WorldWideScience

Sample records for metabolic reaction spaces

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

    Directory of Open Access Journals (Sweden)

    Sayed-Rzgar Hosseini

    2015-08-01

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

  2. Quantum chemical approach to estimating the thermodynamics of metabolic reactions.

    Science.gov (United States)

    Jinich, Adrian; Rappoport, Dmitrij; Dunn, Ian; Sanchez-Lengeling, Benjamin; Olivares-Amaya, Roberto; Noor, Elad; Even, Arren Bar; Aspuru-Guzik, Alán

    2014-11-12

    Thermodynamics plays an increasingly important role in modeling and engineering metabolism. We present the first nonempirical computational method for estimating standard Gibbs reaction energies of metabolic reactions based on quantum chemistry, which can help fill in the gaps in the existing thermodynamic data. When applied to a test set of reactions from core metabolism, the quantum chemical approach is comparable in accuracy to group contribution methods for isomerization and group transfer reactions and for reactions not including multiply charged anions. The errors in standard Gibbs reaction energy estimates are correlated with the charges of the participating molecules. The quantum chemical approach is amenable to systematic improvements and holds potential for providing thermodynamic data for all of metabolism.

  3. Phase Space Bottlenecks in Enzymatic Reactions.

    Science.gov (United States)

    Antoniou, Dimitri; Schwartz, Steven D

    2016-01-28

    The definition of a transition state on an individual reactive trajectory is made via a committor analysis. In the past, the bottleneck definition has often been applied in configuration space. This is an approximation, and in order to expand this definition, we are revisiting an enzyme in which we had identified a fast subpicosecond motion that makes the reaction possible. First we used a time-series analysis method to identify the exact time when this motion initiates donor-acceptor compression. Then we modified the standard committor analysis of transition path sampling to identify events in phase space and found that there is a dividing surface in phase space significantly earlier than the configurationally defined transition-state crossing.

  4. Estimating the size of the solution space of metabolic networks

    Directory of Open Access Journals (Sweden)

    Mulet Roberto

    2008-05-01

    Full Text Available Abstract Background Cellular metabolism is one of the most investigated system of biological interactions. While the topological nature of individual reactions and pathways in the network is quite well understood there is still a lack of comprehension regarding the global functional behavior of the system. In the last few years flux-balance analysis (FBA has been the most successful and widely used technique for studying metabolism at system level. This method strongly relies on the hypothesis that the organism maximizes an objective function. However only under very specific biological conditions (e.g. maximization of biomass for E. coli in reach nutrient medium the cell seems to obey such optimization law. A more refined analysis not assuming extremization remains an elusive task for large metabolic systems due to algorithmic limitations. Results In this work we propose a novel algorithmic strategy that provides an efficient characterization of the whole set of stable fluxes compatible with the metabolic constraints. Using a technique derived from the fields of statistical physics and information theory we designed a message-passing algorithm to estimate the size of the affine space containing all possible steady-state flux distributions of metabolic networks. The algorithm, based on the well known Bethe approximation, can be used to approximately compute the volume of a non full-dimensional convex polytope in high dimensions. We first compare the accuracy of the predictions with an exact algorithm on small random metabolic networks. We also verify that the predictions of the algorithm match closely those of Monte Carlo based methods in the case of the Red Blood Cell metabolic network. Then we test the effect of gene knock-outs on the size of the solution space in the case of E. coli central metabolism. Finally we analyze the statistical properties of the average fluxes of the reactions in the E. coli metabolic network. Conclusion We propose a

  5. Chemical reaction vector embeddings: towards predicting drug metabolism in the human gut microbiome.

    Science.gov (United States)

    Mallory, Emily K; Acharya, Ambika; Rensi, Stefano E; Turnbaugh, Peter J; Bright, Roselie A; Altman, Russ B

    2018-01-01

    Bacteria in the human gut have the ability to activate, inactivate, and reactivate drugs with both intended and unintended effects. For example, the drug digoxin is reduced to the inactive metabolite dihydrodigoxin by the gut Actinobacterium E. lenta, and patients colonized with high levels of drug metabolizing strains may have limited response to the drug. Understanding the complete space of drugs that are metabolized by the human gut microbiome is critical for predicting bacteria-drug relationships and their effects on individual patient response. Discovery and validation of drug metabolism via bacterial enzymes has yielded >50 drugs after nearly a century of experimental research. However, there are limited computational tools for screening drugs for potential metabolism by the gut microbiome. We developed a pipeline for comparing and characterizing chemical transformations using continuous vector representations of molecular structure learned using unsupervised representation learning. We applied this pipeline to chemical reaction data from MetaCyc to characterize the utility of vector representations for chemical reaction transformations. After clustering molecular and reaction vectors, we performed enrichment analyses and queries to characterize the space. We detected enriched enzyme names, Gene Ontology terms, and Enzyme Consortium (EC) classes within reaction clusters. In addition, we queried reactions against drug-metabolite transformations known to be metabolized by the human gut microbiome. The top results for these known drug transformations contained similar substructure modifications to the original drug pair. This work enables high throughput screening of drugs and their resulting metabolites against chemical reactions common to gut bacteria.

  6. Real-Time Polymerase Chain Reaction (PCR) Capability in Space

    Data.gov (United States)

    National Aeronautics and Space Administration — The goal of this project is enabling the real-time polymerase chain reaction (real-time PCR) technology in space. In space, the real-time PCR technology can be used...

  7. Integration of metabolome data with metabolic networks reveals reporter reactions

    DEFF Research Database (Denmark)

    Çakir, Tunahan; Patil, Kiran Raosaheb; Önsan, Zeynep Ilsen

    2006-01-01

    network topology. The algorithm thus enables identification of reporter reactions, which are reactions where there are significant coordinated changes in the level of surrounding metabolites following environmental/genetic perturbations. Applicability of the algorithm is demonstrated by using data from......Interpreting quantitative metabolome data is a difficult task owing to the high connectivity in metabolic networks and inherent interdependency between enzymatic regulation, metabolite levels and fluxes. Here we present a hypothesis-driven algorithm for the integration of such data with metabolic...... is measured. By combining the results with transcriptome data, we further show that it is possible to infer whether the reactions are hierarchically or metabolically regulated. Hereby, the reported approach represents an attempt to map different layers of regulation within metabolic networks through...

  8. Fusion Reactions and Matter-Antimatter Annihilation for Space Propulsion

    Science.gov (United States)

    2005-07-13

    FUSION REACTIONS AND MATTER- ANTIMATTER ANNIHILATION FOR SPACE PROPULSION Claude DEUTSCH LPGP (UMR-CNRS 8578), Bât. 210, UPS, 91405 Orsay...REPORT TYPE N/A 3. DATES COVERED - 4. TITLE AND SUBTITLE šFusion Reactions And Matter- Antimatter Annihilation For Space Propulsion 5a...which is possible with successful MCF or ICF. Appropriate vessel designs will be presented for fusion as well as for antimatter propulsion. In

  9. METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks

    Directory of Open Access Journals (Sweden)

    Holzhütter Hermann-Georg

    2007-01-01

    Full Text Available Abstract Background One central goal of computational systems biology is the mathematical modelling of complex metabolic reaction networks. The first and most time-consuming step in the development of such models consists in the stoichiometric reconstruction of the network, i. e. compilation of all metabolites, reactions and transport processes relevant to the considered network and their assignment to the various cellular compartments. Therefore an information system is required to collect and manage data from different databases and scientific literature in order to generate a metabolic network of biochemical reactions that can be subjected to further computational analyses. Results The computer program METANNOGEN facilitates the reconstruction of metabolic networks. It uses the well-known database of biochemical reactions KEGG of biochemical reactions as primary information source from which biochemical reactions relevant to the considered network can be selected, edited and stored in a separate, user-defined database. Reactions not contained in KEGG can be entered manually into the system. To aid the decision whether or not a reaction selected from KEGG belongs to the considered network METANNOGEN contains information of SWISSPROT and ENSEMBL and provides Web links to a number of important information sources like METACYC, BRENDA, NIST, and REACTOME. If a reaction is reported to occur in more than one cellular compartment, a corresponding number of reactions is generated each referring to one specific compartment. Transport processes of metabolites are entered like chemical reactions where reactants and products have different compartment attributes. The list of compartmentalized biochemical reactions and membrane transport processes compiled by means of METANNOGEN can be exported as an SBML file for further computational analysis. METANNOGEN is highly customizable with respect to the content of the SBML output file, additional data

  10. High energy reactions in normal metabolism and ageing of animals

    International Nuclear Information System (INIS)

    Avdonina, E.N.; Nesmeyanov, N.

    1983-01-01

    Processes involving reactions on highly excited states are thought to be of great importance for normal metabolism and aging. Excess energy of the organism is transferred to result in the formation of highly excited states of macromolecules. UV, visible light or ionizing radiation created partially by the organism itself can change metabolic process rates. According to the authors, aging is associated with the defects of macromolecules owing to high energy processes. Gerontological changes in biological materials result from the elimination of low molecular weight molecules and from the formation of unsaturated compounds. Crosslinking of the compounds, accumulation of collagen and connective tissues, the energetic overload of the organism are listed as important features of aging. (V.N.)

  11. In silico strain optimization by adding reactions to metabolic models.

    Science.gov (United States)

    Correia, Sara; Rocha, Miguel

    2012-07-24

    Nowadays, the concerns about the environment and the needs to increase the productivity at low costs, demand for the search of new ways to produce compounds with industrial interest. Based on the increasing knowledge of biological processes, through genome sequencing projects, and high-throughput experimental techniques as well as the available computational tools, the use of microorganisms has been considered as an approach to produce desirable compounds. However, this usually requires to manipulate these organisms by genetic engineering and/ or changing the enviromental conditions to make the production of these compounds possible. In many cases, it is necessary to enrich the genetic material of those microbes with hereologous pathways from other species and consequently adding the potential to produce novel compounds. This paper introduces a new plug-in for the OptFlux Metabolic Engineering platform, aimed at finding suitable sets of reactions to add to the genomes of selected microbes (wild type strain), as well as finding complementary sets of deletions, so that the mutant becomes able to overproduce compounds with industrial interest, while preserving their viability. The necessity of adding reactions to the metabolic model arises from existing gaps in the original model or motivated by the productions of new compounds by the organism. The optimization methods used are metaheuristics such as Evolutionary Algorithms and Simulated Annealing. The usefulness of this plug-in is demonstrated by a case study, regarding the production of vanillin by the bacterium E. coli.

  12. Standard Gibbs energy of metabolic reactions: II. Glucose-6-phosphatase reaction and ATP hydrolysis.

    Science.gov (United States)

    Meurer, Florian; Do, Hoang Tam; Sadowski, Gabriele; Held, Christoph

    2017-04-01

    ATP (adenosine triphosphate) is a key reaction for metabolism. Tools from systems biology require standard reaction data in order to predict metabolic pathways accurately. However, literature values for standard Gibbs energy of ATP hydrolysis are highly uncertain and differ strongly from each other. Further, such data usually neglect the activity coefficients of reacting agents, and published data like this is apparent (condition-dependent) data instead of activity-based standard data. In this work a consistent value for the standard Gibbs energy of ATP hydrolysis was determined. The activity coefficients of reacting agents were modeled with electrolyte Perturbed-Chain Statistical Associating Fluid Theory (ePC-SAFT). The Gibbs energy of ATP hydrolysis was calculated by combining the standard Gibbs energies of hexokinase reaction and of glucose-6-phosphate hydrolysis. While the standard Gibbs energy of hexokinase reaction was taken from previous work, standard Gibbs energy of glucose-6-phosphate hydrolysis reaction was determined in this work. For this purpose, reaction equilibrium molalities of reacting agents were measured at pH7 and pH8 at 298.15K at varying initial reacting agent molalities. The corresponding activity coefficients at experimental equilibrium molalities were predicted with ePC-SAFT yielding the Gibbs energy of glucose-6-phosphate hydrolysis of -13.72±0.75kJ·mol -1 . Combined with the value for hexokinase, the standard Gibbs energy of ATP hydrolysis was finally found to be -31.55±1.27kJ·mol -1 . For both, ATP hydrolysis and glucose-6-phosphate hydrolysis, a good agreement with own and literature values were obtained when influences of pH, temperature, and activity coefficients were explicitly taken into account in order to calculate standard Gibbs energy at pH7, 298.15K and standard state. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Mass effects and internal space geometry in triatomic reaction dynamics

    Science.gov (United States)

    Yanao, Tomohiro; Koon, Wang S.; Marsden, Jerrold E.

    2006-05-01

    The effect of the distribution of mass in triatomic reaction dynamics is analyzed using the geometry of the associated internal space. Atomic masses are appropriately incorporated into internal coordinates as well as the associated non-Euclidean internal space metric tensor after a separation of the rotational degrees of freedom. Because of the non-Euclidean nature of the metric in the internal space, terms such as connection coefficients arise in the internal equations of motion, which act as velocity-dependent forces in a coordinate chart. By statistically averaging these terms, an effective force field is deduced, which accounts for the statistical tendency of geodesics in the internal space. This force field is shown to play a crucial role in determining mass-related branching ratios of isomerization and dissociation dynamics of a triatomic molecule. The methodology presented can be useful for qualitatively predicting branching ratios in general triatomic reactions, and may be applied to the study of isotope effects.

  14. Research Opportunities in Nutrition and Metabolism in Space

    Science.gov (United States)

    Altman, Philip L. (Editor); Fisher, Kenneth D. (Editor)

    1986-01-01

    The objectives of the Life Sciences Research Office (LSRO) study on nutrient requirements for meeting metabolic needs in manned space flights are as follows: review extant knowledge on the subject; identify significant gaps in knowledge; formulate suggestions for possible research; and produce a documented report of the foregoing items that can be used for program planning. In accordance with NASA's request for this study, the report focuses on issues of nutrition and metabolism that relate primarily to the contemplated United States Space Station, secondarily to the Shuttle Program as an orbital test bed for operational studies, and incidentally to scenarios for future long-term space flights. Members of the LSRO ad hoc Working Group on Nutrition and Metabolism were provided with pertinent articles and summaries on the subject. At the meeting of the Working Group, presentations were made by NASA Headquarters program staff on past experiences relative to space-flight nutrition and metabolism, as well as scenarios for future flights. The discussions of the ad hoc Working Group focused on the following: (1) metabolic needs related to work and exercise; (2) nutrients required to meet such needs; (3) food types, management, and records; and (4) nutritional amelioration or prevention of space-related physiological and behavioral changes.

  15. Geometrical Models of the Phase Space Structures Governing Reaction Dynamics

    Science.gov (United States)

    2009-08-01

    of Mathematical Sciences . Springer, Berlin. [Child & Pollak(1980)] Child, M. S. & Pollak, E. (1980). Analytical reaction dynamics: Origin and implica...state region, i.e. the phase space point at which a trajectory enters the transition state region can be mapped analytically to the phase space point...Neishtadt, A. I. (1988). Mathematical aspects of classical and celestial mechanics. In V. I. Arnol’d, editor, Dynamical Systems III, volume 3 of Encyclopaedia

  16. Chemistry in interstellar space. [environment characteristics influencing reaction dynamics

    Science.gov (United States)

    Donn, B.

    1973-01-01

    The particular characteristics of chemistry in interstellar space are determined by the unique environmental conditions involved. Interstellar matter is present at extremely low densities. Large deviations from thermodynamic equilibrium are, therefore, to be expected. A relatively intense ultraviolet radiation is present in many regions. The temperatures are in the range from 5 to 200 K. Data concerning the inhibiting effect of small activation energies in interstellar clouds are presented in a table. A summary of measured activation energies or barrier heights for exothermic exchange reactions is also provided. Problems of molecule formation are discussed, taking into account gas phase reactions and surface catalyzed processes.

  17. The role of depressed metabolism in space biology: An overview

    Science.gov (United States)

    Saunders, J.

    1973-01-01

    Organization and research activities of the entire NASA Space Biology Program are outlined. Various technical approaches are reported to study depressed metabolism particularly in the situation of 100% oxygen and reduced ambient pressures. These include hibernation and hypothermia, thermal regulation, and diluent gases.

  18. Radiation reaction in curved space-time:. local method

    Science.gov (United States)

    Gal'Tsov, Dmitri; Spirin, Pavel; Staub, Simona

    Although consensus seems to exist about the validity of equations accounting for radiation reaction in curved space-time, their previous derivations were criticized recently as not fully satisfactory: some ambiguities were noticed in the procedure of integration of the field momentum over the tube surrounding the world-line. To avoid these problems we suggest a purely local derivation dealing with the field quantities defined only on the world-line. We consider point particle interacting with scalar, vector (electromagnetic) and linearized gravitational fields in the (generally non-vacuum) curved space-time. To properly renormalize the self-action in the gravitational case, we use a manifestly reparameterization-invariant formulation of the theory. Scalar and vector divergences are shown to cancel for a certain ratio of the corresponding charges. We also report on a modest progress in extending the results for the gravitational radiation reaction to the case of non-vacuum background.

  19. Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D

    OpenAIRE

    Preciat Gonzalez, German Andres; El Assal, Lemmer; Noronha, Alberto; Thiele, Ines; Haraldsdottir, Hulda; Fleming, Ronan MT

    2017-01-01

    The mechanism of each chemical reaction in a metabolic network can be represented as a set of atom mappings, each of which relates an atom in a substrate metabolite to an atom of the same element in a product metabolite. Genome-scale metabolic network reconstructions typically represent biochemistry at the level of reaction stoichiometry. However, a more detailed representation at the underlying level of atom mappings opens the possibility for a broader range of biological, biomedical and bio...

  20. Low Energy Reaction cell for advanced space power applications

    International Nuclear Information System (INIS)

    Miley, George H.; Rice, Eric

    2001-01-01

    Power units using Low Energy Reactions (LENRs) are under study as a radical new approach to power units that could potentially replace nuclear and chemical power sources for a number of space applications. These cells employ thin metallic films (order of 500 deg., using variously Ni, Pd and Ti) as cathodes with various electrolytes such as 0.5-1 molar lithium sulfate in light water. Power densities exceeding 10 W/cm3 in the thin-films have been achieved. An ultimate goal is to incorporate this thin-film technology into a 'tightly packed' cell design where the film material occupies ∼20% of the total cell volume. If this is achieved, overall power densities of ∼20 W/cm3 appear feasible, opening the way to a number of potential applications ranging from distributed power units in spacecraft to advanced propulsion

  1. Quantitative Assessment of Thermodynamic Constraints on the Solution Space of Genome-Scale Metabolic Models

    Science.gov (United States)

    Hamilton, Joshua J.; Dwivedi, Vivek; Reed, Jennifer L.

    2013-01-01

    Constraint-based methods provide powerful computational techniques to allow understanding and prediction of cellular behavior. These methods rely on physiochemical constraints to eliminate infeasible behaviors from the space of available behaviors. One such constraint is thermodynamic feasibility, the requirement that intracellular flux distributions obey the laws of thermodynamics. The past decade has seen several constraint-based methods that interpret this constraint in different ways, including those that are limited to small networks, rely on predefined reaction directions, and/or neglect the relationship between reaction free energies and metabolite concentrations. In this work, we utilize one such approach, thermodynamics-based metabolic flux analysis (TMFA), to make genome-scale, quantitative predictions about metabolite concentrations and reaction free energies in the absence of prior knowledge of reaction directions, while accounting for uncertainties in thermodynamic estimates. We applied TMFA to a genome-scale network reconstruction of Escherichia coli and examined the effect of thermodynamic constraints on the flux space. We also assessed the predictive performance of TMFA against gene essentiality and quantitative metabolomics data, under both aerobic and anaerobic, and optimal and suboptimal growth conditions. Based on these results, we propose that TMFA is a useful tool for validating phenotypes and generating hypotheses, and that additional types of data and constraints can improve predictions of metabolite concentrations. PMID:23870272

  2. Mathematical Modeling and Dynamic Simulation of Metabolic Reaction Systems Using Metabolome Time Series Data.

    Science.gov (United States)

    Sriyudthsak, Kansuporn; Shiraishi, Fumihide; Hirai, Masami Yokota

    2016-01-01

    The high-throughput acquisition of metabolome data is greatly anticipated for the complete understanding of cellular metabolism in living organisms. A variety of analytical technologies have been developed to acquire large-scale metabolic profiles under different biological or environmental conditions. Time series data are useful for predicting the most likely metabolic pathways because they provide important information regarding the accumulation of metabolites, which implies causal relationships in the metabolic reaction network. Considerable effort has been undertaken to utilize these data for constructing a mathematical model merging system properties and quantitatively characterizing a whole metabolic system in toto. However, there are technical difficulties between benchmarking the provision and utilization of data. Although, hundreds of metabolites can be measured, which provide information on the metabolic reaction system, simultaneous measurement of thousands of metabolites is still challenging. In addition, it is nontrivial to logically predict the dynamic behaviors of unmeasurable metabolite concentrations without sufficient information on the metabolic reaction network. Yet, consolidating the advantages of advancements in both metabolomics and mathematical modeling remain to be accomplished. This review outlines the conceptual basis of and recent advances in technologies in both the research fields. It also highlights the potential for constructing a large-scale mathematical model by estimating model parameters from time series metabolome data in order to comprehensively understand metabolism at the systems level.

  3. Genome-scale Metabolic Reaction Modeling: a New Approach to Geomicrobial Kinetics

    Science.gov (United States)

    McKernan, S. E.; Shapiro, B.; Jin, Q.

    2014-12-01

    Geomicrobial rates, rates of microbial metabolism in natural environments, are a key parameter of theoretical and practical problems in geobiology and biogeochemistry. Both laboratory- and field-based approaches have been applied to study rates of geomicrobial processes. Laboratory-based approaches analyze geomicrobial kinetics by incubating environmental samples under controlled laboratory conditions. Field methods quantify geomicrobial rates by observing the progress of geomicrobial processes. To take advantage of recent development in biogeochemical modeling and genome-scale metabolic modeling, we suggest that geomicrobial rates can also be predicted by simulating metabolic reaction networks of microbes. To predict geomicrobial rates, we developed a genome-scale metabolic model that describes enzyme reaction networks of microbial metabolism, and simulated the network model by accounting for the kinetics and thermodynamics of enzyme reactions. The model is simulated numerically to solve cellular enzyme abundance and hence metabolic rates under the constraints of cellular physiology. The new modeling approach differs from flux balance analysis of system biology in that it accounts for the thermodynamics and kinetics of enzymatic reactions. It builds on subcellular metabolic reaction networks, and hence also differs from classical biogeochemical reaction modeling. We applied the new approach to Methanosarcina acetivorans, an anaerobic, marine methanogen capable of disproportionating acetate to carbon dioxide and methane. The input of the new model includes (1) enzyme reaction network of acetoclastic methanogenesis, and (2) representative geochemical conditions of freshwater sedimentary environments. The output of the simulation includes the proteomics, metabolomics, and energy and matter fluxes of M. acetivorans. Our simulation results demonstrate the predictive power of the new modeling approach. Specifically, the results illustrate how methanogenesis rates vary

  4. The biochemistry of drug metabolism--an introduction: part 4. reactions of conjugation and their enzymes.

    Science.gov (United States)

    Testa, Bernard; Krämer, Stefanie D

    2008-11-01

    This review continues a general presentation of the metabolism of drugs and other xenobiotics begun in three recent issues of Chemistry & Biodiversity. The present Part is dedicated to reactions of conjugation, namely methylation, sulfonation, and phosphorylation, glucuronidation and other glycosidations, acetylation and other acylations, the formation and fate of coenzyme A conjugates, glutathione conjugation, and the reaction of amines with carbonyl compounds. It presents the many transferases involved, their nomenclature, relevant biochemical properties, catalytic mechanisms, and the reactions they catalyze. Nonenzymatic reactions, mainly of glutathione conjugation, also receive due attention. A number of medicinally, environmentally, and toxicologically relevant examples are presented and discussed.

  5. Atmospheric reaction systems as null-models to identify structural traces of evolution in metabolism.

    Directory of Open Access Journals (Sweden)

    Petter Holme

    Full Text Available The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same physics that gives molecules their stability and affinity to react. These fundamental factors cannot be captured by standard null-models based on randomization. The unique property of organismal metabolism is that it is controlled, to some extent, by an enzymatic machinery that is subject to evolution. In this paper, we explore the possibility that reaction systems of planetary atmospheres can serve as a null-model against which we can define metabolic structure and trace the influence of evolution. We find that the two types of data can be distinguished by their respective degree distributions. This is especially clear when looking at the degree distribution of the reaction network (of reaction connected to each other if they involve the same molecular species. For the Earth's atmospheric network and the human metabolic network, we look into more detail for an underlying explanation of this deviation. However, we cannot pinpoint a single cause of the difference, rather there are several concurrent factors. By examining quantities relating to the modular-functional organization of the metabolism, we confirm that metabolic networks have a more complex modular organization than the atmospheric networks, but not much more. We interpret the more variegated modular arrangement of metabolism as a trace of evolved functionality. On the other hand, it is quite remarkable how similar the structures of these two types of networks are, which emphasizes that the constraints from the chemical properties of the molecules has a larger influence in shaping the reaction system than does natural selection.

  6. Alkalizing reactions streamline cellular metabolism in acidogenic microorganisms.

    Directory of Open Access Journals (Sweden)

    Stefania Arioli

    Full Text Available An understanding of the integrated relationships among the principal cellular functions that govern the bioenergetic reactions of an organism is necessary to determine how cells remain viable and optimise their fitness in the environment. Urease is a complex enzyme that catalyzes the hydrolysis of urea to ammonia and carbonic acid. While the induction of urease activity by several microorganisms has been predominantly considered a stress-response that is initiated to generate a nitrogen source in response to a low environmental pH, here we demonstrate a new role of urease in the optimisation of cellular bioenergetics. We show that urea hydrolysis increases the catabolic efficiency of Streptococcus thermophilus, a lactic acid bacterium that is widely used in the industrial manufacture of dairy products. By modulating the intracellular pH and thereby increasing the activity of β-galactosidase, glycolytic enzymes and lactate dehydrogenase, urease increases the overall change in enthalpy generated by the bioenergetic reactions. A cooperative altruistic behaviour of urease-positive microorganisms on the urease-negative microorganisms within the same environment was also observed. The physiological role of a single enzymatic activity demonstrates a novel and unexpected view of the non-transcriptional regulatory mechanisms that govern the bioenergetics of a bacterial cell, highlighting a new role for cytosol-alkalizing biochemical pathways in acidogenic microorganisms.

  7. Biological and Metabolic Response in STS-135 Space-flown Mouse Skin

    Data.gov (United States)

    National Aeronautics and Space Administration — Changes in gene expression profiles implicated in oxidative stress and in ECM remodeling in mouse skin were examined after space flight. The metabolic effects of...

  8. Metabolic regulation and maximal reaction optimization in the central metabolism of a yeast cell

    Science.gov (United States)

    Kasbawati, Gunawan, A. Y.; Hertadi, R.; Sidarto, K. A.

    2015-03-01

    Regulation of fluxes in a metabolic system aims to enhance the production rates of biotechnologically important compounds. Regulation is held via modification the cellular activities of a metabolic system. In this study, we present a metabolic analysis of ethanol fermentation process of a yeast cell in terms of continuous culture scheme. The metabolic regulation is based on the kinetic formulation in combination with metabolic control analysis to indicate the key enzymes which can be modified to enhance ethanol production. The model is used to calculate the intracellular fluxes in the central metabolism of the yeast cell. Optimal control is then applied to the kinetic model to find the optimal regulation for the fermentation system. The sensitivity results show that there are external and internal control parameters which are adjusted in enhancing ethanol production. As an external control parameter, glucose supply should be chosen in appropriate way such that the optimal ethanol production can be achieved. For the internal control parameter, we find three enzymes as regulation targets namely acetaldehyde dehydrogenase, pyruvate decarboxylase, and alcohol dehydrogenase which reside in the acetaldehyde branch. Among the three enzymes, however, only acetaldehyde dehydrogenase has a significant effect to obtain optimal ethanol production efficiently.

  9. Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D.

    Science.gov (United States)

    Preciat Gonzalez, German A; El Assal, Lemmer R P; Noronha, Alberto; Thiele, Ines; Haraldsdóttir, Hulda S; Fleming, Ronan M T

    2017-06-14

    The mechanism of each chemical reaction in a metabolic network can be represented as a set of atom mappings, each of which relates an atom in a substrate metabolite to an atom of the same element in a product metabolite. Genome-scale metabolic network reconstructions typically represent biochemistry at the level of reaction stoichiometry. However, a more detailed representation at the underlying level of atom mappings opens the possibility for a broader range of biological, biomedical and biotechnological applications than with stoichiometry alone. Complete manual acquisition of atom mapping data for a genome-scale metabolic network is a laborious process. However, many algorithms exist to predict atom mappings. How do their predictions compare to each other and to manually curated atom mappings? For more than four thousand metabolic reactions in the latest human metabolic reconstruction, Recon 3D, we compared the atom mappings predicted by six atom mapping algorithms. We also compared these predictions to those obtained by manual curation of atom mappings for over five hundred reactions distributed among all top level Enzyme Commission number classes. Five of the evaluated algorithms had similarly high prediction accuracy of over 91% when compared to manually curated atom mapped reactions. On average, the accuracy of the prediction was highest for reactions catalysed by oxidoreductases and lowest for reactions catalysed by ligases. In addition to prediction accuracy, the algorithms were evaluated on their accessibility, their advanced features, such as the ability to identify equivalent atoms, and their ability to map hydrogen atoms. In addition to prediction accuracy, we found that software accessibility and advanced features were fundamental to the selection of an atom mapping algorithm in practice.

  10. Reactions and enzymes in the metabolism of drugs and other xenobiotics.

    Science.gov (United States)

    Testa, Bernard; Pedretti, Alessandro; Vistoli, Giulio

    2012-06-01

    In this article, we offer an overview of the compared quantitative importance of biotransformation reactions in the metabolism of drugs and other xenobiotics, based on a meta-analysis of current research interests. Also, we assess the relative significance the enzyme (super)families or categories catalysing these reactions. We put the facts unveiled by the analysis into a drug discovery context and draw some implications. The results confirm the primary role of cytochrome P450-catalysed oxidations and UDP-glucuronosyl-catalysed glucuronidations, but they also document the marked significance of several other reactions. Thus, there is a need for several drug discovery scientists to better grasp the variety of drug metabolism reactions and enzymes and their consequences. Copyright © 2012 Elsevier Ltd. All rights reserved.

  11. Radiation effects on K+-activated metabolic reactions

    International Nuclear Information System (INIS)

    Rink, H.; Bergeder, H.D.

    1976-01-01

    A study has been made of the effects of a minor radiation-induced decrease in K + -content on a K + -dependent enzyme, the aldehyde dehydrogenase in yeast cells. Irradiated (200 rad X-rays) and unirradiated starved cell suspensions were incubated with acetaldehyde and varying K + concentrations, and the intracellular K + -content determined by flame photometry. Oxygen consumption (equivalent to the utilized amount of substrate) was measured under the same conditions of incubation, using the Warburg technique. The results demonstrated that irradiated and unirradiated cells behaved qualitatively in the same way, but there were essential quantitative differences. The highest intracellular K + content and highest O 2 -concentration were always reached at the same extracellular K + -concentration. These extracellular concentrations were always higher for irradiated samples, and the maximum values of K + -content and O 2 -consumption were always smaller in irradiated cells than in controls. A reduction in K + content as small as 15 μMol.g -1 was sufficient to affect the turnover rate, confirming that the K + -decrease accompanying irradiation can be sufficient to cause secondary disturbances in metabolism which will contribute to biological radiation effects. (U.K.)

  12. Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates

    DEFF Research Database (Denmark)

    Nielsen, Jens Bredal

    1997-01-01

    of the thermokinetic description of reaction rates to include the influence of effecters. Here the reaction rate is written as a linear function of the logarithm of the metabolite concentrations. With this type of rate function it is shown that the approach of Delgado and Liao [Biochem. J. (1992) 282, 919-927] can......Metabolic control analysis is a powerful technique for the evaluation of flux control within biochemical pathways. Its foundation is the elasticity coefficients and the flux control coefficients (FCCs). On the basis of a thermokinetic description of reaction rates it is here shown...... that the elasticity coefficients can be calculated directly from the pool levels of metabolites at steady state. The only requirement is that one thermodynamic parameter be known, namely the reaction affinity at the intercept of the tangent in the inflection point of the curve of reaction rate against reaction...

  13. Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates

    DEFF Research Database (Denmark)

    Nielsen, Jens Bredal

    1997-01-01

    Metabolic control analysis is a powerful technique for the evaluation of flux control within biochemical pathways. Its foundation is the elasticity coefficients and the flux control coefficients (FCCs). On the basis of a thermokinetic description of reaction rates it is here shown...... that the elasticity coefficients can be calculated directly from the pool levels of metabolites at steady state. The only requirement is that one thermodynamic parameter be known, namely the reaction affinity at the intercept of the tangent in the inflection point of the curve of reaction rate against reaction...... of the thermokinetic description of reaction rates to include the influence of effecters. Here the reaction rate is written as a linear function of the logarithm of the metabolite concentrations. With this type of rate function it is shown that the approach of Delgado and Liao [Biochem. J. (1992) 282, 919-927] can...

  14. Sequence-based Network Completion Reveals the Integrality of Missing Reactions in Metabolic Networks*

    Science.gov (United States)

    Krumholz, Elias W.; Libourel, Igor G. L.

    2015-01-01

    Genome-scale metabolic models are central in connecting genotypes to metabolic phenotypes. However, even for well studied organisms, such as Escherichia coli, draft networks do not contain a complete biochemical network. Missing reactions are referred to as gaps. These gaps need to be filled to enable functional analysis, and gap-filling choices influence model predictions. To investigate whether functional networks existed where all gap-filling reactions were supported by sequence similarity to annotated enzymes, four draft networks were supplemented with all reactions from the Model SEED database for which minimal sequence similarity was found in their genomes. Quadratic programming revealed that the number of reactions that could partake in a gap-filling solution was vast: 3,270 in the case of E. coli, where 72% of the metabolites in the draft network could connect a gap-filling solution. Nonetheless, no network could be completed without the inclusion of orphaned enzymes, suggesting that parts of the biochemistry integral to biomass precursor formation are uncharacterized. However, many gap-filling reactions were well determined, and the resulting networks showed improved prediction of gene essentiality compared with networks generated through canonical gap filling. In addition, gene essentiality predictions that were sensitive to poorly determined gap-filling reactions were of poor quality, suggesting that damage to the network structure resulting from the inclusion of erroneous gap-filling reactions may be predictable. PMID:26041773

  15. Sequence-based Network Completion Reveals the Integrality of Missing Reactions in Metabolic Networks.

    Science.gov (United States)

    Krumholz, Elias W; Libourel, Igor G L

    2015-07-31

    Genome-scale metabolic models are central in connecting genotypes to metabolic phenotypes. However, even for well studied organisms, such as Escherichia coli, draft networks do not contain a complete biochemical network. Missing reactions are referred to as gaps. These gaps need to be filled to enable functional analysis, and gap-filling choices influence model predictions. To investigate whether functional networks existed where all gap-filling reactions were supported by sequence similarity to annotated enzymes, four draft networks were supplemented with all reactions from the Model SEED database for which minimal sequence similarity was found in their genomes. Quadratic programming revealed that the number of reactions that could partake in a gap-filling solution was vast: 3,270 in the case of E. coli, where 72% of the metabolites in the draft network could connect a gap-filling solution. Nonetheless, no network could be completed without the inclusion of orphaned enzymes, suggesting that parts of the biochemistry integral to biomass precursor formation are uncharacterized. However, many gap-filling reactions were well determined, and the resulting networks showed improved prediction of gene essentiality compared with networks generated through canonical gap filling. In addition, gene essentiality predictions that were sensitive to poorly determined gap-filling reactions were of poor quality, suggesting that damage to the network structure resulting from the inclusion of erroneous gap-filling reactions may be predictable. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  16. Cancer metabolism in space and time: Beyond the Warburg effect.

    Science.gov (United States)

    Danhier, Pierre; Bański, Piotr; Payen, Valéry L; Grasso, Debora; Ippolito, Luigi; Sonveaux, Pierre; Porporato, Paolo E

    2017-08-01

    Altered metabolism in cancer cells is pivotal for tumor growth, most notably by providing energy, reducing equivalents and building blocks while several metabolites exert a signaling function promoting tumor growth and progression. A cancer tissue cannot be simply reduced to a bulk of proliferating cells. Tumors are indeed complex and dynamic structures where single cells can heterogeneously perform various biological activities with different metabolic requirements. Because tumors are composed of different types of cells with metabolic activities affected by different spatial and temporal contexts, it is important to address metabolism taking into account cellular and biological heterogeneity. In this review, we describe this heterogeneity also in metabolic fluxes, thus showing the relative contribution of different metabolic activities to tumor progression according to the cellular context. This article is part of a Special Issue entitled Mitochondria in Cancer, edited by Giuseppe Gasparre, Rodrigue Rossignol and Pierre Sonveaux. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

    Mochizuki, Atsushi; Fiedler, Bernold

    2015-02-21

    In biological cells, chemical reaction pathways lead to complex network systems like metabolic networks. One experimental approach to the dynamics of such systems examines their "sensitivity": each enzyme mediating a reaction in the system is increased/decreased or knocked out separately, and the responses in the concentrations of chemicals or their fluxes are observed. In this study, we present a mathematical method, named structural sensitivity analysis, to determine the sensitivity of reaction systems from information on the network alone. We investigate how the sensitivity responses of chemicals in a reaction network depend on the structure of the network, and on the position of the perturbed reaction in the network. We establish and prove some general rules which relate the sensitivity response to the structure of the underlying network. We describe a hierarchical pattern in the flux response which is governed by branchings in the network. We apply our method to several hypothetical and real life chemical reaction networks, including the metabolic network of the Escherichia coli TCA cycle. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. Deoxyfluorination with Sulfonyl Fluorides: Navigating Reaction Space with Machine Learning.

    Science.gov (United States)

    Nielsen, Matthew K; Ahneman, Derek T; Riera, Orestes; Doyle, Abigail G

    2018-03-27

    Through fine-tuning of reagent and base structure, sulfonyl fluorides can efficiently fluorinate diverse classes of alcohols. We show that machine learning can map the intricate reaction landscape and enable accurate prediction of high-yielding conditions for untested substrates.

  19. Analysis of reaction torque-based control of a redundant free-floating space robot

    Directory of Open Access Journals (Sweden)

    Minghe JIN

    2017-10-01

    Full Text Available Owing to the dynamics coupling between a free-floating base and a manipulator, the non-stationary base of a space robot will face the issue of base disturbance due to a manipulator’s motion. The reaction torque acted on the satellite base’s centroid is an important index to measure the satellite base’s disturbance. In this paper, a comprehensive analysis of the reaction torque is made, and a novel way to derive the analytical form of the reaction torque is proposed. In addition, the reaction torque null-space is derived, in which the manipulator’s joint motion is dynamically decoupled from the motion of the satellite base, and its novel expression demonstrates the equivalence between the reaction torque null-space and the reaction null-space. Furthermore, the reaction torque acted as an optimization index can be utilized to achieve satellite base disturbance minimization in the generalized Jacobian-based end-effector Cartesian path tracking task. Besides, supposing that the redundant degrees of freedom are abundant to achieve reaction torque-based active control, the reaction torque can be used to realize satellite base attitude control, that is, base attitude adjustment or maintenance. Moreover, because reaction torque-based control is a second-order control scheme, joint torque minimization can be regarded as the optimization task in reaction torque-based active or in-active control. A real-time simulation system of a 7-DOF space robot under Linux/RTAI is developed to verify and test the feasibility and reliability of the proposed ideas. Our extensive empirical results demonstrate that the corresponding analysis about the reaction torque is correct and the proposed methods are feasible.

  20. Small-Scale, Methane-Fueled Reaction Control Engines for In-Space Propulsion, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Given increasing interest in high-performance, Methane-fueled reaction control engines in the 5-100lbf thrust class, Ventions proposes the design, fabrication and...

  1. Thermodynamic calculations for biochemical transport and reaction processes in metabolic networks.

    Science.gov (United States)

    Jol, Stefan J; Kümmel, Anne; Hatzimanikatis, Vassily; Beard, Daniel A; Heinemann, Matthias

    2010-11-17

    Thermodynamic analysis of metabolic networks has recently generated increasing interest for its ability to add constraints on metabolic network operation, and to combine metabolic fluxes and metabolite measurements in a mechanistic manner. Concepts for the calculation of the change in Gibbs energy of biochemical reactions have long been established. However, a concept for incorporation of cross-membrane transport in these calculations is still missing, although the theory for calculating thermodynamic properties of transport processes is long known. Here, we have developed two equivalent equations to calculate the change in Gibbs energy of combined transport and reaction processes based on two different ways of treating biochemical thermodynamics. We illustrate the need for these equations by showing that in some cases there is a significant difference between the proposed correct calculation and using an approximative method. With the developed equations, thermodynamic analysis of metabolic networks spanning over multiple physical compartments can now be correctly described. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  2. Comparison of TiO2 photocatalysis, electrochemically assisted Fenton reaction and direct electrochemistry for simulation of phase I metabolism reactions of drugs

    NARCIS (Netherlands)

    Ruokolainen, Miina; Gül, Turan; Permentier, Hjalmar; Sikanen, Tiina; Kostiainen, Risto; Kotiaho, Tapio

    2016-01-01

    The feasibility of titanium dioxide (TiO2) photocatalysis, electrochemically assisted Fenton reaction (EC-Fenton) and direct electrochemical oxidation (EC) for simulation of phase I metabolism of drugs was studied by comparing the reaction products of buspirone, promazine, testosterone and

  3. Exact Green's function of the reversible ABCD reaction in two space dimensions

    OpenAIRE

    Prüstel, Thorsten; Meier-Schellersheim, Martin

    2013-01-01

    We derive an exact expression for the Green's functions in the time domain of the reversible diffusion-influenced ABCD reaction $A+B\\leftrightarrow C+D$ in two space dimensions. Furthermore, we calculate the corresponding survival and reaction probabilities. The obtained expressions should prove useful for the study of reversible membrane-bound reactions in cell biology and can serve as a useful ingredient of enhanced stochastic particle-based simulation algorithms.

  4. Quantification of reaction time and time perception during Space Shuttle operations

    Science.gov (United States)

    Ratino, D. A.; Repperger, D. W.; Goodyear, C.; Potor, G.; Rodriguez, L. E.

    1988-01-01

    A microprocessor-based test battery containing simple reaction time, choice reaction time, and time perception tasks was flown aboard a 1985 Space Shuttle flight. Data were obtained from four crew members. Individual subject means indicate a correlation between change in reaction time during the flight and the presence of space motion sickness symptoms. The time perception task results indicate that the shortest duration task time (2 s) is progressively overestimated as the mission proceeds and is statistically significant when comparing preflight and postflight baselines. The tasks that required longer periods of time to estimate (8, 12, and 16 s) are less affected.

  5. [A review on urban metabolism research based on physical space entities for environmental management].

    Science.gov (United States)

    Liu, Ye; Liu, Dan

    2015-07-01

    Urban metabolism is a basic theory for coping with global environmental problems, which is coherent with the aims of national environmental management. This paper analyzed the concept of urban metabolism, and pointed out the meaning for urban metabolism in physical space entities; reviewed the current methods for urban metabolism and its merits and shortages; analyzed the system boundaries, connotation, and methodologies; and summarized the advances on urban meta-bolism practices in physical space entities. At last, we made conclusions that there were shortages, including conception system, basic theory system, and interdisciplinary integrated theory system in current urban metabolism research, and the current cases studied in urban metabolism were limited and not suitable to the harmony development between society, economy, and environment. In the future, we need to strengthen comparison between different case studies from different countries, develop the prior modes of typical urban metabolism research, identify the mechanism for urban ecosystem, and strengthen the spatial decision support system of environmental management taking urban spatial entity spaces as units.

  6. Conditions for extinction events in chemical reaction networks with discrete state spaces.

    Science.gov (United States)

    Johnston, Matthew D; Anderson, David F; Craciun, Gheorghe; Brijder, Robert

    2018-05-01

    We study chemical reaction networks with discrete state spaces and present sufficient conditions on the structure of the network that guarantee the system exhibits an extinction event. The conditions we derive involve creating a modified chemical reaction network called a domination-expanded reaction network and then checking properties of this network. Unlike previous results, our analysis allows algorithmic implementation via systems of equalities and inequalities and suggests sequences of reactions which may lead to extinction events. We apply the results to several networks including an EnvZ-OmpR signaling pathway in Escherichia coli.

  7. Metabolic activity, experiment M171. [space flight effects on human metabolism

    Science.gov (United States)

    Michel, E. L.; Rummel, J. A.

    1973-01-01

    The Skylab metabolic activity experiment determines if man's metabolic effectiveness in doing mechanical work is progressively altered by a simulated Skylab environment, including environmental factors such as slightly increased pCO2. This test identified several hardware/procedural anomalies. The most important of these were: (1) the metabolic analyzer measured carbon dioxide production and expired water too high; (2) the ergometer load module failed under continuous high workload conditions; (3) a higher than desirable number of erroneous blood pressure measurements were recorded; (4) vital capacity measurements were unreliable; and (5) anticipated crew personal exercise needs to be more structured.

  8. Effects of dietary bread crust Maillard reaction products on calcium and bone metabolism in rats.

    Science.gov (United States)

    Roncero-Ramos, Irene; Delgado-Andrade, Cristina; Haro, Ana; Ruiz-Roca, Beatriz; Morales, Francisco J; Navarro, María Pilar

    2013-06-01

    Maillard reaction products (MRP) consumption has been related with the development of bone degenerative disorders, probably linked to changes in calcium metabolism. We aimed to investigate the effects of MRP intake from bread crust on calcium balance and its distribution, and bone metabolism. During 88 days, rats were fed control diet or diets containing bread crust as source of MRP, or its soluble high molecular weight, soluble low molecular weight or insoluble fractions (bread crust, HMW, LMW and insoluble diets, respectively). In the final week, a calcium balance was performed, then animals were sacrified and some organs removed to analyse calcium levels. A second balance was carried out throughout the experimental period to calculate global calcium retention. Biochemical parameters and bone metabolism markers were measured in serum or urine. Global calcium bioavailability was unmodified by consumption of bread crust or its isolate fractions, corroborating the previously described low affinity of MRP to bind calcium. Despite this, a higher calcium concentration was found in femur due to smaller bones having a lower relative density. The isolate consumption of the fractions altered some bone markers, reflecting a situation of increased bone resorption or higher turnover; this did not take place in the animals fed the bread crust diet. Thus, the bread crust intake does not affect negatively calcium bioavailability and bone metabolism.

  9. An analytic algorithm for the space-time fractional reaction-diffusion equation

    Directory of Open Access Journals (Sweden)

    M. G. Brikaa

    2015-11-01

    Full Text Available In this paper, we solve the space-time fractional reaction-diffusion equation by the fractional homotopy analysis method. Solutions of different examples of the reaction term will be computed and investigated. The approximation solutions of the studied models will be put in the form of convergent series to be easily computed and simulated. Comparison with the approximation solution of the classical case of the studied modeled with their approximation errors will also be studied.

  10. Statistical probabilistic mapping in the individual brain space: decreased metabolism in epilepsy with FDG PET

    International Nuclear Information System (INIS)

    Oh, Jung Su; Lee, Jae Sung; Kim, Yu Kyeong; Chung, June Key; Lee, Myung Chul; Lee, Dong Soo

    2005-01-01

    In the statistical probabilistic mapping, commonly, differences between two or more groups of subjects are statistically analyzed following spatial normalization. However, to our best knowledge, there is few study which performed the statistical mapping in the individual brain space rather than in the stereotaxic brain space, i.e., template space. Therefore, in the current study, a new method for mapping the statistical results in the template space onto individual brain space has been developed. Four young subjects with epilepsy and their age-matched thirty normal healthy subjects were recruited. Both FDG PET and T1 structural MRI was scanned in these groups. Statistical analysis on the decreased FDG metabolism in epilepsy was performed on the SPM with two sample t-test (p < 0.001, intensity threshold 100). To map the statistical results onto individual space, inverse deformation was performed as follows. With SPM deformation toolbox, DCT (discrete cosine transform) basis-encoded deformation fields between individual T1 images and T1 MNI template were obtained. Afterward, inverse of those fields, i.e., inverse deformation fields were obtained. Since both PET and T1 images have been already normalized in the same MNI space, inversely deformed results in PET is on the individual brain MRI space. By applying inverse deformation field on the statistical results of the PET, the statistical map of decreased metabolism in individual spaces were obtained. With statistical results in the template space, localization of decreased metabolism was in the inferior temporal lobe, which was slightly inferior to the hippocampus. The statistical results in the individual space were commonly located in the hippocampus, where the activation should be decreased according to a priori knowledge of neuroscience. With our newly developed statistical mapping on the individual spaces, the localization of the brain functional mapping became more appropriate in the sense of neuroscience

  11. Oxygen consumption through metabolism and photodynamic reactions in cells cultured on microbeads

    International Nuclear Information System (INIS)

    Schunck, T.; Poulet, P.

    2000-01-01

    Oxygen consumption by cultured cells, through metabolism and photosensitization reactions, has been calculated theoretically. From this result, we have derived the partial oxygen pressure P O 2 in the perfusion medium flowing across sensitized cultured cells during photodynamic experiments. The P O 2 variations in the perfusate during light irradiation are related to the rate of oxygen consumption through photoreactions, and to the number of cells killed per mole of oxygen consumed through metabolic processes. After irradiation, the reduced metabolic oxygen consumption yields information on the cell death rate, and on the photodynamic cell killing efficiency. The aim of this paper is to present an experimental set-up and the corresponding theoretical model that allows us to control the photodynamic efficiency for a given cell-sensitizer pair, under well defined and controlled conditions of irradiation and oxygen supply. To demonstrate the usefulness of the methodology described, CHO cells cultured on microbeads were sensitized with pheophorbide a and irradiated with different light fluence rates. The results obtained, i.e. oxygen consumption of about 0.1 μMs -1 m -3 under a light fluence rate of 1 W m -2 , 10 5 cells killed per mole of oxygen consumed and a decay rate of about 1 h -1 of living cells after irradiation, are in good agreement with the theoretical predictions and with previously published data. (author)

  12. Impact of Fungicide Residues on Polymerase Chain Reaction and on Yeast Metabolism

    Directory of Open Access Journals (Sweden)

    Gildo Almeida da Silva

    Full Text Available ABSTRACT The indiscriminate use of pesticides on grape crops is harmful for consumers´ healthin “in natura” consumption and in the ingestion of wine and grape juice. During winemaking, a rapid and efficient fermentation stage is critical to avoid proliferation of contaminating microorganisms and to guarantee the product´s quality. Polymerase chain reaction (PCR has the advantage of detecting these contaminants in the early stages of fermentation. However,this enzymatic reaction may also be susceptible to specific problems, reducing its efficiency. Agricultural practices, such as fungicide treatments, may be a source of PCR inhibiting factors and may also interfere in the normal course of fermentation.The action of the pesticides captan and folpet on PCR and on yeast metabolism was evaluated, once these phthalimide compounds are widely employed in Brazilian vineyards. DNA amplification was only observed at 75 and 37.5 µg/mL of captan concentrations, whereas with folpet, amplification was observed only in the two lowest concentrations tested (42.2 and 21.1µg/mL.Besides the strong inhibition on Taq polymerase activity, phthalimides also inhibited yeast metabolism at all concentrations analyzed.Grape must containing captan and folpet residues could not be transformed into wine due to stuck fermentation caused by the inhibition of yeast metabolism. Non-compliance with the waiting period for phthalimide fungicides may result in financial liabilities to the viticulture sector.The use of yeasts with high fungicide sensitivity should be selected for must fermentation as a strategy for sustainable wine production and to assure that products comply with health and food safety standards.

  13. Phase space conduits for reaction in multidimensional systems : HCN isomerization in three dimensions

    NARCIS (Netherlands)

    Waalkens, Holger; Burbanks, Andrew; Wiggins, Stephen

    2004-01-01

    The three-dimensional hydrogen cyanide/isocyanide isomerization problem is taken as an example to present a general theory for computing the phase space structures which govern classical reaction dynamics in systems with an arbitrary (finite) number of degrees of freedom. The theory, which is

  14. Dynamical Studies of Chemical Reactions Relevant to the Local Atmosphere of the Orbiting Space Shuttle

    National Research Council Canada - National Science Library

    Casavecchia, Piergiorgio

    1998-01-01

    ...: The contractor will measure differential cross sections for reactions of O(3P), 0(1D) and OH(2P) with various radial and molecules present in the local atmosphere of the space shuttle in low earth orbit as described in the original proposal for this work.

  15. Fisher Information Study in Position and Momentum Spaces for Elementary Chemical Reactions.

    Science.gov (United States)

    López-Rosa, Sheila; Esquivel, Rodolfo O; Angulo, Juan Carlos; Antolín, Juan; Dehesa, Jesús S; Flores-Gallegos, Nelson

    2010-01-12

    The utility of the Fisher information measure is analyzed to detect the transition state, the stationary points of a chemical reaction, and the bond breaking/forming regions of elementary reactions such as the simplest hydrogen abstraction and the identity SN2 exchange ones. This is performed by following the intrinsic reaction path calculated at the MP2 and QCISD(T) levels of theory with a 6-311++G(3df, 2p) basis set. Selected descriptors of both position and momentum space densities are utilized to support the observations, such as the molecular electrostatic potential (MEP), the hardness, the dipole moment, along with geometrical parameters. Our results support the concept of a continuum of transient of Zewail and Polanyi for the transition state rather than a single state, which is also in agreement with reaction force analyses.

  16. MCNP6 simulation of reactions of interest to FRIB, medical, and space applications

    International Nuclear Information System (INIS)

    Mashnik, Stepan G.

    2015-01-01

    The latest production-version of the Los Alamos Monte Carlo N-Particle transport code MCNP6 has been used to simulate a variety of particle-nucleus and nucleus-nucleus reactions of academic and applied interest to research subjects at the Facility for Rare Isotope Beams (FRIB), medical isotope production, space-radiation shielding, cosmic-ray propagation, and accelerator applications, including several reactions induced by radioactive isotopes, analyzing production of both stable and radioactive residual nuclei. Here, we discuss examples of validation and verification of MCNP6 by comparing with recent neutron spectra measured at the Heavy Ion Medical Accelerator in Chiba, Japan; spectra of light fragments from several reactions measured recently at GANIL, France; INFN Laboratori Nazionali del Sud, Catania, Italy; COSY of the Jülich Research Center, Germany; and cross sections of products from several reactions measured lately at GSI, Darmstadt, Germany; ITEP, Moscow, Russia; and, LANSCE, LANL, Los Alamos, U.S.A. As a rule, MCNP6 provides quite good predictions for most of the reactions we analyzed so far, allowing us to conclude that it can be used as a reliable and useful simulation tool for various applications for FRIB, medical, and space applications involving stable and radioactive isotopes. (author)

  17. Energy metabolism and ATP balance in animal cell cultivation using a stoichiometrically based reaction network.

    Science.gov (United States)

    Xie, L; Wang, D I

    1996-12-05

    A metabolic reaction network is developed for the estimation of the stoichiometric production of adenosine triphosphate (ATP) in animal cell culture. By using the material balance data from fed-batch and batch cultures of hybridoma cells, the stoichiometric ATP productions are determined with estimated effective P/O ratios of 2 for NADH and 1.2 for FADH(2). A significant percentage of the ATP requirement (16-41%) in hybridoma cells is generated directly from free energy release without the participation of oxygen. The oxidative phosphorylation of NADH accounts for about 60% of the total ATP production in the fed-batch cultures and about 47% in the batch culture. The oxidative phosphorylation of FADH(2) accounts for less then 20% of the total ATP production in all cases.A fractional model is devised to analyze the contribution of each nutrient to the ATP production. Results show that a majority of the ATP is produced from glucose metabolism (60-76%). Less than 30% of the ATP is derived from glutamine, and less than 11% is derived from other essential amino acids. The analysis also shows that the glycolytic pathway generates more ATP in the batch (41%) than in the fed-batch (demand estimated from the dry cell weight and cell composition is significantly lower than that calculated from the maximum ATP yield, indicating that the non-growth-associated ATP demand may contain other factors than what is considered in the estimation of the biosynthetic ATP demand.

  18. WNT and DKK Determine Hair Follicle Spacing Through a Reaction-Diffusion Mechanism

    Science.gov (United States)

    Sick, Stefanie; Reinker, Stefan; Timmer, Jens; Schlake, Thomas

    2006-12-01

    Mathematical reaction-diffusion models have been suggested to describe formation of animal pigmentation patterns and distribution of epidermal appendages. However, the crucial signals and in vivo mechanisms are still elusive. Here we identify WNT and its inhibitor DKK as primary determinants of murine hair follicle spacing, using a combined experimental and computational modeling approach. Transgenic DKK overexpression reduces overall appendage density. Moderate suppression of endogenous WNT signaling forces follicles to form clusters during an otherwise normal morphogenetic program. These results confirm predictions of a WNT/DKK-specific mathematical model and provide in vivo corroboration of the reaction-diffusion mechanism for epidermal appendage formation.

  19. Comparison of TiO2 photocatalysis, electrochemically assisted Fenton reaction and direct electrochemistry for simulation of phase I metabolism reactions of drugs.

    Science.gov (United States)

    Ruokolainen, Miina; Gul, Turan; Permentier, Hjalmar; Sikanen, Tiina; Kostiainen, Risto; Kotiaho, Tapio

    2016-02-15

    The feasibility of titanium dioxide (TiO2) photocatalysis, electrochemically assisted Fenton reaction (EC-Fenton) and direct electrochemical oxidation (EC) for simulation of phase I metabolism of drugs was studied by comparing the reaction products of buspirone, promazine, testosterone and 7-ethoxycoumarin with phase I metabolites of the same compounds produced in vitro by human liver microsomes (HLM). Reaction products were analysed by UHPLC-MS. TiO2 photocatalysis simulated the in vitro phase I metabolism in HLM more comprehensively than did EC-Fenton or EC. Even though TiO2 photocatalysis, EC-Fenton and EC do not allow comprehensive prediction of phase I metabolism, all three methods produce several important metabolites without the need for demanding purification steps to remove the biological matrix. Importantly, TiO2 photocatalysis produces aliphatic and aromatic hydroxylation products where direct EC fails. Furthermore, TiO2 photocatalysis is an extremely rapid, simple and inexpensive way to generate oxidation products in a clean matrix and the reaction can be simply initiated and quenched by switching the UV lamp on/off. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. An Efficient Implicit FEM Scheme for Fractional-in-Space Reaction-Diffusion Equations

    KAUST Repository

    Burrage, Kevin

    2012-01-01

    Fractional differential equations are becoming increasingly used as a modelling tool for processes associated with anomalous diffusion or spatial heterogeneity. However, the presence of a fractional differential operator causes memory (time fractional) or nonlocality (space fractional) issues that impose a number of computational constraints. In this paper we develop efficient, scalable techniques for solving fractional-in-space reaction diffusion equations using the finite element method on both structured and unstructured grids via robust techniques for computing the fractional power of a matrix times a vector. Our approach is show-cased by solving the fractional Fisher and fractional Allen-Cahn reaction-diffusion equations in two and three spatial dimensions, and analyzing the speed of the traveling wave and size of the interface in terms of the fractional power of the underlying Laplacian operator. © 2012 Society for Industrial and Applied Mathematics.

  1. A computational approach to extinction events in chemical reaction networks with discrete state spaces.

    Science.gov (United States)

    Johnston, Matthew D

    2017-12-01

    Recent work of Johnston et al. has produced sufficient conditions on the structure of a chemical reaction network which guarantee that the corresponding discrete state space system exhibits an extinction event. The conditions consist of a series of systems of equalities and inequalities on the edges of a modified reaction network called a domination-expanded reaction network. In this paper, we present a computational implementation of these conditions written in Python and apply the program on examples drawn from the biochemical literature. We also run the program on 458 models from the European Bioinformatics Institute's BioModels Database and report our results. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Individual variation in metabolic reaction norms over ambient temperature causes low correlation between basal and standard metabolic rate

    NARCIS (Netherlands)

    Briga, Michael; Verhulst, Simon

    2017-01-01

    Basal metabolic rate (BMR) is often assumed to be indicative of the energy turnover at ambient temperatures (T-a) below the thermoneutral zone (SMR), but this assumption has remained largely untested. Using a new statistical approach, we quantified the consistency in nocturnal metabolic rate across

  3. Space Weather Influence on the Earth Climate: Possible Manifestations in Wheat Markets Reaction

    Science.gov (United States)

    Pustilnik, Lev; Yom Din, Gregory; Zagnetko, Alexander

    We consider problem of a possible influence of unfavorable states of the space weather on agri-culture market through chain of connections: "space weather"-"earth weather"-"agriculture crops"-"price reaction". We show that new manifestations of "space weather"-"earth weather" relations discovered in the last time allow to revise wide field of expected solar-terrestrial con-nections. In the previous works we proposed possible mechanisms of wheat market reaction in the form of price bursts on the specific unfavorable states of space weather. We show that implementation of considered "price reaction scenarios" is possible only for condition of simul-taneous realization of several necessary conditions: high sensitivity of local earth weather in selected region to space weather; state of "high risk agriculture" in selected agriculture zone; high sensitivity of agricultural market to possible deficit of supply. Results of previous works included application of this approach to wheat market in Medieval England and to modern USA durum market showed that real connection between wheat price bursts and space weather state is observed with high confidence level. The aim of present work is answer on the ques-tion, why wheat markets in one region are sensitive to space weather factor, while another regional wheat markets demonstrate absolute indifferent reaction on this factor. For this aim we consider distribution of sensitivity of wheat markets in Europe to space weather as function of localization in different climatic zones. We analyze giant database of 95 European wheat markets from 14 countries during about 600-year period (1260-1912). We show that observed sensitivity of wheat market to space weather effects controlled, first of all, by type of predomi-nant climate in different zones of agriculture. Wheat markets in the North and part of Central Europe (England, Iceland, Holland) shows reliable sensitivity to space weather in minimum states of solar activity with low

  4. Diels–Alder reactions in confined spaces: the influence of catalyst structure and the nature of active sites for the retro-Diels–Alder reaction

    Directory of Open Access Journals (Sweden)

    Ángel Cantín

    2016-10-01

    Full Text Available Diels–Alder cycloaddition between cyclopentadiene and p-benzoquinone has been studied in the confined space of a pure silica zeolite Beta and the impact on reaction rate due to the concentration effect within the pore and diffusion limitations are discussed. Introduction of Lewis or Brønsted acid sites on the walls of the zeolite strongly increases the reaction rate. However, contrary to what occurs with mesoporous molecular sieves (MCM-41, Beta zeolite does not catalyse the retro-Diels–Alder reaction, resulting in a highly selective catalyst for the cycloaddition reaction.

  5. Development of an Objective Space Suit Mobility Performance Metric Using Metabolic Cost and Functional Tasks

    Science.gov (United States)

    McFarland, Shane M.; Norcross, Jason

    2016-01-01

    Existing methods for evaluating EVA suit performance and mobility have historically concentrated on isolated joint range of motion and torque. However, these techniques do little to evaluate how well a suited crewmember can actually perform during an EVA. An alternative method of characterizing suited mobility through measurement of metabolic cost to the wearer has been evaluated at Johnson Space Center over the past several years. The most recent study involved six test subjects completing multiple trials of various functional tasks in each of three different space suits; the results indicated it was often possible to discern between different suit designs on the basis of metabolic cost alone. However, other variables may have an effect on real-world suited performance; namely, completion time of the task, the gravity field in which the task is completed, etc. While previous results have analyzed completion time, metabolic cost, and metabolic cost normalized to system mass individually, it is desirable to develop a single metric comprising these (and potentially other) performance metrics. This paper outlines the background upon which this single-score metric is determined to be feasible, and initial efforts to develop such a metric. Forward work includes variable coefficient determination and verification of the metric through repeated testing.

  6. Individual variation in metabolic reaction norms over ambient temperature causes low correlation between basal and standard metabolic rate

    OpenAIRE

    Briga, Michael; Verhulst, Simon

    2017-01-01

    Basal metabolic rate (BMR) is often assumed to be indicative of the energy turnover at ambient temperatures (T-a) below the thermoneutral zone (SMR), but this assumption has remained largely untested. Using a new statistical approach, we quantified the consistency in nocturnal metabolic rate across a temperature range in zebra finches (N=3213 measurements on 407 individuals) living permanently in eight outdoor aviaries. Foraging conditions were either benign or harsh, and body mass and mass-a...

  7. Individual variation in metabolic reaction norms over ambient temperature causes low correlation between basal and standard metabolic rate.

    Science.gov (United States)

    Briga, Michael; Verhulst, Simon

    2017-09-15

    Basal metabolic rate (BMR) is often assumed to be indicative of the energy turnover at ambient temperatures ( T a ) below the thermoneutral zone (SMR), but this assumption has remained largely untested. Using a new statistical approach, we quantified the consistency in nocturnal metabolic rate across a temperature range in zebra finches ( N =3213 measurements on 407 individuals) living permanently in eight outdoor aviaries. Foraging conditions were either benign or harsh, and body mass and mass-adjusted BMR (BMR m ) and SMR (SMR m ) were lower in individuals living in a harsh foraging environment. The correlation between SMR m at different T a was high ( r =0.91), independent of foraging environment, showing that individuals are consistently ranked according to their SMR m However, the correlations between BMR m and SMR m were always lower (average: r =0.29; range: 0metabolic response to lower T a at least in part reflected differential body temperature ( T b ) regulation: early morning T b was lower at low T a , and more so in individuals with a weaker metabolic response to lower T a Our findings have implications for the use of BMR in the estimation of time-energy budgets and comparative analyses: we suggest that the use of metabolic rates at ecologically relevant T a , such as the easily tractable SMR, will be more informative than the use of BMR as a proxy for energy turnover. © 2017. Published by The Company of Biologists Ltd.

  8. Towards human exploration of space: The THESEUS review series on nutrition and metabolism research priorities.

    Science.gov (United States)

    Bergouignan, Audrey; Stein, T Peter; Habold, Caroline; Coxam, Veronique; O' Gorman, Donal; Blanc, Stéphane

    2016-01-01

    Nutrition has multiple roles during space flight from providing sufficient nutrients to meet the metabolic needs of the body and to maintain good health, to the beneficial psychosocial aspects related to the meals. Nutrition is central to the functioning of the body; poor nutrition compromises all the physiological systems. Nutrition is therefore likely to have a key role in counteracting the negative effects of space flight (e.g., radiation, immune deficits, oxidative stress, and bone and muscle loss). As missions increase in duration, any dietary/nutritional deficiencies will become progressively more detrimental. Moreover, it has been recognized that the human diet contains, in addition to essential macronutrients, a complex array of naturally occurring bioactive micronutrients that may confer significant long-term health benefits. It is therefore critical that astronauts be adequately nourished during missions. Problems of nutritional origin are often treatable by simply providing the appropriate nutrients and adequate recommendations. This review highlights six key issues that have been identified as space research priorities in nutrition field: in-flight energy balance; altered feeding behavior; development of metabolic stress; micronutrient deficiency; alteration of gut microflora; and altered fluid and electrolytes balance. For each of these topics, relevance for space exploration, knowledge gaps and proposed investigations are described. Finally, the nutritional questions related to bioastronautics research are very relevant to multiple ground-based-related health issues. The potential spin-offs are both interesting scientifically and potentially of great clinical importance.

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

    Science.gov (United States)

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

    1981-01-01

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

  10. Expansion of chemical space for natural products by uncommon P450 reactions.

    Science.gov (United States)

    Zhang, Xingwang; Li, Shengying

    2017-08-30

    Covering: 2000 to 2017Cytochrome P450 enzymes (P450s) are the most versatile biocatalysts in nature. The catalytic competence of these extraordinary hemoproteins is broadly harnessed by numerous chemical defenders such as bacteria, fungi, and plants for the generation of diverse and complex natural products. Rather than the common tailoring reactions (e.g. hydroxylation and epoxidation) mediated by the majority of biosynthetic P450s, in this review, we will focus on the unusual P450 enzymes in relation to new chemistry, skeleton construction, and structure re-shaping via their own unique catalytic power or the intriguing protein-protein interactions between P450s and other proteins. These uncommon P450 reactions lead to a higher level of chemical space expansion for natural products, through which a broader spectrum of bioactivities can be gained by the host organisms.

  11. Thermodynamic calculations for biochemical transport and reaction processes in metabolic networks

    NARCIS (Netherlands)

    Jol, Stefan J; Kümmel, Anne; Hatzimanikatis, Vassily; Beard, Daniel A; Heinemann, Matthias

    2010-01-01

    Thermodynamic analysis of metabolic networks has recently generated increasing interest for its ability to add constraints on metabolic network operation, and to combine metabolic fluxes and metabolite measurements in a mechanistic manner. Concepts for the calculation of the change in Gibbs energy

  12. Phase-space geometry and reaction dynamics near index 2 saddles

    International Nuclear Information System (INIS)

    Ezra, Gregory S; Wiggins, Stephen

    2009-01-01

    We study the phase-space geometry associated with index 2 saddles of a potential energy surface and its influence on reaction dynamics for n degree-of-freedom (DoF) Hamiltonian systems. In recent years, similar studies have been carried out for index 1 saddles of potential energy surfaces, and the phase-space geometry associated with classical transition state theory has been elucidated. In this case, the existence of a normally hyperbolic invariant manifold (NHIM) of saddle stability type has been shown, where the NHIM serves as the 'anchor' for the construction of dividing surfaces having the no-recrossing property and minimal flux. For the index 1 saddle case, the stable and unstable manifolds of the NHIM are co-dimension 1 in the energy surface and have the structure of spherical cylinders, and thus act as the conduits for reacting trajectories in phase space. The situation for index 2 saddles is quite different, and their relevance for reaction dynamics has not previously been fully recognized. We show that NHIMs with their stable and unstable manifolds still exist, but that these manifolds by themselves lack sufficient dimension to act as barriers in the energy surface in order to constrain reactions. Rather, in the index 2 case there are different types of invariant manifolds, containing the NHIM and its stable and unstable manifolds, that act as co-dimension 1 barriers in the energy surface. These barriers divide the energy surface in the vicinity of the index 2 saddle into regions of qualitatively different trajectories exhibiting a wider variety of dynamical behavior than for the case of index 1 saddles. In particular, we can identify a class of trajectories, which we refer to as 'roaming trajectories', which are not associated with reaction along the classical minimum energy path (MEP). We illustrate the significance of our analysis of the index 2 saddle for reaction dynamics with two examples. The first involves isomerization on a potential energy

  13. Construction of Metabolism Prediction Models for CYP450 3A4, 2D6, and 2C9 Based on Microsomal Metabolic Reaction System

    Directory of Open Access Journals (Sweden)

    Shuai-Bing He

    2016-10-01

    Full Text Available During the past decades, there have been continuous attempts in the prediction of metabolism mediated by cytochrome P450s (CYP450s 3A4, 2D6, and 2C9. However, it has indeed remained a huge challenge to accurately predict the metabolism of xenobiotics mediated by these enzymes. To address this issue, microsomal metabolic reaction system (MMRS—a novel concept, which integrates information about site of metabolism (SOM and enzyme—was introduced. By incorporating the use of multiple feature selection (FS techniques (ChiSquared (CHI, InfoGain (IG, GainRatio (GR, Relief and hybrid classification procedures (Kstar, Bayes (BN, K-nearest neighbours (IBK, C4.5 decision tree (J48, RandomForest (RF, Support vector machines (SVM, AdaBoostM1, Bagging, metabolism prediction models were established based on metabolism data released by Sheridan et al. Four major biotransformations, including aliphatic C-hydroxylation, aromatic C-hydroxylation, N-dealkylation and O-dealkylation, were involved. For validation, the overall accuracies of all four biotransformations exceeded 0.95. For receiver operating characteristic (ROC analysis, each of these models gave a significant area under curve (AUC value >0.98. In addition, an external test was performed based on dataset published previously. As a result, 87.7% of the potential SOMs were correctly identified by our four models. In summary, four MMRS-based models were established, which can be used to predict the metabolism mediated by CYP3A4, 2D6, and 2C9 with high accuracy.

  14. Scalable implicit methods for reaction-diffusion equations in two and three space dimensions

    Energy Technology Data Exchange (ETDEWEB)

    Veronese, S.V.; Othmer, H.G. [Univ. of Utah, Salt Lake City, UT (United States)

    1996-12-31

    This paper describes the implementation of a solver for systems of semi-linear parabolic partial differential equations in two and three space dimensions. The solver is based on a parallel implementation of a non-linear Alternating Direction Implicit (ADI) scheme which uses a Cartesian grid in space and an implicit time-stepping algorithm. Various reordering strategies for the linearized equations are used to reduce the stride and improve the overall effectiveness of the parallel implementation. We have successfully used this solver for large-scale reaction-diffusion problems in computational biology and medicine in which the desired solution is a traveling wave that may contain rapid transitions. A number of examples that illustrate the efficiency and accuracy of the method are given here; the theoretical analysis will be presented.

  15. Effect of Prolonged Simulated Microgravity on Metabolic Proteins in Rat Hippocampus: Steps toward Safe Space Travel.

    Science.gov (United States)

    Wang, Yun; Javed, Iqbal; Liu, Yahui; Lu, Song; Peng, Guang; Zhang, Yongqian; Qing, Hong; Deng, Yulin

    2016-01-04

    Mitochondria are not only the main source of energy in cells but also produce reactive oxygen species (ROS), which result in oxidative stress when in space. This oxidative stress is responsible for energy imbalances and cellular damage. In this study, a rat tail suspension model was used in individual experiments for 7 and 21 days to explore the effect of simulated microgravity (SM) on metabolic proteins in the hippocampus, a vital brain region involved in learning, memory, and navigation. A comparative (18)O-labeled quantitative proteomic strategy was used to observe the differential expression of metabolic proteins. Forty-two and sixty-seven mitochondrial metabolic proteins were differentially expressed after 21 and 7 days of SM, respectively. Mitochondrial Complex I, III, and IV, isocitrate dehydrogenase and malate dehydrogenase were down-regulated. Moreover, DJ-1 and peroxiredoxin 6, which defend against oxidative damage, were up-regulated in the hippocampus. Western blot analysis of proteins DJ-1 and COX 5A confirmed the mass spectrometry results. Despite these changes in mitochondrial protein expression, no obvious cell apoptosis was observed after 21 days of SM. The results of this study indicate that the oxidative stress induced by SM has profound effects on metabolic proteins.

  16. Metabolic Rate and Ground Reaction Force During Motorized and Non-Motorized Treadmill Exercise

    Science.gov (United States)

    Everett, Meghan E.; Loehr, James A.; DeWitt, John K.; Laughlin, Mitzi; Lee, Stuart M. C.

    2010-01-01

    PURPOSE: To measure vertical ground reaction force (vGRF) and oxygen consumption (VO2) at several velocities during exercise using a ground-based version of the ISS treadmill in the M and NM modes. METHODS: Subjects (n = 20) walked or ran at 0.89, 1.34, 1.79, 2.24, 2.68, and 3.12 m/s while VO2 and vGRF data were collected. VO2 was measured using open-circuit spirometry (TrueOne 2400, Parvo-Medics). Data were averaged over the last 2 min of each 5-min stage. vGRF was measured in separate 15-s bouts at 125 Hz using custom-fitted pressure-sensing insoles (F-Scan Sport Sensors, Tekscan, Inc). A repeated-measures ANOVA was used to test for differences in VO2 and vGRF between M and NM and across speeds. Significance was set at P < 0.05. RESULTS: Most subjects were unable to exercise for 5 min at treadmill speeds above 1.79 m/s in the NM mode; however, vGRF data were obtained for all subjects at each speed in both modes. VO2 was approx.40% higher during NM than M exercise across treadmill speeds. vGRF increased with treadmill speed but was not different between modes. CONCLUSION: Higher VO2 with no change in vGRF suggests that the additional metabolic cost associated with NM treadmill exercise is accounted for in the horizontal forces required to move the treadmill belt. Although this may limit the exercise duration at faster speeds, high-intensity NM exercise activates the hamstrings and plantarflexors, which are not specifically targeted or well protected by other in-flight countermeasures.

  17. Velocity-space observation regions of high-resolution two-step reaction gamma-ray spectroscopy

    DEFF Research Database (Denmark)

    Salewski, Mirko; Nocente, M.; Gorini, G.

    2015-01-01

    High-resolution γ-ray spectroscopy (GRS) measurements resolve spectral shapes of Dopplerbroadened γ-rays. We calculate weight functions describing velocity-space sensitivities of any two-step reaction GRS measurements in magnetized plasmas using the resonant nuclear reaction 9Be(α, nγ)12C...

  18. Instantaneous Metabolic Cost of Walking: Joint-Space Dynamic Model with Subject-Specific Heat Rate.

    Directory of Open Access Journals (Sweden)

    Dustyn Roberts

    Full Text Available A subject-specific model of instantaneous cost of transport (ICOT is introduced from the joint-space formulation of metabolic energy expenditure using the laws of thermodynamics and the principles of multibody system dynamics. Work and heat are formulated in generalized coordinates as functions of joint kinematic and dynamic variables. Generalized heat rates mapped from muscle energetics are estimated from experimental walking metabolic data for the whole body, including upper-body and bilateral data synchronization. Identified subject-specific energetic parameters-mass, height, (estimated maximum oxygen uptake, and (estimated maximum joint torques-are incorporated into the heat rate, as opposed to the traditional in vitro and subject-invariant muscle parameters. The total model metabolic energy expenditure values are within 5.7 ± 4.6% error of the measured values with strong (R2 > 0.90 inter- and intra-subject correlations. The model reliably predicts the characteristic convexity and magnitudes (0.326-0.348 of the experimental total COT (0.311-0.358 across different subjects and speeds. The ICOT as a function of time provides insights into gait energetic causes and effects (e.g., normalized comparison and sensitivity with respect to walking speed and phase-specific COT, which are unavailable from conventional metabolic measurements or muscle models. Using the joint-space variables from commonly measured or simulated data, the models enable real-time and phase-specific evaluations of transient or non-periodic general tasks that use a range of (aerobic energy pathway similar to that of steady-state walking.

  19. Distributed BOLD-response in association cortex vector state space predicts reaction time during selective attention.

    Science.gov (United States)

    Musso, Francesco; Konrad, Andreas; Vucurevic, Goran; Schäffner, Cornelius; Friedrich, Britta; Frech, Peter; Stoeter, Peter; Winterer, Georg

    2006-02-15

    Human cortical information processing is thought to be dominated by distributed activity in vector state space (Churchland, P.S., Sejnowski, T.J., 1992. The Computational Brain. MIT Press, Cambridge.). In principle, it should be possible to quantify distributed brain activation with independent component analysis (ICA) through vector-based decomposition, i.e., through a separation of a mixture of sources. Using event-related functional magnetic resonance imaging (fMRI) during a selective attention-requiring task (visual oddball), we explored how the number of independent components within activated cortical areas is related to reaction time. Prior to ICA, the activated cortical areas were determined on the basis of a General linear model (GLM) voxel-by-voxel analysis of the target stimuli (checkerboard reversal). Two activated cortical areas (temporoparietal cortex, medial prefrontal cortex) were further investigated as these cortical regions are known to be the sites of simultaneously active electromagnetic generators which give rise to the compound event-related potential P300 during oddball task conditions. We found that the number of independent components more strongly predicted reaction time than the overall level of "activation" (GLM BOLD-response) in the left temporoparietal area whereas in the medial prefrontal cortex both ICA and GLM predicted reaction time equally well. Comparable correlations were not seen when principle components were used instead of independent components. These results indicate that the number of independently activated components, i.e., a high level of cortical activation complexity in cortical vector state space, may index particularly efficient information processing during selective attention-requiring tasks. To our best knowledge, this is the first report describing a potential relationship between neuronal generators of cognitive processes, the associated electrophysiological evidence for the existence of distributed networks

  20. Space-flight simulations of calcium metabolism using a mathematical model of calcium regulation

    Science.gov (United States)

    Brand, S. N.

    1985-01-01

    The results of a series of simulation studies of calcium matabolic changes which have been recorded during human exposure to bed rest and space flight are presented. Space flight and bed rest data demonstrate losses of total body calcium during exposure to hypogravic environments. These losses are evidenced by higher than normal rates of urine calcium excretion and by negative calcium balances. In addition, intestinal absorption rates and bone mineral content are assumed to decrease. The bed rest and space flight simulations were executed on a mathematical model of the calcium metabolic system. The purpose of the simulations is to theoretically test hypotheses and predict system responses which are occurring during given experimental stresses. In this case, hypogravity occurs through the comparison of simulation and experimental data and through the analysis of model structure and system responses. The model reliably simulates the responses of selected bed rest and space flight parameters. When experimental data are available, the simulated skeletal responses and regulatory factors involved in the responses agree with space flight data collected on rodents. In addition, areas within the model that need improvement are identified.

  1. Reaction Norms in Natural Conditions: How Does Metabolic Performance Respond to Weather Variations in a Small Endotherm Facing Cold Environments?

    Science.gov (United States)

    Petit, Magali; Vézina, François

    2014-01-01

    Reaction norms reflect an organisms' capacity to adjust its phenotype to the environment and allows for identifying trait values associated with physiological limits. However, reaction norms of physiological parameters are mostly unknown for endotherms living in natural conditions. Black-capped chickadees (Poecile atricapillus) increase their metabolic performance during winter acclimatization and are thus good model to measure reaction norms in the wild. We repeatedly measured basal (BMR) and summit (Msum) metabolism in chickadees to characterize, for the first time in a free-living endotherm, reaction norms of these parameters across the natural range of weather variation. BMR varied between individuals and was weakly and negatively related to minimal temperature. Msum varied with minimal temperature following a Z-shape curve, increasing linearly between 24°C and −10°C, and changed with absolute humidity following a U-shape relationship. These results suggest that thermal exchanges with the environment have minimal effects on maintenance costs, which may be individual-dependent, while thermogenic capacity is responding to body heat loss. Our results suggest also that BMR and Msum respond to different and likely independent constraints. PMID:25426860

  2. Using in vitro derived enzymatic reaction rates of metabolism to inform pesticide body burdens in amphibians

    Science.gov (United States)

    Understanding how pesticide exposure to non-target species influences toxicity is necessary to accurately assess the ecological risks these compounds pose. To assess the potential metabolic activation of broad use pesticides in amphibians, in vitro and in vivo metabolic rate cons...

  3. Integer programming-based method for designing synthetic metabolic networks by Minimum Reaction Insertion in a Boolean model.

    Science.gov (United States)

    Lu, Wei; Tamura, Takeyuki; Song, Jiangning; Akutsu, Tatsuya

    2014-01-01

    In this paper, we consider the Minimum Reaction Insertion (MRI) problem for finding the minimum number of additional reactions from a reference metabolic network to a host metabolic network so that a target compound becomes producible in the revised host metabolic network in a Boolean model. Although a similar problem for larger networks is solvable in a flux balance analysis (FBA)-based model, the solution of the FBA-based model tends to include more reactions than that of the Boolean model. However, solving MRI using the Boolean model is computationally more expensive than using the FBA-based model since the Boolean model needs more integer variables. Therefore, in this study, to solve MRI for larger networks in the Boolean model, we have developed an efficient Integer Programming formalization method in which the number of integer variables is reduced by the notion of feedback vertex set and minimal valid assignment. As a result of computer experiments conducted using the data of metabolic networks of E. coli and reference networks downloaded from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, we have found that the developed method can appropriately solve MRI in the Boolean model and is applicable to large scale-networks for which an exhaustive search does not work. We have also compared the developed method with the existing connectivity-based methods and FBA-based methods, and show the difference between the solutions of our method and the existing methods. A theoretical analysis of MRI is also conducted, and the NP-completeness of MRI is proved in the Boolean model. Our developed software is available at "http://sunflower.kuicr.kyoto-u.ac.jp/~rogi/minRect/minRect.html."

  4. Novel reaction control techniques for redundant space manipulators: Theory and simulated microgravity tests

    Science.gov (United States)

    Cocuzza, Silvio; Pretto, Isacco; Debei, Stefano

    2011-06-01

    This paper presents two novel redundancy resolution schemes aimed at locally minimizing the reaction torque transferred to the spacecraft during manipulator manoeuvres. The subject is of particular interest in space robotics because reduced reactions result in reduced energy consumption and longer operating life of the attitude control system. The first presented solution is based on a weighted Jacobian pseudoinverse and is derived by using Lagrangian multipliers. The weight matrix is defined by means of the inertia matrix which appears in the spacecraft reaction torque dynamics. The second one is based on a least squares formulation of the minimization problem. In this formulation the linearity of the forward kinematics and of the reaction torque dynamics equations with respect to the joint accelerations is used. A closed-form solution is derived for both the presented methods, and their equivalence is proven analytically. Moreover, the proposed solutions, which are suitable for real-time implementation, are extended in order to take into account the physical limits of the manipulator joints directly inside the solution algorithms. A software simulator has been developed in order to simulate the performance of the presented solutions for the selected test cases. The proposed solutions have then been experimentally tested using a 3D free-flying robot previously tested in an ESA parabolic flight campaign. In the test campaign the 3D robot has been converted in a 2D robot thanks to its modularity in order to perform planar tests, in which the microgravity environment can be simulated without time constraints. Air-bearings are used to sustain the links weight, and a dynamometer is used to measure the reaction torque. The experimental validation of the presented inverse kinematics solutions, with an insight on the effect of joint flexibility on their performance, has been carried out, and the experimental results confirmed the good performance of the proposed methods

  5. From bare to renormalized order parameter in gauge space: Structure and reactions

    Science.gov (United States)

    Potel, G.; Idini, A.; Barranco, F.; Vigezzi, E.; Broglia, R. A.

    2017-09-01

    It is not physically obvious why one can calculate with similar accuracy, as compared to the experimental data, the absolute cross section associated with two-nucleon transfer processes between members of pairing rotational bands, making use of simple BCS (constant matrix elements) or of many-body [Nambu-Gorkov (NG), nuclear field theory (NFT)] spectroscopic amplitudes. Restoration of spontaneous symmetry breaking and associated emergent generalized rigidity in gauge space provides the answer and points to a new emergence: A physical sum rule resulting from the intertwining of structure and reaction processes, closely connected with the central role induced pairing interaction plays in structure, together with the fact that successive transfer dominates Cooper pair tunneling.

  6. Evaluation of an S-system root-finding method for estimating parameters in a metabolic reaction model.

    Science.gov (United States)

    Iwata, Michio; Miyawaki-Kuwakado, Atsuko; Yoshida, Erika; Komori, Soichiro; Shiraishi, Fumihide

    2018-02-02

    In a mathematical model, estimation of parameters from time-series data of metabolic concentrations in cells is a challenging task. However, it seems that a promising approach for such estimation has not yet been established. Biochemical Systems Theory (BST) is a powerful methodology to construct a power-law type model for a given metabolic reaction system and to then characterize it efficiently. In this paper, we discuss the use of an S-system root-finding method (S-system method) to estimate parameters from time-series data of metabolite concentrations. We demonstrate that the S-system method is superior to the Newton-Raphson method in terms of the convergence region and iteration number. We also investigate the usefulness of a translocation technique and a complex-step differentiation method toward the practical application of the S-system method. The results indicate that the S-system method is useful to construct mathematical models for a variety of metabolic reaction networks. Copyright © 2018 Elsevier Inc. All rights reserved.

  7. Development of reaction-sintered SiC mirror for space-borne optics

    Science.gov (United States)

    Yui, Yukari Y.; Kimura, Toshiyoshi; Tange, Yoshio

    2017-11-01

    We are developing high-strength reaction-sintered silicon carbide (RS-SiC) mirror as one of the new promising candidates for large-diameter space-borne optics. In order to observe earth surface or atmosphere with high spatial resolution from geostationary orbit, larger diameter primary mirrors of 1-2 m are required. One of the difficult problems to be solved to realize such optical system is to obtain as flat mirror surface as possible that ensures imaging performance in infrared - visible - ultraviolet wavelength region. This means that homogeneous nano-order surface flatness/roughness is required for the mirror. The high-strength RS-SiC developed and manufactured by TOSHIBA is one of the most excellent and feasible candidates for such purpose. Small RS-SiC plane sample mirrors have been manufactured and basic physical parameters and optical performances of them have been measured. We show the current state of the art of the RS-SiC mirror and the feasibility of a large-diameter RS-SiC mirror for space-borne optics.

  8. Plant metabolism and cell wall formation in space (microgravity) and on Earth

    Science.gov (United States)

    Lewis, Norman G.

    1994-01-01

    Variations in cell wall chemistry provide vascular plants with the ability to withstand gravitational forces, as well as providing facile mechanisms for correctional responses to various gravitational stimuli, e.g., in reaction wood formation. A principal focus of our current research is to precisely and systematically dissect the essentially unknown mechanism(s) of vascular plant cell wall assembly, particularly with respect to formation of its phenolic constituents, i.e., lignins and suberins, and how gravity impacts upon these processes. Formation of these phenolic polymers is of particular interest, since it appears that elaboration of their biochemical pathways was essential for successful land adaptation. By extrapolation, we are also greatly intrigued as to how the microgravity environment impacts upon 'normal' cell wall assembly mechanisms/metabolism.

  9. Quantitative analysis of energy metabolic pathways in MCF-7 breast cancer cells by selected reaction monitoring assay.

    Science.gov (United States)

    Drabovich, Andrei P; Pavlou, Maria P; Dimitromanolakis, Apostolos; Diamandis, Eleftherios P

    2012-08-01

    To investigate the quantitative response of energy metabolic pathways in human MCF-7 breast cancer cells to hypoxia, glucose deprivation, and estradiol stimulation, we developed a targeted proteomics assay for accurate quantification of protein expression in glycolysis/gluconeogenesis, TCA cycle, and pentose phosphate pathways. Cell growth conditions were selected to roughly mimic the exposure of cells in the cancer tissue to the intermittent hypoxia, glucose deprivation, and hormonal stimulation. Targeted proteomics assay allowed for reproducible quantification of 76 proteins in four different growth conditions after 24 and 48 h of perturbation. Differential expression of a number of control and metabolic pathway proteins in response to the change of growth conditions was found. Elevated expression of the majority of glycolytic enzymes was observed in hypoxia. Cancer cells, as opposed to near-normal MCF-10A cells, exhibited significantly increased expression of key energy metabolic pathway enzymes (FBP1, IDH2, and G6PD) that are known to redirect cellular metabolism and increase carbon flux through the pentose phosphate pathway. Our quantitative proteomic protocol is based on a mass spectrometry-compatible acid-labile detergent and is described in detail. Optimized parameters of a multiplex selected reaction monitoring (SRM) assay for 76 proteins, 134 proteotypic peptides, and 401 transitions are included and can be downloaded and used with any SRM-compatible mass spectrometer. The presented workflow is an integrated tool for hypothesis-driven studies of mammalian cells as well as functional studies of proteins, and can greatly complement experimental methods in systems biology, metabolic engineering, and metabolic transformation of cancer cells.

  10. [Integrated evaluation on system reliability of a space metabolism simulation device].

    Science.gov (United States)

    Du, Zhen-hua; Chen, Jin-dun; Zhao, Yu; Wang, Li-dong

    2003-08-01

    To define the lower confidence limit of the system reliability of the space metabolism simulation device by using the test data of the comprising units in their development phases. A new method for defining the environmental conversion factors of failure times has been given basing on the AMSAA model, and the MTBF point evaluated values and lower confidence limits of the units were defined, at last, the lower confidence limit of the system reliability was obtained using L-M method. The lower confidence limit of the system reliability under confidence level of 0.8 is 0.9281, which is consistent with the result obtained by the classic system reliability evaluation method. Integrated system reliability evaluation using the proposed method can well satisfy the need in engineering.

  11. Exploring the Space of Viable Configurations in a Model of Metabolism-Boundary Co-construction.

    Science.gov (United States)

    Agmon, Eran; Gates, Alexander J; Churavy, Valentin; Beer, Randall D

    2016-01-01

    We introduce a spatial model of concentration dynamics that supports the emergence of spatiotemporal inhomogeneities that engage in metabolism-boundary co-construction. These configurations exhibit disintegration following some perturbations, and self-repair in response to others. We define robustness as a viable configuration's tendency to return to its prior configuration in response to perturbations, and plasticity as a viable configuration's tendency to change to other viable configurations. These properties are demonstrated and quantified in the model, allowing us to map a space of viable configurations and their possible transitions. Combining robustness and plasticity provides a measure of viability as the average expected survival time under ongoing perturbation, and allows us to measure how viability is affected as the configuration undergoes transitions. The framework introduced here is independent of the specific model we used, and is applicable for quantifying robustness, plasticity, and viability in any computational model of artificial life that demonstrates the conditions for viability that we promote.

  12. Using in vitro derived enzymatic reaction rates of metabolism to inform pesticide body burdens in amphibians.

    Science.gov (United States)

    Glinski, Donna A; Henderson, W Matthew; Van Meter, Robin J; Purucker, S Thomas

    2018-02-13

    Understanding how pesticide exposure to non-target species influences toxicity is necessary to accurately assess the ecological risks these compounds pose. To assess the potential metabolic activation of broad use pesticides in amphibians, in vitro and in vivo metabolic rate constants were derived from toad (Anaxyrus terrestris) livers in experiments measuring the depletion of atrazine (ATZ), triadimefon (TDN), and fipronil (FIP) as well as formation of their metabolites. To determine the predictability of these in vitro derived rate constants, Fowler's toads (Anaxyrus fowleri) were exposed to soil contaminated with each of the pesticides at maximum application rate. Desethyl atrazine (DEA) and deisopropyl atrazine (DIA), both metabolites of ATZ, exhibited similar velocities (V max ) while the K M constant for DIA was two times higher than DEA. TDN was metabolized into two diastereomers of triadimenol (TDL A and TDL B), where TDL B had a V max around two times higher than TDL A. The metabolite fipronil sulfone's V max and K M were 150 pmol min -1  mg -1 and 29 μM, respectively. While intrinsic clearance rates for the pesticides ranged from 0.54 to 38.31 mL min -1  kg -1 . Thus, gaining knowledge on differences in metabolism of pesticides within amphibians is important in estimating risk to these non-target species since the inherent toxicity of metabolites can differ from the parent compound. Copyright © 2018 Elsevier B.V. All rights reserved.

  13. Metabolic engineering of free-energy (ATP) conserving reactions in Saccharomyces cerevisiae

    NARCIS (Netherlands)

    De Kok, S.

    2012-01-01

    Metabolic engineering – the improvement of cellular activities by manipulation of enzymatic, transport and regulatory functions of the cell – has enabled the industrial production of a wide variety of biological molecules from renewable resources. Microbial production of fuels and chemicals thereby

  14. Fourier spectral methods for fractional-in-space reaction-diffusion equations

    KAUST Repository

    Bueno-Orovio, Alfonso

    2014-04-01

    © 2014, Springer Science+Business Media Dordrecht. Fractional differential equations are becoming increasingly used as a powerful modelling approach for understanding the many aspects of nonlocality and spatial heterogeneity. However, the numerical approximation of these models is demanding and imposes a number of computational constraints. In this paper, we introduce Fourier spectral methods as an attractive and easy-to-code alternative for the integration of fractional-in-space reaction-diffusion equations described by the fractional Laplacian in bounded rectangular domains of ℝ. The main advantages of the proposed schemes is that they yield a fully diagonal representation of the fractional operator, with increased accuracy and efficiency when compared to low-order counterparts, and a completely straightforward extension to two and three spatial dimensions. Our approach is illustrated by solving several problems of practical interest, including the fractional Allen–Cahn, FitzHugh–Nagumo and Gray–Scott models, together with an analysis of the properties of these systems in terms of the fractional power of the underlying Laplacian operator.

  15. Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules-Search Options and Applications in Food Science.

    Science.gov (United States)

    Minkiewicz, Piotr; Darewicz, Małgorzata; Iwaniak, Anna; Bucholska, Justyna; Starowicz, Piotr; Czyrko, Emilia

    2016-12-06

    Internet databases of small molecules, their enzymatic reactions, and metabolism have emerged as useful tools in food science. Database searching is also introduced as part of chemistry or enzymology courses for food technology students. Such resources support the search for information about single compounds and facilitate the introduction of secondary analyses of large datasets. Information can be retrieved from databases by searching for the compound name or structure, annotating with the help of chemical codes or drawn using molecule editing software. Data mining options may be enhanced by navigating through a network of links and cross-links between databases. Exemplary databases reviewed in this article belong to two classes: tools concerning small molecules (including general and specialized databases annotating food components) and tools annotating enzymes and metabolism. Some problems associated with database application are also discussed. Data summarized in computer databases may be used for calculation of daily intake of bioactive compounds, prediction of metabolism of food components, and their biological activity as well as for prediction of interactions between food component and drugs.

  16. Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules—Search Options and Applications in Food Science

    Directory of Open Access Journals (Sweden)

    Piotr Minkiewicz

    2016-12-01

    Full Text Available Internet databases of small molecules, their enzymatic reactions, and metabolism have emerged as useful tools in food science. Database searching is also introduced as part of chemistry or enzymology courses for food technology students. Such resources support the search for information about single compounds and facilitate the introduction of secondary analyses of large datasets. Information can be retrieved from databases by searching for the compound name or structure, annotating with the help of chemical codes or drawn using molecule editing software. Data mining options may be enhanced by navigating through a network of links and cross-links between databases. Exemplary databases reviewed in this article belong to two classes: tools concerning small molecules (including general and specialized databases annotating food components and tools annotating enzymes and metabolism. Some problems associated with database application are also discussed. Data summarized in computer databases may be used for calculation of daily intake of bioactive compounds, prediction of metabolism of food components, and their biological activity as well as for prediction of interactions between food component and drugs.

  17. Metabolism

    Science.gov (United States)

    ... functions: Anabolism (uh-NAB-uh-liz-um), or constructive metabolism, is all about building and storing. It ... in infants and young children. Hypothyroidism slows body processes and causes fatigue (tiredness), slow heart rate, excessive ...

  18. Metabolism

    Science.gov (United States)

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

  19. Novel approach for evaluation of air change rate in naturally ventilated occupied spaces based on metabolic CO2 time variation

    DEFF Research Database (Denmark)

    Melikov, Arsen Krikor; Markov, Detelin G.

    2014-01-01

    IAQ in many residential buildings relies on non-organized natural ventilation. Accurate evaluation of air change rate (ACR) in this situation is difficult due to the nature of the phenomenon - intermittent infiltration-exfiltration periods of mass exchange between the room air and the outdoor air...... at low rate. This paper describes a new approach for ACR evaluation in naturally ventilated occupied spaces. Actual metabolic CO2 time variation record in an interval of time is compared with the computed variation of metabolic CO2 for the same time interval under reference conditions: sleeping occupants......, air-tight space, constant indoor pressure and temperature. The proposed approach for ACR evaluation can be applied to time intervals with any length, even with varying parameters of both indoor and outdoor air, in which metabolic CO2 generation rate is known and constant. This approach makes possible...

  20. Phosphorus-31 NMR magnetization transfer measurements of metabolic reaction rates in the rat heart and kidney in vivo

    International Nuclear Information System (INIS)

    Koretsky, A.P.

    1984-01-01

    31 P NMR is a unique tool to study bioenergetics in living cells. The application of magnetization transfer techniques to the measurement of steady-state enzyme reaction rates provides a new approach to understanding the regulation of high energy phosphate metabolism. This dissertation is concerned with the measurement of the rates of ATP synthesis in the rat kidney and of the creatine kinase catalyzed reaction in the rat heart in situ. The theoretical considerations of applying magnetization transfer techniques to intact organs are discussed with emphasis on the problems associated with multiple exchange reactions and compartmentation of reactants. Experimental measurements of the ATP synthesis rate were compared to whole kidney oxygen consumption and Na + reabsorption rates to derive ATP/O values. The problems associated with ATP synthesis rate measurements in kidney, e.g. the heterogeneity of the inorganic phosphate resonance, are discussed and experiments to overcome these problems proposed. In heart, the forward rate through creatine kinase was measured to be larger than the reverse rate. To account for the difference in forward and reverse rates a model is proposed based on the compartmentation of a small pool of ATP

  1. MICROSCALE METABOLIC, REDOX AND ABIOTIC REACTIONS IN HANFORD 300 AREA SUBSURFACE SEDIMENTS

    Energy Technology Data Exchange (ETDEWEB)

    Beyenal, Haluk [WSU; McLEan, Jeff [JCVI; Majors, Paul [PNNL; Fredrickson, Jim [PNNL

    2013-11-14

    The Hanford 300 Area is a unique site due to periodic hydrologic influence of river water resulting in changes in groundwater elevation and flow direction. This area is also highly subject to uranium remobilization, the source of which is currently believed to be the region at the base of the vadose zone that is subject to period saturation due to the changes in the water levels in the Columbia River. We found that microbial processes and redox and abiotic reactions which operate at the microscale were critical to understanding factors controlling the macroscopic fate and transport of contaminants in the subsurface. The combined laboratory and field research showed how microscale conditions control uranium mobility and how biotic, abiotic and redox reactions relate to each other. Our findings extended the current knowledge to examine U(VI) reduction and immobilization using natural 300 Area communities as well as selected model organisms on redox-sensitive and redox-insensitive minerals. Using innovative techniques developed specifically to probe biogeochemical processes at the microscale, our research expanded our current understanding of the roles played by mineral surfaces, bacterial competition, and local biotic, abiotic and redox reaction rates on the reduction and immobilization of uranium.

  2. Are Neutral-Neutral Reactions Effective for the Carbon-Chain Growth of Cyanopolyynes and Polyacetylenes in Interstellar Space?

    International Nuclear Information System (INIS)

    Fukuzawa, K.; Osamura, Y.; Schaefer, H.F. III

    1998-01-01

    Ab initio molecular quantum-mechanical methods have been applied to explore the possibility of neutral-neutral reactions leading to the formation of cyanopolyynes and polyacetylenes in interstellar cloud. Potential energy surfaces for the reactions between the CN radical and polyacetylenes indicate that all reactions, C 2n H 2 + CN (n = 1 endash 4), which form HC 2n+1 N molecules, are exothermic and have no energy barriers. We have also examined the possibility of the various product channels from the reactions C 2n H 2 + CN based on the thermochemical relationships. The theoretical results show that none of the product channels is exothermic except the case which produces HC 2n+1 N, with the carbon chain being longer than the reactant polyacetylene. Similar results are obtained for the regioselectivity of the reactions, C 2n H 2 + C 2 H (n = 1 endash 4), to produce hydrocarbons. The only possible products from the latter reactions are shown to be HC 2n+2 H + H under the conditions of interstellar space. These results clearly demonstrate the importance of the neutral-neutral reactions on the carbon-chain growth of cyanopolyynes and polyacetylenes. copyright copyright 1998. The American Astronomical Society

  3. An incomplete assembly with thresholding algorithm for systems of reaction-diffusion equations in three space dimensions IAT for reaction-diffusion systems

    International Nuclear Information System (INIS)

    Moore, Peter K.

    2003-01-01

    Solving systems of reaction-diffusion equations in three space dimensions can be prohibitively expensive both in terms of storage and CPU time. Herein, I present a new incomplete assembly procedure that is designed to reduce storage requirements. Incomplete assembly is analogous to incomplete factorization in that only a fixed number of nonzero entries are stored per row and a drop tolerance is used to discard small values. The algorithm is incorporated in a finite element method-of-lines code and tested on a set of reaction-diffusion systems. The effect of incomplete assembly on CPU time and storage and on the performance of the temporal integrator DASPK, algebraic solver GMRES and preconditioner ILUT is studied

  4. The enzymes of biotin dependent CO2 metabolism: What structures reveal about their reaction mechanisms

    Science.gov (United States)

    Waldrop, Grover L; Holden, Hazel M; Maurice, Martin St

    2012-01-01

    Biotin is the major cofactor involved in carbon dioxide metabolism. Indeed, biotin-dependent enzymes are ubiquitous in nature and are involved in a myriad of metabolic processes including fatty acid synthesis and gluconeogenesis. The cofactor, itself, is composed of a ureido ring, a tetrahydrothiophene ring, and a valeric acid side chain. It is the ureido ring that functions as the CO2 carrier. A complete understanding of biotin-dependent enzymes is critically important for translational research in light of the fact that some of these enzymes serve as targets for anti-obesity agents, antibiotics, and herbicides. Prior to 1990, however, there was a dearth of information regarding the molecular architectures of biotin-dependent enzymes. In recent years there has been an explosion in the number of three-dimensional structures reported for these proteins. Here we review our current understanding of the structures and functions of biotin-dependent enzymes. In addition, we provide a critical analysis of what these structures have and have not revealed about biotin-dependent catalysis. PMID:22969052

  5. Mineral balance, experiment M071. [space flight effects on human mineral metabolism

    Science.gov (United States)

    Whedon, G. D.; Rambaut, P. C.; Smith, M. C., Jr.

    1973-01-01

    Concern for the long term metabolic consequences of weightless flight was the basis for the conception of the Skylab medical experiment to measure mineral balance. Proper interpretation of obtained data that diminished atmospheric pressure has no appreciable effect, or at least no protective effect, on calcium metabolism. The absence of changes in calcium metabolism indicates that a stable baseline observation has been made for Skylab as far as the effects of atmosphere or calcium metabolism are concerned.

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

    Science.gov (United States)

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

    2015-01-01

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

  7. Sodium ascorbate kills Candida albicans in vitro via iron-catalyzed Fenton reaction: importance of oxygenation and metabolism.

    Science.gov (United States)

    Avci, Pinar; Freire, Fernanda; Banvolgyi, Andras; Mylonakis, Eleftherios; Wikonkal, Norbert M; Hamblin, Michael R

    2016-12-01

    Ascorbate can inhibit growth and even decrease viability of various microbial species including Candida albicans. However the optimum conditions and the mechanism of action are unclear. Materials/methodology: Candida albicans shaken for 90 min in a buffered solution of ascorbate (90 mM) gave a 5-log reduction of cell viability, while there was no killing without shaking, in growth media with different carbon sources or at 4°C. Killing was inhibited by the iron chelator 2,2'-bipyridyl. Hydroxyphenyl fluorescein probe showed the intracellular generation of hydroxyl radicals. Ascorbate-mediated killing of C. albicans depends on oxygenation and metabolism, involves iron-catalyzed generation of hydroxyl radicals via Fenton reaction and depletion of intracellular NADH. Ascorbate could serve as a component of a topical antifungal therapy.

  8. Genotype networks, innovation, and robustness in sulfur metabolism

    Science.gov (United States)

    2011-01-01

    Background A metabolism is a complex network of chemical reactions. This network synthesizes multiple small precursor molecules of biomass from chemicals that occur in the environment. The metabolic network of any one organism is encoded by a metabolic genotype, defined as the set of enzyme-coding genes whose products catalyze the network's reactions. Each metabolic genotype has a metabolic phenotype. We define this metabolic phenotype as the spectrum of different sources of a chemical element that a metabolism can use to synthesize biomass. We here focus on the element sulfur. We study properties of the space of all possible metabolic genotypes in sulfur metabolism by analyzing random metabolic genotypes that are viable on different numbers of sulfur sources. Results We show that metabolic genotypes with the same phenotype form large connected genotype networks - networks of metabolic networks - that extend far through metabolic genotype space. How far they reach through this space depends linearly on the number of super-essential reactions. A super-essential reaction is an essential reaction that occurs in all networks viable in a given environment. Metabolic networks can differ in how robust their phenotype is to the removal of individual reactions. We find that this robustness depends on metabolic network size, and on other variables, such as the size of minimal metabolic networks whose reactions are all essential in a specific environment. We show that different neighborhoods of any genotype network harbor very different novel phenotypes, metabolic innovations that can sustain life on novel sulfur sources. We also analyze the ability of evolving populations of metabolic networks to explore novel metabolic phenotypes. This ability is facilitated by the existence of genotype networks, because different neighborhoods of these networks contain very different novel phenotypes. Conclusions We show that the space of metabolic genotypes involved in sulfur metabolism

  9. ReacKnock: identifying reaction deletion strategies for microbial strain optimization based on genome-scale metabolic network.

    Directory of Open Access Journals (Sweden)

    Zixiang Xu

    Full Text Available Gene knockout has been used as a common strategy to improve microbial strains for producing chemicals. Several algorithms are available to predict the target reactions to be deleted. Most of them apply mixed integer bi-level linear programming (MIBLP based on metabolic networks, and use duality theory to transform bi-level optimization problem of large-scale MIBLP to single-level programming. However, the validity of the transformation was not proved. Solution of MIBLP depends on the structure of inner problem. If the inner problem is continuous, Karush-Kuhn-Tucker (KKT method can be used to reformulate the MIBLP to a single-level one. We adopt KKT technique in our algorithm ReacKnock to attack the intractable problem of the solution of MIBLP, demonstrated with the genome-scale metabolic network model of E. coli for producing various chemicals such as succinate, ethanol, threonine and etc. Compared to the previous methods, our algorithm is fast, stable and reliable to find the optimal solutions for all the chemical products tested, and able to provide all the alternative deletion strategies which lead to the same industrial objective.

  10. Current status and future prospect of space and time reversal symmetry violation on low energy neutron reactions

    International Nuclear Information System (INIS)

    Masuda, Yasuhiro

    1993-01-01

    In this report, the papers on symmetry violation under space reflection and time reversal and neutron spin, neutron spin rotation and P-violation, parity nonconservation in neutron capture reaction, some advantage of the search for CP-violation in neutron scattering, dynamic polarization of 139 La target, alexandrite laser for optical pumping, polarized 3 He system for T- and P-violation neutron experiments, control of neutron spin in T-violation neutron experiment, symmetry regarding time and space and angular distribution and angular correlation of radiation and particle beams, T-violation due to low temperature nuclear polarization and axion exploration using nuclear transition are collected. (K.I.)

  11. Metallographic Preparation of Space Shuttle Reaction Control System Thruster Electron Beam Welds for Electron Backscatter Diffraction

    Science.gov (United States)

    Martinez, James

    2011-01-01

    A Space Shuttle Reaction Control System (RCS) thruster failed during a firing test at the NASA White Sands Test Facility (WSTF), Las Cruces, New Mexico. The firing test was being conducted to investigate a previous electrical malfunction. A number of cracks were found associated with the fuel closure plate/injector assembly (Fig 1). The firing test failure generated a flight constraint to the launch of STS-133. A team comprised of several NASA centers and other research institutes was assembled to investigate and determine the root cause of the failure. The JSC Materials Evaluation Laboratory was asked to compare and characterize the outboard circumferential electron beam (EB) weld between the fuel closure plate (Titanium 6Al-4V) and the injector (Niobium C-103 alloy) of four different RCS thrusters, including the failed RCS thruster. Several metallographic challenges in grinding/polishing, and particularly in etching were encountered because of the differences in hardness, ductility, and chemical resistance between the two alloys and the bimetallic weld. Segments from each thruster were sectioned from the outboard weld. The segments were hot-compression mounted using a conductive, carbon-filled epoxy. A grinding/polishing procedure for titanium alloys was used [1]. This procedure worked well on the titanium; but a thin, disturbed layer was visible on the niobium surface by means of polarized light. Once polished, each sample was micrographed using bright field, differential interference contrast optical microscopy, and scanning electron microscopy (SEM) using a backscatter electron (BSE) detector. No typical weld anomalies were observed in any of the cross sections. However, areas of large atomic contrast were clearly visible in the weld nugget, particularly along fusion line interfaces between the titanium and the niobium. This prompted the need to better understand the chemistry and microstructure of the weld (Fig 2). Energy Dispersive X-Ray Spectroscopy (EDS

  12. Evidence of cross-cutting and redox reaction in Khatyrka meteorite reveals metallic-Al minerals formed in outer space.

    Science.gov (United States)

    Lin, Chaney; Hollister, Lincoln S; MacPherson, Glenn J; Bindi, Luca; Ma, Chi; Andronicos, Christopher L; Steinhardt, Paul J

    2017-05-09

    We report on a fragment of the quasicrystal-bearing CV3 carbonaceous chondrite Khatyrka recovered from fine-grained, clay-rich sediments in the Koryak Mountains, Chukotka (Russia). We show higher melting-point silicate glass cross-cutting lower melting-point Al-Cu-Fe alloys, as well as unambiguous evidence of a reduction-oxidation reaction history between Al-Cu-Fe alloys and silicate melt. The redox reactions involve reduction of FeO and SiO 2 to Fe and Fe-Si metal, and oxidation of metallic Al to Al 2 O 3 , occurring where silicate melt was in contact with Al-Cu-Fe alloys. In the reaction zone, there are metallic Fe and Fe-Si beads, aluminous spinel rinds on the Al-Cu-Fe alloys, and Al 2 O 3 enrichment in the silicate melt surrounding the alloys. From this and other evidence, we demonstrate that Khatyrka must have experienced at least two distinct events: first, an event as early as 4.564 Ga in which the first Al-Cu-Fe alloys formed; and, second, a more recent impact-induced shock in space that led to transformations of and reactions between the alloys and the meteorite matrix. The new evidence firmly establishes that the Al-Cu-Fe alloys (including quasicrystals) formed in outer space in a complex, multi-stage process.

  13. MbT-Tool: An open-access tool based on Thermodynamic Electron Equivalents Model to obtain microbial-metabolic reactions to be used in biotechnological process

    Directory of Open Access Journals (Sweden)

    Pablo Araujo Granda

    2016-01-01

    Full Text Available Modelling cellular metabolism is a strategic factor in investigating microbial behaviour and interactions, especially for bio-technological processes. A key factor for modelling microbial activity is the calculation of nutrient amounts and products generated as a result of the microbial metabolism. Representing metabolic pathways through balanced reactions is a complex and time-consuming task for biologists, ecologists, modellers and engineers. A new computational tool to represent microbial pathways through microbial metabolic reactions (MMRs using the approach of the Thermodynamic Electron Equivalents Model has been designed and implemented in the open-access framework NetLogo. This computational tool, called MbT-Tool (Metabolism based on Thermodynamics can write MMRs for different microbial functional groups, such as aerobic heterotrophs, nitrifiers, denitrifiers, methanogens, sulphate reducers, sulphide oxidizers and fermenters. The MbT-Tool's code contains eighteen organic and twenty inorganic reduction-half-reactions, four N-sources (NH4+, NO3−, NO2−, N2 to biomass synthesis and twenty-four microbial empirical formulas, one of which can be determined by the user (CnHaObNc. MbT-Tool is an open-source program capable of writing MMRs based on thermodynamic concepts, which are applicable in a wide range of academic research interested in designing, optimizing and modelling microbial activity without any extensive chemical, microbiological and programing experience.

  14. Enzyme oscillation can enhance the thermodynamic efficiency of cellular metabolism: consequence of anti-phase coupling between reaction flux and affinity

    Science.gov (United States)

    Himeoka, Yusuke; Kaneko, Kunihiko

    2016-04-01

    Cells generally convert nutrient resources to products via energy transduction. Accordingly, the thermodynamic efficiency of this conversion process is one of the most essential characteristics of living organisms. However, although these processes occur under conditions of dynamic metabolism, most studies of cellular thermodynamic efficiency have been restricted to examining steady states; thus, the relevance of dynamics to this efficiency has not yet been elucidated. Here, we develop a simple model of metabolic reactions with anabolism-catabolism coupling catalyzed by enzymes. Through application of external oscillation in the enzyme abundances, the thermodynamic efficiency of metabolism was found to be improved. This result is in strong contrast with that observed in the oscillatory input, in which the efficiency always decreased with oscillation. This improvement was effectively achieved by separating the anabolic and catabolic reactions, which tend to disequilibrate each other, and taking advantage of the temporal oscillations so that each of the antagonistic reactions could progress near equilibrium. In this case, anti-phase oscillation between the reaction flux and chemical affinity through oscillation of enzyme abundances is essential. This improvement was also confirmed in a model capable of generating autonomous oscillations in enzyme abundances. Finally, the possible relevance of the improvement in thermodynamic efficiency is discussed with respect to the potential for manipulation of metabolic oscillations in microorganisms.

  15. Studies on the effect of vanillin (food additive on some metabolic reactions of the experimental animals

    Directory of Open Access Journals (Sweden)

    El-Massry, R. A.

    1991-12-01

    Full Text Available Vanillin (4-hydroxy-3-methoxybenzaldehyde was administrated to hypercholesterolemic albino rats at low and high doses (1.0 and 2.0%, respectively for nine weeks period. Lipid pattern, as well as liver and kidneys functions were determined in normal, hypercholesterolemic and hypercholesterolemic rats administrated vanillin. Hypercholesterolemia was characterized by significant increase in the average levels of total lipids, total cholesterol and triglycerides and a significant decrease in phospholipids content. Also, liver function (S.GOT, S.GPT, alkaline and acid phosphatase as well as kidneys function were elevated compared to control group. Administration of vanillin significantly reduced liver and kidneys total lipids. Spleen and heart followed nearly the same trend but with moderate effect, while brain was not affected. Liver, kidneys, spleen and heart total cholesterol was significantly reduced while brain total cholesterol was not affected. Triglycerides were significantly decreased in liver and spleen, while that of kidneys and brain was not affected. Also, there was a significant decrease in the high activity of S.GOT, S.GPT, alkaline and acid phosphatase and the values were nearly attained to the initial level. Administration of vanillin exertes potent anabolic effects for protein metabolism as shown from the results of uric acid and creatinine.

    Se administró vanillina (4-hidroxi-3-metoxibenzaldehído a ratas albino hipercolesterolémicas en dosis bajas y altas (1,0 y 2,0% respectivamente por un período de nueve semanas. La forma lipídica así como las funciones hepáticas y renales se determinaron en ratas normales, hipercolesterolémicas e hipercolesterolémicas a las que se les administró vanillina. La hipercolesterolemia se caracterizó por un aumento significativo en los niveles medios de lípidos totales, colesterol total y triglicéridos, y una disminución significativa en el contenido de fosfolípidos. También, la

  16. Reaction Automata

    OpenAIRE

    Okubo, Fumiya; Kobayashi, Satoshi; Yokomori, Takashi

    2011-01-01

    Reaction systems are a formal model that has been introduced to investigate the interactive behaviors of biochemical reactions. Based on the formal framework of reaction systems, we propose new computing models called reaction automata that feature (string) language acceptors with multiset manipulation as a computing mechanism, and show that reaction automata are computationally Turing universal. Further, some subclasses of reaction automata with space complexity are investigated and their la...

  17. Diffusional screening in treelike spaces: An exactly solvable diffusion-reaction model

    Science.gov (United States)

    Mayo, Michael; Gheorghiu, Stefan; Pfeifer, Peter

    2012-01-01

    A renormalization approach is used to derive an analytic formula for the total current crossing the reactive surface of a Cayley tree of cylindrical tubes under a Helmholtz-type approximation to the full diffusion-reaction problem. We provide analytic conditions for the emergence of a plateau in the current—a region of maximum insensitivity of the current to variations in either the reaction rate (membrane permeability) or the diffusivity. The occurrence of such a plateau is associated with a partial screening regime wherein most of the active surface is screened to incoming diffusing particles. Large trees trade efficiency for fault tolerance, a valuable feature which may provide robustness to mammalian respiratory systems and tolerance to catalytic poisoning in chemical reactors.

  18. Systematic Search for Chemical Reactions in Gas Phase Contributing to Methanol Formation in Interstellar Space.

    Science.gov (United States)

    Gamez-Garcia, Victoria G; Galano, Annia

    2017-10-05

    A massive search for chemical routes leading to methanol formation in gas phase has been conducted using computational chemistry, at the CBS-QB3 level of theory. The calculations were performed at five different temperatures (100, 80, 50, 20, and 10 K) and at three pressures (0.1, 0.01, and 0.001 atm) for each temperature. The search was focused on identifying reactions with the necessary features to be viable in the interstellar medium (ISM). A searching strategy was applied to that purpose, which allowed to reduce an initial set of 678 possible reactions to a subset of 11 chemical routes that are recommended, for the first time, as potential candidates for contributing to methanol formation in the gas phase of the ISM. They are all barrier-less, and thus they are expected to take place at collision rates. Hopefully, including these reactions in the currently available models, for the gas-phase methanol formation in the ISM, would help improving the predicted fractional abundance of this molecule in dark clouds. Further investigations, especially those dealing with grain chemistry and electronic excited states, would be crucial to get a complete picture of the methanol formation in the ISM.

  19. Preliminary study of the effects of a reversible chemical reaction on gas bubble dissolution. [for space glass refining

    Science.gov (United States)

    Weinberg, M. C.

    1982-01-01

    A preliminary investigation is carried out of the effects of a reversible chemical reaction on the dissolution of an isolated, stationary gas bubble in a glass melt. The exact governing equations for the model system are formulated and analyzed. The approximate quasi-steady-state version of these equations is solved analytically, and a calculation is made of bubble dissolution rates. The results are then compared with numerical solutions obtained from the finite difference form of the exact governing equations. It is pointed out that in the microgravity condition of space, the buoyant rise of a gas bubble in a glass melt will be negligible on the time scale of most experiments. For this reason, a determination of the behavior of a stationary gas bubble in a melt is relevant for an understanding of glass refining in space.

  20. Acorn: A grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface

    Directory of Open Access Journals (Sweden)

    Bushell Michael E

    2011-05-01

    Full Text Available Abstract Background Constraint-based approaches facilitate the prediction of cellular metabolic capabilities, based, in turn on predictions of the repertoire of enzymes encoded in the genome. Recently, genome annotations have been used to reconstruct genome scale metabolic reaction networks for numerous species, including Homo sapiens, which allow simulations that provide valuable insights into topics, including predictions of gene essentiality of pathogens, interpretation of genetic polymorphism in metabolic disease syndromes and suggestions for novel approaches to microbial metabolic engineering. These constraint-based simulations are being integrated with the functional genomics portals, an activity that requires efficient implementation of the constraint-based simulations in the web-based environment. Results Here, we present Acorn, an open source (GNU GPL grid computing system for constraint-based simulations of genome scale metabolic reaction networks within an interactive web environment. The grid-based architecture allows efficient execution of computationally intensive, iterative protocols such as Flux Variability Analysis, which can be readily scaled up as the numbers of models (and users increase. The web interface uses AJAX, which facilitates efficient model browsing and other search functions, and intuitive implementation of appropriate simulation conditions. Research groups can install Acorn locally and create user accounts. Users can also import models in the familiar SBML format and link reaction formulas to major functional genomics portals of choice. Selected models and simulation results can be shared between different users and made publically available. Users can construct pathway map layouts and import them into the server using a desktop editor integrated within the system. Pathway maps are then used to visualise numerical results within the web environment. To illustrate these features we have deployed Acorn and created a

  1. Metabolism in time and space – exploring the frontier of developmental biology

    Czech Academy of Sciences Publication Activity Database

    Krejčí, Alena; Tennessen, J. M.

    2017-01-01

    Roč. 144, č. 18 (2017), s. 3193-3198 ISSN 0950-1991 Institutional support: RVO:60077344 Keywords : metabolism * mitochondria * aerobic glycolysis Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Genetics and heredity (medical genetics to be 3) Impact factor: 5.843, year: 2016 http://dev.biologists.org/content/144/18/3193

  2. Heritable variation in reaction norms of metabolism and activity across temperatures in a wild-derived population of white-footed mice (Peromyscus leucopus).

    Science.gov (United States)

    Kaseloo, Paul A; Crowell, Madelyn G; Heideman, Paul D

    2014-05-01

    Heritable variation in metabolic traits is likely to affect fitness. In this study, white-footed mice from wild-derived photoresponsive [R, infertile in short day length (SD)] and non-photoresponsive (NR, fertile in SD) selection lines were maintained under short-day (SD 8Light:16Dark), sub-thermoneutral conditions (22 or 12 °C). Mice had significantly higher levels of food intake and resting metabolic rates (RMR) at low temperature. RMR differed significantly between lines (greater in NR mice). In contrast to previous work under thermoneutral conditions, there was no significant difference in overall activity or average daily metabolic rates (ADMR) of mice from the two lines. Reduced activity may reflect behavioral changes under cooler conditions (e.g., nest building) reducing the overall energetic cost of fertility (for NR mice). There was no significant difference in maximal rate of oxygen consumption ([Formula: see text]) between lines. R mice had significantly greater brown adipose tissue and white abdominal fat mass due to both line and temperature. Reaction norms for intake, resting metabolism (RMR/BMR) and level of activity from current (12 and 22 °C) and previously published data (28 °C) demonstrate independent effects of genetics (line) and environment (temperature) for resting metabolism, but a clear interaction between these for activity. The results suggest that fertility under winter conditions imposes metabolic costs that are related to the level of reproductive development. Under the coldest conditions tested, however, mice that remained fertile in SD reduced activity, ADMR and food requirements, decreasing the differential between selection lines. Heritable variation in reaction norms suggests a genetic by environment effect that could be subject to selection.

  3. Drug Metabolism

    Indian Academy of Sciences (India)

    IAS Admin

    Chemistry of Drug Metabolism. Drug metabolism is a chemical process, where enzymes play a crucial role in the conversion of one chemical species to another. The major family of enzymes associated with these metabolic reactions is the cytochrome P450 family. The structural features and functional activity of these ...

  4. The Effects of Space Flight on Some Liver Enzymes Concerned with Carbohydrate and Lipid Metabolism in Rats

    Science.gov (United States)

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

    1978-01-01

    The activities of about 30 enzymes concerned with carbohydrate and lipid metabolism and the levels of glycogen and of individual fatty acids were measured in livers of rats ex- posed to prolonged space flight (18.5 days) aboard COSMOS 986 Biosatellite. When flight stationary, (FS) and flight centrifuged (FC) rats were compared at recovery (R(sub 0)), decrceases in the activities of glycogen phosphorylase, alpha glycerphosphate, acyl transferase, diglyceride acyl transferase, acconitase and Epsilon-phosphogluconate dehydrogenase were noted in the weightless group (FS). The significance of these findings was strengthened since all activities, showing alterations at R(sub 0), returned to normal 25 days post-flight. Differences were also seen in levels of two liver constituents. When glycogen and total fatty acids of the two groups of flight animals were determined, differences that could be attributed to reduced gravity were observed, the FS group at R(sub 0) contained, on the average, more than twice the amount of glycogen than did controls ad a remarkable shift in the ratio of palmitate to palmitoleate were noted. These metabolic alterations appear to be unique to the weightless condition. Our data justify the conclusion that centrifugation during space flight is equivalent to terrestrial gravity.

  5. Dietary and Urinary Sulfur can Predict Changes in Bone Metabolism During Space Flight

    Science.gov (United States)

    Zwart, Sara R.; Heer, Martina; Shackelford, Linda; Smith, Scott M.

    2015-01-01

    Mitigating space flight-induced bone loss is critical for space exploration, and diet can play a major role in this effort. Previous ground-based studies provide evidence that dietary composition can influence bone resorption during bed rest. In this study we examined the role of dietary intake patterns as one factor that can influence bone mineral loss in astronauts during space flight. Crew members were asked to consume, for 4 days at a time, prescribed menus with either a low (0.3-0.6 g/mEq) or high (1.0-1.3 g/mEq) ratio of animal protein to potassium (APro:K). Menus were developed for each crewmember, and were designed to meet both crew preferences and study constraints. Intakes of energy, total protein, calcium, and sodium were held relatively constant between the two diets. The order of the menus was randomized, and crews completed each set (low and high) once before and twice during space flight, for a total of 6 controlled diet sessions. One inflight session and three postflight sessions (R+30, R+180, R+365) monitored typical dietary intake. As of this writing, data are available from 14 crew members. The final three subjects' inflight samples are awaiting return from the International Space Station via Space-X. On the last day of each of the 4-d controlled diet sessions, 24-h urine samples were collected, along with a fasting blood sample on the morning of the 5th day. Preliminary analyses show that urinary excretion of sulfate (normalized to lean body mass) is a significant predictor of urinary n-telopeptide (NTX). Dietary sulfate (normalized to lean body mass) is also a significant predictor of urinary NTX. The results from this study, will be important to better understand diet and bone interrelationships during space flight as well as on Earth. This study was funded by the Human Health Countermeasures Element of the NASA Human Research Program.

  6. Facile charge-displacement at silicon gives spaced-out reaction.

    Science.gov (United States)

    Ebrahimi, Maryam; Huang, Kai; Lu, Xuekun; McNab, Iain R; Polanyi, John C; Waqar, Zafar; Yang, Jody; Lin, Haiping; Hofer, Werner A

    2011-10-19

    Adsorbates on metals, but not previously on semiconductors, have been observed to display long-range repulsive interactions. On metals, due to efficient dissipation, the repulsions are weak, typically on the order of 5 meV at 10 Å. On the 7×7 reconstruction of the Si(111) surface, charge transport through the surface has been demonstrated by others using charge injection by STM tips. Here we show that for both physisorbed brominated molecules, and for chemisorbed Br-atoms, induced charge-transfer in the Si(111)-7×7 surface can lead to a strong repulsive interaction between adsorbates, calculated as 200 meV at 13.4 Å. This large repulsive interaction must be channeled through the surface since it causes widely spaced "one-per-corner-hole" patterns of physisorption (three cases--directly observed here) and subsequent chemisorption (four cases observed). The patterns were observed by ultrahigh vacuum scanning tunneling microscopy for four different brominated hydrocarbon adsorbates; 1,2-dibromoethane, 1-bromopropane, 1-bromopentane, and bromobenzene, deposited individually on the surface. In every case, adsorbates were overwhelmingly more likely to be found singly than multiply adjacent to a corner-hole, constituting a distinctive pattern having a probability p = 7 × 10(-5) compared to a random distribution.

  7. Reaction torque control of redundant space robotic systems for orbital maintenance and simulated microgravity tests

    Science.gov (United States)

    Cocuzza, Silvio; Pretto, Isacco; Debei, Stefano

    2010-08-01

    This paper presents the theoretical formulation and the experimental validation of a novel solution for the inverse kinematics of redundant space robotic systems aimed at locally minimizing the torque transferred to the spacecraft due to the robotic arm movement. The differential kinematics is formulated at the acceleration level and an additional constraint is imposed in order to locally minimize the torque transferred to the spacecraft center of mass. This problem can be expressed as a constrained linear least squares problem and a closed-form solution is obtained. An extension of this method is presented in order to take into account the physical limits of the manipulator, by limiting the joint accelerations under acceptable values. In this case the problem can be expressed as a constrained linear least squares problem with both equality and inequality constraints. The proposed solution has been experimentally tested using a 3D free-flying robot previously tested in an ESA Parabolic Flight Campaign. In this test campaign the 3D robot has been converted in a 2D robot taking advantage of its modular structure, and it has been suspended by means of air-bearings on a granite plane. In this way it is possible to perform simulated microgravity tests without time constraints. The base of the robot is fixed on ground by means of a custom design dynamometer, which measures the torque transferred to ground to be minimized. The experimental results validated the proposed solutions and confirmed their good performance.

  8. Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism

    DEFF Research Database (Denmark)

    Ryu, Jae Yong; Kim, Hyun Uk; Lee, Sang Yup

    2017-01-01

    Alternative splicing plays important roles in generating different transcripts from one gene, and consequently various protein isoforms. However, there has been no systematic approach that facilitates characterizing functional roles of protein isoforms in the context of the entire human metabolism....... Here, we present a systematic framework for the generation of gene-transcript-proteinreaction associations (GeTPRA) in the human metabolism. The framework in this study generated 11,415 GeTPRA corresponding to 1,106 metabolic genes for both principal and nonprincipal transcripts (PTs and NPTs......) of metabolic genes. The framework further evaluates GeTPRA, using a human genome-scale metabolic model (GEM) that is biochemically consistent and transcript-level data compatible, and subsequently updates the human GEM. A generic human GEM, Recon 2M. 1, was developed for this purpose, and subsequently updated...

  9. Urinary Acid Excretion Can Predict Changes in Bone Metabolism During Space Flight

    Science.gov (United States)

    Zwart, Sara R.; Smith, Scott M.

    2011-01-01

    Mitigating space flight-induced bone loss is critical for space exploration, and a dietary countermeasure would be ideal. We present here preliminary data from a study where we examined the role of dietary intake patterns as one factor that can influence bone mineral loss in astronauts during space flight. Crewmembers (n=5) were asked to consume a prescribed diet with either a low (0.3-0.6) or high (1.0-1.3) ratio of animal protein to potassium (APro:K) before and during space flight for 4-d periods. Diets were controlled for energy, total protein, calcium, and sodium. 24-h urine samples were collected on the last day of each of the 4-d controlled diet sessions. 24-h urinary acid excretion, which was predicted by dietary potential renal acid load, was correlated with urinary n-telopeptide (NTX, Pearson R = 0.99 and 0.80 for the high and low APro:K sessions, respectively, p<0.001). The amount of protein when expressed as the percentage of total energy (but not as total grams) was also correlated with urinary NTX (R = 0.66, p<0.01). These results, from healthy individuals in a unique environment, will be important to better understand diet and bone interrelationships during space flight as well as on Earth. The study was funded by the NASA Human Research Program.

  10. Condensed Matter Cluster Reactions in LENR Power Cells for a Radical New Type of Space Power Source

    Science.gov (United States)

    Yang, Xiaoling; Miley, George H.; Hora, Heinz

    2009-03-01

    This paper reviews previous theoretical and experimental study on the possibility of nuclear events in multilayer thin film electrodes (Lipson et al., 2004 and 2005; Miley et al., 2007), including the correlation between excess heat and transmutations (Miley and Shrestha, 2003) and the cluster theory that predicts it. As a result of this added understanding of cluster reactions, a new class of electrodes is under development at the University of Illinois. These electrodes are designed to enhance cluster formation and subsequent reactions. Two approaches are under development. The first employs improved loading-unloading techniques, intending to obtain a higher volumetric density of sites favoring cluster formation. The second is designed to create nanostructures on the electrode where the cluster state is formed by electroless deposition of palladium on nickel micro structures. Power units employing these electrodes should offer unique advantages for space applications. This is a fundamental new nuclear energy source that is environmentally compatible with a minimum of radiation involvement, high specific power, very long lifetime, and scalable from micro power to kilowatts.

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

    Science.gov (United States)

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

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

  12. Apparent Bicarbonate Space in Children

    OpenAIRE

    Repetto, Horacio A.; Penna, Roberto

    2006-01-01

    The amount needed to change the concentration of a solute requires the knowledge of its volume of distribution in the solution. Electrolytes that do not participate in active metabolic reactions have a fixed volume of distribution that corresponds to the volume of water in which they solubilize. Bicarbonate infusion is used to correct hyperchloremic metabolic acidosis. Its volume of distribution (bicarbonate space) changes with its participation in the blood buffer systems. In other words, it...

  13. An Updated Look at the Pro K Experiment: Urinary Acid Excretion Can Predict Changes in Bone Metabolism During Space Flight

    Science.gov (United States)

    Zwart, Sara R.; Heer, Martina; Shackelford, Linda; Smith, Scott M.

    2015-01-01

    Mitigating space flight-induced bone loss is critical for space exploration, and diet can play a major role in this effort (1). Previous ground-based studies provide evidence that dietary composition can influence bone resorption during bed rest (2). In this study we examined the role of dietary intake patterns as one factor that can influence bone mineral loss in astronauts during space flight. Crew members were asked to consume, for 4 days at a time, prescribed menus with either a low (0.3-0.6 g/mEq) or high (1.0-1.3 g/mEq) ratio of animal protein to potassium (APro:K). Menus were developed for each crewmember, and were designed to meet both crew preferences and study constraints. Intakes of energy, total protein, calcium, and sodium were held relatively constant between the two diets. The order of the menus was randomized, and crews completed each set (low and high) once before and twice during space flight, for a total of 6 controlled diet sessions. One inflight session and three postflight sessions (R+30, R+180, R+365) monitored typical dietary intake. As of this writing, data are available from 14 crew members. Two subject's samples are awaiting return from ISS via Space-X, and the final subject has one more collection session planned in November 2014. On the last day of each of the 4-d controlled diet sessions, 24-h urine samples were collected, along with a fasting blood sample on the morning of the 5th day. Preliminary analyses will show the relationships between diet and flight on markers of bone metabolism. The results from this study, which represent healthy individuals in a unique environment, will be important to better understand diet and bone interrelationships during space flight as well as on Earth. These data will be important as nutritional requirements and food systems are developed for future exploration-class missions. This study was funded by the Human Health Countermeasures Element of NASA Human Research Program.

  14. Development of Eddy Current Technique for the Detection of Stress Corrosion Cracking in Space Shuttle Primary Reaction Control Thrusters

    Science.gov (United States)

    Wincheski, Buzz; Simpson, John; Koshti, Ajay

    2006-01-01

    A recent identification of stress corrosion cracking in the Space Shuttle Primary Reaction Control System (PRCS) thrusters triggered an extensive nondestructive evaluation effort to develop techniques capable of identifying such damage on installed shuttle hardware. As a part of this effort, specially designed eddy current probes inserted into the acoustic cavity were explored for the detection of such flaws and for evaluation of the remaining material between the crack tip and acoustic cavity. The technique utilizes two orthogonal eddy current probes which are scanned under stepper motor control in the acoustic cavity to identify cracks hidden with as much as 0.060 remaining wall thickness to the cavity. As crack growth rates in this area have been determined to be very slow, such an inspection provides a large safety margin for continued operation of the critical shuttle hardware. Testing has been performed on thruster components with both actual and fabricated defects. This paper will review the design and performance of the developed eddy current inspection system. Detection of flaws as a function of remaining wall thickness will be presented along with the proposed system configuration for depot level or on-vehicle inspection capabilities.

  15. Risk of Visual Impairment and Intracranial Hypertension After Space Flight: Evaluation of the Role of Polymorphism of Enzymes Involved in One-Carbon Metabolism

    Science.gov (United States)

    Smith, S. M.; Gregory, J. F.; Zeisel, G. H.; Gibson, C. R.; Mader, T. H.; Kinchen, J.; Ueland, P.; Ploutz-Snyder, R.; Heer, M.; Zwart, S. R.

    2016-01-01

    Data from the Nutritional Status Assessment protocol provided biochemical evidence that the one-carbon metabolic pathway may be altered in individuals experiencing vision-related issues during and after space flight (1, 2). Briefly, serum concentrations of homocysteine, cystathionine, 2-methylcitric acid, and methylmalonic acid were significantly (Pvisual disturbances (3). Block regression showed that B-vitamin status at landing and genetics were significant predictors for many of the ophthalmic outcomes studied (3). In conclusion, we document an association between MTRR 66 and SHMT1 1420 polymorphisms and space flightinduced vision changes. These data document that individuals with an altered 1-carbon metabolic pathway may be predisposed to anatomic and/or physiologic changes that render them susceptible to ophthalmic damage during space flight.

  16. Prenatal dietary load of Maillard reaction products combined with postnatal Coca-Cola drinking affects metabolic status of female Wistar rats.

    Science.gov (United States)

    Gurecká, Radana; Koborová, Ivana; Janšáková, Katarína; Tábi, Tamás; Szökő, Éva; Somoza, Veronika; Šebeková, Katarína; Celec, Peter

    2015-04-01

    To assess the impact of prenatal exposure to Maillard reaction products (MRPs) -rich diet and postnatal Coca-Cola consumption on metabolic status of female rats. Diet rich in MRPs and consumption of saccharose/fructose sweetened soft drinks is presumed to impose increased risk of development of cardiometabolic afflictions, such as obesity or insulin resistance. At the first day of pregnancy, 9 female Wistar rats were randomized into two groups, pair-fed either with standard rat chow (MRP-) or MRPs-rich diet (MRP+). Offspring from each group of mothers was divided into two groups and given either water (Cola-) or Coca-Cola (Cola+) for drinking ad libitum for 18 days. Oral glucose tolerance test was performed, and circulating markers of inflammation, oxidative stress, glucose and lipid metabolism were assessed. MRP+ groups had higher weight gain, significantly so in the MRP+/Cola- vs MRP-/Cola-. Both prenatal and postnatal intervention increased carboxymethyllysine levels and semicarbazide-sensitive amine oxidase activity, both significantly higher in MRP+/Cola + than in MRP-/Cola-. Total antioxidant capacity was lower in MRP+ groups, with significant decrease in MRP+/Cola + vs MRP-/Cola+. Rats drinking Coca-Cola had higher insulin, homeostatic model assessment of insulin resistance, heart rate, advanced oxidation of protein products, triacylglycerols, and oxidative stress markers measured as thiobarbituric acid reactive substances compared to rats drinking water, with no visible effect of MRPs-rich diet. Metabolic status of rats was affected both by prenatal and postnatal dietary intervention. Our results suggest that combined effect of prenatal MRPs load and postnatal Coca-Cola drinking may play a role in development of metabolic disorders in later life.

  17. Efficient numerical simulation of non-integer-order space-fractional reaction-diffusion equation via the Riemann-Liouville operator

    Science.gov (United States)

    Owolabi, Kolade M.

    2018-03-01

    In this work, we are concerned with the solution of non-integer space-fractional reaction-diffusion equations with the Riemann-Liouville space-fractional derivative in high dimensions. We approximate the Riemann-Liouville derivative with the Fourier transform method and advance the resulting system in time with any time-stepping solver. In the numerical experiments, we expect the travelling wave to arise from the given initial condition on the computational domain (-∞, ∞), which we terminate in the numerical experiments with a large but truncated value of L. It is necessary to choose L large enough to allow the waves to have enough space to distribute. Experimental results in high dimensions on the space-fractional reaction-diffusion models with applications to biological models (Fisher and Allen-Cahn equations) are considered. Simulation results reveal that fractional reaction-diffusion equations can give rise to a range of physical phenomena when compared to non-integer-order cases. As a result, most meaningful and practical situations are found to be modelled with the concept of fractional calculus.

  18. A method to build an analytic model of the 10B(n,alpha)7Li reaction rate space distribution for boron neutron capture therapy (BNCT).

    Science.gov (United States)

    Morand, Josselin; Moss, Raymond; Hachem, Sabet; Sauerwein, Wolfgang

    2009-07-01

    This work provides the basis of a methodology to build a deterministic model for the spatial distribution of the (10)B(n,alpha)(7)Li reaction rate in boron neutron capture therapy (BNCT), as a function of space variables, boron concentration and beam incidence angle in homogeneous isotropic environments but also in different heterogeneous environments. Building the analytic function in a simple homogeneous environment with numerical methods leads to a mathematical formulation of the (10)B(n,alpha)(7)Li reactions rate.

  19. The Non-Linear Child: Ontogeny, Isoniazid Concentration, and NAT2 Genotype Modulate Enzyme Reaction Kinetics and Metabolism.

    Science.gov (United States)

    Rogers, Zoe; Hiruy, Hiwot; Pasipanodya, Jotam G; Mbowane, Chris; Adamson, John; Ngotho, Lihle; Karim, Farina; Jeena, Prakash; Bishai, William; Gumbo, Tawanda

    2016-09-01

    N-acetyltransferase 2 (NAT2) catalyzes the acetylation of isoniazid to N-acetylisoniazid. NAT2 polymorphism explains 88% of isoniazid clearance variability in adults. We examined the effects of clinical and genetic factors on Michaelis-Menten reaction kinetic constants of maximum velocity (V max ) and affinity (K m ) in children 0-10years old. We measured the rates of isoniazid elimination and N-acetylisoniazid production in the blood of 30 children. Since maturation effects could be non-linear, we utilized a pharmacometric approach and the artificial intelligence method, multivariate adaptive regression splines (MARS), to identify factors predicting NAT2 V max and K m by examining clinical, genetic, and laboratory factors in toto. Isoniazid concentration predicted both V max and K m and superseded the contribution of NAT2 genotype. Age non-linearly modified the NAT2 genotype contribution until maturation at ≥5.3years. Thus, enzyme efficiency was constrained by substrate concentration, genes, and age. Since MARS output is in the form of basis functions and equations, it allows multiscale systems modeling from the level of cellular chemical reactions to whole body physiological parameters, by automatic selection of significant predictors by the algorithm. Copyright © 2016 Forschungsgesellschaft für Arbeitsphysiologie und Arbeitschutz e.V. Published by Elsevier B.V. All rights reserved.

  20. The Non-Linear Child: Ontogeny, Isoniazid Concentration, and NAT2 Genotype Modulate Enzyme Reaction Kinetics and Metabolism

    Directory of Open Access Journals (Sweden)

    Zoe Rogers

    2016-09-01

    Full Text Available N-acetyltransferase 2 (NAT2 catalyzes the acetylation of isoniazid to N-acetylisoniazid. NAT2 polymorphism explains 88% of isoniazid clearance variability in adults. We examined the effects of clinical and genetic factors on Michaelis-Menten reaction kinetic constants of maximum velocity (Vmax and affinity (Km in children 0–10 years old. We measured the rates of isoniazid elimination and N-acetylisoniazid production in the blood of 30 children. Since maturation effects could be non-linear, we utilized a pharmacometric approach and the artificial intelligence method, multivariate adaptive regression splines (MARS, to identify factors predicting NAT2 Vmax and Km by examining clinical, genetic, and laboratory factors in toto. Isoniazid concentration predicted both Vmax and Km and superseded the contribution of NAT2 genotype. Age non-linearly modified the NAT2 genotype contribution until maturation at ≥5.3 years. Thus, enzyme efficiency was constrained by substrate concentration, genes, and age. Since MARS output is in the form of basis functions and equations, it allows multiscale systems modeling from the level of cellular chemical reactions to whole body physiological parameters, by automatic selection of significant predictors by the algorithm.

  1. Propagation of kinetic uncertainties through a canonical topology of the TLR4 signaling network in different regions of biochemical reaction space

    Directory of Open Access Journals (Sweden)

    St Laurent Georges

    2010-03-01

    Full Text Available Abstract Background Signal transduction networks represent the information processing systems that dictate which dynamical regimes of biochemical activity can be accessible to a cell under certain circumstances. One of the major concerns in molecular systems biology is centered on the elucidation of the robustness properties and information processing capabilities of signal transduction networks. Achieving this goal requires the establishment of causal relations between the design principle of biochemical reaction systems and their emergent dynamical behaviors. Methods In this study, efforts were focused in the construction of a relatively well informed, deterministic, non-linear dynamic model, accounting for reaction mechanisms grounded on standard mass action and Hill saturation kinetics, of the canonical reaction topology underlying Toll-like receptor 4 (TLR4-mediated signaling events. This signaling mechanism has been shown to be deployed in macrophages during a relatively short time window in response to lypopolysaccharyde (LPS stimulation, which leads to a rapidly mounted innate immune response. An extensive computational exploration of the biochemical reaction space inhabited by this signal transduction network was performed via local and global perturbation strategies. Importantly, a broad spectrum of biologically plausible dynamical regimes accessible to the network in widely scattered regions of parameter space was reconstructed computationally. Additionally, experimentally reported transcriptional readouts of target pro-inflammatory genes, which are actively modulated by the network in response to LPS stimulation, were also simulated. This was done with the main goal of carrying out an unbiased statistical assessment of the intrinsic robustness properties of this canonical reaction topology. Results Our simulation results provide convincing numerical evidence supporting the idea that a canonical reaction mechanism of the TLR4

  2. Distributed space scales in a semilinear reaction-diffusion system including a parabolic variational inequality : a well-posedness study

    OpenAIRE

    Fatima, T Tasnim; Muntean, A Adrian; Aiki, T

    2012-01-01

    This paper treats the solvability of a semilinear reaction-diffusion system, which incorporates transport (diffusion) and reaction effects emerging from two separated spatial scales: $x$ - macro and $y$ - micro. The system's origin connects to the modeling of concrete corrosion in sewer concrete pipes. It consists of three partial differential equations which are mass-balances of concentrations, as well as, one ordinary differential equation tracking the damage-by-corrosion. The system is sem...

  3. Assessment of nitric oxide (NO) redox reactions contribution to nitrous oxide (N2 O) formation during nitrification using a multispecies metabolic network model.

    Science.gov (United States)

    Perez-Garcia, Octavio; Chandran, Kartik; Villas-Boas, Silas G; Singhal, Naresh

    2016-05-01

    Over the coming decades nitrous oxide (N2O) is expected to become a dominant greenhouse gas and atmospheric ozone depleting substance. In wastewater treatment systems, N2O is majorly produced by nitrifying microbes through biochemical reduction of nitrite (NO2(-)) and nitric oxide (NO). However it is unknown if the amount of N2O formed is affected by alternative NO redox reactions catalyzed by oxidative nitrite oxidoreductase (NirK), cytochromes (i.e., P460 [CytP460] and 554 [Cyt554 ]) and flavohemoglobins (Hmp) in ammonia- and nitrite-oxidizing bacteria (AOB and NOB, respectively). In this study, a mathematical model is developed to assess how N2O formation is affected by such alternative nitrogen redox transformations. The developed multispecies metabolic network model captures the nitrogen respiratory pathways inferred from genomes of eight AOB and NOB species. The performance of model variants, obtained as different combinations of active NO redox reactions, was assessed against nine experimental datasets for nitrifying cultures producing N2O at different concentration of electron donor and acceptor. Model predicted metabolic fluxes show that only variants that included NO oxidation to NO2(-) by CytP460 and Hmp in AOB gave statistically similar estimates to observed production rates of N2O, NO, NO2(-) and nitrate (NO3(-)), together with fractions of AOB and NOB species in biomass. Simulations showed that NO oxidation to NO2(-) decreased N2O formation by 60% without changing culture's NO2(-) production rate. Model variants including NO reduction to N2O by Cyt554 and cNor in NOB did not improve the accuracy of experimental datasets estimates, suggesting null N2O production by NOB during nitrification. Finally, the analysis shows that in nitrifying cultures transitioning from dissolved oxygen levels above 3.8 ± 0.38 to <1.5 ± 0.8 mg/L, NOB cells can oxidize the NO produced by AOB through reactions catalyzed by oxidative NirK. © 2015 Wiley Periodicals, Inc.

  4. EcoCyc: Enyclopedia of Escherichia coli Genes and Metabolism.

    Science.gov (United States)

    Karp, P D; Riley, M; Paley, S M; Pellegrini-Toole, A; Krummenacker, M

    1997-01-01

    The Encyclopedia of Genes and Metabolism (EcoCyc) is a database that combines information about the genome and the intermediary metabolism of Escherichia coli. It describes 2970 genes of E.coli, 547 enzymes encoded by these genes, 702 metabolic reactions that occur in E.coli and the organization of these reactions into 107 metabolic pathways. The EcoCyc graphical user interface allows scientists to query and explore the EcoCyc database using visualization tools such as genomic-map browsers and automatic layouts of metabolic pathways. EcoCyc spans the space from sequence to function to allow scientists to investigate an unusually broad range of questions. EcoCyc can be thought of as both an electronic review article because of its copious references to the primary literature, and as an in silicio model of E.coli metabolism that can be probed and analyzed through computational means.

  5. Prevalence of CHD-related metabolic comorbidity of diabetes mellitus in Northern Chinese adults: the REACTION study.

    Science.gov (United States)

    Gao, Nannan; Yuan, Zhongshang; Tang, Xulei; Zhou, Xiaoming; Zhao, Meng; Liu, Lu; Ji, Jiadong; Xue, Fuzhong; Ning, Guang; Zhao, Jiajun; Zhang, Haiqing; Gao, Ling

    2016-03-01

    To gain more precise understanding of the epidemiology of comorbidities with diabetes and to clarify the correlation with coronary heart disease (CHD) in Chinese population. Based on REACTION study, 18,696 participants aged over 40 years were included in the cross-sectional analysis. Prevalence and patterns of comorbid diseases were demonstrated, and their impact on CHD was also analyzed by logistic regression. Diabetes was more prevalent in patients with older age and lower education level, with relatively low awareness (36.3%), treatment (27.9%) and control (34.7%) rate. The proportion of diabetics with additional condition was 88.8%; 53.2% had more than two comorbidities. Compared with patients with comorbidities, diabetics only had the highest controlled HbA1c rate (37.9%). Dyslipidemia (71.97%) was the most common comorbidity, followed by hypertension (58.19%), and hypothyroidism (21.24%). A strong gradient existed between the number of comorbidities and CHD versus "diabetes only" group; the odds ratio was 1.38, 2.48 and 3.01 for diabetics with one, two and three additional diseases, respectively. Low glycemic control and high prevalence of diabetes comorbidities are common in China, which increases the risk of CHD. Full-scale and individualized guidelines for diabetics should be planned. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. The formation of urea in space. I. Ion-molecule, neutral-neutral, and radical gas-phase reactions

    Science.gov (United States)

    Brigiano, Flavio Siro; Jeanvoine, Yannick; Largo, Antonio; Spezia, Riccardo

    2018-02-01

    Context. Many organic molecules have been observed in the interstellar medium thanks to advances in radioastronomy, and very recently the presence of urea was also suggested. While those molecules were observed, it is not clear what the mechanisms responsible to their formation are. In fact, if gas-phase reactions are responsible, they should occur through barrierless mechanisms (or with very low barriers). In the past, mechanisms for the formation of different organic molecules were studied, providing only in a few cases energetic conditions favorable to a synthesis at very low temperature. A particularly intriguing class of such molecules are those containing one N-C-O peptide bond, which could be a building block for the formation of biological molecules. Urea is a particular case because two nitrogen atoms are linked to the C-O moiety. Thus, motivated also by the recent tentative observation of urea, we have considered the synthetic pathways responsible to its formation. Aims: We have studied the possibility of forming urea in the gas phase via different kinds of bi-molecular reactions: ion-molecule, neutral, and radical. In particular we have focused on the activation energy of these reactions in order to find possible reactants that could be responsible for to barrierless (or very low energy) pathways. Methods: We have used very accurate, highly correlated quantum chemistry calculations to locate and characterize the reaction pathways in terms of minima and transition states connecting reactants to products. Results: Most of the reactions considered have an activation energy that is too high; but the ion-molecule reaction between NH2OHNH2OH2+ and formamide is not too high. These reactants could be responsible not only for the formation of urea but also of isocyanic acid, which is an organic molecule also observed in the interstellar medium.

  7. Defining Sequence Space and Reaction Products within the Cyanuric Acid Hydrolase (AtzD)/Barbiturase Protein Family

    OpenAIRE

    Seffernick, Jennifer L.; Erickson, Jasmine S.; Cameron, Stephan M.; Cho, Seunghee; Dodge, Anthony G.; Richman, Jack E.; Sadowsky, Michael J.; Wackett, Lawrence P.

    2012-01-01

    Cyanuric acid hydrolases (AtzD) and barbiturases are homologous, found almost exclusively in bacteria, and comprise a rare protein family with no discernible linkage to other protein families or an X-ray structural class. There has been confusion in the literature and in genome projects regarding the reaction products, the assignment of individual sequences as either cyanuric acid hydrolases or barbiturases, and spurious connection of this family to another protein family. The present study h...

  8. Defining sequence space and reaction products within the cyanuric acid hydrolase (AtzD)/barbiturase protein family.

    Science.gov (United States)

    Seffernick, Jennifer L; Erickson, Jasmine S; Cameron, Stephan M; Cho, Seunghee; Dodge, Anthony G; Richman, Jack E; Sadowsky, Michael J; Wackett, Lawrence P

    2012-09-01

    Cyanuric acid hydrolases (AtzD) and barbiturases are homologous, found almost exclusively in bacteria, and comprise a rare protein family with no discernible linkage to other protein families or an X-ray structural class. There has been confusion in the literature and in genome projects regarding the reaction products, the assignment of individual sequences as either cyanuric acid hydrolases or barbiturases, and spurious connection of this family to another protein family. The present study has addressed those issues. First, the published enzyme reaction products of cyanuric acid hydrolase are incorrectly identified as biuret and carbon dioxide. The current study employed (13)C nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry to show that cyanuric acid hydrolase releases carboxybiuret, which spontaneously decarboxylates to biuret. This is significant because it revealed that homologous cyanuric acid hydrolases and barbiturases catalyze completely analogous reactions. Second, enzymes that had been annotated incorrectly in genome projects have been reassigned here by bioinformatics, gene cloning, and protein characterization studies. Third, the AtzD/barbiturase family has previously been suggested to consist of members of the amidohydrolase superfamily, a large class of metallohydrolases. Bioinformatics and the lack of bound metals both argue against a connection to the amidohydrolase superfamily. Lastly, steady-state kinetic measurements and observations of protein stability suggested that the AtzD/barbiturase family might be an undistinguished protein family that has undergone some resurgence with the recent introduction of industrial s-triazine compounds such as atrazine and melamine into the environment.

  9. Food environment, walkability, and public open spaces are associated with incident development of cardio-metabolic risk factors in a biomedical cohort.

    Science.gov (United States)

    Paquet, Catherine; Coffee, Neil T; Haren, Matthew T; Howard, Natasha J; Adams, Robert J; Taylor, Anne W; Daniel, Mark

    2014-07-01

    We investigated whether residential environment characteristics related to food (unhealthful/healthful food sources ratio), walkability and public open spaces (POS; number, median size, greenness and type) were associated with incidence of four cardio-metabolic risk factors (pre-diabetes/diabetes, hypertension, dyslipidaemia, abdominal obesity) in a biomedical cohort (n=3205). Results revealed that the risk of developing pre-diabetes/diabetes was lower for participants in areas with larger POS and greater walkability. Incident abdominal obesity was positively associated with the unhealthful food environment index. No associations were found with hypertension or dyslipidaemia. Results provide new evidence for specific, prospective associations between the built environment and cardio-metabolic risk factors. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Rapid and accurate liquid chromatography and tandem mass spectrometry method for the simultaneous quantification of ten metabolic reactions catalyzed by hepatic cytochrome P450 enzymes.

    Science.gov (United States)

    Shi, Rong; Ma, Bingliang; Wu, Jiasheng; Wang, Tianming; Ma, Yueming

    2015-10-01

    The hepatic cytochrome P450 enzymes play a central role in the biotransformation of endogenous and exogenous substances. A sensitive high-throughput liquid chromatography with tandem mass spectrometry assay was developed and validated for the simultaneous quantification of the products of ten metabolic reactions catalyzed by hepatic cytochrome P450 enzymes. After the substrates were incubated separately, the samples were pooled and analyzed by liquid chromatography with tandem mass spectrometry using an electrospray ionization source in the positive and negative ion modes. The method exhibited linearity over a broad concentration range, insensitivity to matrix effects, and high accuracy, precision, and stability. The novel method was successfully applied to study the kinetics of phenacetin-O deethylation, coumarin-7 hydroxylation, bupropion hydroxylation, taxol-6 hydroxylation, omeprazole-5 hydroxylation, dextromethorphan-O demethylation, tolbutamide-4 hydroxylation, chlorzoxazone-6 hydroxylation, testosterone-6β hydroxylation, and midazolam-1 hydroxylation in rat liver microsomes. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Modeling complex metabolic reactions, ecological systems, and financial and legal networks with MIANN models based on Markov-Wiener node descriptors.

    Science.gov (United States)

    Duardo-Sánchez, Aliuska; Munteanu, Cristian R; Riera-Fernández, Pablo; López-Díaz, Antonio; Pazos, Alejandro; González-Díaz, Humberto

    2014-01-27

    The use of numerical parameters in Complex Network analysis is expanding to new fields of application. At a molecular level, we can use them to describe the molecular structure of chemical entities, protein interactions, or metabolic networks. However, the applications are not restricted to the world of molecules and can be extended to the study of macroscopic nonliving systems, organisms, or even legal or social networks. On the other hand, the development of the field of Artificial Intelligence has led to the formulation of computational algorithms whose design is based on the structure and functioning of networks of biological neurons. These algorithms, called Artificial Neural Networks (ANNs), can be useful for the study of complex networks, since the numerical parameters that encode information of the network (for example centralities/node descriptors) can be used as inputs for the ANNs. The Wiener index (W) is a graph invariant widely used in chemoinformatics to quantify the molecular structure of drugs and to study complex networks. In this work, we explore for the first time the possibility of using Markov chains to calculate analogues of node distance numbers/W to describe complex networks from the point of view of their nodes. These parameters are called Markov-Wiener node descriptors of order k(th) (W(k)). Please, note that these descriptors are not related to Markov-Wiener stochastic processes. Here, we calculated the W(k)(i) values for a very high number of nodes (>100,000) in more than 100 different complex networks using the software MI-NODES. These networks were grouped according to the field of application. Molecular networks include the Metabolic Reaction Networks (MRNs) of 40 different organisms. In addition, we analyzed other biological and legal and social networks. These include the Interaction Web Database Biological Networks (IWDBNs), with 75 food webs or ecological systems and the Spanish Financial Law Network (SFLN). The calculated W

  12. Addressing fear of crime in public space: gender differences in reaction to safety measures in train transit.

    Science.gov (United States)

    Yavuz, Nilay; Welch, Eric W

    2010-01-01

    Research has identified several factors that affect fear of crime in public space. However, the extent to which gender moderates the effectiveness of fear-reducing measures has received little attention. Using data from the Chicago Transit Authority Customer Satisfaction Survey of 2003, this study aims to understand whether train transit security practices and service attributes affect men and women differently. Findings indicate that, while the presence of video cameras has a lower effect on women's feelings of safety compared with men, frequent and on-time service matters more to male passengers. Additionally, experience with safety-related problems affects women significantly more than men. Conclusions discuss the implications of the study for theory and gender-specific policies to improve perceptions of transit safety.

  13. A Bayesian approach to the evolution of metabolic networks on a phylogeny.

    Directory of Open Access Journals (Sweden)

    Aziz Mithani

    2010-08-01

    Full Text Available The availability of genomes of many closely related bacteria with diverse metabolic capabilities offers the possibility of tracing metabolic evolution on a phylogeny relating the genomes to understand the evolutionary processes and constraints that affect the evolution of metabolic networks. Using simple (independent loss/gain of reactions or complex (incorporating dependencies among reactions stochastic models of metabolic evolution, it is possible to study how metabolic networks evolve over time. Here, we describe a model that takes the reaction neighborhood into account when modeling metabolic evolution. The model also allows estimation of the strength of the neighborhood effect during the course of evolution. We present Gibbs samplers for sampling networks at the internal node of a phylogeny and for estimating the parameters of evolution over a phylogeny without exploring the whole search space by iteratively sampling from the conditional distributions of the internal networks and parameters. The samplers are used to estimate the parameters of evolution of metabolic networks of bacteria in the genus Pseudomonas and to infer the metabolic networks of the ancestral pseudomonads. The results suggest that pathway maps that are conserved across the Pseudomonas phylogeny have a stronger neighborhood structure than those which have a variable distribution of reactions across the phylogeny, and that some Pseudomonas lineages are going through genome reduction resulting in the loss of a number of reactions from their metabolic networks.

  14. Metabolism and resistance of Fusarium spp. to the manzamine alkaloids via a putative retro pictet-spengler reaction and utility of the rational design of antimalarial and antifungal agents.

    Science.gov (United States)

    Kasanah, Noer; Farr, Lorelei Lucas; Gholipour, Abbas; Wedge, David E; Hamann, Mark T

    2014-08-01

    As a part of our continuing investigation of the manzamine alkaloids we studied the in vitro activity of the β-carboline containing manzamine alkaloids against Fusarium solani, Fusarium oxysporium, and Fusarium proliferatum by employing several bioassay techniques including one-dimensional direct bioautography, dilution, and plate susceptibility, and microtiter broth assays. In addition, we also studied the metabolism of the manzamine alkaloids by Fusarium spp. in order to facilitate the redesign of the compounds to prevent resistance of Fusarium spp. through metabolism. The present research reveals that the manzamine alkaloids are inactive against Fusarium spp. and the fungi transform manzamines via hydrolysis, reduction, and a retro Pictet-Spengler reaction. This is the first report to demonstrate an enzymatically retro Pictet-Spengler reaction. The results of this study reveal the utility of the rational design of metabolically stable antifungal agents from this class and the development of manzamine alkaloids as antimalarial drugs through the utilization of Fusarium's metabolic products to reconstruct the molecule.

  15. Effect of space availability at feed bunk and rest area on metabolic conditions and productive responses in dairy cows

    Directory of Open Access Journals (Sweden)

    L. Stefanini

    2011-03-01

    Full Text Available It has been estimated that dairy cows spend 3 to 5 h/d eating, consuming 9 to 14 meals per day. In addition, they ruminate 7 to 10 h/d, spend approximately 30 min/d drinking, 2 to 3 h/d being milked, and require approximately 10 h/d for lying time (Grant and Albright, 2000. Management decisions on dairy must not interfere with the cow’s ability to perform these activities which comprises her daily routines. It is well known that feed bunk space modifies eating behaviour, while the amount and characteristics of rest area modify resting activity of the cows. The traditional recommendation of 0.6 linear meter of bunk space per cow is the minimal amount of space needed for all cows to eat at one time (Grant and Albright, 2001.......

  16. The Pine Ridge-Mayo National Aeronautics and Space Administration telemedicine project: program activities and participant reactions.

    Science.gov (United States)

    Kottke, T E; Little Finger, L; Trapp, M A; Panser, L A; Novotny, P J

    1996-04-01

    To determine the response of participants to the Pine Ridge-Mayo National Aeronautics and Space Administration telemedicine project. We describe a 3-month demonstration project of medical education and clinical consultations conducted by means of satellite transmission. Postparticipation questionnaires and a postproject survey were used to assess the success of the activity. Patients and employees at the Pine Ridge Indian Health Service Hospital in southwestern South Dakota and employees at Mayo Clinic Rochester participated in a telemedicine project, after which they completed exit surveys and a postproject questionnaire to ascertain the acceptability of this mode of health care. Almost all Pine Ridge and Mayo Clinic participants viewed the project as beneficial. The educational sessions received favorable evaluations, and almost two-thirds of the patients who completed evaluations thought the consultation had contributed to their medical care. More than 90% of the respondents from Pine Ridge and more than 85% of the respondents from Mayo Clinic Rochester said that they would recommend participation in this project to others. More than 90% of respondents from Pine Ridge and 80% of Mayo respondents agreed with the statement that the project should continue. These data suggest that a program of clinical consultation services, professional education, and patient education available by telemedicine might be viewed as beneficial.

  17. On Data Space Selection and Data Processing for Parameter Identification in a Reaction-Diffusion Model Based on FRAP Experiments

    Directory of Open Access Journals (Sweden)

    Stefan Kindermann

    2015-01-01

    Full Text Available Fluorescence recovery after photobleaching (FRAP is a widely used measurement technique to determine the mobility of fluorescent molecules within living cells. While the experimental setup and protocol for FRAP experiments are usually fixed, data (preprocessing represents an important issue. The aim of this paper is twofold. First, we formulate and solve the problem of relevant FRAP data selection. The theoretical findings are illustrated by the comparison of the results of parameter identification when the full data set was used and the case when the irrelevant data set (data with negligible impact on the confidence interval of the estimated parameters was removed from the data space. Second, we analyze and compare two approaches of FRAP data processing. Our proposition, surprisingly for the FRAP community, claims that the data set represented by the FRAP recovery curves in form of a time series (integrated data approach commonly used by the FRAP community leads to a larger confidence interval compared to the full (spatiotemporal data approach.

  18. Metabolism and inflammatory mediators in the peritendinous space measured by microdialysis during intermittent isometric exercise in humans

    DEFF Research Database (Denmark)

    Langberg, Henning; Skovgaard, D; Karamouzis, M

    1999-01-01

    1. The metabolic processes that occur around the tendon during mechanical loading and exercise are undescribed in man. These processes are important for understanding the development of overuse inflammation and injury. 2. A microdialysis technique was used to determine interstitial concentrations...... healthy humans were studied at rest, during 30 min of intermittent static plantar flexion of the ankle at a workload corresponding to individual body weight, and during 60 min of recovery. Microdialysis was performed in both legs with simultaneous determination of blood flow by 133Xe washout in the same...

  19. New Resolution Strategy for Multi-scale Reaction Waves using Time Operator Splitting and Space Adaptive Multiresolution: Application to Human Ischemic Stroke*

    Directory of Open Access Journals (Sweden)

    Louvet Violaine

    2011-12-01

    Full Text Available We tackle the numerical simulation of reaction-diffusion equations modeling multi-scale reaction waves. This type of problems induces peculiar difficulties and potentially large stiffness which stem from the broad spectrum of temporal scales in the nonlinear chemical source term as well as from the presence of large spatial gradients in the reactive fronts, spatially very localized. A new resolution strategy was recently introduced ? that combines a performing time operator splitting with high oder dedicated time integration methods and space adaptive multiresolution. Based on recent theoretical studies of numerical analysis, such a strategy leads to a splitting time step which is not restricted neither by the fastest scales in the source term nor by stability limits related to the diffusion problem, but only by the physics of the phenomenon. In this paper, the efficiency of the method is evaluated through 2D and 3D numerical simulations of a human ischemic stroke model, conducted on a simplified brain geometry, for which a simple parallelization strategy for shared memory architectures was implemented, in order to reduce computing costs related to “detailed chemistry” features of the model.

  20. Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks

    Science.gov (United States)

    Haraldsdóttir, Hulda S.; Fleming, Ronan M. T.

    2016-01-01

    Conserved moieties are groups of atoms that remain intact in all reactions of a metabolic network. Identification of conserved moieties gives insight into the structure and function of metabolic networks and facilitates metabolic modelling. All moiety conservation relations can be represented as nonnegative integer vectors in the left null space of the stoichiometric matrix corresponding to a biochemical network. Algorithms exist to compute such vectors based only on reaction stoichiometry but their computational complexity has limited their application to relatively small metabolic networks. Moreover, the vectors returned by existing algorithms do not, in general, represent conservation of a specific moiety with a defined atomic structure. Here, we show that identification of conserved moieties requires data on reaction atom mappings in addition to stoichiometry. We present a novel method to identify conserved moieties in metabolic networks by graph theoretical analysis of their underlying atom transition networks. Our method returns the exact group of atoms belonging to each conserved moiety as well as the corresponding vector in the left null space of the stoichiometric matrix. It can be implemented as a pipeline of polynomial time algorithms. Our implementation completes in under five minutes on a metabolic network with more than 4,000 mass balanced reactions. The scalability of the method enables extension of existing applications for moiety conservation relations to genome-scale metabolic networks. We also give examples of new applications made possible by elucidating the atomic structure of conserved moieties. PMID:27870845

  1. Reaction Decoder Tool (RDT): extracting features from chemical reactions

    OpenAIRE

    Rahman, Syed Asad; Torrance, Gilliean; Baldacci, Lorenzo; Mart?nez Cuesta, Sergio; Fenninger, Franz; Gopal, Nimish; Choudhary, Saket; May, John W.; Holliday, Gemma L.; Steinbeck, Christoph; Thornton, Janet M.

    2016-01-01

    Summary: Extracting chemical features like Atom?Atom Mapping (AAM), Bond Changes (BCs) and Reaction Centres from biochemical reactions helps us understand the chemical composition of enzymatic reactions. Reaction Decoder is a robust command line tool, which performs this task with high accuracy. It supports standard chemical input/output exchange formats i.e. RXN/SMILES, computes AAM, highlights BCs and creates images of the mapped reaction. This aids in the analysis of metabolic pathways and...

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

    Science.gov (United States)

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

    2011-01-01

    About 20% of astronauts on International Space Station missions have developed measurable ophthalmic changes after flight. This study was conducted to determine whether the folate-dependent 1-carbon pathway is altered in these individuals. Data were modeled to evaluate differences between individuals with ophthalmic changes (n=5) and those without them (n=15). We also correlated mean preflight serum concentrations of the 1-carbon metabolites with changes in measured refraction after flight. Serum homocysteine (HCy), cystathionine, 2-methylcitric acid, and methylmalonic acid concentrations were 25%-45% higher (P<0.001) in astronauts with ophthalmic changes than in those without them. These differences existed before, during, and after flight. Preflight serum HCy and cystathionine, and in-flight serum folate, were significantly (P<0.05) correlated with postflight change in refraction, and preflight serum concentrations of 2-methylcitric acid tended to be associated (P=0.06) with ophthalmic changes. The biochemical differences observed in those with vision issues strongly suggests impairment of the folate-dependent 1-carbon transfer pathway. Impairment of this pathway, by polymorphisms, diet or other means, may interact with components of the microgravity environment to influence these pathophysiologic changes. This study was funded by the NASA Human Research Program.

  3. Chemical transport reactions

    CERN Document Server

    Schäfer, Harald

    2013-01-01

    Chemical Transport Reactions focuses on the processes and reactions involved in the transport of solid or liquid substances to form vapor phase reaction products. The publication first offers information on experimental and theoretical principles and the transport of solid substances and its special applications. Discussions focus on calculation of the transport effect of heterogeneous equilibria for a gas motion between equilibrium spaces; transport effect and the thermodynamic quantities of the transport reaction; separation and purification of substances by means of material transport; and

  4. Space space space

    CERN Document Server

    Trembach, Vera

    2014-01-01

    Space is an introduction to the mysteries of the Universe. Included are Task Cards for independent learning, Journal Word Cards for creative writing, and Hands-On Activities for reinforcing skills in Math and Language Arts. Space is a perfect introduction to further research of the Solar System.

  5. The Mice Drawer System (MDS) Tissue Sharing Programme: effect of space conditions on skin metabolic activity and vascularization and potential impact of radiations in mice.

    Science.gov (United States)

    Nusgens, Betty; Lambert, Charles; Liu, Yi; Cancedda, Ranieri; Tavella, Sara; Ruggiu, Alessandra; Colige, Alain

    Our aim was to investigate the effect of prolonged microgravity on skin physiology in mice and to identify potentially altered metabolic and vascular parameters. Osteoporosis-induced microgravity is a well documented space flight problem in Man and animals.We have previously demonstrated that fibroblasts from the dermis also sense and react to mechanical forces issued from the surrounding extracellular matrix. Conversely, fibroblasts are able to remodel their environment by a dynamic process of synthesis and degradation. Fibroblasts and cells of the vascular network also react to soluble mediators secreted by the keratinocytes such as IL-1, IL-6, VEGF, .... Skin fibroblasts upon relaxation of mechanical tension adopt a catabolic phenotype and produce significant amount of IL-1 and IL-6, of various matrix metalloproteinases (MMP) while the collagen synthesis is reduced. In microgravity, we have shown that the expression of MMP-1 and IL-6 by dermal fibroblasts is increased indicating that cell might interpret micro-gravity as a mechanical relaxation. This concept is supported by a reduction of the actin stress fibers and focal adhesions in fibroblasts in microgravity. Altogether, microgravity might alter metabolic equilibrium of the skin and perhaps of other soft connective tissues such as tendons or interstitial matrix of internal organs. The Mice Drawer System (MDS) is an Italian Space Agency facility which is able to support mice onboard the International Space Station during long-duration exploration missions by providing living space, food, water, ventilation and light-ing. Details on the mission that took place from August 28, 2009 to November 27, 2009, can be found at the URL indicated below. A similar ground control mission has been performed using the same wild type and transgenic mice overexpressing OSF-1. Upon receiving mice at KSC, the team has collected pieces of skin that were handled for histological, transcriptomic and biochemical analyses. The

  6. Systems Biology of Metabolism.

    Science.gov (United States)

    Nielsen, Jens

    2017-06-20

    Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology are described, and two different types of mathematical models used for studying metabolism are discussed: kinetic models and genome-scale metabolic models. The use of different omics technologies, including transcriptomics, proteomics, metabolomics, and fluxomics, for studying metabolism is presented. Finally, the application of systems biology for analyzing global regulatory structures, engineering the metabolism of cell factories, and analyzing human diseases is discussed.

  7. Effects of introducing heterologous pathways on microbial metabolism with respect to metabolic optimality

    DEFF Research Database (Denmark)

    Kim, Hyun Uk; Kim, Byoungjin; Seung, Do Young

    2014-01-01

    Although optimality of microbial metabolism under genetic and environmental perturbations is well studied, the effects of introducing heterologous reactions on the overall metabolism are not well understood. This point is important in the field of metabolic engineering because heterologous reacti...

  8. High-Performance Reaction Wheel Optimization for Fine-Pointing Space Platforms: Minimizing Induced Vibration Effects on Jitter Performance plus Lessons Learned from Hubble Space Telescope for Current and Future Spacecraft Applications

    Science.gov (United States)

    Hasha, Martin D.

    2016-01-01

    The Hubble Space Telescope (HST) applies large-diameter optics (2.5-m primary mirror) for diffraction-limited resolution spanning an extended wavelength range (approx. 100-2500 nm). Its Pointing Control System (PCS) Reaction Wheel Assemblies (RWAs), in the Support Systems Module (SSM), acquired an unprecedented set of high-sensitivity Induced Vibration (IV) data for 5 flight-certified RWAs: dwelling at set rotation rates. Focused on 4 key ratios, force and moment harmonic values (in 3 local principal directions) are extracted in the RWA operating range (0-3000 RPM). The IV test data, obtained under ambient lab conditions, are investigated in detail, evaluated, compiled, and curve-fitted; variational trends, core causes, and unforeseen anomalies are addressed. In aggregate, these values constitute a statistically-valid basis to quantify ground test-to-test variations and facilitate extrapolations to on-orbit conditions. Accumulated knowledge of bearing-rotor vibrational sources, corresponding harmonic contributions, and salient elements of IV key variability factors are discussed. An evolved methodology is presented for absolute assessments and relative comparisons of macro-level IV signal magnitude due to micro-level construction-assembly geometric details/imperfections stemming from both electrical drive and primary bearing design parameters. Based upon studies of same-size/similar-design momentum wheels' IV changes, upper estimates due to transitions from ground tests to orbital conditions are derived. Recommended HST RWA choices are discussed relative to system optimization/tradeoffs of Line-Of-Sight (LOS) vector-pointing focal-plane error driven by higher IV transmissibilities through low-damped structural dynamics that stimulate optical elements. Unique analytical disturbance results for orbital HST accelerations are described applicable to microgravity efforts. Conclusions, lessons learned, historical context/insights, and perspectives on future applications

  9. Horizontal and vertical growth of S. cerevisiae metabolic network.

    KAUST Repository

    Grassi, Luigi

    2011-10-14

    BACKGROUND: The growth and development of a biological organism is reflected by its metabolic network, the evolution of which relies on the essential gene duplication mechanism. There are two current views about the evolution of metabolic networks. The retrograde model hypothesizes that a pathway evolves by recruiting novel enzymes in a direction opposite to the metabolic flow. The patchwork model is instead based on the assumption that the evolution is based on the exploitation of broad-specificity enzymes capable of catalysing a variety of metabolic reactions. RESULTS: We analysed a well-studied unicellular eukaryotic organism, S. cerevisiae, and studied the effect of the removal of paralogous gene products on its metabolic network. Our results, obtained using different paralog and network definitions, show that, after an initial period when gene duplication was indeed instrumental in expanding the metabolic space, the latter reached an equilibrium and subsequent gene duplications were used as a source of more specialized enzymes rather than as a source of novel reactions. We also show that the switch between the two evolutionary strategies in S. cerevisiae can be dated to about 350 million years ago. CONCLUSIONS: Our data, obtained through a novel analysis methodology, strongly supports the hypothesis that the patchwork model better explains the more recent evolution of the S. cerevisiae metabolic network. Interestingly, the effects of a patchwork strategy acting before the Euascomycete-Hemiascomycete divergence are still detectable today.

  10. Evaluation of modafinil as a perpetrator of metabolic drug-drug interactions using a model informed cocktail reaction phenotyping trial protocol.

    Science.gov (United States)

    Rowland, Angela; van Dyk, Madelé; Warncken, David; Mangoni, Arduino A; Sorich, Michael J; Rowland, Andrew

    2018-03-01

    To evaluate the capacity for modafinil to be a perpetrator of metabolic drug-drug interactions by altering cytochrome P450 activity following a single dose and dosing to steady state. A single centre, open label, single sequence cocktail drug interaction trial. On days 0, 2 and 8 participants were administered an oral drug cocktail comprising 100 mg caffeine, 30 mg dextromethorphan, 25 mg losartan, 1 mg midazolam and 20 mg enteric-coated omeprazole. Timed blood samples were collected prior to and for up to 6 h post cocktail dosing. Between days 2 and 8 participants orally self-administered 200 mg modafinil each morning. Following a single 200 mg dose of modafinil mean (± 95% CI) AUC ratios for caffeine, dextromethorphan, losartan, midazolam and omeprazole were 0.95 (± 0.08), 1.01 (± 0.35), 0.97 (± 0.10), 0.98 (± 0.10) and 1.36 (± 0.06), respectively. Following dosing of modafinil to steady state (200 mg for 7 days), AUC ratios for caffeine, dextromethorphan, losartan, midazolam and omeprazole were 0.90 (± 0.16), 0.79 (± 0.09), 0.98 (± 0.11), 0.66 (± 0.12) and 1.90 (± 0.53), respectively. These data support consideration of the risk of clinically relevant metabolic drug-drug interactions perpetrated by modafinil when this drug is co-administered with drugs that are primarily cleared by CYP2C19 (single modafinil dose or steady state modafinil dosing) or CYP3A4 (steady state modafinil dosing only) catalysed metabolic pathways. © 2017 The British Pharmacological Society.

  11. Regulatory Biology: Depressed Metabolic States

    Science.gov (United States)

    Holton, E. M. (Editor)

    1973-01-01

    Exobiological aspects of depressed metabolism and thermoregulation are discussed for subsequent development of biological space flight experiments. Included is a brief description of differential hypothermia in cancer chemotherapy.

  12. A novel tool for studying auxin-metabolism: the inhibition of grapevine indole-3-acetic acid-amido synthetases by a reaction intermediate analogue.

    Directory of Open Access Journals (Sweden)

    Christine Böttcher

    Full Text Available An important process for the regulation of auxin levels in plants is the inactivation of indole-3-acetic acid (IAA by conjugation to amino acids. The conjugation reaction is catalysed by IAA-amido synthetases belonging to the family of GH3 proteins. Genetic approaches to study the biological significance of these enzymes have been hampered by large gene numbers and a high degree of functional redundancy. To overcome these difficulties a chemical approach based on the reaction mechanism of GH3 proteins was employed to design a small molecule inhibitor of IAA-amido synthetase activity. Adenosine-5'-[2-(1H-indol-3-ylethyl]phosphate (AIEP mimics the adenylated intermediate of the IAA-conjugation reaction and was therefore proposed to compete with the binding of MgATP and IAA in the initial stages of catalysis. Two grapevine IAA-amido synthetases with different catalytic properties were chosen to test the inhibitory effects of AIEP in vitro. GH3-1 has previously been implicated in the grape berry ripening process and is restricted to two amino acid substrates, whereas GH3-6 conjugated IAA to 13 amino acids. AIEP is the most potent inhibitor of GH3 enzymes so far described and was shown to be competitive against MgATP and IAA binding to both enzymes with K(i-values 17-68-fold lower than the respective K(m-values. AIEP also exhibited in vivo activity in an ex planta test system using young grape berries. Exposure to 5-20 µM of the inhibitor led to decreased levels of the common conjugate IAA-Asp and reduced the accumulation of the corresponding Asp-conjugate upon treatment with a synthetic auxin. AIEP therefore represents a novel chemical probe with which to study IAA-amido synthetase function.

  13. Extending the Derek-Meteor Workflow to Predict Chemical-Toxicity Space Impacted by Metabolism: Application to ToxCast and Tox21 Chemical Inventories

    Science.gov (United States)

    A central aim of EPA’s ToxCast project is to use in vitro high-throughput screening (HTS) profiles to build predictive models of in vivo toxicity. Where assays lack metabolic capability, such efforts may need to anticipate the role of metabolic activation (or deactivation). A wo...

  14. Effect of preoperative consumption of high carbohydrate drink (Pre-Op) on postoperative metabolic stress reaction in patients undergoing radical prostatectomy.

    Science.gov (United States)

    Canbay, Özgür; Adar, Serdar; Karagöz, Ayşe Heves; Çelebi, Nalan; Bilen, Cenk Yücel

    2014-07-01

    To investigate the effects of oral carbohydrate solution consumed until 2 h before the surgery in the patients that would undergo open radical retropubic prostatectomy on postoperative metabolic stress, patient anxiety, and comfort. A total of 50 adult patients, who were in ASA I-II group and would undergo open radical retropubic prostatectomy, were included in the study. While Group 1 = CH (n = 25) received oral glucose solution, Group 2 = FAM (n = 25) was famished starting from 24:00 h. Blood glucose, insulin, and procalcitonin levels of the patients were recorded, and the patients completed state-trait anxiety inventory (STAI) test, which reflects the anxiety level of the patients, both before surgery and on the postoperative 24th hour. In order to evaluate patient comfort, senses of hunger, thirst, nausea, and cold were assessed in the morning prior to the surgery. No difference was observed between the two groups in terms of demographic data and insulin resistance levels (p > 0.05). Comparing with the preoperative levels, insulin resistance showed statistically significant elevation in both groups (p 0.05). With regard to preoperative patient comfort, sense of hunger was present in lesser number of subjects and at lower level in Group 1 (p hunger and thirst in the preoperative period in open radical retropubic prostatectomies.

  15. A possible association between space weather conditions and the risk of acute coronary syndrome in patients with diabetes and the metabolic syndrome.

    Science.gov (United States)

    Vencloviene, Jone; Babarskiene, Ruta Marija; Kiznys, Deivydas

    2017-01-01

    Hyperglycemia negatively affects cardiovascular variables that are also adversely affected by increased geomagnetic activity. It is likely that geomagnetic storms (GS) could have a stronger negative impact on these patients. We analyzed data on 1548 randomly selected patients with acute coronary syndrome (ACS) who were admitted inpatient treatment in Kaunas city, during 2000-2003. We evaluated the associations of GS, solar proton events (SPE), and high-speed solar wind (HSSW) (solar wind speed ≥600 km/s) with the risk of ACS in patients with diabetes mellitus (DM) and the metabolic syndrome (MS) by using logistic regression with categorical predictors. During days of HSSW, the risk of ACS in DM patients increased by 1.95 times (OR = 1.95, 95 % CI 1.36-2.79) as compared to days without either of these events or 2 days prior to or after them. In the multivariate model, the risk of ACS in DM patients was associated with days of HSSW and 1-2 days after (OR = 1.40, 95 % CI 1.01-1.93), with days of GS lasting >1 day and occurring on days of HSSW or 1-2 days after (OR = 2.31, 95 % CI 1.28-4.17), and with the onset of SPE (OR = 2.72 (1.09-6.83)). The risk of ACS in MS patients was associated with days of GS and 1-2 days prior or after GS (OR = 1.31 (1.00-1.73)); an additional impact was established if these days coincided with days of HSSW or 1-2 days before (OR = 2.16 (1.39-3.35)). These findings suggest that not only GS but also HSSW and changes in space weather conditions prior to SPE affect the human cardiovascular system.

  16. Fluoroacetylcarnitine: metabolism and metabolic effects in mitochondria

    Energy Technology Data Exchange (ETDEWEB)

    Bremer, J.; Davis, E.J.

    1973-01-01

    The metabolism and metabolic effects of fluoroacetylcarnitine have been investigated. Carnitineacetyltransferase transfers the fluoro-acetyl group of fluoroacetylcarnitine nearly as rapidly to CoA as the acetyl group of acetylcarnitine. Fluorocitrate is then formed by citrate synthase, but this second reaction is relatively slow. The fluorocitrate formed intramitochondrially inhibits the metabolism of citrate. In heart and skeletal muscle mitochondria the accumulated citrate inhibits citrate synthesis and the ..beta..-oxidation of fatty acids. Free acetate is formed, presumably because accumulated acetyl-CoA is hydrolyzed. In liver mitochondria the accumulation of citrate leads to a relatively increased rate of ketogenesis. Increased ketogenesis is obtained also upon the addition of citrate to the reaction mixture.

  17. The thermodynamics of protein aggregation reactions may underpin the enhanced metabolic efficiency associated with heterosis, some balancing selection, and the evolution of ploidy levels.

    Science.gov (United States)

    Ginn, B R

    2017-07-01

    Identifying the physical basis of heterosis (or "hybrid vigor") has remained elusive despite over a hundred years of research on the subject. The three main theories of heterosis are dominance theory, overdominance theory, and epistasis theory. Kacser and Burns (1981) identified the molecular basis of dominance, which has greatly enhanced our understanding of its importance to heterosis. This paper aims to explain how overdominance, and some features of epistasis, can similarly emerge from the molecular dynamics of proteins. Possessing multiple alleles at a gene locus results in the synthesis of different allozymes at reduced concentrations. This in turn reduces the rate at which each allozyme forms soluble oligomers, which are toxic and must be degraded, because allozymes co-aggregate at low efficiencies. The model developed in this paper can explain how heterozygosity impacts the metabolic efficiency of an organism. It can also explain why the viabilities of some inbred lines seem to decline rapidly at high inbreeding coefficients (F > 0.5), which may provide a physical basis for truncation selection for heterozygosity. Finally, the model has implications for the ploidy level of organisms. It can explain why polyploids are frequently found in environments where severe physical stresses promote the formation of soluble oligomers. The model can also explain why complex organisms, which need to synthesize aggregation-prone proteins that contain intrinsically unstructured regions (IURs) and multiple domains because they facilitate complex protein interaction networks (PINs), tend to be diploid while haploidy tends to be restricted to relatively simple organisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Multi-objective shadow prices point at principles of metabolic regulation.

    Science.gov (United States)

    Sajitz-Hermstein, Max; Nikoloski, Zoran

    2016-08-01

    Perturbations in environmental and intracellular conditions often lead to changes across all cellular layers, from transcription to metabolism. Regulatory mechanisms are key to mediating these changes to maintain homeostasis and to ensure viability. Since changes in metabolic reaction rates are partly due to perturbations in metabolite concentrations, it is expected that metabolites with large effect on those reaction rates which govern metabolic functionality are tightly regulated. The extent of metabolic regulation has been quantified by the sensitivity of an individual metabolic function to changes in metabolite concentrations, in particular by shadow prices in the constraint-based modeling framework. However, the system-wide characterization of the extent to which metabolite concentrations are regulated in the more realistic scenario of multiple contending tasks remains elusive. Here we examine multi-objective shadow prices for the central carbon metabolism of Escherichia coli whose reaction rates are shaped by several contending metabolic functions. We determine shadow prices for sampled solutions of the Pareto front, which characterizes the space of multi-objective optima, for three contending metabolic functions that provide the best agreement with (13)C-labeling experiments. By analyzing the parts of the Pareto front closest to the experimentally determined flux phenotypes, we show that E. coli operates in the vicinity of an area of the Pareto front which facilitates robust and efficient regulation. In addition, we find significant associations between features of the transcriptional regulatory network and the sensitivity of E. coli's metabolic functionality to changes in metabolite concentrations. We demonstrate that the structural constraints of the metabolic network together with data on condition-specific flux phenotypes can be effectively used to dissect metabolic regulation on a system-wide level. Copyright © 2016 The Author(s). Published by Elsevier

  19. Genome scale metabolic reconstruction of Chlorella variabilis for exploring its metabolic potential for biofuels.

    Science.gov (United States)

    Juneja, Ankita; Chaplen, Frank W R; Murthy, Ganti S

    2016-08-01

    A compartmentalized genome scale metabolic network was reconstructed for Chlorella variabilis to offer insight into various metabolic potentials from this alga. The model, iAJ526, was reconstructed with 1455 reactions, 1236 metabolites and 526 genes. 21% of the reactions were transport reactions and about 81% of the total reactions were associated with enzymes. Along with gap filling reactions, 2 major sub-pathways were added to the model, chitosan synthesis and rhamnose metabolism. The reconstructed model had reaction participation of 4.3 metabolites per reaction and average lethality fraction of 0.21. The model was effective in capturing the growth of C. variabilis under three light conditions (white, red and red+blue light) with fair agreement. This reconstructed metabolic network will serve an important role in systems biology for further exploration of metabolism for specific target metabolites and enable improved characteristics in the strain through metabolic engineering. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Measurement of Fragment Production Cross Sections in the $^{12}$C+$^{12}$C and $^{12}$C+$^{197}$Au Reactions at 62 $A$ MeV for Hadrontherapy and Space Radiation Protection

    CERN Document Server

    Tropea, S; Agodi, C; Blancato, A A; Bondì, M; Cappuzzello, F; Carbone, D; Cavallaro, M; Cirrone, G A P; Cuttone, G; Giacoppo, F; Nicolosi, D; Pandola, L; Raciti, G; Rapisarda, E; Romano, F; Sardina, D; Scuderi, V; Sfienti, C

    2014-01-01

    Over the last twenty years, there has been a renewed interest in nuclear fragmentation studies for both hadrontherapy applications and space radiation protection. In both fields, fragmentation cross sections are needed to predict the effects of the ions nuclear interactions within the patient’s and the astronaut’s body. Indeed, the Monte Carlo codes used in planning tumor treatments and space missions must be tuned and validated by experimental data. However, only a limited set of fragmentation cross sections are available in literature, especially at Fermi energies. Therefore, we have studied the production of secondary fragments in the 12 C+ 12 C and 12 C+ 197 Au reactions at 62 A MeV. In this work, the measured 4 He cross sections angular distributions at four selected angles are presented and compared.

  1. Metabolic Panel

    Science.gov (United States)

    A metabolic panel is a group of tests that measures different chemicals in the blood. These tests are usually done on ... and liver. There are two types: basic metabolic panel (BMP) and comprehensive metabolic panel (CMP). The BMP ...

  2. Space-time information analysis for resource-conscious urban planning and design: A stakeholder based identification of urban metabolism data gaps

    NARCIS (Netherlands)

    Voskamp, I.M.; Spiller, M.; Stremke, S.; Bregt, A.K.; Vreugdenhil, L.C.; Rijnaarts, H.H.M.

    2018-01-01

    The research presented here examined at which spatial and temporal resolution urban metabolism should be analysed to generate results that are useful for implementation of urban planning and design interventions aiming at optimization of resource flows. Moreover, it was researched whether a lack of

  3. Reaction Decoder Tool (RDT): extracting features from chemical reactions.

    Science.gov (United States)

    Rahman, Syed Asad; Torrance, Gilliean; Baldacci, Lorenzo; Martínez Cuesta, Sergio; Fenninger, Franz; Gopal, Nimish; Choudhary, Saket; May, John W; Holliday, Gemma L; Steinbeck, Christoph; Thornton, Janet M

    2016-07-01

    Extracting chemical features like Atom-Atom Mapping (AAM), Bond Changes (BCs) and Reaction Centres from biochemical reactions helps us understand the chemical composition of enzymatic reactions. Reaction Decoder is a robust command line tool, which performs this task with high accuracy. It supports standard chemical input/output exchange formats i.e. RXN/SMILES, computes AAM, highlights BCs and creates images of the mapped reaction. This aids in the analysis of metabolic pathways and the ability to perform comparative studies of chemical reactions based on these features. This software is implemented in Java, supported on Windows, Linux and Mac OSX, and freely available at https://github.com/asad/ReactionDecoder : asad@ebi.ac.uk or s9asad@gmail.com. © The Author 2016. Published by Oxford University Press.

  4. Biosignature Preservation Vulnerability Associated with Stress Response Metabolic Redox Mode Switching in a Mars Analogue Coupled Microbial Mat Transiting Near-Space

    Science.gov (United States)

    Archer, R.; Ralat, A.

    2016-05-01

    Examination of a coupled microbial mat recovered from Death Valley failed to detect rosickyte, both before and after exposure to near-space conditions; associated redox proxies suggest diagenesis caused by rapid adaptive microbial stress response.

  5. Time- and space-resolved study of the methanol to hydrocarbons (MTH) reaction - influence of zeolite topology on axial deactivation patterns.

    Science.gov (United States)

    Rojo-Gama, Daniel; Etemadi, Samaneh; Kirby, Eliot; Lillerud, Karl Petter; Beato, Pablo; Svelle, Stian; Olsbye, Unni

    2017-04-28

    Zeolites representing seven different topologies were subjected to life-time assessment studies as methanol to hydrocarbons (MTH) catalysts at 400 °C, P(MeOH) = 13 kPa and P(tot) = 100 kPa. The following topologies were studied: ZSM-22 (TON), ZSM-23 (MTT), IM-5 (IMF), ITQ-13 (ITH), ZSM-5 (MFI), mordenite (MOR) and beta (BEA). Two experimental approaches were used. In the first approach, each catalyst was tested at three different contact times, all giving 100% initial conversion. The life-time before conversion decreased to 50% at each contact time was measured and used to calculate critical contact times (i.e. the contact time needed to launch the autocatalytic MTH reaction) and deactivation rates. It was found that the critical contact time is strongly correlated with pore size: the smaller the pore size, the longer the critical contact time. The second experimental approach consisted of testing the catalysts in a double tube reactor with 100% initial conversion, and quenching the reaction after 4 consecutive times on stream, representing full, partial, and zero conversion. After quenching, the catalyst bed was divided into four segments, which were individually characterised for coke content (temperature-programmed oxidation) and specific surface area (N 2 adsorption). The axial deactivation pattern was found to depend on pore size. With increasing pore size, the main source of coke formation changed from methanol conversion (1D 10-ring structures), to partly methanol, partly product conversion (3D 10-ring structures) and finally mainly product conversion (3D 12-ring structure). As a result, the methanol conversion capacity changed little with contact time for ZSM-5, while it increased with increasing contact time for the catalysts with smaller pore sizes, and decreased with increasing contact time for pore sizes larger than ZSM-5.

  6. Studying Biological Rhythms of Person's Skin-galvanic Reaction and Dynamics of Light Transmission by Isomeric Substance in Space Flight Conditions

    Science.gov (United States)

    Glushko, Vladimir

    2004-01-01

    Intensity and amplitude of human functional systems and human most important organs are wavelike, rhythmic by nature. These waves have constant periodicity, phase and amplitude. The mentioned characteristics can vary, however their variations have a pronounced reiteration in the course of time. This indicates a hashing of several wave processes and their interference. Stochastic changes in wave processes characteristics of a human organism are explained either by 'pulsations' associated with hashing (superposition) of several wave processes and their interference, or by single influence of environmental physical factors on a human organism. Human beings have respectively periods of higher and lower efficiency, state of health and so on, depending not only of environmental factors, but also of 'internal' rhythmic factor. Sometimes peaks and falls periodicity of some or other characteristics is broken. Disturbance of steady-state biological rhythms is usually accompanied by reduction of activity steadiness of the most important systems of a human organism. In its turn this has an effect on organism's adaptation to changing living conditions as well as on general condition and efficiency of a human being. The latter factor is very important for space medicine. Biological rhythmology is a special branch of biology and medicine, it studies rhythmic activity mechanisms of organs, their systems, individuals and species. Appropriate researches were also carried out in space medicine.

  7. Nuclear reactions

    International Nuclear Information System (INIS)

    Lane, A.M.

    1980-01-01

    In reviewing work at Harwell over the past 25 years on nuclear reactions it is stated that a balance has to be struck in both experiment and theory between work on cross-sections of direct practical relevance to reactors and on those relevant to an overall understanding of reaction processes. The compound nucleus and direct process reactions are described. Having listed the contributions from AERE, Harwell to developments in nuclear reaction research in the period, work on the optical model, neutron capture theory, reactions at doorway states with fine structure, and sum-rules for spectroscopic factors are considered in more detail. (UK)

  8. Exercise Countermeasures for Bone Loss During Space Flight: A Method for the Study of Ground Reaction Forces and their Implications for Bone Strain

    Science.gov (United States)

    Peterman, M.; McCrory, J. L.; Sharkey, N. A.; Piazza, S.; Cavanagh, P. R.

    1999-01-01

    Effective countermeasures to prevent loss of bone mineral during long duration space flight remain elusive. Despite an exercise program on MIR flights, the data from LeBlanc et al. (1996) indicated that there was still a mean rate of loss of bone mineral density in the proximal femur of 1.58% per month (n=18, flight duration 4 - 14.4 months). The specific mechanisms regulating bone mass are not known, but most investigators agree that bone maintenance is largely dependent upon mechanical demand and the resultant local bone strains. A plausible hypothesis is that bone loss during space flight, such as that reported by LeBlanc et al. (1996), may result from failure to effectively load the skeleton in order to generate localized bone strains of sufficient magnitude to prevent disuse osteoporosis. A variety of methods have been proposed to simulate locomotor exercise in reduced gravity. In such simulations, and in an actual microgravity environment, a gravity replacement load (GRL) must always be added to return the exercising subject to the support surface and the resulting skeletal load is critically dependent upon the magnitude of the GRL. To our knowledge, GRLs during orbital flight have only been measured once (on STS 81) and it is likely that most or all prior treadmill exercise in space has used GRLs that were less than one body weight. McCrory (1997) has shown that subjects walking and running in simulated zero-G can tolerate GRLs of 1 if an appropriate harness is used. Several investigators have attempted to measure in vivo strains and forces in the bones of humans, but have faced ethical and technical limitations. The anteromedial aspect of the tibial midshaft has been a common site for the placement of strain gauges; one reason to measure strains in the anterior tibia is that this region is surgically accessible. Aamodt et al. (1997) were able to measure strains on the lateral surface of the proximal femur only because their experimental subjects were

  9. An Evaluation of Collagen Metabolism in Non Human Primates Associated with the Bion 11 Space Program-Markers of Urinary Collagen Turnover and Muscle Connective Tissue

    Science.gov (United States)

    Vailas, Arthur C.; Martinez, Daniel A.

    1999-01-01

    Patients exhibiting changes in connective tissue and bone metabolism also show changes in urinary by-products of tissue metabolism. Furthermore, the changes in urinary connective tissue and bone metabolites precede alterations at the tissue macromolecular level. Astronauts and Cosmonauts have also shown suggestive increases in urinary by-products of mineralized and non-mineralized tissue degradation. Thus, the idea of assessing connective tissue and bone response in spaceflight monkeys by measurement of biomarkers in urine has merit. Other investigations of bone and connective histology, cytology and chemistry in the Bion 11 monkeys will allow for further validation of the relationship of urinary biomarkers and tissue response. In future flights the non-invasive procedure of urinary analysis may be useful in early detection of changes in these tissues. The purpose of this grant investigation was to evaluate mineralized and non-mineralized connective tissue responses of non-human primates to microgravity by the non-invasive analysis of urinary biomarkers. Secondly, we also wanted to assess muscle connective tissue adaptive changes in three weight-bearing skeletal muscles: the soleus, media] gastrocnemius and tibialis anterior by obtaining pre-flight and post-flight small biopsy specimens in collaboration with Dr. V. Reggie Edgerton's laboratory at the University of California at Los Angeles.

  10. RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity.

    Science.gov (United States)

    Hu, Qian-Nan; Deng, Zhe; Hu, Huanan; Cao, Dong-Sheng; Liang, Yi-Zeng

    2011-09-01

    Biochemical reactions play a key role to help sustain life and allow cells to grow. RxnFinder was developed to search biochemical reactions from KEGG reaction database using three search criteria: molecular structures, molecular fragments and reaction similarity. RxnFinder is helpful to get reference reactions for biosynthesis and xenobiotics metabolism. RxnFinder is freely available via: http://sdd.whu.edu.cn/rxnfinder. qnhu@whu.edu.cn.

  11. Genome-scale reconstruction of the Streptococcus pyogenes M49 metabolic network reveals growth requirements and indicates potential drug targets

    NARCIS (Netherlands)

    Levering, J.; Fiedler, T.; Sieg, A.; van Grinsven, K.W.A.; Hering, S.; Veith, N.; Olivier, B.G.; Klett, L.; Hugenholtz, J.; Teusink, B.; Kreikemeyer, B.; Kummer, U.

    2016-01-01

    Genome-scale metabolic models comprise stoichiometric relations between metabolites, as well as associations between genes and metabolic reactions and facilitate the analysis of metabolism. We computationally reconstructed the metabolic network of the lactic acid bacterium Streptococcus pyogenes

  12. Automated metabolic reconstruction for Methanococcus jannaschii

    Science.gov (United States)

    Tsoka, Sophia; Simon, David; Ouzounis, Christos A.

    2004-01-01

    We present the computational prediction and synthesis of the metabolic pathways in Methanococcus jannaschii from its genomic sequence using the PathoLogic software. Metabolic reconstruction is based on a reference knowledge base of metabolic pathways and is performed with minimal manual intervention. We predict the existence of 609 metabolic reactions that are assembled in 113 metabolic pathways and an additional 17 super-pathways consisting of one or more component pathways. These assignments represent significantly improved enzyme and pathway predictions compared with previous metabolic reconstructions, and some key metabolic reactions, previously missing, have been identified. Our results, in the form of enzymatic assignments and metabolic pathway predictions, form a database (MJCyc) that is accessible over the World Wide Web for further dissemination among members of the scientific community. PMID:15810431

  13. Automated metabolic reconstruction for Methanococcus jannaschii

    Directory of Open Access Journals (Sweden)

    Sophia Tsoka

    2004-01-01

    Full Text Available We present the computational prediction and synthesis of the metabolic pathways in Methanococcus jannaschii from its genomic sequence using the PathoLogic software. Metabolic reconstruction is based on a reference knowledge base of metabolic pathways and is performed with minimal manual intervention. We predict the existence of 609 metabolic reactions that are assembled in 113 metabolic pathways and an additional 17 super-pathways consisting of one or more component pathways. These assignments represent significantly improved enzyme and pathway predictions compared with previous metabolic reconstructions, and some key metabolic reactions, previously missing, have been identified. Our results, in the form of enzymatic assignments and metabolic pathway predictions, form a database (MJCyc that is accessible over the World Wide Web for further dissemination among members of the scientific community.

  14. Metabolic Syndrome

    Science.gov (United States)

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

  15. Reaction Wheel Disturbance Model Extraction Software Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Reaction wheel mechanical noise is one of the largest sources of disturbance forcing on space-based observatories. Such noise arises from mass imbalance, bearing...

  16. Genome-scale metabolic network of Cordyceps militaris useful for comparative analysis of entomopathogenic fungi.

    Science.gov (United States)

    Vongsangnak, Wanwipa; Raethong, Nachon; Mujchariyakul, Warasinee; Nguyen, Nam Ninh; Leong, Hon Wai; Laoteng, Kobkul

    2017-08-30

    The first genome-scale metabolic network of Cordyceps militaris (iWV1170) was constructed representing its whole metabolisms, which consisted of 894 metabolites and 1,267 metabolic reactions across five compartments, including the plasma membrane, cytoplasm, mitochondria, peroxisome and extracellular space. The iWV1170 could be exploited to explain its phenotypes of growth ability, cordycepin and other metabolites production on various substrates. A high number of genes encoding extracellular enzymes for degradation of complex carbohydrates, lipids and proteins were existed in C. militaris genome. By comparative genome-scale analysis, the adenine metabolic pathway towards putative cordycepin biosynthesis was reconstructed, indicating their evolutionary relationships across eleven species of entomopathogenic fungi. The overall metabolic routes involved in the putative cordycepin biosynthesis were also identified in C. militaris, including central carbon metabolism, amino acid metabolism (glycine, l-glutamine and l-aspartate) and nucleotide metabolism (adenosine and adenine). Interestingly, a lack of the sequence coding for ribonucleotide reductase inhibitor was observed in C. militaris that might contribute to its over-production of cordycepin. Copyright © 2017. Published by Elsevier B.V.

  17. Cyanohydrin reactions enhance glycolytic oscillations in yeast

    DEFF Research Database (Denmark)

    Hald, Bjørn Olav; Nielsen, Astrid Gram; Tortzen, Christian

    2015-01-01

    Synchronous metabolic oscillations can be induced in yeast by addition of glucose and removal of extracellular acetaldehyde (ACAx). Compared to other means of ACAx removal, cyanide robustly induces oscillations, indicating additional cyanide reactions besides ACA to lactonitrile conversion. Here...

  18. Structural correlations in bacterial metabolic networks

    Directory of Open Access Journals (Sweden)

    Lizana Ludvig

    2011-01-01

    Full Text Available Abstract Background Evolution of metabolism occurs through the acquisition and loss of genes whose products acts as enzymes in metabolic reactions, and from a presumably simple primordial metabolism the organisms living today have evolved complex and highly variable metabolisms. We have studied this phenomenon by comparing the metabolic networks of 134 bacterial species with known phylogenetic relationships, and by studying a neutral model of metabolic network evolution. Results We consider the 'union-network' of 134 bacterial metabolisms, and also the union of two smaller subsets of closely related species. Each reaction-node is tagged with the number of organisms it belongs to, which we denote organism degree (OD, a key concept in our study. Network analysis shows that common reactions are found at the centre of the network and that the average OD decreases as we move to the periphery. Nodes of the same OD are also more likely to be connected to each other compared to a random OD relabelling based on their occurrence in the real data. This trend persists up to a distance of around five reactions. A simple growth model of metabolic networks is used to investigate the biochemical constraints put on metabolic-network evolution. Despite this seemingly drastic simplification, a 'union-network' of a collection of unrelated model networks, free of any selective pressure, still exhibit similar structural features as their bacterial counterpart. Conclusions The OD distribution quantifies topological properties of the evolutionary history of bacterial metabolic networks, and lends additional support to the importance of horizontal gene transfer during bacterial metabolic evolution where new reactions are attached at the periphery of the network. The neutral model of metabolic network growth can reproduce the main features of real networks, but we observe that the real networks contain a smaller common core, while they are more similar at the periphery

  19. Structural correlations in bacterial metabolic networks.

    Science.gov (United States)

    Bernhardsson, Sebastian; Gerlee, Philip; Lizana, Ludvig

    2011-01-20

    Evolution of metabolism occurs through the acquisition and loss of genes whose products acts as enzymes in metabolic reactions, and from a presumably simple primordial metabolism the organisms living today have evolved complex and highly variable metabolisms. We have studied this phenomenon by comparing the metabolic networks of 134 bacterial species with known phylogenetic relationships, and by studying a neutral model of metabolic network evolution. We consider the 'union-network' of 134 bacterial metabolisms, and also the union of two smaller subsets of closely related species. Each reaction-node is tagged with the number of organisms it belongs to, which we denote organism degree (OD), a key concept in our study. Network analysis shows that common reactions are found at the centre of the network and that the average OD decreases as we move to the periphery. Nodes of the same OD are also more likely to be connected to each other compared to a random OD relabelling based on their occurrence in the real data. This trend persists up to a distance of around five reactions. A simple growth model of metabolic networks is used to investigate the biochemical constraints put on metabolic-network evolution. Despite this seemingly drastic simplification, a 'union-network' of a collection of unrelated model networks, free of any selective pressure, still exhibit similar structural features as their bacterial counterpart. The OD distribution quantifies topological properties of the evolutionary history of bacterial metabolic networks, and lends additional support to the importance of horizontal gene transfer during bacterial metabolic evolution where new reactions are attached at the periphery of the network. The neutral model of metabolic network growth can reproduce the main features of real networks, but we observe that the real networks contain a smaller common core, while they are more similar at the periphery of the network. This suggests that natural selection and

  20. Primary Metabolic Pathways and Metabolic Flux Analysis

    DEFF Research Database (Denmark)

    Villadsen, John

    2015-01-01

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

  1. Genetic and Proteomics Analyses of Space Flown Mice Skin

    Science.gov (United States)

    Terada, Masahiro; Takahashi, Rika; Yamada, Shin; Masaya, Seki; Higashibata, Akira; Majima, Hideyuki J.; Ohira, Yoshinobu; Mukai, Chiaki; Ishioka, Noriaki

    2013-02-01

    Many astronauts stay in the International Space Station (ISS) for a long period of time. Therefore, the development of astronaut health care technologies is very important. Especially, an understanding of the effects of the space environment, such as microgravity and radiation, on protein, gene, and mineral metabolism is important for developing countermeasures against the adverse effects experienced by astronauts who are in space for long periods of time. Since December 2009, the Japan Aerospace Exploration Agency (JAXA) has initiated a human research study to investigate the effects of long-term space flight on gene expression and mineral metabolism by analyzing hair samples from ISS crew members who have been in space (experiment nicknamed “HAIR”). As animal control experiments, we could have an opportunity to analyze rodents samples by participating the tissue sharing program of space-flown mice organized by Italian Space Agency (AGI) and National Aeronautics and Space Administration (NASA). It will reasonably complement human hair experiment because we able to conduct more detailed skin analysis which is enable in human experiment. The purpose of this flown-mice experiment is to study the effects of long-term exposure to space environment. In this experiment, we analyzed mice skin contained hair roots. The samples were taken from space-flown (3-month and 2-week) and 3-month hindlimb suspensioned and 3-month 2G exposed mice, and ground-control mice. For the skin contained hair roots, the extracted and amplified RNA was used to DNA microarray analysis, and was further analyzed with expression on the interesting genes by real time Reverse Transcription Polymerase Chain Reaction (RT-PCR) method. And the extracted protein was used to Mass Spectrometer analysis. Data analysis on the specimen are in progress.

  2. Surface Reactions in the Space Environment

    Science.gov (United States)

    1988-01-01

    From the beginning, a central goal of this effort has been to establish a coordinated multidisciplinary Center of Excellence program concentrating...References 1. M. Faraday, "Sur la Coloration produite par la lumiere, dans une espece particuliere de carreaux de vitres", Annale de Chimie et de

  3. Reaction mechanisms

    International Nuclear Information System (INIS)

    Nguyen Trong Anh

    1988-01-01

    The 1988 progress report of the Reaction Mechanisms laboratory (Polytechnic School, France), is presented. The research topics are: the valence bond methods, the radical chemistry, the modelling of the transition states by applying geometric constraints, the long range interactions (ion - molecule) in gaseous phase, the reaction sites in gaseous phase and the mass spectroscopy applications. The points of convergence between the investigations of the mass spectroscopy and the theoretical chemistry teams, as well as the purposes guiding the research programs, are discussed. The published papers, the conferences, the congress communications and the thesis, are also reported [fr

  4. Spontaneous emergence of a metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Bagley, R.J.; Farmer, J.D. (Los Alamos National Lab., NM (USA) Santa Fe Inst., NM (USA))

    1990-01-01

    Networks of catalyzed reactions with nonlinear feedback have been proposed to play an important role in the origin of life. We investigate this possibility in a polymer chemistry with catalyzed cleavage and condensation reactions. We study the properties of a well-stirred reactor driven away from equilibrium by the flow of mass. Under appropriate non-equilibrium conditions. The nonlinear feedback of the reaction network focuses the material of the system into a few specific polymer species. The network of catalytic reactions digests'' the material of its environment, incorporating it into its own form. We call the result an autocatalytic metabolism. Under some variations it persists almost unchanged, while in other cases it dies. We argue that the dynamical stability of autocatalytic metabolisms gives them regenerative properties that allow them to repair themselves and to propagate through time. 43 refs., 16 figs., 3 tabs.

  5. Nucleotide Metabolism

    DEFF Research Database (Denmark)

    Martinussen, Jan; Willemoës, M.; Kilstrup, Mogens

    2011-01-01

    Metabolic pathways are connected through their utilization of nucleotides as supplier of energy, allosteric effectors, and their role in activation of intermediates. Therefore, any attempt to exploit a given living organism in a biotechnological process will have an impact on nucleotide metabolism...

  6. Capture reactions

    NARCIS (Netherlands)

    Endt, P.M.

    1956-01-01

    Capture reactions will be considered here from the viewpoint of the nuclear spectroscopist. Especially important to him are the capture of neutrons, protons, and alpha particles, which may proceed through narrow resonances, offering a well defined initial state for the subsequent deexcitation

  7. Allergic reactions

    Science.gov (United States)

    ... that don't bother most people (such as venom from bee stings and certain foods, medicines, and pollens) can ... person. If the allergic reaction is from a bee sting, scrape the ... more venom. If the person has emergency allergy medicine on ...

  8. cycloaddition reactions

    Indian Academy of Sciences (India)

    Unknown

    ... has shown very severe limitations in predicting the regioselectivity. In comparison,. DFT-based descriptors are better suited to model the regioselectivity of cycloaddition reactions. Acknowledgements. GG thanks the Council of Scientific and Industrial. Research for a fellowship. References. 1. Winkler J D 1996 Chem. Rev.

  9. A compendium of inborn errors of metabolism mapped onto the human metabolic network.

    Science.gov (United States)

    Sahoo, Swagatika; Franzson, Leifur; Jonsson, Jon J; Thiele, Ines

    2012-10-01

    Inborn errors of metabolism (IEMs) are hereditary metabolic defects, which are encountered in almost all major metabolic pathways occurring in man. Many IEMs are screened for in neonates through metabolomic analysis of dried blood spot samples. To enable the mapping of these metabolomic data onto the published human metabolic reconstruction, we added missing reactions and pathways involved in acylcarnitine (AC) and fatty acid oxidation (FAO) metabolism. Using literary data, we reconstructed an AC/FAO module consisting of 352 reactions and 139 metabolites. When this module was combined with the human metabolic reconstruction, the synthesis of 39 acylcarnitines and 22 amino acids, which are routinely measured, was captured and 235 distinct IEMs could be mapped. We collected phenotypic and clinical features for each IEM enabling comprehensive classification. We found that carbohydrate, amino acid, and lipid metabolism were most affected by the IEMs, while the brain was the most commonly affected organ. Furthermore, we analyzed the IEMs in the context of metabolic network topology to gain insight into common features between metabolically connected IEMs. While many known examples were identified, we discovered some surprising IEM pairs that shared reactions as well as clinical features but not necessarily causal genes. Moreover, we could also re-confirm that acetyl-CoA acts as a central metabolite. This network based analysis leads to further insight of hot spots in human metabolism with respect to IEMs. The presented comprehensive knowledge base of IEMs will provide a valuable tool in studying metabolic changes involved in inherited metabolic diseases.

  10. Incremental parameter estimation of kinetic metabolic network models

    Directory of Open Access Journals (Sweden)

    Jia Gengjie

    2012-11-01

    Full Text Available Abstract Background An efficient and reliable parameter estimation method is essential for the creation of biological models using ordinary differential equation (ODE. Most of the existing estimation methods involve finding the global minimum of data fitting residuals over the entire parameter space simultaneously. Unfortunately, the associated computational requirement often becomes prohibitively high due to the large number of parameters and the lack of complete parameter identifiability (i.e. not all parameters can be uniquely identified. Results In this work, an incremental approach was applied to the parameter estimation of ODE models from concentration time profiles. Particularly, the method was developed to address a commonly encountered circumstance in the modeling of metabolic networks, where the number of metabolic fluxes (reaction rates exceeds that of metabolites (chemical species. Here, the minimization of model residuals was performed over a subset of the parameter space that is associated with the degrees of freedom in the dynamic flux estimation from the concentration time-slopes. The efficacy of this method was demonstrated using two generalized mass action (GMA models, where the method significantly outperformed single-step estimations. In addition, an extension of the estimation method to handle missing data is also presented. Conclusions The proposed incremental estimation method is able to tackle the issue on the lack of complete parameter identifiability and to significantly reduce the computational efforts in estimating model parameters, which will facilitate kinetic modeling of genome-scale cellular metabolism in the future.

  11. Metabolism of xenobiotics of human environments.

    Science.gov (United States)

    Croom, Edward

    2012-01-01

    Xenobiotics have been defined as chemicals to which an organism is exposed that are extrinsic to the normal metabolism of that organism. Without metabolism, many xenobiotics would reach toxic concentrations. Most metabolic activity inside the cell requires energy, cofactors, and enzymes in order to occur. Xenobiotic-metabolizing enzymes can be divided into phase I, phase II, and transporter enzymes. Lipophilic xenobiotics are often first metabolized by phase I enzymes, which function to make xenobiotics more polar and provide sites for conjugation reactions. Phase II enzymes are conjugating enzymes and can directly interact with xenobiotics but more commonly interact with metabolites produced by phase I enzymes. Through both passive and active transport, these more polar metabolites are eliminated. Most xenobiotics are cleared through multiple enzymes and pathways. The relationship between chemical concentrations, enzyme affinity and quantity, and cofactor availability often determine which metabolic reactions dominate in a given individual. Copyright © 2012 Elsevier Inc. All rights reserved.

  12. Drug Metabolism

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 19; Issue 3. Drug Metabolism: A Fascinating Link Between Chemistry and Biology. Nikhil Taxak Prasad V Bharatam. General Article Volume 19 Issue 3 March 2014 pp 259-282 ...

  13. Drug Metabolism

    Indian Academy of Sciences (India)

    IAS Admin

    Drug metabolism may be defined as the biochemical modifica- tion of one chemical form to another, occurring usually through ..... Endogenous. Enzyme. Drugs. Cofactor. Glucuronidation. UDP glucoronic. UDP-. Chloramphenicol, acid glucuronosyltransferase morphine, paracetamol, salicylic acid, fenoprofen, desipramine,.

  14. Metabolic Myopathies.

    Science.gov (United States)

    Tarnopolsky, Mark A

    2016-12-01

    Metabolic myopathies are genetic disorders that impair intermediary metabolism in skeletal muscle. Impairments in glycolysis/glycogenolysis (glycogen-storage disease), fatty acid transport and oxidation (fatty acid oxidation defects), and the mitochondrial respiratory chain (mitochondrial myopathies) represent the majority of known defects. The purpose of this review is to develop a diagnostic and treatment algorithm for the metabolic myopathies. The metabolic myopathies can present in the neonatal and infant period as part of more systemic involvement with hypotonia, hypoglycemia, and encephalopathy; however, most cases present in childhood or in adulthood with exercise intolerance (often with rhabdomyolysis) and weakness. The glycogen-storage diseases present during brief bouts of high-intensity exercise, whereas fatty acid oxidation defects and mitochondrial myopathies present during a long-duration/low-intensity endurance-type activity or during fasting or another metabolically stressful event (eg, surgery, fever). The clinical examination is often normal between acute events, and evaluation involves exercise testing, blood testing (creatine kinase, acylcarnitine profile, lactate, amino acids), urine organic acids (ketones, dicarboxylic acids, 3-methylglutaconic acid), muscle biopsy (histology, ultrastructure, enzyme testing), MRI/spectroscopy, and targeted or untargeted genetic testing. Accurate and early identification of metabolic myopathies can lead to therapeutic interventions with lifestyle and nutritional modification, cofactor treatment, and rapid treatment of rhabdomyolysis.

  15. Animal metabolism

    International Nuclear Information System (INIS)

    Walburg, H.E.

    1977-01-01

    Studies on placental transport included the following: clearance of tritiated water as a baseline measurement for transport of materials across perfused placentas; transport of organic and inorganic mercury across the perfused placenta of the guinea pig in late gestation; and transport of cadmium across the perfused placenta of the guinea pig in late gestation. Studies on cadmium absorption and metabolism included the following: intestinal absorption and retention of cadmium in neonatal rats; uptake and distribution of an oral dose of cadmium in postweanling male and female, iron-deficient and normal rats; postnatal viability and growth in rat pups after oral cadmium administration during gestation; and the effect of calcium and phosphorus on the absorption and toxicity of cadmium. Studies on gastrointestinal absorption and mineral metabolism included: uptake and distribution of orally administered plutonium complex compounds in male mice; gastrointestinal absorption of 144 Ce in the newborn mouse, rat, and pig; and gastrointestinal absorption of 95 Nb by rats of different ages. Studies on iodine metabolism included the following: influence of thyroid status and thiocyanate on iodine metabolism in the bovine; effects of simulated fallout radiation on iodine metabolism in dairy cattle; and effects of feeding iodine binding agents on iodine metabolism in the calf

  16. Noise propagation in synthetic gene circuits for metabolic control.

    Science.gov (United States)

    Oyarzún, Diego A; Lugagne, Jean-Baptiste; Stan, Guy-Bart V

    2015-02-20

    Dynamic control of enzyme expression can be an effective strategy to engineer robust metabolic pathways. It allows a synthetic pathway to self-regulate in response to changes in bioreactor conditions or the metabolic state of the host. The implementation of this regulatory strategy requires gene circuits that couple metabolic signals with the genetic machinery, which is known to be noisy and one of the main sources of cell-to-cell variability. One of the unexplored design aspects of these circuits is the propagation of biochemical noise between enzyme expression and pathway activity. In this article, we quantify the impact of a synthetic feedback circuit on the noise in a metabolic product in order to propose design criteria to reduce cell-to-cell variability. We consider a stochastic model of a catalytic reaction under negative feedback from the product to enzyme expression. On the basis of stochastic simulations and analysis, we show that, depending on the repression strength and promoter strength, transcriptional repression of enzyme expression can amplify or attenuate the noise in the number of product molecules. We obtain analytic estimates for the metabolic noise as a function of the model parameters and show that noise amplification/attenuation is a structural property of the model. We derive an analytic condition on the parameters that lead to attenuation of metabolic noise, suggesting that a higher promoter sensitivity enlarges the parameter design space. In the theoretical case of a switch-like promoter, our analysis reveals that the ability of the circuit to attenuate noise is subject to a trade-off between the repression strength and promoter strength.

  17. Spallation reactions

    International Nuclear Information System (INIS)

    Cugon, J.

    1996-01-01

    Spallation reactions dominate the interactions of hadrons with nuclei in the GeV range (from ∼ 0.1 to ∼ 10 GeV). They correspond to a sometimes important ejection of light particles leaving most of the time a residue of mass commensurate with the target mass. The main features of the experimental data are briefly reviewed. The most successful theoretical model, namely the intranuclear cascade + evaporation model, is presented. Its physical content, results and possible improvements are critically discussed. Alternative approaches are shortly reviewed. (author)

  18. Space debris; challenges and solutions

    NARCIS (Netherlands)

    Van Beurden, E.; Prins, C.

    2013-01-01

    Space debris has been a hot topic for the last few decades, ever since the space industry started growing exponentially. Everyone agrees that space debris is a growing problem and the saturation point has almost been reached. With a big risk of a chain reaction, called the Kessler syndrome, billions

  19. Stickland reactions of dental plaque.

    Science.gov (United States)

    Curtis, M A; Kemp, C W; Robrish, S A; Bowen, W H

    1983-01-01

    Dental plaque samples from monkeys (Macaca fascicularis) were shown to contain proline reduction activity in coupled Stickland reactions with other amino acids and also with certain end products of bacterial glucose metabolism. The unusually high concentration of bound and free proline in the oral environment may be of importance in both the production of base and in the removal of acid from the tooth surface after dietary carbohydrate ingestion. PMID:6618673

  20. Microalgal Metabolic Network Model Refinement through High-Throughput Functional Metabolic Profiling

    International Nuclear Information System (INIS)

    Chaiboonchoe, Amphun; Dohai, Bushra Saeed; Cai, Hong; Nelson, David R.; Jijakli, Kenan; Salehi-Ashtiani, Kourosh

    2014-01-01

    Metabolic modeling provides the means to define metabolic processes at a systems level; however, genome-scale metabolic models often remain incomplete in their description of metabolic networks and may include reactions that are experimentally unverified. This shortcoming is exacerbated in reconstructed models of newly isolated algal species, as there may be little to no biochemical evidence available for the metabolism of such isolates. The phenotype microarray (PM) technology (Biolog, Hayward, CA, USA) provides an efficient, high-throughput method to functionally define cellular metabolic activities in response to a large array of entry metabolites. The platform can experimentally verify many of the unverified reactions in a network model as well as identify missing or new reactions in the reconstructed metabolic model. The PM technology has been used for metabolic phenotyping of non-photosynthetic bacteria and fungi, but it has not been reported for the phenotyping of microalgae. Here, we introduce the use of PM assays in a systematic way to the study of microalgae, applying it specifically to the green microalgal model species Chlamydomonas reinhardtii. The results obtained in this study validate a number of existing annotated metabolic reactions and identify a number of novel and unexpected metabolites. The obtained information was used to expand and refine the existing COBRA-based C. reinhardtii metabolic network model iRC1080. Over 254 reactions were added to the network, and the effects of these additions on flux distribution within the network are described. The novel reactions include the support of metabolism by a number of d-amino acids, l-dipeptides, and l-tripeptides as nitrogen sources, as well as support of cellular respiration by cysteamine-S-phosphate as a phosphorus source. The protocol developed here can be used as a foundation to functionally profile other microalgae such as known microalgae mutants and novel isolates.

  1. Microalgal Metabolic Network Model Refinement through High Throughput Functional Metabolic Profiling

    Directory of Open Access Journals (Sweden)

    Amphun eChaiboonchoe

    2014-12-01

    Full Text Available Metabolic modeling provides the means to define metabolic processes at a systems level; however, genome-scale metabolic models often remain incomplete in their description of metabolic networks and may include reactions that are experimentally unverified. This shortcoming is exacerbated in reconstructed models of newly isolated algal species, as there may be little to no biochemical evidence available for the metabolism of such isolates. The Phenotype Microarray (PM technology (Biolog, Hayward, CA, USA provides an efficient, high throughput method to functionally define cellular metabolic activities in response to a large array of entry metabolites. The platform can experimentally verify many of the unverified reactions in a network model as well as identify missing or new reactions in the reconstructed metabolic model. The PM technology has been used for metabolic phenotyping of non-photosynthetic bacteria and fungi but it has not been reported for the phenotyping of microalgae. Here we introduce the use of PM assays in a systematic way to the study of microalgae, applying it specifically to the green microalgal model species Chlamydomonas reinhardtii. The results obtained in this study validate a number of existing annotated metabolic reactions and identify a number of novel and unexpected metabolites. The obtained information was used to expand and refine the existing COBRA-based C. reinhardtii metabolic network model iRC1080. Over 254 reactions were added to the network, and the effects of these additions on flux distribution within the network are described. The novel reactions include the support of metabolism by a number of D-amino acids, L-dipeptides, and L-tripeptides as nitrogen sources, as well as support of cellular respiration by cysteamine-S-phosphate as a phosphorus source. The protocol developed here can be used as a foundation to functionally profile other microalgae such as known microalgae mutants and novel isolates.

  2. Microalgal Metabolic Network Model Refinement through High-Throughput Functional Metabolic Profiling.

    Science.gov (United States)

    Chaiboonchoe, Amphun; Dohai, Bushra Saeed; Cai, Hong; Nelson, David R; Jijakli, Kenan; Salehi-Ashtiani, Kourosh

    2014-01-01

    Metabolic modeling provides the means to define metabolic processes at a systems level; however, genome-scale metabolic models often remain incomplete in their description of metabolic networks and may include reactions that are experimentally unverified. This shortcoming is exacerbated in reconstructed models of newly isolated algal species, as there may be little to no biochemical evidence available for the metabolism of such isolates. The phenotype microarray (PM) technology (Biolog, Hayward, CA, USA) provides an efficient, high-throughput method to functionally define cellular metabolic activities in response to a large array of entry metabolites. The platform can experimentally verify many of the unverified reactions in a network model as well as identify missing or new reactions in the reconstructed metabolic model. The PM technology has been used for metabolic phenotyping of non-photosynthetic bacteria and fungi, but it has not been reported for the phenotyping of microalgae. Here, we introduce the use of PM assays in a systematic way to the study of microalgae, applying it specifically to the green microalgal model species Chlamydomonas reinhardtii. The results obtained in this study validate a number of existing annotated metabolic reactions and identify a number of novel and unexpected metabolites. The obtained information was used to expand and refine the existing COBRA-based C. reinhardtii metabolic network model iRC1080. Over 254 reactions were added to the network, and the effects of these additions on flux distribution within the network are described. The novel reactions include the support of metabolism by a number of d-amino acids, l-dipeptides, and l-tripeptides as nitrogen sources, as well as support of cellular respiration by cysteamine-S-phosphate as a phosphorus source. The protocol developed here can be used as a foundation to functionally profile other microalgae such as known microalgae mutants and novel isolates.

  3. What is Metabolic Syndrome?

    Science.gov (United States)

    ... Research Home / Metabolic Syndrome Metabolic Syndrome What Is Metabolic syndrome is the name for a group of risk ... three metabolic risk factors to be diagnosed with metabolic syndrome. A large waistline. This also is called abdominal ...

  4. In-time and in-space tandem mass spectrometry to determine the metabolic profiling of flavonoids in a typical sweet cherry (Prunus avium L.) cultivar from Southern Italy.

    Science.gov (United States)

    Crupi, Pasquale; Genghi, Rosalinda; Antonacci, Donato

    2014-10-01

    This paper presents a comprehensive analytical methodology, based on 'in-time' and 'in-space' tandem mass spectrometry (MS) techniques, to identify and quantify flavonoid compounds in a typical Italian sweet cherry cultivar (cv. Ferrovia). Five anthocyanins, four flavan-3-ols and nine flavonols were determined by means of hyphenated high-performance liquid chromatography - multi-stage MS (HPLC-MS(n)) analyses (MS(n) up to MS(4)), among which quercetin-3-O-rutinoside-7-O-glucoside, kaempferol-3-O-rutinoside-7-O-glucoside, quercetin-3-O-galactosyl-rhamnoside and quercetin-3-O-coumaroylglucoside were tentatively identified in sweet cherries for the first time. Ultrafast HPLC and tandem MS (UHPLC-MS/MS) analyses through multiple reaction monitoring experiments showed that cyanidin-3-O-rutinoside and cyanidin-3-O-glucoside were the main anthocyanins of cv. Ferrovia at maturity. Moreover, consistent levels of catechin and epicatechin as well as quercetin-3-O-rutinoside and kaempferol-3-O-rutinoside were also found. Because flavonoids have been ascribed as potential health-promoting compounds, gathered findings provide new insight into the knowledge of the quali-quantitative profile of these phytochemicals into a widespread fruit such as sweet cherry. Copyright © 2014 John Wiley & Sons, Ltd.

  5. Nuclear reactions

    International Nuclear Information System (INIS)

    Corner, J.; Richardson, K.; Fenton, N.

    1990-01-01

    Nuclear reactions' marks a new development in the study of television as an agency of public policy debate. During the Eighties, nuclear energy became a major international issue. The disasters at Three-mile Island and Chernobyl created a global anxiety about its risks and a new sensitivity to it among politicians and journalists. This book is a case-study into documentary depictions of nuclear energy in television and video programmes and into the interpretations and responses of viewers drawn from many different occupational groupings. How are the complex and specialist arguments about benefit, risk and proof conveyed through the different conventions of commentary, interview and film sequence? What symbolic associations does the visual language of television bring to portrayals of the issue? And how do viewers make sense of various and conflicting accounts, connecting what they see and hear on the screen with their pre-existing knowledge, experience and 'civic' expectations. The authors examine some of the contrasting forms and themes which have been used by programme makers to explain and persuade, and then give a sustained analysis of the nature and sources of viewers' own accounts. 'Nuclear Reactions' inquires into the public meanings surrounding energy and the environment, spelling out in its conclusion some of the implications for future media treatments of this issue. It is also a key contribution to the international literature on 'television knowledge' and the processes of active viewing. (author)

  6. Microfabricated electrochemiluminescence cell for chemical reaction detection

    Science.gov (United States)

    Northrup, M. Allen; Hsueh, Yun-Tai; Smith, Rosemary L.

    2003-01-01

    A detector cell for a silicon-based or non-silicon-based sleeve type chemical reaction chamber that combines heaters, such as doped polysilicon for heating, and bulk silicon for convection cooling. The detector cell is an electrochemiluminescence cell constructed of layers of silicon with a cover layer of glass, with spaced electrodes located intermediate various layers forming the cell. The cell includes a cavity formed therein and fluid inlets for directing reaction fluid therein. The reaction chamber and detector cell may be utilized in any chemical reaction system for synthesis or processing of organic, inorganic, or biochemical reactions, such as the polymerase chain reaction (PCR) and/or other DNA reactions, such as the ligase chain reaction, which are examples of a synthetic, thermal-cycling-based reaction. The ECL cell may also be used in synthesis instruments, particularly those for DNA amplification and synthesis.

  7. [Metabolic myopathies].

    Science.gov (United States)

    Papazian, Óscar; Rivas-Chacón, Rafael

    2013-09-06

    To review the metabolic myopathies manifested only by crisis of myalgias, cramps and rigidity of the muscles with decreased voluntary contractions and normal inter crisis neurologic examination in children and adolescents. These metabolic myopathies are autosomic recessive inherited enzymatic deficiencies of the carbohydrates and lipids metabolisms. The end result is a reduction of intra muscle adenosine triphosphate, mainly through mitochondrial oxidative phosphorylation, with decrease of available energy for muscle contraction. The one secondary to carbohydrates intra muscle metabolism disorders are triggered by high intensity brief (fatty acids metabolism disorders are triggered by low intensity prolonged (> 10 min) exercises. The conditions in the first group in order of decreasing frequency are the deficiencies of myophosforilase (GSD V), muscle phosphofructokinase (GSD VII), phosphoglycerate mutase 1 (GSD X) and beta enolase (GSD XIII). The conditions in the second group in order of decreasing frequency are the deficiencies of carnitine palmitoyl transferase II and very long chain acyl CoA dehydrogenase. The differential characteristics of patients in each group and within each group will allow to make the initial presumptive clinical diagnosis in the majority and then to order only the necessary tests to achieve the final diagnosis. Treatment during the crisis includes hydration, glucose and alkalinization of urine if myoglobin in blood and urine are elevated. Prevention includes avoiding exercise which may induce the crisis and fasting. The prognosis is good with the exception of rare cases of acute renal failure due to hipermyoglobinemia because of severe rabdomyolisis.

  8. Neuroinflammatory basis of metabolic syndrome.

    Science.gov (United States)

    Purkayastha, Sudarshana; Cai, Dongsheng

    2013-10-05

    Inflammatory reaction is a fundamental defense mechanism against threat towards normal integrity and physiology. On the other hand, chronic diseases such as obesity, type 2 diabetes, hypertension and atherosclerosis, have been causally linked to chronic, low-grade inflammation in various metabolic tissues. Recent cross-disciplinary research has led to identification of hypothalamic inflammatory changes that are triggered by overnutrition, orchestrated by hypothalamic immune system, and sustained through metabolic syndrome-associated pathophysiology. While continuing research is actively trying to underpin the identity and mechanisms of these inflammatory stimuli and actions involved in metabolic syndrome disorders and related diseases, proinflammatory IκB kinase-β (IKKβ), the downstream nuclear transcription factor NF-κB and some related molecules in the hypothalamus were discovered to be pathogenically significant. This article is to summarize recent progresses in the field of neuroendocrine research addressing the central integrative role of neuroinflammation in metabolic syndrome components ranging from obesity, glucose intolerance to cardiovascular dysfunctions.

  9. Optimal flux patterns in cellular metabolic networks

    Energy Technology Data Exchange (ETDEWEB)

    Almaas, E

    2007-01-20

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

  10. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network

    DEFF Research Database (Denmark)

    Förster, Jochen; Famili, I.; Fu, P.

    2003-01-01

    and the environment were included. A total of 708 structural open reading frames (ORFs) were accounted for in the reconstructed network, corresponding to 1035 metabolic reactions. Further, 140 reactions were included on the basis of biochemical evidence resulting in a genome-scale reconstructed metabolic network...... with Escherichia coli. The reconstructed metabolic network is the first comprehensive network for a eukaryotic organism, and it may be used as the basis for in silico analysis of phenotypic functions....

  11. Response to trauma and metabolic changes: posttraumatic metabolism.

    Science.gov (United States)

    Şimşek, Turgay; Şimşek, Hayal Uzelli; Cantürk, Nuh Zafer

    2014-01-01

    Stress response caused by events such as surgical trauma includes endocrine, metabolic and immunological changes. Stress hormones and cytokines play a role in these reactions. More reactions are induced by greater stress, ultimately leading to greater catabolic effects. Cuthbertson reported the characteristic response that occurs in trauma patients: protein and fat consumption and protection of body fluids and electrolytes because of hypermetabolism in the early period. The oxygen and energy requirement increases in proportion to the severity of trauma. The awareness of alterations in amino acid, lipid, and carbohydrate metabolism changes in surgical patients is important in determining metabolic and nutritional support. The main metabolic change in response to injury that leads to a series of reactions is the reduction of the normal anabolic effect of insulin, i.e. the development of insulin resistance. Free fatty acids are primary sources of energy after trauma. Triglycerides meet 50 to 80 % of the consumed energy after trauma and in critical illness. Surgical stress and trauma result in a reduction in protein synthesis and moderate protein degradation. Severe trauma, burns and sepsis result in increased protein degradation. The aim of glucose administration to surgical patients during fasting is to reduce proteolysis and to prevent loss of muscle mass. In major stress such as sepsis and trauma, it is important both to reduce the catabolic response that is the key to faster healing after surgery and to obtain a balanced metabolism in the shortest possible time with minimum loss. For these reasons, the details of metabolic response to trauma should be known in managing these situations and patients should be treated accordingly.

  12. Quantitative determination of five metabolites of aspirin by UHPLC-MS/MS coupled with enzymatic reaction and its application to evaluate the effects of aspirin dosage on the metabolic profile.

    Science.gov (United States)

    Li, Jian-Ping; Guo, Jian-Ming; Shang, Er-Xin; Zhu, Zhen-Hua; Liu, Yang; Zhao, Bu-Chang; Zhao, Jing; Tang, Zhi-Shu; Duan, Jin-Ao

    2017-05-10

    Acetylsalicylic acid (Aspirin, ASA) is a famous drug for cardiovascular diseases in recent years. Effects of ASA dosage on the metabolic profile have not been fully understood. The purpose of our study is to establish a rapid and reliable method to quantify ASA metabolites in biological matrices, especially for glucuronide metabolites whose standards are not commercially available. Then we applied this method to evaluate the effects of ASA dosage on the metabolic and excretion profile of ASA metabolites in rat urine. Salicylic acid (SA), gentisic acid (GA) and salicyluric acid (SUA) were determined directly by UHPLC-MS/MS, while salicyl phenolic glucuronide (SAPG) and salicyluric acid phenolic glucuronide (SUAPG) were quantified indirectly by measuring the released SA and SUA from SAPG and SUAPG after β-glucuronidase digestion. SUA and SUAPG were the major metabolites of ASA in rat urine 24h after ASA administration, which accounted for 50% (SUA) and 26% (SUAPG). When ASA dosage was increased, the contributions dropped to 32% and 18%, respectively. The excretion of other three metabolites (GA, SA and SAPG) however showed remarkable increases by 16%, 6% and 4%, respectively. In addition, SUA and SUAPG were mainly excreted in the time period of 12-24h, while GA was excreted in the earlier time periods (0-4h and 4-8h). SA was mainly excreted in the time period of 0-4h and 12-24h. And the excretion of SAPG was equally distributed in the four time periods. We went further to show that the excretion of five metabolites in rat urine was delayed when ASA dosage was increased. In conclusion, we have developed a rapid and sensitive method to determine the five ASA metabolites (SA, GA, SUA, SAPG and SUAPG) in rat urine. We showed that ASA dosage could significantly influence the metabolic and excretion profile of ASA metabolites in rat urine. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Space Detectives

    Science.gov (United States)

    Tyszka, Steph; Saraiva, Jose; Doran, Rosa

    2017-04-01

    NUCLIO is a Portuguese non-profit organization with a strong record of investing in science education and outreach. We have developed and implemented many activities mostly directed to a young audience, in a bid to awaken and reinforce the interest that young people devote to Astronomy and all things spatial. In this framework, we have created a week-long program called Space Detectives, supported by the Municipality of Cascais, based on a story-line that provided a number of challenges and opportunities for learning matters as diverse as the electro-magnetic spectrum, means of communication, space travel, the martian environment, coding and robotics. We report on the first session that took place in December 2016. We had as participants several kids aged 9 to 12, with a mixed background in terms of interest in the sciences. Their response varied from enthusiastic to somewhat less interested, depending on the nature of the subject and the way it was presented - a reaction not necessarily related to its complexity. This week was taken as something of a trial run, in preparation for the European Commission- funded project "Stories of Tomorrow", to be implemented in schools. The individual activities and the way they were related to the story-line, as well as the smooth transition from one to the next, were subject to an analysis that will allow for improvements in the next installments of this program. We believe this is an excellent approach to the goals of using Space and Astronomy as an anchor for generating and keeping interest in the scientific areas, and of finding new and richer ways of learning.

  14. Modelling Tethered Enzymatic Reactions

    Science.gov (United States)

    Solis Salas, Citlali; Goyette, Jesse; Coker-Gordon, Nicola; Bridge, Marcus; Isaacson, Samuel; Allard, Jun; Maini, Philip; Dushek, Omer

    Enzymatic reactions are key to cell functioning, and whilst much work has been done in protein interaction in cases where diffusion is possible, interactions of tethered proteins are poorly understood. Yet, because of the large role cell membranes play in enzymatic reactions, several reactions may take place where one of the proteins is bound to a fixed point in space. We develop a model to characterize tethered signalling between the phosphatase SHP-1 interacting with a tethered, phosphorylated protein. We compare our model to experimental data obtained using surface plasmon resonance (SPR). We show that a single SPR experiment recovers 5 independent biophysical/biochemical constants. We also compare the results between a three dimensional model and a two dimensional model. The work gives the opportunity to use known techniques to learn more about signalling processes, and new insights into how enzyme tethering alters cellular signalling. With support from the Mexican Council for Science and Technology (CONACyT), the Public Education Secretariat (SEP), and the Mexican National Autonomous University's Foundation (Fundacion UNAM).

  15. Reaction Wheel with Embedded MEMS IMU, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — The innovation is to embed a MEMS IMU Sensor Chip into a reaction wheel to measure its spin rate as well as wheel attitude rate. We propose to use a reaction wheel...

  16. Reaction Wheel with Embedded MEMS IMU Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Reaction wheels are used to stabilize satellites and to slew their orientation from object to object with precision and accuracy by varying the rotational speed of...

  17. Reaction Wheel Disturbance Model Extraction Software Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Reaction wheel disturbances are some of the largest sources of noise on sensitive telescopes. Such wheel-induced mechanical noises are not well characterized....

  18. Metabolic Engineering

    Indian Academy of Sciences (India)

    IAS Admin

    and in vitro to be able to alter properties of the encoded enzyme, and (6) assemble an array of genes for their expression inside the host cell. Although bacteria and yeast are the pioneering hosts for metabolic engineering, other organisms such as fungi, animal as well as plant cells are also used nowadays for similar experi ...

  19. Metabolic Engineering

    Indian Academy of Sciences (India)

    IAS Admin

    Metabolic engineering is a process for modulating the me- tabolism of the organisms so as to produce the required amounts of the desired metabolite through genetic manipula- tions. Considering its advantages over the other chemical synthesis routes, this area of biotechnology is likely to revolu- tionize the way in which ...

  20. Metabolic syndrome

    Science.gov (United States)

    ... gov/pubmed/26718656 . Ruderman NB, Shulman GI. Metabolic syndrome. In: Jameson JL, De Groot LJ, de Kretser DM, et al, eds. Endocrinology: Adult and Pediatric . 7th ed. Philadelphia, PA: Elsevier Saunders; 2016:chap 43. Review ... NIH MedlinePlus Magazine Read more Health ...

  1. Metabolic Disorders

    Science.gov (United States)

    Metabolism is the process your body uses to get or make energy from the food you eat. Food is made up of proteins, carbohydrates, and fats. Chemicals in your digestive system break the food parts down into sugars and acids, your body's ...

  2. Chain reaction

    International Nuclear Information System (INIS)

    Balogh, Brian.

    1991-01-01

    Chain Reaction is a work of recent American political history. It seeks to explain how and why America came to depend so heavily on its experts after World War II, how those experts translated that authority into political clout, and why that authority and political discretion declined in the 1970s. The author's research into the internal memoranda of the Atomic Energy Commission substantiates his argument in historical detail. It was not the ravages of American anti-intellectualism, as so many scholars have argued, that brought the experts back down to earth. Rather, their decline can be traced to the very roots of their success after World War II. The need to over-state anticipated results in order to garner public support, incessant professional and bureaucratic specialization, and the sheer proliferation of expertise pushed arcane and insulated debates between experts into public forums at the same time that a broad cross section of political participants found it easier to gain access to their own expertise. These tendencies ultimately undermined the political influence of all experts. (author)

  3. Biochemical Hypermedia: Galactose Metabolism.

    Directory of Open Access Journals (Sweden)

    J.K. Sugai

    2013-05-01

    Full Text Available Introduction: Animations of biochemical processes and virtual laboratory environments lead to true molecular simulations. The use of interactive software’s in education can improve cognitive capacity, better learning and, mainly, it makes information acquisition easier. Material and Methods: This work presents the development of a biochemical hypermedia to understanding of the galactose metabolism. It was developed with the help of concept maps, ISIS Draw, ADOBE Photoshop and FLASH MX Program. Results and Discussion: A step by step animation process shows the enzymatic reactions of galactose conversion to glucose-1-phosphate (to glycogen synthesis, glucose-6-phosphate (glycolysis intermediary, UDP-galactose (substrate to mucopolysaccharides synthesis and collagen’s glycosylation. There are navigation guide that allow scrolling the mouse over the names of the components of enzymatic reactions of via the metabolism of galactose. Thus, explanatory text box, chemical structures and animation of the actions of enzymes appear to navigator. Upon completion of the module, the user’s response to the proposed exercise can be checked immediately through text box with interactive content of the answer. Conclusion: This hypermedia was presented for undergraduate students (UFSC who revealed that it was extremely effective in promoting the understanding of the theme.

  4. Metabolic alkalosis.

    Science.gov (United States)

    Khanna, A; Kurtzman, N A

    2006-01-01

    Metabolic alkalosis is a primary pathophysiologic event characterized by the gain of bicarbonate or the loss of nonvolatile acid from extracellular fluid. The kidney preserves normal acid-base balance by two mechanisms: bicarbonate reclamation mainly in the proximal tubule and bicarbonate generation predominantly in the distal nephron. Bicarbonate reclamation is mediated mainly by a Na-H antiporter and to a smaller extent by the H-ATPase. The principal factors affecting HCO 3 reabsorption include effective arterial blood volume, glomerular filtration rate, chloride, and potassium. Bicarbonate regeneration is primarily affected by distal Na delivery and reabsorption, aldosterone, arterial pH, and arterial pCO2. To generate metabolic alkalosis, either a gain of base or a loss of acid, must occur. The loss of acid may be via the GI tract or by the kidney. Excess base may be gained by oral or parenteral HCO 3 administration or by lactate, acetate, or citrate administration. Factors that help maintain metabolic alkalosis include decreased glomerular filtration rate (GFR), volume contraction, hypokalemia, hypochloremia, and aldosterone excess. Clinical states associated with metabolic alkalosis are vomiting, mineralocorticoid excess, the adrenogenital syndrome, licorice ingestion, diuretic administration, and Bartter's and Gitelma's Syndromes. The effects of metabolic alkalosis on the body are varied and include effects on the central nervous system, myocardium, skeletal muscle, and the liver. Treatment of this disorder is simple, once the pathophysiology of the cause is delineated. Therapy consists of reversing the contributory factors promoting alkalosis and in severe cases, administration of carbonic anhydrase inhibitors, acid infusion, and low bicarbonate dialysis.

  5. Reaction rates for reaction-diffusion kinetics on unstructured meshes.

    Science.gov (United States)

    Hellander, Stefan; Petzold, Linda

    2017-02-14

    The reaction-diffusion master equation is a stochastic model often utilized in the study of biochemical reaction networks in living cells. It is applied when the spatial distribution of molecules is important to the dynamics of the system. A viable approach to resolve the complex geometry of cells accurately is to discretize space with an unstructured mesh. Diffusion is modeled as discrete jumps between nodes on the mesh, and the diffusion jump rates can be obtained through a discretization of the diffusion equation on the mesh. Reactions can occur when molecules occupy the same voxel. In this paper, we develop a method for computing accurate reaction rates between molecules occupying the same voxel in an unstructured mesh. For large voxels, these rates are known to be well approximated by the reaction rates derived by Collins and Kimball, but as the mesh is refined, no analytical expression for the rates exists. We reduce the problem of computing accurate reaction rates to a pure preprocessing step, depending only on the mesh and not on the model parameters, and we devise an efficient numerical scheme to estimate them to high accuracy. We show in several numerical examples that as we refine the mesh, the results obtained with the reaction-diffusion master equation approach those of a more fine-grained Smoluchowski particle-tracking model.

  6. Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms

    Directory of Open Access Journals (Sweden)

    Carbonell Pablo

    2012-02-01

    Full Text Available Abstract Background We consider the possibility of engineering metabolic pathways in a chassis organism in order to synthesize novel target compounds that are heterologous to the chassis. For this purpose, we model metabolic networks through hypergraphs where reactions are represented by hyperarcs. Each hyperarc represents an enzyme-catalyzed reaction that transforms set of substrates compounds into product compounds. We follow a retrosynthetic approach in order to search in the metabolic space (hypergraphs for pathways (hyperpaths linking the target compounds to a source set of compounds. Results To select the best pathways to engineer, we have developed an objective function that computes the cost of inserting a heterologous pathway in a given chassis organism. In order to find minimum-cost pathways, we propose in this paper two methods based on steady state analysis and network topology that are to the best of our knowledge, the first to enumerate all possible heterologous pathways linking a target compounds to a source set of compounds. In the context of metabolic engineering, the source set is composed of all naturally produced chassis compounds (endogenuous chassis metabolites and the target set can be any compound of the chemical space. We also provide an algorithm for identifying precursors which can be supplied to the growth media in order to increase the number of ways to synthesize specific target compounds. Conclusions We find the topological approach to be faster by several orders of magnitude than the steady state approach. Yet both methods are generally scalable in time with the number of pathways in the metabolic network. Therefore this work provides a powerful tool for pathway enumeration with direct application to biosynthetic pathway design.

  7. Metabolic engineering: the ultimate paradigm for continuous pharmaceutical manufacturing.

    Science.gov (United States)

    Yadav, Vikramaditya G; Stephanopoulos, Gregory

    2014-07-01

    Research and development (R&D) expenditures by pharmaceutical companies doubled over the past decade, yet candidate attrition rates and development times rose markedly during this period. Understandably, companies have begun downsizing their pipelines and diverting investments away from R&D in favor of manufacturing. It is estimated that transitioning to continuous manufacturing could enable companies to compete for a share in emerging markets. Accordingly, the model for continuous manufacturing that has emerged commences with the conversion of late-stage intermediates into the active pharmaceutical ingredient (API) in a series of continuous flow reactors, followed by continuous solid processing to form finished tablets. The use of flow reactions for API synthesis will certainly generate purer products at higher yields in shorter times compared to equivalent batch reactions. However, transitioning from batch to flow configuration simply alleviates transport limitations within the reaction milieu. As the catalogue of reactions used in flow syntheses is a subset of batch-based chemistries, molecules such as natural products will continue to evade drug prospectors. Also, it is uncertain whether flow synthesis can deliver improvements in the atom and energy economies of API production at the scales that would achieve the levels of revenue growth targeted by companies. Instead, it is argued that implementing metabolic engineering for the production of oxidized scaffolds as gateway molecules for flow-based addition of electrophiles is a more effective and scalable strategy for accessing natural product chemical space. This new paradigm for manufacturing, with metabolic engineering as its engine, would also permit rapid optimization of production variables and allow facile scale-up from gram to ton scale to meet material requirements for clinical trials, thus recasting manufacturing as a tool for discovery. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Investigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model.

    Science.gov (United States)

    Islam, M Ahsanul; Zengler, Karsten; Edwards, Elizabeth A; Mahadevan, Radhakrishnan; Stephanopoulos, Gregory

    2015-08-01

    Moorella thermoacetica is a strictly anaerobic, endospore-forming, and metabolically versatile acetogenic bacterium capable of conserving energy by both autotrophic (acetogenesis) and heterotrophic (homoacetogenesis) modes of metabolism. Its metabolic diversity and the ability to efficiently convert a wide range of compounds, including syngas (CO + H2) into acetyl-CoA have made this thermophilic bacterium a promising host for industrial biotechnology applications. However, lack of detailed information on M. thermoacetica's metabolism is a major impediment to its use as a microbial cell factory. In order to overcome this issue, a genome-scale constraint-based metabolic model of Moorella thermoacetica, iAI558, has been developed using its genome sequence and physiological data from published literature. The reconstructed metabolic network of M. thermoacetica comprises 558 metabolic genes, 705 biochemical reactions, and 698 metabolites. Of the total 705 model reactions, 680 are gene-associated while the rest are non-gene associated reactions. The model, in addition to simulating both autotrophic and heterotrophic growth of M. thermoacetica, revealed degeneracy in its TCA-cycle, a common characteristic of anaerobic metabolism. Furthermore, the model helped elucidate the poorly understood energy conservation mechanism of M. thermoacetica during autotrophy. Thus, in addition to generating experimentally testable hypotheses regarding its physiology, such a detailed model will facilitate rapid strain designing and metabolic engineering of M. thermoacetica for industrial applications.

  9. Rebinding in biochemical reactions on membranes

    Science.gov (United States)

    Lawley, Sean D.; Keener, James P.

    2017-10-01

    The behavior of many biochemical processes depends crucially on molecules rapidly rebinding after dissociating. In the case of multisite protein modification, the importance of rebinding has been demonstrated both experimentally and through several recent computational studies involving stochastic spatial simulations. As rebinding stems from spatio-temporal correlations, theorists have resorted to models that explicitly include space to properly account for the effects of rebinding. However, for reactions in three space dimensions it was recently shown that well-mixed ordinary differential equation (ODE) models can incorporate rebinding by adding connections to the reaction network. The rate constants for these new connections involve the probability that a pair of molecules rapidly rebinds after dissociation. In order to study biochemical reactions on membranes, in this paper we derive an explicit formula for this rebinding probability for reactions in two space dimensions. We show that ODE models can use the formula to replicate detailed stochastic spatial simulations, and that the formula can predict ultrasensitivity for reactions involving multisite modification of membrane-bound proteins. Further, we compute a new concentration-dependent rebinding probability for reactions in three space dimensions. Our analysis predicts that rebinding plays a much larger role in reactions on membranes compared to reactions in cytoplasm.

  10. Engineered Alloy Structures by Friction Stir Reaction Processing, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — This SBIR Phase I effort examines the feasibility of an innovative surface modification technology incorporating friction stir reaction processing for producing...

  11. Metabolic and Transcriptional Response to Cofactor Perturbations in Escherichia coli

    DEFF Research Database (Denmark)

    Holm, Anders Koefoed; Blank, L.M.; Oldiges, M.

    2010-01-01

    Metabolic cofactors such as NADH and ATP play important roles in a large number of cellular reactions, and it is of great interest to dissect the role of these cofactors in different aspects of metabolism. Toward this goal, we overexpressed NADH oxidase and the soluble F1-ATPase in Escherichia coli...... of redox and energy metabolism and should help in developing metabolic engineering strategies in E. coli....

  12. Genome-Scale Reconstruction of the Human Astrocyte Metabolic Network

    OpenAIRE

    Mart?n-Jim?nez, Cynthia A.; Salazar-Barreto, Diego; Barreto, George E.; Gonz?lez, Janneth

    2017-01-01

    Astrocytes are the most abundant cells of the central nervous system; they have a predominant role in maintaining brain metabolism. In this sense, abnormal metabolic states have been found in different neuropathological diseases. Determination of metabolic states of astrocytes is difficult to model using current experimental approaches given the high number of reactions and metabolites present. Thus, genome-scale metabolic networks derived from transcriptomic data can be used as a framework t...

  13. ReactionPredictor: prediction of complex chemical reactions at the mechanistic level using machine learning.

    Science.gov (United States)

    Kayala, Matthew A; Baldi, Pierre

    2012-10-22

    Proposing reasonable mechanisms and predicting the course of chemical reactions is important to the practice of organic chemistry. Approaches to reaction prediction have historically used obfuscating representations and manually encoded patterns or rules. Here we present ReactionPredictor, a machine learning approach to reaction prediction that models elementary, mechanistic reactions as interactions between approximate molecular orbitals (MOs). A training data set of productive reactions known to occur at reasonable rates and yields and verified by inclusion in the literature or textbooks is derived from an existing rule-based system and expanded upon with manual curation from graduate level textbooks. Using this training data set of complex polar, hypervalent, radical, and pericyclic reactions, a two-stage machine learning prediction framework is trained and validated. In the first stage, filtering models trained at the level of individual MOs are used to reduce the space of possible reactions to consider. In the second stage, ranking models over the filtered space of possible reactions are used to order the reactions such that the productive reactions are the top ranked. The resulting model, ReactionPredictor, perfectly ranks polar reactions 78.1% of the time and recovers all productive reactions 95.7% of the time when allowing for small numbers of errors. Pericyclic and radical reactions are perfectly ranked 85.8% and 77.0% of the time, respectively, rising to >93% recovery for both reaction types with a small number of allowed errors. Decisions about which of the polar, pericyclic, or radical reaction type ranking models to use can be made with >99% accuracy. Finally, for multistep reaction pathways, we implement the first mechanistic pathway predictor using constrained tree-search to discover a set of reasonable mechanistic steps from given reactants to given products. Webserver implementations of both the single step and pathway versions of Reaction

  14. The compositional and evolutionary logic of metabolism

    International Nuclear Information System (INIS)

    Braakman, Rogier; Smith, Eric

    2013-01-01

    Metabolism is built on a foundation of organic chemistry, and employs structures and interactions at many scales. Despite these sources of complexity, metabolism also displays striking and robust regularities in the forms of modularity and hierarchy, which may be described compactly in terms of relatively few principles of composition. These regularities render metabolic architecture comprehensible as a system, and also suggests the order in which layers of that system came into existence. In addition metabolism also serves as a foundational layer in other hierarchies, up to at least the levels of cellular integration including bioenergetics and molecular replication, and trophic ecology. The recapitulation of patterns first seen in metabolism, in these higher levels, motivates us to interpret metabolism as a source of causation or constraint on many forms of organization in the biosphere. Many of the forms of modularity and hierarchy exhibited by metabolism are readily interpreted as stages in the emergence of catalytic control by living systems over organic chemistry, sometimes recapitulating or incorporating geochemical mechanisms. We identify as modules, either subsets of chemicals and reactions, or subsets of functions, that are re-used in many contexts with a conserved internal structure. At the small molecule substrate level, module boundaries are often associated with the most complex reaction mechanisms, catalyzed by highly conserved enzymes. Cofactors form a biosynthetically and functionally distinctive control layer over the small-molecule substrate. The most complex members among the cofactors are often associated with the reactions at module boundaries in the substrate networks, while simpler cofactors participate in widely generalized reactions. The highly tuned chemical structures of cofactors (sometimes exploiting distinctive properties of the elements of the periodic table) thereby act as ‘keys’ that incorporate classes of organic reactions

  15. A comprehensive survey of nuclear reactions; Panorama des reactions nucleaires

    Energy Technology Data Exchange (ETDEWEB)

    Cugnon, J. [Liege Univ., IFPA, AGO Dept. (Belgium)

    2007-07-01

    The various mechanisms of nuclear reactions are surveyed and classified in different regimes, based on the notions of coherent mechanisms and hard versus soft processes. The emphasis is put on the concepts at the basis of the understanding of these regimes and on the elements of nuclear structure which are involved in these different regimes, as well as the on the possibility of extracting this information. Due to lack of space and for pedagogical reasons, the discussion is limited to nucleon-induced and light-ion-induced reactions. However, a few remarks are given concerning some specific probes, such as weakly bound projectiles or neutron-rich nuclei. (author)

  16. The Impact of Oxygen on Metabolic Evolution: A Chemoinformatic Investigation

    Science.gov (United States)

    Qin, Tao; Li, Xiao; Caetano-Anollés, Gustavo; Zhang, Hong-Yu

    2012-01-01

    The appearance of planetary oxygen likely transformed the chemical and biochemical makeup of life and probably triggered episodes of organismal diversification. Here we use chemoinformatic methods to explore the impact of the rise of oxygen on metabolic evolution. We undertake a comprehensive comparative analysis of structures, chemical properties and chemical reactions of anaerobic and aerobic metabolites. The results indicate that aerobic metabolism has expanded the structural and chemical space of metabolites considerably, including the appearance of 130 novel molecular scaffolds. The molecular functions of these metabolites are mainly associated with derived aspects of cellular life, such as signal transfer, defense against biotic factors, and protection of organisms from oxidation. Moreover, aerobic metabolites are more hydrophobic and rigid than anaerobic compounds, suggesting they are better fit to modulate membrane functions and to serve as transmembrane signaling factors. Since higher organisms depend largely on sophisticated membrane-enabled functions and intercellular signaling systems, the metabolic developments brought about by oxygen benefit the diversity of cellular makeup and the complexity of cellular organization as well. These findings enhance our understanding of the molecular link between oxygen and evolution. They also show the significance of chemoinformatics in addressing basic biological questions. PMID:22438800

  17. Reaction Wheel Disturbance Model Extraction Software, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — Reaction wheel mechanical noise is one of the largest sources of disturbance forcing on space-based observatories. Such noise arises from mass imbalance, bearing...

  18. Acoustic Resonance Reaction Control Thruster (ARCTIC), Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — ORBITEC proposes to develop and demonstrate the innovative Acoustic Resonance Reaction Control Thruster (ARCTIC) to provide rapid and reliable in-space impulse...

  19. Curation and Computational Design of Bioenergy-Related Metabolic Pathways

    Energy Technology Data Exchange (ETDEWEB)

    Karp, Peter D. [SRI International, Menlo Park, CA (United States)

    2014-09-12

    . The pathways were to be generated using metabolic reactions from a reference database (DB). 5: Develop computational tools for ranking the pathways generated in objective (4) according to their optimality. The ranking criteria include stoichiometric yield, the number and cost of additional inputs and the cofactor compounds required by the pathway, pathway length, and pathway energetics. 6: Develop tools for visualizing generated pathways to facilitate the evaluation of a large space of generated pathways.

  20. Simulating metabolism with statistical thermodynamics.

    Science.gov (United States)

    Cannon, William R

    2014-01-01

    New methods are needed for large scale modeling of metabolism that predict metabolite levels and characterize the thermodynamics of individual reactions and pathways. Current approaches use either kinetic simulations, which are difficult to extend to large networks of reactions because of the need for rate constants, or flux-based methods, which have a large number of feasible solutions because they are unconstrained by the law of mass action. This report presents an alternative modeling approach based on statistical thermodynamics. The principles of this approach are demonstrated using a simple set of coupled reactions, and then the system is characterized with respect to the changes in energy, entropy, free energy, and entropy production. Finally, the physical and biochemical insights that this approach can provide for metabolism are demonstrated by application to the tricarboxylic acid (TCA) cycle of Escherichia coli. The reaction and pathway thermodynamics are evaluated and predictions are made regarding changes in concentration of TCA cycle intermediates due to 10- and 100-fold changes in the ratio of NAD+:NADH concentrations. Finally, the assumptions and caveats regarding the use of statistical thermodynamics to model non-equilibrium reactions are discussed.

  1. Phase space quark counting rule

    International Nuclear Information System (INIS)

    Wei-gin, C.; Lo, S.

    1980-01-01

    A simple quark counting rule based on phase space consideration suggested before is used to fit all 39 recent experimental data points on inclusive reactions. Parameter free relations are found to agree with experiments. Excellent detail fits are obtained for 11 inclusive reactions

  2. Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity.

    Science.gov (United States)

    Rolfsson, Óttar; Paglia, Giuseppe; Magnusdóttir, Manuela; Palsson, Bernhard Ø; Thiele, Ines

    2013-01-15

    Metabolic network reconstructions define metabolic information within a target organism and can therefore be used to address incomplete metabolic information. In the present study we used a computational approach to identify human metabolites whose metabolism is incomplete on the basis of their detection in humans but exclusion from the human metabolic network reconstruction RECON 1. Candidate solutions, composed of metabolic reactions capable of explaining the metabolism of these compounds, were then identified computationally from a global biochemical reaction database. Solutions were characterized with respect to how metabolites were incorporated into RECON 1 and their biological relevance. Through detailed case studies we show that biologically plausible non-intuitive hypotheses regarding the metabolism of these compounds can be proposed in a semi-automated manner, in an approach that is similar to de novo network reconstruction. We subsequently experimentally validated one of the proposed hypotheses and report that C9orf103, previously identified as a candidate tumour suppressor gene, encodes a functional human gluconokinase. The results of the present study demonstrate how semi-automatic gap filling can be used to refine and extend metabolic reconstructions, thereby increasing their biological scope. Furthermore, we illustrate how incomplete human metabolic knowledge can be coupled with gene annotation in order to prioritize and confirm gene functions.

  3. Metabolism of fluoroacetate by lettuce

    Energy Technology Data Exchange (ETDEWEB)

    Ward, P.F.V.

    1973-10-01

    The metabolism of fluoroacetate was studied at sub-toxic levels. In order to isolate sufficient metabolites for structural studies, a plant system was chosen, since plants are able to withstand much higher levels of fluoroacetate than most animals. Lettuce was used because of its convenient size and ready availability throughout the year. The reaction between fluroacetate and glutathione is discussed; it strongly resembles the metabolism of many aliphatic and aromatic halogen compounds by mammalian liver. It is possible that this detoxifying reaction occurs in the liver of fluoroacetate-poisoned animals since the level of citrate found in this organ is always less than in the other organs tested. 20 references, 9 figures, 2 tables.

  4. Subdiffusion-reaction processes with A →B reactions versus subdiffusion-reaction processes with A +B→B reactions

    Science.gov (United States)

    Kosztołowicz, Tadeusz; Lewandowska, Katarzyna D.

    2014-09-01

    We consider the subdiffusion-reaction process with reactions of a type A +B→B (in which particles A are assumed to be mobile, whereas B are assumed to be static) in comparison to the subdiffusion-reaction process with A →B reactions which was studied by Sokolov, Schmidt, and Sagués [Phys. Rev. E 73, 031102 (2006), 10.1103/PhysRevE.73.031102]. In both processes a rule that reactions can only occur between particles which continue to exist is taken into account. Although in both processes a probability of the vanishing of particle A due to a reaction is independent of both time and space variables (assuming that in the system with the A +B→B reactions, particles B are distributed homogeneously), we show that subdiffusion-reaction equations describing these processes as well as their Green's functions are qualitatively different. The reason for this difference is as follows. In the case of the former reaction, particles A and B have to meet with some probability before the reaction occurs in contradiction with the case of the latter reaction. For the subdiffusion process with the A +B→B reactions we consider three models which differ in some details concerning a description of the reactions. We base the method considered in this paper on a random walk model in a system with both discrete time and discrete space variables. Then the system with discrete variables is transformed into a system with both continuous time and continuous space variables. Such a method seems to be convenient in analyzing subdiffusion-reaction processes with partially absorbing or partially reflecting walls. The reason is that within this method we can determine Green's functions without a necessity of solving a fractional differential subdiffusion-reaction equation with boundary conditions at the walls. As an example, we use the model to find the Green's functions for a subdiffusive reaction system (with the reactions mentioned above), which is bounded by a partially absorbing wall

  5. Slave nodes and the controllability of metabolic networks

    International Nuclear Information System (INIS)

    Kim, Dong-Hee; Motter, Adilson E

    2009-01-01

    Recent work on synthetic rescues has shown that the targeted deletion of specific metabolic genes can often be used to rescue otherwise non-viable mutants. This raises a fundamental biophysical question: to what extent can the whole-cell behavior of a large metabolic network be controlled by constraining the flux of one or more reactions in the network? This touches upon the issue of the number of degrees of freedom contained by one such network. Using the metabolic network of Escherichia coli as a model system, here we address this question theoretically by exploring not only reaction deletions, but also a continuum of all possible reaction expression levels. We show that the behavior of the metabolic network can be largely manipulated by the pinned expression of a single reaction. In particular, a relevant fraction of the metabolic reactions exhibits canalizing interactions, in that the specification of one reaction flux determines cellular growth as well as the fluxes of most other reactions in optimal steady states. The activity of individual reactions can thus be used as surrogates to monitor and possibly control cellular growth and other whole-cell behaviors. In addition to its implications for the study of control processes, our methodology provides a new approach to study how the integrated dynamics of the entire metabolic network emerges from the coordinated behavior of its component parts.

  6. Network reconstruction of platelet metabolism identifies metabolic signature for aspirin resistance

    Science.gov (United States)

    Thomas, Alex; Rahmanian, Sorena; Bordbar, Aarash; Palsson, Bernhard Ø.; Jamshidi, Neema

    2014-01-01

    Recently there has not been a systematic, objective assessment of the metabolic capabilities of the human platelet. A manually curated, functionally tested, and validated biochemical reaction network of platelet metabolism, iAT-PLT-636, was reconstructed using 33 proteomic datasets and 354 literature references. The network contains enzymes mapping to 403 diseases and 231 FDA approved drugs, alluding to an expansive scope of biochemical transformations that may affect or be affected by disease processes in multiple organ systems. The effect of aspirin (ASA) resistance on platelet metabolism was evaluated using constraint-based modeling, which revealed a redirection of glycolytic, fatty acid, and nucleotide metabolism reaction fluxes in order to accommodate eicosanoid synthesis and reactive oxygen species stress. These results were confirmed with independent proteomic data. The construction and availability of iAT-PLT-636 should stimulate further data-driven, systems analysis of platelet metabolism towards the understanding of pathophysiological conditions including, but not strictly limited to, coagulopathies.

  7. Glycaemic Adverse Drug Reactions from Anti-Neoplastics Used in ...

    African Journals Online (AJOL)

    2017-06-01

    Jun 1, 2017 ... in cancer treatment. The aim was to analyze the blood glucose‑related ADR of antineoplastics in treating pancreatic cancer. Materials and Methods: .... Figure 2: Record numbers on general adverse drug reactions (metabolism and nutrition disorder ratio = metabolism and nutrition disorder/total number.

  8. A compendium of inborn errors of metabolism mapped onto the human metabolic network.

    OpenAIRE

    Sahoo, Swagatika; Franzson, Leifur; Jonsson, Jon J; Thiele, Ines

    2012-01-01

    Efst á síðunni er hægt að nálgast greinina í heild sinni með því að smella á hlekkinn Inborn errors of metabolism (IEMs) are hereditary metabolic defects, which are encountered in almost all major metabolic pathways occurring in man. Many IEMs are screened for in neonates through metabolomic analysis of dried blood spot samples. To enable the mapping of these metabolomic data onto the published human metabolic reconstruction, we added missing reactions and pathways involved in acylcarnitin...

  9. Chemical reactions in low-g

    Science.gov (United States)

    Grodzka, P. G.; Facemire, B. R.

    1978-01-01

    The Apollo-Soyuz flight experiment, 'Chemical Foams' demonstrated that foams and air/liquid dispersions are much more stable in low-gravity than on the ground. It thus should be possible to conduct unique chemical reactions in space foams. The low-g results and subsequent ground work on the formaldehyde clock reaction indicate that the reaction is strongly influenced by (1) dissociated and undissociated solution species being adsorbed at solid/liquid and gas/liquid surfaces and (2) chemical reaction rates apparently being affected by long-range forces determined by the liquid mass and the extent and nature of all surface interfaces.

  10. Hierarchical analysis of dependency in metabolic networks.

    Science.gov (United States)

    Gagneur, Julien; Jackson, David B; Casari, Georg

    2003-05-22

    Elucidation of metabolic networks for an increasing number of organisms reveals that even small networks can contain thousands of reactions and chemical species. The intimate connectivity between components complicates their decomposition into biologically meaningful sub-networks. Moreover, traditional higher-order representations of metabolic networks as metabolic pathways, suffers from the lack of rigorous definition, yielding pathways of disparate content and size. We introduce a hierarchical representation that emphasizes the gross organization of metabolic networks in largely independent pathways and sub-systems at several levels of independence. The approach highlights the coupling of different pathways and the shared compounds responsible for those couplings. By assessing our results on Escherichia coli (E.coli metabolic reactions, Genetic Circuits Research Group, University of California, San Diego, http://gcrg.ucsd.edu/organisms/ecoli.html, 'model v 1.01. reactions') against accepted biochemical annotations, we provide the first systematic synopsis of an organism's metabolism. Comparison with operons of E.coli shows that low-level clusters are reflected in genome organization and gene regulation. Source code, data sets and supplementary information are available at http://www.mas.ecp.fr/labo/equipe/gagneur/hierarchy/hierarchy.html

  11. Metabolism of 25-hydroxyvitamin D3 by microsomal and mitochondrial vitamin D3 25-hydroxylases (CYP2D25 and CYP27A1): a novel reaction by CYP27A1.

    Science.gov (United States)

    Araya, Zufan; Hosseinpour, Fardin; Bodin, Karl; Wikvall, Kjell

    2003-06-10

    The metabolism of 25-hydroxyvitamin D(3) was studied with a crude mitochondrial cytochrome P450 extract from pig kidney and with recombinant human CYP27A1 (mitochondrial vitamin D(3) 25-hydroxylase) and porcine CYP2D25 (microsomal vitamin D(3) 25-hydroxylase). The kidney mitochondrial cytochrome P450 catalyzed the formation of 1alpha,25-dihydroxyvitamin D(3), 24,25-dihydroxyvitamin D(3) and 25,27-dihydroxyvitamin D(3). An additional metabolite that was separated from the other hydroxylated products on HPLC was also formed. The formation of this 25-hydroxyvitamin D(3) metabolite was dependent on NADPH and the mitochondrial electron transferring protein components. A monoclonal antibody directed against purified pig liver CYP27A1 immunoprecipitated the 1alpha- and 27-hydroxylase activities towards 25-hydroxyvitamin D(3) as well as the formation of the unknown metabolite. These results together with substrate inhibition experiments indicate that CYP27A1 is responsible for the formation of the unknown 25-hydroxyvitamin D(3) metabolite in kidney. Recombinant human CYP27A1 was found to convert 25-hydroxyvitamin D(3) into 1alpha,25-dihydroxyvitamin D(3), 25,27-dihydroxyvitamin D(3) and a major metabolite with the same retention time on HPLC as that formed by kidney mitochondrial cytochrome P450. Gas chromatography-mass spectrometry (GC-MS) analysis of the unknown enzymatic product revealed it to be a triol different from other known hydroxylated 25-hydroxyvitamin D(3) metabolites such as 1alpha,25-, 23,25-, 24,25-, 25,26- or 25,27-dihydroxyvitamin D(3). The product had the mass spectrometic properties expected for 4beta,25-dihydroxyvitamin D(3). Recombinant porcine CYP2D25 converted 25-hydroxyvitamin D(3) into 1alpha,25-dihydroxyvitamin D(3) and 25,26-dihydroxyvitamin D(3). It can be concluded that both CYP27A1 and CYP2D25 are able to carry out multiple hydroxylations of 25-hydroxyvitamin D(3).

  12. Catalysis of Photochemical Reactions.

    Science.gov (United States)

    Albini, A.

    1986-01-01

    Offers a classification system of catalytic effects in photochemical reactions, contrasting characteristic properties of photochemical and thermal reactions. Discusses catalysis and sensitization, examples of catalyzed reactions of excepted states, complexing ground state substrates, and catalysis of primary photoproducts. (JM)

  13. Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism

    Science.gov (United States)

    Saha, Rajib; Suthers, Patrick F.; Maranas, Costas D.

    2011-01-01

    The scope and breadth of genome-scale metabolic reconstructions have continued to expand over the last decade. Herein, we introduce a genome-scale model for a plant with direct applications to food and bioenergy production (i.e., maize). Maize annotation is still underway, which introduces significant challenges in the association of metabolic functions to genes. The developed model is designed to meet rigorous standards on gene-protein-reaction (GPR) associations, elementally and charged balanced reactions and a biomass reaction abstracting the relative contribution of all biomass constituents. The metabolic network contains 1,563 genes and 1,825 metabolites involved in 1,985 reactions from primary and secondary maize metabolism. For approximately 42% of the reactions direct literature evidence for the participation of the reaction in maize was found. As many as 445 reactions and 369 metabolites are unique to the maize model compared to the AraGEM model for A. thaliana. 674 metabolites and 893 reactions are present in Zea mays iRS1563 that are not accounted for in maize C4GEM. All reactions are elementally and charged balanced and localized into six different compartments (i.e., cytoplasm, mitochondrion, plastid, peroxisome, vacuole and extracellular). GPR associations are also established based on the functional annotation information and homology prediction accounting for monofunctional, multifunctional and multimeric proteins, isozymes and protein complexes. We describe results from performing flux balance analysis under different physiological conditions, (i.e., photosynthesis, photorespiration and respiration) of a C4 plant and also explore model predictions against experimental observations for two naturally occurring mutants (i.e., bm1 and bm3). The developed model corresponds to the largest and more complete to-date effort at cataloguing metabolism for a plant species. PMID:21755001

  14. On Thermonuclear Reaction Rates

    OpenAIRE

    Haubold, H. J.; Mathai, A. M.

    1996-01-01

    Nuclear reactions govern major aspects of the chemical evolution of galaxies and stars. Analytic study of the reaction rates and reaction probability integrals is attempted here. Exact expressions for the reaction rates and reaction probability integrals for nuclear reactions in the cases of nonresonant, modified nonresonant, screened nonresonant and resonant cases are given. These are expressed in terms of H-functions, G-functions and in computable series forms. Computational aspects are als...

  15. Analog regulation of metabolic demand

    Directory of Open Access Journals (Sweden)

    Muskhelishvili Georgi

    2011-03-01

    Full Text Available Abstract Background The 3D structure of the chromosome of the model organism Escherichia coli is one key component of its gene regulatory machinery. This type of regulation mediated by topological transitions of the chromosomal DNA can be thought of as an analog control, complementing the digital control, i.e. the network of regulation mediated by dedicated transcription factors. It is known that alterations in the superhelical density of chromosomal DNA lead to a rich pattern of differential expressed genes. Using a network approach, we analyze these expression changes for wild type E. coli and mutants lacking nucleoid associated proteins (NAPs from a metabolic and transcriptional regulatory network perspective. Results We find a significantly higher correspondence between gene expression and metabolism for the wild type expression changes compared to mutants in NAPs, indicating that supercoiling induces meaningful metabolic adjustments. As soon as the underlying regulatory machinery is impeded (as for the NAP mutants, this coherence between expression changes and the metabolic network is substantially reduced. This effect is even more pronounced, when we compute a wild type metabolic flux distribution using flux balance analysis and restrict our analysis to active reactions. Furthermore, we are able to show that the regulatory control exhibited by DNA supercoiling is not mediated by the transcriptional regulatory network (TRN, as the consistency of the expression changes with the TRN logic of activation and suppression is strongly reduced in the wild type in comparison to the mutants. Conclusions So far, the rich patterns of gene expression changes induced by alterations of the superhelical density of chromosomal DNA have been difficult to interpret. Here we characterize the effective networks formed by supercoiling-induced gene expression changes mapped onto reconstructions of E. coli's metabolic and transcriptional regulatory network. Our

  16. Inferring differences in the distribution of reaction rates across conditions

    NARCIS (Netherlands)

    Hendrickx, D.M.; Hoefsloot, H.C.J.; Hendriks, M.M.W.B.; Vis, D.J.; Canelas, A.B.; Teusink, B.; Smilde, A.K.

    2012-01-01

    Elucidating changes in the distribution of reaction rates in metabolic pathways under different conditions is a central challenge in systems biology. Here we present a method for inferring regulation mechanisms responsible for changes in the distribution of reaction rates across conditions from

  17. Metabolic Modulation in Macrophage Effector Function

    Directory of Open Access Journals (Sweden)

    Ciana Diskin

    2018-02-01

    Full Text Available Traditionally cellular respiration or metabolism has been viewed as catabolic and anabolic pathways generating energy and biosynthetic precursors required for growth and general cellular maintenance. However, growing literature provides evidence of a much broader role for metabolic reactions and processes in controlling immunological effector functions. Much of this research into immunometabolism has focused on macrophages, cells that are central in pro- as well as anti-inflammatory responses—responses that in turn are a direct result of metabolic reprogramming. As we learn more about the precise role of metabolic pathways and pathway intermediates in immune function, a novel opportunity to target immunometabolism therapeutically has emerged. Here, we review the current understanding of the regulation of macrophage function through metabolic remodeling.

  18. Finding metabolic pathways using atom tracking

    Science.gov (United States)

    Heath, Allison P.; Bennett, George N.; Kavraki, Lydia E.

    2010-01-01

    Motivation: Finding novel or non-standard metabolic pathways, possibly spanning multiple species, has important applications in fields such as metabolic engineering, metabolic network analysis and metabolic network reconstruction. Traditionally, this has been a manual process, but the large volume of metabolic data now available has created a need for computational tools to automatically identify biologically relevant pathways. Results: We present new algorithms for finding metabolic pathways, given a desired start and target compound, that conserve a given number of atoms by tracking the movement of atoms through metabolic networks containing thousands of compounds and reactions. First, we describe an algorithm that identifies linear pathways. We then present a new algorithm for finding branched metabolic pathways. Comparisons to known metabolic pathways demonstrate that atom tracking enables our algorithms to avoid many unrealistic connections, often found in previous approaches, and return biologically meaningful pathways. Our results also demonstrate the potential of the algorithms to find novel or non-standard pathways that may span multiple organisms. Availability: The software is freely available for academic use at: http://www.kavrakilab.org/atommetanet Contact: kavraki@rice.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20421197

  19. A reaction-diffusion model of cytosolic hydrogen peroxide.

    Science.gov (United States)

    Lim, Joseph B; Langford, Troy F; Huang, Beijing K; Deen, William M; Sikes, Hadley D

    2016-01-01

    As a signaling molecule in mammalian cells, hydrogen peroxide (H2O2) determines the thiol/disulfide oxidation state of several key proteins in the cytosol. Localization is a key concept in redox signaling; the concentrations of signaling molecules within the cell are expected to vary in time and in space in manner that is essential for function. However, as a simplification, all theoretical studies of intracellular hydrogen peroxide and many experimental studies to date have treated the cytosol as a well-mixed compartment. In this work, we incorporate our previously reported reduced kinetic model of the network of reactions that metabolize hydrogen peroxide in the cytosol into a model that explicitly treats diffusion along with reaction. We modeled a bolus addition experiment, solved the model analytically, and used the resulting equations to quantify the spatiotemporal variations in intracellular H2O2 that result from this kind of perturbation to the extracellular H2O2 concentration. We predict that micromolar bolus additions of H2O2 to suspensions of HeLa cells (0.8 × 10(9)cells/l) result in increases in the intracellular concentration that are localized near the membrane. These findings challenge the assumption that intracellular concentrations of H2O2 are increased uniformly throughout the cell during bolus addition experiments and provide a theoretical basis for differing phenotypic responses of cells to intracellular versus extracellular perturbations to H2O2 levels. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Novel Composite Membrane for Space Life Supporting System, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Space life-supporting systems require effective removal of metabolic CO2 from the cabin atmosphere with minimal loss of O2. Conventional techniques, using either...

  1. Novel Composite Membrane for Space Life Supporting System Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Space life-supporting systems require effective removal of metabolic CO2 from the cabin atmosphere with minimal loss of O2. Conventional techniques, using either...

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

    Science.gov (United States)

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

    2017-01-01

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

  3. Topics in heavy ion reactions

    International Nuclear Information System (INIS)

    Feshbach, H.

    1980-01-01

    Methods are discussed which, by straightforward extensions of currently available concepts and procedures, can be used for the description of reactions induced by heavy ions. The first section describes a nuclear Weiszaecker-Williams method for peripheral collisions of nuclei which is here extended to pion production in peripheral collisions. The second section emphasizes the relationship between the collision of an energetic proton and that of an energetic heavy ion with a nucleus. The comparatively remarkable behavior of the observed energy dependence of the angular distribution and average energy of the fragments produced in proton collision is described and a qualitative explanation offered. The third section is concerned with the'pre-equilibrium' reactions as well as the multi-step direct reactions which are known to play an important role in heavy ion collisions. A statistical theory of multi-step direct and multi-step compound reactions providing explicit expressions for the energy and angular distributions is formulated. A diffusion equation in momentum space is obtained as an approximation to these formulas. The extension of these results to heavy ion reactions in which phenomena involving deformation, mass and charge transfer and multi-particle final states are important, is made. (author)

  4. The reconstruction and analysis of tissue specific human metabolic networks.

    Science.gov (United States)

    Hao, Tong; Ma, Hong-Wu; Zhao, Xue-Ming; Goryanin, Igor

    2012-02-01

    Human tissues have distinct biological functions. Many proteins/enzymes are known to be expressed only in specific tissues and therefore the metabolic networks in various tissues are different. Though high quality global human metabolic networks and metabolic networks for certain tissues such as liver have already been studied, a systematic study of tissue specific metabolic networks for all main tissues is still missing. In this work, we reconstruct the tissue specific metabolic networks for 15 main tissues in human based on the previously reconstructed Edinburgh Human Metabolic Network (EHMN). The tissue information is firstly obtained for enzymes from Human Protein Reference Database (HPRD) and UniprotKB databases and transfers to reactions through the enzyme-reaction relationships in EHMN. As our knowledge of tissue distribution of proteins is still very limited, we replenish the tissue information of the metabolic network based on network connectivity analysis and thorough examination of the literature. Finally, about 80% of proteins and reactions in EHMN are determined to be in at least one of the 15 tissues. To validate the quality of the tissue specific network, the brain specific metabolic network is taken as an example for functional module analysis and the results reveal that the function of the brain metabolic network is closely related with its function as the centre of the human nervous system. The tissue specific human metabolic networks are available at .

  5. Metabolism and the triggering of germination of Bacillus megaterium

    International Nuclear Information System (INIS)

    Scott, I.R.; Ellar, D.J.

    1978-01-01

    L-[2,3- 3 H]Alanine was used to probe for metabolism of alanine during triggering of germination of spores of Bacillus megaterium KM. No detectable incorporation of label into any compound, including water, was found, indicating that any metabolism involving the alanine germinant must be at a very low rate and also that alanine racemase is absent from spores of this strain. Spores were germinated in 3 H 2 0 to find if any of the many metabolic reactions causing irreversible incorporation of 3 H into reaction products took place during triggering og germination. No incorporation was detected until 2-3 min after addition of germinants. It is therefore concluded that a wide variety of metabolic routes, including glycolysis, the tricarboxylic acid cycle, the pentose phosphate pathway and amino acid metabolism are either not involved in the reactions causing the triggering of germination or operate at an extremely low rate during this process. (author)

  6. Metabolic pathways variability and sequence/networks comparisons

    Science.gov (United States)

    Tun, Kyaw; Dhar, Pawan K; Palumbo, Maria Concetta; Giuliani, Alessandro

    2006-01-01

    Background In this work a simple method for the computation of relative similarities between homologous metabolic network modules is presented. The method is similar to classical sequence alignment and allows for the generation of phenotypic trees amenable to be compared with correspondent sequence based trees. The procedure can be applied to both single metabolic modules and whole metabolic network data without the need of any specific assumption. Results We demonstrate both the ability of the proposed method to build reliable biological classification of a set of microrganisms and the strong correlation between the metabolic network wiringand involved enzymes sequence space. Conclusion The method represents a valuable tool for the investigation of genotype/phenotype correlationsallowing for a direct comparison of different species as for their metabolic machinery. In addition the detection of enzymes whose sequence space is maximally correlated with the metabolicnetwork space gives an indication of the most crucial (on an evolutionary viewpoint) steps of the metabolic process. PMID:16420696

  7. Metabolic pathways variability and sequence/networks comparisons

    Directory of Open Access Journals (Sweden)

    Palumbo Maria

    2006-01-01

    Full Text Available Abstract Background In this work a simple method for the computation of relative similarities between homologous metabolic network modules is presented. The method is similar to classical sequence alignment and allows for the generation of phenotypic trees amenable to be compared with correspondent sequence based trees. The procedure can be applied to both single metabolic modules and whole metabolic network data without the need of any specific assumption. Results We demonstrate both the ability of the proposed method to build reliable biological classification of a set of microrganisms and the strong correlation between the metabolic network wiringand involved enzymes sequence space. Conclusion The method represents a valuable tool for the investigation of genotype/phenotype correlationsallowing for a direct comparison of different species as for their metabolic machinery. In addition the detection of enzymes whose sequence space is maximally correlated with the metabolicnetwork space gives an indication of the most crucial (on an evolutionary viewpoint steps of the metabolic process.

  8. Attributions of teacher reactions to diabetes self-care behaviors.

    Science.gov (United States)

    Hains, Anthony A; Berlin, Kristoffer S; Davies, W Hobart; Sato, Amy F; Smothers, Melissa K; Clifford, Lisa C; Alemzadeh, Ramin

    2009-01-01

    This study had two objectives: examine relationships among negative attributions of teacher reactions, anticipated adherence difficulties, teacher support, diabetes stress, and metabolic control; and develop questionnaires to test these relationships. One hundred and two youths with type 1 insulin-dependent diabetes completed instruments measuring attribution of teacher reactions, anticipated adherence, teacher support, and diabetes stress. Metabolic control was measured by percentage of hemoglobin A(1c). Structural equation modeling demonstrated that negative attributions had direct effects on anticipated adherence difficulties and diabetes stress. Diabetes stress had a direct effect on metabolic control. Negative attributions had a significant indirect effect on metabolic control through associations with diabetes stress. Teacher support moderated the path between negative attributions and anticipated adherence difficulties. Youths making negative attributions about teacher's reactions are likely to find adherence difficult in school situations and have increased stress. Results are discussed in terms of a social information processing model of adjustment and practical applications.

  9. Metabolic disorders of purine metabolism affecting the nervous system.

    Science.gov (United States)

    Jinnah, H A; Sabina, Richard L; Van Den Berghe, Georges

    2013-01-01

    The purines are a group of molecules used by all cells for many vital biochemical processes including energy-requiring enzymatic reactions, cofactor-requiring reactions, synthesis of DNA or RNA, signaling pathways within and between cells, and other processes. Defects in some of the enzymes of purine metabolism are known to be associated with specific clinical disorders, and neurological problems may be a presenting sign or the predominant clinical problem for several of them. This chapter describes three disorders for which the clinical features and metabolic basis are well characterized. Deficiency of adenylosuccinate-lyase (ADSL) causes psychomotor retardation, epilepsy, and autistic features. Lesch-Nyhan disease is caused by deficiency of hypoxanthine-guanine phosphoribosyltransferase (HPRT) and is characterized by hyperuricemia, motor and cognitive disability, and self-injurious behavior. Deficiency of myoadenylate deaminase (mAMPD) is associated with myopathic features. In addition to these disorders, several other disorders are briefly summarized. These include defects of phosphoribosylpyrophosphate synthase, adenosine deaminase (ADA), purine nucleoside phosphorylase (PND), deoxyguanosine kinase (dGK), or IMP dehydrogenase (IMPDH). Each of these disorders provides an unusual window on the unique importance of purine metabolism for function of different parts of the nervous system. Copyright © 2013 Elsevier B.V. All rights reserved.

  10. Carbohydrate Metabolism Disorders

    Science.gov (United States)

    ... you eat. Food is made up of proteins, carbohydrates, and fats. Chemicals in your digestive system (enzymes) ... metabolic disorder, something goes wrong with this process. Carbohydrate metabolism disorders are a group of metabolic disorders. ...

  11. Sulphite metabolism

    International Nuclear Information System (INIS)

    Fromageot, P.; Chapeville, F.

    1960-01-01

    Although the formation of sulphite by micro-organisms was observed as early as 1914 by Neuberg, it was only in 1932 that Nightingale showed it to be present inside cells, in the case of tomato leaf stalks, its formation being due to the reaction: SO 3 H - + (S 2 O 3 ) 2 -- → S 2 O 3 -- + O 3 S 2 O 3 -- . The presence of the thiosulphate formed was shown by the high refractive index of its barium salt. Today we have a certain amount of data concerning the formation and use of sulphite in the living cell, even through the knowledge is still incomplete. In this article we will describe and discuss the facts which are known, with particular reference to the oxidation of sulphite. (author) [fr

  12. Metabolism during hypodynamia

    Science.gov (United States)

    Federov, I. V.

    1980-01-01

    Physical immobilization, inaction due to space travel, a sedentary occupation, or bed confinement due to a chronic illness elicit similar alternations in the metabolism of man and animals (rat, rabbit, dog, mouse). After a preliminary period of weight loss, there is eventually weight gain due to increased lipid storage. Protein catabolism is enhanced and anabolism depressed, with elevated urinary excretion of amino acids, creatine, and ammonia. Glycogen stores are depleted and glyconeogenesis is accelerated. Polyuria develops with subsequent redistribution of body fluids in which the blood volume of the systemic circulation is decreased and that of pulmonary circulation increased. This results in depressed production of vasopressin by the posterior pituitary which further enhances urinary water and salt loss.

  13. Sobolev spaces

    CERN Document Server

    Adams, Robert A

    2003-01-01

    Sobolev Spaces presents an introduction to the theory of Sobolev Spaces and other related spaces of function, also to the imbedding characteristics of these spaces. This theory is widely used in pure and Applied Mathematics and in the Physical Sciences.This second edition of Adam''s ''classic'' reference text contains many additions and much modernizing and refining of material. The basic premise of the book remains unchanged: Sobolev Spaces is intended to provide a solid foundation in these spaces for graduate students and researchers alike.* Self-contained and accessible for readers in other disciplines.* Written at elementary level making it accessible to graduate students.

  14. Sacred Space.

    Science.gov (United States)

    Adelstein, Pamela

    2018-01-01

    A space can be sacred, providing those who inhabit a particular space with sense of transcendence-being connected to something greater than oneself. The sacredness may be inherent in the space, as for a religious institution or a serene place outdoors. Alternatively, a space may be made sacred by the people within it and events that occur there. As medical providers, we have the opportunity to create sacred space in our examination rooms and with our patient interactions. This sacred space can be healing to our patients and can bring us providers opportunities for increased connection, joy, and gratitude in our daily work.

  15. Design Constraints on a Synthetic Metabolism

    Science.gov (United States)

    Bilgin, Tugce; Wagner, Andreas

    2012-01-01

    A metabolism is a complex network of chemical reactions that converts sources of energy and chemical elements into biomass and other molecules. To design a metabolism from scratch and to implement it in a synthetic genome is almost within technological reach. Ideally, a synthetic metabolism should be able to synthesize a desired spectrum of molecules at a high rate, from multiple different nutrients, while using few chemical reactions, and producing little or no waste. Not all of these properties are achievable simultaneously. We here use a recently developed technique to create random metabolic networks with pre-specified properties to quantify trade-offs between these and other properties. We find that for every additional molecule to be synthesized a network needs on average three additional reactions. For every additional carbon source to be utilized, it needs on average two additional reactions. Networks able to synthesize 20 biomass molecules from each of 20 alternative sole carbon sources need to have at least 260 reactions. This number increases to 518 reactions for networks that can synthesize more than 60 molecules from each of 80 carbon sources. The maximally achievable rate of biosynthesis decreases by approximately 5 percent for every additional molecule to be synthesized. Biochemically related molecules can be synthesized at higher rates, because their synthesis produces less waste. Overall, the variables we study can explain 87 percent of variation in network size and 84 percent of the variation in synthesis rate. The constraints we identify prescribe broad boundary conditions that can help to guide synthetic metabolism design. PMID:22768162

  16. Metabolic Imaging of Breast Cancer and the Normal Brain

    DEFF Research Database (Denmark)

    Asghar Butt, Sadia

    biological systems - breast cancer and normal brain. Breast cancer metabolism was longitudinally monitored in a mouse model using MRS of hyperpolirized pyruvate. The results demonstrated that we could monitor the changes in metabolism with increasing disease severity. The normal cerebral metabolism of α......Cellular metabolism is a set of biochemical reactions that happen in living organisms to maintain life. Enzymes act as catalysts and allow these reactions to proceed quickly and efficiently in order to maintain the cellular function and reproduction. Metabolic Magnetic Resonance Spectroscopy (MRS......) of hyperpolarized substrates enables the visualization, characterization, and quantification of biological processes taking without perturbing them. Biologic processes can, thus, be studied in their own physiologically authentic environment. This ability to measure fine metabolic changes opens up an incredible...

  17. Automated, Miniaturized Instrument for Measuring Gene Expression in Space

    Science.gov (United States)

    Pohorille, A.; Peyvan, K.; Danley, D.; Ricco, A. J.

    2010-01-01

    To facilitate astrobiological studies on the survival and adaptation of microorganisms and mixed microbial cultures to space environment, we have been developing a fully automated, miniaturized system for measuring their gene expression on small spacecraft. This low-cost, multi-purpose instrument represents a major scientific and technological advancement in our ability to study the impact of the space environment on biological systems by providing data on cellular metabolism and regulation orders of magnitude richer than what is currently available. The system supports growth of the organism, lyse it to release the expressed RNA, label the RNA, read the expression levels of a large number of genes by microarray analysis of labeled RNA and transmit the measurements to Earth. To measure gene expression we use microarray technology developed by CombiMatrix, which is based on electrochemical reactions on arrays of electrodes on a semiconductor substrate. Since the electrical integrity of the microarray remains intact after probe synthesis, the circuitry can be employed to sense nucleic acid binding at each electrode. CombiMatrix arrays can be sectored to allow multiple samples per chip. In addition, a single array can be used for several assays. The array has been integrated into an automated microfluidic cartridge that uses flexible reagent blisters and pinch pumping to move liquid reagents between chambers. The proposed instrument will help to understand adaptation of terrestrial life to conditions beyond the planet of origin, identify deleterious effects of the space environment, develop effective countermeasures against these effects, and test our ability to sustain and grow in space organisms that can be used for life support and in situ resource utilization during long-duration space exploration. The instrument is suitable for small satellite platforms, which provide frequent, low cost access to space. It can be also used on any other platform in space

  18. Method for predicting enzyme-catalyzed reactions

    Science.gov (United States)

    Hlavacek, William S.; Unkefer, Clifford J.; Mu, Fangping; Unkefer, Pat J.

    2013-03-19

    The reactivity of given metabolites is assessed using selected empirical atomic properties in the potential reaction center. Metabolic reactions are represented as biotransformation rules. These rules are generalized from the patterns in reactions. These patterns are not unique to reactants but are widely distributed among metabolites. Using a metabolite database, potential substructures are identified in the metabolites for a given biotransformation. These substructures are divided into reactants or non-reactants, depending on whether they participate in the biotransformation or not. Each potential substructure is then modeled using descriptors of the topological and electronic properties of atoms in the potential reaction center; molecular properties can also be used. A Support Vector Machine (SVM) or classifier is trained to classify a potential reactant as a true or false reactant using these properties.

  19. Russian space

    Science.gov (United States)

    As well as authorizing NASA's funding for FY 1998 and 1999, the Civilian Space Authorization Act (H.R. 1275) would affect U.S.-Russia interactions in space. Regarding the International Space Station, the bill: prohibits transferring funds to Russia to pay for work on elements that are Russia's responsibility;

  20. Space administration

    OpenAIRE

    Worthington, Scott; Worthington, Scott

    2015-01-01

    My dissertation consists of two parts. The larger portion is an hour-long piece for double bass, electronics, and projected text called Space Administration. The second portion, this essay, discusses my musical background leading up to Space Administration, details of the composition itself, and what new directions I see in my work that in part stem from creating the piece Space Administration

  1. Profiling metabolic networks to study cancer metabolism.

    Science.gov (United States)

    Hiller, Karsten; Metallo, Christian M

    2013-02-01

    Cancer is a disease of unregulated cell growth and survival, and tumors reprogram biochemical pathways to aid these processes. New capabilities in the computational and bioanalytical characterization of metabolism have now emerged, facilitating the identification of unique metabolic dependencies that arise in specific cancers. By understanding the metabolic phenotype of cancers as a function of their oncogenic profiles, metabolic engineering may be applied to design synthetically lethal therapies for some tumors. This process begins with accurate measurement of metabolic fluxes. Here we review advanced methods of quantifying pathway activity and highlight specific examples where these approaches have uncovered potential opportunities for therapeutic intervention. Copyright © 2012 Elsevier Ltd. All rights reserved.

  2. Principal Metabolic Flux Mode Analysis.

    Science.gov (United States)

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

    2018-02-06

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

  3. Prediction of cytochrome P450 mediated metabolism

    DEFF Research Database (Denmark)

    Olsen, Lars; Oostenbrink, Chris; Jørgensen, Flemming Steen

    2015-01-01

    Cytochrome P450 enzymes (CYPs) form one of the most important enzyme families involved in the metabolism of xenobiotics. CYPs comprise many isoforms, which catalyze a wide variety of reactions, and potentially, a large number of different metabolites can be formed. However, it is often hard...

  4. Effective dynamics along given reaction coordinates, and reaction rate theory.

    Science.gov (United States)

    Zhang, Wei; Hartmann, Carsten; Schütte, Christof

    2016-12-22

    In molecular dynamics and related fields one considers dynamical descriptions of complex systems in full (atomic) detail. In order to reduce the overwhelming complexity of realistic systems (high dimension, large timescale spread, limited computational resources) the projection of the full dynamics onto some reaction coordinates is examined in order to extract statistical information like free energies or reaction rates. In this context, the effective dynamics that is induced by the full dynamics on the reaction coordinate space has attracted considerable attention in the literature. In this article, we contribute to this discussion: we first show that if we start with an ergodic diffusion process whose invariant measure is unique then these properties are inherited by the effective dynamics. Then, we give equations for the effective dynamics, discuss whether the dominant timescales and reaction rates inferred from the effective dynamics are accurate approximations of such quantities for the full dynamics, and compare our findings to results from approaches like Mori-Zwanzig, averaging, or homogenization. Finally, by discussing the algorithmic realization of the effective dynamics, we demonstrate that recent algorithmic techniques like the "equation-free" approach and the "heterogeneous multiscale method" can be seen as special cases of our approach.

  5. Metabolism Disrupting Chemicals and Metabolic Disorders

    Science.gov (United States)

    Heindel, Jerrold J.; Blumberg, Bruce; Cave, Mathew; Machtinger, Ronit; Mantovani, Alberto; Mendez, Michelle A.; Nadal, Angel; Palanza, Paola; Panzica, Giancarlo; Sargis, Robert; Vandenberg, Laura N.; Saal, Frederick vom

    2016-01-01

    The recent epidemics of metabolic diseases, obesity, type 2 diabetes(T2D), liver lipid disorders and metabolic syndrome have largely been attributed to genetic background and changes in diet, exercise and aging. However, there is now considerable evidence that other environmental factors may contribute to the rapid increase in the incidence of these metabolic diseases. This review will examine changes to the incidence of obesity, T2D and non-alcoholic fatty liver disease (NAFLD), the contribution of genetics to these disorders and describe the role of the endocrine system in these metabolic disorders. It will then specifically focus on the role of endocrine disrupting chemicals (EDCs) in the etiology of obesity, T2D and NAFLD while finally integrating the information on EDCs on multiple metabolic disorders that could lead to metabolic syndrome. We will specifically examine evidence linking EDC exposures during critical periods of development with metabolic diseases that manifest later in life and across generations. PMID:27760374

  6. Computational Modeling of Lipid Metabolism in Yeast

    Directory of Open Access Journals (Sweden)

    Vera Schützhold

    2016-09-01

    Full Text Available Lipid metabolism is essential for all major cell functions and has recently gained increasing attention in research and health studies. However, mathematical modeling by means of classical approaches such as stoichiometric networks and ordinary differential equation systems has not yet provided satisfactory insights, due to the complexity of lipid metabolism characterized by many different species with only slight differences and by promiscuous multifunctional enzymes.Here, we present a object-oriented stochastic model approach as a way to cope with the complex lipid metabolic network. While all lipid species are treated objects in the model, they can be modified by the respective converting reactions based on reaction rules, a hybrid method that integrates benefits of agent-based and classical stochastic simulation. This approach allows to follow the dynamics of all lipid species with different fatty acids, different degrees of saturation and different headgroups over time and to analyze the effect of parameter changes, potential mutations in the catalyzing enzymes or provision of different precursors. Applied to yeast metabolism during one cell cycle period, we could analyze the distribution of all lipids to the various membranes in time-dependent manner.The presented approach allows to efficiently treat the complexity of cellular lipid metabolism and to derive conclusions on the time- and location-dependent distributions of lipid species and their properties such as saturation. It is widely applicable, easily extendable and will provide further insights in healthy and diseased states of cell metabolism.

  7. Design spaces

    DEFF Research Database (Denmark)

    2005-01-01

    of digital technology with space poses new challenges that call for new approaches. Creative alternatives to traditional systems methodologies are called for when designers use digital media to create new possibilities for action in space. Design Spaces explores how design and media art can provide creative......Digital technologies and media are becoming increasingly embodied and entangled in the spaces and places at work and at home. However, our material environment is more than a geometric abstractions of space: it contains familiar places, social arenas for human action. For designers, the integration...... alternatives for integrating digital technology with space. Connecting practical design work with conceptual development and theorizing, art with technology, and usesr-centered methods with social sciences, Design Spaces provides a useful research paradigm for designing ubiquitous computing. This book...

  8. Design spaces

    DEFF Research Database (Denmark)

    2005-01-01

    Digital technologies and media are becoming increasingly embodied and entangled in the spaces and places at work and at home. However, our material environment is more than a geometric abstractions of space: it contains familiar places, social arenas for human action. For designers, the integration...... of digital technology with space poses new challenges that call for new approaches. Creative alternatives to traditional systems methodologies are called for when designers use digital media to create new possibilities for action in space. Design Spaces explores how design and media art can provide creative...... alternatives for integrating digital technology with space. Connecting practical design work with conceptual development and theorizing, art with technology, and usesr-centered methods with social sciences, Design Spaces provides a useful research paradigm for designing ubiquitous computing. This book...

  9. C2 metabolism in Euglena.

    Science.gov (United States)

    Nakazawa, Masami

    2017-01-01

    Euglenoids are able to assimilate fatty acids and alcohols with various carbon-chain lengths, and ethanol is known to be one of the best carbon sources to support the growth of Euglena gracilis. Ethanol is first oxidized to acetate by the sequential reactions of alcohol dehydrogenase and acetaldehyde dehydrogenase in the mitochondria, and then converted to acetyl coenzyme A (acetyl-CoA). Acetyl-CoA is metabolized through the glyoxylate cycle which is a modified tricarboxylic acid (TCA) cycle in which isocitrate lyase (ICL) and malate synthase (MS) function to bypass the two decarboxylation steps of the TCA cycle, enabling the net synthesis of carbohydrates from C2 compounds. ICL and MS form a unique bifunctional enzyme localized in Euglena mitochondria, not in glyoxysome as in other eukaryotes. The unique glyoxylate and glycolate metabolism during photorespiration is also discussed in this chapter.

  10. [Adverse reactions to insulin].

    Science.gov (United States)

    Liñana, J J; Montoro, F J; Hernández, M D; Basomba, A

    1997-07-01

    The prevalence of allergic reactions to insuline has decreased during the last few years. Probably this is due to the use of the newly-developed recombinant human insuline. At present, adverse reactions to insuline occur in 5-10% of patients on therapy with insuline. Adverse reactions may be local (more frequent) or systemic (rare). Insuline resistance consists in a different type of immunological reaction. Diagnosis of allergy to insuline is based on clinical history and cutaneous and serological tests. Treatment depends upon the severity of the reaction. When insuline is indispensable despite a previous allergic reaction, a desensitization protocol may be implemented.

  11. Conservation Laws in Biochemical Reaction Networks

    DEFF Research Database (Denmark)

    Mahdi, Adam; Ferragut, Antoni; Valls, Claudia

    2017-01-01

    We study the existence of linear and nonlinear conservation laws in biochemical reaction networks with mass-action kinetics. It is straightforward to compute the linear conservation laws as they are related to the left null-space of the stoichiometry matrix. The nonlinear conservation laws...... are difficult to identify and have rarely been considered in the context of mass-action reaction networks. Here, using the Darboux theory of integrability, we provide necessary structural (i.e., parameterindependent) conditions on a reaction network to guarantee the existence of nonlinear conservation laws...

  12. Biomedical Analyses of Mice Body Hair Exposed to Long-term Space Flight as a Compliment of Human Research

    Science.gov (United States)

    Mukai, Chiaki

    Introduction: To understand the effect of space environment characterized by microgravity and radiation on protein and mineral metabolisms is important for developing the countermeasures to the adverse effects happening on the astronauts who stay long-term in space. Thus JAXA has started a human research to study the effects of long-term exposure in space flight on gene expression and mineral metabolism by analyzing astronaut's hair grown in space since December 2009 (Experiment nicknamed "HAIR"). Ten human subjects who are the crew of the International Space Station (ISS) will be expected to complete this experiment. Thanks to the tissue sharing program of space-flown mice which is presented and organized by AGI(Italian Space Agency), we can also have an opportunity to analyze rodents samples which will greatly compliment human hair experiment by enable us to conduct more detailed analysis with the expansion of skin analysis which is not include in human experiment. The purpose of this flown-mice experiment is to study the effects of long-term exposure to space environment such as microgravity and space radiation on mineral and protein metabolism, the biological responses to the stress levels, and the initial process of skin carcinogenesis by analyzing hair shaft, its root cells, and skin. Approach and Method In this experiment, we analyzed hair shaft, hair root and skin. Hair samples with skin were taken from 3-month space-flown mice and ground-control mice in the AGI's tissue sharing program in 2009. The sample numbers of space-flown mice and control-mice were three and six, respectively. And they were at the Mice Drawer System (MDS) in ISS and in the laboratory of Geneva University. For the hair shaft, the mineral balance is investi-gated by energy dispersive X-ray spectroscopy (SEM-EDX). For hair root, the extracted RNA undergoes DNA microarray analysis, and will be further examined particular interests of gene-expression by real time Reverse Transcription

  13. Metabolism of fluoroacetate in lettuce

    Energy Technology Data Exchange (ETDEWEB)

    Ward, P.F.V.; Huskisson, N.S.

    1972-01-01

    Whole lettuce plants were incubated with (1) (l-/sup 14/C)acetate, (2) fluoroacetate followed by (l-/sup 14/C)acetate, (3) fluoro(l-/sup 14/C)acetate, (4) fluoro(2-/sup 14/C)acetate or (5) S-carboxy-(/sup 14/C)methylglutathione. 2. Fluoroacetate did not affect the expiration of /sup 14/CO/sub 2/ from (l-/sup 14/C)acetate and only a small amount of /sup 14/CO/sub 2/ was produced from either fluoro(l-/sup 14/C)-acetate or fluoro(2-/sup 14/C)acetate in 43 h. 3. Fluoroacetate at 50 mg/kg wet wt. doubled the plant citrate concentration after 43 h incubation, and depending on the age and size of the plant 50-100% of the compound was metabolized. 4. With both fluoro(l-/sup 14/C)acetate and fluoro(2-/sup 14/C)acetate all the radioactivity except that in the CO/sub 2/ was found in the water-soluble fraction. About 2% was in fluorocitrate and the remainder, apart from unchanged fluoroacetate, was in a number of compounds devoid of fluorine but containing nitrogen and sulphur. These were peptide-like and could be separated by chromatography on an amino acid analyser. 5. Identical compounds were obtained from the spontaneous reaction between iodo(2-/sup 14/C)acetate and glutathione, the major product being S-carboxy-methylglutathione. 6. S-Carboxymethylcysteine was also isolated and its mass spectrum compared with a commercial sample. 7. Reaction rates of all the monohaloacetates with glutathione were studied at pH 7 at 25/sup 0/C. No reaction was observed with fluoroacetate. 8. The metabolism of fluoroacetate by lettuce is discussed in relation to that of aliphatic and aromatic halogen compounds, including fluoroacetate, by mammalian liver and to the metabolism of fluoroacetate by different plants reported by other workers.

  14. Space Commercialization

    Science.gov (United States)

    Martin, Gary L.

    2011-01-01

    A robust and competitive commercial space sector is vital to continued progress in space. The United States is committed to encouraging and facilitating the growth of a U.S. commercial space sector that supports U.S. needs, is globally competitive, and advances U.S. leadership in the generation of new markets and innovation-driven entrepreneurship. Energize competitive domestic industries to participate in global markets and advance the development of: satellite manufacturing; satellite-based services; space launch; terrestrial applications; and increased entrepreneurship. Purchase and use commercial space capabilities and services to the maximum practical extent Actively explore the use of inventive, nontraditional arrangements for acquiring commercial space goods and services to meet United States Government requirements, including measures such as public-private partnerships, . Refrain from conducting United States Government space activities that preclude, discourage, or compete with U.S. commercial space activities. Pursue potential opportunities for transferring routine, operational space functions to the commercial space sector where beneficial and cost-effective.

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

    Directory of Open Access Journals (Sweden)

    Tyler W. H. Backman

    2018-01-01

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

  16. Positron emission tomography for measuring metabolism in vivo

    International Nuclear Information System (INIS)

    Feinendegen, L.E.

    1985-01-01

    Nuclear medical imaging always relates to changes at the cellular or molecular level of organization of the body. For years, such changes, summarily called metabolism, permitted radionuclides as tracers to produce information on rather gross organ structure and function. Yet, more recently, increasing emphasis is placed on metabolic reactions themselves; this development is of considerable promise to the clinician, because disease begins and nearly always expresses itself by alterations of metabolism. PET greatly helps to investigate and describe in vivo individual steps within the complex network of enzyme catalized reactions that maintain life; in fact, PET allows studies of biochemistry in vivo. (Author)

  17. Preequilibrium Nuclear Reactions

    International Nuclear Information System (INIS)

    Strohmaier, B.

    1988-01-01

    After a survey on existing experimental data on precompound reactions and a description of preequilibrium reactions, theoretical models and quantum mechanical theories of preequilibrium emission are presented. The 25 papers of this meeting are analyzed separately

  18. Microfluidic chemical reaction circuits

    Science.gov (United States)

    Lee, Chung-cheng [Irvine, CA; Sui, Guodong [Los Angeles, CA; Elizarov, Arkadij [Valley Village, CA; Kolb, Hartmuth C [Playa del Rey, CA; Huang, Jiang [San Jose, CA; Heath, James R [South Pasadena, CA; Phelps, Michael E [Los Angeles, CA; Quake, Stephen R [Stanford, CA; Tseng, Hsian-rong [Los Angeles, CA; Wyatt, Paul [Tipperary, IE; Daridon, Antoine [Mont-Sur-Rolle, CH

    2012-06-26

    New microfluidic devices, useful for carrying out chemical reactions, are provided. The devices are adapted for on-chip solvent exchange, chemical processes requiring multiple chemical reactions, and rapid concentration of reagents.

  19. Oral Hypersensitivity Reactions

    Science.gov (United States)

    ... such as cinnamon, peppermint, eugenol and menthol. Even dental floss and denture cleansers may contain ingredients known to cause a hypersensitivity reaction. Q: How can dental treatment trigger a hypersensitivity reaction? A: Some dental ...

  20. Topics in Xenobiochemistry: do metabolic pathways exist for xenobiotics? The micro-metabolism hypothesis.

    Science.gov (United States)

    Wilson, I D; Nicholson, J K

    2003-09-01

    1. The relevance of the concept of 'the metabolic pathway' for the understanding of xenobiotic metabolism is discussed in the light of advances in modern analytical methods that have enabled the detection and identification of minor metabolites present at ever lower concentrations. 2. A model is suggested where the overall metabolic fate of a xenobiotic is the sum of all the possible metabolic reactions permitted by the solution chemistry of the compound modulated by factors such as the metabolizing enzyme complement of the organism, the affinity of those enzymes for the xenobiotic substrates and the probabilities of all of these processes. 3. In this probabilistic, rather than deterministic, system, the resulting proportions of particular metabolites will, therefore, depend on the sums of the probabilities of particular biotransformation reactions occurring and the stability (chemical or metabolic) of the resulting metabolite. 4. In this model, all the potential metabolic possibilities that could result for any individual xenobiotic will occur to some extent. However, in actuality, many of the resulting metabolites will be produced or excreted in such small quantities as to defy ready detection with current methods.

  1. Adaptive Evolution of Phosphorus Metabolism in Prochlorococcus

    DEFF Research Database (Denmark)

    Casey, John R; Mardinoglu, Adil; Nielsen, Jens

    2016-01-01

    Inorganic phosphorus is scarce in the eastern Mediterranean Sea, where the high-light-adapted ecotype HLI of the marine picocyanobacterium Prochlorococcus marinus thrives. Physiological and regulatory control of phosphorus acquisition and partitioning has been observed in HLI both in culture...... and in the field; however, the optimization of phosphorus metabolism and associated gains for its phosphorus-limited-growth (PLG) phenotype have not been studied. Here, we reconstructed a genome-scale metabolic network of the HLI axenic strain MED4 (iJC568), consisting of 568 metabolic genes in relation to 794...... reactions involving 680 metabolites distributed in 6 subcellular locations. iJC568 was used to quantify metabolic fluxes under PLG conditions, and we observed a close correspondence between experimental and computed fluxes. We found that MED4 has minimized its dependence on intracellular phosphate, not only...

  2. Thermonuclear reaction rates. III

    International Nuclear Information System (INIS)

    Harris, M.J.; Fowler, W.A.; Caughlan, G.R.; Zimmerman, B.A.

    1983-01-01

    Stellar thermonuclear reaction rates are revised and updated, adding a number of new important reaction rates. Several reactions with large negative Q-values are included, and examples of them are discussed. The importance of the decay rates for Mg-26(p,n) exp 26 Al and Al-26(n,p) exp 26 Mg for stellar studies is emphasized. 19 references

  3. Cluster knockout reactions

    Indian Academy of Sciences (India)

    2014-04-07

    Apr 7, 2014 ... advancements in the area of (α, 2α) reactions and heavy cluster knockout reactions are discussed. Importance of the finite-range vertex and the final-state interactions are brought out. Keywords. Cluster knockout reactions; FR-DWIA calculations; t-matrix effective interaction. PACS Nos 14.20.Pt; 24.10.

  4. ORGANIC REACTION MECHANISM CONTROVERSY ...

    African Journals Online (AJOL)

    Preferred Customer

    However, there are so many chemical reactions notably in organic chemistry where reactions may not directly lead to products. ... There are concepts that support these ideas but can they be proven to the ... Reaction mechanism is one such issue in organic chemistry that has attracted a lot of controversial comments from ...

  5. Maillard Reaction: review

    Directory of Open Access Journals (Sweden)

    Júlia d'Almeida Francisquini

    2017-11-01

    Full Text Available Maillard reaction is an important subject of study in food science and technology and different areas of knowledge are involved such as chemistry, food engineering, nutrition and food technology. The objective of this paper is to present the basic concepts of the Maillard reaction, such as the reaction stages, the main compounds producced and some technological consequences for dairy products.

  6. Resonant thermonuclear reaction rate

    International Nuclear Information System (INIS)

    Haubold, H.J.; Mathai, A.M.

    1986-01-01

    Basic physical principles for the resonant and nonresonant thermonuclear reaction rates are applied to find their standard representations for nuclear astrophysics. Closed-form representations for the resonant reaction rate are derived in terms of Meijer's G-function. Analytic representations of the resonant and nonresonant nuclear reaction rates are compared and the appearance of Meijer's G-function is discussed in physical terms

  7. Wang-Landau Reaction Ensemble Method: Simulation of Weak Polyelectrolytes and General Acid-Base Reactions.

    Science.gov (United States)

    Landsgesell, Jonas; Holm, Christian; Smiatek, Jens

    2017-02-14

    We present a novel method for the study of weak polyelectrolytes and general acid-base reactions in molecular dynamics and Monte Carlo simulations. The approach combines the advantages of the reaction ensemble and the Wang-Landau sampling method. Deprotonation and protonation reactions are simulated explicitly with the help of the reaction ensemble method, while the accurate sampling of the corresponding phase space is achieved by the Wang-Landau approach. The combination of both techniques provides a sufficient statistical accuracy such that meaningful estimates for the density of states and the partition sum can be obtained. With regard to these estimates, several thermodynamic observables like the heat capacity or reaction free energies can be calculated. We demonstrate that the computation times for the calculation of titration curves with a high statistical accuracy can be significantly decreased when compared to the original reaction ensemble method. The applicability of our approach is validated by the study of weak polyelectrolytes and their thermodynamic properties.

  8. Kinugasa Reactions in Water: From Green Chemistry to Bioorthogonal Labelling

    Directory of Open Access Journals (Sweden)

    Mariya Chigrinova

    2015-04-01

    Full Text Available The Kinugasa reaction has become an efficient method for the direct synthesis of β-lactams from substituted nitrones and copper(I acetylides. In recent years, the reaction scope has been expanded to include the use of water as the solvent, and with micelle-promoted [3+2] cycloadditions followed by rearrangement furnishing high yields of β-lactams. The high yields of stable products under aqueous conditions render the modified Kinugasa reaction amenable to metabolic labelling and bioorthogonal applications. Herein, the development of methods for use of the Kinugasa reaction in aqueous media is reviewed, with emphasis on its potential use as a bioorthogonal coupling strategy.

  9. Kinugasa reactions in water: from green chemistry to bioorthogonal labelling.

    Science.gov (United States)

    Chigrinova, Mariya; MacKenzie, Douglas A; Sherratt, Allison R; Cheung, Lawrence L W; Pezacki, John Paul; Pezacki, Paul

    2015-04-16

    The Kinugasa reaction has become an efficient method for the direct synthesis of β-lactams from substituted nitrones and copper(I) acetylides. In recent years, the reaction scope has been expanded to include the use of water as the solvent, and with micelle-promoted [3+2] cycloadditions followed by rearrangement furnishing high yields of β-lactams. The high yields of stable products under aqueous conditions render the modified Kinugasa reaction amenable to metabolic labelling and bioorthogonal applications. Herein, the development of methods for use of the Kinugasa reaction in aqueous media is reviewed, with emphasis on its potential use as a bioorthogonal coupling strategy.

  10. Reconstruction of the central carbon metabolism of Aspergillus niger

    DEFF Research Database (Denmark)

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

    2003-01-01

    between the different intracellular compartments and between the cell and the extracellular medium. The stoichiometry of the metabolic reactions was used in combination with biosynthetic requirements for growth and pseudo-steady state mass balances over intracellular metabolites for the quanti. cation...... of metabolic fluxes using metabolite balancing. This framework was employed to perform an in silico characterisation of the phenotypic behaviour of A. niger grown on different carbon sources. The effects on growth of single reaction deletions were assessed and essential biochemical reactions were identified...

  11. In silico prediction of xenobiotic metabolism in humans

    Energy Technology Data Exchange (ETDEWEB)

    Mu, Fangping [Los Alamos National Laboratory

    2009-01-01

    Xenobiotic metabolism in humans is catalyzed by a few enzymes with broad substrate specificities, which provide the overall broad chemical specificity for nearly all xenobiotics that humans encounter. Xenobiotic metabolism are classified into functional group biotransformations. Based on bona fide reactions and negative examples for each reaction class, support vector machine (SVM) classifiers are built. The input to SVM is a set of atomic and molecular features to define the electrostatic, steric, energetic, geometrical and topological environment of the atoms in the reaction center under the molecule. Results show that the overall sensitivity and specificity of classifiers is around 87%.

  12. Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii.

    Science.gov (United States)

    Nagarajan, Harish; Sahin, Merve; Nogales, Juan; Latif, Haythem; Lovley, Derek R; Ebrahim, Ali; Zengler, Karsten

    2013-11-25

    The metabolic capabilities of acetogens to ferment a wide range of sugars, to grow autotrophically on H2/CO2, and more importantly on synthesis gas (H2/CO/CO2) make them very attractive candidates as production hosts for biofuels and biocommodities. Acetogenic metabolism is considered one of the earliest modes of bacterial metabolism. A thorough understanding of various factors governing the metabolism, in particular energy conservation mechanisms, is critical for metabolic engineering of acetogens for targeted production of desired chemicals. Here, we present the genome-scale metabolic network of Clostridium ljungdahlii, the first such model for an acetogen. This genome-scale model (iHN637) consisting of 637 genes, 785 reactions, and 698 metabolites captures all the major central metabolic and biosynthetic pathways, in particular pathways involved in carbon fixation and energy conservation. A combination of metabolic modeling, with physiological and transcriptomic data provided insights into autotrophic metabolism as well as aided the characterization of a nitrate reduction pathway in C. ljungdahlii. Analysis of the iHN637 metabolic model revealed that flavin based electron bifurcation played a key role in energy conservation during autotrophic growth and helped identify genes for some of the critical steps in this mechanism. iHN637 represents a predictive model that recapitulates experimental data, and provides valuable insights into the metabolic response of C. ljungdahlii to genetic perturbations under various growth conditions. Thus, the model will be instrumental in guiding metabolic engineering of C. ljungdahlii for the industrial production of biocommodities and biofuels.

  13. Views from Space

    Science.gov (United States)

    Kitmacher, Gary H.

    2002-01-01

    Only in the last century have human beings flown in space and men and machines have explored the worlds of our solar system. Robots have gone to most of the our neighboring worlds, the valleys of Mars and the clouds and moons of Jupiter. Instruments like the Hubble Space Telescope have looked into deep space. Those of us on the earth have been able to participate as vicarious explorers through the records, and experiences and the photographs that have been returned. At the beginning of the space program hardly anyone thought of photographs from space as anything more than a branch of industrial photography. There were pictures of the spaceships, and launches and of astronauts in training, but these were all pictures taken on the ground. When John Glenn became America's first man in orbit, bringing a camera was an afterthought. An Ansco Autoset was purchased in a drug store and hastily modified so the astronaut could use it more easily while in his pressure suit. In 1962, everything that Glenn did was deemed an experiment. At the beginning of the program, no one knew for certain whether weightlessness would prevent a man from seeing, or from breathing, or from eating and swallowing. Photography was deemed nothing more than a recreational extra. Not only was little expected of those first pictures taken from space, but there was serious concern that taking pictures of other nations from orbit would be seen as an act of ill will and even one of war- as sovereign sensitive nations would resent having pictures taken by Americans orbiting overhead. A few years earlier, in 1957, in reaction to the Soviet launch of the first Sputnik satellite, scientists told congressman of the necessity of orbiting our own robot spacecraft-they predicted that one day we would take daily pictures of the world's weather. Congressman were incredulous. But space photography developed quickly. For security purposes, spy satellites took over many of the responsibilities we had depended upon

  14. Principles for circadian orchestration of metabolic pathways

    Science.gov (United States)

    Thurley, Kevin; Herbst, Christopher; Wesener, Felix; Koller, Barbara; Wallach, Thomas; Maier, Bert; Kramer, Achim

    2017-01-01

    Circadian rhythms govern multiple aspects of animal metabolism. Transcriptome-, proteome- and metabolome-wide measurements have revealed widespread circadian rhythms in metabolism governed by a cellular genetic oscillator, the circadian core clock. However, it remains unclear if and under which conditions transcriptional rhythms cause rhythms in particular metabolites and metabolic fluxes. Here, we analyzed the circadian orchestration of metabolic pathways by direct measurement of enzyme activities, analysis of transcriptome data, and developing a theoretical method called circadian response analysis. Contrary to a common assumption, we found that pronounced rhythms in metabolic pathways are often favored by separation rather than alignment in the times of peak activity of key enzymes. This property holds true for a set of metabolic pathway motifs (e.g., linear chains and branching points) and also under the conditions of fast kinetics typical for metabolic reactions. By circadian response analysis of pathway motifs, we determined exact timing separation constraints on rhythmic enzyme activities that allow for substantial rhythms in pathway flux and metabolite concentrations. Direct measurements of circadian enzyme activities in mouse skeletal muscle confirmed that such timing separation occurs in vivo. PMID:28159888

  15. Computational Functional Analysis of Lipid Metabolic Enzymes.

    Science.gov (United States)

    Bagnato, Carolina; Have, Arjen Ten; Prados, María B; Beligni, María V

    2017-01-01

    The computational analysis of enzymes that participate in lipid metabolism has both common and unique challenges when compared to the whole protein universe. Some of the hurdles that interfere with the functional annotation of lipid metabolic enzymes that are common to other pathways include the definition of proper starting datasets, the construction of reliable multiple sequence alignments, the definition of appropriate evolutionary models, and the reconstruction of phylogenetic trees with high statistical support, particularly for large datasets. Most enzymes that take part in lipid metabolism belong to complex superfamilies with many members that are not involved in lipid metabolism. In addition, some enzymes that do not have sequence similarity catalyze similar or even identical reactions. Some of the challenges that, albeit not unique, are more specific to lipid metabolism refer to the high compartmentalization of the routes, the catalysis in hydrophobic environments and, related to this, the function near or in biological membranes.In this work, we provide guidelines intended to assist in the proper functional annotation of lipid metabolic enzymes, based on previous experiences related to the phospholipase D superfamily and the annotation of the triglyceride synthesis pathway in algae. We describe a pipeline that starts with the definition of an initial set of sequences to be used in similarity-based searches and ends in the reconstruction of phylogenies. We also mention the main issues that have to be taken into consideration when using tools to analyze subcellular localization, hydrophobicity patterns, or presence of transmembrane domains in lipid metabolic enzymes.

  16. Metabolism of [3-{sup 3}H]oleanolic acid in the isolated ``Calendula officinalis`` leaf cells and transport of the synthesized glycosides, to the cell wall and the extracellular space

    Energy Technology Data Exchange (ETDEWEB)

    Szakiel, A.; Wasiukiewicz, I.; Janiszowska, W. [Warsaw Univ. (Poland). Katedra Biochemii

    1995-12-31

    It has been shown for the first time that [3-{sup 3}H]oleanolic acid glycosides formed in the cytosol of ``C. officinalis`` leaf cells are transported to the extracellular space in the form of pentaglucoside VI (44%), whereas glucuronides derived from [3-{sup 3}H]oleanolic acid 3-O-monoglucuronide (29%) as well as a part of glucosides (24%) were transported into the cell walls. (author). 15 refs, 2 figs, 1 tab.

  17. Automatic NMR-based identification of chemical reaction types in mixtures of co-occurring reactions.

    Directory of Open Access Journals (Sweden)

    Diogo A R S Latino

    Full Text Available The combination of chemoinformatics approaches with NMR techniques and the increasing availability of data allow the resolution of problems far beyond the original application of NMR in structure elucidation/verification. The diversity of applications can range from process monitoring, metabolic profiling, authentication of products, to quality control. An application related to the automatic analysis of complex mixtures concerns mixtures of chemical reactions. We encoded mixtures of chemical reactions with the difference between the (1H NMR spectra of the products and the reactants. All the signals arising from all the reactants of the co-occurring reactions were taken together (a simulated spectrum of the mixture of reactants and the same was done for products. The difference spectrum is taken as the representation of the mixture of chemical reactions. A data set of 181 chemical reactions was used, each reaction manually assigned to one of 6 types. From this dataset, we simulated mixtures where two reactions of different types would occur simultaneously. Automatic learning methods were trained to classify the reactions occurring in a mixture from the (1H NMR-based descriptor of the mixture. Unsupervised learning methods (self-organizing maps produced a reasonable clustering of the mixtures by reaction type, and allowed the correct classification of 80% and 63% of the mixtures in two independent test sets of different similarity to the training set. With random forests (RF, the percentage of correct classifications was increased to 99% and 80% for the same test sets. The RF probability associated to the predictions yielded a robust indication of their reliability. This study demonstrates the possibility of applying machine learning methods to automatically identify types of co-occurring chemical reactions from NMR data. Using no explicit structural information about the reactions participants, reaction elucidation is performed without structure

  18. Automatic NMR-based identification of chemical reaction types in mixtures of co-occurring reactions.

    Science.gov (United States)

    Latino, Diogo A R S; Aires-de-Sousa, João

    2014-01-01

    The combination of chemoinformatics approaches with NMR techniques and the increasing availability of data allow the resolution of problems far beyond the original application of NMR in structure elucidation/verification. The diversity of applications can range from process monitoring, metabolic profiling, authentication of products, to quality control. An application related to the automatic analysis of complex mixtures concerns mixtures of chemical reactions. We encoded mixtures of chemical reactions with the difference between the (1)H NMR spectra of the products and the reactants. All the signals arising from all the reactants of the co-occurring reactions were taken together (a simulated spectrum of the mixture of reactants) and the same was done for products. The difference spectrum is taken as the representation of the mixture of chemical reactions. A data set of 181 chemical reactions was used, each reaction manually assigned to one of 6 types. From this dataset, we simulated mixtures where two reactions of different types would occur simultaneously. Automatic learning methods were trained to classify the reactions occurring in a mixture from the (1)H NMR-based descriptor of the mixture. Unsupervised learning methods (self-organizing maps) produced a reasonable clustering of the mixtures by reaction type, and allowed the correct classification of 80% and 63% of the mixtures in two independent test sets of different similarity to the training set. With random forests (RF), the percentage of correct classifications was increased to 99% and 80% for the same test sets. The RF probability associated to the predictions yielded a robust indication of their reliability. This study demonstrates the possibility of applying machine learning methods to automatically identify types of co-occurring chemical reactions from NMR data. Using no explicit structural information about the reactions participants, reaction elucidation is performed without structure elucidation of

  19. Metabolic host responses to infection by intracellular bacterial pathogens

    Directory of Open Access Journals (Sweden)

    Wolfgang eEisenreich

    2013-07-01

    Full Text Available The interaction of bacterial pathogens with mammalian hosts leads to a variety of physiological responses of the interacting partners aimed at an adaptation to the new situation. These responses include multiple metabolic changes in the affected host cells which are most obvious when the pathogen replicates within host cells as in case of intracellular bacterial pathogens. While the pathogen tries to deprive nutrients from the host cell, the host cell in return takes various metabolic countermeasures against the nutrient theft. During this conflicting interaction, the pathogen triggers metabolic host cell responses by means of common cell envelope components and specific virulence-associated factors. These host reactions generally promote replication of the pathogen. There is growing evidence that pathogen-specific factors may interfere in different ways with the complex regulatory network that controls the carbon and nitrogen metabolism of mammalian cells. The host cell defence answers include general metabolic reactions, like the generation of oxygen- and/or nitrogen-reactive species, and more specific measures aimed to prevent access to essential nutrients for the respective pathogen. Accurate results on metabolic host cell responses are often hampered by the use of cancer cell lines that already exhibit various de-regulated reactions in the primary carbon metabolism. Hence, there is an urgent need for cellular models that more closely reflect the in vivo infection conditions. The exact knowledge of the metabolic host cell responses may provide new interesting concepts for antibacterial therapies.

  20. Early anaerobic metabolisms

    Science.gov (United States)

    Canfield, Don E; Rosing, Minik T; Bjerrum, Christian

    2006-01-01

    Before the advent of oxygenic photosynthesis, the biosphere was driven by anaerobic metabolisms. We catalogue and quantify the source strengths of the most probable electron donors and electron acceptors that would have been available to fuel early-Earth ecosystems. The most active ecosystems were probably driven by the cycling of H2 and Fe2+ through primary production conducted by anoxygenic phototrophs. Interesting and dynamic ecosystems would have also been driven by the microbial cycling of sulphur and nitrogen species, but their activity levels were probably not so great. Despite the diversity of potential early ecosystems, rates of primary production in the early-Earth anaerobic biosphere were probably well below those rates observed in the marine environment. We shift our attention to the Earth environment at 3.8 Gyr ago, where the earliest marine sediments are preserved. We calculate, consistent with the carbon isotope record and other considerations of the carbon cycle, that marine rates of primary production at this time were probably an order of magnitude (or more) less than today. We conclude that the flux of reduced species to the Earth surface at this time may have been sufficient to drive anaerobic ecosystems of sufficient activity to be consistent with the carbon isotope record. Conversely, an ecosystem based on oxygenic photosynthesis was also possible with complete removal of the oxygen by reaction with reduced species from the mantle. PMID:17008221

  1. Borel Spaces

    CERN Document Server

    Berberian, S K

    2002-01-01

    A detailed exposition of G.W. Mackey's theory of Borel spaces (standard, substandard, analytic), based on results in Chapter 9 of Bourbaki's General Topology. Appended are five informal lectures on the subject (given at the CIMPA/ICPAM Summer School, Nice, 1986), sketching the connection between Borel spaces and representations of operator algebras.

  2. Space psychology

    Science.gov (United States)

    Parin, V. V.; Gorbov, F. D.; Kosmolinskiy, F. P.

    1974-01-01

    Psychological selection of astronauts considers mental responses and adaptation to the following space flight stress factors: (1) confinement in a small space; (2) changes in three dimensional orientation; (3) effects of altered gravity and weightlessness; (4) decrease in afferent nerve pulses; (5) a sensation of novelty and danger; and (6) a sense of separation from earth.

  3. Performative Spaces

    DEFF Research Database (Denmark)

    Svaneklink, Annette

    2009-01-01

    that can be related to traditional architectural concepts in terms of dealing with space, body, time and movement. The paper considers this performativity and dual spatiality as being a processual architecture, constantly reconfiguring new hybrids between space, image and user. This dual spatiality raises...

  4. Space Microbiology

    Science.gov (United States)

    Horneck, Gerda; Klaus, David M.; Mancinelli, Rocco L.

    2010-01-01

    Summary: The responses of microorganisms (viruses, bacterial cells, bacterial and fungal spores, and lichens) to selected factors of space (microgravity, galactic cosmic radiation, solar UV radiation, and space vacuum) were determined in space and laboratory simulation experiments. In general, microorganisms tend to thrive in the space flight environment in terms of enhanced growth parameters and a demonstrated ability to proliferate in the presence of normally inhibitory levels of antibiotics. The mechanisms responsible for the observed biological responses, however, are not yet fully understood. A hypothesized interaction of microgravity with radiation-induced DNA repair processes was experimentally refuted. The survival of microorganisms in outer space was investigated to tackle questions on the upper boundary of the biosphere and on the likelihood of interplanetary transport of microorganisms. It was found that extraterrestrial solar UV radiation was the most deleterious factor of space. Among all organisms tested, only lichens (Rhizocarpon geographicum and Xanthoria elegans) maintained full viability after 2 weeks in outer space, whereas all other test systems were inactivated by orders of magnitude. Using optical filters and spores of Bacillus subtilis as a biological UV dosimeter, it was found that the current ozone layer reduces the biological effectiveness of solar UV by 3 orders of magnitude. If shielded against solar UV, spores of B. subtilis were capable of surviving in space for up to 6 years, especially if embedded in clay or meteorite powder (artificial meteorites). The data support the likelihood of interplanetary transfer of microorganisms within meteorites, the so-called lithopanspermia hypothesis. PMID:20197502

  5. Space Robotics

    Directory of Open Access Journals (Sweden)

    Alex Ellery

    2004-09-01

    Full Text Available In this second of three short papers, I introduce some of the basic concepts of space robotics with an emphasis on some specific challenging areas of research that are peculiar to the application of robotics to space infrastructure development. The style of these short papers is pedagogical and the concepts in this paper are developed from fundamental manipulator robotics. This second paper considers the application of space manipulators to on-orbit servicing (OOS, an application which has considerable commercial application. I provide some background to the notion of robotic on-orbit servicing and explore how manipulator control algorithms may be modified to accommodate space manipulators which operate in the micro-gravity of space.

  6. [Acid-base homeostasis: metabolic acidosis and metabolic alkalosis].

    Science.gov (United States)

    Dussol, Bertrand

    2014-07-01

    Acid-base homeostasis ensured by the kidneys, which maintain the equilibrium between proton generation by cellular metabolism and proton excretion in urine. This requirement is lifesaving because of the protons' ability to bind to anionic proteins in the extracellular space, modifying their structure and functions. The kidneys also regenerate bicarbonates. The kidney is not the sole organ in charge of maintaining blood pH in a very narrow range; lungs are also involved since they allow a large amount of volatile acid generated by cellular respiration to be eliminated. Copyright © 2014 Association Société de néphrologie. Published by Elsevier SAS. All rights reserved.

  7. Construction of a Genome-Scale Metabolic Model of Arthrospira platensis NIES-39 and Metabolic Design for Cyanobacterial Bioproduction.

    Directory of Open Access Journals (Sweden)

    Katsunori Yoshikawa

    Full Text Available Arthrospira (Spirulina platensis is a promising feedstock and host strain for bioproduction because of its high accumulation of glycogen and superior characteristics for industrial production. Metabolic simulation using a genome-scale metabolic model and flux balance analysis is a powerful method that can be used to design metabolic engineering strategies for the improvement of target molecule production. In this study, we constructed a genome-scale metabolic model of A. platensis NIES-39 including 746 metabolic reactions and 673 metabolites, and developed novel strategies to improve the production of valuable metabolites, such as glycogen and ethanol. The simulation results obtained using the metabolic model showed high consistency with experimental results for growth rates under several trophic conditions and growth capabilities on various organic substrates. The metabolic model was further applied to design a metabolic network to improve the autotrophic production of glycogen and ethanol. Decreased flux of reactions related to the TCA cycle and phosphoenolpyruvate reaction were found to improve glycogen production. Furthermore, in silico knockout simulation indicated that deletion of genes related to the respiratory chain, such as NAD(PH dehydrogenase and cytochrome-c oxidase, could enhance ethanol production by using ammonium as a nitrogen source.

  8. Construction of a Genome-Scale Metabolic Model of Arthrospira platensis NIES-39 and Metabolic Design for Cyanobacterial Bioproduction

    Science.gov (United States)

    Yoshikawa, Katsunori; Aikawa, Shimpei; Kojima, Yuta; Toya, Yoshihiro; Furusawa, Chikara; Kondo, Akihiko; Shimizu, Hiroshi

    2015-01-01

    Arthrospira (Spirulina) platensis is a promising feedstock and host strain for bioproduction because of its high accumulation of glycogen and superior characteristics for industrial production. Metabolic simulation using a genome-scale metabolic model and flux balance analysis is a powerful method that can be used to design metabolic engineering strategies for the improvement of target molecule production. In this study, we constructed a genome-scale metabolic model of A. platensis NIES-39 including 746 metabolic reactions and 673 metabolites, and developed novel strategies to improve the production of valuable metabolites, such as glycogen and ethanol. The simulation results obtained using the metabolic model showed high consistency with experimental results for growth rates under several trophic conditions and growth capabilities on various organic substrates. The metabolic model was further applied to design a metabolic network to improve the autotrophic production of glycogen and ethanol. Decreased flux of reactions related to the TCA cycle and phosphoenolpyruvate reaction were found to improve glycogen production. Furthermore, in silico knockout simulation indicated that deletion of genes related to the respiratory chain, such as NAD(P)H dehydrogenase and cytochrome-c oxidase, could enhance ethanol production by using ammonium as a nitrogen source. PMID:26640947

  9. Space polypropulsion

    Science.gov (United States)

    Kellett, B. J.; Griffin, D. K.; Bingham, R.; Campbell, R. N.; Forbes, A.; Michaelis, M. M.

    2008-05-01

    Hybrid space propulsion has been a feature of most space missions. Only the very early rocket propulsion experiments like the V2, employed a single form of propulsion. By the late fifties multi-staging was routine and the Space Shuttle employs three different kinds of fuel and rocket engines. During the development of chemical rockets, other forms of propulsion were being slowly tested, both theoretically and, relatively slowly, in practice. Rail and gas guns, ion engines, "slingshot" gravity assist, nuclear and solar power, tethers, solar sails have all seen some real applications. Yet the earliest type of non-chemical space propulsion to be thought of has never been attempted in space: laser and photon propulsion. The ideas of Eugen Saenger, Georgii Marx, Arthur Kantrowitz, Leik Myrabo, Claude Phipps and Robert Forward remain Earth-bound. In this paper we summarize the various forms of nonchemical propulsion and their results. We point out that missions beyond Saturn would benefit from a change of attitude to laser-propulsion as well as consideration of hybrid "polypropulsion" - which is to say using all the rocket "tools" available rather than possibly not the most appropriate. We conclude with three practical examples, two for the next decades and one for the next century; disposal of nuclear waste in space; a grand tour of the Jovian and Saturnian moons - with Huygens or Lunoxod type, landers; and eventually mankind's greatest space dream: robotic exploration of neighbouring planetary systems.

  10. Inborn errors of metabolism

    Science.gov (United States)

    Metabolism - inborn errors of ... Bodamer OA. Approach to inborn errors of metabolism. In: Goldman L, Schafer AI, eds. Goldman-Cecil Medicine . 25th ed. Philadelphia, PA: Elsevier Saunders; 2016:chap 205. Rezvani I, Rezvani GA. An ...

  11. Lipid Metabolism Disorders

    Science.gov (United States)

    ... metabolic disorder, something goes wrong with this process. Lipid metabolism disorders, such as Gaucher disease and Tay-Sachs disease, involve lipids. Lipids are fats or fat-like substances. They ...

  12. Cold-induced metabolism

    NARCIS (Netherlands)

    Lichtenbelt, W. van Marken; Daanen, H.A.M.

    2003-01-01

    Purpose of review Cold response can be insulative (drop in peripheral temperature) or metabolic (increase in energy expenditure). Nonshivering thermogenesis by sympathetic, norepinephrine-induced mitochondrial heat production in brown adipose tissue is a well known component of this metabolic

  13. Investigation of metabolic encephalopathy

    African Journals Online (AJOL)

    , and. Table 1. Confirmed IMD cases associated with metabolic encephalopathy diagnosed at Red Cross Children's Hospital Metabolic Disease. Laboratory, 2006 - 2012. Name of disorder. Number of cases. Glutaric aciduria type 1 (GA1)*. 23.

  14. Reaction Wheel Disturbance Model Extraction Software, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Reaction wheel disturbances are some of the largest sources of noise on sensitive telescopes. Such wheel-induced mechanical noises are not well characterized....

  15. Mars Ascent Vehicle Reaction Control System, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — During this Phase I NASA program, Valley Tech Systems (VTS) will develop an innovative solid Reaction Control System (RCS) architecture concept design that can...

  16. Miniature Reaction Wheel for Small Satellite Control, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — The overall goal of this project is to design, develop, demonstrate, and deliver a miniature, high torque, low-vibration reaction wheel for use on small satellites....

  17. A Reaction Sphere for High Performance Attitude Control, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Our innovative reaction sphere (Doty pending patent application serial number 61/164,868) has the potential to provide much higher performance than a conventional...

  18. Knowledge spaces

    CERN Document Server

    Doignon, Jean-Paul

    1999-01-01

    Knowledge spaces offer a rigorous mathematical foundation for various practical systems of knowledge assessment. An example is offered by the ALEKS system (Assessment and LEarning in Knowledge Spaces), a software for the assessment of mathematical knowledge. From a mathematical standpoint, knowledge spaces generalize partially ordered sets. They are investigated both from a combinatorial and a stochastic viewpoint. The results are applied to real and simulated data. The book gives a systematic presentation of research and extends the results to new situations. It is of interest to mathematically oriented readers in education, computer science and combinatorics at research and graduate levels. The text contains numerous examples and exercises and an extensive bibliography.

  19. Space Bugz!

    DEFF Research Database (Denmark)

    Birke, Alexander; Schoenau-Fog, Henrik; Reng, Lars

    2012-01-01

    This paper presents Space Bugz! - a novel crowd game for large venues or cinemas that utilises the audience's smartphones as controllers for the game. This paper explains what crowd gaming is and describes how the approach used in Space Bugz! enables more advanced gameplay concepts and individual...... player control than current technologies allow. The gameplay of Space Bugz! is then explained along with the technical architecture of the game. After this, the iterative design process used to create the game is described together with future perspectives. The article concludes with links to a video...

  20. Neuroendocrine Regulation of Metabolism

    OpenAIRE

    Cornejo, Maria P.; Hentges, Shane T.; Maliqueo, Manuel; Coirini, Hector; Becu-Villalobos, Damasia; Elias, Carol F.

    2016-01-01

    Given the current environment in most developed countries, it is a challenge to maintain a good balance between calories consumed and calories burned, although maintenance of metabolic balance is key to good health. Therefore, understanding how metabolic regulation is achieved and how the dysregulation of metabolism affects health is an area of intense research. Most studies are focused on the hypothalamus, which is a brain area that acts as a key regulator of metabolism. Among the nuclei tha...

  1. A network perspective on metabolic inconsistency

    Directory of Open Access Journals (Sweden)

    Sonnenschein Nikolaus

    2012-05-01

    Full Text Available Abstract Background Integrating gene expression profiles and metabolic pathways under different experimental conditions is essential for understanding the coherence of these two layers of cellular organization. The network character of metabolic systems can be instrumental in developing concepts of agreement between expression data and pathways. A network-driven interpretation of gene expression data has the potential of suggesting novel classifiers for pathological cellular states and of contributing to a general theoretical understanding of gene regulation. Results Here, we analyze the coherence of gene expression patterns and a reconstruction of human metabolism, using consistency scores obtained from network and constraint-based analysis methods. We find a surprisingly strong correlation between the two measures, demonstrating that a substantial part of inconsistencies between metabolic processes and gene expression can be understood from a network perspective alone. Prompted by this finding, we investigate the topological context of the individual biochemical reactions responsible for the observed inconsistencies. On this basis, we are able to separate the differential contributions that bear physiological information about the system, from the unspecific contributions that unravel gaps in the metabolic reconstruction. We demonstrate the biological potential of our network-driven approach by analyzing transcriptome profiles of aldosterone producing adenomas that have been obtained from a cohort of Primary Aldosteronism patients. We unravel systematics in the data that could not have been resolved by conventional microarray data analysis. In particular, we discover two distinct metabolic states in the adenoma expression patterns. Conclusions The methodology presented here can help understand metabolic inconsistencies from a network perspective. It thus serves as a mediator between the topology of metabolic systems and their dynamical

  2. Nuclear reaction studies

    International Nuclear Information System (INIS)

    Alexander, J.M.; Lacey, R.A.

    1994-01-01

    Research focused on the statistical and dynamical properties of ''hot'' nuclei formed in symmetric heavy-ion reactions. Theses included ''flow'' measurements and the mechanism for multifragment disassembly. Model calculations are being performed for the reactions C+C, Ne+Al, Ar+Sc, Kr+Nb, and Xe+La. It is planned to study 40 Ar reactions from 27 to 115 MeV/nucleon. 2 figs., 41 refs

  3. Metabolic Engineering X Conference

    Energy Technology Data Exchange (ETDEWEB)

    Flach, Evan [American Institute of Chemical Engineers

    2015-05-07

    The International Metabolic Engineering Society (IMES) and the Society for Biological Engineering (SBE), both technological communities of the American Institute of Chemical Engineers (AIChE), hosted the Metabolic Engineering X Conference (ME-X) on June 15-19, 2014 at the Westin Bayshore in Vancouver, British Columbia. It attracted 395 metabolic engineers from academia, industry and government from around the globe.

  4. Sleeve reaction chamber system

    Science.gov (United States)

    Northrup, M Allen [Berkeley, CA; Beeman, Barton V [San Mateo, CA; Benett, William J [Livermore, CA; Hadley, Dean R [Manteca, CA; Landre, Phoebe [Livermore, CA; Lehew, Stacy L [Livermore, CA; Krulevitch, Peter A [Pleasanton, CA

    2009-08-25

    A chemical reaction chamber system that combines devices such as doped polysilicon for heating, bulk silicon for convective cooling, and thermoelectric (TE) coolers to augment the heating and cooling rates of the reaction chamber or chambers. In addition the system includes non-silicon-based reaction chambers such as any high thermal conductivity material used in combination with a thermoelectric cooling mechanism (i.e., Peltier device). The heat contained in the thermally conductive part of the system can be used/reused to heat the device, thereby conserving energy and expediting the heating/cooling rates. The system combines a micromachined silicon reaction chamber, for example, with an additional module/device for augmented heating/cooling using the Peltier effect. This additional module is particularly useful in extreme environments (very hot or extremely cold) where augmented heating/cooling would be useful to speed up the thermal cycling rates. The chemical reaction chamber system has various applications for synthesis or processing of organic, inorganic, or biochemical reactions, including the polymerase chain reaction (PCR) and/or other DNA reactions, such as the ligase chain reaction.

  5. Sodium-concrete reactions

    International Nuclear Information System (INIS)

    Gadd, P.G.

    1982-09-01

    Reaction products of all the major constituents of commercial concrete with liquid sodium have been identified using X-Ray Powder Diffraction. Eight different aggregate materials were chosen to represent the main rock classes available and Ordinary Portland Cement was used throughout. A Differential Thermal Analysis apparatus which enabled continuous stirring of the reactants was designed to improve contact between the powdered concrete components and the liquid sodium. Heats of reaction were calculated from peak areas, the apparatus having been calibrated using reactions of sodium with simple binary oxides whose heats of reaction were known. The heat evolution from aggregates was rationalised on the basis of their mineralogical composition, thus providing a means of choosing an optimum aggregate for use in the concrete of a LMFBR. The reaction of SiO 2 with liquid sodium was shown to depend on the oxygen concentration of the sodium. Reaction products are identified. The reaction of Al 2 O 3 with sodium has been shown also to depend on the oxygen concentration. Reaction products are identified. The evolution of hydrogen during a sodium-cement reaction has been studied using an electrochemical hydrogen meter and the penetration of the liquid metal into cement blocks was also investigated. (author)

  6. Tattoo reaction: Case series

    Directory of Open Access Journals (Sweden)

    Muneer Mohamed

    2018-04-01

    Full Text Available Tattoo is going to be a very common practice especially among young people and we are witnessing a gradual increase of numerous potential complications to tattoo placement which are often seen by physicians, but generally unknown to the public. The most common skin reactions to tattoo include a transient acute inflammatory reaction due to trauma of the skin with needles and medical complications such as superficial and deep local infections, systemic infections, allergic contact dermatitis, photodermatitis, granulomatous and lichenoid reactions, and skin diseases localized on tattooed area (eczema, psoriasis, lichen, and morphea. In this series we present three cases of tattoo reaction.

  7. Riesz spaces

    CERN Document Server

    Zaanen, A C

    1983-01-01

    While Volume I (by W.A.J. Luxemburg and A.C. Zaanen, NHML Volume 1, 1971) is devoted to the algebraic aspects of the theory, this volume emphasizes the analytical theory of Riesz spaces and operators between these spaces. Though the numbering of chapters continues on from the first volume, this does not imply that everything covered in Volume I is required for this volume, however the two volumes are to some extent complementary.

  8. Pharmacotherapeutic Aspects of Space Medicine

    Science.gov (United States)

    Putcha, Lakshmi

    2004-01-01

    Medications are used for a wide variety of indications during space flight. For example, astronauts have taken drugs in flight to ameliorate or prevent symptoms of space motion sickness, headache, sleeplessness, backache, nasal congestion, and constipation. Russian cosmonauts reportedly take medications to prevent metabolic disturbances of the myocardium and intestinal flora, and to optimize their work capacity. Although the discomfort associated with some acute responses to microgravity (e.g., space motion sickness) is expected to diminish with length of time in flight, other responses that have delayed onset (e.g., maintaining nutritional status, bone and muscle strength, and perhaps immune response) may affect health and quality of life during longer missions. Therefore, as the duration of space flights increases, the need for treatment with medications is expected to increase accordingly. Medications carried on Space Shuttle missions have varied somewhat from flight to flight, depending on the individual needs of the crewmembers. Medications use during Shuttle flights seems to be more prevalent than during earlier programs, perhaps because drugs are provided in easy-to-use forms. In fact, nearly all medications taken to date have been ingested orally in tablet form. However, given that the oral route may not be ideal for those suffering motion-sickness symptoms, intramuscular and intranasal preparations are being tested. For example, intramuscular administration of promethazine hydrochloride (Phenergan(Registered TradeMark)) has been reported to be more effective in alleviating motion-sickness symptoms. The difficulties involved in conducting definitive studies of drug efficacy during U.S. space flights have been compounded by the absence of a systematic approach to determining which drugs were taken by whom and under what circumstances. The use of some drugs in space has been less efficacious than expected. The onset, intensity, and duration of the response

  9. Space dosimetry

    International Nuclear Information System (INIS)

    Doke, Tadayoshi

    1988-01-01

    Japan will take part in the LML-1 (International Microgravity Laboratory 1) program that is scheduled to be carried out with space shuttles to be launched in 1991. The program will be followed by the LS-J (Space Laboratory-Japan) and IML-2 programs. A reliable dosimetry system is currently required to be established to evaluate the radiations in space. The present article reviews major features of different types of space radiations and requirements of dosimeters for these radiations. The radiations in the space environment consist of: 1) electrons and protons that have been trapped by the terrestrial magnetism, 2) corpuscular, gamma-and X-rays released from the sun, and 3) galactic cosmic rays (corpuscular, gamma-and X-rays). The effects of the trapped radiations will be low if a spacecraft can get through the zone of such radiations in a short period of time. The effects of galactic cosmic rays are much smaller than those of the trapped radiations. A solar flare can give significant contributions to the total radiations received by a spacecraft. An extremely large flare can release a fatal amount of radiations to the crew of a spacecraft. Prediction of such a large flare is of great important for a long trip through the space. Significant improvements should be made on existing dosimeters. (Nogami, K.)

  10. A genome-scale metabolic network reconstruction of tomato (Solanum lycopersicum L.) and its application to photorespiratory metabolism.

    Science.gov (United States)

    Yuan, Huili; Cheung, C Y Maurice; Poolman, Mark G; Hilbers, Peter A J; van Riel, Natal A W

    2016-01-01

    Tomato (Solanum lycopersicum L.) has been studied extensively due to its high economic value in the market, and high content in health-promoting antioxidant compounds. Tomato is also considered as an excellent model organism for studying the development and metabolism of fleshy fruits. However, the growth, yield and fruit quality of tomatoes can be affected by drought stress, a common abiotic stress for tomato. To investigate the potential metabolic response of tomato plants to drought, we reconstructed iHY3410, a genome-scale metabolic model of tomato leaf, and used this metabolic network to simulate tomato leaf metabolism. The resulting model includes 3410 genes and 2143 biochemical and transport reactions distributed across five intracellular organelles including cytosol, plastid, mitochondrion, peroxisome and vacuole. The model successfully described the known metabolic behaviour of tomato leaf under heterotrophic and phototrophic conditions. The in silico investigation of the metabolic characteristics for photorespiration and other relevant metabolic processes under drought stress suggested that: (i) the flux distributions through the mevalonate (MVA) pathway under drought were distinct from that under normal conditions; and (ii) the changes in fluxes through core metabolic pathways with varying flux ratio of RubisCO carboxylase to oxygenase may contribute to the adaptive stress response of plants. In addition, we improved on previous studies of reaction essentiality analysis for leaf metabolism by including potential alternative routes for compensating reaction knockouts. Altogether, the genome-scale model provides a sound framework for investigating tomato metabolism and gives valuable insights into the functional consequences of abiotic stresses. © 2015 The Authors.The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

  11. A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell growth: The WarburQ effect.

    Science.gov (United States)

    Damiani, Chiara; Colombo, Riccardo; Gaglio, Daniela; Mastroianni, Fabrizia; Pescini, Dario; Westerhoff, Hans Victor; Mauri, Giancarlo; Vanoni, Marco; Alberghina, Lilia

    2017-09-01

    Cancer cells share several metabolic traits, including aerobic production of lactate from glucose (Warburg effect), extensive glutamine utilization and impaired mitochondrial electron flow. It is still unclear how these metabolic rearrangements, which may involve different molecular events in different cells, contribute to a selective advantage for cancer cell proliferation. To ascertain which metabolic pathways are used to convert glucose and glutamine to balanced energy and biomass production, we performed systematic constraint-based simulations of a model of human central metabolism. Sampling of the feasible flux space allowed us to obtain a large number of randomly mutated cells simulated at different glutamine and glucose uptake rates. We observed that, in the limited subset of proliferating cells, most displayed fermentation of glucose to lactate in the presence of oxygen. At high utilization rates of glutamine, oxidative utilization of glucose was decreased, while the production of lactate from glutamine was enhanced. This emergent phenotype was observed only when the available carbon exceeded the amount that could be fully oxidized by the available oxygen. Under the latter conditions, standard Flux Balance Analysis indicated that: this metabolic pattern is optimal to maximize biomass and ATP production; it requires the activity of a branched TCA cycle, in which glutamine-dependent reductive carboxylation cooperates to the production of lipids and proteins; it is sustained by a variety of redox-controlled metabolic reactions. In a K-ras transformed cell line we experimentally assessed glutamine-induced metabolic changes. We validated computational results through an extension of Flux Balance Analysis that allows prediction of metabolite variations. Taken together these findings offer new understanding of the logic of the metabolic reprogramming that underlies cancer cell growth.

  12. Intermediary metabolism during brief and prolonged low tissue temperature. [mammalian thermoregulation during hibernation and hypothermia

    Science.gov (United States)

    Enteman, C.

    1973-01-01

    The intermediary metabolism of the depressed metabolic state in the hypothermic hamster and the hibernating ground squirrel was studied by observing acetate and palmitic acid metabolisms in their tissues. The oxidative metabolism seemed to be dominant in the depressed state although synthetic reactions such as fat synthesis proceeded in some cases at a faster rate than normothermic metabolism for the same tissues. Fat syntheses proceeded in all tissues with brown fat and liver especially active. Enzymes for the synthesis of cholesterol seemed to be more temperature sensitive than enzymes for fatty acid synthesis. It was concluded that there are no great differences between metabolisms in hypothermic and hibernating animals.

  13. Metabolite damage and repair in metabolic engineering design

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Jiayi; Jeffryes, James G.; Henry, Christopher S.; Bruner, Steven D.; Hanson, Andrew D.

    2017-11-01

    The necessarily sharp focus of metabolic engineering and metabolic synthetic biology on pathways and their fluxes has tended to divert attention from the damaging enzymatic and chemical side-reactions that pathway metabolites can undergo. Although historically overlooked and underappreciated, such metabolite damage reactions are now known to occur throughout metabolism and to generate (formerly enigmatic) peaks detected in metabolomics datasets. It is also now known that metabolite damage is often countered by dedicated repair enzymes that undo or prevent it. Metabolite damage and repair are highly relevant to engineered pathway design: metabolite damage reactions can reduce flux rates and product yields, and repair enzymes can provide robust, host-independent solutions. Herein, after introducing the core principles of metabolite damage and repair, we use case histories to document how damage and repair processes affect efficient operation of engineered pathways - particularly those that are heterologous, non-natural, or cell-free. We then review how metabolite damage reactions can be predicted, how repair reactions can be prospected, and how metabolite damage and repair can be built into genome-scale metabolic models. Lastly, we propose a versatile 'plug and play' set of well-characterized metabolite repair enzymes to solve metabolite damage problems known or likely to occur in metabolic engineering and synthetic biology projects.

  14. A new dynamical layout algorithm for complex biochemical reaction networks

    OpenAIRE

    Kummer Ursula; Wegner Katja

    2005-01-01

    Abstract Background To study complex biochemical reaction networks in living cells researchers more and more rely on databases and computational methods. In order to facilitate computational approaches, visualisation techniques are highly important. Biochemical reaction networks, e.g. metabolic pathways are often depicted as graphs and these graphs should be drawn dynamically to provide flexibility in the context of different data. Conventional layout algorithms are not sufficient for every k...

  15. The politics of space - Who owns what? Earth law for space

    Science.gov (United States)

    Hosenball, S. N.

    1983-01-01

    Topics of concern in developing space law, i.e., international disagreements, the present status of space law, and requirements for future space activities, are discussed. Factors inhibiting agreements include governments that wish to control specific regions of GEO, the refusal of several countries to permit international DBS television broadcasts over their boundaries, the possibility that weapons may be placed in space, and the lack of international laws governing humans and industries in space. It is noted that any state entering an international agreement has relinquished some of its sovereignty. The Outer Space Treaty has removed celestial bodies from claims of national appropriation. States retain sovereignty over their citizens who travel in space, a problematical concept once internationally-manned settlements in space or on the moon are established. It is recommended that space law develop mainly in reaction to the implementation of new space capabilities in order to avoid hindering space activities.

  16. Nuclear Propulsion for Space Applications

    Science.gov (United States)

    Houts, M. G.; Bechtel, R. D.; Borowski, S. K.; George, J. A.; Kim, T.; Emrich, W. J.; Hickman, R. R.; Broadway, J. W.; Gerrish, H. P.; Adams, R. B.

    2013-01-01

    Basics of Nuclear Systems: Long history of use on Apollo and space science missions. 44 RTGs and hundreds of RHUs launched by U.S. during past 4 decades. Heat produced from natural alpha (a) particle decay of Plutonium (Pu-238). Used for both thermal management and electricity production. Used terrestrially for over 65 years. Fissioning 1 kg of uranium yields as much energy as burning 2,700,000 kg of coal. One US space reactor (SNAP-10A) flown (1965). Former U.S.S.R. flew 33 space reactors. Heat produced from neutron-induced splitting of a nucleus (e.g. U-235). At steady-state, 1 of the 2 to 3 neutrons released in the reaction causes a subsequent fission in a "chain reaction" process. Heat converted to electricity, or used directly to heat a propellant. Fission is highly versatile with many applications.

  17. Program BETA for simulation of particle decays and reactions

    International Nuclear Information System (INIS)

    Takhtamyshev, G.G.; Merkulova, T.A.

    1997-01-01

    Program BETA is designed for simulation of particle decays and reactions. The program also produces integration over the phase space and decay rate or the reaction cross section are calculated as a result of such integration. At the simulation process the adaptive random number generator SMART may be used, what is found to be useful for some difficult cases

  18. Nonlinear analysis of a reaction-diffusion system: Amplitude equations

    Energy Technology Data Exchange (ETDEWEB)

    Zemskov, E. P., E-mail: zemskov@ccas.ru [Russian Academy of Sciences, Dorodnicyn Computing Center (Russian Federation)

    2012-10-15

    A reaction-diffusion system with a nonlinear diffusion term is considered. Based on nonlinear analysis, the amplitude equations are obtained in the cases of the Hopf and Turing instabilities in the system. Turing pattern-forming regions in the parameter space are determined for supercritical and subcritical instabilities in a two-component reaction-diffusion system.

  19. Ensemble Kinetic Modeling of Metabolic Networks from Dynamic Metabolic Profiles

    Science.gov (United States)

    Jia, Gengjie; Stephanopoulos, Gregory; Gunawan, Rudiyanto

    2012-01-01

    Kinetic modeling of metabolic pathways has important applications in metabolic engineering, but significant challenges still remain. The difficulties faced vary from finding best-fit parameters in a highly multidimensional search space to incomplete parameter identifiability. To meet some of these challenges, an ensemble modeling method is developed for characterizing a subset of kinetic parameters that give statistically equivalent goodness-of-fit to time series concentration data. The method is based on the incremental identification approach, where the parameter estimation is done in a step-wise manner. Numerical efficacy is achieved by reducing the dimensionality of parameter space and using efficient random parameter exploration algorithms. The shift toward using model ensembles, instead of the traditional “best-fit” models, is necessary to directly account for model uncertainty during the application of such models. The performance of the ensemble modeling approach has been demonstrated in the modeling of a generic branched pathway and the trehalose pathway in Saccharomyces cerevisiae using generalized mass action (GMA) kinetics. PMID:24957767

  20. Ensemble Kinetic Modeling of Metabolic Networks from Dynamic Metabolic Profiles

    Directory of Open Access Journals (Sweden)

    Gengjie Jia

    2012-11-01

    Full Text Available Kinetic modeling of metabolic pathways has important applications in metabolic engineering, but significant challenges still remain. The difficulties faced vary from finding best-fit parameters in a highly multidimensional search space to incomplete parameter identifiability. To meet some of these challenges, an ensemble modeling method is developed for characterizing a subset of kinetic parameters that give statistically equivalent goodness-of-fit to time series concentration data. The method is based on the incremental identification approach, where the parameter estimation is done in a step-wise manner. Numerical efficacy is achieved by reducing the dimensionality of parameter space and using efficient random parameter exploration algorithms. The shift toward using model ensembles, instead of the traditional “best-fit” models, is necessary to directly account for model uncertainty during the application of such models. The performance of the ensemble modeling approach has been demonstrated in the modeling of a generic branched pathway and the trehalose pathway in Saccharomyces cerevisiae using generalized mass action (GMA kinetics.

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

    Indian Academy of Sciences (India)

    2015-09-28

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

  2. Altered metabolism in cancer

    Directory of Open Access Journals (Sweden)

    Locasale Jason W

    2010-06-01

    Full Text Available Abstract Cancer cells have different metabolic requirements from their normal counterparts. Understanding the consequences of this differential metabolism requires a detailed understanding of glucose metabolism and its relation to energy production in cancer cells. A recent study in BMC Systems Biology by Vasquez et al. developed a mathematical model to assess some features of this altered metabolism. Here, we take a broader look at the regulation of energy metabolism in cancer cells, considering their anabolic as well as catabolic needs. See research article: http://www.biomedcentral.com/1752-0509/4/58/

  3. Cancer stem cell metabolism.

    Science.gov (United States)

    Peiris-Pagès, Maria; Martinez-Outschoorn, Ubaldo E; Pestell, Richard G; Sotgia, Federica; Lisanti, Michael P

    2016-05-24

    Cancer is now viewed as a stem cell disease. There is still no consensus on the metabolic characteristics of cancer stem cells, with several studies indicating that they are mainly glycolytic and others pointing instead to mitochondrial metabolism as their principal source of energy. Cancer stem cells also seem to adapt their metabolism to microenvironmental changes by conveniently shifting energy production from one pathway to another, or by acquiring intermediate metabolic phenotypes. Determining the role of cancer stem cell metabolism in carcinogenesis has become a major focus in cancer research, and substantial efforts are conducted towards discovering clinical targets.

  4. Engineering Cellular Metabolism

    DEFF Research Database (Denmark)

    Nielsen, Jens; Keasling, Jay

    2016-01-01

    Metabolic engineering is the science of rewiring the metabolism of cells to enhance production of native metabolites or to endow cells with the ability to produce new products. The potential applications of such efforts are wide ranging, including the generation of fuels, chemicals, foods, feeds...... of metabolic engineering and will discuss how new technologies can enable metabolic engineering to be scaled up to the industrial level, either by cutting off the lines of control for endogenous metabolism or by infiltrating the system with disruptive, heterologous pathways that overcome cellular regulation....

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

    Science.gov (United States)

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

    2018-01-01

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

  6. The plasticity of cyanobacterial carbon metabolism.

    Science.gov (United States)

    Xiong, Wei; Cano, Melissa; Wang, Bo; Douchi, Damien; Yu, Jianping

    2017-12-01

    This opinion article aims to raise awareness of a fundamental issue which governs sustainable production of biofuels and bio-chemicals from photosynthetic cyanobacteria. Discussed is the plasticity of carbon metabolism, by which the cyanobacterial cells flexibly distribute intracellular carbon fluxes towards target products and adapt to environmental/genetic alterations. This intrinsic feature in cyanobacterial metabolism is being understood through recent identification of new biochemical reactions and engineering on low-throughput pathways. We focus our discussion on new insights into the nature of metabolic plasticity in cyanobacteria and its impact on hydrocarbons (e.g. ethylene and isoprene) production. We discuss approaches that need to be developed to rationally rewire photosynthetic carbon fluxes throughout primary metabolism. We outline open questions about the regulatory mechanisms of the metabolic network that remain to be answered, which might shed light on photosynthetic carbon metabolism and help optimize design principles in order to improve the production of fuels and chemicals in cyanobacteria. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. The effect of the structure of polychlorinated biphenyls on their hydroxylation, oxidation, and glutathionyl conjugation reactions.

    Science.gov (United States)

    Song, Er Qun; Ma, Xiao Yan; Tian, Xing Guo; Liu, Jing; Liu, Li Chao; Dong, Hui; Song, Yang

    2013-02-01

    To compare the nature of the metabolites formed from the phase I metabolism (hydroxylation and oxidation) and phase II metabolism (glutathionyl conjugation) of PCBs that have different chlorine substitution patterns. To discuss the structure-activity relationships and metabolic mechanisms of PCBs. 4-Cl-biphenyl (PCB3), 4,4'-Cl-biphenyl (PCB15), 3,4,3',4'-Cl-biphenyl (PCB77) were used for in vitro metabolic study. LC/MS and UV-Vis studies were performed for metabolites identification. The cytochrome P-450 catalyzed hydroxylation rate decreased as the number of chlorine substitutions increased. In this reaction, PCB3 was fully metabolized, approximately half of the PCB15 was metabolized and PCB77 was not metabolized at all. The oxidation rate of PCB15-HQ was higher than that of PCB3-HQ under various oxidation conditions. The LC/MS and UV-Vis data suggest that in the conjugation reaction of PCB15-Q and GSH, the Michael addition reaction occurs preferentially over the displacement reaction. The metabolic profiles of polychlorinated biphenyls (PCBs) are dramatically affected by chlorine substitution patterns. It is suggested that the metabolic profiles of PCBs are related to their chlorine substitution patterns, which may have implications for the toxicity of PCB exposure. Copyright © 2013 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

  8. public spaces

    Directory of Open Access Journals (Sweden)

    Elena Grigoryeva

    2013-01-01

    Full Text Available The topic of this issue is PUBLIC SPACES. It is familiar and clear to every citizen. The streets and courtyards as childhood experiences remain with us forever. And these are the places where we come with our parents at weekends, where we meet friends, where we have dates and where we already come for a walk with our children.The history of public spaces is long and captivating. It was the main city squares where the most important events took place in history. The Agoras of Ancient Greece and the Roman Forums, the squares of Vatican, Paris and London, Moscow and Saint Petersburg… Greve, Trafalgar, Senate, Palace, Red, Bolotnaya – behind every name there is life of capitals, countries and nations.Public spaces, their shapes, image and development greatly influence the perception of the city as a whole. Both visitors and inhabitants can see in public spaces not only the visage but the heart, the soul and the mind of the city.Unfortunately, sometimes we have to prove the value of public spaces and defend them from those who consider them nothing but a blank space, nobody’s land destined for barbarous development.What should happen to make citizens perceive public spaces as their own and to make authorities consider development and maintenance of squares and parks their priority task against the  background of increasing competition between cities and the fight for human capital? Lately they more often say about “a high-quality human capital”. And now, when they say “the city should be liveable” they add “for all groups of citizens, including the creative class”.

  9. Underground spaces/cybernetic spaces

    Directory of Open Access Journals (Sweden)

    Tomaž Novljan

    2000-01-01

    Full Text Available A modern city space is a space where in the vertical and horizontal direction dynamic, non-linear processes exist, similar as in nature. Alongside the “common” city surface, cities have underground spaces as well that are increasingly affecting the functioning of the former. It is the space of material and cybernetic communication/transport. The psychophysical specifics of using underground places have an important role in their conceptualisation. The most evident facts being their limited volume and often limited connections to the surface and increased level of potential dangers of all kinds. An efficient mode for alleviating the effects of these specific features are artistic interventions, such as: shape, colour, lighting, all applications of the basic principles of fractal theory.

  10. Clock Reaction: Outreach Attraction

    Science.gov (United States)

    Carpenter, Yuen-ying; Phillips, Heather A.; Jakubinek, Michael B.

    2010-01-01

    Chemistry students are often introduced to the concept of reaction rates through demonstrations or laboratory activities involving the well-known iodine clock reaction. For example, a laboratory experiment involving thiosulfate as an iodine scavenger is part of the first-year general chemistry laboratory curriculum at Dalhousie University. With…

  11. Nuclear Reaction Data Centers

    International Nuclear Information System (INIS)

    McLane, V.; Nordborg, C.; Lemmel, H.D.; Manokhin, V.N.

    1988-01-01

    The cooperating Nuclear Reaction Data Centers are involved in the compilation and exchange of nuclear reaction data for incident neutrons, charged particles and photons. Individual centers may also have services in other areas, e.g., evaluated data, nuclear structure and decay data, reactor physics, nuclear safety; some of this information may also be exchanged between interested centers. 20 refs., 1 tab

  12. Hydrogen evolution reaction catalyst

    Science.gov (United States)

    Subbaraman, Ram; Stamenkovic, Vojislav; Markovic, Nenad; Tripkovic, Dusan

    2016-02-09

    Systems and methods for a hydrogen evolution reaction catalyst are provided. Electrode material includes a plurality of clusters. The electrode exhibits bifunctionality with respect to the hydrogen evolution reaction. The electrode with clusters exhibits improved performance with respect to the intrinsic material of the electrode absent the clusters.

  13. Applications of Reaction Rate

    Science.gov (United States)

    Cunningham, Kevin

    2007-01-01

    This article presents an assignment in which students are to research and report on a chemical reaction whose increased or decreased rate is of practical importance. Specifically, students are asked to represent the reaction they have chosen with an acceptable chemical equation, identify a factor that influences its rate and explain how and why it…

  14. Degradations and Rearrangement Reactions

    Science.gov (United States)

    Zhang, Jianbo

    This section deals with recent reports concerning degradation and rearrangement reactions of free sugars as well as some glycosides. The transformations are classified in chemical and enzymatic ways. In addition, the Maillard reaction will be discussed as an example of degradation and rearrangement transformation and its application in current research in the fields of chemistry and biology.

  15. Computational modelling of cellular level metabolism

    International Nuclear Information System (INIS)

    Calvetti, D; Heino, J; Somersalo, E

    2008-01-01

    The steady and stationary state inverse problems consist of estimating the reaction and transport fluxes, blood concentrations and possibly the rates of change of some of the concentrations based on data which are often scarce noisy and sampled over a population. The Bayesian framework provides a natural setting for the solution of this inverse problem, because a priori knowledge about the system itself and the unknown reaction fluxes and transport rates can compensate for the insufficiency of measured data, provided that the computational costs do not become prohibitive. This article identifies the computational challenges which have to be met when analyzing the steady and stationary states of multicompartment model for cellular metabolism and suggest stable and efficient ways to handle the computations. The outline of a computational tool based on the Bayesian paradigm for the simulation and analysis of complex cellular metabolic systems is also presented

  16. Allergic reactions during anesthesia.

    Science.gov (United States)

    Levy, J H

    1988-01-01

    Any drug or blood product administered in the perioperative period has the potential to produce a life-threatening allergic (immune reaction) called anaphylaxis. Anaphylactic reactions represent adverse reactions mediated by immunospecific antibodies (IgE and IgG) that interact with mast cells, basophils, or the complement system to liberate vasoactive mediators and recruit other inflammatory cells. Activation of humoral and cellular pathways produces characteristic responses in the respiratory (bronchospasm and upper airway edema), cardiovascular (vasodilation and increased capillary permeability), and cutaneous systems (wheal and flare). Other predictable adverse drug reactions may mimic anaphylaxis to produce similar physiologic consequences independent of allergy (immune responses). Rapid and timely cardiopulmonary intervention with airway maintenance, epinephrine, and volume expansion is essential to avoid an adverse outcome. Severe reactions may be protracted, especially during anesthesia, requiring even larger doses of catecholamines and intensive care observation.

  17. Glycogen metabolism in humans.

    Science.gov (United States)

    Adeva-Andany, María M; González-Lucán, Manuel; Donapetry-García, Cristóbal; Fernández-Fernández, Carlos; Ameneiros-Rodríguez, Eva

    2016-06-01

    In the human body, glycogen is a branched polymer of glucose stored mainly in the liver and the skeletal muscle that supplies glucose to the blood stream during fasting periods and to the muscle cells during muscle contraction. Glycogen has been identified in other tissues such as brain, heart, kidney, adipose tissue, and erythrocytes, but glycogen function in these tissues is mostly unknown. Glycogen synthesis requires a series of reactions that include glucose entrance into the cell through transporters, phosphorylation of glucose to glucose 6-phosphate, isomerization to glucose 1-phosphate, and formation of uridine 5'-diphosphate-glucose, which is the direct glucose donor for glycogen synthesis. Glycogenin catalyzes the formation of a short glucose polymer that is extended by the action of glycogen synthase. Glycogen branching enzyme introduces branch points in the glycogen particle at even intervals. Laforin and malin are proteins involved in glycogen assembly but their specific function remains elusive in humans. Glycogen is accumulated in the liver primarily during the postprandial period and in the skeletal muscle predominantly after exercise. In the cytosol, glycogen breakdown or glycogenolysis is carried out by two enzymes, glycogen phosphorylase which releases glucose 1-phosphate from the linear chains of glycogen, and glycogen debranching enzyme which untangles the branch points. In the lysosomes, glycogen degradation is catalyzed by α-glucosidase. The glucose 6-phosphatase system catalyzes the dephosphorylation of glucose 6-phosphate to glucose, a necessary step for free glucose to leave the cell. Mutations in the genes encoding the enzymes involved in glycogen metabolism cause glycogen storage diseases.

  18. Space Station Water Quality

    Science.gov (United States)

    Willis, Charles E. (Editor)

    1987-01-01

    The manned Space Station will exist as an isolated system for periods of up to 90 days. During this period, safe drinking water and breathable air must be provided for an eight member crew. Because of the large mass involved, it is not practical to consider supplying the Space Station with water from Earth. Therefore, it is necessary to depend upon recycled water to meet both the human and nonhuman water needs on the station. Sources of water that will be recycled include hygiene water, urine, and cabin humidity condensate. A certain amount of fresh water can be produced by CO2 reduction process. Additional fresh water will be introduced into the total pool by way of food, because of the free water contained in food and the water liberated by metabolic oxidation of the food. A panel of scientists and engineers with extensive experience in the various aspects of wastewater reuse was assembled for a 2 day workshop at NASA-Johnson. The panel included individuals with expertise in toxicology, chemistry, microbiology, and sanitary engineering. A review of Space Station water reclamation systems was provided.

  19. Environmental spaces

    DEFF Research Database (Denmark)

    Larsen, Henrik Gutzon

    Using the development of intergovernmental environmental cooperation in the Baltic Sea area as a concrete example, the aim of this study is to explore how the 'environment' in situations of environmental interdependence is identified and institutionalised as political-geographical objects....... 'Environmental interdependence' is to this end conceptualised as a tension between 'political spaces' of discrete state territories and 'environmental spaces' of spatially nested ecosystems. This tension between geographies of political separateness and environmental wholeness is the implicit or explicit basis...... for a large and varied literature. But in both its critical and problemsolving manifestations, this literature tends to naturalise the spatiality of environmental concerns: environmental spaces are generally taken for granted. On the suggestion that there is a subtle politics to the specification...

  20. Tsirelson's space

    CERN Document Server

    Casazza, Peter G

    1989-01-01

    This monograph provides a structure theory for the increasingly important Banach space discovered by B.S. Tsirelson. The basic construction should be accessible to graduate students of functional analysis with a knowledge of the theory of Schauder bases, while topics of a more advanced nature are presented for the specialist. Bounded linear operators are studied through the use of finite-dimensional decompositions, and complemented subspaces are studied at length. A myriad of variant constructions are presented and explored, while open questions are broached in almost every chapter. Two appendices are attached: one dealing with a computer program which computes norms of finitely-supported vectors, while the other surveys recent work on weak Hilbert spaces (where a Tsirelson-type space provides an example).

  1. Space doubt

    OpenAIRE

    Rega, Joseph Mark

    2003-01-01

    Dissertação (mestrado) - Universidade Federal de Santa Catarina, Centro de Comunicação e Expressão. Programa de Pós-Graduação em Inglês e Literatura Correspondente. The recent surge in cyberspace science fiction follows previous trends within the genre, i.e. those connected with future city-space and outer space, and is an inevitable result of economic forces. There has always been a close relationship between capitalism and spatial expansion, compelled by technological innovations that ha...

  2. Einstein spaces

    CERN Document Server

    Petrov, Aleksej Z

    1969-01-01

    Einstein Spaces presents the mathematical basis of the theory of gravitation and discusses the various spaces that form the basis of the theory of relativity. This book examines the contemporary development of the theory of relativity, leading to the study of such problems as gravitational radiation, the interaction of fields, and the behavior of elementary particles in a gravitational field. Organized into nine chapters, this book starts with an overview of the principles of the special theory of relativity, with emphasis on the mathematical aspects. This text then discusses the need for a ge

  3. Entering Space

    Science.gov (United States)

    Zubrin, Robert

    The authors is giving a classification of civilisations depending on the degree of colonisation of the Earth, Solar System and Our Galaxy. The problems of: History of geographic discoveries (The great geographical discoveries during the Middle Age, the concurence of Chinnese and Europeans in this Area); The Astrophysics, such as: Asteroids, Water and Atmosphere on outer planets, Planet Mars Planet, Agriculture on outer planets, Minerals on outer planets; Cosmic flights: Fuels, Robotics, Moon (as an intermediary basis for interplanetary flights), Mars colonisation; Interstellar flights, Space research costs, strategy and tactics of the space colonisation; Policy: War and Peace, International Collaboration are discussed.

  4. Transit space

    DEFF Research Database (Denmark)

    Raahauge, Kirsten Marie

    2008-01-01

    This article deals with representations of one specific city, Århus, Denmark, especially its central district. The analysis is based on anthropological fieldwork conducted in Skåde Bakker and Fedet, two well-off neighborhoods. The overall purpose of the project is to study perceptions of space...... and the interaction of cultural, social, and spatial organizations, as seen from the point of view of people living in Skåde Bakker and Fedet. The focus is on the city dwellers’ representations of the central district of Århus with specific reference to the concept of transit space. When applied to various Århusian...

  5. CardioNet: A human metabolic network suited for the study of cardiomyocyte metabolism

    Directory of Open Access Journals (Sweden)

    Karlstädt Anja

    2012-08-01

    Full Text Available Abstract Background Availability of oxygen and nutrients in the coronary circulation is a crucial determinant of cardiac performance. Nutrient composition of coronary blood may significantly vary in specific physiological and pathological conditions, for example, administration of special diets, long-term starvation, physical exercise or diabetes. Quantitative analysis of cardiac metabolism from a systems biology perspective may help to a better understanding of the relationship between nutrient supply and efficiency of metabolic processes required for an adequate cardiac output. Results Here we present CardioNet, the first large-scale reconstruction of the metabolic network of the human cardiomyocyte comprising 1793 metabolic reactions, including 560 transport processes in six compartments. We use flux-balance analysis to demonstrate the capability of the network to accomplish a set of 368 metabolic functions required for maintaining the structural and functional integrity of the cell. Taking the maintenance of ATP, biosynthesis of ceramide, cardiolipin and further important phospholipids as examples, we analyse how a changed supply of glucose, lactate, fatty acids and ketone bodies may influence the efficiency of these essential processes. Conclusions CardioNet is a functionally validated metabolic network of the human cardiomyocyte that enables theorectical studies of cellular metabolic processes crucial for the accomplishment of an adequate cardiac output.

  6. Enhancing chemical reactions

    Science.gov (United States)

    Morrey, John R.

    1978-01-01

    Methods of enhancing selected chemical reactions. The population of a selected high vibrational energy state of a reactant molecule is increased substantially above its population at thermal equilibrium by directing onto the molecule a beam of radiant energy from a laser having a combination of frequency and intensity selected to pump the selected energy state, and the reaction is carried out with the temperature, pressure, and concentrations of reactants maintained at a combination of values selected to optimize the reaction in preference to thermal degradation by transforming the absorbed energy into translational motion. The reaction temperature is selected to optimize the reaction. Typically a laser and a frequency doubler emit radiant energy at frequencies of .nu. and 2.nu. into an optical dye within an optical cavity capable of being tuned to a wanted frequency .delta. or a parametric oscillator comprising a non-centrosymmetric crystal having two indices of refraction, to emit radiant energy at the frequencies of .nu., 2.nu., and .delta. (and, with a parametric oscillator, also at 2.nu.-.delta.). Each unwanted frequency is filtered out, and each desired frequency is focused to the desired radiation flux within a reaction chamber and is reflected repeatedly through the chamber while reactants are fed into the chamber and reaction products are removed therefrom.

  7. Respiratory transfusion reactions

    Directory of Open Access Journals (Sweden)

    Ivica Marić

    2017-11-01

    Full Text Available Respiratory transfusion-related reactions are not very frequent, partly also because recognition and reporting transfusion reactions is still underemphasized. Tis article describes the most important respiratory transfusion reactions, their pathophysiology, clinical picture and treatment strategies. Respiratory transfusion related reactions can be primary or secondary. The most important primary transfusion-related reactions are TRALI - transfusion-related acute lung injury, TACO – transfusion-associated circulatory overload, and TAD - transfusion-associated dyspnea. TRALI is immuneassociated injury of alveolar basal membrane, which becomes highly permeable and causes noncardiogenic pulmonary edema. Treatment of TRALI is mainly supportive with oxygen, fluids (in case of hypotension and in cases of severe acute respiratory failure also mechanic ventilation. TACO is caused by volume overload in predisposed individuals, such as patients with heart failure, the elderly, infants, patients with anemia and patients with positive fluid balance. Clinical picture is that of a typical pulmonary cardiogenic edema, and the therapy is classical: oxygen and diuretics, and in severe cases also non-invasive or invasive mechanical ventilation. TAD is usually a mild reaction of unknown cause and cannot be classified as TACO or TRALI, nor can it be ascribed to patient’s preexisting diseases. Although the transfusion-related reactions are not very common, knowledge about them can prevent serious consequences. On the one hand preventive measures should be sought, and on the other early recognition is beneficial, so that proper treatment can take place.

  8. Learning the Fructose Metabolism by Hypermedia

    Directory of Open Access Journals (Sweden)

    J.K. Sugai et al

    2014-08-01

    Full Text Available Introduction: Learning of biochemistry among other factors depends on create an educational environment favorable to the reality of the students and offer better educational tools for the teachers. Objective: The goal of this hypermedia is to motivate and strengthen the students learning about the metabolism of fructose. Materials And Methods:This work presents the development of a biochemical hypermedia to understanding of the fructose metabolism. It was developed with the help of concept maps, ISIS Draw, ADOBE Photoshop and FLASH MX Program. Results and Discussion: A step by step animation process shows the enzymatic reactions of three pathways of the fructose metabolism (principal route-fructokinase, sorbitol and hexokinase pathways.There are navigation guide that allow scrolling the mouse over the names of the components of enzymatic reactions of via the metabolism of fructose. Thus, explanatory text box, chemical structures and animation of the actions of enzymes appear to navigator. Upon completion of the module, the user’s response to the proposed exercise can be checked immediately through text box with interactive content of the answer. Conclusion:This hypermedia was presented for undergraduate students (UFSC. Its use allowed to users to reach the goal of understanding of the subject independently of their agility or background, since it was possible to each student navigate through the hypermedia according with his individual rhythm and as many times as needed. Interactive hypermedia is proving to be

  9. Organics in Space: Results from SPace Exposure Platforms and Nanosatellites

    Science.gov (United States)

    Ehrenfreund, Pascale; Foing, Bernard H.; Salama, Farid

    2015-08-01

    A series of successful “laboratory astrophysics” experiments performed on International Space Station (ISS) external platforms such as EXPOSE have provided insights into the evolution of organic and biological materials in space and planetary environments. The study of the reactions, destruction, and longevity of organics in the space environment is of fundamental interest. To provide an accurate outer space environment for extended durations, exposure experiments in low Earth orbit have been conducted in the last decades in order to examine the consequences of actual space conditions including combinations of solar and cosmic radiation, space vacuum, and microgravity. The O/OREOS (Organism/ORganic Exposure to Orbital Stresses) nanosatellite studied in situ during the 6-month primary and 1-year extended mission the photochemical processing of selected PAHs in low Earth orbit (650 km altitude); results were autonomously telemetered to Earth. We report on the methods and flight preparation of samples for space exposure platforms and results on the stability of organic thin-films. The UV-vis degradation process of thin-films was recorded over time, which revealed intriguing and counter-intuitive photolytic kinetics that will be re-investigated on the ISS in a space environment.

  10. Effects of kinins on glucose metabolism in vivo.

    Science.gov (United States)

    Hartl, W H; Jauch, K W; Wolfe, R R; Schildberg, F W

    1990-01-01

    Current concepts of the physiological importance of the kinin/prostaglandin system view these tissue factors as part of a defense system, which protects tissues from potentially noxious factors, such as hypoxia or destructive inflammatory reactions. This kinin-triggered defense reaction includes an improvement in cellular energy metabolism. The latter is brought about in peripheral tissues by an increased availability of glucose for anaerobic and aerobic glycolysis, whereas in liver tissue, energy-consuming reactions such as gluconeogenesis are attenuated. There is evidence that such favorable effects can also be produced in man when kinins are administered systemically. Prostaglandins are most likely the second messengers of kinin-induced metabolic effects. Thus, it may be advantageous to increase the availability of kinins either by exogenous infusion or by inhibiting endogenous degradation during postoperative stress or in diseases such as diabetes mellitus, in which glucose metabolism is severely disturbed.

  11. The Reaction Wheel Pendulum

    CERN Document Server

    Block, Daniel J; Spong, Mark W

    2007-01-01

    This monograph describes the Reaction Wheel Pendulum, the newest inverted-pendulum-like device for control education and research. We discuss the history and background of the reaction wheel pendulum and other similar experimental devices. We develop mathematical models of the reaction wheel pendulum in depth, including linear and nonlinear models, and models of the sensors and actuators that are used for feedback control. We treat various aspects of the control problem, from linear control of themotor, to stabilization of the pendulum about an equilibrium configuration using linear control, t

  12. Electron transfer reactions

    CERN Document Server

    Cannon, R D

    2013-01-01

    Electron Transfer Reactions deals with the mechanisms of electron transfer reactions between metal ions in solution, as well as the electron exchange between atoms or molecules in either the gaseous or solid state. The book is divided into three parts. Part 1 covers the electron transfer between atoms and molecules in the gas state. Part 2 tackles the reaction paths of oxidation states and binuclear intermediates, as well as the mechanisms of electron transfer. Part 3 discusses the theories and models of the electron transfer process; theories and experiments involving bridged electron transfe

  13. Training Spaces

    Science.gov (United States)

    Weinstein, Margery

    2010-01-01

    Creating a balanced learning space for employees is about more than trying different types of seating. It is a challenge that an affect how well employees absorb the lessons and whether they will be able to product better results for the company. The possible solutions are as diverse as the learners. This article describes how three companies…

  14. Space Conquest

    CERN Multimedia

    2005-01-01

    An old water tank from the time of the ISR is being converted into a temporary store for ATLAS muon chambers. This is the last chapter in the big programme by the PH Department to make better use of space at CERN.

  15. Transit space

    DEFF Research Database (Denmark)

    Raahauge, Kirsten Marie

    2008-01-01

    and the interaction of cultural, social, and spatial organizations, as seen from the point of view of people living in Skåde Bakker and Fedet. The focus is on the city dwellers’ representations of the central district of Århus with specific reference to the concept of transit space. When applied to various Århusian...

  16. Space Gerontology

    Science.gov (United States)

    Miquel, J. (Editor); Economos, A. C. (Editor)

    1982-01-01

    Presentations are given which address the effects of space flght on the older person, the parallels between the physiological responses to weightlessness and the aging process, and experimental possibilities afforded by the weightless environment to fundamental research in gerontology and geriatrics.

  17. Hilbert space

    Directory of Open Access Journals (Sweden)

    David N. Keck

    2003-01-01

    Full Text Available We investigate a class of abstract functional integro-differential stochastic evolution equations in a real separable Hilbert space. Global existence results concerning mild and periodic solutions are formulated under various growth and compactness conditions. Also, related convergence results are established and an example arising in the mathematical modeling of heat conduction is discussed to illustrate the abstract theory.

  18. Trading Spaces

    Science.gov (United States)

    Cort, Cliff

    2006-01-01

    Education administrators face the dual dilemma of crowded, aging facilities and tightening capital budgets. The challenge is to build the necessary classroom, laboratory and activity space while minimizing the length and expense of the construction process. One solution that offers an affordable alternative is modular construction, a method that…

  19. Trace spaces

    DEFF Research Database (Denmark)

    Fajstrup, Lisbeth; Goubault, Eric; Haucourt, Emmanuel

    2012-01-01

    State-space reduction techniques, used primarily in model-checkers, all rely on the idea that some actions are independent, hence could be taken in any (respective) order while put in parallel, without changing the semantics. It is thus not necessary to consider all execution paths...

  20. Sexual dimorphism in human lipid metabolism.

    Science.gov (United States)

    Mittendorfer, Bettina

    2005-04-01

    The existing work demonstrates that striking differences exist between men and women in lipid kinetics. These differences cannot be explained simply by the presence and action of sex hormones and are not always due to secondary, phenotypic traits that characterize men and women (e.g., body-composition, regional fat distribution). In fact, some of these secondary traits may even be the result of sexual dimorphism in metabolism, and being of female or male genotype also determines intermediary metabolism. This review provides an overview of the currently available information regarding sexual dimorphism in human lipid metabolism but does not provide an in-depth account of current knowledge (due to limited space); it will be a broad introduction to those interested in the field and will, hopefully, stimulate further efforts to unravel the secrets of male and female metabolism. What has been discovered so far regarding differences in lipid metabolism between men and women is likely only the tip of the iceberg; clearly, more work is necessary to fully understand human substrate metabolism and the implications the presence of sexual dimorphism in the control of substrate kinetics has on the prevention and treatment of disease.

  1. Nutrition for Space Exploration

    Science.gov (United States)

    Smith, Scott M.

    2005-01-01

    Nutrition has proven to be critical throughout the history of human exploration, on both land and water. The importance of nutrition during long-duration space exploration is no different. Maintaining optimal nutritional status is critical for all bodily systems, especially in light of the fact that that many are also affected by space flight itself. Major systems of concern are bone, muscle, the cardiovascular system, the immune system, protection against radiation damage, and others. The task ahead includes defining the nutritional requirements for space travelers, ensuring adequacy of the food system, and assessing crew nutritional status before, during, and after flight. Accomplishing these tasks will provide significant contributions to ensuring crew health on long-duration missions. In addition, development and testing of nutritional countermeasures to effects of space flight is required, and assessment of the impact of other countermeasures (such as exercise and pharmaceuticals) on nutrition is also critical for maintaining overall crew health. Vitamin D stores of crew members are routinely low after long-duration space flight. This occurs even when crew members take vitamin D supplements, suggesting that vitamin D metabolism may be altered during space flight. Vitamin D is essential for efficient absorption of calcium, and has numerous other benefits for other tissues with vitamin D receptors. Protein is a macronutrient that requires additional study to define the optimal intake for space travelers. Administration of protein to bed rest subjects can effectively mitigate muscle loss associated with disuse, but too much or too little protein can also have negative effects on bone. In another bed rest study, we found that the ratio of protein to potassium was correlated with the level of bone resorption: the higher the ratio, the more bone resorption. These relationships warrant further study to optimize the beneficial effect of protein on both bone and muscle

  2. Selected aspects of fusion reactions

    International Nuclear Information System (INIS)

    Lacroix, D.

    2003-01-01

    In this lecture, we present selected aspects of nuclear fusion. The importance of the initial geometry of the reaction and its relation to fusion barrier are first discussed. The effect of deformation leading to the notion of barrier distribution is then illustrated. After a brief overview of the advantages of macroscopic theories, the dynamics of nuclear system under large amplitude motion is reviewed. The di-nuclear concept is presented to understand the competition between fusion and quasi-fission. This concept is then generalized to account for the dissipative dynamics in multidimensional collective space. The last part of this lecture is devoted to new aspects encountered with radioactive beams specific properties of very extended neutron rich system, influence of pygmy or soft dipole resonances and charge exchange far from stability are discussed. (author)

  3. Studies on the reaction of glutathione and formaldehyde using NMR.

    Science.gov (United States)

    Hopkinson, Richard J; Barlow, Philippa S; Schofield, Christopher J; Claridge, Timothy D W

    2010-11-07

    Within cells it is proposed that a major mechanism for the metabolism of formaldehyde is via its reaction with glutathione (GSH) to form S-hydroxymethylglutathione (HMG), which undergoes subsequent oxidation. In addition to HMG and the previously reported (5R,10S)-5-(carboxymethylcarbamoyl)-7-oxo-3-thia-1,6-diazabicyclo[4.4.1]undecane-10-carboxylic acid (BiGF(2)), NMR studies on the reaction of GSH with formaldehyde reveal two previously unassigned monocyclic structures. The results imply that the biologically relevant reactions between aldehydes and peptides/proteins may be more complex than presently perceived.

  4. Glycaemic adverse drug reactions from anti-neoplastics used in ...

    African Journals Online (AJOL)

    235625 records ... Glycaemic adverse drug reactions from anti-neoplastics used in treating pancreatic cancer. ... Based on the emphasized nine antineoplastic drugs with high hyperglycemic ADR incidence, we found: fluorouracil, sorafenib and pemetrexed with high ADR record of metabolism and nutrition disorders; ...

  5. Metabolic assessments during extra-vehicular activity

    Science.gov (United States)

    Osipov, Yu. Yu.; Spichkov, A. N.; Filipenkov, S. N.

    Extra-vehicular activity (EVA) has a significant role during extended space flights. It demonstrates that humans can survive and perform useful work outside the Orbital Space Stations (OSS) while wearing protective space suits (SS). When the International Space Station 'Alpha'(ISSA) is fully operational, EVA assembly, installation, maintenance and repair operations will become an everyday repetitive work activity in space. It needs new ergonomic evaluation of the work/rest schedule for an increasing of the labor amount per EVA hour. The metabolism assessment is a helpful method to control the productivity of the EVA astronaut and to optimize the work/rest regime. Three following methods were used in Russia to estimate real-time metabolic rates during EVA: 1. Oxygen consumption, computed from the pressure drop in a high pressure bottle per unit time (with actual thermodynamic oxygen properties under high pressure and oxygen leakage taken into account). 2. Carbon dioxide production, computed from CO 2 concentration at the contaminant control cartridge and gas flow rate in the life support subsystem closed loop (nominal mode) or gas leakage in the SS open loop (emergency mode). 3. Heat removal, computed from the difference between the temperatures of coolant water or gas and its flow rate in a unit of time (with assumed humidity and wet oxygen state taken into account). Comparison of heat removal values with metabolic rates enables us to determine the thermal balance during an operative medical control of EVA at "Salyut-6", "Salyut-7" and "Mir" OSS. Complex analysis of metabolism, body temperature and heat rate supports a differential diagnosis between emotional and thermal components of stress during EVA. It gives a prognosis of human homeostasis during EVA. Available information has been acquired into an EVA data base which is an effective tool for ergonomical optimization.

  6. DREAMS of metabolism.

    Science.gov (United States)

    Soh, Keng Cher; Hatzimanikatis, Vassily

    2010-10-01

    Metabolic networks have been studied for several decades, and sophisticated computational frameworks are needed to augment experimental approaches to harness these complex networks. BNICE (Biochemical Network Integrated Computational Explorer), a computational approach for the discovery of novel biochemical pathways that is based on biochemical transformations, overcomes many of the current limitations. BNICE and similar frameworks can be used in several different areas: (i) 'Design' of novel pathways for metabolic engineering; (ii) 'Retrosynthesis' of metabolic compounds; (iii) 'Evolution' analysis between metabolic pathways of different organisms; (iv) 'Analysis' of metabolic pathways; (v) 'Mining' of omics data; and (vi) 'Selection' of targets for enzyme engineering. Here, we discuss the issues and challenges in building such frameworks as well as the gamut of applications in biotechnology, metabolic engineering and synthetic biology. Copyright © 2010 Elsevier Ltd. All rights reserved.

  7. [Menopause and metabolic syndrome].

    Science.gov (United States)

    Meirelles, Ricardo M R

    2014-03-01

    The incidence of cardiovascular disease increases considerably after the menopause. One reason for the increased cardiovascular risk seems to be determined by metabolic syndrome, in which all components (visceral obesity, dyslipidemia, hypertension, and glucose metabolism disorder) are associated with higher incidence of coronary artery disease. After menopause, metabolic syndrome is more prevalent than in premenopausal women, and may plays an important role in the occurrence of myocardial infarction and other atherosclerotic and cardiovascular morbidities. Obesity, an essential component of the metabolic syndrome, is also associated with increased incidence of breast, endometrial, bowel, esophagus, and kidney cancer. The treatment of metabolic syndrome is based on the change in lifestyle and, when necessary, the use of medication directed to its components. In the presence of symptoms of the climacteric syndrome, hormonal therapy, when indicated, will also contribute to the improvement of the metabolic syndrome.

  8. Calbindins decreased after space flight.

    Science.gov (United States)

    Sergeev, I N; Rhoten, W B; Carney, M D

    1996-12-01

    Exposure of the body to microgravity during space flight causes a series of well-documented changes in Ca2+ metabolism, yet the cellular and molecular mechanisms leading to these changes are poorly understood. Calbindins, vitamin D-dependent Ca2+ binding proteins, are believed to have a significant role in maintaining cellular Ca2+ homeostasis. In this study, we used biochemical and immunocytochemical approaches to analyze the expression of calbindin-D28k and calbindin-D9k in kidneys, small intestine, and pancreas of rats flown for 9 d aboard the space shuttle. The effects of microgravity on calbindins in rats from space were compared with synchronous Animal Enclosure Module controls, modeled weightlessness animals (tail suspension), and their controls. Exposure to microgravity resulted in a significant and sustained decrease in calbindin-D28k content in the kidney and calbindin-D9k in the small intestine of flight animals, as measured by enzyme-linked immunosorbent assay (ELISA). Modeled weightlessness animals exhibited a similar decrease in calbindins by ELISA. Immunocytochemistry (ICC) in combination with quantitative computer image analysis was used to measure in situ the expression of calbindins in the kidney and the small intestine, and the expression of insulin in pancreas. There was a large decrease of immunoreactivity in renal distal tubular cell-associated calbindin-D28k and in intestinal absorptive cell-associated calbindin-D9k of space flight and modeled weightlessness animals compared with matched controls. No consistent difference in pancreatic insulin immunoreactivity between space flight, modeled weightlessness, and controls was observed. Regression analysis of results obtained by quantitative ICC and ELISA for space flight, modeled weightlessness animals, and their controls demonstrated a significant correlation. These findings after a short-term exposure to microgravity or modeled weightlessness suggest that a decreased expression of calbindins

  9. Metabolic syndrome and menopause

    OpenAIRE

    Jouyandeh, Zahra; Nayebzadeh, Farnaz; Qorbani, Mostafa; Asadi, Mojgan

    2013-01-01

    Abstract Background The metabolic syndrome is defined as an assemblage of risk factors for cardiovascular diseases, and menopause is associated with an increase in metabolic syndrome prevalence. The aim of this study was to assess the prevalence of metabolic syndrome and its components among postmenopausal women in Tehran, Iran. Methods In this cross-sectional study in menopause clinic in Tehran, 118 postmenopausal women were investigated. We used the adult treatment panel 3 (ATP3) criteria t...

  10. Nutrition and metabolic syndrome.

    OpenAIRE

    Albornoz López, Raúl; Pérez Rodrigo, Iciar

    2012-01-01

    The metabolic syndrome comprises a cluster of metabolic abnormalities that increase the risk for cardiovascular disease and type 2 diabetes mellitus. The exact etiology is unclear, although it is known thatthere is a complex interaction between genetic, metabolic and environmental factors. Among the environmental factors, dietary habits play an important role in the treatment and prevention of this condition. General classic recommendations include control of obesity, increased physical activ...

  11. Systems Biology of Metabolism: Annual Review of Biochemistry

    DEFF Research Database (Denmark)

    Nielsen, Jens

    2017-01-01

    Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology......, the application of systems biology for analyzing global regulatory structures, engineering the metabolism of cell factories, and analyzing human diseases is discussed....

  12. Reactor for exothermic reactions

    Science.gov (United States)

    Smith, L.A. Jr.; Hearn, D.; Jones, E.M. Jr.

    1993-03-02

    A liquid phase process is described for oligomerization of C[sub 4] and C[sub 5] isoolefins or the etherification thereof with C[sub 1] to C[sub 6] alcohols wherein the reactants are contacted in a reactor with a fixed bed acid cation exchange resin catalyst at an LHSV of 5 to 20, pressure of 0 to 400 psig and temperature of 120 to 300 F. Wherein the improvement is the operation of the reactor at a pressure to maintain the reaction mixture at its boiling point whereby at least a portion but less than all of the reaction mixture is vaporized. By operating at the boiling point and allowing a portion of the reaction mixture to vaporize, the exothermic heat of reaction is dissipated by the formation of more boil up and the temperature in the reactor is controlled.

  13. Bad Reaction to Cosmetics?

    Science.gov (United States)

    ... Consumers Protect Yourself Health Fraud Bad Reactions to Cosmetics? Tell FDA! Share Tweet Linkedin Pin it More ... Radiation-Emitting Products Vaccines, Blood & Biologics Animal & Veterinary Cosmetics Tobacco Products

  14. Transfusion reaction - hemolytic

    Science.gov (United States)

    ... Names Blood transfusion reaction Images Surface proteins causing rejection References Choate JD, Maitta RW, Tormey CA, Wu ... PA: Elsevier Saunders; 2016:chap 177. Hall JE. Blood types; transfusion; tissue and organ transplantation. In: Hall JE, ...

  15. Reaction Qualifications Revisited

    DEFF Research Database (Denmark)

    Lippert-Rasmussen, Kasper

    2009-01-01

    to a person's effectiveness by causing a favourable reaction in customers, co-workers etc. (for short: recipients) - are involved, this assumption is false. Building on work by Wertheimer, Mason, and Miller, this paper proposes an account of the reaction qualifications that count, from the point of view...... preferences, recipients should not respond to the applicant actually hired on the basis of their (the recipients') racial preferences. My account decomposes the meritocratic ideal into four separate norms, one of which applies to recipients rather than to selectors. Finally, it defends the view that reaction...... qualifications based on antimeritocratic reactions, while not unproblematic, are not entirely irrelevant from the point of view of merit. Notably, selectors need not discount them when no one - including the targets of the objectionable preferences - is unfairly disadvantaged. Because not all problematic...

  16. Sequential charged particle reaction

    International Nuclear Information System (INIS)

    Hori, Jun-ichi; Ochiai, Kentaro; Sato, Satoshi; Yamauchi, Michinori; Nishitani, Takeo

    2004-01-01

    The effective cross sections for producing the sequential reaction products in F82H, pure vanadium and LiF with respect to the 14.9-MeV neutron were obtained and compared with the estimation ones. Since the sequential reactions depend on the secondary charged particles behavior, the effective cross sections are corresponding to the target nuclei and the material composition. The effective cross sections were also estimated by using the EAF-libraries and compared with the experimental ones. There were large discrepancies between estimated and experimental values. Additionally, we showed the contribution of the sequential reaction on the induced activity and dose rate in the boundary region with water. From the present study, it has been clarified that the sequential reactions are of great importance to evaluate the dose rates around the surface of cooling pipe and the activated corrosion products. (author)

  17. Firefighter Nozzle Reaction

    DEFF Research Database (Denmark)

    Chin, Selena K.; Sunderland, Peter B.; Jomaas, Grunde

    2017-01-01

    to anchor forces, the hose becomes straight. The nozzle reaction is found to equal the jet momentum flow rate, and it does not change when an elbow connects the hose to the nozzle. A forward force must be exerted by a firefighter or another anchor that matches the forward force that the jet would exert...... on a perpendicular wall. Three reaction expressions are derived, allowing it to be determined in terms of hose diameter, jet diameter, flow rate, and static pressure upstream of the nozzle. The nozzle reaction predictions used by the fire service are 56% to 90% of those obtained here for typical firefighting hand......Nozzle reaction and hose tension are analyzed using conservation of fluid momentum and assuming steady, inviscid flow and a flexible hose in frictionless contact with the ground. An expression that is independent of the bend angle is derived for the hose tension. If this tension is exceeded owing...

  18. Nucleon induced reactions

    International Nuclear Information System (INIS)

    Gmuca, S.; Antalik, R.; Kristiak, J.

    1988-01-01

    The collection contains full texts of 37 contributions; all fall within the INIS Subject Scope. The topics treated include some unsolved problems of nuclear reactions and relevant problems of nuclear structure at low and intermediate energies. (Z.S.)

  19. Mass-Related Dynamical Barriers in Triatomic Reactions

    Science.gov (United States)

    Yanao, T.; Koon, W. S.; Marsden, J. E.

    2006-06-01

    A methodology is given to determine the effect of different mass distributions for triatomic reactions using the geometry of shape space. Atomic masses are incorporated into the non-Euclidean shape space metric after the separation of rotations. Using the equations of motion in this non-Euclidean shape space, an averaged field of velocity-dependent fictitious forces is determined. This force field, as opposed to the force arising from the potential, dominates branching ratios of isomerization dynamics of a triatomic molecule. This methodology may be useful for qualitative prediction of branching ratios in general triatomic reactions.

  20. Reaction: Chemistry Driven by the Harsh Space Environment

    Science.gov (United States)

    Farrell, William M.

    2018-01-01

    The studies by Solar System Exploration Research Virtual Institute (SSERVI) teams such as REVEALS and DREAM2 not only connect back to the highest planetary science decadal goals regarding volatiles but also feed forward to understanding the chemical origins of potential resources at the surface useful for human exploration. See https://sservi.nasa.gov for more about SSERVI and its dynamic teams.

  1. Jets in hadronic reactions

    Energy Technology Data Exchange (ETDEWEB)

    Paige, F.E.

    1983-01-01

    Recent experimental data on the properties of jets in hadronic reactions are reviewed and compared with theoretical expectations. Jets are clearly established as the dominant process for high E/sub T/ events in hadronic reactions. The cross section and the other properties of these events are in qualitative and even semiquantitative agreement with expectations based on perturbative QCD. However, we can not yet make precise tests of QCD, primarily because there are substantial uncertainties in the theoretical calculations. 45 references. (WHK)

  2. Oxygen evolution reaction catalysis

    Science.gov (United States)

    Haber, Joel A.; Jin, Jian; Xiang, Chengxiang; Gregoire, John M.; Jones, Ryan J.; Guevarra, Dan W.; Shinde, Aniketa A.

    2016-09-06

    An Oxygen Evolution Reaction (OER) catalyst includes a metal oxide that includes oxygen, cerium, and one or more second metals. In some instances, the cerium is 10 to 80 molar % of the metals in the metal oxide and/or the catalyst includes two or more second metals. The OER catalyst can be included in or on an electrode. The electrode can be arranged in an oxygen evolution system such that the Oxygen Evolution Reaction occurs at the electrode.

  3. Anaphylactic reaction to orthoiodohippurate

    Energy Technology Data Exchange (ETDEWEB)

    Stoeckel, M.; Roedbro, P.; Ennow, K.; Kristensen, K.

    1983-02-01

    A case of an anaphylactic reaction following administration of /sup 125/I- and /sup 131/-I-o-iodohippurate in a 32-year-old woman is reported. The patient had a renography performed because of hematuria. She was known to react to an intravenous pyelography previously performed with an anaphylactic shock. The importance of reporting all adverse reactions to radiopharmaceuticals for central registration is stressed.

  4. Mathematical modelling of metabolism

    DEFF Research Database (Denmark)

    Gombert, Andreas Karoly; Nielsen, Jens

    2000-01-01

    Mathematical models of the cellular metabolism have a special interest within biotechnology. Many different kinds of commercially important products are derived from the cell factory, and metabolic engineering can be applied to improve existing production processes, as well as to make new processes...... available. Both stoichiometric and kinetic models have been used to investigate the metabolism, which has resulted in defining the optimal fermentation conditions, as well as in directing the genetic changes to be introduced in order to obtain a good producer strain or cell line. With the increasing...... availability of genomic information and powerful analytical techniques, mathematical models also serve as a tool for understanding the cellular metabolism and physiology....

  5. Engineering of Secondary Metabolism.

    Science.gov (United States)

    O'Connor, Sarah E

    2015-01-01

    Secondary (specialized) metabolites, produced by bacteria, fungi, plants, and other organisms, exhibit enormous structural variation, and consequently display a wide range of biological activities. Secondary metabolism improves and modulates the phenotype of the host producer. Furthermore, these biological activities have resulted in the use of secondary metabolites in a variety of industrial and pharmaceutical applications. Metabolic engineering presents a powerful strategy to improve access to these valuable molecules. A critical overview of engineering approaches in secondary metabolism is presented, both in heterologous and native hosts. The recognition of the increasing role of compartmentalization in metabolic engineering is highlighted. Engineering approaches to modify the structure of key secondary metabolite classes are also critically evaluated.

  6. Soft Connected Spaces and Soft Paracompact Spaces

    OpenAIRE

    Fucai Lin

    2013-01-01

    Soft topological spaces are considered as mathematical tools for dealing with uncertainties, and a fuzzy topological space is a special case of the soft topological space. The purpose of this paper is to study soft topological spaces. We introduce some new concepts in soft topological spaces such as soft closed mapping, soft open mappings, soft connected spaces and soft paracompact spaces. We also redefine the concept of soft points such that it is reasonable in soft topological spaces. Mo...

  7. On-chip electromembrane extraction for monitoring drug metabolism in real time by electrospray ionization mass spectrometry

    DEFF Research Database (Denmark)

    Petersen, Nickolaj J.; Pedersen, Jacob Sønderby; Poulsen, Nicklas Nørgård

    2012-01-01

    the in vitro metabolism of amitriptyline in real time. There was no need to stop the metabolisms by protein precipitation as in conventional metabolic studies, since the EME selectively extracted the drug and metabolites from the reaction solution comprised of rat liver microsomes in buffer. Compositional...

  8. Adverse drug reactions.

    Science.gov (United States)

    Patton, K; Borshoff, D C

    2018-01-01

    Adverse drug reactions are a cause of significant morbidity and mortality to patients and a source of financial burden to the healthcare system. Of the wide spectrum of adverse drug reactions, the most concerning to the anaesthetist remain anaphylaxis and malignant hyperthermia. Although the incidence of anaphylaxis under anaesthesia is difficult to ascertain, it occurs commonly enough that most anaesthetists will manage at least one case in their career. The wide range of drugs given in the peri-operative period and the variable presentation in the anaesthetised patient can delay diagnosis and treatment, and adversely affect outcome. Furthermore, despite improvements in testing, causative drugs can still be difficult to identify, as adverse reactions may be mediated by mechanisms other than IgE activation. With an increase in the reporting of anaphylaxis to newer anaesthetic drugs such as sugammadex, combined with change over the recent decades in the most likely causative peri-operative agents, it is imperative anaesthetists remain up to date on recent developments. In addition, they should be vigilant to patient characteristics, including pharmacogenetic variations that may predispose to adverse drug reactions, in order to help minimise risks of a reaction. The severity of adverse drug reactions to peri-operative drugs means morbidity and mortality remain high. © 2018 The Association of Anaesthetists of Great Britain and Ireland.

  9. Simulating mesoscopic reaction-diffusion systems using the Gillespie algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Bernstein, David

    2004-12-12

    We examine an application of the Gillespie algorithm to simulating spatially inhomogeneous reaction-diffusion systems in mesoscopic volumes such as cells and microchambers. The method involves discretizing the chamber into elements and modeling the diffusion of chemical species by the movement of molecules between neighboring elements. These transitions are expressed in the form of a set of reactions which are added to the chemical system. The derivation of the rates of these diffusion reactions is by comparison with a finite volume discretization of the heat equation on an unevenly spaced grid. The diffusion coefficient of each species is allowed to be inhomogeneous in space, including discontinuities. The resulting system is solved by the Gillespie algorithm using the fast direct method. We show that in an appropriate limit the method reproduces exact solutions of the heat equation for a purely diffusive system and the nonlinear reaction-rate equation describing the cubic autocatalytic reaction.

  10. Predicting novel metabolic pathways through subgraph mining.

    Science.gov (United States)

    Sankar, Aravind; Ranu, Sayan; Raman, Karthik

    2017-12-15

    The ability to predict pathways for biosynthesis of metabolites is very important in metabolic engineering. It is possible to mine the repertoire of biochemical transformations from reaction databases, and apply the knowledge to predict reactions to synthesize new molecules. However, this usually involves a careful understanding of the mechanism and the knowledge of the exact bonds being created and broken. There is a need for a method to rapidly predict reactions for synthesizing new molecules, which relies only on the structures of the molecules, without demanding additional information such as thermodynamics or hand-curated reactant mapping, which are often hard to obtain accurately. We here describe a robust method based on subgraph mining, to predict a series of biochemical transformations, which can convert between two (even previously unseen) molecules. We first describe a reliable method based on subgraph edit distance to map reactants and products, using only their chemical structures. Having mapped reactants and products, we identify the reaction centre and its neighbourhood, the reaction signature, and store this in a reaction rule network. This novel representation enables us to rapidly predict pathways, even between previously unseen molecules. We demonstrate this ability by predicting pathways to molecules not present in the KEGG database. We also propose a heuristic that predominantly recovers natural biosynthetic pathways from amongst hundreds of possible alternatives, through a directed search of the reaction rule network, enabling us to provide a reliable ranking of the different pathways. Our approach scales well, even to databases with >100 000 reactions. A Java-based implementation of our algorithms is available at https://github.com/RamanLab/ReactionMiner. sayanranu@cse.iitd.ac.in or kraman@iitm.ac.in. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For

  11. Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry.

    Science.gov (United States)

    Rappoport, Dmitrij; Galvin, Cooper J; Zubarev, Dmitry Yu; Aspuru-Guzik, Alán

    2014-03-11

    While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for modeling complex structures and large-scale chemical systems. Here, we present a heuristics-aided quantum chemical methodology applicable to complex chemical reaction networks such as those arising in cell metabolism and prebiotic chemistry. Chemical heuristics offer an expedient way of traversing high-dimensional reactive potential energy surfaces and are combined here with quantum chemical structure optimizations, which yield the structures and energies of the reaction intermediates and products. Application of heuristics-aided quantum chemical methodology to the formose reaction reproduces the experimentally observed reaction products, major reaction pathways, and autocatalytic cycles.

  12. Fatty acid metabolism: target for metabolic syndrome

    OpenAIRE

    Wakil, Salih J.; Abu-Elheiga, Lutfi A.

    2009-01-01

    Fatty acids are a major energy source and important constituents of membrane lipids, and they serve as cellular signaling molecules that play an important role in the etiology of the metabolic syndrome. Acetyl-CoA carboxylases 1 and 2 (ACC1 and ACC2) catalyze the synthesis of malonyl-CoA, the substrate for fatty acid synthesis and the regulator of fatty acid oxidation. They are highly regulated and play important roles in the energy metabolism of fatty acids in animals, including humans. They...

  13. Methylenetetrahydrofolate Reductase Activity and Folate Metabolism

    Directory of Open Access Journals (Sweden)

    Nursen Keser

    2014-04-01

    Full Text Available Folate is a vital B vitamin which is easily water-soluble. It is a natural source which is found in the herbal and animal foods. Folate has important duties in the human metabolism, one of them is the adjustment of the level of plasma homocysteine. Reduction in MTHFR (methylenetetrahydrofolate reductase,which is in charge of the metabolism of homocysteine activity affects the level of homocysteine. Therefore MTHFR is an important enzyme in folate metabolism. Some of the mutations occurring in the MTHFR gene is a risk factor for various diseases and may be caused the hyperhomocysteinemia or the homocystinuria, and they also may lead to metabolic problems. MTHFR is effective in the important pathways such as DNA synthesis, methylation reactions and synthesis of RNA. C677T and A1298C are the most commonly occurring polymorphisms in the gene of MTHFR. The frequency of these polymorphisms show differences in the populations. MTHFR, folate distribution, metabolism of homocysteine and S-adenosylmethionine, by the MTHFR methylation the genetic defects have the potential of affecting the risk of disease in the negative or positive way.

  14. Phenotype spaces.

    Science.gov (United States)

    Mynard, Frédéric; Seal, Gavin J

    2010-02-01

    The topological viewpoint on spaces of phenotypes presented in Stadler et al. (J Theor Biol 213:241-274, 2001) is revisited, and a quantified version is proposed. While necessary probabilistic information can be encoded in a topological- like fashion, it turns out that it is not reflected adequately by the concept of continuity. We propose alternative models, but the behavior of maps make these models non-topological in fundamental ways.

  15. Communication spaces.

    Science.gov (United States)

    Coiera, Enrico

    2014-01-01

    Annotations to physical workspaces such as signs and notes are ubiquitous. When densely annotated, work areas become communication spaces. This study aims to characterize the types and purpose of such annotations. A qualitative observational study was undertaken in two wards and the radiology department of a 440-bed metropolitan teaching hospital. Images were purposefully sampled; 39 were analyzed after excluding inferior images. Annotation functions included signaling identity, location, capability, status, availability, and operation. They encoded data, rules or procedural descriptions. Most aggregated into groups that either created a workflow by referencing each other, supported a common workflow without reference to each other, or were heterogeneous, referring to many workflows. Higher-level assemblies of such groupings were also observed. Annotations make visible the gap between work done and the capability of a space to support work. Annotations are repairs of an environment, improving fitness for purpose, fixing inadequacy in design, or meeting emergent needs. Annotations thus record the missing information needed to undertake tasks, typically added post-implemented. Measuring annotation levels post-implementation could help assess the fit of technology to task. Physical and digital spaces could meet broader user needs by formally supporting user customization, 'programming through annotation'. Augmented reality systems could also directly support annotation, addressing existing information gaps, and enhancing work with context sensitive annotation. Communication spaces offer a model of how work unfolds. Annotations make visible local adaptation that makes technology fit for purpose post-implementation and suggest an important role for annotatable information systems and digital augmentation of the physical environment.

  16. Space Radiation

    Energy Technology Data Exchange (ETDEWEB)

    Corliss, William R.

    1968-01-01

    This booklet discusses three kinds of space radiation, cosmic rays, Van Allen Belts, and solar plasma. Cosmic rays are penetrating particles that we cannot see, hear or feel, which come from distant stars. Van Allen Belts, named after their discoverer are great belts of protons and electrons that the earth has captured in its magnetic trap. Solar plasma is a gaseous, electrically neutral mixture of positive and negative ions that the sun spews out from convulsed regions on its surface.

  17. Space Operations

    Science.gov (United States)

    2013-05-29

    attack Laser attack Jamming Indications and warning Cyber attack Environmental monitoring System status     Re-entry Detect and track Cataloging...vulnerable to interference or attack. Space segments are vulnerable to attacks or interference such as direct-ascent anti- satellite interceptors, laser ...blinding, and dazzling . Additionally, ground-to-satellite link segments are susceptible to jamming and other forms of interference, and ground

  18. Space Nutrition

    Science.gov (United States)

    Smith, Scott M.

    2009-01-01

    Optimal nutrition will be critical for crew members who embark on space exploration missions. Nutritional assessment provides an opportunity to ensure that crewmembers begin their missions in optimal nutritional status, to document changes during a mission and, if necessary, to provide intervention to maintain that status throughout the mission, and to assesses changes after landing in order to facilitate the return to their normal status as soon as possible after landing. We report here the findings from our nutritional assessment of astronauts who participated in the International Space Station (ISS) missions, along with flight and ground-based research findings. We also present ongoing and planned nutrition research activities. These studies provide evidence that bone loss, compromised vitamin status, and oxidative damage are the critical nutritional concerns for space travelers. Other nutrient issues exist, including concerns about the stability of nutrients in the food system, which are exposed to longterm storage and radiation during flight. Defining nutrient requirements, and being able to provide and maintain those nutrients on exploration missions, will be critical for maintaining crew member health.

  19. Game Spaces

    DEFF Research Database (Denmark)

    Kristiansen, Erik

    2015-01-01

    , called “pervasive games.” These are games that are based on computer technology, but use a physical space as the game space as opposed to video games. Coupling spatial configuration with performance theory of rituals as liminal phenomena, I put forward a model and a new understanding of the magic circle......When we play games of any kind, from tennis to board games, it is easy to notice that games seem to be configured in space, often using stripes or a kind of map on a board. Some games are clearly performed within this marked border, while it may be difficult to pinpoint such a border in games like...... hide-and-seek, but even these games are still spatially configured. The border (visible or not) both seem to separate and uphold the game that it is meant for. This chapter sets out to analyse the possible border that separates a game from the surrounding world. Johan Huizinga noted this “separateness...

  20. Inertial effects in diffusion-limited reactions

    International Nuclear Information System (INIS)

    Dorsaz, N; Foffi, G; De Michele, C; Piazza, F

    2010-01-01

    Diffusion-limited reactions are commonly found in biochemical processes such as enzyme catalysis, colloid and protein aggregation and binding between different macromolecules in cells. Usually, such reactions are modeled within the Smoluchowski framework by considering purely diffusive boundary problems. However, inertial effects are not always negligible in real biological or physical media on typical observation time frames. This is all the more so for non-bulk phenomena involving physical boundaries, that introduce additional time and space constraints. In this paper, we present and test a novel numerical scheme, based on event-driven Brownian dynamics, that allows us to explore a wide range of velocity relaxation times, from the purely diffusive case to the underdamped regime. We show that our algorithm perfectly reproduces the solution of the Fokker-Planck problem with absorbing boundary conditions in all the regimes considered and is thus a good tool for studying diffusion-guided reactions in complex biological environments.

  1. Supercritical water oxidation of products of human metabolism

    Science.gov (United States)

    Tester, Jefferson W.; Orge A. achelling, Richard K. ADTHOMASSON; Orge A. achelling, Richard K. ADTHOMASSON

    1986-01-01

    Although the efficient destruction of organic material was demonstrated in the supercritical water oxidation process, the reaction kinetics and mechanisms are unknown. The kinetics and mechanisms of carbon monoxide and ammonia oxidation in and reaction with supercritical water were studied experimentally. Experimental oxidation of urine and feces in a microprocessor controlled system was performed. A minaturized supercritical water oxidation process for space applications was design, including preliminary mass and energy balances, power, space and weight requirements.

  2. Some questions of space bioengineering

    Science.gov (United States)

    Nyiri, L. K.

    1977-01-01

    Zero-gravity offers selective effect on growth and metabolic activity unicellular organisms as well as unique opportunities in purification of organic compounds. These make it possible to consider the biosynthesis and recovery of certain metabolites economically feasible in space. Design, construction and operation of systems for the above mentioned purposes requires interdisciplinary actions within the scope of a new discipline: space bioengineering. The problems and perspectives of this discipline particularly in the application of bioreactor-recovery systems in space to manufacture metabolites of high economic and scientific value. Special attention is paid to pivotal factors such as various mass transport phenomena, contamination control, automatic control of optimum environment and synchronization of the operation of the biological (biosynthesis) and the physiochemical (recovery-purification) systems.

  3. Characterizing multistationarity regimes in biochemical reaction networks.

    Directory of Open Access Journals (Sweden)

    Irene Otero-Muras

    Full Text Available Switch like responses appear as common strategies in the regulation of cellular systems. Here we present a method to characterize bistable regimes in biochemical reaction networks that can be of use to both direct and reverse engineering of biological switches. In the design of a synthetic biological switch, it is important to study the capability for bistability of the underlying biochemical network structure. Chemical Reaction Network Theory (CRNT may help at this level to decide whether a given network has the capacity for multiple positive equilibria, based on their structural properties. However, in order to build a working switch, we also need to ensure that the bistability property is robust, by studying the conditions leading to the existence of two different steady states. In the reverse engineering of biological switches, knowledge collected about the bistable regimes of the underlying potential model structures can contribute at the model identification stage to a drastic reduction of the feasible region in the parameter space of search. In this work, we make use and extend previous results of the CRNT, aiming not only to discriminate whether a biochemical reaction network can exhibit multiple steady states, but also to determine the regions within the whole space of parameters capable of producing multistationarity. To that purpose we present and justify a condition on the parameters of biochemical networks for the appearance of multistationarity, and propose an efficient and reliable computational method to check its satisfaction through the parameter space.

  4. Interplay of drug metabolizing enzymes with cellular transporters.

    Science.gov (United States)

    Böhmdorfer, Michaela; Maier-Salamon, Alexandra; Riha, Juliane; Brenner, Stefan; Höferl, Martina; Jäger, Walter

    2014-11-01

    Many endogenous and xenobiotic substances and their metabolites are substrates for drug metabolizing enzymes and cellular transporters. These proteins may not only contribute to bioavailability of molecules but also to uptake into organs and, consequently, to overall elimination. The coordinated action of uptake transporters, metabolizing enzymes, and efflux pumps, therefore, is a precondition for detoxification and elimination of drugs. As the understanding of the underlying mechanisms is important to predict alterations in drug disposal, adverse drug reactions and, finally, drug-drug interactions, this review illustrates the interplay between selected uptake/efflux transporters and phase I/II metabolizing enzymes.

  5. DRUM: A New Framework for Metabolic Modeling under Non-Balanced Growth. Application to the Carbon Metabolism of Unicellular Microalgae

    Science.gov (United States)

    Baroukh, Caroline; Muñoz-Tamayo, Rafael; Steyer, Jean-Philippe; Bernard, Olivier

    2014-01-01

    Metabolic modeling is a powerful tool to understand, predict and optimize bioprocesses, particularly when they imply intracellular molecules of interest. Unfortunately, the use of metabolic models for time varying metabolic fluxes is hampered by the lack of experimental data required to define and calibrate the kinetic reaction rates of the metabolic pathways. For this reason, metabolic models are often used under the balanced growth hypothesis. However, for some processes such as the photoautotrophic metabolism of microalgae, the balanced-growth assumption appears to be unreasonable because of the synchronization of their circadian cycle on the daily light. Yet, understanding microalgae metabolism is necessary to optimize the production yield of bioprocesses based on this microorganism, as for example production of third-generation biofuels. In this paper, we propose DRUM, a new dynamic metabolic modeling framework that handles the non-balanced growth condition and hence accumulation of intracellular metabolites. The first stage of the approach consists in splitting the metabolic network into sub-networks describing reactions which are spatially close, and which are assumed to satisfy balanced growth condition. The left metabolites interconnecting the sub-networks behave dynamically. Then, thanks to Elementary Flux Mode analysis, each sub-network is reduced to macroscopic reactions, for which simple kinetics are assumed. Finally, an Ordinary Differential Equation system is obtained to describe substrate consumption, biomass production, products excretion and accumulation of some internal metabolites. DRUM was applied to the accumulation of lipids and carbohydrates of the microalgae Tisochrysis lutea under day/night cycles. The resulting model describes accurately experimental data obtained in day/night conditions. It efficiently predicts the accumulation and consumption of lipids and carbohydrates. PMID:25105494

  6. DRUM: a new framework for metabolic modeling under non-balanced growth. Application to the carbon metabolism of unicellular microalgae.

    Directory of Open Access Journals (Sweden)

    Caroline Baroukh

    Full Text Available Metabolic modeling is a powerful tool to understand, predict and optimize bioprocesses, particularly when they imply intracellular molecules of interest. Unfortunately, the use of metabolic models for time varying metabolic fluxes is hampered by the lack of experimental data required to define and calibrate the kinetic reaction rates of the metabolic pathways. For this reason, metabolic models are often used under the balanced growth hypothesis. However, for some processes such as the photoautotrophic metabolism of microalgae, the balanced-growth assumption appears to be unreasonable because of the synchronization of their circadian cycle on the daily light. Yet, understanding microalgae metabolism is necessary to optimize the production yield of bioprocesses based on this microorganism, as for example production of third-generation biofuels. In this paper, we propose DRUM, a new dynamic metabolic modeling framework that handles the non-balanced growth condition and hence accumulation of intracellular metabolites. The first stage of the approach consists in splitting the metabolic network into sub-networks describing reactions which are spatially close, and which are assumed to satisfy balanced growth condition. The left metabolites interconnecting the sub-networks behave dynamically. Then, thanks to Elementary Flux Mode analysis, each sub-network is reduced to macroscopic reactions, for which simple kinetics are assumed. Finally, an Ordinary Differential Equation system is obtained to describe substrate consumption, biomass production, products excretion and accumulation of some internal metabolites. DRUM was applied to the accumulation of lipids and carbohydrates of the microalgae Tisochrysis lutea under day/night cycles. The resulting model describes accurately experimental data obtained in day/night conditions. It efficiently predicts the accumulation and consumption of lipids and carbohydrates.

  7. PPARa governs glycerol metabolism

    NARCIS (Netherlands)

    Patsouris, D.A.; Mandard, S.J.; Voshol, P.J.; Escher, P.; Tan, N.S.; Havekes, L.M.; Koenig, W.; März, W.; Müller, M.R.; Kersten, A.H.

    2004-01-01

    Glycerol, a product of adipose tissue lipolysis, is an important substrate for hepatic glucose synthesis. However, little is known about the regulation of hepatic glycerol metabolism. Here we show that several genes involved in the hepatic metabolism of glycerol, i.e., cytosolic and mitochondrial

  8. Metabolic syndrome and menopause

    Directory of Open Access Journals (Sweden)

    Jouyandeh Zahra

    2013-01-01

    Full Text Available Abstract Background The metabolic syndrome is defined as an assemblage of risk factors for cardiovascular diseases, and menopause is associated with an increase in metabolic syndrome prevalence. The aim of this study was to assess the prevalence of metabolic syndrome and its components among postmenopausal women in Tehran, Iran. Methods In this cross-sectional study in menopause clinic in Tehran, 118 postmenopausal women were investigated. We used the adult treatment panel 3 (ATP3 criteria to classify subjects as having metabolic syndrome. Results Total prevalence of metabolic syndrome among our subjects was 30.1%. Waist circumference, HDL-cholesterol, fasting blood glucose, diastolic blood pressure ,Systolic blood pressure, and triglyceride were significantly higher among women with metabolic syndrome (P-value Conclusions Our study shows that postmenopausal status is associated with an increased risk of metabolic syndrome. Therefore, to prevent cardiovascular disease there is a need to evaluate metabolic syndrome and its components from the time of the menopause.

  9. Circadian Systems and Metabolism

    NARCIS (Netherlands)

    Roenneberg, Till; Merrow, Martha

    1999-01-01

    Circadian systems direct many metabolic parameters and, at the same time, they appear to be exquisitely shielded from metabolic variations. Although the recent decade of circadian research has brought insights into how circadian periodicity may be generated at the molecular level, little is known

  10. Comprehensive metabolic panel

    Science.gov (United States)

    Metabolic panel - comprehensive; Chem-20; SMA20; Sequential multi-channel analysis with computer-20; SMAC20; Metabolic panel 20 ... Normal values for the panel tests are: Albumin : 3.4 to 5.4 g/dL (34 to 54 g/L) Alkaline phosphatase : 44 to 147 ...

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

    Science.gov (United States)

    Angermayr, S Andreas; Gorchs Rovira, Aleix; Hellingwerf, Klaas J

    2015-06-01

    Through metabolic engineering cyanobacteria can be employed in biotechnology. Combining the capacity for oxygenic photosynthesis and carbon fixation with an engineered metabolic pathway allows carbon-based product formation from CO(2), light, and water directly. Such cyanobacterial 'cell factories' are constructed to produce biofuels, bioplastics, and commodity chemicals. Efforts of metabolic engineers and synthetic biologists allow the modification of the intermediary metabolism at various branching points, expanding the product range. The new biosynthesis routes 'tap' the metabolism ever more efficiently, particularly through the engineering of driving forces and utilization of cofactors generated during the light reactions of photosynthesis, resulting in higher product titers. High rates of carbon rechanneling ultimately allow an almost-complete allocation of fixed carbon to product above biomass. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions

    Directory of Open Access Journals (Sweden)

    Orth Jeffrey D

    2012-05-01

    Full Text Available Abstract Background The iJO1366 reconstruction of the metabolic network of Escherichia coli is one of the most complete and accurate metabolic reconstructions available for any organism. Still, because our knowledge of even well-studied model organisms such as this one is incomplete, this network reconstruction contains gaps and possible errors. There are a total of 208 blocked metabolites in iJO1366, representing gaps in the network. Results A new model improvement workflow was developed to compare model based phenotypic predictions to experimental data to fill gaps and correct errors. A Keio Collection based dataset of E. coli gene essentiality was obtained from literature data and compared to model predictions. The SMILEY algorithm was then used to predict the most likely missing reactions in the reconstructed network, adding reactions from a KEGG based universal set of metabolic reactions. The feasibility of these putative reactions was determined by comparing updated versions of the model to the experimental dataset, and genes were predicted for the most feasible reactions. Conclusions Numerous improvements to the iJO1366 metabolic reconstruction were suggested by these analyses. Experiments were performed to verify several computational predictions, including a new mechanism for growth on myo-inositol. The other predictions made in this study should be experimentally verifiable by similar means. Validating all of the predictions made here represents a substantial but important undertaking.

  13. Fomepizole for severe disulfiram-ethanol reactions.

    Science.gov (United States)

    Sande, Margaret; Thompson, David; Monte, Andrew A

    2012-01-01

    Ingestion of ethanol in the presence of disulfiram may cause a histamine-like reaction due to accumulation of acetaldehyde. These disulfiram-ethanol reactions (DERs) are manifested by hypotension, tachycardia, gastritis, and angioedema. Fomepizole, an inhibitor of alcohol dehydrogenase, may halt progression of this reaction by blocking ethanol metabolism to acetaldehyde. We present 2 cases of disulfiram and alcohol overdose leading to severe reactions unresponsive to fluid resuscitation and treated with a single dose of fomepizole. Case 1: A 20-year-old woman presented after ingestion of vodka and disulfiram. After 11 hours of resuscitation, she had skin flushing, lip swelling, tachycardia, and hypotension. Antihistamines, steroids, and an additional 2 L of normal saline were given without improvement. Fomepizole 15 mg/kg was given with improvement within 1.5 hours, and she was ultimately discharged with no clinical sequelae. Case 2: A 47-year-old woman presented after overdose of vodka and disulfiram. She was tachycardic and hypotensive upon presentation. After administration of 3 L of normal saline, she remained hypotensive and tachycardic. One dose of fomepizole 15 mg/kg was given. Within 1 hour following fomepizole infusion, her blood pressure and heart rate normalized, and she had no further sequelae from her ingestion. Fomepizole may be a safe and effective treatment of severe DERs. We suggest that 1 dose of fomepizole for severe DERs with hypotension unresponsive to fluid resuscitation or for angioedema unresponsive to antihistamines be administered.

  14. Immediate reaction to clarithromycin.

    Science.gov (United States)

    Gangemi, S; Ricciardi, L; Fedele, R; Isola, S; Purello-D'Ambrosio, F

    2001-01-01

    We present the case of bronchospastic reaction to clarithromycin had during a drug challenge test. Personal allergic history was negative for respiratory allergies and positive for adverse drug reactions to general and regional anesthesia and to ceftriaxone. After the administration of 1/4 of therapeutic dose of clarithromycin the patient showed dyspnea, cough and bronchospasm in all the lung fields. The positivity of the test was confirmed by the negativity to the administration of placebo. The quickness and the clinical characteristic of the adverse reaction suggest a pathogenic mechanism of immediate-type hypersensitivity. On reviewing the literature we have found no reports of bronchospastic reaction to clarithromycin. Macrolides are a class of antibiotics mainly used in the last years in place of beta-lactams because of a broad spectrum of action and a low allergic power. In fact, there are few reports on allergic reactions to these molecules. Clarithromycin is one of the latest macrolides, characterised by the presence of a 14-carbon-atom lactone ring as erythromycin, active on a wide spectrum of pathogens.

  15. Mycobacterium tuberculosis Metabolism

    Science.gov (United States)

    Warner, Digby F.

    2015-01-01

    Metabolism underpins the physiology and pathogenesis of Mycobacterium tuberculosis. However, although experimental mycobacteriology has provided key insights into the metabolic pathways that are essential for survival and pathogenesis, determining the metabolic status of bacilli during different stages of infection and in different cellular compartments remains challenging. Recent advances—in particular, the development of systems biology tools such as metabolomics—have enabled key insights into the biochemical state of M. tuberculosis in experimental models of infection. In addition, their use to elucidate mechanisms of action of new and existing antituberculosis drugs is critical for the development of improved interventions to counter tuberculosis. This review provides a broad summary of mycobacterial metabolism, highlighting the adaptation of M. tuberculosis as specialist human pathogen, and discusses recent insights into the strategies used by the host and infecting bacillus to influence the outcomes of the host–pathogen interaction through modulation of metabolic functions. PMID:25502746

  16. Metabolic Engineering VII Conference

    Energy Technology Data Exchange (ETDEWEB)

    Kevin Korpics

    2012-12-04

    The aims of this Metabolic Engineering conference are to provide a forum for academic and industrial researchers in the field; to bring together the different scientific disciplines that contribute to the design, analysis and optimization of metabolic pathways; and to explore the role of Metabolic Engineering in the areas of health and sustainability. Presentations, both written and oral, panel discussions, and workshops will focus on both applications and techniques used for pathway engineering. Various applications including bioenergy, industrial chemicals and materials, drug targets, health, agriculture, and nutrition will be discussed. Workshops focused on technology development for mathematical and experimental techniques important for metabolic engineering applications will be held for more in depth discussion. This 2008 meeting will celebrate our conference tradition of high quality and relevance to both industrial and academic participants, with topics ranging from the frontiers of fundamental science to the practical aspects of metabolic engineering.

  17. Chemical kinetics of gas reactions

    CERN Document Server

    Kondrat'Ev, V N

    2013-01-01

    Chemical Kinetics of Gas Reactions explores the advances in gas kinetics and thermal, photochemical, electrical discharge, and radiation chemical reactions. This book is composed of 10 chapters, and begins with the presentation of general kinetic rules for simple and complex chemical reactions. The next chapters deal with the experimental methods for evaluating chemical reaction mechanisms and some theories of elementary chemical processes. These topics are followed by discussions on certain class of chemical reactions, including unimolecular, bimolecular, and termolecular reactions. The rema

  18. Risperidone and Venlafaxine Metabolic Ratios Strongly Predict a CYP2D6 Poor Metabolizing Genotype.

    Science.gov (United States)

    Mannheimer, Buster; Haslemo, Tore; Lindh, Jonatan D; Eliasson, Erik; Molden, Espen

    2016-02-01

    To investigate the predictive value of the risperidone and venlafaxine metabolic ratios and CYP2D6 genotype. The determination of risperidone, 9-hydroxyrisperidone, and venlafaxine, O-desmethylvenlafaxine, N-desmethylvenlafaxine and CYP2D6 genotype was performed in 425 and 491 patients, respectively. The receiver operator characteristic method and the area under the receiver operator characteristic curve were used to illustrate the predictive value of risperidone metabolic ratio for the individual CYP2D6 genotype. To evaluate the proposed cutoff levels of >1 to identify individuals with a poor CYP2D6 genotype, the sensitivity, specificity, positive predictive values, and negative predictive values were calculated. Area under the receiver operator characteristic curve to predict poor metabolizers for risperidone/9-hydroxyrisperidone and N-desmethylvenlafaxine/O-desmethylvenlafaxine ratios was 93% and 99%, respectively. The sensitivity, specificity, positive predictive value, and negative predictive value (confidence interval) of a risperidone/9-hydroxyrisperidone ratio >1 to predict a CYP2D6 poor metabolizer genotype were 91% (76%-97%), 86% (83%-89%), 35% (26%-46%), and 99% (97%-100%), respectively. The corresponding measures for N-desmethylvenlafaxine/O-desmethylvenlafaxine were 93% (76%-97%), 87% (83%-89%), 40% (32%-51%), and 99% (98%-100%). Risperidone/9-hydroxyrisperidone and N-desmethylvenlafaxine/O-desmethylvenlafaxine metabolic ratios >1 strongly predict individuals with poor metabolizer genotype, which could guide psychotropic drug treatment to avoid adverse drug reactions and to increase their therapeutic efficacy in patients prescribed these drugs.

  19. Adverse drug reactions and organ damage: The skin.

    Science.gov (United States)

    Marzano, Angelo V; Borghi, Alessandro; Cugno, Massimo

    2016-03-01

    Cutaneous adverse drug reactions are frequent, affecting 2-3% of hospitalized patients and in one twentieth of them are potentially life-threatening. Almost any pharmacologic agent can induce skin reactions, and certain drug classes, such as non-steroidal anti-inflammatory drugs, antibiotics and antiepileptics, have drug eruption rates ranging from 1% to 5%. Cutaneous drug reactions recognize several different pathomechanisms: some skin manifestations are immune-mediated like allergic reactions while others are the result of non immunological causes such as cumulative toxicity, photosensitivity, interaction with other drugs or different metabolic pathways. Cutaneous adverse drug reactions can be classified into two groups: common non-severe and rare life-threatening adverse drug reactions. Non-severe reactions are often exanthematous or urticarial whereas life-threatening reactions typically present with skin detachment or necrosis of large areas of the body and mucous membrane involvement, as in the Stevens-Johnson syndrome or toxic epidermal necrolysis. Clinicians should carefully evaluate the signs and symptoms of all cutaneous adverse drug reactions thought to be due to drugs and immediately discontinue drugs that are not essential. Short cycles of systemic corticosteroids in combination with antihistamines may be necessary for widespread exanthematous rashes, while more aggressive corticosteroid regimens or intravenous immunoglobulins associated with supportive treatment should be used for patients with Stevens-Johnson syndrome or toxic epidermal necrolysis. Copyright © 2015 European Federation of Internal Medicine. Published by Elsevier B.V. All rights reserved.

  20. Mining chemical reactions using neighborhood behavior and condensed graphs of reactions approaches.

    Science.gov (United States)

    de Luca, Aurélie; Horvath, Dragos; Marcou, Gilles; Solov'ev, Vitaly; Varnek, Alexandre

    2012-09-24

    This work addresses the problem of similarity search and classification of chemical reactions using Neighborhood Behavior (NB) and Condensed Graphs of Reaction (CGR) approaches. The CGR formalism represents chemical reactions as a classical molecular graph with dynamic bonds, enabling descriptor calculations on this graph. Different types of the ISIDA fragment descriptors generated for CGRs in combination with two metrics--Tanimoto and Euclidean--were considered as chemical spaces, to serve for reaction dissimilarity scoring. The NB method has been used to select an optimal combination of descriptors which distinguish different types of chemical reactions in a database containing 8544 reactions of 9 classes. Relevance of NB analysis has been validated in generic (multiclass) similarity search and in clustering with Self-Organizing Maps (SOM). NB-compliant sets of descriptors were shown to display enhanced mapping propensities, allowing the construction of better Self-Organizing Maps and similarity searches (NB and classical similarity search criteria--AUC ROC--correlate at a level of 0.7). The analysis of the SOM clusters proved chemically meaningful CGR substructures representing specific reaction signatures.

  1. Metabolic self-destruction in critically ill patients: origins, mechanisms and therapeutic principles.

    Science.gov (United States)

    Hartl, Wolfgang H; Jauch, Karl-Walter

    2014-03-01

    The aim of this study was to describe the evolution and nature of self-destructive metabolic responses observed in critically ill patients, and to analyze therapeutic principles on how best to avoid or diminish these responses. We electronically identified articles through a search of PubMed and Google Scholar. Metabolic reactions associated with surgical injury or infections comprise hyperglycemia, insulin resistance, increased hepatic glucose production, and muscle protein breakdown. From an evolutionary perspective, these responses have been necessary and successful to overcome spontaneously survivable insults (minor surgical trauma). If prolonged and exaggerated, however, these reactions may become self-destructive, causing secondary metabolic damage. There is overwhelming evidence that extreme metabolic responses have not been selected by evolution, but are brought about by modern medicine enabling survival of severe, otherwise lethal insults and giving patients the chance to develop such exaggerated self-destructive metabolic reactions. Poorly adapted metabolic responses to severe insults, however, may have persisted because of unavoidable evolutionary constraints. Self-destructive metabolic responses cannot be prevented by adjuvant therapies such as artificial nutrition, which may only help to ameliorate secondary metabolic damage. Minor surgical trauma is associated with a beneficial adaptive metabolic response. After a severe insult, however, emergence of self-destructive responses will be unavoidable if the patient survives the acute phase. Effective treatment is only possible by an aggressive therapy of underlying pathologies (such as shock, trauma or infection) thereby interrupting secondary metabolic trigger mechanisms at an early stage. Copyright © 2014 Elsevier Inc. All rights reserved.

  2. Inflammatory reaction in chondroblastoma

    Energy Technology Data Exchange (ETDEWEB)

    Yamamura, Sigeki [Dept. of Orthopedic Surgery, Nagoya Univ. School of Medicine (Japan); Sato, Keiji [Dept. of Orthopedic Surgery, Nagoya Univ. School of Medicine (Japan); Sugiura, Hideshi [Dept. of Orthopedic Surgery, Nagoya Univ. School of Medicine (Japan); Iwata, Hisashi [Dept. of Orthopedic Surgery, Nagoya Univ. School of Medicine (Japan)

    1996-05-01

    The objective of this study was to evaluate the inflammatory reaction accompanying chondroblastoma and to define the value of the finding in clinical practice. We reviewed the clinical, radiographic, and magnetic resonance (MR) findings in six patients with histologically proven chondroblastoma. In all cases, MR imaging showered marrow and soft tissue edema. In four of six cases, periosteal reaction related to intra-osseous edema was more clearly demonstrated on MR imaging than on radiographs. Follow-up MR studies after surgery were available in three patients and all showed disappearance of inflammatory responses such as marrow and soft tissue edema, and reactive synovitis. We propose that these inflammatory reactions of chondroblastomas are inportant signs for detecting residual tumor in recurrences after surgery, as well as for making a precise diagnosis. The MR changes may also be valuable in demonstrating eradication of the tumor. (orig./MG)

  3. Nanoparticle Reactions on Chip

    Science.gov (United States)

    Köhler, J. M.; Kirner, Th.; Wagner, J.; Csáki, A.; Möller, R.; Fritzsche, W.

    The handling of heterogenous systems in micro reactors is difficult due to their adhesion and transport behaviour. Therefore, the formation of precipitates and gas bubbles has to be avoided in micro reaction technology, in most cases. But, micro channels and other micro reactors offer interesting possibilities for the control of reaction conditions and transport by diffusion and convection due to the laminar flow caused by small Reynolds numbers. This can be used for the preparation and modification of objects, which are much smaller than the cross section of microchannels. The formation of colloidal solutions and the change of surface states of nano particles are two important tasks for the application of chip reactors in nanoparticle technology. Some concepts for the preparation and reaction of nanoparticles in modular chip reactor arrangements will be discussed.

  4. Space exploration

    CERN Document Server

    2009-01-01

    Space Exploration, is one book in the Britannica Illustrated Science Library Series that is correlated to the science curriculum in grades 5-8. The Britannica Illustrated Science Library is a visually compelling set that covers earth science, life science, and physical science in 16 volumes.  Created for ages 10 and up, each volume provides an overview on a subject and thoroughly explains it through detailed and powerful graphics-more than 1,000 per volume-that turn complex subjects into information that students can grasp.  Each volume contains a glossary with full definitions for vocabulary help and an index.

  5. Space Pharmacology

    CERN Document Server

    Wotring, Virginia E

    2012-01-01

    Space Pharmacology” is a review of the current knowledge regarding the use of pharmaceuticals during spaceflights. It is a comprehensive review of the literature, addressing each area of pharmacokinetics and each major physiological system in turn. Every section begins with a topic overview, and is followed by a discussion of published data from spaceflight, and from ground experiments meant to model the spaceflight situation. Includes a discussion looking forward to the new medical challenges we are likely to face on longer duration exploration missions. This book is a snapshot of our current knowledge that also highlights areas of unknown.

  6. Metabolic and functional characterization of effects of developmental temperature in Drosophila melanogaster

    DEFF Research Database (Denmark)

    Schou, Mads F; Kristensen, Torsten Nygaard; Karlsson, Goran B

    2017-01-01

    , and in particular, how physiological stress at extreme temperatures may counteract beneficial acclimation responses at benign temperatures. We exposed Drosophila melanogaster to ten developmental temperatures covering their entire permissible temperature range. We obtained metabolic profiles and reaction norms...

  7. Optimization of a blueprint for in vitro glycolysis by metabolic real-time analysis

    NARCIS (Netherlands)

    Bujara, Matthias; Schümperli, Michael; Pellaux, René; Heinemann, Matthias; Panke, Sven

    Recruiting complex metabolic reaction networks for chemical synthesis has attracted considerable attention but frequently requires optimization of network composition and dynamics to reach sufficient productivity. As a design framework to predict optimal levels for all enzymes in the network is

  8. The evolution of metabolic networks of E. coli

    Directory of Open Access Journals (Sweden)

    Baumler David J

    2011-11-01

    Full Text Available Abstract Background Despite the availability of numerous complete genome sequences from E. coli strains, published genome-scale metabolic models exist only for two commensal E. coli strains. These models have proven useful for many applications, such as engineering strains for desired product formation, and we sought to explore how constructing and evaluating additional metabolic models for E. coli strains could enhance these efforts. Results We used the genomic information from 16 E. coli strains to generate an E. coli pangenome metabolic network by evaluating their collective 76,990 ORFs. Each of these ORFs was assigned to one of 17,647 ortholog groups including ORFs associated with reactions in the most recent metabolic model for E. coli K-12. For orthologous groups that contain an ORF already represented in the MG1655 model, the gene to protein to reaction associations represented in this model could then be easily propagated to other E. coli strain models. All remaining orthologous groups were evaluated to see if new metabolic reactions could be added to generate a pangenome-scale metabolic model (iEco1712_pan. The pangenome model included reactions from a metabolic model update for E. coli K-12 MG1655 (iEco1339_MG1655 and enabled development of five additional strain-specific genome-scale metabolic models. These additional models include a second K-12 strain (iEco1335_W3110 and four pathogenic strains (two enterohemorrhagic E. coli O157:H7 and two uropathogens. When compared to the E. coli K-12 models, the metabolic models for the enterohemorrhagic (iEco1344_EDL933 and iEco1345_Sakai and uropathogenic strains (iEco1288_CFT073 and iEco1301_UTI89 contained numerous lineage-specific gene and reaction differences. All six E. coli models were evaluated by comparing model predictions to carbon source utilization measurements under aerobic and anaerobic conditions, and to batch growth profiles in minimal media with 0.2% (w/v glucose. An ancestral

  9. Velocity pump reaction turbine

    Science.gov (United States)

    House, P.A.

    An expanding hydraulic/two-phase velocity pump reaction turbine including a dual concentric rotor configuration with an inter-rotor annular flow channel in which the inner rotor is mechanically driven by the outer rotor. In another embodiment, the inner rotor is immobilized and provided with gas recovery ports on its outer surface by means of which gas in solution may be recovered. This velocity pump reaction turbine configuration is capable of potential energy conversion efficiencies of up to 70%, and is particularly suited for geothermal applications.

  10. Reactions to dietary tartrazine.

    OpenAIRE

    David, T J

    1987-01-01

    Double blind challenges with tartrazine and benzoic acid were performed in hospital in 24 children whose parents gave a definite history of a purely behavioural immediate adverse reaction to one of these substances. The patients, whose ages ranged from 1.6 to 12.4 years, were on a diet that avoided these items, and in all there was a clear history that any lapse of the diet caused an obvious adverse behavioural reaction within two hours. In no patient was any change in behaviour noted either ...

  11. Allergic reactions in anaesthesia

    DEFF Research Database (Denmark)

    Krøigaard, M; Garvey, L H; Menné, T

    2005-01-01

    match, the right substance being suspected, but investigations showed an additional allergen or several substances, including the right substance being suspected. CONCLUSIONS: An informed guess is not a reliable way of determining the cause of a supposed allergic reaction during anaesthesia and may put...... a significant number of patients at unnecessary risk. Some patients may be labelled with a wrong allergy, leading to unnecessary warnings against harmless substances, and some patients may be put at risk of subsequent re-exposure to the real allergen. Patients with suspected allergic reactions during...

  12. Introduction to nuclear reactions

    International Nuclear Information System (INIS)

    Satchler, G.R.

    1980-01-01

    This introduction to nuclear reaction phenomena is aimed primarily but not exclusively at readers at the undergraduate student level. An overview of the subject is presented in the first two chapters entitled - Some background information and Introduction to nuclear reactions. The third chapter reviews scattering theory with emphasis on the underlying physical ideas and also provides schematic entrees to the more advanced topics. The physical models which have been developed to account for the various aspects of nuclear phenomena are described in more detail in chapter 4. References and exercises are appended to each chapter. (U.K.)

  13. Modeling of Reaction Calorimeter

    OpenAIRE

    Farzad, Reza

    2014-01-01

    The purpose of this project was to model the reaction calorimeter in order to calculate the heat of absorption which is the most important parameter in this work. Reaction calorimeter is an apparatus which is used in measuring the heat of absorption of CO2 as well as the total pressure in vapor phase based on vapor-liquid equilibrium state. Mixture of monoethanolamine (MEA) and water was used as a solvent to absorb the CO2.Project was divided in to three parts in order to make the programming...

  14. Anniversary reactions in therapists.

    Science.gov (United States)

    Granet, R B; Kalman, T P

    1982-12-01

    The authors provide three case examples of anniversary reactions in psychotherapists evoked in the course of treating patients. They note that psychotherapy has always been discussed in terms of time and phases, which lend themselves to periodicities and may provide the potential for anniversary phenomena. The authors recommend that therapists be aware of such phenomena; monitor their own losses, defenses, and dreams; and continue their own supervision. Possible positive aspects of identification of therapists' anniversary reactions are increased empathy with patients and help in completing unresolved therapeutic and personal issues.

  15. USSR Space Life Sciences Digest, issue 29

    Science.gov (United States)

    Stone, Lydia Razran (Editor); Teeter, Ronald (Editor); Rowe, Joseph (Editor)

    1991-01-01

    This is the twenty-ninth issue of NASA's Space Life Sciences Digest. It is a double issue covering two issues of the Soviet Space Biology and Aerospace Medicine Journal. Issue 29 contains abstracts of 60 journal papers or book chapters published in Russian and of three Soviet monographs. Selected abstracts are illustrated with figures and tables from the original. A review of a book on environmental hygiene and a list of papers presented at a Soviet conference on space biology and medicine are also included. The materials in this issue were identified as relevant to 28 areas of space biology and medicine. The areas are: adaptation, aviation medicine, biological rhythms, body fluids, botany, cardiovascular and respiratory systems, developmental biology, digestive system, endocrinology, equipment and instrumentation, genetics, habitability and environment effects, hematology, human performance, immunology, life support systems, mathematical modeling, metabolism, musculoskeletal system, neurophysiology, nutrition, personnel selection, psychology, radiobiology, reproductive system, space biology and medicine, and the economics of space flight.

  16. Metabolic disorders in menopause.

    Science.gov (United States)

    Stachowiak, Grzegorz; Pertyński, Tomasz; Pertyńska-Marczewska, Magdalena

    2015-03-01

    Metabolic disorders occurring in menopause, including dyslipidemia, disorders of carbohydrate metabolism (impaired glucose tolerance - IGT, type 2 diabetes mellitus - T2DM) or components of metabolic syndrome, constitute risk factors for cardiovascular disease in women. A key role could be played here by hyperinsulinemia, insulin resistance and visceral obesity, all contributing to dyslipidemia, oxidative stress, inflammation, alter coagulation and atherosclerosis observed during the menopausal period. Undiagnosed and untreated, metabolic disorders may adversely affect the length and quality of women's life. Prevention and treatment preceded by early diagnosis should be the main goal for the physicians involved in menopausal care. This article represents a short review of the current knowledge concerning metabolic disorders (e.g. obesity, polycystic ovary syndrome or thyroid diseases) in menopause, including the role of a tailored menopausal hormone therapy (HT). According to current data, HT is not recommend as a preventive strategy for metabolic disorders in menopause. Nevertheless, as part of a comprehensive strategy to prevent chronic diseases after menopause, menopausal hormone therapy, particularly estrogen therapy may be considered (after balancing benefits/risks and excluding women with absolute contraindications to this therapy). Life-style modifications, with moderate physical activity and healthy diet at the forefront, should be still the first choice recommendation for all patients with menopausal metabolic abnormalities.

  17. Metabolic disorders in menopause

    Directory of Open Access Journals (Sweden)

    Grzegorz Stachowiak

    2015-04-01

    Full Text Available Metabolic disorders occurring in menopause, including dyslipidemia, disorders of carbohydrate metabolism (impaired glucose tolerance – IGT, type 2 diabetes mellitus – T2DM or components of metabolic syndrome, constitute risk factors for cardiovascular disease in women. A key role could be played here by hyperinsulinemia, insulin resistance and visceral obesity, all contributing to dyslipidemia, oxidative stress, inflammation, alter coagulation and atherosclerosis observed during the menopausal period. Undiagnosed and untreated, metabolic disorders may adversely affect the length and quality of women’s life. Prevention and treatment preceded by early diagnosis should be the main goal for the physicians involved in menopausal care. This article represents a short review of the current knowledge concerning metabolic disorders (e.g. obesity, polycystic ovary syndrome or thyroid diseases in menopause, including the role of a tailored menopausal hormone therapy (HT. According to current data, HT is not recommend as a preventive strategy for metabolic disorders in menopause. Nevertheless, as part of a comprehensive strategy to prevent chronic diseases after menopause, menopausal hormone therapy, particularly estrogen therapy may be considered (after balancing benefits/risks and excluding women with absolute contraindications to this therapy. Life-style modifications, with moderate physical activity and healthy diet at the forefront, should be still the first choice recommendation for all patients with menopausal metabolic abnormalities.

  18. Interdisciplinary Pathways for Urban Metabolism Research

    Science.gov (United States)

    Newell, J. P.

    2011-12-01

    With its rapid rise as a metaphor to express coupled natural-human systems in cities, the concept of urban metabolism is evolving into a series of relatively distinct research frameworks amongst various disciplines, with varying definitions, theories, models, and emphases. In industrial ecology, housed primarily within the disciplinary domain of engineering, urban metabolism research has focused on quantifying material and energy flows into, within, and out of cities, using methodologies such as material flow analysis and life cycle assessment. In the field of urban ecology, which is strongly influenced by ecology and urban planning, research focus has been placed on understanding and modeling the complex patterns and processes of human-ecological systems within urban areas. Finally, in political ecology, closely aligned with human geography and anthropology, scholars theorize about the interwoven knots of social and natural processes, material flows, and spatial structures that form the urban metabolism. This paper offers three potential interdisciplinary urban metabolism research tracks that might integrate elements of these three "ecologies," thereby bridging engineering and the social and physical sciences. First, it presents the idea of infrastructure ecology, which explores the complex, emergent interdependencies between gray (water and wastewater, transportation, etc) and green (e.g. parks, greenways) infrastructure systems, as nested within a broader socio-economic context. For cities to be sustainable and resilient over time-space, the theory follows, these is a need to understand and redesign these infrastructure linkages. Second, there is the concept of an urban-scale carbon metabolism model which integrates consumption-based material flow analysis (including goods, water, and materials), with the carbon sink and source dynamics of the built environment (e.g. buildings, etc) and urban ecosystems. Finally, there is the political ecology of the material

  19. Reaction Formulation: A Bibliography.

    Science.gov (United States)

    Pedrini, D. T.; Pedrini, Bonnie C.

    Reaction formation was studied by Sigmund Freud. This defense mechanism may be related to repression, substitution, reversal, and compensation (or over-compensation). Alfred Adler considered compensation a basic process in his individual psychology. Anna Freud discussed some defense mechanisms, and Bibring, Dwyer, Huntington, and Valenstein…

  20. Cluster knockout reactions

    Indian Academy of Sciences (India)

    2014-04-07

    Apr 7, 2014 ... Cluster knockout reactions are expected to reveal the amount of clustering (such as that of , d and even of heavier clusters such as 12C, 16O etc.) in the target nucleus. In simple terms, incident medium high-energy nuclear projectile interacts strongly with the cluster (present in the target nucleus) as if it ...