae Model

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    Serge Feyder

    2015-01-01

    Full Text Available The yeast Saccharomyces cerevisiae is one of the best characterized eukaryotic models. The secretory pathway was the first trafficking pathway clearly understood mainly thanks to the work done in the laboratory of Randy Schekman in the 1980s. They have isolated yeast sec mutants unable to secrete an extracellular enzyme and these SEC genes were identified as encoding key effectors of the secretory machinery. For this work, the 2013 Nobel Prize in Physiology and Medicine has been awarded to Randy Schekman; the prize is shared with James Rothman and Thomas Südhof. Here, we present the different trafficking pathways of yeast S. cerevisiae. At the Golgi apparatus newly synthesized proteins are sorted between those transported to the plasma membrane (PM, or the external medium, via the exocytosis or secretory pathway (SEC, and those targeted to the vacuole either through endosomes (vacuolar protein sorting or VPS pathway or directly (alkaline phosphatase or ALP pathway. Plasma membrane proteins can be internalized by endocytosis (END and transported to endosomes where they are sorted between those targeted for vacuolar degradation and those redirected to the Golgi (recycling or RCY pathway. Studies in yeast S. cerevisiae allowed the identification of most of the known effectors, protein complexes, and trafficking pathways in eukaryotic cells, and most of them are conserved among eukaryotes.

  11. In-silico identification and characterization of organic and inorganic chemical stress responding genes in yeast (Saccharomyces cerevisiae).

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    Barozai, Muhammad Younas Khan; Bashir, Farrukh; Muzaffar, Shafia; Afzal, Saba; Behlil, Farida; Khan, Muzaffar

    2014-10-15

    To study the life processes of all eukaryotes, yeast (Saccharomyces cerevisiae) is a significant model organism. It is also one of the best models to study the responses of genes at transcriptional level. In a living organism, gene expression is changed by chemical stresses. The genes that give response to chemical stresses will provide good source for the strategies in engineering and formulating mechanisms which are chemical stress resistant in the eukaryotic organisms. The data available through microarray under the chemical stresses like lithium chloride, lactic acid, weak organic acids and tomatidine were studied by using computational tools. Out of 9335 yeast genes, 388 chemical stress responding genes were identified and characterized under different chemical stresses. Some of these are: Enolases 1 and 2, heat shock protein-82, Yeast Elongation Factor 3, Beta Glucanase Protein, Histone H2A1 and Histone H2A2 Proteins, Benign Prostatic Hyperplasia, ras GTPase activating protein, Establishes Silent Chromatin protein, Mei5 Protein, Nondisjunction Protein and Specific Mitogen Activated Protein Kinase. Characterization of these genes was also made on the basis of their molecular functions, biological processes and cellular components. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. Influence of organic acids and organochlorinated insecticides on metabolism of Saccharomyces cerevisiae

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    Pejin Dušanka J.

    2005-01-01

    Full Text Available Saccharomyces cerevisiae is exposed to different stress factors during the production: osmotic, temperature, oxidative. The response to these stresses is the adaptive mechanism of cells. The raw materials Saccharomyces cerevisiae is produced from, contain metabolism products of present microorganisms and protective agents used during the growth of sugar beet for example the influence of acetic and butyric acid and organochlorinated insecticides, lindan and heptachlor, on the metabolism of Saccharomyces cerevisiae was investigated and presented in this work. The mentioned compounds affect negatively the specific growth rate, yield, content of proteins, phosphorus, total ribonucleic acids. These compounds influence the increase of trechalose and glycogen content in the Saccharomyces cerevisiae cells.

  13. A mathematical model of the mating signal transduction pathway in the yeast Saccharomyces cerevisiae. Final report

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    Thomas Ivan Milac

    1998-09-14

    Outline of two major goals in my proposal for this fellowship. First goal having no previous training in biology, was to become knowledgeable of the paradigms, experimental techniques, and current research interests of molecular biology. Second goal was to construct a mathematical model of the mating signal transduction pathway in the yeast Saccharomyces cerevisiae.

  14. Self-organization of magnetite nanoparticles in providing Saccharomyces cerevisiae Yeasts with magnetic properties

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    Gorobets, S. V.; Yu, Gorobets O.; Demianenko, I. V.; Nikolaenko, R. N.

    2013-07-01

    The compared analyze of four methods of the magnetic nanoparticles clusters parameters estimation were developed and performed, such as, method, which takes into account two magneto-force scans of surface for calculation, geometry distance measurement between two centers of clusters in chains using the functions of NOVA-program, which is the standard computer equipment for scanning probe microscopy SOLVER PRO-M and the model, which takes into account the table meaning of magnetite magnetization and atomic-force microscopy. The magnetically-controllable biosorbent based on the culture of Saccharomyces cerevisiae was used as a model object for adequacy analyze of these models. As the result of the work we get the information about the depth of clusters penetration inside biomembrane, the typical sizes of clusters and the dispersion of magnetic clusters sizes. This analyze shows that all four methods can be used for single magnetic clusters, but for clusters, which lay in chains with small distance between their centers, the mode, which takes into account the table meaning of magnetite magnetization, cannot be used, because this model does not take into account the nearest neighbors contribution of interaction of magnetic fields dipole with magnetic probe.

  15. Effectiveness of Saccharomyces boulardii in a rat model of colitis

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    Mujde Soyturk; Saba Mukaddes Saygili; Huseyin Baskin; Ozgul Sagol; Osman Yilmaz; Fatih Saygili; Hale Akpinar

    2012-01-01

    AIM:To investigate the effects of Saccharomyces boulardii (S.boulardii) in an experimental rat model of trinitrobenzene sulfonic acid (TNBS)-induced colitis.METHODS:Thirty-two Wistar albino female rats were categorized into five groups.On the first day of the study,50 mg TNBS was administered via a rectal catheter in order to induce colitis in all rats,except those in the control group.For 14 d,the rats were fed a standard diet,without the administration of any additional supplements to either the control or TNBS groups,in addition to 1 mg/kg per day S.boulardii to the S.boulardii group,1 mg/kg per day methyl prednisolone (MP)to the MP group.The animals in the S.boulardii + MP group were coadministered these doses of S.boulardii and MP.During the study,weight loss,stool consistency,and the presence of obvious blood in the stool were evaluated,and the disease activity index (DAI) for colitis was recorded.The intestines were examined and colitis was macro-and microscopically scored.The serum and tissue levels of tumor necrosis factor-α (TNF-α)and nitric oxide (NO) were determined,and fungemia was evaluated in the blood samples.RESULTS:The mean DAI scores for the MP and S.boulardii + MP groups was significantly lower than the TNBS group (3.69 ± 0.61 vs 4.46 ± 0.34,P =0.018and 3.77 ± 0.73 vs 4.46 ± 0.34,P =0.025,respectively).While no significant differences between the TNBS and the S.boulardii or MP groups could be determined in terms of serum NO levels,the level of serum NO in the S.boulardii + MP group was significantly higher than in the TNBS and S.boulardii groups (8.12 ± 4.25μmol/L vs 3.18 ± 1.19 μmol/L,P =0.013; 8.12 ± 4.25μmol/L vs 3.47 ± 1.66 μmol/L,P =0.012,respectively).The tissue NO levels in the S.boulardii,MP and S.boulardii + MP groups were significantly lower than the TNBS group (16.62 ± 2.27 iμmol/L vs 29.72 ± 6.10μmol/L,P =0.002; 14.66 ± 5.18 μmol/L vs 29.72 ± 6.10μmol/L,P =0.003; 11.95 ± 2.34 μmol/L vs 29.72 ± 6.10

  16. Web Resources for Model Organism Studies

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    Bixia Tang; Yanqing Wang; Junwei Zhu; Wenming Zhao

    2015-01-01

    An ever-growing number of resources on model organisms have emerged with the continued development of sequencing technologies. In this paper, we review 13 databases of model organisms, most of which are reported by the National Institutes of Health of the United States (NIH; http://www.nih.gov/science/models/). We provide a brief description for each database, as well as detail its data source and types, functions, tools, and availability of access. In addition, we also provide a quality assessment about these databases. Significantly, the organism databases instituted in the early 1990s––such as the Mouse Genome Database (MGD), Saccharomyces Genome Database (SGD), and FlyBase––have developed into what are now comprehensive, core authority resources. Furthermore, all of the databases mentioned here update continually according to user feedback and with advancing technologies.

  17. Mathematical model of GAL regulon dynamics in Saccharomyces cerevisiae.

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    Apostu, Raluca; Mackey, Michael C

    2012-01-21

    Genetic switches are prevalent in nature and provide cells with a strategy to adapt to changing environments. The GAL switch is an intriguing example which is not understood in all detail. The GAL switch allows organisms to metabolize galactose, and controls whether the machinery responsible for the galactose metabolism is turned on or off. Currently, it is not known exactly how the galactose signal is sensed by the transcriptional machinery. Here we utilize quantitative tools to understand the S. cerevisiae cell response to galactose challenge, and to analyze the plausible molecular mechanisms underlying its operation. We work at a population level to develop a dynamic model based on the interplay of the key regulatory proteins Gal4p, Gal80p, and Gal3p. To our knowledge, the model presented here is the first to reproduce qualitatively the bistable network behavior found experimentally. Given the current understanding of the GAL circuit induction (Wightman et al., 2008; Jiang et al., 2009), we propose that the most likely in vivo mechanism leading to the transcriptional activation of the GAL genes is the physical interaction between galactose-activated Gal3p and Gal80p, with the complex Gal3p-Gal80p remaining bound at the GAL promoters. Our mathematical model is in agreement with the flow cytometry profiles of wild type, gal3Δ and gal80Δ mutant strains from Acar et al. (2005), and involves a fraction of actively transcribing cells with the same qualitative features as in the data set collected by Acar et al. (2010). Furthermore, the computational modeling provides an explanation for the contradictory results obtained by independent laboratories when tackling experimentally the issue of binary versus graded response to galactose induction.

  18. Incorporating Protein Biosynthesis into the Saccharomyces cerevisiae Genome-scale Metabolic Model

    DEFF Research Database (Denmark)

    Olivares Hernandez, Roberto

    Based on stoichiometric biochemical equations that occur into the cell, the genome-scale metabolic models can quantify the metabolic fluxes, which are regarded as the final representation of the physiological state of the cell. For Saccharomyces Cerevisiae the genome scale model has been......, translation initiation, translation elongation, translation termination, translation elongation, and mRNA decay. Considering these information from the mechanisms of transcription and translation, we will include this stoichiometric reactions into the genome scale model for S. Cerevisiae to obtain the first...

  19. Compositions and methods for modeling Saccharomyces cerevisiae metabolism

    DEFF Research Database (Denmark)

    2012-01-01

    The invention provides an in silica model for determining a S. cerevisiae physiological function. The model includes a data structure relating a plurality of S. cerevisiae reactants to a plurality of S. cerevisiae reactions, a constraint set for the plurality of S. cerevisiae reactions......, and commands for determining a distribution of flux through the reactions that is predictive of a S. cerevisiae physiological function. A model of the invention can further include a gene database containing information characterizing the associated gene or genes. The invention further provides methods...... for making an in silica S. cerevisiae model and methods for determining a S. cerevisiae physiological function using a model of the invention. The invention provides an in silica model for determining a S. cerevisiae physiological function. The model includes a data structure relating a plurality of S...

  20. Fungal genomics beyond Saccharomyces cerevisiae?

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    Hofmann, Gerald; Mcintyre, Mhairi; Nielsen, Jens

    2003-01-01

    Fungi are used extensively in both fundamental research and industrial applications. Saccharomyces cerevisiae has been the model organism for fungal research for many years, particularly in functional genomics. However, considering the diversity within the fungal kingdom, it is obvious that the a......Fungi are used extensively in both fundamental research and industrial applications. Saccharomyces cerevisiae has been the model organism for fungal research for many years, particularly in functional genomics. However, considering the diversity within the fungal kingdom, it is obvious...... that the application of the existing methods of genome, transcriptome, proteome and metabolome analysis to other fungi has enormous potential, especially for the production of food and food ingredients. The developments in the past year demonstrate that we have only just started to exploit this potential....

  1. Growth of Saccharomyces cerevisiae CBS 426 on mixtures of glucose and succinic acid: a model

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    Bonnet, J.A.B.A.F.; Koellmann, C.J.W.; Dekkers-de Kok, H.E.; Roels, J.A.

    1984-03-01

    Saccharomyces cerevisiae CBS 426 was grown in continuous culture in a defined medium with a mixture of glucose and succinic acid as the carbon source. Growth on succinic acid was possible after long adaptation periods. The flows of glucose, succinic acid, oxygen, carbon dioxide, and biomass to and from the system were measured. It proved necessary to expand our previous model to accommodate the active transport of succinic acid by the cell. The values found for the efficiency of the oxidative phosphorylation (PIO) and the amount of ATP needed for production of biomass from monomers gave the same values as found for substrate mixtures taken up passively. (Refs. 13).

  2. Effects of organic and inorganic additives on flotation recovery of washed cells of Saccharomyces cerevisiae resuspended in water.

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    DeSousa, Sandro Rogério; Laluce, Cecilia; Jafelicci, Miguel

    2006-03-01

    Separation of microbial cells by flotation recovery is usually carried out in industrial reactors or wastewater treatment systems, which contain a complex mixture of microbial nutrients and excretion products. In the present study, the separation of yeast cells by flotation recovery was carried out using a simple flotation recovery systems containing washed yeast cells resuspended in water in order to elucidate the effects of additives (defined amounts of organic and inorganic acids, ethanol, surfactants and sodium chloride) on the cellular interactions at interfaces (cell/aqueous phase and cell/air bubble). When sodium chloride, organic acids (notably propionic, succinic and acetic acids) and organic surfactants (sodium dodecyl sulphate (SDS), cetyltrimethylammonium bromide (CTAB) and Nonidet P40) were added to the flotation recovery system, significant increases in the cell recovery of yeast hydrophobic cells (Saccharomyces cerevisiae, strain FLT-01) were observed. The association of ethanol to acetic acid solution (a minor by-product of alcoholic fermentation) in the flotation recovery system, containing washed cells of strain FLT-01 resuspended in water, leading to an increased flotation recovery at pH 5.5. Thus, the association among products of the cellular metabolism (e.g., ethanol and acetic acid) can improve yeast cell recovery by flotation recovery.

  3. Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae

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    Oliveira Ana

    2009-01-01

    Full Text Available Abstract Background In the yeast Saccharomyces cerevisiae, the presence of high levels of glucose leads to an array of down-regulatory effects known as glucose repression. This process is complex due to the presence of feedback loops and crosstalk between different pathways, complicating the use of intuitive approaches to analyze the system. Results We established a logical model of yeast glucose repression, formalized as a hypergraph. The model was constructed based on verified regulatory interactions and it includes 50 gene transcripts, 22 proteins, 5 metabolites and 118 hyperedges. We computed the logical steady states of all nodes in the network in order to simulate wildtype and deletion mutant responses to different sugar availabilities. Evaluation of the model predictive power was achieved by comparing changes in the logical state of gene nodes with transcriptome data. Overall, we observed 71% true predictions, and analyzed sources of errors and discrepancies for the remaining. Conclusion Though the binary nature of logical (Boolean models entails inherent limitations, our model constitutes a primary tool for storing regulatory knowledge, searching for incoherencies in hypotheses and evaluating the effect of deleting regulatory elements involved in glucose repression.

  4. A MultiSite GatewayTM vector set for the functional analysis of genes in the model Saccharomyces cerevisiae

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    Nagels Durand Astrid

    2012-09-01

    Full Text Available Abstract Background Recombinatorial cloning using the GatewayTM technology has been the method of choice for high-throughput omics projects, resulting in the availability of entire ORFeomes in GatewayTM compatible vectors. The MultiSite GatewayTM system allows combining multiple genetic fragments such as promoter, ORF and epitope tag in one single reaction. To date, this technology has not been accessible in the yeast Saccharomyces cerevisiae, one of the most widely used experimental systems in molecular biology, due to the lack of appropriate destination vectors. Results Here, we present a set of three-fragment MultiSite GatewayTM destination vectors that have been developed for gene expression in S. cerevisiae and that allow the assembly of any promoter, open reading frame, epitope tag arrangement in combination with any of four auxotrophic markers and three distinct replication mechanisms. As an example of its applicability, we used yeast three-hybrid to provide evidence for the assembly of a ternary complex of plant proteins involved in jasmonate signalling and consisting of the JAZ, NINJA and TOPLESS proteins. Conclusion Our vectors make MultiSite GatewayTM cloning accessible in S. cerevisiae and implement a fast and versatile cloning method for the high-throughput functional analysis of (heterologous proteins in one of the most widely used model organisms for molecular biology research.

  5. Saccharomyces cerivisiae as a model system for kidney disease: what can yeast tell us about renal function?

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    Kolb, Alexander R; Buck, Teresa M; Brodsky, Jeffrey L

    2011-07-01

    Ion channels, solute transporters, aquaporins, and factors required for signal transduction are vital for kidney function. Because mutations in these proteins or in associated regulatory factors can lead to disease, an investigation into their biogenesis, activities, and interplay with other proteins is essential. To this end, the yeast, Saccharomyces cerevisiae, represents a powerful experimental system. Proteins expressed in yeast include the following: 1) ion channels, including the epithelial sodium channel, members of the inward rectifying potassium channel family, and cystic fibrosis transmembrane conductance regulator; 2) plasma membrane transporters, such as the Na(+)-K(+)-ATPase, the Na(+)-phosphate cotransporter, and the Na(+)-H(+) ATPase; 3) aquaporins 1-4; and 4) proteins such as serum/glucocorticoid-induced kinase 1, phosphoinositide-dependent kinase 1, Rh glycoprotein kidney, and trehalase. The variety of proteins expressed and studied emphasizes the versatility of yeast, and, because of the many available tools in this organism, results can be obtained rapidly and economically. In most cases, data gathered using yeast have been substantiated in higher cell types. These attributes validate yeast as a model system to explore renal physiology and suggest that research initiated using this system may lead to novel therapeutics.

  6. Effects of Bacillus subtilis var. natto and Saccharomyces cerevisiae fermented liquid feed on growth performance, relative organ weight, intestinal microflora, and organ antioxidant status in Landes geese.

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    Chen, W; Zhu, X Z; Wang, J P; Wang, Z X; Huang, Y Q

    2013-02-01

    The aim of this study was to investigate the effect of Bacillus subtilis var. natto N21 (BAC) and Saccharomyces cerevisiae Y10 (SAC) fermented liquid feed (FLF) during different incubation times on the growth performance, relative organ weight, intestinal microflora, and organ antioxidative status in Landes geese. Two hundred forty male Landes geese (10 wk old) with the BW of 4.163 ± 0.108 kg were selected for a 3-wk trial and randomly allotted to 3 treatments according to their BW (10 replicates/treatment and 8 geese/replicate). The treatments included 1) CON, dry basal feed (corn-soybean basal diet mixed with water) before feeding (2:1 wt/wt), 2) FLF24, 24 h FLF, and 3) FLF48, 48 h FLF. The FLF diet was prepared by storing basal diet with 10(9) cfu/g feed of each BAC and SAC and water (2:1 wt/wt) in a closed tank at 20°C fermented for 24 or 48 h. The BW gain and feed intake of geese fed FLF24 and FLF48 was greater (P Feeding geese with FLF24 and FLF48 feeds increased (P feeding geese with BAC and SAC mix FLF can improve growth and feed intake, modulate the intestine ecology, and decrease the blood cholesterol concentrations; it also can improve the antioxidative status of organs and breast muscle.

  7. Effect of Saccharomyces cerevisiae strain UFMG A-905 in experimental model of inflammatory bowel disease.

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    Tiago, F C P; Porto, B A A; Ribeiro, N S; Moreira, L M C; Arantes, R M E; Vieira, A T; Teixeira, M M; Generoso, S V; Nascimento, V N; Martins, F S; Nicoli, J R

    2015-01-01

    In the present study, the protective potential of Saccharomyces cerevisiae strain UFMG A-905 was evaluated in a murine model of acute ulcerative colitis (UC). Six groups of Balb/c mice were used: not treated with yeast and not challenged with dextran sulphate sodium (DSS) (control); treated with S. cerevisiae UFMG A-905 (905); treated with the non-probiotic S. cerevisiae W303 (W303); challenged with DSS (DSS); treated with S. cerevisiae UFMG A-905 and challenged with DSS (905 + DSS); and treated with S. cerevisiae W303 and challenged with DSS (W303 + DSS). Seven days after induction of UC, mice were euthanised to remove colon for enzymatic, immunological, and histopathological analysis. In vivo intestinal permeability was also evaluated. An improvement of clinical manifestations of experimental UC was observed only in mice of the 905 + DSS group when compared to animals from DSS and W303 + DSS groups. This observation was confirmed by histological and morphometrical data and determination of myeloperoxidase and eosinophil peroxidase activities, intestinal permeability and some pro-inflammatory cytokines. S. cerevisiae UFMG A-905 showed to be a potential alternative treatment for UC when used in an experimental animal model of the disease.

  8. Saccharomyces boulardii

    Science.gov (United States)

    ... bowel syndrome. Some people use Saccharomyces boulardii for lactose intolerance, urinary tract infections (UTIs), vaginal yeast infections, high ... cholesterol. Lyme disease. Hives. Fever blisters. Canker sores. Lactose intolerance. Other conditions. More evidence is needed to rate ...

  9. Quantitative analysis of the modes of growth inhibition by weak organic acids in Saccharomyces cerevisiae

    NARCIS (Netherlands)

    Ullah, A.; Orij, R.; Brul, S.; Smits, G.J.

    2012-01-01

    Weak organic acids are naturally occurring compounds that are commercially used as preservatives in the food and beverage industries. They extend the shelf life of food products by inhibiting microbial growth. There are a number of theories that explain the antifungal properties of these weak acids,

  10. Beneficial Effects of Prebiotic Saccharomyces cerevisiae Mannan on Allergic Asthma Mouse Models

    Directory of Open Access Journals (Sweden)

    D. Betty Lew

    2017-01-01

    Full Text Available One of the unmet needs for asthma management is a new therapeutic agent with both anti-inflammatory and anti-smooth muscle (ASM remodeling effects. The mannose receptor (MR family plays an important role in allergen uptake and processing of major allergens Der p 1 and Fel d 1. We have previously reported that ASM cells express a mannose receptor (ASM-MR and that mannan derived from Saccharomyces cerevisiae (SC-MN inhibits mannosyl-rich lysosomal hydrolase-induced bovine ASM cell proliferation. Using a humanized transgenic mouse strain (huASM-MRC2 expressing the human MRC2 receptor in a SM tissue-specific manner, we have demonstrated that ASM hyperplasia/hypertrophy can occur as early as 15 days after allergen challenge in this mouse model and this phenomenon is preventable with SC-MN treatment. This proof-of-concept study would facilitate future development of a potential asthma therapeutic agent with dual function of anti-inflammatory and anti-smooth muscle remodeling effects.

  11. Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Henriksen, Peter; Wagner, Sebastian Alexander; Weinert, Brian Tate;

    2012-01-01

    Post-translational modification of proteins by lysine acetylation plays important regulatory roles in living cells. The budding yeast Saccharomyces cerevisiae is a widely used unicellular eukaryotic model organism in biomedical research. S. cerevisiae contains several evolutionary conserved lysin...

  12. Structural insights into Saccharomyces cerevisiae Msh4-Msh5 complex function using homology modeling.

    Directory of Open Access Journals (Sweden)

    Ramaswamy Rakshambikai

    Full Text Available The Msh4-Msh5 protein complex in eukaryotes is involved in stabilizing Holliday junctions and its progenitors to facilitate crossing over during Meiosis I. These functions of the Msh4-Msh5 complex are essential for proper chromosomal segregation during the first meiotic division. The Msh4/5 proteins are homologous to the bacterial mismatch repair protein MutS and other MutS homologs (Msh2, Msh3, Msh6. Saccharomyces cerevisiae msh4/5 point mutants were identified recently that show two fold reduction in crossing over, compared to wild-type without affecting chromosome segregation. Three distinct classes of msh4/5 point mutations could be sorted based on their meiotic phenotypes. These include msh4/5 mutations that have a crossover and viability defects similar to msh4/5 null mutants; b intermediate defects in crossing over and viability and c defects only in crossing over. The absence of a crystal structure for the Msh4-Msh5 complex has hindered an understanding of the structural aspects of Msh4-Msh5 function as well as molecular explanation for the meiotic defects observed in msh4/5 mutations. To address this problem, we generated a structural model of the S. cerevisiae Msh4-Msh5 complex using homology modeling. Further, structural analysis tailored with evolutionary information is used to predict sites with potentially critical roles in Msh4-Msh5 complex formation, DNA binding and to explain asymmetry within the Msh4-Msh5 complex. We also provide a structural rationale for the meiotic defects observed in the msh4/5 point mutations. The mutations are likely to affect stability of the Msh4/5 proteins and/or interactions with DNA. The Msh4-Msh5 model will facilitate the design and interpretation of new mutational data as well as structural studies of this important complex involved in meiotic chromosome segregation.

  13. Modeling and optimization of ethanol fermentation using Saccharomyces cerevisiae: Response surface methodology and artificial neural network

    Directory of Open Access Journals (Sweden)

    Esfahanian Mehri

    2013-01-01

    Full Text Available In this study, the capabilities of response surface methodology (RSM and artificial neural networks (ANN for modeling and optimization of ethanol production from glucoseusing Saccharomyces cerevisiae in batch fermentation process were investigated. Effect of three independent variables in a defined range of pH (4.2-5.8, temperature (20-40ºC and glucose concentration (20-60 g/l on the cell growth and ethanol production was evaluated. Results showed that prediction accuracy of ANN was apparently similar to RSM. At optimum condition of temperature (32°C, pH (5.2 and glucose concentration (50 g/l suggested by the statistical methods, the maximum cell dry weight and ethanol concentration obtained from RSM were 12.06 and 16.2 g/l whereas experimental values were 12.09 and 16.53 g/l, respectively. The present study showed that using ANN as fitness function, the maximum cell dry weight and ethanol concentration were 12.05 and 16.16 g/l, respectively. Also, the coefficients of determination for biomass and ethanol concentration obtained from RSM were 0.9965 and 0.9853 and from ANN were 0.9975 and 0.9936, respectively. The process parameters optimization was successfully conducted using RSM and ANN; however prediction by ANN was slightly more precise than RSM. Based on experimental data maximum yield of ethanol production of 0.5 g ethanol/g substrate (97 % of theoretical yield was obtained.

  14. Teaching biology with model organisms

    Science.gov (United States)

    Keeley, Dolores A.

    The purpose of this study is to identify and use model organisms that represent each of the kingdoms biologists use to classify organisms, while experiencing the process of science through guided inquiry. The model organisms will be the basis for studying the four high school life science core ideas as identified by the Next Generation Science Standards (NGSS): LS1-From molecules to organisms, LS2-Ecosystems, LS3- Heredity, and LS4- Biological Evolution. NGSS also have identified four categories of science and engineering practices which include developing and using models and planning and carrying out investigations. The living organisms will be utilized to increase student interest and knowledge within the discipline of Biology. Pre-test and posttest analysis utilizing student t-test analysis supported the hypothesis. This study shows increased student learning as a result of using living organisms as models for classification and working in an inquiry-based learning environment.

  15. MODEL ORGANISMS USED IN MOLECULAR BIOLOGY OR MEDICAL RESEARCH

    Directory of Open Access Journals (Sweden)

    Pandey Govind

    2011-11-01

    Full Text Available A model organism is a non-human species that is studied to understand specific biological phenomena with the expectation that investigations made in the organism model will provide insight into the workings of other organisms. The model organisms are widely used to explore potential causes and treatments for human as well as animal diseases when experiments on animals or humans would be unfeasible or considered less ethical. Studying model organisms may be informative, but care must be taken when generalizing from one organism to another. Often, model organisms are chosen on the basis that they are amenable to experimental manipulation. When researchers look for an organism to use in their studies, they look for several traits. Among these are size, generation time, accessibility, manipulation, genetics, conservation of mechanisms and potential economic benefit. As comparative molecular biology has become more common, some researchers have sought model organisms from a wider assortment of lineages on the tree of life. There are many model organisms, such as viruses (e.g., Phage lambda virus, Tobacco mosaic virus, etc., bacteria (e.g., Bacillus subtilis, Escherichia coli, Pseudomonas fluorescens, Vibrio fischeri, etc., algae (e.g., Chlamydomonas reinhardtii, Emiliania huxleyi, etc., molds (e.g., Aspergillus nidulans, Neurospora crassa, etc., yeasts (e.g., Saccharomyces cerevisiae, Ustilago maydis, etc., higher plants (e.g., Arabidopsis thaliana, Lemna gibba, Lotus japonicus, Nicotiana tabaccum, Oryza sativa, Physcomitrella patens, Zea mays, etc. and animals (e.g., Caenorhabditis elegans, guinea pig, hamster, mouse, rat, cat, chicken, dog, frog, Hydra, Drosophila melanogaster fruit fly, fish, etc..

  16. De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology

    NARCIS (Netherlands)

    Nijkamp, J.F.; Van den Broek, M.A.; Datema, E.; De Kok, S.; Bosman, L.; Luttik, M.A.H.; Daran-Lapujade, P.A.S.; Vongsangnak, W.; Nielsen, J.; Heijne. W.H.M.; Klaassen, P.; Paddon, C.J.; Platt, D.; Kötter, P.; Van Ham, R.C.; Reinders, M.J.T.; Pronk, J.T.; De Ridder, D.; Daran, J.M.

    2012-01-01

    Saccharomyces cerevisiae CEN.PK 113-7D is widely used for metabolic engineering and systems biology research in industry and academia. We sequenced, assembled, annotated and analyzed its genome. Single-nucleotide variations (SNV), insertions/deletions (indels) and differences in genome organization

  17. Construction of robust dynamic genome-scale metabolic model structures of Saccharomyces cerevisiae through iterative re-parameterization.

    Science.gov (United States)

    Sánchez, Benjamín J; Pérez-Correa, José R; Agosin, Eduardo

    2014-09-01

    Dynamic flux balance analysis (dFBA) has been widely employed in metabolic engineering to predict the effect of genetic modifications and environmental conditions in the cell׳s metabolism during dynamic cultures. However, the importance of the model parameters used in these methodologies has not been properly addressed. Here, we present a novel and simple procedure to identify dFBA parameters that are relevant for model calibration. The procedure uses metaheuristic optimization and pre/post-regression diagnostics, fixing iteratively the model parameters that do not have a significant role. We evaluated this protocol in a Saccharomyces cerevisiae dFBA framework calibrated for aerobic fed-batch and anaerobic batch cultivations. The model structures achieved have only significant, sensitive and uncorrelated parameters and are able to calibrate different experimental data. We show that consumption, suboptimal growth and production rates are more useful for calibrating dynamic S. cerevisiae metabolic models than Boolean gene expression rules, biomass requirements and ATP maintenance.

  18. Simple generic model for dynamic experiments with Saccharomyces cerevisiae in continuous culture. Decoupling between anabolism and catabolism

    DEFF Research Database (Denmark)

    Duboc, Philippe Jean; von Stockar, U.; Villadsen, John

    1998-01-01

    The dynamic behavior of a continuous culture of Saccharomyces cerevisiae subjected to a sudden increase in the dilution rate has been successfully modelled for anaerobic growth on glucose, and for aerobic growth on acetate, on ethanol, and on glucose. The catabolism responded by an immediate jump...... whereas biosynthesis did not. Thus catabolism was in excess to anabolism. The model considers the decoupling between biosynthesis and catabolism, both types of reactions being modelled by first-order kinetic expressions evolving towards maximal values. Yield parameters and maximal reaction rates were...... identified in steady state continuous cultures or during batch experiments. Only the time constant of biosynthesis regeneration, tau(x), and the time constant of catabolic capacity regeneration, tau(cat), had to be identified during transient experiments. In most experiments 7, was around 3 h, and tau...

  19. Yeast Biocontrol of a Fungal Plant Disease: A Model for Studying Organism Interrelationships

    Science.gov (United States)

    Chanchaichaovivat, Arun; Panijpan, Bhinyo; Ruenwongsa, Pintip

    2008-01-01

    An experiment on the action of the yeast, "Saccharomyces cerevisiae", against a fungal plant disease is proposed for secondary students (Grade 11) to support their study of organism interrelationship. This biocontrol experiment serves as the basis for discussing relationships among three organisms (red chilli fruit, "Saccharomyces cerevisiae," and…

  20. Yeast Biocontrol of a Fungal Plant Disease: A Model for Studying Organism Interrelationships

    Science.gov (United States)

    Chanchaichaovivat, Arun; Panijpan, Bhinyo; Ruenwongsa, Pintip

    2008-01-01

    An experiment on the action of the yeast, "Saccharomyces cerevisiae", against a fungal plant disease is proposed for secondary students (Grade 11) to support their study of organism interrelationship. This biocontrol experiment serves as the basis for discussing relationships among three organisms (red chilli fruit, "Saccharomyces cerevisiae," and…

  1. The effect of high hydrostatic pressure on the survival of Saccharomyces cerevisiae in model suspensions and beetroot juice

    Science.gov (United States)

    Sokołowska, B.; Skąpska, S.; Fonberg-Broczek, M.; Niezgoda, J.; Rutkowska, M.; Chotkiewicz, M.; Dekowska, A.; Rzoska, S. J.

    2013-03-01

    The inactivation of Saccharomyces cerevisiae NCFB 3191 using high hydrostatic pressure of 300 MPa at 20°C with a holding time of 0, 1, 5 and 10 min was investigated with model suspensions in phosphate-buffered saline and in beetroot juice. The reduction in S. cerevisiae NCFB 3191 in model suspensions was about 5 log after 10 min of pressurization, irrespective of the initial level of cell concentration in the samples (5.4-8.7 log cfu/mL). The baroprotective effect of beetroot juice on yeast cells during pressurization was observed; the reduction was lower and was only 3.5 log (the inoculum was 5.4 log cfu/mL). No sublethal injury among the surviving cells of the studied yeast strain was found.

  2. A reference model systesm of industrial yeasts Saccharomyces cerevisiae is needed for development of the next-generation biocatalyst toward advanced biofuels production

    Science.gov (United States)

    Diploid industrial yeast Saccharomyces cerevisiae has demonstrated distinct characteristics that differ from haploid laboratory model strains. However, as a workhorse for a broad range of fermentation-based industrial applications, it was poorly characterized at the genome level. Observations on the...

  3. Screening for new brewing yeasts in the non-Saccharomyces sector with Torulaspora delbrueckii as model.

    Science.gov (United States)

    Michel, Maximilian; Kopecká, Jana; Meier-Dörnberg, Tim; Zarnkow, Martin; Jacob, Fritz; Hutzler, Mathias

    2016-04-01

    This study describes a screening system for future brewing yeasts focusing on non-Saccharomyces yeasts. The aim was to find new yeast strains that can ferment beer wort into a respectable beer. Ten Torulaspora delbrueckii strains were put through the screening system, which included sugar utilization tests, hop resistance tests, ethanol resistance tests, polymerase chain reaction fingerprinting, propagation tests, amino acid catabolism and anabolism, phenolic off-flavour tests and trial fermentations. Trial fermentations were analysed for extract reduction, pH drop, yeast concentration in bulk fluid and fermentation by-products. All investigated strains were able to partly ferment wort sugars and showed high tolerance to hop compounds and ethanol. One of the investigated yeast strains fermented all the wort sugars and produced a respectable fruity flavour and a beer of average ethanol content with a high volatile flavour compound concentration. Two other strains could possibly be used for pre-fermentation as a bio-flavouring agent for beers that have been post-fermented by Saccharomyces strains as a consequence of their low sugar utilization but good flavour-forming properties.

  4. Asymmetric Synthesis of (—)—1—Trimethylsiyl—ethanol with Immobilized Saccharomyces Cerevisiae Cells in Water/Organic Solvent Biphasic System

    Institute of Scientific and Technical Information of China (English)

    娄文勇; 宗敏华; 范晓丹

    2003-01-01

    Asymmetric synthesis of (-)-1-trimethylsilyl-ethanol with immobilized Saccharomyces cerevisiae cells in water/organic solvent biphasic system was studied,The effects of shake speed,hydrophobictiy of organic solvent ,volume ratio of water phase to organic phase,pH value of aqueous phase and reaction temperature on the initial reaction rate,maximum yield and enantiomeric excess(ee) of the product were systematically explored,All the above-mentioned factors had significant infuence on the reaction.n-Hexane was found to be the best organic solvent for the reaction.The optimum shake speed,volume ratio of water phase to organic phase,pH value and reaction temperature were 150 r.min-1,1/2,8 and 30℃ respectively,under which the maximum yield and enantiomeric excess of the product were as high as 96.8% and 95.7%,which are 15% and 16% higher than those of the corresponding reaction performed in aqueous phase ,To our best knowledge,this is the most satisfactory result obtained.

  5. Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Bojsen, Rasmus K; Andersen, Kaj Scherz; Regenberg, Birgitte

    2012-01-01

    Microbial biofilms can be defined as multi-cellular aggregates adhering to a surface and embedded in an extracellular matrix (ECM). The nonpathogenic yeast, Saccharomyces cerevisiae, follows the common traits of microbial biofilms with cell-cell and cell-surface adhesion. S. cerevisiae is shown...... pathways including the protein kinase A and a mitogen-activated protein kinase pathway. Advanced genetic tools and resources have been developed for S. cerevisiae including a deletion mutant-strain collection in a biofilm-forming strain background and GFP-fusion protein collections. Furthermore, S....... cerevisiae biofilm is well applied for confocal laser scanning microscopy and fluorophore tagging of proteins, DNA and RNA. These techniques can be used to uncover the molecular mechanisms for biofilm development, drug resistance and for the study of molecular interactions, cell response to environmental...

  6. Saccharomyces cerevisiae strain UFMG 905 protects against bacterial translocation, preserves gut barrier integrity and stimulates the immune system in a murine intestinal obstruction model.

    Science.gov (United States)

    Generoso, Simone V; Viana, Mirelle; Santos, Rosana; Martins, Flaviano S; Machado, José A N; Arantes, Rosa M E; Nicoli, Jacques R; Correia, Maria I T D; Cardoso, Valbert N

    2010-06-01

    Probiotic is a preparation containing microorganisms that confers beneficial effect to the host. This work assessed whether oral treatment with viable or heat-killed yeast Saccharomyces cerevisiae strain UFMG 905 prevents bacterial translocation (BT), intestinal barrier integrity, and stimulates the immunity, in a murine intestinal obstruction (IO) model. Four groups of mice were used: mice undergoing only laparotomy (CTL), undergoing intestinal obstruction (IO) and undergoing intestinal obstruction after previous treatment with viable or heat-killed yeast. BT, determined as uptake of (99m)Tc-E. coli in blood, mesenteric lymph nodes, liver, spleen and lungs, was significantly higher in IO group than in CTL group. Treatments with both yeasts reduced BT in blood and all organs investigated. The treatment with both yeasts also reduced intestinal permeability as determined by blood uptake of (99m)Tc-DTPA. Immunological data demonstrated that both treatments were able to significantly increase IL-10 levels, but only viable yeast had the same effect on sIgA levels. Intestinal lesions were more severe in IO group when compared to CTL and yeasts groups. Concluding, both viable and heat-killed cells of yeast prevent BT, probably by immunomodulation and by maintaining gut barrier integrity. Only the stimulation of IgA production seems to depend on the yeast viability.

  7. Evolution-based strategy to generate non-genetically modified organisms Saccharomyces cerevisiae strains impaired in sulfate assimilation pathway.

    Science.gov (United States)

    De Vero, L; Solieri, L; Giudici, P

    2011-11-01

    An evolution-based strategy was designed to screen novel yeast strains impaired in sulfate assimilation. Specifically, molybdate and chromate resistance was used as selectable phenotype to select sulfate permease-deficient variants that unable to produce sulfites and hydrogen sulfide (H(2) S). Four Saccharomyces cerevisiae parent strains were induced to sporulate. After tetrad digestion, spore suspensions were observed under the microscope to monitor the conjugation of gametes. Then, the cell suspension was inoculated in tubes containing YPD medium supplemented with ammonium molybdate or potassium chromate. Forty-four resistant strains were obtained and then tested in microvinifications. Three strains with a low sulfite production (SO2 sulfites were selected. Our strategy enabled the selection of improved yeasts with desired oenological characteristics. Particularly, resistance to toxic analogues of sulfate allowed us to detect strains that unable to assimilate sulfates. This strategy that combines the sexual recombination of spores and application of a specific selective pressure provides a rapid screening method to generate genetic variants and select improved wine yeast strains with an impaired metabolism regarding the production of sulfites and H2S. © 2011 The Authors. Letters in Applied Microbiology © 2011 The Society for Applied Microbiology.

  8. Antiproliferative effects of Matricaria chamomilla on Saccharomyces cerevisiae

    OpenAIRE

    Hosseinpour Maryam; Mobini-Dehkordi Mohsen; Saffar Behnaz; Teimori Hossein

    2013-01-01

    Introduction: The Matricaria chamomilla plant is one of the most important plants used for the therapeutic purposes. More than 120 chemical constituents have been identified in Matricaria chamomile plant including 28 terpenoids and 36 flavonoids. This plant has a variety of therapeutic applications including the treatment of diabetes, eczema, wounds and gastrointestinal diseases. The Saccharomyces cerevisiae yeast is a non-pathogenic organism that is used as a model for pathogenic yeasts in o...

  9. Modeling Gene Networks in Saccharomyces cerevisiae Based on Gene Expression Profiles

    Directory of Open Access Journals (Sweden)

    Yulin Zhang

    2015-01-01

    Full Text Available Detailed and innovative analysis of gene regulatory network structures may reveal novel insights to biological mechanisms. Here we study how gene regulatory network in Saccharomyces cerevisiae can differ under aerobic and anaerobic conditions. To achieve this, we discretized the gene expression profiles and calculated the self-entropy of down- and upregulation of gene expression as well as joint entropy. Based on these quantities the uncertainty coefficient was calculated for each gene triplet, following which, separate gene logic networks were constructed for the aerobic and anaerobic conditions. Four structural parameters such as average degree, average clustering coefficient, average shortest path, and average betweenness were used to compare the structure of the corresponding aerobic and anaerobic logic networks. Five genes were identified to be putative key components of the two energy metabolisms. Furthermore, community analysis using the Newman fast algorithm revealed two significant communities for the aerobic but only one for the anaerobic network. David Gene Functional Classification suggests that, under aerobic conditions, one such community reflects the cell cycle and cell replication, while the other one is linked to the mitochondrial respiratory chain function.

  10. Recombinant Saccharomyces cerevisiae strain expressing a model cytochrome P450 in the rat digestive environment: viability and bioconversion activity.

    Science.gov (United States)

    Garrait, G; Jarrige, J F; Blanquet, S; Beyssac, E; Alric, M

    2007-06-01

    An innovative "biodrug" concept, based on the oral administration of living recombinant microorganisms, has recently emerged for the prevention or treatment of various diseases. An engineered Saccharomyces cerevisiae strain expressing plant P450 73A1 (cinnamate-4-hydroxylase [CA4H] activity) was used, and its survival and ability to convert trans-cinnamic acid (CIN) into p-coumaric acid (COU) were investigated in vivo. In rats, the recombinant yeast was resistant to gastric and small intestinal secretions but was more sensitive to the conditions found in the large intestine. After oral administration of yeast and CIN, the CA4H activity was shown in vivo, with COU being found throughout the rat's digestive tract and in its urine. The bioconversion reaction occurred very fast, with most of the COU being produced within the first 5 min. The gastrointestinal sac technique demonstrated that the recombinant yeast was able to convert CIN into COU (conversion rate ranging from 2 to 5%) in all the organs of the rat's digestive tract: stomach, duodenum, jejunum, ileum, cecum, and colon. These results promise new opportunities for the development of drug delivery systems based on engineered yeasts catalyzing a bioconversion reaction directly in the digestive tract.

  11. An organic acid-tolerant HAA1-overexpression mutant of an industrial bioethanol strain of Saccharomyces cerevisiae and its application to the production of bioethanol from sugarcane molasses.

    Science.gov (United States)

    Inaba, Takuya; Watanabe, Daisuke; Yoshiyama, Yoko; Tanaka, Koichi; Ogawa, Jun; Takagi, Hiroshi; Shimoi, Hitoshi; Shima, Jun

    2013-12-30

    Bacterial contamination is known as a major cause of the reduction in ethanol yield during bioethanol production by Saccharomyces cerevisiae. Acetate is an effective agent for the prevention of bacterial contamination, but it negatively affects the fermentation ability of S. cerevisiae. We have proposed that the combined use of organic acids including acetate and lactate and yeast strains tolerant to organic acids may be effective for the elimination of principally lactic acid bacterial (LAB) contamination. In a previous study employing laboratory S. cerevisiae strains, we showed that overexpression of the HAA1 gene, which encodes a transcriptional activator, could be a useful molecular breeding method for acetate-tolerant yeast strains. In the present study, we constructed a HAA1-overexpressing diploid strain (MATa/α, named ER HAA1-OP) derived from the industrial bioethanol strain Ethanol Red (ER). ER HAA1-OP showed tolerance not only to acetate but also to lactate, and this tolerance was dependent on the increased expression of HAA1 gene. The ethanol production ability of ER HAA1-OP was almost equivalent to that of the parent strain during the bioethanol production process from sugarcane molasses in the absence of acetate. The addition of acetate at 0.5% (w/v, pH 4.5) inhibited the fermentation ability of the parent strain, but such an inhibition was not observed in the ethanol production process using ER HAA1-OP.

  12. A dynamic flux balance model and bottleneck identification of glucose, xylose, xylulose co-fermentation in Saccharomyces cerevisiae

    Science.gov (United States)

    Economically viable production of lignocellulosic ethanol requires efficient conversion of feedstock sugars to ethanol. Saccharomyces cerevisiae cannot ferment xylose, the main five-carbon sugars in biomass, but can ferment xylulose, an enzymatically derived isomer. Xylulose fermentation is slow rel...

  13. Performance of several Saccharomyces strains for the alcoholic fermentation of sugar-sweetened high-strength wastewaters: Comparative analysis and kinetic modelling.

    Science.gov (United States)

    Comelli, Raúl N; Seluy, Lisandro G; Isla, Miguel A

    2016-12-25

    This work focuses on the performance of ten commercial Saccharomyces yeast strains in the batch alcoholic fermentation of sugars contained in selected industrial wastewaters from the soft drink industry. Fermentation has been applied successfully to treat these effluents prior to their disposal. Although many strains were investigated, similar behaviour was observed between all of the Saccharomyces strains tested. When media were inoculated with 2gL(-1) of yeast, all strains were able to completely consume the available sugars in less than 14h. Thus, any of the strains studied in this work could be used in non-conventional wastewater treatment processes based on alcoholic fermentation. However, ethanol production varied between strains, and these differences could be significant from a production point of view. Saccharomyces bayanus produced the most ethanol, with a mean yield of 0.44gethanolgsugarconsumed(-1) and an ethanol specific production rate of 5.96gethanol (Lh)(-1). As the assayed soft drinks wastewaters contain about 105gsugar/L of fermentable sugars, the concentration of ethanol achieved after the fermentations process was 46.2gethanol/L. A rigorous kinetic modelling methodology was used to model the Saccharomyces bayanus fermentation process. The kinetic model included coupled mass balances and a minimal number of parameters. A simple unstructured model based on the Andrews equation (substrate inhibition) was developed. This model satisfactorily described biomass growth, sugar consumption and bioethanol production. In addition to providing insights into the fermentative performance of potentially relevant strains, this work can facilitate the design of large-scale ethanol production processes that use wastewaters from the sugar-sweetened beverage industry as feedstock. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Disruption of Saccharomyces cerevisiae by Plantaricin 149 and investigation of its mechanism of action with biomembrane model systems.

    Science.gov (United States)

    Lopes, José Luiz S; Nobre, Thatyane M; Siano, Alvaro; Humpola, Verónica; Bossolan, Nelma R S; Zaniquelli, Maria E D; Tonarelli, Georgina; Beltramini, Leila M

    2009-10-01

    The action of a synthetic antimicrobial peptide analog of Plantaricin 149 (Pln149a) against Saccharomyces cerevisiae and its interaction with biomembrane model systems were investigated. Pln149a was shown to inhibit S. cerevisiae growth by more than 80% in YPD medium, causing morphological changes in the yeast wall and remaining active and resistant to the yeast proteases even after 24 h of incubation. Different membrane model systems and carbohydrates were employed to better describe the Pln149a interaction with cellular components using circular dichroism and fluorescence spectroscopies, adsorption kinetics and surface elasticity in Langmuir monolayers. These assays showed that Pln149a does not interact with either mono/polysaccharides or zwitterionic LUVs, but is strongly adsorbed to and incorporated into negatively charged surfaces, causing a conformational change in its secondary structure from random-coil to helix upon adsorption. From the concurrent analysis of Pln149a adsorption kinetics and dilatational surface elasticity data, we determined that 2.5 muM is the critical concentration at which Pln149a will disrupt a negative DPPG monolayer. Furthermore, Pln149a exhibited a carpet-like mechanism of action, in which the peptide initially binds to the membrane, covering its surface and acquiring a helical structure that remains associated to the negatively charged phospholipids. After this electrostatic interaction, another peptide region causes a strain in the membrane, promoting its disruption.

  15. Metabolism of phosphatidylcholine and its implications for lipid acyl chain composition in Saccharomyces cerevisiae

    NARCIS (Netherlands)

    de Kroon, A.I.P.M.

    2007-01-01

    Phosphatidylcholine (PC) is a very abundant membrane lipid in most eukaryotes including the model organism Saccharomyces cerevisiae. Consequently, the molecular species profile of PC, i.e. the ensemble of PC molecules with acyl chains differing in number of carbon atoms and double bonds, is importan

  16. Sensitivity to Lovastatin of Saccharomyces cerevisiae Strains Deleted for Pleiotropic Drug Resistance (PDR) Genes

    DEFF Research Database (Denmark)

    Formenti, Luca Riccardo; Kielland-Brandt, Morten

    2011-01-01

    The use of statins is well established in human therapy, and model organisms such as Saccharomyces cerevisiae are commonly used in studies of drug action at molecular and cellular levels. The investigation of the resistance mechanisms towards statins may suggest new approaches to improve therapy...

  17. Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Regenberg, Birgitte; Grotkjaer, Thomas; Winther, Ole

    2006-01-01

    Growth rate is central to the development of cells in all organisms. However, little is known about the impact of changing growth rates. We used continuous cultures to control growth rate and studied the transcriptional program of the model eukaryote Saccharomyces cerevisiae, with generation time...

  18. Proteolytic activity of Saccharomyces cerevisiae strains associated with Italian dry-fermented sausages in a model system.

    Science.gov (United States)

    Chaves-López, Clemencia; Paparella, Antonello; Tofalo, Rosanna; Suzzi, Giovanna

    2011-10-17

    Strains of Saccharomyces cerevisiae isolated from Italian salami were screened for proteolytic activity in a model system containing sarcoplasmic (SMS) or myofibrillar (MMS) proteins, at 20°C for 14days, to evaluate the possible influence on the proteolysis of fermented sausages. SDS-PAGE revealed that 14 of the most osmotolerant strains were responsible for the extensive hydrolysis of the main myofibrillar proteins, while only one strain was able to hydrolyze sarcoplasmic proteins. Free amino acids (FAA) accumulated during proteolysis were strain-dependent with different patterns from sarcoplasmic or myofibrillar protein fraction. In general, proteolysis lead Cys, Glu, Lys and Val as the most abundant FAA in the inoculated MMS samples. Volatile compound analysis, determined by SPME-GC-MS, evidenced 3-methyl butanol in MMS, and 2-methyl propanol and 3-methyl-1-butanol in SMS as major compounds. Our findings highlight that S. cerevisiae could influence the composition in amino acids and volatile compounds in fermented sausages, with a strain-dependent activity.

  19. Saccharomyces cerevisiae UFMG A-905 treatment reduces intestinal damage in a murine model of irinotecan-induced mucositis.

    Science.gov (United States)

    Bastos, R W; Pedroso, S H S P; Vieira, A T; Moreira, L M C; França, C S; Cartelle, C T; Arantes, R M E; Generoso, S V; Cardoso, V N; Neves, M J; Nicoli, J R; Martins, F S

    2016-09-01

    Indigenous microbiota plays a crucial role in the development of several intestinal diseases, including mucositis. Gastrointestinal mucositis is a major and serious side effect of cancer therapy, and there is no effective therapy for this clinical condition. However, some probiotics have been shown to attenuate such conditions. To evaluate the effects of Saccharomyces cerevisiae UFMG A-905 (Sc-905), a potential probiotic yeast, we investigated whether pre- or post-treatment with viable or inactivated Sc-905 could prevent weight loss and intestinal lesions, and maintain integrity of the mucosal barrier in a mucositis model induced by irinotecan in mice. Only post-treatment with viable Sc-905 was able to protect mice against the damage caused by chemotherapy, reducing the weight loss, increase of intestinal permeability and jejunal lesions (villous shortening). Besides, this treatment reduced oxidative stress, prevented the decrease of goblet cells and stimulated the replication of cells in the intestinal crypts of mice with experimental mucositis. In conclusion, Sc-905 protects animals against irinotecan-induced mucositis when administered as a post-treatment with viable cells, and this effect seems to be related with the reduction of oxidative stress and preservation of intestinal mucosa.

  20. Model Organisms Fact Sheet: Using Model Organisms to Study Health and Disease

    Science.gov (United States)

    ... Model Organisms to Study Health and Disease Using Model Organisms to Study Health and Disease Tagline (Optional) ... and treating disease in humans. What is a model? The word model has many meanings, but in ...

  1. A mathematical model for ethanol fermentation from oil palm trunk sap using Saccharomyces cerevisiae

    Science.gov (United States)

    Sultana, S.; Jamil, Norazaliza Mohd; Saleh, E. A. M.; Yousuf, A.; Faizal, Che Ku M.

    2017-09-01

    This paper presents a mathematical model and solution strategy of ethanol fermentation for oil palm trunk (OPT) sap by considering the effect of substrate limitation, substrate inhibition product inhibition and cell death. To investigate the effect of cell death rate on the fermentation process we extended and improved the current mathematical model. The kinetic parameters of the model were determined by nonlinear regression using maximum likelihood function. The temporal profiles of sugar, cell and ethanol concentrations were modelled by a set of ordinary differential equations, which were solved numerically by the 4th order Runge-Kutta method. The model was validated by the experimental data and the agreement between the model and experimental results demonstrates that the model is reasonable for prediction of the dynamic behaviour of the fermentation process.

  2. Exploring Protein Function Using the Saccharomyces Genome Database.

    Science.gov (United States)

    Wong, Edith D

    2017-01-01

    Elucidating the function of individual proteins will help to create a comprehensive picture of cell biology, as well as shed light on human disease mechanisms, possible treatments, and cures. Due to its compact genome, and extensive history of experimentation and annotation, the budding yeast Saccharomyces cerevisiae is an ideal model organism in which to determine protein function. This information can then be leveraged to infer functions of human homologs. Despite the large amount of research and biological data about S. cerevisiae, many proteins' functions remain unknown. Here, we explore ways to use the Saccharomyces Genome Database (SGD; http://www.yeastgenome.org ) to predict the function of proteins and gain insight into their roles in various cellular processes.

  3. Saccharomyces cerevisiae: a versatile eukaryotic system in virology

    Directory of Open Access Journals (Sweden)

    Breinig Tanja

    2007-10-01

    Full Text Available Abstract The yeast Saccharomyces cerevisiae is a well-established model system for understanding fundamental cellular processes relevant to higher eukaryotic organisms. Less known is its value for virus research, an area in which Saccharomyces cerevisiae has proven to be very fruitful as well. The present review will discuss the main achievements of yeast-based studies in basic and applied virus research. These include the analysis of the function of individual proteins from important pathogenic viruses, the elucidation of key processes in viral replication through the development of systems that allow the replication of higher eukayotic viruses in yeast, and the use of yeast in antiviral drug development and vaccine production.

  4. Requirements of Slm proteins for proper eisosome organization, endocytic trafficking and recycling in the yeast Saccharomyces cerevisiae

    Indian Academy of Sciences (India)

    Chitra Kamble; Sandhya Jain; Erin Murphy; Kyoungtae Kim

    2011-03-01

    Eisosomes are large immobile assemblies at the cortex of a cell under the membrane compartment of Can1 (MCC) in yeast. Slm1 has recently been identified as an MCC component that acts downstream of Mss4 in a pathway that regulates actin cytoskeleton organization in response to stress. In this study, we showed that inactivation of Slm proteins disrupts proper localization of the primary eisosome marker Pil1, providing evidence that Slm proteins play a role in eisosome organization. Furthermore, we found that slmts mutant cells exhibit actin defects in both the ability to polarize cortical F-actin and the formation of cytoplasmic actin cables even at the permissive temperature (30°C). We further demonstrated that the actin defect accounts for the slow traffic of FM4-64-labelled endosome in the cytoplasm, supporting the notion that intact actin is essential for endosome trafficking. However, our real-time microscopic analysis of Abp1-RFP revealed that the actin defect in slmts cells was not accompanied by a noticeable defect in actin patch internalization during receptor-mediated endocytosis. In addition, we found that slmts cells displayed impaired membrane recycling and that recycling occurred in an actin-independent manner. Our data provide evidence for the requirement of Slm proteins in eisosome organization and endosome trafficking and recycling.

  5. Modeling the growth and proteinase A production in continuous cultures of recombinant Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Carlsen, Morten; Jochumsen, Kirsten Væver; Emborg, Claus

    1997-01-01

    . The model is based on an assumption of a limited respiratory capacity as suggested by Sonnleitner and Kappeli but extended to describe production of an extracellular protein. The model predicts correctly the critical dilution rate to be between 0.15 and 0.16 h(-1), the decrease in the biomass yield above...

  6. Mathematical modeling and validation of the ergosterol pathway in Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Fernando Alvarez-Vasquez

    Full Text Available The de novo biosynthetic machinery for both sphingolipid and ergosterol production in yeast is localized in the endoplasmic reticulum (ER and Golgi. The interconnections between the two pathways are still poorly understood, but they may be connected in specialized membrane domains, and specific knockouts strongly suggest that both routes have different layers of mutual control and are co-affected by drugs. With the goal of shedding light on the functional integration of the yeast sphingolipid-ergosterol (SL-E pathway, we constructed a dynamic model of the ergosterol pathway using the guidelines of Biochemical Systems Theory (BST (Savageau., J. theor. Biol., 25, 365-9, 1969. The resulting model was merged with a previous mathematical model of sphingolipid metabolism in yeast (Alvarez-Vasquez et al., J. theor. Biol., 226, 265-91, 2004; Alvarez-Vasquez et al., Nature433, 425-30, 2005. The S-system format within BST was used for analyses of consistency, stability, and sensitivity of the SL-E model, while the GMA format was used for dynamic simulations and predictions. Model validation was accomplished by comparing predictions from the model with published results on sterol and sterol-ester dynamics in yeast. The validated model was used to predict the metabolomic dynamics of the SL-E pathway after drug treatment. Specifically, we simulated the action of drugs affecting sphingolipids in the endoplasmic reticulum and studied changes in ergosterol associated with microdomains of the plasma membrane (PM.

  7. Mathematical modeling and validation of the ergosterol pathway in Saccharomyces cerevisiae.

    Science.gov (United States)

    Alvarez-Vasquez, Fernando; Riezman, Howard; Hannun, Yusuf A; Voit, Eberhard O

    2011-01-01

    The de novo biosynthetic machinery for both sphingolipid and ergosterol production in yeast is localized in the endoplasmic reticulum (ER) and Golgi. The interconnections between the two pathways are still poorly understood, but they may be connected in specialized membrane domains, and specific knockouts strongly suggest that both routes have different layers of mutual control and are co-affected by drugs. With the goal of shedding light on the functional integration of the yeast sphingolipid-ergosterol (SL-E) pathway, we constructed a dynamic model of the ergosterol pathway using the guidelines of Biochemical Systems Theory (BST) (Savageau., J. theor. Biol., 25, 365-9, 1969). The resulting model was merged with a previous mathematical model of sphingolipid metabolism in yeast (Alvarez-Vasquez et al., J. theor. Biol., 226, 265-91, 2004; Alvarez-Vasquez et al., Nature433, 425-30, 2005). The S-system format within BST was used for analyses of consistency, stability, and sensitivity of the SL-E model, while the GMA format was used for dynamic simulations and predictions. Model validation was accomplished by comparing predictions from the model with published results on sterol and sterol-ester dynamics in yeast. The validated model was used to predict the metabolomic dynamics of the SL-E pathway after drug treatment. Specifically, we simulated the action of drugs affecting sphingolipids in the endoplasmic reticulum and studied changes in ergosterol associated with microdomains of the plasma membrane (PM).

  8. Asymmetric Reduction of3,5-Bistrifluoromethyl Acetophenone with NADH Regeneration by Immobilized Cells of Saccharomyces rhodotorula in Aqueous-Organic Solvent Biphasic System%Asymmetric Reduction of 3,5-Bistrifluoromethyl Acetophenone with NADH Regeneration by Immobilized Cells of Saccharomyces rhodotorula in Aqueous-Organic Solvent Biphasic System

    Institute of Scientific and Technical Information of China (English)

    ZHANGFang; XUEYing; LILi; WANG Min

    2011-01-01

    Asymmetric reduction of 3,5-bistrifluoromethyl acetophenone to produce (S)-3,5-bistrifluoromethylphenyl ethanol was successfully carried out with sodium alginate immobilized Saccharomyces rhodotorula cells in an aqueous-organic solvent biphasic system.The possible influential factors were examined thoroughly according to their effects on conversion rate and e.e of the product.Organic solvents were rated by their biocompatibility and conversion potential.The immobilized cells [125 mg/mL in 20 mmol/L Tris-HCl buffer and 5%(φ) octane at pH 8] showed the best conversion with a substrate concentration of 1.42 g/L at 30C with glucose as co-substrate for cofactor regeneration.Sequential 8-batch process was carried out with immobilized cells with a slow decrease in conversion and e.e.The immobilized cells showed stable catalytic activity with 50% reserved activity and are superior especially in reusability in comparison with resting cells.

  9. A kinetic model of catabolic adaptation and protein reprofiling in Saccharomyces cerevisiae during temperature shifts

    NARCIS (Netherlands)

    Mensonides, Femke I. C.; Brul, Stanley; Hellingwerf, Klaas J.; Bakker, Barbara M.; de Mattos, M. Joost Teixeira

    2014-01-01

    In this article, we aim to find an explanation for the surprisingly thin line, with regard to temperature, between cell growth, growth arrest and ultimately loss of cell viability. To this end, we used an integrative approach including both experimental and modelling work. We measured the shortand l

  10. Incorporating Protein Biosynthesis into the Saccharomyces cerevisiae Genome-scale Metabolic Model

    DEFF Research Database (Denmark)

    Olivares Hernandez, Roberto

    by a rapidly growing cell. To extend the model including protein synthesis, from the survey of the available literature was possible to identify a few enzymatic reactions and gene functions in the early steps of gene expression for proteins: mRNA transcription, mRNA processing, mRNA export out of the nucleus...

  11. Flavour compound production by Yarrowia lipolytica, Saccharomyces cerevisiae and Debaryomyces hansenii in a cheese-surface model

    DEFF Research Database (Denmark)

    Sørensen, Louise Marie; Gori, Klaus; Petersen, Mikael Agerlin

    2011-01-01

    produced sulphides, furanes and short-chain ketones; Saccharomyces cerevisiae D7 primarily produced esters and Debaryomyces hansenii D18335 primarily produced branched-chain aldehydes and alcohols. For several of the detected flavour compounds, an increase in production was observed upon exposure to dairy......A simple cheese model mimicking a cheese surface was developed for the detection of cheese flavour formation of yeasts. A total of 56 flavour compounds were detected by dynamic headspace sampling followed by gas chromatography - mass spectrometry analysis. Yarrowia lipolytica CBS2075 primarily...

  12. Organization customer behavior: Elected models

    Directory of Open Access Journals (Sweden)

    Maričić Branko

    2008-01-01

    Full Text Available Paper is dealing with business-to-business marketing issues with particular attention to some of models oriented to explain differences relative to FMCG marketing. Author describe the core principles of selected models including their basic features. In this paper some of models are in focus - Window and Webster-Window model as well as Sheets model, Nielsen model and Multivariation tools.

  13. A Thermodynamic Model of Monovalent Cation Homeostasis in the Yeast Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Susanne Gerber

    2016-01-01

    Full Text Available Cationic and heavy metal toxicity is involved in a substantial number of diseases in mammals and crop plants. Therefore, the understanding of tightly regulated transporter activities, as well as conceiving the interplay of regulatory mechanisms, is of substantial interest. A generalized thermodynamic description is developed for the complex interplay of the plasma membrane ion transporters, membrane potential and the consumption of energy for maintaining and restoring specific intracellular cation concentrations. This concept is applied to the homeostasis of cation concentrations in the yeast cells of S. cerevisiae. The thermodynamic approach allows to model passive ion fluxes driven by the electrochemical potential differences, but also primary or secondary active transport processes driven by the inter- play of different ions (symport, antiport or by ATP consumption (ATPases. The model-confronted with experimental data-reproduces the experimentally observed potassium and proton fluxes induced by the external stimuli KCl and glucose. The estimated phenomenological constants combine kinetic parameters and transport coefficients. These are in good agreement with the biological understanding of the transporters thus providing a better understanding of the control exerted by the coupled fluxes. The model predicts the flux of additional ion species, like e.g. chloride, as a potential candidate for counterbalancing positive charges. Furthermore, the effect of a second KCl stimulus is simulated, predicting a reduced cellular response for cells that were first exposed to a high KCl stimulus compared to cells pretreated with a mild KCl stimulus. By describing the generalized forces that are responsible for a given flow, the model provides information and suggestions for new experiments. Furthermore, it can be extended to other systems such as e.g. Candida albicans, or selected plant cells.

  14. A Thermodynamic Model of Monovalent Cation Homeostasis in the Yeast Saccharomyces cerevisiae.

    Science.gov (United States)

    Gerber, Susanne; Fröhlich, Martina; Lichtenberg-Fraté, Hella; Shabala, Sergey; Shabala, Lana; Klipp, Edda

    2016-01-01

    Cationic and heavy metal toxicity is involved in a substantial number of diseases in mammals and crop plants. Therefore, the understanding of tightly regulated transporter activities, as well as conceiving the interplay of regulatory mechanisms, is of substantial interest. A generalized thermodynamic description is developed for the complex interplay of the plasma membrane ion transporters, membrane potential and the consumption of energy for maintaining and restoring specific intracellular cation concentrations. This concept is applied to the homeostasis of cation concentrations in the yeast cells of S. cerevisiae. The thermodynamic approach allows to model passive ion fluxes driven by the electrochemical potential differences, but also primary or secondary active transport processes driven by the inter- play of different ions (symport, antiport) or by ATP consumption (ATPases). The model-confronted with experimental data-reproduces the experimentally observed potassium and proton fluxes induced by the external stimuli KCl and glucose. The estimated phenomenological constants combine kinetic parameters and transport coefficients. These are in good agreement with the biological understanding of the transporters thus providing a better understanding of the control exerted by the coupled fluxes. The model predicts the flux of additional ion species, like e.g. chloride, as a potential candidate for counterbalancing positive charges. Furthermore, the effect of a second KCl stimulus is simulated, predicting a reduced cellular response for cells that were first exposed to a high KCl stimulus compared to cells pretreated with a mild KCl stimulus. By describing the generalized forces that are responsible for a given flow, the model provides information and suggestions for new experiments. Furthermore, it can be extended to other systems such as e.g. Candida albicans, or selected plant cells.

  15. Integral Membrane Protein Expression in Saccharomyces cerevisiae.

    Science.gov (United States)

    Boswell-Casteel, Rebba C; Johnson, Jennifer M; Stroud, Robert M; Hays, Franklin A

    2016-01-01

    Eukaryotic integral membrane proteins are challenging targets for crystallography or functional characterization in a purified state. Since expression is often a limiting factor when studying this difficult class of biological macromolecules, the intent of this chapter is to focus on the expression of eukaryotic integral membrane proteins (IMPs) using the model organism Saccharomyces cerevisiae. S. cerevisiae is a prime candidate for the expression of eukaryotic IMPs because it offers the convenience of using episomal expression plasmids, selection of positive transformants, posttranslational modifications, and it can properly fold and target IMPs. Here we present a generalized protocol and insights based on our collective knowledge as an aid to overcoming the challenges faced when expressing eukaryotic IMPs in S. cerevisiae.

  16. Antifungal Activities of Antineoplastic Agents: Saccharomyces cerevisiae as a Model System To Study Drug Action

    Science.gov (United States)

    Cardenas, Maria E.; Cruz, M. Cristina; Del Poeta, Maurizio; Chung, Namjin; Perfect, John R.; Heitman, Joseph

    1999-01-01

    Recent evolutionary studies reveal that microorganisms including yeasts and fungi are more closely related to mammals than was previously appreciated. Possibly as a consequence, many natural-product toxins that have antimicrobial activity are also toxic to mammalian cells. While this makes it difficult to discover antifungal agents without toxic side effects, it also has enabled detailed studies of drug action in simple genetic model systems. We review here studies on the antifungal actions of antineoplasmic agents. Topics covered include the mechanisms of action of inhibitors of topoisomerases I and II; the immunosuppressants rapamycin, cyclosporin A, and FK506; the phosphatidylinositol 3-kinase inhibitor wortmannin; the angiogenesis inhibitors fumagillin and ovalicin; the HSP90 inhibitor geldanamycin; and agents that inhibit sphingolipid metabolism. In general, these natural products inhibit target proteins conserved from microorganisms to humans. These studies highlight the potential of microorganisms as screening tools to elucidate the mechanisms of action of novel pharmacological agents with unique effects against specific mammalian cell types, including neoplastic cells. In addition, this analysis suggests that antineoplastic agents and derivatives might find novel indications in the treatment of fungal infections, for which few agents are presently available, toxicity remains a serious concern, and drug resistance is emerging. PMID:10515904

  17. Dynamics models of soil organic carbon

    Institute of Scientific and Technical Information of China (English)

    YANGLi-xia; PANJian-jun

    2003-01-01

    As the largest pool of terrestrial organic carbon, soils interact strongly with atmosphere composition, climate, and land change. Soil organic carbon dynamics in ecosystem plays a great role in global carbon cycle and global change. With development of mathematical models that simulate changes in soil organic carbon, there have been considerable advances in understanding soil organic carbon dynamics. This paper mainly reviewed the composition of soil organic matter and its influenced factors, and recommended some soil organic matter models worldwide. Based on the analyses of the developed results at home and abroad, it is suggested that future soil organic matter models should be developed toward based-process models, and not always empirical ones. The models are able to reveal their interaction between soil carbon systems, climate and land cover by technique and methods of GIS (Geographical Information System) and RS (Remote Sensing). These models should be developed at a global scale, in dynamically describing the spatial and temporal changes of soil organic matter cycle. Meanwhile, the further researches on models should be strengthen for providing theory basis and foundation in making policy of green house gas emission in China.

  18. Effect of Saccharomyces cerevisiae of different generationon the organic acids metabolism%不同代数酿酒酵母对有机酸代谢的影响

    Institute of Scientific and Technical Information of China (English)

    张利; 成建国; 张善飞; 王硕; 董亮; 赵长新

    2012-01-01

    The fermentation broth of different generation saccharomyces cerevisiae were compared by high performance liquid chromatography and found that six kinds of organic acids in different algebraic Saccharomyces cerevisiae had significant differences and regularity.After several experiments to prove:the yeast had higher activity within five generations,the amount of organic production was more harmonious,to give the pure taste of wine.%实验通过高效液相色谱法(HPLC)对酵母发酵液中6种有机酸测定分析,发现不同代数酵母发酵液中6种有机酸有明显的差异性和规律性。经过多次实验证明:五代以内的酵母活性较高,产有机酸的量较为规律、稳定,能够赋予酒类纯正的口感。

  19. Progress in Metabolic Engineering of Saccharomyces cerevisiae

    OpenAIRE

    Nevoigt, Elke

    2008-01-01

    Summary: The traditional use of the yeast Saccharomyces cerevisiae in alcoholic fermentation has, over time, resulted in substantial accumulated knowledge concerning genetics, physiology, and biochemistry as well as genetic engineering and fermentation technologies. S. cerevisiae has become a platform organism for developing metabolic engineering strategies, methods, and tools. The current review discusses the relevance of several engineering strategies, such as rational and inverse metabolic...

  20. Project-matrix models of marketing organization

    Directory of Open Access Journals (Sweden)

    Gutić Dragutin

    2009-01-01

    Full Text Available Unlike theory and practice of corporation organization, in marketing organization numerous forms and contents at its disposal are not reached until this day. It can be well estimated that marketing organization today in most of our companies and in almost all its parts, noticeably gets behind corporation organization. Marketing managers have always been occupied by basic, narrow marketing activities as: sales growth, market analysis, market growth and market share, marketing research, introduction of new products, modification of products, promotion, distribution etc. They rarely found it necessary to focus a bit more to different aspects of marketing management, for example: marketing planning and marketing control, marketing organization and leading. This paper deals with aspects of project - matrix marketing organization management. Two-dimensional and more-dimensional models are presented. Among two-dimensional, these models are analyzed: Market management/products management model; Products management/management of product lifecycle phases on market model; Customers management/marketing functions management model; Demand management/marketing functions management model; Market positions management/marketing functions management model. .

  1. Cardiac Electromechanical Models: From Cell to Organ

    Directory of Open Access Journals (Sweden)

    Natalia A Trayanova

    2011-08-01

    Full Text Available The heart is a multiphysics and multiscale system that has driven the development of the most sophisticated mathematical models at the frontiers of computation physiology and medicine. This review focuses on electromechanical (EM models of the heart from the molecular level of myofilaments to anatomical models of the organ. Because of the coupling in terms of function and emergent behaviors at each level of biological hierarchy, separation of behaviors at a given scale is difficult. Here, a separation is drawn at the cell level so that the first half addresses subcellular/single cell models and the second half addresses organ models. At the subcelluar level, myofilament models represent actin-myosin interaction and Ca-based activation. Myofilament models and their refinements represent an overview of the development in the field. The discussion of specific models emphasizes the roles of cooperative mechanisms and sarcomere length dependence of contraction force, considered the cellular basis of the Frank-Starling law. A model of electrophysiology and Ca handling can be coupled to a myofilament model to produce an EM cell model, and representative examples are summarized to provide an overview of the progression of field. The second half of the review covers organ-level models that require solution of the electrical component as a reaction-diffusion system and the mechanical component, in which active tension generated by the myocytes produces deformation of the organ as described by the equations of continuum mechanics. As outlined in the review, different organ-level models have chosen to use different ionic and myofilament models depending on the specific application; this choice has been largely dictated by compromises between model complexity and computational tractability. The review also addresses application areas of EM models such as cardiac resynchronization therapy and the role of mechano-electric coupling in arrhythmias and

  2. The Zebrafish Model Organism Database (ZFIN)

    Data.gov (United States)

    U.S. Department of Health & Human Services — ZFIN serves as the zebrafish model organism database. It aims to: a) be the community database resource for the laboratory use of zebrafish, b) develop and support...

  3. Modeling Virtual Organization Architecture with the Virtual Organization Breeding Methodology

    Science.gov (United States)

    Paszkiewicz, Zbigniew; Picard, Willy

    While Enterprise Architecture Modeling (EAM) methodologies become more and more popular, an EAM methodology tailored to the needs of virtual organizations (VO) is still to be developed. Among the most popular EAM methodologies, TOGAF has been chosen as the basis for a new EAM methodology taking into account characteristics of VOs presented in this paper. In this new methodology, referred as Virtual Organization Breeding Methodology (VOBM), concepts developed within the ECOLEAD project, e.g. the concept of Virtual Breeding Environment (VBE) or the VO creation schema, serve as fundamental elements for development of VOBM. VOBM is a generic methodology that should be adapted to a given VBE. VOBM defines the structure of VBE and VO architectures in a service-oriented environment, as well as an architecture development method for virtual organizations (ADM4VO). Finally, a preliminary set of tools and methods for VOBM is given in this paper.

  4. Modeling Virtual Organization Architecture with the Virtual Organization Breeding Methodology

    CERN Document Server

    Paszkiewicz, Zbigniew

    2011-01-01

    While Enterprise Architecture Modeling (EAM) methodologies become more and more popular, an EAM methodology tailored to the needs of virtual organizations (VO) is still to be developed. Among the most popular EAM methodologies, TOGAF has been chosen as the basis for a new EAM methodology taking into account characteristics of VOs presented in this paper. In this new methodology, referred as Virtual Organization Breeding Methodology (VOBM), concepts developed within the ECOLEAD project, e.g. the concept of Virtual Breeding Environment (VBE) or the VO creation schema, serve as fundamental elements for development of VOBM. VOBM is a generic methodology that should be adapted to a given VBE. VOBM defines the structure of VBE and VO architectures in a service-oriented environment, as well as an architecture development method for virtual organizations (ADM4VO). Finally, a preliminary set of tools and methods for VOBM is given in this paper.

  5. Modeling personnel turnover in the parametric organization

    Science.gov (United States)

    Dean, Edwin B.

    1991-01-01

    A model is developed for simulating the dynamics of a newly formed organization, credible during all phases of organizational development. The model development process is broken down into the activities of determining the tasks required for parametric cost analysis (PCA), determining the skills required for each PCA task, determining the skills available in the applicant marketplace, determining the structure of the model, implementing the model, and testing it. The model, parameterized by the likelihood of job function transition, has demonstrated by the capability to represent the transition of personnel across functional boundaries within a parametric organization using a linear dynamical system, and the ability to predict required staffing profiles to meet functional needs at the desired time. The model can be extended by revisions of the state and transition structure to provide refinements in functional definition for the parametric and extended organization.

  6. Complex Systems and Self-organization Modelling

    CERN Document Server

    Bertelle, Cyrille; Kadri-Dahmani, Hakima

    2009-01-01

    The concern of this book is the use of emergent computing and self-organization modelling within various applications of complex systems. The authors focus their attention both on the innovative concepts and implementations in order to model self-organizations, but also on the relevant applicative domains in which they can be used efficiently. This book is the outcome of a workshop meeting within ESM 2006 (Eurosis), held in Toulouse, France in October 2006.

  7. Condensing Organic Aerosols in a Microphysical Model

    Science.gov (United States)

    Gao, Y.; Tsigaridis, K.; Bauer, S.

    2015-12-01

    The condensation of organic aerosols is represented in a newly developed box-model scheme, where its effect on the growth and composition of particles are examined. We implemented the volatility-basis set (VBS) framework into the aerosol mixing state resolving microphysical scheme Multiconfiguration Aerosol TRacker of mIXing state (MATRIX). This new scheme is unique and advances the representation of organic aerosols in models in that, contrary to the traditional treatment of organic aerosols as non-volatile in most climate models and in the original version of MATRIX, this new scheme treats them as semi-volatile. Such treatment is important because low-volatility organics contribute significantly to the growth of particles. The new scheme includes several classes of semi-volatile organic compounds from the VBS framework that can partition among aerosol populations in MATRIX, thus representing the growth of particles via condensation of low volatility organic vapors. Results from test cases representing Mexico City and a Finish forrest condistions show good representation of the time evolutions of concentration for VBS species in the gas phase and in the condensed particulate phase. Emitted semi-volatile primary organic aerosols evaporate almost completely in the high volatile range, and they condense more efficiently in the low volatility range.

  8. Kinetic Model for the ATP-Dependent Translocation of Saccharomyces cerevisiae RSC along Double-Stranded DNA†

    Science.gov (United States)

    Fischer, Christopher J.; Saha, Anjanabha; Cairns, Bradley R.

    2008-01-01

    The chromatin remodeling complex RSC from Saccharomyces cerevisiae is a DNA translocase that moves with directionality along double-stranded DNA in a reaction that is coupled to ATP hydrolysis. To better understand how this basic molecular motor functions, a novel method of analysis has been developed to study the kinetics of RSC translocation along double-stranded DNA. The data provided are consistent with RSC translocation occurring through a series of repeating uniform steps with an overall processivity of P = 0.949 ± 0.003; this processivity corresponds to an average translocation distance of 20 ± 1 base pairs (bp) before dissociation. Interestingly, a slow initiation process, following DNA binding, is required to make RSC competent for DNA translocation. These results are further discussed in the context of previously published studies of RSC and other DNA translocases. PMID:17918861

  9. Putting "Organizations" into an Organization Theory Course: A Hybrid CAO Model for Teaching Organization Theory

    Science.gov (United States)

    Hannah, David R.; Venkatachary, Ranga

    2010-01-01

    In this article, the authors present a retrospective analysis of an instructor's multiyear redesign of a course on organization theory into what is called a hybrid Classroom-as-Organization model. It is suggested that this new course design served to apprentice students to function in quasi-real organizational structures. The authors further argue…

  10. Mathematical Modeling Social Responsibility for Dynamic Organizations

    Directory of Open Access Journals (Sweden)

    Farzaneh Chavoshbashi

    2012-03-01

    Full Text Available Dynamic organizations as accountable organizations, for transparency and accountability to its stakeholders to stakeholders for their toward performance there should express their commitment to social responsibility are through their values and ensure that this commitment throughout the organization are now and thus will have a social responsibility for their mutual benefit, so there is more and more coherent in their ethical approach takes advantage and the community and stakeholders and the organization will have better performance and strengths. Because of interest in social responsibility, in this paper dynamic model is presented for Corporate Social Responsibility of Bionic organization. Model presented a new model is inspired by chaos theory and natural systems theory based on bifurcation in creation to be all natural systems, realizing the value of responsibility as one of the fundamental values of social and institutional development that the relationship between business and work environment in the global market economy and range will be specified. First Social Responsibility factors identified, then experts and scholars determine the weight of the components and technical coefficient for modeling and paired comparison has been done using MATLAB mathematical Software.

  11. Polymer models of chromosome (re)organization

    Science.gov (United States)

    Mirny, Leonid

    Chromosome Conformation Capture technique (Hi-C) provides comprehensive information about frequencies of spatial interactions between genomic loci. Inferring 3D organization of chromosomes from these data is a challenging biophysical problem. We develop a top-down approach to biophysical modeling of chromosomes. Starting with a minimal set of biologically motivated interactions we build ensembles of polymer conformations that can reproduce major features observed in Hi-C experiments. I will present our work on modeling organization of human metaphase and interphase chromosomes. Our works suggests that active processes of loop extrusion can be a universal mechanism responsible for formation of domains in interphase and chromosome compaction in metaphase.

  12. Microtechnology-Based Multi-Organ Models

    Directory of Open Access Journals (Sweden)

    Seung Hwan Lee

    2017-05-01

    Full Text Available Drugs affect the human body through absorption, distribution, metabolism, and elimination (ADME processes. Due to their importance, the ADME processes need to be studied to determine the efficacy and side effects of drugs. Various in vitro model systems have been developed and used to realize the ADME processes. However, conventional model systems have failed to simulate the ADME processes because they are different from in vivo, which has resulted in a high attrition rate of drugs and a decrease in the productivity of new drug development. Recently, a microtechnology-based in vitro system called “organ-on-a-chip” has been gaining attention, with more realistic cell behavior and physiological reactions, capable of better simulating the in vivo environment. Furthermore, multi-organ-on-a-chip models that can provide information on the interaction between the organs have been developed. The ultimate goal is the development of a “body-on-a-chip”, which can act as a whole body model. In this review, we introduce and summarize the current progress in the development of multi-organ models as a foundation for the development of body-on-a-chip.

  13. Microtechnology-Based Multi-Organ Models.

    Science.gov (United States)

    Lee, Seung Hwan; Sung, Jong Hwan

    2017-05-21

    Drugs affect the human body through absorption, distribution, metabolism, and elimination (ADME) processes. Due to their importance, the ADME processes need to be studied to determine the efficacy and side effects of drugs. Various in vitro model systems have been developed and used to realize the ADME processes. However, conventional model systems have failed to simulate the ADME processes because they are different from in vivo, which has resulted in a high attrition rate of drugs and a decrease in the productivity of new drug development. Recently, a microtechnology-based in vitro system called "organ-on-a-chip" has been gaining attention, with more realistic cell behavior and physiological reactions, capable of better simulating the in vivo environment. Furthermore, multi-organ-on-a-chip models that can provide information on the interaction between the organs have been developed. The ultimate goal is the development of a "body-on-a-chip", which can act as a whole body model. In this review, we introduce and summarize the current progress in the development of multi-organ models as a foundation for the development of body-on-a-chip.

  14. New Federated Collaborative Networked Organization Model (FCNOM

    Directory of Open Access Journals (Sweden)

    Morcous M. Yassa

    2012-01-01

    Full Text Available Formation of Collaborative Networked Organization (CNO usually comes upon expected business opportunities and needs huge of negotiation during its lifecycle, especially to increase the Dynamic Virtual Organization (DVO configuration automation. Decision makers need more comprehensive information about CNO system to support their decisions. Unfortunately, there is no single formal modeling, tool, approach or any comprehensive methodology that covers all perspectives. In spite of there are some approaches to model CNO have been existed, these approaches model the CNO either with respect to the technology, or business without considering organizational behavior, federation modeling, and external environments. The aim of this paper is to propose an integrated framework that combines the existed modeling perspectives, as well as, proposes new ones. Also, it provides clear CNO boundaries. By using this approach the view of CNO environment becomes clear and unified. Also, it minimizes the negotiations within CNO components during its life cycle, supports DVO configuration automation, as well as, helps decision making for DVO, and achieves harmonization between CNO partners. The proposed FCNOM utilizes CommonKADS methodology organization model for describing CNO components. Insurance Collaborative Network has been used as an example to proof the proposed FCNOM model.

  15. 酿酒酵母对弱有机酸胁迫的应激机制研究进展%Research progress on weak organic acid stress mechanism of Saccharomyces cerevisiae

    Institute of Scientific and Technical Information of China (English)

    刘兴艳; 贾博; 赵芳; 王成; 李静援; 战吉宬; 黄卫东

    2013-01-01

    Yeast Saccharomyces cerevisiae is the main microorganism in the production of liquor,but fermentation environment is always disadvantageous to its growth.It is always exposed to several stress conditions including low pH stress resulting from weak organic acid.Yeast cells have developed a common response to environmental adverse conditions,but there are some differences among different stress.Researches on weak organic acid stress mechanism of Saccharomyces cerevisiae in recent years are reviewed in this paper,including gene expression,transcript expression and protein expression.ATP binding cassette transporter Pdrl2 and its transcription factor Warlp,HOG-MAPK pathway,FPS1 aquaglyceroporin,plasma membrane H+-ATPase,superoxide dismutase (SOD),catalase(CAT) and interaction of weak acid stress with other stress are all discussed.We hope it could provide certain reference for better research on weak acid stress mechanism of Saccharomyces cerevisiae.%酿酒酵母是生产酒类产品的主要微生物,而生产中的发酵环境对酿酒酵母来说是一种不利的生长代谢环境,存在多种胁迫因素,其中就包括弱有机酸引起的低pH胁迫.酿酒酵母应对胁迫环境,有自身一套完备的适应机制,不同胁迫应对机制既有相同之处亦有不同之处.本文概括了近年来酿酒酵母对弱有机酸应激机制的研究热点,主要从弱有机酸胁迫的基因表达、转录表达以及蛋白质表达3个水平进行阐述,涉及ATP结合区转运子Pdrl2及其转录因子Warlp,HOG-MAPK途径,水通道蛋白Fpslp,质膜H+-ATP酶,SOD,CAT,以及弱有机酸与其他胁迫的交互作用,旨在为更好地研究酿酒酵母的弱有机酸应激机制提供一定的参考.

  16. Organic production in a dynamic CGE model

    DEFF Research Database (Denmark)

    Jacobsen, Lars Bo

    2004-01-01

    Concerns about the impact of modern agriculture on the environment have in recent years led to an interest in supporting the development of organic farming. In addition to environmental benefits, the aim is to encourage the provision of other “multifunctional” properties of organic farming...... such as rural amenities and rural development that are spillover benefit additional to the supply of food. In this paper we further develop an existing dynamic general equilibrium model of the Danish economy to specifically incorporate organic farming. In the model and input-output data each primary...... to illustrate the working of our theory by constructing a long term forecast for the development of the Danish economy. Moreover we simulate the effect of the recent agreed 2003 reform of the common agricultural policy....

  17. Safety Cultural Competency Modeling in Nuclear Organizations

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sa Kil; Oh, Yeon Ju; Luo, Meiling; Lee, Yong Hee [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2014-05-15

    The nuclear safety cultural competency model should be supplemented through a bottom-up approach such as behavioral event interview. The developed model, however, is meaningful for determining what should be dealt for enhancing safety cultural competency of nuclear organizations. The more details of the developing process, results, and applications will be introduced later. Organizational culture include safety culture in terms of its organizational characteristics.

  18. Expanding on Successful Concepts, Models, and Organization

    Science.gov (United States)

    If the goal of the AEP framework was to replace existing exposure models or databases for organizing exposure data with a concept, we would share Dr. von Göetz concerns. Instead, the outcome we promote is broader use of an organizational framework for exposure science. The f...

  19. Evaluation of milk production and somatic cell count of dairy cow supplemented with Saccharomyces cerevisiae as a source of organic zinc/ Avaliação da produção de leite e contagem de células somáticas em bovinos leiteiros suplementads com Saccharomyces cerevisiae como fonte de zinco orgânico

    Directory of Open Access Journals (Sweden)

    Adalberto José Crocci

    2007-08-01

    Full Text Available The aim of the evaluation of milk production and somatic cell count of dairy cow supplemented with Saccharomyces cerevisiae as a source of organic zinc for 180 days, 25 Holstein cows were selected, randomly chosen from a flock of 189 lactating cows. The animals were distributed in two groups, namely group 1 (G1 which holded 10 cows supplemented and group 2 (G2 with 15 animals without supplementation. The production of milk was measured by the control official milkman of the Assocition Paranaense of Creators of Bovine of the Holstein in seven moments during the 180 days. The samples of milk were collected of each animal, being submitted to the electronic counting of somatic cells. The results demonstrate that the supplemented of organic zinc didn’t alter the production of milk, however it was capable to maintain low the counting of somatic cells. The data of the present work suggest that to use supplemented of organic zinc in the diet of cows milk, increase the quality of the produced milk and consequently the remuneration for the producer.Com o objetivo de avaliar a produção de leite e a contagem de células somáticas de bovinos leiteiros, suplementados com Saccharomyces cerevisiae, como fonte de zinco orgânico, por 180 dias, foram separadas aleatoriamente 25 vacas holandesas, em um rebanho de 189 vacas em lactação. Os animais foram distribuídos em dois grupos, sendo grupo 1 (G1 composto por 10 vacas suplementadas e grupo 2 (G2 15 animais sem suplementação. A produção de leite foi mensurada pelo controle leiteiro oficial da Associação Paranaense de Criadores de Bovinos da Raça Holandesa em sete momentos durante os 180 dias. As amostras de leite foram coletadas de cada animal, sendo submetidas à contagem eletrônica de células somáticas. Os resultados demonstram que a suplementação de zinco orgânico não alterou a produção de leite, contudo foi capaz de manter baixa a contagem de células somáticas. Os dados do presente

  20. Emergent organization in a model market

    Science.gov (United States)

    Yadav, Avinash Chand; Manchanda, Kaustubh; Ramaswamy, Ramakrishna

    2017-09-01

    We study the collective behaviour of interacting agents in a simple model of market economics that was originally introduced by Nørrelykke and Bak. A general theoretical framework for interacting traders on an arbitrary network is presented, with the interaction consisting of buying (namely consumption) and selling (namely production) of commodities. Extremal dynamics is introduced by having the agent with least profit in the market readjust prices, causing the market to self-organize. In addition to examining this model market on regular lattices in two-dimensions, we also study the cases of random complex networks both with and without community structures. Fluctuations in an activity signal exhibit properties that are characteristic of avalanches observed in models of self-organized criticality, and these can be described by power-law distributions when the system is in the critical state.

  1. Emergent organization in a model market

    CERN Document Server

    Yadav, Avinash Chand; Ramaswamy, Ramakrishna

    2016-01-01

    We study the collective behavior of interacting agents in a simple model of market economics originally introduced by N{\\o}rrelykke and Bak. A general theoretical framework for interacting traders on an arbitrary network is presented, with the interaction consisting of buying (namely, consumption) and selling (namely, production) of commodities. Extremal dynamics is introduced by having the agent with least profit in the market readjust prices, causing the market to self--organize. We study this model market on regular lattices in two--dimension as well as on random complex networks; in the critical state fluctuations in an activity signal exhibit properties that are characteristic of avalanches observed in models of self-organized criticality, and these can be described by power--law distributions.

  2. Self-organized model of cascade spreading

    Science.gov (United States)

    Gualdi, S.; Medo, M.; Zhang, Y.-C.

    2011-01-01

    We study simultaneous price drops of real stocks and show that for high drop thresholds they follow a power-law distribution. To reproduce these collective downturns, we propose a minimal self-organized model of cascade spreading based on a probabilistic response of the system elements to stress conditions. This model is solvable using the theory of branching processes and the mean-field approximation. For a wide range of parameters, the system is in a critical state and displays a power-law cascade-size distribution similar to the empirically observed one. We further generalize the model to reproduce volatility clustering and other observed properties of real stocks.

  3. Recursive self-organizing network models.

    Science.gov (United States)

    Hammer, Barbara; Micheli, Alessio; Sperduti, Alessandro; Strickert, Marc

    2004-01-01

    Self-organizing models constitute valuable tools for data visualization, clustering, and data mining. Here, we focus on extensions of basic vector-based models by recursive computation in such a way that sequential and tree-structured data can be processed directly. The aim of this article is to give a unified review of important models recently proposed in literature, to investigate fundamental mathematical properties of these models, and to compare the approaches by experiments. We first review several models proposed in literature from a unifying perspective, thereby making use of an underlying general framework which also includes supervised recurrent and recursive models as special cases. We shortly discuss how the models can be related to different neuron lattices. Then, we investigate theoretical properties of the models in detail: we explicitly formalize how structures are internally stored in different context models and which similarity measures are induced by the recursive mapping onto the structures. We assess the representational capabilities of the models, and we shortly discuss the issues of topology preservation and noise tolerance. The models are compared in an experiment with time series data. Finally, we add an experiment for one context model for tree-structured data to demonstrate the capability to process complex structures.

  4. De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology.

    Science.gov (United States)

    Nijkamp, Jurgen F; van den Broek, Marcel; Datema, Erwin; de Kok, Stefan; Bosman, Lizanne; Luttik, Marijke A; Daran-Lapujade, Pascale; Vongsangnak, Wanwipa; Nielsen, Jens; Heijne, Wilbert H M; Klaassen, Paul; Paddon, Chris J; Platt, Darren; Kötter, Peter; van Ham, Roeland C; Reinders, Marcel J T; Pronk, Jack T; de Ridder, Dick; Daran, Jean-Marc

    2012-03-26

    Saccharomyces cerevisiae CEN.PK 113-7D is widely used for metabolic engineering and systems biology research in industry and academia. We sequenced, assembled, annotated and analyzed its genome. Single-nucleotide variations (SNV), insertions/deletions (indels) and differences in genome organization compared to the reference strain S. cerevisiae S288C were analyzed. In addition to a few large deletions and duplications, nearly 3000 indels were identified in the CEN.PK113-7D genome relative to S288C. These differences were overrepresented in genes whose functions are related to transcriptional regulation and chromatin remodelling. Some of these variations were caused by unstable tandem repeats, suggesting an innate evolvability of the corresponding genes. Besides a previously characterized mutation in adenylate cyclase, the CEN.PK113-7D genome sequence revealed a significant enrichment of non-synonymous mutations in genes encoding for components of the cAMP signalling pathway. Some phenotypic characteristics of the CEN.PK113-7D strains were explained by the presence of additional specific metabolic genes relative to S288C. In particular, the presence of the BIO1 and BIO6 genes correlated with a biotin prototrophy of CEN.PK113-7D. Furthermore, the copy number, chromosomal location and sequences of the MAL loci were resolved. The assembled sequence reveals that CEN.PK113-7D has a mosaic genome that combines characteristics of laboratory strains and wild-industrial strains.

  5. Proteomic and Real-Time PCR analyses of Saccharomyces cerevisiae VL3 exposed to microcystin-LR reveals a set of protein alterations transversal to several eukaryotic models.

    Science.gov (United States)

    Valério, Elisabete; Campos, Alexandre; Osório, Hugo; Vasconcelos, Vitor

    2016-03-15

    Some of the most common toxins present in freshwater, in particular microcystins (MCs), are produced by cyanobacteria. These toxins have a negative impact on human health, being associated with episodes of acute hepatotoxicity and being considered potentially carcinogenic to humans. To date the exact mechanisms of MC-induced toxicity and tumor promotion were not completely elucidated. To get new insights underlying microcystin-LR (MCLR) molecular mechanisms of toxicity we have performed the proteomic profiling using two-dimensional electrophoresis and MALDI-TOF/TOF of Saccharomyces cerevisiae cells exposed for 4 h-1 nM and 1 μM of MCLR, and compared them to the control (cells not exposed to MCLR). We identified 14 differentially expressed proteins. The identified proteins are involved in metabolism, genotoxicity, cytotoxicity and stress response. Furthermore, we evaluated the relative expression of yeast's PP1 and PP2A genes and also of genes from the Base Excision Repair (BER) DNA-repair system, and observed that three out of the five genes analyzed displayed dose-dependent responses. Overall, the different proteins and genes affected are related to oxidative stress and apoptosis, thus reinforcing that it is probably the main mechanism of MCLR toxicity transversal to several organisms, especially at lower doses. Notwithstanding these MCLR responsive proteins could be object of further studies to evaluate their suitability as biomarkers of exposure to the toxin.

  6. Modeling plasmonic efficiency enhancement in organic photovoltaics.

    Science.gov (United States)

    Taff, Y; Apter, B; Katz, E A; Efron, U

    2015-09-10

    Efficiency enhancement of bulk heterojunction (BHJ) organic solar cells by means of the plasmonic effect is investigated by using finite-difference time-domain (FDTD) optical simulations combined with analytical modeling of exciton dissociation and charge transport efficiencies. The proposed method provides an improved analysis of the cell performance compared to previous FDTD studies. The results of the simulations predict an 11.8% increase in the cell's short circuit current with the use of Ag nano-hexagons.

  7. Self-organized model of cascade spreading

    CERN Document Server

    Gualdi, Stanislao; Zhang, Yi-Cheng

    2010-01-01

    We study simultaneous price drops of real stocks and show that for high drop thresholds they follow a power-law distribution. To reproduce these collective downturns, we propose a self-organized model of cascade spreading based on a probabilistic response of the system's elements to stress conditions. This model is solvable using the theory of branching processes and the mean-field approximation and displays a power-law cascade-size distribution-similar to the empirically observed one-over a wide range of parameters.

  8. Models for the a subunits of the Thermus thermophilus V/A-ATPase and Saccharomyces cerevisiae V-ATPase enzymes by cryo-EM and evolutionary covariance.

    Science.gov (United States)

    Schep, Daniel G; Zhao, Jianhua; Rubinstein, John L

    2016-03-22

    Rotary ATPases couple ATP synthesis or hydrolysis to proton translocation across a membrane. However, understanding proton translocation has been hampered by a lack of structural information for the membrane-embedded a subunit. The V/A-ATPase from the eubacterium Thermus thermophilus is similar in structure to the eukaryotic V-ATPase but has a simpler subunit composition and functions in vivo to synthesize ATP rather than pump protons. We determined the T. thermophilus V/A-ATPase structure by cryo-EM at 6.4 Å resolution. Evolutionary covariance analysis allowed tracing of the a subunit sequence within the map, providing a complete model of the rotary ATPase. Comparing the membrane-embedded regions of the T. thermophilus V/A-ATPase and eukaryotic V-ATPase from Saccharomyces cerevisiae allowed identification of the α-helices that belong to the a subunit and revealed the existence of previously unknown subunits in the eukaryotic enzyme. Subsequent evolutionary covariance analysis enabled construction of a model of the a subunit in the S. cerevisae V-ATPase that explains numerous biochemical studies of that enzyme. Comparing the two a subunit structures determined here with a structure of the distantly related a subunit from the bovine F-type ATP synthase revealed a conserved pattern of residues, suggesting a common mechanism for proton transport in all rotary ATPases.

  9. Biotechnology of non-Saccharomyces yeasts-the basidiomycetes.

    Science.gov (United States)

    Johnson, Eric A

    2013-09-01

    Yeasts are the major producer of biotechnology products worldwide, exceeding production in capacity and economic revenues of other groups of industrial microorganisms. Yeasts have wide-ranging fundamental and industrial importance in scientific, food, medical, and agricultural disciplines (Fig. 1). Saccharomyces is the most important genus of yeast from fundamental and applied perspectives and has been expansively studied. Non-Saccharomyces yeasts (non-conventional yeasts) including members of the Ascomycetes and Basidiomycetes also have substantial current utility and potential applicability in biotechnology. In an earlier mini-review, "Biotechnology of non-Saccharomyces yeasts-the ascomycetes" (Johnson Appl Microb Biotechnol 97: 503-517, 2013), the extensive biotechnological utility and potential of ascomycetous yeasts are described. Ascomycetous yeasts are particularly important in food and ethanol formation, production of single-cell protein, feeds and fodder, heterologous production of proteins and enzymes, and as model and fundamental organisms for the delineation of genes and their function in mammalian and human metabolism and disease processes. In contrast, the roles of basidiomycetous yeasts in biotechnology have mainly been evaluated only in the past few decades and compared to the ascomycetous yeasts and currently have limited industrial utility. From a biotechnology perspective, the basidiomycetous yeasts are known mainly for the production of enzymes used in pharmaceutical and chemical synthesis, for production of certain classes of primary and secondary metabolites such as terpenoids and carotenoids, for aerobic catabolism of complex carbon sources, and for bioremediation of environmental pollutants and xenotoxicants. Notwithstanding, the basidiomycetous yeasts appear to have considerable potential in biotechnology owing to their catabolic utilities, formation of enzymes acting on recalcitrant substrates, and through the production of unique primary

  10. MODEL ORGANISMS USED IN MOLECULAR BIOLOGY OR MEDICAL RESEARCH

    OpenAIRE

    Pandey Govind

    2011-01-01

    A model organism is a non-human species that is studied to understand specific biological phenomena with the expectation that investigations made in the organism model will provide insight into the workings of other organisms. The model organisms are widely used to explore potential causes and treatments for human as well as animal diseases when experiments on animals or humans would be unfeasible or considered less ethical. Studying model organisms may be informative, but care must be taken ...

  11. Antiproliferative effects of Matricaria chamomilla on Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Hosseinpour Maryam

    2013-04-01

    Full Text Available Introduction: The Matricaria chamomilla plant is one of the most important plants used for the therapeutic purposes. More than 120 chemical constituents have been identified in Matricaria chamomile plant including 28 terpenoids and 36 flavonoids. This plant has a variety of therapeutic applications including the treatment of diabetes, eczema, wounds and gastrointestinal diseases. The Saccharomyces cerevisiae yeast is a non-pathogenic organism that is used as a model for pathogenic yeasts in order to identify compounds with antifungal properties and also to identify functional mechanism of these compounds. The aim of this study is to investigate the antifungal effect of Matricaria chamomilla hydroalcoholic extract on S. cerevisiae yeast. Methods: In this study Matricaria chamomilla extract was prepared by maceration method. In order to study the extract effect on growth and survival rate of the yeast cell, the spectrophotometry and methylene blue staining methods were used. Excel and SPSS 11 softwares were used to determine amounts and to infer the difference between control and treatment samples. Results: Results obtained from spectrophotometry and analyses of methylene blue staining showed that the Matricaria chamomilla extract at the concentration of 3000 μg/ml caused a significant decrease in the yeast growth and reduced the cells survival rate up to 48% (p< 0.05. Conclusion: Results of this research confirm that the hydroalcoholic extract of Matricaria chamomilla has antiproliferative effect on Saccharomyces cerevisiae.

  12. Expanding on Successful Concepts, Models, and Organization

    Energy Technology Data Exchange (ETDEWEB)

    Teeguarden, Justin G.; Tan, Yu-Mei; Edwards, Stephen W.; Leonard, Jeremy A.; Anderson, Kim A.; Corley, Richard A.; Kile, Molly L.; L. Massey Simonich, Staci; Stone, David; Tanguay, Robert L.; Waters, Katrina M.; Harper, Stacey L.; Williams, David E.

    2016-09-06

    In her letter to the editor1 regarding our recent Feature Article “Completing the Link between Exposure Science and Toxicology for Improved Environmental Health Decision Making: The Aggregate Exposure Pathway Framework” 2, Dr. von Göetz expressed several concerns about terminology, and the perception that we propose the replacement of successful approaches and models for exposure assessment with a concept. We are glad to have the opportunity to address these issues here. If the goal of the AEP framework was to replace existing exposure models or databases for organizing exposure data with a concept, we would share Dr. von Göetz concerns. Instead, the outcome we promote is broader use of an organizational framework for exposure science. The framework would support improved generation, organization, and interpretation of data as well as modeling and prediction, not replacement of models. The field of toxicology has seen the benefits of wide use of one or more organizational frameworks (e.g., mode and mechanism of action, adverse outcome pathway). These frameworks influence how experiments are designed, data are collected, curated, stored and interpreted and ultimately how data are used in risk assessment. Exposure science is poised to similarly benefit from broader use of a parallel organizational framework, which Dr. von Göetz correctly points out, is currently used in the exposure modeling community. In our view, the concepts used so effectively in the exposure modeling community, expanded upon in the AEP framework, could see wider adoption by the field as a whole. The value of such a framework was recognized by the National Academy of Sciences.3 Replacement of models, databases, or any application with the AEP framework was not proposed in our article. The positive role broader more consistent use of such a framework might have in enabling and advancing “general activities such as data acquisition, organization…,” and exposure modeling was discussed

  13. Modeling disordered morphologies in organic semiconductors.

    Science.gov (United States)

    Neumann, Tobias; Danilov, Denis; Lennartz, Christian; Wenzel, Wolfgang

    2013-12-05

    Organic thin film devices are investigated for many diverse applications, including light emitting diodes, organic photovoltaic and organic field effect transistors. Modeling of their properties on the basis of their detailed molecular structure requires generation of representative morphologies, many of which are amorphous. Because time-scales for the formation of the molecular structure are slow, we have developed a linear-scaling single molecule deposition protocol which generates morphologies by simulation of vapor deposition of molecular films. We have applied this protocol to systems comprising argon, buckminsterfullerene, N,N-Di(naphthalene-1-yl)-N,N'-diphenyl-benzidine, mer-tris(8-hydroxy-quinoline)aluminum(III), and phenyl-C61-butyric acid methyl ester, with and without postdeposition relaxation of the individually deposited molecules. The proposed single molecule deposition protocol leads to formation of highly ordered morphologies in argon and buckminsterfullerene systems when postdeposition relaxation is used to locally anneal the configuration in the vicinity of the newly deposited molecule. The other systems formed disordered amorphous morphologies and the postdeposition local relaxation step has only a small effect on the characteristics of the disordered morphology in comparison to the materials forming crystals.

  14. Virtuous organization: A structural equation modeling approach

    Directory of Open Access Journals (Sweden)

    Majid Zamahani

    2013-02-01

    Full Text Available For years, the idea of virtue was unfavorable among researchers and virtues were traditionally considered as culture-specific, relativistic and they were supposed to be associated with social conservatism, religious or moral dogmatism, and scientific irrelevance. Virtue and virtuousness have been recently considered seriously among organizational researchers. The proposed study of this paper examines the relationships between leadership, organizational culture, human resource, structure and processes, care for community and virtuous organization. Structural equation modeling is employed to investigate the effects of each variable on other components. The data used in this study consists of questionnaire responses from employees in Payam e Noor University in Yazd province. A total of 250 questionnaires were sent out and a total of 211 valid responses were received. Our results have revealed that all the five variables have positive and significant impacts on virtuous organization. Among the five variables, organizational culture has the most direct impact (0.80 and human resource has the most total impact (0.844 on virtuous organization.

  15. De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology

    Directory of Open Access Journals (Sweden)

    Nijkamp Jurgen F

    2012-03-01

    Full Text Available Abstract Saccharomyces cerevisiae CEN.PK 113-7D is widely used for metabolic engineering and systems biology research in industry and academia. We sequenced, assembled, annotated and analyzed its genome. Single-nucleotide variations (SNV, insertions/deletions (indels and differences in genome organization compared to the reference strain S. cerevisiae S288C were analyzed. In addition to a few large deletions and duplications, nearly 3000 indels were identified in the CEN.PK113-7D genome relative to S288C. These differences were overrepresented in genes whose functions are related to transcriptional regulation and chromatin remodelling. Some of these variations were caused by unstable tandem repeats, suggesting an innate evolvability of the corresponding genes. Besides a previously characterized mutation in adenylate cyclase, the CEN.PK113-7D genome sequence revealed a significant enrichment of non-synonymous mutations in genes encoding for components of the cAMP signalling pathway. Some phenotypic characteristics of the CEN.PK113-7D strains were explained by the presence of additional specific metabolic genes relative to S288C. In particular, the presence of the BIO1 and BIO6 genes correlated with a biotin prototrophy of CEN.PK113-7D. Furthermore, the copy number, chromosomal location and sequences of the MAL loci were resolved. The assembled sequence reveals that CEN.PK113-7D has a mosaic genome that combines characteristics of laboratory strains and wild-industrial strains.

  16. Learning a weighted sequence model of the nucleosome core and linker yields more accurate predictions in Saccharomyces cerevisiae and Homo sapiens.

    Directory of Open Access Journals (Sweden)

    Sheila M Reynolds

    Full Text Available DNA in eukaryotes is packaged into a chromatin complex, the most basic element of which is the nucleosome. The precise positioning of the nucleosome cores allows for selective access to the DNA, and the mechanisms that control this positioning are important pieces of the gene expression puzzle. We describe a large-scale nucleosome pattern that jointly characterizes the nucleosome core and the adjacent linkers and is predominantly characterized by long-range oscillations in the mono, di- and tri-nucleotide content of the DNA sequence, and we show that this pattern can be used to predict nucleosome positions in both Homo sapiens and Saccharomyces cerevisiae more accurately than previously published methods. Surprisingly, in both H. sapiens and S. cerevisiae, the most informative individual features are the mono-nucleotide patterns, although the inclusion of di- and tri-nucleotide features results in improved performance. Our approach combines a much longer pattern than has been previously used to predict nucleosome positioning from sequence-301 base pairs, centered at the position to be scored-with a novel discriminative classification approach that selectively weights the contributions from each of the input features. The resulting scores are relatively insensitive to local AT-content and can be used to accurately discriminate putative dyad positions from adjacent linker regions without requiring an additional dynamic programming step and without the attendant edge effects and assumptions about linker length modeling and overall nucleosome density. Our approach produces the best dyad-linker classification results published to date in H. sapiens, and outperforms two recently published models on a large set of S. cerevisiae nucleosome positions. Our results suggest that in both genomes, a comparable and relatively small fraction of nucleosomes are well-positioned and that these positions are predictable based on sequence alone. We believe that the

  17. Learning a weighted sequence model of the nucleosome core and linker yields more accurate predictions in Saccharomyces cerevisiae and Homo sapiens.

    Science.gov (United States)

    Reynolds, Sheila M; Bilmes, Jeff A; Noble, William Stafford

    2010-07-08

    DNA in eukaryotes is packaged into a chromatin complex, the most basic element of which is the nucleosome. The precise positioning of the nucleosome cores allows for selective access to the DNA, and the mechanisms that control this positioning are important pieces of the gene expression puzzle. We describe a large-scale nucleosome pattern that jointly characterizes the nucleosome core and the adjacent linkers and is predominantly characterized by long-range oscillations in the mono, di- and tri-nucleotide content of the DNA sequence, and we show that this pattern can be used to predict nucleosome positions in both Homo sapiens and Saccharomyces cerevisiae more accurately than previously published methods. Surprisingly, in both H. sapiens and S. cerevisiae, the most informative individual features are the mono-nucleotide patterns, although the inclusion of di- and tri-nucleotide features results in improved performance. Our approach combines a much longer pattern than has been previously used to predict nucleosome positioning from sequence-301 base pairs, centered at the position to be scored-with a novel discriminative classification approach that selectively weights the contributions from each of the input features. The resulting scores are relatively insensitive to local AT-content and can be used to accurately discriminate putative dyad positions from adjacent linker regions without requiring an additional dynamic programming step and without the attendant edge effects and assumptions about linker length modeling and overall nucleosome density. Our approach produces the best dyad-linker classification results published to date in H. sapiens, and outperforms two recently published models on a large set of S. cerevisiae nucleosome positions. Our results suggest that in both genomes, a comparable and relatively small fraction of nucleosomes are well-positioned and that these positions are predictable based on sequence alone. We believe that the bulk of the

  18. Organic acid modeling and model validation: Workshop summary. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Sullivan, T.J.; Eilers, J.M.

    1992-08-14

    A workshop was held in Corvallis, Oregon on April 9--10, 1992 at the offices of E&S Environmental Chemistry, Inc. The purpose of this workshop was to initiate research efforts on the entitled ``Incorporation of an organic acid representation into MAGIC (Model of Acidification of Groundwater in Catchments) and testing of the revised model using Independent data sources.`` The workshop was attended by a team of internationally-recognized experts in the fields of surface water acid-bass chemistry, organic acids, and watershed modeling. The rationale for the proposed research is based on the recent comparison between MAGIC model hindcasts and paleolimnological inferences of historical acidification for a set of 33 statistically-selected Adirondack lakes. Agreement between diatom-inferred and MAGIC-hindcast lakewater chemistry in the earlier research had been less than satisfactory. Based on preliminary analyses, it was concluded that incorporation of a reasonable organic acid representation into the version of MAGIC used for hindcasting was the logical next step toward improving model agreement.

  19. Organic acid modeling and model validation: Workshop summary

    Energy Technology Data Exchange (ETDEWEB)

    Sullivan, T.J.; Eilers, J.M.

    1992-08-14

    A workshop was held in Corvallis, Oregon on April 9--10, 1992 at the offices of E S Environmental Chemistry, Inc. The purpose of this workshop was to initiate research efforts on the entitled Incorporation of an organic acid representation into MAGIC (Model of Acidification of Groundwater in Catchments) and testing of the revised model using Independent data sources.'' The workshop was attended by a team of internationally-recognized experts in the fields of surface water acid-bass chemistry, organic acids, and watershed modeling. The rationale for the proposed research is based on the recent comparison between MAGIC model hindcasts and paleolimnological inferences of historical acidification for a set of 33 statistically-selected Adirondack lakes. Agreement between diatom-inferred and MAGIC-hindcast lakewater chemistry in the earlier research had been less than satisfactory. Based on preliminary analyses, it was concluded that incorporation of a reasonable organic acid representation into the version of MAGIC used for hindcasting was the logical next step toward improving model agreement.

  20. Modeling charge transport in organic photovoltaic materials.

    Science.gov (United States)

    Nelson, Jenny; Kwiatkowski, Joe J; Kirkpatrick, James; Frost, Jarvist M

    2009-11-17

    The performance of an organic photovoltaic cell depends critically on the mobility of charge carriers within the constituent molecular semiconductor materials. However, a complex combination of phenomena that span a range of length and time scales control charge transport in disordered organic semiconductors. As a result, it is difficult to rationalize charge transport properties in terms of material parameters. Until now, efforts to improve charge mobilities in molecular semiconductors have proceeded largely by trial and error rather than through systematic design. However, recent developments have enabled the first predictive simulation studies of charge transport in disordered organic semiconductors. This Account describes a set of computational methods, specifically molecular modeling methods, to simulate molecular packing, quantum chemical calculations of charge transfer rates, and Monte Carlo simulations of charge transport. Using case studies, we show how this combination of methods can reproduce experimental mobilities with few or no fitting parameters. Although currently applied to material systems of high symmetry or well-defined structure, further developments of this approach could address more complex systems such anisotropic or multicomponent solids and conjugated polymers. Even with an approximate treatment of packing disorder, these computational methods simulate experimental mobilities within an order of magnitude at high electric fields. We can both reproduce the relative values of electron and hole mobility in a conjugated small molecule and rationalize those values based on the symmetry of frontier orbitals. Using fully atomistic molecular dynamics simulations of molecular packing, we can quantitatively replicate vertical charge transport along stacks of discotic liquid crystals which vary only in the structure of their side chains. We can reproduce the trends in mobility with molecular weight for self-organizing polymers using a cheap, coarse

  1. Effects of pentamidine isethionate on Saccharomyces cerevisiae.

    OpenAIRE

    Ludewig, G.; Williams, J M; Li, Y.; Staben, C

    1994-01-01

    We used Saccharomyces cerevisiae as a model system in which to examine the mechanism of action of the anti-Pneumocystis drug pentamidine. Pentamidine at low concentrations inhibited S. cerevisiae growth on nonfermentable carbon sources (50% inhibitory concentration [IC50] of 1.25 micrograms/ml in glycerol). Pentamidine inhibited growth on fermentable energy sources only at much higher concentrations (IC50 of 250 micrograms/ml in glucose). Inhibition at low pentamidine concentrations in glycer...

  2. Increasing NADH oxidation reduces overflow metabolism in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Vemuri, Goutham; Eiteman, M.A; McEwen, J.E

    2007-01-01

    Respiratory metabolism plays an important role in energy production in the form of ATP in all aerobically growing cells. However, a limitation in respiratory capacity results in overflow metabolism, leading to the formation of byproducts, a phenomenon known as ‘‘overflow metabolism’’ or ‘‘the...... Crabtree effect.’’ The yeast Saccharomyces cerevisiae has served as an important model organism for studying the Crabtree effect. When subjected to increasing glycolytic fluxes under aerobic conditions, there is a threshold value of the glucose uptake rate at which the metabolism shifts from purely...... by overexpression of a water-forming NADH oxidase reduced aerobic glycerol formation. The metabolic response to elevated alternative oxidase occurred predominantly in the mitochondria, whereas NADH oxidase affected genes that catalyze cytosolic reactions. Moreover, NADH oxidase restored the deficiency of cytosolic...

  3. A new atmospheric aerosol phase equilibrium model (UHAERO: organic systems

    Directory of Open Access Journals (Sweden)

    N. R. Amundson

    2007-09-01

    Full Text Available In atmospheric aerosols, water and volatile inorganic and organic species are distributed between the gas and aerosol phases in accordance with thermodynamic equilibrium. Within an atmospheric particle, liquid and solid phases can exist at equilibrium. Models exist for computation of phase equilibria for inorganic/water mixtures typical of atmospheric aerosols; when organic species are present, the phase equilibrium problem is complicated by organic/water interactions as well as the potentially large number of organic species. We present here an extension of the UHAERO inorganic thermodynamic model (Amundson et al., 2006c to organic/water systems. Phase diagrams for a number of model organic/water systems characteristic of both primary and secondary organic aerosols are computed. Also calculated are inorganic/organic/water phase diagrams that show the effect of organics on inorganic deliquescence behavior. The effect of the choice of activity coefficient model for organics on the computed phase equilibria is explored.

  4. A new atmospheric aerosol phase equilibrium model (UHAERO: organic systems

    Directory of Open Access Journals (Sweden)

    N. R. Amundson

    2007-06-01

    Full Text Available In atmospheric aerosols, water and volatile inorganic and organic species are distributed between the gas and aerosol phases in accordance with thermodynamic equilibrium. Within an atmospheric particle, liquid and solid phases can exist at equilibrium. Models exist for computation of phase equilibria for inorganic/water mixtures typical of atmospheric aerosols; when organic species are present, the phase equilibrium problem is complicated by organic/water interactions as well as the potentially large number of organic species. We present here an extension of the UHAERO inorganic thermodynamic model (Amundson et al., 2006c to organic/water systems. Phase diagrams for a number of model organic/water systems characteristic of both primary and secondary organic aerosols are computed. Also calculated are inorganic/organic/water phase diagrams that show the effect of organics on inorganic deliquescence behavior. The effect of the choice of activity coefficient model for organics on the computed phase equilibria is explored.

  5. Fermentation Process Modeling with Levenberg-Marquardt Algorithm and Runge-Kutta Method on Ethanol Production by Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Dengfeng Liu

    2014-01-01

    Full Text Available The core of the Chinese rice wine making is a typical simultaneous saccharification and fermentation (SSF process. In order to control and optimize the SSF process of Chinese rice wine brewing, it is necessary to construct kinetic model and study the influence of temperature on the Chinese rice wine brewing process. An unstructured kinetic model containing 12 kinetics parameters was developed and used to describe the changing of kinetic parameters in Chinese rice wine fermentation at 22, 26, and 30°C. The effects of substrate and product inhibitions were included in the model, and four variable, including biomass, ethanol, sugar and substrate were considered. The R-square values for the model are all above 0.95 revealing that the model prediction values could match experimental data very well. Our model conceivably contributes significantly to the improvement of the industrial process for the production of Chinese rice wine.

  6. Regulation of Cation Balance in Saccharomyces cerevisiae

    Science.gov (United States)

    Cyert, Martha S.; Philpott, Caroline C.

    2013-01-01

    All living organisms require nutrient minerals for growth and have developed mechanisms to acquire, utilize, and store nutrient minerals effectively. In the aqueous cellular environment, these elements exist as charged ions that, together with protons and hydroxide ions, facilitate biochemical reactions and establish the electrochemical gradients across membranes that drive cellular processes such as transport and ATP synthesis. Metal ions serve as essential enzyme cofactors and perform both structural and signaling roles within cells. However, because these ions can also be toxic, cells have developed sophisticated homeostatic mechanisms to regulate their levels and avoid toxicity. Studies in Saccharomyces cerevisiae have characterized many of the gene products and processes responsible for acquiring, utilizing, storing, and regulating levels of these ions. Findings in this model organism have often allowed the corresponding machinery in humans to be identified and have provided insights into diseases that result from defects in ion homeostasis. This review summarizes our current understanding of how cation balance is achieved and modulated in baker’s yeast. Control of intracellular pH is discussed, as well as uptake, storage, and efflux mechanisms for the alkali metal cations, Na+ and K+, the divalent cations, Ca2+ and Mg2+, and the trace metal ions, Fe2+, Zn2+, Cu2+, and Mn2+. Signal transduction pathways that are regulated by pH and Ca2+ are reviewed, as well as the mechanisms that allow cells to maintain appropriate intracellular cation concentrations when challenged by extreme conditions, i.e., either limited availability or toxic levels in the environment. PMID:23463800

  7. Biotechnology of non-Saccharomyces yeasts--the ascomycetes.

    Science.gov (United States)

    Johnson, Eric A

    2013-01-01

    Saccharomyces cerevisiae and several other yeast species are among the most important groups of biotechnological organisms. S. cerevisiae and closely related ascomycetous yeasts are the major producer of biotechnology products worldwide, exceeding other groups of industrial microorganisms in productivity and economic revenues. Traditional industrial attributes of the S. cerevisiae group include their primary roles in food fermentations such as beers, cider, wines, sake, distilled spirits, bakery products, cheese, sausages, and other fermented foods. Other long-standing industrial processes involving S. cerevisae yeasts are production of fuel ethanol, single-cell protein (SCP), feeds and fodder, industrial enzymes, and small molecular weight metabolites. More recently, non-Saccharomyces yeasts (non-conventional yeasts) have been utilized as industrial organisms for a variety of biotechnological roles. Non-Saccharomyces yeasts are increasingly being used as hosts for expression of proteins, biocatalysts and multi-enzyme pathways for the synthesis of fine chemicals and small molecular weight compounds of medicinal and nutritional importance. Non-Saccharomyces yeasts also have important roles in agriculture as agents of biocontrol, bioremediation, and as indicators of environmental quality. Several of these products and processes have reached commercial utility, while others are in advanced development. The objective of this mini-review is to describe processes currently used by industry and those in developmental stages and close to commercialization primarily from non-Saccharomyces yeasts with an emphasis on new opportunities. The utility of S. cerevisiae in heterologous production of selected products is also described.

  8. Model for Railway Infrastructure Management Organization

    Directory of Open Access Journals (Sweden)

    Gordan Stojić

    2012-03-01

    Full Text Available The provision of appropriate quality rail services has an important role in terms of railway infrastructure: quality of infrastructure maintenance, regulation of railway traffic, line capacity, speed, safety, train station organization, the allowable lines load and other infrastructure parameters.The analysis of experiences in transforming the railway systems points to the conclusion that there is no unique solution in terms of choice for institutional rail infrastructure management modes, although more than nineteen years have passed from the beginning of the implementation of the Directive 91/440/EEC. Depending on the approach to the process of restructuring the national railway company, adopted regulations and caution in its implementation, the existence or absence of a clearly defined transport strategy, the willingness to liberalize the transport market, there are several different ways for institutional management of railway infrastructure.A hybrid model for selection of modes of institutional rail infrastructure management was developed based on the theory of artificial intelligence, theory of fuzzy sets and theory of multicriteria optimization.KEY WORDSmanagement, railway infrastructure, organizational structure, hybrid model

  9. Knowledge Management Model on Educational Organization

    Directory of Open Access Journals (Sweden)

    Elsina Ferdinandus

    2015-12-01

    Key Words: model, knowledge management, educational organizations Abstrak: Penelitian ini bertujuan mendeskripsikan proses knowledge management yang dilakukan pada SMA Negeri 1 Pulau-pulau Aru dan SMA Yos Sudarso Dobo di Kabupaten Kepulauan Aru. Penelitian ini menggunakan jenis penelitian kualitatif dengan rancangan studi multi kasus. Data dikumpulkan dengan teknik observasi, wawancara mendalam dan dokumentasi kemudian dianalisis dengan teknik analisis data kasus individu dan analisis data lintas kasus. Temuan penelitian ini menggambarkan (1 guru-guru sudah melakukan transformasi pengetahuan explicit to tacit dengan baik ketika melakukan persiapan pembelajaran, transformasi pengetahuan tacit to explicit belum dilakukan dengan baik, dan transformasi pengetahuan tacit to tacit sudah dilakukan dengan baik; (2  sosialisasi dilakukan dengan baik, namun belum maksimal; (3  kepala sekolah SMA Negeri 1 Pulau-pulau Aru lebih demokratis dan kepala sekolah SMA Yos Sudarso Dobo lebih paternalistis; (4 peningkatan berupa upaya memasukan pengetahuan dari luar sekolah sudah dilakukan oleh kedua sekolah; dan (5  proses knowledge capture di kedua sekolah sudah berjalan dengan baik. Kata kunci: model, knowledge management, organisasi pendidikan

  10. Interspecies variation reveals a conserved repressor of alpha-specific genes in Saccharomyces yeasts.

    Science.gov (United States)

    Zill, Oliver A; Rine, Jasper

    2008-06-15

    The mating-type determination circuit in Saccharomyces yeast serves as a classic paradigm for the genetic control of cell type in all eukaryotes. Using comparative genetics, we discovered a central and conserved, yet previously undetected, component of this genetic circuit: active repression of alpha-specific genes in a cells. Upon inactivation of the SUM1 gene in Saccharomyces bayanus, a close relative of Saccharomyces cerevisiae, a cells acquired mating characteristics of alpha cells and displayed autocrine activation of their mating response pathway. Sum1 protein bound to the promoters of alpha-specific genes, repressing their transcription. In contrast to the standard model, alpha1 was important but not required for alpha-specific gene activation and mating of alpha cells in the absence of Sum1. Neither Sum1 protein expression, nor its association with target promoters was mating-type-regulated. Thus, the alpha1/Mcm1 coactivators did not overcome repression by occluding Sum1 binding to DNA. Surprisingly, the mating-type regulatory function of Sum1 was conserved in S. cerevisiae. We suggest that a comprehensive understanding of some genetic pathways may be best attained through the expanded phenotypic space provided by study of those pathways in multiple related organisms.

  11. COMPUTER MODEL FOR ORGANIC FERTILIZER EVALUATION

    Directory of Open Access Journals (Sweden)

    Zdenko Lončarić

    2009-12-01

    Full Text Available Evaluation of manures, composts and growing media quality should include enough properties to enable an optimal use from productivity and environmental points of view. The aim of this paper is to describe basic structure of organic fertilizer (and growing media evaluation model to present the model example by comparison of different manures as well as example of using plant growth experiment for calculating impact of pH and EC of growing media on lettuce plant growth. The basic structure of the model includes selection of quality indicators, interpretations of indicators value, and integration of interpreted values into new indexes. The first step includes data input and selection of available data as a basic or additional indicators depending on possible use as fertilizer or growing media. The second part of the model uses inputs for calculation of derived quality indicators. The third step integrates values into three new indexes: fertilizer, growing media, and environmental index. All three indexes are calculated on the basis of three different groups of indicators: basic value indicators, additional value indicators and limiting factors. The possible range of indexes values is 0-10, where range 0-3 means low, 3-7 medium and 7-10 high quality. Comparing fresh and composted manures, higher fertilizer and environmental indexes were determined for composted manures, and the highest fertilizer index was determined for composted pig manure (9.6 whereas the lowest for fresh cattle manure (3.2. Composted manures had high environmental index (6.0-10 for conventional agriculture, but some had no value (environmental index = 0 for organic agriculture because of too high zinc, copper or cadmium concentrations. Growing media indexes were determined according to their impact on lettuce growth. Growing media with different pH and EC resulted in very significant impacts on height, dry matter mass and leaf area of lettuce seedlings. The highest lettuce

  12. Formal Modelling of Goals in Organizations

    NARCIS (Netherlands)

    Popova, Viara; Sharpanskykh, Alexei

    2008-01-01

    Each organization exists or is created for the achievement of one or more goals. To ensure continued success, the organization should monitor its performance with respect to the formulated goals. In practice the performance of an organization is often evaluated by estimating its performance indicato

  13. The Time Is Right to Focus on Model Organism Metabolomes

    Directory of Open Access Journals (Sweden)

    Arthur S. Edison

    2016-02-01

    Full Text Available Model organisms are an essential component of biological and biomedical research that can be used to study specific biological processes. These organisms are in part selected for facile experimental study. However, just as importantly, intensive study of a small number of model organisms yields important synergies as discoveries in one area of science for a given organism shed light on biological processes in other areas, even for other organisms. Furthermore, the extensive knowledge bases compiled for each model organism enable systems-level understandings of these species, which enhance the overall biological and biomedical knowledge for all organisms, including humans. Building upon extensive genomics research, we argue that the time is now right to focus intensively on model organism metabolomes. We propose a grand challenge for metabolomics studies of model organisms: to identify and map all metabolites onto metabolic pathways, to develop quantitative metabolic models for model organisms, and to relate organism metabolic pathways within the context of evolutionary metabolomics, i.e., phylometabolomics. These efforts should focus on a series of established model organisms in microbial, animal and plant research.

  14. The Time Is Right to Focus on Model Organism Metabolomes

    Science.gov (United States)

    Edison, Arthur S.; Hall, Robert D.; Junot, Christophe; Karp, Peter D.; Kurland, Irwin J.; Mistrik, Robert; Reed, Laura K.; Saito, Kazuki; Salek, Reza M.; Steinbeck, Christoph; Sumner, Lloyd W.; Viant, Mark R.

    2016-01-01

    Model organisms are an essential component of biological and biomedical research that can be used to study specific biological processes. These organisms are in part selected for facile experimental study. However, just as importantly, intensive study of a small number of model organisms yields important synergies as discoveries in one area of science for a given organism shed light on biological processes in other areas, even for other organisms. Furthermore, the extensive knowledge bases compiled for each model organism enable systems-level understandings of these species, which enhance the overall biological and biomedical knowledge for all organisms, including humans. Building upon extensive genomics research, we argue that the time is now right to focus intensively on model organism metabolomes. We propose a grand challenge for metabolomics studies of model organisms: to identify and map all metabolites onto metabolic pathways, to develop quantitative metabolic models for model organisms, and to relate organism metabolic pathways within the context of evolutionary metabolomics, i.e., phylometabolomics. These efforts should focus on a series of established model organisms in microbial, animal and plant research. PMID:26891337

  15. The Time Is Right to Focus on Model Organism Metabolomes

    NARCIS (Netherlands)

    Edison, Arthur; Hall, Robert; Junot, Christophe; Karp, Peter; Kurland, Irwin; Mistrik, Robert; Reed, Laura; Saito, Kazuki; Salek, Reza; Steinbeck, Christoph; Sumner, Lloyd; Viant, Mark

    2016-01-01

    Model organisms are an essential component of biological and biomedical research that can be used to study specific biological processes. These organisms are in part selected for facile experimental study. However, just as importantly, intensive study of a small number of model organisms yields

  16. The Time Is Right to Focus on Model Organism Metabolomes.

    Science.gov (United States)

    Edison, Arthur S; Hall, Robert D; Junot, Christophe; Karp, Peter D; Kurland, Irwin J; Mistrik, Robert; Reed, Laura K; Saito, Kazuki; Salek, Reza M; Steinbeck, Christoph; Sumner, Lloyd W; Viant, Mark R

    2016-02-15

    Model organisms are an essential component of biological and biomedical research that can be used to study specific biological processes. These organisms are in part selected for facile experimental study. However, just as importantly, intensive study of a small number of model organisms yields important synergies as discoveries in one area of science for a given organism shed light on biological processes in other areas, even for other organisms. Furthermore, the extensive knowledge bases compiled for each model organism enable systems-level understandings of these species, which enhance the overall biological and biomedical knowledge for all organisms, including humans. Building upon extensive genomics research, we argue that the time is now right to focus intensively on model organism metabolomes. We propose a grand challenge for metabolomics studies of model organisms: to identify and map all metabolites onto metabolic pathways, to develop quantitative metabolic models for model organisms, and to relate organism metabolic pathways within the context of evolutionary metabolomics, i.e., phylometabolomics. These efforts should focus on a series of established model organisms in microbial, animal and plant research.

  17. Integration of metabolic modeling and phenotypic data in evaluation and improvement of ethanol production using respiration-deficient mutants of Saccharomyces cerevisiae.

    Science.gov (United States)

    Dikicioglu, Duygu; Pir, Pinar; Onsan, Z Ilsen; Ulgen, Kutlu O; Kirdar, Betul; Oliver, Stephen G

    2008-09-01

    Flux balance analysis and phenotypic data were used to provide clues to the relationships between the activities of gene products and the phenotypes resulting from the deletion of genes involved in respiratory function in Saccharomyces cerevisiae. The effect of partial or complete respiratory deficiency on the ethanol production and growth characteristics of hap4Delta/hap4Delta, mig1Delta/mig1Delta, qdr3Delta/qdr3Delta, pdr3Delta/pdr3Delta, qcr7Delta/qcr7Delta, cyt1Delta/cyt1Delta, and rip1Delta/rip1Delta mutants grown in microaerated chemostats was investigated. The study provided additional evidence for the importance of the selection of a physiologically relevant objective function, and it may improve quantitative predictions of exchange fluxes, as well as qualitative estimations of changes in intracellular fluxes. Ethanol production was successfully predicted by flux balance analysis in the case of the qdr3Delta/qdr3Delta mutant, with maximization of ethanol production as the objective function, suggesting an additional role for Qdr3p in respiration. The absence of similar changes in estimated intracellular fluxes in the qcr7Delta/qcr7Delta mutant compared to the rip1Delta/rip1Delta and cyt1Delta/cyt1Delta mutants indicated that the effect of the deletion of this subunit of complex III was somehow compensated for. Analysis of predicted flux distributions indicated self-organization of intracellular fluxes to avoid NAD(+)/NADH imbalance in rip1Delta/rip1Delta and cyt1Delta/cyt1Delta mutants, but not the qcr7Delta/qcr7Delta mutant. The flux through the glycerol efflux channel, Fps1p, was estimated to be zero in all strains under the investigated conditions. This indicates that previous strategies for improving ethanol production, such as the overexpression of the glutamate synthase gene GLT1 in a GDH1 deletion background or deletion of the glycerol efflux channel gene FPS1 and overexpression of GLT1, are unnecessary in a respiration-deficient background.

  18. Mathematical models for determining metabolic fluxes through the citric acid and the glyoxylate cycles in Saccharomyces cerevisiae by 13C-NMR spectroscopy.

    Science.gov (United States)

    Tran-Dinh, S; Bouet, F; Huynh, Q T; Herve, M

    1996-12-15

    We propose, first, a practical method for studying the isotopic transformation of glutamate or any other metabolite isotopomers in the citric acid and the glyoxylate cycles; second, two mathematical models, one for evaluating the flux through the citric acid cycle and the other for evaluating the flux through the latter coupled to the glyoxylate cycle in yeast. These models are based on the analysis of 13C-NMR spectra of glutamate obtained from Saccharomyces cerevisiae, NCYC strain, fed with 100% enriched [2-13C]acetate. The population of each glutamate isotopomer, the change in intensity of each multiplet component or the enrichment of any glutamate carbon is expressed by a specific analytical equation from which the flux in the citric acid and the glyoxylate cycles can be deduced. The aerobic metabolism of 100% [2-13C]acetate in acetate-grown S. cerevisiae cells was studied as a function of time using 13C-NMR. 1H-NMR and biochemical techniques. The C1 and C6 doublet and singlet of labeled trehalose increase continuously with time indicating that there is no isotopic transformation between trehalose isotopomers even though the corresponding formation rates are different. By contrast, the glutamate C4 singlet increases then decreases with time. The C4 doublet, which is lower than the singlet for t 90 min. A similar observation was made for the C2 resonance singlet and doublet. In addition, the glutamate C2 multiplet consists of only seven instead of nine peaks as in random labeling. These results agree well with our models and demonstrate that, in the presence of acetate, anaplerotic carbon sources involved in the synthesis of acetyl-CoA are negligible in yeast. The flux in the citric acid cycle was deduced from a plot of the C4 area versus incubation time, while the flux within the glyoxylate cycle was determined from the relative intensity of the glutamate C4 doublet and singlet. The fluxes in the citric acid and the glyoxylate cycles were found to be comparable

  19. Kinetic model of continuous ethanol fermentation in closed-circulating process with pervaporation membrane bioreactor by Saccharomyces cerevisiae.

    Science.gov (United States)

    Fan, Senqing; Chen, Shiping; Tang, Xiaoyu; Xiao, Zeyi; Deng, Qing; Yao, Peina; Sun, Zhaopeng; Zhang, Yan; Chen, Chunyan

    2015-02-01

    Unstructured kinetic models were proposed to describe the principal kinetics involved in ethanol fermentation in a continuous and closed-circulating fermentation (CCCF) process with a pervaporation membrane bioreactor. After ethanol was removed in situ from the broth by the membrane pervaporation, the secondary metabolites accumulated in the broth became the inhibitors to cell growth. The cell death rate related to the deterioration of the culture environment was described as a function of the cell concentration and fermentation time. In CCCF process, 609.8 g L(-1) and 750.1 g L(-1) of ethanol production were obtained in the first run and second run, respectively. The modified Gompertz model, correlating the ethanol production with the fermentation period, could be used to describe the ethanol production during CCCF process. The fitting results by the models showed good agreement with the experimental data. These models could be employed for the CCCF process technology development for ethanol fermentation. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Self-Organized Criticality in a Random Network Model

    OpenAIRE

    Nirei, Makoto

    1998-01-01

    A new model of self-organized criticality is defined by incorporating a random network model in order to explain endogenous complex fluctuations of economic aggregates. The model can feature many globally interactive systems such as economies or societies.

  1. Study of Self-Organization Model of Multiple Mobile Robot

    OpenAIRE

    Li Shu-qin; Ceng Xian-yi; Xia De-shen

    2006-01-01

    A good organization model of multiple mobile robot should be able to improve the efficiency of the system, reduce the complication of robot interactions, and detract the difficulty of computation. From the sociology aspect of topology, structure and organization, this paper studies the multiple mobile robot organization formation and running mechanism in the dynamic, complicated and unknown environment. It presents and describes in detail a Hierarchical- Web Recursive Organization Model (HWRO...

  2. An apoptotic cell cycle mutant in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Villadsen, Ingrid

    1996-01-01

    The simple eukaryote Saccharomyces cerevisiae has proved to be a useful organism for elucidating the mechanisms that govern cell cycle progression in eukaryotic cells. The excellent in vivo system permits a cell cycle study using temperature sensitive mutants. In addition, it is possible to study...... many genes and gene products from higher eukaryotes in Saccharomyces cerevisiae because many genes and biological processes are homologous or similar in lower and in higher eukaryotes. The highly developed methods of genetics and molecular biology greatly facilitates studies of higher eukaryotic...... processes.Programmmed cell death with apoptosis plays a major role in development and homeostatis in most, if not all, animal cells. Apoptosis is a morphologically distinct form of death, that requires the activation of a highly regulated suicide program. Saccharomyces cerevisiae provides a new system...

  3. A Topological Model for C2 Organizations

    Science.gov (United States)

    2011-06-01

    functions of the organization, and the capabilities of its members, as these sets somehow efine the boundaries of organizational performance and the...and functions of the organization, and the capabilities of its members, as these sets somehow efine the boundaries of organizational performance and

  4. 3D Bioprinting of Tissue/Organ Models.

    Science.gov (United States)

    Pati, Falguni; Gantelius, Jesper; Svahn, Helene Andersson

    2016-04-04

    In vitro tissue/organ models are useful platforms that can facilitate systematic, repetitive, and quantitative investigations of drugs/chemicals. The primary objective when developing tissue/organ models is to reproduce physiologically relevant functions that typically require complex culture systems. Bioprinting offers exciting prospects for constructing 3D tissue/organ models, as it enables the reproducible, automated production of complex living tissues. Bioprinted tissues/organs may prove useful for screening novel compounds or predicting toxicity, as the spatial and chemical complexity inherent to native tissues/organs can be recreated. In this Review, we highlight the importance of developing 3D in vitro tissue/organ models by 3D bioprinting techniques, characterization of these models for evaluating their resemblance to native tissue, and their application in the prioritization of lead candidates, toxicity testing, and as disease/tumor models.

  5. Modeling of combined effects of citral, linalool and beta-pinene used against Saccharomyces cerevisiae in citrus-based beverages subjected to a mild heat treatment.

    Science.gov (United States)

    Belletti, Nicoletta; Kamdem, Sylvain Sado; Tabanelli, Giulia; Lanciotti, Rosalba; Gardini, Fausto

    2010-01-01

    The aim of this work was to evaluate the antimicrobial activity of three terpenes (citral, linalool and beta-pinene), in combination with a mild heat treatment (55 degrees C, 15 min). The study has been carried out on an orange based soft drink inoculated using a wild strain of Saccharomyces cerevisiae. The results, expressed as growth/no-growth data, were analyzed with the logistic regression. A model comprising only of significant individual parameters (p beta-pinene were combined, the citral concentration required to achieve a 50% probability of having stable bottles (P=0.5) dropped from 100.9 microL/L in the absence of beta-pinene to 49.3 microL/L in the presence of 20 microL/L of beta-pinene. The mixture of citral and linalool was less effective, in fact, the same probability (P=0.5) was obtained combining 60 microL/L of linalool with 35.1 microL/L of citral. The addition of 20 microL/L of linalool and beta-pinene reinforced citral bioactivity and the concentration of citral needed to reach P=0.5 fell from 100.9 microL/L in the presence of citral alone to 42.0 microL/L. The presence of both linalool and beta-pinene at a concentration of 40 or 60 microL/L in the absence of citral led to a lower spoilage probability (P=0.58 and P=0.93, respectively). It can be concluded that the antimicrobial potential of the three terpenes alone can be strengthened combining appropriate concentrations of each of them. This study confirmed also the potentiating effect of a mild temperature treatment on the antimicrobial efficacy of the molecules. Neither the thermal treatment alone nor the presence of the terpenes at their maximum concentrations (without thermal treatment) were able to guarantee the microbial stability of the beverages.

  6. Novel insights into iron metabolism by integrating deletome and transcriptome analysis in an iron deficiency model of the yeast Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Arkin Adam P

    2009-03-01

    Full Text Available Abstract Background Iron-deficiency anemia is the most prevalent form of anemia world-wide. The yeast Saccharomyces cerevisiae has been used as a model of cellular iron deficiency, in part because many of its cellular pathways are conserved. To better understand how cells respond to changes in iron availability, we profiled the yeast genome with a parallel analysis of homozygous deletion mutants to identify essential components and cellular processes required for optimal growth under iron-limited conditions. To complement this analysis, we compared those genes identified as important for fitness to those that were differentially-expressed in the same conditions. The resulting analysis provides a global perspective on the cellular processes involved in iron metabolism. Results Using functional profiling, we identified several genes known to be involved in high affinity iron uptake, in addition to novel genes that may play a role in iron metabolism. Our results provide support for the primary involvement in iron homeostasis of vacuolar and endosomal compartments, as well as vesicular transport to and from these compartments. We also observed an unexpected importance of the peroxisome for growth in iron-limited media. Although these components were essential for growth in low-iron conditions, most of them were not differentially-expressed. Genes with altered expression in iron deficiency were mainly associated with iron uptake and transport mechanisms, with little overlap with those that were functionally required. To better understand this relationship, we used expression-profiling of selected mutants that exhibited slow growth in iron-deficient conditions, and as a result, obtained additional insight into the roles of CTI6, DAP1, MRS4 and YHR045W in iron metabolism. Conclusion Comparison between functional and gene expression data in iron deficiency highlighted the complementary utility of these two approaches to identify important functional

  7. Interactions between Drosophila and its natural yeast symbionts—Is Saccharomyces cerevisiae a good model for studying the fly-yeast relationship?

    Directory of Open Access Journals (Sweden)

    Don Hoang

    2015-08-01

    Full Text Available Yeasts play an important role in the biology of the fruit fly, Drosophila melanogaster. In addition to being a valuable source of nutrition, yeasts affect D. melanogaster behavior and interact with the host immune system. Most experiments investigating the role of yeasts in D. melanogaster biology use the baker’s yeast, Saccharomyces cerevisiae. However, S. cerevisiae is rarely found with natural populations of D. melanogaster or other Drosophila species. Moreover, the strain of S. cerevisiae used most often in D. melanogaster experiments is a commercially and industrially important strain that, to the best of our knowledge, was not isolated from flies. Since disrupting natural host–microbe interactions can have profound effects on host biology, the results from D. melanogaster–S. cerevisiae laboratory experiments may not be fully representative of host–microbe interactions in nature. In this study, we explore the D. melanogaster-yeast relationship using five different strains of yeast that were isolated from wild Drosophila populations. Ingested live yeasts have variable persistence in the D. melanogaster gastrointestinal tract. For example, Hanseniaspora occidentalis persists relative to S. cerevisiae, while Brettanomyces naardenensis is removed. Despite these differences in persistence relative to S. cerevisiae, we find that all yeasts decrease in total abundance over time. Reactive oxygen species (ROS are an important component of the D. melanogaster anti-microbial response and can inhibit S. cerevisiae growth in the intestine. To determine if sensitivity to ROS explains the differences in yeast persistence, we measured yeast growth in the presence and absence of hydrogen peroxide. We find that B. naardenesis is completely inhibited by hydrogen peroxide, while H. occidentalis is not, which is consistent with yeast sensitivity to ROS affecting persistence within the D. melanogaster gastrointestinal tract. We also compared the feeding

  8. using stereochemistry models in teaching organic compounds ...

    African Journals Online (AJOL)

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    (ii) provide the students with basic knowledge in chemical concepts and ... ethanol, ethan-l-ol and ethyl alcohol in some textbooks and they are the same. ... Considering class level, what is the performance of the students in naming organic.

  9. A Modeling Exercise for the Organic Classroom

    Science.gov (United States)

    Whitlock, Christine R.

    2010-01-01

    An in-class molecular modeling exercise is described. Groups of students are given molecular models to investigate and questions about the models to answer. This exercise is a quick and effective way to review nomenclature, stereochemistry, and conformational analysis.

  10. Self-Organizing Map Models of Language Acquisition

    Directory of Open Access Journals (Sweden)

    Ping eLi

    2013-11-01

    Full Text Available Connectionist models have had a profound impact on theories of language. While most early models were inspired by the classic PDP architecture, recent models of language have explored various other types of models, including self-organizing models for language acquisition. In this paper we aim at providing a review of the latter type of models, and highlight a number of simulation experiments that we have conducted based on these models. We show that self-organizing connectionist models can provide significant insights into long-standing debates in both monolingual and bilingual language development.

  11. MODELING OF MANAGEMENT PROCESSES IN AN ORGANIZATION

    Directory of Open Access Journals (Sweden)

    Stefan Iovan

    2016-05-01

    Full Text Available When driving any major change within an organization, strategy and execution are intrinsic to a project’s success. Nevertheless, closing the gap between strategy and execution remains a challenge for many organizations [1]. Companies tend to focus more on execution than strategy for quick results, instead of taking the time needed to understand the parts that make up the whole, so the right execution plan can be put in place to deliver the best outcomes. A large part of this understands that business operations don’t fit neatly within the traditional organizational hierarchy. Business processes are often messy, collaborative efforts that cross teams, departments and systems, making them difficult to manage within a hierarchical structure [2]. Business process management (BPM fills this gap by redefining an organization according to its end-to-end processes, so opportunities for improvement can be identified and processes streamlined for growth, revenue and transformation. This white paper provides guidelines on what to consider when using business process applications to solve your BPM initiatives, and the unique capabilities software systems provides that can help ensure both your project’s success and the success of your organization as a whole. majority of medium and small businesses, big companies and even some guvermental organizations [2].

  12. 面包酵母催化不对称还原EOPB反应中的溶剂效应%Effect of organic solvents on asymmetric reduction of ethyl-2-oxo-4-phenylbutyrate mediated by saccharomyces cerevisiae

    Institute of Scientific and Technical Information of China (English)

    石玉刚; 励建荣; 唐琼

    2011-01-01

    The asymmetric reduction of ethyl-2-oxo-4-phenylbutyrate (EOPB) catalyzed by saccharomyces cerevisiae in organic phase to synthesize chiral ethyl-2-hydroxy-4-phenylbutyrate (EHPB) was investigated. In diethyl ether with the initial EOPB concentration of 6 mmol·L-1 , the e. e.(R)-EHPB was increased 19% by using wet baker's yeast (WB) as biocatalyst compared to that by dry baker's yeast (DB). However, the catalytic activity and stability of WB was lower than that of DB. The enantioselectivity of the reduction to produce (R) -EHPB was reduced with the increase of the log P value (0.82-3.2 ) of employed organic solvents. Although dimethylbenzene and cyclohexane had the same log p value (3.2), the enantioselectivity of the reduction was reversed from R to S when dimethylbenzene was in place of cyclohexane as reaction media. Significant changes were observed in the UV absorption and fluorescence spectrum of the YADH from the yeast pretreated by the solvents. These facts indicated that the synergistic effect of solvent polarity and its spatial structure led to the change of the catalytic behavior of baker's yeast%研究了非水介质中面包酵母催化不对称还原2-氧代-4-苯基丁酸乙酯(EOPB)合成手性2-羟基-4-苯36基丁酸乙酯(EHPB)的反应.乙醚体系中湿酵母(WB)催化6mmol·L-1EOPB合成(R)-EHPB的e.e.值较之于干酵母(DB)提高了近19%,但WB稳定性较差.DB催化该反应的立体选择性随溶剂logP(0.82-3.2)的增加而降低,反应从相同logP值(3.2)的二甲苯转换至环己烷后产物构型由R转为S,经有机溶剂预处理后酵母醇脱氢酶(YADH)的紫外及荧光光谱的特征变化表明溶剂分子极性与结构的协同作用下酵母催化行为发生了改变.

  13. MARTINI Model for Physisorption of Organic Molecules on Graphite

    NARCIS (Netherlands)

    Gobbo, Cristian; Beurroies, Isabelle; de Ridder, David; Eelkema, Rienk; Marrink, Siewert J.; De Feyter, Steven; van Esch, Jan H.; de Vries, Alex H.

    2013-01-01

    An extension to the MARTINI coarse-grained model is presented to describe the adsorption of organic molecules on graphite surfaces. The model allows the study of the dynamics of the preferential adsorption of long-chain organic molecules from solvent and the formation of ordered structures on the su

  14. Yeast and filamentous fungi as model organisms in microbody research

    NARCIS (Netherlands)

    Klei, Ida J. van der; Veenhuis, Marten

    2006-01-01

    Yeast and filamentous fungi are important model organisms in microbody research. The value of these organisms as models for higher eukaryotes is underscored by the observation that the principles of various aspects of microbody biology are strongly conserved from lower to higher eukaryotes. This has

  15. The initiative on Model Organism Proteomes (iMOP) Session

    DEFF Research Database (Denmark)

    Schrimpf, Sabine P; Mering, Christian von; Bendixen, Emøke

    2012-01-01

    iMOP – the Initiative on Model Organism Proteomes – was accepted as a new HUPO initiative at the Ninth HUPO meeting in Sydney in 2010. A goal of iMOP is to integrate research groups working on a great diversity of species into a model organism community. At the Tenth HUPO meeting in Geneva...

  16. Modeling the Explicit Chemistry of Anthropogenic and Biogenic Organic Aerosols

    Energy Technology Data Exchange (ETDEWEB)

    Madronich, Sasha [Univ. Corporation for Atmospheric Research, Boulder, CO (United States)

    2015-12-09

    The atmospheric burden of Secondary Organic Aerosols (SOA) remains one of the most important yet uncertain aspects of the radiative forcing of climate. This grant focused on improving our quantitative understanding of SOA formation and evolution, by developing, applying, and improving a highly detailed model of atmospheric organic chemistry, the Generation of Explicit Chemistry and Kinetics of Organics in the Atmosphere (GECKO-A) model. Eleven (11) publications have resulted from this grant.

  17. Early manifestations of replicative aging in the yeast Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Maksim I. Sorokin

    2014-01-01

    Full Text Available The yeast Saccharomyces cerevisiae is successfully used as a model organism to find genes responsible for lifespan control of higher organisms. As functional decline of higher eukaryotes can start as early as one quarter of the average lifespan, we asked whether S. cerevisiae can be used to model this manifestation of aging. While the average replicative lifespan of S. cerevisiae mother cells ranges between 15 and 30 division cycles, we found that resistances to certain stresses start to decrease much earlier. Looking into the mechanism, we found that knockouts of genes responsible for mitochondriato-nucleus (retrograde signaling, RTG1 or RTG3, significantly decrease the resistance of cells that generated more than four daughters, but not of the younger ones. We also found that even young mother cells frequently contain mitochondria with heterogeneous transmembrane potential and that the percentage of such cells correlates with replicative age. Together, these facts suggest that retrograde signaling starts to malfunction in relatively young cells, leading to accumulation of heterogeneous mitochondria within one cell. The latter may further contribute to a decline in stress resistances.

  18. Examining the role of membrane lipid composition in determining the ethanol tolerance of Saccharomyces cerevisiae.

    Science.gov (United States)

    Henderson, Clark M; Block, David E

    2014-05-01

    Yeast (Saccharomyces cerevisiae) has an innate ability to withstand high levels of ethanol that would prove lethal to or severely impair the physiology of other organisms. Significant efforts have been undertaken to elucidate the biochemical and biophysical mechanisms of how ethanol interacts with lipid bilayers and cellular membranes. This research has implicated the yeast cellular membrane as the primary target of the toxic effects of ethanol. Analysis of model membrane systems exposed to ethanol has demonstrated ethanol's perturbing effect on lipid bilayers, and altering the lipid composition of these model bilayers can mitigate the effect of ethanol. In addition, cell membrane composition has been correlated with the ethanol tolerance of yeast cells. However, the physical phenomena behind this correlation are likely to be complex. Previous work based on often divergent experimental conditions and time-consuming low-resolution methodologies that limit large-scale analysis of yeast fermentations has fallen short of revealing shared mechanisms of alcohol tolerance in Saccharomyces cerevisiae. Lipidomics, a modern mass spectrometry-based approach to analyze the complex physiological regulation of lipid composition in yeast and other organisms, has helped to uncover potential mechanisms for alcohol tolerance in yeast. Recent experimental work utilizing lipidomics methodologies has provided a more detailed molecular picture of the relationship between lipid composition and ethanol tolerance. While it has become clear that the yeast cell membrane composition affects its ability to tolerate ethanol, the molecular mechanisms of yeast alcohol tolerance remain to be elucidated.

  19. MODEL OF LEARNING ORGANIZATION IN BROADCASTING ORGANIZATION OF ISLAMIC REPUBLIC OF IRAN

    Directory of Open Access Journals (Sweden)

    Reza Najafbagy

    2010-11-01

    Full Text Available This article tries to present a model of learning organization for Iran Broadcasting Organization which is under the management of the spiritual leader of Iran. The study is based on characteristics of Peter Senge’s original learning organization namely, personal stery, mental models, shared vision, team learning and systems thinking. The methodology was a survey research employed questionnaire among sample employees and managers of the Organization.Findings showed that the Organization is fairly far from an ffective learning organization.Moreover, it seems that employees’ performance in team learning and changes in mental models are more satisfactory than managers. Regarding other characteristics of learning organizations, there are similarities in learning attempts by employees and managers. The rganization lacks organizational vision, and consequently there is no shared vision in the Organization. It also is in need of organizational culture. As a kind of state-owned organization, there s no need of financial support which affect the need for learning organization. It also does not face the threat of sustainabilitybecause there is no competitive organization.Findings also show that IBO need a fundamental change in its rganizational learning process. In this context, the general idea is to unfreeze the mindset of leadership of IBO and creating a visionand organizational culture based on learning and staff development. Then gradually through incremental effective change and continual organizational learning process in dividual, team and organization levels engage in development and reinforcement of skills of personal mastery, mental models, shared vision, team learning and systems thinking, should lead IBO to learning organization.

  20. Integrated modelling of two xenobiotic organic compounds

    DEFF Research Database (Denmark)

    Lindblom, Erik Ulfson; Gernaey, K.V.; Henze, Mogens

    2006-01-01

    compounds, is carried out. Sorption and specific biological degradation processes are integrated with standardised water process models to model the fate of both compounds. Simulated mass flows of the two compounds during one dry weather day and one wet weather day are compared for realistic influent flow...... rate and concentration profiles. The wet weather day induces resuspension of stored sediments, which increases the pollutant load on the downstream system. The potential of the model to elucidate important phenomena related to origin and fate of the model compounds is demonstrated....

  1. Evolutionary Model to Traditional Culture and Program Organization

    Institute of Scientific and Technical Information of China (English)

    ZHANG Jing-xiao; JIN Wei-xing; YANG De-qin

    2006-01-01

    To study the relationship between the evolutions of Chinese Traditional Culture (CTC) and program organization, an outline of the CTC is generalized by reviewing literature, and which is also compartmentalized into two aspects according to economic philosophy views: traditional philosophy aspect and value judgment. Based on three dimensions, which are the philosophy aspect (P), program organization model (P), and value judgment from economic philosophy views (V), and this evolution sequence, the CTC's influence on the program organization model in the evolution is discussed; then the cultural spatial evolution model for program organization based on the three dimensions (PPV) is constructed. From analyzing the plane matrix of P-P and empirical investigating on the organizational model of construction enterprises, it is found that the ancient Chinese government organizational model still has prevailing influence on the modern program organizational model in China.

  2. Mathematical models of cell self-organization

    Directory of Open Access Journals (Sweden)

    Benoît Perthame

    2011-04-01

    More recently nonlinear hyperbolic and kinetic models also have been used to describe the phenomena at a smaller scale. We explain here some motivations for ‘microscopic’ descriptions, the mathematical difficulties arising in their analysis and how kinetic models can help in understanding the unity of these descriptions.

  3. Exploring Organic Mechanistic Puzzles with Molecular Modeling

    Science.gov (United States)

    Horowitz, Gail; Schwartz, Gary

    2004-01-01

    The molecular modeling was used to reinforce more general skills such as deducing and drawing reaction mechanisms, analyzing reaction kinetics and thermodynamics and drawing reaction coordinate energy diagrams. This modeling was done through the design of mechanistic puzzles, involving reactions not familiar to the students.

  4. [Models of the organization of neonatal screening].

    Science.gov (United States)

    Cassio, A; Piazzi, S; Colli, C; Balsamo, A; Bozza, D; Salardi, S; Sprovieri, G; Cacciari, E

    1994-01-01

    The authors evaluate the different organizational strategies of a congenital hypothyroidism screening program. Positive and negative aspects of laboratory screening tests (TSH only, T4-supplemental TSH, TSH and T4), organization strategies (centralization or decentralization), recall and first follow-up criteria are examined. The authors consider that the necessity for an early diagnostic confirmation can be associated with a precise etiologic diagnosis and an evaluation of the prenatal severity of congenital hypothyroidism factors. Some European and North-American experiences are compared with the activity of a regional Italian screening center.

  5. Modeling the influence of organic acids on soil weathering

    Science.gov (United States)

    Lawrence, Corey; Harden, Jennifer; Maher, Kate

    2014-08-01

    Biological inputs and organic matter cycling have long been regarded as important factors in the physical and chemical development of soils. In particular, the extent to which low molecular weight organic acids, such as oxalate, influence geochemical reactions has been widely studied. Although the effects of organic acids are diverse, there is strong evidence that organic acids accelerate the dissolution of some minerals. However, the influence of organic acids at the field-scale and over the timescales of soil development has not been evaluated in detail. In this study, a reactive-transport model of soil chemical weathering and pedogenic development was used to quantify the extent to which organic acid cycling controls mineral dissolution rates and long-term patterns of chemical weathering. Specifically, oxalic acid was added to simulations of soil development to investigate a well-studied chronosequence of soils near Santa Cruz, CA. The model formulation includes organic acid input, transport, decomposition, organic-metal aqueous complexation and mineral surface complexation in various combinations. Results suggest that although organic acid reactions accelerate mineral dissolution rates near the soil surface, the net response is an overall decrease in chemical weathering. Model results demonstrate the importance of organic acid input concentrations, fluid flow, decomposition and secondary mineral precipitation rates on the evolution of mineral weathering fronts. In particular, model soil profile evolution is sensitive to kaolinite precipitation and oxalate decomposition rates. The soil profile-scale modeling presented here provides insights into the influence of organic carbon cycling on soil weathering and pedogenesis and supports the need for further field-scale measurements of the flux and speciation of reactive organic compounds.

  6. Modeling the influence of organic acids on soil weathering

    Science.gov (United States)

    Lawrence, Corey R.; Harden, Jennifer W.; Maher, Kate

    2014-01-01

    Biological inputs and organic matter cycling have long been regarded as important factors in the physical and chemical development of soils. In particular, the extent to which low molecular weight organic acids, such as oxalate, influence geochemical reactions has been widely studied. Although the effects of organic acids are diverse, there is strong evidence that organic acids accelerate the dissolution of some minerals. However, the influence of organic acids at the field-scale and over the timescales of soil development has not been evaluated in detail. In this study, a reactive-transport model of soil chemical weathering and pedogenic development was used to quantify the extent to which organic acid cycling controls mineral dissolution rates and long-term patterns of chemical weathering. Specifically, oxalic acid was added to simulations of soil development to investigate a well-studied chronosequence of soils near Santa Cruz, CA. The model formulation includes organic acid input, transport, decomposition, organic-metal aqueous complexation and mineral surface complexation in various combinations. Results suggest that although organic acid reactions accelerate mineral dissolution rates near the soil surface, the net response is an overall decrease in chemical weathering. Model results demonstrate the importance of organic acid input concentrations, fluid flow, decomposition and secondary mineral precipitation rates on the evolution of mineral weathering fronts. In particular, model soil profile evolution is sensitive to kaolinite precipitation and oxalate decomposition rates. The soil profile-scale modeling presented here provides insights into the influence of organic carbon cycling on soil weathering and pedogenesis and supports the need for further field-scale measurements of the flux and speciation of reactive organic compounds.

  7. Comparing risk attitudes of organic and non-organic farmers with a Bayesian random coefficient model

    NARCIS (Netherlands)

    Gardebroek, C.

    2006-01-01

    Organic farming is usually considered to be more risky than conventional farming, but the risk aversion of organic farmers compared with that of conventional farmers has not been studied. Using a non-structural approach to risk estimation, a Bayesian random coefficient model is used to obtain indivi

  8. Current methods in quantifying ROS and oxidative damage in Caenorhabditis elegans and other model organism of aging.

    Science.gov (United States)

    Labuschagne, Christiaan F; Brenkman, Arjan B

    2013-09-01

    Accumulation of oxidative damage has been proposed to be causal to aging as defined by the Free radical Theory of Aging, which has been subject to recent debate. However, a major hurdle in understanding the biological roles of reactive oxygen species (ROS) signaling and their oxidative damage has been the widely recognized methodological difficulties to measure oxidative damage and ROS in vivo. In this review we describe the various novel approaches that have recently been developed to overcome this challenge in the nematode Caenorhabditis elegans, which is a paradigm invertebrate model organism for studying aging and age-related disease given its short lifespan, easy genetics and transparency. In addition, we also discuss these methods in other important model organisms of aging, including the budding yeast Saccharomyces cerevisiae, the fruitfly Drosophila melanogaster and the mouse Mus musculus. After an introduction on the various ROS that can be encountered, we discuss approaches for the detection and quantification of ROS and ROS damage of DNA, lipids and proteins, highlighting examples from literature to demonstrate the applicability and caveats of each method. As will become clear, combinations of approaches have now become possible and will prove essential for thoroughly understanding the involvement of ROS and ROS damage in the biology of aging and disease.

  9. Daphnia as an Emerging Epigenetic Model Organism

    Directory of Open Access Journals (Sweden)

    Kami D. M. Harris

    2012-01-01

    Full Text Available Daphnia offer a variety of benefits for the study of epigenetics. Daphnia’s parthenogenetic life cycle allows the study of epigenetic effects in the absence of confounding genetic differences. Sex determination and sexual reproduction are epigenetically determined as are several other well-studied alternate phenotypes that arise in response to environmental stressors. Additionally, there is a large body of ecological literature available, recently complemented by the genome sequence of one species and transgenic technology. DNA methylation has been shown to be altered in response to toxicants and heavy metals, although investigation of other epigenetic mechanisms is only beginning. More thorough studies on DNA methylation as well as investigation of histone modifications and RNAi in sex determination and predator-induced defenses using this ecologically and evolutionarily important organism will contribute to our understanding of epigenetics.

  10. MODELLING CONSUMERS' DEMAND FOR ORGANIC FOOD PRODUCTS: THE SWEDISH EXPERIENCE

    OpenAIRE

    Manuchehr Irandoust

    2016-01-01

    This paper attempts to examine a few factors characterizing consumer preferences and behavior towards organic food products in the south of Sweden using a proportional odds model which captures the natural ordering of dependent variables and any inherent nonlinearities. The findings show that consumer's choice for organic food depends on perceived benefits of organic food (environment, health, and quality) and consumer's perception and attitudes towards labelling system, message framing, and ...

  11. Organic production in a dynamic CGE model

    DEFF Research Database (Denmark)

    Jacobsen, Lars Bo

    2004-01-01

    accumulation relationship for land, and an explicit modeling of the rate of stock accumulation (i.e., of land investment). We assume that land is industry specific, with land rentals adjusting to ensure that land supply equals land demand for each industry. Once the decision has been made to transform land...

  12. Nematodes: Model Organisms in High School Biology

    Science.gov (United States)

    Bliss, TJ; Anderson, Margery; Dillman, Adler; Yourick, Debra; Jett, Marti; Adams, Byron J.; Russell, RevaBeth

    2007-01-01

    In a collaborative effort between university researchers and high school science teachers, an inquiry-based laboratory module was designed using two species of insecticidal nematodes to help students apply scientific inquiry and elements of thoughtful experimental design. The learning experience and model are described in this article. (Contains 4…

  13. Representational Translation with Concrete Models in Organic Chemistry

    Science.gov (United States)

    Stull, Andrew T.; Hegarty, Mary; Dixon, Bonnie; Stieff, Mike

    2012-01-01

    In representation-rich domains such as organic chemistry, students must be facile and accurate when translating between different 2D representations, such as diagrams. We hypothesized that translating between organic chemistry diagrams would be more accurate when concrete models were used because difficult mental processes could be augmented by…

  14. Apparent ploidy effects on silencing are post-transcriptional at HML and telomeres in Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Jenny M McLaughlan

    Full Text Available The repression of genes in regions of heterochromatin is known as transcriptional silencing. It occurs in a wide range of organisms and can have importance in adaptation to the environment, developmental changes and disease. The model organism Saccharomyces cerevisiae has been used for many years to study transcriptional silencing, but until recently no study has been made in relation to ploidy. The aim of this work was to compare transcriptional silencing in haploids and diploids at both telomeres and the hidden mating-type (HM loci. Transcriptional silencing was assayed, by growth on 5-fluoroorotic acid (5-FOA media or by flow cytometry, on strains where a telomere or HM locus was marked. RNA levels were measured by quantitative RT-PCR to confirm that effects were transcriptional. 5-FOA assays and flow cytometry were consistent with transcriptional silencing at telomeres and at HML being reduced as ploidy increases which agreed with conclusions in previous publications. However, QRT-PCR revealed that transcriptional silencing was unaffected by ploidy and thus protein levels were increasing independently of RNA levels. At telomere XI left (XI-L, changes in protein level were strongly influenced by mating-type, whereas at HML mating-type had much less influence. The post-transcriptional effects seen in this study, illustrate the often ignored need to measure RNA levels when assaying transcriptional silencing in Saccharomyces cerevisiae.

  15. levadura Saccharomyces Cerevisiae

    Directory of Open Access Journals (Sweden)

    B. Aguilar Uscanga

    2005-01-01

    Full Text Available La pared celular de levaduras representa entre 20 a 30 % de la célula en peso seco. Está compuesta de polisacáridos complejos de β-glucanos, manoproteínas y quitina. Se estudió la composición de los polisacáridos contenidos en la pared celular de la Saccharomyces cerevisiae CEN.PK 113 y se observó el efecto de la variación de la fuente carbono (glucosa, sacarosa, galactosa, maltosa, manosa, etanol y pH (3, 4, 5, 6 en un medio mineral “cell factory”. Las células fueron recolectadas en fase exponencial y se extrajo la pared celular. Los extractos de pared se hidrolizaron con H2SO4 al 72% y las muestras fueron analizadas por cromatografía HPLC. Se realizó una prueba de resistencia al rompimiento celular con una β(1,3-glucanasa, y las células cultivadas a diferentes fuentes carbono y pH. Los resultados del análisis por HPLC, mostraron que la composición de los polisacáridos en la pared celular, varía considerablemente con las modificaciones del medio de cultivo. Se observó que las levaduras cultivadas en sacarosa tienen mayor porcentaje de pared celular (25% y mayor cantidad de glucanos (115µg/mg peso seco y mananos (131µg/mg peso seco, que aquellas levaduras cultivadas en etanol (13% en peso seco. Las levaduras cultivadas a pH 5 presentaron 19% de pared celular en peso seco, mientras que a pH 6 el porcentaje fue menor (14%. El análisis de resistencia al rompimiento celular, mostró que las células cultivadas en etanol y galactosa fueron resistentes al rompimiento enzimático. Se comparó este resultado con el contenido de polisacáridos en la pared celular y concluimos que la resistencia de la célula al rompimiento, no está ligada con la cantidad de β-glucanos contenidos en la pared celular, sino que va a depender del número de enlaces β(1,3 y β(1,6-glucanos, los cuales juegan un rol importante durante el ensamblaje de la pared

  16. Proteomics of Saccharomyces cerevisiae Organelles

    NARCIS (Netherlands)

    Wiederhold, Elena; Veenhoff, Liesbeth M.; Poolman, Bert; Slotboom, Dirk Jan

    2010-01-01

    Knowledge of the subcellular localization of proteins is indispensable to understand their physiological roles. In the past decade, 18 studies have been performed to analyze the protein content of isolated organelles from Saccharomyces cerevisiae. Here, we integrate the data sets and compare them wi

  17. Investigating ecological speciation in non-model organisms

    DEFF Research Database (Denmark)

    Foote, Andrew David

    2012-01-01

    Background: Studies of ecological speciation tend to focus on a few model biological systems. In contrast, few studies on non-model organisms have been able to infer ecological speciation as the underlying mechanism of evolutionary divergence. Questions: What are the pitfalls in studying ecological...... speciation in non-model organisms that lead to this bias? What alternative approaches might redress the balance? Organism: Genetically differentiated types of the killer whale (Orcinus orca) exhibiting differences in prey preference, habitat use, morphology, and behaviour. Methods: Review of the literature...... variation underlie reproductive isolation between sympatric killer whale types. Perhaps ecological speciation has occurred, but it is hard to prove. We will probably face this outcome whenever we wish to address non-model organisms – species in which it is not easy to apply experimental approaches...

  18. Self-organizing map models of language acquisition

    Science.gov (United States)

    Li, Ping; Zhao, Xiaowei

    2013-01-01

    Connectionist models have had a profound impact on theories of language. While most early models were inspired by the classic parallel distributed processing architecture, recent models of language have explored various other types of models, including self-organizing models for language acquisition. In this paper, we aim at providing a review of the latter type of models, and highlight a number of simulation experiments that we have conducted based on these models. We show that self-organizing connectionist models can provide significant insights into long-standing debates in both monolingual and bilingual language development. We suggest future directions in which these models can be extended, to better connect with behavioral and neural data, and to make clear predictions in testing relevant psycholinguistic theories. PMID:24312061

  19. Self-organizing map models of language acquisition.

    Science.gov (United States)

    Li, Ping; Zhao, Xiaowei

    2013-11-19

    Connectionist models have had a profound impact on theories of language. While most early models were inspired by the classic parallel distributed processing architecture, recent models of language have explored various other types of models, including self-organizing models for language acquisition. In this paper, we aim at providing a review of the latter type of models, and highlight a number of simulation experiments that we have conducted based on these models. We show that self-organizing connectionist models can provide significant insights into long-standing debates in both monolingual and bilingual language development. We suggest future directions in which these models can be extended, to better connect with behavioral and neural data, and to make clear predictions in testing relevant psycholinguistic theories.

  20. Labour Quality Model for Organic Farming Food Chains

    OpenAIRE

    Gassner, B.; Freyer, B.; Leitner, H.

    2008-01-01

    The debate on labour quality in science is controversial as well as in the organic agriculture community. Therefore, we reviewed literature on different labour quality models and definitions, and had key informant interviews on labour quality issues with stakeholders in a regional oriented organic agriculture bread food chain. We developed a labour quality model with nine quality categories and discussed linkages to labour satisfaction, ethical values and IFOAM principles.

  1. Kineic Modelling of Degradation of Organic Compounds in Soils

    Institute of Scientific and Technical Information of China (English)

    WANGZONGSHENG; ZHANGSHUIMING; 等

    1997-01-01

    A set of equations in suggested to describe the kinetics of degradation of organic ompounds applied to soils ad the kinetics of growth of the inolved microorganisms:-dx/dt=jx+kxm dm/dt=-fm+gxm where x is the concentration of organic compound at time t,m is the numer of microorganisms capable of degrading the organic compound at time t,while j,k,f and g are positive constants,This model can satisfactorily be used to explain the degradation curve of organic compounds and the growth curve of the involved microorganisms.

  2. BUSINESS PROCESS MODELLING FOR PROJECTS COSTS MANAGEMENT IN AN ORGANIZATION

    Directory of Open Access Journals (Sweden)

    PĂTRAŞCU AURELIA

    2014-05-01

    Full Text Available Using Information Technologies in organizations represents an evident progress for company, money economy, time economy and generates value for the organization. In this paper the author proposes to model the business processes for an organization that manages projects costs, because modelling is an important part of any software development process. Using software for projects costs management is essential because it allows the management of all operations according to the established parameters, the management of the projects groups, as well as the management of the projects and subprojects, at different complexity levels.

  3. Mathematical model for cyclodextrin alteration of bioavailability of organic pollutants.

    Science.gov (United States)

    Liu, Huihui; Cai, Xiyun; Chen, Jingwen

    2013-06-04

    While many cyclodextrin-based applications have been developed to assess or enhance bioavailability of organic pollutants, the choice of cyclodextrin (CD) is largely empirical, with little consideration of pollutant diversity and environmental matrix effects. This study aimed at developing a mathematical model for quantifying CD alteration of bioavailability of organic pollutants. Cyclodextrin appears to have multiple effects, together contributing to its bioavailability-enhancing property. Cyclodextrin is adsorbed onto the adsorbent matrix to different extents. The adsorbed CD is capable of sequestrating organic pollutants, highlighting the role of a pseudophase similar to solid environmental matrix. Aqueous CD can reduce adsorption of organic pollutants via inclusion complexation. The two effects cancel each other to a certain degree, which determines the levels of organic pollutants dissolved (comprising freely dissolved and CD-included forms). Additionally, the CD-included form is nearly identical in biological activity to the free form. A mathematical model of one variable (i.e., CD concentration) was derived to quantify effects of CD on the bioavailability of organic pollutants. Model analysis indicates that alteration of bioavailability of organic pollutants by CD depends on both CD (type and level) and environmental matrix. The selection of CD type and amendment level for a given application may be predicted by the model.

  4. A survey of financial planning models for health care organizations.

    Science.gov (United States)

    Coleman, J R; Kaminsky, F C; McGee, F

    1978-01-01

    This paper describes "what if?" financial planning models developed for health care administrators and financial managers to study and evaluate the economic impact of changes in a health care organization's charge structure, operating policies, reimbursement plans, and services and resources. Models for inpatient and outpatient care systems are presented. The models are described in terms of input, output, and application. An assessment of the state of the art of financial planning and prospects for the future of what if?models are given.

  5. Drosophila melanogaster as a model organism to study nanotoxicity.

    Science.gov (United States)

    Ong, Cynthia; Yung, Lin-Yue Lanry; Cai, Yu; Bay, Boon-Huat; Baeg, Gyeong-Hun

    2015-05-01

    Drosophila melanogaster has been used as an in vivo model organism for the study of genetics and development since 100 years ago. Recently, the fruit fly Drosophila was also developed as an in vivo model organism for toxicology studies, in particular, the field of nanotoxicity. The incorporation of nanomaterials into consumer and biomedical products is a cause for concern as nanomaterials are often associated with toxicity in many in vitro studies. In vivo animal studies of the toxicity of nanomaterials with rodents and other mammals are, however, limited due to high operational cost and ethical objections. Hence, Drosophila, a genetically tractable organism with distinct developmental stages and short life cycle, serves as an ideal organism to study nanomaterial-mediated toxicity. This review discusses the basic biology of Drosophila, the toxicity of nanomaterials, as well as how the Drosophila model can be used to study the toxicity of various types of nanomaterials.

  6. Clinical Saccharomyces cerevisiae isolates cannot cross the epithelial barrier in vitro.

    Science.gov (United States)

    Pérez-Torrado, Roberto; Llopis, Silvia; Jespersen, Lene; Fernández-Espinar, Teresa; Querol, Amparo

    2012-06-15

    Saccharomyces cerevisiae is generally considered to be a safe organism and is essential to produce many different kinds of foods as well as being widely used as a dietary supplement. However, several isolates, which are genetically related to brewing and baking yeasts, have shown virulent traits, being able to produce human infections in immunodeficient patients. Previously it has been shown that the administration of S. cerevisiae clinical isolates can lead to systemic infections, reaching several organs in murine systems. In this work, we studied S. cerevisiae clinical isolates in an in vitro intestinal epithelial barrier model, comparing their behaviour with that of several strains of the related pathogens Candida glabrata and Candida albicans. The results showed that, in contrast to C. glabrata and C. albicans, S. cerevisiae was not able to cross the intestinal barrier. We concluded that S. cerevisiae can only perform opportunistic or passive crossings when epithelial barrier integrity is previously compromised.

  7. Systems Biology of Saccharomyces cerevisiae Physiology and its DNA Damage Response

    DEFF Research Database (Denmark)

    Fazio, Alessandro

    set of growth dependent genes by using a multi-factorial experimental design. Moreover, new insights into the metabolic response and transcriptional regulation of these genes have been provided by using systems biology tools (Chapter 3). One of the prerequisite of systems biology should......The yeast Saccharomyces cerevisiae is a model organism in biology, being widely used in fundamental research, the first eukaryotic organism to be fully sequenced and the platform for the development of many genomics techniques. Therefore, it is not surprising that S. cerevisiae has also been widely...... used in the field of systems biology during the last decade. This thesis investigates S. cerevisiae growth physiology and DNA damage response by using a systems biology approach. Elucidation of the relationship between growth rate and gene expression is important to understand the mechanisms regulating...

  8. Cellular Memory of Acquired Stress Resistance in Saccharomyces cerevisiae

    OpenAIRE

    Guan, Qiaoning; Haroon, Suraiya; Bravo, Diego González; Will, Jessica L.; Gasch, Audrey P.

    2012-01-01

    Cellular memory of past experiences has been observed in several organisms and across a variety of experiences, including bacteria “remembering” prior nutritional status and amoeba “learning” to anticipate future environmental conditions. Here, we show that Saccharomyces cerevisiae maintains a multifaceted memory of prior stress exposure. We previously demonstrated that yeast cells exposed to a mild dose of salt acquire subsequent tolerance to severe doses of H2O2. We set out to characterize ...

  9. Viruses and prions of Saccharomyces cerevisiae.

    Science.gov (United States)

    Wickner, Reed B; Fujimura, Tsutomu; Esteban, Rosa

    2013-01-01

    Saccharomyces cerevisiae has been a key experimental organism for the study of infectious diseases, including dsRNA viruses, ssRNA viruses, and prions. Studies of the mechanisms of virus and prion replication, virus structure, and structure of the amyloid filaments that are the basis of yeast prions have been at the forefront of such studies in these classes of infectious entities. Yeast has been particularly useful in defining the interactions of the infectious elements with cellular components: chromosomally encoded proteins necessary for blocking the propagation of the viruses and prions, and proteins involved in the expression of viral components. Here, we emphasize the L-A dsRNA virus and its killer-toxin-encoding satellites, the 20S and 23S ssRNA naked viruses, and the several infectious proteins (prions) of yeast.

  10. Phytoremediation and its models for organic contaminated soils

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Soil pollution has been attracting considerable public attentions over the last decades. Sorts of traditional physiochemical methods have been used to remove the organic pollutants from soils. However, the enormous costs and low efficiencies associated with these remediation technologies limit their availabilities. Phytoremediation is an emerging technology that uses plants to cleanup pollutants in soils. As overwhelmingly positive results have been shown, phytoremediation is a most economical and effective remediation technique for organic contaminated soils. In this paper phytoremediation and its models for organic contaminated soils is overviewed. The mechanisms of phytoremediation mainly include the direct plant uptake of organic pollutants, degradation by plant-derived degradative enzymes, and stimulated biodegradation in plant rhizosphere. Phytoremediation efficiency is tightly related to physicochemical properties of organic pollutants, environmental characteristics, and plant types. It is no doubt that soil amendments such as surfactants change the solubilities and availabilities of organic pollutants in soils. However, little information is available about effects of soil amendments on phytoremediation efficiencies. Phytoremediation models have been developed to simulate and predict the environmental behavior of organic pollutants, and progress of models is illustrated. In many ways phytoremediation is still in its initial stage, and recommendations for the future research on phytoremediation are presented.

  11. Modeling secondary organic aerosol formation through cloud processing of organic compounds

    Directory of Open Access Journals (Sweden)

    J. Chen

    2007-06-01

    Full Text Available Interest in the potential formation of secondary organic aerosol (SOA through reactions of organic compounds in condensed aqueous phases is growing. In this study, the potential formation of SOA from irreversible aqueous-phase reactions of organic species in clouds was investigated. A new proposed aqueous-phase chemistry mechanism (AqChem is coupled with the existing gas-phase Caltech Atmospheric Chemistry Mechanism (CACM and the Model to Predict the Multiphase Partitioning of Organics (MPMPO that simulate SOA formation. AqChem treats irreversible organic reactions that lead mainly to the formation of carboxylic acids, which are usually less volatile than the corresponding aldehydic compounds. Zero-dimensional model simulations were performed for tropospheric conditions with clouds present for three consecutive hours per day. Zero-dimensional model simulations show that 48-h averaged SOA formation are increased by 27% for a rural scenario with strong monoterpene emissions and 7% for an urban scenario with strong emissions of aromatic compounds, respectively, when irreversible organic reactions in clouds are considered. AqChem was also incorporated into the Community Multiscale Air Quality Model (CMAQ version 4.4 with CACM/MPMPO and applied to a previously studied photochemical episode (3–4 August 2004 focusing on the eastern United States. The CMAQ study indicates that the maximum contribution of SOA formation from irreversible reactions of organics in clouds is 0.28 μg m−3 for 24-h average concentrations and 0.60 μg m−3 for one-hour average concentrations at certain locations. On average, domain-wide surface SOA predictions for the episode are increased by 8.6% when irreversible, in-cloud processing of organics is considered.

  12. A Workforce Design Model: Providing Energy to Organizations in Transition

    Science.gov (United States)

    Halm, Barry J.

    2011-01-01

    The purpose of this qualitative study was to examine the change in performance realized by a professional services organization, which resulted in the Life Giving Workforce Design (LGWD) model through a grounded theory research design. This study produced a workforce design model characterized as an organizational blueprint that provides virtuous…

  13. Simple model of self-organized biological evolution

    Science.gov (United States)

    de Boer, Jan; Derrida, Bernard; Flyvbjerg, Henrik; Jackson, Andrew D.; Wettig, Tilo

    1994-08-01

    We give an exact solution of a recently proposed self-organized critical model of biological evolution. We show that the model has a power law distribution of durations of coevolutionary ``avalanches'' with a mean field exponent 3/2. We also calculate analytically the finite size effects which cut off this power law at times of the order of the system size.

  14. Modeling organic compounds in the estuarine and coastal environment

    NARCIS (Netherlands)

    R.W.P.M. Laane; D. van de Meent; P. de Voogt; J. Parsons; J. Hendriks; J. van Gils

    2011-01-01

    This chapter describes the historical development and present applications of water-quality models for organic chemical compounds (e.g., polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs)). Various types of water-quality models are described, varying in the amount of compar

  15. Fruit tree model for uptake of organic compounds from soil

    DEFF Research Database (Denmark)

    Trapp, Stefan; Rasmussen, D.; Samsoe-Petersen, L.

    2003-01-01

    soils, regressions or models are in use, which were not intended to be used for tree fruits. A simple model for uptake of neutral organic contaminants into fruits is developed. It considers xylem and phloem transport to fruits through the stem. The mass balance is solved for the steady...

  16. Towards an Intelligent Project Based Organization Business Model

    Directory of Open Access Journals (Sweden)

    Alami Marrouni Oussama

    2013-01-01

    Full Text Available Global economy is undergoing a recession phase that had made competition tougher and imposed new business framework. Businesses have to shift from the classical management approaches to an Intelligent Project Based Organization (IPBO model that provides flexibility and agility. IPBO model is intended to reinforce the proven advantages of Project Based Organization (PBO by the use of suitable Enterprise Intelligence (EI Systems. The goal of this paper is to propose an IPBO model that combines benefits of PBO and EI and helps overcoming their pitfalls

  17. Xanthusbase: adapting wikipedia principles to a model organism database.

    Science.gov (United States)

    Arshinoff, Bradley I; Suen, Garret; Just, Eric M; Merchant, Sohel M; Kibbe, Warren A; Chisholm, Rex L; Welch, Roy D

    2007-01-01

    xanthusBase (http://www.xanthusbase.org) is the official model organism database (MOD) for the social bacterium Myxococcus xanthus. In many respects, M.xanthus represents the pioneer model organism (MO) for studying the genetic, biochemical, and mechanistic basis of prokaryotic multicellularity, a topic that has garnered considerable attention due to the significance of biofilms in both basic and applied microbiology research. To facilitate its utility, the design of xanthusBase incorporates open-source software, leveraging the cumulative experience made available through the Generic Model Organism Database (GMOD) project, MediaWiki (http://www.mediawiki.org), and dictyBase (http://www.dictybase.org), to create a MOD that is both highly useful and easily navigable. In addition, we have incorporated a unique Wikipedia-style curation model which exploits the internet's inherent interactivity, thus enabling M.xanthus and other myxobacterial researchers to contribute directly toward the ongoing genome annotation.

  18. An Ising model for metal-organic frameworks

    Science.gov (United States)

    Höft, Nicolas; Horbach, Jürgen; Martín-Mayor, Victor; Seoane, Beatriz

    2017-08-01

    We present a three-dimensional Ising model where lines of equal spins are frozen such that they form an ordered framework structure. The frame spins impose an external field on the rest of the spins (active spins). We demonstrate that this "porous Ising model" can be seen as a minimal model for condensation transitions of gas molecules in metal-organic frameworks. Using Monte Carlo simulation techniques, we compare the phase behavior of a porous Ising model with that of a particle-based model for the condensation of methane (CH4) in the isoreticular metal-organic framework IRMOF-16. For both models, we find a line of first-order phase transitions that end in a critical point. We show that the critical behavior in both cases belongs to the 3D Ising universality class, in contrast to other phase transitions in confinement such as capillary condensation.

  19. The expanding epigenetic landscape of non-model organisms.

    Science.gov (United States)

    Bonasio, Roberto

    2015-01-01

    Epigenetics studies the emergence of different phenotypes from a single genotype. Although these processes are essential to cellular differentiation and transcriptional memory, they are also widely used in all branches of the tree of life by organisms that require plastic but stable adaptation to their physical and social environment. Because of the inherent flexibility of epigenetic regulation, a variety of biological phenomena can be traced back to evolutionary adaptations of few conserved molecular pathways that converge on chromatin. For these reasons chromatin biology and epigenetic research have a rich history of chasing discoveries in a variety of model organisms, including yeast, flies, plants and humans. Many more fascinating examples of epigenetic plasticity lie outside the realm of model organisms and have so far been only sporadically investigated at a molecular level; however, recent progress on sequencing technology and genome editing tools have begun to blur the lines between model and non-model organisms, opening numerous new avenues for investigation. Here, I review examples of epigenetic phenomena in non-model organisms that have emerged as potential experimental systems, including social insects, fish and flatworms, and are becoming accessible to molecular approaches.

  20. Regional Persistent Organic Pollutants' Environmental Impact Assessment and Control Model

    Directory of Open Access Journals (Sweden)

    Jurgis Staniskis

    2008-10-01

    Full Text Available The sources of formation, environmental distribution and fate of persistent organic pollutants (POPs are increasingly seen as topics to be addressed and solved at the global scale. Therefore, there are already two international agreements concerning persistent organic pollutants: the Protocol of 1998 to the 1979 Convention on the Long-Range Transboundary Air Pollution on Persistent Organic Pollutants (Aarhus Protocol; and the Stockholm Convention on Persistent Organic Pollutants. For the assessment of environmental pollution of POPs, for the risk assessment, for the evaluation of new pollutants as potential candidates to be included in the POPs list of the Stokholmo or/and Aarhus Protocol, a set of different models are developed or under development. Multimedia models help describe and understand environmental processes leading to global contamination through POPs and actual risk to the environment and human health. However, there is a lack of the tools based on a systematic and integrated approach to POPs management difficulties in the region.

  1. Quantitative model studies for interfaces in organic electronic devices

    Science.gov (United States)

    Gottfried, J. Michael

    2016-11-01

    In organic light-emitting diodes and similar devices, organic semiconductors are typically contacted by metal electrodes. Because the resulting metal/organic interfaces have a large impact on the performance of these devices, their quantitative understanding is indispensable for the further rational development of organic electronics. A study by Kröger et al (2016 New J. Phys. 18 113022) of an important single-crystal based model interface provides detailed insight into its geometric and electronic structure and delivers valuable benchmark data for computational studies. In view of the differences between typical surface-science model systems and real devices, a ‘materials gap’ is identified that needs to be addressed by future research to make the knowledge obtained from fundamental studies even more beneficial for real-world applications.

  2. MODELLING CONSUMERS' DEMAND FOR ORGANIC FOOD PRODUCTS: THE SWEDISH EXPERIENCE

    Directory of Open Access Journals (Sweden)

    Manuchehr Irandoust

    2016-07-01

    Full Text Available This paper attempts to examine a few factors characterizing consumer preferences and behavior towards organic food products in the south of Sweden using a proportional odds model which captures the natural ordering of dependent variables and any inherent nonlinearities. The findings show that consumer's choice for organic food depends on perceived benefits of organic food (environment, health, and quality and consumer's perception and attitudes towards labelling system, message framing, and local origin. In addition, high willingness to pay and income level will increase the probability to buy organic food, while the cultural differences and socio-demographic characteristics have no effect on consumer behaviour and attitudes towards organic food products. Policy implications are offered.

  3. Glucose repression in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Kayikci, Omur; Nielsen, Jens

    2015-01-01

    Glucose is the primary source of energy for the budding yeast Saccharomyces cerevisiae. Although yeast cells can utilize a wide range of carbon sources, presence of glucose suppresses molecular activities involved in the use of alternate carbon sources as well as it represses respiration and gluc......Glucose is the primary source of energy for the budding yeast Saccharomyces cerevisiae. Although yeast cells can utilize a wide range of carbon sources, presence of glucose suppresses molecular activities involved in the use of alternate carbon sources as well as it represses respiration...... and gluconeogenesis. This dominant effect of glucose on yeast carbon metabolism is coordinated by several signaling and metabolic interactions that mainly regulate transcriptional activity but are also effective at post-transcriptional and post-translational levels. This review describes effects of glucose repression...

  4. Lotka-Volterra competition models for sessile organisms.

    Science.gov (United States)

    Spencer, Matthew; Tanner, Jason E

    2008-04-01

    Markov models are widely used to describe the dynamics of communities of sessile organisms, because they are easily fitted to field data and provide a rich set of analytical tools. In typical ecological applications, at any point in time, each point in space is in one of a finite set of states (e.g., species, empty space). The models aim to describe the probabilities of transitions between states. In most Markov models for communities, these transition probabilities are assumed to be independent of state abundances. This assumption is often suspected to be false and is rarely justified explicitly. Here, we start with simple assumptions about the interactions among sessile organisms and derive a model in which transition probabilities depend on the abundance of destination states. This model is formulated in continuous time and is equivalent to a Lotka-Volterra competition model. We fit this model and a variety of alternatives in which transition probabilities do not depend on state abundances to a long-term coral reef data set. The Lotka-Volterra model describes the data much better than all models we consider other than a saturated model (a model with a separate parameter for each transition at each time interval, which by definition fits the data perfectly). Our approach provides a basis for further development of stochastic models of sessile communities, and many of the methods we use are relevant to other types of community. We discuss possible extensions to spatially explicit models.

  5. Modeling nanostructure-enhanced light trapping in organic solar cells

    DEFF Research Database (Denmark)

    Adam, Jost

    A promising approach for improving the power conversion efficiencies of organic solar cells (OSCs) is by incorporating nanostructures in their thin film architecture to improve the light absorption in the device’s active polymer layers. Here, we present a modelling framework for the prediction....... Diffraction by fractal metallic supergratings. Optics Express, 15(24), 15628–15636 (2007) [3] Goszczak, A. J. et al. Nanoscale Aluminum dimples for light trapping in organic thin films (submitted)...

  6. Modelling the formation of organic particles in the atmosphere

    Science.gov (United States)

    Anttila, T.; Kerminen, V.-M.; Kulmala, M.; Laaksonen, A.; O'Dowd, C.

    2003-12-01

    A modelling study investigating the formation of organic particles from inorganic, thermodynamically stable clusters was carried out. A recently-developed theory, the so-called nano-Köhler theory, which describes a thermodynamic equilibrium between a nanometer-size cluster, water and water-soluble organic compound, was implemented in a dynamical model along with a treatment of the appropriate aerosol and gas-phase processes. The obtained results suggest that both gaseous sulphuric acid and organic vapours contribute to organic particle formation. The initial growth of freshly-nucleated clusters having a diameter around 1 nm is driven by condensation of gaseous sulphuric acid and by a lesser extent cluster self-coagulation. After the clusters have reached sizes of around 2 nm in diameter, low-volatile organic vapours start to condense spontaneously into the clusters, thereby accelerating their growth to detectable sizes. A shortage of gaseous sulphuric acid or organic vapours limit, or suppress altogether, the particle formation, since freshly-nucleated clusters are rapidly coagulated away by pre-existing particles. The obtained modelling results were applied to explaining the observed seasonal cycle in the number of aerosol formation events in a continental forest site.

  7. Precisely parameterized experimental and computational models of tissue organization.

    Science.gov (United States)

    Molitoris, Jared M; Paliwal, Saurabh; Sekar, Rajesh B; Blake, Robert; Park, JinSeok; Trayanova, Natalia A; Tung, Leslie; Levchenko, Andre

    2016-02-01

    Patterns of cellular organization in diverse tissues frequently display a complex geometry and topology tightly related to the tissue function. Progressive disorganization of tissue morphology can lead to pathologic remodeling, necessitating the development of experimental and theoretical methods of analysis of the tolerance of normal tissue function to structural alterations. A systematic way to investigate the relationship of diverse cell organization to tissue function is to engineer two-dimensional cell monolayers replicating key aspects of the in vivo tissue architecture. However, it is still not clear how this can be accomplished on a tissue level scale in a parameterized fashion, allowing for a mathematically precise definition of the model tissue organization and properties down to a cellular scale with a parameter dependent gradual change in model tissue organization. Here, we describe and use a method of designing precisely parameterized, geometrically complex patterns that are then used to control cell alignment and communication of model tissues. We demonstrate direct application of this method to guiding the growth of cardiac cell cultures and developing mathematical models of cell function that correspond to the underlying experimental patterns. Several anisotropic patterned cultures spanning a broad range of multicellular organization, mimicking the cardiac tissue organization of different regions of the heart, were found to be similar to each other and to isotropic cell monolayers in terms of local cell-cell interactions, reflected in similar confluency, morphology and connexin-43 expression. However, in agreement with the model predictions, different anisotropic patterns of cell organization, paralleling in vivo alterations of cardiac tissue morphology, resulted in variable and novel functional responses with important implications for the initiation and maintenance of cardiac arrhythmias. We conclude that variations of tissue geometry and topology

  8. The postmitotic Saccharomyces cerevisiae after spaceflight showed higher viability

    Science.gov (United States)

    Yi, Zong-Chun; Li, Xiao-Fei; Wang, Yan; Wang, Jie; Sun, Yan; Zhuang, Feng-Yuan

    2011-06-01

    The budding yeast Saccharomyces cerevisiae has been proposed as an ideal model organism for clarifying the biological effects caused by spaceflight conditions. The postmitotic S. cerevisiae cells onboard Practice eight recoverable satellite were subjected to spaceflight for 15 days. After recovery, the viability, the glycogen content, the activities of carbohydrate metabolism enzymes, the DNA content and the lipid peroxidation level in yeast cells were analyzed. The viability of the postmitotic yeast cells after spaceflight showed a three-fold increase as compared with that of the ground control cells. Compared to the ground control cells, the lipid peroxidation level in the spaceflight yeast cells markedly decreased. The spaceflight yeast cells also showed an increase in G2/M cell population and a decrease in Sub-G1 cell population. The glycogen content and the activities of hexokinase and succinate dehydrogenase significantly decreased in the yeast cells after spaceflight. In contrast, the activity of malate dehydrogenase showed an obvious increase after spaceflight. These results suggested that microgravity or spaceflight could promote the survival of postmitotic S. cerevisiae cells through regulating carbohydrate metabolism, ROS level and cell cycle progression.

  9. Role of social wasps in Saccharomyces cerevisiae ecology and evolution.

    Science.gov (United States)

    Stefanini, Irene; Dapporto, Leonardo; Legras, Jean-Luc; Calabretta, Antonio; Di Paola, Monica; De Filippo, Carlotta; Viola, Roberto; Capretti, Paolo; Polsinelli, Mario; Turillazzi, Stefano; Cavalieri, Duccio

    2012-08-14

    Saccharomyces cerevisiae is one of the most important model organisms and has been a valuable asset to human civilization. However, despite its extensive use in the last 9,000 y, the existence of a seasonal cycle outside human-made environments has not yet been described. We demonstrate the role of social wasps as vector and natural reservoir of S. cerevisiae during all seasons. We provide experimental evidence that queens of social wasps overwintering as adults (Vespa crabro and Polistes spp.) can harbor yeast cells from autumn to spring and transmit them to their progeny. This result is mirrored by field surveys of the genetic variability of natural strains of yeast. Microsatellites and sequences of a selected set of loci able to recapitulate the yeast strain's evolutionary history were used to compare 17 environmental wasp isolates with a collection of strains from grapes from the same region and more than 230 strains representing worldwide yeast variation. The wasp isolates fall into subclusters representing the overall ecological and industrial yeast diversity of their geographic origin. Our findings indicate that wasps are a key environmental niche for the evolution of natural S. cerevisiae populations, the dispersion of yeast cells in the environment, and the maintenance of their diversity. The close relatedness of several wasp isolates with grape and wine isolates reflects the crucial role of human activities on yeast population structure, through clonal expansion and selection of specific strains during the biotransformation of fermented foods, followed by dispersal mediated by insects and other animals.

  10. Modeling of Spatially Correlated Energetic Disorder in Organic Semiconductors.

    Science.gov (United States)

    Kordt, Pascal; Andrienko, Denis

    2016-01-12

    Mesoscale modeling of organic semiconductors relies on solving an appropriately parametrized master equation. Essential ingredients of the parametrization are site energies (driving forces), which enter the charge transfer rate between pairs of neighboring molecules. Site energies are often Gaussian-distributed and are spatially correlated. Here, we propose an algorithm that generates these energies with a given Gaussian distribution and spatial correlation function. The method is tested on an amorphous organic semiconductor, DPBIC, illustrating that the accurate description of correlations is essential for the quantitative modeling of charge transport in amorphous mesophases.

  11. Biobanking of a Marine Invertebrate Model Organism: The Sea Urchin

    Directory of Open Access Journals (Sweden)

    Estefania Paredes

    2016-01-01

    Full Text Available The sea urchin has long been used as an invertebrate model organism in developmental biology, membrane transport and sperm oocyte interactions, and for the assessment of marine pollution. This review explores the effects of cryopreservation and biobanking in the biology and development of sea urchins, all the way from germaplasm through to juveniles. This review will provide an integral view of the process and all that is known so far about the biology of cryopreserved sea urchins, as well as provide an insight on the applications of the biobanking of these model organisms.

  12. Workshop meeting report Organs-on-Chips: human disease models.

    Science.gov (United States)

    van de Stolpe, Anja; den Toonder, Jaap

    2013-09-21

    The concept of "Organs-on-Chips" has recently evolved and has been described as 3D (mini-) organs or tissues consisting of multiple and different cell types interacting with each other under closely controlled conditions, grown in a microfluidic chip, and mimicking the complex structures and cellular interactions in and between different cell types and organs in vivo, enabling the real time monitoring of cellular processes. In combination with the emerging iPSC (induced pluripotent stem cell) field this development offers unprecedented opportunities to develop human in vitro models for healthy and diseased organ tissues, enabling the investigation of fundamental mechanisms in disease development, drug toxicity screening, drug target discovery and drug development, and the replacement of animal testing. Capturing the genetic background of the iPSC donor in the organ or disease model carries the promise to move towards "in vitro clinical trials", reducing costs for drug development and furthering the concept of personalized medicine and companion diagnostics. During the Lorentz workshop (Leiden, September 2012) an international multidisciplinary group of experts discussed the current state of the art, available and emerging technologies, applications and how to proceed in the field. Organ-on-a-chip platform technologies are expected to revolutionize cell biology in general and drug development in particular.

  13. Stochastic models for plant microtubule self-organization and structure.

    Science.gov (United States)

    Eren, Ezgi C; Dixit, Ram; Gautam, Natarajan

    2015-12-01

    One of the key enablers of shape and growth in plant cells is the cortical microtubule (CMT) system, which is a polymer array that forms an appropriately-structured scaffolding in each cell. Plant biologists have shown that stochastic dynamics and simple rules of interactions between CMTs can lead to a coaligned CMT array structure. However, the mechanisms and conditions that cause CMT arrays to become organized are not well understood. It is prohibitively time-consuming to use actual plants to study the effect of various genetic mutations and environmental conditions on CMT self-organization. In fact, even computer simulations with multiple replications are not fast enough due to the spatio-temporal complexity of the system. To redress this shortcoming, we develop analytical models and methods for expeditiously computing CMT system metrics that are related to self-organization and array structure. In particular, we formulate a mean-field model to derive sufficient conditions for the organization to occur. We show that growth-prone dynamics itself is sufficient to lead to organization in presence of interactions in the system. In addition, for such systems, we develop predictive methods for estimation of system metrics such as expected average length and number of CMTs over time, using a stochastic fluid-flow model, transient analysis, and approximation algorithms tailored to our problem. We illustrate the effectiveness of our approach through numerical test instances and discuss biological insights.

  14. Implementing Marine Organic Aerosols Into the GEOS-Chem Model

    Science.gov (United States)

    Johnson, Matthew S.

    2015-01-01

    Marine-sourced organic aerosols (MOA) have been shown to play an important role in tropospheric chemistry by impacting surface mass, cloud condensation nuclei, and ice nuclei concentrations over remote marine and coastal regions. In this work, an online marine primary organic aerosol emission parameterization, designed to be used for both global and regional models, was implemented into the GEOS-Chem model. The implemented emission scheme improved the large under-prediction of organic aerosol concentrations in clean marine regions (normalized mean bias decreases from -79% when using the default settings to -12% when marine organic aerosols are added). Model predictions were also in good agreement (correlation coefficient of 0.62 and normalized mean bias of -36%) with hourly surface concentrations of MOA observed during the summertime at an inland site near Paris, France. Our study shows that MOA have weaker coastal-to-inland concentration gradients than sea-salt aerosols, leading to several inland European cities having > 10% of their surface submicron organic aerosol mass concentration with a marine source. The addition of MOA tracers to GEOS-Chem enabled us to identify the regions with large contributions of freshly-emitted or aged aerosol having distinct physicochemical properties, potentially indicating optimal locations for future field studies.

  15. Self-organized Criticality Model for Ocean Internal Waves

    Institute of Scientific and Technical Information of China (English)

    WANG Gang; LIN Min; QIAO Fang-Li; HOU Yi-Jun

    2009-01-01

    In this paper, we present a simple spring-block model for ocean internal waves based on the self-organized criticality (SOC). The oscillations of the water blocks in the model display power-law behavior with an exponent of-2 in the frequency domain, which is similar to the current and sea water temperature spectra in the actual ocean and the universal Garrett and Munk deep ocean internal wave model [Geophysical Fluid Dynamics 2 (1972) 225; J. Geophys. Res. 80 (1975) 291]. The influence of the ratio of the driving force to the spring coefficient to SOC behaviors in the model is also discussed.

  16. Financial market model based on self-organized percolation

    Institute of Scientific and Technical Information of China (English)

    YANG Chunxia; WANG Jie; ZHOU Tao; LIU Jun; XU Min; ZHOU Peiling; WANG Binghong

    2005-01-01

    Starting with the self-organized evolution of the trader group's structure, a parsimonious percolation model for stock market is established, which can be considered as a kind of betterment of the Cont-Bouchaud model. The return distribution of the present model obeys Lévy form in the center and displays fat-tail property, in accord with the stylized facts observed in real-life financial time series. Furthermore, this model reveals the power-law relationship between the peak value of the probability distribution and the time scales, in agreement with the empirical studies on the Hang Seng Index.

  17. Green Algae as Model Organisms for Biological Fluid Dynamics.

    Science.gov (United States)

    Goldstein, Raymond E

    2015-01-01

    In the past decade the volvocine green algae, spanning from the unicellular Chlamydomonas to multicellular Volvox, have emerged as model organisms for a number of problems in biological fluid dynamics. These include flagellar propulsion, nutrient uptake by swimming organisms, hydrodynamic interactions mediated by walls, collective dynamics and transport within suspensions of microswimmers, the mechanism of phototaxis, and the stochastic dynamics of flagellar synchronization. Green algae are well suited to the study of such problems because of their range of sizes (from 10 μm to several millimetres), their geometric regularity, the ease with which they can be cultured and the availability of many mutants that allow for connections between molecular details and organism-level behavior. This review summarizes these recent developments and highlights promising future directions in the study of biological fluid dynamics, especially in the context of evolutionary biology, that can take advantage of these remarkable organisms.

  18. There Is No Simple Model of the Plasma Membrane Organization

    Science.gov (United States)

    Bernardino de la Serna, Jorge; Schütz, Gerhard J.; Eggeling, Christian; Cebecauer, Marek

    2016-01-01

    Ever since technologies enabled the characterization of eukaryotic plasma membranes, heterogeneities in the distributions of its constituents were observed. Over the years this led to the proposal of various models describing the plasma membrane organization such as lipid shells, picket-and-fences, lipid rafts, or protein islands, as addressed in numerous publications and reviews. Instead of emphasizing on one model we in this review give a brief overview over current models and highlight how current experimental work in one or the other way do not support the existence of a single overarching model. Instead, we highlight the vast variety of membrane properties and components, their influences and impacts. We believe that highlighting such controversial discoveries will stimulate unbiased research on plasma membrane organization and functionality, leading to a better understanding of this essential cellular structure. PMID:27747212

  19. Review of existing terrestrial bioaccumulation models and terrestrial bioaccumulation modeling needs for organic chemicals

    Science.gov (United States)

    Protocols for terrestrial bioaccumulation assessments are far less-developed than for aquatic systems. This manuscript reviews modeling approaches that can be used to assess the terrestrial bioaccumulation potential of commercial organic chemicals. Models exist for plant, inver...

  20. A dynamical phyllotaxis model to determine floral organ number.

    Directory of Open Access Journals (Sweden)

    Miho S Kitazawa

    2015-05-01

    Full Text Available How organisms determine particular organ numbers is a fundamental key to the development of precise body structures; however, the developmental mechanisms underlying organ-number determination are unclear. In many eudicot plants, the primordia of sepals and petals (the floral organs first arise sequentially at the edge of a circular, undifferentiated region called the floral meristem, and later transition into a concentric arrangement called a whorl, which includes four or five organs. The properties controlling the transition to whorls comprising particular numbers of organs is little explored. We propose a development-based model of floral organ-number determination, improving upon earlier models of plant phyllotaxis that assumed two developmental processes: the sequential initiation of primordia in the least crowded space around the meristem and the constant growth of the tip of the stem. By introducing mutual repulsion among primordia into the growth process, we numerically and analytically show that the whorled arrangement emerges spontaneously from the sequential initiation of primordia. Moreover, by allowing the strength of the inhibition exerted by each primordium to decrease as the primordium ages, we show that pentamerous whorls, in which the angular and radial positions of the primordia are consistent with those observed in sepal and petal primordia in Silene coeli-rosa, Caryophyllaceae, become the dominant arrangement. The organ number within the outmost whorl, corresponding to the sepals, takes a value of four or five in a much wider parameter space than that in which it takes a value of six or seven. These results suggest that mutual repulsion among primordia during growth and a temporal decrease in the strength of the inhibition during initiation are required for the development of the tetramerous and pentamerous whorls common in eudicots.

  1. Modeling organic matter stabilization during windrow composting of livestock effluents.

    Science.gov (United States)

    Oudart, D; Paul, E; Robin, P; Paillat, J M

    2012-01-01

    Composting is a complex bioprocess, requiring a lot of empirical experiments to optimize the process. A dynamical mathematical model for the biodegradation of the organic matter during the composting process has been developed. The initial organic matter expressed by chemical oxygen demand (COD) is decomposed into rapidly and slowly degraded compartments and an inert one. The biodegradable COD is hydrolysed and consumed by microorganisms and produces metabolic water and carbon dioxide. This model links a biochemical characterization of the organic matter by Van Soest fractionating with COD. The comparison of experimental and simulation results for carbon dioxide emission, dry matter and carbon content balance showed good correlation. The initial sizes of the biodegradable COD compartments are explained by the soluble, hemicellulose-like and lignin fraction. Their sizes influence the amplitude of the carbon dioxide emission peak. The initial biomass is a sensitive variable too, influencing the time at which the emission peak occurs.

  2. Simple model of self-organized biological evolution

    Energy Technology Data Exchange (ETDEWEB)

    de Boer, J.; Derrida, B.; Flyvbjerg, H.; Jackson, A.D.; Wettig, T. (Department of Physics, State University of New York at Stony Brook, Stony Brook, New York 11794-3800 (United States) The Isaac Newton Institute for Mathematical Sciences, 20 Clarkson Road, Cambridge, CB4 0EH (United Kingdom) Laboratoire de Physique Statistique, Ecole Normale Superieure, 24 rue Lhomond, F-75005 Paris (France) Service de Physique Theorique, Centre de Etudes Nucleaires de Saclay, F-91191, Gif-Sur-Yvette (France) CONNECT, The Niels Bohr Institute, Blegdamsvej 17, DK-2100 Copenhagen (Denmark))

    1994-08-08

    We give an exact solution of a recently proposed self-organized critical model of biological evolution. We show that the model has a power law distribution of durations of coevolutionary avalanches'' with a mean field exponent 3/2. We also calculate analytically the finite size effects which cut off this power law at times of the order of the system size.

  3. BeetleBase: the model organism database for Tribolium castaneum

    OpenAIRE

    Wang, Liangjiang; Wang, Suzhi; Li, Yonghua; Paradesi, Martin S. R.; Brown, Susan J

    2006-01-01

    BeetleBase () is an integrated resource for the Tribolium research community. The red flour beetle (Tribolium castaneum) is an important model organism for genetics, developmental biology, toxicology and comparative genomics, the genome of which has recently been sequenced. BeetleBase is constructed to integrate the genomic sequence data with information about genes, mutants, genetic markers, expressed sequence tags and publications. BeetleBase uses the Chado data model and software component...

  4. A two-site bipolaron model for organic magnetoresistance

    Science.gov (United States)

    Wagemans, W.; Bloom, F. L.; Bobbert, P. A.; Wohlgenannt, M.; Koopmans, B.

    2008-04-01

    The recently proposed bipolaron model for large "organic magnetoresistance" (OMAR) at room temperature is extended to an analytically solvable two-site scheme. It is shown that even this extremely simplified approach reproduces some of the key features of OMAR, viz., the possibility to have both positive and negative magnetoresistance, as well as its universal line shapes. Specific behavior and limiting cases are discussed. Extensions of the model, to guide future experiments and numerical Monte Carlo studies, are suggested.

  5. Validation and Scenario Analysis of a Soil Organic Carbon Model

    Institute of Scientific and Technical Information of China (English)

    HUANG Yao; LIU Shi-liang; SHEN Qi-rong; ZONG Liang-gang; JIANG Ding-an; HUANG Hong-guang

    2002-01-01

    A model developed by the authors was validated against independent data sets. The data sets were obtained from field experiments of crop residue decomposition and a 7-year soil improvement in Yixing City, Jiangsu Province. Model validation indicated that soil organic carbon dynamics can be simulated from the weather variables of temperature, sunlight and precipitation, soil clay content and bulk density, grain yield of previous crops, qualities and quantities of the added organic matter. Model simulation in general agreed with the measurements. The comparison between computed and measured resulted in correlation coefficient γ2 values of 0.9291 * * * (n = 48) and 0. 6431 * * (n = 65) for the two experiments, respectively. Model prediction under three scenarios of no additional organic matter input, with an annual incorporation of rice and wheat straw at rates of 6.75t/ha and 9.0t/ha suggested that the soil organic carbon in Wanshi Township of Yixing City would be from an initial value of 7.85g/kg in 1983 to 6.30g/kg, 11.42g/kg and 13g/kg in 2014, respectively. Consequently, total nitrogen content of the soil was predicted to be respectively 0.49g/kg,0.89g/kg and 1.01g/kg under the three scenarios.

  6. Waste Reduction Model (WARM) Resources for Small Businesses and Organizations

    Science.gov (United States)

    This page provides a brief overview of how EPA’s Waste Reduction Model (WARM) can be used by small businesses and organizations. The page includes a brief summary of uses of WARM for the audience and links to other resources.

  7. An Integrated Model for Effective Knowledge Management in Chinese Organizations

    Science.gov (United States)

    An, Xiaomi; Deng, Hepu; Wang, Yiwen; Chao, Lemen

    2013-01-01

    Purpose: The purpose of this paper is to provide organizations in the Chinese cultural context with a conceptual model for an integrated adoption of existing knowledge management (KM) methods and to improve the effectiveness of their KM activities. Design/methodology/approaches: A comparative analysis is conducted between China and the western…

  8. Promoting Representational Competence with Molecular Models in Organic Chemistry

    Science.gov (United States)

    Stull, Andrew T.; Gainer, Morgan; Padalkar, Shamin; Hegarty, Mary

    2016-01-01

    Mastering the many different diagrammatic representations of molecules used in organic chemistry is challenging for students. This article summarizes recent research showing that manipulating 3-D molecular models can facilitate the understanding and use of these representations. Results indicate that students are more successful in translating…

  9. Editorial: Plant organ abscission: from models to crops

    Science.gov (United States)

    The shedding of plant organs is a highly coordinated process essential for both vegetative and reproductive development (Addicott, 1982; Sexton and Roberts, 1982; Roberts et al., 2002; Leslie et al., 2007; Roberts and Gonzalez-Carranza, 2007; Estornell et al., 2013). Research with model plants, name...

  10. A Process Model for the Comprehension of Organic Chemistry Notation

    Science.gov (United States)

    Havanki, Katherine L.

    2012-01-01

    This dissertation examines the cognitive processes individuals use when reading organic chemistry equations and factors that affect these processes, namely, visual complexity of chemical equations and participant characteristics (expertise, spatial ability, and working memory capacity). A six stage process model for the comprehension of organic…

  11. SOMPROF: A vertically explicit soil organic matter model

    NARCIS (Netherlands)

    Braakhekke, M.C.; Beer, M.; Hoosbeek, M.R.; Kruijt, B.; Kabat, P.

    2011-01-01

    Most current soil organic matter (SOM) models represent the soil as a bulk without specification of the vertical distribution of SOM in the soil profile. However, the vertical SOM profile may be of great importance for soil carbon cycling, both on short (hours to years) time scale, due to

  12. Promoting Representational Competence with Molecular Models in Organic Chemistry

    Science.gov (United States)

    Stull, Andrew T.; Gainer, Morgan; Padalkar, Shamin; Hegarty, Mary

    2016-01-01

    Mastering the many different diagrammatic representations of molecules used in organic chemistry is challenging for students. This article summarizes recent research showing that manipulating 3-D molecular models can facilitate the understanding and use of these representations. Results indicate that students are more successful in translating…

  13. Asymmetric Synthesis of (-)-1-Trimethylsilyl-ethanol with Immobilized Saccharomyces Cerevisiae Cells in Water/Organic Solvent Biphasic System%水/有机溶剂双相中固定化啤酒酵母细胞催化三甲基硅乙酮不对称还原

    Institute of Scientific and Technical Information of China (English)

    娄文勇; 宗敏华; 范晓丹

    2003-01-01

    Asymmetric synthesis of (-)-1-trimethylsilyl-ethanol with immobilized Saccharomyces cerevisiae cells in water/organic solvent biphasic system was studied. The effects of shake speed, hydrophobicity of organic solvent,volume ratio of water phase to organic phase, pH value of aqueous phase and reaction temperature on the initial reaction rate, maximum yield and enantiomeric excess (ee) of the product were systematically explored. All the above-mentioned factors had significant influence on the reaction. n-Hexane was found to be the best organic solvent for the reaction. The optimum shake speed, volume ratio of water phase to organic phase, pH value and reaction temperature were 150 r.min- 1, 1/2, 8 and 30℃ respectively, under which the maximum yield and enantiomeric excess of the product were as high as 96.8% and 95.7%, which are 15% and 16% higher than those of the corresponding reaction performed in aqueous phase. To our best knowledge, this is the most satisfactory result obtained.

  14. Supramolecular organization of functional organic materials in the bulk and at organic/organic interfaces: a modeling and computer simulation approach.

    Science.gov (United States)

    Muccioli, Luca; D'Avino, Gabriele; Berardi, Roberto; Orlandi, Silvia; Pizzirusso, Antonio; Ricci, Matteo; Roscioni, Otello Maria; Zannoni, Claudio

    2014-01-01

    The molecular organization of functional organic materials is one of the research areas where the combination of theoretical modeling and experimental determinations is most fruitful. Here we present a brief summary of the simulation approaches used to investigate the inner structure of organic materials with semiconducting behavior, paying special attention to applications in organic photovoltaics and clarifying the often obscure jargon hindering the access of newcomers to the literature of the field. Special attention is paid to the choice of the computational "engine" (Monte Carlo or Molecular Dynamics) used to generate equilibrium configurations of the molecular system under investigation and, more importantly, to the choice of the chemical details in describing the molecular interactions. Recent literature dealing with the simulation of organic semiconductors is critically reviewed in order of increasing complexity of the system studied, from low molecular weight molecules to semiflexible polymers, including the challenging problem of determining the morphology of heterojunctions between two different materials.

  15. Modeling secondary organic aerosol formation through cloud processing of organic compounds

    Directory of Open Access Journals (Sweden)

    J. Chen

    2007-10-01

    Full Text Available Interest in the potential formation of secondary organic aerosol (SOA through reactions of organic compounds in condensed aqueous phases is growing. In this study, the potential formation of SOA from irreversible aqueous-phase reactions of organic species in clouds was investigated. A new proposed aqueous-phase chemistry mechanism (AqChem is coupled with the existing gas-phase Caltech Atmospheric Chemistry Mechanism (CACM and the Model to Predict the Multiphase Partitioning of Organics (MPMPO that simulate SOA formation. AqChem treats irreversible organic reactions that lead mainly to the formation of carboxylic acids, which are usually less volatile than the corresponding aldehydic compounds. Zero-dimensional model simulations were performed for tropospheric conditions with clouds present for three consecutive hours per day. Zero-dimensional model simulations show that 48-h average SOA formation is increased by 27% for a rural scenario with strong monoterpene emissions and 7% for an urban scenario with strong emissions of aromatic compounds, respectively, when irreversible organic reactions in clouds are considered. AqChem was also incorporated into the Community Multiscale Air Quality Model (CMAQ version 4.4 with CACM/MPMPO and applied to a previously studied photochemical episode (3–4 August 2004 focusing on the eastern United States. The CMAQ study indicates that the maximum contribution of SOA formation from irreversible reactions of organics in clouds is 0.28 μg m−3 for 24-h average concentrations and 0.60 μg m−3 for one-hour average concentrations at certain locations. On average, domain-wide surface SOA predictions for the episode are increased by 9% when irreversible, in-cloud processing of organics is considered. Because aldehydes of carbon number greater than four are assumed to convert fully to the corresponding carboxylic acids upon reaction with OH in cloud droplets and this assumption may overestimate

  16. Sustainable Organic Farming For Environmental Health A Social Development Model

    Directory of Open Access Journals (Sweden)

    Ijun Rijwan Susanto

    2015-05-01

    Full Text Available ABSTRACT In this study the researcher attempted 1 to understand the basic features of organic farming in The Paguyuban Pasundans Cianjur 2 to describe and understand how the stakeholders were are able to internalize the challenges of organic farming on their lived experiences in the community 3 to describe and understand how the stakeholders were are able to internalize and applied the values of benefits of organic farming in support of environmental health on their lived experiences in the community 4 The purpose was to describe and understand how the stakeholders who are able to articulate their ideas regarding the model of sustainable organic farming 5 The Policy Recommendation for Organic Farming. The researcher employed triangulation thorough finding that provides breadth and depth to an investigation offering researchers a more accurate picture of the phenomenon. In the implementation of triangulation researchers conducted several interviews to get saturation. After completion of the interview results are written compiled and shown to the participants to check every statement by every participant. In addition researchers also checked the relevant documents and direct observation in the field The participants of this study were the stakeholders namely 1 The leader of Paguyuban Pasundans Organic Farmer Cianjur PPOFC 2 Members of Paguyuban Pasundans Organic FarmersCianjur 3 Leader of NGO 4 Government officials of agriculture 5 Business of organic food 6 and Consumer of organic food. Generally the findings of the study revealed the following 1 PPOFC began to see the reality as the impact of modern agriculture showed in fertility problems due to contaminated soil by residues of agricultural chemicals such as chemical fertilizers and chemical pesticides. So he wants to restore the soil fertility through environmentally friendly of farming practices 2 the challenges of organic farming on their lived experiences in the community farmers did not

  17. Saccharomyces species in the Production of Beer

    Directory of Open Access Journals (Sweden)

    Graham G. Stewart

    2016-12-01

    Full Text Available The characteristic flavour and aroma of any beer is, in large part, determined by the yeast strain employed and the wort composition. In addition, properties such as flocculation, wort fermentation ability (including the uptake of wort sugars, amino acids, and peptides, ethanol and osmotic pressure tolerance together with oxygen requirements have a critical impact on fermentation performance. Yeast management between fermentations is also a critical brewing parameter. Brewer’s yeasts are mostly part of the genus Saccharomyces. Ale yeasts belong to the species Saccharomyces cerevisiae and lager yeasts to the species Saccharomyces pastorianus. The latter is an interspecies hybrid between S. cerevisiae and Saccharomyces eubayanus. Brewer’s yeast strains are facultative anaerobes—they are able to grow in the presence or absence of oxygen and this ability supports their property as an important industrial microorganism. This article covers important aspects of Saccharomyces molecular biology, physiology, and metabolism that is involved in wort fermentation and beer production.

  18. Global Modeling of the Oceanic Source of Organic Aerosols

    Directory of Open Access Journals (Sweden)

    Stelios Myriokefalitakis

    2010-01-01

    Full Text Available The global marine organic aerosol budget is investigated by a 3-dimensional chemistry-transport model considering recently proposed parameterisations of the primary marine organic aerosol (POA and secondary organic aerosol (SOA formation from the oxidation of marine volatile organic compounds. MODIS and SeaWiFS satellite data of Chlorophyll-a and ECMWF solar incoming radiation, wind speed, and temperature are driving the oceanic emissions in the model. Based on the adopted parameterisations, the SOA and the submicron POA marine sources are evaluated at about 5 Tg yr−1 (∼1.5 Tg C yr−1 and 7 to 8 Tg yr−1 (∼4 Tg C yr−1, respectively. The computed marine SOA originates from the dimethylsulfide oxidation (∼78%, the potentially formed dialkyl amine salts (∼21%, and marine hydrocarbon oxidation (∼0.1%. Comparison of calculations with observations indicates an additional marine source of soluble organic carbon that could be partially encountered by marine POA chemical ageing.

  19. Oral treatment with Saccharomyces cerevisiae strain UFMG 905 modulates immune responses and interferes with signal pathways involved in the activation of inflammation in a murine model of typhoid fever.

    Science.gov (United States)

    Martins, Flaviano S; Elian, Samir D A; Vieira, Angélica T; Tiago, Fabiana C P; Martins, Ariane K S; Silva, Flávia C P; Souza, Ericka L S; Sousa, Lirlândia P; Araújo, Helena R C; Pimenta, Paulo F; Bonjardim, Cláudio A; Arantes, Rosa M E; Teixeira, Mauro M; Nicoli, Jacques R

    2011-04-01

    Salmonella spp. are Gram-negative, facultative, intracellular pathogens that cause several diarrheal diseases ranging from self-limiting gastroenteritis to typhoid fever. Previous results from our laboratory showed that Saccharomyces cerevisiae strain UFMG 905 isolated from 'cachaça' production presented probiotic properties due to its ability to protect against experimental infection with Salmonella enterica serovar Typhimurium. In this study, the effects of oral treatment with S. cerevisiae 905 were evaluated at the immunological level in a murine model of typhoid fever. Treatment with S. cerevisiae 905 inhibited weight loss and increased survival rate after Salmonella challenge. Immunological data demonstrated that S. cerevisiae 905 decreased levels of proinflammatory cytokines and modulated the activation of mitogen-activated protein kinases (p38 and JNK, but not ERK1/2), NF-κB and AP-1, signaling pathways which are involved in the transcriptional activation of proinflammatory mediators. Experiments in germ-free mice revealed that probiotic effects were due, at least in part, to the binding of Salmonella to the yeast. In conclusion, S. cerevisiae 905 acts as a potential new biotherapy against S. Typhimurium infection due to its ability to bind bacteria and modulate signaling pathways involved in the activation of inflammation in a murine model of typhoid fever.

  20. Accounting for microbial habitats in modeling soil organic matter dynamics

    Science.gov (United States)

    Chenu, Claire; Garnier, Patricia; Nunan, Naoise; Pot, Valérie; Raynaud, Xavier; Vieublé, Laure; Otten, Wilfred; Falconer, Ruth; Monga, Olivier

    2017-04-01

    The extreme heterogeneity of soils constituents, architecture and inhabitants at the microscopic scale is increasingly recognized. Microbial communities exist and are active in a complex 3-D physical framework of mineral and organic particles defining pores of various sizes, more or less inter-connected. This results in a frequent spatial disconnection between soil carbon, energy sources and the decomposer organisms and a variety of microhabitats that are more or less suitable for microbial growth and activity. However, current biogeochemical models account for C dynamics at the macroscale (cm, m) and consider time- and spatially averaged relationships between microbial activity and soil characteristics. Different modelling approaches have intended to account for this microscale heterogeneity, based either on considering aggregates as surrogates for microbial habitats, or pores. Innovative modelling approaches are based on an explicit representation of soil structure at the fine scale, i.e. at µm to mm scales: pore architecture and their saturation with water, localization of organic resources and of microorganisms. Three recent models are presented here, that describe the heterotrophic activity of either bacteria or fungi and are based upon different strategies to represent the complex soil pore system (Mosaic, LBios and µFun). These models allow to hierarchize factors of microbial activity in soil's heterogeneous architecture. Present limits of these approaches and challenges are presented, regarding the extensive information required on soils at the microscale and to up-scale microbial functioning from the pore to the core scale.

  1. Model Based Fuzzy Expert System for Measuring Organization Knowledge Management

    Directory of Open Access Journals (Sweden)

    Houshang Taghizadeh

    2012-02-01

    Full Text Available This paper presents a model based on fuzzy set theory for determining the score of knowledge management in organization. The introduced model has five stages. In the first stage, input and output variable of model are characterized by available theories. Inputs are as follows: knowledge acquisition, knowledge storage, knowledge creation, knowledge sharing and knowledge transfer. The output is as follow score of knowledge management in organization. In the second stage, the input and output are converted into fuzzy numbers after classification. Inference rules are explained in the third stage. In the fourth stage, defuzzification is performed, and in the fifth stage, the devised system is tested. The test result shows that the presented model has high validity. Ultimately, by using the designed model, the score of knowledge management for Tabriz Kar machinery industry was calculated. The statistical population consists of 50 members of this organization. All the population has been studied. A questionnaire was devised, and its validity and reliability were confirmed. The result indicated that the score of knowledge management in Tabriz Kar machinery industry with the membership rank of 0.924 was at an average level and with the membership rank of 0.076 was at a high

  2. Modeling organic nitrogen conversions in activated sludge bioreactors.

    Science.gov (United States)

    Makinia, Jacek; Pagilla, Krishna; Czerwionka, Krzysztof; Stensel, H David

    2011-01-01

    For biological nutrient removal (BNR) systems designed to maximize nitrogen removal, the effluent total nitrogen (TN) concentration may range from 2.0 to 4.0 g N/m(3) with about 25-50% in the form of organic nitrogen (ON). In this study, current approaches to modeling organic N conversions (separate processes vs. constant contents of organic fractions) were compared. A new conceptual model of ON conversions was developed and combined with Activated Sludge Model No. 2d (ASM2d). The model addresses a new insight into the processes of ammonification, biomass decay and hydrolysis of particulate and colloidal ON (PON and CON, respectively). Three major ON fractions incorporated are defined as dissolved (DON) (model parameter set, the behaviors of both inorganic N forms (NH4-N, NOX-N) and ON forms (DON, CON) in the batch experiments were predicted. The challenges to accurately simulate and predict effluent ON levels from BNR systems are due to analytical methods of direct ON measurement (replacing TKN) and lack of large enough database (in-process measurements, dynamic variations of the ON concentrations) which can be used to determine parameter value ranges.

  3. THE MODEL OF EXTERNSHIP ORGANIZATION FOR FUTURE TEACHERS: QUALIMETRIC APPROACH

    Directory of Open Access Journals (Sweden)

    Taisiya A. Isaeva

    2015-01-01

    Full Text Available The aim of the paper is to present author’s model for bachelors – future teachers of vocational training. The model is been worked out from the standpoint of qualimetric approach and provides a pedagogical training.Methods. The process is based on the literature analysis of externship organization for students in higher education and includes the SWOT-analysis techniques in pedagogical training. The method of group expert evaluation is the main method of pedagogical qualimetry. Structural components of professional pedagogical competency of students-future teachers are defined. It allows us to determine a development level and criterion of estimation on mastering programme «Vocational training (branch-wise».Results. This article interprets the concept «pedagogical training»; its basic organization principles during students’ practice are stated. The methods of expert group formation are presented: self-assessment and personal data.Scientific novelty. The externship organization model for future teachers is developed. This model is based on pedagogical training, using qualimetric approach and the SWOT-analysis techniques. Proposed criterion-assessment procedures are managed to determine the developing levels of professional and pedagogical competency.Practical significance. The model is introduced into pedagogical training of educational process of Kalashnikov’s Izhevsk State Technical University, and can be used in other similar educational establishments.

  4. Self-organizing model of motor cortical activities during drawing

    Science.gov (United States)

    Lin, Siming H.; Si, Jennie; Schwartz, Andrew B.

    1996-05-01

    The population vector algorithm has been developed to combine the simultaneous direction- related activities of a population of motor cortical neurons to predict the trajectory of the arm movement. In our study, we consider a self-organizing model of a neural representation of the arm trajectory based on neuronal discharge rates. Self-organizing feature mapping (SOFM) is used to select the optimal set of weights in the model to determine the contribution of individual neuron to the overall movement. The correspondence between the movement directions and the discharge patterns of the motor cortical neurons is established in the output map. The topology preserving property of the SOFM is used to analyze real recorded data of a behavior monkey. The data used in this analysis were taken while the monkey was drawing spirals and doing the center out movement. Using such a statistical model, the monkey's arm moving directions could be well predicted based on the motor cortex neuronal firing information.

  5. Rotation in turbulence of aquatic organisms modeled as particles

    Science.gov (United States)

    Variano, Evan; Byron, Margaret; Bellani, Gabriele

    2012-11-01

    We investigate which length and time scales are relevant for determining the rotation of aquatic organisms and their gametes. We are interested in parameter space beyond the Stokes regime, and also the effect of particle shape on rotation. We report experimental measurements that use custom-manufactured particles to model aquatic organisms, which are designed with the necessary optical properties so that we can measure their rotation, simultaneously with the vorticity statistics of the surrounding fluid. Lagrangian timeseries of particles' angular velocity allows investigation of rotational diffusion.

  6. Modeling stable isotope and organic carbon in hillslope stormflow

    Science.gov (United States)

    Dusek, Jaromir; Vogel, Tomas; Dohnal, Michal; Marx, Anne; Jankovec, Jakub; Sanda, Martin; Votrubova, Jana; Barth, Johannes A. C.; Cislerova, Milena

    2016-04-01

    Reliable prediction of water movement and fluxes of dissolved substances (such as stable isotopes and organic carbon) at both the hillslope and the catchment scales remains a challenge due to complex boundary conditions and soil spatial heterogeneity. In addition, microbially mediated transformations of dissolved organic carbon (DOC) are known to affect balance of DOC in soils, hence the transformations need to be included in a conceptual model of a DOC transport. So far, only few studies utilized stable isotope information in modeling and even fewer linked dissolved carbon fluxes to mixing and/or transport models. In this study, stormflow dynamics of oxygen-18 isotope and dissolved organic carbon was analyzed using a physically based modeling approach. One-dimensional dual-continuum vertical flow and transport model, based on Richards and advection-dispersion equations, was used to simulate the subsurface transport processes in a forest soil during several observed rainfall-runoff episodes. The transport of heat in the soil profile was described by conduction-advection equation. Water flow and transport of solutes and heat were assumed to take place in two mutually communicating porous domains, the soil matrix and the network of preferential pathways. The rate of microbial transformations of DOC was assumed to depend on soil water content and soil temperature. Oxygen-18 and dissolved organic carbon concentrations were observed in soil pore water, hillslope stormflow (collected in the experimental hillslope trench), and stream discharge (at the catchment outlet). The modeling was used to analyze the transformation of input solute signals into output hillslope signals observed in the trench stormflow. Signatures of oxygen-18 isotope in hillslope stormflow as well as isotope concentration in soil pore water were predicted reasonably well. Due to complex nature of microbial transformations, prediction of DOC rate and transport was associated with a high uncertainty.

  7. Molecular mechanisms of Saccharomyces cerevisiae stress adaptation and programmed cell death in response to acetic acid

    Directory of Open Access Journals (Sweden)

    Sergio eGiannattasio

    2013-02-01

    Full Text Available Beyond its classical biotechnological applications such as food and beverage production or as a cell factory, the yeast Saccharomyces cerevisiae is a valuable model organism to study fundamental mechanisms of cell response to stressful environmental changes. Acetic acid is a physiological product of yeast fermentation and it is a well-known food preservative due to its antimicrobial action. Acetic acid has recently been shown to cause yeast cell death and aging. Here we shall focus on the molecular mechanisms of S. cerevisiae stress adaptation and programmed cell death in response to acetic acid. We shall elaborate on the intracellular signaling pathways involved in the cross-talk of pro-survival and pro-death pathways underlying the importance of understanding fundamental aspects of yeast cell homeostasis to improve the performance of a given yeast strain in biotechnological applications.

  8. Translational thermotolerance in Saccharomyces cerevisiae

    OpenAIRE

    Hallberg, Elizabeth M.; Hallberg, Richard L.

    1996-01-01

    While protein synthesis is rapidly inactivated in Saccharomyces cerevisiae, cells shifted from log growth at 30°C to 43°C, a 1-h 37°C treatment given to cells just prior to the shift to 43°C partially blocks this inactivation. By contrast, such a pre-heat shock treament has no protective effect on translational inactivation at 45°C or higher. Cells allowed to approach stationary phase not only develop an enhanced thermotolerance relative to log cells but also exhibit a pronounced resistance t...

  9. Experimentation and modeling of organic photocontamination on lithographic optics

    Science.gov (United States)

    Kunz, Roderick R.; Liberman, Vladimir; Downs, Deanna K.

    2000-07-01

    Photodeposition of organic films on transparent substrates irradiated in the presence of trace levels of hydrocarbons has been experimentally investigated and a model is presented that describes the film growth behavior. The efficacy of a given organic precursor at forming a deposit is proportional to the product of its surface coverage and by its photon absorption cross section. These measurement are important in predicting the transmission characteristics of lithographic optics operating at 157-, 193-, and 248-nm wavelength. For example, a lens element irradiated continuously for one year in the presence of 1 part per billion of t-butyl benzene would exhibit a transmission of approximately 87 percent at 193 nm. The effects of oxygen- containing ambients are also documented, and methods for elimination and/or prevention of organic contamination are suggested.

  10. Organic livestock production systems as a model of sustainability development

    Directory of Open Access Journals (Sweden)

    Mariano Pauselli

    2010-01-01

    Full Text Available Organic farming and livestock production offer effective means of satisfying consumer demand for healthy and safe foods and reducing the environmental pressure of agricultural production. In Mediterranean areas organic livestock production could be considered a feasible systems to improve rural development in unfavourable areas and to maintain rural landscape. Constrains, like pasture availability during the year, determine the evolution of different strategies in livestock rearing to improve or maintain net income of population. Moreover the evaluation of the sustainability using a holistic approach using assessment criteria like Life Cycle Assessment (LCA and Emergy Assessment could be considered models to evaluate organic and conventional livestock production sustainability and at the same time new research fields.

  11. IT Business Value Model for Information Intensive Organizations

    Directory of Open Access Journals (Sweden)

    Antonio Carlos Gastaud Maçada

    2012-01-01

    Full Text Available Many studies have highlighted the capacity Information Technology (IT has for generating value for organizations. Investments in IT made by organizations have increased each year. Therefore, the purpose of the present study is to analyze the IT Business Value for Information Intensive Organizations (IIO - e.g. banks, insurance companies and securities brokers. The research method consisted of a survey that used and combined the models from Weill and Broadbent (1998 and Gregor, Martin, Fernandez, Stern and Vitale (2006. Data was gathered using an adapted instrument containing 5 dimensions (Strategic, Informational, Transactional, Transformational and Infra-structure with 27 items. The instrument was refined by employing statistical techniques such as Exploratory and Confirmatory Factorial Analysis through Structural Equations (first and second order Model Measurement. The final model is composed of four factors related to IT Business Value: Strategic, Informational, Transactional and Transformational, arranged in 15 items. The dimension Infra-structure was excluded during the model refinement process because it was discovered during interviews that managers were unable to perceive it as a distinct dimension of IT Business Value.

  12. Modeling self-organizing traffic lights with elementary cellular automata

    CERN Document Server

    Gershenson, Carlos

    2009-01-01

    There have been several highway traffic models proposed based on cellular automata. The simplest one is elementary cellular automaton rule 184. We extend this model to city traffic with cellular automata coupled at intersections using only rules 184, 252, and 136. The simplicity of the model offers a clear understanding of the main properties of city traffic and its phase transitions. We use the proposed model to compare two methods for coordinating traffic lights: a green-wave method that tries to optimize phases according to expected flows and a self-organizing method that adapts to the current traffic conditions. The self-organizing method delivers considerable improvements over the green-wave method. For low densities, the self-organizing method promotes the formation and coordination of platoons that flow freely in four directions, i.e. with a maximum velocity and no stops. For medium densities, the method allows a constant usage of the intersections, exploiting their maximum flux capacity. For high dens...

  13. Nonequilibrium drift-diffusion model for organic semiconductor devices

    Science.gov (United States)

    Felekidis, Nikolaos; Melianas, Armantas; Kemerink, Martijn

    2016-07-01

    Two prevailing formalisms are currently used to model charge transport in organic semiconductor devices. Drift-diffusion calculations, on the one hand, are time effective but assume local thermodynamic equilibrium, which is not always realistic. Kinetic Monte Carlo models, on the other hand, do not require this assumption but are computationally expensive. Here, we present a nonequilibrium drift-diffusion model that bridges this gap by fusing the established multiple trap and release formalism with the drift-diffusion transport equation. For a prototypical photovoltaic system the model is shown to quantitatively describe, with a single set of parameters, experiments probing (1) temperature-dependent steady-state charge transport—space-charge limited currents, and (2) time-resolved charge transport and relaxation of nonequilibrated photocreated charges. Moreover, the outputs of the developed kinetic drift-diffusion model are an order of magnitude, or more, faster to compute and in good agreement with kinetic Monte Carlo calculations.

  14. Modeling regional secondary organic aerosol using the Master Chemical Mechanism

    Science.gov (United States)

    Li, Jingyi; Cleveland, Meredith; Ziemba, Luke D.; Griffin, Robert J.; Barsanti, Kelley C.; Pankow, James F.; Ying, Qi

    2015-02-01

    A modified near-explicit Master Chemical Mechanism (MCM, version 3.2) with 5727 species and 16,930 reactions and an equilibrium partitioning module was incorporated into the Community Air Quality Model (CMAQ) to predict the regional concentrations of secondary organic aerosol (SOA) from volatile organic compounds (VOCs) in the eastern United States (US). In addition to the semi-volatile SOA from equilibrium partitioning, reactive surface uptake processes were used to simulate SOA formation due to isoprene epoxydiol, glyoxal and methylglyoxal. The CMAQ-MCM-SOA model was applied to simulate SOA formation during a two-week episode from August 28 to September 7, 2006. The southeastern US has the highest SOA, with a maximum episode-averaged concentration of ∼12 μg m-3. Primary organic aerosol (POA) and SOA concentrations predicted by CMAQ-MCM-SOA agree well with AMS-derived hydrocarbon-like organic aerosol (HOA) and oxygenated organic aerosol (OOA) urban concentrations at the Moody Tower at the University of Houston. Predicted molecular properties of SOA (O/C, H/C, N/C and OM/OC ratios) at the site are similar to those reported in other urban areas, and O/C values agree with measured O/C at the same site. Isoprene epoxydiol is predicted to be the largest contributor to total SOA concentration in the southeast US, followed by methylglyoxal and glyoxal. The semi-volatile SOA components are dominated by products from β-caryophyllene oxidation, but the major species and their concentrations are sensitive to errors in saturation vapor pressure estimation. A uniform decrease of saturation vapor pressure by a factor of 100 for all condensable compounds can lead to a 150% increase in total SOA. A sensitivity simulation with UNIFAC-calculated activity coefficients (ignoring phase separation and water molecule partitioning into the organic phase) led to a 10% change in the predicted semi-volatile SOA concentrations.

  15. Model Establishment for Simulating Soil Organic Carbon Dynamics

    Institute of Scientific and Technical Information of China (English)

    HUANG Yao; LIU Shi-liang; SHEN Qi-rong; ZONG Liang-gang

    2002-01-01

    Assuming that decomposition of organic matter in soils follows the first-order kinetics reaction,a computer model was developed to simulate soil organic matter dynamics. Organic matter in soils is divided up into two parts that include incorporated organic carbon from crop residues or other organic fertilizer and soil intrinsic carbon. The incorporated organic carbon was assumed to consist of two components, labile-C and resistant-C. The model was represented by a differential equation of dCi/dt = Ki× fT × fw × fs × Ci ( i = l,r, S ) and an integral equation of Cit = Cio × EXP ( Ki X fT X fw X fs X t ). Effect of soil parameters of temperature, moisture and texture on the decomposition was functioned by the fT, fw and fs, respectively.Data from laboratory incubation experiments were used to determine the first-order decay rate Ki and the fraction of labile-C of crop residues by employing a nonlinear method. The values of K for the components of labile-C and resistant-C and the soil intrinsic carbon were evaluated to be 0. 025,0. 080 × 10-2 and 0. 065 ×10-3d-1, respectively. The labile-C fraction of wheat straw, wheat roots, rice straw and rice roots were0.50, 0.25, 0.40 and 0.20, respectively. These values are related to the initial residue carbon-to-nitrogen ratio ( C/N) and lignin content.

  16. A refined atomic scale model of the Saccharomyces cerevisiae K+-translocation protein Trk1p combined with experimental evidence confirms the role of selectivity filter glycines and other key residues.

    Science.gov (United States)

    Zayats, Vasilina; Stockner, Thomas; Pandey, Saurabh Kumar; Wörz, Katharina; Ettrich, Rüdiger; Ludwig, Jost

    2015-05-01

    Potassium ion (K+) uptake in yeast is mediated mainly by the Trk1/2 proteins that enable cells to survive on external K+ concentration as low as a few μM. Fungal Trks are related to prokaryotic TRK and Ktr and plant HKT K+ transport systems. Overall sequence similarity is very low, thus requiring experimental verification of homology models. Here a refined structural model of the Saccharomyces cerevisiae Trk1 is presented that was obtained by combining homology modeling, molecular dynamics simulation and experimental verification through functional analysis of mutants. Structural models and experimental results showed that glycines within the selectivity filter, conserved among the K-channel/transporter family, are not only important for protein function, but are also required for correct folding/membrane targeting. A conserved aspartic acid in the PA helix (D79) and a lysine in the M2D helix (K1147) were proposed earlier to interact. Our results suggested individual roles of these residues in folding, structural integrity and function. While mutations of D79 completely abolished protein folding, mutations at position 1147 were tolerated to some extent. Intriguingly, a secondary interaction of D79 with R76 could enhance folding/stability of Trk1 and enable a fraction of Trk1[K1147A] to fold. The part of the ion permeation path containing the selectivity filter is shaped similar to that of ion channels. However below the selectivity filter it is obstructed or regulated by a proline containing loop. The presented model could provide the structural basis for addressing the long standing question if Trk1 is a passive or active ion-translocation system.

  17. Mobility dependent recombination models for organic solar cells

    Science.gov (United States)

    Wagenpfahl, Alexander

    2017-09-01

    Modern solar cell technologies are driven by the effort to enhance power conversion efficiencies. A main mechanism limiting power conversion efficiencies is charge carrier recombination which is a direct function of the encounter probability of both recombination partners. In inorganic solar cells with rather high charge carrier mobilities, charge carrier recombination is often dominated by energetic states which subsequently trap both recombination partners for recombination. Free charge carriers move fast enough for Coulomb attraction to be irrelevant for the encounter probability. Thus, charge carrier recombination is independent of charge carrier mobilities. In organic semiconductors charge carrier mobilities are much lower. Therefore, electrons and holes have more time react to mutual Coulomb-forces. This results in the strong charge carrier mobility dependencies of the observed charge carrier recombination rates. In 1903 Paul Langevin published a fundamental model to describe the recombination of ions in gas-phase or aqueous solutions, known today as Langevin recombination. During the last decades this model was used to interpret and model recombination in organic semiconductors. However, certain experiments especially with bulk-heterojunction solar cells reveal much lower recombination rates than predicted by Langevin. In search of an explanation, many material and device properties such as morphology and energetic properties have been examined in order to extend the validity of the Langevin model. A key argument for most of these extended models is, that electron and hole must find each other at a mutual spatial location. This encounter may be limited for instance by trapping of charges in trap states, by selective electrodes separating electrons and holes, or simply by the morphology of the involved semiconductors, making it impossible for electrons and holes to recombine at high rates. In this review, we discuss the development of mobility limited

  18. Model evaluation of marine primary organic aerosol emission schemes

    Directory of Open Access Journals (Sweden)

    B. Gantt

    2012-09-01

    Full Text Available In this study, several marine primary organic aerosol (POA emission schemes have been evaluated using the GEOS-Chem chemical transport model in order to provide guidance for their implementation in air quality and climate models. These emission schemes, based on varying dependencies of chlorophyll a concentration ([chl a] and 10 m wind speed (U10, have large differences in their magnitude, spatial distribution, and seasonality. Model comparison with weekly and monthly mean values of the organic aerosol mass concentration at two coastal sites shows that the source function exclusively related to [chl a] does a better job replicating surface observations. Sensitivity simulations in which the negative U10 and positive [chl a] dependence of the organic mass fraction of sea spray aerosol are enhanced show improved prediction of the seasonality of the marine POA concentrations. A top-down estimate of submicron marine POA emissions based on the parameterization that compares best to the observed weekly and monthly mean values of marine organic aerosol surface concentrations has a global average emission rate of 6.3 Tg yr−1. Evaluation of existing marine POA source functions against a case study during which marine POA contributed the major fraction of submicron aerosol mass shows that none of the existing parameterizations are able to reproduce the hourly-averaged observations. Our calculations suggest that in order to capture episodic events and short-term variability in submicron marine POA concentration over the ocean, new source functions need to be developed that are grounded in the physical processes unique to the organic fraction of sea spray aerosol.

  19. Model evaluation of marine primary organic aerosol emission schemes

    Science.gov (United States)

    Gantt, B.; Johnson, M. S.; Meskhidze, N.; Sciare, J.; Ovadnevaite, J.; Ceburnis, D.; O'Dowd, C. D.

    2012-09-01

    In this study, several marine primary organic aerosol (POA) emission schemes have been evaluated using the GEOS-Chem chemical transport model in order to provide guidance for their implementation in air quality and climate models. These emission schemes, based on varying dependencies of chlorophyll a concentration ([chl a]) and 10 m wind speed (U10), have large differences in their magnitude, spatial distribution, and seasonality. Model comparison with weekly and monthly mean values of the organic aerosol mass concentration at two coastal sites shows that the source function exclusively related to [chl a] does a better job replicating surface observations. Sensitivity simulations in which the negative U10 and positive [chl a] dependence of the organic mass fraction of sea spray aerosol are enhanced show improved prediction of the seasonality of the marine POA concentrations. A top-down estimate of submicron marine POA emissions based on the parameterization that compares best to the observed weekly and monthly mean values of marine organic aerosol surface concentrations has a global average emission rate of 6.3 Tg yr-1. Evaluation of existing marine POA source functions against a case study during which marine POA contributed the major fraction of submicron aerosol mass shows that none of the existing parameterizations are able to reproduce the hourly-averaged observations. Our calculations suggest that in order to capture episodic events and short-term variability in submicron marine POA concentration over the ocean, new source functions need to be developed that are grounded in the physical processes unique to the organic fraction of sea spray aerosol.

  20. Dissecting genetic and environmental mutation signatures with model organisms.

    Science.gov (United States)

    Segovia, Romulo; Tam, Annie S; Stirling, Peter C

    2015-08-01

    Deep sequencing has impacted on cancer research by enabling routine sequencing of genomes and exomes to identify genetic changes associated with carcinogenesis. Researchers can now use the frequency, type, and context of all mutations in tumor genomes to extract mutation signatures that reflect the driving mutational processes. Identifying mutation signatures, however, may not immediately suggest a mechanism. Consequently, several recent studies have employed deep sequencing of model organisms exposed to discrete genetic or environmental perturbations. These studies exploit the simpler genomes and availability of powerful genetic tools in model organisms to analyze mutation signatures under controlled conditions, forging mechanistic links between mutational processes and signatures. We discuss the power of this approach and suggest that many such studies may be on the horizon.

  1. Semantic network based component organization model for program mining

    Institute of Scientific and Technical Information of China (English)

    王斌; 张尧学; 陈松乔

    2003-01-01

    Based on the definition of component ontology, an effective component classification mechanism and a facet named component relationship are proposed. Then an application domain oriented, hierarchical component organization model is established. At last a hierarchical component semantic network (HCSN) described by ontology interchange language(OIL) is presented and then its function is described. Using HCSN and cooperating with other components retrieving algorithms based on component description, other components information and their assembly or composite modes related to the key component can be found. Based on HCSN, component directory library is catalogued and a prototype system is constructed. The prototype system proves that component library organization based on this model gives guarantee to the reliability of component assembly during program mining.

  2. Cube Kohonen self-organizing map (CKSOM) model with new equations in organizing unstructured data.

    Science.gov (United States)

    Lim, Seng Poh; Haron, Habibollah

    2013-09-01

    Surface reconstruction by using 3-D data is used to represent the surface of an object and perform important tasks. The type of data used is important and can be described as either structured or unstructured. For unstructured data, there is no connectivity information between data points. As a result, incorrect shapes will be obtained during the imaging process. Therefore, the data should be reorganized by finding the correct topology so that the correct shape can be obtained. Previous studies have shown that the Kohonen self-organizing map (KSOM) could be used to solve data organizing problems. However, 2-D Kohonen maps are limited because they are unable to cover the whole surface of closed 3-D surface data. Furthermore, the neurons inside the 3-D KSOM structure should be removed in order to create a correct wireframe model. This is because only the outside neurons are used to represent the surface of an object. The aim of this paper is to use KSOM to organize unstructured data for closed surfaces. KSOM isused in this paper by testing its ability to organize medical image data because KSOM is mostly used in constructing engineering field data. Enhancements are added to the model by introducing class number and the index vector, and new equations are created. Various grid sizes and maximum iterations are tested in the experiments. Based on the results, the number of redundancies is found to be directly proportional to the grid size. When we increase the maximum iterations, the surface of the image becomes smoother. An area formula is used and manual calculations are performed to validate the results. This model is implemented and images are created using Dev C++ and GNUPlot.

  3. Mechanical models for the self-organization of tubular patterns.

    Science.gov (United States)

    Guo, Chin-Lin

    2013-01-01

    Organogenesis, such as long tubule self-organization, requires long-range coordination of cell mechanics to arrange cell positions and to remodel the extracellular matrix. While the current mainstream in the field of tissue morphogenesis focuses primarily on genetics and chemical signaling, the influence of cell mechanics on the programming of patterning cues in tissue morphogenesis has not been adequately addressed. Here, we review experimental evidence and propose quantitative mechanical models by which cells can create tubular patterns.

  4. Spatial self-organization in hybrid models of multicellular adhesion

    Science.gov (United States)

    Bonforti, Adriano; Duran-Nebreda, Salva; Montañez, Raúl; Solé, Ricard

    2016-10-01

    Spatial self-organization emerges in distributed systems exhibiting local interactions when nonlinearities and the appropriate propagation of signals are at work. These kinds of phenomena can be modeled with different frameworks, typically cellular automata or reaction-diffusion systems. A different class of dynamical processes involves the correlated movement of agents over space, which can be mediated through chemotactic movement or minimization of cell-cell interaction energy. A classic example of the latter is given by the formation of spatially segregated assemblies when cells display differential adhesion. Here, we consider a new class of dynamical models, involving cell adhesion among two stochastically exchangeable cell states as a minimal model capable of exhibiting well-defined, ordered spatial patterns. Our results suggest that a whole space of pattern-forming rules is hosted by the combination of physical differential adhesion and the value of probabilities modulating cell phenotypic switching, showing that Turing-like patterns can be obtained without resorting to reaction-diffusion processes. If the model is expanded allowing cells to proliferate and die in an environment where diffusible nutrient and toxic waste are at play, different phases are observed, characterized by regularly spaced patterns. The analysis of the parameter space reveals that certain phases reach higher population levels than other modes of organization. A detailed exploration of the mean-field theory is also presented. Finally, we let populations of cells with different adhesion matrices compete for reproduction, showing that, in our model, structural organization can improve the fitness of a given cell population. The implications of these results for ecological and evolutionary models of pattern formation and the emergence of multicellularity are outlined.

  5. Sulfurous Gases As Biological Messengers and Toxins: Comparative Genetics of Their Metabolism in Model Organisms

    Directory of Open Access Journals (Sweden)

    Neal D. Mathew

    2011-01-01

    Full Text Available Gasotransmitters are biologically produced gaseous signalling molecules. As gases with potent biological activities, they are toxic as air pollutants, and the sulfurous compounds are used as fumigants. Most investigations focus on medical aspects of gasotransmitter biology rather than toxicity toward invertebrate pests of agriculture. In fact, the pathways for the metabolism of sulfur containing gases in lower organisms have not yet been described. To address this deficit, we use protein sequences from Homo sapiens to query Genbank for homologous proteins in Caenorhabditis elegans, Drosophila melanogaster, and Saccharomyces cerevisiae. In C. elegans, we find genes for all mammalian pathways for synthesis and catabolism of the three sulfur containing gasotransmitters, H2S, SO2 and COS. The genes for H2S synthesis have actually increased in number in C. elegans. Interestingly, D. melanogaster and Arthropoda in general, lack a gene for 3-mercaptopyruvate sulfurtransferase, an enzym for H2S synthesis under reducing conditions.

  6. Numerical model of multilayer organic light-emitting devices

    Institute of Scientific and Technical Information of China (English)

    Hu Yue; Rao Hai-Bo

    2009-01-01

    A numerical model of multilayer organic light-emitting devices is presented in this article.This model is based on the drift-diffusion equations which include charge injection,transport,space charge effects,trapping,heterojunction interface and recombination process.The device structure in the simulation is ITO/CuPc(20 nm)/NPD(40 nm)/Alq3(60 nm)/LiF/Al.There are two heterojunctions which should be dealt with in the simulation.The Ⅰ-Ⅴ characteristics,carrier distribution and recombination rate of a device are calculated.The simulation results and measured data are in good agreement.

  7. Conceptual hierarchical modeling to describe wetland plant community organization

    Science.gov (United States)

    Little, A.M.; Guntenspergen, G.R.; Allen, T.F.H.

    2010-01-01

    Using multivariate analysis, we created a hierarchical modeling process that describes how differently-scaled environmental factors interact to affect wetland-scale plant community organization in a system of small, isolated wetlands on Mount Desert Island, Maine. We followed the procedure: 1) delineate wetland groups using cluster analysis, 2) identify differently scaled environmental gradients using non-metric multidimensional scaling, 3) order gradient hierarchical levels according to spatiotem-poral scale of fluctuation, and 4) assemble hierarchical model using group relationships with ordination axes and post-hoc tests of environmental differences. Using this process, we determined 1) large wetland size and poor surface water chemistry led to the development of shrub fen wetland vegetation, 2) Sphagnum and water chemistry differences affected fen vs. marsh / sedge meadows status within small wetlands, and 3) small-scale hydrologic differences explained transitions between forested vs. non-forested and marsh vs. sedge meadow vegetation. This hierarchical modeling process can help explain how upper level contextual processes constrain biotic community response to lower-level environmental changes. It creates models with more nuanced spatiotemporal complexity than classification and regression tree procedures. Using this process, wetland scientists will be able to generate more generalizable theories of plant community organization, and useful management models. ?? Society of Wetland Scientists 2009.

  8. Self-organized Collaboration Network Model Based on Module Emerging

    Science.gov (United States)

    Yang, Hongyong; Lu, Lan; Liu, Qiming

    Recently, the studies of the complex network have gone deep into many scientific fields, such as computer science, physics, mathematics, sociology, etc. These researches enrich the realization for complex network, and increase understands for the new characteristic of complex network. Based on the evolvement characteristic of the author collaboration in the scientific thesis, a self-organized network model of the scientific cooperation network is presented by module emerging. By applying the theoretical analysis, it is shown that this network model is a scale-free network, and the strength degree distribution and the module degree distribution of the network nodes have the same power law. In order to make sure the validity of the theoretical analysis for the network model, we create the computer simulation and demonstration collaboration network. By analyzing the data of the network, the results of the demonstration network and the computer simulation are consistent with that of the theoretical analysis of the model.

  9. Comparative genomics and transcriptomics in Saccharomyces

    OpenAIRE

    Ibáñez Martínez, Clara

    2015-01-01

    Las levaduras del género Saccharomyces (principalmente Saccharomyces cerevisiae) son las responsables de la fermentación alcohólica (Pretorius, 2000). Aunque S. cerevisiae es la especie más frecuente en fermentaciones vínicas, y modelo de estudio (Pretorius, 2000; Serra et al., 2005; Barrio et al., 2006), también pueden estar presentes durante el proceso especies como S. uvarum (Naumov et al., 2002; Rementería et al., 2003; Demuyter et al., 2004), Saccharomyces paradoxus, aislada de viñedos c...

  10. Modelling nitrous oxide emissions from organic soils in Europe

    Science.gov (United States)

    Leppelt, Thomas; Dechow, Rene; Gebbert, Sören; Freibauer, Annette

    2013-04-01

    The greenhouse gas emission potential of peatland ecosystems are mandatory for a complete annual emission budget in Europe. The GHG-Europe project aims to improve the modelling capabilities for greenhouse gases, e.g., nitrous oxide. The heterogeneous and event driven fluxes of nitrous oxide are challenging to model on European scale, especially regarding the upscaling purpose and certain parameter estimations. Due to these challenges adequate techniques are needed to create a robust empirical model. Therefore a literature study of nitrous oxide fluxes from organic soils has been carried out. This database contains flux data from boreal and temperate climate zones and covers the different land use categories: cropland, grassland, forest, natural and peat extraction sites. Especially managed crop- and grassland sites feature high emission potential. Generally nitrous oxide emissions increases significantly with deep drainage and intensive application of nitrogen fertilisation. Whereas natural peatland sites with a near surface groundwater table can act as nitrous oxide sink. An empirical fuzzy logic model has been applied to predict annual nitrous oxide emissions from organic soils. The calibration results in two separate models with best model performances for bogs and fens, respectively. The derived parameter combinations of these models contain mean groundwater table, nitrogen fertilisation, annual precipitation, air temperature, carbon content and pH value. Influences of the calibrated parameters on nitrous oxide fluxes are verified by several studies in literature. The extrapolation potential has been tested by an implemented cross validation. Furthermore the parameter ranges of the calibrated models are compared to occurring values on European scale. This avoid unknown systematic errors for the regionalisation purpose. Additionally a sensitivity analysis specify the model behaviour for each alternating parameter. The upscaling process for European peatland

  11. Modelling erosion and its interaction with soil organic carbon.

    Science.gov (United States)

    Oyesiku-Blakemore, Joseph; Verrot, Lucile; Geris, Josie; Zhang, Ganlin; Peng, Xinhua; Hallett, Paul; Smith, Jo

    2017-04-01

    Water driven soil erosion removes and relocates a significant quantity of soil organic carbon. In China the quantity of carbon removed from the soil through water erosion has been reported to be 180+/-80 Mt y-1 (Yue et al., 2011). Being able to effectively model the movement of such a large quantity of carbon is important for the assessment of soil quality and carbon storage in the region and further afield. A large selection of erosion models are available and much work has been done on evaluating the performance of these in developed countries (Merritt et al., 2006). Fewer studies have evaluated the application of these models on soils in developing countries. Here we evaluate and compare the performance of two of these models, WEPP (Laflen et al., 1997) and RUSLE (Renard et al., 1991), for simulations of soil erosion and deposition at the slope scale on a Chinese Red Soil under cultivation using measurements taken at the site. We also describe work to dynamically couple the movement of carbon presented in WEPP to a model of soil organic matter and nutrient turnover, ECOSSE (Smith et al., 2010). This aims to improve simulations of both erosion and carbon cycling by using the simulated rates of erosion to alter the distribution of soil carbon, the depth of soil and the clay content across the slopes, changing the simulated rate of carbon turnover. This, in turn, affects the soil carbon available to be eroded in the next timestep, so improving estimates of carbon erosion. We compare the simulations of this coupled modelling approach with those of the unaltered ECOSSE and WEPP models to determine the importance of coupling erosion and turnover models on the simulation of carbon losses at catchment scale.

  12. Spatiotemporal Organization of Spin-Coated Supported Model Membranes

    Science.gov (United States)

    Simonsen, Adam Cohen

    All cells of living organisms are separated from their surroundings and organized internally by means of flexible lipid membranes. In fact, there is consensus that the minimal requirements for self-replicating life processes include the following three features: (1) information carriers (DNA, RNA), (2) a metabolic system, and (3) encapsulation in a container structure [1]. Therefore, encapsulation can be regarded as an essential part of life itself. In nature, membranes are highly diverse interfacial structures that compartmentalize cells [2]. While prokaryotic cells only have an outer plasma membrane and a less-well-developed internal membrane structure, eukaryotic cells have a number of internal membranes associated with the organelles and the nucleus. Many of these membrane structures, including the plasma membrane, are complex layered systems, but with the basic structure of a lipid bilayer. Biomembranes contain hundreds of different lipid species in addition to embedded or peripherally associated membrane proteins and connections to scaffolds such as the cytoskeleton. In vitro, lipid bilayers are spontaneously self-organized structures formed by a large group of amphiphilic lipid molecules in aqueous suspensions. Bilayer formation is driven by the entropic properties of the hydrogen bond network in water in combination with the amphiphilic nature of the lipids. The molecular shapes of the lipid constituents play a crucial role in bilayer formation, and only lipids with approximately cylindrical shapes are able to form extended bilayers. The bilayer structure of biomembranes was discovered by Gorter and Grendel in 1925 [3] using monolayer studies of lipid extracts from red blood cells. Later, a number of conceptual models were developed to rationalize the organization of lipids and proteins in biological membranes. One of the most celebrated is the fluid-mosaic model by Singer and Nicolson (1972) [4]. According to this model, the lipid bilayer component of

  13. Incorporating microbial ecology into the metabolic modelling of polyphosphate accumulating organisms and glycogen accumulating organisms.

    Science.gov (United States)

    Oehmen, A; Carvalho, G; Lopez-Vazquez, C M; van Loosdrecht, M C M; Reis, M A M

    2010-09-01

    In the enhanced biological phosphorus removal (EBPR) process, the competition between polyphosphate accumulating organisms (PAO) and glycogen accumulating organisms (GAO) has been studied intensively in recent years by both microbiologists and engineers, due to its important effects on phosphorus removal performance and efficiency. This study addresses the impact of microbial ecology on assessing the PAO-GAO competition through metabolic modelling, focussing on reviewing recent developments, discussion of how the results from molecular studies can impact the way we model the process, and offering perspectives for future research opportunities based on unanswered questions concerning PAO and GAO metabolism. Indeed, numerous findings that are seemingly contradictory could in fact be explained by the metabolic behaviour of different sub-groups of PAOs and/or GAOs exposed to different environmental and operational conditions. Some examples include the glycolysis pathway (i.e. Embden-Meyerhof-Parnas (EMP) vs. Entner-Doudoroff (ED)), denitrification capacity, anaerobic tricarboxylic acid (TCA) cycle activity and PAOs' ability to adjust their metabolism to e.g. a GAO-like metabolism. Metabolic modelling may further yield far-reaching influences on practical applications as well, and serves as a bridge between molecular/biochemical research studies and the optimisation of wastewater treatment plant operation. Copyright © 2010 Elsevier Ltd. All rights reserved.

  14. MIANN models in medicinal, physical and organic chemistry.

    Science.gov (United States)

    González-Díaz, Humberto; Arrasate, Sonia; Sotomayor, Nuria; Lete, Esther; Munteanu, Cristian R; Pazos, Alejandro; Besada-Porto, Lina; Ruso, Juan M

    2013-01-01

    Reducing costs in terms of time, animal sacrifice, and material resources with computational methods has become a promising goal in Medicinal, Biological, Physical and Organic Chemistry. There are many computational techniques that can be used in this sense. In any case, almost all these methods focus on few fundamental aspects including: type (1) methods to quantify the molecular structure, type (2) methods to link the structure with the biological activity, and others. In particular, MARCH-INSIDE (MI), acronym for Markov Chain Invariants for Networks Simulation and Design, is a well-known method for QSAR analysis useful in step (1). In addition, the bio-inspired Artificial-Intelligence (AI) algorithms called Artificial Neural Networks (ANNs) are among the most powerful type (2) methods. We can combine MI with ANNs in order to seek QSAR models, a strategy which is called herein MIANN (MI & ANN models). One of the first applications of the MIANN strategy was in the development of new QSAR models for drug discovery. MIANN strategy has been expanded to the QSAR study of proteins, protein-drug interactions, and protein-protein interaction networks. In this paper, we review for the first time many interesting aspects of the MIANN strategy including theoretical basis, implementation in web servers, and examples of applications in Medicinal and Biological chemistry. We also report new applications of the MIANN strategy in Medicinal chemistry and the first examples in Physical and Organic Chemistry, as well. In so doing, we developed new MIANN models for several self-assembly physicochemical properties of surfactants and large reaction networks in organic synthesis. In some of the new examples we also present experimental results which were not published up to date.

  15. Modeling uptake of hydrophobic organic contaminants into polyethylene passive samplers.

    Science.gov (United States)

    Thompson, Jay M; Hsieh, Ching-Hong; Luthy, Richard G

    2015-02-17

    Single-phase passive samplers are gaining acceptance as a method to measure hydrophobic organic contaminant (HOC) concentration in water. Although the relationship between the HOC concentration in water and passive sampler is linear at equilibrium, mass transfer models are needed for nonequilibrium conditions. We report measurements of organochlorine pesticide diffusion and partition coefficients with respect to polyethylene (PE), and present a Fickian approach to modeling HOC uptake by PE in aqueous systems. The model is an analytic solution to Fick's second law applied through an aqueous diffusive boundary layer and a polyethylene layer. Comparisons of the model with existing methods indicate agreement at appropriate boundary conditions. Laboratory release experiments on the organochlorine pesticides DDT, DDE, DDD, and chlordane in well-mixed slurries support the model's applicability to aqueous systems. In general, the advantage of the model is its application in the cases of well-agitated systems, low values of polyethylene-water partioning coefficients, thick polyethylene relative to the boundary layer thickness, and/or short exposure times. Another significant advantage is the ability to estimate, or at least bound, the needed exposure time to reach a desired CPE without empirical model inputs. A further finding of this work is that polyethylene diffusivity does not vary by transport direction through the sampler thickness.

  16. OBJECT ORIENTED MODELLING, A MODELLING METHOD OF AN ECONOMIC ORGANIZATION ACTIVITY

    Directory of Open Access Journals (Sweden)

    TĂNĂSESCU ANA

    2014-05-01

    Full Text Available Now, most economic organizations use different information systems types in order to facilitate their activity. There are different methodologies, methods and techniques that can be used to design information systems. In this paper, I propose to present the advantages of using the object oriented modelling at the information system design of an economic organization. Thus, I have modelled the activity of a photo studio, using Visual Paradigm for UML as a modelling tool. For this purpose, I have identified the use cases for the analyzed system and I have presented the use case diagram. I have, also, realized the system static and dynamic modelling, through the most known UML diagrams.

  17. Engineering of Saccharomyces cerevisiae for Efficient Anaerobic Alcoholic Fermentation of L-Arabinose

    NARCIS (Netherlands)

    Wisselink, H.W.; Toirkens, M.J.; Del Rosario Franco Berriel, M.; Winkler, A.A.; Van Dijken, J.P.; Pronk, J.T.; Van Maris, A.J.A.

    2007-01-01

    For cost-effective and efficient ethanol production from lignocellulosic fractions of plant biomass, the conversion of not only major constituents, such as glucose and xylose, but also less predominant sugars, such as L-arabinose, is required. Wild-type strains of Saccharomyces cerevisiae, the organ

  18. Dissection of transcriptional regulation networks and prediction of gene functions in Saccharomyces cerevisiae

    NARCIS (Netherlands)

    Boorsma, A.

    2008-01-01

    Molecular biology aims to unravel the functions of cells by studying cellular processes at the molecular level. Amodel organism that is well established in molecular biology is bakers yeast (Saccharomyces cerevisiae). Bakers yeast cells are remarkably similar to human cells, but much easier to grow

  19. Conditions With High Intracellular Glucose Inhibit Sensing Through Glucose Sensor Snf3 in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Karhumaa, Kaisa; Wu, B.Q.; Kielland-Brandt, Morten

    2010-01-01

    Gene expression in micro-organisms is regulated according to extracellular conditions and nutrient concentrations. In Saccharomyces cerevisiae, non-transporting sensors with high sequence similarity to transporters, that is, transporter-like sensors, have been identified for sugars as well...

  20. Calorie restriction does not elicit a robust extension of replicative lifespan in Saccharomyces cerevisiae

    NARCIS (Netherlands)

    Huberts, Daphne H.E.W.; Gonzalez Hernandez, Javier; Lee, Sung Sik; Litsios, Athanasios; Hubmann, Georg; Wit, Ernst C.; Heinemann, Matthias

    2014-01-01

    Calorie restriction (CR) is often described as the most robust manner to extend lifespan in a large variety of organisms. Hence, considerable research effort is directed toward understanding the mechanisms underlying CR, especially in the yeast Saccharomyces cerevisiae. However, the effect of CR on

  1. The role of the nutrients in G1 phase progression of Saccharomyces cerevisiae

    NARCIS (Netherlands)

    Paalman, Johannes Wilhelmus Gerardus

    2001-01-01

    Organisms that have optimally integrated fast reproduction with high survival have a strategic advantage over less adapted species during evolution. This thesis focusses on the main decision point in the life cycle of the yeast Saccharomyces cerevisiae, at which the cell decides to rapidly grow and

  2. Dissection of transcriptional regulation networks and prediction of gene functions in Saccharomyces cerevisiae

    NARCIS (Netherlands)

    Boorsma, A.

    2008-01-01

    Molecular biology aims to unravel the functions of cells by studying cellular processes at the molecular level. Amodel organism that is well established in molecular biology is bakers yeast (Saccharomyces cerevisiae). Bakers yeast cells are remarkably similar to human cells, but much easier to grow

  3. Multiscale Modeling and Simulation of Organic Solar Cells

    CERN Document Server

    de Falco, Carlo; Sacco, Riccardo; Verri, Maurizio

    2012-01-01

    In this article, we continue our mathematical study of organic solar cells (OSCs) and propose a two-scale (micro- and macro-scale) model of heterojunction OSCs with interface geometries characterized by an arbitrarily complex morphology. The microscale model consists of a system of partial and ordinary differential equations in an heterogeneous domain, that provides a full description of excitation/transport phenomena occurring in the bulk regions and dissociation/recombination processes occurring in a thin material slab across the interface. The macroscale model is obtained by a micro-to-macro scale transition that consists of averaging the mass balance equations in the normal direction across the interface thickness, giving rise to nonlinear transmission conditions that are parametrized by the interfacial width. These conditions account in a lumped manner for the volumetric dissociation/recombination phenomena occurring in the thin slab and depend locally on the electric field magnitude and orientation. Usi...

  4. Controlling self-organized criticality in sandpile models

    CERN Document Server

    Cajueiro, Daniel O

    2013-01-01

    We introduce an external control to reduce the size of avalanches in some sandpile models exhibiting self organized criticality. This rather intuitive approach seems to be missing in the vast literature on such systems. The control action, which amounts to triggering avalanches in sites that are near to be come critical, reduces the probability of very large events, so that energy dissipation occurs most locally. The control is applied to a directed Abelian sandpile model driven by both uncorrelated and correlated deposition. The latter is essential to design an efficient and simple control heuristic, but has only small influence in the uncontrolled avalanche probability distribution. The proposed control seeks a tradeoff between control cost and large event risk. Preliminary results hint that the proposed control works also for an undirected sandpile model.

  5. Genome Editing and Its Applications in Model Organisms

    Directory of Open Access Journals (Sweden)

    Dongyuan Ma

    2015-12-01

    Full Text Available Technological advances are important for innovative biological research. Development of molecular tools for DNA manipulation, such as zinc finger nucleases (ZFNs, transcription activator-like effector nucleases (TALENs, and the clustered regularly-interspaced short palindromic repeat (CRISPR/CRISPR-associated (Cas, has revolutionized genome editing. These approaches can be used to develop potential therapeutic strategies to effectively treat heritable diseases. In the last few years, substantial progress has been made in CRISPR/Cas technology, including technical improvements and wide application in many model systems. This review describes recent advancements in genome editing with a particular focus on CRISPR/Cas, covering the underlying principles, technological optimization, and its application in zebrafish and other model organisms, disease modeling, and gene therapy used for personalized medicine.

  6. Intelligent Model for Measuring Organization Maturity in E-Business

    Directory of Open Access Journals (Sweden)

    Sadra Ahmadi

    2009-07-01

    Full Text Available E-Business is one of the most fascinating areas of information Technology. Managers should seek out means for making decision towards optimizing resource development in this area in order to control their expense and capital allocations at a higher, strategic level. To do this, manager must first identify their level of e-business development and plan to improve the status quo by identifying factors contributing to the growth in this approach. The present paper aims to construct and develop intelligent models for determining the organization status quo and management decision-making towards improving the situation using fuzzy [logic] tools. Thus for modeling these factors and their impact, the contributing factors in development of e-business approaches were identified by literature survey. These were later categorized using Delphi Method. Furthermore the FCM model was used to graphically illustrate the causal relationships among factors, including the mode and means of their mutual impact.

  7. Self-organized criticality model for brain plasticity.

    Science.gov (United States)

    de Arcangelis, Lucilla; Perrone-Capano, Carla; Herrmann, Hans J

    2006-01-20

    Networks of living neurons exhibit an avalanche mode of activity, experimentally found in organotypic cultures. Here we present a model that is based on self-organized criticality and takes into account brain plasticity, which is able to reproduce the spectrum of electroencephalograms (EEG). The model consists of an electrical network with threshold firing and activity-dependent synapse strengths. The system exhibits an avalanche activity in a power-law distribution. The analysis of the power spectra of the electrical signal reproduces very robustly the power-law behavior with the exponent 0.8, experimentally measured in EEG spectra. The same value of the exponent is found on small-world lattices and for leaky neurons, indicating that universality holds for a wide class of brain models.

  8. Genome Editing and Its Applications in Model Organisms.

    Science.gov (United States)

    Ma, Dongyuan; Liu, Feng

    2015-12-01

    Technological advances are important for innovative biological research. Development of molecular tools for DNA manipulation, such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the clustered regularly-interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas), has revolutionized genome editing. These approaches can be used to develop potential therapeutic strategies to effectively treat heritable diseases. In the last few years, substantial progress has been made in CRISPR/Cas technology, including technical improvements and wide application in many model systems. This review describes recent advancements in genome editing with a particular focus on CRISPR/Cas, covering the underlying principles, technological optimization, and its application in zebrafish and other model organisms, disease modeling, and gene therapy used for personalized medicine.

  9. Model for Triplet State Engineering in Organic Light Emitting Diodes

    CERN Document Server

    Prodhan, Suryoday; Ramasesha, S

    2014-01-01

    Engineering the position of the lowest triplet state (T1) relative to the first excited singlet state (S1) is of great importance in improving the efficiencies of organic light emitting diodes and organic photovoltaic cells. We have carried out model exact calculations of substituted polyene chains to understand the factors that affect the energy gap between S1 and T1. The factors studied are backbone dimerisation, different donor-acceptor substitutions and twisted geometry. The largest system studied is an eighteen carbon polyene which spans a Hilbert space of about 991 million. We show that for reverse intersystem crossing (RISC) process, the best system involves substituting all carbon sites on one half of the polyene with donors and the other half with acceptors.

  10. Table of 3D organ model IDs and organ names (IS-A Tree) - BodyParts3D | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us BodyParts3D Table of 3D organ model IDs and organ names (IS-A Tree) Data detail Data name Table of 3D organ model...ontents List of downloadable 3D organ models in a tab-delimited text file format, describing the correspondence between 3D organ mode...| Contact Us Table of 3D organ model IDs and organ names (IS-A Tree) - BodyParts3D | LSDB Archive ...

  11. Developing an Enzyme Mediated Soil Organic Carbon Decomposition Model

    Science.gov (United States)

    Mayes, M. A.; Post, W. M.; Wang, G.; Jagadamma, S.; Steinweg, J. M.; Schadt, C. W.

    2012-12-01

    We developed the Microbial-ENzyme-mediated Decomposition (MEND) model in order to mechanistically model the decomposition of soil organic carbon (C). This presentation is an overview of the concept and development of the model and of the design of complementary lab-scale experiments. The model divides soil C into five pools of particulate, mineral-associated, dissolved, microbial, and enzyme organic C (Wang et al. 2012). There are three input types - cellulose, lignin, and dissolved C. Decomposition is mediated via microbial extracellular enzymes using the Michaelis-Menten equation, resulting in the production of a common pool of dissolved organic C. Parameters for the Michaelis-Menten equation are obtained through a literature review (Wang and Post, 2012a). The dissolved C is taken up by microbial biomass and proportioned according to microbial maintenance and growth, which were recalculated according to Wang and Post (2012b). The model allows dissolved C to undergo adsorption and desorption reactions with the mineral-associated C, which was also parameterized based upon a literature review and complementary laboratory experiments. In the lab, four 14C-labeled substrates (cellulose, fatty acid, glucose, and lignin-like) were incubated with either the particulate C pool, the mineral-associated C pool, or to bulk soils. The rate of decomposition was measured via the production of 14CO2 over time, along with incorporation into microbial biomass, production of dissolved C, and estimation of sorbed C. We performed steady-state and dynamic simulations and sensitivity analyses under temperature increases of 1-5°C for a period of 100 y. Simulations indicated an initial decrease in soil organic C consisting of both cellulose and lignin pools. Over longer time intervals (> 6 y), however, a shrinking microbial population, a concomitant decrease in enzyme production, and a decrease in microbial carbon use efficiency together decreased CO2 production and resulted in greater

  12. Thermodynamic Modeling of Organic-Inorganic Aerosols with the Group-Contribution Model AIOMFAC

    Science.gov (United States)

    Zuend, A.; Marcolli, C.; Luo, B. P.; Peter, T.

    2009-04-01

    Liquid aerosol particles are - from a physicochemical viewpoint - mixtures of inorganic salts, acids, water and a large variety of organic compounds (Rogge et al., 1993; Zhang et al., 2007). Molecular interactions between these aerosol components lead to deviations from ideal thermodynamic behavior. Strong non-ideality between organics and dissolved ions may influence the aerosol phases at equilibrium by means of liquid-liquid phase separations into a mainly polar (aqueous) and a less polar (organic) phase. A number of activity models exists to successfully describe the thermodynamic equilibrium of aqueous electrolyte solutions. However, the large number of different, often multi-functional, organic compounds in mixed organic-inorganic particles is a challenging problem for the development of thermodynamic models. The group-contribution concept as introduced in the UNIFAC model by Fredenslund et al. (1975), is a practical method to handle this difficulty and to add a certain predictability for unknown organic substances. We present the group-contribution model AIOMFAC (Aerosol Inorganic-Organic Mixtures Functional groups Activity Coefficients), which explicitly accounts for molecular interactions between solution constituents, both organic and inorganic, to calculate activities, chemical potentials and the total Gibbs energy of mixed systems (Zuend et al., 2008). This model enables the computation of vapor-liquid (VLE), liquid-liquid (LLE) and solid-liquid (SLE) equilibria within one framework. Focusing on atmospheric applications we considered eight different cations, five anions and a wide range of alcohols/polyols as organic compounds. With AIOMFAC, the activities of the components within an aqueous electrolyte solution are very well represented up to high ionic strength. We show that the semi-empirical middle-range parametrization of direct organic-inorganic interactions in alcohol-water-salt solutions enables accurate computations of vapor-liquid and liquid

  13. Contemporary model of language organization: an overview for neurosurgeons.

    Science.gov (United States)

    Chang, Edward F; Raygor, Kunal P; Berger, Mitchel S

    2015-02-01

    Classic models of language organization posited that separate motor and sensory language foci existed in the inferior frontal gyrus (Broca's area) and superior temporal gyrus (Wernicke's area), respectively, and that connections between these sites (arcuate fasciculus) allowed for auditory-motor interaction. These theories have predominated for more than a century, but advances in neuroimaging and stimulation mapping have provided a more detailed description of the functional neuroanatomy of language. New insights have shaped modern network-based models of speech processing composed of parallel and interconnected streams involving both cortical and subcortical areas. Recent models emphasize processing in "dorsal" and "ventral" pathways, mediating phonological and semantic processing, respectively. Phonological processing occurs along a dorsal pathway, from the posterosuperior temporal to the inferior frontal cortices. On the other hand, semantic information is carried in a ventral pathway that runs from the temporal pole to the basal occipitotemporal cortex, with anterior connections. Functional MRI has poor positive predictive value in determining critical language sites and should only be used as an adjunct for preoperative planning. Cortical and subcortical mapping should be used to define functional resection boundaries in eloquent areas and remains the clinical gold standard. In tracing the historical advancements in our understanding of speech processing, the authors hope to not only provide practicing neurosurgeons with additional information that will aid in surgical planning and prevent postoperative morbidity, but also underscore the fact that neurosurgeons are in a unique position to further advance our understanding of the anatomy and functional organization of language.

  14. Performance Evaluation Based on EFQM Excellence Model in Sport Organizations

    Directory of Open Access Journals (Sweden)

    Rasoul Faraji

    2012-06-01

    Full Text Available The present study aims to evaluate the performance of physical education (P.E. general office of Tehran province through model of European Foundation for Quality Management (EFQM. Questionnaire approach was used in this study. Therefore validity of the 50-item EFQM questionnaire verified by the experts and the reliability also calculated in a pilot study (α=0.928. 95 questionnaires distributed between subjects (N=n and 80 questionnaires returned and concluded in the statistical analysis. From nine EFQM criteria, the highest scores were gained in key performance results (37.62% and the lowest gained in people results (27.94%. Totally, this organization achieved 337.11 pointes out of a total of 1000. Additionally, there was a strong relationship (r=0.827, p=0.001 between enablers and results (P<0.05. Based on scores gained in the criteria, improving measures in all criteria is essential for this organization, especially in the people criterion from enablers and people results criterion from results domain. Furthermore, it is believed that the physical education area is one of the best fields for application of the excellence model towards the performance excellence and gaining better results and hence, it seems that the model has a high potential in responding to problems commonly seen in sport sector.

  15. Modeling of secondary organic aerosol yields from laboratory chamber data

    Directory of Open Access Journals (Sweden)

    M. N. Chan

    2009-04-01

    Full Text Available A product-specific model for secondary organic aerosol (SOA formation and composition based on equilibrium gas-particle partitioning is evaluated. The model is applied to represent laboratory data on the ozonolysis of α-pinene under dry, dark, and low-NOx conditions in the presence of ammonium sulfate seed aerosol. Using five major identified products, the model is fit to the chamber data. From the optimal fitting, SOA oxygen-to-carbon (O/C and hydrogen-to-carbon (H/C ratios are modeled. The discrepancy between measured H/C ratios and those based on the oxidation products used in the model fitting suggests the potential importance of particle-phase reactions. Data fitting is also carried out using the volatility basis set, wherein oxidation products are parsed into volatility bins. The product-specific model is best used for an SOA precursor for which a substantial fraction of the aerosol-phase oxidation products has been identified.

  16. A Revised Iranian Model of Organ Donation as an Answer to the Current Organ Shortage Crisis.

    Science.gov (United States)

    Hamidian Jahromi, Alireza; Fry-Revere, Sigrid; Bastani, Bahar

    2015-09-01

    Kidney transplantation has become the treatment of choice for patients with end-stage renal disease. Six decades of success in the field of transplantation have made it possible to save thousands of lives every year. Unfortunately, in recent years success has been overshadowed by an ever-growing shortage of organs. In the United States, there are currently more than 100 000 patients waiting for kidneys. However, the supply of kidneys (combined cadaveric and live donations) has stagnated around 17 000 per year. The ever-widening gap between demand and supply has resulted in an illegal black market and unethical transplant tourism of global proportions. While we believe there is much room to improve the Iranian model of regulated incentivized live kidney donation, with some significant revisions, the Iranian Model could serve as an example for how other countries could make significant strides to lessening their own organ shortage crises.

  17. Real-time Monitoring of Non-specific Toxicity Using a Saccharomyces cerevisiae Reporter System

    Directory of Open Access Journals (Sweden)

    Matti Karp

    2008-10-01

    Full Text Available Baker’s yeast, Saccharomyces cerevisiae, is the simplest and most well-known representative of eukaryotic cells and thus a convenient model organism for evaluating toxic effects in human cells and tissues. Yeast cell sensors are easy to maintain with short generation times, which makes the analytical method of assessing antifungal toxicity cheap and less-time consuming. In this work, the toxicity of test compounds was assessed in bioassays based on bioluminescence inhibition and on traditional growth inhibition on agar plates. The model organism in both tests was a modified S. cerevisiae sensor strain that produces light when provided with D-luciferin in an insect luciferase reporter gene activity assay. The bioluminescence assay showed toxic effects for yeast cell sensor of 5,6-benzo-flavone, rapamycin, nystatin and cycloheximide at concentrations of nM to µM. In addition, arsenic compounds, cadmium chloride, copper sulfate and lead acetate were shown to be potent non-specific inhibitors of the reporter organism described here. The results from a yeast agar diffusion assay correlated with the bioluminescence assay results.

  18. Microfluidic reactor for continuous cultivation of Saccharomyces cerevisiae.

    Science.gov (United States)

    Edlich, Astrid; Magdanz, Veronika; Rasch, Detlev; Demming, Stefanie; Aliasghar Zadeh, Shobeir; Segura, Rodrigo; Kähler, Christian; Radespiel, Rolf; Büttgenbach, Stephanus; Franco-Lara, Ezequiel; Krull, Rainer

    2010-01-01

    A diffusion-based microreactor system operated with a reaction volume of 8 μL is presented and characterized to intensify the process understanding in microscale cultivations. Its potential as screening tool for biological processes is evaluated. The advantage of the designed microbioreactor is the use for the continuous cultivation mode by integrating online measurement technique for dissolved oxygen (DO) and optical density (OD). A further advantage is the broaden application for biological systems. The bioreactor geometry was chosen to achieve homogeneous flow during continuous process operation. The device consisted of a microstructured top layer made of poly(dimethylsiloxane) (PDMS), which was designed and fabricated using UV-depth and soft lithography assembled with a glass bottom. CFD simulation data used for geometry design were verified via microparticle-image-velocimetry (μPIV). In the used microreactor geometry no concentration gradients occurred along the entire reaction volume because of rapid diffusive mixing, the homogeneous medium flow inside the growth chamber of the microreactor could be realized. Undesirable bubble formation before and during operation was reduced by using degassed medium as well as moistened and moderate incident air flow above the gas permeable PDMS membrane. Because of this a passive oxygen supply of the culture medium in the device is ensured by diffusion through the PDMS membrane. The oxygen supply itself was monitored online via integrated DO sensors based on a fluorescent dye complex. An adequate overall volumetric oxygen transfer coefficient K(L)a as well as mechanical stability of the device were accomplished for a membrane thickness of 300 μm. Experimental investigations considering measurements of OD (online) and several metabolite concentrations (offline) in a modified Verduyn medium. The used model organism Saccharomyces cerevisiae DSM 2155 tended to strong reactor wall growth resembling a biofilm. © 2010

  19. Modeling the role of microplastics in Bioaccumulation of organic chemicals to marine aquatic organisms. Critical Review

    NARCIS (Netherlands)

    Koelmans, A.A.

    2015-01-01

    It has been shown that ingestion of microplastics may increase bioaccumulation of organic chemicals by aquatic organisms. This paper critically reviews the literature on the effects of plastic ingestion on the bioaccumulation of organic chemicals, emphasizing quantitative approaches and mechanistic

  20. Modeling the adsorption of weak organic acids on goethite: the ligand and charge distribution model

    NARCIS (Netherlands)

    Filius, J.D.

    2001-01-01

    A detailed study is presented in which the CD-MUSIC modeling approach is used in a new modeling approach that can describe the binding of large organic molecules by metal (hydr)oxides taking the full speciation of the adsorbed molecule into account. Batch equilibration experiments were performed usi

  1. Generic Modelling of Faecal Indicator Organism Concentrations in the UK

    Directory of Open Access Journals (Sweden)

    Carl M. Stapleton

    2011-06-01

    Full Text Available To meet European Water Framework Directive requirements, data are needed on faecal indicator organism (FIO concentrations in rivers to enable the more heavily polluted to be targeted for remedial action. Due to the paucity of FIO data for the UK, especially under high-flow hydrograph event conditions, there is an urgent need by the policy community for generic models that can accurately predict FIO concentrations, thus informing integrated catchment management programmes. This paper reports the development of regression models to predict base- and high-flow faecal coliform (FC and enterococci (EN concentrations for 153 monitoring points across 14 UK catchments, using land cover, population (human and livestock density and other variables that may affect FIO source strength, transport and die-off. Statistically significant models were developed for both FC and EN, with greater explained variance achieved in the high-flow models. Both land cover and, in particular, population variables are significant predictors of FIO concentrations, with r2 maxima for EN of 0.571 and 0.624, respectively. It is argued that the resulting models can be applied, with confidence, to other UK catchments, both to predict FIO concentrations in unmonitored watercourses and evaluate the likely impact of different land use/stocking level and human population change scenarios.

  2. Modeling financial markets by self-organized criticality

    Science.gov (United States)

    Biondo, Alessio Emanuele; Pluchino, Alessandro; Rapisarda, Andrea

    2015-10-01

    We present a financial market model, characterized by self-organized criticality, that is able to generate endogenously a realistic price dynamics and to reproduce well-known stylized facts. We consider a community of heterogeneous traders, composed by chartists and fundamentalists, and focus on the role of informative pressure on market participants, showing how the spreading of information, based on a realistic imitative behavior, drives contagion and causes market fragility. In this model imitation is not intended as a change in the agent's group of origin, but is referred only to the price formation process. We introduce in the community also a variable number of random traders in order to study their possible beneficial role in stabilizing the market, as found in other studies. Finally, we also suggest some counterintuitive policy strategies able to dampen fluctuations by means of a partial reduction of information.

  3. Modeling financial markets by self-organized criticality.

    Science.gov (United States)

    Biondo, Alessio Emanuele; Pluchino, Alessandro; Rapisarda, Andrea

    2015-10-01

    We present a financial market model, characterized by self-organized criticality, that is able to generate endogenously a realistic price dynamics and to reproduce well-known stylized facts. We consider a community of heterogeneous traders, composed by chartists and fundamentalists, and focus on the role of informative pressure on market participants, showing how the spreading of information, based on a realistic imitative behavior, drives contagion and causes market fragility. In this model imitation is not intended as a change in the agent's group of origin, but is referred only to the price formation process. We introduce in the community also a variable number of random traders in order to study their possible beneficial role in stabilizing the market, as found in other studies. Finally, we also suggest some counterintuitive policy strategies able to dampen fluctuations by means of a partial reduction of information.

  4. Modelling Financial Markets by Self-Organized Criticality

    CERN Document Server

    Biondo, A E; Rapisarda, A

    2015-01-01

    We present a financial market model, characterized by self-organized criticality, that is able to generate endogenously a realistic price dynamics and to reproduce well-known stylized facts. We consider a community of heterogeneous traders, composed by chartists and fundamentalists, and focus on the role of informative pressure on market participants, showing how the spreading of information, based on a realistic imitative behavior, drives contagion and causes market fragility. In this model imitation is not intended as a change in the agent's group of origin, but is referred only to the price formation process. We introduce in the community also a variable number of random traders in order to study their possible beneficial role in stabilizing the market, as found in other studies. Finally we also suggest some counterintuitive policy strategies able to dampen fluctuations by means of a partial reduction of information.

  5. Partitioning of Nanoparticles into Organic Phases and Model Cells

    Energy Technology Data Exchange (ETDEWEB)

    Posner, J.D.; Westerhoff, P.; Hou, W-C.

    2011-08-25

    There is a recognized need to understand and predict the fate, transport and bioavailability of engineered nanoparticles (ENPs) in aquatic and soil ecosystems. Recent research focuses on either collection of empirical data (e.g., removal of a specific NP through water or soil matrices under variable experimental conditions) or precise NP characterization (e.g. size, degree of aggregation, morphology, zeta potential, purity, surface chemistry, and stability). However, it is almost impossible to transition from these precise measurements to models suitable to assess the NP behavior in the environment with complex and heterogeneous matrices. For decades, the USEPA has developed and applies basic partitioning parameters (e.g., octanol-water partition coefficients) and models (e.g., EPI Suite, ECOSAR) to predict the environmental fate, bioavailability, and toxicity of organic pollutants (e.g., pesticides, hydrocarbons, etc.). In this project we have investigated the hypothesis that NP partition coefficients between water and organic phases (octanol or lipid bilayer) is highly dependent on their physiochemical properties, aggregation, and presence of natural constituents in aquatic environments (salts, natural organic matter), which may impact their partitioning into biological matrices (bioaccumulation) and human exposure (bioavailability) as well as the eventual usage in modeling the fate and bioavailability of ENPs. In this report, we use the terminology "partitioning" to operationally define the fraction of ENPs distributed among different phases. The mechanisms leading to this partitioning probably involve both chemical force interactions (hydrophobic association, hydrogen bonding, ligand exchange, etc.) and physical forces that bring the ENPs in close contact with the phase interfaces (diffusion, electrostatic interactions, mixing turbulence, etc.). Our work focuses on partitioning, but also provides insight into the relative behavior of ENPs as either "more like

  6. Partitioning of Nanoparticles into Organic Phases and Model Cells

    Energy Technology Data Exchange (ETDEWEB)

    Posner, J.D.; Westerhoff, P.; Hou, W-C.

    2011-08-25

    There is a recognized need to understand and predict the fate, transport and bioavailability of engineered nanoparticles (ENPs) in aquatic and soil ecosystems. Recent research focuses on either collection of empirical data (e.g., removal of a specific NP through water or soil matrices under variable experimental conditions) or precise NP characterization (e.g. size, degree of aggregation, morphology, zeta potential, purity, surface chemistry, and stability). However, it is almost impossible to transition from these precise measurements to models suitable to assess the NP behavior in the environment with complex and heterogeneous matrices. For decades, the USEPA has developed and applies basic partitioning parameters (e.g., octanol-water partition coefficients) and models (e.g., EPI Suite, ECOSAR) to predict the environmental fate, bioavailability, and toxicity of organic pollutants (e.g., pesticides, hydrocarbons, etc.). In this project we have investigated the hypothesis that NP partition coefficients between water and organic phases (octanol or lipid bilayer) is highly dependent on their physiochemical properties, aggregation, and presence of natural constituents in aquatic environments (salts, natural organic matter), which may impact their partitioning into biological matrices (bioaccumulation) and human exposure (bioavailability) as well as the eventual usage in modeling the fate and bioavailability of ENPs. In this report, we use the terminology "partitioning" to operationally define the fraction of ENPs distributed among different phases. The mechanisms leading to this partitioning probably involve both chemical force interactions (hydrophobic association, hydrogen bonding, ligand exchange, etc.) and physical forces that bring the ENPs in close contact with the phase interfaces (diffusion, electrostatic interactions, mixing turbulence, etc.). Our work focuses on partitioning, but also provides insight into the relative behavior of ENPs as either "more like

  7. Correlated earthquakes in a self-organized model

    Directory of Open Access Journals (Sweden)

    M. Baiesi

    2009-03-01

    Full Text Available Motivated by the fact that empirical time series of earthquakes exhibit long-range correlations in space and time and the Gutenberg-Richter distribution of magnitudes, we propose a simple fault model that can account for these types of scale-invariance. It is an avalanching process that displays power-laws in the event sizes, in the epicenter distances as well as in the waiting-time distributions, and also aftershock rates obeying a generalized Omori law. We thus confirm that there is a relation between temporal and spatial clustering of the activity in this kind of models. The fluctuating boundaries of possible slipping areas show that the size of the largest possible earthquake is not always maximal, and the average correlation length is a fraction of the system size. This suggests that there is a concrete alternative to the extreme interpretation of self-organized criticality as a process in which every small event can cascade to an arbitrary large one: the new picture includes fluctuating domains of coherent stress field as part of the global self-organization. Moreover, this picture can be more easily compared with other scenarios discussing fluctuating correlations lengths in seismicity.

  8. Terrestrial and marine perspectives on modeling organic matter degradation pathways.

    Science.gov (United States)

    Burd, Adrian B; Frey, Serita; Cabre, Anna; Ito, Takamitsu; Levine, Naomi M; Lønborg, Christian; Long, Matthew; Mauritz, Marguerite; Thomas, R Quinn; Stephens, Brandon M; Vanwalleghem, Tom; Zeng, Ning

    2016-01-01

    Organic matter (OM) plays a major role in both terrestrial and oceanic biogeochemical cycles. The amount of carbon stored in these systems is far greater than that of carbon dioxide (CO2 ) in the atmosphere, and annual fluxes of CO2 from these pools to the atmosphere exceed those from fossil fuel combustion. Understanding the processes that determine the fate of detrital material is important for predicting the effects that climate change will have on feedbacks to the global carbon cycle. However, Earth System Models (ESMs) typically utilize very simple formulations of processes affecting the mineralization and storage of detrital OM. Recent changes in our view of the nature of this material and the factors controlling its transformation have yet to find their way into models. In this review, we highlight the current understanding of the role and cycling of detrital OM in terrestrial and marine systems and examine how this pool of material is represented in ESMs. We include a discussion of the different mineralization pathways available as organic matter moves from soils, through inland waters to coastal systems and ultimately into open ocean environments. We argue that there is strong commonality between aspects of OM transformation in both terrestrial and marine systems and that our respective scientific communities would benefit from closer collaboration.

  9. Advances in metabolic engineering of yeast Saccharomyces cerevisiae for production of chemicals

    DEFF Research Database (Denmark)

    Borodina, Irina; Nielsen, Jens

    2014-01-01

    Yeast Saccharomyces cerevisiae is an important industrial host for production of enzymes, pharmaceutical and nutraceutical ingredients and recently also commodity chemicals and biofuels. Here, we review the advances in modeling and synthetic biology tools and how these tools can speed up the deve......Yeast Saccharomyces cerevisiae is an important industrial host for production of enzymes, pharmaceutical and nutraceutical ingredients and recently also commodity chemicals and biofuels. Here, we review the advances in modeling and synthetic biology tools and how these tools can speed up...

  10. 2μ plasmid in Saccharomyces species and in Saccharomyces cerevisiae.

    Science.gov (United States)

    Strope, Pooja K; Kozmin, Stanislav G; Skelly, Daniel A; Magwene, Paul M; Dietrich, Fred S; McCusker, John H

    2015-12-01

    We determined that extrachromosomal 2μ plasmid was present in 67 of the Saccharomyces cerevisiae 100-genome strains; in addition to variation in the size and copy number of 2μ, we identified three distinct classes of 2μ. We identified 2μ presence/absence and class associations with populations, clinical origin and nuclear genotypes. We also screened genome sequences of S. paradoxus, S. kudriavzevii, S. uvarum, S. eubayanus, S. mikatae, S. arboricolus and S. bayanus strains for both integrated and extrachromosomal 2μ. Similar to S. cerevisiae, we found no integrated 2μ sequences in any S. paradoxus strains. However, we identified part of 2μ integrated into the genomes of some S. uvarum, S. kudriavzevii, S. mikatae and S. bayanus strains, which were distinct from each other and from all extrachromosomal 2μ. We identified extrachromosomal 2μ in one S. paradoxus, one S. eubayanus, two S. bayanus and 13 S. uvarum strains. The extrachromosomal 2μ in S. paradoxus, S. eubayanus and S. cerevisiae were distinct from each other. In contrast, the extrachromosomal 2μ in S. bayanus and S. uvarum strains were identical with each other and with one of the three classes of S. cerevisiae 2μ, consistent with interspecific transfer.

  11. Modeling organic micro pollutant degradation kinetics during sewage sludge composting.

    Science.gov (United States)

    Sadef, Yumna; Poulsen, Tjalfe Gorm; Bester, Kai

    2014-11-01

    Degradation of 13 different organic micro-pollutants in sewage sludge during aerobic composting at 5 different temperatures over a 52 day period was investigated. Adequacy of two kinetic models: a single first order, and a dual first order expression (using an early (first 7 days) and a late-time (last 45 days) degradation coefficient), for describing micro-pollutant degradation, and kinetic constant dependency on composting temperature were evaluated. The results showed that both models provide relatively good descriptions of the degradation process, with the dual first order model being most accurate. The single first order degradation coefficient was 0.025 d(-1) on average across all compounds and temperatures. At early times, degradation was about three times faster than at later times. Average values of the early and late time degradation coefficients for the dual first order model were 0.066 d(-1) and 0.022 d(-1), respectively. On average 30% of the initial micro-pollutant mass present in the compost was degraded rapidly during the early stages of the composting process. Single first order and late time dual first order kinetic constants were strongly dependent on composting temperature with maximum values at temperatures of 35-65°C. In contrast the early time degradation coefficients were relatively independent of composting temperature.

  12. Mathematical modeling of wastewater-derived biodegradable dissolved organic nitrogen.

    Science.gov (United States)

    Simsek, Halis

    2016-11-01

    Wastewater-derived dissolved organic nitrogen (DON) typically constitutes the majority of total dissolved nitrogen (TDN) discharged to surface waters from advanced wastewater treatment plants (WWTPs). When considering the stringent regulations on nitrogen discharge limits in sensitive receiving waters, DON becomes problematic and needs to be reduced. Biodegradable DON (BDON) is a portion of DON that is biologically degradable by bacteria when the optimum environmental conditions are met. BDON in a two-stage trickling filter WWTP was estimated using artificial intelligence techniques, such as adaptive neuro-fuzzy inference systems, multilayer perceptron, radial basis neural networks (RBNN), and generalized regression neural networks. Nitrite, nitrate, ammonium, TDN, and DON data were used as input neurons. Wastewater samples were collected from four different locations in the plant. Model performances were evaluated using root mean square error, mean absolute error, mean bias error, and coefficient of determination statistics. Modeling results showed that the R(2) values were higher than 0.85 in all four models for all wastewater samples, except only R(2) in the final effluent sample for RBNN modeling was low (0.52). Overall, it was found that all four computing techniques could be employed successfully to predict BDON.

  13. Priming and substrate quality interactions in soil organic matter models

    Directory of Open Access Journals (Sweden)

    T. Wutzler

    2012-12-01

    Full Text Available Interactions between different qualities of soil organic matter (SOM affecting their turnover are rarely represented in models. In this study we propose three mathematical strategies at different levels of abstraction for representing those interactions. Implementing these strategies into the Introductory Carbon Balance Model (ICBM and applying them to several scenarios of litter input show that the different levels of abstraction are applicable on different time scales. We present a simple one-parameter equation of substrate limitation applicable at decadal time scale that is straightforward to implement into other models of SOM dynamics. We show how substrate quality interactions can explain priming effects, acceleration of turnover times in FACE experiments, and the slowdown of decomposition in long-term bare fallow experiments as an effect of energy limitation of microbial biomass. The mechanisms of those interactions need to be further scrutinized empirically for a more complete understanding. Overall, substrate quality interactions offer a valuable way of understanding and quantitatively modelling SOM dynamics.

  14. Modeling organic aerosols during MILAGRO: importance of biogenic secondary organic aerosols

    Directory of Open Access Journals (Sweden)

    A. Hodzic

    2009-09-01

    Full Text Available The meso-scale chemistry-transport model CHIMERE is used to assess our understanding of major sources and formation processes leading to a fairly large amount of organic aerosols – OA, including primary OA (POA and secondary OA (SOA – observed in Mexico City during the MILAGRO field project (March 2006. Chemical analyses of submicron aerosols from aerosol mass spectrometers (AMS indicate that organic particles found in the Mexico City basin contain a large fraction of oxygenated organic species (OOA which have strong correspondence with SOA, and that their production actively continues downwind of the city. The SOA formation is modeled here by the one-step oxidation of anthropogenic (i.e. aromatics, alkanes, biogenic (i.e. monoterpenes and isoprene, and biomass-burning SOA precursors and their partitioning into both organic and aqueous phases. Conservative assumptions are made for uncertain parameters to maximize the amount of SOA produced by the model. The near-surface model evaluation shows that predicted OA correlates reasonably well with measurements during the campaign, however it remains a factor of 2 lower than the measured total OA. Fairly good agreement is found between predicted and observed POA within the city suggesting that anthropogenic and biomass burning emissions are reasonably captured. Consistent with previous studies in Mexico City, large discrepancies are encountered for SOA, with a factor of 2–10 model underestimate. When only anthropogenic SOA precursors were considered, the model was able to reproduce within a factor of two the sharp increase in OOA concentrations during the late morning at both urban and near-urban locations but the discrepancy increases rapidly later in the day, consistent with previous results, and is especially obvious when the column-integrated SOA mass is considered instead of the surface concentration. The increase in the missing SOA mass in the afternoon coincides with the sharp drop in POA

  15. Mechanisms of ethanol tolerance in Saccharomyces cerevisiae.

    Science.gov (United States)

    Ma, Menggen; Liu, Z Lewis

    2010-07-01

    Saccharomyces cerevisiae is a superb ethanol producer, yet is also sensitive to higher ethanol concentrations especially under high gravity or very high gravity fermentation conditions. Ethanol tolerance is associated with interplay of complex networks at the genome level. Although significant efforts have been made to study ethanol stress response in past decades, mechanisms of ethanol tolerance are not well known. With developments of genome sequencing and genomic technologies, our understanding of yeast biology has been revolutionarily advanced. More evidence of mechanisms of ethanol tolerance have been discovered involving multiple loci, multi-stress, and complex interactions as well as signal transduction pathways and regulatory networks. Transcription dynamics and profiling studies of key gene sets including heat shock proteins provided insight into tolerance mechanisms. A transient gene expression response or a stress response to ethanol does not necessarily lead to ethanol tolerance in yeast. Reprogrammed pathways and interactions of cofactor regeneration and redox balance observed from studies of tolerant yeast demonstrated the significant importance of a time-course study for ethanol tolerance. In this review, we focus on current advances of our understanding for ethanol-tolerance mechanisms of S. cerevisiae including gene expression responses, pathway-based analysis, signal transduction and regulatory networks. A prototype of global system model for mechanisms of ethanol tolerance is presented.

  16. Modeling biogenic and anthropogenic secondary organic aerosol in China

    Science.gov (United States)

    Hu, Jianlin; Wang, Peng; Ying, Qi; Zhang, Hongliang; Chen, Jianjun; Ge, Xinlei; Li, Xinghua; Jiang, Jingkun; Wang, Shuxiao; Zhang, Jie; Zhao, Yu; Zhang, Yingyi

    2017-01-01

    A revised Community Multi-scale Air Quality (CMAQ) model with updated secondary organic aerosol (SOA) yields and a more detailed description of SOA formation from isoprene oxidation was applied to study the spatial and temporal distribution of SOA in China in the entire year of 2013. Predicted organic carbon (OC), elemental carbon and volatile organic compounds agreed favorably with observations at several urban areas, although the high OC concentrations in wintertime in Beijing were under-predicted. Predicted summer SOA was generally higher (10-15 µg m-3) due to large contributions of isoprene (country average, 61 %), although the relative importance varies in different regions. Winter SOA was slightly lower and was mostly due to emissions of alkane and aromatic compounds (51 %). Contributions of monoterpene SOA was relatively constant (8-10 %). Overall, biogenic SOA accounted for approximately 75 % of total SOA in summer, 50-60 % in autumn and spring, and 24 % in winter. The Sichuan Basin had the highest predicted SOA concentrations in the country in all seasons, with hourly concentrations up to 50 µg m-3. Approximately half of the SOA in all seasons was due to the traditional equilibrium partitioning of semivolatile components followed by oligomerization, while the remaining SOA was mainly due to reactive surface uptake of isoprene epoxide (5-14 %), glyoxal (14-25 %) and methylglyoxal (23-28 %). Sensitivity analyses showed that formation of SOA from biogenic emissions was significantly enhanced due to anthropogenic emissions. Removing all anthropogenic emissions while keeping the biogenic emissions unchanged led to total SOA concentrations of less than 1 µg m-3, which suggests that manmade emissions facilitated biogenic SOA formation and controlling anthropogenic emissions would result in reduction of both anthropogenic and biogenic SOA.

  17. Nephrology around Europe: organization models and management strategies: Spain.

    Science.gov (United States)

    de Francisco, Angel L M; Piñera, Celestino

    2011-01-01

    The main aim of this report is to present a picture of the current organization of nephrology in Spain. The Spanish health system offers almost universal coverage, a wide variety of services and a high-quality network of hospitals and primary care centers. Spain has a specialized health care training system that is highly developed, highly regulated, with the capacity to provide high-quality training in 54 different specialties. Nephrology is basically a hospital-based specialty. There are no private dialysis patients in Spain. Hemodialysis centers are 40% public, 15% private and 45% run by companies. The National Health System covers 95% of the population, and there is no cost to patients for treatment of renal disease (dialysis and transplant). We observed a clear decrease of nephrology in residents' election rankings, with position 29 out of 47 specialties in 2007. Some of the reasons for this are the complexity of the subject, no clear information at the university, reduction of professional posts and a very good public service with minimal private practice. In Spain, a model of organization for transplantation was adopted based on a decentralized transplant coordinating network. For cadaveric donors, it compares favorably with rates in other Western countries. Living donor transplantation is very low in Spain--just 10% of total renal transplantation activity. New programs due to financial constraints need to include reduced dialysis costs, greater cost-effectiveness of prescriptions, better handling of ethical issues related to the need for using a clinical score of chronic kidney disease patients to make decisions about conservative or renal replacement therapy and an action plan for improvement of organ donation and transplantation. Recovery of skills (acute kidney injury, biopsies, vascular access, etc.), research and advances in autonomous activities (imaging, surgical and medical vascular training, etc.) are some of the future educational paths needed in

  18. Enhancement of the fungicidal activity of amphotericin B by allicin, an allyl-sulfur compound from garlic, against the yeast Saccharomyces cerevisiae as a model system.

    Science.gov (United States)

    Ogita, Akira; Fujita, Ken-ichi; Taniguchi, Makoto; Tanaka, Toshio

    2006-10-01

    Amphotericin B (AmB) is a representative antibiotic for the control of serious fungal infections, and its fungicidal activity was greatly enhanced by allicin, an allyl-sulfur compound from garlic. In addition to the plasma membrane permeability change, AmB induced vacuole membrane damage so that the organelles were visible as small discrete particles. Although allicin was ineffective in promoting AmB-induced plasma membrane disability, this compound enhanced AmB-induced structural damage to the vacuolar membrane even at a non-lethal dose of the antibiotic. Allicin could also enhance the antifungal activity of AmB against the pathogenic fungus Candida albicans and against Aspergillus fumigatus. In contrast, allicin did not enhance the cytotoxic activity of AmB against cells of human promyelocytic leukemia (HL-60), a vacuole-less organism.

  19. Trans-sulfuration Pathway Seleno-amino Acids Are Mediators of Selenomethionine Toxicity in Saccharomyces cerevisiae*

    Science.gov (United States)

    Lazard, Myriam; Dauplais, Marc; Blanquet, Sylvain; Plateau, Pierre

    2015-01-01

    Toxicity of selenomethionine, an organic derivative of selenium widely used as supplement in human diets, was studied in the model organism Saccharomyces cerevisiae. Several DNA repair-deficient strains hypersensitive to selenide displayed wild-type growth rate properties in the presence of selenomethionine indicating that selenide and selenomethionine exert their toxicity via distinct mechanisms. Cytotoxicity of selenomethionine decreased when the extracellular concentration of methionine or S-adenosylmethionine was increased. This protection resulted from competition between the S- and Se-compounds along the downstream metabolic pathways inside the cell. By comparing the sensitivity to selenomethionine of mutants impaired in the sulfur amino acid pathway, we excluded a toxic effect of Se-adenosylmethionine, Se-adenosylhomocysteine, or of any compound in the methionine salvage pathway. Instead, we found that selenomethionine toxicity is mediated by the trans-sulfuration pathway amino acids selenohomocysteine and/or selenocysteine. Involvement of superoxide radicals in selenomethionine toxicity in vivo is suggested by the hypersensitivity of a Δsod1 mutant strain, increased resistance afforded by the superoxide scavenger manganese, and inactivation of aconitase. In parallel, we showed that, in vitro, the complete oxidation of the selenol function of selenocysteine or selenohomocysteine by dioxygen is achieved within a few minutes at neutral pH and produces superoxide radicals. These results establish a link between superoxide production and trans-sulfuration pathway seleno-amino acids and emphasize the importance of the selenol function in the mechanism of organic selenium toxicity. PMID:25745108

  20. Multi-Capillary Column-Ion Mobility Spectrometry of Volatile Metabolites Emitted by Saccharomyces Cerevisiae

    Directory of Open Access Journals (Sweden)

    Christoph Halbfeld

    2014-09-01

    Full Text Available Volatile organic compounds (VOCs produced during microbial fermentations determine the flavor of fermented food and are of interest for the production of fragrances or food additives. However, the microbial synthesis of these compounds from simple carbon sources has not been well investigated so far. Here, we analyzed the headspace over glucose minimal salt medium cultures of Saccharomyces cerevisiae using multi-capillary column-ion mobility spectrometry (MCC-IMS. The high sensitivity and fast data acquisition of the MCC-IMS enabled online analysis of the fermentation off-gas and 19 specific signals were determined. To four of these volatile compounds, we could assign the metabolites ethanol, 2-pentanone, isobutyric acid, and 2,3-hexanedione by MCC-IMS measurements of pure standards and cross validation with thermal desorption–gas chromatography-mass spectrometry measurements. Despite the huge biochemical knowledge of the biochemistry of the model organism S. cerevisiae, only the biosynthetic pathways for ethanol and isobutyric acid are fully understood, demonstrating the considerable lack of research of volatile metabolites. As monitoring of VOCs produced during microbial fermentations can give valuable insight into the metabolic state of the organism, fast and non-invasive MCC-IMS analyses provide valuable data for process control.

  1. Modeling evolutionary dynamics of epigenetic mutations in hierarchically organized tumors.

    Directory of Open Access Journals (Sweden)

    Andrea Sottoriva

    2011-05-01

    Full Text Available The cancer stem cell (CSC concept is a highly debated topic in cancer research. While experimental evidence in favor of the cancer stem cell theory is apparently abundant, the results are often criticized as being difficult to interpret. An important reason for this is that most experimental data that support this model rely on transplantation studies. In this study we use a novel cellular Potts model to elucidate the dynamics of established malignancies that are driven by a small subset of CSCs. Our results demonstrate that epigenetic mutations that occur during mitosis display highly altered dynamics in CSC-driven malignancies compared to a classical, non-hierarchical model of growth. In particular, the heterogeneity observed in CSC-driven tumors is considerably higher. We speculate that this feature could be used in combination with epigenetic (methylation sequencing studies of human malignancies to prove or refute the CSC hypothesis in established tumors without the need for transplantation. Moreover our tumor growth simulations indicate that CSC-driven tumors display evolutionary features that can be considered beneficial during tumor progression. Besides an increased heterogeneity they also exhibit properties that allow the escape of clones from local fitness peaks. This leads to more aggressive phenotypes in the long run and makes the neoplasm more adaptable to stringent selective forces such as cancer treatment. Indeed when therapy is applied the clone landscape of the regrown tumor is more aggressive with respect to the primary tumor, whereas the classical model demonstrated similar patterns before and after therapy. Understanding these often counter-intuitive fundamental properties of (non-hierarchically organized malignancies is a crucial step in validating the CSC concept as well as providing insight into the therapeutical consequences of this model.

  2. Spectrophotometry and organic matter on Iapetus. 1: Composition models

    Science.gov (United States)

    Wilson, Peter D.; Sagan, Carl

    1995-01-01

    Iapetus shows a greater hemispheric albedo asymmetry than any other body in the solar system. Hapke scattering theory and optical constants measured in the laboratory are used to identify possible compositions for the dark material on the leading hemisphere of Iapetus. The materials considered are poly-HCN, kerogen, Murchison organic residue, Titan tholin, ice tholin, and water ice. Three-component mixtures of these materials are modeled in intraparticle mixture of 25% poly-HCN, 10% Murchison residue, and 65% water ice is found to best fit the spectrum, albedo, and phase behavior of the dark material. The Murchison residue and/or water ice can be replaced by kerogen and ice tholin, respectively, and still produce very good fits. Areal and particle mixtures of poly-HCN, Titan tholin, and either ice tholin or Murchison residue are also possible models. Poly-HCN is a necessary component in almost all good models. The presence of poly-HCN can be further tested by high-resolution observations near 4.5 micrometers.

  3. In Vivo RNAi-Based Screens: Studies in Model Organisms

    Directory of Open Access Journals (Sweden)

    Miki Yamamoto-Hino

    2013-11-01

    Full Text Available RNA interference (RNAi is a technique widely used for gene silencing in organisms and cultured cells, and depends on sequence homology between double-stranded RNA (dsRNA and target mRNA molecules. Numerous cell-based genome-wide screens have successfully identified novel genes involved in various biological processes, including signal transduction, cell viability/death, and cell morphology. However, cell-based screens cannot address cellular processes such as development, behavior, and immunity. Drosophila and Caenorhabditis elegans are two model organisms whose whole bodies and individual body parts have been subjected to RNAi-based genome-wide screening. Moreover, Drosophila RNAi allows the manipulation of gene function in a spatiotemporal manner when it is implemented using the Gal4/UAS system. Using this inducible RNAi technique, various large-scale screens have been performed in Drosophila, demonstrating that the method is straightforward and valuable. However, accumulated results reveal that the results of RNAi-based screens have relatively high levels of error, such as false positives and negatives. Here, we review in vivo RNAi screens in Drosophila and the methods that could be used to remove ambiguity from screening results.

  4. Multiscale modelling of charge transport in organic electronic materials

    Science.gov (United States)

    Nelson, Jenny

    2010-03-01

    Charge transport in disordered organic semiconductors is controlled by a complex combination of phenomena that span a range of length and time scales. As a result, it is difficult to rationalize charge transport properties in terms of material parameters. Until now, efforts to improve charge mobilities in molecular semiconductors have proceeded largely by trial and error rather than through systematic design. However, recent developments have enabled the first predictive simulation studies of charge transport in disordered organic semiconductors. In this presentation we will show how a set of computational methods, namely molecular modelling methods to simulate molecular packing, quantum chemical calculations of charge transfer rates, and Monte Carlo simulations of charge transport can be used to reproduce experimental charge mobilities with few or no fitting parameters. Using case studies, we will show how such simulations can explain the relative values of electron and hole mobility and the effects of grain size, side chains and polymer molecular weight on charge mobility. Although currently applied to material systems of relatively high symmetry or well defined structure, this approach can be developed to address more complex systems such as multicomponent solids and conjugated polymers.

  5. Dosage Effects of Salt and pH Stresses on Saccharomyces cerevisiae as Monitored via Metabolites by Using Two Dimensional NMR Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Chae, Young Kee; Kim, Seol Hyun [Sejong Univ., Seoul (Korea, Republic of); Ellinger, James E.; Markley, John L. [Univ. of Wisconsin-Madison Madison (United States)

    2013-12-15

    Saccharomyces cerevisiae, which is a common species of yeast, is by far the most extensively studied model of a eukaryote because although it is one of the simplest eukaryotes, its basic cellular processes resemble those of higher organisms. In addition, yeast is a commercially valuable organism for ethanol production. Since the yeast data can be extrapolated to the important aspects of higher organisms, many researchers have studied yeast metabolism under various conditions. In this report, we analyzed and compared metabolites of Saccharomyces cerevisiae under salt and pH stresses of various strengths by using two-dimensional NMR spectroscopy. A total of 31 metabolites were identified for most of the samples. The levels of many identified metabolites showed gradual or drastic increases or decreases depending on the severity of the stresses involved. The statistical analysis produced a holistic outline: pH stresses were clustered together, but salt stresses were spread out depending on the severity. This work could provide a link between the metabolite profiles and mRNA or protein profiles under representative and well studied stress conditions.

  6. Translational thermotolerance in Saccharomyces cerevisiae

    Science.gov (United States)

    Hallberg, Elizabeth M.; Hallberg, Richard L.

    1996-01-01

    While protein synthesis is rapidly inactivated in Saccharomyces cerevisiae, cells shifted from log growth at 30°C to 43°C, a 1-h 37°C treatment given to cells just prior to the shift to 43°C partially blocks this inactivation. By contrast, such a pre-heat shock treament has no protective effect on translational inactivation at 45°C or higher. Cells allowed to approach stationary phase not only develop an enhanced thermotolerance relative to log cells but also exhibit a pronounced resistance to inactivation of protein synthesis at 43°C as well as at 45°C. We have found that this ‘translational thermotolerance’ can also be induced in S. cerevisiae by briefly treating log phase cells at 30°C with cycloheximide. Using such a procedure to induce stabilization of protein synthesis at 43°C, we have been able to show that heat shock-induced proteins are not responsible for the establishment of this protective effect. This work shows that enhanced thermotolerance can be induced in log cells even after a shift to 43°C, as long as a prior translational thermotolerance has been established. Futhermore, we show that the capacity of plateau cells to maintain translation at 43°C contributes significantly to their state of enhanced thermotolerance. PMID:9222591

  7. EcoCyc: fusing model organism databases with systems biology.

    Science.gov (United States)

    Keseler, Ingrid M; Mackie, Amanda; Peralta-Gil, Martin; Santos-Zavaleta, Alberto; Gama-Castro, Socorro; Bonavides-Martínez, César; Fulcher, Carol; Huerta, Araceli M; Kothari, Anamika; Krummenacker, Markus; Latendresse, Mario; Muñiz-Rascado, Luis; Ong, Quang; Paley, Suzanne; Schröder, Imke; Shearer, Alexander G; Subhraveti, Pallavi; Travers, Mike; Weerasinghe, Deepika; Weiss, Verena; Collado-Vides, Julio; Gunsalus, Robert P; Paulsen, Ian; Karp, Peter D

    2013-01-01

    EcoCyc (http://EcoCyc.org) is a model organism database built on the genome sequence of Escherichia coli K-12 MG1655. Expert manual curation of the functions of individual E. coli gene products in EcoCyc has been based on information found in the experimental literature for E. coli K-12-derived strains. Updates to EcoCyc content continue to improve the comprehensive picture of E. coli biology. The utility of EcoCyc is enhanced by new tools available on the EcoCyc web site, and the development of EcoCyc as a teaching tool is increasing the impact of the knowledge collected in EcoCyc.

  8. A self-organized critical model for evolution

    Energy Technology Data Exchange (ETDEWEB)

    Flyvbjerg, H.; Bak, P.; Jensen, M.H.; Sneppen, K.

    1996-01-01

    A simple mathematical model of biological macroevolution is presented. It describes an ecology of adapting, interacting species. Species evolve to maximize their individual fitness in their environment. The environment of any given species is affected by other evolving species; hence it is not constant in time. The ecology evolves to a ``self-organized critical`` state where periods of stasis alternate with avalanches of causally connected evolutionary changes. This characteristic intermittent behaviour of natural history, known as ``punctuated equilibrium,`` thus finds a theoretical explanation as a selforganized critical phenomenon. In particular, large bursts of apparently simultaneous evolutionary activity require no external cause. They occur as the less frequent result of the very same dynamics that governs the more frequent small-scale evolutionary activity. Our results are compared with data from the fossil record collected by J. Sepkoski, Jr., and others.

  9. Modeling nanostructure-enhanced light trapping in organic solar cells

    DEFF Research Database (Denmark)

    Adam, Jost

    A promising approach for improving the power conversion efficiencies of organic solar cells (OSCs) is by incorporating nanostructures in their thin film architecture to improve the light absorption in the device’s active polymer layers. Here, we present a modelling framework for the prediction...... of optical and plasmonic field enhancement by nanostructures in (or close to) the active layers and electrodes in OSCs. We incorporate finite-difference time-domain (FDTD) calculations alongside semi- analytical approaches, as the rigorous coupled-wave analysis (RCWA) and mode-coupling theory. Our simulation......-compatible method for non-periodic electrode structuring by pores of controlled dimensions, formed through anodic oxidation of sputter-deposited high-purity aluminium films [3]. [1] Kluge, C., et al. Multi-periodic nanostructures for photon control. Optics Express, 22 (S5), A1363. (2014) [2] Skigin, D., et al...

  10. Corporate Social Responsibility And Islamic Business Organizations: A Proposed Model

    Directory of Open Access Journals (Sweden)

    Rusnah Muhamad

    2008-01-01

    Full Text Available The issue of corporate social responsibility (CSR has been of growing concern among business communities in recent years. Various corporate leaders maintain that business is considered to contribute fully to the society if it is effi cient, profi table and socially responsible. Islam is considered as addin (a way of life, thus, providing comprehensive guidelines in every aspects of the believers’ life. It is the aim of this paper to propose an Islamic model of corporate social responsibility based on human relationships with the God (hablun min’Allah; with other fellow human being (hablun min’an-nas and with the environment.Keywords : Corporate Social Responsibility, Islamic Business Organization

  11. Azolla - A Model Organism for Plant Genomic Studies

    Institute of Scientific and Technical Information of China (English)

    Yin-Long Qiu; Jun Yu

    2003-01-01

    The aquatic ferns of the genus Azolla are nitrogen-fixing plants that have great potentials in agricultural production and environmental conservation. Azolla in many aspects is qualified to serve as a model organism for genomic studies because of its importance in agriculture, its unique position in plant evolution, its symbiotic relationship with the N2-fixing cyanobacterium, Anabaena azollae, and its moderate-sized genome. The goals of this genome project are not only to understand the biology of the Azolla genome to promote its applications in biological research and agriculture practice but also to gain critical insights about evolution of plant genomes. Together with the strategic and technical improvement as well as cost reduction of DNA sequencing, the deciphering of their genetic code is imminent.

  12. Azolla—A Model Organism for Plant Genomic Studies

    Institute of Scientific and Technical Information of China (English)

    Yin-LongQiu; JunYu

    2003-01-01

    The aquatic ferns of the genus Azolla are nitrogen-fixing plants that have great potentials in agricultural production and environmental conservation.Azolla in many aspects is qualified to serve as a model organism for genomic studies because of its importance in agriculture,its unique position in plant evolution,its symbiotic relationship with the N2-fixing cyanobacterium,Anabaena azollae,and its moderate-sized genome.The goals of this genome project are not only to understand the biology of the Azolla genome to promote its applications in biological research and agriculture practice but also to gain critical insights about evolution of plant genomes.Together with the strategic and technical improvement as well as cost reduction of DNA sequencing,the deciphering of their genetic code is imminent.

  13. Giant plasma membrane vesicles: models for understanding membrane organization.

    Science.gov (United States)

    Levental, Kandice R; Levental, Ilya

    2015-01-01

    The organization of eukaryotic membranes into functional domains continues to fascinate and puzzle cell biologists and biophysicists. The lipid raft hypothesis proposes that collective lipid interactions compartmentalize the membrane into coexisting liquid domains that are central to membrane physiology. This hypothesis has proven controversial because such structures cannot be directly visualized in live cells by light microscopy. The recent observations of liquid-liquid phase separation in biological membranes are an important validation of the raft hypothesis and enable application of the experimental toolbox of membrane physics to a biologically complex phase-separated membrane. This review addresses the role of giant plasma membrane vesicles (GPMVs) in refining the raft hypothesis and expands on the application of GPMVs as an experimental model to answer some of key outstanding problems in membrane biology. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Self-organized criticality in a computer network model

    Science.gov (United States)

    Yuan; Ren; Shan

    2000-02-01

    We study the collective behavior of computer network nodes by using a cellular automaton model. The results show that when the load of network is constant, the throughputs and buffer contents of nodes are power-law distributed in both space and time. Also the feature of 1/f noise appears in the power spectrum of the change of the number of nodes that bear a fixed part of the system load. It can be seen as yet another example of self-organized criticality. Power-law decay in the distribution of buffer contents implies that heavy network congestion occurs with small probability. The temporal power-law distribution for throughput might be a reasonable explanation for the observed self-similarity in computer network traffic.

  15. Comparing and modelling land use organization in cities

    Science.gov (United States)

    Lenormand, Maxime; Picornell, Miguel; Cantú-Ros, Oliva G.; Louail, Thomas; Herranz, Ricardo; Barthelemy, Marc; Frías-Martínez, Enrique; San Miguel, Maxi; Ramasco, José J.

    2015-01-01

    The advent of geolocated information and communication technologies opens the possibility of exploring how people use space in cities, bringing an important new tool for urban scientists and planners, especially for regions where data are scarce or not available. Here we apply a functional network approach to determine land use patterns from mobile phone records. The versatility of the method allows us to run a systematic comparison between Spanish cities of various sizes. The method detects four major land use types that correspond to different temporal patterns. The proportion of these types, their spatial organization and scaling show a strong similarity between all cities that breaks down at a very local scale, where land use mixing is specific to each urban area. Finally, we introduce a model inspired by Schelling's segregation, able to explain and reproduce these results with simple interaction rules between different land uses. PMID:27019730

  16. Comparing and modeling land use organization in cities

    CERN Document Server

    Lenormand, Maxime; Cantú-Ros, Oliva G; Louail, Thomas; Herranz, Ricardo; Barthelemy, Marc; Frías-Martínez, Enrique; Miguel, Maxi San; Ramasco, José J

    2015-01-01

    The advent of geolocated ICT technologies opens the possibility of exploring how people use space in cities, bringing an important new tool for urban scientists and planners, especially for regions where data is scarce or not available. Here we apply a functional network approach to determine land use patterns from mobile phone records. The versatility of the method allows us to run a systematic comparison between Spanish cities of various sizes. The method detects four major land use types that correspond to different temporal patterns. The proportion of these types, their spatial organization and scaling show a strong similarity between all cities that breaks down at a very local scale, where land use mixing is specific to each urban area. Finally, we introduce a model inspired by Schelling's segregation, able to explain and reproduce these results with simple interaction rules between different land uses.

  17. CONCEPTUAL MODEL OF MARKETING STRATEGIC PLANNING SPECIFIC TO PUBLIC ORGANIZATIONS

    Directory of Open Access Journals (Sweden)

    Ionescu Florin Tudor

    2012-12-01

    Full Text Available In public services, the political component of the marketing environment has a major importance, as all decisions adopted within central administration influence both the objectives and measures implemented by units of local government and other public service providers. Any discontinuity in the activity of such entities might result in neglecting the real needs of citizens and slowing the reform process in the public sector. Therefore, all initiatives of public organizations must have a unitary goal and integrate harmoniously within a single process. A tool from the management-marketing literature that both contributes to this purpose and leads to an increased customer satisfaction and organizational performance is strategic marketing planning. This paper presents, firstly, requirements and particularities of this process in the public sector, focusing on the need for bottom-up planning, meaning from the functional levels of public service organizations, to the corporate level, where strategic decisions are taken. To achieve this goal, there should be included in the planning process the clients and other audiences, which can provide useful information about the services they want, the quality or the accessibility thereof, and news about the services they need in the future. There are also mentioned the factors that can influence the quality of strategic marketing planning in public services domain: the importance of marketing within the organization, marketing knowledge of employees in marketing departments and/or of management personnel, the efficiency of activities within the organization, and the manager’s marketing vision. In the final part of the paper there are presented the stages of the conceptual model of strategic marketing planning in public services field: (1 accepting the idea of bottom-up planning, (2 avoid or eliminate discrepancies between measures taken at high levels and executions carried out at operational

  18. ORGANIZING SCENARIO VARIABLES BY APPLYING THE INTERPRETATIVE STRUCTURAL MODELING (ISM

    Directory of Open Access Journals (Sweden)

    Daniel Estima de Carvalho

    2009-10-01

    Full Text Available The scenario building method is a thought mode - taken to effect in an optimized, strategic manner - based on trends and uncertain events, concerning a large variety of potential results that may impact the future of an organization.In this study, the objective is to contribute towards a possible improvement in Godet and Schoemaker´s scenario preparation methods, by employing the Interpretative Structural Modeling (ISM as a tool for the analysis of variables.Given this is an exploratory theme, bibliographical research with tool definition and analysis, examples extraction from literature and a comparison exercise of referred methods, were undertaken.It was verified that ISM may substitute or complement the original tools for the analysis of variables of scenarios per Godet and Schoemaker’s methods, given the fact that it enables an in-depth analysis of relations between variables in a shorter period of time, facilitating both structuring and construction of possible scenarios.Key-words: Strategy. Future studies. Interpretative Structural Modeling.

  19. Self-Organization of Aging in a Modified Penna Model

    Science.gov (United States)

    Kim, Gi Ok; Shim, Sugie

    The Penna model for biological aging is modified so that the fertility of each individual is determined by means of the number of activated mutations at that time. A new concept of "good" mutation, which makes an individual to mature enough to reproduce, is introduced. It is assumed that each individual can reproduce only during adulthood, which is determined by the number of activated mutations. The results of Monte Carlo calculations using the modified model show that the ranges of the reproductive age are broadened as time goes by, thus showing self-organization in the biological aging to the direction of the maximum self-conservation. In addition, the population, the survival rate, and the average life span were calculated and analyzed by changing the number of new mutations at birth. It is observed that the higher is the considered number of new mutations at birth, the shorter is the obtained average life span. The mortality functions are also calculated and they showed the exponential increase in adulthood, satisfying the Gompertz law.

  20. Development of an analytical model for organic-fluid fouling

    Energy Technology Data Exchange (ETDEWEB)

    Panchal, C.B.; Watkinson, A.P.

    1994-10-01

    The research goal of this project is to determine ways to effectively mitigate fouling in organic fluids: hydrocarbons and derived fluids. The fouling research focuses on the development of methodology for determining threshold conditions for fouling. Initially, fluid containing chemicals known to produce foulant is analyzed; subsequently, fouling of industrial fluids is investigated. The fouling model developed for determining the effects of physical parameters is the subject of this report. The fouling model is developed on the premise that the chemical reaction for generation of precursor can take place in the bulk fluid, in the thermal-boundary layer, or at the fluid/wall interface, depending upon the interactive effects of fluid dynamics, heat and mass transfer, and the controlling chemical reaction. In the analysis, the experimental data are examined for fouling deposition of polyperoxide produced by autoxidation of indene in kerosene. The effects of fluid and wall temperatures for two flow geometries are analyzed. The results show that the relative effects of physical parameters on the fouling rate differ for the three fouling mechanisms. Therefore, to apply the closed-flow-loop data to industrial conditions, the controlling mechanism must be identified.

  1. Purification of fluorescently labeled Saccharomyces cerevisiae Spindle Pole Bodies

    Science.gov (United States)

    Davis, Trisha N.

    2016-01-01

    Centrosomes are components of the mitotic spindle responsible for organizing microtubules and establishing a bipolar spindle for accurate chromosome segregation. In budding yeast, Saccharomyces cerevisiae, the centrosome is called the spindle pole body, a highly organized tri-laminar structure embedded in the nuclear envelope. Here we describe a detailed protocol for the purification of fluorescently labeled spindle pole bodes from S. cerevisiae. Spindle pole bodies are purified from yeast using a TAP-tag purification followed by velocity sedimentation. This highly reproducible TAP-tag purification method improves upon previous techniques and expands the scope of in vitro characterization of yeast spindle pole bodies. The genetic flexibility of this technique allows for the study of spindle pole body mutants as well as the study of spindle pole bodies during different stages of the cell cycle. The ease and reproducibility of the technique makes it possible to study spindle pole bodies using a variety of biochemical, biophysical, and microscopic techniques. PMID:27193850

  2. Transcriptional profiling of Saccharomyces cerevisiae exposed to propolis

    Science.gov (United States)

    2012-01-01

    prominent pathways are related to oxidative stress, mitochondrial electron transport chain, vacuolar acidification, regulation of macroautophagy associated with protein target to vacuole, cellular response to starvation, and negative regulation of transcription from RNA polymerase II promoter. Our work emphasizes again the importance of S. cerevisiae as a model system to understand at molecular level the mechanism whereby propolis causes cell death in this organism at the concentration herein tested. Our study is the first one that investigates systematically by using functional genomics how propolis influences and modulates the mRNA abundance of an organism and may stimulate further work on the propolis-mediated cell death mechanisms in fungi. PMID:23092287

  3. Diversion of flux toward sesquiterpene production in Saccharomyces cerevisiae by fusion of host and heterologous enzymes

    DEFF Research Database (Denmark)

    Albertsen, Line; Chen, Yun; Bach, Lars Stougaard

    2011-01-01

    The ability to transfer metabolic pathways from the natural producer organisms to the well-characterized cell factory Saccharomyces cerevisiae is well documented. However, as many secondary metabolites are produced by collaborating enzymes assembled in complexes, metabolite production in yeast ma...... demonstrates that engineering the spatial organization of metabolic enzymes around a branch point has great potential for diverting flux toward a desired product. ©American Society for Microbiology. All rights reserved.......The ability to transfer metabolic pathways from the natural producer organisms to the well-characterized cell factory Saccharomyces cerevisiae is well documented. However, as many secondary metabolites are produced by collaborating enzymes assembled in complexes, metabolite production in yeast may...... increased the production of patchoulol, the main sesquiterpene produced by PTS, up to 2-fold. Moreover, we have demonstrated that the fusion strategy can be used in combination with traditional metabolic engineering to further increase the production of patchoulol. This simple test case of synthetic biology...

  4. A Study of Some Leading Organ Transplant Models in Health Care Systems

    Directory of Open Access Journals (Sweden)

    Yasin Uzuntarla

    2016-04-01

    Full Text Available The most effective treatment method for patients with organ failure is an organ transplant. Although numerous patients are waiting to get organ transplants, the inadequacy in the supply of organs has become a chronic health problem around the whole world. Countries have made various regulations in their health systems that increase the supply of organs and, as a result, various organ transplantation models have been established. Organ transplantation models applied in Spain, the USA, the European Union, Iran, and Turkey have been examined in this study.

  5. KICS: A Model of Motivational Leadership in Organizations

    Directory of Open Access Journals (Sweden)

    John N. N. Ugoani

    2015-09-01

    Full Text Available This pure research gave birth to a Model of Motivational Leadership – KICS: which embraces knowledge, intelligence, collaboration and synergy. It is a synergistic  proposition based on the theory of emotional intelligence as the index of competencies needed for effective leadership. It opened with a general discussion on traditional models of leadership, then the roles of knowledge, intelligence, collaboration and synergy as they relate to motivational leadership. Issues of emotional intelligence clusters and synthesis of the model’s elements were discussed, emphasizing how KICS-based motivational leadership skills can be developed and sustained. Motivational leadership entails exciting people’s imaginations and inspiring them to move in a desired direction. It takes more than simple power to motivate and lead in organizations. Realizing that unity and cohesiveness are built from personal bonds, the best leaders ensure to deepen their rapport with employees and colleagues which enhances organizational performance. This pure research argues that the synergy of related emotional intelligence competencies can lead to motivational leadership behaviour. Knowledge is critical to leadership because there are different types of leadership and different situations require different kinds of knowledge, and the person possessing the knowledge demanded by a certain situation in most cases, tends to become the best leader. A knowledgeable person is one who is trained to consider his actions to undertake them deliberately, in a disciplined manner. Added to this ability is the intelligence to endure in a chosen course in the face of distraction, confusion and difficulty, all combined in producing a motivational leader. Knowledge tends to be procedural in nature and to operate outside of focal awareness. It also reflects the structure of the situation more closely than it does in the structure of formal disciplinary knowledge. The survey research design

  6. Genetic engineering of AtAOX1a in Saccharomyces cerevisiae prevents oxidative damage and maintains redox homeostasis.

    Science.gov (United States)

    Vishwakarma, Abhaypratap; Dalal, Ahan; Tetali, Sarada Devi; Kirti, Pulugurtha Bharadwaja; Padmasree, Kollipara

    2016-02-01

    This study aimed to validate the physiological importance of Arabidopsis thaliana alternative oxidase 1a (AtAOX1a) in alleviating oxidative stress using Saccharomyces cerevisiae as a model organism. The AOX1a transformant (pYES2AtAOX1a) showed cyanide resistant and salicylhydroxamic acid (SHAM)-sensitive respiration, indicating functional expression of AtAOX1a in S. cerevisiae. After exposure to oxidative stress, pYES2AtAOX1a showed better survival and a decrease in reactive oxygen species (ROS) when compared to S. cerevisiae with empty vector (pYES2). Furthermore, pYES2AtAOX1a sustained growth by regulating GPX2 and/or TSA2, and cellular NAD (+)/NADH ratio. Thus, the expression of AtAOX1a in S. cerevisiae enhances its respiratory tolerance which, in turn, maintains cellular redox homeostasis and protects from oxidative damage.

  7. Review of existing terrestrial bioaccumulation models and terrestrial bioaccumulation modeling needs for organic chemicals.

    Science.gov (United States)

    Gobas, Frank A P C; Burkhard, Lawrence P; Doucette, William J; Sappington, Keith G; Verbruggen, Eric M J; Hope, Bruce K; Bonnell, Mark A; Arnot, Jon A; Tarazona, Jose V

    2016-01-01

    Protocols for terrestrial bioaccumulation assessments are far less-developed than for aquatic systems. This article reviews modeling approaches that can be used to assess the terrestrial bioaccumulation potential of commercial organic chemicals. Models exist for plant, invertebrate, mammal, and avian species and for entire terrestrial food webs, including some that consider spatial factors. Limitations and gaps in terrestrial bioaccumulation modeling include the lack of QSARs for biotransformation and dietary assimilation efficiencies for terrestrial species; the lack of models and QSARs for important terrestrial species such as insects, amphibians and reptiles; the lack of standardized testing protocols for plants with limited development of plant models; and the limited chemical domain of existing bioaccumulation models and QSARs (e.g., primarily applicable to nonionic organic chemicals). There is an urgent need for high-quality field data sets for validating models and assessing their performance. There is a need to improve coordination among laboratory, field, and modeling efforts on bioaccumulative substances in order to improve the state of the science for challenging substances.

  8. Anti-Saccharomyces cerevisiae antibody titers are stable over time in Crohn's patients and are not inducible in murine models of colitis

    Institute of Scientific and Technical Information of China (English)

    Stefan Müller; Maya Styner; Beatrice Seibold-Schmid; Beatrice Flogerzi; Michael M(a)hler; Astrid Konrad; Frank Seibold

    2005-01-01

    AIM: To investigate ASCA production over time in CD and murine colitis in order to further our understanding of their etiology.MATERIALS AND METHODS: Sixty-six CD patients were compared to ulcerative colitis (UC) and irritable bowel syndrome patients with respect to ASCA production as measured by ELISA. ASCA IgG or IgA positivity as well as change in titers over a period of up to 3 years (ΔIgG/A) was correlated with clinical parameters such as CD activity index (CDAI) and C-reactive protein levels (CRP). Moreover, two murine models of colitis (DSS and IL-10 knock out) were compared to control animals with respect to ASCA titers after oral yeast exposure.RESULTS: ASCA IgG and IgA titers are stable over time in CD and non-CD patients. Fistular disease was associated with a higher rate of ASCA IgA positivity (P = 0.014). Ileal disease was found to have a significant influence on the ΔIgG of ASCA (P=0.032). There was no correlation found between ASCA positivity or ΔIgG/A and clinical parameters of CD: CDAI and CRP. In mice,neither healthy animals nor animals with DSS-induced or spontaneous colitis exhibited a marked increase in ASCA titers after high-dose yeast exposure. On the other hand, mice immunized intraperitoneally with mannan plus adjuvant showed a marked and significant increase in ASCA titers compared to adjuvant-only immunized controls (P=0.014).CONCLUSION: The propensity to produce ASCA in a subgroup of CD patients is largely genetically predetermined as evidenced by their stability and lack of correlation with clinical disease activity parameters. Furthermore,in animal models of colitis, mere oral exposure of mice to yeast does not lead to the induction of marked ASCA titers irrespective of concomitant colonic inflammation.Hence, environment may play only a minor role in inducing ASCA.

  9. 3D modeling of organic haze in Pluto's atmosphere

    Science.gov (United States)

    Bertrand, Tanguy; Forget, François

    2017-05-01

    The New Horizons spacecraft, which flew by Pluto on July 14, 2015, revealed the presence of haze in Pluto's atmosphere that were formed by CH4/N2 photochemistry at high altitudes in Pluto's atmosphere, as on Titan and Triton. In order to help the analysis of the observations and further investigate the formation of organic haze and its evolution at global scales, we have implemented a simple parameterization of the formation of organic haze in our Pluto General Circulation Model. The production of haze in our model is based on the different steps of aerosol formation as understood on Titan and Triton: photolysis of CH4 in the upper atmosphere by Lyman-α UV radiation, production of various gaseous species, and conversion into solid particles through accumulation and aggregation processes. The simulations use properties of aerosols similar to those observed in the detached haze layer on Titan. We compared two reference simulations ran with a particle radius of 50 nm: with, and without South Pole N2 condensation. We discuss the impact of the particle radius and the lifetime of the precursors on the haze distribution. We simulate CH4 photolysis and the haze formation up to 600 km above the surface. Results show that CH4 photolysis in Pluto's atmosphere in 2015 occurred mostly in the sunlit summer hemisphere with a peak at an altitude of 250 km, though the interplanetary source of Lyman-α flux can induce some photolysis even in the Winter hemisphere. We obtained an extensive haze up to altitudes comparable with the observations, and with non-negligible densities up to 500 km altitude. In both reference simulations, the haze density is not strongly impacted by the meridional circulation. With No South Pole N2 condensation, the maximum nadir opacity and haze extent is obtained at the North Pole. With South Pole N2 condensation, the descending parcel of air above the South Pole leads to a latitudinally more homogeneous haze density with a slight density peak at the South

  10. Omics analysis of acetic acid tolerance in Saccharomyces cerevisiae.

    Science.gov (United States)

    Geng, Peng; Zhang, Liang; Shi, Gui Yang

    2017-05-01

    Acetic acid is an inhibitor in industrial processes such as wine making and bioethanol production from cellulosic hydrolysate. It causes energy depletion, inhibition of metabolic enzyme activity, growth arrest and ethanol productivity losses in Saccharomyces cerevisiae. Therefore, understanding the mechanisms of the yeast responses to acetic acid stress is essential for improving acetic acid tolerance and ethanol production. Although 329 genes associated with acetic acid tolerance have been identified in the Saccharomyces genome and included in the database ( http://www.yeastgenome.org/observable/resistance_to_acetic_acid/overview ), the cellular mechanistic responses to acetic acid remain unclear in this organism. Post-genomic approaches such as transcriptomics, proteomics, metabolomics and chemogenomics are being applied to yeast and are providing insight into the mechanisms and interactions of genes, proteins and other components that together determine complex quantitative phenotypic traits such as acetic acid tolerance. This review focuses on these omics approaches in the response to acetic acid in S. cerevisiae. Additionally, several novel strains with improved acetic acid tolerance have been engineered by modifying key genes, and the application of these strains and recently acquired knowledge to industrial processes is also discussed.

  11. Towards Increased Relevance: Context-Adapted Models of the Learning Organization

    Science.gov (United States)

    Örtenblad, Anders

    2015-01-01

    Purpose: The purposes of this paper are to take a closer look at the relevance of the idea of the learning organization for organizations in different generalized organizational contexts; to open up for the existence of multiple, context-adapted models of the learning organization; and to suggest a number of such models.…

  12. Towards Increased Relevance: Context-Adapted Models of the Learning Organization

    Science.gov (United States)

    Örtenblad, Anders

    2015-01-01

    Purpose: The purposes of this paper are to take a closer look at the relevance of the idea of the learning organization for organizations in different generalized organizational contexts; to open up for the existence of multiple, context-adapted models of the learning organization; and to suggest a number of such models.…

  13. Evaluation of approaches focused on modelling of organic carbon stocks using the RothC model

    Science.gov (United States)

    Koco, Štefan; Skalský, Rastislav; Makovníková, Jarmila; Tarasovičová, Zuzana; Barančíková, Gabriela

    2014-05-01

    The aim of current efforts in the European area is the protection of soil organic matter, which is included in all relevant documents related to the protection of soil. The use of modelling of organic carbon stocks for anticipated climate change, respectively for land management can significantly help in short and long-term forecasting of the state of soil organic matter. RothC model can be applied in the time period of several years to centuries and has been tested in long-term experiments within a large range of soil types and climatic conditions in Europe. For the initialization of the RothC model, knowledge about the carbon pool sizes is essential. Pool size characterization can be obtained from equilibrium model runs, but this approach is time consuming and tedious, especially for larger scale simulations. Due to this complexity we search for new possibilities how to simplify and accelerate this process. The paper presents a comparison of two approaches for SOC stocks modelling in the same area. The modelling has been carried out on the basis of unique input of land use, management and soil data for each simulation unit separately. We modeled 1617 simulation units of 1x1 km grid on the territory of agroclimatic region Žitný ostrov in the southwest of Slovakia. The first approach represents the creation of groups of simulation units based on the evaluation of results for simulation unit with similar input values. The groups were created after the testing and validation of modelling results for individual simulation units with results of modelling the average values of inputs for the whole group. Tests of equilibrium model for interval in the range 5 t.ha-1 from initial SOC stock showed minimal differences in results comparing with result for average value of whole interval. Management inputs data from plant residues and farmyard manure for modelling of carbon turnover were also the same for more simulation units. Combining these groups (intervals of initial

  14. Development and evaluation of a new sorption model for organic cations in soil: contributions from organic matter and clay minerals.

    Science.gov (United States)

    Droge, Steven T J; Goss, Kai-Uwe

    2013-12-17

    This study evaluates a newly proposed cation-exchange model that defines the sorption of organic cations to soil as a summed contribution of sorption to organic matter (OM) and sorption to phyllosilicate clay minerals. Sorption to OM is normalized to the fraction organic carbon (fOC), and sorption to clay is normalized to the estimated cation-exchange capacity attributed to clay minerals (CECCLAY). Sorption affinity is specified to a fixed medium composition, with correction factors for other electrolyte concentrations. The model applies measured sorption coefficients to one reference OM material and one clay mineral. If measured values are absent, then empirical relationships are available on the basis of molecular volume and amine type in combination with corrective increments for specific polar moieties. The model is tested using new sorption data generated at pH 6 for two Eurosoils, one enriched in clay and the other, OM, using 29 strong bases (pKa > 8). Using experimental data on reference materials for all tested compounds, model predictions for the two soils differed on average by only -0.1 ± 0.4 log units from measured sorption affinities. Within the chemical applicability domain, the model can also be applied successfully to various reported soil sorption data for organic cations. Particularly for clayish soils, the model shows that sorption of organic cations to clay minerals accounts for more than 90% of the overall affinity.

  15. Chemical Composition and Antioxidant Properties of Juniper Berry (Juniperus communis L.) Essential Oil. Action of the Essential Oil on the Antioxidant Protection of Saccharomyces cerevisiae Model Organism

    Science.gov (United States)

    Höferl, Martina; Stoilova, Ivanka; Schmidt, Erich; Wanner, Jürgen; Jirovetz, Leopold; Trifonova, Dora; Krastev, Lutsian; Krastanov, Albert

    2014-01-01

    The essential oil of juniper berries (Juniperus communis L., Cupressaceae) is traditionally used for medicinal and flavoring purposes. As elucidated by gas chromatography/flame ionization detector (GC/FID) and gas chromatography/mass spectrometry (GC/MS methods), the juniper berry oil from Bulgaria is largely comprised of monoterpene hydrocarbons such as α-pinene (51.4%), myrcene (8.3%), sabinene (5.8%), limonene (5.1%) and β-pinene (5.0%). The antioxidant capacity of the essential oil was evaluated in vitro by 2,2-Diphenyl-1-picrylhydrazyl (DPPH) scavenging, 2,2-azino-bis-3-ethylbenzothiazoline-6 sulfonic acid (ABTS) radical cation scavenging, hydroxyl radical (ОН•) scavenging and chelating capacity, superoxide radical (•O2−) scavenging and xanthine oxidase inhibitory effects, hydrogen peroxide scavenging. The antioxidant activity of the oil attributable to electron transfer made juniper berry essential oil a strong antioxidant, whereas the antioxidant activity attributable to hydrogen atom transfer was lower. Lipid peroxidation inhibition by the essential oil in both stages, i.e., hydroperoxide formation and malondialdehyde formation, was less efficient than the inhibition by butylated hydroxytoluene (BHT). In vivo studies confirmed these effects of the oil which created the possibility of blocking the oxidation processes in yeast cells by increasing activity of the antioxidant enzymes superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx). PMID:26784665

  16. Vienna Soil-Organic-Matter Modeler--Generating condensed-phase models of humic substances.

    Science.gov (United States)

    Sündermann, Axel; Solc, Roland; Tunega, Daniel; Haberhauer, Georg; Gerzabek, Martin H; Oostenbrink, Chris

    2015-11-01

    Humic substances are ubiquitous in the environment and have manifold functions. While their composition is well known, information on the chemical structure and three-dimensional conformation is scarce. Here we describe the Vienna Soil-Organic-Matter Modeler, which is an online tool to generate condensed phase computer models of humic substances (http://somm.boku.ac.at). Many different models can be created that reflect the diversity in composition and conformations of the constituting molecules. To exemplify the modeler, 18 different models are generated based on two experimentally determined compositions, to explicitly study the effect of varying e.g. the amount of water molecules in the models or the pH. Molecular dynamics simulations were performed on the models, which were subsequently analyzed in terms of structure, interactions and dynamics, linking macroscopic observables to the microscopic composition of the systems. We are convinced that this new tool opens the way for a wide range of in silico studies on soil organic matter.

  17. Modeling adsorption and reactions of organic molecules at metal surfaces.

    Science.gov (United States)

    Liu, Wei; Tkatchenko, Alexandre; Scheffler, Matthias

    2014-11-18

    CONSPECTUS: The understanding of adsorption and reactions of (large) organic molecules at metal surfaces plays an increasingly important role in modern surface science and technology. Such hybrid inorganic/organic systems (HIOS) are relevant for many applications in catalysis, light-emitting diodes, single-molecule junctions, molecular sensors and switches, and photovoltaics. Obviously, the predictive modeling and understanding of the structure and stability of such hybrid systems is an essential prerequisite for tuning their electronic properties and functions. At present, density-functional theory (DFT) is the most promising approach to study the structure, stability, and electronic properties of complex systems, because it can be applied to both molecules and solids comprising thousands of atoms. However, state-of-the-art approximations to DFT do not provide a consistent and reliable description for HIOS, which is largely due to two issues: (i) the self-interaction of the electrons with themselves arising from the Hartree term of the total energy that is not fully compensated in approximate exchange-correlation functionals, and (ii) the lack of long-range part of the ubiquitous van der Waals (vdW) interactions. The self-interaction errors sometimes lead to incorrect description of charge transfer and electronic level alignment in HIOS, although for molecules adsorbed on metals these effects will often cancel out in total energy differences. Regarding vdW interactions, several promising vdW-inclusive DFT-based methods have been recently demonstrated to yield remarkable accuracy for intermolecular interactions in the gas phase. However, the majority of these approaches neglect the nonlocal collective electron response in the vdW energy tail, an effect that is particularly strong in condensed phases and at interfaces between different materials. Here we show that the recently developed DFT+vdW(surf) method that accurately accounts for the collective electronic

  18. The prisoner as model organism: malaria research at Stateville Penitentiary

    Science.gov (United States)

    Comfort, Nathaniel

    2009-01-01

    In a military-sponsored research project begun during the Second World War, inmates of the Stateville Penitentiary in Illinois were infected with malaria and treated with experimental drugs that sometimes had vicious side effects. They were made into reservoirs for the disease and they provided a food supply for the mosquito cultures. They acted as secretaries and technicians, recording data on one another, administering malarious mosquito bites and experimental drugs to one another, and helping decide who was admitted to the project and who became eligible for early parole as a result of his participation. Thus, the prisoners were not simply research subjects; they were deeply constitutive of the research project. Because a prisoner’s time on the project was counted as part of his sentence, and because serving on the project could shorten one’s sentence, the project must be seen as simultaneously serving the functions of research and punishment. Michel Foucault wrote about such ‘mixed mechanisms’ in his Discipline and punish. His shining example of such a ‘transparent’ and subtle style of punishment was the panopticon, Jeremy Bentham’s architectural invention of prison cellblocks arrayed around a central guard tower. Stateville prison was designed on Bentham’s model; Foucault featured it in his own discussion. This paper, then, explores the power relations in this highly idiosyncratic experimental system, in which the various roles of model organism, reagent, and technician are all occupied by sentient beings who move among them fluidly. This, I argue, created an environment in the Stateville hospital wing more panoptic than that in the cellblocks. Research and punishment were completely interpenetrating, and mutually reinforcing. PMID:19720327

  19. The prisoner as model organism: malaria research at Stateville Penitentiary.

    Science.gov (United States)

    Comfort, Nathaniel

    2009-09-01

    In a military-sponsored research project begun during the Second World War, inmates of the Stateville Penitentiary in Illinois were infected with malaria and treated with experimental drugs that sometimes had vicious side effects. They were made into reservoirs for the disease and they provided a food supply for the mosquito cultures. They acted as secretaries and technicians, recording data on one another, administering malarious mosquito bites and experimental drugs to one another, and helping decide who was admitted to the project and who became eligible for early parole as a result of his participation. Thus, the prisoners were not simply research subjects; they were deeply constitutive of the research project. Because a prisoner's time on the project was counted as part of his sentence, and because serving on the project could shorten one's sentence, the project must be seen as simultaneously serving the functions of research and punishment. Michel Foucault wrote about such 'mixed mechanisms' in his Discipline and punish. His shining example of such a 'transparent' and subtle style of punishment was the panopticon, Jeremy Bentham's architectural invention of prison cellblocks arrayed around a central guard tower. Stateville prison was designed on Bentham's model; Foucault featured it in his own discussion. This paper, then, explores the power relations in this highly idiosyncratic experimental system, in which the various roles of model organism, reagent, and technician are all occupied by sentient beings who move among them fluidly. This, I argue, created an environment in the Stateville hospital wing more panoptic than that in the cellblocks. Research and punishment were completely interpenetrating, and mutually reinforcing.

  20. Modelling and Optimization of Organization of Workplaces in a Foundry

    Directory of Open Access Journals (Sweden)

    Kukla S.

    2016-09-01

    Full Text Available The paper presents a practical example of improvement of foundry production systems in terms of post-finishing of nodular iron castings produced in the conditions of bulk production for automotive industry. The attention was paid to high labour-intensive efforts, which are difficult to be subjected to mechanization and automation. The times of actions related to grinding processing of castings in three grinding positions connected with a belt conveyor were estimated with the use of a time study method. A bottleneck as well as limiting factors were specified in a system. A number of improvements were proposed, aimed at improving work organization on the castings post-finishing line. An analysis of work ergonomics at the workplace was made in order to eliminate unnecessary and onerous for the employee actions. A model of production system using the Arena software, on which a simulation experiment was conducted, was drawn up in order to visualize the analysed phenomena. The effects of the project were shown on graphs comparing times, costs, work ergonomics and overall efficiency of production equipment indicator.

  1. [Epidemiological intelligence as a model of organization in health].

    Science.gov (United States)

    Rodrigues-Júnior, Antonio Luiz

    2012-03-01

    The concept of epidemiological intelligence, as a construction of information societies, goes beyond monitoring a list of diseases and the ability to elicit rapid responses. The concept should consider the complexity of the definition of epidemiology in the identification of this object of study without being limited to a set of actions in a single government sector. The activities of epidemiological intelligence include risk assessment, strategies for prevention and protection, subsystems of information, crisis management rooms, geographical analysis, etc. This concept contributes to the understanding of policies in health, in multisectorial and geopolitical dimensions, as regards the organization of services around public health emergencies, primary healthcare, as well as disasters. The activities of epidemiological intelligence should not be restricted to scientific research, but the researchers must beware of threats to public health. Lalonde's model enabled consideration of epidemiological intelligence as a way to restructure policies and share resources by creating communities of intelligence, whose purpose is primarily to deal with public health emergencies and disasters.

  2. Modelling Competences for Partner Selection in Service-Oriented Virtual Organization Breeding Environments

    CERN Document Server

    Paszkiewicz, Zbigniew

    2011-01-01

    In the context of globalization and dynamic markets, collaboration among organizations is a condition sine qua non for organizations, especially small and medium enterprises, to remain competitive. Virtual organizations have been proposed as an organizational structure adapted to collaboration among organizations. The concept of Virtual Organization Breeding Environment (VOBE) has been proposed as a means to support the creation and operation of virtual organizations. With the rise of the service-oriented architecture (SOA), the concept of service-oriented VOBE (SOVOBE) has been proposed as a VOBE systematically organized around the concept of services. In the context of SOVOBEs, novel competence models supporting both service orientation and collaboration among organizations have to be developed to support efficiently partner selection, a key aspect of VO creation. In this paper, such a competence model is presented. Our competence model consists of a competence description model, a competence verification m...

  3. The yeast Saccharomyces cerevisiae: an overview of methods to study autophagy progression

    Science.gov (United States)

    Delorme-Axford, Elizabeth; Guimaraes, Rodrigo Soares; Reggiori, Fulvio; Klionsky, Daniel J.

    2014-01-01

    Macroautophagy (hereafter autophagy) is a highly evolutionarily conserved process essential for sustaining cellular integrity, homeostasis, and survival. Most eukaryotic cells constitutively undergo autophagy at a low basal level. However, various stimuli, including starvation, organelle deterioration, stress, and pathogen infection, potently upregulate autophagy. The hallmark morphological feature of autophagy is the formation of the double-membrane vesicle known as the autophagosome. In yeast, flux through the pathway culminates in autophagosome-vacuole fusion, and the subsequent degradation of the resulting autophagic bodies and cargo by vacuolar hydrolases, followed by efflux of the breakdown products. Importantly, aberrant autophagy is associated with diverse human pathologies. Thus, there is a need for ongoing work in this area to further understand the cellular factors regulating this process. The field of autophagy research has grown exponentially in recent years, and although numerous model organisms are being used to investigate autophagy, the baker’s yeast Saccharomyces cerevisiae remains highly relevant, as there are significant and unique benefits to working with this organism. In this review, we will focus on the current methods available to evaluate and monitor autophagy in S. cerevisiae, which in several cases have also been subsequently exploited in higher eukaryotes. PMID:25526918

  4. Suspended Animation Extends Survival Limits of Caenorhabditis elegans and Saccharomyces cerevisiae at Low Temperature

    Science.gov (United States)

    Chan, Kin; Goldmark, Jesse P.

    2010-01-01

    The orderly progression through the cell division cycle is of paramount importance to all organisms, as improper progression through the cycle could result in defects with grave consequences. Previously, our lab has shown that model eukaryotes such as Saccharomyces cerevisiae, Caenorhabditis elegans, and Danio rerio all retain high viability after prolonged arrest in a state of anoxia-induced suspended animation, implying that in such a state, progression through the cell division cycle is reversibly arrested in an orderly manner. Here, we show that S. cerevisiae (both wild-type and several cold-sensitive strains) and C. elegans embryos exhibit a dramatic decrease in viability that is associated with dysregulation of the cell cycle when exposed to low temperatures. Further, we find that when the yeast or worms are first transitioned into a state of anoxia-induced suspended animation before cold exposure, the associated cold-induced viability defects are largely abrogated. We present evidence that by imposing an anoxia-induced reversible arrest of the cell cycle, the cells are prevented from engaging in aberrant cell cycle events in the cold, thus allowing the organisms to avoid the lethality that would have occurred in a cold, oxygenated environment. PMID:20462960

  5. The effects of dietary administration with chemical treated Saccharomyces cerevisiae strain YG3-1 on the growth of aquatic invertebrates in Artemia

    Institute of Scientific and Technical Information of China (English)

    Behnam Shekarchi; Ali Nekuiefard; Ramin Manaffar

    2016-01-01

    Objective: To investigate the biological effects of β-glucans in cell wall of new identified strain Saccharomyces cerevisiae strain YG3-1 on the growth of aquatic invertebrates, in Artemia as model organism. Methods: All yeasts used in the present study were isolated from Rainbow trout intestine and then cultured in yeast extract-peptone-glycerol medium. Activation of β-glucan in yeasts was performed by chemical treatment with 2-mercaptoethanol (2ME) (3.5% v/v). Then nauplii and larvae individuals of Artemia urmiana and Artemia franciscana (two different species of Artemia as test organisms) were fed with 2ME-treated yeasts during the culture. At the end of experiment, after feeding individual length (total length and growth rate) in adult individuals of Artemia was measured. Results: Following this administration, growth in both species of Artemia was improved (P Conclusions: This study suggested that 2ME-treated Saccharomyces cerevisiae strain YG3-1 yeasts can be used for enhancing the growth of other aquatic invertebrates like shrimps as probiotic supplement and growth promoter.

  6. The effects of dietary administration with chemical treated Saccharomyces cerevisiae strain YG3-1 on the growth of aquatic invertebrates in Artemia

    Directory of Open Access Journals (Sweden)

    Behnam Shekarchi

    2016-02-01

    Full Text Available Objective: To investigate the biological effects of β-glucans in cell wall of new identified strain Saccharomyces cerevisiae strain YG3-1 on the growth of aquatic invertebrates, in Artemia as model organism. Methods: All yeasts used in the present study were isolated from Rainbow trout intestine and then cultured in yeast extract-peptone-glycerol medium. Activation of β-glucan in yeasts was performed by chemical treatment with 2-mercaptoethanol (2ME (3.5% v/v. Then nauplii and larvae individuals of Artemia urmiana and Artemia franciscana (two different species of Artemia as test organisms were fed with 2ME-treated yeasts during the culture. At the end of experiment, after feeding individual length (total length and growth rate in adult individuals of Artemia was measured. Results: Following this administration, growth in both species of Artemia was improved (P < 0.05. So, the results showed that Artemia urmiana adults individuals that fed with 2MEtreated yeasts had the highest growth and total length. These results were confirmed with growth measurement in adult individuals of Artemia. Conclusions: This study suggested that 2ME-treated Saccharomyces cerevisiae strain YG3-1 yeasts can be used for enhancing the growth of other aquatic invertebrates like shrimps as probiotic supplement and growth promoter.

  7. Phenotypic evaluation of natural and industrial Saccharomyces yeasts for different traits desirable in industrial bioethanol production.

    Science.gov (United States)

    Mukherjee, Vaskar; Steensels, Jan; Lievens, Bart; Van de Voorde, Ilse; Verplaetse, Alex; Aerts, Guido; Willems, Kris A; Thevelein, Johan M; Verstrepen, Kevin J; Ruyters, Stefan

    2014-11-01

    Saccharomyces cerevisiae is the organism of choice for many food and beverage fermentations because it thrives in high-sugar and high-ethanol conditions. However, the conditions encountered in bioethanol fermentation pose specific challenges, including extremely high sugar and ethanol concentrations, high temperature, and the presence of specific toxic compounds. It is generally considered that exploring the natural biodiversity of Saccharomyces strains may be an interesting route to find superior bioethanol strains and may also improve our understanding of the challenges faced by yeast cells during bioethanol fermentation. In this study, we phenotypically evaluated a large collection of diverse Saccharomyces strains on six selective traits relevant for bioethanol production with increasing stress intensity. Our results demonstrate a remarkably large phenotypic diversity among different Saccharomyces species and among S. cerevisiae strains from different origins. Currently applied bioethanol strains showed a high tolerance to many of these relevant traits, but several other natural and industrial S. cerevisiae strains outcompeted the bioethanol strains for specific traits. These multitolerant strains performed well in fermentation experiments mimicking industrial bioethanol production. Together, our results illustrate the potential of phenotyping the natural biodiversity of yeasts to find superior industrial strains that may be used in bioethanol production or can be used as a basis for further strain improvement through genetic engineering, experimental evolution, or breeding. Additionally, our study provides a basis for new insights into the relationships between tolerance to different stressors.

  8. Dissecting Ubiquitin Folding Using the Self-Organized Polymer Model.

    Science.gov (United States)

    Reddy, Govardhan; Thirumalai, D

    2015-08-27

    Folding of Ubiquitin (Ub), a functionally important protein found in eukaryotic organisms, is investigated at low and neutral pH at different temperatures using simulations of the coarse-grained self-organized-polymer model with side chains (SOP-SC). The melting temperatures (Tm's), identified with the peaks in the heat capacity curves, decrease as pH decreases, in qualitative agreement with experiments. The calculated radius of gyration, showing dramatic variations with pH, is in excellent agreement with scattering experiments. At Tm, Ub folds in a two-state manner at low and neutral pH. Clustering analysis of the conformations sampled in equilibrium folding trajectories at Tm, with multiple transitions between the folded and unfolded states, shows a network of metastable states connecting the native and unfolded states. At low and neutral pH, Ub folds with high probability through a preferred set of conformations resulting in a pH-dependent dominant folding pathway. Folding kinetics reveal that Ub assembly at low pH occurs by multiple pathways involving a combination of nucleation-collapse and diffusion collision mechanism. The mechanism by which Ub folds is dictated by the stability of the key secondary structural elements responsible for establishing long-range contacts and collapse of Ub. Nucleation collapse mechanism holds if the stability of these elements are marginal, as would be the case at elevated temperatures. If the lifetimes associated with these structured microdomains are on the order of hundreds of microseconds, then Ub folding follows the diffusion-collision mechanism with intermediates, many of which coincide with those found in equilibrium. Folding at neutral pH is a sequential process with a populated intermediate resembling that sampled at equilibrium. The transition state structures, obtained using a Pfold analysis, are homogeneous and globular with most of the secondary and tertiary structures being native-like. Many of our findings for

  9. Flocculation of Saccharomyces cerevisiae tup1 mutants.

    OpenAIRE

    1984-01-01

    Strains of Saccharomyces cerevisiae carrying a mutation in the TUP1 locus exhibited calcium-dependent flocculation. The flocculation had none of the characteristics of sexual agglutination. The flocculation differed from that exhibited by a FLO1 strain in the effect of pH on cation dependence and sensitivity to chemical inactivation.

  10. Heterooligomeric phosphoribosyl diphosphate synthase of Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Hove-Jensen, Bjarne

    2004-01-01

    The yeast Saccharomyces cerevisiae contains five phosphoribosyl diphosphate (PRPP) synthase-homologous genes (PRS1-5), which specify PRPP synthase subunits 1-5. Expression of the five S. cerevisiae PRS genes individually in an Escherichia coli PRPP-less strain (Deltaprs) showed that a single PRS...

  11. Fatal Saccharomyces Cerevisiae Aortic Graft Infection

    Science.gov (United States)

    Meyer, Michael (Technical Monitor); Smith, Davey; Metzgar, David; Wills, Christopher; Fierer, Joshua

    2002-01-01

    Saccharomyces cerevisiae is a yeast commonly used in baking and a frequent colonizer of human mucosal surfaces. It is considered relatively nonpathogenic in immunocompetent adults. We present a case of S. cerevisiae fungemia and aortic graft infection in an immunocompetent adult. This is the first reported case of S. cerevisiue fungemia where the identity of the pathogen was confirmed by rRNA sequencing.

  12. Tangential Ultrafiltration of Aqueous "Saccharomyces Cerevisiae" Suspensions

    Science.gov (United States)

    Silva, Carlos M.; Neves, Patricia S.; Da Silva, Francisco A.; Xavier, Ana M. R. B.; Eusebio, M. F. J.

    2008-01-01

    Experimental work on ultrafiltration is presented to illustrate the practical and theoretical principles of this separation technique. The laboratory exercise comprises experiments with pure water and with aqueous "Saccharomyces cerevisiae" (from commercial Baker's yeast) suspensions. With this work students detect the characteristic phenomena…

  13. Models,Characteristics and Upgrade of Rural Tourism Industrial Organizations in Beijing Suburbs

    Institute of Scientific and Technical Information of China (English)

    Hongli; GENG

    2013-01-01

    This paper firstly introduces theoretical basis of researches on industrial organizations of rural tourism.It sums up major models of industrial organizations of rural tourism in Beijing suburbs.Then,it presents benefits and major problems of different models,sums up characteristics of development of rural tourism industrial organizations in Beijing suburbs.Finally,it comes up with recommendations for upgrade and development of rural tourism industrial organizations in Beijing suburbs.

  14. Modelling the subgenual organ of the honeybee, Apis mellifera

    DEFF Research Database (Denmark)

    Storm, Jesper; Kilpinen, Ole

    1998-01-01

    In a recent study on the honeybee (Apis mellifera), the subgenual organ was observed moving inside the leg during sinusoidal vibrations of the leg (Kilpinen and Storm 1997). The subgenual organ of the honeybee is suspended in a haemolymph channel in the tibia of each leg. When the leg accelerates...

  15. Improving Organizations by Replacing the "Mechanical" Model with the "Organic" one

    Directory of Open Access Journals (Sweden)

    2007-01-01

    Full Text Available Organizations are currently viewed as artificial structures. However, in our opinion, organizations seem to match a biological structure much better. This paper explores this new approach with some interesting conclusions and results: organizations aim at perpetual exis-tence and continuous adaptation. We advance the ideas of organizational "instincts", organizational pathology and organizational optimization using genetic algorithms. In competitive markets, organizations are in a natural selection process, which actually is part of a natural genetic algorithm. This process may be simulated in an artificial multidisciplinary optimization environment, based on minimizing a Total Costs and Risks objective function. Unlike the gradient optimization methods, the genetic algorithms may be applied to such problems with thousands of degrees of freedom. This opens the way to the organizational structure optimization through genetic algorithms.

  16. Participatory plant breeding and organic agriculture: A synergistic model for organic variety development in the United States

    Directory of Open Access Journals (Sweden)

    Adrienne C. Shelton

    2016-12-01

    Full Text Available Abstract Organic farmers require improved varieties that have been adapted to their unique soils, nutrient inputs, management practices, and pest pressures. One way to develop adapted varieties is to situate breeding programs in the environment of intended use, such as directly on organic farms, and in collaboration with organic farmers. This model is a form of participatory plant breeding, and was originally created in order to meet the needs of under-served, small-scale farmers in developing countries. A robust body of literature supports the quantitative genetic selection theory of participatory plant breeding, and helps to explain its increasing prevalence among organic breeding projects in the United States. The history of the organic farming movement in the United States highlights the cultural relevance of engaging organic farmers in the breeding process, complementing the biological rationale for participatory plant breeding. In addition, limited private investment in organic plant breeding encourages the involvement of plant breeders at public institutions. This paper synthesizes the biological, cultural, and economic justifications for utilizing participatory plant breeding as an appropriate methodology for organic cultivar development.

  17. Design of control adaptability system model for TV media organization structure

    Institute of Scientific and Technical Information of China (English)

    WANG Dong-dong; WANG Ya-lin; MA Tao

    2008-01-01

    To resolve the control adaptability problem of TV media in complex competitive environment, a con-trol system model of TV media organization structure was designed. Based on the designed system model for TV media organization structure, the relations among the main factors of the system constitution, missions, organi-zing decision entity, and carrying bodies were analyzed. By means of applying multi-objective decision method and complex control system theory, and combining the integration model of TV media organization structure, the basic model was concluded and the corresponding parameters were designed. The current organization process of TV media is analyzed by this model, which comes to the adaptability appearance with different parameters. The results indicate that the model can estimate current TV media organization structure for the chain appearance of communications and the correlation between platforms and policy-making agencies.

  18. 76 FR 29249 - Medicare Program; Pioneer Accountable Care Organization Model: Request for Applications

    Science.gov (United States)

    2011-05-20

    ... participate in the Pioneer Accountable Care Organization Model for a period beginning in 2011 and ending...://innovations.cms.gov/areas-of-focus/seamless-and-coordinated-care-models/pioneer-aco . Application Submission... Accountable Care Organization Model or the application process. SUPPLEMENTARY INFORMATION: I. Background...

  19. 76 FR 34712 - Medicare Program; Pioneer Accountable Care Organization Model; Extension of the Submission...

    Science.gov (United States)

    2011-06-14

    ...: This notice extends the deadlines for the submission of the Pioneer Accountable Care Organization Model...-coordinated-care-models/pioneer-aco . Application Submission Deadline: Applications must be postmarked on or before August 19, 2011. The Pioneer Accountable Care Organization Model ] Application is available...

  20. Stage-structured matrix models for organisms with non-geometric development times

    Science.gov (United States)

    Andrew Birt; Richard M. Feldman; David M. Cairns; Robert N. Coulson; Maria Tchakerian; Weimin Xi; James M. Guldin

    2009-01-01

    Matrix models have been used to model population growth of organisms for many decades. They are popular because of both their conceptual simplicity and their computational efficiency. For some types of organisms they are relatively accurate in predicting population growth; however, for others the matrix approach does not adequately model...

  1. Current developments in soil organic matter modeling and the expansion of model applications: a review

    Science.gov (United States)

    Campbell, Eleanor E.; Paustian, Keith

    2015-12-01

    Soil organic matter (SOM) is an important natural resource. It is fundamental to soil and ecosystem functions across a wide range of scales, from site-specific soil fertility and water holding capacity to global biogeochemical cycling. It is also a highly complex material that is sensitive to direct and indirect human impacts. In SOM research, simulation models play an important role by providing a mathematical framework to integrate, examine, and test the understanding of SOM dynamics. Simulation models of SOM are also increasingly used in more ‘applied’ settings to evaluate human impacts on ecosystem function, and to manage SOM for greenhouse gas mitigation, improved soil health, and sustainable use as a natural resource. Within this context, there is a need to maintain a robust connection between scientific developments in SOM modeling approaches and SOM model applications. This need forms the basis of this review. In this review we first provide an overview of SOM modeling, focusing on SOM theory, data-model integration, and model development as evidenced by a quantitative review of SOM literature. Second, we present the landscape of SOM model applications, focusing on examples in climate change policy. We conclude by discussing five areas of recent developments in SOM modeling including: (1) microbial roles in SOM stabilization; (2) modeling SOM saturation kinetics; (3) temperature controls on decomposition; (4) SOM dynamics in deep soil layers; and (5) SOM representation in earth system models. Our aim is to comprehensively connect SOM model development to its applications, revealing knowledge gaps in need of focused interdisciplinary attention and exposing pitfalls that, if avoided, can lead to best use of SOM models to support policy initiatives and sustainable land management solutions.

  2. A 360° Vision for Virtual Organizations Characterization and Modelling: Two Intentional Level Aspects

    Science.gov (United States)

    Priego-Roche, Luz-María; Rieu, Dominique; Front, Agnès

    Nowadays, organizations aiming to be successful in an increasingly competitive market tend to group together into virtual organizations. Designing the information system (IS) of such virtual organizations on the basis of the IS of those participating is a real challenge. The IS of a virtual organization plays an important role in the collaboration and cooperation of the participants organizations and in reaching the common goal. This article proposes criteria allowing virtual organizations to be identified and classified at an intentional level, as well as the information necessary for designing the organizations’ IS. Instantiation of criteria for a specific virtual organization and its participants, will allow simple graphical models to be generated in a modelling tool. The models will be used as bases for the IS design at organizational and operational levels. The approach is illustrated by the example of the virtual organization UGRT (a regional stockbreeders union in Tabasco, Mexico).

  3. Modelling organic crystal structures using distributed multipole and polarizability-based model intermolecular potentials.

    Science.gov (United States)

    Price, Sarah L; Leslie, Maurice; Welch, Gareth W A; Habgood, Matthew; Price, Louise S; Karamertzanis, Panagiotis G; Day, Graeme M

    2010-08-14

    Crystal structure prediction for organic molecules requires both the fast assessment of thousands to millions of crystal structures and the greatest possible accuracy in their relative energies. We describe a crystal lattice simulation program, DMACRYS, emphasizing the features that make it suitable for use in crystal structure prediction for pharmaceutical molecules using accurate anisotropic atom-atom model intermolecular potentials based on the theory of intermolecular forces. DMACRYS can optimize the lattice energy of a crystal, calculate the second derivative properties, and reduce the symmetry of the spacegroup to move away from a transition state. The calculated terahertz frequency k = 0 rigid-body lattice modes and elastic tensor can be used to estimate free energies. The program uses a distributed multipole electrostatic model (Q, t = 00,...,44s) for the electrostatic fields, and can use anisotropic atom-atom repulsion models, damped isotropic dispersion up to R(-10), as well as a range of empirically fitted isotropic exp-6 atom-atom models with different definitions of atomic types. A new feature is that an accurate model for the induction energy contribution to the lattice energy has been implemented that uses atomic anisotropic dipole polarizability models (alpha, t = (10,10)...(11c,11s)) to evaluate the changes in the molecular charge density induced by the electrostatic field within the crystal. It is demonstrated, using the four polymorphs of the pharmaceutical carbamazepine C(15)H(12)N(2)O, that whilst reproducing crystal structures is relatively easy, calculating the polymorphic energy differences to the accuracy of a few kJ mol(-1) required for applications is very demanding of assumptions made in the modelling. Thus DMACRYS enables the comparison of both known and hypothetical crystal structures as an aid to the development of pharmaceuticals and other speciality organic materials, and provides a tool to develop the modelling of the

  4. Organic chemistry in the atmosphere. [laboratory modeling of Titan atmosphere

    Science.gov (United States)

    Sagan, C.

    1974-01-01

    The existence of an at least moderately complex organic chemistry on Titan is stipulated based on clear evidence of methane, and at least presumptive evidence of hydrogen in its atmosphere. The ratio of methane to hydrogen is the highest of any atmosphere in the solar system. Irradiation of hydrogen/methane mixtures produces aromatic and aliphatic hydrocarbons. A very reasonable hypothesis assumes that the red cloud cover of Titan is made of organic chemicals. Two-carbon hydrocarbons experimentally produced from irradiated mixtures of methane, ammonia, water, and hydrogen bear out the possible organic chemistry of the Titanian environment.

  5. PROCESS DOCUMENTATION: A MODEL FOR KNOWLEDGE MANAGEMENT IN ORGANIZATIONS.

    Science.gov (United States)

    Haddadpoor, Asefeh; Taheri, Behjat; Nasri, Mehran; Heydari, Kamal; Bahrami, Gholamreza

    2015-10-01

    Continuous and interconnected processes are a chain of activities that turn the inputs of an organization to its outputs and help achieve partial and overall goals of the organization. These activates are carried out by two types of knowledge in the organization called explicit and implicit knowledge. Among these, implicit knowledge is the knowledge that controls a major part of the activities of an organization, controls these activities internally and will not be transferred to the process owners unless they are present during the organization's work. Therefore the goal of this study is identification of implicit knowledge and its integration with explicit knowledge in order to improve human resources management, physical resource management, information resource management, training of new employees and other activities of Isfahan University of Medical Science. The project for documentation of activities in department of health of Isfahan University of Medical Science was carried out in several stages. First the main processes and related sub processes were identified and categorized with the help of planning expert. The categorization was carried out from smaller processes to larger ones. In this stage the experts of each process wrote down all their daily activities and organized them into general categories based on logical and physical relations between different activities. Then each activity was assigned a specific code. The computer software was designed after understanding the different parts of the processes, including main and sup processes, and categorization, which will be explained in the following sections. The findings of this study showed that documentation of activities can help expose implicit knowledge because all of inputs and outputs of a process along with the length, location, tools and different stages of the process, exchanged information, storage location of the information and information flow can be identified using proper

  6. Clinical Saccharomyces cerevisiae isolates cannot cross the epithelial barrier in vitro

    DEFF Research Database (Denmark)

    Pérez-Torrado, Roberto; Llopis, Silvia; Jespersen, Lene

    2012-01-01

    Saccharomyces cerevisiae is generally considered to be a safe organism and is essential to produce many different kinds of foods as well as being widely used as a dietary supplement. However, several isolates, which are genetically related to brewing and baking yeasts, have shown virulent traits,...

  7. Clinical Saccharomyces cerevisiae isolates cannot cross the epithelial barrier in vitro

    DEFF Research Database (Denmark)

    Pérez-Torrado, Roberto; Llopis, Silvia; Jespersen, Lene

    2012-01-01

    Saccharomyces cerevisiae is generally considered to be a safe organism and is essential to produce many different kinds of foods as well as being widely used as a dietary supplement. However, several isolates, which are genetically related to brewing and baking yeasts, have shown virulent traits,...

  8. Kinetic mechanism of an aldehyde reductase of Saccharomyces cerevisiae that relieves toxicity of furfural and 5-hydroxymethylfurfural

    Science.gov (United States)

    An effective means of relieving the toxicity of furan aldehydes, furfural (FFA) and 5-hydroxymethylfurfural (HMF), on fermenting organisms is essential for achieving efficient fermentation of lignocellulosic biomass to ethanol and other products. Ari1p, an aldehyde reductase from Saccharomyces cerev...

  9. Multi-Capillary Column-Ion Mobility Spectrometry of Volatile Metabolites Emitted by Saccharomyces Cerevisiae

    OpenAIRE

    Christoph Halbfeld; Ebert, Birgitta E.; Blank, Lars M.

    2014-01-01

    Volatile organic compounds (VOCs) produced during microbial fermentations determine the flavor of fermented food and are of interest for the production of fragrances or food additives. However, the microbial synthesis of these compounds from simple carbon sources has not been well investigated so far. Here, we analyzed the headspace over glucose minimal salt medium cultures of Saccharomyces cerevisiae using multi-capillary column-ion mobility spectrometry (MCC-IMS). The high sensitivity and f...

  10. The effect of millimeter waves at the yeast Saccharomyces cerevisiae during heliogeophysical disturbances

    Science.gov (United States)

    Rogacheva, Svetlana M.; Babaeva, Milena I.

    2013-02-01

    The isolated and combined effect of heliogeophysical factors and low intensive electromagnetic radiation of millimeter diapason at the metachromasia reaction of the yeast Saccharomyces cerevisiae was studied. It was established that longterm influence of EMR 65 GHz induced changes in the response of cells towards heliogeomagnetic disturbance. On our opinion millimeter waves may reduce the effect of heliogeophysical factors on living organisms because of destabilization of the intracellular water structure.

  11. Replication of Avocado Sunblotch Viroid in the Yeast Saccharomyces cerevisiae▿

    Science.gov (United States)

    Delan-Forino, Clémentine; Maurel, Marie-Christine; Torchet, Claire

    2011-01-01

    Viroids are the smallest known pathogenic agents. They are noncoding, single-stranded, closed-circular, “naked” RNAs, which replicate through RNA-RNA transcription. Viroids of the Avsunviroidae family possess a hammerhead ribozyme in their sequence, allowing self-cleavage during their replication. To date, viroids have only been detected in plant cells. Here, we investigate the replication of Avocado sunblotch viroid (ASBVd) of the Avsunviroidae family in a nonconventional host, the yeast Saccharomyces cerevisiae. We demonstrate that ASBVd RNA strands of both polarities are able to self-cleave and to replicate in a unicellular eukaryote cell. We show that the viroid monomeric RNA is destabilized by the nuclear 3′ and the cytoplasmic 5′ RNA degradation pathways. For the first time, our results provide evidence that viroids can replicate in other organisms than plants and that yeast contains all of the essential cellular elements for the replication of ASBVd. PMID:21270165

  12. ACTIVITY OF SUPEROXIDE DISMUTASE ENZYME IN YEAST SACCHAROMYCES CEREVISIAE

    Directory of Open Access Journals (Sweden)

    Blažena Lavová

    2014-02-01

    Full Text Available Reactive oxygen species (ROS with reactive nitrogen species (RNS are known to play dual role in biological systems, they can be harmful or beneficial to living systems. ROS can be important mediators of damage to cell structures, including proteins, lipids and nucleic acids termed as oxidative stress. The antioxidant enzymes protect the organism against the oxidative damage caused by active oxygen forms. The role of superoxide dismutase (SOD is to accelerate the dismutation of the toxic superoxide radical, produced during oxidative energy processes, to hydrogen peroxide and molecular oxygen. In this study, SOD activity of three yeast strains Saccharomyces cerevisiae was determined. It was found that SOD activity was the highest (23.7 U.mg-1 protein in strain 612 after 28 hours of cultivation. The lowest SOD activity from all tested strains was found after 56 hours of cultivation of strain Gyöng (0.7 U.mg-1 protein.

  13. Cytotoxicity of orthodontic materials assessed by survival tests in Saccharomyces cerevisiae.

    Science.gov (United States)

    Limberger, Karen M; Westphalen, Graziela H; Menezes, Luciane M; Medina-Silva, Renata

    2011-05-01

    The aim of this study was to assess the cytotoxicity of orthodontic materials (brackets, wires, resin, elastomers and silver solder) using Saccharomyces cerevisiae as a model organism. The induction of cytotoxicity was assessed by two different tests using the wild-type S. cerevisiae strain FF18733: (1) direct exposure to orthodontic materials in YPD broth, and (2) exposure to artificial commercial saliva pre-treated with orthodontic materials. Only the silver solder was tested in mutant S. cerevisiae strains to investigate the origin of the observed cytotoxicity. Colony forming units per mL counts were carried out in all experiments and compared to controls to detect significant survival differences. The results showed that only the silver solder induced significant cytotoxicity, which might have occurred via oxidative stress, although this mechanism is not completely understood. Moreover, S. cerevisiae proved to be a reliable and useful model microorganism for evaluating the cytotoxicity of clinical materials. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

  14. Public attitudes to financial incentive models for organs

    DEFF Research Database (Denmark)

    Hoeyer, Klaus; Schicktanz, Silke; Deleuran, Ida

    2013-01-01

    Waiting lists for organs have stimulated interest in the use of financial incentives for organ donation (FIs), but the literature does not contain an adequate overview of studies of public attitudes toward this mode of procurement. We conducted a literature review of international peer......-reviewed research published between 2002 and 2012 on how members of the public position themselves toward FIs. We identified and analyzed 23 studies using MEDLINE, PsycINFO, Sociological Abstracts and cross-reference search. The search included whole organs, donation, quantitative and empirical qualitative social...... scientific studies on, public attitudes (excluding professionals and medical students). The review reveals a broad divergence of public opinions on financial incentives. However, quantitative studies showed a low overall level of acceptance of payment for organs in living donation (LD); only a slightly...

  15. Dynamic flux balancing elucidates NAD(P)H production as limiting response to furfural inhibition in Saccharomyces cerevisiae.

    Science.gov (United States)

    Pornkamol, Unrean; Franzen, Carl J

    2015-08-01

    Achieving efficient and economical lignocellulose-based bioprocess requires a robust organism tolerant to furfural, a major inhibitory compound present in lignocellulosic hydrolysate. The aim of this study was to develop a model that could generate quantitative descriptions of cell metabolism for elucidating the cell's adaptive response to furfural. Such a modelling tool could provide strategies for the design of more robust cells. A dynamic flux balance (dFBA) model of Saccharomyces cerevisiae was created by coupling a kinetic fermentation model with a previously published genome-scale stoichiometric model. The dFBA model was used for studying intracellular and extracellular flux responses to furfural perturbations under steady state and dynamic conditions. The predicted effects of furfural on dynamic flux profiles agreed well with previously published experimental results. The model showed that the yeast cell adjusts its metabolism in response to furfural challenge by increasing fluxes through the pentose phosphate pathway, TCA cycle, and proline and serine biosynthesis in order to meet the high demand of NAD(P)H cofactors. The model described here can be used to aid in systematic optimization of the yeast, as well as of the fermentation process, for efficient lignocellulosic ethanol production.

  16. Modeling the neurodynamic organizations and interactions of teams.

    Science.gov (United States)

    Stevens, Ronald H; Galloway, Trysha L

    2016-01-01

    Across-brain neurodynamic organizations arise when teams perform coordinated tasks. We describe a symbolic electroencephalographic (EEG) approach that identifies when team neurodynamic organizations occur and demonstrate its utility with scientific problem solving and submarine navigation tasks. Each second, neurodynamic symbols (NS) were created showing the 1-40 Hz EEG power spectral densities for each team member. These data streams contained a performance history of the team's across-brain neurodynamic organizations. The degree of neurodynamic organization was calculated each second from a moving window average of the Shannon entropy over the task. Decreased NS entropy (i.e., greater neurodynamic organization) was prominent in the ~16 Hz EEG bins during problem solving, while during submarine navigation, the maximum NS entropy decreases were ~10 Hz and were associated with establishing the ship's location. Decreased NS entropy also occurred in the 20-40 Hz bins of both teams and was associated with uncertainty or stress. The highest mutual information levels, calculated from the EEG values of team dyads, were associated with decreased NS entropy, suggesting a link between these two measures. These studies show entropy and mutual information mapping of symbolic EEG data streams from teams can be useful for identifying organized across-brain team activation patterns.

  17. An evaluation of the applicability of the EPA Organic Leachate Model to leaching of solvent and non-solvent wastes

    OpenAIRE

    Bosserman, Carolyn Whitney

    1989-01-01

    The author evaluated the applicability of the Environmental Protection Agency's Organic Leachate Model to wastes containing organic solvents and other organic compounds ("non-solvents"), and determined that the model tends to overestimate the leaching of organic solvents and other organic compounds. Furthermore, when evaluated for its ability to predict leaching of organic compounds, the model was found to predict the leaching of organic solvent compounds with some accuracy, with a correlatio...

  18. On the Implications of aerosol liquid water and phase separation for modeled organic aerosol mass

    Science.gov (United States)

    Current chemical transport models assume that organic aerosol (OA)-forming compounds partition mostly to a water-poor, organic-rich phase in accordance with their vapor pressures. However, in the southeast United States, a significant fraction of ambient organic compounds are wat...

  19. Quantitative comparison of transient growth of Saccharomyces cerevisiae, Saccharomyces kluyveri, and Kluyveromyces lactis.

    Science.gov (United States)

    Herwig, Christoph; Von Stockar, Urs

    2003-03-30

    A multitude of metabolic regulations occur in yeast, particularly under dynamic process conditions, such as under sudden glucose excess. However, quantification of regulations and classification of yeast strains under these conditions have yet to be elucidated, which requires high-frequency and consistent quantification of the metabolic response. The present study aimed at quantifying the dynamic regulation of the central metabolism of strains Saccharomyces cerevisiae, S. kluyveri, and Kluyveromyces lactis upon sudden glucose excess, accomplished by a shift-up in dilution rate inside of the oxidative region using a small metabolic flux model. It was found that, under transient growth conditions, S. kluyveri behaved like K. lactis, while classification using steady-state conditions would position S. kluyveri close to S. cerevisiae. For transient conditions and based on the observation whether excess glucose is initially used for catabolism (energy) or anabolism (carbon), we propose to classify strains into energy-driven, such as S. cerevisiae, and carbon-driven, such as S. kluyveri and K. lactis, strains. Furthermore, it was found that the delayed onset of fermentative catabolism in carbon-driven strains is a consequence of low catabolic flux and the initial shunt of glucose in non-nitrogen-containing biomass constituents. The MFA model suggests that energy limitation forced the cell to ultimately increase catabolic flux, while the capacity of oxidative catabolism is not sufficient to process this flux oxidatively. The combination of transient experiments and its exploitation with reconciled intrinsic rates using a small metabolic model could corroborate earlier findings of metabolic regulations, such as tight glucose control in carbon-driven strains and transient changes in biomass composition, as well as explore new regulations, such as assimilation of ethanol before glucose. The benefit from using small metabolic flux models is the richness of information and the

  20. A depositional model for organic-rich Duvernay Formation mudstones

    Science.gov (United States)

    Knapp, Levi J.; McMillan, Julia M.; Harris, Nicholas B.

    2017-01-01

    The Upper Devonian Duvernay Formation of western Canada is an organic-rich shale formation now targeted as a hydrocarbon reservoir. We present a detailed sedimentological analysis of the Duvernay Formation in order to better understand organic-rich mudstone depositional processes and conditions and to characterize the vertical and lateral heterogeneity of mudstone lithofacies that affect petrophysical and geomechanical rock properties. Organic-rich mudstone facies of the Duvernay Formation were deposited in a dynamic depositional environment by a variety of sediment transport mechanisms, including suspension settling, turbidity currents, and bottom water currents in variably oxygenated bottom waters. Suspension settling dominated in distal relatively deep areas of the basin, but evidence for weak turbidity currents and bottom water currents was observed in the form of graded beds and thin grain-supported siltstone laminae. Organic enrichment primarily occurred in distal areas as a result of bottom water anoxia and low depositional rates of inorganic sediment. In deep water locations near platform margins, alternating silty-sandy contourite beds and organic-rich mudstone beds are present, the former interpreted to have been deposited and reworked by bottom water currents flowing parallel to slope. In shallower, more oxygenated settings, mudstone lithologies vary from calcareous to argillaceous. These sediments were deposited from suspension settling, turbidity currents, and bottom water currents, although primary sedimentary structures are often obscured by extensive bioturbation. Locally, organic enrichment in dysoxic rather than anoxic bottom waters was driven by a slightly increased sedimentation rate and possibly also by aggregation of sedimentary particles in the water column due to interaction between organic matter and clay minerals. Large variations observed in sediment composition, from siliceous to calcareous to argillaceous, reflect multiple biogenic

  1. Application of several activity coefficient models to water-organic-electrolyte aerosols of atmospheric interest

    Directory of Open Access Journals (Sweden)

    T. Raatikainen

    2005-01-01

    Full Text Available In this work, existing and modified activity coefficient models are examined in order to assess their capabilities to describe the properties of aqueous solution droplets relevant in the atmosphere. Five different water-organic-electrolyte activity coefficient models were first selected from the literature. Only one of these models included organics and electrolytes which are common in atmospheric aerosol particles. In the other models, organic species were solvents such as alcohols, and important atmospheric ions like NH4+ could be missing. The predictions of these models were compared to experimental activity and solubility data in aqueous single electrolyte solutions with 31 different electrolytes. Based on the deviations from experimental data and on the capabilities of the models, four predictive models were selected for fitting of new parameters for binary and ternary solutions of common atmospheric electrolytes and organics. New electrolytes (H+, NH4+, Na+, Cl-, NO3- and SO42- and organics (dicarboxylic and some hydroxy acids were added and some modifications were made to the models if it was found useful. All new and most of the existing parameters were fitted to experimental single electrolyte data as well as data for aqueous organics and aqueous organic-electrolyte solutions. Unfortunately, there are very few data available for organic activities in binary solutions and for organic and electrolyte activities in aqueous organic-electrolyte solutions. This reduces model capabilities in predicting solubilities. After the parameters were fitted, deviations from measurement data were calculated for all fitted models, and for different data types. These deviations and the calculated property values were compared with those from other non-electrolyte and organic-electrolyte models found in the literature. Finally, hygroscopic growth factors were calculated for four 100 nm organic-electrolyte particles and these predictions were compared to

  2. Comparison of activity coefficient models for atmospheric aerosols containing mixtures of electrolytes, organics, and water

    Science.gov (United States)

    Tong, Chinghang; Clegg, Simon L.; Seinfeld, John H.

    Atmospheric aerosols generally comprise a mixture of electrolytes, organic compounds, and water. Determining the gas-particle distribution of volatile compounds, including water, requires equilibrium or mass transfer calculations, at the heart of which are models for the activity coefficients of the particle-phase components. We evaluate here the performance of four recent activity coefficient models developed for electrolyte/organic/water mixtures typical of atmospheric aerosols. Two of the models, the CSB model [Clegg, S.L., Seinfeld, J.H., Brimblecombe, P., 2001. Thermodynamic modelling of aqueous aerosols containing electrolytes and dissolved organic compounds. Journal of Aerosol Science 32, 713-738] and the aerosol diameter dependent equilibrium model (ADDEM) [Topping, D.O., McFiggans, G.B., Coe, H., 2005. A curved multi-component aerosol hygroscopicity model framework: part 2—including organic compounds. Atmospheric Chemistry and Physics 5, 1223-1242] treat ion-water and organic-water interactions but do not include ion-organic interactions; these can be referred to as "decoupled" models. The other two models, reparameterized Ming and Russell model 2005 [Raatikainen, T., Laaksonen, A., 2005. Application of several activity coefficient models to water-organic-electrolyte aerosols of atmospheric interest. Atmospheric Chemistry and Physics 5, 2475-2495] and X-UNIFAC.3 [Erdakos, G.B., Change, E.I., Pandow, J.F., Seinfeld, J.H., 2006. Prediction of activity coefficients in liquid aerosol particles containing organic compounds, dissolved inorganic salts, and water—Part 3: Organic compounds, water, and ionic constituents by consideration of short-, mid-, and long-range effects using X-UNIFAC.3. Atmospheric Environment 40, 6437-6452], include ion-organic interactions; these are referred to as "coupled" models. We address the question—Does the inclusion of a treatment of ion-organic interactions substantially improve the performance of the coupled models over

  3. Models of Micro-Organisms: Children's Knowledge and Understanding of Micro-Organisms from 7 to 14 Years Old

    Science.gov (United States)

    Byrne, Jenny

    2011-01-01

    This paper describes the expressed models that children aged 7, 11, and 14 years have about micro-organisms and microbial activity. These were elicited using a variety of data collection techniques that complemented each other, resulting in a rich dataset, and provided information about the level of knowledge and progression of ideas across the…

  4. Health biomarkers in a rat model after intake of organically grown carrots

    DEFF Research Database (Denmark)

    Melballe Jensen, Maja; Jørgensen, Henry; Halekoh, Ulrich

    2012-01-01

    BACKGROUND:Organic foodis perceived as beingofbetter quality andhealthier than conventional foods although the scientific research on organic foodstuffs is highly contradictory. The aim of the present study was to investigate if intake of carrots from four different cultivation systems grown in two...... consecutive years would influence various biomarkers of health in a rat model. All rats were fed a diet with 40% carrot content. The carrots were grown under conventional (C), ‘minimalistic’ organic (O1), organic (O2), or ‘very’ organic cultivation systems (O3). A control group (CO) being fed standard rat...... as a framework for further studies of health in relation to organic foodstuff....

  5. 76 FR 33306 - Medicare Program; Pioneer Accountable Care Organization Model, Request for Applications; Correction

    Science.gov (United States)

    2011-06-08

    ... Care Organization Model: Request for Applications.'' FOR FURTHER INFORMATION CONTACT: Maria Alexander... http://innovations.cms.gov/areas-of-focus/seamless-and-coordinated-care-models/pioneer-aco... HUMAN SERVICES Centers for Medicare & Medicaid Services Medicare Program; Pioneer Accountable...

  6. Importance of global aerosol modeling including secondary organic aerosol formed from monoterpene

    OpenAIRE

    Goto, Daisuke; Takemura, Toshihiko; Nakajima, Teruyuki

    2008-01-01

    A global three-dimensional aerosol transport-radiation model, coupled to an atmospheric general circulation model (AGCM), has been extended to improve the model process for organic aerosols, particularly secondary organic aerosols (SOA), and to estimate SOA contributions to direct and indirect radiative effects. Because the SOA formation process is complicated and unknown, the results in different model simulations include large differences. In this work, we simulate SOA production assuming v...

  7. The network architecture of the Saccharomyces cerevisiae genome.

    Directory of Open Access Journals (Sweden)

    Stephen A Hoang

    Full Text Available We propose a network-based approach for surmising the spatial organization of genomes from high-throughput interaction data. Our strategy is based on methods for inferring architectural features of networks. Specifically, we employ a community detection algorithm to partition networks of genomic interactions. These community partitions represent an intuitive interpretation of genomic organization from interaction data. Furthermore, they are able to recapitulate known aspects of the spatial organization of the Saccharomyces cerevisiae genome, such as the rosette conformation of the genome, the clustering of centromeres, as well as tRNAs, and telomeres. We also demonstrate that simple architectural features of genomic interaction networks, such as cliques, can give meaningful insight into the functional role of the spatial organization of the genome. We show that there is a correlation between inter-chromosomal clique size and replication timing, as well as cohesin enrichment. Together, our network-based approach represents an effective and intuitive framework for interpreting high-throughput genomic interaction data. Importantly, there is a great potential for this strategy, given the rich literature and extensive set of existing tools in the field of network analysis.

  8. Fair Trade Organizations and Social Enterprise. Social Innovation through Hybrid Organization Models

    OpenAIRE

    Huybrechts, Benjamin

    2012-01-01

    For several decades, Fair Trade Social Enterprises (FTSEs) have set up partnerships with producer groups in the South and distributed the latter’s products through different types of channels in the North. However, while pioneers in the early years were relatively homogeneous (nonprofit organizations relying on voluntary work and selling through “worldshops”), organizational diversity has tremendously increased in recent times, including other types of legal forms, architectures, and governan...

  9. Keeping the Faith: A Model of Cultural Transmission in Formal Organizations.

    Science.gov (United States)

    Harrison, J. Richard; Carroll, Glenn R.

    1991-01-01

    Develops a cultural transmission model with the following variables: worker entry and exit rate, organization growth rate, recruiting selectivity, socialization intensity, and the rate that socialization decays if not reinforced. A computer simulation of the model found that cultural systems in organizations are highly robust and reach equilibrium…

  10. From Learning Object to Learning Cell: A Resource Organization Model for Ubiquitous Learning

    Science.gov (United States)

    Yu, Shengquan; Yang, Xianmin; Cheng, Gang; Wang, Minjuan

    2015-01-01

    This paper presents a new model for organizing learning resources: Learning Cell. This model is open, evolving, cohesive, social, and context-aware. By introducing a time dimension into the organization of learning resources, Learning Cell supports the dynamic evolution of learning resources while they are being used. In addition, by introducing a…

  11. The Family FIRO Model: A Modest Proposal for Organizing Family Treatment.

    Science.gov (United States)

    Doherty, William J.; Colangelo, Nicholas

    1984-01-01

    Presents a model for organizing family issues and family treatment. Schutz's Fundamental Interpersonal Relations Orientation (FIRO) model is offered as a framework for organizing family issues into inclusion, control, and affection categories, constituting a logical hierarchy of core issues to be dealt with in treating multiproblem families. (JAC)

  12. Plastic as a Carrier of POPs to Aquatic Organisms: A Model Analysis

    NARCIS (Netherlands)

    Koelmans, A.A.; Besseling, E.; Wegner, A.; Foekema, E.M.

    2013-01-01

    It has been hypothesized that persistent organic pollutants (POPs) in microplastic may pose a risk to aquatic organisms. Here we develop and analyze a conceptual model that simulates the effects of plastic on bioaccumulation of POPs. The model accounts for dilution of exposure concentration by sorpt

  13. Modelling the fate of oxidisable organic contaminants in groundwater

    DEFF Research Database (Denmark)

    Barry, D.A.; Prommer, H.; Miller, C.T.

    2002-01-01

    Subsurface contamination by organic chemicals is a pervasive environmental problem, susceptible to remediation by natural or enhanced attenuation approaches or more highly engineered methods such as pump-and-treat, amongst others. Such remediation approaches, along with risk assessment or the pre...

  14. Modeling emissions of volatile organic compounds from silage

    Science.gov (United States)

    Photochemical smog is a major air pollution problem and a significant cause of premature death in the U.S. Smog forms in the presence of volatile organic compounds (VOCs), which are emitted primarily from industry and motor vehicles in the U.S. However, dairy farms may be an important source in so...

  15. Mitochondrial damage and ageing using skin as a model organ.

    Science.gov (United States)

    Hudson, Laura; Bowman, Amy; Rashdan, Eyman; Birch-Machin, Mark A

    2016-11-01

    Ageing describes the progressive functional decline of an organism over time, leading to an increase in susceptibility to age-related diseases and eventually to death, and it is a phenomenon observed across a wide range of organisms. Despite a vast repertoire of ageing studies performed over the past century, the exact causes of ageing remain unknown. For over 50 years it has been speculated that mitochondria play a key role in the ageing process, due mainly to correlative data showing an increase in mitochondrial dysfunction, mitochondrial DNA (mtDNA) damage, and reactive oxygen species (ROS) with age. However, the exact role of the mitochondria in the ageing process remains unknown. The skin is often used to study human ageing, due to its easy accessibility, and the observation that the ageing process is able to be accelerated in this organ via environmental insults, such as ultra violet radiation (UVR). This provides a useful tool to investigate the mechanisms regulating ageing and, in particular, the role of the mitochondria. Observations from dermatological and photoageing studies can provide useful insights into chronological ageing of the skin and other organs such as the brain and liver. Moreover, a wide range of diseases are associated with ageing; therefore, understanding the cause of the ageing process as well as regulatory mechanisms involved could provide potentially advantageous therapeutic targets for the prevention or treatment of such diseases. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  16. Modelling Organic Surfaces with Self-Assembled Monolayers

    Science.gov (United States)

    1989-05-01

    reactive organic liquids. Fluorinated thiols form monolayers that are more water and oil-repellent than Teflon. The hydrophobicity and oleophobicity of...and are both hydrophobic and oleophobic . The surface of a monolayer containing an approximately equal mixture of the two components 13 resembles a

  17. Modeling the Current and Future Roles of Particulate Organic Nitrates in the Southeastern United States.

    Science.gov (United States)

    Pye, Havala O T; Luecken, Deborah J; Xu, Lu; Boyd, Christopher M; Ng, Nga L; Baker, Kirk R; Ayres, Benjamin R; Bash, Jesse O; Baumann, Karsten; Carter, William P L; Edgerton, Eric; Fry, Juliane L; Hutzell, William T; Schwede, Donna B; Shepson, Paul B

    2015-12-15

    Organic nitrates are an important aerosol constituent in locations where biogenic hydrocarbon emissions mix with anthropogenic NOx sources. While regional and global chemical transport models may include a representation of organic aerosol from monoterpene reactions with nitrate radicals (the primary source of particle-phase organic nitrates in the Southeast United States), secondary organic aerosol (SOA) models can underestimate yields. Furthermore, SOA parametrizations do not explicitly take into account organic nitrate compounds produced in the gas phase. In this work, we developed a coupled gas and aerosol system to describe the formation and subsequent aerosol-phase partitioning of organic nitrates from isoprene and monoterpenes with a focus on the Southeast United States. The concentrations of organic aerosol and gas-phase organic nitrates were improved when particulate organic nitrates were assumed to undergo rapid (τ = 3 h) pseudohydrolysis resulting in nitric acid and nonvolatile secondary organic aerosol. In addition, up to 60% of less oxidized-oxygenated organic aerosol (LO-OOA) could be accounted for via organic nitrate mediated chemistry during the Southern Oxidants and Aerosol Study (SOAS). A 25% reduction in nitrogen oxide (NO + NO2) emissions was predicted to cause a 9% reduction in organic aerosol for June 2013 SOAS conditions at Centreville, Alabama.

  18. Modelling the cloud condensation nucleus activity of organic acids

    Directory of Open Access Journals (Sweden)

    Z. Varga

    2007-04-01

    Full Text Available In this study vapour pressure osmometry was used to determine water activity in solutions of organic acids. The surface tension of the solutions was also monitored in parallel and then Köhler curves were calculated for nine organic acids (oxalic, malonic, succinic, glutaric, adipic acid, maleic acid, malic acid, citric acid and pinonic acid. Surface tension depression is negligible for most of the organic acids in dilute (≤1 w/w% solutions. Therefore, these compounds affect the supersaturation only in the beginning phase of droplet formation but not necessarily at the critical size. An exception is cis-pinonic acid which remarkably depress surface tension also in dilute (0.1 w/w% solution and hence at the critical point. The surface tension of organic acid solutions is influenced by the solubility of the compound, the length of the carbon chain and also by the polar functional groups present in the molecule. Similarly to surface tension solubility plays an important role also in water activity: compounds with higher solubility (e.g. malonic, maleic, and glutaric acid reduce water activity significantly in the early phase of droplet formation while less soluble acids (e.g. succinic and adipic acid are saturated in small droplets and the solution starts diluting only in bigger droplets. As a consequence, compounds with lower solubility have a minor effect on water activity in the early phase of droplet formation. To deduce the total effect Köhler curves were calculated and critical supersaturations were determined for the organic acids using measured surface tension and water activity. It was found that critical supersaturation grew with growing carbon number. Oxalic acid had the lowest critical supersaturation in the size range studied and it was comparable to the activation of ammonium sulfate. The Sc values obtained in this study were compared to data from CCNC measurements. In most cases good agreement was found.

  19. Designing an Effective Female Leadership Model in Governmental Organizations

    Directory of Open Access Journals (Sweden)

    Nosratollah MALEKI

    2011-10-01

    Full Text Available Since leadership is a critical factor for improving organizational performance, failure or success of an organization highly depends on the efficiency of leadership at all levels. Scholars elaborated that leadership is the ability of influencing one's attitudes, aptitudes and beliefs, in the way that it will lead to meet organizational objectives. The main purpose of this study is to consider two domains of efficient leadership and women’s leadership style, in order to determine and elaborate the dimensions of the new concept of “Women’s Efficient Leadership”. We intend to describe the characteristics of women’s efficient leadership in state organizations in Iran by means of offering a logical pattern, in order to be able to propose a favorable pattern, leading to increased efficiency in governmental organizations of the country. Innovation of this study can be divided into two parts: one is theoretical contribution and developing the knowledge of efficient leadership as well as women’s leadership style, and the second one is scientific contribution and proposing a pattern for women’s efficient leadership in state organizations, using compound approach. The outcomes of this study show that women’s efficient leadership in state organizations consists of 7 subjects, 17 dimensions, and 85 components, which represent various characteristics in different periods of time. The thesis that women’s efficient leadership has an evolving nature was approved and that it consists of a combination of factors such as capability of team making, having vision, cognitive and psychological capabilities, able to bring continuous improvement of organizational performance, mentoring and making effective relations. In this study, the influence of mentioned factors on women’s efficient leadership has been investigated by means of questionnaires and has been approved.

  20. Studies of Saccharomyces cerevisiae and Non-Saccharomyces Yeasts during Alcoholic Fermentation

    DEFF Research Database (Denmark)

    Kemsawasd, Varongsiri

    The early death of non-Saccharomyces yeasts during mixed culture spontaneous wine fermentation has traditionally been attributed to the lower capacity of these yeast species to withstand high levels of ethanol, low pH, and other media properties that are a part of progressing fermentation. However......, other yeast-yeast interactions, such as cell-cell contact mediated growth arrest and/or toxininduced death may also be a significant factor in the relative fragility of these non-Saccharomyces yeasts in mixed culture fermentation. In the present work we evaluate the combined roles of cell-cell contact...... and/or antimicrobial peptides on the early death of Lachancea thermotolerans during mixed culture fermentations with Saccharomyces cerevisiae. Using a specially designed double compartment fermentation system, we established that both cell-to-cell contact and antimicrobial peptides contribute...

  1. AGAPE (Automated Genome Analysis PipelinE for pan-genome analysis of Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Giltae Song

    Full Text Available The characterization and public release of genome sequences from thousands of organisms is expanding the scope for genetic variation studies. However, understanding the phenotypic consequences of genetic variation remains a challenge in eukaryotes due to the complexity of the genotype-phenotype map. One approach to this is the intensive study of model systems for which diverse sources of information can be accumulated and integrated. Saccharomyces cerevisiae is an extensively studied model organism, with well-known protein functions and thoroughly curated phenotype data. To develop and expand the available resources linking genomic variation with function in yeast, we aim to model the pan-genome of S. cerevisiae. To initiate the yeast pan-genome, we newly sequenced or re-sequenced the genomes of 25 strains that are commonly used in the yeast research community using advanced sequencing technology at high quality. We also developed a pipeline for automated pan-genome analysis, which integrates the steps of assembly, annotation, and variation calling. To assign strain-specific functional annotations, we identified genes that were not present in the reference genome. We classified these according to their presence or absence across strains and characterized each group of genes with known functional and phenotypic features. The functional roles of novel genes not found in the reference genome and associated with strains or groups of strains appear to be consistent with anticipated adaptations in specific lineages. As more S. cerevisiae strain genomes are released, our analysis can be used to collate genome data and relate it to lineage-specific patterns of genome evolution. Our new tool set will enhance our understanding of genomic and functional evolution in S. cerevisiae, and will be available to the yeast genetics and molecular biology community.

  2. AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces cerevisiae.

    Science.gov (United States)

    Song, Giltae; Dickins, Benjamin J A; Demeter, Janos; Engel, Stacia; Gallagher, Jennifer; Choe, Kisurb; Dunn, Barbara; Snyder, Michael; Cherry, J Michael

    2015-01-01

    The characterization and public release of genome sequences from thousands of organisms is expanding the scope for genetic variation studies. However, understanding the phenotypic consequences of genetic variation remains a challenge in eukaryotes due to the complexity of the genotype-phenotype map. One approach to this is the intensive study of model systems for which diverse sources of information can be accumulated and integrated. Saccharomyces cerevisiae is an extensively studied model organism, with well-known protein functions and thoroughly curated phenotype data. To develop and expand the available resources linking genomic variation with function in yeast, we aim to model the pan-genome of S. cerevisiae. To initiate the yeast pan-genome, we newly sequenced or re-sequenced the genomes of 25 strains that are commonly used in the yeast research community using advanced sequencing technology at high quality. We also developed a pipeline for automated pan-genome analysis, which integrates the steps of assembly, annotation, and variation calling. To assign strain-specific functional annotations, we identified genes that were not present in the reference genome. We classified these according to their presence or absence across strains and characterized each group of genes with known functional and phenotypic features. The functional roles of novel genes not found in the reference genome and associated with strains or groups of strains appear to be consistent with anticipated adaptations in specific lineages. As more S. cerevisiae strain genomes are released, our analysis can be used to collate genome data and relate it to lineage-specific patterns of genome evolution. Our new tool set will enhance our understanding of genomic and functional evolution in S. cerevisiae, and will be available to the yeast genetics and molecular biology community.

  3. Speciation of volatile organic compound emissions for regional air quality modeling of particulate matter and ozone

    Science.gov (United States)

    Makar, P. A.; Moran, M. D.; Scholtz, M. T.; Taylor, A.

    2003-01-01

    A new classification scheme for the speciation of organic compound emissions for use in air quality models is described. The scheme uses 81 organic compound classes to preserve both net gas-phase reactivity and particulate matter (PM) formation potential. Chemical structure, vapor pressure, hydroxyl radical (OH) reactivity, freezing point/boiling point, and solubility data were used to create the 81 compound classes. Volatile, semivolatile, and nonvolatile organic compounds are included. The new classification scheme has been used in conjunction with the Canadian Emissions Processing System (CEPS) to process 1990 gas-phase and particle-phase organic compound emissions data for summer and winter conditions for a domain covering much of eastern North America. A simple postprocessing model was used to analyze the speciated organic emissions in terms of both gas-phase reactivity and potential to form organic PM. Previously unresolved compound classes that may have a significant impact on ozone formation include biogenic high-reactivity esters and internal C6-8 alkene-alcohols and anthropogenic ethanol and propanol. Organic radical production associated with anthropogenic organic compound emissions may be 1 or more orders of magnitude more important than biogenic-associated production in northern United States and Canadian cities, and a factor of 3 more important in southern U.S. cities. Previously unresolved organic compound classes such as low vapour pressure PAHs, anthropogenic diacids, dialkyl phthalates, and high carbon number alkanes may have a significant impact on organic particle formation. Primary organic particles (poorly characterized in national emissions databases) dominate total organic particle concentrations, followed by secondary formation and primary gas-particle partitioning. The influence of the assumed initial aerosol water concentration on subsequent thermodynamic calculations suggests that hydrophobic and hydrophilic compounds may form external

  4. Democracy versus Dictatorship in Self-Organized Models of Financial Markets

    CERN Document Server

    D'Hulst, R

    1999-01-01

    Models to mimic the transmission of information in financial markets are introduced. As an attempt to generate the demand process, we distinguish between dictatorship associations, where groups of agents rely on one of them to make decision, and democratic associations, where each agent takes part in the group decision. In the dictatorship model, agents segregate into two distinct populations, while the democratic model is driven towards a critical state where groups of agents of all sizes exist. Hence, both models display a level of organization, but only the democratic model is self-organized. We show that the dictatorship model generates less volatile markets than the democratic model.

  5. Explicit modeling of organic chemistry and secondary organic aerosol partitioning for Mexico City and its outflow plume

    Energy Technology Data Exchange (ETDEWEB)

    Lee-Taylor, J.; Madronich, Sasha; Aumont, B.; Baker, A.; Camredon, M.; Hodzic, Alma; Tyndall, G. S.; Apel, Eric; Zaveri, Rahul A.

    2011-12-21

    The evolution of organic aerosols (OA) in Mexico City and its outflow is investigated with the nearly explicit gas phase photochemistry model GECKO-A (Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere), wherein precursor hydrocarbons are oxidized to numerous intermediate species for which vapor pressures are computed and used to determine gas/particle partitioning in a chemical box model. Precursor emissions included observed C3-10 alkanes, alkenes, and light aromatics, as well as larger n-alkanes (up to C25) not directly observed but estimated by scaling to particulate emissions according to their volatility. Conditions were selected for comparison with observations made in March 2006 (MILAGRO). The model successfully reproduces the magnitude and diurnal shape for both primary (POA) and secondary (SOA) organic aerosols, with POA peaking in the early morning at 15-20 ug m-3, and SOA peaking at 10-15 μg m-3 during mid-day. The majority (> 75%) of the model SOA stems from the large n-alkanes, with the remainder mostly from the light aromatics. Simulated OA elemental composition reproduces observed H/C and O/C ratios reasonably well, although modeled ratios develop more slowly than observations suggest. SOA chemical composition is initially dominated by *- hydroxy ketones and nitrates from the large alkanes, with contributions from peroxy acyl nitrates and, at later times when NOx is lower, organic hydroperoxides. The simulated plume-integrated OA mass continues to increase for several days downwind despite dilution-induced particle evaporation, since oxidation chemistry leading to SOA formation remains strong. In this model, the plume SOA burden several days downwind exceeds that leaving the city by a factor of >3. These results suggest significant regional radiative impacts of SOA.

  6. Explicit modeling of organic chemistry and secondary organic aerosol partitioning for Mexico City and its outflow plume

    Directory of Open Access Journals (Sweden)

    J. Lee-Taylor

    2011-06-01

    Full Text Available The evolution of organic aerosols (OA in Mexico City and its outflow is investigated with the nearly explicit gas phase photochemistry model GECKO-A (Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere, wherein precursor hydrocarbons are oxidized to numerous intermediate species for which vapor pressures are computed and used to determine gas/particle partitioning in a chemical box model. Precursor emissions included observed C3–10 alkanes, alkenes, and light aromatics, as well as larger n-alkanes (up to C25 not directly observed but estimated by scaling to particulate emissions according to their volatility. Conditions were selected for comparison with observations made in March 2006 (MILAGRO. The model successfully reproduces the magnitude and diurnal shape for both primary (POA and secondary (SOA organic aerosols, with POA peaking in the early morning at 15–20 μg m−3, and SOA peaking at 10–15 μg m−3 during mid-day. The majority (≥75 % of the model SOA stems from the large n-alkanes, with the remainder mostly from the light aromatics. Simulated OA elemental composition reproduces observed H/C and O/C ratios reasonably well, although modeled ratios develop more slowly than observations suggest. SOA chemical composition is initially dominated by δ-hydroxy ketones and nitrates from the large alkanes, with contributions from peroxy acyl nitrates and, at later times when NOx is lower, organic hydroperoxides. The simulated plume-integrated OA mass continues to increase for several days downwind despite dilution-induced particle evaporation, since oxidation chemistry leading to SOA formation remains strong. In this model, the plume SOA burden several days downwind exceeds that leaving the city by a factor of >3. These results suggest significant regional radiative impacts of SOA.

  7. Self-organized Critical Model Based on Complex Brain Networks with Hierarchical Organization

    Institute of Scientific and Technical Information of China (English)

    ZHANG Ying-Yue; ZHANG Gui-Qing; YANG Qiu-Ying; CHEN Tian-Lun

    2008-01-01

    The dynamical behavior in the cortical brain network of macaque is studied by modelling each cortical area with a subnetwork of interacting excitable neurons.We find that the avalanche of our model on different levels exhibits power-law.Furthermore the power-law exponent of the distribution and the average avalanche Size are affected by the topology of the network.

  8. Modelling the fate of organic micropollutants in stormwater ponds

    DEFF Research Database (Denmark)

    Vezzaro, Luca; Eriksson, Eva; Ledin, Anna;

    2011-01-01

    substance inherent properties to calculate MP fate but differ in their ability to represent the small physical scale and high temporal variability of stormwater treatment systems. Therefore the three models generate different results. A Global Sensitivity Analysis (GSA) highlighted that settling....../resuspension of particulate matter was themost sensitive process for the dynamic model. The uncertainty of the estimated MP fluxes can be reduced by calibrating the dynamic model against total suspended solids data. This reduction in uncertainty was more significant for the substances with strong tendency to sorb, i...... models. The fate of four different MP in a stormwater retention pond was simulated by applying two steady-state multimedia fate models (EPI Suite and SimpleBox) commonly applied in chemical risk assessment and a dynamic multimedia fate model (Stormwater Treatment Unit Model for Micro Pollutants — STUMP...

  9. Encapsulation-Induced Stress Helps Saccharomyces cerevisiae Resist Convertible Lignocellulose Derived Inhibitors

    Directory of Open Access Journals (Sweden)

    Johan O. Westman

    2012-09-01

    Full Text Available The ability of macroencapsulated Saccharomyces cerevisiae CBS8066 to withstand readily and not readily in situ convertible lignocellulose-derived inhibitors was investigated in anaerobic batch cultivations. It was shown that encapsulation increased the tolerance against readily convertible furan aldehyde inhibitors and to dilute acid spruce hydrolysate, but not to organic acid inhibitors that cannot be metabolized anaerobically. Gene expression analysis showed that the protective effect arising from the encapsulation is evident also on the transcriptome level, as the expression of the stress-related genes YAP1, ATR1 and FLR1 was induced upon encapsulation. The transcript levels were increased due to encapsulation already in the medium without added inhibitors, indicating that the cells sensed low stress level arising from the encapsulation itself. We present a model, where the stress response is induced by nutrient limitation, that this helps the cells to cope with the increased stress added by a toxic medium, and that superficial cells in the capsules degrade convertible inhibitors, alleviating the inhibition for the cells deeper in the capsule.

  10. Controlling promoter strength and regulation in Saccharomyces cerevisiae using synthetic hybrid promoters.

    Science.gov (United States)

    Blazeck, John; Garg, Rishi; Reed, Ben; Alper, Hal S

    2012-11-01

    A dynamic range of well-controlled constitutive and tunable promoters are essential for metabolic engineering and synthetic biology applications in all host organisms. Here, we apply a synthetic hybrid promoter approach for the creation of strong promoter libraries in the model yeast, Saccharomyces cerevisiae. Synthetic hybrid promoters are composed of two modular components-the enhancer element, consisting of tandem repeats or combinations of upstream activation sequences (UAS), and the core promoter element. We demonstrate the utility of this approach with three main case studies. First, we establish a dynamic range of constitutive promoters and in doing so expand transcriptional capacity of the strongest constitutive yeast promoter, P(GPD) , by 2.5-fold in terms of mRNA levels. Second, we demonstrate the capacity to impart synthetic regulation through a hybrid promoter approach by adding galactose activation and removing glucose repression. Third, we establish a collection of galactose-inducible hybrid promoters that span a nearly 50-fold dynamic range of galactose-induced expression levels and increase the transcriptional capacity of the Gal1 promoter by 15%. These results demonstrate that promoters in S. cerevisiae, and potentially all yeast, are enhancer limited and a synthetic hybrid promoter approach can expand, enhance, and control promoter activity.

  11. Molecular characterization of propolis-induced cell death in Saccharomyces cerevisiae.

    Science.gov (United States)

    de Castro, Patrícia Alves; Savoldi, Marcela; Bonatto, Diego; Barros, Mário Henrique; Goldman, Maria Helena S; Berretta, Andresa A; Goldman, Gustavo Henrique

    2011-03-01

    Propolis, a natural product of plant resins, is used by the bees to seal holes in their honeycombs and protect the hive entrance. However, propolis has also been used in folk medicine for centuries. Here, we apply the power of Saccharomyces cerevisiae as a model organism for studies of genetics, cell biology, and genomics to determine how propolis affects fungi at the cellular level. Propolis is able to induce an apoptosis cell death response. However, increased exposure to propolis provides a corresponding increase in the necrosis response. We showed that cytochrome c but not endonuclease G (Nuc1p) is involved in propolis-mediated cell death in S. cerevisiae. We also observed that the metacaspase YCA1 gene is important for propolis-mediated cell death. To elucidate the gene functions that may be required for propolis sensitivity in eukaryotes, the full collection of about 4,800 haploid S. cerevisiae deletion strains was screened for propolis sensitivity. We were able to identify 138 deletion strains that have different degrees of propolis sensitivity compared to the corresponding wild-type strains. Systems biology revealed enrichment for genes involved in the mitochondrial electron transport chain, vacuolar acidification, negative regulation of transcription from RNA polymerase II promoter, regulation of macroautophagy associated with protein targeting to vacuoles, and cellular response to starvation. Validation studies indicated that propolis sensitivity is dependent on the mitochondrial function and that vacuolar acidification and autophagy are important for yeast cell death caused by propolis.

  12. Polyhydroxyfullerene binds cadmium ions and alleviates metal-induced oxidative stress in Saccharomyces cerevisiae.

    Science.gov (United States)

    Pradhan, Arunava; Pinheiro, José Paulo; Seena, Sahadevan; Pascoal, Cláudia; Cássio, Fernanda

    2014-09-01

    The water-soluble polyhydroxyfullerene (PHF) is a functionalized carbon nanomaterial with several industrial and commercial applications. There have been controversial reports on the toxicity and/or antioxidant properties of fullerenes and their derivatives. Conversely, metals have been recognized as toxic mainly due to their ability to induce oxidative stress in living organisms. We investigated the interactive effects of PHF and cadmium ions (Cd) on the model yeast Saccharomyces cerevisiae by exposing cells to Cd (≤5 mg liter(-1)) in the absence or presence of PHF (≤500 mg liter(-1)) at different pHs (5.8 to 6.8). In the absence of Cd, PHF stimulated yeast growth up to 10.4%. Cd inhibited growth up to 79.7%, induced intracellular accumulation of reactive oxygen species (ROS), and promoted plasma membrane disruption in a dose- and pH-dependent manner. The negative effects of Cd on growth were attenuated by the presence of PHF, and maximum growth recovery (53.8%) was obtained at the highest PHF concentration and pH. The coexposure to Cd and PHF decreased ROS accumulation up to 36.7% and membrane disruption up to 30.7% in a dose- and pH-dependent manner. Two mechanisms helped to explain the role of PHF in alleviating Cd toxicity to yeasts: PHF decreased Cd-induced oxidative stress and bound significant amounts of Cd in the extracellular medium, reducing its bioavailability to the cells.

  13. Biosynthesis and function of GPI proteins in the yeast Saccharomyces cerevisiae.

    Science.gov (United States)

    Pittet, Martine; Conzelmann, Andreas

    2007-03-01

    Like most other eukaryotes, Saccharomyces cerevisiae harbors a GPI anchoring machinery and uses it to attach proteins to membranes. While a few GPI proteins reside permanently at the plasma membrane, a majority of them gets further processed and is integrated into the cell wall by a covalent attachment to cell wall glucans. The GPI biosynthetic pathway is necessary for growth and survival of yeast cells. The GPI lipids are synthesized in the ER and added onto proteins by a pathway comprising 12 steps, carried out by 23 gene products, 19 of which are essential. Some of the estimated 60 GPI proteins predicted from the genome sequence serve enzymatic functions required for the biosynthesis and the continuous shape adaptations of the cell wall, others seem to be structural elements of the cell wall and yet others mediate cell adhesion. Because of its genetic tractability S. cerevisiae is an attractive model organism not only for studying GPI biosynthesis in general, but equally for investigating the intracellular transport of GPI proteins and the peculiar role of GPI anchoring in the elaboration of fungal cell walls.

  14. Mapping condition-dependent regulation of lipid metabolism in Saccharomyces cerevisiae.

    Science.gov (United States)

    Jewett, Michael C; Workman, Christopher T; Nookaew, Intawat; Pizarro, Francisco A; Agosin, Eduardo; Hellgren, Lars I; Nielsen, Jens

    2013-11-06

    Lipids play a central role in cellular function as constituents of membranes, as signaling molecules, and as storage materials. Although much is known about the role of lipids in regulating specific steps of metabolism, comprehensive studies integrating genome-wide expression data, metabolite levels, and lipid levels are currently lacking. Here, we map condition-dependent regulation controlling lipid metabolism in Saccharomyces cerevisiae by measuring 5636 mRNAs, 50 metabolites, 97 lipids, and 57 (13)C-reaction fluxes in yeast using a three-factor full-factorial design. Correlation analysis across eight environmental conditions revealed 2279 gene expression level-metabolite/lipid relationships that characterize the extent of transcriptional regulation in lipid metabolism relative to major metabolic hubs within the cell. To query this network, we developed integrative methods for correlation of multi-omics datasets that elucidate global regulatory signatures. Our data highlight many characterized regulators of lipid metabolism and reveal that sterols are regulated more at the transcriptional level than are amino acids. Beyond providing insights into the systems-level organization of lipid metabolism, we anticipate that our dataset and approach can join an emerging number of studies to be widely used for interrogating cellular systems through the combination of mathematical modeling and experimental biology.

  15. Genome wide transcriptional response of Saccharomyces cerevisiae to stress-induced perturbations

    Directory of Open Access Journals (Sweden)

    Hilal eTaymaz-Nikerel

    2016-02-01

    Full Text Available Cells respond to environmental and/or genetic perturbations in order to survive and proliferate. Characterization of the changes after various stimuli at different -omics levels is crucial to comprehend the adaptation of cells to changing conditions. Genome wide quantification and analysis of transcript levels, the genes affected by perturbations, extends our understanding of cellular metabolism by pointing out the mechanisms that play role in sensing the stress caused by those perturbations and related signaling pathways, and in this way guides us to achieve endeavors such as rational engineering of cells or interpretation of disease mechanisms. Saccharomyces cerevisiae as a model system has been studied in response to different perturbations and corresponding transcriptional profiles were followed either statically or/and dynamically, short- and long- term. This review focuses on response of yeast cells to diverse stress inducing perturbations including nutritional changes, ionic stress, salt stress, oxidative stress, osmotic shock, as well as to genetic interventions such as deletion and over-expression of genes. It is aimed to conclude on common regulatory phenomena that allow yeast to organize its transcriptomic response after any perturbation under different external conditions.

  16. Benchmarking two commonly used Saccharomyces cerevisiae strains for heterologous vanillin-β-glucoside production

    Directory of Open Access Journals (Sweden)

    Tomas Strucko

    2015-12-01

    Full Text Available The yeast Saccharomyces cerevisiae is a widely used eukaryotic model organism and a key cell factory for production of biofuels and wide range of chemicals. From the broad palette of available yeast strains, the most popular are those derived from laboratory strain S288c and the industrially relevant CEN.PK strain series. Importantly, in recent years these two strains have been subjected to comparative “-omics” analyzes pointing out significant genotypic and phenotypic differences. It is therefore possible that the two strains differ significantly with respect to their potential as cell factories for production of specific compounds. To examine this possibility, we have reconstructed a de novo vanillin-β-glucoside pathway in an identical manner in S288c and CEN.PK strains. Characterization of the two resulting strains in two standard conditions revealed that the S288c background strain produced up to 10-fold higher amounts of vanillin-β-glucoside compared to CEN.PK. This study demonstrates that yeast strain background may play a major role in the outcome of newly developed cell factories for production of a given product.

  17. Glucose starvation as a selective tool for the study of adaptive mutations in Saccharomyces cerevisiae.

    Science.gov (United States)

    Heidenreich, Erich; Steinboeck, Ferdinand

    2017-01-01

    Mutations not only arise in proliferating cells but also in resting - thus non-replicating - cells. Such stationary-phase mutations may occasionally enable an escape from growth repression and e.g. contribute to cancerogenesis or development of drug resistance. The most widely used condition for the study of such adaptive mutations in the eukaryotic model organism Saccharomyces cerevisiae is the starvation for a single amino acid. To overcome some limitations of this experimental setup we developed a new adaptive mutation assay that allows a screening for mutagenic processes during a more regular cell cycle arrest induced by the lack of a fermentable carbon source. We blocked one essential step of gluconeogenesis by inactivation of the FBP1 gene. This drives the cells into a cell cycle arrest when glucose is not available in the medium although a non-fermentable carbon source is present. As another component of the new mutation assay, we established a custom-designed test allele that contains a microsatellite sequence as a target for mutations. We demonstrated the feasibility and validity of this novel experimental setup by the observation and characterization of adaptive mutants.

  18. Molecular Characterization of Propolis-Induced Cell Death in Saccharomyces cerevisiae▿†

    Science.gov (United States)

    de Castro, Patrícia Alves; Savoldi, Marcela; Bonatto, Diego; Barros, Mário Henrique; Goldman, Maria Helena S.; Berretta, Andresa A.; Goldman, Gustavo Henrique

    2011-01-01

    Propolis, a natural product of plant resins, is used by the bees to seal holes in their honeycombs and protect the hive entrance. However, propolis has also been used in folk medicine for centuries. Here, we apply the power of Saccharomyces cerevisiae as a model organism for studies of genetics, cell biology, and genomics to determine how propolis affects fungi at the cellular level. Propolis is able to induce an apoptosis cell death response. However, increased exposure to propolis provides a corresponding increase in the necrosis response. We showed that cytochrome c but not endonuclease G (Nuc1p) is involved in propolis-mediated cell death in S. cerevisiae. We also observed that the metacaspase YCA1 gene is important for propolis-mediated cell death. To elucidate the gene functions that may be required for propolis sensitivity in eukaryotes, the full collection of about 4,800 haploid S. cerevisiae deletion strains was screened for propolis sensitivity. We were able to identify 138 deletion strains that have different degrees of propolis sensitivity compared to the corresponding wild-type strains. Systems biology revealed enrichment for genes involved in the mitochondrial electron transport chain, vacuolar acidification, negative regulation of transcription from RNA polymerase II promoter, regulation of macroautophagy associated with protein targeting to vacuoles, and cellular response to starvation. Validation studies indicated that propolis sensitivity is dependent on the mitochondrial function and that vacuolar acidification and autophagy are important for yeast cell death caused by propolis. PMID:21193549

  19. Modeling of multiphase transport of multicomponent organic contaminants and heat in the subsurface: Numerical model formulation

    Science.gov (United States)

    Adenekan, A. E.; Patzek, T. W.; Pruess, K.

    1993-11-01

    A numerical compositional simulator (Multiphase Multicomponent Nonisothermal Organics Transport Simulator (M2NOTS)) has been developed for modeling transient, three-dimensional, nonisothermal, and multiphase transport of multicomponent organic contaminants in the subsurface. The governing equations include (1) advection of all three phases in response to pressure, capillary, and gravity forces; (2) interphase mass transfer that allows every component to partition into each phase present; (3) diffusion; and (4) transport of sensible and latent heat energy. Two other features distinguish M2NOTS from other simulators reported in the groundwater literature: (1) the simulator allows for any number of chemical components and every component is allowed to partition into all fluid phases present, and (2) each phase is allowed to completely disappear from, or appear in, any region of the domain during a simulation. These features are required to model realistic field problems involving transport of mixtures of nonaqueous phase liquid contaminants, and to quantify performance of existing and emerging remediation methods such as vacuum extraction and steam injection.

  20. Neotropical electric fishes (Gymnotiformes as model organisms for bioassays

    Directory of Open Access Journals (Sweden)

    Milena Ferreira

    2015-04-01

    Full Text Available Electric fishes (Gymnotiformes inhabit Central and South America and form a relatively large group with more than 200 species. Besides a taxonomic challenge due to their still unresolved systematic, wide distribution and the variety of habitats they occupy, these fishes have been intensively studied due to their peculiar use of bioelectricity for electrolocation and communication. Conventional analysis of cells, tissues and organs have been complemented with the studies on the electric organ discharges of these fishes. This review compiles the results of 13 bioassays developed during the last 50 years, which used the quickness, low costs and functionality of the bioelectric data collection of Gymnotiformes to evaluate the effects of environmental contaminants and neuroactive drugs.

  1. Neotropical electric fishes (Gymnotiformes) as model organisms for bioassays

    Institute of Scientific and Technical Information of China (English)

    Milena Ferreira; Isac Silva de Jesus; Eliana Feldberg; JoséAntônioAlves-Gomes

    2015-01-01

    Electric fishes (Gymnotiformes) inhabit Central and South America and form a relatively large group with more than 200 species. Besides a taxonomic challenge due to their still unresolved systematic, wide distribution and the variety of habitats they occupy, these fishes have been intensively studied due to their peculiar use of bioelectricity for electrolocation and communication. Conventional analysis of cells, tissues and organs have been complemented with the studies on the electric organ discharges of these fishes. This review compiles the results of 13 bioassays developed during the last 50 years, which used the quickness, low costs and functionality of the bioelectric data collection of Gymnotiformes to evaluate the effects of environmental contaminants and neuroactive drugs.

  2. Organizations

    DEFF Research Database (Denmark)

    Hatch, Mary Jo

    Most of us recognize that organizations are everywhere. You meet them on every street corner in the form of families and shops, study in them, work for them, buy from them, pay taxes to them. But have you given much thought to where they came from, what they are today, and what they might become...... in the future? How and why do they have so much influence over us, and what influences them? How do they contribute to and detract from the meaningfulness of lives, and how might we improve them so they better serve our needs and desires? This Very Short Introductions addresses all of these questions...

  3. [Emission model of volatile organic compounds from materials used indoors].

    Science.gov (United States)

    Han, K

    1998-11-30

    Various materials, such as wall-paper, floor-wax, paint, multicolor wall-coat, air freshener and mothball were experimented in a simulated test chamber under constant selected temperature, humidity and air exchange rate. The relation between the total VOCs concentration and time was regressed by four emission models and the surface emission rate was calculated. The regressed results indicated the similarity among four emission models for the liquid materials with volatile-solvent such as paint and multicolor wall-coat. But for low volatile solid materials, such as wall-paper, floor-wax, mothball, the sink model and the empirical model were better than the dilution model and vapor pressure model. Only for air freshener, it was improper to the total VOCs concentration as a parameter.

  4. Modeling the release of organic contaminants during compost decomposition in soil.

    Science.gov (United States)

    Geng, Chunnu; Haudin, Claire-Sophie; Zhang, Yuan; Lashermes, Gwenaëlle; Houot, Sabine; Garnier, Patricia

    2015-01-01

    Composts, incorporated in soils as amendments, may release organic contaminants during their decomposition. COP-Soil is presented here as a new model to simulate the interaction between organic contaminants and compost, using one module for organic matter and one for organic pollutants, with these modules being linked by several assumptions. Published results of laboratory soil incubations using labeled carbon pollutants from compost were used to test the model for one polycyclic aromatic hydrocarbon (PAH), two surfactants and one herbicide. Several simulation scenarios were tested using (i) the organic pollutant module either alone or coupled to the organic matter module, (ii) various methods to estimate the adsorption coefficients (Kd) of contaminants on organic matter and (iii) different degrading biomasses. The simulations were improved if the organic pollutant module was coupled with the organic matter module. Multiple linear regression model for Kd as a function of organic matter quality yielded the most accurate simulation results. The inclusion of specific biomass in the model made it possible to successfully predict the PAH mineralization.

  5. CONCEPTUAL MODEL OF MARKETING STRATEGIC PLANNING SPECIFIC TO PUBLIC ORGANIZATIONS

    OpenAIRE

    Ionescu Florin Tudor; Barbu Andreea Mihaela

    2012-01-01

    In public services, the political component of the marketing environment has a major importance, as all decisions adopted within central administration influence both the objectives and measures implemented by units of local government and other public service providers. Any discontinuity in the activity of such entities might result in neglecting the real needs of citizens and slowing the reform process in the public sector. Therefore, all initiatives of public organizations must have a unit...

  6. Organisms modeling: The question of radial basis function networks

    Directory of Open Access Journals (Sweden)

    Muzy Alexandre

    2014-01-01

    Full Text Available There exists usually a gap between bio-inspired computational techniques and what biologists can do with these techniques in their current researches. Although biology is the root of system-theory and artifical neural networks, computer scientists are tempted to build their own systems independently of biological issues. This publication is a first-step re-evalution of an usual machine learning technique (radial basis funtion(RBF networks in the context of systems and biological reactive organisms.

  7. Ames Culture Chamber System: Enabling Model Organism Research Aboard the international Space Station

    Science.gov (United States)

    Steele, Marianne

    2014-01-01

    Understanding the genetic, physiological, and behavioral effects of spaceflight on living organisms and elucidating the molecular mechanisms that underlie these effects are high priorities for NASA. Certain organisms, known as model organisms, are widely studied to help researchers better understand how all biological systems function. Small model organisms such as nem-atodes, slime mold, bacteria, green algae, yeast, and moss can be used to study the effects of micro- and reduced gravity at both the cellular and systems level over multiple generations. Many model organisms have sequenced genomes and published data sets on their transcriptomes and proteomes that enable scientific investigations of the molecular mechanisms underlying the adaptations of these organisms to space flight.

  8. Protochordate amphioxus is an emerging model organism for comparative immunology

    Institute of Scientific and Technical Information of China (English)

    Shicui Zhang; Yujun Liang; Guangdong Jia; Zhimeng Zhuang

    2009-01-01

    Protochordate amphioxus is an extant invertebrate regarded quite recently as a basal chordate. It has a vertebrate-like body plan including a circulation system with an organization similar to that of vertebrates. However, amphioxus is less complex than vertebrates for having a genome uncomplicated by extensive genomic duplication, and lacking lymphoid organs and free circulating blood cells.Recent studies on immunity have demonstrated the presence in amphioxus of both the constituent elements of key molecules involved in adaptive immunity such as proto-major histocompatibility complex (proto-MHC), V region-containing chitin-binding protein (VCBP)and V and C domain-bearing protein (VCP), and the complement system operating via the alternative and lectin pathways resembling those seen in vertebrates. In addition, the acute phase response profile in amphioxus has been shown to be similar to that observed in vertebrates. These findings together with the relative structural and genomic simplicity make amphioxus an ideal organism for gaining insights into the origin and evolution of the vertebrate immune system, especially adaptive immunity, and the composition and mech-anisms of the vertebrate innate immunity.

  9. Dynamic root uptake model for neutral lipophilic organics

    DEFF Research Database (Denmark)

    Trapp, Stefan

    2002-01-01

    and output to stem with the transpiration stream plus first-order metabolism and dilution by exponential growth. For chemicals with low or intermediate lipophilicity (log Kow , 2), there was no relevant difference between dynamic model and equilibrium approach. For lipophilic compounds, the dynamic model...... approach. Very lipophilic compounds (e.g., DDT) diffuse very slowly into plant tissue, so they are likely to remain in the peel of root vegetables. In addition, a dynamic (steady-state) flux model for uptake with transpiration water into thick roots is presented. The model considers input from soil...

  10. Phenotypic characterisation of Saccharomyces spp. for tolerance to 1-butanol.

    Science.gov (United States)

    Zaki, A M; Wimalasena, T T; Greetham, D

    2014-11-01

    Biofuels are expected to play a role in replacing crude oil as a liquid transportation fuel, and research into butanol has highlighted the importance of this alcohol as a fuel. Butanol has a higher energy density than ethanol, butanol-gasoline blends do not separate in the presence of water, and butanol is miscible with gasoline (Szulczyk, Int J Energy Environ 1(1):2876-2895, 40). Saccharomyces cerevisiae has been used as a fermentative organism in the biofuel industry producing ethanol from glucose derived from starchy plant material; however, it typically cannot tolerate butanol concentrations greater than 2 % (Luong, Biotechnol Bioeng 29 (2):242-248, 27). 90 Saccharomyces spp. strains were screened for tolerance to 1-butanol via a phenotypic microarray assay and we observed significant variation in response with the most tolerant strains (S. cerevisiae DBVPG1788, S. cerevisiae DBVPG6044 and S. cerevisiae YPS128) exhibiting tolerance to 4 % 1-butanol compared with S. uvarum and S. castelli strains, which were sensitive to 3 % 1-butanol. Response to butanol was confirmed using traditional yeast methodologies such as growth; it was observed that fermentations in the presence of butanol, when using strains with a tolerant background, were significantly faster. Assessing for genetic rationale for tolerance, it was observed that 1-butanol-tolerant strains, when compared with 1-butanol-sensitive strains, had an up-regulation of RPN4, a transcription factor which regulates proteasome genes. Analysing for the importance of RPN4, we observed that a Δrpn4 strain displayed a reduced rate of fermentation in the presence of 1-butanol when compared with the BY4741 background strain. This data will aid the development of breeding programmes to produce better strains for future bio-butanol production.

  11. Copper Tolerance and Biosorption of Saccharomyces cerevisiae during Alcoholic Fermentation.

    Science.gov (United States)

    Sun, Xiang-Yu; Zhao, Yu; Liu, Ling-Ling; Jia, Bo; Zhao, Fang; Huang, Wei-Dong; Zhan, Ji-Cheng

    2015-01-01

    At high levels, copper in grape mash can inhibit yeast activity and cause stuck fermentations. Wine yeast has limited tolerance of copper and can reduce copper levels in wine during fermentation. This study aimed to understand copper tolerance of wine yeast and establish the mechanism by which yeast decreases copper in the must during fermentation. Three strains of Saccharomyces cerevisiae (lab selected strain BH8 and industrial strains AWRI R2 and Freddo) and a simple model fermentation system containing 0 to 1.50 mM Cu2+ were used. ICP-AES determined Cu ion concentration in the must decreasing differently by strains and initial copper levels during fermentation. Fermentation performance was heavily inhibited under copper stress, paralleled a decrease in viable cell numbers. Strain BH8 showed higher copper-tolerance than strain AWRI R2 and higher adsorption than Freddo. Yeast cell surface depression and intracellular structure deformation after copper treatment were observed by scanning electron microscopy and transmission electron microscopy; electronic differential system detected higher surface Cu and no intracellular Cu on 1.50 mM copper treated yeast cells. It is most probably that surface adsorption dominated the biosorption process of Cu2+ for strain BH8, with saturation being accomplished in 24 h. This study demonstrated that Saccharomyces cerevisiae strain BH8 has good tolerance and adsorption of Cu, and reduces Cu2+ concentrations during fermentation in simple model system mainly through surface adsorption. The results indicate that the strain selected from China's stress-tolerant wine grape is copper tolerant and can reduce copper in must when fermenting in a copper rich simple model system, and provided information for studies on mechanisms of heavy metal stress.

  12. Copper Tolerance and Biosorption of Saccharomyces cerevisiae during Alcoholic Fermentation

    Science.gov (United States)

    Liu, Ling-ling; Jia, Bo; Zhao, Fang; Huang, Wei-dong; Zhan, Ji-cheng

    2015-01-01

    At high levels, copper in grape mash can inhibit yeast activity and cause stuck fermentations. Wine yeast has limited tolerance of copper and can reduce copper levels in wine during fermentation. This study aimed to understand copper tolerance of wine yeast and establish the mechanism by which yeast decreases copper in the must during fermentation. Three strains of Saccharomyces cerevisiae (lab selected strain BH8 and industrial strains AWRI R2 and Freddo) and a simple model fermentation system containing 0 to 1.50 mM Cu2+ were used. ICP-AES determined Cu ion concentration in the must decreasing differently by strains and initial copper levels during fermentation. Fermentation performance was heavily inhibited under copper stress, paralleled a decrease in viable cell numbers. Strain BH8 showed higher copper-tolerance than strain AWRI R2 and higher adsorption than Freddo. Yeast cell surface depression and intracellular structure deformation after copper treatment were observed by scanning electron microscopy and transmission electron microscopy; electronic differential system detected higher surface Cu and no intracellular Cu on 1.50 mM copper treated yeast cells. It is most probably that surface adsorption dominated the biosorption process of Cu2+ for strain BH8, with saturation being accomplished in 24 h. This study demonstrated that Saccharomyces cerevisiae strain BH8 has good tolerance and adsorption of Cu, and reduces Cu2+ concentrations during fermentation in simple model system mainly through surface adsorption. The results indicate that the strain selected from China’s stress-tolerant wine grape is copper tolerant and can reduce copper in must when fermenting in a copper rich simple model system, and provided information for studies on mechanisms of heavy metal stress. PMID:26030864

  13. Modeling the surface tension of complex, reactive organic-inorganic mixtures

    Science.gov (United States)

    Schwier, A. N.; Viglione, G. A.; Li, Z.; McNeill, V. Faye

    2013-11-01

    Atmospheric aerosols can contain thousands of organic compounds which impact aerosol surface tension, affecting aerosol properties such as heterogeneous reactivity, ice nucleation, and cloud droplet formation. We present new experimental data for the surface tension of complex, reactive organic-inorganic aqueous mixtures mimicking tropospheric aerosols. Each solution contained 2-6 organic compounds, including methylglyoxal, glyoxal, formaldehyde, acetaldehyde, oxalic acid, succinic acid, leucine, alanine, glycine, and serine, with and without ammonium sulfate. We test two semi-empirical surface tension models and find that most reactive, complex, aqueous organic mixtures which do not contain salt are well described by a weighted Szyszkowski-Langmuir (S-L) model which was first presented by Henning et al. (2005). Two approaches for modeling the effects of salt were tested: (1) the Tuckermann approach (an extension of the Henning model with an additional explicit salt term), and (2) a new implicit method proposed here which employs experimental surface tension data obtained for each organic species in the presence of salt used with the Henning model. We recommend the use of method (2) for surface tension modeling of aerosol systems because the Henning model (using data obtained from organic-inorganic systems) and Tuckermann approach provide similar modeling results and goodness-of-fit (χ2) values, yet the Henning model is a simpler and more physical approach to modeling the effects of salt, requiring less empirically determined parameters.

  14. Modeling the surface tension of complex, reactive organic-inorganic mixtures

    Directory of Open Access Journals (Sweden)

    A. N. Schwier

    2013-01-01

    Full Text Available Atmospheric aerosols can contain thousands of organic compounds which impact aerosol surface tension, affecting aerosol properties such as cloud condensation nuclei (CCN ability. We present new experimental data for the surface tension of complex, reactive organic-inorganic aqueous mixtures mimicking tropospheric aerosols. Each solution contained 2–6 organic compounds, including methylglyoxal, glyoxal, formaldehyde, acetaldehyde, oxalic acid, succinic acid, leucine, alanine, glycine, and serine, with and without ammonium sulfate. We test two surface tension models and find that most reactive, complex, aqueous organic mixtures which do not contain salt are well-described by a weighted Szyszkowski–Langmuir (S–L model which was first presented by Henning et al. (2005. Two approaches for modeling the effects of salt were tested: (1 the Tuckermann approach (an extension of the Henning model with an additional explicit salt term, and (2 a new implicit method proposed here which employs experimental surface tension data obtained for each organic species in the presence of salt used with the Henning model. We recommend the use of method (2 for surface tension modeling because the Henning model (using data obtained from organic-inorganic systems and Tuckermann approach provide similar modeling fits and goodness of fit (χ2 values, yet the Henning model is a simpler and more physical approach to modeling the effects of salt, requiring less empirically determined parameters.

  15. Molecular Dynamics Modeling of Tethered Organics in Confined Spaces

    Energy Technology Data Exchange (ETDEWEB)

    Waksburg, Avi [Monash University, Australia; Nguyen, M [Monash University, Australia; Chaffe, Alan [Monash University, Australia; Kidder, Michelle [ORNL; Buchanan III, A C [ORNL; Britt, Phillip F [ORNL

    2011-01-01

    A computational method for constructing and evaluating the dynamic behaviour of functionalised hexagonal mesoporous silica (HMS) MCM-41 models is reported. HMS with three pore diameters (1.7, 2.2 and 2.9 nm) were prepared, and, from these, two series of derivative structures were constructed - one with 1,3-diphenylpropyl (DPP) tethers and the other with smaller dimethylsilyl (DMS) tethers attached to the mesopores internal surfaces. Comparison with experimental data shows that simulation results correctly predict the maximum tether density that can be achieved for each tether and each pore diameter. For the smaller pore models, the extent of DPP functionalisation that can be achieved is limited by the available pore volume. However, for the larger pore model, the extent of functionalisation is limited by access to potentially reactive sites on the pore surface. The dynamic behaviour of the models was investigated over a range of temperatures (240-648 K). At lower temperatures (< 400 K), the mobility of DPP tethers in the 2.9 nm model is actually less than that observed in either the 2.2 nm model or the 1.7 nm model due to the extensive non-bonded interactions that are able to develop between tethers and the silica surface at this diameter. At higher temperatures, the free ends of these tethers break away from the surface, extend further into the pore space and the DPP mobility in the 2.9 nm model is higher than in the smaller pore systems.

  16. Modeling cadmium in the feed chain and cattle organs

    NARCIS (Netherlands)

    Fels-Klerx, van der H.J.; Romkens, P.F.A.M.; Franz, E.; Raamsdonk, van L.W.D.

    2011-01-01

    The objectives of this study were to estimate cadmium contamination levels in different scenarios related to soil characteristics and assumptions regarding cadmium accumulation in the animal tissues, using quantitative supply chain modeling. The model takes into account soil cadmium levels, soil pH,

  17. Modeling cadmium in the feed chain and cattle organs

    NARCIS (Netherlands)

    Fels-Klerx, van der H.J.; Romkens, P.F.A.M.; Franz, E.; Raamsdonk, van L.W.D.

    2011-01-01

    The objectives of this study were to estimate cadmium contamination levels in different scenarios related to soil characteristics and assumptions regarding cadmium accumulation in the animal tissues, using quantitative supply chain modeling. The model takes into account soil cadmium levels, soil pH,

  18. Drosophila melanogaster as a Model Organism of Brain Diseases

    Directory of Open Access Journals (Sweden)

    Werner Paulus

    2009-02-01

    Full Text Available Drosophila melanogaster has been utilized to model human brain diseases. In most of these invertebrate transgenic models, some aspects of human disease are reproduced. Although investigation of rodent models has been of significant impact, invertebrate models offer a wide variety of experimental tools that can potentially address some of the outstanding questions underlying neurological disease. This review considers what has been gleaned from invertebrate models of neurodegenerative diseases, including Alzheimer’s disease, Parkinson’s disease, metabolic diseases such as Leigh disease, Niemann-Pick disease and ceroid lipofuscinoses, tumor syndromes such as neurofibromatosis and tuberous sclerosis, epilepsy as well as CNS injury. It is to be expected that genetic tools in Drosophila will reveal new pathways and interactions, which hopefully will result in molecular based therapy approaches.

  19. Incorporating sorption/desorption of organic pollutants into river water quality model

    Institute of Scientific and Technical Information of China (English)

    LOU Bao-feng; ZHU Li-zhong; YANG Kun

    2004-01-01

    Preliminary research was conducted about how to incorporate sorption/desorption of organic pollutants with suspended solids and sediments into single-chemical and one-dimensional water quality model of Jinghang Canal.Sedimentation-resuspension coefficient k3 was deduced; characteristics of organic pollutants, concentrations and components of suspended solids/sediments and hydrological and hydraulic conditions were integrated into k3 and further into river water quality model; impact of sorption/desorption of organic pollutants with suspended solids and sediments on prediction function of the model was discussed. Results demonstrated that this impact is pronounced for organic pollutants with relatively large Koc and Kow, especially when they are also conservative and foc of river suspended solids/sediments is high, and that incorporation of sorption/ desorption of organic pollutants into river water quality model can improve its prediction accuracy.

  20. EXTERNALITIES AND THE SIX FACETS MODEL OF TECHNOLOGY MANAGEMENT: GENETICALLY MODIFIED ORGANISMS IN AGRIBUSINESS

    OpenAIRE

    STEPHEN R. LUXMORE; CLYDE EIRÍKUR HULL

    2010-01-01

    The Six Facets Model of technology management has previously only been applied to process innovation at the firm and the industry level. In this article, the model is applied to product innovation for the first time. In the context of genetically-modified organisms in the agribusiness industry, we examine radical product innovation through the Six Facets Model. We propose, based on the history of genetically-modified organisms in agribusiness, that when applied to product innovation the Six F...

  1. Modeling of iodine radiation chemistry in the presence of organic compounds

    Energy Technology Data Exchange (ETDEWEB)

    Taghipour, Fariborz; Evans, Greg J. E-mail: evansg@chem-eng.toronto.edu

    2002-06-01

    A kinetic-based model was developed that simulates the radiation chemistry of iodine in the presence of organic compounds. The model's mechanistic description of iodine chemistry and generic semi-mechanistic reactions for various classes of organics, provided a reasonable representation of experimental results. The majority of the model and experimental results of iodine volatilization rates were in agreement within an order of magnitude.

  2. Engineering of a Nepetalactol-Producing Platform Strain of Saccharomyces cerevisiae for the Production of Plant Seco-Iridoids.

    Science.gov (United States)

    Campbell, Alex; Bauchart, Philippe; Gold, Nicholas D; Zhu, Yun; De Luca, Vincenzo; Martin, Vincent J J

    2016-05-20

    The monoterpene indole alkaloids (MIAs) are a valuable family of chemicals that include the anticancer drugs vinblastine and vincristine. These compounds are of global significance-appearing on the World Health Organization's list of model essential medicines-but remain exorbitantly priced due to low in planta levels. Chemical synthesis and genetic manipulation of MIA producing plants such as Catharanthus roseus have so far failed to find a solution to this problem. Synthetic biology holds a potential answer, by building the pathway into more tractable organisms such as Saccharomyces cerevisiae. Recent work has taken the first steps in this direction by producing small amounts of the intermediate strictosidine in yeast. In order to help improve on these titers, we aimed to optimize the early biosynthetic steps of the MIA pathway to the metabolite nepetalactol. We combined a number of strategies to create a base strain producing 11.4 mg/L of the precursor geraniol. We also show production of the critical intermediate 10-hydroxygeraniol and demonstrate nepetalactol production in vitro. Lastly we demonstrate that activity of the iridoid synthase toward the intermediates geraniol and 10-hydroxygeraniol results in the synthesis of the nonproductive intermediates citronellol and 10-hydroxycitronellol. This discovery has serious implications for the reconstruction of the MIA in heterologous organisms.

  3. Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae.

    Science.gov (United States)

    Wang, Ji-Ping; Fondufe-Mittendorf, Yvonne; Xi, Liqun; Tsai, Guei-Feng; Segal, Eran; Widom, Jonathan

    2008-09-12

    The exact lengths of linker DNAs connecting adjacent nucleosomes specify the intrinsic three-dimensional structures of eukaryotic chromatin fibers. Some studies suggest that linker DNA lengths preferentially occur at certain quantized values, differing one from another by integral multiples of the DNA helical repeat, approximately 10 bp; however, studies in the literature are inconsistent. Here, we investigate linker DNA length distributions in the yeast Saccharomyces cerevisiae genome, using two novel methods: a Fourier analysis of genomic dinucleotide periodicities adjacent to experimentally mapped nucleosomes and a duration hidden Markov model applied to experimentally defined dinucleosomes. Both methods reveal that linker DNA lengths in yeast are preferentially periodic at the DNA helical repeat ( approximately 10 bp), obeying the forms 10n+5 bp (integer n). This 10 bp periodicity implies an ordered superhelical intrinsic structure for the average chromatin fiber in yeast.

  4. Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Ji-Ping Wang

    Full Text Available The exact lengths of linker DNAs connecting adjacent nucleosomes specify the intrinsic three-dimensional structures of eukaryotic chromatin fibers. Some studies suggest that linker DNA lengths preferentially occur at certain quantized values, differing one from another by integral multiples of the DNA helical repeat, approximately 10 bp; however, studies in the literature are inconsistent. Here, we investigate linker DNA length distributions in the yeast Saccharomyces cerevisiae genome, using two novel methods: a Fourier analysis of genomic dinucleotide periodicities adjacent to experimentally mapped nucleosomes and a duration hidden Markov model applied to experimentally defined dinucleosomes. Both methods reveal that linker DNA lengths in yeast are preferentially periodic at the DNA helical repeat ( approximately 10 bp, obeying the forms 10n+5 bp (integer n. This 10 bp periodicity implies an ordered superhelical intrinsic structure for the average chromatin fiber in yeast.

  5. Self-Organizing Maps for Fast LES Combustion Modeling Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Tremendous advances have been made in the development of large and accurate detailed reaction chemistry models for hydrocarbon fuels. Comparable progress has also...

  6. Soil Organic Matter Mapping by Decision Tree Modeling

    Institute of Scientific and Technical Information of China (English)

    ZHOU Bin; ZHANG Xing-Gang; WANG Fan; WANG Ren-Chao

    2005-01-01

    Based on a case study of Longyou County, Zhejiang Province, the decision tree, a data mining method, was used to analyze the relationships between soil organic matter (SOM) and other environmental and satellite sensing spatial data.The decision tree associated SOM content with some extensive easily observable landscape attributes, such as landform,geology, land use, and remote sensing images, thus transforming the SOM-related information into a clear, quantitative,landscape factor-associated regular system. This system could be used to predict continuous SOM spatial distribution.By analyzing factors such as elevation, geological unit, soil type, land use, remotely sensed data, upslope contributing area, slope, aspect, planform curvature, and profile curvature, the decision tree could predict distribution of soil organic matter levels. Among these factors, elevation, land use, aspect, soil type, the first principle component of bitemporal Landsat TM, and upslope contributing area were considered the most important variables for predicting SOM. Results of the prediction between SOM content and landscape types sorted by the decision tree showed a close relationship with an accuracy of 81.1%.

  7. Presenting a comprehensive market oriented model and evaluating its impact on organization performance

    Directory of Open Access Journals (Sweden)

    Mohammad Taqi Amini

    2013-08-01

    Full Text Available Like other innovative strategies, companies have paid more attention to market oriented strategies in recent years. This has been focused by organizations for improved effectiveness and the organization performance accelerated a lot in business competition. In responding to this fact, organizations are trying to formulate many of the issues familiar to large organizations, which have involved with market oriented strategy planning. This paper reviews key elements in market-oriented strategy planning with regard to competitiveness and performance in large organizations and outlines a comprehensive model for strategy planning in profit organizations. These elements include environment, top management, organization structure and market oriented strategy. Professional question of this study has a particularly important role in formulating relations of this model. These elements are well positioned to evaluate the impact of market-oriented strategy planning on organizations and their expected impacts on organization performance. A well-organized questionnaire to help organizations with their planning is proposed in this survey. Based on the proposed questionnaire, data obtained from Tehran food industry experts and analyzed by using SEM method. Results accepted eight hypotheses and rejected one.

  8. Retention modeling in combined pH/organic solvent gradient reversed-phase HPLC.

    Science.gov (United States)

    Zisi, Ch; Fasoula, S; Nikitas, P; Pappa-Louisi, A

    2013-07-07

    An approach for retention modeling of double pH/organic solvent gradient data easily generated by automatically mixing two mobile phases with different pH and organic content according to a linear pump program is proposed. This approach is based on retention models arising from the evaluation of the retention data of a set of 17 OPA derivatives of amino acids obtained in 27 combined pH/organic solvent gradient runs performed between fixed initial pH/organic modifier values but different final ones and for different gradient duration. The derived general model is a ninth parameter equation easily manageable through a linear least-squares fitting but it requires eighteen initial pH/organic modifier gradient experiments for a satisfactory retention prediction in various double gradients of the same kind with those used in the fitting procedure. Two simplified versions of the general model, which were parameterized based on six only initial pH/organic modifier gradients, were also proposed, when one of the final double gradient conditions, pH or organic content was kept constant. The full and the simplified models allowed us to predict the experimental retention data in simultaneous pH/organic solvent double gradient mode very satisfactorily without the solution of the fundamental equation of gradient elution.

  9. Investigation of autonomous cell cycle oscillation in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Hansen, Morten Skov

    2007-01-01

    Autonome Oscillationer i kontinuert kultivering af Saccharomyces cerevisiae Udgangspunktet for dette Ph.d. projekt var at søge at forstå, hvad der gør det muligt at opnå multiple statiske tilstande ved kontinuert kultivering af Saccharomyces cerevisiae med glukose som begrænsende substrat...

  10. Functional expression of rat VPAC1 receptor in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Hansen, M.K.; Tams, J.W.; Fahrenkrug, Jan;

    1999-01-01

    G protein-coupled receptor; heterologous expression; membrane protein; Saccharomyces cerevisiae, vasoactive intestinal polypeptide; yeast mating factor-pre-pro *Ga-leader peptide......G protein-coupled receptor; heterologous expression; membrane protein; Saccharomyces cerevisiae, vasoactive intestinal polypeptide; yeast mating factor-pre-pro *Ga-leader peptide...

  11. TREATMENT OF DIARRHEA-PREDOMINANT IRRITABLE BOWEL SYNDROME WITH MESALAZINE AND/OR SACCHAROMYCES BOULARDII

    Directory of Open Access Journals (Sweden)

    Mauro BAFUTTO

    2013-12-01

    Full Text Available Context Irritable bowel syndrome (IBS is a functional bowel disease characterized by abdominal pain and altered intestinal habits. The pathophysiology of IBS remains unclear. Recent studies have demonstrated that some IBS patients, especially in diarrhea-predominant IBS (IBS-D, display persistent signs of minor mucosal inflammation and a modified intestinal microflora. The mesalazine has known intestinal anti-inflammatory properties. Saccharomyces boulardii is a probiotic used for a long time in treatment of diarrhea, including infectious diarrhea. Objective Evaluate the effects of mesalazine alone, combined therapy of mesalazine with liophylised Saccharomyces boulardii or alone on symptoms of IBS-D patients. Methods Based on Rome III criteria, 53 IBS-D patients (18 year or more were included. To exclude organic diseases all patients underwent colonoscopy, stool culture, serum anti-endomisium antibody, lactose tolerance test and ova and parasite exam. Patients were divided in three groups: mesalazine group (MG - 20 patients received mesalazine 800 mg t.i.d. for 30 days; mesalazine and Saccharomyces boulardii group (MSbG - 21 patients received mesalazine 800 mg t.i.d. and Saccharomyces boulardii 200 mg t.i.d. for 30 days and; Saccharomyces boulardii group (SbG – 12 patients received Sb 200 mg t.i.d. for 30 days. Drugs that might have any effect on intestinal motility or secretion were not allowed. Symptom evaluations at baseline and after treatment were performed by means of a 4-point likert scale including: stool frequency, stool form and consistency (Bristol scale, abdominal pain and distension. Paired t test and Kruskal-Wallis test were used for statistical analyses. Results Compared to baseline, there were statistically significant reduction of symptom score after 30 th day therapy in all three groups: MG (P<0.0001; MSbG (P<0.0001 and in SbG (P = 0.003. There were statistically significant differences in the symptom score at 30 th day

  12. Modeling the effects of organic nitrogen uptake by plants on the carbon cycling of boreal ecosystems

    Directory of Open Access Journals (Sweden)

    Q. Zhu

    2013-08-01

    Full Text Available Boreal forest and tundra are the major ecosystems in the northern high latitudes in which a large amount of carbon is stored. These ecosystems are nitrogen-limited due to slow mineralization rate of the soil organic nitrogen. Recently, abundant field studies have found that organic nitrogen is another important nitrogen supply for boreal ecosystems. In this study, we incorporated a mechanism that allowed boreal plants to uptake small molecular amino acids into a process-based biogeochemical model, the Terrestrial Ecosystem Model (TEM, to evaluate the impact of organic nitrogen uptake on ecosystem carbon cycling. The new version of the model was evaluated at both boreal forest and tundra sites. We found that the modeled organic nitrogen uptake accounted for 36–87% of total nitrogen uptake by plants in tundra ecosystems and 26–50% for boreal forests, suggesting that tundra ecosystem might have more relied on the organic form of nitrogen than boreal forests. The simulated monthly gross ecosystem production (GPP and net ecosystem production (NEP tended to be larger with the new version of the model since the plant uptake of organic nitrogen alleviated the soil nitrogen limitation especially during the growing season. The sensitivity study indicated that the most important factors controlling the plant uptake of organic nitrogen were the maximum root uptake rate (Imax and the radius of the root (r0 in our model. The model uncertainty due to uncertain parameters associated with organic nitrogen uptake at tundra ecosystem was larger than at boreal forest ecosystems. This study suggests that considering the organic nitrogen uptake by plants is important to boreal ecosystem carbon modeling.

  13. Growth temperature exerts differential physiological and transcriptional responses in laboratory and wine strains of Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Pizarra, Francisco J.; Jewett, Michael Christopher; Nielsen, Jens;

    2008-01-01

    Laboratory strains of Saccharomyces cerevisiae have been widely used as a model for studying eukaryotic cells and mapping the molecular mechanisms of many different human diseases. Industrial wine yeasts, on the other hand, have been selected on the basis of their adaptation to stringent environm......Laboratory strains of Saccharomyces cerevisiae have been widely used as a model for studying eukaryotic cells and mapping the molecular mechanisms of many different human diseases. Industrial wine yeasts, on the other hand, have been selected on the basis of their adaptation to stringent......-limited, anaerobic, steady-state chemostat cultures. Physiological characterization revealed that the growth temperature strongly impacted the biomass yield of both strains. Moreover, we found that the wine yeast was better adapted to mobilizing resources for biomass production and that the laboratory yeast...... global insight into how growth temperature affects differential physiological and transcriptional responses in laboratory and wine strains of S. cerevisiae....

  14. Study of elastic-plastic damage model of cement consolidated soil with high organic content

    Institute of Scientific and Technical Information of China (English)

    CHEN Huie; WANG Qing; CAI Keyi

    2009-01-01

    On the basis of elastic-plastic damage model of cement consolidated soil, the authors took organic contents into reasonable damage variable evolution equation in order to seek relation between the organic contents and parameters in the equation, and established the elastic-plastic damage model of cement consolidated soil considering organic contents. The results show that the parameters change correspondingly with difference of the organic contents. The higher the organic contents are, the less the valves of the parameters such as elastic modulus (E), material parameters (K, n) and damage evolution parameter (ε) become, but the larger strain damage threshold value (εd) of the sample is. Meanwhile, the calculation results obtained from established model are compared with the test data in the condition of common indoors test, which is testified with reliability.

  15. Role of Corporate Culture in Model of Logic Levels of Organization

    Directory of Open Access Journals (Sweden)

    Mariya А. Aleksandrova

    2012-05-01

    Full Text Available The article deals with the level of corporate culture in a model of logic levels of the organization. The modern organization is influenced by the external factors, and therefore it should have the ability to form and accumulate potential for corporate culture in order to ensure a timely response to the external environment and effectively manage the operation and development of numerous elements and subsystems of the organization.

  16. Study on the Organization Model of Wagon Flows in Railway Terminal

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Railway terminal is an important part of railway network. Transport organization of railway terminal is the key of the railway transport organization. Moreover, the organization of transport work is based on the organization of wagon flows in the railway terminal. Because of the great amounts of equipment and a large number of train operations, the study on railway terminal transport organization is mostly focused on a marshalling station in railway terminal or a part of it. Systematic study taking railway terminal as a whole is very few. In this paper, the organization of wagon flows in a railway terminal is analyzed and a wagon flow model in a railway terminal is established. The main principles of organization of local trains are also presented.

  17. Electromagnetic Model Reliably Predicts Radar Scattering Characteristics of Airborne Organisms

    Science.gov (United States)

    Mirkovic, Djordje; Stepanian, Phillip M.; Kelly, Jeffrey F.; Chilson, Phillip B.

    2016-10-01

    The radar scattering characteristics of aerial animals are typically obtained from controlled laboratory measurements of a freshly harvested specimen. These measurements are tedious to perform, difficult to replicate, and typically yield only a small subset of the full azimuthal, elevational, and polarimetric radio scattering data. As an alternative, biological applications of radar often assume that the radar cross sections of flying animals are isotropic, since sophisticated computer models are required to estimate the 3D scattering properties of objects having complex shapes. Using the method of moments implemented in the WIPL-D software package, we show for the first time that such electromagnetic modeling techniques (typically applied to man-made objects) can accurately predict organismal radio scattering characteristics from an anatomical model: here the Brazilian free-tailed bat (Tadarida brasiliensis). The simulated scattering properties of the bat agree with controlled measurements and radar observations made during a field study of bats in flight. This numerical technique can produce the full angular set of quantitative polarimetric scattering characteristics, while eliminating many practical difficulties associated with physical measurements. Such a modeling framework can be applied for bird, bat, and insect species, and will help drive a shift in radar biology from a largely qualitative and phenomenological science toward quantitative estimation of animal densities and taxonomic identification.

  18. Modeling equilibrium adsorption of organic micropollutants onto activated carbon

    KAUST Repository

    De Ridder, David J.

    2010-05-01

    Solute hydrophobicity, polarizability, aromaticity and the presence of H-bond donor/acceptor groups have been identified as important solute properties that affect the adsorption on activated carbon. However, the adsorption mechanisms related to these properties occur in parallel, and their respective dominance depends on the solute properties as well as carbon characteristics. In this paper, a model based on multivariate linear regression is described that was developed to predict equilibrium carbon loading on a specific activated carbon (F400) for solutes reflecting a wide range of solute properties. In order to improve prediction accuracy, groups (bins) of solutes with similar solute properties were defined and solute removals were predicted for each bin separately. With these individual linear models, coefficients of determination (R2) values ranging from 0.61 to 0.84 were obtained. With the mechanistic approach used in developing this predictive model, a strong relation with adsorption mechanisms is established, improving the interpretation and, ultimately, acceptance of the model. © 2010 Elsevier Ltd.

  19. Modeling emissions of volatile organic compounds from silage storages and feed lanes

    Science.gov (United States)

    An initial volatile organic compound (VOC) emission model for silage sources, developed using experimental data from previous studies, was incorporated into the Integrated Farm System Model (IFSM), a whole-farm simulation model used to assess the performance, environmental impacts, and economics of ...

  20. An Introduction to Topic Modeling as an Unsupervised Machine Learning Way to Organize Text Information

    Science.gov (United States)

    Snyder, Robin M.

    2015-01-01

    The field of topic modeling has become increasingly important over the past few years. Topic modeling is an unsupervised machine learning way to organize text (or image or DNA, etc.) information such that related pieces of text can be identified. This paper/session will present/discuss the current state of topic modeling, why it is important, and…

  1. A Modified Earthquake Model of Self-Organized Criticality on Small World Networks

    Institute of Scientific and Technical Information of China (English)

    LIN Min; ZHAO Xiao-Wei; CHEN Tian-Lun

    2004-01-01

    A modified Olami Feder-Christensen model of self-organized criticality on a square lattice with the properties of small world networks has been studied.We find that our model displays power-law behavior and the exponent τ of the model depends on φ,the density of long-range connections in our network.

  2. Teaching Diversified Organic Crop Production Using the Community Supported Agriculture Farming System Model

    Science.gov (United States)

    Falk, Constance L.; Pao, Pauline; Cramer, Christopher S.

    2005-01-01

    An organic garden operated as a community supported agriculture (CSA) venture on the New Mexico State University (NMSU) main campus was begun in January 2002. Students enroll in an organic vegetable production class during spring and fall semesters to help manage and work on the project. The CSA model of farming involves the sale of shares to…

  3. Modelling energy level alignment at organic interfaces and density functional theory

    DEFF Research Database (Denmark)

    Flores, F.; Ortega, J.; Vazquez, Patricia

    2009-01-01

    A review of our theoretical understanding of the band alignment at organic interfaces is presented with particular emphasis on the metal/organic (MO) case. The unified IDIS (induced density of interface states) and the ICT (integer charge transfer) models are reviewed and shown to describe qualit...

  4. The model selection in the process of teambuilding for the management of the organization

    Directory of Open Access Journals (Sweden)

    Sergey Petrov

    2010-10-01

    Full Text Available Improving competitiveness of organizations necessary for their success in a market economy is no longer possible only due to material resources. This implies need for qualitatively new approach to human capital. The author reviews approaches to team building and suggests team management model based on situations-cases in which the organized one way or another team reaches goal.

  5. The control structure of team-based organizations : A diagnostic model for empowerment

    NARCIS (Netherlands)

    Kuipers, Benjamin; de Witte, M.C.

    2005-01-01

    This article describes a diagnostic model for empowerment in team-based organizations that portrays four dimensions of the organization's control structure: the level of routine, the nature of expertise, the level of dependence and the line of command. The combined positions of the set of job

  6. For the Arts To Have Meaning...A Model of Adult Education in Performing Arts Organizations.

    Science.gov (United States)

    Kitinoja, L.; Heimlich, J. E.

    A model of adult education appears to function in the outreach programs of three Columbus (Ohio) performing arts organizations. The first tier represents the arts organization's board of trustees, and the second represents the internal administration of the company. Two administrative bodies are arbitrarily labelled as education and marketing,…

  7. Risk management in organic coffee supply chains : testing the usefulness of critical risk models

    NARCIS (Netherlands)

    Brusselaers, J.F.; Benninga, J.; Hennen, W.H.G.J.

    2011-01-01

    This report documents the findings of the analysis of the supply chain of organic coffee from Uganda to the Netherlands using a Chain Risk Model (CRM). The CRM considers contamination of organic coffee with chemicals as a threat for the supply chain, and analyses the consequences of contamination in

  8. The control structure of team-based organizations : A diagnostic model for empowerment

    NARCIS (Netherlands)

    Kuipers, Benjamin; de Witte, M.C.

    2005-01-01

    This article describes a diagnostic model for empowerment in team-based organizations that portrays four dimensions of the organization's control structure: the level of routine, the nature of expertise, the level of dependence and the line of command. The combined positions of the set of job regula

  9. Teaching Diversified Organic Crop Production Using the Community Supported Agriculture Farming System Model

    Science.gov (United States)

    Falk, Constance L.; Pao, Pauline; Cramer, Christopher S.

    2005-01-01

    An organic garden operated as a community supported agriculture (CSA) venture on the New Mexico State University (NMSU) main campus was begun in January 2002. Students enroll in an organic vegetable production class during spring and fall semesters to help manage and work on the project. The CSA model of farming involves the sale of shares to…

  10. [Structural models of simple sense organs by the example of first metazoans].

    Science.gov (United States)

    Aronova, M Z

    2009-01-01

    Basic variants of the evolutional program for formation of simple sensor system--structural models of gravitation receptor, organ of vision, chemoreceptor organ as well as of the nervous system at early stages of the metazoan phylogenesis--are considered from results of our own morphofunctional studies and literature data.

  11. Modelling soil organic carbon in Danish agricultural soils suggests low potential for future carbon sequestration

    DEFF Research Database (Denmark)

    Taghizadeh-Toosi, Arezoo; Olesen, Jørgen Eivind

    2016-01-01

    Soil organic carbon (SOC) is in active exchange with the atmosphere. The amount of organic carbon (OC) input into the soil and SOC turnover rate are important for predicting the carbon (C) sequestration potential of soils subject to changes in land-use and climate. The C-TOOL model was developed...

  12. Characteristics of sterol uptake in Saccharomyces cerevisiae.

    OpenAIRE

    Lorenz, R T; Rodriguez, R J; Lewis, T A; Parks, L W

    1986-01-01

    A Saccharomyces cerevisiae sterol auxotroph, FY3 (alpha hem1 erg7 ura), was used to probe the characteristics of sterol uptake in S. cerevisiae. The steady-state cellular concentration of free sterol at the late exponential phase of growth could be adjusted within a 10-fold range by varying the concentration of exogenously supplied sterol. When cultured on 1 microgram of sterol ml-1, the cells contained a minimal cellular free-cholesterol concentration of 0.85 nmol/mg (dry weight) and were te...

  13. Isocitrate lyase localisation in Saccharomyces cerevisiae cells.

    Science.gov (United States)

    Chaves, R S; Herrero, P; Ordiz, I; Angeles del Brio, M; Moreno, F

    1997-10-01

    The isocitrate lyase from Saccharomyces cerevisiae was only located in the cell cytoplasm. This protein was found not to be associated with cell organelles, even under growth conditions that induce peroxisome proliferation. This conclusion is supported by experiments carried out by damaging the protoplast plasma membrane with DEAE-dextran, by differential centrifugation of osmotically lysed protoplast and by using the green fluorescent protein (GFP) of Aequorea victoria as a reporter fusion tag to localise the subcellular compartment to which isocitrate lyase is targeted.

  14. Computational Modeling of Cultural Dimensions in Adversary Organizations

    Science.gov (United States)

    2010-01-01

    sons of soil” and contraband- financed civil war types last longer than other types (coups/popular revolutions, anti-colonial wars, and wars in...University of California Press. [122] Cioffi-Revilla, C., and M. I. Midlarsky. 2004. Highest-magnitude warfare: Power laws, scaling, and fractals in the...Terrorism: An Agent-Based Approach.” Chaos, Solitons & Fractals 20. 1 (April 2004): 63-68. [176] Levis, A. H. “Executable Models of Decision

  15. Environmental modelling of use of treated organic waste on agricultural land

    DEFF Research Database (Denmark)

    Hansen, Trine Lund; Christensen, Thomas Højlund; Schmidt, S.

    2006-01-01

    . THE IFEU PROJECT, ORWARE and EASEWASTE are life cycle assessment (LCA) models containing more detailed land application modules. A case study estimating the environmental impacts from land application of 1 ton of composted source sorted organic household waste was performed to compare the results from......Modelling of environmental impacts from the application of treated organic municipal solid waste (MSW) in agriculture differs widely between different models for environmental assessment of waste systems. In this comparative study five models were examined concerning quantification and impact...... assessment of environmental effects from land application of treated organic MSW: DST (Decision Support Tool, USA), IWM (Integrated Waste Management, UK), THE IFEU PROJECT (Germany), ORWARE (ORganic WAste REsearch, Sweden) and EASEWASTE (Environmental Assessment of Solid Waste Systems and Technologies...

  16. Effects of Some Neurobiological Factors in a Self-organized Critical Model Based on Neural Networks

    Institute of Scientific and Technical Information of China (English)

    ZHOU Li-Ming; ZHANG Ying-Yue; CHEN Tian-Lun

    2005-01-01

    Based on an integrate-and-fire mechanism, we investigate the effect of changing the efficacy of the synapse,the transmitting time-delayed, and the relative refractoryperiod on the self-organized criticality in our neural network model.

  17. Modeling the Role of Alkanes, Polycyclic Aromatic Hydrocarbons, and Their Oligomers in Secondary Organic Aerosol Formation

    Science.gov (United States)

    A computationally efficient method to treat secondary organic aerosol (SOA) from various length and structure alkanes as well as SOA from polycyclic aromatic hydrocarbons (PAHs) is implemented in the Community Multiscale Air Quality (CMAQ) model to predict aerosol concentrations ...

  18. Organic-matter maturation and petroleum generation model in the Yinggehai and Qiongdongnan basins

    Institute of Scientific and Technical Information of China (English)

    郝芳; 李思田; 孙永传; 张启明

    1996-01-01

    The enhancement of organic-matter maturation and petroleum generation by the migration and accumulation of active hydrothermal fluids in the high thermal-gradient, strongly overpressured environments in the Yinggehai and Qiongdongnan basins is systematically demonstrated by combination of geological, geochemical analysis and basin modeling. The retardation of organic-matter thermal evolution by abnormal pore-pressure is recognized, its manifestation and dynamic mechanism are illustrated, and chemical kinetic modeling of the pressure retardation is carried out. On this basis, the model of organic-matter thermal evolution and petroleum generation in high thermal-gradient, strongly overpressured environments is summarized. A correct understanding of the effects of active hydrothermal fluids and abnormal pore-fluid pressures on organic-matter thermal evolution is of great theoretical and practical significance for thermal history analysis, basin modeling and petroleum resource evaluation.

  19. Lessons Learned About Organic Aerosol Formation in the Southeast U.S. Using Observations and Modeling

    Science.gov (United States)

    Isoprene emitted by vegetation is an important precursor of secondary organic aerosol (SOA). In this work, modeling of isoprene SOA via heterogeneous uptake is explored and compared to observations from the Southern Oxidant and Aerosol Study (SOAS).

  20. Tardigrades as a Potential Model Organism in Space Research

    Science.gov (United States)

    Jönsson, K. Ingemar

    2007-10-01

    Exposure of living organisms to open space requires a high level of tolerance to desiccation, cold, and radiation. Among animals, only anhydrobiotic species can fulfill these requirements. The invertebrate phylum Tardigrada includes many anhydrobiotic species, which are adapted to survive in very dry or cold environmental conditions. As a likely by-product of the adaptations for desiccation and freezing, tardigrades also show a very high tolerance to a number of other, unnatural conditions, including exposure to ionizing radiation. This makes tardigrades an interesting candidate for experimental exposure to open space. This paper reviews the tolerances that make tardigrades suitable for astrobiological studies and the reported radiation tolerance in other anhydrobiotic animals. Several studies have shown that tardigrades can survive γ-irradiation well above 1 kilogray, and desiccated and hydrated (active) tardigrades respond similarly to irradiation. Thus, tolerance is not restricted to the dry anhydrobiotic state, and I discuss the possible involvement of an efficient, but yet undocumented, mechanism for DNA repair. Other anhydrobiotic animals (Artemia, Polypedium), when dessicated, show a higher tolerance to γ-irradiation than hydrated animals, possibly due to the presence of high levels of the protective disaccharide trehalose in the dry state. Tardigrades and other anhydrobiotic animals provide a unique opportunity to study the effects of space exposure on metabolically inactive but vital metazoans.