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Sample records for model incorporating enzyme

  1. Modeling nitrous oxide production and reduction in soil through explicit representation of denitrification enzyme kinetics.

    Science.gov (United States)

    Zheng, Jianqiu; Doskey, Paul V

    2015-02-17

    An enzyme-explicit denitrification model with representations for pre- and de novo synthesized enzymes was developed to improve predictions of nitrous oxide (N2O) accumulations in soil and emissions from the surface. The metabolic model of denitrification is based on dual-substrate utilization and Monod growth kinetics. Enzyme synthesis/activation was incorporated into each sequential reduction step of denitrification to regulate dynamics of the denitrifier population and the active enzyme pool, which controlled the rate function. Parameterizations were developed from observations of the dynamics of N2O production and reduction in soil incubation experiments. The model successfully reproduced the dynamics of N2O and N2 accumulation in the incubations and revealed an important regulatory effect of denitrification enzyme kinetics on the accumulation of denitrification products. Pre-synthesized denitrification enzymes contributed 20, 13, 43, and 62% of N2O that accumulated in 48 h incubations of soil collected from depths of 0-5, 5-10, 10-15, and 15-25 cm, respectively. An enzyme activity function (E) was defined to estimate the relative concentration of active enzymes and variation in response to environmental conditions. The value of E allows for activities of pre-synthesized denitrification enzymes to be differentiated from de novo synthesized enzymes. Incorporating explicit representations of denitrification enzyme kinetics into biogeochemical models is a promising approach for accurately simulating dynamics of the production and reduction of N2O in soils.

  2. Effects of Straw Incorporation on Soil Nutrients, Enzymes, and Aggregate Stability in Tobacco Fields of China

    Directory of Open Access Journals (Sweden)

    Jiguang Zhang

    2016-07-01

    Full Text Available To determine the effects of straw incorporation on soil nutrients, enzyme activity, and aggregates in tobacco fields, we conducted experiments with different amounts of wheat and maize straw in Zhucheng area of southeast Shandong province for three years (2010–2012. In the final year of experiment (2012, straw incorporation increased soil organic carbon (SOC and related parameters, and improved soil enzyme activity proportionally with the amount of straw added, except for catalase when maize straw was used. And maize straw incorporation was more effective than wheat straw in the tobacco field. The percentage of aggregates >2 mm increased with straw incorporation when measured by either dry or wet sieving. The mean weight diameter (MWD and geometric mean diameter (GMD in straw incorporation treatments were higher than those in the no-straw control (CK. Maize straw increased soil aggregate stability more than wheat straw with the same incorporation amount. Alkaline phosphatase was significantly and negatively correlated with soil pH. Sucrase and urease were both significantly and positively correlated with soil alkali-hydrolysable N. Catalase was significantly but negatively correlated with soil extractable K (EK. The MWD and GMD by dry sieving had significantly positive correlations with SOC, total N, total K, and EK, but only significantly correlated with EK by wet sieving. Therefore, soil nutrients, metabolic enzyme activity, and aggregate stability might be increased by increasing the SOC content through the maize or wheat straw incorporation. Moreover, incorporation of maize straw at 7500 kg·hm−2 was the best choice to enhance soil fertility in the tobacco area of Eastern China.

  3. An enzyme-linked immunosorbent assay for bromodeoxyuridine incorporation using fixed microcultures

    International Nuclear Information System (INIS)

    Muir, D.; Varon, S.; Manthorpe, M.

    1990-01-01

    We report a quantitative method by which a single microculture can be examined for cell morphology; cell number; DNA synthesis; and expression of cell antigens. This method first involves measuring by enzyme-linked immunosorbent assay (ELISA) the total bromodeoxyuridine (BrdU) incorporation into DNA by monolayer microcultures. The BrdU-ELISA measurement was followed by simultaneous immunostaining for BrdU-positive nuclei and for a cytoplasmic antigen. The method was applied to the measurement of mitogen-induced proliferation of rat sciatic nerve Schwann cell and cerebral astroglia microcultures. The ELISA measurement of BrdU incorporation compares favorably with measurements of tritiated thymidine incorporation and offers the additional advantages that the same microculture can subsequently be examined for cell number, for cell morphology, and for the percentage of cells having BrdU-labeled nuclei and other antigens

  4. An enzyme-linked immunosorbent assay for bromodeoxyuridine incorporation using fixed microcultures

    Energy Technology Data Exchange (ETDEWEB)

    Muir, D.; Varon, S.; Manthorpe, M. (Univ. of California, San Diego, La Jolla (USA))

    1990-03-01

    We report a quantitative method by which a single microculture can be examined for cell morphology; cell number; DNA synthesis; and expression of cell antigens. This method first involves measuring by enzyme-linked immunosorbent assay (ELISA) the total bromodeoxyuridine (BrdU) incorporation into DNA by monolayer microcultures. The BrdU-ELISA measurement was followed by simultaneous immunostaining for BrdU-positive nuclei and for a cytoplasmic antigen. The method was applied to the measurement of mitogen-induced proliferation of rat sciatic nerve Schwann cell and cerebral astroglia microcultures. The ELISA measurement of BrdU incorporation compares favorably with measurements of tritiated thymidine incorporation and offers the additional advantages that the same microculture can subsequently be examined for cell number, for cell morphology, and for the percentage of cells having BrdU-labeled nuclei and other antigens.

  5. 40 CFR 174.525 - E. coli B-D-glucuronidase enzyme as a plant-incorporated protectant inert ingredient; exemption...

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false E. coli B-D-glucuronidase enzyme as a... E. coli B-D-glucuronidase enzyme as a plant-incorporated protectant inert ingredient; exemption from the requirement of a tolerance. Residues of E. coli B-D-glucuronidase enzyme are exempt from the...

  6. Ultrarapid sonochemical synthesis of enzyme-incorporated copper nanoflowers and their application to mediatorless glucose biofuel cell

    Science.gov (United States)

    Chung, Minsoo; Nguyen, Tuan Loi; Tran, Thao Quynh Ngan; Yoon, Hyon Hee; Kim, Il Tae; Kim, Moon Il

    2018-01-01

    We have developed a mediatorless glucose biofuel cell based on hybrid nanoflowers incorporating enzymes including glucose oxidase (GOx), laccase, or catalase with copper phosphate, which were further mixed and compressed with conductive multi-walled carbon nanotube (CNT). The nanoflowers were simply synthesized within 5 min at room temperature using sonication method but yielded greatly improved stability as well as highly retained activity by the proper incorporation of enzyme molecules inside the flower-like structure. With glucose as biofuel, GOx and laccase nanoflowers were applied to form enzyme anode and cathode, respectively, and catalase nanoflowers were additionally employed to catalyze the decomposition of hydrogen peroxide, which may be deleterious for GOx, into oxygen and water. Using the enzyme nanoflowers-based biofuel cell system without any involved mediator, a high power density up to 200 μW cm-2 were obtained, which was approximately 80% to that from the biofuel cell system prepared with the corresponding free enzymes. Importantly, the enzyme nanoflowers-based biofuel cell maintained their initial power density over 90% during storage for two months at 4 °C, while most of the glucose biofuel cells in the literature present meaningful stability only in the range of one or two weeks. Based on this result, we expect that this simple but efficient strategy to prepare highly stable glucose biofuel cell using the rapidly-synthesized enzyme-inorganic hybrid nanoflowers can be readily extended to diverse applications in medical and environmental chemistry.

  7. Structural differences of matrix metalloproteinases. Homology modeling and energy minimization of enzyme-substrate complexes

    DEFF Research Database (Denmark)

    Terp, G E; Christensen, I T; Jørgensen, Flemming Steen

    2000-01-01

    Matrix metalloproteinases are extracellular enzymes taking part in the remodeling of extracellular matrix. The structures of the catalytic domain of MMP1, MMP3, MMP7 and MMP8 are known, but structures of enzymes belonging to this family still remain to be determined. A general approach...... to the homology modeling of matrix metalloproteinases, exemplified by the modeling of MMP2, MMP9, MMP12 and MMP14 is described. The models were refined using an energy minimization procedure developed for matrix metalloproteinases. This procedure includes incorporation of parameters for zinc and calcium ions...... in the AMBER 4.1 force field, applying a non-bonded approach and a full ion charge representation. Energy minimization of the apoenzymes yielded structures with distorted active sites, while reliable three-dimensional structures of the enzymes containing a substrate in active site were obtained. The structural...

  8. Multi-enzyme Process Modeling

    DEFF Research Database (Denmark)

    Andrade Santacoloma, Paloma de Gracia

    are affected (in a positive or negative way) by the presence of the other enzymes and compounds in the media. In this thesis the concept of multi-enzyme in-pot term is adopted for processes that are carried out by the combination of enzymes in a single reactor and implemented at pilot or industrial scale...... features of the process and provides the information required to structure the process model by using a step-by-step procedure with the required tools and methods. In this way, this framework increases efficiency of the model development process with respect to time and resources needed (fast and effective....... In this way the model parameters that drives the main dynamic behavior can be identified and thus a better understanding of this type of processes. In order to develop, test and verify the methodology, three case studies were selected, specifically the bi-enzyme process for the production of lactobionic acid...

  9. Functional Enzyme-Based Approach for Linking Microbial Community Functions with Biogeochemical Process Kinetics

    Energy Technology Data Exchange (ETDEWEB)

    Li, Minjing [School; Qian, Wei-jun [Pacific Northwest National Laboratory, Richland, Washington 99354, United States; Gao, Yuqian [Pacific Northwest National Laboratory, Richland, Washington 99354, United States; Shi, Liang [School; Liu, Chongxuan [Pacific Northwest National Laboratory, Richland, Washington 99354, United States; School

    2017-09-28

    The kinetics of biogeochemical processes in natural and engineered environmental systems are typically described using Monod-type or modified Monod-type models. These models rely on biomass as surrogates for functional enzymes in microbial community that catalyze biogeochemical reactions. A major challenge to apply such models is the difficulty to quantitatively measure functional biomass for constraining and validating the models. On the other hand, omics-based approaches have been increasingly used to characterize microbial community structure, functions, and metabolites. Here we proposed an enzyme-based model that can incorporate omics-data to link microbial community functions with biogeochemical process kinetics. The model treats enzymes as time-variable catalysts for biogeochemical reactions and applies biogeochemical reaction network to incorporate intermediate metabolites. The sequences of genes and proteins from metagenomes, as well as those from the UniProt database, were used for targeted enzyme quantification and to provide insights into the dynamic linkage among functional genes, enzymes, and metabolites that are necessary to be incorporated in the model. The application of the model was demonstrated using denitrification as an example by comparing model-simulated with measured functional enzymes, genes, denitrification substrates and intermediates

  10. Seeing & Feeling How Enzymes Work Using Tangible Models

    Science.gov (United States)

    Lau, Kwok-chi

    2013-01-01

    This article presents a tangible model used to help students tackle some misconceptions about enzyme actions, particularly the induced-fit model, enzyme-substrate complementarity, and enzyme inhibition. The model can simulate how substrates induce a change in the shape of the active site and the role of attraction force during enzyme-substrate…

  11. Incorporation of chemical kinetic models into process control

    International Nuclear Information System (INIS)

    Herget, C.J.; Frazer, J.W.

    1981-01-01

    An important consideration in chemical process control is to determine the precise rationing of reactant streams, particularly when a large time delay exists between the mixing of the reactants and the measurement of the product. In this paper, a method is described for incorporating chemical kinetic models into the control strategy in order to achieve optimum operating conditions. The system is first characterized by determining a reaction rate surface as a function of all input reactant concentrations over a feasible range. A nonlinear constrained optimization program is then used to determine the combination of reactants which produces the specified yield at minimum cost. This operating condition is then used to establish the nominal concentrations of the reactants. The actual operation is determined through a feedback control system employing a Smith predictor. The method is demonstrated on a laboratory bench scale enzyme reactor

  12. A stochastic model of enzyme kinetics

    Science.gov (United States)

    Stefanini, Marianne; Newman, Timothy; McKane, Alan

    2003-10-01

    Enzyme kinetics is generally modeled by deterministic rate equations, and in the simplest case leads to the well-known Michaelis-Menten equation. It is plausible that stochastic effects will play an important role at low enzyme concentrations. We have addressed this by constructing a simple stochastic model which can be exactly solved in the steady-state. Throughout a wide range of parameter values Michaelis-Menten dynamics is replaced by a new and simple theoretical result.

  13. A quantitative systems pharmacology approach, incorporating a novel liver model, for predicting pharmacokinetic drug-drug interactions.

    Science.gov (United States)

    Cherkaoui-Rbati, Mohammed H; Paine, Stuart W; Littlewood, Peter; Rauch, Cyril

    2017-01-01

    All pharmaceutical companies are required to assess pharmacokinetic drug-drug interactions (DDIs) of new chemical entities (NCEs) and mathematical prediction helps to select the best NCE candidate with regard to adverse effects resulting from a DDI before any costly clinical studies. Most current models assume that the liver is a homogeneous organ where the majority of the metabolism occurs. However, the circulatory system of the liver has a complex hierarchical geometry which distributes xenobiotics throughout the organ. Nevertheless, the lobule (liver unit), located at the end of each branch, is composed of many sinusoids where the blood flow can vary and therefore creates heterogeneity (e.g. drug concentration, enzyme level). A liver model was constructed by describing the geometry of a lobule, where the blood velocity increases toward the central vein, and by modeling the exchange mechanisms between the blood and hepatocytes. Moreover, the three major DDI mechanisms of metabolic enzymes; competitive inhibition, mechanism based inhibition and induction, were accounted for with an undefined number of drugs and/or enzymes. The liver model was incorporated into a physiological-based pharmacokinetic (PBPK) model and simulations produced, that in turn were compared to ten clinical results. The liver model generated a hierarchy of 5 sinusoidal levels and estimated a blood volume of 283 mL and a cell density of 193 × 106 cells/g in the liver. The overall PBPK model predicted the pharmacokinetics of midazolam and the magnitude of the clinical DDI with perpetrator drug(s) including spatial and temporal enzyme levels changes. The model presented herein may reduce costs and the use of laboratory animals and give the opportunity to explore different clinical scenarios, which reduce the risk of adverse events, prior to costly human clinical studies.

  14. A quantitative systems pharmacology approach, incorporating a novel liver model, for predicting pharmacokinetic drug-drug interactions.

    Directory of Open Access Journals (Sweden)

    Mohammed H Cherkaoui-Rbati

    Full Text Available All pharmaceutical companies are required to assess pharmacokinetic drug-drug interactions (DDIs of new chemical entities (NCEs and mathematical prediction helps to select the best NCE candidate with regard to adverse effects resulting from a DDI before any costly clinical studies. Most current models assume that the liver is a homogeneous organ where the majority of the metabolism occurs. However, the circulatory system of the liver has a complex hierarchical geometry which distributes xenobiotics throughout the organ. Nevertheless, the lobule (liver unit, located at the end of each branch, is composed of many sinusoids where the blood flow can vary and therefore creates heterogeneity (e.g. drug concentration, enzyme level. A liver model was constructed by describing the geometry of a lobule, where the blood velocity increases toward the central vein, and by modeling the exchange mechanisms between the blood and hepatocytes. Moreover, the three major DDI mechanisms of metabolic enzymes; competitive inhibition, mechanism based inhibition and induction, were accounted for with an undefined number of drugs and/or enzymes. The liver model was incorporated into a physiological-based pharmacokinetic (PBPK model and simulations produced, that in turn were compared to ten clinical results. The liver model generated a hierarchy of 5 sinusoidal levels and estimated a blood volume of 283 mL and a cell density of 193 × 106 cells/g in the liver. The overall PBPK model predicted the pharmacokinetics of midazolam and the magnitude of the clinical DDI with perpetrator drug(s including spatial and temporal enzyme levels changes. The model presented herein may reduce costs and the use of laboratory animals and give the opportunity to explore different clinical scenarios, which reduce the risk of adverse events, prior to costly human clinical studies.

  15. Compounds from silicones alter enzyme activity in curing barnacle glue and model enzymes.

    Science.gov (United States)

    Rittschof, Daniel; Orihuela, Beatriz; Harder, Tilmann; Stafslien, Shane; Chisholm, Bret; Dickinson, Gary H

    2011-02-17

    Attachment strength of fouling organisms on silicone coatings is low. We hypothesized that low attachment strength on silicones is, in part, due to the interaction of surface available components with natural glues. Components could alter curing of glues through bulk changes or specifically through altered enzyme activity. GC-MS analysis of silicone coatings showed surface-available siloxanes when the coatings were gently rubbed with a cotton swab for 15 seconds or given a 30 second rinse with methanol. Mixtures of compounds were found on 2 commercial and 8 model silicone coatings. The hypothesis that silicone components alter glue curing enzymes was tested with curing barnacle glue and with commercial enzymes. In our model, barnacle glue curing involves trypsin-like serine protease(s), which activate enzymes and structural proteins, and a transglutaminase which cross-links glue proteins. Transglutaminase activity was significantly altered upon exposure of curing glue from individual barnacles to silicone eluates. Activity of purified trypsin and, to a greater extent, transglutaminase was significantly altered by relevant concentrations of silicone polymer constituents. Surface-associated silicone compounds can disrupt glue curing and alter enzyme properties. Altered curing of natural glues has potential in fouling management.

  16. Enzymes activities involving bacterial cytochromes incorporated in clays

    International Nuclear Information System (INIS)

    Lojou, E.; Giudici-Orticoni, M.Th.; Bianco, P.

    2005-01-01

    With the development of bio electrochemistry, researches appeared on the enzymes immobilization at the surface of electrodes for the realization of bioreactors and bio sensors. One of the main challenges is the development of host matrix able to immobilize the protein material preserving its integrity. In this framework the authors developed graphite electrodes modified by clay films. These electrodes are examined for two enzyme reactions involving proteins of sulfate-reduction bacteria. Then in the framework of the hydrogen biological production and bioreactors for the environmental pollution de-pollution, the electrochemical behavior of the cytochrome c3 in two different clays deposed at the electrode is examined

  17. Effects of wheat straw incorporation on the availability of soil nutrients and enzyme activities in semiarid areas.

    Directory of Open Access Journals (Sweden)

    Ting Wei

    Full Text Available Soil infertility is the main barrier to dryland agricultural production in China. To provide a basis for the establishment of a soil amelioration technical system for rainfed fields in the semiarid area of northwest China, we conducted a four-year (2007-2011 field experiment to determine the effects of wheat straw incorporation on the arid soil nutrient levels of cropland cultivated with winter wheat after different straw incorporation levels. Three wheat straw incorporation levels were tested (H: 9000 kg hm(-2, M: 6000 kg hm(-2, and L: 3000 kg hm(-2 and no straw incorporation was used as the control (CK. The levels of soil nutrients, soil organic carbon (SOC, soil labile organic carbon (LOC, and enzyme activities were analyzed each year after the wheat harvest. After straw incorporation for four years, the results showed that variable straw amounts had different effects on the soil fertility indices, where treatment H had the greatest effect. Compared with CK, the average soil available N, available P, available K, SOC, and LOC levels were higher in the 0-40 cm soil layers after straw incorporation treatments, i.e., 9.1-30.5%, 9.8-69.5%, 10.3-27.3%, 0.7-23.4%, and 44.4-49.4% higher, respectively. On average, the urease, phosphatase, and invertase levels in the 0-40 cm soil layers were 24.4-31.3%, 9.9-36.4%, and 42.9-65.3% higher, respectively. Higher yields coupled with higher nutrient contents were achieved with H, M and L compared with CK, where these treatments increased the crop yields by 26.75%, 21.51%, and 7.15%, respectively.

  18. MOLECULAR MODELLING OF HUMAN ALDEHYDE OXIDASE AND IDENTIFICATION OF THE KEY INTERACTIONS IN THE ENZYME-SUBSTRATE COMPLEX

    Directory of Open Access Journals (Sweden)

    Siavoush Dastmalchi

    2005-05-01

    Full Text Available Aldehyde oxidase (EC 1.2.3.1, a cytosolic enzyme containing FAD, molybdenum and iron-sulphur cluster, is a member of non-cytochrome P-450 enzymes called molybdenum hydroxylases which is involved in the metabolism of a wide range of endogenous compounds and many drug substances. Drug metabolism is one of the important characteristics which influences many aspects of a therapeutic agent such as routes of administration, drug interaction and toxicity and therefore, characterisation of the key interactions between enzymes and substrates is very important from drug development point of view. The aim of this study was to generate a three-dimensional model of human aldehyde oxidase (AO in order to assist us to identify the mode of interaction between enzyme and a set of phethalazine/quinazoline derivatives. Both sequence-based (BLAST and inverse protein fold recognition methods (THREADER were used to identify the crystal structure of bovine xanthine dehydrogenase (pdb code of 1FO4 as the suitable template for comparative modelling of human AO. Model structure was generated by aligning and then threading the sequence of human AO onto the template structure, incorporating the associated cofactors, and molecular dynamics simulations and energy minimization using GROMACS program. Different criteria which were measured by the PROCHECK, QPACK, VERIFY-3D were indicative of a proper fold for the predicted structural model of human AO. For example, 97.9 percentages of phi and psi angles were in the favoured and most favoured regions in the ramachandran plot, and all residues in the model are assigned environmentally positive compatibility scores. Further evaluation on the model quality was performed by investigation of AO-mediated oxidation of a set of phthalazine/quinazoline derivatives to develop QSAR model capable of describing the extent of the oxidation. Substrates were aligned by docking onto the active site of the enzyme using GOLD technology and then

  19. Incorporating parametric uncertainty into population viability analysis models

    Science.gov (United States)

    McGowan, Conor P.; Runge, Michael C.; Larson, Michael A.

    2011-01-01

    Uncertainty in parameter estimates from sampling variation or expert judgment can introduce substantial uncertainty into ecological predictions based on those estimates. However, in standard population viability analyses, one of the most widely used tools for managing plant, fish and wildlife populations, parametric uncertainty is often ignored in or discarded from model projections. We present a method for explicitly incorporating this source of uncertainty into population models to fully account for risk in management and decision contexts. Our method involves a two-step simulation process where parametric uncertainty is incorporated into the replication loop of the model and temporal variance is incorporated into the loop for time steps in the model. Using the piping plover, a federally threatened shorebird in the USA and Canada, as an example, we compare abundance projections and extinction probabilities from simulations that exclude and include parametric uncertainty. Although final abundance was very low for all sets of simulations, estimated extinction risk was much greater for the simulation that incorporated parametric uncertainty in the replication loop. Decisions about species conservation (e.g., listing, delisting, and jeopardy) might differ greatly depending on the treatment of parametric uncertainty in population models.

  20. Phage lytic enzymes: a history.

    Science.gov (United States)

    Trudil, David

    2015-02-01

    There are many recent studies regarding the efficacy of bacteriophage-related lytic enzymes: the enzymes of 'bacteria-eaters' or viruses that infect bacteria. By degrading the cell wall of the targeted bacteria, these lytic enzymes have been shown to efficiently lyse Gram-positive bacteria without affecting normal flora and non-related bacteria. Recent studies have suggested approaches for lysing Gram-negative bacteria as well (Briersa Y, et al., 2014). These enzymes include: phage-lysozyme, endolysin, lysozyme, lysin, phage lysin, phage lytic enzymes, phageassociated enzymes, enzybiotics, muralysin, muramidase, virolysin and designations such as Ply, PAE and others. Bacteriophages are viruses that kill bacteria, do not contribute to antimicrobial resistance, are easy to develop, inexpensive to manufacture and safe for humans, animals and the environment. The current focus on lytic enzymes has been on their use as anti-infectives in humans and more recently in agricultural research models. The initial translational application of lytic enzymes, however, was not associated with treating or preventing a specific disease but rather as an extraction method to be incorporated in a rapid bacterial detection assay (Bernstein D, 1997).The current review traces the translational history of phage lytic enzymes-from their initial discovery in 1986 for the rapid detection of group A streptococcus in clinical specimens to evolving applications in the detection and prevention of disease in humans and in agriculture.

  1. Comparison of Enzymes / Non-Enzymes Proteins Classification Models Based on 3D, Composition, Sequences and Topological Indices

    OpenAIRE

    Munteanu, Cristian Robert

    2014-01-01

    Comparison of Enzymes / Non-Enzymes Proteins Classification Models Based on 3D, Composition, Sequences and Topological Indices, German Conference on Bioinformatics (GCB), Potsdam, Germany (September, 2007)

  2. Modeling metabolic response to changes of enzyme amount in ...

    African Journals Online (AJOL)

    Based on the work of Hynne et al. (2001), in an in silico model of glycolysis, Saccharomyces cerevisiae is established by introducing an enzyme amount multiple factor (.) into the kinetic equations. The model is aimed to predict the metabolic response to the change of enzyme amount. With the help of .α, the amounts of ...

  3. Stability of Enzymes in Granular Enzyme Products for Laundry Detergents

    DEFF Research Database (Denmark)

    Biran, Suzan; Bach, Poul; Simonsen, Ole

    Enzymes have long been of interest to the detergent industry due to their ability to improve the cleaning efficiency of synthetic detergents, contribute to shortening washing times, and reduce energy and water consumption, provision of environmentally friendlier wash water effluents and fabric care....... However, incorporating enzymes in detergent formulations gives rise to numerous practical problems due to their incompatibility with and stability against various detergent components. In powdered detergent formulations, these issues can be partly overcome by physically isolating the enzymes in separate...... particles. However, enzymes may loose a significant part of their activity over a time period of several weeks. Possible causes of inactivation of enzymes in a granule may be related to the release of hydrogen peroxide from the bleaching chemicals in a moisture-containing atmosphere, humidity, autolysis...

  4. Improving a natural enzyme activity through incorporation of unnatural amino acids.

    Science.gov (United States)

    Ugwumba, Isaac N; Ozawa, Kiyoshi; Xu, Zhi-Qiang; Ely, Fernanda; Foo, Jee-Loon; Herlt, Anthony J; Coppin, Chris; Brown, Sue; Taylor, Matthew C; Ollis, David L; Mander, Lewis N; Schenk, Gerhard; Dixon, Nicholas E; Otting, Gottfried; Oakeshott, John G; Jackson, Colin J

    2011-01-19

    The bacterial phosphotriesterases catalyze hydrolysis of the pesticide paraoxon with very fast turnover rates and are thought to be near to their evolutionary limit for this activity. To test whether the naturally evolved turnover rate could be improved through the incorporation of unnatural amino acids and to probe the role of peripheral active site residues in nonchemical steps of the catalytic cycle (substrate binding and product release), we replaced the naturally occurring tyrosine amino acid at position 309 with unnatural L-(7-hydroxycoumarin-4-yl)ethylglycine (Hco) and L-(7-methylcoumarin-4-yl)ethylglycine amino acids, as well as leucine, phenylalanine, and tryptophan. Kinetic analysis suggests that the 7-hydroxyl group of Hco, particularly in its deprotonated state, contributes to an increase in the rate-limiting product release step of substrate turnover as a result of its electrostatic repulsion of the negatively charged 4-nitrophenolate product of paraoxon hydrolysis. The 8-11-fold improvement of this already highly efficient catalyst through a single rationally designed mutation using an unnatural amino acid stands in contrast to the difficulty in improving this native activity through screening hundreds of thousands of mutants with natural amino acids. These results demonstrate that designer amino acids provide easy access to new and valuable sequence and functional space for the engineering and evolution of existing enzyme functions.

  5. Incorporating groundwater flow into the WEPP model

    Science.gov (United States)

    William Elliot; Erin Brooks; Tim Link; Sue Miller

    2010-01-01

    The water erosion prediction project (WEPP) model is a physically-based hydrology and erosion model. In recent years, the hydrology prediction within the model has been improved for forest watershed modeling by incorporating shallow lateral flow into watershed runoff prediction. This has greatly improved WEPP's hydrologic performance on small watersheds with...

  6. Infrared Analysis Of Enzymes Adsorbed Onto Model Surfaces

    Science.gov (United States)

    Story, Gloria M.; Rauch, Deborah S.; Brode, Philip F.; Marcott, Curtis A.

    1989-12-01

    The adsorption of the enzymes, subtilisin BPN' and lysozyme, onto model surfaces was examined using attenuated total reflectance (ATR) infrared (IR) spectroscopy. Using a cylindrical internal reflection (CIRcle) cell with a Germanium (Ge) internal reflection element (IRE), model hydrophilic surfaces were made by plasma cleaning the IRE and model hydrophobic surfaces were made by precoating the IRE with a thin film of polystyrene. Gas chromatography (GC)-IR data collection software was used to monitor adsorption kinetics during the first five minutes after injection of the enzyme into the CIRcle cell. It was found that for both lysozyme and BPN', most of the enzyme that was going to adsorb onto the model surface did so within ten seconds after injection. Nearly an order-of-magnitude more BPN' adsorbed on the hydrophobic Ge surface than the hydrophilic one, while lysozyme adsorbed somewhat more strongly to the hydrophilic Ge surface. Overnight, the lysozyme layer continued to increase in thickness, while BPN' maintained its initial coverage. The appearance of carboxylate bands in some of the adsorbed BPN' spectra suggests the occurrence of peptide bond hydrolysis. A Au/Pd coating on the CIRcle cell o-rings had a significant effect on the adsorption of BPN'. (This coating was applied in an attempt to eliminate interfering Teflon absorption bands.) An apparent electrochemical reaction occurred, involving BPN', Ge, Au/Pd, and the salt solution used to stabilize BPN'. The result of this reaction was enhanced adsorption of the enzyme around the coated o-rings, etching of the Ge IRE at the o-ring site, and some autolysis of the enzyme. No such reaction was observed with lysozyme.

  7. Model for Quantitative Evaluation of Enzyme Replacement Treatment

    Directory of Open Access Journals (Sweden)

    Radeva B.

    2009-12-01

    Full Text Available Gaucher disease is the most frequent lysosomal disorder. Its enzyme replacement treatment was the new progress of modern biotechnology, successfully used in the last years. The evaluation of optimal dose of each patient is important due to health and economical reasons. The enzyme replacement is the most expensive treatment. It must be held continuously and without interruption. Since 2001, the enzyme replacement therapy with Cerezyme*Genzyme was formally introduced in Bulgaria, but after some time it was interrupted for 1-2 months. The dose of the patients was not optimal. The aim of our work is to find a mathematical model for quantitative evaluation of ERT of Gaucher disease. The model applies a kind of software called "Statistika 6" via the input of the individual data of 5-year-old children having the Gaucher disease treated with Cerezyme. The output results of the model gave possibilities for quantitative evaluation of the individual trends in the development of the disease of each child and its correlation. On the basis of this results, we might recommend suitable changes in ERT.

  8. Incorporating direct marketing activity into latent attrition models

    NARCIS (Netherlands)

    Schweidel, David A.; Knox, George

    2013-01-01

    When defection is unobserved, latent attrition models provide useful insights about customer behavior and accurate forecasts of customer value. Yet extant models ignore direct marketing efforts. Response models incorporate the effects of direct marketing, but because they ignore latent attrition,

  9. Coupled enzyme reactions performed in heterogeneous reaction media: experiments and modeling for glucose oxidase and horseradish peroxidase in a PEG/citrate aqueous two-phase system.

    Science.gov (United States)

    Aumiller, William M; Davis, Bradley W; Hashemian, Negar; Maranas, Costas; Armaou, Antonios; Keating, Christine D

    2014-03-06

    The intracellular environment in which biological reactions occur is crowded with macromolecules and subdivided into microenvironments that differ in both physical properties and chemical composition. The work described here combines experimental and computational model systems to help understand the consequences of this heterogeneous reaction media on the outcome of coupled enzyme reactions. Our experimental model system for solution heterogeneity is a biphasic polyethylene glycol (PEG)/sodium citrate aqueous mixture that provides coexisting PEG-rich and citrate-rich phases. Reaction kinetics for the coupled enzyme reaction between glucose oxidase (GOX) and horseradish peroxidase (HRP) were measured in the PEG/citrate aqueous two-phase system (ATPS). Enzyme kinetics differed between the two phases, particularly for the HRP. Both enzymes, as well as the substrates glucose and H2O2, partitioned to the citrate-rich phase; however, the Amplex Red substrate necessary to complete the sequential reaction partitioned strongly to the PEG-rich phase. Reactions in ATPS were quantitatively described by a mathematical model that incorporated measured partitioning and kinetic parameters. The model was then extended to new reaction conditions, i.e., higher enzyme concentration. Both experimental and computational results suggest mass transfer across the interface is vital to maintain the observed rate of product formation, which may be a means of metabolic regulation in vivo. Although outcomes for a specific system will depend on the particulars of the enzyme reactions and the microenvironments, this work demonstrates how coupled enzymatic reactions in complex, heterogeneous media can be understood in terms of a mathematical model.

  10. Dynamic relationships between microbial biomass, respiration, inorganic nutrients and enzyme activities: informing enzyme based decomposition models

    Directory of Open Access Journals (Sweden)

    Daryl L Moorhead

    2013-08-01

    Full Text Available We re-examined data from a recent litter decay study to determine if additional insights could be gained to inform decomposition modeling. Rinkes et al. (2013 conducted 14-day laboratory incubations of sugar maple (Acer saccharum or white oak (Quercus alba leaves, mixed with sand (0.4% organic C content or loam (4.1% organic C. They measured microbial biomass C, carbon dioxide efflux, soil ammonium, nitrate, and phosphate concentrations, and β-glucosidase (BG, β-N-acetyl-glucosaminidase (NAG, and acid phosphatase (AP activities on days 1, 3, and 14. Analyses of relationships among variables yielded different insights than original analyses of individual variables. For example, although respiration rates per g soil were higher for loam than sand, rates per g soil C were actually higher for sand than loam, and rates per g microbial C showed little difference between treatments. Microbial biomass C peaked on day 3 when biomass-specific activities of enzymes were lowest, suggesting uptake of litter C without extracellular hydrolysis. This result refuted a common model assumption that all enzyme production is constitutive and thus proportional to biomass, and/or indicated that part of litter decay is independent of enzyme activity. The length and angle of vectors defined by ratios of enzyme activities (BG/NAG versus BG/AP represent relative microbial investments in C (length, and N and P (angle acquiring enzymes. Shorter lengths on day 3 suggested low C limitation, whereas greater lengths on day 14 suggested an increase in C limitation with decay. The soils and litter in this study generally had stronger P limitation (angles > 45˚. Reductions in vector angles to < 45˚ for sand by day 14 suggested a shift to N limitation. These relational variables inform enzyme-based models, and are usually much less ambiguous when obtained from a single study in which measurements were made on the same samples than when extrapolated from separate studies.

  11. Incorporating unnatural amino acids to engineer biocatalysts for industrial bioprocess applications.

    Science.gov (United States)

    Ravikumar, Yuvaraj; Nadarajan, Saravanan Prabhu; Hyeon Yoo, Tae; Lee, Chong-Soon; Yun, Hyungdon

    2015-12-01

    The bioprocess engineering with biocatalysts broadly spans its development and actual application of enzymes in an industrial context. Recently, both the use of bioprocess engineering and the development and employment of enzyme engineering techniques have been increasing rapidly. Importantly, engineering techniques that incorporate unnatural amino acids (UAAs) in vivo has begun to produce enzymes with greater stability and altered catalytic properties. Despite the growth of this technique, its potential value in bioprocess applications remains to be fully exploited. In this review, we explore the methodologies involved in UAA incorporation as well as ways to synthesize these UAAs. In addition, we summarize recent efforts to increase the yield of UAA engineered proteins in Escherichia coli and also the application of this tool in enzyme engineering. Furthermore, this protein engineering tool based on the incorporation of UAA can be used to develop immobilized enzymes that are ideal for bioprocess applications. Considering the potential of this tool and by exploiting these engineered enzymes, we expect the field of bioprocess engineering to open up new opportunities for biocatalysis in the near future. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Bioprospecting of Thermostable Cellulolytic Enzymes through Modeling and Virtual Screening Method

    Directory of Open Access Journals (Sweden)

    R. Navanietha Krishnaraj

    2017-04-01

    Full Text Available Cellulolytic enzymes are promising candidates for the use of cellulose in any bioprocess operations and for the disposal of the cellulosic wastes in an environmentally benign manner. Cellulases from thermophiles have the advantage of hydrolyzing cellulose at wider range of operating conditions unlike the normal enzymes. Herein we report the modeled structures of cellulolytic enzymes (endoglucanase, cellobiohydrolase and ß-glucosidase from a thermophilic bacterium,Clostridium thermocellumand their validation using Root Mean Square Deviation (RMSD and Ramachandran plot analyses. Further, the molecular interactions of the modeled enzyme with cellulose were analyzed using molecular docking technique. The results of molecular docking showed that the endoglucanase, cellobiohydrolase and ß-glucosidase had the binding affinities of -10.7, -9.0 and -10.8 kcal/mol, respectively. A correlation between the binding affinity of the endoglucanase with cellulose and the enzyme activity was also demonstrated. The results showed that the binding affinities of cellulases with cellulose could be used as a tool to assess the hydrolytic activity of cellulases. The results obtained could be used in virtual screening of cellulolytic enzymes based on the molecular interactions with the substrate, and aid in developing systems biology models of thermophiles for industrial biotechnology applications.

  13. Enzymes involved in cholesterol homeostasis in outer vs inner cortices of the guinea pig adrenal

    International Nuclear Information System (INIS)

    Brody, R.I.

    1988-01-01

    Adrenocortical cells require cholesterol for steroid hormone synthesis. Intracellular free cholesterol levels are maintained by the actions of three key enzymes: HMG CoA reductase, a rate limiting enzyme of cholesterol biosynthesis, acyl CoA:cholesterol acyltransferase (ACAT), which esterifies cholesterol to fatty acids, and cholesterol ester hydrolase (CEH), which releases stored cholesterol by clearing the ester bond. The guinea pig adrenal cortex, which can be separated into a lipid-rich outer zone and a lipid-poor inner zone, provides a good model in which to determine whether the morphological differences in these regions correlate with functional distinctions in enzymes of cholesterol homeostasis. These studies have shown that there are great differences in these enzymes in the outer and inner zones of the guinea pig adrenal cortex. The cholesterol-rich outer zone possesses greater activities of ACAT and CEH than the inner zone, and, in untreated animals, these enzymes are nearly maximally stimulated. Both zones had substantial levels of HMG CoA reductase, as measured by enzyme assay and ELISA, and these levels increased following ACTH stimulation. However, only the outer zone incorporated 14 C-acetate into steroids and cholesterol to any great degree in vitro, and only in this zone was incorporation increased following incubation of cultures with ACTH. The discrepancies between HMG CoA reductase levels and 14 C-acetate incorporation in the inner zone indicate that cholesterol synthesis must be regulated differently in this zone

  14. Evaluation of the energy efficiency of enzyme fermentation by mechanistic modeling.

    Science.gov (United States)

    Albaek, Mads O; Gernaey, Krist V; Hansen, Morten S; Stocks, Stuart M

    2012-04-01

    Modeling biotechnological processes is key to obtaining increased productivity and efficiency. Particularly crucial to successful modeling of such systems is the coupling of the physical transport phenomena and the biological activity in one model. We have applied a model for the expression of cellulosic enzymes by the filamentous fungus Trichoderma reesei and found excellent agreement with experimental data. The most influential factor was demonstrated to be viscosity and its influence on mass transfer. Not surprisingly, the biological model is also shown to have high influence on the model prediction. At different rates of agitation and aeration as well as headspace pressure, we can predict the energy efficiency of oxygen transfer, a key process parameter for economical production of industrial enzymes. An inverse relationship between the productivity and energy efficiency of the process was found. This modeling approach can be used by manufacturers to evaluate the enzyme fermentation process for a range of different process conditions with regard to energy efficiency. Copyright © 2011 Wiley Periodicals, Inc.

  15. True dose from incorporated activities. Models for internal dosimetry

    International Nuclear Information System (INIS)

    Breustedt, B.; Eschner, W.; Nosske, D.

    2012-01-01

    The assessment of doses after incorporation of radionuclides cannot use direct measurements of the doses, as for example dosimetry in external radiation fields. The only observables are activities in the body or in excretions. Models are used to calculate the doses based on the measured activities. The incorporated activities and the resulting doses can vary by more than seven orders of magnitude between occupational and medical exposures. Nevertheless the models and calculations applied in both cases are similar. Since the models for the different applications have been developed independently by ICRP and MIRD different terminologies have been used. A unified terminology is being developed. (orig.)

  16. Incorporating interfacial phenomena in solidification models

    Science.gov (United States)

    Beckermann, Christoph; Wang, Chao Yang

    1994-01-01

    A general methodology is available for the incorporation of microscopic interfacial phenomena in macroscopic solidification models that include diffusion and convection. The method is derived from a formal averaging procedure and a multiphase approach, and relies on the presence of interfacial integrals in the macroscopic transport equations. In a wider engineering context, these techniques are not new, but their application in the analysis and modeling of solidification processes has largely been overlooked. This article describes the techniques and demonstrates their utility in two examples in which microscopic interfacial phenomena are of great importance.

  17. High-Strain Rate Failure Modeling Incorporating Shear Banding and Fracture

    Science.gov (United States)

    2017-11-22

    High Strain Rate Failure Modeling Incorporating Shear Banding and Fracture The views, opinions and/or findings contained in this report are those of...SECURITY CLASSIFICATION OF: 1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND SUBTITLE 13. SUPPLEMENTARY NOTES 12. DISTRIBUTION AVAILIBILITY STATEMENT 6. AUTHORS...Report as of 05-Dec-2017 Agreement Number: W911NF-13-1-0238 Organization: Columbia University Title: High Strain Rate Failure Modeling Incorporating

  18. Incorporating the life course model into MCH nutrition leadership education and training programs.

    Science.gov (United States)

    Haughton, Betsy; Eppig, Kristen; Looney, Shannon M; Cunningham-Sabo, Leslie; Spear, Bonnie A; Spence, Marsha; Stang, Jamie S

    2013-01-01

    Life course perspective, social determinants of health, and health equity have been combined into one comprehensive model, the life course model (LCM), for strategic planning by US Health Resources and Services Administration's Maternal and Child Health Bureau. The purpose of this project was to describe a faculty development process; identify strategies for incorporation of the LCM into nutrition leadership education and training at the graduate and professional levels; and suggest broader implications for training, research, and practice. Nineteen representatives from 6 MCHB-funded nutrition leadership education and training programs and 10 federal partners participated in a one-day session that began with an overview of the models and concluded with guided small group discussions on how to incorporate them into maternal and child health (MCH) leadership training using obesity as an example. Written notes from group discussions were compiled and coded emergently. Content analysis determined the most salient themes about incorporating the models into training. Four major LCM-related themes emerged, three of which were about training: (1) incorporation by training grants through LCM-framed coursework and experiences for trainees, and similarly framed continuing education and skills development for professionals; (2) incorporation through collaboration with other training programs and state and community partners, and through advocacy; and (3) incorporation by others at the federal and local levels through policy, political, and prevention efforts. The fourth theme focused on anticipated challenges of incorporating the model in training. Multiple methods for incorporating the LCM into MCH training and practice are warranted. Challenges to incorporating include the need for research and related policy development.

  19. 75 FR 20265 - Airworthiness Directives; Liberty Aerospace Incorporated Model XL-2 Airplanes

    Science.gov (United States)

    2010-04-19

    ... Office, 1701 Columbia Avenue, College Park, Georgia 30337; telephone: (404) 474-5524; facsimile: (404... Airworthiness Directives; Liberty Aerospace Incorporated Model XL-2 Airplanes AGENCY: Federal Aviation...-08- 05, which applies to certain Liberty Aerospace Incorporated Model XL-2 airplanes. AD 2009-08-05...

  20. NRSA enzyme decomposition model data

    Data.gov (United States)

    U.S. Environmental Protection Agency — Microbial enzyme activities measured at more than 2000 US streams and rivers. These enzyme data were then used to predict organic matter decomposition and microbial...

  1. Modelling non-redox enzymes: Anaerobic and aerobic acetylene ...

    Indian Academy of Sciences (India)

    Administrator

    Modelling non-redox enzymes: Anaerobic and aerobic acetylene hydratase. SABYASACHI SARKAR. Department of Chemistry, Indian Institute of Technology, Kanpur 208 016,. India. Acetaldehyde is the first metabolite produced during acetylene degradation by bacteria either aerobically or anaerobically. Conversion of ...

  2. Modelling of different enzyme productions by solid-state fermentation on several agro-industrial residues.

    Science.gov (United States)

    Diaz, Ana Belen; Blandino, Ana; Webb, Colin; Caro, Ildefonso

    2016-11-01

    A simple kinetic model, with only three fitting parameters, for several enzyme productions in Petri dishes by solid-state fermentation is proposed in this paper, which may be a valuable tool for simulation of this type of processes. Basically, the model is able to predict temporal fungal enzyme production by solid-state fermentation on complex substrates, maximum enzyme activity expected and time at which these maxima are reached. In this work, several fermentations in solid state were performed in Petri dishes, using four filamentous fungi grown on different agro-industrial residues, measuring xylanase, exo-polygalacturonase, cellulose and laccase activities over time. Regression coefficients after fitting experimental data to the proposed model turned out to be quite high in all cases. In fact, these results are very interesting considering, on the one hand, the simplicity of the model and, on the other hand, that enzyme activities correspond to different enzymes, produced by different fungi on different substrates.

  3. A Numerical Procedure for Model Identifiability Analysis Applied to Enzyme Kinetics

    DEFF Research Database (Denmark)

    Daele, Timothy, Van; Van Hoey, Stijn; Gernaey, Krist

    2015-01-01

    The proper calibration of models describing enzyme kinetics can be quite challenging. In the literature, different procedures are available to calibrate these enzymatic models in an efficient way. However, in most cases the model structure is already decided on prior to the actual calibration...... and Pronzato (1997) and which can be easily set up for any type of model. In this paper the proposed approach is applied to the forward reaction rate of the enzyme kinetics proposed by Shin and Kim(1998). Structural identifiability analysis showed that no local structural model problems were occurring......) identifiability problems. By using the presented approach it is possible to detect potential identifiability problems and avoid pointless calibration (and experimental!) effort....

  4. A Refined Model for the Structure of Acireductone Dioxygenase from Klebsiella ATCC 8724 Incorporating Residual Dipolar Couplings

    Energy Technology Data Exchange (ETDEWEB)

    Pochapsky, Thomas C., E-mail: pochapsk@brandeis.edu; Pochapsky, Susan S.; Ju Tingting [Brandeis University, Department of Chemistry (United States); Hoefler, Chris [Brandeis University, Department of Biochemistry (United States); Liang Jue [Brandeis University, Department of Chemistry (United States)

    2006-02-15

    Acireductone dioxygenase (ARD) from Klebsiella ATCC 8724 is a metalloenzyme that is capable of catalyzing different reactions with the same substrates (acireductone and O{sub 2}) depending upon the metal bound in the active site. A model for the solution structure of the paramagnetic Ni{sup 2+}-containing ARD has been refined using residual dipolar couplings (RDCs) measured in two media. Additional dihedral restraints based on chemical shift (TALOS) were included in the refinement, and backbone structure in the vicinity of the active site was modeled from a crystallographic structure of the mouse homolog of ARD. The incorporation of residual dipolar couplings into the structural refinement alters the relative orientations of several structural features significantly, and improves local secondary structure determination. Comparisons between the solution structures obtained with and without RDCs are made, and structural similarities and differences between mouse and bacterial enzymes are described. Finally, the biological significance of these differences is considered.

  5. A coarse-grained model for synergistic action of multiple enzymes on cellulose

    Directory of Open Access Journals (Sweden)

    Asztalos Andrea

    2012-08-01

    Full Text Available Abstract Background Degradation of cellulose to glucose requires the cooperative action of three classes of enzymes, collectively known as cellulases. Endoglucanases randomly bind to cellulose surfaces and generate new chain ends by hydrolyzing β-1,4-D-glycosidic bonds. Exoglucanases bind to free chain ends and hydrolyze glycosidic bonds in a processive manner releasing cellobiose units. Then, β-glucosidases hydrolyze soluble cellobiose to glucose. Optimal synergistic action of these enzymes is essential for efficient digestion of cellulose. Experiments show that as hydrolysis proceeds and the cellulose substrate becomes more heterogeneous, the overall degradation slows down. As catalysis occurs on the surface of crystalline cellulose, several factors affect the overall hydrolysis. Therefore, spatial models of cellulose degradation must capture effects such as enzyme crowding and surface heterogeneity, which have been shown to lead to a reduction in hydrolysis rates. Results We present a coarse-grained stochastic model for capturing the key events associated with the enzymatic degradation of cellulose at the mesoscopic level. This functional model accounts for the mobility and action of a single cellulase enzyme as well as the synergy of multiple endo- and exo-cellulases on a cellulose surface. The quantitative description of cellulose degradation is calculated on a spatial model by including free and bound states of both endo- and exo-cellulases with explicit reactive surface terms (e.g., hydrogen bond breaking, covalent bond cleavages and corresponding reaction rates. The dynamical evolution of the system is simulated by including physical interactions between cellulases and cellulose. Conclusions Our coarse-grained model reproduces the qualitative behavior of endoglucanases and exoglucanases by accounting for the spatial heterogeneity of the cellulose surface as well as other spatial factors such as enzyme crowding. Importantly, it captures

  6. A model of extracellular enzymes in free-living microbes: which strategy pays off?

    Science.gov (United States)

    Traving, Sachia J; Thygesen, Uffe H; Riemann, Lasse; Stedmon, Colin A

    2015-11-01

    An initial modeling approach was applied to analyze how a single, nonmotile, free-living, heterotrophic bacterial cell may optimize the deployment of its extracellular enzymes. Free-living cells live in a dilute and complex substrate field, and to gain enough substrate, their extracellular enzymes must be utilized efficiently. The model revealed that surface-attached and free enzymes generate unique enzyme and substrate fields, and each deployment strategy has distinctive advantages. For a solitary cell, surface-attached enzymes are suggested to be the most cost-efficient strategy. This strategy entails potential substrates being reduced to very low concentrations. Free enzymes, on the other hand, generate a radically different substrate field, which suggests significant benefits for the strategy if free cells engage in social foraging or experience high substrate concentrations. Swimming has a slight positive effect for the attached-enzyme strategy, while the effect is negative for the free-enzyme strategy. The results of this study suggest that specific dissolved organic compounds in the ocean likely persist below a threshold concentration impervious to biological utilization. This could help explain the persistence and apparent refractory state of oceanic dissolved organic matter (DOM). Microbial extracellular enzyme strategies, therefore, have important implications for larger-scale processes, such as shaping the role of DOM in ocean carbon sequestration. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  7. Modelling Fungal Fermentations for Enzyme Production

    DEFF Research Database (Denmark)

    Albæk, Mads Orla; Gernaey, Krist; Hansen, Morten S.

    We have developed a process model of fungal fed-batch fermentations for enzyme production. In these processes, oxygen transfer rate is limiting and controls the substrate feeding rate. The model has been shown to describe cultivations of both Aspergillus oryzae and Trichoderma reesei strains in 550......L stirred tank pilot plant reactors well. For each strain, 8 biological parameters are needed as well as a correlation of viscosity, as viscosity has a major influence on oxygen transfer. The parameters were measured averages of at least 9 batches for each strain. The model is successfully able...... to cover a wide range of process conditions (0.3-2 vvm of aeration, 0.2-10.0 kW/m3 of specific agitation power input, and 0.1-1.3 barg head space pressure). Uncertainty and sensitivity analysis have shown that the uncertainty of the model is mainly due to difficulties surrounding the estimation...

  8. A model of extracellular enzymes in free-living microbes: Which strategy pays off?

    DEFF Research Database (Denmark)

    Traving, Sachia J; Thygesen, Uffe Høgsbro; Riemann, Lasse

    2015-01-01

    a slight positive effect for the attached-enzyme strategy, while the effect is negative for the free-enzyme strategy. The results of this study suggest that specific dissolved organic compounds in the ocean likely persist below a threshold concentration impervious to biological utilization. This could help...... must be utilized efficiently. The model revealed that surface-attached and free enzymes generate unique enzyme and substrate fields, and each deployment strategy has distinctive advantages. For a solitary cell, surface-attached enzymes are suggested to be the most cost-efficient strategy. This strategy...

  9. Hybrid quantum and classical methods for computing kinetic isotope effects of chemical reactions in solutions and in enzymes.

    Science.gov (United States)

    Gao, Jiali; Major, Dan T; Fan, Yao; Lin, Yen-Lin; Ma, Shuhua; Wong, Kin-Yiu

    2008-01-01

    A method for incorporating quantum mechanics into enzyme kinetics modeling is presented. Three aspects are emphasized: 1) combined quantum mechanical and molecular mechanical methods are used to represent the potential energy surface for modeling bond forming and breaking processes, 2) instantaneous normal mode analyses are used to incorporate quantum vibrational free energies to the classical potential of mean force, and 3) multidimensional tunneling methods are used to estimate quantum effects on the reaction coordinate motion. Centroid path integral simulations are described to make quantum corrections to the classical potential of mean force. In this method, the nuclear quantum vibrational and tunneling contributions are not separable. An integrated centroid path integral-free energy perturbation and umbrella sampling (PI-FEP/UM) method along with a bisection sampling procedure was summarized, which provides an accurate, easily convergent method for computing kinetic isotope effects for chemical reactions in solution and in enzymes. In the ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT), these three aspects of quantum mechanical effects can be individually treated, providing useful insights into the mechanism of enzymatic reactions. These methods are illustrated by applications to a model process in the gas phase, the decarboxylation reaction of N-methyl picolinate in water, and the proton abstraction and reprotonation process catalyzed by alanine racemase. These examples show that the incorporation of quantum mechanical effects is essential for enzyme kinetics simulations.

  10. Self-Healing Textile: Enzyme Encapsulated Layer-by-Layer Structural Proteins.

    Science.gov (United States)

    Gaddes, David; Jung, Huihun; Pena-Francesch, Abdon; Dion, Genevieve; Tadigadapa, Srinivas; Dressick, Walter J; Demirel, Melik C

    2016-08-10

    Self-healing materials, which enable an autonomous repair response to damage, are highly desirable for the long-term reliability of woven or nonwoven textiles. Polyelectrolyte layer-by-layer (LbL) films are of considerable interest as self-healing coatings due to the mobility of the components comprising the film. In this work mechanically stable self-healing films were fabricated through construction of a polyelectrolyte LbL film containing squid ring teeth (SRT) proteins. SRTs are structural proteins with unique self-healing properties and high elastic modulus in both dry and wet conditions (>2 GPa) due to their semicrystalline architecture. We demonstrate LbL construction of multilayers containing native and recombinant SRT proteins capable of self-healing defects. Additionally, we show these films are capable of utilizing functional biomolecules by incorporating an enzyme into the SRT multilayer. Urease was chosen as a model enzyme of interest to test its activity via fluorescence assay. Successful construction of the SRT films demonstrates the use of mechanically stable self-healing coatings, which can incorporate biomolecules for more complex protective functionalities for advanced functional fabrics.

  11. Modeling the Interaction between β-Amyloid Aggregates and Choline Acetyltransferase Activity and Its Relation with Cholinergic Dysfunction through Two-Enzyme/Two-Compartment Model

    Directory of Open Access Journals (Sweden)

    Hedia Fgaier

    2015-01-01

    Full Text Available The effect of β-amyloid aggregates on activity of choline acetyltransferase (ChAT which is responsible for synthesizing acetylcholine (ACh in human brain is investigated through the two-enzyme/two-compartment (2E2C model where the presynaptic neuron is considered as compartment 1 while both the synaptic cleft and the postsynaptic neuron are considered as compartment 2 through suggesting three different kinetic mechanisms for the inhibition effect. It is found that the incorporation of ChAT inhibition by β-amyloid aggregates into the 2E2C model is able to yield dynamic solutions for concentrations of generated β-amyloid, ACh, choline, acetate, and pH in addition to the rates of ACh synthesis and ACh hydrolysis in compartments 1 and 2. It is observed that ChAT activity needs a high concentration of β-amyloid aggregates production rate. It is found that ChAT activity is reduced significantly when neurons are exposed to high levels of β-amyloid aggregates leading to reduction in levels of ACh which is one of the most significant physiological symptoms of AD. Furthermore, the system of ACh neurocycle is dominated by the oscillatory behavior when ChAT enzyme is completely inhibited by β-amyloid. It is observed that the direct inactivation of ChAT by β-amyloid aggregates may be a probable mechanism contributing to the development of AD.

  12. Evaluation of the energy efficiency of enzyme fermentation by mechanistic modeling

    DEFF Research Database (Denmark)

    Albaek, Mads O.; Gernaey, Krist V.; Hansen, Morten S.

    2012-01-01

    Modeling biotechnological processes is key to obtaining increased productivity and efficiency. Particularly crucial to successful modeling of such systems is the coupling of the physical transport phenomena and the biological activity in one model. We have applied a model for the expression of ce...... was found. This modeling approach can be used by manufacturers to evaluate the enzyme fermentation process for a range of different process conditions with regard to energy efficiency.......Modeling biotechnological processes is key to obtaining increased productivity and efficiency. Particularly crucial to successful modeling of such systems is the coupling of the physical transport phenomena and the biological activity in one model. We have applied a model for the expression...... of cellulosic enzymes by the filamentous fungus Trichoderma reesei and found excellent agreement with experimental data. The most influential factor was demonstrated to be viscosity and its influence on mass transfer. Not surprisingly, the biological model is also shown to have high influence on the model...

  13. Production of specifically structured lipids by enzymatic interesterification in a pilot enzyme bed reactor: process optimization by response surface methodology

    DEFF Research Database (Denmark)

    Xu, Xuebing; Mu, Huiling; Høy, Carl-Erik

    1999-01-01

    Pilot production of specifically structured lipids by Lipozyme IM-catalyzed interesterification was carried out in a continuous enzyme bed reactor without the use of solvent. Medium chain triacylglycerols and oleic acid were used as model substrates. Response surface methodology was applied...... and the production of mono-incorporated and di-incorporated structured lipids with multiple regression and backward elimination. The coefficient of determination (R2) for the incorporation was 0.93, and that for the di-incorporated products was 0.94. The optimal conditions were flow rate, 2 ml/min; temperature, 65...

  14. Immobilized enzyme studies in a microscale bioreactor.

    Science.gov (United States)

    Jones, Francis; Forrest, Scott; Palmer, Jim; Lu, Zonghuan; Elmore, John; Elmore, Bill B

    2004-01-01

    Novel microreactors with immobilized enzymes were fabricated using both silicon and polymer-based microfabrication techniques. The effectiveness of these reactors was examined along with their behavior over time. Urease enzyme was successfully incorporated into microchannels of a polymeric matrix of polydimethylsiloxane and through layer-bylayer self-assembly techniques onto silicon. The fabricated microchannels had cross-sectional dimensions ranging from tens to hundreds of micrometers in width and height. The experimental results for continuous-flow microreactors are reported for the conversion of urea to ammonia by urease enzyme. Urea conversions of >90% were observed.

  15. Steric and thermodynamic limits of design for the incorporation of large unnatural amino acids in aminoacyl-tRNA synthetase enzymes.

    Science.gov (United States)

    Armen, Roger S; Schiller, Stefan M; Brooks, Charles L

    2010-06-01

    Orthogonal aminoacyl-tRNA synthetase/tRNA pairs from archaea have been evolved to facilitate site specific in vivo incorporation of unnatural amino acids into proteins in Escherichia coli. Using this approach, unnatural amino acids have been successfully incorporated with high translational efficiency and fidelity. In this study, CHARMM-based molecular docking and free energy calculations were used to evaluate rational design of specific protein-ligand interactions for aminoacyl-tRNA synthetases. A series of novel unnatural amino acid ligands were docked into the p-benzoyl-L-phenylalanine tRNA synthetase, which revealed that the binding pocket of the enzyme does not provide sufficient space for significantly larger ligands. Specific binding site residues were mutated to alanine to create additional space to accommodate larger target ligands, and then mutations were introduced to improve binding free energy. This approach was used to redesign binding sites for several different target ligands, which were then tested against the standard 20 amino acids to verify target specificity. Only the synthetase designed to bind Man-alpha-O-Tyr was predicted to be sufficiently selective for the target ligand and also thermodynamically stable. Our study suggests that extensive redesign of the tRNA synthatase binding pocket for large bulky ligands may be quite thermodynamically unfavorable.

  16. Incorporation of the capillary hysteresis model HYSTR into the numerical code TOUGH

    International Nuclear Information System (INIS)

    Niemi, A.; Bodvarsson, G.S.; Pruess, K.

    1991-11-01

    As part of the work performed to model flow in the unsaturated zone at Yucca Mountain Nevada, a capillary hysteresis model has been developed. The computer program HYSTR has been developed to compute the hysteretic capillary pressure -- liquid saturation relationship through interpolation of tabulated data. The code can be easily incorporated into any numerical unsaturated flow simulator. A complete description of HYSTR, including a brief summary of the previous hysteresis literature, detailed description of the program, and instructions for its incorporation into a numerical simulator are given in the HYSTR user's manual (Niemi and Bodvarsson, 1991a). This report describes the incorporation of HYSTR into the numerical code TOUGH (Transport of Unsaturated Groundwater and Heat; Pruess, 1986). The changes made and procedures for the use of TOUGH for hysteresis modeling are documented

  17. A model-based framework for design of intensified enzyme-based processes

    DEFF Research Database (Denmark)

    Román-Martinez, Alicia

    This thesis presents a generic and systematic model-based framework to design intensified enzyme-based processes. The development of the presented methodology was motivated by the needs of the bio-based industry for a more systematic approach to achieve intensification in its production plants...... in enzyme-based processes which have found significant application in the pharmaceutical, food, and renewable fuels sector. The framework uses model-based strategies for (bio)-chemical process design and optimization, including the use of a superstructure to generate all potential reaction......(s)-separation(s) options according to a desired performance criteria and a generic mathematical model represented by the superstructure to derive the specific models corresponding to a specific process option. In principle, three methods of intensification of bioprocess are considered in this thesis: 1. enzymatic one...

  18. Metabolic Models of Protein Allocation Call for the Kinetome

    DEFF Research Database (Denmark)

    Nilsson, Avlant; Nielsen, Jens; Palsson, Bernhard

    2017-01-01

    The flux of metabolites in the living cell depend on enzyme activities. Recently, many metabolic phenotypes have been explained by computer models that incorporate enzyme activity data. To move further, the scientific community needs to measure the kinetics of all enzymes in a systematic way....

  19. Cellulase enzyme: Homology modeling, binding site identification and molecular docking

    Science.gov (United States)

    Selvam, K.; Senbagam, D.; Selvankumar, T.; Sudhakar, C.; Kamala-Kannan, S.; Senthilkumar, B.; Govarthanan, M.

    2017-12-01

    Cellulase is an enzyme that degrades the linear polysaccharide like cellulose into glucose by breaking the β-1,4- glycosidic bonds. These enzymes are the third largest enzymes with a great potential towards the ethanol production and play a vital role in degrading the biomass. The production of ethanol depends upon the ability of the cellulose to utilize the wide range of substrates. In this study, the 3D structure of cellulase from Acinetobacter sp. was modeled by using Modeler 9v9 and validated by Ramachandran plot. The accuracy of the predicted 3D structure was checked using Ramachandran plot analysis showed that 81.1% in the favored region, compatibility of an atomic model (3D) with amino acid sequence (1D) for the model was observed as 78.21% and 49.395% for Verify 3D and ERRAT at SAVES server. As the binding efficacy with the substrate might suggests the choice of the substrate as carbon and nitrogen sources, the cellobiose, cellotetraose, cellotetriose and laminaribiose were employed in the docking studies. The docking of cellobiose, cellotetraose, cellotetriose and laminaribiose with cellulase exhibited the binding energy of -6.1523 kJ/mol, -7.8759 kJ/mol,-6.1590 kJ/mol and -6.7185 kJ/mol, respectively. These docking studies revealed that cellulase has the greater potential towards the cellotetraose as a substrate for the high yield of ethanol.

  20. Model for how type I restriction enzymes select cleavage sites in DNA

    International Nuclear Information System (INIS)

    Studier, F.W.; Bandyopadhyay, P.K.

    1988-01-01

    Under appropriate conditions, digestion of phage T7 DNA by the type I restriction enzyme EcoK produces an orderly progression of discrete DNA fragments. All details of the fragmentation pattern can be explained on the basis of the known properties of type I enzymes, together with two further assumptions: (i) in the ATP-stimulated translocation reaction, the enzyme bound at the recognition sequence translocates DNA toward itself from both directions simultaneously; and (ii) when translocation causes neighboring enzymes to meet, they cut the DNA between them. The kinetics of digestion at 37 degree C indicates that the rate of translocation of DNA from each side of a bound enzyme is about 200 base pairs per second, and the cuts are completed within 15-25 sec of the time neighboring enzymes meet. The resulting DNA fragments each contain a single recognition site with an enzyme (or subunit) remaining bound to it. At high enzyme concentrations, such fragments can bu further degraded, apparently by cooperation between the specifically bound and excess enzymes. This model is consistent with a substantial body of previous work on the nuclease activity of EcoB and EcoK, and it explains in a simple way how cleavage sites are selected

  1. Modeling cutinase enzyme regulation in polyethylene terepthalate plastic biodegradation

    International Nuclear Information System (INIS)

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

    2016-01-01

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

  2. Modeling cutinase enzyme regulation in polyethylene terepthalate plastic biodegradation

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-04-06

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

  3. Modeling cutinase enzyme regulation in polyethylene terepthalate plastic biodegradation

    Science.gov (United States)

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

    2016-04-01

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

  4. Modified lingguizhugan decoction incorporated with dietary restriction and exercise ameliorates hyperglycemia, hyperlipidemia and hypertension in a rat model of the metabolic syndrome.

    Science.gov (United States)

    Yao, Limei; Wei, Jingjing; Shi, Si; Guo, Kunbin; Wang, Xiangyu; Wang, Qi; Chen, Dingsheng; Li, Weirong

    2017-02-28

    Modified Lingguizhugan Decoction (MLD) came from famous Chinese medicine Linggui Zhugan Decoction. The MLD is used for the treatment of metabolic syndrome in the clinical setting. Our study focuses on the comprehensive treatment of MLD incorporated with dietary restriction and exercise in a rat model of the metabolic syndrome (MS). Rats were divided into five groups: control group (Cont), high-fat diet group (HFD), high-fat diet incorporated with dietary restriction group (HFD-DR), exercise incorporated with dietary restriction group (HFD-DR-Ex) and MLD incorporated with dietary restriction and exercise group (HFD-DR-Ex-MLD). Treatments were conducted for 1 week after feeding high-fat diet for 12 weeks. The effects of treatments on high fat diet-induced obesity, hyperglycemia, hyperlipidemia, hypertension, hepatic injury and insulin resistance in rats of MS were examined. In addition, the tumor necrosis factor-α (TNF-α), leptin and protein kinase B (PKB) in rats serum and liver were also examined by enzyme-linked immunosorbent assay (ELISA). After a week's intervention by dietary restriction, dietary restriction incorporated with exercise or MLD, compared with HFD rats, the relative weight of liver and fat, levels of triglyceride, total cholesterol, low-density lipoprotein, free fatty acid, aspartate aminotransferase, glutamic-pyruvic transaminase and alkaline phosphatase, insulin, were significantly decreased (p exercise treatment exhibit effects in alleviating high-fat diet-induced obesity, hyperglycemia, hyperlipidemia, hypertension, hepatic injury and insulin resistance, which are possibly due to the down-regulation of TNF-α, leptin and PKB.

  5. Modeling the reactions catalyzed by coenzyme B12-dependent enzymes.

    Science.gov (United States)

    Sandala, Gregory M; Smith, David M; Radom, Leo

    2010-05-18

    catalysis depends on a delicate energy balance. Radical-based enzyme reactions are often difficult to probe experimentally, so theoretical investigations have a particularly valuable role to play in their study. Our research demonstrates that a small-model approach can provide important and revealing insights into the mechanism of action of AdoCbl-dependent enzymes.

  6. Artificial Enzymes, "Chemzymes"

    DEFF Research Database (Denmark)

    Bjerre, Jeannette; Rousseau, Cyril Andre Raphaël; Pedersen, Lavinia Georgeta M

    2008-01-01

    Enzymes have fascinated scientists since their discovery and, over some decades, one aim in organic chemistry has been the creation of molecules that mimic the active sites of enzymes and promote catalysis. Nevertheless, even today, there are relatively few examples of enzyme models that successf......Enzymes have fascinated scientists since their discovery and, over some decades, one aim in organic chemistry has been the creation of molecules that mimic the active sites of enzymes and promote catalysis. Nevertheless, even today, there are relatively few examples of enzyme models...... that successfully perform Michaelis-Menten catalysis under enzymatic conditions (i.e., aqueous medium, neutral pH, ambient temperature) and for those that do, very high rate accelerations are seldomly seen. This review will provide a brief summary of the recent developments in artificial enzymes, so called...... "Chemzymes", based on cyclodextrins and other molecules. Only the chemzymes that have shown enzyme-like activity that has been quantified by different methods will be mentioned. This review will summarize the work done in the field of artificial glycosidases, oxidases, epoxidases, and esterases, as well...

  7. Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints

    DEFF Research Database (Denmark)

    Sanchez, Benjamin J.; Zhang, Xi-Cheng; Nilsson, Avlant

    2017-01-01

    , which act as limitations on metabolic fluxes, are not taken into account. Here, we present GECKO, a method that enhances a GEM to account for enzymes as part of reactions, thereby ensuring that each metabolic flux does not exceed its maximum capacity, equal to the product of the enzyme's abundance...... and turnover number. We applied GECKO to a Saccharomyces cerevisiae GEM and demonstrated that the new model could correctly describe phenotypes that the previous model could not, particularly under high enzymatic pressure conditions, such as yeast growing on different carbon sources in excess, coping...... with stress, or overexpressing a specific pathway. GECKO also allows to directly integrate quantitative proteomics data; by doing so, we significantly reduced flux variability of the model, in over 60% of metabolic reactions. Additionally, the model gives insight into the distribution of enzyme usage between...

  8. A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosis

    Directory of Open Access Journals (Sweden)

    Reifman Jaques

    2009-09-01

    Full Text Available Abstract Background Because metabolism is fundamental in sustaining microbial life, drugs that target pathogen-specific metabolic enzymes and pathways can be very effective. In particular, the metabolic challenges faced by intracellular pathogens, such as Mycobacterium tuberculosis, residing in the infected host provide novel opportunities for therapeutic intervention. Results We developed a mathematical framework to simulate the effects on the growth of a pathogen when enzymes in its metabolic pathways are inhibited. Combining detailed models of enzyme kinetics, a complete metabolic network description as modeled by flux balance analysis, and a dynamic cell population growth model, we quantitatively modeled and predicted the dose-response of the 3-nitropropionate inhibitor on the growth of M. tuberculosis in a medium whose carbon source was restricted to fatty acids, and that of the 5'-O-(N-salicylsulfamoyl adenosine inhibitor in a medium with low-iron concentration. Conclusion The predicted results quantitatively reproduced the experimentally measured dose-response curves, ranging over three orders of magnitude in inhibitor concentration. Thus, by allowing for detailed specifications of the underlying enzymatic kinetics, metabolic reactions/constraints, and growth media, our model captured the essential chemical and biological factors that determine the effects of drug inhibition on in vitro growth of M. tuberculosis cells.

  9. Random-walk enzymes

    Science.gov (United States)

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

    2015-09-01

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

  10. Incorporating neurophysiological concepts in mathematical thermoregulation models

    Science.gov (United States)

    Kingma, Boris R. M.; Vosselman, M. J.; Frijns, A. J. H.; van Steenhoven, A. A.; van Marken Lichtenbelt, W. D.

    2014-01-01

    Skin blood flow (SBF) is a key player in human thermoregulation during mild thermal challenges. Various numerical models of SBF regulation exist. However, none explicitly incorporates the neurophysiology of thermal reception. This study tested a new SBF model that is in line with experimental data on thermal reception and the neurophysiological pathways involved in thermoregulatory SBF control. Additionally, a numerical thermoregulation model was used as a platform to test the function of the neurophysiological SBF model for skin temperature simulation. The prediction-error of the SBF-model was quantified by root-mean-squared-residual (RMSR) between simulations and experimental measurement data. Measurement data consisted of SBF (abdomen, forearm, hand), core and skin temperature recordings of young males during three transient thermal challenges (1 development and 2 validation). Additionally, ThermoSEM, a thermoregulation model, was used to simulate body temperatures using the new neurophysiological SBF-model. The RMSR between simulated and measured mean skin temperature was used to validate the model. The neurophysiological model predicted SBF with an accuracy of RMSR human thermoregulation models can be equipped with SBF control functions that are based on neurophysiology without loss of performance. The neurophysiological approach in modelling thermoregulation is favourable over engineering approaches because it is more in line with the underlying physiology.

  11. Incorporation of composite defects from ultrasonic NDE into CAD and FE models

    Science.gov (United States)

    Bingol, Onur Rauf; Schiefelbein, Bryan; Grandin, Robert J.; Holland, Stephen D.; Krishnamurthy, Adarsh

    2017-02-01

    Fiber-reinforced composites are widely used in aerospace industry due to their combined properties of high strength and low weight. However, owing to their complex structure, it is difficult to assess the impact of manufacturing defects and service damage on their residual life. While, ultrasonic testing (UT) is the preferred NDE method to identify the presence of defects in composites, there are no reasonable ways to model the damage and evaluate the structural integrity of composites. We have developed an automated framework to incorporate flaws and known composite damage automatically into a finite element analysis (FEA) model of composites, ultimately aiding in accessing the residual life of composites and make informed decisions regarding repairs. The framework can be used to generate a layer-by-layer 3D structural CAD model of the composite laminates replicating their manufacturing process. Outlines of structural defects, such as delaminations, are automatically detected from UT of the laminate and are incorporated into the CAD model between the appropriate layers. In addition, the framework allows for direct structural analysis of the resulting 3D CAD models with defects by automatically applying the appropriate boundary conditions. In this paper, we show a working proof-of-concept for the composite model builder with capabilities of incorporating delaminations between laminate layers and automatically preparing the CAD model for structural analysis using a FEA software.

  12. Thermodynamic activity-based intrinsic enzyme kinetic sheds light on enzyme-solvent interactions.

    Science.gov (United States)

    Grosch, Jan-Hendrik; Wagner, David; Nistelkas, Vasilios; Spieß, Antje C

    2017-01-01

    The reaction medium has major impact on biocatalytic reaction systems and on their economic significance. To allow for tailored medium engineering, thermodynamic phenomena, intrinsic enzyme kinetics, and enzyme-solvent interactions have to be discriminated. To this end, enzyme reaction kinetic modeling was coupled with thermodynamic calculations based on investigations of the alcohol dehydrogenase from Lactobacillus brevis (LbADH) in monophasic water/methyl tert-butyl ether (MTBE) mixtures as a model solvent. Substrate concentrations and substrate thermodynamic activities were varied separately to identify the individual thermodynamic and kinetic effects on the enzyme activity. Microkinetic parameters based on concentration and thermodynamic activity were derived to successfully identify a positive effect of MTBE on the availability of the substrate to the enzyme, but a negative effect on the enzyme performance. In conclusion, thermodynamic activity-based kinetic modeling might be a suitable tool to initially curtail the type of enzyme-solvent interactions and thus, a powerful first step to potentially understand the phenomena that occur in nonconventional media in more detail. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:96-103, 2017. © 2016 American Institute of Chemical Engineers.

  13. Developing Baltic cod recruitment models II : Incorporation of environmental variability and species interaction

    DEFF Research Database (Denmark)

    Köster, Fritz; Hinrichsen, H.H.; St. John, Michael

    2001-01-01

    We investigate whether a process-oriented approach based on the results of field, laboratory, and modelling studies can be used to develop a stock-environment-recruitment model for Central Baltic cod (Gadus morhua). Based on exploratory statistical analysis, significant variables influencing...... cod in these areas, suggesting that key biotic and abiotic processes can be successfully incorporated into recruitment models....... survival of early life stages and varying systematically among spawning sites were incorporated into stock-recruitment models, first for major cod spawning sites and then combined for the entire Central Baltic. Variables identified included potential egg production by the spawning stock, abiotic conditions...

  14. Thymidine uptake, thymidine incorporation, and thymidine kinase activity in marine bacterium isolates

    International Nuclear Information System (INIS)

    Jeffrey, W.H.; Paul, J.H.

    1990-01-01

    One assumption made in bacterial production estimates from [ 3 H]thymidine incorporation is that all heterotrophic bacteria can incorporate exogenous thymidine into DNA. Heterotrophic marine bacterium isolates from Tampa Bay, Fla., Chesapeake Bay, Md., and a coral surface microlayer were examined for thymidine uptake (transport), thymidine incorporation, the presence of thymidine kinase genes, and thymidine kinase enzyme activity. Of the 41 isolates tested, 37 were capable of thymidine incorporation into DNA. The four organisms that could not incorporate thymidine also transported the thymidine poorly and lacked thymidine kinase activity. Attempts to detect thymidine kinase genes in the marine isolates by molecular probing with gene probes made from Escherichia coli and herpes simplex virus thymidine kinase genes proved unsuccessful. To determine if the inability to incorporate thymidine was due to the lack of thymidine kinase, one organism, Vibro sp. strain DI9, was transformed with a plasmid (pGQ3) that contained an E. coli thymidine kinase gene. Although enzyme assays indicated high levels of thymidine kinase activity in transformants, these cells still failed to incorporate exogenous thymidine into DNA or to transport thymidine into cells. These results indicate that the inability of certain marine bacteria to incorporate thymidine may not be solely due to the lack of thymidine kinase activity but may also be due to the absence of thymidine transport systems

  15. Modeling metabolic response to changes of enzyme amount in ...

    African Journals Online (AJOL)

    Jane

    2010-10-11

    Oct 11, 2010 ... In this work, we first introduced the enzyme parameter (ɑ) into the kinetic equations and consequently established an in silico glycolysis model of Saccharomyces cerevisiae in XML format (Figure 1), based on the work of Hynn et al. (2001). Equation 1 shows how the ɑis introduced into the kinetic equation.

  16. Mathematical modelling of enzyme synthesis during fermentations: the Q-functions

    Energy Technology Data Exchange (ETDEWEB)

    Nielsen, H K; Martiny, S C

    1981-01-01

    In modeling enzyme synthesis, the Q-function has been generalized to describe ordinary induction and repression as well as mixed induction-repression. The practical use of the Q-function as found in the literature was considered, especially the implications of applying fractional exponents.

  17. Investigations of the efficiency of enzyme production technologies using modelling tools

    DEFF Research Database (Denmark)

    Albæk, Mads Orla; Gernaey, Krist; Hansen, Morten Skov

    Growing markets and new innovative applications of industrial enzymes leads to increased interest in efficient production of these products. Most industrial enzymes are currently produced in traditional stirred tank reactors in submerged fed batch culture. The limiting parameter in such processes...... fermentations of the filamentous fungus Trichoderma reesei in 550litre pilot scale stirred tank reactors for a range of process conditions. Based on the experimental data a process model has been created, which satisfactory simulates the effect of the changing process conditions: Aeration rate, agitation speed...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-09-29

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

  19. A climatological model for risk computations incorporating site- specific dry deposition influences

    International Nuclear Information System (INIS)

    Droppo, J.G. Jr.

    1991-07-01

    A gradient-flux dry deposition module was developed for use in a climatological atmospheric transport model, the Multimedia Environmental Pollutant Assessment System (MEPAS). The atmospheric pathway model computes long-term average contaminant air concentration and surface deposition patterns surrounding a potential release site incorporating location-specific dry deposition influences. Gradient-flux formulations are used to incorporate site and regional data in the dry deposition module for this atmospheric sector-average climatological model. Application of these formulations provide an effective means of accounting for local surface roughness in deposition computations. Linkage to a risk computation module resulted in a need for separate regional and specific surface deposition computations. 13 refs., 4 figs., 2 tabs

  20. Incorporation of copper ions into crystals of T2 copper-depleted laccase from Botrytis aclada

    International Nuclear Information System (INIS)

    Osipov, E. M.; Polyakov, K. M.; Tikhonova, T. V.; Kittl, R.; Dorovatovskii, P.V.; Shleev, S. V.; Popov, V. O.; Ludwig, R.

    2015-01-01

    The restoration of the native form of laccase from B. aclada from the type 2 copper-depleted form of the enzyme was investigated. Copper ions were found to be incorporated into the active site after soaking the depleted enzyme in a Cu + -containing solution. Laccases belong to the class of multicopper oxidases catalyzing the oxidation of phenols accompanied by the reduction of molecular oxygen to water without the formation of hydrogen peroxide. The activity of laccases depends on the number of Cu atoms per enzyme molecule. The structure of type 2 copper-depleted laccase from Botrytis aclada has been solved previously. With the aim of obtaining the structure of the native form of the enzyme, crystals of the depleted laccase were soaked in Cu + - and Cu 2+ -containing solutions. Copper ions were found to be incorporated into the active site only when Cu + was used. A comparative analysis of the native and depleted forms of the enzymes was performed

  1. Methods improvements incorporated into the SAPHIRE ASP models

    International Nuclear Information System (INIS)

    Sattison, M.B.; Blackman, H.S.; Novack, S.D.; Smith, C.L.; Rasmuson, D.M.

    1994-01-01

    The Office for Analysis and Evaluation of Operational Data (AEOD) has sought the assistance of the Idaho National Engineering Laboratory (INEL) to make some significant enhancements to the SAPHIRE-based Accident Sequence Precursor (ASP) models recently developed by the INEL. The challenge of this project is to provide the features of a full-scale PRA within the framework of the simplified ASP models. Some of these features include: (1) uncertainty analysis addressing the standard PRA uncertainties and the uncertainties unique to the ASP models and methodology, (2) incorporation and proper quantification of individual human actions and the interaction among human actions, (3) enhanced treatment of common cause failures, and (4) extension of the ASP models to more closely mimic full-scale PRAs (inclusion of more initiators, explicitly modeling support system failures, etc.). This paper provides an overview of the methods being used to make the above improvements

  2. Methods improvements incorporated into the SAPHIRE ASP models

    International Nuclear Information System (INIS)

    Sattison, M.B.; Blackman, H.S.; Novack, S.D.

    1995-01-01

    The Office for Analysis and Evaluation of Operational Data (AEOD) has sought the assistance of the Idaho National Engineering Laboratory (INEL) to make some significant enhancements to the SAPHIRE-based Accident Sequence Precursor (ASP) models recently developed by the INEL. The challenge of this project is to provide the features of a full-scale PRA within the framework of the simplified ASP models. Some of these features include: (1) uncertainty analysis addressing the standard PRA uncertainties and the uncertainties unique to the ASP models and methods, (2) incorporation and proper quantification of individual human actions and the interaction among human actions, (3) enhanced treatment of common cause failures, and (4) extension of the ASP models to more closely mimic full-scale PRAs (inclusion of more initiators, explicitly modeling support system failures, etc.). This paper provides an overview of the methods being used to make the above improvements

  3. Restriction enzyme body doubles and PCR cloning: on the general use of type IIs restriction enzymes for cloning.

    Science.gov (United States)

    Tóth, Eszter; Huszár, Krisztina; Bencsura, Petra; Kulcsár, Péter István; Vodicska, Barbara; Nyeste, Antal; Welker, Zsombor; Tóth, Szilvia; Welker, Ervin

    2014-01-01

    The procedure described here allows the cloning of PCR fragments containing a recognition site of the restriction endonuclease (Type IIP) used for cloning in the sequence of the insert. A Type IIS endonuclease--a Body Double of the Type IIP enzyme--is used to generate the same protruding palindrome. Thus, the insert can be cloned to the Type IIP site of the vector without digesting the PCR product with the same Type IIP enzyme. We achieve this by incorporating the recognition site of a Type IIS restriction enzyme that cleaves the DNA outside of its recognition site in the PCR primer in such a way that the cutting positions straddle the desired overhang sequence. Digestion of the PCR product by the Body Double generates the required overhang. Hitherto the use of Type IIS restriction enzymes in cloning reactions has only been used for special applications, the approach presented here makes Type IIS enzymes as useful as Type IIP enzymes for general cloning purposes. To assist in finding Body Double enzymes, we summarised the available Type IIS enzymes which are potentially useful for Body Double cloning and created an online program (http://group.szbk.u-szeged.hu/welkergr/body_double/index.html) for the selection of suitable Body Double enzymes and the design of the appropriate primers.

  4. Computational enzyme design: transitioning from catalytic proteins to enzymes.

    Science.gov (United States)

    Mak, Wai Shun; Siegel, Justin B

    2014-08-01

    The widespread interest in enzymes stem from their ability to catalyze chemical reactions under mild and ecologically friendly conditions with unparalleled catalytic proficiencies. While thousands of naturally occurring enzymes have been identified and characterized, there are still numerous important applications for which there are no biological catalysts capable of performing the desired chemical transformation. In order to engineer enzymes for which there is no natural starting point, efforts using a combination of quantum chemistry and force-field based protein molecular modeling have led to the design of novel proteins capable of catalyzing chemical reactions not catalyzed by naturally occurring enzymes. Here we discuss the current status and potential avenues to pursue as the field of computational enzyme design moves forward. Published by Elsevier Ltd.

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

    Science.gov (United States)

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

    2013-12-01

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

  6. An electricity generation planning model incorporating demand response

    International Nuclear Information System (INIS)

    Choi, Dong Gu; Thomas, Valerie M.

    2012-01-01

    Energy policies that aim to reduce carbon emissions and change the mix of electricity generation sources, such as carbon cap-and-trade systems and renewable electricity standards, can affect not only the source of electricity generation, but also the price of electricity and, consequently, demand. We develop an optimization model to determine the lowest cost investment and operation plan for the generating capacity of an electric power system. The model incorporates demand response to price change. In a case study for a U.S. state, we show the price, demand, and generation mix implications of a renewable electricity standard, and of a carbon cap-and-trade policy with and without initial free allocation of carbon allowances. This study shows that both the demand moderating effects and the generation mix changing effects of the policies can be the sources of carbon emissions reductions, and also shows that the share of the sources could differ with different policy designs. The case study provides different results when demand elasticity is excluded, underscoring the importance of incorporating demand response in the evaluation of electricity generation policies. - Highlights: ► We develop an electric power system optimization model including demand elasticity. ► Both renewable electricity and carbon cap-and-trade policies can moderate demand. ► Both policies affect the generation mix, price, and demand for electricity. ► Moderated demand can be a significant source of carbon emission reduction. ► For cap-and-trade policies, initial free allowances change outcomes significantly.

  7. "Violent Intent Modeling: Incorporating Cultural Knowledge into the Analytical Process

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Nibbs, Faith G.

    2007-08-24

    While culture has a significant effect on the appropriate interpretation of textual data, the incorporation of cultural considerations into data transformations has not been systematic. Recognizing that the successful prevention of terrorist activities could hinge on the knowledge of the subcultures, Anthropologist and DHS intern Faith Nibbs has been addressing the need to incorporate cultural knowledge into the analytical process. In this Brown Bag she will present how cultural ideology is being used to understand how the rhetoric of group leaders influences the likelihood of their constituents to engage in violent or radicalized behavior, and how violent intent modeling can benefit from understanding that process.

  8. Design considerations of a hollow microneedle-optofluidic biosensing platform incorporating enzyme-linked assays

    Science.gov (United States)

    Ranamukhaarachchi, Sahan A.; Padeste, Celestino; Häfeli, Urs O.; Stoeber, Boris; Cadarso, Victor J.

    2018-02-01

    A hollow metallic microneedle is integrated with microfluidics and photonic components to form a microneedle-optofluidic biosensor suitable for therapeutic drug monitoring (TDM) in biological fluids, like interstitial fluid, that can be collected in a painless and minimally-invasive manner. The microneedle inner lumen surface is bio-functionalized to trap and bind target analytes on-site in a sample volume as small as 0.6 nl, and houses an enzyme-linked assay on its 0.06 mm2 wall. The optofluidic components are designed to rapidly quantify target analytes present in the sample and collected in the microneedle using a simple and sensitive absorbance scheme. This contribution describes how the biosensor components were optimized to detect in vitro streptavidin-horseradish peroxidase (Sav-HRP) as a model analyte over a large detection range (0-7.21 µM) and a very low limit of detection (60.2 nM). This biosensor utilizes the lowest analyte volume reported for TDM with microneedle technology, and presents significant avenues to improve current TDM methods for patients, by potentially eliminating blood draws for several drug candidates.

  9. Incorporating nitrogen fixing cyanobacteria in the global biogeochemical model HAMOCC

    Science.gov (United States)

    Paulsen, Hanna; Ilyina, Tatiana; Six, Katharina

    2015-04-01

    Nitrogen fixation by marine diazotrophs plays a fundamental role in the oceanic nitrogen and carbon cycle as it provides a major source of 'new' nitrogen to the euphotic zone that supports biological carbon export and sequestration. Since most global biogeochemical models include nitrogen fixation only diagnostically, they are not able to capture its spatial pattern sufficiently. Here we present the incorporation of an explicit, dynamic representation of diazotrophic cyanobacteria and the corresponding nitrogen fixation in the global ocean biogeochemical model HAMOCC (Hamburg Ocean Carbon Cycle model), which is part of the Max Planck Institute for Meteorology Earth system model (MPI-ESM). The parameterization of the diazotrophic growth is thereby based on available knowledge about the cyanobacterium Trichodesmium spp., which is considered as the most significant pelagic nitrogen fixer. Evaluation against observations shows that the model successfully reproduces the main spatial distribution of cyanobacteria and nitrogen fixation, covering large parts of the tropical and subtropical oceans. Besides the role of cyanobacteria in marine biogeochemical cycles, their capacity to form extensive surface blooms induces a number of bio-physical feedback mechanisms in the Earth system. The processes driving these interactions, which are related to the alteration of heat absorption, surface albedo and momentum input by wind, are incorporated in the biogeochemical and physical model of the MPI-ESM in order to investigate their impacts on a global scale. First preliminary results will be shown.

  10. Computational Biochemistry-Enzyme Mechanisms Explored.

    Science.gov (United States)

    Culka, Martin; Gisdon, Florian J; Ullmann, G Matthias

    2017-01-01

    Understanding enzyme mechanisms is a major task to achieve in order to comprehend how living cells work. Recent advances in biomolecular research provide huge amount of data on enzyme kinetics and structure. The analysis of diverse experimental results and their combination into an overall picture is, however, often challenging. Microscopic details of the enzymatic processes are often anticipated based on several hints from macroscopic experimental data. Computational biochemistry aims at creation of a computational model of an enzyme in order to explain microscopic details of the catalytic process and reproduce or predict macroscopic experimental findings. Results of such computations are in part complementary to experimental data and provide an explanation of a biochemical process at the microscopic level. In order to evaluate the mechanism of an enzyme, a structural model is constructed which can be analyzed by several theoretical approaches. Several simulation methods can and should be combined to get a reliable picture of the process of interest. Furthermore, abstract models of biological systems can be constructed combining computational and experimental data. In this review, we discuss structural computational models of enzymatic systems. We first discuss various models to simulate enzyme catalysis. Furthermore, we review various approaches how to characterize the enzyme mechanism both qualitatively and quantitatively using different modeling approaches. © 2017 Elsevier Inc. All rights reserved.

  11. Simulation of Forest Carbon Fluxes Using Model Incorporation and Data Assimilation

    OpenAIRE

    Min Yan; Xin Tian; Zengyuan Li; Erxue Chen; Xufeng Wang; Zongtao Han; Hong Sun

    2016-01-01

    This study improved simulation of forest carbon fluxes in the Changbai Mountains with a process-based model (Biome-BGC) using incorporation and data assimilation. Firstly, the original remote sensing-based MODIS MOD_17 GPP (MOD_17) model was optimized using refined input data and biome-specific parameters. The key ecophysiological parameters of the Biome-BGC model were determined through the Extended Fourier Amplitude Sensitivity Test (EFAST) sensitivity analysis. Then the optimized MOD_17 mo...

  12. INCORPORATING MULTIPLE OBJECTIVES IN PLANNING MODELS OF LOW-RESOURCE FARMERS

    OpenAIRE

    Flinn, John C.; Jayasuriya, Sisira; Knight, C. Gregory

    1980-01-01

    Linear goal programming provides a means of formally incorporating the multiple goals of a household into the analysis of farming systems. Using this approach, the set of plans which come as close as possible to achieving a set of desired goals under conditions of land and cash scarcity are derived for a Filipino tenant farmer. A challenge in making LGP models empirically operational is the accurate definition of the goals of the farm household being modelled.

  13. Enzyme Informatics

    Science.gov (United States)

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

    2012-01-01

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

  14. INCORPORATION OF MECHANISTIC INFORMATION IN THE ARSENIC PBPK MODEL DEVELOPMENT PROCESS

    Science.gov (United States)

    INCORPORATING MECHANISTIC INSIGHTS IN A PBPK MODEL FOR ARSENICElaina M. Kenyon, Michael F. Hughes, Marina V. Evans, David J. Thomas, U.S. EPA; Miroslav Styblo, University of North Carolina; Michael Easterling, Analytical Sciences, Inc.A physiologically based phar...

  15. Predictors of hepatitis B cure using gene therapy to deliver DNA cleavage enzymes: a mathematical modeling approach.

    Directory of Open Access Journals (Sweden)

    Joshua T Schiffer

    Full Text Available Most chronic viral infections are managed with small molecule therapies that inhibit replication but are not curative because non-replicating viral forms can persist despite decades of suppressive treatment. There are therefore numerous strategies in development to eradicate all non-replicating viruses from the body. We are currently engineering DNA cleavage enzymes that specifically target hepatitis B virus covalently closed circular DNA (HBV cccDNA, the episomal form of the virus that persists despite potent antiviral therapies. DNA cleavage enzymes, including homing endonucleases or meganucleases, zinc-finger nucleases (ZFNs, TAL effector nucleases (TALENs, and CRISPR-associated system 9 (Cas9 proteins, can disrupt specific regions of viral DNA. Because DNA repair is error prone, the virus can be neutralized after repeated cleavage events when a target sequence becomes mutated. DNA cleavage enzymes will be delivered as genes within viral vectors that enter hepatocytes. Here we develop mathematical models that describe the delivery and intracellular activity of DNA cleavage enzymes. Model simulations predict that high vector to target cell ratio, limited removal of delivery vectors by humoral immunity, and avid binding between enzyme and its DNA target will promote the highest level of cccDNA disruption. Development of de novo resistance to cleavage enzymes may occur if DNA cleavage and error prone repair does not render the viral episome replication incompetent: our model predicts that concurrent delivery of multiple enzymes which target different vital cccDNA regions, or sequential delivery of different enzymes, are both potentially useful strategies for avoiding multi-enzyme resistance. The underlying dynamics of cccDNA persistence are unlikely to impact the probability of cure provided that antiviral therapy is given concurrently during eradication trials. We conclude by describing experiments that can be used to validate the model, which

  16. Incorporating microbial dormancy dynamics into soil decomposition models to improve quantification of soil carbon dynamics of northern temperate forests

    Science.gov (United States)

    He, Yujie; Yang, Jinyan; Zhuang, Qianlai; Harden, Jennifer W.; McGuire, A. David; Liu, Yaling; Wang, Gangsheng; Gu, Lianhong

    2015-01-01

    Soil carbon dynamics of terrestrial ecosystems play a significant role in the global carbon cycle. Microbial-based decomposition models have seen much growth recently for quantifying this role, yet dormancy as a common strategy used by microorganisms has not usually been represented and tested in these models against field observations. Here we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of microbial dormancy at six temperate forest sites of different forest types. We then extrapolated the model to global temperate forest ecosystems to investigate biogeochemical controls on soil heterotrophic respiration and microbial dormancy dynamics at different temporal-spatial scales. The dormancy model consistently produced better match with field-observed heterotrophic soil CO2 efflux (RH) than the no dormancy model. Our regional modeling results further indicated that models with dormancy were able to produce more realistic magnitude of microbial biomass (analysis showed that soil organic carbon content was the dominating factor (correlation coefficient = 0.4–0.6) in the simulated spatial pattern of soil RHwith both models. In contrast to strong temporal and local controls of soil temperature and moisture on microbial dormancy, our modeling results showed that soil carbon-to-nitrogen ratio (C:N) was a major regulating factor at regional scales (correlation coefficient = −0.43 to −0.58), indicating scale-dependent biogeochemical controls on microbial dynamics. Our findings suggest that incorporating microbial dormancy could improve the realism of microbial-based decomposition models and enhance the integration of soil experiments and mechanistically based modeling.

  17. A code reviewer assignment model incorporating the competence differences and participant preferences

    Directory of Open Access Journals (Sweden)

    Wang Yanqing

    2016-03-01

    Full Text Available A good assignment of code reviewers can effectively utilize the intellectual resources, assure code quality and improve programmers’ skills in software development. However, little research on reviewer assignment of code review has been found. In this study, a code reviewer assignment model is created based on participants’ preference to reviewing assignment. With a constraint of the smallest size of a review group, the model is optimized to maximize review outcomes and avoid the negative impact of “mutual admiration society”. This study shows that the reviewer assignment strategies incorporating either the reviewers’ preferences or the authors’ preferences get much improvement than a random assignment. The strategy incorporating authors’ preference makes higher improvement than that incorporating reviewers’ preference. However, when the reviewers’ and authors’ preference matrixes are merged, the improvement becomes moderate. The study indicates that the majority of the participants have a strong wish to work with reviewers and authors having highest competence. If we want to satisfy the preference of both reviewers and authors at the same time, the overall improvement of learning outcomes may be not the best.

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

    Science.gov (United States)

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

    2018-03-01

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

  19. ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature.

    Science.gov (United States)

    McDonald, Andrew G; Boyce, Sinéad; Moss, Gerard P; Dixon, Henry B F; Tipton, Keith F

    2007-07-27

    We describe the database ExplorEnz, which is the primary repository for EC numbers and enzyme data that are being curated on behalf of the IUBMB. The enzyme nomenclature is incorporated into many other resources, including the ExPASy-ENZYME, BRENDA and KEGG bioinformatics databases. The data, which are stored in a MySQL database, preserve the formatting of chemical and enzyme names. A simple, easy to use, web-based query interface is provided, along with an advanced search engine for more complex queries. The database is publicly available at http://www.enzyme-database.org. The data are available for download as SQL and XML files via FTP. ExplorEnz has powerful and flexible search capabilities and provides the scientific community with the most up-to-date version of the IUBMB Enzyme List.

  20. Incorporating model parameter uncertainty into inverse treatment planning

    International Nuclear Information System (INIS)

    Lian Jun; Xing Lei

    2004-01-01

    Radiobiological treatment planning depends not only on the accuracy of the models describing the dose-response relation of different tumors and normal tissues but also on the accuracy of tissue specific radiobiological parameters in these models. Whereas the general formalism remains the same, different sets of model parameters lead to different solutions and thus critically determine the final plan. Here we describe an inverse planning formalism with inclusion of model parameter uncertainties. This is made possible by using a statistical analysis-based frameset developed by our group. In this formalism, the uncertainties of model parameters, such as the parameter a that describes tissue-specific effect in the equivalent uniform dose (EUD) model, are expressed by probability density function and are included in the dose optimization process. We found that the final solution strongly depends on distribution functions of the model parameters. Considering that currently available models for computing biological effects of radiation are simplistic, and the clinical data used to derive the models are sparse and of questionable quality, the proposed technique provides us with an effective tool to minimize the effect caused by the uncertainties in a statistical sense. With the incorporation of the uncertainties, the technique has potential for us to maximally utilize the available radiobiology knowledge for better IMRT treatment

  1. In silico molecular modeling of neuraminidase enzyme H1N1 avian influenza virus and docking with zanamivir ligands

    Directory of Open Access Journals (Sweden)

    Muthiyan Ramachandran

    2012-12-01

    Full Text Available Objective: Neuraminidase is an enzyme aspartic protease that is essential for the life cycle of H1N1. Methods: Constructed a model of Neuraminidase enzyme the 3D structure as template using with Modeller software. The Neuraminidase enzyme model was predicted and validated by Procheck, What check, Errat, Verify-3D and AutoDock web server for reliability. Results: The Modeller homology-modeling algorithm was demonstrated excellent accuracy in blind predictions. The Neuraminidase enzyme model built with little, 35% identity could be accurate enough to be successfully used in receptor based rational drug design. The closest homologue with the highest sequence identity 100% was selected. Zanamivir drug and analogues were retrieved from PubChem database, as well as subjected to docking interaction with Neuraminidase enzyme used AutoDock programme. Based on the root mean square deviation and lowest binding energy values the best docking orientation was selected. The better lowest binding energy value -6.91 was selected of CID_25209232. Conclusions: This study will be used in broad screening of inhibitors of the protein. However, further implemented experimental and clinical verification is needed to establishment these analogues as drug.

  2. Incorporation of ice sheet models into an Earth system model: Focus on methodology of coupling

    Science.gov (United States)

    Rybak, Oleg; Volodin, Evgeny; Morozova, Polina; Nevecherja, Artiom

    2018-03-01

    Elaboration of a modern Earth system model (ESM) requires incorporation of ice sheet dynamics. Coupling of an ice sheet model (ICM) to an AOGCM is complicated by essential differences in spatial and temporal scales of cryospheric, atmospheric and oceanic components. To overcome this difficulty, we apply two different approaches for the incorporation of ice sheets into an ESM. Coupling of the Antarctic ice sheet model (AISM) to the AOGCM is accomplished via using procedures of resampling, interpolation and assigning to the AISM grid points annually averaged meanings of air surface temperature and precipitation fields generated by the AOGCM. Surface melting, which takes place mainly on the margins of the Antarctic peninsula and on ice shelves fringing the continent, is currently ignored. AISM returns anomalies of surface topography back to the AOGCM. To couple the Greenland ice sheet model (GrISM) to the AOGCM, we use a simple buffer energy- and water-balance model (EWBM-G) to account for orographically-driven precipitation and other sub-grid AOGCM-generated quantities. The output of the EWBM-G consists of surface mass balance and air surface temperature to force the GrISM, and freshwater run-off to force thermohaline circulation in the oceanic block of the AOGCM. Because of a rather complex coupling procedure of GrIS compared to AIS, the paper mostly focuses on Greenland.

  3. Incorporation particle creation and annihilation into Bohm's Pilot Wave model

    Energy Technology Data Exchange (ETDEWEB)

    Sverdlov, Roman [Raman Research Institute, C.V. Raman Avenue, Sadashiva Nagar, Bangalore, Karnataka, 560080 (India)

    2011-07-08

    The purpose of this paper is to come up with a Pilot Wave model of quantum field theory that incorporates particle creation and annihilation without sacrificing determinism; this theory is subsequently coupled with gravity.

  4. Improving Watershed-Scale Hydrodynamic Models by Incorporating Synthetic 3D River Bathymetry Network

    Science.gov (United States)

    Dey, S.; Saksena, S.; Merwade, V.

    2017-12-01

    Digital Elevation Models (DEMs) have an incomplete representation of river bathymetry, which is critical for simulating river hydrodynamics in flood modeling. Generally, DEMs are augmented with field collected bathymetry data, but such data are available only at individual reaches. Creating a hydrodynamic model covering an entire stream network in the basin requires bathymetry for all streams. This study extends a conceptual bathymetry model, River Channel Morphology Model (RCMM), to estimate the bathymetry for an entire stream network for application in hydrodynamic modeling using a DEM. It is implemented at two large watersheds with different relief and land use characterizations: coastal Guadalupe River basin in Texas with flat terrain and a relatively urban White River basin in Indiana with more relief. After bathymetry incorporation, both watersheds are modeled using HEC-RAS (1D hydraulic model) and Interconnected Pond and Channel Routing (ICPR), a 2-D integrated hydrologic and hydraulic model. A comparison of the streamflow estimated by ICPR at the outlet of the basins indicates that incorporating bathymetry influences streamflow estimates. The inundation maps show that bathymetry has a higher impact on flat terrains of Guadalupe River basin when compared to the White River basin.

  5. Reflection on design and testing of pancreatic alpha-amylase inhibitors: an in silico comparison between rat and rabbit enzyme models

    Directory of Open Access Journals (Sweden)

    Khalil-Moghaddam Shiva

    2012-11-01

    Full Text Available Abstract Background Inhibitors of pancreatic alpha-amylase are potential drugs to treat diabetes and obesity. In order to find compounds that would be effective amylase inhibitors, in vitro and in vivo models are usually used. The accuracy of models is limited, but these tools are nonetheless valuable. In vitro models could be used in large screenings involving thousands of chemicals that are tested to find potential lead compounds. In vivo models are still used as preliminary mean of testing compounds behavior in the whole organism. In the case of alpha-amylase inhibitors, both rats and rabbits could be chosen as in vivo models. The question was which animal could present more accuracy with regard to its pancreatic alpha-amylase. Results As there is no crystal structure of these enzymes, a molecular modeling study was done in order to compare the rabbit and rat enzymes with the human one. The overall result is that rabbit enzyme could probably be a better choice in this regard, but in the case of large ligands, which could make putative interactions with the −4 subsite of pancreatic alpha-amylase, interpretation of results should be made cautiously. Conclusion Molecular modeling tools could be used to choose the most suitable model enzyme that would help to identify new enzyme inhibitors. In the case of alpha-amylase, three-dimensional structures of animal enzymes show differences with the human one which should be taken into account when testing potential new drugs.

  6. Network analysis of metabolic enzyme evolution in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Kraulis Per

    2004-02-01

    Full Text Available Abstract Background The two most common models for the evolution of metabolism are the patchwork evolution model, where enzymes are thought to diverge from broad to narrow substrate specificity, and the retrograde evolution model, according to which enzymes evolve in response to substrate depletion. Analysis of the distribution of homologous enzyme pairs in the metabolic network can shed light on the respective importance of the two models. We here investigate the evolution of the metabolism in E. coli viewed as a single network using EcoCyc. Results Sequence comparison between all enzyme pairs was performed and the minimal path length (MPL between all enzyme pairs was determined. We find a strong over-representation of homologous enzymes at MPL 1. We show that the functionally similar and functionally undetermined enzyme pairs are responsible for most of the over-representation of homologous enzyme pairs at MPL 1. Conclusions The retrograde evolution model predicts that homologous enzymes pairs are at short metabolic distances from each other. In general agreement with previous studies we find that homologous enzymes occur close to each other in the network more often than expected by chance, which lends some support to the retrograde evolution model. However, we show that the homologous enzyme pairs which may have evolved through retrograde evolution, namely the pairs that are functionally dissimilar, show a weaker over-representation at MPL 1 than the functionally similar enzyme pairs. Our study indicates that, while the retrograde evolution model may have played a small part, the patchwork evolution model is the predominant process of metabolic enzyme evolution.

  7. Rationally evolving tRNAPyl for efficient incorporation of noncanonical amino acids.

    Science.gov (United States)

    Fan, Chenguang; Xiong, Hai; Reynolds, Noah M; Söll, Dieter

    2015-12-15

    Genetic encoding of noncanonical amino acids (ncAAs) into proteins is a powerful approach to study protein functions. Pyrrolysyl-tRNA synthetase (PylRS), a polyspecific aminoacyl-tRNA synthetase in wide use, has facilitated incorporation of a large number of different ncAAs into proteins to date. To make this process more efficient, we rationally evolved tRNA(Pyl) to create tRNA(Pyl-opt) with six nucleotide changes. This improved tRNA was tested as substrate for wild-type PylRS as well as three characterized PylRS variants (N(ϵ)-acetyllysyl-tRNA synthetase [AcKRS], 3-iodo-phenylalanyl-tRNA synthetase [IFRS], a broad specific PylRS variant [PylRS-AA]) to incorporate ncAAs at UAG codons in super-folder green fluorescence protein (sfGFP). tRNA(Pyl-opt) facilitated a 5-fold increase in AcK incorporation into two positions of sfGFP simultaneously. In addition, AcK incorporation into two target proteins (Escherichia coli malate dehydrogenase and human histone H3) caused homogenous acetylation at multiple lysine residues in high yield. Using tRNA(Pyl-opt) with PylRS and various PylRS variants facilitated efficient incorporation of six other ncAAs into sfGFP. Kinetic analyses revealed that the mutations in tRNA(Pyl-opt) had no significant effect on the catalytic efficiency and substrate binding of PylRS enzymes. Thus tRNA(Pyl-opt) should be an excellent replacement of wild-type tRNA(Pyl) for future ncAA incorporation by PylRS enzymes. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. Adsorption and enzyme activity of asparaginase at lipid Langmuir and Langmuir-Blodgett films

    International Nuclear Information System (INIS)

    Rocha Junior, Carlos da; Caseli, Luciano

    2017-01-01

    In this present work, the surface activity of the enzyme asparaginase was investigated at the air-water interface, presenting surface activity in high ionic strengths. Asparaginase was incorporated in Langmuir monolayers of the phospholipid dipalmitoylphosphatidylcholine (DPPC), forming a mixed film, which was characterized with surface pressure-area isotherms, surface potential-area isotherms, polarization-modulated infrared reflection-absorption spectroscopy (PM-IRRAS), and Brewster angle microscopy (BAM). The adsorption of the enzyme at the air-water interface condensed the lipid monolayer and increased the film compressibility at high surface pressures. Amide bands in the PM-IRRAS spectra were identified, with the C−N and C =O dipole moments lying parallel to monolayer plane, revealing the structuring of the enzyme into α-helices and β-sheets. The floating monolayers were transferred to solid supports as Langmuir-Blodgett (LB) films and characterized with fluorescence spectroscopy and atomic force microscopy. Catalytic activities of the films were measured and compared to the homogenous medium. The enzyme accommodated in the LB films preserved more than 78% of the enzyme activity after 30 days, in contrast for the homogeneous medium, which preserved less than 13%. The method presented in this work not only allows for an enhanced catalytic activity, but also can help explain why certain film architectures exhibit better performance. - Highlights: • Biomembranes are mimicked with Langmuir monolayers. • Asparaginase is incorporated into the lipid monolayer. • Enzyme adsorption is confirmed with tensiometry and infrared spectroscopy. • Langmuir-Blodgett films of the enzyme present enzyme activity.

  9. Adsorption and enzyme activity of asparaginase at lipid Langmuir and Langmuir-Blodgett films

    Energy Technology Data Exchange (ETDEWEB)

    Rocha Junior, Carlos da; Caseli, Luciano, E-mail: lcaseli@unifesp.br

    2017-04-01

    In this present work, the surface activity of the enzyme asparaginase was investigated at the air-water interface, presenting surface activity in high ionic strengths. Asparaginase was incorporated in Langmuir monolayers of the phospholipid dipalmitoylphosphatidylcholine (DPPC), forming a mixed film, which was characterized with surface pressure-area isotherms, surface potential-area isotherms, polarization-modulated infrared reflection-absorption spectroscopy (PM-IRRAS), and Brewster angle microscopy (BAM). The adsorption of the enzyme at the air-water interface condensed the lipid monolayer and increased the film compressibility at high surface pressures. Amide bands in the PM-IRRAS spectra were identified, with the C−N and C =O dipole moments lying parallel to monolayer plane, revealing the structuring of the enzyme into α-helices and β-sheets. The floating monolayers were transferred to solid supports as Langmuir-Blodgett (LB) films and characterized with fluorescence spectroscopy and atomic force microscopy. Catalytic activities of the films were measured and compared to the homogenous medium. The enzyme accommodated in the LB films preserved more than 78% of the enzyme activity after 30 days, in contrast for the homogeneous medium, which preserved less than 13%. The method presented in this work not only allows for an enhanced catalytic activity, but also can help explain why certain film architectures exhibit better performance. - Highlights: • Biomembranes are mimicked with Langmuir monolayers. • Asparaginase is incorporated into the lipid monolayer. • Enzyme adsorption is confirmed with tensiometry and infrared spectroscopy. • Langmuir-Blodgett films of the enzyme present enzyme activity.

  10. Mathematical modeling of enzyme production using Trichoderma harzianum P49P11 and sugarcane bagasse as carbon source.

    Science.gov (United States)

    Gelain, Lucas; da Cruz Pradella, José Geraldo; da Costa, Aline Carvalho

    2015-12-01

    A mathematical model to describe the kinetics of enzyme production by the filamentous fungus Trichoderma harzianum P49P11 was developed using a low cost substrate as main carbon source (pretreated sugarcane bagasse). The model describes the cell growth, variation of substrate concentration and production of three kinds of enzymes (cellulases, beta-glucosidase and xylanase) in different sugarcane bagasse concentrations (5; 10; 20; 30; 40 gL(-1)). The 10 gL(-1) concentration was used to validate the model and the other to parameter estimation. The model for enzyme production has terms implicitly representing induction and repression. Substrate variation was represented by a simple degradation rate. The models seem to represent well the kinetics with a good fit for the majority of the assays. Validation results indicate that the models are adequate to represent the kinetics for a biotechnological process. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Student Collaboration in a Series of Integrated Experiments to Study Enzyme Reactor Modeling with Immobilized Cell-Based Invertase

    Science.gov (United States)

    Taipa, M. A^ngela; Azevedo, Ana M.; Grilo, Anto´nio L.; Couto, Pedro T.; Ferreira, Filipe A. G.; Fortuna, Ana R. M.; Pinto, Ine^s F.; Santos, Rafael M.; Santos, Susana B.

    2015-01-01

    An integrative laboratory study addressing fundamentals of enzyme catalysis and their application to reactors operation and modeling is presented. Invertase, a ß-fructofuranosidase that catalyses the hydrolysis of sucrose, is used as the model enzyme at optimal conditions (pH 4.5 and 45 °C). The experimental work involves 3 h of laboratory time…

  12. Accessory enzymes influence cellulase hydrolysis of the model substrate and the realistic lignocellulosic biomass.

    Science.gov (United States)

    Sun, Fubao Fuebiol; Hong, Jiapeng; Hu, Jinguang; Saddler, Jack N; Fang, Xu; Zhang, Zhenyu; Shen, Song

    2015-11-01

    The potential of cellulase enzymes in the developing and ongoing "biorefinery" industry has provided a great motivation to develop an efficient cellulase mixture. Recent work has shown how important the role that the so-called accessory enzymes can play in an effective enzymatic hydrolysis. In this study, three newest Novozymes Cellic CTec cellulase preparations (CTec 1/2/3) were compared to hydrolyze steam pretreated lignocellulosic substrates and model substances at an identical FPA loading. These cellulase preparations were found to display significantly different hydrolytic performances irrelevant with the FPA. And this difference was even observed on the filter paper itself when the FPA based assay was revisited. The analysis of specific enzyme activity in cellulase preparations demonstrated that different accessory enzymes were mainly responsible for the discrepancy of enzymatic hydrolysis between diversified substrates and various cellulases. Such the active role of accessory enzymes present in cellulase preparations was finally verified by supplementation with β-glucosidase, xylanase and lytic polysaccharide monooxygenases AA9. This paper provides new insights into the role of accessory enzymes, which can further provide a useful reference for the rational customization of cellulase cocktails in order to realize an efficient conversion of natural lignocellulosic substrates. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Moving college students to a better understanding of substrate specificity of enzymes through utilizing multimedia pre-training and an interactive enzyme model

    Science.gov (United States)

    Saleh, Mounir R.

    Scientists' progress in understanding enzyme specificity uncovered a complex natural phenomenon. However, not all of the currently available biology textbooks seem to be up to date on this progress. Students' understanding of how enzymes work is a core requirement in biochemistry and biology tertiary education. Nevertheless, current pre-college science education does not provide students with enough biochemical background to enable them to understand complex material such as this. To bridge this gap, a multimedia pre-training presentation was prepared to fuel the learner's prior knowledge with discrete facts necessary to understand the presented concept. This treatment is also known to manage intrinsic cognitive load during the learning process. An interactive instructional enzyme model was also built to motivate students to learn about substrate specificity of enzymes. Upon testing the effect of this combined treatment on 111 college students, desirable learning outcomes were found in terms of cognitive load, motivation, and achievement. The multimedia pre-training group reported significantly less intrinsic cognitive load, higher motivation, and demonstrated higher transfer performance than the control and post-training groups. In this study, a statistical mediation model is also proposed to explain how cognitive load and motivation work in concert to foster learning from multimedia pre-training. This type of research goes beyond simple forms of "what works" to a deeper understanding of "how it works", thus enabling informed decisions for multimedia instructional design. Multimedia learning plays multiple roles in science education. Therefore, science learners would be some of the first to benefit from improving multimedia instructional design. Accordingly, complex scientific phenomena can be introduced to college students in a motivating, informative, and cognitively efficient learning environment.

  14. Strategies for enzyme saving during saccharification of pretreated lignocellulo-starch biomass: effect of enzyme dosage and detoxification chemicals

    Directory of Open Access Journals (Sweden)

    M.G. Mithra

    2017-08-01

    Full Text Available Two strategies leading to enzyme saving during saccharification of pretreated lignocellulo-starch biomass (LCSB was investigated which included reducing enzyme dosage by varying their levels in enzyme cocktails and enhancing the fermentable sugar yield in enzyme-reduced systems using detoxification chemicals. Time course release of reducing sugars (RS during 24–120 h was significantly higher when an enzyme cocktail containing full dose of cellulase (16 FPU/g cellulose along with half dose each of xylanase (1.5 mg protein/g hemicelluloses and Stargen (12.5 μl/g biomass was used to saccharify conventional dilute sulphuric acid (DSA pretreated biomass compared to a parallel system where only one-fourth the dose of the latter two enzymes was used. The reduction in RS content in the 120 h saccharified mash to the extent of 3–4 g/L compared to the system saccharified with full complement of the three enzymes could be overcome considerably by supplementing the system (half dose of two enzymes with detoxification chemical mix incorporating Tween 20, PEG 4000 and sodium borohydride. Microwave (MW-assisted DSA pretreated biomass on saccharification with enzyme cocktail having full dose of cellulase and half dose of Stargen along with detoxification chemicals gave significantly higher RS yield than DSA pretreated system saccharified using three enzymes. The study showed that xylanase could be eliminated during saccharification of MW-assisted DSA pretreated biomass without affecting RS yield when detoxification chemicals were also supplemented. The Saccharification Efficiency and Overall Conversion Efficiency were also high for the MW-assisted DSA pretreated biomass. Since whole slurry saccharifcation of pretreated biomass is essential to conserve fermentable sugars in LCSB saccharification, detoxification of soluble inhibitors is equally important as channelling out of insoluble lignin remaining in the residue. As one of the major factors contributing

  15. A thermodynamic and theoretical view for enzyme regulation.

    Science.gov (United States)

    Zhao, Qinyi

    2015-01-01

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

  16. Vault Nanoparticles Packaged with Enzymes as an Efficient Pollutant Biodegradation Technology.

    Science.gov (United States)

    Wang, Meng; Abad, Danny; Kickhoefer, Valerie A; Rome, Leonard H; Mahendra, Shaily

    2015-11-24

    Vault nanoparticles packaged with enzymes were synthesized as agents for efficiently degrading environmental contaminants. Enzymatic biodegradation is an attractive technology for in situ cleanup of contaminated environments because enzyme-catalyzed reactions are not constrained by nutrient requirements for microbial growth and often have higher biodegradation rates. However, the limited stability of extracellular enzymes remains a major challenge for practical applications. Encapsulation is a recognized method to enhance enzymatic stability, but it can increase substrate diffusion resistance, lower catalytic rates, and increase the apparent half-saturation constants. Here, we report an effective approach for boosting enzymatic stability by single-step packaging into vault nanoparticles. With hollow core structures, assembled vault nanoparticles can simultaneously contain multiple enzymes. Manganese peroxidase (MnP), which is widely used in biodegradation of organic contaminants, was chosen as a model enzyme in the present study. MnP was incorporated into vaults via fusion to a packaging domain called INT, which strongly interacts with vaults' interior surface. MnP fused to INT and vaults packaged with the MnP-INT fusion protein maintained peroxidase activity. Furthermore, MnP-INT packaged in vaults displayed stability significantly higher than that of free MnP-INT, with slightly increased Km value. Additionally, vault-packaged MnP-INT exhibited 3 times higher phenol biodegradation in 24 h than did unpackaged MnP-INT. These results indicate that the packaging of MnP enzymes in vault nanoparticles extends their stability without compromising catalytic activity. This research will serve as the foundation for the development of efficient and sustainable vault-based bioremediation approaches for removing multiple contaminants from drinking water and groundwater.

  17. Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes: Targeted quantification of functional enzyme dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Li, Minjing [School of Environmental Studies, China University of Geosciences, Wuhan 430074 People' s Republic of China; Gao, Yuqian [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Qian, Wei-Jun [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Shi, Liang [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Liu, Yuanyuan [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Nelson, William C. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Nicora, Carrie D. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Resch, Charles T. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Thompson, Christopher [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Yan, Sen [School of Environmental Studies, China University of Geosciences, Wuhan 430074 People' s Republic of China; Fredrickson, James K. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Zachara, John M. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Liu, Chongxuan [Pacific Northwest National Laboratory, Richland, WA 99354 USA; School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055 People' s Republic of China

    2017-07-13

    Microbially mediated biogeochemical processes are catalyzed by enzymes that control the transformation of carbon, nitrogen, and other elements in environment. The dynamic linkage between enzymes and biogeochemical species transformation has, however, rarely been investigated because of the lack of analytical approaches to efficiently and reliably quantify enzymes and their dynamics in soils and sediments. Herein, we developed a signature peptide-based technique for sensitively quantifying dissimilatory and assimilatory enzymes using nitrate-reducing enzymes in a hyporheic zone sediment as an example. Moreover, the measured changes in enzyme concentration were found to correlate with the nitrate reduction rate in a way different from that inferred from biogeochemical models based on biomass or functional genes as surrogates for functional enzymes. This phenomenon has important implications for understanding and modeling the dynamics of microbial community functions and biogeochemical processes in environments. Our results also demonstrate the importance of enzyme quantification for the identification and interrogation of those biogeochemical processes with low metabolite concentrations as a result of faster enzyme-catalyzed consumption of metabolites than their production. The dynamic enzyme behaviors provide a basis for the development of enzyme-based models to describe the relationship between the microbial community and biogeochemical processes.

  18. Mitomycin C induced alterations in antioxidant enzyme levels in a model insect species, Spodoptera eridania.

    Science.gov (United States)

    Batcabe, J P; MacGill, R S; Zaman, K; Ahmad, S; Pardini, R S

    1994-05-01

    1. An insect species, the southern armyworm Spodoptera eridania, was used as an in vivo model to examine mitomycin C's (MMC) pro-oxidant effect reflected in alterations of antioxidant enzymes. 2. Following a 2-day exposure to 0.01 and 0.05% w/w dietary concentrations, MMC only induced superoxide dismutase activity. All other enzyme activities were not affected, indicating oxidative stress was mild. 3. Following a 5-day exposure to 0.05% w/w dietary MMC, the activities of superoxide dismutase, glutathione-S-transferase and its peroxidase activity and DT-diaphorase were induced. GR activity was not altered. The high constitutive catalase activity was also not affected. These responses of S. eridania's antioxidant enzymes are analogous to those of mammalian systems in alleviating MMC-induced oxidative stress. 4. S. eridania emerges as an appropriate non-mammalian model for initial and cost-effective screening of drug-induced oxidative stress.

  19. Advanced Methods for Incorporating Solar Energy Technologies into Electric Sector Capacity-Expansion Models: Literature Review and Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Sullivan, P.; Eurek, K.; Margolis, R.

    2014-07-01

    Because solar power is a rapidly growing component of the electricity system, robust representations of solar technologies should be included in capacity-expansion models. This is a challenge because modeling the electricity system--and, in particular, modeling solar integration within that system--is a complex endeavor. This report highlights the major challenges of incorporating solar technologies into capacity-expansion models and shows examples of how specific models address those challenges. These challenges include modeling non-dispatchable technologies, determining which solar technologies to model, choosing a spatial resolution, incorporating a solar resource assessment, and accounting for solar generation variability and uncertainty.

  20. In silico investigation of the short QT syndrome, using human ventricle models incorporating electromechanical coupling

    Directory of Open Access Journals (Sweden)

    Ismail eAdeniran

    2013-07-01

    Full Text Available Introduction Genetic forms of the Short QT Syndrome (SQTS arise due to cardiac ion channel mutations leading to accelerated ventricular repolarisation, arrhythmias and sudden cardiac death. Results from experimental and simulation studies suggest that changes to refractoriness and tissue vulnerability produce a substrate favourable to re-entry. Potential electromechanical consequences of the SQTS are less well understood. The aim of this study was to utilize electromechanically coupled human ventricle models to explore electromechanical consequences of the SQTS. Methods and results: The Rice et al. mechanical model was coupled to the ten Tusscher et al. ventricular cell model. Previously validated K+ channel formulations for SQT variants 1 and 3 were incorporated. Functional effects of the SQTS mutations on transients, sarcomere length shortening and contractile force at the single cell level were evaluated with and without the consideration of stretch activated channel current (Isac. Without Isac, the SQTS mutations produced dramatic reductions in the amplitude of transients, sarcomere length shortening and contractile force. When Isac was incorporated, there was a considerable attenuation of the effects of SQTS-associated action potential shortening on Ca2+ transients, sarcomere shortening and contractile force. Single cell models were then incorporated into 3D human ventricular tissue models. The timing of maximum deformation was delayed in the SQTS setting compared to control. Conclusion: The incorporation of Isac appears to be an important consideration in modelling functional effects of SQT 1 and 3 mutations on cardiac electro-mechanical coupling. Whilst there is little evidence of profoundly impaired cardiac contractile function in SQTS patients, our 3D simulations correlate qualitatively with reported evidence for dissociation between ventricular repolarization and the end of mechanical systole.

  1. Investigations of incorporating source directivity into room acoustics computer models to improve auralizations

    Science.gov (United States)

    Vigeant, Michelle C.

    Room acoustics computer modeling and auralizations are useful tools when designing or modifying acoustically sensitive spaces. In this dissertation, the input parameter of source directivity has been studied in great detail to determine first its effect in room acoustics computer models and secondly how to better incorporate the directional source characteristics into these models to improve auralizations. To increase the accuracy of room acoustics computer models, the source directivity of real sources, such as musical instruments, must be included in the models. The traditional method for incorporating source directivity into room acoustics computer models involves inputting the measured static directivity data taken every 10° in a sphere-shaped pattern around the source. This data can be entered into the room acoustics software to create a directivity balloon, which is used in the ray tracing algorithm to simulate the room impulse response. The first study in this dissertation shows that using directional sources over an omni-directional source in room acoustics computer models produces significant differences both in terms of calculated room acoustics parameters and auralizations. The room acoustics computer model was also validated in terms of accurately incorporating the input source directivity. A recently proposed technique for creating auralizations using a multi-channel source representation has been investigated with numerous subjective studies, applied to both solo instruments and an orchestra. The method of multi-channel auralizations involves obtaining multi-channel anechoic recordings of short melodies from various instruments and creating individual channel auralizations. These auralizations are then combined to create a total multi-channel auralization. Through many subjective studies, this process was shown to be effective in terms of improving the realism and source width of the auralizations in a number of cases, and also modeling different

  2. Enzyme release in the skin of mice as an effect of soft X-irradiation

    International Nuclear Information System (INIS)

    Soltesz, L.

    1976-01-01

    The shaved skin of 7-8 week old male mice was irradiated locally on the back by doses of 100, 500, 1000, 2000 or 4000 R of soft X-ray. The enzyme activity of the washing solution and of the homogenate of the removed skin, the nitrogen content and the incorporation of 3 H-thymidine were measured immediately after irradiation or 1,2,4,8,16 hours later. The activity of lysosomal enzymes (acid phosphatase, beta-glucuronidase, cathepsine D) increased in the washing solution, whereas in the homogenate no significant change was observed. The maximal values were measured on the second day after irradiation with 1000 R. Tha activity of alkaline phosphatase and leucinaminopeptidase (non-lysosomal enzymes) did not change. Neither was any change observed in the nitrogen content of the skin. The incorporation of 3 H-thymidine considerably decreased. It can be concluded that small doses (500-1000 R) of local X-irradiation damage the membrane of lysosoms and lead to a release of cell destructing enzymes. (L.E.)

  3. Caseoperoxidase, mixed β-casein-SDS-hemin-imidazole complex: a nano artificial enzyme.

    Science.gov (United States)

    Moosavi-Movahedi, Zainab; Gharibi, Hussein; Hadi-Alijanvand, Hamid; Akbarzadeh, Mohammad; Esmaili, Mansoore; Atri, Maliheh S; Sefidbakht, Yahya; Bohlooli, Mousa; Nazari, Khodadad; Javadian, Soheila; Hong, Jun; Saboury, Ali A; Sheibani, Nader; Moosavi-Movahedi, Ali A

    2015-01-01

    A novel peroxidase-like artificial enzyme, named "caseoperoxidase", was biomimetically designed using a nano artificial amino acid apo-protein hydrophobic pocket. This four-component nano artificial enzyme containing heme-imidazole-β-casein-SDS exhibited high activity growth and k(cat) performance toward the native horseradish peroxidase demonstrated by the steady state kinetics using UV-vis spectrophotometry. The hydrophobicity and secondary structure of the caseoperoxidase were studied by ANS fluorescence and circular dichroism spectroscopy. Camel β-casein (Cβ-casein) was selected as an appropriate apo-protein for the heme active site because of its innate flexibility and exalted hydrophobicity. This selection was confirmed by homology modeling method. Heme docking into the newly obtained Cβ-casein structure indicated one heme was mainly incorporated with Cβ-casein. The presence of a main electrostatic site for the active site in the Cβ-casein was also confirmed by experimental methods through Wyman binding potential and isothermal titration calorimetry. The existence of Cβ-casein protein in this biocatalyst lowered the suicide inactivation and provided a suitable protective role for the heme active-site. Additional experiments confirmed the retention of caseoperoxidase structure and function as an artificial enzyme.

  4. Making a difference: incorporating theories of autonomy into models of informed consent.

    Science.gov (United States)

    Delany, C

    2008-09-01

    Obtaining patients' informed consent is an ethical and legal obligation in healthcare practice. Whilst the law provides prescriptive rules and guidelines, ethical theories of autonomy provide moral foundations. Models of practice of consent, have been developed in the bioethical literature to assist in understanding and integrating the ethical theory of autonomy and legal obligations into the clinical process of obtaining a patient's informed consent to treatment. To review four models of consent and analyse the way each model incorporates the ethical meaning of autonomy and how, as a consequence, they might change the actual communicative process of obtaining informed consent within clinical contexts. An iceberg framework of consent is used to conceptualise how ethical theories of autonomy are positioned and underpin the above surface, and visible clinical communication, including associated legal guidelines and ethical rules. Each model of consent is critically reviewed from the perspective of how it might shape the process of informed consent. All four models would alter the process of obtaining consent. Two models provide structure and guidelines for the content and timing of obtaining patients' consent. The two other models rely on an attitudinal shift in clinicians. They provide ideas for consent by focusing on underlying values, attitudes and meaning associated with the ethical meaning of autonomy. The paper concludes that models of practice that explicitly incorporate the underlying ethical meaning of autonomy as their basis, provide less prescriptive, but more theoretically rich guidance for healthcare communicative practices.

  5. PWR plant operator training used full scope simulator incorporated MAAP model

    International Nuclear Information System (INIS)

    Matsumoto, Y.; Tabuchi, T.; Yamashita, T.; Komatsu, Y.; Tsubouchi, K.; Banka, T.; Mochizuki, T.; Nishimura, K.; Iizuka, H.

    2015-01-01

    NTC makes an effort with the understanding of plant behavior of core damage accident as part of our advanced training. For the Fukushima Daiichi Nuclear Power Station accident, we introduced the MAAP model into PWR operator training full scope simulator and also made the Severe Accident Visual Display unit. From 2014, we will introduce new training program for a core damage accident with PWR operator training full scope simulator incorporated the MAAP model and the Severe Accident Visual Display unit. (author)

  6. Incorporating modelled subglacial hydrology into inversions for basal drag

    Directory of Open Access Journals (Sweden)

    C. P. Koziol

    2017-12-01

    Full Text Available A key challenge in modelling coupled ice-flow–subglacial hydrology is initializing the state and parameters of the system. We address this problem by presenting a workflow for initializing these values at the start of a summer melt season. The workflow depends on running a subglacial hydrology model for the winter season, when the system is not forced by meltwater inputs, and ice velocities can be assumed constant. Key parameters of the winter run of the subglacial hydrology model are determined from an initial inversion for basal drag using a linear sliding law. The state of the subglacial hydrology model at the end of winter is incorporated into an inversion of basal drag using a non-linear sliding law which is a function of water pressure. We demonstrate this procedure in the Russell Glacier area and compare the output of the linear sliding law with two non-linear sliding laws. Additionally, we compare the modelled winter hydrological state to radar observations and find that it is in line with summer rather than winter observations.

  7. Incorporation of stochastic engineering models as prior information in Bayesian medical device trials.

    Science.gov (United States)

    Haddad, Tarek; Himes, Adam; Thompson, Laura; Irony, Telba; Nair, Rajesh

    2017-01-01

    Evaluation of medical devices via clinical trial is often a necessary step in the process of bringing a new product to market. In recent years, device manufacturers are increasingly using stochastic engineering models during the product development process. These models have the capability to simulate virtual patient outcomes. This article presents a novel method based on the power prior for augmenting a clinical trial using virtual patient data. To properly inform clinical evaluation, the virtual patient model must simulate the clinical outcome of interest, incorporating patient variability, as well as the uncertainty in the engineering model and in its input parameters. The number of virtual patients is controlled by a discount function which uses the similarity between modeled and observed data. This method is illustrated by a case study of cardiac lead fracture. Different discount functions are used to cover a wide range of scenarios in which the type I error rates and power vary for the same number of enrolled patients. Incorporation of engineering models as prior knowledge in a Bayesian clinical trial design can provide benefits of decreased sample size and trial length while still controlling type I error rate and power.

  8. Fungal Morphology in Industrial Enzyme Production - Modelling and Monitoring

    DEFF Research Database (Denmark)

    Quintanilla, D.; Hagemann, T.; Hansen, K.

    2015-01-01

    Filamentous fungi are widely used in the biotechnology industry for the production of industrial enzymes. Thus, considerable work has been done with the purpose of characterizing these processes. The ultimate goal of these efforts is to be able to control and predict fermentation performance......, and on the way the data is interpreted-i.e. which models were applied. The main filamentous fungi used in industrial fermentation are introduced, ranging from Trichoderma reesei to Aspergillus species. Due to the fact that secondary metabolites, like antibiotics, are not to be considered bulk products, organisms...

  9. Enzyme-Gelatin Electrochemical Biosensors: Scaling Down

    Directory of Open Access Journals (Sweden)

    Hendrik A. Heering

    2012-03-01

    Full Text Available In this article we investigate the possibility of scaling down enzyme-gelatin modified electrodes by spin coating the enzyme-gelatin layer. Special attention is given to the electrochemical behavior of the selected enzymes inside the gelatin matrix. A glassy carbon electrode was used as a substrate to immobilize, in the first instance, horse heart cytochrome c (HHC in a gelatin matrix. Both a drop dried and a spin coated layer was prepared. On scaling down, a transition from diffusion controlled reactions towards adsorption controlled reactions is observed. Compared to a drop dried electrode, a spin coated electrode showed a more stable electrochemical behavior. Next to HHC, we also incorporated catalase in a spin coated gelatin matrix immobilized on a glassy carbon electrode. By spincoating, highly uniform sub micrometer layers of biocompatible matrices can be constructed. A full electrochemical study and characterization of the modified surfaces has been carried out. It was clear that in the case of catalase, gluteraldehyde addition was needed to prevent leaking of the catalase from the gelatin matrix.

  10. Incorporating microbial dormancy dynamics into soil decomposition models to improve quantification of soil carbon dynamics of northern temperate forests

    Energy Technology Data Exchange (ETDEWEB)

    He, Yujie [Purdue Univ., West Lafayette, IN (United States). Dept. of Earth, Atmospheric, and Planetary Sciences; Yang, Jinyan [Univ. of Georgia, Athens, GA (United States). Warnell School of Forestry and Natural Resources; Northeast Forestry Univ., Harbin (China). Center for Ecological Research; Zhuang, Qianlai [Purdue Univ., West Lafayette, IN (United States). Dept. of Earth, Atmospheric, and Planetary Sciences; Purdue Univ., West Lafayette, IN (United States). Dept. of Agronomy; Harden, Jennifer W. [U.S. Geological Survey, Menlo Park, CA (United States); McGuire, Anthony D. [Alaska Cooperative Fish and Wildlife Research Unit, U.S. Geological Survey, Univ. of Alaska, Fairbanks, AK (United States). U.S. Geological Survey, Alaska Cooperative Fish and Wildlife Research Unit; Liu, Yaling [Purdue Univ., West Lafayette, IN (United States). Dept. of Earth, Atmospheric, and Planetary Sciences; Wang, Gangsheng [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Climate Change Science Inst. and Environmental Sciences Division; Gu, Lianhong [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Environmental Sciences Division

    2015-11-20

    Soil carbon dynamics of terrestrial ecosystems play a significant role in the global carbon cycle. Microbial-based decomposition models have seen much growth recently for quantifying this role, yet dormancy as a common strategy used by microorganisms has not usually been represented and tested in these models against field observations. Here in this study we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of microbial dormancy at six temperate forest sites of different forest types. We then extrapolated the model to global temperate forest ecosystems to investigate biogeochemical controls on soil heterotrophic respiration and microbial dormancy dynamics at different temporal-spatial scales. The dormancy model consistently produced better match with field-observed heterotrophic soil CO2 efflux (RH) than the no dormancy model. Our regional modeling results further indicated that models with dormancy were able to produce more realistic magnitude of microbial biomass (<2% of soil organic carbon) and soil RH (7.5 ± 2.4 PgCyr-1). Spatial correlation analysis showed that soil organic carbon content was the dominating factor (correlation coefficient = 0.4-0.6) in the simulated spatial pattern of soil RH with both models. In contrast to strong temporal and local controls of soil temperature and moisture on microbial dormancy, our modeling results showed that soil carbon-to-nitrogen ratio (C:N) was a major regulating factor at regional scales (correlation coefficient = -0.43 to -0.58), indicating scale-dependent biogeochemical controls on microbial dynamics. Our findings suggest that incorporating microbial dormancy could improve the realism of microbial-based decomposition models and enhance the integration of soil experiments and mechanistically based modeling.

  11. A mathematical model for incorporating biofeedback into human postural control

    Directory of Open Access Journals (Sweden)

    Ersal Tulga

    2013-02-01

    Full Text Available Abstract Background Biofeedback of body motion can serve as a balance aid and rehabilitation tool. To date, mathematical models considering the integration of biofeedback into postural control have represented this integration as a sensory addition and limited their application to a single degree-of-freedom representation of the body. This study has two objectives: 1 to develop a scalable method for incorporating biofeedback into postural control that is independent of the model’s degrees of freedom, how it handles sensory integration, and the modeling of its postural controller; and 2 to validate this new model using multidirectional perturbation experimental results. Methods Biofeedback was modeled as an additional torque to the postural controller torque. For validation, this biofeedback modeling approach was applied to a vibrotactile biofeedback device and incorporated into a two-link multibody model with full-state-feedback control that represents the dynamics of bipedal stance. Average response trajectories of body sway and center of pressure (COP to multidirectional surface perturbations of subjects with vestibular deficits were used for model parameterization and validation in multiple perturbation directions and for multiple display resolutions. The quality of fit was quantified using average error and cross-correlation values. Results The mean of the average errors across all tactor configurations and perturbations was 0.24° for body sway and 0.39 cm for COP. The mean of the cross-correlation value was 0.97 for both body sway and COP. Conclusions The biofeedback model developed in this study is capable of capturing experimental response trajectory shapes with low average errors and high cross-correlation values in both the anterior-posterior and medial-lateral directions for all perturbation directions and spatial resolution display configurations considered. The results validate that biofeedback can be modeled as an additional

  12. A mathematical model for incorporating biofeedback into human postural control

    Science.gov (United States)

    2013-01-01

    Background Biofeedback of body motion can serve as a balance aid and rehabilitation tool. To date, mathematical models considering the integration of biofeedback into postural control have represented this integration as a sensory addition and limited their application to a single degree-of-freedom representation of the body. This study has two objectives: 1) to develop a scalable method for incorporating biofeedback into postural control that is independent of the model’s degrees of freedom, how it handles sensory integration, and the modeling of its postural controller; and 2) to validate this new model using multidirectional perturbation experimental results. Methods Biofeedback was modeled as an additional torque to the postural controller torque. For validation, this biofeedback modeling approach was applied to a vibrotactile biofeedback device and incorporated into a two-link multibody model with full-state-feedback control that represents the dynamics of bipedal stance. Average response trajectories of body sway and center of pressure (COP) to multidirectional surface perturbations of subjects with vestibular deficits were used for model parameterization and validation in multiple perturbation directions and for multiple display resolutions. The quality of fit was quantified using average error and cross-correlation values. Results The mean of the average errors across all tactor configurations and perturbations was 0.24° for body sway and 0.39 cm for COP. The mean of the cross-correlation value was 0.97 for both body sway and COP. Conclusions The biofeedback model developed in this study is capable of capturing experimental response trajectory shapes with low average errors and high cross-correlation values in both the anterior-posterior and medial-lateral directions for all perturbation directions and spatial resolution display configurations considered. The results validate that biofeedback can be modeled as an additional torque to the postural

  13. Bioethanol production by inherent enzymes from rye and wheat with addition of organic farming cheese whey

    DEFF Research Database (Denmark)

    Kádár, Zsófia; Christensen, Anne Deen; Thomsen, Mette Hedegaard

    2011-01-01

    . Throughout our studies, wheat and rye grain was used as raw material in bioethanol production with the purpose of producing in situ enzymes (during germination) for the hydrolysis of starch in the grains and compared with commercial amylase enzyme preparations. Whey permeate was incorporated into the grain...

  14. Making Invasion models useful for decision makers; incorporating uncertainty, knowledge gaps, and decision-making preferences

    Science.gov (United States)

    Denys Yemshanov; Frank H Koch; Mark Ducey

    2015-01-01

    Uncertainty is inherent in model-based forecasts of ecological invasions. In this chapter, we explore how the perceptions of that uncertainty can be incorporated into the pest risk assessment process. Uncertainty changes a decision maker’s perceptions of risk; therefore, the direct incorporation of uncertainty may provide a more appropriate depiction of risk. Our...

  15. Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily

    Science.gov (United States)

    Lukk, Tiit; Sakai, Ayano; Kalyanaraman, Chakrapani; Brown, Shoshana D.; Imker, Heidi J.; Song, Ling; Fedorov, Alexander A.; Fedorov, Elena V.; Toro, Rafael; Hillerich, Brandan; Seidel, Ronald; Patskovsky, Yury; Vetting, Matthew W.; Nair, Satish K.; Babbitt, Patricia C.; Almo, Steven C.; Gerlt, John A.; Jacobson, Matthew P.

    2012-01-01

    The rapid advance in genome sequencing presents substantial challenges for protein functional assignment, with half or more of new protein sequences inferred from these genomes having uncertain assignments. The assignment of enzyme function in functionally diverse superfamilies represents a particular challenge, which we address through a combination of computational predictions, enzymology, and structural biology. Here we describe the results of a focused investigation of a group of enzymes in the enolase superfamily that are involved in epimerizing dipeptides. The first members of this group to be functionally characterized were Ala-Glu epimerases in Eschericiha coli and Bacillus subtilis, based on the operon context and enzymological studies; these enzymes are presumed to be involved in peptidoglycan recycling. We have subsequently studied more than 65 related enzymes by computational methods, including homology modeling and metabolite docking, which suggested that many would have divergent specificities;, i.e., they are likely to have different (unknown) biological roles. In addition to the Ala-Phe epimerase specificity reported previously, we describe the prediction and experimental verification of: (i) a new group of presumed Ala-Glu epimerases; (ii) several enzymes with specificity for hydrophobic dipeptides, including one from Cytophaga hutchinsonii that epimerizes D-Ala-D-Ala; and (iii) a small group of enzymes that epimerize cationic dipeptides. Crystal structures for certain of these enzymes further elucidate the structural basis of the specificities. The results highlight the potential of computational methods to guide experimental characterization of enzymes in an automated, large-scale fashion. PMID:22392983

  16. Incorporation of fungal cellulases in bacterial minicellulosomes yields viable, synergistically acting celluloytic complexes

    NARCIS (Netherlands)

    Mingardon, F.; Chanal, A.; Lopez Contreras, A.M.; Dray, C.; Bayer, E.A.; Fierobe, H.P.

    2007-01-01

    Artificial designer minicellulosomes comprise a chimeric scaffoldin that displays an optional cellulose-binding module (CBM) and bacterial cohesins from divergent species which bind strongly to enzymes engineered to bear complementary dockerins. Incorporation of cellulosomal cellulases from

  17. Quantitative Structure-Activity Relationship Modeling Coupled with Molecular Docking Analysis in Screening of Angiotensin I-Converting Enzyme Inhibitory Peptides from Qula Casein Hydrolysates Obtained by Two-Enzyme Combination Hydrolysis.

    Science.gov (United States)

    Lin, Kai; Zhang, Lanwei; Han, Xue; Meng, Zhaoxu; Zhang, Jianming; Wu, Yifan; Cheng, Dayou

    2018-03-28

    In this study, Qula casein derived from yak milk casein was hydrolyzed using a two-enzyme combination approach, and high angiotensin I-converting enzyme (ACE) inhibitory activity peptides were screened by quantitative structure-activity relationship (QSAR) modeling integrated with molecular docking analysis. Hydrolysates (casein presents an excellent source to produce ACE inhibitory peptides.

  18. Screen-printable sol-gel enzyme-containing carbon inks.

    Science.gov (United States)

    Wang, J; Pamidi, P V; Park, D S

    1996-08-01

    Enzymes usually cannot withstand the high-temperature curing associated with the thick-film fabrication process and require a separate immobilization step in connection with the production of single-use biosensors. We report on the development of sol-gel-derived enzyme-containing carbon inks that display compatibility with the screen-printing process. Such coupling of sol-gel and thick-film technologies offers a one-step fabrication of disposable enzyme electrodes, as it obviates the need for thermal curing. The enzyme-containing sol-gel carbon ink, prepared by dispersing the biocatalyst, along with the graphite powder and a binder, within the sol-gel precursors, is cured very rapidly (10 min) at low temperature (4 °C). The influence of the ink preparation conditions is explored, and the sensor performance is evaluated in connection with the incorporation of glucose oxidase or horseradish peroxidase. The resulting strips are stable for at least 3 months. Such sol-gel-derived carbon inks should serve as hosts for other heat-sensitive biomaterials in connection with the microfabrication of various thick-film biosensors.

  19. Expression of enzymes in yeast for lignocellulose derived oligomer CBP

    Science.gov (United States)

    McBride, John E.; Wiswall, Erin; Shikhare, Indraneel; Xu, Haowen; Thorngren, Naomi; Hau, Heidi H.; Stonehouse, Emily

    2017-08-29

    The present invention provides a multi-component enzyme system that hydrolyzes hemicellulose oligomers from hardwood which can be expressed, for example, in yeast such as Saccharomyces cerevisiae. In some embodiments, this invention provides for the engineering of a series of biocatalysts combining the expression and secretion of components of this enzymatic system with robust, rapid xylose utilization, and ethanol fermentation under industrially relevant process conditions for consolidated bioprocessing. In some embodiments, the invention utilizes co-cultures of strains that can achieve significantly improved performance due to the incorporation of additional enzymes in the fermentation system.

  20. Tantalum strength model incorporating temperature, strain rate and pressure

    Science.gov (United States)

    Lim, Hojun; Battaile, Corbett; Brown, Justin; Lane, Matt

    Tantalum is a body-centered-cubic (BCC) refractory metal that is widely used in many applications in high temperature, strain rate and pressure environments. In this work, we propose a physically-based strength model for tantalum that incorporates effects of temperature, strain rate and pressure. A constitutive model for single crystal tantalum is developed based on dislocation kink-pair theory, and calibrated to measurements on single crystal specimens. The model is then used to predict deformations of single- and polycrystalline tantalum. In addition, the proposed strength model is implemented into Sandia's ALEGRA solid dynamics code to predict plastic deformations of tantalum in engineering-scale applications at extreme conditions, e.g. Taylor impact tests and Z machine's high pressure ramp compression tests, and the results are compared with available experimental data. Sandia National Laboratories is a multi program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  1. A facile and efficient method of enzyme immobilization on silica particles via Michael acceptor film coatings: immobilized catalase in a plug flow reactor.

    Science.gov (United States)

    Bayramoglu, Gulay; Arica, M Yakup; Genc, Aysenur; Ozalp, V Cengiz; Ince, Ahmet; Bicak, Niyazi

    2016-06-01

    A novel method was developed for facile immobilization of enzymes on silica surfaces. Herein, we describe a single-step strategy for generating of reactive double bonds capable of Michael addition on the surfaces of silica particles. This method was based on reactive thin film generation on the surfaces by heating of impregnated self-curable polymer, alpha-morpholine substituted poly(vinyl methyl ketone) p(VMK). The generated double bonds were demonstrated to be an efficient way for rapid incorporation of enzymes via Michael addition. Catalase was used as model enzyme in order to test the effect of immobilization methodology by the reactive film surface through Michael addition reaction. Finally, a plug flow type immobilized enzyme reactor was employed to estimate decomposition rate of hydrogen peroxide. The highly stable enzyme reactor could operate continuously for 120 h at 30 °C with only a loss of about 36 % of its initial activity.

  2. Enzyme stabilization for pesticide degradation

    Energy Technology Data Exchange (ETDEWEB)

    Rivers, D.B.; Frazer, F.R. III; Mason, D.W.; Tice, T.R.

    1988-01-01

    Enzymes offer inherent advantages and limitations as active components of formulations used to decontaminate soil and equipment contaminated with toxic materials such as pesticides. Because of the catalytic nature of enzymes, each molecule of enzyme has the potential to destroy countless molecules of a contaminating toxic compound. This degradation takes place under mild environmental conditions of pH, temperature, pressure, and solvent. The basic limitation of enzymes is their degree of stability during storage and application conditions. Stabilizing methods such as the use of additives, covalent crosslinking, covalent attachment, gel entrapment, and microencapsulation have been directed developing an enzyme preparation that is stable under extremes of pH, temperature, and exposure to organic solvents. Initial studies were conducted using the model enzymes subtilisin and horseradish peroxidase.

  3. Modeling fraud detection and the incorporation of forensic specialists in the audit process

    DEFF Research Database (Denmark)

    Sakalauskaite, Dominyka

    Financial statement audits are still comparatively poor in fraud detection. Forensic specialists can play a significant role in increasing audit quality. In this paper, based on prior academic research, I develop a model of fraud detection and the incorporation of forensic specialists in the audit...... process. The intention of the model is to identify the reasons why the audit is weak in fraud detection and to provide the analytical framework to assess whether the incorporation of forensic specialists can help to improve it. The results show that such specialists can potentially improve the fraud...... detection in the audit, but might also cause some negative implications. Overall, even though fraud detection is one of the main topics in research there are very few studies done on the subject of how auditors co-operate with forensic specialists. Thus, the paper concludes with suggestions for further...

  4. Homology modelling of Drosophila cytochrome P450 enzymes associated with insecticide resistance.

    Science.gov (United States)

    Jones, Robert T; Bakker, Saskia E; Stone, Deborah; Shuttleworth, Sally N; Boundy, Sam; McCart, Caroline; Daborn, Phillip J; ffrench-Constant, Richard H; van den Elsen, Jean M H

    2010-10-01

    Overexpression of the cytochrome P450 gene Cyp6g1 confers resistance against DDT and a broad range of other insecticides in Drosophila melanogaster Meig. In the absence of crystal structures of CYP6G1 or complexes with its substrates, structural studies rely on homology modelling and ligand docking to understand P450-substrate interactions. Homology models are presented for CYP6G1, a P450 associated with resistance to DDT and neonicotinoids, and two other enzymes associated with insecticide resistance in D. melanogaster, CYP12D1 and CYP6A2. The models are based on a template of the X-ray structure of the phylogenetically related human CYP3A4, which is known for its broad substrate specificity. The model of CYP6G1 has a much smaller active site cavity than the template. The cavity is also 'V'-shaped and is lined with hydrophobic residues, showing high shape and chemical complementarity with the molecular characteristics of DDT. Comparison of the DDT-CYP6G1 complex and a non-resistant CYP6A2 homology model implies that tight-fit recognition of this insecticide is important in CYP6G1. The active site can accommodate differently shaped substrates ranging from imidacloprid to malathion but not the pyrethroids permethrin and cyfluthrin. The CYP6G1, CYP12D1 and CYP6A2 homology models can provide a structural insight into insecticide resistance in flies overexpressing P450 enzymes with broad substrate specificities.

  5. Upscaling of enzyme enhanced CO2 capture

    DEFF Research Database (Denmark)

    Gladis, Arne Berthold

    Fossil fuels are the backbone of the energy generation in the coming decades for USA, China, India and Europe, hence high greenhouse gas emissions are expected in future. Carbon capture and storage technology (CCS) is the only technology that can mitigate greenhouse gas emissions from fossil fuel...... the mass transfer of CO2 with slow-capturing but energetically favorable solvents can open up a variety of new process options for this technology. The ubiquitous enzyme carbonic anhydrase (CA), which enhances the mass transfer of CO2 in the lungs by catalyzing the reversible hydration of CO2, is one very...... enhanced CO2 capture technology by identifying the potentials and limitations in lab and in pilot scale and benchmarking the process against proven technologies. The main goal was to derive a realistic process model for technical size absorbers with a wide range of validity incorporating a mechanistic...

  6. Silica Sol-Gel Entrapment of the Enzyme Chloro peroxidase

    International Nuclear Information System (INIS)

    Le, T.; Chan, S.; Ebaid, B.; Sommerhalter, M.

    2015-01-01

    The enzyme chloro peroxidase (CPO) was immobilized in silica sol-gel beads prepared from tetramethoxysilane. The average pore diameter of the silica host structure (∼3 nm) was smaller than the globular CPO diameter (∼6 nm) and the enzyme remained entrapped after sol-gel maturation. The catalytic performance of the entrapped enzyme was assessed via the pyrogallol peroxidation reaction. Sol-gel beads loaded with 4 μg CPO per mL sol solution reached 9-12% relative activity compared to free CPO in solution. Enzyme kinetic analysis revealed a decrease in K_cat but no changes in K_M or K_I . Product release or enzyme damage might thus limit catalytic performance. Yet circular dichroism and visible absorption spectra of transparent CPO sol-gel sheets did not indicate enzyme damage. Activity decline due to methanol exposure was shown to be reversible in solution. To improve catalytic performance the sol-gel protocol was modified. The incorporation of 5, 20, or 40% methyltrimethoxysilane resulted in more brittle sol-gel beads but the catalytic performance increased to 14% relative to free CPO in solution. The use of more acidic casting buffers (ph 4.5 or 5.5 instead of 6.5) resulted in a more porous silica host reaching up to 18% relative activity

  7. Enzymes in lipid modification: From classical biocatalysis with commercial enzymes to advanced protein engineering tools

    Directory of Open Access Journals (Sweden)

    Bornscheuer Uwe T.

    2013-01-01

    Full Text Available In this review, the application of enzymes, especially lipases, for the modification of fats and oils is covered. This includes the lipase-catalyzed selective production of structured triglycerides and the isolation or incorporation of specific fatty acids. Protein engineering methods to modify lipases on a molecular level were used to alter the fatty acid chain-length and ‘‘trans over cis’’ selectivity of lipase A from Candida antarctica. Furthermore, an enzymatic cascade reaction to remove 3-monochloropropanediol and the identification of a phospholipase C for degumming are briefly covered.

  8. Incorporating damage mechanics into explosion simulation models

    International Nuclear Information System (INIS)

    Sammis, C.G.

    1993-01-01

    The source region of an underground explosion is commonly modeled as a nested series of shells. In the innermost open-quotes hydrodynamic regimeclose quotes pressures and temperatures are sufficiently high that the rock deforms as a fluid and may be described using a PVT equation of state. Just beyond the hydrodynamic regime, is the open-quotes non-linear regimeclose quotes in which the rock has shear strength but the deformation is nonlinear. This regime extends out to the open-quotes elastic radiusclose quotes beyond which the deformation is linear. In this paper, we develop a model for the non-linear regime in crystalline source rock where the nonlinearity is mostly due to fractures. We divide the non-linear regime into a open-quotes damage regimeclose quotes in which the stresses are sufficiently high to nucleate new fractures from preexisting ones and a open-quotes crack-slidingclose quotes regime where motion on preexisting cracks produces amplitude dependent attenuation and other non-linear effects, but no new cracks are nucleated. The boundary between these two regimes is called the open-quotes damage radius.close quotes The micromechanical damage mechanics recently developed by Ashby and Sammis (1990) is used to write an analytic expression for the damage radius in terms of the initial fracture spectrum of the source rock, and to develop an algorithm which may be used to incorporate damage mechanics into computer source models for the damage regime. Effects of water saturation and loading rate are also discussed

  9. Highly efficient enzyme encapsulation in a protein nanocage: towards enzyme catalysis in a cellular nanocompartment mimic

    Science.gov (United States)

    Schoonen, Lise; Nolte, Roeland J. M.; van Hest, Jan C. M.

    2016-07-01

    The study of enzyme behavior in small nanocompartments is crucial for the understanding of biocatalytic processes in the cellular environment. We have developed an enzymatic conjugation strategy to attach a model enzyme to the interior of a cowpea chlorotic mottle virus capsid. It is shown that with this methodology high encapsulation efficiencies can be achieved. Additionally, we demonstrate that the encapsulation does not affect the enzyme performance in terms of a decreased activity or a hampered substrate diffusion. Finally, it is shown that the encapsulated enzymes are protected against proteases. We believe that our strategy can be used to study enzyme kinetics in an environment that approaches physiological conditions.The study of enzyme behavior in small nanocompartments is crucial for the understanding of biocatalytic processes in the cellular environment. We have developed an enzymatic conjugation strategy to attach a model enzyme to the interior of a cowpea chlorotic mottle virus capsid. It is shown that with this methodology high encapsulation efficiencies can be achieved. Additionally, we demonstrate that the encapsulation does not affect the enzyme performance in terms of a decreased activity or a hampered substrate diffusion. Finally, it is shown that the encapsulated enzymes are protected against proteases. We believe that our strategy can be used to study enzyme kinetics in an environment that approaches physiological conditions. Electronic supplementary information (ESI) available: Experimental procedures for the cloning, expression, and purification of all proteins, as well as supplementary figures and calculations. See DOI: 10.1039/c6nr04181g

  10. Molecular Modeling of Enzyme Dynamics Towards Understanding Solvent Effects

    DEFF Research Database (Denmark)

    Wedberg, Nils Hejle Rasmus Ingemar

    This thesis describes the development of a molecular simulation methodology to study properties of enzymes in non-aqueous media at fixed thermodynamic water activities. The methodology is applied in a molecular dynamics study of the industrially important enzyme Candida antarctica lipase B (CALB...... of enzyme kinetics in non-aqueous media, it has been a fruitful approach to fix the enzyme hydration level by controlling the water activity of the medium. In this work, a protocol is therefore developed for determining the water activity in non-aqueous protein simulations. The method relies on determining...... integration, while for small systems, it seems to be even better. The method is applied to compute the excess Gibbs energy of the mixtures of water and organic solvents used in the simulations of CALB. This allows to determine the water activity of the simulated systems and thus to compare protein properties...

  11. Mesoscopic dynamics of diffusion-influenced enzyme kinetics.

    Science.gov (United States)

    Chen, Jiang-Xing; Kapral, Raymond

    2011-01-28

    A particle-based mesoscopic model for enzyme kinetics is constructed and used to investigate the influence of diffusion on the reactive dynamics. Enzymes and enzyme-substrate complexes are modeled as finite-size soft spherical particles, while substrate, product, and solvent molecules are point particles. The system is evolved using a hybrid molecular dynamics-multiparticle collision dynamics scheme. Both the nonreactive and reactive dynamics are constructed to satisfy mass, momentum, and energy conservation laws, and reversible reaction steps satisfy detailed balance. Hydrodynamic interactions among the enzymes and complexes are automatically accounted for in the dynamics. Diffusion manifests itself in various ways, notably in power-law behavior in the evolution of the species concentrations. In accord with earlier investigations, regimes where the product production rate exhibits either monotonic or nonmonotonic behavior as a function of time are found. In addition, the species concentrations display both t(-1/2) and t(-3/2) power-law behavior, depending on the dynamical regime under investigation. For high enzyme volume fractions, cooperative effects influence the enzyme kinetics. The time dependent rate coefficient determined from the mass action rate law is computed and shown to depend on the enzyme concentration. Lifetime distributions of substrate molecules newly released in complex dissociation events are determined and shown to have either a power-law form for rebinding to the same enzyme from which they were released or an exponential form for rebinding to different enzymes. The model can be used and extended to explore a variety of issues related concentration effects and diffusion on enzyme kinetics.

  12. Mesoscopic dynamics of diffusion-influenced enzyme kinetics

    Science.gov (United States)

    Chen, Jiang-Xing; Kapral, Raymond

    2011-01-01

    A particle-based mesoscopic model for enzyme kinetics is constructed and used to investigate the influence of diffusion on the reactive dynamics. Enzymes and enzyme-substrate complexes are modeled as finite-size soft spherical particles, while substrate, product, and solvent molecules are point particles. The system is evolved using a hybrid molecular dynamics-multiparticle collision dynamics scheme. Both the nonreactive and reactive dynamics are constructed to satisfy mass, momentum, and energy conservation laws, and reversible reaction steps satisfy detailed balance. Hydrodynamic interactions among the enzymes and complexes are automatically accounted for in the dynamics. Diffusion manifests itself in various ways, notably in power-law behavior in the evolution of the species concentrations. In accord with earlier investigations, regimes where the product production rate exhibits either monotonic or nonmonotonic behavior as a function of time are found. In addition, the species concentrations display both t^{-1/2} and t^{-3/2} power-law behavior, depending on the dynamical regime under investigation. For high enzyme volume fractions, cooperative effects influence the enzyme kinetics. The time dependent rate coefficient determined from the mass action rate law is computed and shown to depend on the enzyme concentration. Lifetime distributions of substrate molecules newly released in complex dissociation events are determined and shown to have either a power-law form for rebinding to the same enzyme from which they were released or an exponential form for rebinding to different enzymes. The model can be used and extended to explore a variety of issues related concentration effects and diffusion on enzyme kinetics.

  13. Enzymatic mineralization of hydrogels for bone tissue engineering by incorporation of alkaline phosphatase.

    NARCIS (Netherlands)

    Douglas, T.E.L.; Messersmith, P.B.; Chasan, S.; Mikos, A.G.; Mulder, E.L.W. de; Dickson, G.; Schaubroeck, D.; Balcaen, L.; Vanhaecke, F.; Dubruel, P.; Jansen, J.A.; Leeuwenburgh, S.C.G.

    2012-01-01

    Alkaline phosphatase (ALP), an enzyme involved in mineralization of bone, is incorporated into three hydrogel biomaterials to induce their mineralization with calcium phosphate (CaP). These are collagen type I, a mussel-protein-inspired adhesive consisting of PEG substituted with catechol groups,

  14. Incorporating vehicle mix in stimulus-response car-following models

    Directory of Open Access Journals (Sweden)

    Saidi Siuhi

    2016-06-01

    Full Text Available The objective of this paper is to incorporate vehicle mix in stimulus-response car-following models. Separate models were estimated for acceleration and deceleration responses to account for vehicle mix via both movement state and vehicle type. For each model, three sub-models were developed for different pairs of following vehicles including “automobile following automobile,” “automobile following truck,” and “truck following automobile.” The estimated model parameters were then validated against other data from a similar region and roadway. The results indicated that drivers' behaviors were significantly different among the different pairs of following vehicles. Also the magnitude of the estimated parameters depends on the type of vehicle being driven and/or followed. These results demonstrated the need to use separate models depending on movement state and vehicle type. The differences in parameter estimates confirmed in this paper highlight traffic safety and operational issues of mixed traffic operation on a single lane. The findings of this paper can assist transportation professionals to improve traffic simulation models used to evaluate the impact of different strategies on ameliorate safety and performance of highways. In addition, driver response time lag estimates can be used in roadway design to calculate important design parameters such as stopping sight distance on horizontal and vertical curves for both automobiles and trucks.

  15. A data-driven model for influenza transmission incorporating media effects.

    Science.gov (United States)

    Mitchell, Lewis; Ross, Joshua V

    2016-10-01

    Numerous studies have attempted to model the effect of mass media on the transmission of diseases such as influenza; however, quantitative data on media engagement has until recently been difficult to obtain. With the recent explosion of 'big data' coming from online social media and the like, large volumes of data on a population's engagement with mass media during an epidemic are becoming available to researchers. In this study, we combine an online dataset comprising millions of shared messages relating to influenza with traditional surveillance data on flu activity to suggest a functional form for the relationship between the two. Using this data, we present a simple deterministic model for influenza dynamics incorporating media effects, and show that such a model helps explain the dynamics of historical influenza outbreaks. Furthermore, through model selection we show that the proposed media function fits historical data better than other media functions proposed in earlier studies.

  16. Incorporating microbiota data into epidemiologic models: examples from vaginal microbiota research.

    Science.gov (United States)

    van de Wijgert, Janneke H; Jespers, Vicky

    2016-05-01

    Next generation sequencing and quantitative polymerase chain reaction technologies are now widely available, and research incorporating these methods is growing exponentially. In the vaginal microbiota (VMB) field, most research to date has been descriptive. The purpose of this article is to provide an overview of different ways in which next generation sequencing and quantitative polymerase chain reaction data can be used to answer clinical epidemiologic research questions using examples from VMB research. We reviewed relevant methodological literature and VMB articles (published between 2008 and 2015) that incorporated these methodologies. VMB data have been analyzed using ecologic methods, methods that compare the presence or relative abundance of individual taxa or community compositions between different groups of women or sampling time points, and methods that first reduce the complexity of the data into a few variables followed by the incorporation of these variables into traditional biostatistical models. To make future VMB research more clinically relevant (such as studying associations between VMB compositions and clinical outcomes and the effects of interventions on the VMB), it is important that these methods are integrated with rigorous epidemiologic methods (such as appropriate study designs, sampling strategies, and adjustment for confounding). Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

  17. Comparison of Natural and Engineered Chlorophenol Bioremediation Enzymes

    Science.gov (United States)

    2015-02-26

    herein addresses the urgent need to incorporate biological strategies into environmental restoration efforts ( bioremediation ) that focus on the catalytic... Bioremediation Enzymes The views, opinions and/or findings contained in this report are those of the author(s) and should not contrued as an official Department...Army Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 dehaloperoxidase, bioremediation , halophenol, Amphitrite ornata, marine

  18. Evaluation of the efficiency of alternative enzyme production technologies

    Energy Technology Data Exchange (ETDEWEB)

    Albaek, M.O.

    2012-03-15

    Enzymes are used in an increasing number of industries. The application of enzymes is extending into the production of lignocellulosic ethanol in processes that economically can compete with fossil fuels. Since lignocellulosic ethanol is based on renewable resources it will have a positive impact on for example the emission of green house gasses. Cellulases and hemi-cellulases are used for enzymatic hydrolysis of pretreated lignocellulosic biomass, and fermentable sugars are released upon the enzymatic process. Even though many years of research has decreased the amount of enzyme needed in the process, the cost of enzymes is still considered a bottleneck in the economic feasibility of lignocellulose utilization. The purpose of this project was to investigate and compare different technologies for production of these enzymes. The filamentous fungus Trichoderma reesei is currently used for industrial production of cellulases and hemi-cellulases. The aim of the thesis was to use modeling tools to identify alternative technologies that have higher energy or raw material efficiency than the current technology. The enzyme production by T. reesei was conducted as an aerobic fed-batch fermentation. The process was carried out in pilot scale stirred tank reactors and based on a range of different process conditions, a process model was constructed which satisfactory described the course of fermentation. The process was governed by the rate limiting mass transfer of oxygen from the gas to the liquid phase. During fermentation, filamentous growth of the fungus lead to increased viscosity which hindered mass transfer. These mechanisms were described by a viscosity model based on the biomass concentration of the fermentation broth and a mass transfer correlation that incorporated a viscosity term. An analysis of the uncertainty and sensitivity of the model indicated the biological parameters to be responsible for most of the model uncertainty. A number of alternative

  19. A Self-Assembling Protein Hydrogel Technology for Enzyme Incorporation onto Electrodes in Biofuel Cells

    Science.gov (United States)

    2015-10-26

    an ordered 3-dimentional space. In the first stage, we constructed protein building blocks able to self-assemble into 3D protein hydrogel upon...Chem 23, 1891-1901 (2012). 26. Jung, S. & Yi, H. Facile Strategy for Protein Conjugation with Chitosan -Poly(ethylene glycol) Hybrid Microparticle...multiple enzymes in an ordered 3-dimentional space. In the first stage, we constructed protein building blocks able to self-assemble into 3D protein

  20. Chronic ethanol feeding modulates the synthesis of digestive enzymes

    International Nuclear Information System (INIS)

    Ponnappa, B.C.; Hoek, J.B.; Rubin, E.

    1987-01-01

    The effects of chronic ethanol feeding on pancreatic protein synthesis were investigated. Protein synthesis was assessed by studying the rate of incorporation of 3 H-leucine into TCA-precipitable proteins in isolated pancreatic acini from rats. Chronic ethanol ingestion increased the rate of pancreatic protein synthesis by 2-4 fold. The onset of the increase in protein synthesis was detectable two days after ethanol feeding, reached a maximum after 7 days and remained unchanged after 4 months on the ethanol-containing diet. The rate of synthesis of individual digestive enzymes was studied by SDS-PAGE on extracts obtained from purified zymogen granules. Ethanol feeding induced an increase in the rate of synthesis of most of the digestive enzymes; chymotrypsinogen, trypsinogen and an unidentified protein were increased to a greater extent than other digestive enzymes. By contrast, the synthesis of amylase was selectively decreased after ethanol feeding. These results suggest that chronic ethanol ingestion has specific effects on the rate of synthesis of individual digestive enzymes in the exocrine pancreas

  1. [Inflammatory pancreatic disease due to enzyme autodigestion: an exceptional model of glandular crinophagy].

    Science.gov (United States)

    Sánchez-Fayos Calabuig, P; Martín Relloso, M Jesús; González Guirado, Agustina; Porres Cubero, Juan Carlos

    2007-01-01

    The exocrine pancreas is a functionally dangerous structure since it is exposed to digestion by its most aggressive enzymes (proteases, etc) despite self-protective measures such as the synthesis of some of these enzymes in the form of inactive zymogens (trypsinogen, etc.). We review inflammatory pancreatic disease by separately analyzing its classical forms of onset: acute and chronic pancreatitis (AP and CP). There is general consensus that the initial pathogenic event in AP is intraacinar activation of trypsinogen into trypsin, followed by that of the remaining proenzymes, giving rise to an unusual model of autophagic inflammation. In contrast, consensus is lacking on the initial pathogenic event in CP (toxic-metabolic lesion, oxidative stress, ductal hypertension, etc.?), although in some cases a sequence due to recurrent episodes of AP seems evident. The pathogenic features shared by both forms of the disease and which justify some recent attempts to formulate an overall explanation of the pathogenesis of pancreatitis are discussed. Such an explanation would place both forms of pancreatitis within the conceptual framework of an pancreatic disease due to enzyme autodigestion>.

  2. Incorporating Social Anxiety Into a Model of College Problem Drinking: Replication and Extension

    OpenAIRE

    Ham, Lindsay S.; Hope, Debra A.

    2006-01-01

    Although research has found an association between social anxiety and alcohol use in noncollege samples, results have been mixed for college samples. College students face many novel social situations in which they may drink to reduce social anxiety. In the current study, the authors tested a model of college problem drinking, incorporating social anxiety and related psychosocial variables among 228 undergraduate volunteers. According to structural equation modeling (SEM) results, social anxi...

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

    NARCIS (Netherlands)

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

    2002-01-01

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

  4. Modeling physiological processes in plankton on enzyme kinetic principles

    Directory of Open Access Journals (Sweden)

    Ted Packard

    2004-04-01

    Full Text Available Many ecologically important chemical transformations in the ocean are controlled by biochemical enzyme reactions in plankton. Nitrogenase regulates the transformation of N2 to ammonium in some cyanobacteria and serves as the entryway for N2 into the ocean biosphere. Nitrate reductase controls the reduction of NO3 to NO2 and hence new production in phytoplankton. The respiratory electron transfer system in all organisms links the carbon oxidation reactions of intermediary metabolism with the reduction of oxygen in respiration. Rubisco controls the fixation of CO2 into organic matter in phytoplankton and thus is the major entry point of carbon into the oceanic biosphere. In addition to these, there are the enzymes that control CO2 production, NH4 excretion and the fluxes of phosphate. Some of these enzymes have been recognized and researched by marine scientists in the last thirty years. However, until recently the kinetic principles of enzyme control have not been exploited to formulate accurate mathematical equations of the controlling physiological expressions. Were such expressions available they would increase our power to predict the rates of chemical transformations in the extracellular environment of microbial populations whether this extracellular environment is culture media or the ocean. Here we formulate from the principles of bisubstrate enzyme kinetics, mathematical expressions for the processes of NO3 reduction, O2 consumption, N2 fixation, total nitrogen uptake.

  5. Incorporating ligament laxity in a finite element model for the upper cervical spine.

    Science.gov (United States)

    Lasswell, Timothy L; Cronin, Duane S; Medley, John B; Rasoulinejad, Parham

    2017-11-01

    Predicting physiological range of motion (ROM) using a finite element (FE) model of the upper cervical spine requires the incorporation of ligament laxity. The effect of ligament laxity can be observed only on a macro level of joint motion and is lost once ligaments have been dissected and preconditioned for experimental testing. As a result, although ligament laxity values are recognized to exist, specific values are not directly available in the literature for use in FE models. The purpose of the current study is to propose an optimization process that can be used to determine a set of ligament laxity values for upper cervical spine FE models. Furthermore, an FE model that includes ligament laxity is applied, and the resulting ROM values are compared with experimental data for physiological ROM, as well as experimental data for the increase in ROM when a Type II odontoid fracture is introduced. The upper cervical spine FE model was adapted from a 50th percentile male full-body model developed with the Global Human Body Models Consortium (GHBMC). FE modeling was performed in LS-DYNA and LS-OPT (Livermore Software Technology Group) was used for ligament laxity optimization. Ordinate-based curve matching was used to minimize the mean squared error (MSE) between computed load-rotation curves and experimental load-rotation curves under flexion, extension, and axial rotation with pure moment loads from 0 to 3.5 Nm. Lateral bending was excluded from the optimization because the upper cervical spine was considered to be primarily responsible for flexion, extension, and axial rotation. Based on recommendations from the literature, four varying inputs representing laxity in select ligaments were optimized to minimize the MSE. Funding was provided by the Natural Sciences and Engineering Research Council of Canada as well as GHMBC. The present study was funded by the Natural Sciences and Engineering Research Council of Canada to support the work of one graduate student

  6. Modeling the effects of tree species and incubation temperature on soil's extracellular enzyme activity in 78-year-old tree plantations

    Science.gov (United States)

    Zhou, Xiaoqi; Wang, Shen S. J.; Chen, Chengrong

    2017-12-01

    Forest plantations have been widely used as an effective measure for increasing soil carbon (C), and nitrogen (N) stocks and soil enzyme activities play a key role in soil C and N losses during decomposition of soil organic matter. However, few studies have been carried out to elucidate the mechanisms behind the differences in soil C and N cycling by different tree species in response to climate warming. Here, we measured the responses of soil's extracellular enzyme activity (EEA) to a gradient of temperatures using incubation methods in 78-year-old forest plantations with different tree species. Based on a soil enzyme kinetics model, we established a new statistical model to investigate the effects of temperature and tree species on soil EEA. In addition, we established a tree species-enzyme-C/N model to investigate how temperature and tree species influence soil C/N contents over time without considering plant C inputs. These extracellular enzymes included C acquisition enzymes (β-glucosidase, BG), N acquisition enzymes (N-acetylglucosaminidase, NAG; leucine aminopeptidase, LAP) and phosphorus acquisition enzymes (acid phosphatases). The results showed that incubation temperature and tree species significantly influenced all soil EEA and Eucalyptus had 1.01-2.86 times higher soil EEA than coniferous tree species. Modeling showed that Eucalyptus had larger soil C losses but had 0.99-2.38 times longer soil C residence time than the coniferous tree species over time. The differences in the residual soil C and N contents between Eucalyptus and coniferous tree species, as well as between slash pine (Pinus elliottii Engelm. var. elliottii) and hoop pine (Araucaria cunninghamii Ait.), increase with time. On the other hand, the modeling results help explain why exotic slash pine can grow faster, as it has 1.22-1.38 times longer residual soil N residence time for LAP, which mediate soil N cycling in the long term, than native coniferous tree species like hoop pine and

  7. New types of experimental data shape the use of enzyme kinetics for dynamic network modeling.

    Science.gov (United States)

    Tummler, Katja; Lubitz, Timo; Schelker, Max; Klipp, Edda

    2014-01-01

    Since the publication of Leonor Michaelis and Maude Menten's paper on the reaction kinetics of the enzyme invertase in 1913, molecular biology has evolved tremendously. New measurement techniques allow in vivo characterization of the whole genome, proteome or transcriptome of cells, whereas the classical enzyme essay only allows determination of the two Michaelis-Menten parameters V and K(m). Nevertheless, Michaelis-Menten kinetics are still commonly used, not only in the in vitro context of enzyme characterization but also as a rate law for enzymatic reactions in larger biochemical reaction networks. In this review, we give an overview of the historical development of kinetic rate laws originating from Michaelis-Menten kinetics over the past 100 years. Furthermore, we briefly summarize the experimental techniques used for the characterization of enzymes, and discuss web resources that systematically store kinetic parameters and related information. Finally, describe the novel opportunities that arise from using these data in dynamic mathematical modeling. In this framework, traditional in vitro approaches may be combined with modern genome-scale measurements to foster thorough understanding of the underlying complex mechanisms. © 2013 FEBS.

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

    Science.gov (United States)

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

    2016-03-02

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

  9. Mononuclear non-heme iron enzymes with the 2-His-1-carboxylate facial triad: recent developments in enzymology and modeling studies.

    Science.gov (United States)

    Bruijnincx, Pieter C A; van Koten, Gerard; Klein Gebbink, Robertus J M

    2008-12-01

    Iron-containing enzymes are one of Nature's main means of effecting key biological transformations. The mononuclear non-heme iron oxygenases and oxidases have received the most attention recently, primarily because of the recent availability of crystal structures of many different enzymes and the stunningly diverse oxidative transformations that these enzymes catalyze. The wealth of available structural data has furthermore established the so-called 2-His-1-carboxylate facial triad as a new common structural motif for the activation of dioxygen. This superfamily of mononuclear iron(ii) enzymes catalyzes a wide range of oxidative transformations, ranging from the cis-dihydroxylation of arenes to the biosynthesis of antibiotics such as isopenicillin and fosfomycin. The remarkable scope of oxidative transformations seems to be even broader than that associated with oxidative heme enzymes. Not only are many of these oxidative transformations of key biological importance, many of these selective oxidations are also unprecedented in synthetic organic chemistry. In this critical review, we wish to provide a concise background on the chemistry of the mononuclear non-heme iron enzymes characterized by the 2-His-1-carboxylate facial triad and to discuss the many recent developments in the field. New examples of enzymes with unique reactivities belonging to the superfamily have been reported. Furthermore, key insights into the intricate mechanistic details and reactive intermediates have been obtained from both enzyme and modeling studies. Sections of this review are devoted to each of these subjects, i.e. the enzymes, biomimetic models, and reactive intermediates (225 references).

  10. Imidazole incorporated semicarbazone derivatives as a new class of anticonvulsants: design, synthesis and in-vivo screening.

    Science.gov (United States)

    Amir, Mohammad; Ali, Israr; Hassan, Mohd Zaheen

    2013-06-01

    A series of novel imidazole incorporated semicarbazones was synthesized using an appropriate synthetic route and characterized by spectral analysis (IR, 1H NMR, 13C NMR and Mass). The anticonvulsant activity of the synthesized compounds was determined using doses of 30, 100, and 300 mg kg-1 against maximal electroshock seizure (MES), subcutaneous pentylenetetrazole (scPTZ) induced seizure and minimal neurotoxicity test. Six compounds exhibited protection in both models and 2-(1-(4-chlorophenyl)-2-(1H-imidazol-1-yl)ethylidene)-N-p-tolylsemicarbazone emerged as the most active compound of the series without any neurotoxicity and significant CNS depressant effect. Liver enzyme estimations (SGOT, SGPT, Alkaline phosphatase) of the compound also showed no significant change in the enzymes levels. Moreover, it caused 80% elevation of γ-amino butyric acid (GABA) levels in the whole mice brain, thus indicating that it could be a promising candidate in designing of a potent anticonvulsant drug.

  11. Enzyme II/sup Mtl/ of the Escherichia coli phosphoenolpyruvate-dependent phosphotransferase system: identification of the activity-linked cysteine on the mannitol carrier

    International Nuclear Information System (INIS)

    Pas, H.H.; Robillard, G.T.

    1988-01-01

    The cysteine of the membrane-bound mannitol-specific enzyme II (EII/sup Mtl/) of the Escherichia coli phosphoenolpyruvate-dependent phosphotransferase system have been labeled with 4-vinylpyridine. After proteolytic breakdown and reversed-phase HPLC, the peptides containing cysteines 110, 384, and 571 could be identified. N-Ethylmaleimide (NEM) treatment of the native unphosphorylated enzyme results in incorporation of one NEM label per molecule and loss of enzymatic activity. NEM treatment and inactivation prevented 4-vinylpyridine incorporation into the Cys-384-containing peptide, identifying this residue as the activity-linked cysteine. Both oxidation and phosphorylation of the native enzyme protected the enzyme against NEM labeling of Cys-384. Positive identification of the activity-linked cysteine was accomplished by inactivation with [ 14 C]iodoacetamide, proteolytic fragmentation, isolation of the peptide, and amino acid sequencing

  12. Burn-induced stimulation of lysosomal enzyme synthesis in skeletal muscle

    International Nuclear Information System (INIS)

    Odessey, R.

    1986-01-01

    A localized burn injury to a rat hindlimb results in atrophy of soleus muscle (in the absence of cellular damage) which is attributable to an increase in muscle protein breakdown. Previous work has shown that lysosomal enzyme activities (cathepsins B, H, L, and D) are elevated in muscle from the burned leg by 50% to 100%. There is no change in endogenous neutral protease activity (+/- Ca ++ ). The increase in protease activity can not be attributed to changes in endogenous protease inhibitors. The latency [(Triton X100 treated - control)/triton treated] of lysosomal enzymes is approximately 50% and is not altered by burn injury. The rate of sucrose uptake is also not altered by burn. These experiments suggest that the rate of substrate supply to the lysosomal apparatus via endocytosis or autophagocytosis is not altered by burn. When muscles are preincubated with 3 H-phenylalanine or 3 H-mannose burn increased incorporation into protein of the fraction containing lysosomes by 100%. Preincubation in the presence of tunicamycin (an inhibitor of glycoprotein synthesis) inhibited incorporation of both labels into a microsomal fraction of the muscle from the burned leg, but has little effect on incorporation in the control muscle. These findings are consistent with the hypothesis that the burn-induced increase in protein breakdown is caused by an increase in lysosomal protease synthesis

  13. The hormetic effect of cadmium on the activity of antioxidant enzymes in the earthworm Eisenia fetida

    International Nuclear Information System (INIS)

    Zhang Yan; Shen Guoqing; Yu Yueshu; Zhu Hongling

    2009-01-01

    The hormetic dose-response relationships induced by environmental toxic agents are often characterized by low-dose stimulation and high-dose inhibition. Confirmation of the general phenomenon of hormesis may have significant implications for ecological risk assessment, although the mechanisms that underlie hormesis remain an enigma. In this study, a model-based approach for describing a dose-response relationship incorporating the hormetic effect was applied to the detection and estimation of the hormetic effect of cadmium (Cd) on the activity of antioxidant enzymes in the earthworm Eisenia fetida. The results showed that Cd at low concentrations induced an increase in the activity of catalase and superoxide dismutase (SOD), but high concentrations inhibited the enzymes, and this was reflected in an inverted U-shaped curve. The maximum hormetic magnitude of SOD activity was higher than that of catalase. The presence of hormesis induced by cadmium in the earthworm may be related to activation of adaptive pathways. - A model-based approach and careful preliminary experiments are needed for detecting and estimating the hormetic effect.

  14. The hormetic effect of cadmium on the activity of antioxidant enzymes in the earthworm Eisenia fetida

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Yan [Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240 (China); Shen Guoqing, E-mail: gqsh@sjtu.edu.c [Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240 (China); Yu Yueshu; Zhu Hongling [Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240 (China)

    2009-11-15

    The hormetic dose-response relationships induced by environmental toxic agents are often characterized by low-dose stimulation and high-dose inhibition. Confirmation of the general phenomenon of hormesis may have significant implications for ecological risk assessment, although the mechanisms that underlie hormesis remain an enigma. In this study, a model-based approach for describing a dose-response relationship incorporating the hormetic effect was applied to the detection and estimation of the hormetic effect of cadmium (Cd) on the activity of antioxidant enzymes in the earthworm Eisenia fetida. The results showed that Cd at low concentrations induced an increase in the activity of catalase and superoxide dismutase (SOD), but high concentrations inhibited the enzymes, and this was reflected in an inverted U-shaped curve. The maximum hormetic magnitude of SOD activity was higher than that of catalase. The presence of hormesis induced by cadmium in the earthworm may be related to activation of adaptive pathways. - A model-based approach and careful preliminary experiments are needed for detecting and estimating the hormetic effect.

  15. [Incorporation of an organic MAGIC (Model of Acidification of Groundwater in Catchments) and testing of the revised model using independent data sources]. [MAGIC Model

    Energy Technology Data Exchange (ETDEWEB)

    Sullivan, T.J.

    1992-09-01

    A project was initiated in March, 1992 to (1) incorporate a rigorous organic acid representation, based on empirical data and geochemical considerations, into the MAGIC model of acidification response, and (2) test the revised model using three sets of independent data. After six months of performance, the project is on schedule and the majority of the tasks outlined for Year 1 have been successfully completed. Major accomplishments to data include development of the organic acid modeling approach, using data from the Adirondack Lakes Survey Corporation (ALSC), and coupling the organic acid model with MAGIC for chemical hindcast comparisons. The incorporation of an organic acid representation into MAGIC can account for much of the discrepancy earlier observed between MAGIC hindcasts and paleolimnological reconstructions of preindustrial pH and alkalinity for 33 statistically-selected Adirondack lakes. Additional work is on-going for model calibration and testing with data from two whole-catchment artificial acidification projects. Results obtained thus far are being prepared as manuscripts for submission to the peer-reviewed scientific literature.

  16. Are adverse effects incorporated in economic models? An initial review of current practice.

    Science.gov (United States)

    Craig, D; McDaid, C; Fonseca, T; Stock, C; Duffy, S; Woolacott, N

    2009-12-01

    To identify methodological research on the incorporation of adverse effects in economic models and to review current practice. Major electronic databases (Cochrane Methodology Register, Health Economic Evaluations Database, NHS Economic Evaluation Database, EconLit, EMBASE, Health Management Information Consortium, IDEAS, MEDLINE and Science Citation Index) were searched from inception to September 2007. Health technology assessment (HTA) reports commissioned by the National Institute for Health Research (NIHR) HTA programme and published between 2004 and 2007 were also reviewed. The reviews of methodological research on the inclusion of adverse effects in decision models and of current practice were carried out according to standard methods. Data were summarised in a narrative synthesis. Of the 719 potentially relevant references in the methodological research review, five met the inclusion criteria; however, they contained little information of direct relevance to the incorporation of adverse effects in models. Of the 194 HTA monographs published from 2004 to 2007, 80 were reviewed, covering a range of research and therapeutic areas. In total, 85% of the reports included adverse effects in the clinical effectiveness review and 54% of the decision models included adverse effects in the model; 49% included adverse effects in the clinical review and model. The link between adverse effects in the clinical review and model was generally weak; only 3/80 (manipulation. Of the models including adverse effects, 67% used a clinical adverse effects parameter, 79% used a cost of adverse effects parameter, 86% used one of these and 60% used both. Most models (83%) used utilities, but only two (2.5%) used solely utilities to incorporate adverse effects and were explicit that the utility captured relevant adverse effects; 53% of those models that included utilities derived them from patients on treatment and could therefore be interpreted as capturing adverse effects. In total

  17. Neo-logistic model for the growth of bacteria

    OpenAIRE

    Tashiro, Tohru; Yoshimura, Fujiko

    2017-01-01

    We propose a neo-logistic model that can describe bacterial growth data precisely. This model is not derived by modifying the logistic model formally, but by incorporating the synthesis of inducible enzymes into the logistic model indirectly. Therefore, the meaning of the parameters of the neo-logistic model becomes physically clear. The neo-logistic model can approximate bacterial growth better than models previously presented, and predict the order of the saturated number of bacteria in the...

  18. Enzyme-Catalyzed Transetherification of Alkoxysilanes

    Directory of Open Access Journals (Sweden)

    Peter G. Taylor

    2013-01-01

    Full Text Available We report the first evidence of an enzyme-catalyzed transetherification of model alkoxysilanes. During an extensive enzymatic screening in the search for new biocatalysts for silicon-oxygen bond formation, we found that certain enzymes promoted the transetherification of alkoxysilanes when tert-butanol or 1-octanol were used as the reaction solvents.

  19. Incorporation of detailed eye model into polygon-mesh versions of ICRP-110 reference phantoms.

    Science.gov (United States)

    Nguyen, Thang Tat; Yeom, Yeon Soo; Kim, Han Sung; Wang, Zhao Jun; Han, Min Cheol; Kim, Chan Hyeong; Lee, Jai Ki; Zankl, Maria; Petoussi-Henss, Nina; Bolch, Wesley E; Lee, Choonsik; Chung, Beom Sun

    2015-11-21

    The dose coefficients for the eye lens reported in ICRP 2010 Publication 116 were calculated using both a stylized model and the ICRP-110 reference phantoms, according to the type of radiation, energy, and irradiation geometry. To maintain consistency of lens dose assessment, in the present study we incorporated the ICRP-116 detailed eye model into the converted polygon-mesh (PM) version of the ICRP-110 reference phantoms. After the incorporation, the dose coefficients for the eye lens were calculated and compared with those of the ICRP-116 data. The results showed generally a good agreement between the newly calculated lens dose coefficients and the values of ICRP 2010 Publication 116. Significant differences were found for some irradiation cases due mainly to the use of different types of phantoms. Considering that the PM version of the ICRP-110 reference phantoms preserve the original topology of the ICRP-110 reference phantoms, it is believed that the PM version phantoms, along with the detailed eye model, provide more reliable and consistent dose coefficients for the eye lens.

  20. Modeling the effects of tree species and incubation temperature on soil's extracellular enzyme activity in 78-year-old tree plantations

    Directory of Open Access Journals (Sweden)

    X. Zhou

    2017-12-01

    Full Text Available Forest plantations have been widely used as an effective measure for increasing soil carbon (C, and nitrogen (N stocks and soil enzyme activities play a key role in soil C and N losses during decomposition of soil organic matter. However, few studies have been carried out to elucidate the mechanisms behind the differences in soil C and N cycling by different tree species in response to climate warming. Here, we measured the responses of soil's extracellular enzyme activity (EEA to a gradient of temperatures using incubation methods in 78-year-old forest plantations with different tree species. Based on a soil enzyme kinetics model, we established a new statistical model to investigate the effects of temperature and tree species on soil EEA. In addition, we established a tree species–enzyme–C∕N model to investigate how temperature and tree species influence soil C∕N contents over time without considering plant C inputs. These extracellular enzymes included C acquisition enzymes (β-glucosidase, BG, N acquisition enzymes (N-acetylglucosaminidase, NAG; leucine aminopeptidase, LAP and phosphorus acquisition enzymes (acid phosphatases. The results showed that incubation temperature and tree species significantly influenced all soil EEA and Eucalyptus had 1.01–2.86 times higher soil EEA than coniferous tree species. Modeling showed that Eucalyptus had larger soil C losses but had 0.99–2.38 times longer soil C residence time than the coniferous tree species over time. The differences in the residual soil C and N contents between Eucalyptus and coniferous tree species, as well as between slash pine (Pinus elliottii Engelm. var. elliottii and hoop pine (Araucaria cunninghamii Ait., increase with time. On the other hand, the modeling results help explain why exotic slash pine can grow faster, as it has 1.22–1.38 times longer residual soil N residence time for LAP, which mediate soil N cycling in the long term, than native

  1. Thermometric enzyme linked immunosorbent assay: TELISA.

    Science.gov (United States)

    Mattiasson, B; Borrebaeck, C; Sanfridson, B; Mosbach, K

    1977-08-11

    A new method, thermometric enzyme linked immunosorbent assay (TELISA), for the assay of endogenous and exogenous compounds in biological fluids is described. It is based on the previously described enzyme linked immunosorbent assay technique, ELISA, but utilizes enzymic heat formation which is measured in an enzyme thermistor unit. In the model system studied determination of human serum albumin down to a concentration of 10(-10) M (5 ng/ml) was achieved, with both normal and catalase labelled human serum albumin competing for the binding sites on the immunosorbent, which was rabbit antihuman serum albumin immobilized onto Sepharose CL-4B.

  2. Thermodynamic Activity-Based Progress Curve Analysis in Enzyme Kinetics.

    Science.gov (United States)

    Pleiss, Jürgen

    2018-03-01

    Macrokinetic Michaelis-Menten models based on thermodynamic activity provide insights into enzyme kinetics because they separate substrate-enzyme from substrate-solvent interactions. Kinetic parameters are estimated from experimental progress curves of enzyme-catalyzed reactions. Three pitfalls are discussed: deviations between thermodynamic and concentration-based models, product effects on the substrate activity coefficient, and product inhibition. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Site-specific bioconjugation of a murine dihydrofolate reductase enzyme by copper(I-catalyzed azide-alkyne cycloaddition with retained activity.

    Directory of Open Access Journals (Sweden)

    Sung In Lim

    Full Text Available Cu(I-catalyzed azide-alkyne cycloaddition (CuAAC is an efficient reaction linking an azido and an alkynyl group in the presence of copper catalyst. Incorporation of a non-natural amino acid (NAA containing either an azido or an alkynyl group into a protein allows site-specific bioconjugation in mild conditions via CuAAC. Despite its great potential, bioconjugation of an enzyme has been hampered by several issues including low yield, poor solubility of a ligand, and protein structural/functional perturbation by CuAAC components. In the present study, we incorporated an alkyne-bearing NAA into an enzyme, murine dihydrofolate reductase (mDHFR, in high cell density cultivation of Escherichia coli, and performed CuAAC conjugation with fluorescent azide dyes to evaluate enzyme compatibility of various CuAAC conditions comprising combination of commercially available Cu(I-chelating ligands and reductants. The condensed culture improves the protein yield 19-fold based on the same amount of non-natural amino acid, and the enzyme incubation under the optimized reaction condition did not lead to any activity loss but allowed a fast and high-yield bioconjugation. Using the established conditions, a biotin-azide spacer was efficiently conjugated to mDHFR with retained activity leading to the site-specific immobilization of the biotin-conjugated mDHFR on a streptavidin-coated plate. These results demonstrate that the combination of reactive non-natural amino acid incorporation and the optimized CuAAC can be used to bioconjugate enzymes with retained enzymatic activity.

  4. Incorporating spatial autocorrelation into species distribution models alters forecasts of climate-mediated range shifts.

    Science.gov (United States)

    Crase, Beth; Liedloff, Adam; Vesk, Peter A; Fukuda, Yusuke; Wintle, Brendan A

    2014-08-01

    Species distribution models (SDMs) are widely used to forecast changes in the spatial distributions of species and communities in response to climate change. However, spatial autocorrelation (SA) is rarely accounted for in these models, despite its ubiquity in broad-scale ecological data. While spatial autocorrelation in model residuals is known to result in biased parameter estimates and the inflation of type I errors, the influence of unmodeled SA on species' range forecasts is poorly understood. Here we quantify how accounting for SA in SDMs influences the magnitude of range shift forecasts produced by SDMs for multiple climate change scenarios. SDMs were fitted to simulated data with a known autocorrelation structure, and to field observations of three mangrove communities from northern Australia displaying strong spatial autocorrelation. Three modeling approaches were implemented: environment-only models (most frequently applied in species' range forecasts), and two approaches that incorporate SA; autologistic models and residuals autocovariate (RAC) models. Differences in forecasts among modeling approaches and climate scenarios were quantified. While all model predictions at the current time closely matched that of the actual current distribution of the mangrove communities, under the climate change scenarios environment-only models forecast substantially greater range shifts than models incorporating SA. Furthermore, the magnitude of these differences intensified with increasing increments of climate change across the scenarios. When models do not account for SA, forecasts of species' range shifts indicate more extreme impacts of climate change, compared to models that explicitly account for SA. Therefore, where biological or population processes induce substantial autocorrelation in the distribution of organisms, and this is not modeled, model predictions will be inaccurate. These results have global importance for conservation efforts as inaccurate

  5. Fuzzy Logic-Based Model That Incorporates Personality Traits for Heterogeneous Pedestrians

    Directory of Open Access Journals (Sweden)

    Zhuxin Xue

    2017-10-01

    Full Text Available Most models designed to simulate pedestrian dynamical behavior are based on the assumption that human decision-making can be described using precise values. This study proposes a new pedestrian model that incorporates fuzzy logic theory into a multi-agent system to address cognitive behavior that introduces uncertainty and imprecision during decision-making. We present a concept of decision preferences to represent the intrinsic control factors of decision-making. To realize the different decision preferences of heterogeneous pedestrians, the Five-Factor (OCEAN personality model is introduced to model the psychological characteristics of individuals. Then, a fuzzy logic-based approach is adopted for mapping the relationships between the personality traits and the decision preferences. Finally, we have developed an application using our model to simulate pedestrian dynamical behavior in several normal or non-panic scenarios, including a single-exit room, a hallway with obstacles, and a narrowing passage. The effectiveness of the proposed model is validated with a user study. The results show that the proposed model can generate more reasonable and heterogeneous behavior in the simulation and indicate that individual personality has a noticeable effect on pedestrian dynamical behavior.

  6. Phytobiotic Utilization as Feed Additive in Feed for Pancreatic Enzyme Activity of Broiler Chicken

    Directory of Open Access Journals (Sweden)

    Sri Purwanti

    2015-09-01

    Full Text Available This research was conducted to evaluate the effect of turmeric water extract, garlic and combination turmeric and garlic as a feed additive in the broiler diet on pancreatic enzyme activity of broiler chicken. Effectivity of treatments was assessed by addition of phytobiotic (control, 015% zinc bacitracin, 2.5% TE, 2.0% GE, 2.5% TGE which were arranged Completely Randomized Design with 4 replications. The variables measured were pancreatic enzyme activity(amylase enzyme activity, protease enzyme activity  and lipase enzyme activity.The results showed that enzyme protein activity content of 2.5% TE supplementation is also high at 82.02 U/ml, then supplemented 2.5% TGE, 2.0% GE, negative control and positive control respectively 75.98 ; 72.02; 68.74; and 66.57 U/ml. The lipase enzyme activity whereas the negative control and a positive control differ significantly higher (P<0.05 to treatment with the addition of 2.5% TE, 2.0% GE and 2.5% TGE phytobiotic. The research concluded that the incorporation of 2.5% TE, 2% GE and combined 2.5% TGE as feed additive enhanced pancreatic enzyme activity.

  7. Cold-Adapted Enzymes

    Science.gov (United States)

    Georlette, D.; Bentahir, M.; Claverie, P.; Collins, T.; D'amico, S.; Delille, D.; Feller, G.; Gratia, E.; Hoyoux, A.; Lonhienne, T.; Meuwis, M.-a.; Zecchinon, L.; Gerday, Ch.

    In the last few years, increased attention has been focused on enzymes produced by cold-adapted micro-organisms. It has emerged that psychrophilic enzymes represent an extremely powerful tool in both protein folding investigations and for biotechnological purposes. Such enzymes are characterised by an increased thermosensitivity and, most of them, by a higher catalytic efficiency at low and moderate temperatures, when compared to their mesophilic counterparts. The high thermosensitivity probably originates from an increased flexibility of either a selected area of the molecular edifice or the overall protein structure, providing enhanced abilities to undergo conformational changes during catalysis at low temperatures. Structure modelling and recent crystallographic data have allowed to elucidate the structural parameters that could be involved in this higher resilience. It was demonstrated that each psychrophilic enzyme adopts its own adaptive strategy. It appears, moreover, that there is a continuum in the strategy of protein adaptation to temperature, as the previously mentioned structural parameters are implicated in the stability of thermophilic proteins. Additional 3D crystal structures, site-directed and random mutagenesis experiments should now be undertaken to further investigate the stability-flexibility-activity relationship.

  8. Developing a stochastic parameterization to incorporate plant trait variability into ecohydrologic modeling

    Science.gov (United States)

    Liu, S.; Ng, G. H. C.

    2017-12-01

    The global plant database has revealed that plant traits can vary more within a plant functional type (PFT) than among different PFTs, indicating that the current paradigm in ecohydrogical models of specifying fixed parameters based solely on plant functional type (PFT) could potentially bias simulations. Although some recent modeling studies have attempted to incorporate this observed plant trait variability, many failed to consider uncertainties due to sparse global observation, or they omitted spatial and/or temporal variability in the traits. Here we present a stochastic parameterization for prognostic vegetation simulations that are stochastic in time and space in order to represent plant trait plasticity - the process by which trait differences arise. We have developed the new PFT parameterization within the Community Land Model 4.5 (CLM 4.5) and tested the method for a desert shrubland watershed in the Mojave Desert, where fixed parameterizations cannot represent acclimation to desert conditions. Spatiotemporally correlated plant trait parameters were first generated based on TRY statistics and were then used to implement ensemble runs for the study area. The new PFT parameterization was then further conditioned on field measurements of soil moisture and remotely sensed observations of leaf-area-index to constrain uncertainties in the sparse global database. Our preliminary results show that incorporating data-conditioned, variable PFT parameterizations strongly affects simulated soil moisture and water fluxes, compared with default simulations. The results also provide new insights about correlations among plant trait parameters and between traits and environmental conditions in the desert shrubland watershed. Our proposed stochastic PFT parameterization method for ecohydrological models has great potential in advancing our understanding of how terrestrial ecosystems are predicted to adapt to variable environmental conditions.

  9. Adolescent Decision-Making Processes regarding University Entry: A Model Incorporating Cultural Orientation, Motivation and Occupational Variables

    Science.gov (United States)

    Jung, Jae Yup

    2013-01-01

    This study tested a newly developed model of the cognitive decision-making processes of senior high school students related to university entry. The model incorporated variables derived from motivation theory (i.e. expectancy-value theory and the theory of reasoned action), literature on cultural orientation and occupational considerations. A…

  10. A Mass Balance Model for Designing Green Roof Systems that Incorporate a Cistern for Re-Use

    Directory of Open Access Journals (Sweden)

    Manoj Chopra

    2012-11-01

    Full Text Available Green roofs, which have been used for several decades in many parts of the world, offer a unique and sustainable approach to stormwater management. Within this paper, evidence is presented on water retention for an irrigated green roof system. The presented green roof design results in a water retention volume on site. A first principle mass balance computer model is introduced to assist with the design of these green roof systems which incorporate a cistern to capture and reuse runoff waters for irrigation of the green roof. The model is used to estimate yearly stormwater retention volume for different cistern storage volumes. Additionally, the Blaney and Criddle equation is evaluated for estimation of monthly evapotranspiration rates for irrigated systems and incorporated into the model. This is done so evapotranspiration rates can be calculated for regions where historical data does not exist, allowing the model to be used anywhere historical weather data are available. This model is developed and discussed within this paper as well as compared to experimental results.

  11. A novel film-pore-surface diffusion model to explain the enhanced enzyme adsorption of corn stover pretreated by ultrafine grinding.

    Science.gov (United States)

    Zhang, Haiyan; Chen, Longjian; Lu, Minsheng; Li, Junbao; Han, Lujia

    2016-01-01

    Ultrafine grinding is an environmentally friendly pretreatment that can alter the degree of polymerization, the porosity and the specific surface area of lignocellulosic biomass and can, thus, enhance cellulose hydrolysis. Enzyme adsorption onto the substrate is a prerequisite for the enzymatic hydrolysis process. Therefore, it is necessary to investigate the enzyme adsorption properties of corn stover pretreated by ultrafine grinding. The ultrafine grinding pretreatment was executed on corn stover. The results showed that ultrafine grinding pretreatment can significantly decrease particle size [from 218.50 μm of sieve-based grinding corn stover (SGCS) to 17.45 μm of ultrafine grinding corn stover (UGCS)] and increase the specific surface area (SSA), pore volume (PV) and surface composition (SSA: from 1.71 m(2)/g of SGCS to 2.63 m(2)/g of UGCS, PV: from 0.009 cm(3)/g of SGCS to 0.024 m(3)/g of UGCS, cellulose surface area: from 168.69 m(2)/g of SGCS to 290.76 m(2)/g of UGCS, lignin surface area: from 91.46 m(2)/g of SGCS to 106.70 m(2)/g of UGCS). The structure and surface composition changes induced by ultrafine grinding increase the enzyme adsorption capacity from 2.83 mg/g substrate of SGCS to 5.61 mg/g substrate of UGCS. A film-pore-surface diffusion model was developed to simultaneously predict the enzyme adsorption kinetics of both the SGCS and UGCS. Satisfactory predictions could be made with the model based on high R (2) and low RMSE values (R (2) = 0.95 and RMSE = 0.16 mg/g for the UGCS, R (2) = 0.93 and RMSE = 0.09 mg/g for the SGCS). The model was further employed to analyze the rate-limiting steps in the enzyme adsorption process. Although both the external-film and internal-pore mass transfer are important for enzyme adsorption on the SGCS and UGCS, the UGCS has a lower internal-pore resistance compared to the SGCS. Ultrafine grinding pretreatment can enhance the enzyme adsorption onto corn stover by altering structure and

  12. Petroacoustic Modelling of Heterolithic Sandstone Reservoirs: A Novel Approach to Gassmann Modelling Incorporating Sedimentological Constraints and NMR Porosity data

    Science.gov (United States)

    Matthews, S.; Lovell, M.; Davies, S. J.; Pritchard, T.; Sirju, C.; Abdelkarim, A.

    2012-12-01

    Heterolithic or 'shaly' sandstone reservoirs constitute a significant proportion of hydrocarbon resources. Petroacoustic models (a combination of petrophysics and rock physics) enhance the ability to extract reservoir properties from seismic data, providing a connection between seismic and fine-scale rock properties. By incorporating sedimentological observations these models can be better constrained and improved. Petroacoustic modelling is complicated by the unpredictable effects of clay minerals and clay-sized particles on geophysical properties. Such effects are responsible for erroneous results when models developed for "clean" reservoirs - such as Gassmann's equation (Gassmann, 1951) - are applied to heterolithic sandstone reservoirs. Gassmann's equation is arguably the most popular petroacoustic modelling technique in the hydrocarbon industry and is used to model elastic effects of changing reservoir fluid saturations. Successful implementation of Gassmann's equation requires well-constrained drained rock frame properties, which in heterolithic sandstones are heavily influenced by reservoir sedimentology, particularly clay distribution. The prevalent approach to categorising clay distribution is based on the Thomas - Stieber model (Thomas & Stieber, 1975), this approach is inconsistent with current understanding of 'shaly sand' sedimentology and omits properties such as sorting and grain size. The novel approach presented here demonstrates that characterising reservoir sedimentology constitutes an important modelling phase. As well as incorporating sedimentological constraints, this novel approach also aims to improve drained frame moduli estimates through more careful consideration of Gassmann's model assumptions and limitations. A key assumption of Gassmann's equation is a pore space in total communication with movable fluids. This assumption is often violated by conventional applications in heterolithic sandstone reservoirs where effective porosity, which

  13. In silico prediction of potential chemical reactions mediated by human enzymes.

    Science.gov (United States)

    Yu, Myeong-Sang; Lee, Hyang-Mi; Park, Aaron; Park, Chungoo; Ceong, Hyithaek; Rhee, Ki-Hyeong; Na, Dokyun

    2018-06-13

    Administered drugs are often converted into an ineffective or activated form by enzymes in our body. Conventional in silico prediction approaches focused on therapeutically important enzymes such as CYP450. However, there are more than thousands of different cellular enzymes that potentially convert administered drug into other forms. We developed an in silico model to predict which of human enzymes including metabolic enzymes as well as CYP450 family can catalyze a given chemical compound. The prediction is based on the chemical and physical similarity between known enzyme substrates and a query chemical compound. Our in silico model was developed using multiple linear regression and the model showed high performance (AUC = 0.896) despite of the large number of enzymes. When evaluated on a test dataset, it also showed significantly high performance (AUC = 0.746). Interestingly, evaluation with literature data showed that our model can be used to predict not only enzymatic reactions but also drug conversion and enzyme inhibition. Our model was able to predict enzymatic reactions of a query molecule with a high accuracy. This may foster to discover new metabolic routes and to accelerate the computational development of drug candidates by enabling the prediction of the potential conversion of administered drugs into active or inactive forms.

  14. Enzyme

    Science.gov (United States)

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

  15. A realistic closed-form radiobiological model of clinical tumor-control data incorporating intertumor heterogeneity

    International Nuclear Information System (INIS)

    Roberts, Stephen A.; Hendry, Jolyon H.

    1998-01-01

    Purpose: To investigate the role of intertumor heterogeneity in clinical tumor control datasets and the relationship to in vitro measurements of tumor biopsy samples. Specifically, to develop a modified linear-quadratic (LQ) model incorporating such heterogeneity that it is practical to fit to clinical tumor-control datasets. Methods and Materials: We developed a modified version of the linear-quadratic (LQ) model for tumor control, incorporating a (lagged) time factor to allow for tumor cell repopulation. We explicitly took into account the interpatient heterogeneity in clonogen number, radiosensitivity, and repopulation rate. Using this model, we could generate realistic TCP curves using parameter estimates consistent with those reported from in vitro studies, subject to the inclusion of a radiosensitivity (or dose)-modifying factor. We then demonstrated that the model was dominated by the heterogeneity in α (tumor radiosensitivity) and derived an approximate simplified model incorporating this heterogeneity. This simplified model is expressible in a compact closed form, which it is practical to fit to clinical datasets. Using two previously analysed datasets, we fit the model using direct maximum-likelihood techniques and obtained parameter estimates that were, again, consistent with the experimental data on the radiosensitivity of primary human tumor cells. This heterogeneity model includes the same number of adjustable parameters as the standard LQ model. Results: The modified model provides parameter estimates that can easily be reconciled with the in vitro measurements. The simplified (approximate) form of the heterogeneity model is a compact, closed-form probit function that can readily be fitted to clinical series by conventional maximum-likelihood methodology. This heterogeneity model provides a slightly better fit to the datasets than the conventional LQ model, with the same numbers of fitted parameters. The parameter estimates of the clinically

  16. Quantum Chemical Examination of the Sequential Halogen Incorporation Scheme for the Modeling of Speciation of I/Br/Cl-Containing Trihalomethanes.

    Science.gov (United States)

    Zhang, Chenyang; Li, Maodong; Han, Xuze; Yan, Mingquan

    2018-02-20

    The recently developed three-step ternary halogenation model interprets the incorporation of chlorine, bromine, and iodine ions into natural organic matter (NOM) and formation of iodine-, bromine-, and chlorine-containing trihalomethanes (THMs) based on the competition of iodine, bromine, and chlorine species at each node of the halogenation sequence. This competition is accounted for using the dimensionless ratios (denoted as γ) of kinetic rates of reactions of the initial attack sites or halogenated intermediates with chlorine, bromine, and iodine ions. However, correlations between the model predictions made and mechanistic aspects of the incorporation of halogen species need to be ascertained in more detail. In this study, quantum chemistry calculations were first used to probe the formation mechanism of 10 species of Cl-/Br-/I- THMs. The HOMO energy (E HOMO ) of each mono-, bi-, or trihalomethanes were calculated by B3LYP method in Gaussian 09 software. Linear correlations were found to exist between the logarithms of experimentally determined kinetic preference coefficients γ reported in prior research and, on the other hand, differences of E HOMO values between brominated/iodinated and chlorinated halomethanes. One notable exception from this trend was that observed for the incorporation of iodine into mono- and di-iodinated intermediates. These observations confirm the three-step halogen incorporation sequence and the factor γ in the statistical model. The combined use of quantum chemistry calculations and the ternary sequential halogenation model provides a new insight into the microscopic nature of NOM-halogen interactions and the trends seen in the behavior of γ factors incorporated in the THM speciation models.

  17. Enzymes improve ECF bleaching of pulp

    Directory of Open Access Journals (Sweden)

    Lachenal, D.

    2006-07-01

    Full Text Available The delignification efficiency of different laccase enzymes was examined on the eucalyptus Kraft pulp. The laccase enzyme from Trametes versicolor showing the highest delignification efficiency was selected and used in the elemental chlorine-free bleaching sequence for improving the pulp bleachability. An appreciable reduction in chlorine dioxide consumption was also obtained. Further reduction in chlorine dioxide consumption was obtained when the same laccase treated pulp was subjected to an acid treatment after the extraction stage followed by the DEPD sequence. Elemental-chlorine free bleaching was also performed using the xylanase-laccase treated pulp. Xylanase treatment was incorporated to the laccase mediator system in the elemental-chlorine free bleaching both sequentially and simultaneously. The bleaching sequence DEPD followed and in both the cases, the reduction in chlorine dioxide consumption was greater in comparison to the control. The chlorine dioxide consumption was reduced further when xylanase-laccase treated pulp was given an additional acid treatment. The final pulp properties of the treated pulps were comparable to the control pulp.

  18. Incorporation of human factors into ship collision risk models focusing on human centred design aspects

    International Nuclear Information System (INIS)

    Sotiralis, P.; Ventikos, N.P.; Hamann, R.; Golyshev, P.; Teixeira, A.P.

    2016-01-01

    This paper presents an approach that more adequately incorporates human factor considerations into quantitative risk analysis of ship operation. The focus is on the collision accident category, which is one of the main risk contributors in ship operation. The approach is based on the development of a Bayesian Network (BN) model that integrates elements from the Technique for Retrospective and Predictive Analysis of Cognitive Errors (TRACEr) and focuses on the calculation of the collision accident probability due to human error. The model takes into account the human performance in normal, abnormal and critical operational conditions and implements specific tasks derived from the analysis of the task errors leading to the collision accident category. A sensitivity analysis is performed to identify the most important contributors to human performance and ship collision. Finally, the model developed is applied to assess the collision risk of a feeder operating in Dover strait using the collision probability estimated by the developed BN model and an Event tree model for calculation of human, economic and environmental risks. - Highlights: • A collision risk model for the incorporation of human factors into quantitative risk analysis is proposed. • The model takes into account the human performance in different operational conditions leading to the collision. • The most important contributors to human performance and ship collision are identified. • The model developed is applied to assess the collision risk of a feeder operating in Dover strait.

  19. Metabolic Diseases Downregulate the Majority of Histone Modification Enzymes, Making a Few Upregulated Enzymes Novel Therapeutic Targets--"Sand Out and Gold Stays".

    Science.gov (United States)

    Shao, Ying; Chernaya, Valeria; Johnson, Candice; Yang, William Y; Cueto, Ramon; Sha, Xiaojin; Zhang, Yi; Qin, Xuebin; Sun, Jianxin; Choi, Eric T; Wang, Hong; Yang, Xiao-feng

    2016-02-01

    To determine whether the expression of histone modification enzymes is regulated in physiological and pathological conditions, we took an experimental database mining approach pioneered in our labs to determine a panoramic expression profile of 164 enzymes in 19 human and 17 murine tissues. We have made the following significant findings: (1) Histone enzymes are differentially expressed in cardiovascular, immune, and other tissues; (2) our new pyramid model showed that heart and T cells are among a few tissues in which histone acetylation/deacetylation, and histone methylation/demethylation are in the highest varieties; and (3) histone enzymes are more downregulated than upregulated in metabolic diseases and regulatory T cell (Treg) polarization/ differentiation, but not in tumors. These results have demonstrated a new working model of "Sand out and Gold stays," where more downregulation than upregulation of histone enzymes in metabolic diseases makes a few upregulated enzymes the potential novel therapeutic targets in metabolic diseases and Treg activity.

  20. Incorporating genetic variation into a model of budburst phenology of coast Douglas-fir (Pseudotsuga menziesii var

    Science.gov (United States)

    Peter J. Gould; Constance A. Harrington; Bradley J. St Clair

    2011-01-01

    Models to predict budburst and other phenological events in plants are needed to forecast how climate change may impact ecosystems and for the development of mitigation strategies. Differences among genotypes are important to predicting phenological events in species that show strong clinal variation in adaptive traits. We present a model that incorporates the effects...

  1. Quantification of N-acetylcysteamine activated methylmalonate incorporation into polyketide biosynthesis

    Directory of Open Access Journals (Sweden)

    Stephan Klopries

    2013-04-01

    Full Text Available Polyketides are biosynthesized through consecutive decarboxylative Claisen condensations between a carboxylic acid and differently substituted malonic acid thioesters, both tethered to the giant polyketide synthase enzymes. Individual malonic acid derivatives are typically required to be activated as coenzyme A-thioesters prior to their enzyme-catalyzed transfer onto the polyketide synthase. Control over the selection of malonic acid building blocks promises great potential for the experimental alteration of polyketide structure and bioactivity. One requirement for this endeavor is the supplementation of the bacterial polyketide fermentation system with tailored synthetic thioester-activated malonates. The membrane permeable N-acetylcysteamine has been proposed as a coenzyme A-mimic for this purpose. Here, the incorporation efficiency into different polyketides of N-acetylcysteamine activated methylmalonate is studied and quantified, showing a surprisingly high and transferable activity of these polyketide synthase substrate analogues in vivo.

  2. Enzyme clustering accelerates processing of intermediates through metabolic channeling

    Science.gov (United States)

    Castellana, Michele; Wilson, Maxwell Z.; Xu, Yifan; Joshi, Preeti; Cristea, Ileana M.; Rabinowitz, Joshua D.; Gitai, Zemer; Wingreen, Ned S.

    2015-01-01

    We present a quantitative model to demonstrate that coclustering multiple enzymes into compact agglomerates accelerates the processing of intermediates, yielding the same efficiency benefits as direct channeling, a well-known mechanism in which enzymes are funneled between enzyme active sites through a physical tunnel. The model predicts the separation and size of coclusters that maximize metabolic efficiency, and this prediction is in agreement with previously reported spacings between coclusters in mammalian cells. For direct validation, we study a metabolic branch point in Escherichia coli and experimentally confirm the model prediction that enzyme agglomerates can accelerate the processing of a shared intermediate by one branch, and thus regulate steady-state flux division. Our studies establish a quantitative framework to understand coclustering-mediated metabolic channeling and its application to both efficiency improvement and metabolic regulation. PMID:25262299

  3. Biochemistry students' ideas about how an enzyme interacts with a substrate.

    Science.gov (United States)

    Linenberger, Kimberly J; Bretz, Stacey Lowery

    2015-01-01

    Enzyme-substrate interactions are a fundamental concept of biochemistry that is built upon throughout multiple biochemistry courses. Central to understanding enzyme-substrate interactions is specific knowledge of exactly how an enzyme and substrate interact. Within this narrower topic, students must understand the various binding sites on an enzyme and be able to reason from simplistic lock and key or induced fit models to the more complex energetics model of transition state theory. Learning to understand these many facets of enzyme-substrate interactions and reasoning from multiple models present challenges where students incorrectly make connections between concepts or make no connection at all. This study investigated biochemistry students' understanding of enzyme-substrate interactions through the use of clinical interviews and a national administration (N = 707) of the Enzyme-Substrate Interactions Concept Inventory. Findings include misconceptions regarding the nature of enzyme-substrate interactions, naïve ideas about the active site, a lack of energetically driven interactions, and an incomplete understanding of the specificity pocket. © 2015 by the International Union of Biochemistry and Molecular Biology.

  4. Production of Antimicrobial Films by Incorporation of Partially Purified Lysozyme into Biodegradable Films of Crude Exopolysaccharides Obtained from Aureobasidium pullulans Fermentation

    Directory of Open Access Journals (Sweden)

    Nilay Kandemir

    2005-01-01

    Full Text Available Antimicrobial films were produced by incorporating partially purified lysozyme into films of crude exopolysaccharides (59 % pullulan obtained from Aureobasidium pullulans fermentation. After film making, the films containing lysozyme at 100, 260, 520 and 780 μg/cm2 showed 23 to 70 % of their expected enzyme activities. The highest recovery of enzyme activity (65–70 % after the film making was obtained in films prepared by incorporating lysozyme at 260 μg/cm2 (1409 U/cm2. The incorporation of disodium EDTA×2H2O and sucrose did not affect the initial lysozyme activity of the films significantly. With or without the presence of disodium EDTA×2H2O at 52 or 520 μg/cm2, lysozyme activity showed sufficient stability in the films during 21 days of cold storage. However, the presence of sucrose at 10 mg/cm2 in the films caused the destabilization of part of enzyme activity (almost 35 % at the end of storage. The combinational incorporation of lysozyme at 780 μg/cm2 (4227 U/cm2 and disodium EDTA×2H2O at 520 μg/cm2 gave antimicrobial films effective on Escherichia coli. However, in the studied lysozyme concentration range the films did not show any antimicrobial activity against Lactobacillus plantarum. This study clearly showed that the partially purified lysozyme and crude exopolysaccharides from Aureobasidium pullulans may be used to obtain antimicrobial films to increase the safety of foods.

  5. Global dynamics of a PDE model for aedes aegypti mosquitoe incorporating female sexual preference

    KAUST Repository

    Parshad, Rana

    2011-01-01

    In this paper we study the long time dynamics of a reaction diffusion system, describing the spread of Aedes aegypti mosquitoes, which are the primary cause of dengue infection. The system incorporates a control attempt via the sterile insect technique. The model incorporates female mosquitoes sexual preference for wild males over sterile males. We show global existence of strong solution for the system. We then derive uniform estimates to prove the existence of a global attractor in L-2(Omega), for the system. The attractor is shown to be L-infinity(Omega) regular and posess state of extinction, if the injection of sterile males is large enough. We also provide upper bounds on the Hausdorff and fractal dimensions of the attractor.

  6. Modelling and Simulation of a Manipulator with Stable Viscoelastic Grasping Incorporating Friction

    Directory of Open Access Journals (Sweden)

    A. Khurshid

    2016-12-01

    Full Text Available Design, dynamics and control of a humanoid robotic hand based on anthropological dimensions, with joint friction, is modelled, simulated and analysed in this paper by using computer aided design and multibody dynamic simulation. Combined joint friction model is incorporated in the joints. Experimental values of coefficient of friction of grease lubricated sliding contacts representative of manipulator joints are presented. Human fingers deform to the shape of the grasped object (enveloping grasp at the area of interaction. A mass-spring-damper model of the grasp is developed. The interaction of the viscoelastic gripper of the arm with objects is analysed by using Bond Graph modelling method. Simulations were conducted for several material parameters. These results of the simulation are then used to develop a prototype of the proposed gripper. Bond graph model is experimentally validated by using the prototype. The gripper is used to successfully transport soft and fragile objects. This paper provides information on optimisation of friction and its inclusion in both dynamic modelling and simulation to enhance mechanical efficiency.

  7. Incorporating NDVI in a gravity model setting to describe spatio-temporal patterns of Lyme borreliosis incidence

    Science.gov (United States)

    Barrios, J. M.; Verstraeten, W. W.; Farifteh, J.; Maes, P.; Aerts, J. M.; Coppin, P.

    2012-04-01

    Lyme borreliosis (LB) is the most common tick-borne disease in Europe and incidence growth has been reported in several European countries during the last decade. LB is caused by the bacterium Borrelia burgdorferi and the main vector of this pathogen in Europe is the tick Ixodes ricinus. LB incidence and spatial spread is greatly dependent on environmental conditions impacting habitat, demography and trophic interactions of ticks and the wide range of organisms ticks parasite. The landscape configuration is also a major determinant of tick habitat conditions and -very important- of the fashion and intensity of human interaction with vegetated areas, i.e. human exposure to the pathogen. Hence, spatial notions as distance and adjacency between urban and vegetated environments are related to human exposure to tick bites and, thus, to risk. This work tested the adequacy of a gravity model setting to model the observed spatio-temporal pattern of LB as a function of location and size of urban and vegetated areas and the seasonal and annual change in the vegetation dynamics as expressed by MODIS NDVI. Opting for this approach implies an analogy with Newton's law of universal gravitation in which the attraction forces between two bodies are directly proportional to the bodies mass and inversely proportional to distance. Similar implementations have proven useful in fields like trade modeling, health care service planning, disease mapping among other. In our implementation, the size of human settlements and vegetated systems and the distance separating these landscape elements are considered the 'bodies'; and the 'attraction' between them is an indicator of exposure to pathogen. A novel element of this implementation is the incorporation of NDVI to account for the seasonal and annual variation in risk. The importance of incorporating this indicator of vegetation activity resides in the fact that alterations of LB incidence pattern observed the last decade have been ascribed

  8. Benefits of incorporating spatial organisation of catchments for a semi-distributed hydrological model

    Science.gov (United States)

    Schumann, Andreas; Oppel, Henning

    2017-04-01

    To represent the hydrological behaviour of catchments a model should reproduce/reflect the hydrologically most relevant catchment characteristics. These are heterogeneously distributed within a watershed but often interrelated and subject of a certain spatial organisation. Since common models are mostly based on fundamental assumptions about hydrological processes, the reduction of variance of catchment properties as well as the incorporation of the spatial organisation of the catchment is desirable. We have developed a method that combines the idea of the width-function used for determination of the geomorphologic unit hydrograph with information about soil or topography. With this method we are able to assess the spatial organisation of selected catchment characteristics. An algorithm was developed that structures a watershed into sub-basins and other spatial units to minimise its heterogeneity. The outcomes of this algorithm are used for the spatial setup of a semi-distributed model. Since the spatial organisation of a catchment is not bound to a single characteristic, we have to embed information of multiple catchment properties. For this purpose we applied a fuzzy-based method to combine the spatial setup for multiple single characteristics into a union, optimal spatial differentiation. Utilizing this method, we are able to propose a spatial structure for a semi-distributed hydrological model, comprising the definition of sub-basins and a zonal classification within each sub-basin. Besides the improved spatial structuring, the performed analysis ameliorates modelling in another way. The spatial variability of catchment characteristics, which is considered by a minimum of heterogeneity in the zones, can be considered in a parameter constrained calibration scheme in a case study both options were used to explore the benefits of incorporating the spatial organisation and derived parameter constraints for the parametrisation of a HBV-96 model. We use two benchmark

  9. Tub-Tag Labeling; Chemoenzymatic Incorporation of Unnatural Amino Acids.

    Science.gov (United States)

    Helma, Jonas; Leonhardt, Heinrich; Hackenberger, Christian P R; Schumacher, Dominik

    2018-01-01

    Tub-tag labeling is a chemoenzymatic method that enables the site-specific labeling of proteins. Here, the natural enzyme tubulin tyrosine ligase incorporates noncanonical tyrosine derivatives to the terminal carboxylic acid of proteins containing a 14-amino acid recognition sequence called Tub-tag. The tyrosine derivative carries a unique chemical reporter allowing for a subsequent bioorthogonal modification of proteins with a great variety of probes. Here, we describe the Tub-tag protein modification protocol in detail and explain its utilization to generate labeled proteins for advanced applications in cell biology, imaging, and diagnostics.

  10. EFFECTS OF EARLY ANGIOTENSIN-CONVERTING ENZYME-INHIBITION IN A PIG MODEL OF MYOCARDIAL-ISCHEMIA AND REPERFUSION

    NARCIS (Netherlands)

    VANWIJNGAARDEN, J; TOBE, TJM; WEERSINK, EGL; BEL, KJ; DEGRAEFF, PA; DELANGEN, CDJ; VANGILST, WH; WESSELING, H

    In a blind, randomized study, the effects of perindopril, a nonsulfhydryl-containing angiotensin-converting enzyme (ACE) inhibitor, were compared with those of placebo in a closed-chest pig model of myocardial infraction. In anesthetized pigs, my ocardinal ischemia and reperfusion were induced by

  11. Recent Progresses in Incorporating Human Land-Water Management into Global Land Surface Models Toward Their Integration into Earth System Models

    Science.gov (United States)

    Pokhrel, Yadu N.; Hanasaki, Naota; Wada, Yoshihide; Kim, Hyungjun

    2016-01-01

    The global water cycle has been profoundly affected by human land-water management. As the changes in the water cycle on land can affect the functioning of a wide range of biophysical and biogeochemical processes of the Earth system, it is essential to represent human land-water management in Earth system models (ESMs). During the recent past, noteworthy progress has been made in large-scale modeling of human impacts on the water cycle but sufficient advancements have not yet been made in integrating the newly developed schemes into ESMs. This study reviews the progresses made in incorporating human factors in large-scale hydrological models and their integration into ESMs. The study focuses primarily on the recent advancements and existing challenges in incorporating human impacts in global land surface models (LSMs) as a way forward to the development of ESMs with humans as integral components, but a brief review of global hydrological models (GHMs) is also provided. The study begins with the general overview of human impacts on the water cycle. Then, the algorithms currently employed to represent irrigation, reservoir operation, and groundwater pumping are discussed. Next, methodological deficiencies in current modeling approaches and existing challenges are identified. Furthermore, light is shed on the sources of uncertainties associated with model parameterizations, grid resolution, and datasets used for forcing and validation. Finally, representing human land-water management in LSMs is highlighted as an important research direction toward developing integrated models using ESM frameworks for the holistic study of human-water interactions within the Earths system.

  12. Using expert knowledge to incorporate uncertainty in cause-of-death assignments for modeling of cause-specific mortality

    Science.gov (United States)

    Walsh, Daniel P.; Norton, Andrew S.; Storm, Daniel J.; Van Deelen, Timothy R.; Heisy, Dennis M.

    2018-01-01

    Implicit and explicit use of expert knowledge to inform ecological analyses is becoming increasingly common because it often represents the sole source of information in many circumstances. Thus, there is a need to develop statistical methods that explicitly incorporate expert knowledge, and can successfully leverage this information while properly accounting for associated uncertainty during analysis. Studies of cause-specific mortality provide an example of implicit use of expert knowledge when causes-of-death are uncertain and assigned based on the observer's knowledge of the most likely cause. To explicitly incorporate this use of expert knowledge and the associated uncertainty, we developed a statistical model for estimating cause-specific mortality using a data augmentation approach within a Bayesian hierarchical framework. Specifically, for each mortality event, we elicited the observer's belief of cause-of-death by having them specify the probability that the death was due to each potential cause. These probabilities were then used as prior predictive values within our framework. This hierarchical framework permitted a simple and rigorous estimation method that was easily modified to include covariate effects and regularizing terms. Although applied to survival analysis, this method can be extended to any event-time analysis with multiple event types, for which there is uncertainty regarding the true outcome. We conducted simulations to determine how our framework compared to traditional approaches that use expert knowledge implicitly and assume that cause-of-death is specified accurately. Simulation results supported the inclusion of observer uncertainty in cause-of-death assignment in modeling of cause-specific mortality to improve model performance and inference. Finally, we applied the statistical model we developed and a traditional method to cause-specific survival data for white-tailed deer, and compared results. We demonstrate that model selection

  13. Analysis of PWR control rod ejection accident with the coupled code system SKETCH-INS/TRACE by incorporating pin power reconstruction model

    International Nuclear Information System (INIS)

    Nakajima, T.; Sakai, T.

    2010-01-01

    The pin power reconstruction model was incorporated in the 3-D nodal kinetics code SKETCH-INS in order to produce accurate calculation of three-dimensional pin power distributions throughout the reactor core. In order to verify the employed pin power reconstruction model, the PWR MOX/UO_2 core transient benchmark problem was analyzed with the coupled code system SKETCH-INS/TRACE by incorporating the model and the influence of pin power reconstruction model was studied. SKETCH-INS pin power distributions for 3 benchmark problems were compared with the PARCS solutions which were provided by the host organisation of the benchmark. SKETCH-INS results were in good agreement with the PARCS results. The capability of employed pin power reconstruction model was confirmed through the analysis of benchmark problems. A PWR control rod ejection benchmark problem was analyzed with the coupled code system SKETCH-INS/ TRACE by incorporating the pin power reconstruction model. The influence of pin power reconstruction model was studied by comparing with the result of conventional node averaged flux model. The results indicate that the pin power reconstruction model has significant effect on the pin powers during transient and hence on the fuel enthalpy

  14. Modelling the Effects of Ageing Time of Starch on the Enzymatic Activity of Three Amylolytic Enzymes

    Science.gov (United States)

    Guerra, Nelson P.; Pastrana Castro, Lorenzo

    2012-01-01

    The effect of increasing ageing time (t) of starch on the activity of three amylolytic enzymes (Termamyl, San Super, and BAN) was investigated. Although all the enzymatic reactions follow michaelian kinetics, v max decreased significantly (P enzymes and the release of the reaction products to the medium. A similar effect was observed when the enzymatic reactions were carried out with unaged starches supplemented with different concentrations of gelatine [G]. The inhibition in the amylolytic activities was best mathematically described by using three modified forms of the Michaelis-Menten model, which included a term to consider, respectively, the linear, exponential, and hyperbolic inhibitory effects of t and [G]. PMID:22666116

  15. Towards a functional model of mental disorders incorporating the laws of thermodynamics.

    Science.gov (United States)

    Murray, George C; McKenzie, Karen

    2013-05-01

    The current paper presents the hypothesis that the understanding of mental disorders can be advanced by incorporating the laws of thermodynamics, specifically relating to energy conservation and energy transfer. These ideas, along with the introduction of the notion that entropic activities are symptomatic of inefficient energy transfer or disorder, were used to propose a model of understanding mental ill health as resulting from the interaction of entropy, capacity and work (environmental demands). The model was applied to Attention Deficit Hyperactivity Disorder, and was shown to be compatible with current thinking about this condition, as well as emerging models of mental disorders as complex networks. A key implication of the proposed model is that it argues that all mental disorders require a systemic functional approach, with the advantage that it offers a number of routes into the assessment, formulation and treatment for mental health problems. Copyright © 2013 Elsevier Ltd. All rights reserved.

  16. Evaluation of the efficiency of alternative enzyme production technologies

    DEFF Research Database (Denmark)

    Albæk, Mads Orla

    Enzymes are used in an increasing number of industries. The application of enzymes is extending into the production of lignocellulosic ethanol in processes that economically can compete with fossil fuels. Since lignocellulosic ethanol is based on renewable resources it will have a positive impact...... production of cellulases and hemi-cellulases. The aim of the thesiswas to use modeling tools to identify alternative technologies that have higher energy or raw material efficiency than the current technology. The enzyme production by T. reesei was conducted as an aerobic fed-batch fermentation. The process...... of the uncertainty and sensitivity of the model indicated the biological parameters to be responsible for most of the model uncertainty. A number of alternative fermentation technologies for enzyme production were identified in the open literature. Their mass transfer capabilities and their energy efficiencies were...

  17. Effect of palytoxin on the sodium–potassium pump: model and simulation

    International Nuclear Information System (INIS)

    Rodrigues, Antônio M; Infantosi, Antonio F C; Almeida, Antônio-Carlos G

    2008-01-01

    We propose a reaction model for the palytoxin–sodium–potassium (PTX–Na + /K + ) pump complex. The model, which is similar to the Albers–Post model for Na + /K + -ATPase, is used to elucidate the effect of PTX on Na + /K + -ATPase during the enzyme interactions with Na + and/or K + ions. Conformational substates and reactions for the pump are incorporated into the Albers–Post model to represent enzymes with or without bound PTX. A mathematical model based on the reaction scheme is used in simulations modeling experimental studies of PTX-induced ionic currents. Our simulations suggest that (i) extracellular Na + as well as K + promotes PTX-induced channel blockage; (ii) extracellular K + accelerates PTX unbinding; and (iii) K + occlusion in the PTX–pump complex is essential for describing the PTX-induced current dynamics

  18. Incorporation of Markov reliability models for digital instrumentation and control systems into existing PRAs

    International Nuclear Information System (INIS)

    Bucci, P.; Mangan, L. A.; Kirschenbaum, J.; Mandelli, D.; Aldemir, T.; Arndt, S. A.

    2006-01-01

    Markov models have the ability to capture the statistical dependence between failure events that can arise in the presence of complex dynamic interactions between components of digital instrumentation and control systems. One obstacle to the use of such models in an existing probabilistic risk assessment (PRA) is that most of the currently available PRA software is based on the static event-tree/fault-tree methodology which often cannot represent such interactions. We present an approach to the integration of Markov reliability models into existing PRAs by describing the Markov model of a digital steam generator feedwater level control system, how dynamic event trees (DETs) can be generated from the model, and how the DETs can be incorporated into an existing PRA with the SAPHIRE software. (authors)

  19. Structural and Functional Models of Non-Heme Iron Enzymes : A Study of the 2-His-1-Carboxylate Facial Triad Structural Motif

    NARCIS (Netherlands)

    Bruijnincx, P.C.A.

    2007-01-01

    The structural and functional modeling of a specific group of non-heme iron enzymes by the synthesis of small synthetic analogues is the topic of this thesis. The group of non-heme iron enzymes with the 2-His-1-carboxylate facial triad has recently been established as a common platform for the

  20. Simultaneous measurement of two enzyme activities using infrared spectroscopy: A comparative evaluation of PARAFAC, TUCKER and N-PLS modeling.

    Science.gov (United States)

    Baum, Andreas; Hansen, Per Waaben; Meyer, Anne S; Mikkelsen, Jørn Dalgaard

    2013-08-06

    Enzymes are used in many processes to release fermentable sugars for green production of biofuel, or the refinery of biomass for extraction of functional food ingredients such as pectin or prebiotic oligosaccharides. The complex biomasses may, however, require a multitude of specific enzymes which are active on specific substrates generating a multitude of products. In this paper we use the plant polymer, pectin, to present a method to quantify enzyme activity of two pectolytic enzymes by monitoring their superimposed spectral evolutions simultaneously. The data is analyzed by three chemometric multiway methods, namely PARAFAC, TUCKER3 and N-PLS, to establish simultaneous enzyme activity assays for pectin lyase and pectin methyl esterase. Correlation coefficients Rpred(2) for prediction test sets are 0.48, 0.96 and 0.96 for pectin lyase and 0.70, 0.89 and 0.89 for pectin methyl esterase, respectively. The retrieved models are compared and prediction test sets show that especially TUCKER3 performs well, even in comparison to the supervised regression method N-PLS. Copyright © 2013 Elsevier B.V. All rights reserved.

  1. A generalized linear-quadratic model incorporating reciprocal time pattern of radiation damage repair

    International Nuclear Information System (INIS)

    Huang, Zhibin; Mayr, Nina A.; Lo, Simon S.; Wang, Jian Z.; Jia Guang; Yuh, William T. C.; Johnke, Roberta

    2012-01-01

    Purpose: It has been conventionally assumed that the repair rate for sublethal damage (SLD) remains constant during the entire radiation course. However, increasing evidence from animal studies suggest that this may not the case. Rather, it appears that the repair rate for radiation-induced SLD slows down with increasing time. Such a slowdown in repair would suggest that the exponential repair pattern would not necessarily accurately predict repair process. As a result, the purpose of this study was to investigate a new generalized linear-quadratic (LQ) model incorporating a repair pattern with reciprocal time. The new formulas were tested with published experimental data. Methods: The LQ model has been widely used in radiation therapy, and the parameter G in the surviving fraction represents the repair process of sublethal damage with T r as the repair half-time. When a reciprocal pattern of repair process was adopted, a closed form of G was derived analytically for arbitrary radiation schemes. The published animal data adopted to test the reciprocal formulas. Results: A generalized LQ model to describe the repair process in a reciprocal pattern was obtained. Subsequently, formulas for special cases were derived from this general form. The reciprocal model showed a better fit to the animal data than the exponential model, particularly for the ED50 data (reduced χ 2 min of 2.0 vs 4.3, p = 0.11 vs 0.006), with the following gLQ parameters: α/β = 2.6-4.8 Gy, T r = 3.2-3.9 h for rat feet skin, and α/β = 0.9 Gy, T r = 1.1 h for rat spinal cord. Conclusions: These results of repair process following a reciprocal time suggest that the generalized LQ model incorporating the reciprocal time of sublethal damage repair shows a better fit than the exponential repair model. These formulas can be used to analyze the experimental and clinical data, where a slowing-down repair process appears during the course of radiation therapy.

  2. Effect of whole-body X-irradiation on lysosomal enzymes

    Energy Technology Data Exchange (ETDEWEB)

    D' souza, D W; Vakil, U K; Srinivasan, A [Bhabha Atomic Research Centre, Bombay (India). Biochemistry and Food Technology Div.

    1974-06-01

    Effects of whole-body x irradiation with sublethal dose (400 rad) on three intestinal lysosomal enzymes, namely, arylsulphatase, cathepsin and acid phosphatases, have been studied. They are almost equally distributed throughout the entire small intestine region. X irradiation adversely affects the integrity of lysosomal membranes. ''Free'' and ''total'' lysosomal enzyme activities exhibit maxima on 6th day. These activities return to normal level on 14th day when there is rapid generation of villi, indicating that lysosomal activities correlate with the progression of injury and of repair mechanism after sublethal dose of x irradiation. The increase in total lysosomal activity may be due to its decreased breakdown, since the rate of protein synthesis in intestinal mucosa is reduced. This is evidenced by reduced incorporation of orally fed /sup 14/C leucine into acid insoluble proteins. (auth)

  3. A study of the fine structure, enzyme activities and pattern of 14CO2 ...

    African Journals Online (AJOL)

    A detailed study of selected grasses has been made with respect to fine structures characteristics, enzyme activities associated with C-4 and C-3 pathway photosynthesis, and short term carbon dioxide-14 incorporation experiments. A good correlation was obtained between the fine structure, the carbon pathway and the ...

  4. Something Old, Something New: Conserved Enzymes and the Evolution of Novelty in Plant Specialized Metabolism1

    Science.gov (United States)

    Moghe, Gaurav D.; Last, Robert L.

    2015-01-01

    Plants produce hundreds of thousands of small molecules known as specialized metabolites, many of which are of economic and ecological importance. This remarkable variety is a consequence of the diversity and rapid evolution of specialized metabolic pathways. These novel biosynthetic pathways originate via gene duplication or by functional divergence of existing genes, and they subsequently evolve through selection and/or drift. Studies over the past two decades revealed that diverse specialized metabolic pathways have resulted from the incorporation of primary metabolic enzymes. We discuss examples of enzyme recruitment from primary metabolism and the variety of paths taken by duplicated primary metabolic enzymes toward integration into specialized metabolism. These examples provide insight into processes by which plant specialized metabolic pathways evolve and suggest approaches to discover enzymes of previously uncharacterized metabolic networks. PMID:26276843

  5. Effects of dibutyl phthalate on lipid metabolism and drug metabolising enzyme system in rats

    International Nuclear Information System (INIS)

    Arakaki, Mitsuo; Ariyoshi, Toshihiko.

    1976-01-01

    Effects of dibutyl phthalate (DBP) on the liver constituents and the drug metabolizing enzyme system were investigated in rats. 1. In the experiments at a single oral dose of DBP (630 or 1260 mg/kg), the glycogen content was decreased only at the high dose, but no effects were observed on the contents of glycogen, triglyceride, microsomal protein and cytochromes, and on the activities of drug metabolizing enzymes. 2. In the repeated oral dose of DBP (630 or 1260 mg/kg/day) for 5 days, the ratio of liver weight to body weight was increased in both female and male rats, whereas the increases of cytochrome P-450 content and aniline hydroxylase activity were noted only in male rats. However, the contents of liver triglyceride, phospholipids, and cholesterol were unchanged. On the other hand, serum cholesterol content which showed the tendency to be decreased at the low dose was significantly decreased at the high dose. 3. In the incorporation of 1- 14 C-acetate into liver and serum lipids after repeated oral dose of DBP (630 mg/kg/day) for 5 days in male rats, the incorporation into triglyceride showed tendency to be increased, whereas the incorporation into cholesterol and cholesterol ester remained unchanged in vivo and in vitro. (auth.)

  6. Effects of synthetic cohesin-containing scaffold protein architecture on binding dockerin-enzyme fusions on the surface of Lactococcus lactis

    Directory of Open Access Journals (Sweden)

    Wieczorek Andrew S

    2012-12-01

    Full Text Available Abstract Background The microbial synthesis of fuels, commodity chemicals, and bioactive compounds necessitates the assemblage of multiple enzyme activities to carry out sequential chemical reactions, often via substrate channeling by means of multi-domain or multi-enzyme complexes. Engineering the controlled incorporation of enzymes in recombinant protein complexes is therefore of interest. The cellulosome of Clostridium thermocellum is an extracellular enzyme complex that efficiently hydrolyzes crystalline cellulose. Enzymes interact with protein scaffolds via type 1 dockerin/cohesin interactions, while scaffolds in turn bind surface anchor proteins by means of type 2 dockerin/cohesin interactions, which demonstrate a different binding specificity than their type 1 counterparts. Recombinant chimeric scaffold proteins containing cohesins of different specificity allow binding of multiple enzymes to specific sites within an engineered complex. Results We report the successful display of engineered chimeric scaffold proteins containing both type 1 and type 2 cohesins on the surface of Lactococcus lactis cells. The chimeric scaffold proteins were able to form complexes with the Escherichia coli β-glucuronidase fused to either type 1 or type 2 dockerin, and differences in binding efficiencies were correlated with scaffold architecture. We used E. coli β-galactosidase, also fused to type 1 or type 2 dockerins, to demonstrate the targeted incorporation of two enzymes into the complexes. The simultaneous binding of enzyme pairs each containing a different dockerin resulted in bi-enzymatic complexes tethered to the cell surface. The sequential binding of the two enzymes yielded insights into parameters affecting assembly of the complex such as protein size and position within the scaffold. Conclusions The spatial organization of enzymes into complexes is an important strategy for increasing the efficiency of biochemical pathways. In this study

  7. DEEPre: sequence-based enzyme EC number prediction by deep learning

    KAUST Repository

    Li, Yu

    2017-10-20

    Annotation of enzyme function has a broad range of applications, such as metagenomics, industrial biotechnology, and diagnosis of enzyme deficiency-caused diseases. However, the time and resource required make it prohibitively expensive to experimentally determine the function of every enzyme. Therefore, computational enzyme function prediction has become increasingly important. In this paper, we develop such an approach, determining the enzyme function by predicting the Enzyme Commission number.We propose an end-to-end feature selection and classification model training approach, as well as an automatic and robust feature dimensionality uniformization method, DEEPre, in the field of enzyme function prediction. Instead of extracting manuallycrafted features from enzyme sequences, our model takes the raw sequence encoding as inputs, extracting convolutional and sequential features from the raw encoding based on the classification result to directly improve the prediction performance. The thorough cross-fold validation experiments conducted on two large-scale datasets show that DEEPre improves the prediction performance over the previous state-of-the-art methods. In addition, our server outperforms five other servers in determining the main class of enzymes on a separate low-homology dataset. Two case studies demonstrate DEEPre\\'s ability to capture the functional difference of enzyme isoforms.The server could be accessed freely at http://www.cbrc.kaust.edu.sa/DEEPre.

  8. DEEPre: sequence-based enzyme EC number prediction by deep learning

    KAUST Repository

    Li, Yu; Wang, Sheng; Umarov, Ramzan; Xie, Bingqing; Fan, Ming; Li, Lihua; Gao, Xin

    2017-01-01

    Annotation of enzyme function has a broad range of applications, such as metagenomics, industrial biotechnology, and diagnosis of enzyme deficiency-caused diseases. However, the time and resource required make it prohibitively expensive to experimentally determine the function of every enzyme. Therefore, computational enzyme function prediction has become increasingly important. In this paper, we develop such an approach, determining the enzyme function by predicting the Enzyme Commission number.We propose an end-to-end feature selection and classification model training approach, as well as an automatic and robust feature dimensionality uniformization method, DEEPre, in the field of enzyme function prediction. Instead of extracting manuallycrafted features from enzyme sequences, our model takes the raw sequence encoding as inputs, extracting convolutional and sequential features from the raw encoding based on the classification result to directly improve the prediction performance. The thorough cross-fold validation experiments conducted on two large-scale datasets show that DEEPre improves the prediction performance over the previous state-of-the-art methods. In addition, our server outperforms five other servers in determining the main class of enzymes on a separate low-homology dataset. Two case studies demonstrate DEEPre's ability to capture the functional difference of enzyme isoforms.The server could be accessed freely at http://www.cbrc.kaust.edu.sa/DEEPre.

  9. TRITON: graphic software for rational engineering of enzymes.

    Science.gov (United States)

    Damboský, J; Prokop, M; Koca, J

    2001-01-01

    Engineering of the catalytic properties of enzymes requires knowledge about amino acid residues interacting with the transition state of the substrate. TRITON is a graphic software package for modelling enzymatic reactions for the analysis of essential interactions between the enzyme and its substrate and for in silico construction of protein mutants. The reactions are modelled using semi-empirical quantum-mechanic methods and the protein mutants are constructed by homology modelling. The users are guided through the calculation and data analysis by wizards.

  10. The Secretion and Action of Brush Border Enzymes in the Mammalian Small Intestine.

    Science.gov (United States)

    Hooton, Diane; Lentle, Roger; Monro, John; Wickham, Martin; Simpson, Robert

    2015-01-01

    Microvilli are conventionally regarded as an extension of the small intestinal absorptive surface, but they are also, as latterly discovered, a launching pad for brush border digestive enzymes. Recent work has demonstrated that motor elements of the microvillus cytoskeleton operate to displace the apical membrane toward the apex of the microvillus, where it vesiculates and is shed into the periapical space. Catalytically active brush border digestive enzymes remain incorporated within the membranes of these vesicles, which shifts the site of BB digestion from the surface of the enterocyte to the periapical space. This process enables nutrient hydrolysis to occur adjacent to the membrane in a pre-absorptive step. The characterization of BB digestive enzymes is influenced by the way in which these enzymes are anchored to the apical membranes of microvilli, their subsequent shedding in membrane vesicles, and their differing susceptibilities to cleavage from the component membranes. In addition, the presence of active intracellular components of these enzymes complicates their quantitative assay and the elucidation of their dynamics. This review summarizes the ontogeny and regulation of BB digestive enzymes and what is known of their kinetics and their action in the peripheral and axial regions of the small intestinal lumen.

  11. A modified Wright-Fisher model that incorporates Ne: A variant of the standard model with increased biological realism and reduced computational complexity.

    Science.gov (United States)

    Zhao, Lei; Gossmann, Toni I; Waxman, David

    2016-03-21

    The Wright-Fisher model is an important model in evolutionary biology and population genetics. It has been applied in numerous analyses of finite populations with discrete generations. It is recognised that real populations can behave, in some key aspects, as though their size that is not the census size, N, but rather a smaller size, namely the effective population size, Ne. However, in the Wright-Fisher model, there is no distinction between the effective and census population sizes. Equivalently, we can say that in this model, Ne coincides with N. The Wright-Fisher model therefore lacks an important aspect of biological realism. Here, we present a method that allows Ne to be directly incorporated into the Wright-Fisher model. The modified model involves matrices whose size is determined by Ne. Thus apart from increased biological realism, the modified model also has reduced computational complexity, particularly so when Ne⪡N. For complex problems, it may be hard or impossible to numerically analyse the most commonly-used approximation of the Wright-Fisher model that incorporates Ne, namely the diffusion approximation. An alternative approach is simulation. However, the simulations need to be sufficiently detailed that they yield an effective size that is different to the census size. Simulations may also be time consuming and have attendant statistical errors. The method presented in this work may then be the only alternative to simulations, when Ne differs from N. We illustrate the straightforward application of the method to some problems involving allele fixation and the determination of the equilibrium site frequency spectrum. We then apply the method to the problem of fixation when three alleles are segregating in a population. This latter problem is significantly more complex than a two allele problem and since the diffusion equation cannot be numerically solved, the only other way Ne can be incorporated into the analysis is by simulation. We have

  12. A MULTI-RESOLUTION FUSION MODEL INCORPORATING COLOR AND ELEVATION FOR SEMANTIC SEGMENTATION

    Directory of Open Access Journals (Sweden)

    W. Zhang

    2017-05-01

    Full Text Available In recent years, the developments for Fully Convolutional Networks (FCN have led to great improvements for semantic segmentation in various applications including fused remote sensing data. There is, however, a lack of an in-depth study inside FCN models which would lead to an understanding of the contribution of individual layers to specific classes and their sensitivity to different types of input data. In this paper, we address this problem and propose a fusion model incorporating infrared imagery and Digital Surface Models (DSM for semantic segmentation. The goal is to utilize heterogeneous data more accurately and effectively in a single model instead of to assemble multiple models. First, the contribution and sensitivity of layers concerning the given classes are quantified by means of their recall in FCN. The contribution of different modalities on the pixel-wise prediction is then analyzed based on visualization. Finally, an optimized scheme for the fusion of layers with color and elevation information into a single FCN model is derived based on the analysis. Experiments are performed on the ISPRS Vaihingen 2D Semantic Labeling dataset. Comprehensive evaluations demonstrate the potential of the proposed approach.

  13. Quantitative aspects of the cytochemical demonstration of glucose-6-phosphate dehydrogenase with tetranitro BT studied in a model system of polyacrylamide films

    NARCIS (Netherlands)

    van Noorden, C. J.; Tas, J.

    1980-01-01

    The cytochemical determination of the activity of glucose-6-phosphate dehydrogenase (G6PDH) with tetranitro blue tetrazolium (TNBT) was studied with model films of polyacrylamide gel incorporating purified enzyme. This model system enabled a quantitative study to be made of different parameters

  14. Directing filtration to optimize enzyme immobilization in reactive membranes

    DEFF Research Database (Denmark)

    Luo, Jianquan; Marpani, Fauziah; Brites, Rita

    2014-01-01

    enzymatic reaction efficiency were evaluated in terms of enzyme loading, conversion rate and biocatalytic stability. Alcohol dehydrogenase (ADH) was selected as a model enzyme. Lower pressure, higher enzyme concentration and lower pH resulted in higher irreversible fouling resistance and lower permeate flux....... High pH during immobilization produced increased permeate flux but declines in conversion rates, likely because of the weak immobilization resulting from strong electrostatic repulsion between enzymes and membrane. The results showed that pore blocking as a fouling mechanism permitted a higher enzyme...... loading but generated more permeability loss, while cake layer formation increased enzyme stability but resulted in low loading rate. Low pH (near isoelectric point) favored hydrophobic and electrostatic adsorption of enzymes on the membrane, which reduced the enzyme stability. Neutral pH, however...

  15. A model to incorporate organ deformation in the evaluation of dose/volume relationship

    International Nuclear Information System (INIS)

    Yan, D.; Jaffray, D.; Wong, J.; Brabbins, D.; Martinez, A. A.

    1997-01-01

    Purpose: Measurements of internal organ motion have demonstrated that daily organ deformation exists during the course of radiation treatment. However, a model to evaluate the resultant dose delivered to a daily deformed organ remains a difficult challenge. Current methods which model such organ deformation as rigid body motion in the dose calculation for treatment planning evaluation are incorrect and misleading. In this study, a new model for treatment planning evaluation is introduced which incorporates patient specific information of daily organ deformation and setup variation. The model was also used to retrospectively analyze the actual treatment data measured using daily CT scans for 5 patients with prostate treatment. Methods and Materials: The model assumes that for each patient, the organ of interest can be measured during the first few treatment days. First, the volume of each organ is delineated from each of the daily measurements and cumulated in a 3D bit-map. A tissue occupancy distribution is then constructed with the 50% isodensity representing the mean, or effective, organ volume. During the course of treatment, each voxel in the effective organ volume is assumed to move inside a local 3D neighborhood with a specific distribution function. The neighborhood and the distribution function are deduced from the positions and shapes of the organ in the first few measurements using the biomechanics model of viscoelastic body. For each voxel, the local distribution function is then convolved with the spatial dose distribution. The latter includes also the variation in dose due to daily setup error. As a result, the cumulative dose to the voxel incorporates the effects of daily setup variation and organ deformation. A ''variation adjusted'' dose volume histogram, aDVH, for the effective organ volume can then be constructed for the purpose of treatment evaluation and optimization. Up to 20 daily CT scans and daily portal images for 5 patients with prostate

  16. Intercalation of cellulase enzyme into a hydrotalcite layer structure

    Science.gov (United States)

    Zou, N.; Plank, J.

    2015-01-01

    A new inorganic-organic hybrid material whereby cellulase enzyme is incorporated into a hydrotalcite type layered double hydroxide (LDH) structure is reported. The Mg2Al-cellulase-LDH was synthesized via co-precipitation from Mg/Al nitrate at pH=9.6. Characterization was performed using X-ray powder diffraction (XRD), small angle X-ray scattering (SAXS), elemental analysis, infrared spectroscopy (IR) and thermogravimetry (TG). From XRD and SAXS measurements, a d-value of ~5.0 nm was identified for the basal spacing of the Mg2Al-cellulase-LDH. Consequently, the cellulase enzyme (hydrodynamic diameter ~6.6 nm) attains a slightly compressed conformation when intercalated. Formation of the LDH hybrid was also confirmed via scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Mg2Al-cellulase-LDH phases appear as ~20 nm thin foils which are intergrown to flower-like aggregates. Activity of the enzyme was retained after deintercalation from the Mg2Al-LDH framework using anion exchange. Accordingly, cellulase is not denatured during the intercalation process, and LDH presents a suitable host structure for time-controlled release of the biomolecule.

  17. Metabolic Diseases Downregulate the Majority of Histone Modification Enzymes, Making a Few Upregulated Enzymes Novel Therapeutic Targets – “Sand out and Gold Stays”

    Science.gov (United States)

    Shao, Ying; Chernaya, Valeria; Johnson, Candice; Yang, William Y.; Cueto, Ramon; Sha, Xiaojin; Zhang, Yi; Qin, Xuebin; Sun, Jianxin; Choi, Eric T.; Wang, Hong; Yang, Xiao-feng

    2016-01-01

    To determine whether the expression of histone modification enzymes is regulated in physiological and pathological conditions, we took an experimental database mining approach pioneered in our labs to determine a panoramic expression profile of 164 enzymes in 19 human and 17 murine tissues. We have made the following significant findings: 1) Histone enzymes are differentially expressed in cardiovascular, immune and other tissues; 2) Our new pyramid model showed that heart and T cells are among a few tissues in which histone acetylation/deacetylation, histone methylation/demethylation are in the highest varieties; and 3) Histone enzymes are more downregulated than upregulated in metabolic diseases and Treg polarization/differentiation, but not in tumors. These results have demonstrated a new working model of “sand out and gold stays,” where more downregulation than upregulation of histone enzymes in metabolic diseases makes a few upregulated enzymes the potential novel therapeutic targets in metabolic diseases and Treg activity. PMID:26746407

  18. Using a cognitive architecture in educational and recreational games : How to incorporate a model in your App

    NARCIS (Netherlands)

    Taatgen, Niels A.; de Weerd, Harmen; Reitter, David; Ritter, Frank

    2016-01-01

    We present a Swift re-implementation of the ACT-R cognitive architecture, which can be used to quickly build iOS Apps that incorporate an ACT-R model as a core feature. We discuss how this implementation can be used in an example model, and explore the breadth of possibilities by presenting six Apps

  19. Dynamic Modelling Reveals 'Hotspots' on the Pathway to Enzyme-Substrate Complex Formation.

    Directory of Open Access Journals (Sweden)

    Shane E Gordon

    2016-03-01

    Full Text Available Dihydrodipicolinate synthase (DHDPS catalyzes the first committed step in the diaminopimelate pathway of bacteria, yielding amino acids required for cell wall and protein biosyntheses. The essentiality of the enzyme to bacteria, coupled with its absence in humans, validates DHDPS as an antibacterial drug target. Conventional drug design efforts have thus far been unsuccessful in identifying potent DHDPS inhibitors. Here, we make use of contemporary molecular dynamics simulation and Markov state models to explore the interactions between DHDPS from the human pathogen Staphylococcus aureus and its cognate substrate, pyruvate. Our simulations recover the crystallographic DHDPS-pyruvate complex without a priori knowledge of the final bound structure. The highly conserved residue Arg140 was found to have a pivotal role in coordinating the entry of pyruvate into the active site from bulk solvent, consistent with previous kinetic reports, indicating an indirect role for the residue in DHDPS catalysis. A metastable binding intermediate characterized by multiple points of intermolecular interaction between pyruvate and key DHDPS residue Arg140 was found to be a highly conserved feature of the binding trajectory when comparing alternative binding pathways. By means of umbrella sampling we show that these binding intermediates are thermodynamically metastable, consistent with both the available experimental data and the substrate binding model presented in this study. Our results provide insight into an important enzyme-substrate interaction in atomistic detail that offers the potential to be exploited for the discovery of more effective DHDPS inhibitors and, in a broader sense, dynamic protein-drug interactions.

  20. Structural basis for the site-specific incorporation of lysine derivatives into proteins.

    Directory of Open Access Journals (Sweden)

    Veronika Flügel

    Full Text Available Posttranslational modifications (PTMs of proteins determine their structure-function relationships, interaction partners, as well as their fate in the cell and are crucial for many cellular key processes. For instance chromatin structure and hence gene expression is epigenetically regulated by acetylation or methylation of lysine residues in histones, a phenomenon known as the 'histone code'. Recently it was shown that these lysine residues can furthermore be malonylated, succinylated, butyrylated, propionylated and crotonylated, resulting in significant alteration of gene expression patterns. However the functional implications of these PTMs, which only differ marginally in their chemical structure, is not yet understood. Therefore generation of proteins containing these modified amino acids site specifically is an important tool. In the last decade methods for the translational incorporation of non-natural amino acids using orthogonal aminoacyl-tRNA synthetase (aaRS:tRNAaaCUA pairs were developed. A number of studies show that aaRS can be evolved to use non-natural amino acids and expand the genetic code. Nevertheless the wild type pyrrolysyl-tRNA synthetase (PylRS from Methanosarcina mazei readily accepts a number of lysine derivatives as substrates. This enzyme can further be engineered by mutagenesis to utilize a range of non-natural amino acids. Here we present structural data on the wild type enzyme in complex with adenylated ε-N-alkynyl-, ε-N-butyryl-, ε-N-crotonyl- and ε-N-propionyl-lysine providing insights into the plasticity of the PylRS active site. This shows that given certain key features in the non-natural amino acid to be incorporated, directed evolution of this enzyme is not necessary for substrate tolerance.

  1. Developing Baltic cod recruitment models II : Incorporation of environmental variability and species interaction

    DEFF Research Database (Denmark)

    Köster, Fritz; Hinrichsen, H.H.; St. John, Michael

    2001-01-01

    We investigate whether a process-oriented approach based on the results of field, laboratory, and modelling studies can be used to develop a stock-environment-recruitment model for Central Baltic cod (Gadus morhua). Based on exploratory statistical analysis, significant variables influencing...... affecting survival of eggs, predation by clupeids on eggs, larval transport, and cannibalism. Results showed that recruitment in the most important spawning area, the Bornholm Basin, during 1976-1995 was related to egg production; however, other factors affecting survival of the eggs (oxygen conditions......, predation) were also significant and when incorporated explained 69% of the variation in 0-group recruitment. In other spawning areas, variable hydrographic conditions did not allow for regular successful egg development. Hence, relatively simple models proved sufficient to predict recruitment of 0-group...

  2. Modeling of pharmacokinetics of cocaine in human reveals the feasibility for development of enzyme therapies for drugs of abuse.

    Directory of Open Access Journals (Sweden)

    Fang Zheng

    Full Text Available A promising strategy for drug abuse treatment is to accelerate the drug metabolism by administration of a drug-metabolizing enzyme. The question is how effectively an enzyme can actually prevent the drug from entering brain and producing physiological effects. In the present study, we have developed a pharmacokinetic model through a combined use of in vitro kinetic parameters and positron emission tomography data in human to examine the effects of a cocaine-metabolizing enzyme in plasma on the time course of cocaine in plasma and brain of human. Without an exogenous enzyme, cocaine half-lives in both brain and plasma are almost linearly dependent on the initial cocaine concentration in plasma. The threshold concentration of cocaine in brain required to produce physiological effects has been estimated to be 0.22±0.07 µM, and the threshold area under the cocaine concentration versus time curve (AUC value in brain (denoted by AUC2(∞ required to produce physiological effects has been estimated to be 7.9±2.7 µM·min. It has been demonstrated that administration of a cocaine hydrolase/esterase (CocH/CocE can considerably decrease the cocaine half-lives in both brain and plasma, the peak cocaine concentration in brain, and the AUC2(∞. The estimated maximum cocaine plasma concentration which a given concentration of drug-metabolizing enzyme can effectively prevent from entering brain and producing physiological effects can be used to guide future preclinical/clinical studies on cocaine-metabolizing enzymes. Understanding of drug-metabolizing enzymes is key to the science of pharmacokinetics. The general insights into the effects of a drug-metabolizing enzyme on drug kinetics in human should be valuable also in future development of enzyme therapies for other drugs of abuse.

  3. Modeling of pharmacokinetics of cocaine in human reveals the feasibility for development of enzyme therapies for drugs of abuse.

    Science.gov (United States)

    Zheng, Fang; Zhan, Chang-Guo

    2012-01-01

    A promising strategy for drug abuse treatment is to accelerate the drug metabolism by administration of a drug-metabolizing enzyme. The question is how effectively an enzyme can actually prevent the drug from entering brain and producing physiological effects. In the present study, we have developed a pharmacokinetic model through a combined use of in vitro kinetic parameters and positron emission tomography data in human to examine the effects of a cocaine-metabolizing enzyme in plasma on the time course of cocaine in plasma and brain of human. Without an exogenous enzyme, cocaine half-lives in both brain and plasma are almost linearly dependent on the initial cocaine concentration in plasma. The threshold concentration of cocaine in brain required to produce physiological effects has been estimated to be 0.22±0.07 µM, and the threshold area under the cocaine concentration versus time curve (AUC) value in brain (denoted by AUC2(∞)) required to produce physiological effects has been estimated to be 7.9±2.7 µM·min. It has been demonstrated that administration of a cocaine hydrolase/esterase (CocH/CocE) can considerably decrease the cocaine half-lives in both brain and plasma, the peak cocaine concentration in brain, and the AUC2(∞). The estimated maximum cocaine plasma concentration which a given concentration of drug-metabolizing enzyme can effectively prevent from entering brain and producing physiological effects can be used to guide future preclinical/clinical studies on cocaine-metabolizing enzymes. Understanding of drug-metabolizing enzymes is key to the science of pharmacokinetics. The general insights into the effects of a drug-metabolizing enzyme on drug kinetics in human should be valuable also in future development of enzyme therapies for other drugs of abuse.

  4. The dynamic basis of energy transduction in enzymes.

    Science.gov (United States)

    Somogyi, B; Welch, G R; Damjanovich, S

    1984-09-06

    The most important idea underlying our treatment herein is the unity of the enzyme molecule and the medium. Appreciation of this relationship is vital, if enzymology is to graduate from its present reductionistic status to a more holistic posture. Enzymes are biological entities firstly, and isolated objects of physicochemical analysis secondly. Perhaps the most crucial 'biological lesson', particularly apropos of enzymes in intermediary metabolism, concerns the 'cytosociology' of enzyme action in vivo [94,128]. The natural habitat of many enzymes in the living cell is far different from that in bulk aqueous solution in vitro. In order to obtain a real grasp of the nature of enzyme function, one must ultimately couch enzymology in concepts emerging from contemporary cell biology [95]. Notwithstanding, analysis precedes synthesis; and one must needs begin with the individual enzyme molecule. The trenchant efforts of the physical chemist and the organic chemist have produced a wealth of information on the nature of the binding and catalytic events at the enzyme active site. While it is not yet possible to explain precisely the complete sequence of events in the catalytic process, nevertheless, the basic mechanisms by which enzymes effect catalysis (i.e., reduce activation energy) now seem apparent [81,129]. The new frontier is to be found, in exploring the dynamic role of the protein matrix [17]. Not only does the protein provide the 3-D scaffolding for active-site processes, but, more importantly, it serves as the local solvent for the bound chemical subsystem. Thus, the dynamical aspects of enzyme catalysis (for thermally based systems) must arise from the fluctuational properties of the protein molecule. This notion is the common denominator in all of the models in subsection IIC. It is the anisotropic nature of this fluctuational behavior, which would characterize the energy-transduction phenomenon leading to localized catalytic events at the active-site. In

  5. A model for arsenic anti-site incorporation in GaAs grown by hydride vapor phase epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Schulte, K. L.; Kuech, T. F. [Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706 (United States)

    2014-12-28

    GaAs growth by hydride vapor phase epitaxy (HVPE) has regained interest as a potential route to low cost, high efficiency thin film photovoltaics. In order to attain the highest efficiencies, deep level defect incorporation in these materials must be understood and controlled. The arsenic anti-site defect, As{sub Ga} or EL2, is the predominant deep level defect in HVPE-grown GaAs. In the present study, the relationships between HVPE growth conditions and incorporation of EL2 in GaAs epilayers were determined. Epitaxial n-GaAs layers were grown under a wide range of deposition temperatures (T{sub D}) and gallium chloride partial pressures (P{sub GaCl}), and the EL2 concentration, [EL2], was determined by deep level transient spectroscopy. [EL2] agreed with equilibrium thermodynamic predictions in layers grown under conditions in which the growth rate, R{sub G}, was controlled by conditions near thermodynamic equilibrium. [EL2] fell below equilibrium levels when R{sub G} was controlled by surface kinetic processes, with the disparity increasing as R{sub G} decreased. The surface chemical composition during growth was determined to have a strong influence on EL2 incorporation. Under thermodynamically limited growth conditions, e.g., high T{sub D} and/or low P{sub GaCl}, the surface vacancy concentration was high and the bulk crystal was close to equilibrium with the vapor phase. Under kinetically limited growth conditions, e.g., low T{sub D} and/or high P{sub GaCl}, the surface attained a high GaCl coverage, blocking As adsorption. This competitive adsorption process reduced the growth rate and also limited the amount of arsenic that incorporated as As{sub Ga}. A defect incorporation model which accounted for the surface concentration of arsenic as a function of the growth conditions, was developed. This model was used to identify optimal growth parameters for the growth of thin films for photovoltaics, conditions in which a high growth rate and low [EL2] could be

  6. Recent developments of the quantum chemical cluster approach for modeling enzyme reactions.

    Science.gov (United States)

    Siegbahn, Per E M; Himo, Fahmi

    2009-06-01

    The quantum chemical cluster approach for modeling enzyme reactions is reviewed. Recent applications have used cluster models much larger than before which have given new modeling insights. One important and rather surprising feature is the fast convergence with cluster size of the energetics of the reactions. Even for reactions with significant charge separation it has in some cases been possible to obtain full convergence in the sense that dielectric cavity effects from outside the cluster do not contribute to any significant extent. Direct comparisons between quantum mechanics (QM)-only and QM/molecular mechanics (MM) calculations for quite large clusters in a case where the results differ significantly have shown that care has to be taken when using the QM/MM approach where there is strong charge polarization. Insights from the methods used, generally hybrid density functional methods, have also led to possibilities to give reasonable error limits for the results. Examples are finally given from the most extensive study using the cluster model, the one of oxygen formation at the oxygen-evolving complex in photosystem II.

  7. Fouling-induced enzyme immobilization for membrane reactors

    DEFF Research Database (Denmark)

    Luo, Jianquan; Meyer, Anne S.; Jonsson, Gunnar Eigil

    2013-01-01

    A simple enzyme immobilization method accomplished by promoting membrane fouling formation is proposed. The immobilization method is based on adsorption and entrapment of the enzymes in/on the membrane. To evaluate the concept, two membrane orientations, skin layer facing feed (normal mode......, but the reverse mode allowed for higher enzyme loading and stability, and irreversible fouling (i.e. pore blocking) developed more readily in the support structure than in the skin layer. Compared with an enzymatic membrane reactor (EMR) with free enzymes, the novel EMR with enzymes immobilized in membrane......) and support layer facing feed (reverse mode), were used to immobilize alcohol dehydrogenase (ADH, EC 1.1.1.1) and glutamate dehydrogenase (GDH, EC 1.4.1.3), respectively. The nature of the fouling in each mode was determined by filtration fouling models. The permeate flux was larger in the normal mode...

  8. Incorporating Yearly Derived Winter Wheat Maps Into Winter Wheat Yield Forecasting Model

    Science.gov (United States)

    Skakun, S.; Franch, B.; Roger, J.-C.; Vermote, E.; Becker-Reshef, I.; Justice, C.; Santamaría-Artigas, A.

    2016-01-01

    Wheat is one of the most important cereal crops in the world. Timely and accurate forecast of wheat yield and production at global scale is vital in implementing food security policy. Becker-Reshef et al. (2010) developed a generalized empirical model for forecasting winter wheat production using remote sensing data and official statistics. This model was implemented using static wheat maps. In this paper, we analyze the impact of incorporating yearly wheat masks into the forecasting model. We propose a new approach of producing in season winter wheat maps exploiting satellite data and official statistics on crop area only. Validation on independent data showed that the proposed approach reached 6% to 23% of omission error and 10% to 16% of commission error when mapping winter wheat 2-3 months before harvest. In general, we found a limited impact of using yearly winter wheat masks over a static mask for the study regions.

  9. Biocatalysis with thermostable enzymes: structure and properties of a thermophilic 'ene'-reductase related to old yellow enzyme.

    Science.gov (United States)

    Adalbjörnsson, Björn V; Toogood, Helen S; Fryszkowska, Anna; Pudney, Christopher R; Jowitt, Thomas A; Leys, David; Scrutton, Nigel S

    2010-01-25

    We report the crystal structure of a thermophilic "ene" reductase (TOYE) isolated from Thermoanaerobacter pseudethanolicus E39. The crystal structure reveals a tetrameric enzyme and an active site that is relatively large compared to most other structurally determined and related Old Yellow Enzymes. The enzyme adopts higher order oligomeric states (octamers and dodecamers) in solution, as revealed by sedimentation velocity and multiangle laser light scattering. Bead modelling indicates that the solution structure is consistent with the basic tetrameric structure observed in crystallographic studies and electron microscopy. TOYE is stable at high temperatures (T(m)>70 degrees C) and shows increased resistance to denaturation in water-miscible organic solvents compared to the mesophilic Old Yellow Enzyme family member, pentaerythritol tetranitrate reductase. TOYE has typical ene-reductase properties of the Old Yellow Enzyme family. There is currently major interest in using Old Yellow Enzyme family members in the preparative biocatalysis of a number of activated alkenes. The increased stability of TOYE in organic solvents is advantageous for biotransformations in which water-miscible organic solvents and biphasic reaction conditions are required to both deliver novel substrates and minimize product racemisation.

  10. Homology modelling and docking studies on Neuraminidase enzyme as a natural product target for combating influenza

    Directory of Open Access Journals (Sweden)

    Nisha Singh

    2017-10-01

    Full Text Available Influenza remains to be dreadful with yearly epidemics and sudden pandemic outbreaks causing significant mortality, even in nations with the most advanced health care systems. Thus, there has been a long-standing interest to develop effective and safe antiviral agents to treat infected individuals. Attempt to identify suitable molecular targets as antiviral compounds have focused recently on the influenza virus neuraminidase (NA, a key enzyme in viral replication [1]. In this research, virtual screening was done on a total of 600 natural compounds from 22 ethno medicinal Indian herbs for activity against neuraminidase enzyme exploiting representative protein conformations selected from molecular dynamics simulations. Neuraminidase enzyme sequences from different existing strains available on National Center of Biotechnology Information [2] (NCBI protein database were aligned using Clustal W [3] and CLC workbench 10 [4] to find the conserved residues. Neuraminidase protein sequence from H1N1 strain available on NCBI was used to structure 3D target model predicted against dataset from Protein data bank using modeller [5]. The target model was validated on different parameter at SAVES Server [6]. Using this target model a pharmacophore model was developed using ligand based strategy exploiting the three known inhibitors. The docking parameters were validated by redocking Zanamivir to its co-complex 2009 H1N1 NA crystal structure (PDB ID: 3TI5 generating best pose with a RMSD value of 0.7543 A°. This model was then used for in silico analysis of a library of natural compounds from 22 ethno medicinal Indian herbs known to have antiviral activity taken downloaded from PubChem database and selected on the basis of drug likeliness. All the compounds were docked in the binding pocket of neuraminidase. Top compounds having binding affinity better than or comparable to the control drug Zanamivir were selected and analyzed for their ADME and toxicity

  11. Pancreatic Enzymes

    Science.gov (United States)

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

  12. A Theoretical Approach to Engineering a New Enzyme

    International Nuclear Information System (INIS)

    Anderson, Greg; Gomatam, Ravi; Behera, Raghu N.

    2016-01-01

    Density function theory, a subfield of quantum mechanics (QM), in combination with molecular mechanics (MM) has opened the way to engineer new artificial enzymes. Herein, we report theoretical calculations done using QM/MM to examine whether the regioselectivity and rate of chlorination of the enzyme chloroperoxidase can be improved by replacing the vanadium of this enzyme with niobium through dialysis. Our calculations show that a niobium substituted chloroperoxidase will be able to enter the initial steps of the catalytic cycle for chlorination. Although the protonation state of the niobium substituted enzyme is calculated to be different from than that of the natural vanadium substituted enzyme, our calculations show that the catalytic cycle can still proceed forward. Using natural bond orbitals, we analyse the electronic differences between the niobium substituted enzyme and the natural enzyme. We conclude by briefly examining how good of a model QM/MM provides for understanding the mechanism of catalysis of chloroperoxidase. (paper)

  13. Digital terrain model generalization incorporating scale, semantic and cognitive constraints

    Science.gov (United States)

    Partsinevelos, Panagiotis; Papadogiorgaki, Maria

    2014-05-01

    Cartographic generalization is a well-known process accommodating spatial data compression, visualization and comprehension under various scales. In the last few years, there are several international attempts to construct tangible GIS systems, forming real 3D surfaces using a vast number of mechanical parts along a matrix formation (i.e., bars, pistons, vacuums). Usually, moving bars upon a structured grid push a stretching membrane resulting in a smooth visualization for a given surface. Most of these attempts suffer either in their cost, accuracy, resolution and/or speed. Under this perspective, the present study proposes a surface generalization process that incorporates intrinsic constrains of tangible GIS systems including robotic-motor movement and surface stretching limitations. The main objective is to provide optimized visualizations of 3D digital terrain models with minimum loss of information. That is, to minimize the number of pixels in a raster dataset used to define a DTM, while reserving the surface information. This neighborhood type of pixel relations adheres to the basics of Self Organizing Map (SOM) artificial neural networks, which are often used for information abstraction since they are indicative of intrinsic statistical features contained in the input patterns and provide concise and characteristic representations. Nevertheless, SOM remains more like a black box procedure not capable to cope with possible particularities and semantics of the application at hand. E.g. for coastal monitoring applications, the near - coast areas, surrounding mountains and lakes are more important than other features and generalization should be "biased"-stratified to fulfill this requirement. Moreover, according to the application objectives, we extend the SOM algorithm to incorporate special types of information generalization by differentiating the underlying strategy based on topologic information of the objects included in the application. The final

  14. Design and modelling of enzyme/poly-pyrrole modified electrodes for bio-catalyzed electro-synthesis processes

    International Nuclear Information System (INIS)

    Gros, Pierre

    1996-01-01

    This research thesis reports a study which aims at developing, analyzing and integrating an electrode-enzyme interface within an electro-enzymatic reactor to develop electrochemical biosensors. The adopted method comprises a confinement of the enzyme at the electrode surface by means of an electro-formed poly-pyrrole film. The author reports an experimental and theoretical study of the coupling between electrochemical reaction, enzymatic reaction and matter transfer in the polymer in order to better understand the operation of so-modified electrodes. Different parameters have an influence on the reaction rate. A numerical model (validated by experiments) allows the identification of the reaction limiting stages. A new elaboration protocol allows the polymer permeability to be increased. The interface is first applied to the reduction of the NAD coenzyme, and the process is also applied to the production of gluconic acid [fr

  15. Gold Incorporated Mesoporous Silica Thin Film Model Surface as a Robust SERS and Catalytically Active Substrate

    Directory of Open Access Journals (Sweden)

    Anandakumari Chandrasekharan Sunil Sekhar

    2016-05-01

    Full Text Available Ultra-small gold nanoparticles incorporated in mesoporous silica thin films with accessible pore channels perpendicular to the substrate are prepared by a modified sol-gel method. The simple and easy spin coating technique is applied here to make homogeneous thin films. The surface characterization using FESEM shows crack-free films with a perpendicular pore arrangement. The applicability of these thin films as catalysts as well as a robust SERS active substrate for model catalysis study is tested. Compared to bare silica film our gold incorporated silica, GSM-23F gave an enhancement factor of 103 for RhB with a laser source 633 nm. The reduction reaction of p-nitrophenol with sodium borohydride from our thin films shows a decrease in peak intensity corresponding to –NO2 group as time proceeds, confirming the catalytic activity. Such model surfaces can potentially bridge the material gap between a real catalytic system and surface science studies.

  16. Incorporating excitation-induced dephasing into the Maxwell-Bloch numerical modeling of photon echoes

    International Nuclear Information System (INIS)

    Burr, G.W.; Harris, Todd L.; Babbitt, Wm. Randall; Jefferson, C. Michael

    2004-01-01

    We describe the incorporation of excitation-induced dephasing (EID) into the Maxwell-Bloch numerical simulation of photon echoes. At each time step of the usual numerical integration, stochastic frequency jumps of ions--caused by excitation of neighboring ions--is modeled by convolving each Bloch vector with the Bloch vectors of nearby frequency detunings. The width of this convolution kernel follows the instantaneous change in overall population, integrated over the simulated bandwidth. This approach is validated by extensive comparison against published and original experimental results. The enhanced numerical model is then used to investigate the accuracy of experiments designed to extrapolate to the intrinsic dephasing time T 2 from data taken in the presence of EID. Such a modeling capability offers improved understanding of experimental results, and should allow quantitative analysis of engineering tradeoffs in realistic optical coherent transient applications

  17. Short-term incorporation of organic manures and biofertilizers influences biochemical and microbial characteristics of soils under an annual crop [Turmeric (Curcuma longa L.)].

    Science.gov (United States)

    Dinesh, R; Srinivasan, V; Hamza, S; Manjusha, A

    2010-06-01

    The study was conducted to determine whether short-term incorporation of organic manures and biofertilizers influence biochemical and microbial variables reflecting soil quality. For the study, soils were collected from a field experiment conducted on turmeric (Curcuma longa L.) involving organic nutrient management (ONM), chemical nutrient management (CNM) and integrated nutrient management (INM). The findings revealed that application of organic manures and biofertilizers (ONM and INM) positively influenced microbial biomass C, N mineralization, soil respiration and enzymes activities. Contrarily, greater metabolic quotient levels in CNM indicated a stressed soil microbial community. Principal component analysis indicated the strong relationship between microbial activity and the availability of labile and easily mineralizable organic matter. The findings imply that even short-term incorporation of organic manures and biofertilizers promoted soil microbial and enzyme activities and these parameters are sensitive enough to detect changes in soil quality due to short-term incorporation of biological fertilizers. (c) 2010 Elsevier Ltd. All rights reserved.

  18. SKPDB: a structural database of shikimate pathway enzymes

    Directory of Open Access Journals (Sweden)

    de Azevedo Walter F

    2010-01-01

    Full Text Available Abstract Background The functional and structural characterisation of enzymes that belong to microbial metabolic pathways is very important for structure-based drug design. The main interest in studying shikimate pathway enzymes involves the fact that they are essential for bacteria but do not occur in humans, making them selective targets for design of drugs that do not directly impact humans. Description The ShiKimate Pathway DataBase (SKPDB is a relational database applied to the study of shikimate pathway enzymes in microorganisms and plants. The current database is updated regularly with the addition of new data; there are currently 8902 enzymes of the shikimate pathway from different sources. The database contains extensive information on each enzyme, including detailed descriptions about sequence, references, and structural and functional studies. All files (primary sequence, atomic coordinates and quality scores are available for downloading. The modeled structures can be viewed using the Jmol program. Conclusions The SKPDB provides a large number of structural models to be used in docking simulations, virtual screening initiatives and drug design. It is freely accessible at http://lsbzix.rc.unesp.br/skpdb/.

  19. Simulation of Forest Carbon Fluxes Using Model Incorporation and Data Assimilation

    Directory of Open Access Journals (Sweden)

    Min Yan

    2016-07-01

    Full Text Available This study improved simulation of forest carbon fluxes in the Changbai Mountains with a process-based model (Biome-BGC using incorporation and data assimilation. Firstly, the original remote sensing-based MODIS MOD_17 GPP (MOD_17 model was optimized using refined input data and biome-specific parameters. The key ecophysiological parameters of the Biome-BGC model were determined through the Extended Fourier Amplitude Sensitivity Test (EFAST sensitivity analysis. Then the optimized MOD_17 model was used to calibrate the Biome-BGC model by adjusting the sensitive ecophysiological parameters. Once the best match was found for the 10 selected forest plots for the 8-day GPP estimates from the optimized MOD_17 and from the Biome-BGC, the values of sensitive ecophysiological parameters were determined. The calibrated Biome-BGC model agreed better with the eddy covariance (EC measurements (R2 = 0.87, RMSE = 1.583 gC·m−2·d−1 than the original model did (R2 = 0.72, RMSE = 2.419 gC·m−2·d−1. To provide a best estimate of the true state of the model, the Ensemble Kalman Filter (EnKF was used to assimilate five years (of eight-day periods between 2003 and 2007 of Global LAnd Surface Satellite (GLASS LAI products into the calibrated Biome-BGC model. The results indicated that LAI simulated through the assimilated Biome-BGC agreed well with GLASS LAI. GPP performances obtained from the assimilated Biome-BGC were further improved and verified by EC measurements at the Changbai Mountains forest flux site (R2 = 0.92, RMSE = 1.261 gC·m−2·d−1.

  20. Incorporating an extended dendritic growth model into the CAFE model for rapidly solidified non-dilute alloys

    International Nuclear Information System (INIS)

    Ma, Jie; Wang, Bo; Zhao, Shunli; Wu, Guangxin; Zhang, Jieyu; Yang, Zhiliang

    2016-01-01

    We have extended the dendritic growth model first proposed by Boettinger, Coriell and Trivedi (here termed EBCT) for microstructure simulations of rapidly solidified non-dilute alloys. The temperature-dependent distribution coefficient, obtained from calculations of phase equilibria, and the continuous growth model (CGM) were adopted in the present EBCT model to describe the solute trapping behaviors. The temperature dependence of the physical properties, which were not used in previous dendritic growth models, were also considered in the present EBCT model. These extensions allow the present EBCT model to be used for microstructure simulations of non-dilute alloys. The comparison of the present EBCT model with the BCT model proves that the considerations of the distribution coefficient and physical properties are necessary for microstructure simulations, especially for small particles with high undercoolings. Finally, the EBCT model was incorporated into the cellular automaton-finite element (CAFE) model to simulate microstructures of gas-atomized ASP30 high speed steel particles that were then compared with experimental results. Both the simulated and experimental results reveal that a columnar dendritic microstructure preferentially forms in small particles and an equiaxed microstructure forms otherwise. The applications of the present EBCT model provide a convenient way to predict the microstructure of non-dilute alloys. - Highlights: • A dendritic growth model was developed considering non-equilibrium distribution coefficient. • The physical properties with temperature dependence were considered in the extended model. • The extended model can be used to non-dilute alloys and the extensions are necessary in small particles. • Microstructure of ASP30 steel was investigated using the present model and verified by experiment.

  1. Incorporating an extended dendritic growth model into the CAFE model for rapidly solidified non-dilute alloys

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Jie; Wang, Bo [State Key Laboratory of Advanced Special Steel, Shanghai University, Shanghai 200072 (China); Shanghai Engineering Technology Research Center of Special Casting, Shanghai 201605 (China); Zhao, Shunli [Research Institute, Baoshan Iron & Steel Co., Ltd, Shanghai 201900 (China); Wu, Guangxin [State Key Laboratory of Advanced Special Steel, Shanghai University, Shanghai 200072 (China); Shanghai Engineering Technology Research Center of Special Casting, Shanghai 201605 (China); Zhang, Jieyu, E-mail: zjy6162@staff.shu.edu.cn [State Key Laboratory of Advanced Special Steel, Shanghai University, Shanghai 200072 (China); Shanghai Engineering Technology Research Center of Special Casting, Shanghai 201605 (China); Yang, Zhiliang [State Key Laboratory of Advanced Special Steel, Shanghai University, Shanghai 200072 (China); Shanghai Engineering Technology Research Center of Special Casting, Shanghai 201605 (China)

    2016-05-25

    We have extended the dendritic growth model first proposed by Boettinger, Coriell and Trivedi (here termed EBCT) for microstructure simulations of rapidly solidified non-dilute alloys. The temperature-dependent distribution coefficient, obtained from calculations of phase equilibria, and the continuous growth model (CGM) were adopted in the present EBCT model to describe the solute trapping behaviors. The temperature dependence of the physical properties, which were not used in previous dendritic growth models, were also considered in the present EBCT model. These extensions allow the present EBCT model to be used for microstructure simulations of non-dilute alloys. The comparison of the present EBCT model with the BCT model proves that the considerations of the distribution coefficient and physical properties are necessary for microstructure simulations, especially for small particles with high undercoolings. Finally, the EBCT model was incorporated into the cellular automaton-finite element (CAFE) model to simulate microstructures of gas-atomized ASP30 high speed steel particles that were then compared with experimental results. Both the simulated and experimental results reveal that a columnar dendritic microstructure preferentially forms in small particles and an equiaxed microstructure forms otherwise. The applications of the present EBCT model provide a convenient way to predict the microstructure of non-dilute alloys. - Highlights: • A dendritic growth model was developed considering non-equilibrium distribution coefficient. • The physical properties with temperature dependence were considered in the extended model. • The extended model can be used to non-dilute alloys and the extensions are necessary in small particles. • Microstructure of ASP30 steel was investigated using the present model and verified by experiment.

  2. Incorporation of oxygen contribution by plant roots into classical dissolved oxygen deficit model for a subsurface flow treatment wetland.

    Science.gov (United States)

    Bezbaruah, Achintya N; Zhang, Tian C

    2009-01-01

    It has been long established that plants play major roles in a treatment wetland. However, the role of plants has not been incorporated into wetland models. This study tries to incorporate wetland plants into a biochemical oxygen demand (BOD) model so that the relative contributions of the aerobic and anaerobic processes to meeting BOD can be quantitatively determined. The classical dissolved oxygen (DO) deficit model has been modified to simulate the DO curve for a field subsurface flow constructed wetland (SFCW) treating municipal wastewater. Sensitivities of model parameters have been analyzed. Based on the model it is predicted that in the SFCW under study about 64% BOD are degraded through aerobic routes and 36% is degraded anaerobically. While not exhaustive, this preliminary work should serve as a pointer for further research in wetland model development and to determine the values of some of the parameters used in the modified DO deficit and associated BOD model. It should be noted that nitrogen cycle and effects of temperature have not been addressed in these models for simplicity of model formulation. This paper should be read with this caveat in mind.

  3. Measuring the Enzyme Activity of Arabidopsis Deubiquitylating Enzymes.

    Science.gov (United States)

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

    2016-01-01

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

  4. Bioethanol from lignocellulose - pretreatment, enzyme immobilization and hydrolysis kinetics

    DEFF Research Database (Denmark)

    Tsai, Chien Tai

    , the cost of enzyme is still the bottle neck, re-using the enzyme is apossible way to reduce the input of enzyme in the process. In the point view of engineering, the prediction of enzymatic hydrolysis kinetics under different substrate loading, enzyme combination is usful for process design. Therefore...... lignocellulose is the required high cellulase enzyme dosages that increase the processing costs. One method to decrease the enzyme dosage is to re-use BG, which hydrolyze the soluble substrate cellobiose. Based on the hypothesis that immobilized BG can be re-used, how many times the enzyme could be recycled...... liquid and pretreatment time can be reduced, the influence of substrate concentration, pretreatment time and temperature were investigated and optimized. Pretreatment of barley straw by [EMIM]Ac, correlative models were constructed using 3 different pretreatment parameters (temperature, time...

  5. A constitutive mechanical model for gas hydrate bearing sediments incorporating inelastic mechanisms

    KAUST Repository

    Sánchez, Marcelo

    2016-11-30

    Gas hydrate bearing sediments (HBS) are natural soils formed in permafrost and sub-marine settings where the temperature and pressure conditions are such that gas hydrates are stable. If these conditions shift from the hydrate stability zone, hydrates dissociate and move from the solid to the gas phase. Hydrate dissociation is accompanied by significant changes in sediment structure and strongly affects its mechanical behavior (e.g., sediment stiffenss, strength and dilatancy). The mechanical behavior of HBS is very complex and its modeling poses great challenges. This paper presents a new geomechanical model for hydrate bearing sediments. The model incorporates the concept of partition stress, plus a number of inelastic mechanisms proposed to capture the complex behavior of this type of soil. This constitutive model is especially well suited to simulate the behavior of HBS upon dissociation. The model was applied and validated against experimental data from triaxial and oedometric tests conducted on manufactured and natural specimens involving different hydrate saturation, hydrate morphology, and confinement conditions. Particular attention was paid to model the HBS behavior during hydrate dissociation under loading. The model performance was highly satisfactory in all the cases studied. It managed to properly capture the main features of HBS mechanical behavior and it also assisted to interpret the behavior of this type of sediment under different loading and hydrate conditions.

  6. Modeling enzyme production with Aspergillus oryzae in pilot scale vessels with different agitation, aeration, and agitator types

    DEFF Research Database (Denmark)

    Albæk, Mads Orla; Gernaey, Krist; Hansen, Morten S.

    2011-01-01

    The purpose of this article is to demonstrate how a model can be constructed such that the progress of a submerged fed‐batch fermentation of a filamentous fungus can be predicted with acceptable accuracy. The studied process was enzyme production with Aspergillus oryzae in 550 L pilot plant stirred...

  7. In Silico Phylogenetic Analysis and Molecular Modelling Study of 2-Haloalkanoic Acid Dehalogenase Enzymes from Bacterial and Fungal Origin

    Directory of Open Access Journals (Sweden)

    Raghunath Satpathy

    2016-01-01

    Full Text Available 2-Haloalkanoic acid dehalogenase enzymes have broad range of applications, starting from bioremediation to chemical synthesis of useful compounds that are widely distributed in fungi and bacteria. In the present study, a total of 81 full-length protein sequences of 2-haloalkanoic acid dehalogenase from bacteria and fungi were retrieved from NCBI database. Sequence analysis such as multiple sequence alignment (MSA, conserved motif identification, computation of amino acid composition, and phylogenetic tree construction were performed on these primary sequences. From MSA analysis, it was observed that the sequences share conserved lysine (K and aspartate (D residues in them. Also, phylogenetic tree indicated a subcluster comprised of both fungal and bacterial species. Due to nonavailability of experimental 3D structure for fungal 2-haloalkanoic acid dehalogenase in the PDB, molecular modelling study was performed for both fungal and bacterial sources of enzymes present in the subcluster. Further structural analysis revealed a common evolutionary topology shared between both fungal and bacterial enzymes. Studies on the buried amino acids showed highly conserved Leu and Ser in the core, despite variation in their amino acid percentage. Additionally, a surface exposed tryptophan was conserved in all of these selected models.

  8. Enzymes for Enhanced Oil Recovery (EOR)

    Energy Technology Data Exchange (ETDEWEB)

    Nasiri, Hamidreza

    2011-04-15

    enzymes on interactions in the oil/brine/solid system was studied. It was found that enzymes can change the adhesion behavior of the crude oil on glass surfaces from adhesion to non-adhesion when they are added to the brine solution. This was confirmed by contact angle measurements, which showed that contact angles became more water-wet (i.e. decreased) after exposure to enzyme solutions. Possible mechanisms giving rise to these observations, including catalysis of ester hydrolysis and enzyme adsorption, were discussed and tested. An experimental study of changes in oil-water interfacial properties by addition of enzymes and proteins, including measurements of interfacial tension and electrophoretic mobility, has been performed. It was found that the effect of enzymes on oil-water properties is minor compared to their effect on oil-water-solid properties. Their contribution to change interfacial tension between oil and water is not significant while they affect the electrophoretic mobility of emulsified oil in enzyme-brine solution to some extent. Attempts were also made to study changes in both oil and water phase composition after equilibration with enzymes. However, since the chemical composition of crude oil is highly complex, a model oil was used in some of the experiments. The model oil was chosen to be a water insoluble ester (ethyl decanoate) solved in mineral oil in an effort to verify the possible role of catalysis of ester hydrolysis. Dynamic core displacements using sandstone and carbonate rocks were conducted to show the potential of improved oil recovery by enzyme- and combined enzyme-surfactant flooding. Most of the core flooding experiments commenced with water flooding from initial water saturation, Swi, (established with synthetic sea water) which will be referred to as secondary mode displacements. Accordingly, tertiary oil recovery processes were used to describe injection of enzyme and/or enzyme-surfactant solutions from residual oil saturation, Sor

  9. Incorporating wind availability into land use regression modelling of air quality in mountainous high-density urban environment.

    Science.gov (United States)

    Shi, Yuan; Lau, Kevin Ka-Lun; Ng, Edward

    2017-08-01

    Urban air quality serves as an important function of the quality of urban life. Land use regression (LUR) modelling of air quality is essential for conducting health impacts assessment but more challenging in mountainous high-density urban scenario due to the complexities of the urban environment. In this study, a total of 21 LUR models are developed for seven kinds of air pollutants (gaseous air pollutants CO, NO 2 , NO x , O 3 , SO 2 and particulate air pollutants PM 2.5 , PM 10 ) with reference to three different time periods (summertime, wintertime and annual average of 5-year long-term hourly monitoring data from local air quality monitoring network) in Hong Kong. Under the mountainous high-density urban scenario, we improved the traditional LUR modelling method by incorporating wind availability information into LUR modelling based on surface geomorphometrical analysis. As a result, 269 independent variables were examined to develop the LUR models by using the "ADDRESS" independent variable selection method and stepwise multiple linear regression (MLR). Cross validation has been performed for each resultant model. The results show that wind-related variables are included in most of the resultant models as statistically significant independent variables. Compared with the traditional method, a maximum increase of 20% was achieved in the prediction performance of annual averaged NO 2 concentration level by incorporating wind-related variables into LUR model development. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Nanomaterials with enzyme-like characteristics (nanozymes): next-generation artificial enzymes.

    Science.gov (United States)

    Wei, Hui; Wang, Erkang

    2013-07-21

    Over the past few decades, researchers have established artificial enzymes as highly stable and low-cost alternatives to natural enzymes in a wide range of applications. A variety of materials including cyclodextrins, metal complexes, porphyrins, polymers, dendrimers and biomolecules have been extensively explored to mimic the structures and functions of naturally occurring enzymes. Recently, some nanomaterials have been found to exhibit unexpected enzyme-like activities, and great advances have been made in this area due to the tremendous progress in nano-research and the unique characteristics of nanomaterials. To highlight the progress in the field of nanomaterial-based artificial enzymes (nanozymes), this review discusses various nanomaterials that have been explored to mimic different kinds of enzymes. We cover their kinetics, mechanisms and applications in numerous fields, from biosensing and immunoassays, to stem cell growth and pollutant removal. We also summarize several approaches to tune the activities of nanozymes. Finally, we make comparisons between nanozymes and other catalytic materials (other artificial enzymes, natural enzymes, organic catalysts and nanomaterial-based catalysts) and address the current challenges and future directions (302 references).

  11. A Novel Approach of Understanding and Incorporating Error of Chemical Transport Models into a Geostatistical Framework

    Science.gov (United States)

    Reyes, J.; Vizuete, W.; Serre, M. L.; Xu, Y.

    2015-12-01

    The EPA employs a vast monitoring network to measure ambient PM2.5 concentrations across the United States with one of its goals being to quantify exposure within the population. However, there are several areas of the country with sparse monitoring spatially and temporally. One means to fill in these monitoring gaps is to use PM2.5 modeled estimates from Chemical Transport Models (CTMs) specifically the Community Multi-scale Air Quality (CMAQ) model. CMAQ is able to provide complete spatial coverage but is subject to systematic and random error due to model uncertainty. Due to the deterministic nature of CMAQ, often these uncertainties are not quantified. Much effort is employed to quantify the efficacy of these models through different metrics of model performance. Currently evaluation is specific to only locations with observed data. Multiyear studies across the United States are challenging because the error and model performance of CMAQ are not uniform over such large space/time domains. Error changes regionally and temporally. Because of the complex mix of species that constitute PM2.5, CMAQ error is also a function of increasing PM2.5 concentration. To address this issue we introduce a model performance evaluation for PM2.5 CMAQ that is regionalized and non-linear. This model performance evaluation leads to error quantification for each CMAQ grid. Areas and time periods of error being better qualified. The regionalized error correction approach is non-linear and is therefore more flexible at characterizing model performance than approaches that rely on linearity assumptions and assume homoscedasticity of CMAQ predictions errors. Corrected CMAQ data are then incorporated into the modern geostatistical framework of Bayesian Maximum Entropy (BME). Through cross validation it is shown that incorporating error-corrected CMAQ data leads to more accurate estimates than just using observed data by themselves.

  12. Electron paramagnetic resonance spin label titration: a novel method to investigate random and site-specific immobilization of enzymes onto polymeric membranes with different properties

    International Nuclear Information System (INIS)

    Butterfield, D. Allan; Colvin, Joshua; Liu Jiangling; Wang Jianquan; Bachas, Leonidas; Bhattacharrya, Dibakar

    2002-01-01

    The immobilization of biological molecules onto polymeric membranes to produce biofunctional membranes is used for selective catalysis, separation, analysis, and artificial organs. Normally, random immobilization of enzymes onto polymeric membranes leads to dramatic reduction in activity due to chemical reactions involved in enzyme immobilization, multiple-point binding, etc., and the extent of activity reduction is a function of membrane hydrophilicity (e.g. activity in cellulosic membrane >> polysulfone membrane). We have used molecular biology to effect site-specific immobilization of enzymes in a manner that orients the active site away from the polymeric membrane surface, thus resulting in higher enzyme activity that approaches that in solution and in increased stability of the enzyme relative to the enzyme in solution. A prediction of this site-specific method of enzyme immobilization, which in this study with subtilisin and organophosphorus hydrolase consists of a fusion tag genetically added to these enzymes and subsequent immobilization via the anti-tag antibody and membrane-bound protein A, is that the active site conformation will more closely resemble that of the enzyme in solution than is the case for random immobilization. This hypothesis was confirmed using a new electron paramagnetic resonance (EPR) spin label active site titration method that determines the amount of spin label bound to the active site of the immobilized enzyme. This value nearly perfectly matched the enzyme activity, and the results suggested: (a) a spectroscopic method for measuring activity and thus the extent of active enzyme immobilization in membrane, which may have advantages in cases where optical methods can not be used due to light scattering interference; (b) higher spin label incorporation (and hence activity) in enzymes that had been site-specifically immobilized versus random immobilization; (c) higher spin label incorporation in enzymes immobilized onto hydrophilic

  13. [Advances on enzymes and enzyme inhibitors research based on microfluidic devices].

    Science.gov (United States)

    Hou, Feng-Hua; Ye, Jian-Qing; Chen, Zuan-Guang; Cheng, Zhi-Yi

    2010-06-01

    With the continuous development in microfluidic fabrication technology, microfluidic analysis has evolved from a concept to one of research frontiers in last twenty years. The research of enzymes and enzyme inhibitors based on microfluidic devices has also made great progress. Microfluidic technology improved greatly the analytical performance of the research of enzymes and enzyme inhibitors by reducing the consumption of reagents, decreasing the analysis time, and developing automation. This review focuses on the development and classification of enzymes and enzyme inhibitors research based on microfluidic devices.

  14. Xenobiotica-metabolizing enzymes in the skin of rat, mouse, pig, guinea pig, man, and in human skin models.

    Science.gov (United States)

    Oesch, F; Fabian, E; Landsiedel, Robert

    2018-06-18

    Studies on the metabolic fate of medical drugs, skin care products, cosmetics and other chemicals intentionally or accidently applied to the human skin have become increasingly important in order to ascertain pharmacological effectiveness and to avoid toxicities. The use of freshly excised human skin for experimental investigations meets with ethical and practical limitations. Hence information on xenobiotic-metabolizing enzymes (XME) in the experimental systems available for pertinent studies compared with native human skin has become crucial. This review collects available information of which-taken with great caution because of the still very limited data-the most salient points are: in the skin of all animal species and skin-derived in vitro systems considered in this review cytochrome P450 (CYP)-dependent monooxygenase activities (largely responsible for initiating xenobiotica metabolism in the organ which provides most of the xenobiotica metabolism of the mammalian organism, the liver) are very low to undetectable. Quite likely other oxidative enzymes [e.g. flavin monooxygenase, COX (cooxidation by prostaglandin synthase)] will turn out to be much more important for the oxidative xenobiotic metabolism in the skin. Moreover, conjugating enzyme activities such as glutathione transferases and glucuronosyltransferases are much higher than the oxidative CYP activities. Since these conjugating enzymes are predominantly detoxifying, the skin appears to be predominantly protected against CYP-generated reactive metabolites. The following recommendations for the use of experimental animal species or human skin in vitro models may tentatively be derived from the information available to date: for dermal absorption and for skin irritation esterase activity is of special importance which in pig skin, some human cell lines and reconstructed skin models appears reasonably close to native human skin. With respect to genotoxicity and sensitization reactive

  15. Direct comparison of enzyme histochemical and immunohistochemical methods to localize an enzyme

    NARCIS (Netherlands)

    van Noorden, Cornelis J. F.

    2002-01-01

    Immunohistochemical localization of enzymes is compared directly with localization of enzyme activity with (catalytic) enzyme histochemical methods. The two approaches demonstrate principally different aspects of an enzyme. The immunohistochemical method localizes the enzyme protein whether it is

  16. Structures of the multicomponent Rieske non-heme iron toluene 2, 3-dioxygenase enzyme system

    Energy Technology Data Exchange (ETDEWEB)

    Friemann, Rosmarie [Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, 751 24 Uppsala (Sweden); Lee, Kyoung [Department of Microbiology, Changwon National University, Changwon, Kyoungnam 641-773 (Korea, Republic of); Department of Microbiology, The University of Iowa, Iowa City, Iowa 52242 (United States); Brown, Eric N. [Department of Biochemistry, The University of Iowa, Iowa City, Iowa 52242 (United States); Gibson, David T. [Department of Microbiology, The University of Iowa, Iowa City, Iowa 52242 (United States); Eklund, Hans [Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, 751 24 Uppsala (Sweden); Ramaswamy, S., E-mail: s-ramaswamy@uiowa.edu [Department of Biochemistry, The University of Iowa, Iowa City, Iowa 52242 (United States); Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, 751 24 Uppsala (Sweden)

    2009-01-01

    The crystal structures of the three-component toluene 2, 3-dioxygenase system provide a model for electron transfer among bacterial Rieske non-heme iron dioxygenases. Bacterial Rieske non-heme iron oxygenases catalyze the initial hydroxylation of aromatic hydrocarbon substrates. The structures of all three components of one such system, the toluene 2, 3-dioxygenase system, have now been determined. This system consists of a reductase, a ferredoxin and a terminal dioxygenase. The dioxygenase, which was cocrystallized with toluene, is a heterohexamer containing a catalytic and a structural subunit. The catalytic subunit contains a Rieske [2Fe–2S] cluster and mononuclear iron at the active site. This iron is not strongly bound and is easily removed during enzyme purification. The structures of the enzyme with and without mononuclear iron demonstrate that part of the structure is flexible in the absence of iron. The orientation of the toluene substrate in the active site is consistent with the regiospecificity of oxygen incorporation seen in the product formed. The ferredoxin is Rieske type and contains a [2Fe–2S] cluster close to the protein surface. The reductase belongs to the glutathione reductase family of flavoenzymes and consists of three domains: an FAD-binding domain, an NADH-binding domain and a C-terminal domain. A model for electron transfer from NADH via FAD in the reductase and the ferredoxin to the terminal active-site mononuclear iron of the dioxygenase is proposed.

  17. Enzymes in CO2 Capture

    DEFF Research Database (Denmark)

    Fosbøl, Philip Loldrup; Gladis, Arne; Thomsen, Kaj

    The enzyme Carbonic Anhydrase (CA) can accelerate the absorption rate of CO2 into aqueous solutions by several-fold. It exist in almost all living organisms and catalyses different important processes like CO2 transport, respiration and the acid-base balances. A new technology in the field...... of carbon capture is the application of enzymes for acceleration of typically slow ternary amines or inorganic carbonates. There is a hidden potential to revive currently infeasible amines which have an interesting low energy consumption for regeneration but too slow kinetics for viable CO2 capture. The aim...... of this work is to discuss the measurements of kinetic properties for CA promoted CO2 capture solvent systems. The development of a rate-based model for enzymes will be discussed showing the principles of implementation and the results on using a well-known ternary amine for CO2 capture. Conclusions...

  18. Demonstration of de novo synthesis of enzymes by density labelling with stable isotopes

    International Nuclear Information System (INIS)

    Huebner, G.; Hirschberg, K.

    1977-01-01

    The technique of in vivo density labelling of proteins with H 2 18 O and 2 H 2 O has been used to investigate hormonal regulation and developmental expression of enzymes in plant cells. Buoyant density data obtained from isopycnic equilibrium centrifugation demonstrated that the cytokinine-induced nitrate reductase activity and the gibberellic acid-induced phosphatase activity in isolated embryos of Agrostemma githago are activities of enzymes synthesized de novo. The increase in alanine-specific aminopeptidase in germinating A. githago seeds is not due to de novo synthesis but to the release of preformed enzyme. On the basis of this result it is possible to apply the enzyme aminopeptidase as an internal density standard in equilibrium centrifugation. Density labelling experiments on proteins in pea cotyledons have been used to study the change in the activity of acid phosphatase, alanine-specific aminopeptidase, and peroxidase during germination. The activities of these enzymes increase in cotyledons of Pisum sativum. Density labelling by 18 O and 2 H demonstrates de novo synthesis of these three enzymes. The differential time course of enzyme induction shows the advantage of using H 2 18 O as labelling substance in cases when the enzyme was synthesized immediately at the beginning of germination. At this stage of development the amino-acid pool available for synthesis is formed principally by means of hydrolysis of storage proteins. The incorporation of 2 H into the new proteins takes place in a measurable amount at a stage of growth in which the amino acids are also synthesized de novo. The enzyme acid phosphatase of pea cotyledons was chosen to demonstrate the possibility of using the density labelling technique to detect protein turnover. (author)

  19. Chemical and protein structural basis for biological crosstalk between PPAR α and COX enzymes

    Science.gov (United States)

    Cleves, Ann E.; Jain, Ajay N.

    2015-02-01

    We have previously validated a probabilistic framework that combined computational approaches for predicting the biological activities of small molecule drugs. Molecule comparison methods included molecular structural similarity metrics and similarity computed from lexical analysis of text in drug package inserts. Here we present an analysis of novel drug/target predictions, focusing on those that were not obvious based on known pharmacological crosstalk. Considering those cases where the predicted target was an enzyme with known 3D structure allowed incorporation of information from molecular docking and protein binding pocket similarity in addition to ligand-based comparisons. Taken together, the combination of orthogonal information sources led to investigation of a surprising predicted relationship between a transcription factor and an enzyme, specifically, PPAR α and the cyclooxygenase enzymes. These predictions were confirmed by direct biochemical experiments which validate the approach and show for the first time that PPAR α agonists are cyclooxygenase inhibitors.

  20. Data characterizing the energetics of enzyme-catalyzed hydrolysis and transglycosylation reactions by DFT cluster model calculations

    Directory of Open Access Journals (Sweden)

    Jitrayut Jitonnom

    2018-04-01

    Full Text Available The data presented in this paper are related to the research article entitled “QM/MM modeling of the hydrolysis and transfructosylation reactions of fructosyltransferase from Aspergillus japonicas, an enzyme that produces prebiotic fructooligosaccharide” (Jitonnom et al., 2018 [1]. This paper presents the procedure and data for characterizing the whole relative energy profiles of hydrolysis and transglycosylation reactions whose elementary steps differ in chemical composition. The data also reflects the choices of the QM cluster model, the functional/basis set method and the equations in determining the reaction energetics.

  1. Engineering Cellulase Enzymes for Bioenergy

    Science.gov (United States)

    Atreya, Meera Elizabeth

    methods. Protein engineering targets to improve cellulases include reducing enzyme inhibition, improving inter-enzyme synergy, and increasing enzyme thermotolerance. Ameliorating enzyme inhibition could improve catalytic activity and thus the speed of conversion from biomass to fermentable sugars. Improved enzyme synergy could reduce the enzyme loading required to achieve equivalent biomass conversion. Finally, thermostable enzymes could enable more biomass to be processed at a time, due to high temperatures decreasing the viscosity of biomass slurries. A high-temperature enzyme saccharification reaction could also decrease the risk of contamination in the resulting concentrated sugar solution. Throughout my PhD, I have explored research projects broadly across all of these topics, with the most success in addressing the issue of enzyme inhibition. Cellulase enzyme Cel7A is the most abundant cellulase employed by natural systems for cellulose hydrolysis. Cellobiohydrolase enzymes like Cel7A break down cellulose into cellobiose (two glucose molecules). Unfortunately, upon cleavage, this product molecule interferes with continued hydrolysis activity of Cel7A; the strong binding of cellobiose in the active site can obstruct the enzyme from processing down the cellulase chain. This phenomenon, known as product inhibition, is a bottleneck to efficient biomass breakdown. Using insights from computational protein modeling studies, I experimentally generated and tested mutant Cel7A enzymes for improved tolerance to cellobiose. Indeed, this strategy yielded Cel7A enzymes exhibiting reduced product inhibition, including some mutants completely impervious to cellobiose. The improvements in tolerance to cellobiose, however, resulted in an overall reduction of enzyme activity for the mutants tested. Nevertheless, my findings substantiated computational reports with experimental evidence and pinpointed an amino acid residue in the Cel7A product binding site that is of interest for

  2. Ionic liquid pretreatment of poplar wood at room temperature: swelling and incorporation of nanoparticles.

    Science.gov (United States)

    Lucas, Marcel; Macdonald, Brian A; Wagner, Gregory L; Joyce, Stephen A; Rector, Kirk D

    2010-08-01

    Lignocellulosic biomass offers economic and environmental advantages over corn starch for biofuels production. However, its fractionation currently requires energy-intensive pretreatments, due to the lignin chemical resistance and complex cell wall structure. Recently, ionic liquids have been used to dissolve biomass at high temperatures. In this study, thin sections of poplar wood were swollen by ionic liquid (1-ethyl-3-methylimidazolium acetate) pretreatment at room temperature. The samples contract when rinsed with deionized water. The controlled expansion and contraction of the wood structure can be used to incorporate enzymes and catalysts deep into the wood structure for improved pretreatments and accelerated cellulose hydrolysis. As a proof of concept, silver and gold nanoparticles of diameters ranging from 20 to 100 nm were incorporated at depths up to 4 mum. Confocal surface-enhanced Raman images at different depths show that a significant number of nanoparticles were incorporated into the pretreated sample, and they remained on the samples after rinsing. Quantitative X-ray fluorescence microanalyses indicate that the majority of nanoparticle incorporation occurs after an ionic liquid pretreatment of less than 1 h. In addition to improved pretreatments, the incorporation of materials and chemicals into wood and paper products enables isotope tracing, development of new sensing, and imaging capabilities.

  3. A neural population model incorporating dopaminergic neurotransmission during complex voluntary behaviors.

    Directory of Open Access Journals (Sweden)

    Stefan Fürtinger

    2014-11-01

    Full Text Available Assessing brain activity during complex voluntary motor behaviors that require the recruitment of multiple neural sites is a field of active research. Our current knowledge is primarily based on human brain imaging studies that have clear limitations in terms of temporal and spatial resolution. We developed a physiologically informed non-linear multi-compartment stochastic neural model to simulate functional brain activity coupled with neurotransmitter release during complex voluntary behavior, such as speech production. Due to its state-dependent modulation of neural firing, dopaminergic neurotransmission plays a key role in the organization of functional brain circuits controlling speech and language and thus has been incorporated in our neural population model. A rigorous mathematical proof establishing existence and uniqueness of solutions to the proposed model as well as a computationally efficient strategy to numerically approximate these solutions are presented. Simulated brain activity during the resting state and sentence production was analyzed using functional network connectivity, and graph theoretical techniques were employed to highlight differences between the two conditions. We demonstrate that our model successfully reproduces characteristic changes seen in empirical data between the resting state and speech production, and dopaminergic neurotransmission evokes pronounced changes in modeled functional connectivity by acting on the underlying biological stochastic neural model. Specifically, model and data networks in both speech and rest conditions share task-specific network features: both the simulated and empirical functional connectivity networks show an increase in nodal influence and segregation in speech over the resting state. These commonalities confirm that dopamine is a key neuromodulator of the functional connectome of speech control. Based on reproducible characteristic aspects of empirical data, we suggest a number

  4. Incorporating Social System Dynamics into the Food-Energy-Water System Resilience-Sustainability Modeling Process

    Science.gov (United States)

    Givens, J.; Padowski, J.; Malek, K.; Guzman, C.; Boll, J.; Adam, J. C.; Witinok-Huber, R.

    2017-12-01

    In the face of climate change and multi-scalar governance objectives, achieving resilience of food-energy-water (FEW) systems requires interdisciplinary approaches. Through coordinated modeling and management efforts, we study "Innovations in the Food-Energy-Water Nexus (INFEWS)" through a case-study in the Columbia River Basin. Previous research on FEW system management and resilience includes some attention to social dynamics (e.g., economic, governance); however, more research is needed to better address social science perspectives. Decisions ultimately taken in this river basin would occur among stakeholders encompassing various institutional power structures including multiple U.S. states, tribal lands, and sovereign nations. The social science lens draws attention to the incompatibility between the engineering definition of resilience (i.e., return to equilibrium or a singular stable state) and the ecological and social system realities, more explicit in the ecological interpretation of resilience (i.e., the ability of a system to move into a different, possibly more resilient state). Social science perspectives include but are not limited to differing views on resilience as normative, system persistence versus transformation, and system boundary issues. To expand understanding of resilience and objectives for complex and dynamic systems, concepts related to inequality, heterogeneity, power, agency, trust, values, culture, history, conflict, and system feedbacks must be more tightly integrated into FEW research. We identify gaps in knowledge and data, and the value and complexity of incorporating social components and processes into systems models. We posit that socio-biophysical system resilience modeling would address important complex, dynamic social relationships, including non-linear dynamics of social interactions, to offer an improved understanding of sustainable management in FEW systems. Conceptual modeling that is presented in our study, represents

  5. Statistical Mechanics Analysis of ATP Binding to a Multisubunit Enzyme

    International Nuclear Information System (INIS)

    Zhang Yun-Xin

    2014-01-01

    Due to inter-subunit communication, multisubunit enzymes usually hydrolyze ATP in a concerted fashion. However, so far the principle of this process remains poorly understood. In this study, from the viewpoint of statistical mechanics, a simple model is presented. In this model, we assume that the binding of ATP will change the potential of the corresponding enzyme subunit, and the degree of this change depends on the state of its adjacent subunits. The probability of enzyme in a given state satisfies the Boltzmann's distribution. Although it looks much simple, this model can fit the recent experimental data of chaperonin TRiC/CCT well. From this model, the dominant state of TRiC/CCT can be obtained. This study provide a new way to understand biophysical processe by statistical mechanics analysis. (interdisciplinary physics and related areas of science and technology)

  6. Effect of polymers on the retention and aging of enzyme on bioactive papers.

    Science.gov (United States)

    Khan, Mohidus Samad; Haniffa, Sharon B M; Slater, Alison; Garnier, Gil

    2010-08-01

    The effect of polymer on the retention and the thermal stability of bioactive enzymatic papers was measured using a colorimetric technique quantifying the intensity of the enzyme-substrate product complex. Alkaline phosphatase (ALP) was used as model enzyme. Three water soluble polymers: a cationic polyacrylamide (CPAM), an anionic polyacrylic acid (PAA) and a neutral polyethylene oxide (PEO) were selected as retention aids. The model polymers increased the enzyme adsorption on paper by around 50% and prevented enzyme desorption upon rewetting of the papers. The thermal deactivation of ALP retained on paper with polymers follows two sequential first order reactions. This was also observed for ALP simply physisorbed on paper. The retention aid polymers instigated a rapid initial deactivation which significantly decreased the longevity of the enzymatic papers. This suggests some enzyme-polymer interaction probably affecting the enzyme tertiary structure. A deactivation mathematical model predicting the enzymatic paper half-life was developed. Crown Copyright 2010. Published by Elsevier B.V. All rights reserved.

  7. A Fibrocontractive Mechanochemical Model of Dermal Wound Closure Incorporating Realistic Growth Factor Kinetics

    KAUST Repository

    Murphy, Kelly E.

    2012-01-13

    Fibroblasts and their activated phenotype, myofibroblasts, are the primary cell types involved in the contraction associated with dermal wound healing. Recent experimental evidence indicates that the transformation from fibroblasts to myofibroblasts involves two distinct processes: The cells are stimulated to change phenotype by the combined actions of transforming growth factor β (TGFβ) and mechanical tension. This observation indicates a need for a detailed exploration of the effect of the strong interactions between the mechanical changes and growth factors in dermal wound healing. We review the experimental findings in detail and develop a model of dermal wound healing that incorporates these phenomena. Our model includes the interactions between TGFβ and collagenase, providing a more biologically realistic form for the growth factor kinetics than those included in previous mechanochemical descriptions. A comparison is made between the model predictions and experimental data on human dermal wound healing and all the essential features are well matched. © 2012 Society for Mathematical Biology.

  8. A Fibrocontractive Mechanochemical Model of Dermal Wound Closure Incorporating Realistic Growth Factor Kinetics

    KAUST Repository

    Murphy, Kelly E.; Hall, Cameron L.; Maini, Philip K.; McCue, Scott W.; McElwain, D. L. Sean

    2012-01-01

    Fibroblasts and their activated phenotype, myofibroblasts, are the primary cell types involved in the contraction associated with dermal wound healing. Recent experimental evidence indicates that the transformation from fibroblasts to myofibroblasts involves two distinct processes: The cells are stimulated to change phenotype by the combined actions of transforming growth factor β (TGFβ) and mechanical tension. This observation indicates a need for a detailed exploration of the effect of the strong interactions between the mechanical changes and growth factors in dermal wound healing. We review the experimental findings in detail and develop a model of dermal wound healing that incorporates these phenomena. Our model includes the interactions between TGFβ and collagenase, providing a more biologically realistic form for the growth factor kinetics than those included in previous mechanochemical descriptions. A comparison is made between the model predictions and experimental data on human dermal wound healing and all the essential features are well matched. © 2012 Society for Mathematical Biology.

  9. Modeling the role of covalent enzyme modification in Escherichia coli nitrogen metabolism

    International Nuclear Information System (INIS)

    Kidd, Philip B; Wingreen, Ned S

    2010-01-01

    In the bacterium Escherichia coli, the enzyme glutamine synthetase (GS) converts ammonium into the amino acid glutamine. GS is principally active when the cell is experiencing nitrogen limitation, and its activity is regulated by a bicyclic covalent modification cascade. The advantages of this bicyclic-cascade architecture are poorly understood. We analyze a simple model of the GS cascade in comparison to other regulatory schemes and conclude that the bicyclic cascade is suboptimal for maintaining metabolic homeostasis of the free glutamine pool. Instead, we argue that the lag inherent in the covalent modification of GS slows the response to an ammonium shock and thereby allows GS to transiently detoxify the cell, while maintaining homeostasis over longer times

  10. Biosynthesis of quinoxaline antibiotics: Purification and characterization of the quinoxaline-2-carboxylic acid activating enzyme from Streptomyces triostinicus

    International Nuclear Information System (INIS)

    Glund, K.; Schlumbohm, W.; Bapat, M.; Keller, U.

    1990-01-01

    A quinoxaline-2-carboxylic acid activating enzyme was purified to homogeneity from triostin-producing Streptomyces triostinicus. It could also be purified from quinomycin-producing Streptomyces echinatus. Triostins and quinomycins are peptide lactones that contain quinoxaline-2-carboxylic acid as chromophoric moiety. The enzyme catalyzes the ATP-pyrophosphate exchange reaction dependent on quinoxaline-2-carboxylic acid and the formation of the corresponding adenylate. Besides quinoxaline-2-carboxylic acid, the enzyme also catalyzes the formation of adenylates from quinoline-2-carboxylic acid and thieno[3,2-b]pyridine-5-carboxylic acid. No adenylates were seen from quinoline-3-carboxylic acid, quinoline-4-carboxylic acid, pyridine-2-carboxylic acid, and 2-pyrazinecarboxylic acid. Previous work revealed that quinoline-2-carboxylic acid and thieno[3,2-b]pyridine-5-carboxylic acid became efficiently incorporated into the corresponding quinoxaline antibiotic analogues in vivo. Together with the data described here, this suggests that the enzyme is part of the quinoxaline antibiotics synthesizing enzyme system. The enzyme displays a native molecular weight of 42,000, whereas in its denatured form it is a polypeptide of Mr 52,000-53,000. It resembles in its behavior actinomycin synthetase I, the chromophore activating enzyme involved in actinomycin biosynthesis

  11. Stabilization of enzymes in ionic liquids via modification of enzyme charge.

    Science.gov (United States)

    Nordwald, Erik M; Kaar, Joel L

    2013-09-01

    Due to the propensity of ionic liquids (ILs) to inactivate enzymes, the development of strategies to improve enzyme utility in these solvents is critical to fully exploit ILs for biocatalysis. We have developed a strategy to broadly improve enzyme utility in ILs based on elucidating the effect of charge modifications on the function of enzymes in IL environments. Results of stability studies in aqueous-IL mixtures indicated a clear connection between the ratio of enzyme-containing positive-to-negative sites and enzyme stability in ILs. Stability studies of the effect of [BMIM][Cl] and [EMIM][EtSO4 ] on chymotrypsin specifically found an optimum ratio of positively-charged amine-to-negatively-charged acid groups (0.39). At this ratio, the half-life of chymotrypsin was increased 1.6- and 4.3-fold relative to wild-type chymotrypsin in [BMIM][Cl] and [EMIM][EtSO4 ], respectively. The half-lives of lipase and papain were similarly increased as much as 4.0 and 2.4-fold, respectively, in [BMIM][Cl] by modifying the ratio of positive-to-negative sites of each enzyme. More generally, the results of stability studies found that modifications that reduce the ratio of enzyme-containing positive-to-negative sites improve enzyme stability in ILs. Understanding the impact of charge modification on enzyme stability in ILs may ultimately be exploited to rationally engineer enzymes for improved function in IL environments. Copyright © 2013 Wiley Periodicals, Inc.

  12. [Treatment of burn surfaces by proteinases: mathematical description of an enzyme distribution].

    Science.gov (United States)

    Khalili, A S; Domogatskiĭ, S P; Blizniukov, O P; Ruuge, E K

    2003-01-01

    The process of penetration of a proteolytic enzyme applied to the surface of burn wound into the depth of necrotic tissue was considered. The model approximation describes three factors by a series of mathematical equations: inward-directed enzyme diffusion, counter-flow filtration of interstitial fluid (exudates), and irreversible inactivation of the enzyme by specific inhibitors present in exudates. According to the model, a quasi-stationary distribution of enzymatic activity through the thickness of the necrotic layer is achieved within 3 h and persists as long as the enzyme concentration on the wound surface is constant. The enzyme activity diminishes linearly from the wound surface to the mid-part of the necrotic layer. No enzyme activity is retained in the inner mid-part of the necrotic layer completely protected by the prevalent inhibitor. The ratio of enzyme concentration on the wound surface to inhibitor concentration in the interstitial fluid is the same as the ratio of the depth of active enzyme area to the depth of the inhibitor-protected area through the necrotic layer. The dynamics of accumulation of the active enzyme in the necrotic zone and the rate of enzyme inactivation in the wound by inhibitors were described by formulas applicable for practical purposes.

  13. Effect of diffusion on enzyme activity in a microreactor

    NARCIS (Netherlands)

    Swarts, J.W.; Kolfschoten, R.C.; Jansen, M.C.A.A.; Janssen, A.E.M.; Boom, R.M.

    2010-01-01

    To establish general rules for setting up an enzyme microreactor system, we studied the effect of diffusion on enzyme activity in a microreactor. As a model system we used the hydrolysis of ortho-nitrophenyl-ß-d-galactopyranoside by ß-galactosidase from Kluyveromyces lactis. We found that the

  14. GENPLAT: an automated platform for biomass enzyme discovery and cocktail optimization.

    Science.gov (United States)

    Walton, Jonathan; Banerjee, Goutami; Car, Suzana

    2011-10-24

    The high cost of enzymes for biomass deconstruction is a major impediment to the economic conversion of lignocellulosic feedstocks to liquid transportation fuels such as ethanol. We have developed an integrated high throughput platform, called GENPLAT, for the discovery and development of novel enzymes and enzyme cocktails for the release of sugars from diverse pretreatment/biomass combinations. GENPLAT comprises four elements: individual pure enzymes, statistical design of experiments, robotic pipeting of biomass slurries and enzymes, and automated colorimeteric determination of released Glc and Xyl. Individual enzymes are produced by expression in Pichia pastoris or Trichoderma reesei, or by chromatographic purification from commercial cocktails or from extracts of novel microorganisms. Simplex lattice (fractional factorial) mixture models are designed using commercial Design of Experiment statistical software. Enzyme mixtures of high complexity are constructed using robotic pipeting into a 96-well format. The measurement of released Glc and Xyl is automated using enzyme-linked colorimetric assays. Optimized enzyme mixtures containing as many as 16 components have been tested on a variety of feedstock and pretreatment combinations. GENPLAT is adaptable to mixtures of pure enzymes, mixtures of commercial products (e.g., Accellerase 1000 and Novozyme 188), extracts of novel microbes, or combinations thereof. To make and test mixtures of ˜10 pure enzymes requires less than 100 μg of each protein and fewer than 100 total reactions, when operated at a final total loading of 15 mg protein/g glucan. We use enzymes from several sources. Enzymes can be purified from natural sources such as fungal cultures (e.g., Aspergillus niger, Cochliobolus carbonum, and Galerina marginata), or they can be made by expression of the encoding genes (obtained from the increasing number of microbial genome sequences) in hosts such as E. coli, Pichia pastoris, or a filamentous fungus such

  15. Insights into the Thiamine Diphosphate Enzyme Activation Mechanism: Computational Model for Transketolase Using a Quantum Mechanical/Molecular Mechanical Method.

    Science.gov (United States)

    Nauton, Lionel; Hélaine, Virgil; Théry, Vincent; Hecquet, Laurence

    2016-04-12

    We propose the first computational model for transketolase (TK), a thiamine diphosphate (ThDP)-dependent enzyme, using a quantum mechanical/molecular mechanical method on the basis of crystallographic TK structures from yeast and Escherichia coli, together with experimental kinetic data reported in the literature with wild-type and mutant TK. This model allowed us to define a new route for ThDP activation in the enzyme environment. We evidenced a strong interaction between ThDP and Glu418B of the TK active site, itself stabilized by Glu162A. The crucial point highlighted here is that deprotonation of ThDP C2 is not performed by ThDP N4' as reported in the literature, but by His481B, involving a HOH688A molecule bridge. Thus, ThDP N4' is converted from an amino form to an iminium form, ensuring the stabilization of the C2 carbanion or carbene. Finally, ThDP activation proceeds via an intermolecular process and not by an intramolecular one as reported in the literature. More generally, this proposed ThDP activation mechanism can be applied to some other ThDP-dependent enzymes and used to define the entire TK mechanism with donor and acceptor substrates more accurately.

  16. A mathematical model for maximizing the value of phase 3 drug development portfolios incorporating budget constraints and risk.

    Science.gov (United States)

    Patel, Nitin R; Ankolekar, Suresh; Antonijevic, Zoran; Rajicic, Natasa

    2013-05-10

    We describe a value-driven approach to optimizing pharmaceutical portfolios. Our approach incorporates inputs from research and development and commercial functions by simultaneously addressing internal and external factors. This approach differentiates itself from current practices in that it recognizes the impact of study design parameters, sample size in particular, on the portfolio value. We develop an integer programming (IP) model as the basis for Bayesian decision analysis to optimize phase 3 development portfolios using expected net present value as the criterion. We show how this framework can be used to determine optimal sample sizes and trial schedules to maximize the value of a portfolio under budget constraints. We then illustrate the remarkable flexibility of the IP model to answer a variety of 'what-if' questions that reflect situations that arise in practice. We extend the IP model to a stochastic IP model to incorporate uncertainty in the availability of drugs from earlier development phases for phase 3 development in the future. We show how to use stochastic IP to re-optimize the portfolio development strategy over time as new information accumulates and budget changes occur. Copyright © 2013 John Wiley & Sons, Ltd.

  17. Comparison in the calculation of committed effective dose using the ICRP 30 and ICRP 60 models for a repeated incorporation by inhalation of I-125

    International Nuclear Information System (INIS)

    Carreno P, A.L.; Cortes C, A.; Alonso V, G.; Serrano P, F.

    2005-01-01

    Presently work, a comparison in the calculation of committed effective dose using the models of the ICRP 30 and those of the ICRP 60 for the analysis of internal dose due to repeated incorporation of I-125 is shown. The estimations of incorporated activity are obtained starting from the proportionate data for an exercise of inter comparison, with which it should be determined the internal dose later on. For to estimate the initial activity incorporated by repeated dose was assumed that this it was given through of multiple individual incorporations which happened in the middle points of the monitoring periods. The results using the models of the ICRP 30 and of the ICRP 60 are compared and the causes of the differences are analyzed. (Author)

  18. Thermometric enzyme linked immunosorbent assay in continuous flow system: optimization and evaluation using human serum albumin as a model system.

    Science.gov (United States)

    Borrebaeck, C; Börjeson, J; Mattiasson, B

    1978-06-15

    Thermometric enzyme-linked immunosorbent assay (TELISA) is described. After the procedure of optimization, human serum albumin was assayed using anti-human serum albumin bound to Sepharose CL 4-B in the enzyme thermistor unit and catalase as label on the free antigen. The model system was used for assays down to 10(-13)M and the preparation of immobilized antibodies was used repeatedly up to 100 times. Comparative studies of the TELISA technique with bromocresol green, immunoturbidimetric and rocket immunoelectrophoretic methods were carried out and showed that TELISA could be used as an alternative method.

  19. Size determination of an equilibrium enzymic system by radiation inactivation

    International Nuclear Information System (INIS)

    Simon, P.; Swillens, S.; Dumont, J.E.

    1982-01-01

    Radiation inactivation of complex enzymic systems is currently used to determine the enzyme size and the molecular organization of the components in the system. An equilibrium model was simulated describing the regulation of enzyme activity by association of the enzyme with a regulatory unit. It is assumed that, after irradiation, the system equilibrates before the enzyme activity is assayed. The theoretical results show that the target-size analysis of these numerical data leads to a bad estimate of the enzyme size. Moreover, some implicit assumptions such as the transfer of radiation energy between non-covalently bound molecules should be verified before interpretation of target-size analysis. It is demonstrated that the apparent target size depends on the parameters of the system, namely the size and the concentration of the components, the equilibrium constant, the relative activities of free enzyme and enzymic complex, the existence of energy transfer, and the distribution of the components between free and bound forms during the irradiation. (author)

  20. Printing of polymer microcapsules for enzyme immobilization on paper substrate.

    Science.gov (United States)

    Savolainen, Anne; Zhang, Yufen; Rochefort, Dominic; Holopainen, Ulla; Erho, Tomi; Virtanen, Jouko; Smolander, Maria

    2011-06-13

    Poly(ethyleneimine) (PEI) microcapsules containing laccase from Trametes hirsuta (ThL) and Trametes versicolor (TvL) were printed onto paper substrate by three different methods: screen printing, rod coating, and flexo printing. Microcapsules were fabricated via interfacial polycondensation of PEI with the cross-linker sebacoyl chloride, incorporated into an ink, and printed or coated on the paper substrate. The same ink components were used for three printing methods, and it was found that laccase microcapsules were compatible with the ink. Enzymatic activity of microencapsulated TvL was maintained constant in polymer-based ink for at least eight weeks. Thick layers with high enzymatic activity were obtained when laccase-containing microcapsules were screen printed on paper substrate. Flexo printed bioactive paper showed very low activity, since by using this printing method the paper surface was not fully covered by enzyme microcapsules. Finally, screen printing provided a bioactive paper with high water-resistance and the highest enzyme lifetime.

  1. The development, characterization, and application of biomimetic nanoscale enzyme immobilization

    Science.gov (United States)

    Haase, Nicholas R.

    The utilization of enzymes is of interest for applications such as biosensors and biofuel cells. Immobilizing enzymes provides a means to develop these applications. Previous immobilization efforts have been accomplished by exposing surfaces on which silica-forming molecules are present to solutions containing an enzyme and a silica precursor. This approach leads to the enzyme being entrapped in a matrix three orders of magnitude larger than the enzyme itself, resulting in low retention of enzyme activity. The research herein introduces a method for the immobilization of enzymes during the layer-by-layer buildup of Si-O and Ti-O coatings which are nanoscale in thickness. This approach is an application of a peptide-induced mineral deposition method developed in the Sandhage and Kroger groups, and it involves the alternating exposure of a surface to solutions containing the peptide protamine and then an aqueous precursor solution of silicon- or titanium-oxide at near-neutral pH. A method has been developed that enables in situ immobilization of enzymes in the protamine/mineral oxide coatings. Depending on the layer and mineral (silica or titania) within which the enzyme is incorporated, the resulting multilayer biocatalytic hybrid materials retain 20 -- 100% of the enzyme activity. Analyses of kinetic properties of the immobilized enzyme, coupled with characterization of physical properties of the mineral-bearing layers (thickness, porosity, pore size distribution), indicates that the catalytic activities of the enzymes immobilized in the different layers are largely determined by substrate diffusion. The enzyme was also found to be substantially stabilized against heat-induced denaturation and largely protected from proteolytic attack. These functional coatings are then developed for use as antimicrobial materials. Glucose oxidase, which catalyzes production of the cytotoxic agent hydrogen peroxide, was immobilized with silver nanoparticles, can release

  2. Cost evaluation of cellulase enzyme for industrial-scale cellulosic ethanol production based on rigorous Aspen Plus modeling.

    Science.gov (United States)

    Liu, Gang; Zhang, Jian; Bao, Jie

    2016-01-01

    Cost reduction on cellulase enzyme usage has been the central effort in the commercialization of fuel ethanol production from lignocellulose biomass. Therefore, establishing an accurate evaluation method on cellulase enzyme cost is crucially important to support the health development of the future biorefinery industry. Currently, the cellulase cost evaluation methods were complicated and various controversial or even conflict results were presented. To give a reliable evaluation on this important topic, a rigorous analysis based on the Aspen Plus flowsheet simulation in the commercial scale ethanol plant was proposed in this study. The minimum ethanol selling price (MESP) was used as the indicator to show the impacts of varying enzyme supply modes, enzyme prices, process parameters, as well as enzyme loading on the enzyme cost. The results reveal that the enzyme cost drives the cellulosic ethanol price below the minimum profit point when the enzyme is purchased from the current industrial enzyme market. An innovative production of cellulase enzyme such as on-site enzyme production should be explored and tested in the industrial scale to yield an economically sound enzyme supply for the future cellulosic ethanol production.

  3. The ultrasound technology for modifying enzyme activity

    Directory of Open Access Journals (Sweden)

    Meliza Lindsay

    2016-06-01

    Full Text Available Enzymes are protein complexes compounds widely studied and used due to their ability to catalyze reactions. The food processing mainly aims the inactivation of enzymes due to various undesirable effects. However, there are many processes that can be optimized by its catalytic activity. In this context, different technologies have been applied both to inactivate or to improve the enzymes efficiency. The Ultrasound technology emerges as an alternative mainly applied to achieve the enzyme inactivation. On the contrary, very few investigations show the ability of this technology under certain conditions to achieve the opposite effect (i.e. increase the catalytic activity of enzymes. The objective of this study was to correlate the ultrasonic energy delivered to the sample (J/mL with the residual enzymatic activity and explain the possible mechanisms which results in the enzymatic activation/inactivation complex behavior. The activity of POD in coconut water was evaluated as a model. The enzymatic activity initially increased, followed by reduction with a trend to enzyme inactivation. This complex behavior is directly related to the applied ultrasonic energy and their direct mechanical effects on the product, as well as the effect in the enzymatic infinite intermediate states and its structural conformation changes. The obtained results are useful for both academic and industrial perspectives.

  4. Rapid intranasal delivery of chloramphenicol acetyltransferase in the active form to different brain regions as a model for enzyme therapy in the CNS.

    Science.gov (United States)

    Appu, Abhilash P; Arun, Peethambaran; Krishnan, Jishnu K S; Moffett, John R; Namboodiri, Aryan M A

    2016-02-01

    The blood brain barrier (BBB) is critical for maintaining central nervous system (CNS) homeostasis by restricting entry of potentially toxic substances. However, the BBB is a major obstacle in the treatment of neurotoxicity and neurological disorders due to the restrictive nature of the barrier to many medications. Intranasal delivery of active enzymes to the brain has therapeutic potential for the treatment of numerous CNS enzyme deficiency disorders and CNS toxicity caused by chemical threat agents. The aim of this work is to provide a sensitive model system for analyzing the rapid delivery of active enzymes into various regions of the brain with therapeutic bioavailability. We tested intranasal delivery of chloramphenicol acetyltransferase (CAT), a relatively large (75kD) enzyme, in its active form into different regions of the brain. CAT was delivered intranasally to anaesthetized rats and enzyme activity was measured in different regions using a highly specific High Performance Thin Layer Chromatography (HP-TLC)-radiometry coupled assay. Active enzyme reached all examined areas of the brain within 15min (the earliest time point tested). In addition, the yield of enzyme activity in the brain was almost doubled in the brains of rats pre-treated with matrix metalloproteinase-9 (MMP-9). Intranasal administration of active enzymes in conjunction with MMP-9 to the CNS is both rapid and effective. The present results suggest that intranasal enzyme therapy is a promising method for counteracting CNS chemical threat poisoning, as well as for treating CNS enzyme deficiency disorders. Published by Elsevier B.V.

  5. A computational model incorporating neural stem cell dynamics reproduces glioma incidence across the lifespan in the human population.

    Directory of Open Access Journals (Sweden)

    Roman Bauer

    Full Text Available Glioma is the most common form of primary brain tumor. Demographically, the risk of occurrence increases until old age. Here we present a novel computational model to reproduce the probability of glioma incidence across the lifespan. Previous mathematical models explaining glioma incidence are framed in a rather abstract way, and do not directly relate to empirical findings. To decrease this gap between theory and experimental observations, we incorporate recent data on cellular and molecular factors underlying gliomagenesis. Since evidence implicates the adult neural stem cell as the likely cell-of-origin of glioma, we have incorporated empirically-determined estimates of neural stem cell number, cell division rate, mutation rate and oncogenic potential into our model. We demonstrate that our model yields results which match actual demographic data in the human population. In particular, this model accounts for the observed peak incidence of glioma at approximately 80 years of age, without the need to assert differential susceptibility throughout the population. Overall, our model supports the hypothesis that glioma is caused by randomly-occurring oncogenic mutations within the neural stem cell population. Based on this model, we assess the influence of the (experimentally indicated decrease in the number of neural stem cells and increase of cell division rate during aging. Our model provides multiple testable predictions, and suggests that different temporal sequences of oncogenic mutations can lead to tumorigenesis. Finally, we conclude that four or five oncogenic mutations are sufficient for the formation of glioma.

  6. Enzyme-free electrochemical immunosensor configured with Au-Pd nanocrystals and N-doped graphene sheets for sensitive detection of AFP.

    Science.gov (United States)

    Zhao, Lifang; Li, Songjun; He, Jing; Tian, Guihong; Wei, Qin; Li, He

    2013-11-15

    A novel electrochemical immunosensor capable of enzyme-free detection of alpha fetoprotein (AFP) is reported. This immunosensor was fabricated in a sandwich-like format where catalytic Au-Pd nanocrystals and highly conductive N-doped graphene sheets were incorporated. The significant catalysis by Au-Pd nanocrystals toward hydrogen peroxide, along with the increased electron transfer by graphene sheets, caused signal generation and increased sensitivity, which enables the enzyme-free detection of AFP. With a low detection limit at 0.005 ng mL(-1), this novel immunosensor worked well over the broad linear range of 0.05-30 ng mL(-1). Unlike previously reported enzyme-based electrochemical immunosensors, which often involve the complicated steps for enzyme loading and necessary treatments to keep the activity of enzyme, this novel immunosensor is simple in nature and employed catalytic Au-Pd nanoparticles and highly conductive graphene, which thus enables reliable and sensitive detection for clinic usage. Copyright © 2013 Elsevier B.V. All rights reserved.

  7. Incorporation of a Wind Generator Model into a Dynamic Power Flow Analysis

    Directory of Open Access Journals (Sweden)

    Angeles-Camacho C.

    2011-07-01

    Full Text Available Wind energy is nowadays one of the most cost-effective and practical options for electric generation from renewable resources. However, increased penetration of wind generation causes the power networks to be more depend on, and vulnerable to, the varying wind speed. Modeling is a tool which can provide valuable information about the interaction between wind farms and the power network to which they are connected. This paper develops a realistic characterization of a wind generator. The wind generator model is incorporated into an algorithm to investigate its contribution to the stability of the power network in the time domain. The tool obtained is termed dynamic power flow. The wind generator model takes on account the wind speed and the reactive power consumption by induction generators. Dynamic power flow analysis is carried-out using real wind data at 10-minute time intervals collected for one meteorological station. The generation injected at one point into the network provides active power locally and is found to reduce global power losses. However, the power supplied is time-varying and causes fluctuations in voltage magnitude and power fl ows in transmission lines.

  8. A Model of Oxidative Stress Management: Moderation of Carbohydrate Metabolizing Enzymes in SOD1-Null Drosophila melanogaster

    Science.gov (United States)

    Bernard, Kristine E.; Parkes, Tony L.; Merritt, Thomas J. S.

    2011-01-01

    The response to oxidative stress involves numerous genes and mutations in these genes often manifest in pleiotropic ways that presumably reflect perturbations in ROS-mediated physiology. The Drosophila melanogaster SOD1-null allele (cSODn108) is proposed to result in oxidative stress by preventing superoxide breakdown. In SOD1-null flies, oxidative stress management is thought to be reliant on the glutathione-dependent antioxidants that utilize NADPH to cycle between reduced and oxidized form. Previous studies suggest that SOD1-null Drosophila rely on lipid catabolism for energy rather than carbohydrate metabolism. We tested these connections by comparing the activity of carbohydrate metabolizing enzymes, lipid and triglyceride concentration, and steady state NADPH:NADP+ in SOD1-null and control transgenic rescue flies. We find a negative shift in the activity of carbohydrate metabolizing enzymes in SOD1-nulls and the NADP+-reducing enzymes were found to have significantly lower activity than the other enzymes assayed. Little evidence for the catabolism of lipids as preferential energy source was found, as the concentration of lipids and triglycerides were not significantly lower in SOD1-nulls compared with controls. Using a starvation assay to impact lipids and triglycerides, we found that lipids were indeed depleted in both genotypes when under starvation stress, suggesting that oxidative damage was not preventing the catabolism of lipids in SOD1-null flies. Remarkably, SOD1-nulls were also found to be relatively resistant to starvation. Age profiles of enzyme activity, triglyceride and lipid concentration indicates that the trends observed are consistent over the average lifespan of the SOD1-nulls. Based on our results, we propose a model of physiological response in which organisms under oxidative stress limit the production of ROS through the down-regulation of carbohydrate metabolism in order to moderate the products exiting the electron transport chain. PMID

  9. Methods for Creating and Animating a Computer Model Depicting the Structure and Function of the Sarcoplasmic Reticulum Calcium ATPase Enzyme.

    Science.gov (United States)

    Chen, Alice Y.; McKee, Nancy

    1999-01-01

    Describes the developmental process used to visualize the calcium ATPase enzyme of the sarcoplasmic reticulum which involves evaluating scientific information, consulting scientists, model making, storyboarding, and creating and editing in a computer medium. (Author/CCM)

  10. Incorporating population viability models into species status assessment and listing decisions under the U.S. Endangered Species Act

    Directory of Open Access Journals (Sweden)

    Conor P. McGowan

    2017-10-01

    Full Text Available Assessment of a species' status is a key part of management decision making for endangered and threatened species under the U.S. Endangered Species Act. Predicting the future state of the species is an essential part of species status assessment, and projection models can play an important role in developing predictions. We built a stochastic simulation model that incorporated parametric and environmental uncertainty to predict the probable future status of the Sonoran desert tortoise in the southwestern United States and North Central Mexico. Sonoran desert tortoise was a Candidate species for listing under the Endangered Species Act, and decision makers wanted to use model predictions in their decision making process. The model accounted for future habitat loss and possible effects of climate change induced droughts to predict future population growth rates, abundances, and quasi-extinction probabilities. Our model predicts that the population will likely decline over the next few decades, but there is very low probability of quasi-extinction less than 75 years into the future. Increases in drought frequency and intensity may increase extinction risk for the species. Our model helped decision makers predict and characterize uncertainty about the future status of the species in their listing decision. We incorporated complex ecological processes (e.g., climate change effects on tortoises in transparent and explicit ways tailored to support decision making processes related to endangered species.

  11. Incorporating population viability models into species status assessment and listing decisions under the U.S. Endangered Species Act

    Science.gov (United States)

    McGowan, Conor P.; Allan, Nathan; Servoss, Jeff; Hedwall, Shaula J.; Wooldridge, Brian

    2017-01-01

    Assessment of a species' status is a key part of management decision making for endangered and threatened species under the U.S. Endangered Species Act. Predicting the future state of the species is an essential part of species status assessment, and projection models can play an important role in developing predictions. We built a stochastic simulation model that incorporated parametric and environmental uncertainty to predict the probable future status of the Sonoran desert tortoise in the southwestern United States and North Central Mexico. Sonoran desert tortoise was a Candidate species for listing under the Endangered Species Act, and decision makers wanted to use model predictions in their decision making process. The model accounted for future habitat loss and possible effects of climate change induced droughts to predict future population growth rates, abundances, and quasi-extinction probabilities. Our model predicts that the population will likely decline over the next few decades, but there is very low probability of quasi-extinction less than 75 years into the future. Increases in drought frequency and intensity may increase extinction risk for the species. Our model helped decision makers predict and characterize uncertainty about the future status of the species in their listing decision. We incorporated complex ecological processes (e.g., climate change effects on tortoises) in transparent and explicit ways tailored to support decision making processes related to endangered species.

  12. Modeling water scarcity over south Asia: Incorporating crop growth and irrigation models into the Variable Infiltration Capacity (VIC) model

    Science.gov (United States)

    Troy, Tara J.; Ines, Amor V. M.; Lall, Upmanu; Robertson, Andrew W.

    2013-04-01

    Large-scale hydrologic models, such as the Variable Infiltration Capacity (VIC) model, are used for a variety of studies, from drought monitoring to projecting the potential impact of climate change on the hydrologic cycle decades in advance. The majority of these models simulates the natural hydrological cycle and neglects the effects of human activities such as irrigation, which can result in streamflow withdrawals and increased evapotranspiration. In some parts of the world, these activities do not significantly affect the hydrologic cycle, but this is not the case in south Asia where irrigated agriculture has a large water footprint. To address this gap, we incorporate a crop growth model and irrigation model into the VIC model in order to simulate the impacts of irrigated and rainfed agriculture on the hydrologic cycle over south Asia (Indus, Ganges, and Brahmaputra basin and peninsular India). The crop growth model responds to climate signals, including temperature and water stress, to simulate the growth of maize, wheat, rice, and millet. For the primarily rainfed maize crop, the crop growth model shows good correlation with observed All-India yields (0.7) with lower correlations for the irrigated wheat and rice crops (0.4). The difference in correlation is because irrigation provides a buffer against climate conditions, so that rainfed crop growth is more tied to climate than irrigated crop growth. The irrigation water demands induce hydrologic water stress in significant parts of the region, particularly in the Indus, with the streamflow unable to meet the irrigation demands. Although rainfall can vary significantly in south Asia, we find that water scarcity is largely chronic due to the irrigation demands rather than being intermittent due to climate variability.

  13. A selenium-deficient Caco-2 cell model for assessing differential incorporation of chemical or food selenium into glutathione peroxidase.

    Science.gov (United States)

    Zeng, Huawei; Botnen, James H; Johnson, Luann K

    2008-01-01

    Assessing the ability of a selenium (Se) sample to induce cellular glutathione peroxidase (GPx) activity in Se-deficient animals is the most commonly used method to determine Se bioavailability. Our goal is to establish a Se-deficient cell culture model with differential incorporation of Se chemical forms into GPx, which may complement the in vivo studies. In the present study, we developed a Se-deficient Caco-2 cell model with a serum gradual reduction method. It is well recognized that selenomethionine (SeMet) is the major nutritional source of Se; therefore, SeMet, selenite, or methylselenocysteine (SeMSC) was added to cell culture media with different concentrations and treatment time points. We found that selenite and SeMSC induced GPx more rapidly than SeMet. However, SeMet was better retained as it is incorporated into proteins in place of methionine; compared with 8-, 24-, or 48-h treatment, 72-h Se treatment was a more sensitive time point to measure the potential of GPx induction in all tested concentrations. Based on induction of GPx activity, the cellular bioavailability of Se from an extract of selenobroccoli after a simulated gastrointestinal digestion was comparable with that of SeMSC and SeMet. These in vitro data are, for the first time, consistent with previous published data regarding selenite and SeMet bioavailability in animal models and Se chemical speciation studies with broccoli. Thus, Se-deficient Caco-2 cell model with differential incorporation of chemical or food forms of Se into GPx provides a new tool to study the cellular mechanisms of Se bioavailability.

  14. Enzyme detection by microfluidics

    DEFF Research Database (Denmark)

    2013-01-01

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

  15. A new factor from enteric bacteria of rats amplifying induction of liver enzyme by glucocorticoid. Pt. 2

    International Nuclear Information System (INIS)

    Kido, Hiroshi; Higashi, Takao; Katanuma, Nobuhiko

    1977-01-01

    1) An amplifier of the action of glucocorticoid was purified from Proteus mirabilis as described previously. It was found that it amplified the induction of liver tyrosine aminotransferase by dexamethasone markedly with doses of dexamethasone that caused minimal enzyme induction, but had little effect with doses that caused maximal induction. Thus the amplification may represent a saving of glucocorticoid. The amplification of enzyme activity was brought about by increase in amount of enzyme. 2) The amplification was observed when the amplifier was administered before or with dexamethasone, but not when it was given 2 h after dexamethasone. These results and the finding that actinomycin D inhibited the amplification indicate that the amplifier does not act on the translational level of enzyme induction. 3) It was found that the amplifier increased both incorporation of [ 3 H]dexamethasone into the cytosol and binding of [ 3 H]dexamethasone to cytosol protein and that it decreased decay of the [ 3 H]dexamethasone protein complex. (orig.) [de

  16. Incorporating Measurement Error from Modeled Air Pollution Exposures into Epidemiological Analyses.

    Science.gov (United States)

    Samoli, Evangelia; Butland, Barbara K

    2017-12-01

    Outdoor air pollution exposures used in epidemiological studies are commonly predicted from spatiotemporal models incorporating limited measurements, temporal factors, geographic information system variables, and/or satellite data. Measurement error in these exposure estimates leads to imprecise estimation of health effects and their standard errors. We reviewed methods for measurement error correction that have been applied in epidemiological studies that use model-derived air pollution data. We identified seven cohort studies and one panel study that have employed measurement error correction methods. These methods included regression calibration, risk set regression calibration, regression calibration with instrumental variables, the simulation extrapolation approach (SIMEX), and methods under the non-parametric or parameter bootstrap. Corrections resulted in small increases in the absolute magnitude of the health effect estimate and its standard error under most scenarios. Limited application of measurement error correction methods in air pollution studies may be attributed to the absence of exposure validation data and the methodological complexity of the proposed methods. Future epidemiological studies should consider in their design phase the requirements for the measurement error correction method to be later applied, while methodological advances are needed under the multi-pollutants setting.

  17. Combining polysaccharide biosynthesis and transport in a single enzyme: dual-function cell wall glycan synthases.

    Directory of Open Access Journals (Sweden)

    Jonathan Kent Davis

    2012-06-01

    Full Text Available Extracellular polysaccharides are synthesized by a wide variety of species, from unicellular bacteria and Archaea to the largest multicellular plants and animals in the biosphere. In every case, the biosynthesis of these polymers requires transport across a membrane, from the cytosol to either the lumen of secretory pathway organelles or directly into the extracellular space. Although some polysaccharide biosynthetic substrates are moved across the membrane to sites of polysaccharide synthesis by separate transporter proteins before being incorporated into polymers by glycosyltransferase proteins, many polysaccharide biosynthetic enzymes appear to have both transporter and transferase activities. In these cases, the biosynthetic enzymes utilize substrate on one side of the membrane and deposit the polymer product on the other side. This review discusses structural characteristics of plant cell wall glycan synthases that couple synthesis with transport, drawing on what is known about such dual-function enzymes in other species.

  18. Mathematical modeling of liver metastases tumour growth and control with radiotherapy

    International Nuclear Information System (INIS)

    Campbell, Adrienne; Sivakumaran, Thiru; Wong, Eugene; Davidson, Melanie; Lock, Michael

    2008-01-01

    Generating an optimized radiation treatment plan requires understanding the factors affecting tumour control. Mathematical models of tumour dynamics may help in future studies of factors predicting tumour sensitivity to radiotherapy. In this study, a time-dependent differential model, incorporating biological cancer markers, is presented to describe pre-treatment tumour growth, response to radiation, and recurrence. The model uses Gompertzian-Exponential growth to model pre-treatment tumour growth. The effect of radiotherapy is handled by a realistic cell-kill term that includes a volume-dependent change in tumour sensitivity. Post-treatment, a Gompertzian, accelerated, delayed repopulation is employed. As proof of concept, we examined the fit of the model's prediction using various liver enzyme levels as markers of metastatic liver tumour growth in a liver cancer patient. A tumour clonogen population model was formulated. Each enzyme was coupled to the same tumour population, and served as surrogates of the tumour. This dynamical model was solved numerically and compared to the measured enzyme levels. By minimizing the mean-squared error of the model enzyme predictions, we determined the following tumour model parameters: growth rate prior to treatment was 0.52% per day; the fractional radiation cell kill for the prescribed dose (60 Gy in 15 fractions) was 42% per day, and the tumour repopulation rate was 2.9% per day. These preliminary results provided the basis to test the model in a larger series of patients, to apply biological markers for improving the efficacy of radiotherapy by determining the underlying tumour dynamics.

  19. Aβ-degrading enzymes: potential for treatment of Alzheimer disease.

    Science.gov (United States)

    Miners, James Scott; Barua, Neil; Kehoe, Patrick Gavin; Gill, Steven; Love, Seth

    2011-11-01

    There is increasing evidence that deficient clearance of β-amyloid (Aβ) contributes to its accumulation in late-onset Alzheimer disease (AD). Several Aβ-degrading enzymes, including neprilysin (NEP), insulin-degrading enzyme, and endothelin-converting enzyme reduce Aβ levels and protect against cognitive impairment in mouse models of AD. The activity of several Aβ-degrading enzymes rises with age and increases still further in AD, perhaps as a physiological response to minimize the buildup of Aβ. The age- and disease-related changes in expression of more recently recognized Aβ-degrading enzymes (e.g. NEP-2 and cathepsin B) remain to be investigated, and there is strong evidence that reduced NEP activity contributes to the development of cerebral amyloid angiopathy. Regardless of the role of Aβ-degrading enzymes in the development of AD, experimental data indicate that increasing the activity of these enzymes (NEP in particular) has therapeutic potential in AD, although targeting their delivery to the brain remains a major challenge. The most promising current approaches include the peripheral administration of agents that enhance the activity of Aβ-degrading enzymes and the direct intracerebral delivery of NEP by convection-enhanced delivery. In the longer term, genetic approaches to increasing the intracerebral expression of NEP or other Aβ-degrading enzymes may offer advantages.

  20. Design of novel nano-carriers for multi-enzyme co-localization

    Energy Technology Data Exchange (ETDEWEB)

    Jia, Feng [Iowa State Univ., Ames, IA (United States)

    2013-01-01

    The main objective of this project is to design novel nano-structured carriers and strategies to co-localize multiple enzymes to mimic the functionalities of MECs. In order to achieve this goal, distinct approaches for enzyme co-localization were developed and evaluated. Specifically, we investigated different polymeric nano-carriers, both flexible and rigid, as platforms for co-localization, as well as distinct enzyme attachment techniques using model enzyme systems using glucose oxidase and horseradish peroxidase to control the spatial arrangement of the multiple enzymes on the nanocarriers. This platform technology can be potentially used to co-localize various enzyme systems and its broad applicability will be tested using the sclareol biosynthesis process to control the formation of products through the formation of MECs with multiple enzymes NgCPS and sSsSS to regulate the pathway of reactive intermediate to enhance the final product conversion rate.

  1. [Treatment of surface burns with proteolytic enzymes: mathematic description of lysis kinetics].

    Science.gov (United States)

    Domogatskaia, A S; Domogatskiĭ, S P; Ruuge, E K

    2003-01-01

    The lysis of necrotic tissue by a proteolytic enzyme applied to the surface of a burn wound was studied. A mathematical model was proposed, which describes changes in the thickness of necrotic tissue as a function of the proteolytic activity of the enzyme. The model takes into account the inward-directed diffusion of the enzyme, the counterflow of interstitial fluid (exudates) containing specific inhibitors, and the extracellular matrix proteolysis. It was shown in terms of the quasi-stationary approach that the thickness of the necrotic tissue layer decreases exponentially with time; i.e., the lysis slows down as the thickness of the necrotic tissue layer decreases. The dependence of the characteristic time of this decrease on enzyme concentration was obtained. It was shown that, at high enzyme concentrations (more than 5 mg/ml), the entire time of lysis (after the establishment of quasi-stationary equilibrium) is inversely proportional to the concentration of the enzyme.

  2. The role of the enzyme alpha-amylase in binding of An(III)/Ln(III) by oral ingestion

    Energy Technology Data Exchange (ETDEWEB)

    Barkleit, A.; Bernhard, G. [Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, P.O. Box 510119, 01314 Dresden (Germany); Division of Radiochemistry and Resource Ecology, Technische Universitaet Dresden, 01062 Dresden (Germany); Heller, A. [Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, P.O. Box 510119, 01314 Dresden (Germany)

    2014-07-01

    In case of incorporation, radionuclides represent a serious health risk to humans due to their (radio-)toxicity. Thus, the determination of their speciation and transport on a molecular level is crucial for the understanding of the transport, metabolism, deposition and elimination in the human organisms. In case of oral ingestion of contaminated food or radioactive substances the first contact medium in the mouth is the aqueous bio-fluid saliva which contains inorganic ions (mainly Na{sup +}, K{sup +}, Ca{sup 2+}, Cl{sup -}, CO{sub 3}{sup 2-}, PO{sub 4}{sup 3-}) and numerous biomolecules, mainly proteins. One of the major proteins in saliva is the digestive enzyme α-amylase which catalyzes the hydrolysis of the α-1,4 glycosidic linkages of polysaccharides like starch or glycogen. [1] In this study the speciation of curium(III) and europium(III) in saliva as the first contact medium at oral incorporation was investigated with time-resolved laser-induced fluorescence spectroscopy (TRLFS). For TRLFS measurements, fresh saliva samples from human sources have been spiked in vitro with Eu(III) or Cm(III). The identification of the dominant species was achieved by a comparison of the spectroscopic data with reference spectra obtained from synthetic saliva and the main single components of the bio-fluid. In the pH range from 6.8 to 7.4 similar spectra were obtained. With respect to reference data, the spectra indicate the formation of a ternary metal complex containing phosphate and carbonate anions and, in addition, a coordination of organic matter, namely α-amylase, to the central metal cation is suggested. To get more information about the binding behavior of α-amylase various investigations with Eu(III) as inactive analog for An(III) were carried out with porcine pancreatic α-amylase (PPA) which serves as model system for various α-amylase species. Sorption experiments showed a high affinity of Eu(III) to α-amylase in a wide pH range, namely between pH 4 and 8

  3. Kinetic modelling of in vitro data of PI3K, mTOR1, PTEN enzymes and on-target inhibitors Rapamycin, BEZ235, and LY294002.

    Science.gov (United States)

    Goltsov, Alexey; Tashkandi, Ghassan; Langdon, Simon P; Harrison, David J; Bown, James L

    2017-01-15

    The phosphatidylinositide 3-kinases (PI3K) and mammalian target of rapamycin-1 (mTOR1) are two key targets for anti-cancer therapy. Predicting the response of the PI3K/AKT/mTOR1 signalling pathway to targeted therapy is made difficult because of network complexities. Systems biology models can help explore those complexities but the value of such models is dependent on accurate parameterisation. Motivated by a need to increase accuracy in kinetic parameter estimation, and therefore the predictive power of the model, we present a framework to integrate kinetic data from enzyme assays into a unified enzyme kinetic model. We present exemplar kinetic models of PI3K and mTOR1, calibrated on in vitro enzyme data and founded on Michaelis-Menten (MM) approximation. We describe the effects of an allosteric mTOR1 inhibitor (Rapamycin) and ATP-competitive inhibitors (BEZ235 and LY294002) that show dual inhibition of mTOR1 and PI3K. We also model the kinetics of phosphatase and tensin homolog (PTEN), which modulates sensitivity of the PI3K/AKT/mTOR1 pathway to these drugs. Model validation with independent data sets allows investigation of enzyme function and drug dose dependencies in a wide range of experimental conditions. Modelling of the mTOR1 kinetics showed that Rapamycin has an IC 50 independent of ATP concentration and that it is a selective inhibitor of mTOR1 substrates S6K1 and 4EBP1: it retains 40% of mTOR1 activity relative to 4EBP1 phosphorylation and inhibits completely S6K1 activity. For the dual ATP-competitive inhibitors of mTOR1 and PI3K, LY294002 and BEZ235, we derived the dependence of the IC 50 on ATP concentration that allows prediction of the IC 50 at different ATP concentrations in enzyme and cellular assays. Comparison of drug effectiveness in enzyme and cellular assays showed that some features of these drugs arise from signalling modulation beyond the on-target action and MM approximation and require a systems-level consideration of the whole PI3K

  4. Discontinuous Galerkin Time-Domain Modeling of Graphene Nano-Ribbon Incorporating the Spatial Dispersion Effects

    KAUST Repository

    Li, Ping; Jiang, Li Jun; Bagci, Hakan

    2018-01-01

    It is well known that graphene demonstrates spatial dispersion properties, i.e., its conductivity is nonlocal and a function of spectral wave number (momentum operator) q. In this paper, to account for effects of spatial dispersion on transmission of high speed signals along graphene nano-ribbon (GNR) interconnects, a discontinuous Galerkin time-domain (DGTD) algorithm is proposed. The atomically-thick GNR is modeled using a nonlocal transparent surface impedance boundary condition (SIBC) incorporated into the DGTD scheme. Since the conductivity is a complicated function of q (and one cannot find an analytical Fourier transform pair between q and spatial differential operators), an exact time domain SIBC model cannot be derived. To overcome this problem, the conductivity is approximated by its Taylor series in spectral domain under low-q assumption. This approach permits expressing the time domain SIBC in the form of a second-order partial differential equation (PDE) in current density and electric field intensity. To permit easy incorporation of this PDE with the DGTD algorithm, three auxiliary variables, which degenerate the second-order (temporal and spatial) differential operators to first-order ones, are introduced. Regarding to the temporal dispersion effects, the auxiliary differential equation (ADE) method is utilized to eliminates the expensive temporal convolutions. To demonstrate the applicability of the proposed scheme, numerical results, which involve characterization of spatial dispersion effects on the transfer impedance matrix of GNR interconnects, are presented.

  5. Discontinuous Galerkin Time-Domain Modeling of Graphene Nano-Ribbon Incorporating the Spatial Dispersion Effects

    KAUST Repository

    Li, Ping

    2018-04-13

    It is well known that graphene demonstrates spatial dispersion properties, i.e., its conductivity is nonlocal and a function of spectral wave number (momentum operator) q. In this paper, to account for effects of spatial dispersion on transmission of high speed signals along graphene nano-ribbon (GNR) interconnects, a discontinuous Galerkin time-domain (DGTD) algorithm is proposed. The atomically-thick GNR is modeled using a nonlocal transparent surface impedance boundary condition (SIBC) incorporated into the DGTD scheme. Since the conductivity is a complicated function of q (and one cannot find an analytical Fourier transform pair between q and spatial differential operators), an exact time domain SIBC model cannot be derived. To overcome this problem, the conductivity is approximated by its Taylor series in spectral domain under low-q assumption. This approach permits expressing the time domain SIBC in the form of a second-order partial differential equation (PDE) in current density and electric field intensity. To permit easy incorporation of this PDE with the DGTD algorithm, three auxiliary variables, which degenerate the second-order (temporal and spatial) differential operators to first-order ones, are introduced. Regarding to the temporal dispersion effects, the auxiliary differential equation (ADE) method is utilized to eliminates the expensive temporal convolutions. To demonstrate the applicability of the proposed scheme, numerical results, which involve characterization of spatial dispersion effects on the transfer impedance matrix of GNR interconnects, are presented.

  6. Incorporating Psychological Predictors of Treatment Response into Health Economic Simulation Models: A Case Study in Type 1 Diabetes.

    Science.gov (United States)

    Kruger, Jen; Pollard, Daniel; Basarir, Hasan; Thokala, Praveen; Cooke, Debbie; Clark, Marie; Bond, Rod; Heller, Simon; Brennan, Alan

    2015-10-01

    . Health economic modeling has paid limited attention to the effects that patients' psychological characteristics have on the effectiveness of treatments. This case study tests 1) the feasibility of incorporating psychological prediction models of treatment response within an economic model of type 1 diabetes, 2) the potential value of providing treatment to a subgroup of patients, and 3) the cost-effectiveness of providing treatment to a subgroup of responders defined using 5 different algorithms. . Multiple linear regressions were used to investigate relationships between patients' psychological characteristics and treatment effectiveness. Two psychological prediction models were integrated with a patient-level simulation model of type 1 diabetes. Expected value of individualized care analysis was undertaken. Five different algorithms were used to provide treatment to a subgroup of predicted responders. A cost-effectiveness analysis compared using the algorithms to providing treatment to all patients. . The psychological prediction models had low predictive power for treatment effectiveness. Expected value of individualized care results suggested that targeting education at responders could be of value. The cost-effectiveness analysis suggested, for all 5 algorithms, that providing structured education to a subgroup of predicted responders would not be cost-effective. . The psychological prediction models tested did not have sufficient predictive power to make targeting treatment cost-effective. The psychological prediction models are simple linear models of psychological behavior. Collection of data on additional covariates could potentially increase statistical power. . By collecting data on psychological variables before an intervention, we can construct predictive models of treatment response to interventions. These predictive models can be incorporated into health economic models to investigate more complex service delivery and reimbursement strategies.

  7. Phospholipid synthesis in the squid giant axon: incorporation of lipid precursors

    Energy Technology Data Exchange (ETDEWEB)

    Gould, R.M.; Pant, H.; Gainer, H.; Tytell, M.

    1983-05-01

    The squid giant axon and extruded axoplasm from the giant axon were used to study the capacity of axoplasm for phospholipid synthesis. Extruded axoplasm, suspended in chemically defined media, catalyzed the synthesis of phospholipids from all of the precursors tested. /sup 32/P-Labeled inorganic phosphate and gamma-labeled ATP were actively incorporated into phosphatidylinositol phosphate, while (2-/sup 3/H)myo-inositol and L-(/sup 3/H(G))serine were actively incorporated into phosphatidylinositol and phosphatidylserine, respectively. Though less well utilized. (2-/sup 3/H)glycerol was incorporated into phosphatidic acid, phosphatidylinositol, and triglyceride, and methyl-3H)choline and (1-/sup 3/H)ethanolamine were incorporated into phosphatidylcholine and phosphatidylethanolamine, respectively. Isolated squid giant axons were incubated in artificial seawater containing the above precursors. The axoplasm was extruded following the incubations. Although most of the product lipids were recovered in the sheath (composed of cortical axoplasm, axolemma, and surrounding satellite cells), significant amounts (4-20%) were present in the extruded axoplasm. With tritiated choline and myo-inositol, the major labeled phospholipids found in both the extruded axoplasm and the sheath were phosphatidylcholine and phosphatidylinositol, respectively. With both glycerol and phosphate, phosphatidylethanolamine was a major labeled lipid in both axoplasm and sheath. These findings demonstrate that all classes of phospholipids are formed by endogenous synthetic enzymes in axoplasm. In addition, we feel that the different patterns of incorporation by intact axons and extruded axoplasm indicate that surrounding sheath cells contribute lipids to axoplasm. A comprehensive picture of axonal lipid metabolism should include axoplasmic synthesis and glial-axon transfer as pathways complementing the axonal transport of perikaryally formed lipids.

  8. Optimum concrete compression strength using bio-enzyme

    Directory of Open Access Journals (Sweden)

    Bagio Tony Hartono

    2017-01-01

    Full Text Available To make concrete with high compressive strength and has a certain concrete specifications other than the main concrete materials are also needed concrete mix quality control and other added material is also in line with the current technology of concrete mix that produces concrete with specific characteristics. Addition of bio enzyme on five concrete mixture that will be compared with normal concrete in order to know the optimum level bio-enzyme in concrete to increase the strength of the concrete. Concrete with bio-enzyme 200 ml/m3, 400 ml/m3, 600 ml/m3, 800 ml/m3, 1000 ml/m3 and normal concrete. Refer to the crushing test result, its tends to the mathematical model using 4th degree polynomial regression (least quartic, as represent on the attached data series, which is for the design mix fc′ = 25 MPa generate optimum value for 33,98 MPa, on the bio-additive dosage of 509 ml bio enzymes.

  9. Incorporating a Time Horizon in Rate-of-Return Estimations: Discounted Cash Flow Model in Electric Transmission Rate Cases

    International Nuclear Information System (INIS)

    Chatterjee, Bishu; Sharp, Peter A.

    2006-01-01

    Electric transmission and other rate cases use a form of the discounted cash flow model with a single long-term growth rate to estimate rates of return on equity. It cannot incorporate information about the appropriate time horizon for which analysts' estimates of earnings growth have predictive powers. Only a non-constant growth model can explicitly recognize the importance of the time horizon in an ROE calculation. (author)

  10. 7 CFR 58.436 - Rennet, pepsin, other milk clotting enzymes and flavor enzymes.

    Science.gov (United States)

    2010-01-01

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

  11. Incorporating time-delays in S-System model for reverse engineering genetic networks.

    Science.gov (United States)

    Chowdhury, Ahsan Raja; Chetty, Madhu; Vinh, Nguyen Xuan

    2013-06-18

    In any gene regulatory network (GRN), the complex interactions occurring amongst transcription factors and target genes can be either instantaneous or time-delayed. However, many existing modeling approaches currently applied for inferring GRNs are unable to represent both these interactions simultaneously. As a result, all these approaches cannot detect important interactions of the other type. S-System model, a differential equation based approach which has been increasingly applied for modeling GRNs, also suffers from this limitation. In fact, all S-System based existing modeling approaches have been designed to capture only instantaneous interactions, and are unable to infer time-delayed interactions. In this paper, we propose a novel Time-Delayed S-System (TDSS) model which uses a set of delay differential equations to represent the system dynamics. The ability to incorporate time-delay parameters in the proposed S-System model enables simultaneous modeling of both instantaneous and time-delayed interactions. Furthermore, the delay parameters are not limited to just positive integer values (corresponding to time stamps in the data), but can also take fractional values. Moreover, we also propose a new criterion for model evaluation exploiting the sparse and scale-free nature of GRNs to effectively narrow down the search space, which not only reduces the computation time significantly but also improves model accuracy. The evaluation criterion systematically adapts the max-min in-degrees and also systematically balances the effect of network accuracy and complexity during optimization. The four well-known performance measures applied to the experimental studies on synthetic networks with various time-delayed regulations clearly demonstrate that the proposed method can capture both instantaneous and delayed interactions correctly with high precision. The experiments carried out on two well-known real-life networks, namely IRMA and SOS DNA repair network in

  12. Elevated Liver Enzymes

    Science.gov (United States)

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

  13. Enzyme structure, enzyme function and allozyme diversity in ...

    African Journals Online (AJOL)

    In estimates of population genetic diversity based on allozyme heterozygosity, some enzymes are regularly more variable than others. Evolutionary theory suggests that functionally less important molecules, or parts of molecules, evolve more rapidly than more important ones; the latter enzymes should then theoretically be ...

  14. The ultrasound technology for modifying enzyme activity

    Directory of Open Access Journals (Sweden)

    Meliza Lindsay Rojas

    2016-01-01

    Full Text Available Enzymes are protein complexes compounds widely studied and used due to their ability to catalyze reactions. The food processing mainly a ims the inactivation of enzymes due to various undesirable effects. However, there are many processes that can be optimized by its catalytic activity. In this context, different technologies have been applied both to inactivate or to improve the enzymes ef ficiency. The Ultrasound technology emerges as an alternative mainly applied to achieve the enzyme inactivation. On the contrary, very few investigations show the ability of this technology under certain conditions to achieve the opposite effect (i.e. increase the catalytic activity of enzymes. The objective of this study was to correlate the ultrasonic energy delivered to the sample (J/mL with the residual enzymatic activity and explain the possible mechanisms which results in the enzymatic activation/in activation complex behavior. The activity of POD in coconut water was evaluated as a model. The enzymatic activity initially increased, followed by reduction with a trend to enzyme inactivation. This complex behavior is directly related to the applied ultr asonic energy and their direct mechanical effects on the product, as well as the effect in the enzymatic infinite intermediate states and its structural conformation changes. The obtained results are useful for both academic and industrial perspectives.

  15. Cell In Situ Zymography: Imaging Enzyme-Substrate Interactions.

    Science.gov (United States)

    Chhabra, Aastha; Rani, Vibha

    2017-01-01

    Zymography has long been used for the detection of substrate-specific enzyme activity. In situ zymography (ISZ), an adaptation from the conventional substrate zymography, is a widely employed technique useful for the detection, localization, and estimation of enzyme-substrate interactions in tissues. Here, we describe a protocol to detect 'in position' matrix metalloproteinase (MMP) activity in cells utilizing H9c2 cardiomyoblasts as a model. This technique is primarily adopted from the method used for histological sections and is termed as 'Cell in situ Zymography'. It is a simple, sensitive, and quantifiable methodology to assess the functional activity of an enzyme 'on site/in position' in cell culture.

  16. Light-Addressed Electrodeposition of Enzyme-Entrapped Chitosan Membranes for Multiplexed Enzyme-Based Bioassays Using a Digital Micromirror Device

    Directory of Open Access Journals (Sweden)

    Yeu-Long Jiang

    2013-08-01

    Full Text Available This paper describes a light-addressed electrolytic system used to perform an electrodeposition of enzyme-entrapped chitosan membranes for multiplexed enzyme-based bioassays using a digital micromirror device (DMD. In this system, a patterned light illumination is projected onto a photoconductive substrate serving as a photo-cathode to electrolytically produce hydroxide ions, which leads to an increased pH gradient. The high pH generated at the cathode can cause a local gelation of chitosan through sol-gel transition. By controlling the illumination pattern on the DMD, a light-addressed electrodeposition of chitosan membranes with different shapes and sizes, as well as multiplexed micropatterning, was performed. The effect of the illumination time of the light pattern on the dimensional resolution of chitosan membrane formation was examined experimentally. Moreover, multiplexed enzyme-based bioassay of enzyme-entrapped chitosan membranes was also successfully demonstrated through the electrodeposition of the chitosan membranes with various shapes/sizes and entrapping different enzymes. As a model experiment, glucose and ethanol were simultaneously detected in a single detection chamber without cross-talk using shape-coded chitosan membranes entrapped with glucose oxidase (GOX, peroxidase (POD, and Amplex Red (AmR or alcohol oxidase (AOX, POD, and AmR by using same fluorescence indicator (AmR.

  17. Simple and robust determination of the activity signature of key carbohydrate metabolism enzymes for physiological phenotyping in model and crop plants

    DEFF Research Database (Denmark)

    Jammer, Alexandra; Gasperl, Anna; Luschin-Ebengreuth, Nora

    2015-01-01

    The analysis of physiological parameters is important to understand the link between plant phenotypes and their genetic bases, and therefore is needed as an important element in the analysis of model and crop plants. The activities of enzymes involved in primary carbohydrate metabolism have been...... shown to be strongly associated with growth performance, crop yield, and quality, as well as stress responses. A simple, fast, and cost-effective method to determine activities for 13 key enzymes involved in carbohydrate metabolism has been established, mainly based on coupled spectrophotometric kinetic...

  18. Exciton delocalization incorporated drift-diffusion model for bulk-heterojunction organic solar cells

    Science.gov (United States)

    Wang, Zi Shuai; Sha, Wei E. I.; Choy, Wallace C. H.

    2016-12-01

    Modeling the charge-generation process is highly important to understand device physics and optimize power conversion efficiency of bulk-heterojunction organic solar cells (OSCs). Free carriers are generated by both ultrafast exciton delocalization and slow exciton diffusion and dissociation at the heterojunction interface. In this work, we developed a systematic numerical simulation to describe the charge-generation process by a modified drift-diffusion model. The transport, recombination, and collection of free carriers are incorporated to fully capture the device response. The theoretical results match well with the state-of-the-art high-performance organic solar cells. It is demonstrated that the increase of exciton delocalization ratio reduces the energy loss in the exciton diffusion-dissociation process, and thus, significantly improves the device efficiency, especially for the short-circuit current. By changing the exciton delocalization ratio, OSC performances are comprehensively investigated under the conditions of short-circuit and open-circuit. Particularly, bulk recombination dependent fill factor saturation is unveiled and understood. As a fundamental electrical analysis of the delocalization mechanism, our work is important to understand and optimize the high-performance OSCs.

  19. Optimization of parameters for enhanced oil recovery from enzyme treated wild apricot kernels.

    Science.gov (United States)

    Rajaram, Mahatre R; Kumbhar, Baburao K; Singh, Anupama; Lohani, Umesh Chandra; Shahi, Navin C

    2012-08-01

    Present investigation was undertaken with the overall objective of optimizing the enzymatic parameters i.e. moisture content during hydrolysis, enzyme concentration, enzyme ratio and incubation period on wild apricot kernel processing for better oil extractability and increased oil recovery. Response surface methodology was adopted in the experimental design. A central composite rotatable design of four variables at five levels was chosen. The parameters and their range for the experiments were moisture content during hydrolysis (20-32%, w.b.), enzyme concentration (12-16% v/w of sample), combination of pectolytic and cellulolytic enzyme i.e. enzyme ratio (30:70-70:30) and incubation period (12-16 h). Aspergillus foetidus and Trichoderma viride was used for production of crude enzyme i.e. pectolytic and cellulolytic enzyme respectively. A complete second order model for increased oil recovery as the function of enzymatic parameters fitted the data well. The best fit model for oil recovery was also developed. The effect of various parameters on increased oil recovery was determined at linear, quadric and interaction level. The increased oil recovery ranged from 0.14 to 2.53%. The corresponding conditions for maximum oil recovery were 23% (w.b.), 15 v/w of the sample, 60:40 (pectolytic:cellulolytic), 13 h. Results of the study indicated that incubation period during enzymatic hydrolysis is the most important factor affecting oil yield followed by enzyme ratio, moisture content and enzyme concentration in the decreasing order. Enzyme ratio, incubation period and moisture content had insignificant effect on oil recovery. Second order model for increased oil recovery as a function of enzymatic hydrolysis parameters predicted the data adequately.

  20. Growth performance, digestive enzyme activity and immune response of Macrobrachium rosenbergii fed with probiotic Clostridium butyricum incorporated diets

    Directory of Open Access Journals (Sweden)

    Mohammad Saifuddin Sumon

    2018-01-01

    Full Text Available To determine antagonistic effect of Clostridium butyricum against Vibrio harveyi and its probiotic effect on growth performance, digestibility and immune response of fresh water prawn, Macrobrachium rosenbergii juveniles were examined following feeding with C. butyricum incorporated feed for 60 days. Significant reduction of V. harveyi growth was found at 8 hr and onward in in-vitro and at 10 days and onward in in-vivo challenge test. After rearing prawn with the bacteria in feed treatment for 60 days, body weight and growth rate of prawns was significantly higher (p  0.05 compared to control group. This study revealed that probiotic, C. butyricum incorporated diets were found to be beneficial for M. rosenbergii culture in terms of hindering the growth of pathogenic bacteria and increasing the growth, protease and amylase activities of prawn. Results from this study will be helpful to improve fresh water prawn farming.

  1. Chemosensors and biosensors based on polyelectrolyte microcapsules containing fluorescent dyes and enzymes.

    Science.gov (United States)

    Kazakova, Lyubov I; Shabarchina, Lyudmila I; Anastasova, Salzitsa; Pavlov, Anton M; Vadgama, Pankaj; Skirtach, Andre G; Sukhorukov, Gleb B

    2013-02-01

    The concept of enzyme-assisted substrate sensing based on use of fluorescent markers to detect the products of enzymatic reaction has been investigated by fabrication of micron-scale polyelectrolyte capsules containing enzymes and dyes in one entity. Microcapsules approximately 5 μm in size entrap glucose oxidase or lactate oxidase, with peroxidase, together with the corresponding markers Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride (Ru(dpp)) complex and dihydrorhodamine 123 (DHR123), which are sensitive to oxygen and hydrogen peroxide, respectively. These capsules are produced by co-precipitation of calcium carbonate particles with the enzyme followed by layer-by-layer assembly of polyelectrolytes over the surface of the particles and incorporation of the dye in the capsule interior or in the multilayer shell. After dissolution of the calcium carbonate the enzymes and dyes remain in the multilayer capsules. In this study we produced enzyme-containing microcapsules sensitive to glucose and lactate. Calibration curves based on fluorescence intensity of Ru(dpp) and DHR123 were linearly dependent on substrate concentration, enabling reliable sensing in the millimolar range. The main advantages of using these capsules with optical recording is the possibility of building single capsule-based sensors. The response from individual capsules was observed by confocal microscopy as increasing fluorescence intensity of the capsule on addition of lactate at millimolar concentrations. Because internalization of the micron-sized multi-component capsules was feasible, they could be further optimized for in-situ intracellular sensing and metabolite monitoring on the basis of fluorescence reporting.

  2. Incorporation of 14C glucose into glycogen and glucose-6-phosphate dehydrogenase activity in rat brain following carbon monoxide intoxication

    International Nuclear Information System (INIS)

    Sikorska, M.; Gorzkowski, B.; Szumanska, G.; Smialek, M.

    1975-01-01

    Incorporation of 14 C glucose into glycogen and glucose-6-phosphate dehydrogenase activity in rat brain following carbon monoxide intoxication was studied. In brains of rats tested on the 20, 30 and 60th minute of exposure to CO and immediately after removal from the chamber the enzyme activity showed no essential deviation from the control level. In the group of rats tested 1 hour after taking them out from the chamber increase of the enzyme activity was noticed, amounting to about 33% of the control value. The brains tested 24 hours after exposure showed the largest increase of the enzyme activity by about 94%. In the next time periods, 48 and 72 hours after intoxication, the enzyme activity was decreasing. The glycogen content in brains of control animals increased 3 hours after CO intoxication by about 69%. The increase of glycogen synthesis was expressed by increase of the total radioactivity, which amounted to 160% of the control value. (Z.M.)

  3. Incorporating Context Dependency of Species Interactions in Species Distribution Models.

    Science.gov (United States)

    Lany, Nina K; Zarnetske, Phoebe L; Gouhier, Tarik C; Menge, Bruce A

    2017-07-01

    Species distribution models typically use correlative approaches that characterize the species-environment relationship using occurrence or abundance data for a single species. However, species distributions are determined by both abiotic conditions and biotic interactions with other species in the community. Therefore, climate change is expected to impact species through direct effects on their physiology and indirect effects propagated through their resources, predators, competitors, or mutualists. Furthermore, the sign and strength of species interactions can change according to abiotic conditions, resulting in context-dependent species interactions that may change across space or with climate change. Here, we incorporated the context dependency of species interactions into a dynamic species distribution model. We developed a multi-species model that uses a time-series of observational survey data to evaluate how abiotic conditions and species interactions affect the dynamics of three rocky intertidal species. The model further distinguishes between the direct effects of abiotic conditions on abundance and the indirect effects propagated through interactions with other species. We apply the model to keystone predation by the sea star Pisaster ochraceus on the mussel Mytilus californianus and the barnacle Balanus glandula in the rocky intertidal zone of the Pacific coast, USA. Our method indicated that biotic interactions between P. ochraceus and B. glandula affected B. glandula dynamics across >1000 km of coastline. Consistent with patterns from keystone predation, the growth rate of B. glandula varied according to the abundance of P. ochraceus in the previous year. The data and the model did not indicate that the strength of keystone predation by P. ochraceus varied with a mean annual upwelling index. Balanus glandula cover increased following years with high phytoplankton abundance measured as mean annual chlorophyll-a. M. californianus exhibited the same

  4. A Model Study on the Possible Effects of an External Electrical Field on Enzymes Having Dinuclear Iron Cluster [2Fe-2S

    Directory of Open Access Journals (Sweden)

    Lemi Türker

    2012-01-01

    Full Text Available Hydrogenases which catalyze the H2 ↔ 2H+ + 2e− reaction are metalloenzymes that can be divided into two classes, the NiFe and Fe enzymes, on the basis of their metal content. Iron-sulfur clusters [2Fe-2S] and [4Fe-4S] are common in ironhydrogenases. In the present model study, [2Fe-2S] cluster has been considered to visualize the effect of external electric field on various quantum chemical properties of it. In the model, all the cysteinyl residues are in the amide form. The PM3 type semiempirical calculations have been performed for the geometry optimization of the model structure in the absence and presence of the external field. Then, single point DFT calculations (B3LYP/6-31+G(d have been carried out. Depending on the direction of the field, the chemical reactivity of the model enzyme varies which suggests that an external electric field could, under proper conditions, improve the enzymatic hydrogen production.

  5. Energy system investment model incorporating heat pumps with thermal storage in buildings and buffer tanks

    DEFF Research Database (Denmark)

    Hedegaard, Karsten; Balyk, Olexandr

    2013-01-01

    Individual compression heat pumps constitute a potentially valuable resource in supporting wind power integration due to their economic competitiveness and possibilities for flexible operation. When analysing the system benefits of flexible heat pump operation, effects on investments should...... be taken into account. In this study, we present a model that facilitates analysing individual heat pumps and complementing heat storages in integration with the energy system, while optimising both investments and operation. The model incorporates thermal building dynamics and covers various heat storage...... of operating heat pumps flexibly. This includes prioritising heat pump operation for hours with low marginal electricity production costs, and peak load shaving resulting in a reduced need for peak and reserve capacity investments....

  6. Perspectives on electrostatics and conformational motions in enzyme catalysis.

    Science.gov (United States)

    Hanoian, Philip; Liu, C Tony; Hammes-Schiffer, Sharon; Benkovic, Stephen

    2015-02-17

    CONSPECTUS: Enzymes are essential for all living organisms, and their effectiveness as chemical catalysts has driven more than a half century of research seeking to understand the enormous rate enhancements they provide. Nevertheless, a complete understanding of the factors that govern the rate enhancements and selectivities of enzymes remains elusive, due to the extraordinary complexity and cooperativity that are the hallmarks of these biomolecules. We have used a combination of site-directed mutagenesis, pre-steady-state kinetics, X-ray crystallography, nuclear magnetic resonance (NMR), vibrational and fluorescence spectroscopies, resonance energy transfer, and computer simulations to study the implications of conformational motions and electrostatic interactions on enzyme catalysis in the enzyme dihydrofolate reductase (DHFR). We have demonstrated that modest equilibrium conformational changes are functionally related to the hydride transfer reaction. Results obtained for mutant DHFRs illustrated that reductions in hydride transfer rates are correlated with altered conformational motions, and analysis of the evolutionary history of DHFR indicated that mutations appear to have occurred to preserve both the hydride transfer rate and the associated conformational changes. More recent results suggested that differences in local electrostatic environments contribute to finely tuning the substrate pKa in the initial protonation step. Using a combination of primary and solvent kinetic isotope effects, we demonstrated that the reaction mechanism is consistent across a broad pH range, and computer simulations suggested that deprotonation of the active site Tyr100 may play a crucial role in substrate protonation at high pH. Site-specific incorporation of vibrational thiocyanate probes into the ecDHFR active site provided an experimental tool for interrogating these microenvironments and for investigating changes in electrostatics along the DHFR catalytic cycle

  7. Substrate-Competitive Activity-Based Profiling of Ester Prodrug Activating Enzymes.

    Science.gov (United States)

    Xu, Hao; Majmudar, Jaimeen D; Davda, Dahvid; Ghanakota, Phani; Kim, Ki H; Carlson, Heather A; Showalter, Hollis D; Martin, Brent R; Amidon, Gordon L

    2015-09-08

    Understanding the mechanistic basis of prodrug delivery and activation is critical for establishing species-specific prodrug sensitivities necessary for evaluating preclinical animal models and potential drug-drug interactions. Despite significant adoption of prodrug methodologies for enhanced pharmacokinetics, functional annotation of prodrug activating enzymes is laborious and often unaddressed. Activity-based protein profiling (ABPP) describes an emerging chemoproteomic approach to assay active site occupancy within a mechanistically similar enzyme class in native proteomes. The serine hydrolase enzyme family is broadly reactive with reporter-linked fluorophosphonates, which have shown to provide a mechanism-based covalent labeling strategy to assay the activation state and active site occupancy of cellular serine amidases, esterases, and thioesterases. Here we describe a modified ABPP approach using direct substrate competition to identify activating enzymes for an ethyl ester prodrug, the influenza neuraminidase inhibitor oseltamivir. Substrate-competitive ABPP analysis identified carboxylesterase 1 (CES1) as an oseltamivir-activating enzyme in intestinal cell homogenates. Saturating concentrations of oseltamivir lead to a four-fold reduction in the observed rate constant for CES1 inactivation by fluorophosphonates. WWL50, a reported carbamate inhibitor of mouse CES1, blocked oseltamivir hydrolysis activity in human cell homogenates, confirming CES1 is the primary prodrug activating enzyme for oseltamivir in human liver and intestinal cell lines. The related carbamate inhibitor WWL79 inhibited mouse but not human CES1, providing a series of probes for analyzing prodrug activation mechanisms in different preclinical models. Overall, we present a substrate-competitive activity-based profiling approach for broadly surveying candidate prodrug hydrolyzing enzymes and outline the kinetic parameters for activating enzyme discovery, ester prodrug design, and

  8. The pathogenomics of McArdle disease--genes, enzymes, models, and therapeutic implications.

    Science.gov (United States)

    Nogales-Gadea, Gisela; Santalla, Alfredo; Brull, Astrid; de Luna, Noemi; Lucia, Alejandro; Pinós, Tomàs

    2015-03-01

    Numerous biomedical advances have been made since Carl and Gerty Cori discovered the enzyme phosphorylase in the 1940s and the Scottish physician Brian McArdle reported in 1951 a previously 'undescribed disorder characterized by a gross failure of the breakdown in muscle of glycogen'. Today we know that this disorder, commonly known as 'McArdle disease', is caused by inherited deficiency of the muscle isoform of glycogen phosphorylase (GP). Here we review the main aspects of the 'pathogenomics' of this disease including, among others: the spectrum of mutations in the gene (PYGM) encoding muscle GP; the interplay between the different tissue GP isoforms in cellular cultures and in patients; what can we learn from naturally occurring and recently laboratory-generated animal models of the disease; and potential therapies.

  9. Immobilized enzymes: understanding enzyme - surface interactions at the molecular level.

    Science.gov (United States)

    Hoarau, Marie; Badieyan, Somayesadat; Marsh, E Neil G

    2017-11-22

    Enzymes immobilized on solid supports have important and industrial and medical applications. However, their uses are limited by the significant reductions in activity and stability that often accompany the immobilization process. Here we review recent advances in our understanding of the molecular level interactions between proteins and supporting surfaces that contribute to changes in stability and activity. This understanding has been facilitated by the application of various surface-sensitive spectroscopic techniques that allow the structure and orientation of enzymes at the solid/liquid interface to be probed, often with monolayer sensitivity. An appreciation of the molecular interactions between enzyme and surface support has allowed the surface chemistry and method of enzyme attachement to be fine-tuned such that activity and stability can be greatly enhanced. These advances suggest that a much wider variety of enzymes may eventually be amenable to immobilization as green catalysts.

  10. DYNAMIC MODELLING AND ADVANCED PREDICTIVE CONTROL OF A CONTINUOUS PROCESS OF ENZYME PURIFICATION

    Directory of Open Access Journals (Sweden)

    Dechechi E.C.

    1997-01-01

    Full Text Available A dynamic mathematical model, simulation and computer control of a Continuous Affinity Recycle Extraction (CARE process, a protein purification technique based on protein adsorption on solid-phase adsorbents is described in this work. This process, consisting of three reactors, is a multivariable process with considerable time delay in the on-line analyses of the controlled variable. An advanced predictive control configuration, specifically the Dynamic Matrix Control (DMC, was applied. The DMC algorithm was applied in process schemes where the aim was to maintain constant the enzyme concentration in the outlet of the third reactor. The performance of the DMC controller was analyzed in the feed-flow disturbances and the results are presented.

  11. Hydrolytic enzymes in the central vacuole of plant cells.

    Science.gov (United States)

    Boller, T; Kende, H

    1979-06-01

    The hydrolase content of vacuoles isolated from protoplasts of suspension-cultured tobacco cells, of tulip petals, and of pineapple leaves, and the sedimentation behavior of tobacco tonoplasts were studied. Three precautions were found to be important for the analysis of vacuolar hydrolases and of the tonoplast. (a) Purification of protoplasts in a Ficoll gradient was necessary to remove cell debris which contained contaminating hydrolases adsorbed from the fungal cell-wall-degrading enzyme preparation. (b) Hydrolase activities in the homogenates of the intact cells or the tissue used and of the purified protoplasts had to be compared to verify the absence of contaminating hydrolases in the protoplast preparation. (c) Vacuoles obtained from the protoplasts by an osmotic shock had to be purified from the lysate in a Ficoll gradient. Since the density of the central vacuole approximates that of the protoplasts, about a 10% contamination of the vacuolar preparation by surviving protoplasts could not be eliminated and had to be taken into account when the distribution of enzymes and of radioactivity was calculated.THE INTRACELLULAR ACTIVITIES OF THE FOLLOWING ACID HYDROLASES WERE PRIMARILY LOCALIZED IN THE VACUOLE OF TOBACCO CELLS: alpha-mannosidase, beta-N-acetylglucosaminidase, beta-fructosidase, nuclease, phosphatase, phosphodiesterase. A similar composition of acid hydrolases was found in vacuoles obtained from protoplasts of tulip petals. Proteinase, a hydrolase with low activity in tobacco cells and tulip petals and therefore difficult to localize unequivocally, was found to be vacuolar in pineapple leaves, a tissue containing high levels of this enzyme. Our data support the hypothesis that the central vacuole of higher plant cells has an enzyme composition analogous to that of the animal lysosome.None of the vacuolar enzymes investigated was found to be bound to the tonoplast. When vacuoles were isolated from cells labeled with radioactive choline, the vacuolar

  12. Thermodynamics of information processing based on enzyme kinetics: An exactly solvable model of an information pump.

    Science.gov (United States)

    Cao, Yuansheng; Gong, Zongping; Quan, H T

    2015-06-01

    Motivated by the recent proposed models of the information engine [Proc. Natl. Acad. Sci. USA 109, 11641 (2012)] and the information refrigerator [Phys. Rev. Lett. 111, 030602 (2013)], we propose a minimal model of the information pump and the information eraser based on enzyme kinetics. This device can either pump molecules against the chemical potential gradient by consuming the information to be encoded in the bit stream or (partially) erase the information initially encoded in the bit stream by consuming the Gibbs free energy. The dynamics of this model is solved exactly, and the "phase diagram" of the operation regimes is determined. The efficiency and the power of the information machine is analyzed. The validity of the second law of thermodynamics within our model is clarified. Our model offers a simple paradigm for the investigating of the thermodynamics of information processing involving the chemical potential in small systems.

  13. Evaluation method for the drying performance of enzyme containing formulations

    DEFF Research Database (Denmark)

    Sloth, Jakob; Bach, P.; Jensen, Anker Degn

    2008-01-01

    A method is presented for fast and cheap evaluation of the performance of enzyme containing formulations in terms of preserving the highest enzyme activity during spray drying. The method is based on modeling the kinetics of the thermal inactivation reaction which occurs during the drying process....... Relevant kinetic parameters are determined from differential scanning calorimeter (DSC) experiments and the model is used to simulate the severity of the inactivation reaction for temperatures and moisture levels relevant for spray drying. After conducting experiments and subsequent simulations...... for a number of different formulations it may be deduced which formulation performs best. This is illustrated by a formulation design study where 4 different enzyme containing formulations are evaluated. The method is validated by comparison to pilot scale spray dryer experiments....

  14. Detoxification of Hg(II) from aqueous and enzyme media: Pristine vs. tailored calcium alginate hydrogels.

    Science.gov (United States)

    Sarkar, Kangkana; Ansari, Zarina; Sen, Kamalika

    2016-10-01

    Calcium alginate (CA) hydrogels were tailored using phenolic compounds (PC) like, thymol, morin, catechin, hesperidin, during their preparation. The PC incorporated gels show modified surface features as indicated by scanning electron microscopic images (SEM). The rheological studies show that excepting the hesperidin incorporated gels all the other kinds including calcium alginate pristine have similar mechanical strength. The hesperidine incorporated CA gels had the maximum capacity to adsorb Hg. The Freundlich adsorption isotherms show higher values of adsorption capacity for all PC incorporated CA beads than the pristine CA (PCA). The hesperidin incorporated CA gels were found to show the best adsorption condition at neutral pH and an optimum contact time of 2.5h at 25°C. Considering the possibility of ingested Hg detoxification from human alimentary tract, the hesperidin and morin incorporated CA beads were further modified through incorporation of cod liver oil as the digestion time of fat in stomach is higher. In vitro uptake capacities of Hg in pepsin and pancreatin containing enzyme media were studied with hesperidin and morin incorporated beads and their corresponding fat incorporated beads also. In the pepsin medium, there was no uptake by hesperidin and fat-hesperidin incorporated beads, which is possibly due to the higher acidity of the medium. But in pancreatin medium Hg was taken up by both kinds of beads. Morin and morin-fat incorporated beads were efficient to uptake Hg from both the pepsin and pancreatin medium. The tailored CA beads may therefore serve as efficient scaffolds to rescue Hg ingested individuals. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Expanding the Halohydrin Dehalogenase Enzyme Family: Identification of Novel Enzymes by Database Mining.

    Science.gov (United States)

    Schallmey, Marcus; Koopmeiners, Julia; Wells, Elizabeth; Wardenga, Rainer; Schallmey, Anett

    2014-12-01

    Halohydrin dehalogenases are very rare enzymes that are naturally involved in the mineralization of halogenated xenobiotics. Due to their catalytic potential and promiscuity, many biocatalytic reactions have been described that have led to several interesting and industrially important applications. Nevertheless, only a few of these enzymes have been made available through recombinant techniques; hence, it is of general interest to expand the repertoire of these enzymes so as to enable novel biocatalytic applications. After the identification of specific sequence motifs, 37 novel enzyme sequences were readily identified in public sequence databases. All enzymes that could be heterologously expressed also catalyzed typical halohydrin dehalogenase reactions. Phylogenetic inference for enzymes of the halohydrin dehalogenase enzyme family confirmed that all enzymes form a distinct monophyletic clade within the short-chain dehydrogenase/reductase superfamily. In addition, the majority of novel enzymes are substantially different from previously known phylogenetic subtypes. Consequently, four additional phylogenetic subtypes were defined, greatly expanding the halohydrin dehalogenase enzyme family. We show that the enormous wealth of environmental and genome sequences present in public databases can be tapped for in silico identification of very rare but biotechnologically important biocatalysts. Our findings help to readily identify halohydrin dehalogenases in ever-growing sequence databases and, as a consequence, make even more members of this interesting enzyme family available to the scientific and industrial community. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  16. Incorporating networks in a probabilistic graphical model to find drivers for complex human diseases.

    Science.gov (United States)

    Mezlini, Aziz M; Goldenberg, Anna

    2017-10-01

    Discovering genetic mechanisms driving complex diseases is a hard problem. Existing methods often lack power to identify the set of responsible genes. Protein-protein interaction networks have been shown to boost power when detecting gene-disease associations. We introduce a Bayesian framework, Conflux, to find disease associated genes from exome sequencing data using networks as a prior. There are two main advantages to using networks within a probabilistic graphical model. First, networks are noisy and incomplete, a substantial impediment to gene discovery. Incorporating networks into the structure of a probabilistic models for gene inference has less impact on the solution than relying on the noisy network structure directly. Second, using a Bayesian framework we can keep track of the uncertainty of each gene being associated with the phenotype rather than returning a fixed list of genes. We first show that using networks clearly improves gene detection compared to individual gene testing. We then show consistently improved performance of Conflux compared to the state-of-the-art diffusion network-based method Hotnet2 and a variety of other network and variant aggregation methods, using randomly generated and literature-reported gene sets. We test Hotnet2 and Conflux on several network configurations to reveal biases and patterns of false positives and false negatives in each case. Our experiments show that our novel Bayesian framework Conflux incorporates many of the advantages of the current state-of-the-art methods, while offering more flexibility and improved power in many gene-disease association scenarios.

  17. Metagenomics as a Tool for Enzyme Discovery: Hydrolytic Enzymes from Marine-Related Metagenomes.

    Science.gov (United States)

    Popovic, Ana; Tchigvintsev, Anatoly; Tran, Hai; Chernikova, Tatyana N; Golyshina, Olga V; Yakimov, Michail M; Golyshin, Peter N; Yakunin, Alexander F

    2015-01-01

    This chapter discusses metagenomics and its application for enzyme discovery, with a focus on hydrolytic enzymes from marine metagenomic libraries. With less than one percent of culturable microorganisms in the environment, metagenomics, or the collective study of community genetics, has opened up a rich pool of uncharacterized metabolic pathways, enzymes, and adaptations. This great untapped pool of genes provides the particularly exciting potential to mine for new biochemical activities or novel enzymes with activities tailored to peculiar sets of environmental conditions. Metagenomes also represent a huge reservoir of novel enzymes for applications in biocatalysis, biofuels, and bioremediation. Here we present the results of enzyme discovery for four enzyme activities, of particular industrial or environmental interest, including esterase/lipase, glycosyl hydrolase, protease and dehalogenase.

  18. Incorporation of UDPglucose into cell wall glucans and lipids by intact cotton fibers

    International Nuclear Information System (INIS)

    Dugger, W.M.; Palmer, R.L.

    1986-01-01

    The [ 14 C] moiety from [ 3 H]UDP[ 14 C]glucose was incorporated by intact cotton fibers into hot water soluble, acetic-nitric reagent soluble and insoluble components, and chloroform-methanol soluble lipids; the [ 3 H]UDP moiety was not incorporated. The 3 H-label can be exchanged rapidly with unlabeled substrate in a chase experiment. The cell wall apparent free space of cotton fibers was in the order of 30 picomoles per milligram of dry fibers; 25 picomoles per milligram easily exchanged and about 5 picomoles per milligram more tightly adsorbed. At 50 micromolar UDPglucose, 70% of the [ 14 C]glucose was found in the lipid fraction after both a short labeling period and chase. The percent of [ 14 C]glucose incorporated into total glucan increased within a 30-minute chase period. The data supports the concept that glucan synthesis, including cellulose, as well as the synthesis of steryl glucosides, acetylated steryl glucosides, and glucosyl-phosphoryl-polyprenol from externally supplied UDPglucose occurs at the plasma membrane-cell wall interface. The synthase enzymes for such synthesis must be part of this interfacial membrane system

  19. Effect of microbial enzyme allocation strategies on stoichiometry of soil organic matter (SOM) decomposition

    Science.gov (United States)

    Wutzler, Thomas

    2014-05-01

    We explored different strategies of soil microbial community to invest resources into extracellular enzymes by conceptual modelling. Similar to the EEZY model by Moorhead et al. (2012), microbial community can invest into two separate pools of enzymes that depolymerize two different SOM pools. We show that with assuming that a fixed fraction of substrate uptake is allocated to enzymes, the microbial dynamics decouples from decomposition dynamics. We propose an alternative formulation where investment into enzymes is proportional to microbial biomass. Next, we show that the strategy of optimizing stoichiometry of decomposition flux according to microbial biomass stoichiometry yield less microbial growth than the strategy of optimizing revenue of the currently limiting element. However, both strategies result in better usage of the resources, i.e. less C overflow or N mineralization, than the strategy of equal allocation to both enzymes. Further, we discuss effects of those strategies on decomposition of SOM and priming at different time scales and discuss several abstractions from the detailed model dynamics for usage in larger scale models.

  20. Model for incorporating fuel swelling and clad shrinkage effects in diffusion theory calculations (LWBR Development Program)

    International Nuclear Information System (INIS)

    Schick, W.C. Jr.; Milani, S.; Duncombe, E.

    1980-03-01

    A model has been devised for incorporating into the thermal feedback procedure of the PDQ few-group diffusion theory computer program the explicit calculation of depletion and temperature dependent fuel-rod shrinkage and swelling at each mesh point. The model determines the effect on reactivity of the change in hydrogen concentration caused by the variation in coolant channel area as the rods contract and expand. The calculation of fuel temperature, and hence of Doppler-broadened cross sections, is improved by correcting the heat transfer coefficient of the fuel-clad gap for the effects of clad creep, fuel densification and swelling, and release of fission-product gases into the gap. An approximate calculation of clad stress is also included in the model

  1. Radiation inactivation of multimeric enzymes: application to subunit interactions of adenylate cyclase

    International Nuclear Information System (INIS)

    Verkman, A.S.; Skorecki, K.L.; Ausiello, D.A.

    1986-01-01

    Radiation inactivation has been applied extensively to determine the molecular weight of soluble enzyme and receptor systems from the slope of a linear ln (activity) vs. dose curve. Complex nonlinear inactivation curves are predicted for multimeric enzyme systems, composed of distinct subunits in equilibrium with multimeric complexes. For the system A1 + A2----A1A2, with an active A1A2 complex (associative model), the ln (activity) vs. dose curve is linear for high dissociation constant, K. If a monomer, A1, has all the enzyme activity (dissociative model), the ln (activity) vs. dose curve has an activation hump at low radiation dose if the inactive subunit, A2, has a higher molecular weight than A1 and has upward concavity when A2 is smaller than A1. In general, a radiation inactivation model for a multistep mechanism for enzyme activation fulfills the characteristics of an associative or dissociative model if the reaction step forming active enzyme is an associative or dissociative reaction. Target theory gives the molecular weight of the active enzyme subunit or complex from the limiting slope of the ln (activity) vs. dose curve at high radiation dose. If energy transfer occurs among subunits in the multimer, the ln (activity) vs. dose curve is linear for a single active component and is concave upward for two or more active components. The use of radiation inactivation as a method to determine enzyme size and multimeric subunit assembly is discussed with specific application to the hormone-sensitive adenylate cyclase system. It is shown that the complex inactivation curves presented in the accompanying paper can be used select the best mechanism out of a series of seven proposed mechanisms for the activation of adenylate cyclase by hormone

  2. A three-parameter langmuir-type model for fitting standard curves of sandwich enzyme immunoassays with special attention to the α-fetoprotein assay

    NARCIS (Netherlands)

    Kortlandt, W.; Endeman, H.J.; Hoeke, J.O.O.

    In a simplified approach to the reaction kinetics of enzyme-linked immunoassays, a Langmuir-type equation y = [ax/(b + x)] + c was derived. This model proved to be superior to logit-log and semilog models in the curve-fitting of standard curves. An assay for α-fetoprotein developed in our laboratory

  3. Enzymes and Enzyme Activity Encoded by Nonenveloped Viruses.

    Science.gov (United States)

    Azad, Kimi; Banerjee, Manidipa; Johnson, John E

    2017-09-29

    Viruses are obligate intracellular parasites that rely on host cell machineries for their replication and survival. Although viruses tend to make optimal use of the host cell protein repertoire, they need to encode essential enzymatic or effector functions that may not be available or accessible in the host cellular milieu. The enzymes encoded by nonenveloped viruses-a group of viruses that lack any lipid coating or envelope-play vital roles in all the stages of the viral life cycle. This review summarizes the structural, biochemical, and mechanistic information available for several classes of enzymes and autocatalytic activity encoded by nonenveloped viruses. Advances in research and development of antiviral inhibitors targeting specific viral enzymes are also highlighted.

  4. A new general methodology for incorporating physico-chemical transformations into multi-phase wastewater treatment process models.

    Science.gov (United States)

    Lizarralde, I; Fernández-Arévalo, T; Brouckaert, C; Vanrolleghem, P; Ikumi, D S; Ekama, G A; Ayesa, E; Grau, P

    2015-05-01

    This paper introduces a new general methodology for incorporating physico-chemical and chemical transformations into multi-phase wastewater treatment process models in a systematic and rigorous way under a Plant-Wide modelling (PWM) framework. The methodology presented in this paper requires the selection of the relevant biochemical, chemical and physico-chemical transformations taking place and the definition of the mass transport for the co-existing phases. As an example a mathematical model has been constructed to describe a system for biological COD, nitrogen and phosphorus removal, liquid-gas transfer, precipitation processes, and chemical reactions. The capability of the model has been tested by comparing simulated and experimental results for a nutrient removal system with sludge digestion. Finally, a scenario analysis has been undertaken to show the potential of the obtained mathematical model to study phosphorus recovery. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Prediction of interindividual variation in drug plasma levels in vivo from individual enzyme kinetic data and physiologically based pharmacokinetic modeling

    NARCIS (Netherlands)

    Bogaards, J.J.P.; Hissink, E.M.; Briggs, M.; Weaver, R.; Jochemsen, R.; Jackson, P.; Bertrand, M.; Bladeren, P. van

    2000-01-01

    A strategy is presented to predict interindividual variation in drug plasma levels in vivo by the use of physiologically based pharmacokinetic modeling and human in vitro metabolic parameters, obtained through the combined use of microsomes containing single cytochrome P450 enzymes and a human liver

  6. A stochastic MILP energy planning model incorporating power market dynamics

    International Nuclear Information System (INIS)

    Koltsaklis, Nikolaos E.; Nazos, Konstantinos

    2017-01-01

    Highlights: •Stochastic MILP model for the optimal energy planning of a power system. •Power market dynamics (offers/bids) are incorporated in the proposed model. •Monte Carlo method for capturing the uncertainty of some key parameters. •Analytical supply cost composition per power producer and activity. •Clean dark and spark spreads are calculated for each power unit. -- Abstract: This paper presents an optimization-based methodological approach to address the problem of the optimal planning of a power system at an annual level in competitive and uncertain power markets. More specifically, a stochastic mixed integer linear programming model (MILP) has been developed, combining advanced optimization techniques with Monte Carlo method in order to deal with uncertainty issues. The main focus of the proposed framework is the dynamic formulation of the strategy followed by all market participants in volatile market conditions, as well as detailed economic assessment of the power system’s operation. The applicability of the proposed approach has been tested on a real case study of the interconnected Greek power system, quantifying in detail all the relevant technical and economic aspects of the system’s operation. The proposed work identifies in the form of probability distributions the optimal power generation mix, electricity trade at a regional level, carbon footprint, as well as detailed total supply cost composition, according to the assumed market structure. The paper demonstrates that the proposed optimization approach is able to provide important insights into the appropriate energy strategies designed by market participants, as well as on the strategic long-term decisions to be made by investors and/or policy makers at a national and/or regional level, underscoring potential risks and providing appropriate price signals on critical energy projects under real market operating conditions.

  7. Incorporation of the time aspect into the liability-threshold model for case-control-family data

    DEFF Research Database (Denmark)

    Cederkvist, Luise; Holst, Klaus K.; Andersen, Klaus K.

    2017-01-01

    to estimates that are difficult to interpret and are potentially biased. We incorporate the time aspect into the liability-threshold model for case-control-family data following the same approach that has been applied in the twin setting. Thus, the data are considered as arising from a competing risks setting...... approach using simulation studies and apply it in the analysis of two Danish register-based case-control-family studies: one on cancer diagnosed in childhood and adolescence, and one on early-onset breast cancer....

  8. Incorporation of /sup 14/C glucose into glycogen and glucose-6-phosphate dehydrogenase activity in rat brain following carbon monoxide intoxication

    Energy Technology Data Exchange (ETDEWEB)

    Sikorska, M; Gorzkowski, B; Szumanska, G; Smialek, M [Polska Akademia Nauk, Warsaw. Centrum Medycyny Doswiadczalnej i Klinicznej; Panstwowy Zaklad Higieny, Warsaw (Poland))

    1975-01-01

    Incorporation of /sup 14/C glucose into glycogen and glucose-6-phosphate dehydrogenase activity in rat brain following carbon monoxide intoxication was studied. In brains of rats tested on the 20, 30 and 60th minute of exposure to CO and immediately after removal from the chamber the enzyme activity showed no essential deviation from the control level. In the group of rats tested 1 hour after taking them out from the chamber increase of the enzyme activity was noticed, amounting to about 33% of the control value. The brains tested 24 hours after exposure showed the largest increase of the enzyme activity by about 94%. In the next time periods, 48 and 72 hours after intoxication, the enzyme activity was decreasing. The glycogen content in brains of control animals increased 3 hours after CO intoxication by about 69%. The increase of glycogen synthesis was expressed by increase of the total radioactivity, which amounted to 160% of the control value.

  9. Incorporating human-water dynamics in a hyper-resolution land surface model

    Science.gov (United States)

    Vergopolan, N.; Chaney, N.; Wanders, N.; Sheffield, J.; Wood, E. F.

    2017-12-01

    The increasing demand for water, energy, and food is leading to unsustainable groundwater and surface water exploitation. As a result, the human interactions with the environment, through alteration of land and water resources dynamics, need to be reflected in hydrologic and land surface models (LSMs). Advancements in representing human-water dynamics still leave challenges related to the lack of water use data, water allocation algorithms, and modeling scales. This leads to an over-simplistic representation of human water use in large-scale models; this is in turn leads to an inability to capture extreme events signatures and to provide reliable information at stakeholder-level spatial scales. The emergence of hyper-resolution models allows one to address these challenges by simulating the hydrological processes and interactions with the human impacts at field scales. We integrated human-water dynamics into HydroBlocks - a hyper-resolution, field-scale resolving LSM. HydroBlocks explicitly solves the field-scale spatial heterogeneity of land surface processes through interacting hydrologic response units (HRUs); and its HRU-based model parallelization allows computationally efficient long-term simulations as well as ensemble predictions. The implemented human-water dynamics include groundwater and surface water abstraction to meet agricultural, domestic and industrial water demands. Furthermore, a supply-demand water allocation scheme based on relative costs helps to determine sectoral water use requirements and tradeoffs. A set of HydroBlocks simulations over the Midwest United States (daily, at 30-m spatial resolution for 30 years) are used to quantify the irrigation impacts on water availability. The model captures large reductions in total soil moisture and water table levels, as well as spatiotemporal changes in evapotranspiration and runoff peaks, with their intensity related to the adopted water management strategy. By incorporating human-water dynamics in

  10. Incorporating social groups' responses in a descriptive model for second- and higher-order impact identification

    International Nuclear Information System (INIS)

    Sutheerawatthana, Pitch; Minato, Takayuki

    2010-01-01

    The response of a social group is a missing element in the formal impact assessment model. Previous discussion of the involvement of social groups in an intervention has mainly focused on the formation of the intervention. This article discusses the involvement of social groups in a different way. A descriptive model is proposed by incorporating a social group's response into the concept of second- and higher-order effects. The model is developed based on a cause-effect relationship through the observation of phenomena in case studies. The model clarifies the process by which social groups interact with a lower-order effect and then generate a higher-order effect in an iterative manner. This study classifies social groups' responses into three forms-opposing, modifying, and advantage-taking action-and places them in six pathways. The model is expected to be used as an analytical tool for investigating and identifying impacts in the planning stage and as a framework for monitoring social groups' responses during the implementation stage of a policy, plan, program, or project (PPPPs).

  11. Adapting capillary gel electrophoresis as a sensitive, high-throughput method to accelerate characterization of nucleic acid metabolic enzymes.

    Science.gov (United States)

    Greenough, Lucia; Schermerhorn, Kelly M; Mazzola, Laurie; Bybee, Joanna; Rivizzigno, Danielle; Cantin, Elizabeth; Slatko, Barton E; Gardner, Andrew F

    2016-01-29

    Detailed biochemical characterization of nucleic acid enzymes is fundamental to understanding nucleic acid metabolism, genome replication and repair. We report the development of a rapid, high-throughput fluorescence capillary gel electrophoresis method as an alternative to traditional polyacrylamide gel electrophoresis to characterize nucleic acid metabolic enzymes. The principles of assay design described here can be applied to nearly any enzyme system that acts on a fluorescently labeled oligonucleotide substrate. Herein, we describe several assays using this core capillary gel electrophoresis methodology to accelerate study of nucleic acid enzymes. First, assays were designed to examine DNA polymerase activities including nucleotide incorporation kinetics, strand displacement synthesis and 3'-5' exonuclease activity. Next, DNA repair activities of DNA ligase, flap endonuclease and RNase H2 were monitored. In addition, a multicolor assay that uses four different fluorescently labeled substrates in a single reaction was implemented to characterize GAN nuclease specificity. Finally, a dual-color fluorescence assay to monitor coupled enzyme reactions during Okazaki fragment maturation is described. These assays serve as a template to guide further technical development for enzyme characterization or nucleoside and non-nucleoside inhibitor screening in a high-throughput manner. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Thermodynamics of information processing based on enzyme kinetics: An exactly solvable model of an information pump

    Science.gov (United States)

    Cao, Yuansheng; Gong, Zongping; Quan, H. T.

    2015-06-01

    Motivated by the recent proposed models of the information engine [Proc. Natl. Acad. Sci. USA 109, 11641 (2012), 10.1073/pnas.1204263109] and the information refrigerator [Phys. Rev. Lett. 111, 030602 (2013), 10.1103/PhysRevLett.111.030602], we propose a minimal model of the information pump and the information eraser based on enzyme kinetics. This device can either pump molecules against the chemical potential gradient by consuming the information to be encoded in the bit stream or (partially) erase the information initially encoded in the bit stream by consuming the Gibbs free energy. The dynamics of this model is solved exactly, and the "phase diagram" of the operation regimes is determined. The efficiency and the power of the information machine is analyzed. The validity of the second law of thermodynamics within our model is clarified. Our model offers a simple paradigm for the investigating of the thermodynamics of information processing involving the chemical potential in small systems.

  13. The surface science of enzymes

    DEFF Research Database (Denmark)

    Rod, Thomas Holm; Nørskov, Jens Kehlet

    2002-01-01

    One of the largest challenges to science in the coming years is to find the relation between enzyme structure and function. Can we predict which reactions an enzyme catalyzes from knowledge of its structure-or from its amino acid sequence? Can we use that knowledge to modify enzyme function......? To solve these problems we must understand in some detail how enzymes interact with reactants from its surroundings. These interactions take place at the surface of the enzyme and the question of enzyme function can be viewed as the surface science of enzymes. In this article we discuss how to describe...... catalysis by enzymes, and in particular the analogies between enzyme catalyzed reactions and surface catalyzed reactions. We do this by discussing two concrete examples of reactions catalyzed both in nature (by enzymes) and in industrial reactors (by inorganic materials), and show that although analogies...

  14. Constraining Distributed Catchment Models by Incorporating Perceptual Understanding of Spatial Hydrologic Behaviour

    Science.gov (United States)

    Hutton, Christopher; Wagener, Thorsten; Freer, Jim; Han, Dawei

    2016-04-01

    Distributed models offer the potential to resolve catchment systems in more detail, and therefore simulate the hydrological impacts of spatial changes in catchment forcing (e.g. landscape change). Such models tend to contain a large number of poorly defined and spatially varying model parameters which are therefore computationally expensive to calibrate. Insufficient data can result in model parameter and structural equifinality, particularly when calibration is reliant on catchment outlet discharge behaviour alone. Evaluating spatial patterns of internal hydrological behaviour has the potential to reveal simulations that, whilst consistent with measured outlet discharge, are qualitatively dissimilar to our perceptual understanding of how the system should behave. We argue that such understanding, which may be derived from stakeholder knowledge across different catchments for certain process dynamics, is a valuable source of information to help reject non-behavioural models, and therefore identify feasible model structures and parameters. The challenge, however, is to convert different sources of often qualitative and/or semi-qualitative information into robust quantitative constraints of model states and fluxes, and combine these sources of information together to reject models within an efficient calibration framework. Here we present the development of a framework to incorporate different sources of data to efficiently calibrate distributed catchment models. For each source of information, an interval or inequality is used to define the behaviour of the catchment system. These intervals are then combined to produce a hyper-volume in state space, which is used to identify behavioural models. We apply the methodology to calibrate the Penn State Integrated Hydrological Model (PIHM) at the Wye catchment, Plynlimon, UK. Outlet discharge behaviour is successfully simulated when perceptual understanding of relative groundwater levels between lowland peat, upland peat

  15. Revealing hidden effect of earthworm on C distribution and enzyme activity

    Science.gov (United States)

    Razavi, Bahar S.; Hoang, Duyen; Kuzyakov, Yakov

    2017-04-01

    Despite its importance for terrestrial nutrient and carbon cycling, the spatial organization and localization of microbial activity in soil and in biopores is poorly understood. We hypothesized that biopores created by earthworm play a critical role in reducing the gap of SOM input and microbial activities between topsoil and subsoil. Accordingly, Carbon (C) allocation by earthworms was related to enzyme distribution along soil profile. For the first time we visualized spatial distribution of enzyme activities (β-glucosidase, chitinase and acid phosphatase) and C allocation (by 14C imaging) in earthworm biopores in topsoil and subsoil. Soil zymography (an in situ method for the analysis of the two-dimensional distribution of enzyme activity in soil) was accompanied with 14C imaging (a method that enables to trace distribution of litter and C in soil profile) to visualize change of enzyme activities along with SOM incorporation by earthworms from topsoil to subsoil. Experiment was set up acquiring rhizoboxes (9×1×50 cm) filled up with fresh soil and 3 earthworms (L. terrestris), which were then layered with 14C-labeled plant-litter of 0.3 MBq on the soil surface. 14C imaging and zymography have been carried out after one month. Activities of all enzymes regardless of their nutrient involvement (C, N, P) were higher in the biopores than in bulk soil, but the differences were larger in topsoil compared to subsoil. Among three enzymes, Phosphatase activity was 4-times higher in the biopore than in the bulk soil. Phosphatase activity was closely associated with edge of burrows and correlate positively with 14C activity. These results emphasized especial contribution of hotspheres such as biopores to C allocation in subsoil - which is limited in C input and nutrients - and in stimulation of microbial and enzymatic activity by input of organic residues, e.g. by earthworms. In conclusion, biopore increased enzymatic mobilization of nutrients (e.g. P) inducing allocation

  16. Magnetically responsive enzyme powders

    Energy Technology Data Exchange (ETDEWEB)

    Pospiskova, Kristyna, E-mail: kristyna.pospiskova@upol.cz [Regional Centre of Advanced Technologies and Materials, Palacky University, Slechtitelu 11, 783 71 Olomouc (Czech Republic); Safarik, Ivo, E-mail: ivosaf@yahoo.com [Regional Centre of Advanced Technologies and Materials, Palacky University, Slechtitelu 11, 783 71 Olomouc (Czech Republic); Department of Nanobiotechnology, Institute of Nanobiology and Structural Biology of GCRC, Na Sadkach 7, 370 05 Ceske Budejovice (Czech Republic)

    2015-04-15

    Powdered enzymes were transformed into their insoluble magnetic derivatives retaining their catalytic activity. Enzyme powders (e.g., trypsin and lipase) were suspended in various liquid media not allowing their solubilization (e.g., saturated ammonium sulfate and highly concentrated polyethylene glycol solutions, ethanol, methanol, 2-propanol) and subsequently cross-linked with glutaraldehyde. Magnetic modification was successfully performed at low temperature in a freezer (−20 °C) using magnetic iron oxides nano- and microparticles prepared by microwave-assisted synthesis from ferrous sulfate. Magnetized cross-linked enzyme powders were stable at least for two months in water suspension without leakage of fixed magnetic particles. Operational stability of magnetically responsive enzymes during eight repeated reaction cycles was generally without loss of enzyme activity. Separation of magnetically modified cross-linked powdered enzymes from reaction mixtures was significantly simplified due to their magnetic properties. - Highlights: • Cross-linked enzyme powders were prepared in various liquid media. • Insoluble enzymes were magnetized using iron oxides particles. • Magnetic iron oxides particles were prepared by microwave-assisted synthesis. • Magnetic modification was performed under low (freezing) temperature. • Cross-linked powdered trypsin and lipase can be used repeatedly for reaction.

  17. Enzymes in Fermented Fish.

    Science.gov (United States)

    Giyatmi; Irianto, H E

    Fermented fish products are very popular particularly in Southeast Asian countries. These products have unique characteristics, especially in terms of aroma, flavor, and texture developing during fermentation process. Proteolytic enzymes have a main role in hydrolyzing protein into simpler compounds. Fermentation process of fish relies both on naturally occurring enzymes (in the muscle or the intestinal tract) as well as bacteria. Fermented fish products processed using the whole fish show a different characteristic compared to those prepared from headed and gutted fish. Endogenous enzymes like trypsin, chymotrypsin, elastase, and aminopeptidase are the most involved in the fermentation process. Muscle tissue enzymes like cathepsins, peptidases, transaminases, amidases, amino acid decarboxylases, glutamic dehydrogenases, and related enzymes may also play a role in fish fermentation. Due to the decreased bacterial number during fermentation, contribution of microbial enzymes to proteolysis may be expected prior to salting of fish. Commercial enzymes are supplemented during processing for specific purposes, such as quality improvement and process acceleration. In the case of fish sauce, efforts to accelerate fermentation process and to improve product quality have been studied by addition of enzymes such as papain, bromelain, trypsin, pepsin, and chymotrypsin. © 2017 Elsevier Inc. All rights reserved.

  18. A model for determination of human foetus irradiation during intrauterine development when the mother incorporates iodine 131

    International Nuclear Information System (INIS)

    Vasilev, V.; Doncheva, B.

    1989-01-01

    A model is presented for irradiation calculation of human foetus during weeks 8-15 of the intrauterine development, when the mother chronically incorporates iodine 131. This period is critical for the nervous system of the foetus. Compared to some other author's models, the method proposed eliminates some uncertainties and takes into account the changes in the activity of mother's thyroid in time. The model is built on the base of data from 131 I-kinetics of pregnant women and experimental mice. A formula is proposed for total foetus irradiation calculation including: the internal γ and β irradiation; the external γ and β irradiation from the mother as a whole; and the external γ irradiation from the mother's thyroid

  19. Molecular view of the interaction between iota-carrageenan and a phospholipid film and its role in enzyme immobilization.

    Science.gov (United States)

    Nobre, Thatyane M; de Sousa e Silva, Heurison; Furriel, Rosa P M; Leone, Francisco A; Miranda, Paulo B; Zaniquelli, Maria Elisabete D

    2009-05-28

    Proteins incorporated into phospholipid Langmuir-Blodgett (LB) films are a good model system for biomembranes and enzyme immobilization studies. The specific fluidity of biomembranes, an important requisite for enzymatic activity, is naturally controlled by varying phospholipid compositions. In a model system, instead, LB film fluidity may be varied by covering the top layer with different substances able to interact simultaneously with the phospholipid and the protein to be immobilized. In this study, we immobilized a carbohydrate rich Neurospora crassa alkaline phosphatase (NCAP) in monolayers of the sodium salt of dihexadecylphosphoric acid (DHP), a synthetic phospholipid that provides very condensed Langmuir films. The binding of NCAP to DHP Langmuir-Blodgett (LB) films was mediated by the anionic polysaccharide iota-carrageenan (iota-car). Combining results from surface isotherms and the quartz crystal microbalance technique, we concluded that the polysaccharide was essential to promote the interaction between DHP and NCAP and also to increase the fluidity of the film. An estimate of DHP:iota-car ratio within the film also revealed that the polysaccharide binds to DHP LB film in an extended conformation. Furthermore, the investigation of the polysaccharide conformation at molecular level, using sum-frequency vibrational spectroscopy (SFG), indicated a preferential conformation of the carrageenan molecules with the sulfate groups oriented toward the phospholipid monolayer, and both the hydroxyl and ether groups interacting preferentially with the protein. These results demonstrate how interfacial electric fields can reorient and induce conformational changes in macromolecules, which may significantly affect intermolecular interactions at interfaces. This detailed knowledge of the interaction mechanism between the enzyme and the LB film is relevant to design strategies for enzyme immobilization when orientation and fluidity properties of the film provided by the

  20. Ribosomal incorporation of backbone modified amino acids via an editing-deficient aminoacyl-tRNA synthetase.

    Science.gov (United States)

    Iqbal, Emil S; Dods, Kara K; Hartman, Matthew C T

    2018-02-14

    The ability to incorporate non-canonical amino acids (ncAA) using translation offers researchers the ability to extend the functionality of proteins and peptides for many applications including synthetic biology, biophysical and structural studies, and discovery of novel ligands. Here we describe the high promiscuity of an editing-deficient valine-tRNA synthetase (ValRS T222P). Using this enzyme, we demonstrate ribosomal translation of 11 ncAAs including those with novel side chains, α,α-disubstitutions, and cyclic β-amino acids.

  1. Spinal motor control system incorporates an internal model of limb dynamics.

    Science.gov (United States)

    Shimansky, Y P

    2000-10-01

    The existence and utilization of an internal representation of the controlled object is one of the most important features of the functioning of neural motor control systems. This study demonstrates that this property already exists at the level of the spinal motor control system (SMCS), which is capable of generating motor patterns for reflex rhythmic movements, such as locomotion and scratching, without the aid of the peripheral afferent feedback, but substantially modifies the generated activity in response to peripheral afferent stimuli. The SMCS is presented as an optimal control system whose optimality requires that it incorporate an internal model (IM) of the controlled object's dynamics. A novel functional mechanism for the integration of peripheral sensory signals with the corresponding predictive output from the IM, the summation of information precision (SIP) is proposed. In contrast to other models in which the correction of the internal representation of the controlled object's state is based on the calculation of a mismatch between the internal and external information sources, the SIP mechanism merges the information from these sources in order to optimize the precision of the controlled object's state estimate. It is demonstrated, based on scratching in decerebrate cats as an example of the spinal control of goal-directed movements, that the results of computer modeling agree with the experimental observations related to the SMCS's reactions to phasic and tonic peripheral afferent stimuli. It is also shown that the functional requirements imposed by the mathematical model of the SMCS comply with the current knowledge about the related properties of spinal neuronal circuitry. The crucial role of the spinal presynaptic inhibition mechanism in the neuronal implementation of SIP is elucidated. Important differences between the IM and a state predictor employed for compensating for a neural reflex time delay are discussed.

  2. Profiling the orphan enzymes

    Science.gov (United States)

    2014-01-01

    The emergence of Next Generation Sequencing generates an incredible amount of sequence and great potential for new enzyme discovery. Despite this huge amount of data and the profusion of bioinformatic methods for function prediction, a large part of known enzyme activities is still lacking an associated protein sequence. These particular activities are called “orphan enzymes”. The present review proposes an update of previous surveys on orphan enzymes by mining the current content of public databases. While the percentage of orphan enzyme activities has decreased from 38% to 22% in ten years, there are still more than 1,000 orphans among the 5,000 entries of the Enzyme Commission (EC) classification. Taking into account all the reactions present in metabolic databases, this proportion dramatically increases to reach nearly 50% of orphans and many of them are not associated to a known pathway. We extended our survey to “local orphan enzymes” that are activities which have no representative sequence in a given clade, but have at least one in organisms belonging to other clades. We observe an important bias in Archaea and find that in general more than 30% of the EC activities have incomplete sequence information in at least one superkingdom. To estimate if candidate proteins for local orphans could be retrieved by homology search, we applied a simple strategy based on the PRIAM software and noticed that candidates may be proposed for an important fraction of local orphan enzymes. Finally, by studying relation between protein domains and catalyzed activities, it appears that newly discovered enzymes are mostly associated with already known enzyme domains. Thus, the exploration of the promiscuity and the multifunctional aspect of known enzyme families may solve part of the orphan enzyme issue. We conclude this review with a presentation of recent initiatives in finding proteins for orphan enzymes and in extending the enzyme world by the discovery of new

  3. Microbial Enzyme Activity and Carbon Cycling in Grassland Soil Fractions

    Science.gov (United States)

    Allison, S. D.; Jastrow, J. D.

    2004-12-01

    Extracellular enzymes are necessary to degrade complex organic compounds present in soils. Using physical fractionation procedures, we tested whether old soil carbon is spatially isolated from degradative enzymes across a prairie restoration chronosequence in Illinois, USA. We found that carbon-degrading enzymes were abundant in all soil fractions, including macroaggregates, microaggregates, and the clay fraction, which contains carbon with a mean residence time of ~200 years. The activities of two cellulose-degrading enzymes and a chitin-degrading enzyme were 2-10 times greater in organic matter fractions than in bulk soil, consistent with the rapid turnover of these fractions. Polyphenol oxidase activity was 3 times greater in the clay fraction than in the bulk soil, despite very slow carbon turnover in this fraction. Changes in enzyme activity across the restoration chronosequence were small once adjusted for increases in soil carbon concentration, although polyphenol oxidase activity per unit carbon declined by 50% in native prairie versus cultivated soil. These results are consistent with a `two-pool' model of enzyme and carbon turnover in grassland soils. In light organic matter fractions, enzyme production and carbon turnover both occur rapidly. However, in mineral-dominated fractions, both enzymes and their carbon substrates are immobilized on mineral surfaces, leading to slow turnover. Soil carbon accumulation in the clay fraction and across the prairie restoration chronosequence probably reflects increasing physical isolation of enzymes and substrates on the molecular scale, rather than the micron to millimeter scale.

  4. Modeling and simulation of enzymatic gluconic acid production using immobilized enzyme and CSTR-PFTR circulation reaction system.

    Science.gov (United States)

    Li, Can; Lin, Jianqun; Gao, Ling; Lin, Huibin; Lin, Jianqiang

    2018-04-01

    Production of gluconic acid by using immobilized enzyme and continuous stirred tank reactor-plug flow tubular reactor (CSTR-PFTR) circulation reaction system. A production system is constructed for gluconic acid production, which consists of a continuous stirred tank reactor (CSTR) for pH control and liquid storage and a plug flow tubular reactor (PFTR) filled with immobilized glucose oxidase (GOD) for gluconic acid production. Mathematical model is developed for this production system and simulation is made for the enzymatic reaction process. The pH inhibition effect on GOD is modeled by using a bell-type curve. Gluconic acid can be efficiently produced by using the reaction system and the mathematical model developed for this system can simulate and predict the process well.

  5. Effect of irradiation on immobilized enzymes compared with that on enzymes in solution

    International Nuclear Information System (INIS)

    Schachinger, L.; Schippel, C.; Altmann, E.; Diepold, B.; Yang, C.; Jaenike, M.; Hochhaeuser, E.

    1985-01-01

    Glucose oxidase and catalase were immobilized by attaching them to nylon fibers that had been treated with triethyloxonium-tetrafluoroborate, diaminohexane and glutaraldialdehyde according to Morris, Campell and Hornby (1975). This method assures that the enzymes are bound to a side chain of the polyamide structure. Enzyme activity (as measured by the O 2 -uptake and by microcalorimetry) was found to be unchanged after 2 years. The apparent Ksub(m)-constants of the immobilized enzymes with glucose were the same as those for enzymes in solution. GOD and catalase immobilized in poly(acrylamide) gel had the same Ksub(m)-value. Despite the high stability during storage, the radiation induced inactivation of enzymes immobilized on gel or chromosorb, an inorganic carrier, was of the same order of magnitude as that of the dissolved enzymes. The enzymes bound to nylon fibers showed a higher radiation sensitivity. This might have been caused by an additional attack on the binding site of the carrier. (orig.)

  6. Incorporation of Allium sativum in yogurt: In vitro study on inhibition of diabetes- and hypertension-associated enzymes

    Directory of Open Access Journals (Sweden)

    Shabboo Amirdivani Amirdivani

    2015-06-01

    Full Text Available The effects of inclusion of Allium sativum on yogurt formation and subsequent storage (4°C, up to 28 days on proteolysis, microbial activity, the inhibition of a-amylase, a-glucosidase and angiotensin-1 converting enzyme (ACE-1 in vitro were investigated. A. sativum-yogurt showed higher rates of pH reduction and increment of TA than plain-yogurt during incubation at 41°C. Highest proteolysis,  on day 7 showed in A. sativum-yogurt (62.7±0.80 mg/mL, which was 2-flod higher than plain yogurt (31.0±0.96 mg/mL. Bacterial counts in A.sativum-yogurt were higher for Lactobacillus spp. but lower for S. thermophillus (p<0.05 compared to those in plain yogurt throughout refrigerated storage. Highest inhibitory activities for α-amylase were recorded on day 14 of storage for A. sativum- and plain-yogurts (IC50= 13.7±1.99and 26.3±2.15mg respectively; p<0.05 and on day 7 for α-glucosidase (IC50= 120.7±22.71 and 192.3±33.24mg respectively; p<0.05. The highest anti-ACE-I activity was observed on day 7 of refrigerated storage with A. sativum-yogurt (IC50=6.9±0.23mg being more potent than plain-yogurt (IC50=9.7±0.12mg; p<0.05. A. sativum-yogurt was not favoured for overall aroma, sourness and bitterness in the sensory evaluations but recorded the same overall preference as plain yogurt. A. sativum enhanced the fermentation of yogurt in favour of the population of Lactobacillus spp, stimulated proteolysis of milk proteins and increased the in vitro inhibition of key enzymes associated with diabetes and hypertension.

  7. An investigation into the applicability of the semiempirical method PM7 for modeling the catalytic mechanism in the enzyme chymotrypsin.

    Science.gov (United States)

    Stewart, James J P

    2017-05-01

    The catalytic cycle for the serine protease α-chymotrypsin was investigated in an attempt to determine the suitability of using the semiempirical method PM7 in the program MOPAC for investigating enzyme-catalyzed reactions. All six classical intermediates were modeled using standard methods, and were characterized as stable minima on the potential energy surface. Using a modified saddle point optimization method, five transition states were located and verified both by vibrational and by intrinsic reaction coordinate analysis. Some individual features, such as the hydrogen bonds in the oxyanion hole, the nature of various electrostatic interactions, and the role of Met192, were examined. This involved designing and running computational experiments to model mutations that would allow features of interest, in particular the energies involved, to be isolated. Three features within the enzyme were examined in detail: the reaction site itself, where covalent bonds were made and broken, the electrostatic effects of the buried aspartate anion, a passive but essential component of the catalytic triad, and the oxyanion hole, where hydrogen bonds help stabilize charged intermediates. With one minor exception, all phenomena investigated agreed with previously-reported descriptions. This result, along with the fact that all the techniques used were relatively straightforward, leads to the recommendation that PM7 and related methods, such as PM6-D3H4, are appropriate for modeling similar enzyme-catalyzed reactions. Graphical abstract Fifth of six transition states, showing water splitting into hydroxyl anion and a proton, to form the second tetrahedral intermediate and histidinium ion. Atoms of the water molecule involved in the hydrolysis are indicated by halos.

  8. Direct Electron Transfer of Enzymes in a Biologically Assembled Conductive Nanomesh Enzyme Platform.

    Science.gov (United States)

    Lee, Seung-Woo; Lee, Ki-Young; Song, Yong-Won; Choi, Won Kook; Chang, Joonyeon; Yi, Hyunjung

    2016-02-24

    Nondestructive assembly of a nanostructured enzyme platform is developed in combination of the specific biomolecular attraction and electrostatic coupling for highly efficient direct electron transfer (DET) of enzymes with unprecedented applicability and versatility. The biologically assembled conductive nanomesh enzyme platform enables DET-based flexible integrated biosensors and DET of eight different enzyme with various catalytic activities. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Diversity of beetle genes encoding novel plant cell wall degrading enzymes.

    Directory of Open Access Journals (Sweden)

    Yannick Pauchet

    Full Text Available Plant cell walls are a heterogeneous mixture of polysaccharides and proteins that require a range of different enzymes to degrade them. Plant cell walls are also the primary source of cellulose, the most abundant and useful biopolymer on the planet. Plant cell wall degrading enzymes (PCWDEs are therefore important in a wide range of biotechnological processes from the production of biofuels and food to waste processing. However, despite the fact that the last common ancestor of all deuterostomes was inferred to be able to digest, or even synthesize, cellulose using endogenous genes, all model insects whose complete genomes have been sequenced lack genes encoding such enzymes. To establish if the apparent "disappearance" of PCWDEs from insects is simply a sampling problem, we used 454 mediated pyrosequencing to scan the gut transcriptomes of beetles that feed on a variety of plant derived diets. By sequencing the transcriptome of five beetles, and surveying publicly available ESTs, we describe 167 new beetle PCWDEs belonging to eight different enzyme families. This survey proves that these enzymes are not only present in non-model insects but that the multigene families that encode them are apparently undergoing complex birth-death dynamics. This reinforces the observation that insects themselves, and not just their microbial symbionts, are a rich source of PCWDEs. Further it emphasises that the apparent absence of genes encoding PCWDEs from model organisms is indeed simply a sampling artefact. Given the huge diversity of beetles alive today, and the diversity of their lifestyles and diets, we predict that beetle guts will emerge as an important new source of enzymes for use in biotechnology.

  10. Using enzyme folding to explore the mechanism of therapeutic touch: a feasibility study.

    Science.gov (United States)

    Strickland, Mallory L; Boylan, Helen M

    2010-07-01

    The goal of this research is to design a novel model using protein folding to study Therapeutic Touch, a noncontact form of energy manipulation healing. Presented is a feasibility study suggesting that the denaturation path of ribonuclease A may be a useful model to study the energy exchange underlying therapeutic touch. The folding of ribonuclease A serves as a controlled energy-requiring system in which energy manipulation can be measured by the degree of folding achieved. A kinetic assay and fluorescence spectroscopy are used to assess the enzyme-folding state. The data suggest that the kinetic assay is a useful means of assessing the degree of refolding, and specifically, the enzyme function. However, fluorescence spectroscopy was not shown to be an effective measurement of enzyme structure for the purposes of this work. More research is needed to assess the underlying mechanism of therapeutic touch to complement the existing studies. An enzyme-folding model may provide a useful means of studying the energy exchange in therapeutic touch.

  11. Enzymes for improved biomass conversion

    Science.gov (United States)

    Brunecky, Roman; Himmel, Michael E.

    2016-02-02

    Disclosed herein are enzymes and combinations of the enzymes useful for the hydrolysis of cellulose and the conversion of biomass. Methods of degrading cellulose and biomass using enzymes and cocktails of enzymes are also disclosed.

  12. Effects of commercial pectolytic and cellulolytic enzyme preparations on the apple cell wall.

    Science.gov (United States)

    Dongowski, G; Sembries, S

    2001-09-01

    The action of three different commercial enzyme combinations on apple cell wall material has been examined in a model system under conditions of mash and pomace treatment by using an alcohol-insoluble substance prepared from apples. A part of the total dietary fiber, for example, galacturonan (pectin), appeared in the soluble fraction after enzymatic mash treatment. The soluble fraction increased intensely during pomace treatment. Furthermore, enzyme actions caused a change in the water-binding capacity of residues as well as changes in the monosaccharide composition and in the molecular weight distribution of saccharides in filtrates (soluble parts). The extent of decomposition of cell wall material and the increase of soluble oligomeric and/or polymeric dietary fiber components are caused by both the composition (pectinases, cellulases, and hemicellulases) and the activities of the enzyme preparations. The model experiments allow an insight into the reactions occurring during enzyme action on the plant cell wall, for example, during apple juice production using pectolytic and cellulolytic enzyme preparations.

  13. New CNT/poly(brilliant green) and CNT/poly(3,4-ethylenedioxythiophene) based electrochemical enzyme biosensors.

    Science.gov (United States)

    Barsan, Madalina M; Pifferi, Valentina; Falciola, Luigi; Brett, Christopher M A

    2016-07-13

    A combination of the electroactive polymer poly(brilliant green) (PBG) or conducting polymer poly(3,4-ethylenedioxythiophene) (PEDOT) with carbon nanotubes to obtain CNT/PBG and CNT/PEDOT modified carbon film electrodes (CFE) has been investigated as a new biosensor platform, incorporating the enzymes glucose oxidase (GOx) as test enzyme, alcohol oxidase (AlcOx) or alcohol dehydrogenase (AlcDH). The sensing parameters were optimized for all biosensors based on CNT/PBG/CFE, CNT/PEDOT/CFE platforms. Under optimized conditions, both GOx biosensors exhibited very similar sensitivities, while in the case of AlcOx and AlcDH biosensors, AlcOx/CNT/PBG/CFE was found to give a higher sensitivity and lower detection limit. The influence of dissolved O2 on oxidase-biosensor performance was investigated and was shown to be different for each enzyme. Comparisons were made with similar reported biosensors, showing the advantages of the new biosensors, and excellent selectivity against potential interferents was successfully demonstrated. Finally, alcohol biosensors were successfully used for the determination of ethanol in alcoholic beverages. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Model based design of biochemical micro-reactors

    Directory of Open Access Journals (Sweden)

    Tobias eElbinger

    2016-02-01

    Full Text Available Mathematical modelling of biochemical pathways is an important resource in Synthetic Biology, as the predictive power of simulating synthetic pathways represents an important step in the design of synthetic metabolons. In this paper, we are concerned with the mathematical modeling, simulation and optimization of metabolic processes in biochemical micro-reactors able to carry out enzymatic reactions and to exchange metabolites with their surrounding medium. The results of the reported modeling approach are incorporated in the design of the first micro-reactor prototypes that are under construction. These microreactors consist of compartments separated by membranes carrying specific transporters for the input of substrates and export of products. Inside the compartments multi-enzyme complexes assembled on nano-beads by peptide adapters are used to carry out metabolic reactions.The spatially resolved mathematical model describing the ongoing processes consists of a system of diffusion equations together with boundary and initial conditions. The boundary conditions model the exchange of metabolites with the neighboring compartments and the reactions at the surface of the nano-beads carrying the multi-enzyme complexes. Efficient and accurate approaches for numerical simulation of the mathematical model and for optimal design of the micro-reactor are developed. As a proof-of-concept scenario, a synthetic pathway for the conversion of sucrose to glucose-6-phosphate (G6P was chosen. In this context, the mathematical model is employed to compute the spatio-temporal distributions of the metabolite concentrations, as well as application relevant quantities like the outflow rate of G6P. These computations are performed for different scenarios, where the number of beads as well as their loading capacity are varied. The computed metabolite distributions show spatial patterns which differ for different experimental arrangements. Furthermore, the total output

  15. Incorporating teleconnection information into reservoir operating policies using Stochastic Dynamic Programming and a Hidden Markov Model

    Science.gov (United States)

    Turner, Sean; Galelli, Stefano; Wilcox, Karen

    2015-04-01

    Water reservoir systems are often affected by recurring large-scale ocean-atmospheric anomalies, known as teleconnections, that cause prolonged periods of climatological drought. Accurate forecasts of these events -- at lead times in the order of weeks and months -- may enable reservoir operators to take more effective release decisions to improve the performance of their systems. In practice this might mean a more reliable water supply system, a more profitable hydropower plant or a more sustainable environmental release policy. To this end, climate indices, which represent the oscillation of the ocean-atmospheric system, might be gainfully employed within reservoir operating models that adapt the reservoir operation as a function of the climate condition. This study develops a Stochastic Dynamic Programming (SDP) approach that can incorporate climate indices using a Hidden Markov Model. The model simulates the climatic regime as a hidden state following a Markov chain, with the state transitions driven by variation in climatic indices, such as the Southern Oscillation Index. Time series analysis of recorded streamflow data reveals the parameters of separate autoregressive models that describe the inflow to the reservoir under three representative climate states ("normal", "wet", "dry"). These models then define inflow transition probabilities for use in a classic SDP approach. The key advantage of the Hidden Markov Model is that it allows conditioning the operating policy not only on the reservoir storage and the antecedent inflow, but also on the climate condition, thus potentially allowing adaptability to a broader range of climate conditions. In practice, the reservoir operator would effect a water release tailored to a specific climate state based on available teleconnection data and forecasts. The approach is demonstrated on the operation of a realistic, stylised water reservoir with carry-over capacity in South-East Australia. Here teleconnections relating

  16. Kinetic modeling of cellulosic biomass to ethanol via simultaneous saccharification and fermentation: Part I. Accommodation of intermittent feeding and analysis of staged reactors.

    Science.gov (United States)

    Shao, Xiongjun; Lynd, Lee; Wyman, Charles; Bakker, André

    2009-01-01

    The model of South et al. [South et al. (1995) Enzyme Microb Technol 17(9): 797-803] for simultaneous saccharification of fermentation of cellulosic biomass is extended and modified to accommodate intermittent feeding of substrate and enzyme, cascade reactor configurations, and to be more computationally efficient. A dynamic enzyme adsorption model is found to be much more computationally efficient than the equilibrium model used previously, thus increasing the feasibility of incorporating the kinetic model in a computational fluid dynamic framework in the future. For continuous or discretely fed reactors, it is necessary to use particle conversion in conversion-dependent hydrolysis rate laws rather than reactor conversion. Whereas reactor conversion decreases due to both reaction and exit of particles from the reactor, particle conversion decreases due to reaction only. Using the modified models, it is predicted that cellulose conversion increases with decreasing feeding frequency (feedings per residence time, f). A computationally efficient strategy for modeling cascade reactors involving a modified rate constant is shown to give equivalent results relative to an exhaustive approach considering the distribution of particles in each successive fermenter.

  17. Incorporation of defects into the central atoms model of a metallic glass

    International Nuclear Information System (INIS)

    Lass, Eric A.; Zhu Aiwu; Shiflet, G.J.; Joseph Poon, S.

    2011-01-01

    The central atoms model (CAM) of a metallic glass is extended to incorporate thermodynamically stable defects, similar to vacancies in a crystalline solid, within the amorphous structure. A bond deficiency (BD), which is the proposed defect present in all metallic glasses, is introduced into the CAM equations. Like vacancies in a crystalline solid, BDs are thermodynamically stable entities because of the increase in entropy associated with their creation, and there is an equilibrium concentration present in the glassy phase. When applied to Cu-Zr and Ni-Zr binary metallic glasses, the concentration of thermally induced BDs surrounding Zr atoms reaches a relatively constant value at the glass transition temperature, regardless of composition within a given glass system. Using this 'critical' defect concentration, the predicted temperatures at which the glass transition is expected to occur are in good agreement with the experimentally determined glass transition temperatures for both alloy systems.

  18. Incorporating plant fossil data into species distribution models is not straightforward: Pitfalls and possible solutions

    Science.gov (United States)

    Moreno-Amat, Elena; Rubiales, Juan Manuel; Morales-Molino, César; García-Amorena, Ignacio

    2017-08-01

    The increasing development of species distribution models (SDMs) using palaeodata has created new prospects to address questions of evolution, ecology and biogeography from wider perspectives. Palaeobotanical data provide information on the past distribution of taxa at a given time and place and its incorporation on modelling has contributed to advancing the SDM field. This has allowed, for example, to calibrate models under past climate conditions or to validate projected models calibrated on current species distributions. However, these data also bear certain shortcomings when used in SDMs that may hinder the resulting ecological outcomes and eventually lead to misleading conclusions. Palaeodata may not be equivalent to present data, but instead frequently exhibit limitations and biases regarding species representation, taxonomy and chronological control, and their inclusion in SDMs should be carefully assessed. The limitations of palaeobotanical data applied to SDM studies are infrequently discussed and often neglected in the modelling literature; thus, we argue for the more careful selection and control of these data. We encourage authors to use palaeobotanical data in their SDMs studies and for doing so, we propose some recommendations to improve the robustness, reliability and significance of palaeo-SDM analyses.

  19. Affordances perspective and grammaticalization: Incorporation of language, environment and users in the model of semantic paths

    Directory of Open Access Journals (Sweden)

    Alexander Andrason

    2015-12-01

    Full Text Available The present paper demonstrates that insights from the affordances perspective can contribute to developing a more comprehensive model of grammaticalization. The authors argue that the grammaticalization process is afforded differently depending on the values of three contributing parameters: the factor (schematized as a qualitative-quantitative map or a wave of a gram, environment (understood as the structure of the stream along which the gram travels, and actor (narrowed to certain cognitive-epistemological capacities of the users, in particular to the fact of being a native speaker. By relating grammaticalization to these three parameters and by connecting it to the theory of optimization, the proposed model offers a better approximation to realistic cases of grammaticalization: The actor and environment are overtly incorporated into the model and divergences from canonical grammaticalization paths are both tolerated and explicable.

  20. Nonnatural amino acid incorporation into the methionine 214 position of the metzincin Pseudomonas aeruginosa alkaline protease

    Directory of Open Access Journals (Sweden)

    Honek John F

    2005-10-01

    Full Text Available Abstract Background The alkaline protease from Pseudomonas aeruginosa (AprA is a member of the metzincin superfamily of metalloendoproteases. A key feature of these proteases is a conserved methionine-containing 1,4-tight β turn at the base of the active site zinc binding region. Results To explore the invariant methionine position in this class of protease, incorporation of a nonnatural fluorinated methionine, L-difluoromethionine (DFM, into this site was accomplished. Although overproduction of the N-terminal catalytic fragment of AprA resulted in protein aggregates which could not be resolved, successful heterologous production of the entire AprA was accomplished in the presence and absence of the nonnatural amino acid. DFM incorporation was found to only slightly alter the enzyme kinetics of AprA. In addition, differential scanning calorimetry indicated no significant alteration in the thermal stability of the modified enzyme. Conclusion Although invariant in all metzincin proteases, the methionine 214 position in AprA can be successfully replaced by the nonnatural amino acid DFM resulting in little effect on protein structure and function. This study indicates that the increased size of the methyl group by the introduction of two fluorines is still sufficiently non-sterically demanding, and bodes well for the application of DFM to biophysical studies of protein structure and function in this class of protease.

  1. Nonnatural amino acid incorporation into the methionine 214 position of the metzincin Pseudomonas aeruginosa alkaline protease

    Science.gov (United States)

    Walasek, Paula; Honek, John F

    2005-01-01

    Background The alkaline protease from Pseudomonas aeruginosa (AprA) is a member of the metzincin superfamily of metalloendoproteases. A key feature of these proteases is a conserved methionine-containing 1,4-tight β turn at the base of the active site zinc binding region. Results To explore the invariant methionine position in this class of protease, incorporation of a nonnatural fluorinated methionine, L-difluoromethionine (DFM), into this site was accomplished. Although overproduction of the N-terminal catalytic fragment of AprA resulted in protein aggregates which could not be resolved, successful heterologous production of the entire AprA was accomplished in the presence and absence of the nonnatural amino acid. DFM incorporation was found to only slightly alter the enzyme kinetics of AprA. In addition, differential scanning calorimetry indicated no significant alteration in the thermal stability of the modified enzyme. Conclusion Although invariant in all metzincin proteases, the methionine 214 position in AprA can be successfully replaced by the nonnatural amino acid DFM resulting in little effect on protein structure and function. This study indicates that the increased size of the methyl group by the introduction of two fluorines is still sufficiently non-sterically demanding, and bodes well for the application of DFM to biophysical studies of protein structure and function in this class of protease. PMID:16221305

  2. An overview of technologies for immobilization of enzymes and surface analysis techniques for immobilized enzymes

    Science.gov (United States)

    Mohamad, Nur Royhaila; Marzuki, Nur Haziqah Che; Buang, Nor Aziah; Huyop, Fahrul; Wahab, Roswanira Abdul

    2015-01-01

    The current demands of sustainable green methodologies have increased the use of enzymatic technology in industrial processes. Employment of enzyme as biocatalysts offers the benefits of mild reaction conditions, biodegradability and catalytic efficiency. The harsh conditions of industrial processes, however, increase propensity of enzyme destabilization, shortening their industrial lifespan. Consequently, the technology of enzyme immobilization provides an effective means to circumvent these concerns by enhancing enzyme catalytic properties and also simplify downstream processing and improve operational stability. There are several techniques used to immobilize the enzymes onto supports which range from reversible physical adsorption and ionic linkages, to the irreversible stable covalent bonds. Such techniques produce immobilized enzymes of varying stability due to changes in the surface microenvironment and degree of multipoint attachment. Hence, it is mandatory to obtain information about the structure of the enzyme protein following interaction with the support surface as well as interactions of the enzymes with other proteins. Characterization technologies at the nanoscale level to study enzymes immobilized on surfaces are crucial to obtain valuable qualitative and quantitative information, including morphological visualization of the immobilized enzymes. These technologies are pertinent to assess efficacy of an immobilization technique and development of future enzyme immobilization strategies. PMID:26019635

  3. Sensitizing effect of Z,Z-bilirubin IXα and its photoproducts on enzymes in model solutions

    Science.gov (United States)

    Plavskii, V. Yu.; Mostovnikov, V. A.; Tret'yakova, A. I.; Mostovnikova, G. R.

    2008-05-01

    In model systems, we have studied side effects which may be induced by light during phototherapy of hyperbilirubinemia (jaundice) in newborn infants, with the aim of reducing the Z,Z-bilirubin IXα (Z,Z-BR IXα) level. We have shown that the sensitizing effect of Z,Z-BR IXα, localized at strong binding sites of the human serum albumin (HSA) macromolecule, is primarily directed at the amino acid residues of the carrier protein and does not involve the molecules of the enzyme (lactate dehydrogenase (LDH)) present in the buffer solution. The detected photodynamic damage to LDH is due to sensitization by bilirubin photoisomers, characterized by lower HSA association constants and located (in contrast to native Z,Z-BR IXα) on the surface of the HSA protein globule. Based on study of the spectral characteristics of the photoproducts of Z,Z-BR IXα and comparison of their accumulation kinetics in solution and the enzyme photo-inactivation kinetics, we concluded that the determining role in sensitized damage to LDH is played by lumirubin. The photosensitization effect depends on the wavelength of the radiation used for photoconversion of bilirubin. When (at the beginning of exposure) we make sure that identical numbers of photons are absorbed by the pigment in the different spectral ranges, the side effect is minimal for radiation corresponding to the long-wavelength edge of the bilirubin absorption band. We have shown that for a bilirubin/HSA concentration ratio >2 (when some of the pigment molecules are sorbed on the surface of the protein globule), the bilirubin can act as a photosensitizing agent for the enzyme present in solution. We discuss methods for reducing unfavorable side effects of light on the body of newborn infants during phototherapy of hyperbilirubinemia.

  4. Enzyme inhibition by iminosugars

    DEFF Research Database (Denmark)

    López, Óscar; Qing, Feng-Ling; Pedersen, Christian Marcus

    2013-01-01

    Imino- and azasugar glycosidase inhibitors display pH dependant inhibition reflecting that both the inhibitor and the enzyme active site have groups that change protonation state with pH. With the enzyme having two acidic groups and the inhibitor one basic group, enzyme-inhibitor complexes...

  5. Targeted enzyme prodrug therapies.

    Science.gov (United States)

    Schellmann, N; Deckert, P M; Bachran, D; Fuchs, H; Bachran, C

    2010-09-01

    The cure of cancer is still a formidable challenge in medical science. Long-known modalities including surgery, chemotherapy and radiotherapy are successful in a number of cases; however, invasive, metastasized and inaccessible tumors still pose an unresolved and ongoing problem. Targeted therapies designed to locate, detect and specifically kill tumor cells have been developed in the past three decades as an alternative to treat troublesome cancers. Most of these therapies are either based on antibody-dependent cellular cytotoxicity, targeted delivery of cytotoxic drugs or tumor site-specific activation of prodrugs. The latter is a two-step procedure. In the first step, a selected enzyme is accumulated in the tumor by guiding the enzyme or its gene to the neoplastic cells. In the second step, a harmless prodrug is applied and specifically converted by this enzyme into a cytotoxic drug only at the tumor site. A number of targeting systems, enzymes and prodrugs were investigated and improved since the concept was first envisioned in 1974. This review presents a concise overview on the history and latest developments in targeted therapies for cancer treatment. We cover the relevant technologies such as antibody-directed enzyme prodrug therapy (ADEPT), gene-directed enzyme prodrug therapy (GDEPT) as well as related therapies such as clostridial- (CDEPT) and polymer-directed enzyme prodrug therapy (PDEPT) with emphasis on prodrug-converting enzymes, prodrugs and drugs.

  6. Immobilized enzymes in blood plasma exchangers via radiation grafting

    Science.gov (United States)

    Gombotz, Wayne; Hoffman, Allan; Schmer, Gottfried; Uenoyama, Satoshi

    The enzyme asparaginase was immobilized onto a porous hollow polypropylene (PP) fiber blood plasma exchange device for the treatment of acute lymphocytic leukemia. The devices were first radiation grafted with polymethacrylic acid (poly(MAAc)). This introduces carboxyl groups onto the surface of the fibers. Several variables were studied in the grafting reaction including the effects of solvent type and monomer concentration. The carboxyl groups were activated with N-hydroxy succinimide (NHS) using carbodiimide chemistry. Asparaginase was then covalently immobilized on the activated surfaces. Quantitative relationships were found relating the percent graft to the amount of immobilized enzyme which was active. The enzyme reactor was tested both in vitro and in vivo using a sheep as an animal model.

  7. The biokinetic of incorporates radionuclides; Die Biokinetik von inkorporierten Radionukliden

    Energy Technology Data Exchange (ETDEWEB)

    Breustedt, Bastian [Karlsruher Institut fuer Technologie (KIT), Eggenstein-Leopoldshafen (Germany). Inst. fuer Strahlenforschung; Giussani, Augusto [Bundesamt fuer Strahlenschutz, Oberschleissheim (Germany). Arbeitsgruppe ' ' Externe und interne Dosimetrie, Biokinetik' '

    2017-08-01

    Incorporated radionuclides from nuclear accidents, fission product releases or nuclear medical administration are distributed in the human body in organs and tissue, absorbed 9or excreted. The interpretation of incorporation monitoring results and the estimation of the internal doses that cannot be measured directly need mathematical methods and the formulation of biokinetic models.

  8. Incorporation of Damage and Failure into an Orthotropic Elasto-Plastic Three-Dimensional Model with Tabulated Input Suitable for Use in Composite Impact Problems

    Science.gov (United States)

    Goldberg, Robert K.; Carney, Kelly S.; Dubois, Paul; Hoffarth, Canio; Khaled, Bilal; Rajan, Subramaniam; Blankenhorn, Gunther

    2016-01-01

    A material model which incorporates several key capabilities which have been identified by the aerospace community as lacking in the composite impact models currently available in LS-DYNA(Registered Trademark) is under development. In particular, the material model, which is being implemented as MAT 213 into a tailored version of LS-DYNA being jointly developed by the FAA and NASA, incorporates both plasticity and damage within the material model, utilizes experimentally based tabulated input to define the evolution of plasticity and damage as opposed to specifying discrete input parameters (such as modulus and strength), and is able to analyze the response of composites composed with a variety of fiber architectures. The plasticity portion of the orthotropic, three-dimensional, macroscopic composite constitutive model is based on an extension of the Tsai-Wu composite failure model into a generalized yield function with a non-associative flow rule. The capability to account for the rate and temperature dependent deformation response of composites has also been incorporated into the material model. For the damage model, a strain equivalent formulation is utilized to allow for the uncoupling of the deformation and damage analyses. In the damage model, a diagonal damage tensor is defined to account for the directionally dependent variation of damage. However, in composites it has been found that loading in one direction can lead to damage in multiple coordinate directions. To account for this phenomena, the terms in the damage matrix are semi-coupled such that the damage in a particular coordinate direction is a function of the stresses and plastic strains in all of the coordinate directions. The onset of material failure, and thus element deletion, is being developed to be a function of the stresses and plastic strains in the various coordinate directions. Systematic procedures are being developed to generate the required input parameters based on the results of

  9. A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function.

    Science.gov (United States)

    Lai, Jason; Jin, Jing; Kubelka, Jan; Liberles, David A

    2012-09-21

    Since the dynamic nature of protein structures is essential for enzymatic function, it is expected that functional evolution can be inferred from the changes in protein dynamics. However, dynamics can also diverge neutrally with sequence substitution between enzymes without changes of function. In this study, a phylogenetic approach is implemented to explore the relationship between enzyme dynamics and function through evolutionary history. Protein dynamics are described by normal mode analysis based on a simplified harmonic potential force field applied to the reduced C(α) representation of the protein structure while enzymatic function is described by Enzyme Commission numbers. Similarity of the binding pocket dynamics at each branch of the protein family's phylogeny was analyzed in two ways: (1) explicitly by quantifying the normal mode overlap calculated for the reconstructed ancestral proteins at each end and (2) implicitly using a diffusion model to obtain the reconstructed lineage-specific changes in the normal modes. Both explicit and implicit ancestral reconstruction identified generally faster rates of change in dynamics compared with the expected change from neutral evolution at the branches of potential functional divergences for the α-amylase, D-isomer-specific 2-hydroxyacid dehydrogenase, and copper-containing amine oxidase protein families. Normal mode analysis added additional information over just comparing the RMSD of static structures. However, the branch-specific changes were not statistically significant compared to background function-independent neutral rates of change of dynamic properties and blind application of the analysis would not enable prediction of changes in enzyme specificity. Copyright © 2012 Elsevier Ltd. All rights reserved.

  10. Enzyme-MOF (metal-organic framework) composites.

    Science.gov (United States)

    Lian, Xizhen; Fang, Yu; Joseph, Elizabeth; Wang, Qi; Li, Jialuo; Banerjee, Sayan; Lollar, Christina; Wang, Xuan; Zhou, Hong-Cai

    2017-06-06

    The ex vivo application of enzymes in various processes, especially via enzyme immobilization techniques, has been extensively studied in recent years in order to enhance the recyclability of enzymes, to minimize enzyme contamination in the product, and to explore novel horizons for enzymes in biomedical applications. Possessing remarkable amenability in structural design of the frameworks as well as almost unparalelled surface tunability, Metal-Organic Frameworks (MOFs) have been gaining popularity as candidates for enzyme immobilization platforms. Many MOF-enzyme composites have achieved unprecedented results, far outperforming free enzymes in many aspects. This review summarizes recent developments of MOF-enzyme composites with special emphasis on preparative techniques and the synergistic effects of enzymes and MOFs. The applications of MOF-enzyme composites, primarily in transferation, catalysis and sensing, are presented as well. The enhancement of enzymatic activity of the composites over free enzymes in biologically incompatible conditions is emphasized in many cases.

  11. Modeling of growth and laccase production by Pycnoporus sanguineus.

    Science.gov (United States)

    Saat, Muhammad Naziz; Annuar, Mohamad Suffian Mohamad; Alias, Zazali; Chuan, Ling Tau; Chisti, Yusuf

    2014-05-01

    Production of extracellular laccase by the white-rot fungus Pycnoporus sanguineus was examined in batch submerged cultures in shake flasks, baffled shake flasks and a stirred tank bioreactor. The biomass growth in the various culture systems closely followed a logistic growth model. The production of laccase followed a Luedeking-Piret model. A modified Luedeking-Piret model incorporating logistic growth effectively described the consumption of glucose. Biomass productivity, enzyme productivity and substrate consumption were enhanced in baffled shake flasks relative to the cases for the conventional shake flasks. This was associated with improved oxygen transfer in the presence of the baffles. The best results were obtained in the stirred tank bioreactor. At 28 °C, pH 4.5, an agitation speed of 600 rpm and a dissolved oxygen concentration of ~25 % of air saturation, the laccase productivity in the bioreactor exceeded 19 U L(-1 )days(-1), or 1.5-fold better than the best case for the baffled shake flask. The final concentration of the enzyme was about 325 U L(-1).

  12. Substrate mediated enzyme prodrug therapy.

    Directory of Open Access Journals (Sweden)

    Betina Fejerskov

    Full Text Available In this report, we detail Substrate Mediated Enzyme Prodrug Therapy (SMEPT as a novel approach in drug delivery which relies on enzyme-functionalized cell culture substrates to achieve a localized conversion of benign prodrug(s into active therapeutics with subsequent delivery to adhering cells or adjacent tissues. For proof-of-concept SMEPT, we use surface adhered micro-structured physical hydrogels based on poly(vinyl alcohol, β-glucuronidase enzyme and glucuronide prodrugs. We demonstrate enzymatic activity mediated by the assembled hydrogel samples and illustrate arms of control over rate of release of model fluorescent cargo. SMEPT was not impaired by adhering cells and afforded facile time - and dose - dependent uptake of the in situ generated fluorescent cargo by hepatic cells, HepG2. With the use of a glucuronide derivative of an anticancer drug, SN-38, SMEPT afforded a decrease in cell viability to a level similar to that achieved using parent drug. Finally, dose response was achieved using SMEPT and administration of judiciously chosen concentration of SN-38 glucuronide prodrug thus revealing external control over drug delivery using drug eluting surface. We believe that this highly adaptable concept will find use in diverse biomedical applications, specifically surface mediated drug delivery and tissue engineering.

  13. [Incorporation of an organic MAGIC (Model of Acidification of Groundwater in Catchments) and testing of the revised model using independent data sources]. Progress report, March 16, 1992--September 15, 1992

    Energy Technology Data Exchange (ETDEWEB)

    Sullivan, T.J.

    1992-09-01

    A project was initiated in March, 1992 to (1) incorporate a rigorous organic acid representation, based on empirical data and geochemical considerations, into the MAGIC model of acidification response, and (2) test the revised model using three sets of independent data. After six months of performance, the project is on schedule and the majority of the tasks outlined for Year 1 have been successfully completed. Major accomplishments to data include development of the organic acid modeling approach, using data from the Adirondack Lakes Survey Corporation (ALSC), and coupling the organic acid model with MAGIC for chemical hindcast comparisons. The incorporation of an organic acid representation into MAGIC can account for much of the discrepancy earlier observed between MAGIC hindcasts and paleolimnological reconstructions of preindustrial pH and alkalinity for 33 statistically-selected Adirondack lakes. Additional work is on-going for model calibration and testing with data from two whole-catchment artificial acidification projects. Results obtained thus far are being prepared as manuscripts for submission to the peer-reviewed scientific literature.

  14. Teaching Genetic Counseling Skills: Incorporating a Genetic Counseling Adaptation Continuum Model to Address Psychosocial Complexity.

    Science.gov (United States)

    Shugar, Andrea

    2017-04-01

    Genetic counselors are trained health care professionals who effectively integrate both psychosocial counseling and information-giving into their practice. Preparing genetic counseling students for clinical practice is a challenging task, particularly when helping them develop effective and active counseling skills. Resistance to incorporating these skills may stem from decreased confidence, fear of causing harm or a lack of clarity of psycho-social goals. The author reflects on the personal challenges experienced in teaching genetic counselling students to work with psychological and social complexity, and proposes a Genetic Counseling Adaptation Continuum model and methodology to guide students in the use of advanced counseling skills.

  15. Model for Volatile Incorporation into Soils and Dust on Mars

    Science.gov (United States)

    Clark, B. C.; Yen, A.

    2006-12-01

    Martian soils with high content of compounds of sulfur and chlorine are ubiquitous on Mars, having been found at all five landing sites. Sulfate and chloride salts are implicated by a variety of evidence, but few conclusive specific identifications have been made. Discovery of jarosite and Mg-Ca sulfates in outcrops at Meridiani Planum (MER mission) and regional-scale beds of kieserite and gypsum (Mars Express mission) notwithstanding, the sulfates in soils are uncertain. Chlorides or other Cl-containing minerals have not been uniquely identified directly by any method. Viking and Pathfinder missions found trends in the elemental analytical data consistent with MgSO4, but Viking results are biased by duricrust samples and Pathfinder by soil contamination of rock surfaces. The Mars Exploration Rovers (MER) missions have taken extensive data on soils with no confirmation of trends implicating any particular cation. In our model of martian dust and soil, the S and Cl are initially incorporated by condensation or chemisorption on grains directly from gas phase molecules in the atmosphere. It is shown by modeling that the coatings thus formed cannot quantitatively explain the apparent elemental composition of these materials, and therefore involve the migration of ions and formation of microscopic weathering rinds. Original cation inventories of unweathered particles are isochemically conserved. Exposed rock surfaces should also have micro rinds, depending upon the length of time of exposure. Martian soils may therefore have unusual chemical properties when interacting with aqueous layers or infused fluids. Potential ramifications to the quantitative accuracy of x-ray fluorescence and Moessbauer spectroscopy on unprocessed samples are also assessed.

  16. Nanocaged enzymes with enhanced catalytic activity and increased stability against protease digestion

    Science.gov (United States)

    Zhao, Zhao; Fu, Jinglin; Dhakal, Soma; Johnson-Buck, Alexander; Liu, Minghui; Zhang, Ting; Woodbury, Neal W.; Liu, Yan; Walter, Nils G.; Yan, Hao

    2016-01-01

    Cells routinely compartmentalize enzymes for enhanced efficiency of their metabolic pathways. Here we report a general approach to construct DNA nanocaged enzymes for enhancing catalytic activity and stability. Nanocaged enzymes are realized by self-assembly into DNA nanocages with well-controlled stoichiometry and architecture that enabled a systematic study of the impact of both encapsulation and proximal polyanionic surfaces on a set of common metabolic enzymes. Activity assays at both bulk and single-molecule levels demonstrate increased substrate turnover numbers for DNA nanocage-encapsulated enzymes. Unexpectedly, we observe a significant inverse correlation between the size of a protein and its activity enhancement. This effect is consistent with a model wherein distal polyanionic surfaces of the nanocage enhance the stability of active enzyme conformations through the action of a strongly bound hydration layer. We further show that DNA nanocages protect encapsulated enzymes against proteases, demonstrating their practical utility in functional biomaterials and biotechnology. PMID:26861509

  17. Nanocaged enzymes with enhanced catalytic activity and increased stability against protease digestion

    Science.gov (United States)

    Zhao, Zhao; Fu, Jinglin; Dhakal, Soma; Johnson-Buck, Alexander; Liu, Minghui; Zhang, Ting; Woodbury, Neal W.; Liu, Yan; Walter, Nils G.; Yan, Hao

    2016-02-01

    Cells routinely compartmentalize enzymes for enhanced efficiency of their metabolic pathways. Here we report a general approach to construct DNA nanocaged enzymes for enhancing catalytic activity and stability. Nanocaged enzymes are realized by self-assembly into DNA nanocages with well-controlled stoichiometry and architecture that enabled a systematic study of the impact of both encapsulation and proximal polyanionic surfaces on a set of common metabolic enzymes. Activity assays at both bulk and single-molecule levels demonstrate increased substrate turnover numbers for DNA nanocage-encapsulated enzymes. Unexpectedly, we observe a significant inverse correlation between the size of a protein and its activity enhancement. This effect is consistent with a model wherein distal polyanionic surfaces of the nanocage enhance the stability of active enzyme conformations through the action of a strongly bound hydration layer. We further show that DNA nanocages protect encapsulated enzymes against proteases, demonstrating their practical utility in functional biomaterials and biotechnology.

  18. A multi-period, multi-regional generation expansion planning model incorporating unit commitment constraints

    International Nuclear Information System (INIS)

    Koltsaklis, Nikolaos E.; Georgiadis, Michael C.

    2015-01-01

    Highlights: • A short-term structured investment planning model has been developed. • Unit commitment problem is incorporated into the long-term planning horizon. • Inherent intermittency of renewables is modelled in a comprehensive way. • The impact of CO_2 emission pricing in long-term investment decisions is quantified. • The evolution of system’s marginal price is evaluated for all the planning horizon. - Abstract: This work presents a generic mixed integer linear programming (MILP) model that integrates the unit commitment problem (UCP), i.e., daily energy planning with the long-term generation expansion planning (GEP) framework. Typical daily constraints at an hourly level such as start-up and shut-down related decisions (start-up type, minimum up and down time, synchronization, soak and desynchronization time constraints), ramping limits, system reserve requirements are combined with representative yearly constraints such as power capacity additions, power generation bounds of each unit, peak reserve requirements, and energy policy issues (renewables penetration limits, CO_2 emissions cap and pricing). For modelling purposes, a representative day (24 h) of each month over a number of years has been employed in order to determine the optimal capacity additions, electricity market clearing prices, and daily operational planning of the studied power system. The model has been tested on an illustrative case study of the Greek power system. Our approach aims to provide useful insight into strategic and challenging decisions to be determined by investors and/or policy makers at a national and/or regional level by providing the optimal energy roadmap under real operating and design constraints.

  19. Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted docking

    Directory of Open Access Journals (Sweden)

    Tyagi Sadhna

    2009-06-01

    Full Text Available Abstract Background Previously, ways to adapt docking programs that were developed for modelling inhibitor-receptor interaction have been explored. Two main issues were discussed. First, when trying to model catalysis a reaction intermediate of the substrate is expected to provide more valid information than the ground state of the substrate. Second, the incorporation of protein flexibility is essential for reliable predictions. Results Here we present a predictive and robust method to model substrate specificity and enantioselectivity of lipases and esterases that uses reaction intermediates and incorporates protein flexibility. Substrate-imprinted docking starts with covalent docking of reaction intermediates, followed by geometry optimisation of the resulting enzyme-substrate complex. After a second round of docking the same substrate into the geometry-optimised structures, productive poses are identified by geometric filter criteria and ranked by their docking scores. Substrate-imprinted docking was applied in order to model (i enantioselectivity of Candida antarctica lipase B and a W104A mutant, (ii enantioselectivity and substrate specificity of Candida rugosa lipase and Burkholderia cepacia lipase, and (iii substrate specificity of an acetyl- and a butyrylcholine esterase toward the substrates acetyl- and butyrylcholine. Conclusion The experimentally observed differences in selectivity and specificity of the enzymes were reproduced with an accuracy of 81%. The method was robust toward small differences in initial structures (different crystallisation conditions or a co-crystallised ligand, although large displacements of catalytic residues often resulted in substrate poses that did not pass the geometric filter criteria.

  20. Incorporating the CALPHAD sublattice approach of ordering into the phase-field model with finite interface dissipation

    International Nuclear Information System (INIS)

    Zhang, Lijun; Stratmann, Matthias; Du, Yong; Sundman, Bo; Steinbach, Ingo

    2015-01-01

    A new approach to incorporate the sublattice models in the CALPHAD (CALculation of PHAse Diagram) formalism directly into the phase-field formalism is developed. In binary alloys, the sublattice models can be classified into two types (i.e., “Type I” and “Type II”), depending on whether a direct one-to-one relation between the element site fraction in the CALPHAD database and the phase concentration in the phase-field model exists (Type I), or not (Type II). For “Type II” sublattice models, the specific site fractions, corresponding to a given mole fraction, have to be established via internal relaxation between different sublattices. Internal minimization of sublattice occupancy and solute evolution during microstructure transformation leads, in general, to a solution superior to the separate solution of the individual problems. The present coupling technique is validated for Fe–C and Ni–Al alloys. Finally, the model is extended into multicomponent alloys and applied to simulate the nucleation process of VC monocarbide from austenite matrix in a steel containing vanadium

  1. Capacitive electrolyte-insulator-semiconductor structures functionalised with a polyelectrolyte/enzyme multilayer: New strategy for enhanced field-effect biosensing

    Energy Technology Data Exchange (ETDEWEB)

    Abouzar, Maryam H.; Poghossian, Arshak; Schoening, Michael J. [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Juelich (Germany); Institute of Bio- and Nanosystems (IBN-2), Research Centre Juelich GmbH, Juelich (Germany); Siqueira, Jose R. Jr.; Oliveira, Osvaldo N. Jr. [Physics Institute of Sao Carlos, University of Sao Paulo, Sao Carlos (Brazil); Moritz, Werner [Institute of Chemistry, Humboldt University Berlin (Germany)

    2010-04-15

    A novel strategy for enhanced field-effect biosensing using capacitive electrolyte-insulator-semiconductor (EIS) structures functionalised with pH-responsive weak polyelectrolyte/enzyme or dendrimer/enzyme multilayers is presented. The feasibility of the proposed approach is exemplarily demonstrated by realising a penicillin biosensor based on a capacitive p-Si-SiO{sub 2} EIS structure functionalised with a poly(allylamine hydrochloride) (PAH)/penicillinase and a poly(amidoamine) dendrimer/penicillinase multilayer. The developed sensors response to changes in both the local pH value near the gate surface and the charge of macromolecules induced via enzymatic reaction, resulting in a higher sensitivity. For comparison, an EIS penicillin biosensor with adsorptively immobilised penicillinase has been also studied. The highest penicillin sensitivity of 100 mV/dec has been observed for the EIS sensor functionalised with the PAH/penicillinase multilayer. The lower and upper detection limit was around 20 {mu}M and 10 mM, respectively. In addition, an incorporation of enzymes in a multilayer prepared by layer-by-layer technique provides a larger amount of immobilised enzymes per sensor area, reduces enzyme leaching effects and thus, enhances the biosensor lifetime (the loss of penicillin sensitivity after 2 months was 10-12%). (Abstract Copyright [2010], Wiley Periodicals, Inc.)

  2. Enzyme recycling in lignocellulosic biorefineries

    DEFF Research Database (Denmark)

    Jørgensen, Henning; Pinelo, Manuel

    2017-01-01

    platform. Cellulases are the most important enzymes required in this process, but the complex nature of lignocellulose requires several other enzymes (hemicellulases and auxiliary enzymes) for efficient hydrolysis. Enzyme recycling increases the catalytic productivity of the enzymes by reusing them...... for several batches of hydrolysis, and thereby reduces the overall cost associated with the hydrolysis. Research on this subject has been ongoing for many years and several promising technologies and methods have been developed and demonstrated. But only in a very few cases have these technologies been...... upscaled and tested in industrial settings, mainly because of many difficulties with recycling of enzymes from the complex lignocellulose hydrolyzate at industrially relevant conditions, i.e., high solids loadings. The challenges are associated with the large number of different enzymes required...

  3. Incorporating a hybrid urease-carbon nanotubes sensitive nanofilm on capacitive field-effect sensors for urea detection.

    Science.gov (United States)

    Siqueira, José R; Molinnus, Denise; Beging, Stefan; Schöning, Michael J

    2014-06-03

    The ideal combination among biomolecules and nanomaterials is the key for reaching biosensing units with high sensitivity. The challenge, however, is to find out a stable and sensitive film architecture that can be incorporated on the sensor's surface. In this paper, we report on the benefits of incorporating a layer-by-layer (LbL) nanofilm of polyamidoamine (PAMAM) dendrimer and carbon nanotubes (CNTs) on capacitive electrolyte-insulator-semiconductor (EIS) field-effect sensors for detecting urea. Three sensor arrangements were studied in order to investigate the adequate film architecture, involving the LbL film with the enzyme urease: (i) urease immobilized directly onto a bare EIS [EIS-urease] sensor; (ii) urease atop the LbL film over the EIS [EIS-(PAMAM/CNT)-urease] sensor; and (iii) urease sandwiched between the LbL film and another CNT layer [EIS-(PAMAM/CNT)-urease-CNT]. The surface morphology of all three urea-based EIS biosensors was investigated by atomic force microscopy (AFM), while the biosensing abilities were studied by means of capacitance-voltage (C/V) and dynamic constant-capacitance (ConCap) measureaments at urea concentrations ranging from 0.1 mM to 100 mM. The EIS-urease and EIS-(PAMAM/CNT)-urease sensors showed similar sensitivity (~18 mV/decade) and a nonregular signal behavior as the urea concentration increased. On the other hand, the EIS-(PAMAM/CNT)-urease-CNT sensor exhibited a superior output signal performance and higher sensitivity of about 33 mV/decade. The presence of the additional CNT layer was decisive to achieve a urea based EIS sensor with enhanced properties. Such sensitive architecture demonstrates that the incorporation of an adequate hybrid enzyme-nanofilm as sensing unit opens new prospects for biosensing applications using the field-effect sensor platform.

  4. KRYPTON INCORPORATION IN SPUTTERED SILICON FILMS

    NARCIS (Netherlands)

    GREUTER, MJW; NIESEN, L; HAKVOORT, RA; DEROODE, J; VANVEEN, A; BERNTSEN, AJM; SLOOF, WG

    1993-01-01

    The incorporation of Kr in sputtered a-Si films has been investigated in a systematic way by varying the Kr to Si flux, yielding Kr concentrations up to 5 at %. Compositions were determined with X-ray microanalysis. A model has been applied to describe the composition of the growing film. The layers

  5. Enzymes of industrial purpose - review of the market of enzyme preparations and prospects for its development

    Directory of Open Access Journals (Sweden)

    A. A. Tolkacheva

    2017-01-01

    Full Text Available Microbial enzyme preparations are increasingly replacing conventional chemical catalysts in a number of industrial processes. Such drugs, in addition to environmental friendliness and high activity, have a number of advantages over enzyme preparations of vegetable and animal origin, namely: the production of microbial enzymes in bioreactors is easily controlled and predictable; excreted microbiological enzymes are more stable than intracellular animals and plant enzymes; the genetic diversity of microorganisms makes it possible to produce enzyme preparations with a wide range of specificity; microbiological enzymes can be synthesized year-round, in contrast to the production of plant enzymes, which is often seasonal. The leaders of the world market of enzymes are proteases and amylases, which account for 25% and 15%, respectively. Over the past five years, the world market for carbohydrases, including mainly amylases, cellulases and xylanases, has been the fastest growing segment of the enzyme market with an aggregate annual growth rate of more than 7.0%. Another major product of the industrial enzyme market, which has a great potential for growth, is lipases. From the point of view of designation, the main part is represented by food and food enzymes. The Russian market continues to be unsaturated - the current supply is not able to meet the needs of the Russian feed and food industry in enzyme preparations. Enzyme preparations of domestic producers are in demand in forage production, while food industrial enterprises prefer imported products. The most significant enterprises in the enzymatic industry in Russia at the moment are Sibbiofarm, AgroSistema, Agroferment. In the light of the Russian policy of increasing food security, the development of the domestic enzyme industry is an extremely topical task.

  6. Direct Competitive Enzyme-Linked Immunosorbent Assay (ELISA).

    Science.gov (United States)

    Kohl, Thomas O; Ascoli, Carl A

    2017-07-05

    The competitive enzyme-linked immunosorbent assay (ELISA) (cELISA; also called an inhibition ELISA) is designed so that purified antigen competes with antigen in the test sample for binding to an antibody that has been immobilized in microtiter plate wells. The same concept works if the immobilized molecule is antigen and the competing molecules are purified labeled antibody versus antibody in a test sample. Direct cELISAs incorporate labeled antigen or antibody, whereas indirect assay configurations use reporter-labeled secondary antibodies. The cELISA is very useful for determining the concentration of small-molecule antigens in complex sample mixtures. In the direct cELISA, antigen-specific capture antibody is adsorbed onto the microtiter plate before incubation with either known standards or unknown test samples. Enzyme-linked antigen (i.e., labeled antigen) is also added, which can bind to the capture antibody only when the antibody's binding site is not occupied by either the antigen standard or antigen in the test samples. Unbound labeled and unlabeled antigens are washed away and substrate is added. The amount of antigen in the standard or the test sample determines the amount of reporter-labeled antigen bound to antibody, yielding a signal that is inversely proportional to antigen concentration within the sample. Thus, the higher the antigen concentration in the test sample, the less labeled antigen is bound to the capture antibody, and hence the weaker is the resultant signal. © 2017 Cold Spring Harbor Laboratory Press.

  7. Continuous enzyme reactions with immobilized enzyme tubes prepared by radiation cast-polymerization

    International Nuclear Information System (INIS)

    Kumakura, Minoru; Kaetsu, Isao

    1986-01-01

    Immobilized glucose oxidase tubes were prepared by radiation cast-polymerization of 2-hydroxyethyl methacrylate and tetraethyleneglycol diacrylate monomer at low temperatures. The immobilized enzyme tubes which were spirally set in a water bath were used as reactor, in which the enzyme activity varied with tube size and flow rate of the substrate. The conversion yield of the substrate in continuous enzyme reaction was about 80%. (author)

  8. Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution.

    Science.gov (United States)

    Omelchenko, Marina V; Galperin, Michael Y; Wolf, Yuri I; Koonin, Eugene V

    2010-04-30

    Evolutionarily unrelated proteins that catalyze the same biochemical reactions are often referred to as analogous - as opposed to homologous - enzymes. The existence of numerous alternative, non-homologous enzyme isoforms presents an interesting evolutionary problem; it also complicates genome-based reconstruction of the metabolic pathways in a variety of organisms. In 1998, a systematic search for analogous enzymes resulted in the identification of 105 Enzyme Commission (EC) numbers that included two or more proteins without detectable sequence similarity to each other, including 34 EC nodes where proteins were known (or predicted) to have distinct structural folds, indicating independent evolutionary origins. In the past 12 years, many putative non-homologous isofunctional enzymes were identified in newly sequenced genomes. In addition, efforts in structural genomics resulted in a vastly improved structural coverage of proteomes, providing for definitive assessment of (non)homologous relationships between proteins. We report the results of a comprehensive search for non-homologous isofunctional enzymes (NISE) that yielded 185 EC nodes with two or more experimentally characterized - or predicted - structurally unrelated proteins. Of these NISE sets, only 74 were from the original 1998 list. Structural assignments of the NISE show over-representation of proteins with the TIM barrel fold and the nucleotide-binding Rossmann fold. From the functional perspective, the set of NISE is enriched in hydrolases, particularly carbohydrate hydrolases, and in enzymes involved in defense against oxidative stress. These results indicate that at least some of the non-homologous isofunctional enzymes were recruited relatively recently from enzyme families that are active against related substrates and are sufficiently flexible to accommodate changes in substrate specificity.

  9. Incorporating remote sensing-based ET estimates into the Community Land Model version 4.5

    Directory of Open Access Journals (Sweden)

    D. Wang

    2017-07-01

    Full Text Available Land surface models bear substantial biases in simulating surface water and energy budgets despite the continuous development and improvement of model parameterizations. To reduce model biases, Parr et al. (2015 proposed a method incorporating satellite-based evapotranspiration (ET products into land surface models. Here we apply this bias correction method to the Community Land Model version 4.5 (CLM4.5 and test its performance over the conterminous US (CONUS. We first calibrate a relationship between the observational ET from the Global Land Evaporation Amsterdam Model (GLEAM product and the model ET from CLM4.5, and assume that this relationship holds beyond the calibration period. During the validation or application period, a simulation using the default CLM4.5 (CLM is conducted first, and its output is combined with the calibrated observational-vs.-model ET relationship to derive a corrected ET; an experiment (CLMET is then conducted in which the model-generated ET is overwritten with the corrected ET. Using the observations of ET, runoff, and soil moisture content as benchmarks, we demonstrate that CLMET greatly improves the hydrological simulations over most of the CONUS, and the improvement is stronger in the eastern CONUS than the western CONUS and is strongest over the Southeast CONUS. For any specific region, the degree of the improvement depends on whether the relationship between observational and model ET remains time-invariant (a fundamental hypothesis of the Parr et al. (2015 method and whether water is the limiting factor in places where ET is underestimated. While the bias correction method improves hydrological estimates without improving the physical parameterization of land surface models, results from this study do provide guidance for physically based model development effort.

  10. A LabVIEW model incorporating an open-loop arterial impedance and a closed-loop circulatory system.

    Science.gov (United States)

    Cole, R T; Lucas, C L; Cascio, W E; Johnson, T A

    2005-11-01

    While numerous computer models exist for the circulatory system, many are limited in scope, contain unwanted features or incorporate complex components specific to unique experimental situations. Our purpose was to develop a basic, yet multifaceted, computer model of the left heart and systemic circulation in LabVIEW having universal appeal without sacrificing crucial physiologic features. The program we developed employs Windkessel-type impedance models in several open-loop configurations and a closed-loop model coupling a lumped impedance and ventricular pressure source. The open-loop impedance models demonstrate afterload effects on arbitrary aortic pressure/flow inputs. The closed-loop model catalogs the major circulatory waveforms with changes in afterload, preload, and left heart properties. Our model provides an avenue for expanding the use of the ventricular equations through closed-loop coupling that includes a basic coronary circuit. Tested values used for the afterload components and the effects of afterload parameter changes on various waveforms are consistent with published data. We conclude that this model offers the ability to alter several circulatory factors and digitally catalog the most salient features of the pressure/flow waveforms employing a user-friendly platform. These features make the model a useful instructional tool for students as well as a simple experimental tool for cardiovascular research.

  11. Quantum-Mechanical Methods for Quantifying Incorporation of Contaminants in Proximal Minerals

    Directory of Open Access Journals (Sweden)

    Lindsay C. Shuller-Nickles

    2014-07-01

    Full Text Available Incorporation reactions play an important role in dictating immobilization and release pathways for chemical species in low-temperature geologic environments. Quantum-mechanical investigations of incorporation seek to characterize the stability and geometry of incorporated structures, as well as the thermodynamics and kinetics of the reactions themselves. For a thermodynamic treatment of incorporation reactions, a source of the incorporated ion and a sink for the released ion is necessary. These sources/sinks in a real geochemical system can be solids, but more commonly, they are charged aqueous species. In this contribution, we review the current methods for ab initio calculations of incorporation reactions, many of which do not consider incorporation from aqueous species. We detail a recently-developed approach for the calculation of incorporation reactions and expand on the part that is modeling the interaction of periodic solids with aqueous source and sink phases and present new research using this approach. To model these interactions, a systematic series of calculations must be done to transform periodic solid source and sink phases to aqueous-phase clusters. Examples of this process are provided for three case studies: (1 neptunyl incorporation into studtite and boltwoodite: for the layered boltwoodite, the incorporation energies are smaller (more favorable for reactions using environmentally relevant source and sink phases (i.e., ΔErxn(oxides > ΔErxn(silicates > ΔErxn(aqueous. Estimates of the solid-solution behavior of Np5+/P5+- and U6+/Si4+-boltwoodite and Np5+/Ca2+- and U6+/K+-boltwoodite solid solutions are used to predict the limit of Np-incorporation into boltwoodite (172 and 768 ppm at 300 °C, respectively; (2 uranyl and neptunyl incorporation into carbonates and sulfates: for both carbonates and sulfates, it was found that actinyl incorporation into a defect site is more favorable than incorporation into defect-free periodic

  12. Cell in situ zymography: an in vitro cytotechnology for localization of enzyme activity in cell culture.

    Science.gov (United States)

    Chhabra, Aastha; Jaiswal, Astha; Malhotra, Umang; Kohli, Shrey; Rani, Vibha

    2012-09-01

    In situ zymography is a unique technique for detection and localization of enzyme-substrate interactions majorly in histological sections. Substrate with quenched fluorogenic molecule is incorporated in gel over which tissue sections are mounted and then incubated in buffer. The enzymatic activity is observed in the form of fluorescent signal. With the advancements in the field of biological research, use of in vitro cell culture has become very popular and holds great significance in multiple fields including inflammation, cancer, stem cell biology and the still emerging 3-D cell cultures. The information on analysis of enzymatic activity in cell lines is inadequate presently. We propose a single-step methodology that is simple, sensitive, cost-effective, and functional to perform and study the 'in position' activity of enzyme on substrate for in vitro cell cultures. Quantification of enzymatic activity to carry out comparative studies on cells has also been illustrated. This technique can be applied to a variety of enzyme classes including proteases, amylases, xylanases, and cellulases in cell cultures.

  13. Enzyme activity assay of glycoprotein enzymes based on a boronate affinity molecularly imprinted 96-well microplate.

    Science.gov (United States)

    Bi, Xiaodong; Liu, Zhen

    2014-12-16

    Enzyme activity assay is an important method in clinical diagnostics. However, conventional enzyme activity assay suffers from apparent interference from the sample matrix. Herein, we present a new format of enzyme activity assay that can effectively eliminate the effects of the sample matrix. The key is a 96-well microplate modified with molecularly imprinted polymer (MIP) prepared according to a newly proposed method called boronate affinity-based oriented surface imprinting. Alkaline phosphatase (ALP), a glycoprotein enzyme that has been routinely used as an indicator for several diseases in clinical tests, was taken as a representative target enzyme. The prepared MIP exhibited strong affinity toward the template enzyme (with a dissociation constant of 10(-10) M) as well as superb tolerance for interference. Thus, the enzyme molecules in a complicated sample matrix could be specifically captured and cleaned up for enzyme activity assay, which eliminated the interference from the sample matrix. On the other hand, because the boronate affinity MIP could well retain the enzymatic activity of glycoprotein enzymes, the enzyme captured by the MIP was directly used for activity assay. Thus, additional assay time and possible enzyme or activity loss due to an enzyme release step required by other methods were avoided. Assay of ALP in human serum was successfully demonstrated, suggesting a promising prospect of the proposed method in real-world applications.

  14. Enzymic lactose hydrolysis

    Energy Technology Data Exchange (ETDEWEB)

    Miller, J J; Brand, J C

    1980-01-01

    Acid or enzymic hydrolysis can be used to hydrolyze lactose. Advantages of both are compared and details of enzymic hydrolysis using yeast or fungal enzymes given. The new scheme outlined involves recycling lactase. Because lactose and lactase react to ultrafiltration (UF) membranes differently separation is possible. Milk or milk products are ultrafiltered to separate a concentrate from a lactose-rich permeate which is treated with lactase in a reactor until hydrolysis reaches a required level. The lactase can be removed by UF as it does not permeate the membrane, and it is recycled back to the reactor. Permeate from the second UF stage may or may not be recombined with the concentrate from the first stage to produce a low lactose product (analysis of a typical low-lactose dried whole milk is given). Batch or continuous processes are explained and a batch process without enzyme recovery is discussed. (Refs. 4).

  15. Enzyme Mimics: Advances and Applications.

    Science.gov (United States)

    Kuah, Evelyn; Toh, Seraphina; Yee, Jessica; Ma, Qian; Gao, Zhiqiang

    2016-06-13

    Enzyme mimics or artificial enzymes are a class of catalysts that have been actively pursued for decades and have heralded much interest as potentially viable alternatives to natural enzymes. Aside from having catalytic activities similar to their natural counterparts, enzyme mimics have the desired advantages of tunable structures and catalytic efficiencies, excellent tolerance to experimental conditions, lower cost, and purely synthetic routes to their preparation. Although still in the midst of development, impressive advances have already been made. Enzyme mimics have shown immense potential in the catalysis of a wide range of chemical and biological reactions, the development of chemical and biological sensing and anti-biofouling systems, and the production of pharmaceuticals and clean fuels. This Review concerns the development of various types of enzyme mimics, namely polymeric and dendrimeric, supramolecular, nanoparticulate and proteinic enzyme mimics, with an emphasis on their synthesis, catalytic properties and technical applications. It provides an introduction to enzyme mimics and a comprehensive summary of the advances and current standings of their applications, and seeks to inspire researchers to perfect the design and synthesis of enzyme mimics and to tailor their functionality for a much wider range of applications. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Adsorption of monocomponent enzymes in enzyme mixture analyzed quantitatively during hydrolysis of lignocellulose substrates.

    Science.gov (United States)

    Várnai, Anikó; Viikari, Liisa; Marjamaa, Kaisa; Siika-aho, Matti

    2011-01-01

    The adsorption of purified Trichoderma reesei cellulases (TrCel7A, TrCel6A and TrCel5A) and xylanase TrXyn11 and Aspergillus niger β-glucosidase AnCel3A was studied in enzyme mixture during hydrolysis of two pretreated lignocellulosic materials, steam pretreated and catalytically delignified spruce, along with microcrystalline cellulose (Avicel). The enzyme mixture was compiled to resemble the composition of commercial cellulase preparations. The hydrolysis was carried out at 35 °C to mimic the temperature of the simultaneous saccharification and fermentation (SSF). Enzyme adsorption was followed by analyzing the activity and the protein amount of the individual free enzymes in the hydrolysis supernatant. Most enzymes adsorbed quickly at early stages of the hydrolysis and remained bound throughout the hydrolysis, although the conversion reached was fairly high. Only with the catalytically oxidized spruce samples, the bound enzymes started to be released as the hydrolysis degree reached 80%. The results based on enzyme activities and protein assay were in good accordance. Copyright © 2010 Elsevier Ltd. All rights reserved.

  17. Characterising Complex Enzyme Reaction Data.

    Directory of Open Access Journals (Sweden)

    Handan Melike Dönertaş

    Full Text Available The relationship between enzyme-catalysed reactions and the Enzyme Commission (EC number, the widely accepted classification scheme used to characterise enzyme activity, is complex and with the rapid increase in our knowledge of the reactions catalysed by enzymes needs revisiting. We present a manual and computational analysis to investigate this complexity and found that almost one-third of all known EC numbers are linked to more than one reaction in the secondary reaction databases (e.g., KEGG. Although this complexity is often resolved by defining generic, alternative and partial reactions, we have also found individual EC numbers with more than one reaction catalysing different types of bond changes. This analysis adds a new dimension to our understanding of enzyme function and might be useful for the accurate annotation of the function of enzymes and to study the changes in enzyme function during evolution.

  18. Dipole estimation errors due to not incorporating anisotropic conductivities in realistic head models for EEG source analysis

    Science.gov (United States)

    Hallez, Hans; Staelens, Steven; Lemahieu, Ignace

    2009-10-01

    EEG source analysis is a valuable tool for brain functionality research and for diagnosing neurological disorders, such as epilepsy. It requires a geometrical representation of the human head or a head model, which is often modeled as an isotropic conductor. However, it is known that some brain tissues, such as the skull or white matter, have an anisotropic conductivity. Many studies reported that the anisotropic conductivities have an influence on the calculated electrode potentials. However, few studies have assessed the influence of anisotropic conductivities on the dipole estimations. In this study, we want to determine the dipole estimation errors due to not taking into account the anisotropic conductivities of the skull and/or brain tissues. Therefore, head models are constructed with the same geometry, but with an anisotropically conducting skull and/or brain tissue compartment. These head models are used in simulation studies where the dipole location and orientation error is calculated due to neglecting anisotropic conductivities of the skull and brain tissue. Results show that not taking into account the anisotropic conductivities of the skull yields a dipole location error between 2 and 25 mm, with an average of 10 mm. When the anisotropic conductivities of the brain tissues are neglected, the dipole location error ranges between 0 and 5 mm. In this case, the average dipole location error was 2.3 mm. In all simulations, the dipole orientation error was smaller than 10°. We can conclude that the anisotropic conductivities of the skull have to be incorporated to improve the accuracy of EEG source analysis. The results of the simulation, as presented here, also suggest that incorporation of the anisotropic conductivities of brain tissues is not necessary. However, more studies are needed to confirm these suggestions.

  19. Dipole estimation errors due to not incorporating anisotropic conductivities in realistic head models for EEG source analysis

    International Nuclear Information System (INIS)

    Hallez, Hans; Staelens, Steven; Lemahieu, Ignace

    2009-01-01

    EEG source analysis is a valuable tool for brain functionality research and for diagnosing neurological disorders, such as epilepsy. It requires a geometrical representation of the human head or a head model, which is often modeled as an isotropic conductor. However, it is known that some brain tissues, such as the skull or white matter, have an anisotropic conductivity. Many studies reported that the anisotropic conductivities have an influence on the calculated electrode potentials. However, few studies have assessed the influence of anisotropic conductivities on the dipole estimations. In this study, we want to determine the dipole estimation errors due to not taking into account the anisotropic conductivities of the skull and/or brain tissues. Therefore, head models are constructed with the same geometry, but with an anisotropically conducting skull and/or brain tissue compartment. These head models are used in simulation studies where the dipole location and orientation error is calculated due to neglecting anisotropic conductivities of the skull and brain tissue. Results show that not taking into account the anisotropic conductivities of the skull yields a dipole location error between 2 and 25 mm, with an average of 10 mm. When the anisotropic conductivities of the brain tissues are neglected, the dipole location error ranges between 0 and 5 mm. In this case, the average dipole location error was 2.3 mm. In all simulations, the dipole orientation error was smaller than 10 deg. We can conclude that the anisotropic conductivities of the skull have to be incorporated to improve the accuracy of EEG source analysis. The results of the simulation, as presented here, also suggest that incorporation of the anisotropic conductivities of brain tissues is not necessary. However, more studies are needed to confirm these suggestions.

  20. Enzyme Immobilization: An Overview on Methods, Support Material, and Applications of Immobilized Enzymes.

    Science.gov (United States)

    Sirisha, V L; Jain, Ankita; Jain, Amita

    Immobilized enzymes can be used in a wide range of processes. In recent years, a variety of new approaches have emerged for the immobilization of enzymes that have greater efficiency and wider usage. During the course of the last two decades, this area has rapidly expanded into a multidisciplinary field. This current study is a comprehensive review of a variety of literature produced on the different enzymes that have been immobilized on various supporting materials. These immobilized enzymes have a wide range of applications. These include applications in the sugar, fish, and wine industries, where they are used for removing organic compounds from waste water. This study also reviews their use in sophisticated biosensors for metabolite control and in situ measurements of environmental pollutants. Immobilized enzymes also find significant application in drug metabolism, biodiesel and antibiotic production, bioremediation, and the food industry. The widespread usage of immobilized enzymes is largely due to the fact that they are cheaper, environment friendly, and much easier to use when compared to equivalent technologies. © 2016 Elsevier Inc. All rights reserved.

  1. Hydrolytic enzymes in the central vacuole of plant cells

    International Nuclear Information System (INIS)

    Boller, T.; Kende, H.

    1979-01-01

    The hydrolase content of vacuoles isolated from protoplasts of suspension-cultured tobacco cells, of tulip petals, and pineapple leaves, and the sedimentation behavior of tobacco tonoplasts were studied. Three precautions were found to be important for the analysis of vacuolar hydrolases and of the tonoplast: (a) purification of protoplasts in a Ficoll gradient was necessary to remove cell debris which contained contaminating hydrolases adsorbed from the fungal cell-wall-degrading enzyme preparation; (b) hydrolase activities in the homogenates of the intact cells or the tissue used and of the purified protoplasts had to be compared to verify the absence of contaminating hydrolases in the protoplast preparation; and (c) vacuoles obtained from the protoplasts by an osmotic shock had to be purified from the lysate in a Ficoll gradient. Since the density of the central vacuole approximates that of the protoplasts, about a 10% contamination of the vacuolar preparation by surviving protoplasts could not be eliminated. The intracellular activities of the following acid hydrolases were primarily localized in the vacuole of tobacco cells: α-mannosidase, β-N-acetylglucosaminidase, β-fructosidase, nuclease, phosphatase, phosphodiesterase. A similar composition of acid hydrolases was found in vacuoles obtained from protoplasts of tulip petals. Proteinase, a hydrolase with low activity in tobacco cells and tulip petals was found to be vacuolar in pineapple leaves, a tissue containing high levels of this enzyme. None of the vacuolar enzymes investigated ws found to be bound to the tonoplast. When vacuoles were isolated from cells labeled with radioactive choline, the vacuolar membrane was found to contain radioactivity. On sucrose gradients, the label incorporated into tonoplasts banded around a density of 1.10 grams per cubic centimeter

  2. Incorporation of exogenous L-phenylalanine into C-glycosylflavones in buckwheat cotyledons

    International Nuclear Information System (INIS)

    Margna, U.; Margna, E.

    1978-01-01

    By tracer experiments it was demonstrated that in excised buckwheat cotyledons L-phenylalanine fed exogeneously was incorporated predominantly into the luteolinic C-glycosylflavones orientin and iso-orientin, but not into their simpler apigeninic analogues vitexin and isovitexin, as it could be expected theoretically. Evidence is presented that L-phenylalanine supplied exogenously does not mix with the endogenous pool of that precursor, and that ratios of L-phenylalanine distribution between pathways of apigeninic and luteolinic C-glycosylflavones are different depending on wether the flavonoids are synthesized from endogenous or exogenous material. This phenomenon is suggested to be caused by the differences between enzyme complexes responsible for the biosynthesis of separate C-glycosylflavones in their capability of consuming common endogenous precursors. (author)

  3. Hide unhairing and characterization of commercial enzymes used in leather manufacture

    Directory of Open Access Journals (Sweden)

    A Dettmer

    2011-09-01

    Full Text Available The enzymatic treatment of hides in tannery processes is a promising technology. However, the reaction kinetics of commercial enzymes available to the leather industry are not fully understood and their activities have been mainly determined with model proteins such as casein as substrate, which are not of direct relevance for cattle hides. Therefore, it is important to determine their activities on collagen and keratin, the main proteins of skin, in order to use these enzymes in leather processing. This work describes the study of five proteases, used commercially in tanneries, to assess their ability to act upon collagen and keratin and to determine their unhairing. Results showed that all commercial enzymes tested had more activity on collagen than on keratin. Unhairing was also tested and four out of the five enzymes tested showed some unhairing activity. Optima of the temperature and pH of the enzymes were very similar for all five enzymes, with maximal activities around 55ºC and pH 9 to 12, respectively.

  4. Group spike-and-slab lasso generalized linear models for disease prediction and associated genes detection by incorporating pathway information.

    Science.gov (United States)

    Tang, Zaixiang; Shen, Yueping; Li, Yan; Zhang, Xinyan; Wen, Jia; Qian, Chen'ao; Zhuang, Wenzhuo; Shi, Xinghua; Yi, Nengjun

    2018-03-15

    Large-scale molecular data have been increasingly used as an important resource for prognostic prediction of diseases and detection of associated genes. However, standard approaches for omics data analysis ignore the group structure among genes encoded in functional relationships or pathway information. We propose new Bayesian hierarchical generalized linear models, called group spike-and-slab lasso GLMs, for predicting disease outcomes and detecting associated genes by incorporating large-scale molecular data and group structures. The proposed model employs a mixture double-exponential prior for coefficients that induces self-adaptive shrinkage amount on different coefficients. The group information is incorporated into the model by setting group-specific parameters. We have developed a fast and stable deterministic algorithm to fit the proposed hierarchal GLMs, which can perform variable selection within groups. We assess the performance of the proposed method on several simulated scenarios, by varying the overlap among groups, group size, number of non-null groups, and the correlation within group. Compared with existing methods, the proposed method provides not only more accurate estimates of the parameters but also better prediction. We further demonstrate the application of the proposed procedure on three cancer datasets by utilizing pathway structures of genes. Our results show that the proposed method generates powerful models for predicting disease outcomes and detecting associated genes. The methods have been implemented in a freely available R package BhGLM (http://www.ssg.uab.edu/bhglm/). nyi@uab.edu. Supplementary data are available at Bioinformatics online.

  5. Enzyme-Powered Pumps: From Fundamentals to Applications

    Science.gov (United States)

    Ortiz-Rivera, Isamar

    , covering also the effect of the thermodynamics of the enzymatic reaction in the pumping behavior, and (3) the applicability of enzyme pumps as fluid flow-based inhibitor assays and as drug delivery devices. Our findings in each of these areas, gets us closer to our ultimate goal, where we aim to identify the optimal conditions needed for enzyme micropump operation, and construct a general model that could accurately predict enzyme micropump behavior for any enzyme-substrate combination. The information aforementioned has been divided in four chapters. Chapter 1 gives a quick glance into the development of enzyme-powered micropumps: from the systems and observed behaviors inspiring this work, to the first systems that were developed. The stability, duration, and extent of fluid pumping of enzyme pumps in general, are also discussed, along with the optimization of the enzyme-pump design. This chapter aims to provide a general idea of the motivation behind the concept of "enzyme-powered pumps", what are "enzyme-powered pumps", and which are the key features that characterize these systems. Chapter 2 is an extensive analysis of the mechanisms of actuation proposed for enzyme-powered micropumps. This chapter not only covers the first attempts to understand how enzyme pumps work, but also explores further the behavior of urease-powered pumps, which fluid flow patterns cannot be completely predicted only by considering thermal or solutal gradients. The findings of these studies could allow us to rationally control fluid flow for the directed delivery of payloads at designated locations. In Chapters 3 and 4, our focus was to highlight the potential application of enzyme-powered pumps for sensing and delivery. Chapter 3 explores the use of enzyme pumps as fluid flow-based inhibitor assays. At fixed concentrations of an enzyme and its substrate, the presence of an inhibitor can be detected by monitoring the decrease in fluid flow speed. Using this principle, sensors for toxic

  6. Enzyme Molecules in Solitary Confinement

    Directory of Open Access Journals (Sweden)

    Raphaela B. Liebherr

    2014-09-01

    Full Text Available Large arrays of homogeneous microwells each defining a femtoliter volume are a versatile platform for monitoring the substrate turnover of many individual enzyme molecules in parallel. The high degree of parallelization enables the analysis of a statistically representative enzyme population. Enclosing individual enzyme molecules in microwells does not require any surface immobilization step and enables the kinetic investigation of enzymes free in solution. This review describes various microwell array formats and explores their applications for the detection and investigation of single enzyme molecules. The development of new fabrication techniques and sensitive detection methods drives the field of single molecule enzymology. Here, we introduce recent progress in single enzyme molecule analysis in microwell arrays and discuss the challenges and opportunities.

  7. An expanded Notch-Delta model exhibiting long-range patterning and incorporating MicroRNA regulation.

    Directory of Open Access Journals (Sweden)

    Jerry S Chen

    2014-06-01

    Full Text Available Notch-Delta signaling is a fundamental cell-cell communication mechanism that governs the differentiation of many cell types. Most existing mathematical models of Notch-Delta signaling are based on a feedback loop between Notch and Delta leading to lateral inhibition of neighboring cells. These models result in a checkerboard spatial pattern whereby adjacent cells express opposing levels of Notch and Delta, leading to alternate cell fates. However, a growing body of biological evidence suggests that Notch-Delta signaling produces other patterns that are not checkerboard, and therefore a new model is needed. Here, we present an expanded Notch-Delta model that builds upon previous models, adding a local Notch activity gradient, which affects long-range patterning, and the activity of a regulatory microRNA. This model is motivated by our experiments in the ascidian Ciona intestinalis showing that the peripheral sensory neurons, whose specification is in part regulated by the coordinate activity of Notch-Delta signaling and the microRNA miR-124, exhibit a sparse spatial pattern whereby consecutive neurons may be spaced over a dozen cells apart. We perform rigorous stability and bifurcation analyses, and demonstrate that our model is able to accurately explain and reproduce the neuronal pattern in Ciona. Using Monte Carlo simulations of our model along with miR-124 transgene over-expression assays, we demonstrate that the activity of miR-124 can be incorporated into the Notch decay rate parameter of our model. Finally, we motivate the general applicability of our model to Notch-Delta signaling in other animals by providing evidence that microRNAs regulate Notch-Delta signaling in analogous cell types in other organisms, and by discussing evidence in other organisms of sparse spatial patterns in tissues where Notch-Delta signaling is active.

  8. A mathematical model to determine incorporated quantities of radioactivity from the measured photometric values of tritium-autoradiographs in neuroanatomy

    International Nuclear Information System (INIS)

    Jennissen, J.J.

    1981-01-01

    The mathematical/empirical model developed in this paper helps to determine the incorporated radioactivity from the measured photometric values and the exposure time T. Possible errors of autoradiography due to the exposure time or the preparation are taken into consideration by the empirical model. It is shown that the error of appr. 400% appearing in the sole comparison of the measured photometric values can be corrected. The model is valid for neuroanatomy as optical nerves, i.e. neuroanatomical material, were used to develop it. Its application also to the other sections of the central nervous system seems to be justified due to the reduction of errors thus achieved. (orig.) [de

  9. Integrative computational approach for genome-based study of microbial lipid-degrading enzymes.

    Science.gov (United States)

    Vorapreeda, Tayvich; Thammarongtham, Chinae; Laoteng, Kobkul

    2016-07-01

    Lipid-degrading or lipolytic enzymes have gained enormous attention in academic and industrial sectors. Several efforts are underway to discover new lipase enzymes from a variety of microorganisms with particular catalytic properties to be used for extensive applications. In addition, various tools and strategies have been implemented to unravel the functional relevance of the versatile lipid-degrading enzymes for special purposes. This review highlights the study of microbial lipid-degrading enzymes through an integrative computational approach. The identification of putative lipase genes from microbial genomes and metagenomic libraries using homology-based mining is discussed, with an emphasis on sequence analysis of conserved motifs and enzyme topology. Molecular modelling of three-dimensional structure on the basis of sequence similarity is shown to be a potential approach for exploring the structural and functional relationships of candidate lipase enzymes. The perspectives on a discriminative framework of cutting-edge tools and technologies, including bioinformatics, computational biology, functional genomics and functional proteomics, intended to facilitate rapid progress in understanding lipolysis mechanism and to discover novel lipid-degrading enzymes of microorganisms are discussed.

  10. Enzyme technology: Key to selective biorefining

    DEFF Research Database (Denmark)

    Meyer, Anne S.

    2014-01-01

    to the reaction is a unique trait of enzyme catalysis. Since enzyme selectivity means that a specific reaction is catalysed between particular species to produce definite products, enzymes are particularly fit for converting specific compounds in mixed biomass streams. Since enzymes are protein molecules...... their rational use in biorefinery processes requires an understanding of the basic features of enzymes and reaction traits with respect to specificity, kinetics, reaction optima, stability and structure-function relations – we are now at a stage where it is possible to use nature’s enzyme structures as starting...... point and then improve the functional traits by targeted mutation of the protein. The talk will display some of our recent hypotheses related to enzyme action, recently obtained results within knowledge-based enzyme improvements as well as cast light on research methods used in optimizing enzyme...

  11. Enzyme-assisted extraction of stabilized chlorophyll from spinach.

    Science.gov (United States)

    Özkan, Gülay; Ersus Bilek, Seda

    2015-06-01

    Zinc complex formation with chlorophyll derivatives in spinach pulp was studied by adding 300ppm Zn(2+) for production of stable food colorant, followed by the heating at 110°C for 15min. Zinc complex formation increased at pH values of 7.0 or greater. Pectinex Ultra SP-L was selected for enzyme-assisted release of zinc-chlorophyll derivatives from spinach pulp. Effect of enzyme concentration (1-9%), treatment temperature (30-60°C), and time (30-210min) on total chlorophyll content (TCC) were optimized using response surface methodology. A quadratic regression model (R(2)=0.9486) was obtained from the experimental design. Optimum treatment conditions were 8% enzyme concentration, 45°C, and 30min, which yielded a 50.747mgTCC/100g spinach pulp. Enzymatic treatment was followed by solvent extraction with ethanol at a solvent-to-sample ratio of 2.5:1 at 60°C for 45min for the highest TCC recovery. Pretreatment with enzyme and extraction in ethanol resulted in 39% increase in Zn-chlorophyll derivative yield. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Some considerations concerning the challenge of incorporating social variables into epidemiological models of infectious disease transmission.

    Science.gov (United States)

    Barnett, Tony; Fournié, Guillaume; Gupta, Sunetra; Seeley, Janet

    2015-01-01

    Incorporation of 'social' variables into epidemiological models remains a challenge. Too much detail and models cease to be useful; too little and the very notion of infection - a highly social process in human populations - may be considered with little reference to the social. The French sociologist Émile Durkheim proposed that the scientific study of society required identification and study of 'social currents'. Such 'currents' are what we might today describe as 'emergent properties', specifiable variables appertaining to individuals and groups, which represent the perspectives of social actors as they experience the environment in which they live their lives. Here we review the ways in which one particular emergent property, hope, relevant to a range of epidemiological situations, might be used in epidemiological modelling of infectious diseases in human populations. We also indicate how such an approach might be extended to include a range of other potential emergent properties to represent complex social and economic processes bearing on infectious disease transmission.

  13. A family of spatial interaction models incorporating information flows and choice set constraints applied to U.S. interstate labor flows.

    Science.gov (United States)

    Smith, T R; Slater, P B

    1981-01-01

    "A new family of migration models belonging to the elimination by aspects family is examined, with the spatial interaction model shown to be a special case. The models have simple forms; they incorporate information flow processes and choice set constraints; they are free of problems raised by the Luce Choice Axiom; and are capable of generating intransitive flows. Preliminary calibrations using the Continuous Work History Sample [time] series data indicate that the model fits the migration data well, while providing estimates of interstate job message flows. The preliminary calculations also indicate that care is needed in assuming that destination [attraction] are independent of origins." excerpt

  14. Nanoarmored Enzymes for Organic Enzymology: Synthesis and Characterization of Poly(2-Alkyloxazoline)-Enzyme Conjugates.

    Science.gov (United States)

    Leurs, Melanie; Tiller, Joerg C

    2017-01-01

    The properties of enzymes can be altered significantly by modification with polymers. Numerous different methods are known to obtain such polymer-enzyme conjugates (PECs). However, there is no universal method to render enzymes into PECs that are fully soluble in organic solvents. Here, we present a method, which achieves such high degree of modification of proteins that the majority of modified enzymes will be soluble in organic solvents. This is achieved by preparing poly(2-alkyloxazoline)s (POx) with an NH 2 end group and coupling this functional polymer via pyromellitic acid dianhydride onto the amino groups of the respective protein. The resulting PECs are capable of serving as surfactants for unmodified proteins, rendering the whole mixture organosoluble. Depending on the nature of the POx and the molecular weight and the nature of the enzyme, the PECs are soluble in chloroform or even toluene. Another advantage of this method is that the poly(2-alkyloxazoline) can be activated with the coupling agent and used for the enzyme conjugation without further purification. The POx-enzyme conjugates generated by this modification strategy show modulated catalytic activity in both, aqueous and organic, systems. © 2017 Elsevier Inc. All rights reserved.

  15. Engineering the cell surface display of cohesins for assembly of cellulosome-inspired enzyme complexes on Lactococcus lactis

    Directory of Open Access Journals (Sweden)

    Wieczorek Andrew S

    2010-09-01

    Full Text Available Abstract Background The assembly and spatial organization of enzymes in naturally occurring multi-protein complexes is of paramount importance for the efficient degradation of complex polymers and biosynthesis of valuable products. The degradation of cellulose into fermentable sugars by Clostridium thermocellum is achieved by means of a multi-protein "cellulosome" complex. Assembled via dockerin-cohesin interactions, the cellulosome is associated with the cell surface during cellulose hydrolysis, forming ternary cellulose-enzyme-microbe complexes for enhanced activity and synergy. The assembly of recombinant cell surface displayed cellulosome-inspired complexes in surrogate microbes is highly desirable. The model organism Lactococcus lactis is of particular interest as it has been metabolically engineered to produce a variety of commodity chemicals including lactic acid and bioactive compounds, and can efficiently secrete an array of recombinant proteins and enzymes of varying sizes. Results Fragments of the scaffoldin protein CipA were functionally displayed on the cell surface of Lactococcus lactis. Scaffolds were engineered to contain a single cohesin module, two cohesin modules, one cohesin and a cellulose-binding module, or only a cellulose-binding module. Cell toxicity from over-expression of the proteins was circumvented by use of the nisA inducible promoter, and incorporation of the C-terminal anchor motif of the streptococcal M6 protein resulted in the successful surface-display of the scaffolds. The facilitated detection of successfully secreted scaffolds was achieved by fusion with the export-specific reporter staphylococcal nuclease (NucA. Scaffolds retained their ability to associate in vivo with an engineered hybrid reporter enzyme, E. coli β-glucuronidase fused to the type 1 dockerin motif of the cellulosomal enzyme CelS. Surface-anchored complexes exhibited dual enzyme activities (nuclease and β-glucuronidase, and were

  16. Computer calculation of neutron cross sections with Hauser-Feshbach code STAPRE incorporating the hybrid pre-compound emission model

    International Nuclear Information System (INIS)

    Ivascu, M.

    1983-10-01

    Computer codes incorporating advanced nuclear models (optical, statistical and pre-equilibrium decay nuclear reaction models) were used to calculate neutron cross sections needed for fusion reactor technology. The elastic and inelastic scattering (n,2n), (n,p), (n,n'p), (n,d) and (n,γ) cross sections for stable molybdenum isotopes Mosup(92,94,95,96,97,98,100) and incident neutron energy from about 100 keV or a threshold to 20 MeV were calculated using the consistent set of input parameters. The hydrogen production cross section which determined the radiation damage in structural materials of fusion reactors can be simply deduced from the presented results. The more elaborated microscopic models of nuclear level density are required for high accuracy calculations

  17. A kinematic wave model in Lagrangian coordinates incorporating capacity drop: Application to homogeneous road stretches and discontinuities

    Science.gov (United States)

    Yuan, Kai; Knoop, Victor L.; Hoogendoorn, Serge P.

    2017-01-01

    On freeways, congestion always leads to capacity drop. This means the queue discharge rate is lower than the pre-queue capacity. Our recent research findings indicate that the queue discharge rate increases with the speed in congestion, that is the capacity drop is strongly correlated with the congestion state. Incorporating this varying capacity drop into a kinematic wave model is essential for assessing consequences of control strategies. However, to the best of authors' knowledge, no such a model exists. This paper fills the research gap by presenting a Lagrangian kinematic wave model. "Lagrangian" denotes that the new model is solved in Lagrangian coordinates. The new model can give capacity drops accompanying both of stop-and-go waves (on homogeneous freeway section) and standing queues (at nodes) in a network. The new model can be applied in a network operation. In this Lagrangian kinematic wave model, the queue discharge rate (or the capacity drop) is a function of vehicular speed in traffic jams. Four case studies on links as well as at lane-drop and on-ramp nodes show that the Lagrangian kinematic wave model can give capacity drops well, consistent with empirical observations.

  18. Impact of enzyme loading on the efficacy and recovery of cellulolytic enzymes immobilized on enzymogel nanoparticles.

    Science.gov (United States)

    Samaratunga, Ashani; Kudina, Olena; Nahar, Nurun; Zakharchenko, Andrey; Minko, Sergiy; Voronov, Andriy; Pryor, Scott W

    2015-03-01

    Cellulase and β-glucosidase were adsorbed on a polyacrylic acid polymer brush grafted on silica nanoparticles to produce enzymogels as a form of enzyme immobilization. Enzyme loading on the enzymogels was increased to a saturation level of approximately 110 μg (protein) mg(-1) (particle) for each enzyme. Enzymogels with varied enzyme loadings were then used to determine the impact on hydrolysis rate and enzyme recovery. Soluble sugar concentrations during the hydrolysis of filter paper and Solka-Floc with the enzymogels were 45 and 53%, respectively, of concentrations when using free cellulase. β-Glucosidase enzymogels showed lower performance; hydrolyzate glucose concentrations were just 38% of those using free enzymes. Increasing enzyme loading on the enzymogels did not reduce net efficacy for cellulase and improved efficacy for β-glucosidase. The use of free cellulases and cellulase enzymogels resulted in hydrolyzates with different proportions of cellobiose and glucose, suggesting differential attachment or efficacy of endoglucanases, exoglucanases, and β-glucosidases present in cellulase mixtures. When loading β-glucosidase individually, higher enzyme loadings on the enzymogels produced higher hydrolyzate glucose concentrations. Approximately 96% of cellulase and 66 % of β-glucosidase were recovered on the enzymogels, while enzyme loading level did not impact recovery for either enzyme.

  19. [Interaction between CYP450 enzymes and metabolism of traditional Chinese medicine as well as enzyme activity assay].

    Science.gov (United States)

    Lu, Tu-lin; Su, Lian-lin; Ji, De; Gu, Wei; Mao, Chun-qin

    2015-09-01

    Drugs are exogenous compounds for human bodies, and will be metabolized by many enzymes after administration. CYP450 enzyme, as a major metabolic enzyme, is an important phase I drug metabolizing enzyme. In human bodies, about 75% of drug metabolism is conducted by CYP450 enzymes, and CYP450 enzymes is the key factor for drug interactions between traditional Chinese medicine( TCM) -TCM, TCM-medicine and other drug combination. In order to make clear the interaction between metabolic enzymes and TCM metabolism, we generally chose the enzymatic activity as an evaluation index. That is to say, the enhancement or reduction of CYP450 enzyme activity was used to infer the inducing or inhibitory effect of active ingredients and extracts of traditional Chinese medicine on enzymes. At present, the common method for measuring metabolic enzyme activity is Cocktail probe drugs, and it is the key to select the suitable probe substrates. This is of great significance for study drug's absorption, distribution, metabolism and excretion (ADME) process in organisms. The study focuses on the interaction between TCMs, active ingredients, herbal extracts, cocktail probe substrates as well as CYP450 enzymes, in order to guide future studies.

  20. Bitter taste masking of enzyme-treated soy protein in water and bread.

    Science.gov (United States)

    Bertelsen, Anne S; Laursen, Anne; Knudsen, Tine A; Møller, Stine; Kidmose, Ulla

    2018-08-01

    Bioactive protein hydrolysates are often very bitter. To overcome this challenge, xylitol, sucrose, α-cyclodextrin, maltodextrin and combinations of these were tested systematically as bitter-masking agents of an enzyme-treated soy protein in an aqueous model and in a bread model. Sensory descriptive analysis was used to reveal the bitter-masking effect of the taste-masking blends on the enzyme-treated soy protein. In water, xylitol, sucrose and maltodextrin reduced bitterness significantly, whereas α-cyclodextrin did not. No significant difference was observed in bitterness reduction between xylitol and sucrose. Both reduced bitterness significantly more than maltodextrin. No interactions between the taste-masking agents affecting bitterness reduction were found. Clearer bitter-masking effects were seen in the aqueous model compared with the bread model. The bitter-masking effects of α-cyclodextrin and maltodextrin were similar between water and bread. The effect of xylitol and sucrose on bitterness suppression varied between the systems. In water, bitterness was negatively correlated with sweetness. In bread, bitterness was negatively correlated with freshness, and maltodextrin significantly reduced bitterness of the enzyme-treated soy protein and increased freshness. Bitter-masking effects were generally more discernible in the aqueous model compared with the bread model. © 2018 Society of Chemical Industry. © 2018 Society of Chemical Industry.

  1. Integrative modelling of animal movement: incorporating in situ habitat and behavioural information for a migratory marine predator.

    Science.gov (United States)

    Bestley, Sophie; Jonsen, Ian D; Hindell, Mark A; Guinet, Christophe; Charrassin, Jean-Benoît

    2013-01-07

    A fundamental goal in animal ecology is to quantify how environmental (and other) factors influence individual movement, as this is key to understanding responsiveness of populations to future change. However, quantitative interpretation of individual-based telemetry data is hampered by the complexity of, and error within, these multi-dimensional data. Here, we present an integrative hierarchical Bayesian state-space modelling approach where, for the first time, the mechanistic process model for the movement state of animals directly incorporates both environmental and other behavioural information, and observation and process model parameters are estimated within a single model. When applied to a migratory marine predator, the southern elephant seal (Mirounga leonina), we find the switch from directed to resident movement state was associated with colder water temperatures, relatively short dive bottom time and rapid descent rates. The approach presented here can have widespread utility for quantifying movement-behaviour (diving or other)-environment relationships across species and systems.

  2. BAKERY ENZYMES IN CEREAL TECHNOLOGIES

    Directory of Open Access Journals (Sweden)

    Václav Koman

    2012-10-01

    Full Text Available Normal 0 21 false false false SK X-NONE X-NONE Bread is the most common and traditional food in the world. For years, enzymes such as malt and fungal alpha-amylase have been used in bread making. Due to the changes in the baking industry and the ever-increasing demand for more natural products, enzymes have gained real importance in bread-making. If an enzyme is added, it is often destroyed by the heat during the baking process. For generations, enzymes have been used for the improvement of texture and appearance, enhancement of nutritional values and generation of appealing flavours and aromas. Enzymes used in bakery industry constitute nearly one third of the market. The bakery products have undergone radical improvements in quality over the past years in terms of flavour, texture and shelf-life. The the biggest contributor for these improvementsis the usage of enzymes. Present work seeks to systematically describe bakery enzymes, their classification, benefits, usage and chemical reactions in the bread making process.doi:10.5219/193

  3. HIV-1 incorporates and proteolytically processes human NDR1 and NDR2 serine-threonine kinases

    International Nuclear Information System (INIS)

    Devroe, Eric; Silver, Pamela A.; Engelman, Alan

    2005-01-01

    Mammalian genomes encode two related serine-threonine kinases, nuclear Dbf2 related (NDR)1 and NDR2, which are homologous to the Saccharomyces cerevisiae Dbf2 kinase. Recently, a yeast genetic screen implicated the Dbf2 kinase in Ty1 retrotransposition. Since several virion-incorporated kinases regulate the infectivity of human immunodeficiency virus type 1 (HIV-1), we speculated that the human NDR1 and NDR2 kinases might play a role in the HIV-1 life cycle. Here we show that the NDR1 and NDR2 kinases were incorporated into HIV-1 particles. Furthermore, NDR1 and NDR2 were cleaved by the HIV-1 protease (PR), both within virions and within producer cells. Truncation at the PR cleavage site altered NDR2 subcellular localization and inhibited NDR1 and NDR2 enzymatic activity. These studies identify two new virion-associated host cell enzymes and suggest a novel mechanism by which HIV-1 alters the intracellular environment of human cells

  4. Influence of protoplast fusion between two Trichoderma spp. on extracellular enzymes production and antagonistic activity.

    Science.gov (United States)

    Hassan, Mohamed M

    2014-11-02

    Biological control plays a crucial role in grapevine pathogens disease management. The cell-wall degrading enzymes chitinase, cellulase and β-glucanase have been suggested to be essential for the mycoparasitism activity of Trichoderma species against grapevine fungal pathogens. In order to develop a useful strain as a single source of these vital enzymes, it was intended to incorporate the characteristics of two parental fungicides tolerant mutants of Trichoderma belonging to the high chitinase producing species T. harzianum and the high cellulase producing species T. viride , by fusing their protoplasts. The phylogeny of the parental strains was carried out using a sequence of the 5.8S-ITS region. The BLAST of the obtained sequence identified these isolates as T. harzianum and T. viride . Protoplasts were isolated using lysing enzymes and were fused using polyethylene glycol. The fused protoplasts have been regenerated on protoplast regeneration minimal medium supplemented with two selective fungicides. Among the 40 fast growing fusants, 17 fusants were selected based on their enhanced growth on selective media for further studies. The fusant strains were growing 60%-70% faster than the parents up to third generation. All the 17 selected fusants exhibited morphological variations. Some fusant strains displayed threefold increased chitinase enzyme activity and twofold increase in β-glucanase enzyme activity compared to the parent strains. Most fusants showed powerful antagonistic activity against Macrophomin aphaseolina , Pythium ultimum and Sclerotium rolfsii pathogens. Fusant number 15 showed the highest inhibition percentage (92.8%) against M. phaseolina and P. ultimum, while fusant number 9 showed the highest inhibition percentage (98.2%) against the growth of S. rolfsii. A hyphal intertwining and degradation phenomenon was observed by scanning electron microscope. The Trichoderma antagonistic effect against pathogenic fungal mycelia was due to the

  5. Silica-Immobilized Enzyme Reactors; Application to Cholinesterase-Inhibition Studies

    National Research Council Canada - National Science Library

    Luckarift, Heather R; Johnson, Glenn R; Spain, Jim C

    2006-01-01

    ...) using silica-encapsulated equine butyrycholinestearse (BuChE) as a model system. Peptide-mediated silica formation was used to encapsulate BuChE, directly immobilizing the enzyme within a commercial pre-packed column...

  6. A Non-Isothermal Chemical Lattice Boltzmann Model Incorporating Thermal Reaction Kinetics and Enthalpy Changes

    Directory of Open Access Journals (Sweden)

    Stuart Bartlett

    2017-08-01

    Full Text Available The lattice Boltzmann method is an efficient computational fluid dynamics technique that can accurately model a broad range of complex systems. As well as single-phase fluids, it can simulate thermohydrodynamic systems and passive scalar advection. In recent years, it also gained attention as a means of simulating chemical phenomena, as interest in self-organization processes increased. This paper will present a widely-used and versatile lattice Boltzmann model that can simultaneously incorporate fluid dynamics, heat transfer, buoyancy-driven convection, passive scalar advection, chemical reactions and enthalpy changes. All of these effects interact in a physically accurate framework that is simple to code and readily parallelizable. As well as a complete description of the model equations, several example systems will be presented in order to demonstrate the accuracy and versatility of the method. New simulations, which analyzed the effect of a reversible reaction on the transport properties of a convecting fluid, will also be described in detail. This extra chemical degree of freedom was utilized by the system to augment its net heat flux. The numerical method outlined in this paper can be readily deployed for a vast range of complex flow problems, spanning a variety of scientific disciplines.

  7. Investigation of proteolytic enzymes expression in brain tissue and cultivated retinal pigment epithelial cells at transgenic animal model of Hintington´s disease

    Czech Academy of Sciences Publication Activity Database

    Ardan, Taras; Kocurová, Gabriela; Motlík, Jan

    2015-01-01

    Roč. 78, Suppl 2 (2015), s. 12-12 ISSN 1210-7859. [Conference on Animal Models for neurodegenerative Diseases /3./. 08.11.2015-10.11.2015, Liblice] R&D Projects: GA MŠk ED2.1.00/03.0124; GA MŠk(CZ) 7F14308 Institutional support: RVO:67985904 Keywords : Huntington ´s disease * transgenic porcine model * proteolytic enzymes Subject RIV: EB - Genetics ; Molecular Biology

  8. Crosslinked Enzyme Aggregates in Hierarchically-Ordered Mesoporous Silica: A Simple and Effective Method for Enzyme Stabilization

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Moon Il; Kim, Jungbae; Lee, Jinwoo; Jia, Hongfei; Na, Hyon Bin; Youn, Jongkyu; Kwak, Ja Hun; Dohnalkova, Alice; Grate, Jay W.; Wang, Ping; Hyeon, Taeghwan; Park, Hyun-Gyu; Chang, Ho Nam

    2007-02-01

    alpha-chymotrypsin (CT) and lipase (LP) were immobilized in hierarchically-ordered mesocellular mesoporous silica (HMMS) in a simple but effective way for the enzyme stabilization, which was achieved by the enzyme adsorption followed by glutaraldehyde (GA) crosslinking. This resulted in the formation of nanometer scale crosslinked enzyme aggregates (CLEAs) entrapped in the mesocellular pores of HMMS (37 nm), which did not leach out of HMMS through narrow mesoporous channels (13 nm). CLEA of alpha-chymotrypsin (CLEA-CT) in HMMS showed a high enzyme loading capacity and significantly increased enzyme stability. No activity decrease of CLEA-CT was observed for two weeks under even rigorously shaking condition, while adsorbed CT in HMMS and free CT showed a rapid inactivation due to the enzyme leaching and presumably autolysis, respectively. With the CLEA-CT in HMMS, however, there was no tryptic digestion observed suggesting that the CLEA-CT is not susceptible to autolysis. Moreover, CLEA of lipase (CLEA-LP) in HMMS retained 30% specific activity of free lipase with greatly enhanced stability. This work demonstrates that HMMS can be efficiently employed as host materials for enzyme immobilization leading to highly enhanced stability of the immobilized enzymes with high enzyme loading and activity.

  9. Applying neural networks as software sensors for enzyme engineering.

    Science.gov (United States)

    Linko, S; Zhu, Y H; Linko, P

    1999-04-01

    The on-line control of enzyme-production processes is difficult, owing to the uncertainties typical of biological systems and to the lack of suitable on-line sensors for key process variables. For example, intelligent methods to predict the end point of fermentation could be of great economic value. Computer-assisted control based on artificial-neural-network models offers a novel solution in such situations. Well-trained feedforward-backpropagation neural networks can be used as software sensors in enzyme-process control; their performance can be affected by a number of factors.

  10. A Microdosimetric-Kinetic Model of Cell Killing by Irradiation from Permanently Incorporated Radionuclides.

    Science.gov (United States)

    Hawkins, Roland B

    2018-01-01

    An expression for the surviving fraction of a replicating population of cells exposed to permanently incorporated radionuclide is derived from the microdosimetric-kinetic model. It includes dependency on total implant dose, linear energy transfer (LET), decay rate of the radionuclide, the repair rate of potentially lethal lesions in DNA and the volume doubling time of the target population. This is used to obtain an expression for the biologically effective dose ( BED α / β ) based on the minimum survival achieved by the implant that is equivalent to, and can be compared and combined with, the BED α / β calculated for a fractionated course of radiation treatment. Approximate relationships are presented that are useful in the calculation of BED α / β for alpha- or beta-emitting radionuclides with half-life significantly greater than, or nearly equal to, the approximately 1-h repair half-life of radiation-induced potentially lethal lesions.

  11. Immobilized enzymes and cells

    Energy Technology Data Exchange (ETDEWEB)

    Bucke, C; Wiseman, A

    1981-04-04

    This article reviews the current state of the art of enzyme and cell immobilization and suggests advances which might be made during the 1980's. Current uses of immobilized enzymes include the use of glucoamylase in the production of glucose syrups from starch and glucose isomerase in the production of high fructose corn syrup. Possibilities for future uses of immobilized enzymes and cells include the utilization of whey and the production of ethanol.

  12. Estimating disperser abundance using open population models that incorporate data from continuous detection PIT arrays

    Science.gov (United States)

    Dzul, Maria C.; Yackulic, Charles B.; Korman, Josh

    2017-01-01

    Autonomous passive integrated transponder (PIT) tag antenna systems continuously detect individually marked organisms at one or more fixed points over long time periods. Estimating abundance using data from autonomous antennae can be challenging, because these systems do not detect unmarked individuals. Here we pair PIT antennae data from a tributary with mark-recapture sampling data in a mainstem river to estimate the number of fish moving from the mainstem to the tributary. We then use our model to estimate abundance of non-native rainbow trout Oncorhynchus mykiss that move from the Colorado River to the Little Colorado River (LCR), the latter of which is important spawning and rearing habitat for federally-endangered humpback chub Gila cypha. We estimate 226 rainbow trout (95% CI: 127-370) entered the LCR from October 2013-April 2014. We discuss the challenges of incorporating detections from autonomous PIT antenna systems into mark-recapture population models, particularly in regards to using information about spatial location to estimate movement and detection probabilities.

  13. Incorporating Single-nucleotide Polymorphisms Into the Lyman Model to Improve Prediction of Radiation Pneumonitis

    Energy Technology Data Exchange (ETDEWEB)

    Tucker, Susan L., E-mail: sltucker@mdanderson.org [Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Li Minghuan [Department of Radiation Oncology, Shandong Cancer Hospital, Jinan, Shandong (China); Xu Ting; Gomez, Daniel [Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Yuan Xianglin [Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan (China); Yu Jinming [Department of Radiation Oncology, Shandong Cancer Hospital, Jinan, Shandong (China); Liu Zhensheng; Yin Ming; Guan Xiaoxiang; Wang Lie; Wei Qingyi [Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Mohan, Radhe [Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Vinogradskiy, Yevgeniy [University of Colorado School of Medicine, Aurora, Colorado (United States); Martel, Mary [Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Liao Zhongxing [Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas (United States)

    2013-01-01

    Purpose: To determine whether single-nucleotide polymorphisms (SNPs) in genes associated with DNA repair, cell cycle, transforming growth factor-{beta}, tumor necrosis factor and receptor, folic acid metabolism, and angiogenesis can significantly improve the fit of the Lyman-Kutcher-Burman (LKB) normal-tissue complication probability (NTCP) model of radiation pneumonitis (RP) risk among patients with non-small cell lung cancer (NSCLC). Methods and Materials: Sixteen SNPs from 10 different genes (XRCC1, XRCC3, APEX1, MDM2, TGF{beta}, TNF{alpha}, TNFR, MTHFR, MTRR, and VEGF) were genotyped in 141 NSCLC patients treated with definitive radiation therapy, with or without chemotherapy. The LKB model was used to estimate the risk of severe (grade {>=}3) RP as a function of mean lung dose (MLD), with SNPs and patient smoking status incorporated into the model as dose-modifying factors. Multivariate analyses were performed by adding significant factors to the MLD model in a forward stepwise procedure, with significance assessed using the likelihood-ratio test. Bootstrap analyses were used to assess the reproducibility of results under variations in the data. Results: Five SNPs were selected for inclusion in the multivariate NTCP model based on MLD alone. SNPs associated with an increased risk of severe RP were in genes for TGF{beta}, VEGF, TNF{alpha}, XRCC1 and APEX1. With smoking status included in the multivariate model, the SNPs significantly associated with increased risk of RP were in genes for TGF{beta}, VEGF, and XRCC3. Bootstrap analyses selected a median of 4 SNPs per model fit, with the 6 genes listed above selected most often. Conclusions: This study provides evidence that SNPs can significantly improve the predictive ability of the Lyman MLD model. With a small number of SNPs, it was possible to distinguish cohorts with >50% risk vs <10% risk of RP when they were exposed to high MLDs.

  14. (1,3;1,4)-β-Glucan Biosynthesis by the CSLF6 Enzyme: Position and Flexibility of Catalytic Residues Influence Product Fine Structure.

    Science.gov (United States)

    Dimitroff, George; Little, Alan; Lahnstein, Jelle; Schwerdt, Julian G; Srivastava, Vaibhav; Bulone, Vincent; Burton, Rachel A; Fincher, Geoffrey B

    2016-04-05

    Cellulose synthase-like F6 (CslF6) genes encode polysaccharide synthases responsible for (1,3;1,4)-β-glucan biosynthesis in cereal grains. However, it is not clear how both (1,3)- and (1,4)-linkages are incorporated into a single polysaccharide chain and how the frequency and arrangement of the two linkage types that define the fine structure of the polysaccharide are controlled. Through transient expression in Nicotiana benthamiana leaves, two CSLF6 orthologs from different cereal species were shown to mediate the synthesis of (1,3;1,4)-β-glucans with very different fine structures. Chimeric cDNA constructs with interchanged sections of the barley and sorghum CslF6 genes were developed to identify regions of the synthase enzyme responsible for these differences. A single amino acid residue upstream of the TED motif in the catalytic region was shown to dramatically change the fine structure of the polysaccharide produced. The structural basis of this effect can be rationalized by reference to a homology model of the enzyme and appears to be related to the position and flexibility of the TED motif in the active site of the enzyme. The region and amino acid residue identified provide opportunities to manipulate the solubility of (1,3;1,4)-β-glucan in grains and vegetative tissues of the grasses and, in particular, to enhance the solubility of dietary fibers that are beneficial to human health.

  15. Extended Fitts' model of pointing time in eye-gaze input system - Incorporating effects of target shape and movement direction into modeling.

    Science.gov (United States)

    Murata, Atsuo; Fukunaga, Daichi

    2018-04-01

    This study attempted to investigate the effects of the target shape and the movement direction on the pointing time using an eye-gaze input system and extend Fitts' model so that these factors are incorporated into the model and the predictive power of Fitts' model is enhanced. The target shape, the target size, the movement distance, and the direction of target presentation were set as within-subject experimental variables. The target shape included: a circle, and rectangles with an aspect ratio of 1:1, 1:2, 1:3, and 1:4. The movement direction included eight directions: upper, lower, left, right, upper left, upper right, lower left, and lower right. On the basis of the data for identifying the effects of the target shape and the movement direction on the pointing time, an attempt was made to develop a generalized and extended Fitts' model that took into account the movement direction and the target shape. As a result, the generalized and extended model was found to fit better to the experimental data, and be more effective for predicting the pointing time for a variety of human-computer interaction (HCI) task using an eye-gaze input system. Copyright © 2017. Published by Elsevier Ltd.

  16. Structural basis for proficient incorporation of dTTP opposite O6-methylguanine by human DNA polymerase iota.

    Science.gov (United States)

    Pence, Matthew G; Choi, Jeong-Yun; Egli, Martin; Guengerich, F Peter

    2010-12-24

    O(6)-methylguanine (O(6)-methylG) is highly mutagenic and is commonly found in DNA exposed to methylating agents, even physiological ones (e.g. S-adenosylmethionine). The efficiency of a truncated, catalytic DNA polymerase ι core enzyme was determined for nucleoside triphosphate incorporation opposite O(6)-methylG, using steady-state kinetic analyses. The results presented here corroborate previous work from this laboratory using full-length pol ι, which showed that dTTP incorporation occurs with high efficiency opposite O(6)-methylG. Misincorporation of dTTP opposite O(6)-methylG occurred with ∼6-fold higher efficiency than incorporation of dCTP. Crystal structures of the truncated form of pol ι with O(6)-methylG as the template base and incoming dCTP or dTTP were solved and showed that O(6)-methylG is rotated into the syn conformation in the pol ι active site and that dTTP misincorporation by pol ι is the result of Hoogsteen base pairing with the adduct. Both dCTP and dTTP base paired with the Hoogsteen edge of O(6)-methylG. A single, short hydrogen bond formed between the N3 atom of dTTP and the N7 atom of O(6)-methylG. Protonation of the N3 atom of dCTP and bifurcation of the N3 hydrogen between the N7 and O(6) atoms of O(6)-methylG allow base pairing of the lesion with dCTP. We conclude that differences in the Hoogsteen hydrogen bonding between nucleotides is the main factor in the preferential selectivity of dTTP opposite O(6)-methylG by human pol ι, in contrast to the mispairing modes observed previously for O(6)-methylG in the structures of the model DNA polymerases Sulfolobus solfataricus Dpo4 and Bacillus stearothermophilus DNA polymerase I.

  17. Dual-color plasmonic enzyme-linked immunosorbent assay based on enzyme-mediated etching of Au nanoparticles

    Science.gov (United States)

    Guo, Longhua; Xu, Shaohua; Ma, Xiaoming; Qiu, Bin; Lin, Zhenyu; Chen, Guonan

    2016-09-01

    Colorimetric enzyme-linked immunosorbent assay utilizing 3‧-3-5‧-5-tetramethylbenzidine(TMB) as the chromogenic substrate has been widely used in the hospital for the detection of all kinds of disease biomarkers. Herein, we demonstrate a strategy to change this single-color display into dual-color responses to improve the accuracy of visual inspection. Our investigation firstly reveals that oxidation state of 3‧-3-5‧-5-tetramethylbenzidine (TMB2+) can quantitatively etch gold nanoparticles. Therefore, the incorporation of gold nanoparticles into a commercial TMB-based ELISA kit could generate dual-color responses: the solution color varied gradually from wine red (absorption peak located at ~530 nm) to colorless, and then from colorless to yellow (absorption peak located at ~450 nm) with the increase amount of targets. These dual-color responses effectively improved the sensitivity as well as the accuracy of visual inspection. For example, the proposed dual-color plasmonic ELISA is demonstrated for the detection of prostate-specific antigen (PSA) in human serum with a visual limit of detection (LOD) as low as 0.0093 ng/mL.

  18. Sequence dependent DNA conformations: Raman spectroscopic studies and a model of action of restriction enzymes

    International Nuclear Information System (INIS)

    Nishimura, Y.

    1985-01-01

    Raman spectra have been examined to clarify the polymorphic forms of DNA, A, B, and Z forms. From an analysis the authors found that the guanine ring breathing vibration is sensitive to its local conformation. Examination of nine crystals of guanosine residues in which the local conformations are well established revealed that a guanosine residue with a C3'endo-anti gives a strong line at 666+-2 cm/sup -1/, O4'endo-anti at 682 cm/sup -1/, C1'exo-anti at 673 cm/sup -1/, C2'endo-anti at 677 cm/sup -1/ and syn-forms around 625 cm/sup -1/. Using this characteristic line, they were able to obtain the local conformations of guanosine moieties in poly(dG-dC). Such a sequence derived variation is suggested to be recognized by sequence specific proteins such as restriction enzymes. The authors found a correlation between sequence dependent DNA conformation and a mode of action of restriction enzymes. The cutting mode of restriction enzymes is classified into three groups. The classification of whether the products have blunt ends, two-base-long cohesive ends, or four-base-long cohesive ends depends primarily on the substrate, not on the enzyme. It is suggested that sequence dependent DNA conformation causes such a classification by the use of the Calladine-Dickerson analysis. In the recognition of restriction enzymes, the methyl group in a certain sequence is considered to play an important role by changing the local conformation of DNA

  19. Metabolic fate of lactoferricin-based antimicrobial peptides: effect of truncation and incorporation of amino acid analogs on the in vitro metabolic stability.

    Science.gov (United States)

    Svenson, Johan; Vergote, Valentijn; Karstad, Rasmus; Burvenich, Christian; Svendsen, John S; De Spiegeleer, Bart

    2010-03-01

    A series of promising truncated antibacterial tripeptides derived from lactoferricin has been prepared, and their in vitro metabolic stability in the main metabolic compartments, plasma, liver, kidney, stomach, duodenum, and brain, has been investigated for the first time. The potential stabilizing effect of truncation, C-terminal capping, and introduction of the bulky synthetic amino acid biphenylalanine is also investigated. The drug-like peptides displayed large differences in half-lives in the different matrixes ranging from 4.2 min in stomach and duodenum to 355.9 min in liver. Kinetic analysis of the metabolites revealed that several different degrading enzymes simultaneously target the different peptide bonds and that the outcome of the tested strategies to increase the stability is clearly enzyme-specific. Some of the metabolic enzymes even prefer the synthetic modifications incorporated over the natural counterparts. Collectively, it is shown that the necessary antibacterial pharmacophore generates compounds that are not only potent antibacterial peptides, but excellent substrates for the main degrading enzymes. All the amide bonds are thus rapidly targeted by different enzymes despite the short peptidic sequences of the tested compounds. Hence, our results illustrate that several structural changes are needed before these compounds can be considered for oral administration. Strategies to overcome such metabolic challenges are discussed.

  20. Calculated activity incorporated in the therapy with I131

    International Nuclear Information System (INIS)

    Chica, L.G.; Puerta, J.A.

    1998-01-01

    By means of the product S(T→ S).A s (T e ), the absorbed dose to thyroid delivered by I 131 incorporated is calculated. Where S(T→ S) is the absorbed dose in the thyroid per nuclear transformation (tn.) of I 131 localized in the thyroid and as a potential function of the mass is expressed. A s (T e ) is the number of tn. of I 131 in the thyroid since the moment of the incorporation until the time T e (the effective middle time); to find A s (T e ) to normal as different pathological conditions, the metabolic model of the iodo proposed by the ICRP is used. Of the expressions of the doses, the incorporated activity, l o , is obtained

  1. Energy system investment model incorporating heat pumps with thermal storage in buildings and buffer tanks

    International Nuclear Information System (INIS)

    Hedegaard, Karsten; Balyk, Olexandr

    2013-01-01

    Individual compression heat pumps constitute a potentially valuable resource in supporting wind power integration due to their economic competitiveness and possibilities for flexible operation. When analysing the system benefits of flexible heat pump operation, effects on investments should be taken into account. In this study, we present a model that facilitates analysing individual heat pumps and complementing heat storages in integration with the energy system, while optimising both investments and operation. The model incorporates thermal building dynamics and covers various heat storage options: passive heat storage in the building structure via radiator heating, active heat storage in concrete floors via floor heating, and use of thermal storage tanks for space heating and hot water. It is shown that the model is well qualified for analysing possibilities and system benefits of operating heat pumps flexibly. This includes prioritising heat pump operation for hours with low marginal electricity production costs, and peak load shaving resulting in a reduced need for peak and reserve capacity investments. - Highlights: • Model optimising heat pumps and heat storages in integration with the energy system. • Optimisation of both energy system investments and operation. • Heat storage in building structure and thermal storage tanks included. • Model well qualified for analysing system benefits of flexible heat pump operation. • Covers peak load shaving and operation prioritised for low electricity prices

  2. Early-branching Gut Fungi Possess A Large, And Comprehensive Array Of Biomass-Degrading Enzymes

    Energy Technology Data Exchange (ETDEWEB)

    Solomon, Kevin V.; Haitjema, Charles; Henske, John K.; Gilmore, Sean P.; Borges-Rivera, Diego; Lipzen, Anna; Brewer, Heather M.; Purvine, Samuel O.; Wright, Aaron T.; Theodorou, Michael K.; Grigoriev, Igor V.; Regev, Aviv; Thompson, Dawn; O' Malley, Michelle A.

    2016-03-11

    The fungal kingdom is the source of almost all industrial enzymes in use for lignocellulose bioprocessing. Its more primitive members, however, remain relatively unexploited. We developed a systems-level approach that integrates RNA-Seq, proteomics, phenotype and biochemical studies of relatively unexplored early-branching free-living fungi. Anaerobic gut fungi isolated from herbivores produce a large array of biomass-degrading enzymes that synergistically degrade crude, unpretreated plant biomass, and are competitive with optimized commercial preparations from Aspergillus and Trichoderma. Compared to these model platforms, gut fungal enzymes are unbiased in substrate preference due to a wealth of xylan-degrading enzymes. These enzymes are universally catabolite repressed, and are further regulated by a rich landscape of noncoding regulatory RNAs. Furthermore, we identified several promising sequence divergent enzyme candidates for lignocellulosic bioprocessing.

  3. Key enzymes enabling the growth of Arthrobacter sp. strain JBH1 with nitroglycerin as the sole source of carbon and nitrogen.

    Science.gov (United States)

    Husserl, Johana; Hughes, Joseph B; Spain, Jim C

    2012-05-01

    Flavoprotein reductases that catalyze the transformation of nitroglycerin (NG) to dinitro- or mononitroglycerols enable bacteria containing such enzymes to use NG as the nitrogen source. The inability to use the resulting mononitroglycerols limits most strains to incomplete denitration of NG. Recently, Arthrobacter strain JBH1 was isolated for the ability to grow on NG as the sole source of carbon and nitrogen, but the enzymes and mechanisms involved were not established. Here, the enzymes that enable the Arthrobacter strain to incorporate NG into a productive pathway were identified. Enzyme assays indicated that the transformation of nitroglycerin to mononitroglycerol is NADPH dependent and that the subsequent transformation of mononitroglycerol is ATP dependent. Cloning and heterologous expression revealed that a flavoprotein catalyzes selective denitration of NG to 1-mononitroglycerol (1-MNG) and that 1-MNG is transformed to 1-nitro-3-phosphoglycerol by a glycerol kinase homolog. Phosphorylation of the nitroester intermediate enables the subsequent denitration of 1-MNG in a productive pathway that supports the growth of the isolate and mineralization of NG.

  4. Effect of free cholesterol on incorporation of triolein in phospholipid bilayers

    International Nuclear Information System (INIS)

    Spooner, P.J.R.; Small, D.M.

    1987-01-01

    Triacylglycerols are the major substrates for lipolytic enzymes that act at the surface of emulsion-like particles such as triglyceride-rich lipoproteins, chylomicrons, and intracellular lipid droplets. This study examines the effect of cholesterol on the solubility of a triacylglycerol, triolein, in phospholipid surfaces. Solubilities of [carbonyl- 13 C] triolein in phospholipid bilayer vesicles containing between 0 and 50 mol % free cholesterol, prepared by cosonication, were measured by 13 C NMR. The carbonyl resonances from bilayer-incorporated triglyceride were shifted downfield in the 13 C NMR spectra from those corresponding to excess, nonincorporated material. This enabled solubilities to be determined directly from carbonyl peak intensities at most cholesterol concentration. The bilayer solubility of triolein was inversely proportional to the cholesterol/phospholipid mole ratio. In pure phospholipid vesicles the triolein solubility was 2.2 mol %. The triglyceride incorporation decreased to 1.1 mol % at a cholesterol/phospholipid mole ratio of 0.5, and at a mole ratio of 1.0 for the bilayer lipids, the triolein solubility was reduced to just 0.15 mol %. The effects of free cholesterol were more pronounced and progressive than observed previously on the bilayer solubility of cholestery oleate. As with cholesteryl oleate, they suggest that cholesterol also displaces solubilized triglyceride to deeper regions of the bilayer

  5. Imbalance between pulmonary angiotensin-converting enzyme and angiotensin-converting enzyme 2 activity in acute respiratory distress syndrome

    NARCIS (Netherlands)

    Wösten-van Asperen, Roelie M.; Bos, Albert P.; Bem, Reinout A.; Dierdorp, Barbara S.; Dekker, Tamara; van Goor, Harry; Kamilic, Jelena; van der Loos, Chris M.; van den Berg, Elske; Bruijn, Martijn; van Woensel, Job B.; Lutter, René

    2013-01-01

    Angiotensin-converting enzyme and its effector peptide angiotensin II have been implicated in the pathogenesis of acute respiratory distress syndrome. Recently, angiotensin-converting enzyme 2 was identified as the counter-regulatory enzyme of angiotensin-converting enzyme that converts angiotensin

  6. Imbalance between pulmonary angiotensin-converting enzyme and angiotensin-converting enzyme 2 activity in acute respiratory distress syndrome

    NARCIS (Netherlands)

    Wosten-van Asperen, Roelie M.; Bos, Albert; Bem, Reinout A.; Dierdorp, Barbara S.; Dekker, Tamara; van Goor, Harry; Kamilic, Jelena; van der Loos, Chris M.; van den Berg, Elske; Bruijn, Martijn; van Woensel, Job B.; Lutter, Rene

    2013-01-01

    Objective: Angiotensin-converting enzyme and its effector peptide angiotensin II have been implicated in the pathogenesis of acute respiratory distress syndrome. Recently, angiotensin-converting enzyme 2 was identified as the counter-regulatory enzyme of angiotensin-converting enzyme that converts

  7. Modeling of oxygen incorporation in Th, ThC, and ThN by density functional theory calculations

    Science.gov (United States)

    Pérez Daroca, D.; Llois, A. M.; Mosca, H. O.

    2017-12-01

    Oxygen incorporation in nuclear fuel materials is an important issue deserving investigation due to its influence on thermophysical and structural properties. Even if there has been a renewed interest in thorium and thorium compounds in the last years, there is still not much research done on this topic. In this work, we study, by means of density functional theory calculations, the incorporation of oxygen in Th, ThC, and ThN. We analyze the electronic structure finding a characteristic peak to be attributed to oxygen incorporation. We also calculate incorporation and solution energies and obtain migration energies of oxygen through different paths finding that migration through vacancy sites is more energetically favorable than through interstitial ones.

  8. Immobilization of enzymes using non-ionic colloidal liquid aphrons (CLAs): Surface and enzyme effects.

    Science.gov (United States)

    Ward, Keeran; Xi, Jingshu; Stuckey, David C

    2015-12-01

    The use of non-ionic colloidal liquid aphrons (CLAs) as a support for enzyme immobilisation was investigated. Formulation required the mixing of an aqueous-surfactant solution with a relatively non-polar solvent-surfactant solution, forming a solvent droplet surrounded by a thin stabilised aqueous film (soapy shell). Studies utilising anionic surfactants have showed increased retention, however, very little have been understood about the forces governing immobilisation. This study seeks to determine the effects of enzyme properties on CLA immobilisation by examining a non-ionic/non-polar solvent system comprised of two non-ionic surfactants, Tween 20 and 80, mineral oil and the enzymes lipase, aprotinin and α-chymotrypsin. From these results it was deduced that hydrophobic interactions strongly governed immobilisation. Confocal Scanning Laser Microscopy (CSLM) revealed that immobilisation was predominantly achieved by surface adsorption attributed to hydrophobic interactions between the enzyme and the CLA surface. Enzyme surface affinity was found to increase when added directly to the formulation (pre-manufacture addition), as opposed to the bulk continuous phase (post-manufacture addition), with α-chymotrypsin and aprotinin being the most perturbed, while lipase was relatively unaffected. The effect of zeta potential on immobilisation showed that enzymes adsorbed better closer to their pI, indicating that charge minimisation was necessary for immobilisation. Finally, the effect of increasing enzyme concentration in the aqueous phase resulted in an increase in adsorption for all enzymes due to cooperativity between protein molecules, with saturation occurring faster at higher adsorption rates. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Allosteric regulation of epigenetic modifying enzymes.

    Science.gov (United States)

    Zucconi, Beth E; Cole, Philip A

    2017-08-01

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

  10. Incorporating Born solvation energy into the three-dimensional Poisson-Nernst-Planck model to study ion selectivity in KcsA K+ channels

    Science.gov (United States)

    Liu, Xuejiao; Lu, Benzhuo

    2017-12-01

    Potassium channels are much more permeable to potassium than sodium ions, although potassium ions are larger and both carry the same positive charge. This puzzle cannot be solved based on the traditional Poisson-Nernst-Planck (PNP) theory of electrodiffusion because the PNP model treats all ions as point charges, does not incorporate ion size information, and therefore cannot discriminate potassium from sodium ions. The PNP model can qualitatively capture some macroscopic properties of certain channel systems such as current-voltage characteristics, conductance rectification, and inverse membrane potential. However, the traditional PNP model is a continuum mean-field model and has no or underestimates the discrete ion effects, in particular the ion solvation or self-energy (which can be described by Born model). It is known that the dehydration effect (closely related to ion size) is crucial to selective permeation in potassium channels. Therefore, we incorporated Born solvation energy into the PNP model to account for ion hydration and dehydration effects when passing through inhomogeneous dielectric channel environments. A variational approach was adopted to derive a Born-energy-modified PNP (BPNP) model. The model was applied to study a cylindrical nanopore and a realistic KcsA channel, and three-dimensional finite element simulations were performed. The BPNP model can distinguish different ion species by ion radius and predict selectivity for K+ over Na+ in KcsA channels. Furthermore, ion current rectification in the KcsA channel was observed by both the PNP and BPNP models. The I -V curve of the BPNP model for the KcsA channel indicated an inward rectifier effect for K+ (rectification ratio of ˜3 /2 ) but indicated an outward rectifier effect for Na+ (rectification ratio of ˜1 /6 ) .

  11. DGAT enzymes and triacylglycerol biosynthesis

    Science.gov (United States)

    Yen, Chi-Liang Eric; Stone, Scot J.; Koliwad, Suneil; Harris, Charles; Farese, Robert V.

    2008-01-01

    Triacylglycerols (triglycerides) (TGs) are the major storage molecules of metabolic energy and FAs in most living organisms. Excessive accumulation of TGs, however, is associated with human diseases, such as obesity, diabetes mellitus, and steatohepatitis. The final and the only committed step in the biosynthesis of TGs is catalyzed by acyl-CoA:diacylglycerol acyltransferase (DGAT) enzymes. The genes encoding two DGAT enzymes, DGAT1 and DGAT2, were identified in the past decade, and the use of molecular tools, including mice deficient in either enzyme, has shed light on their functions. Although DGAT enzymes are involved in TG synthesis, they have distinct protein sequences and differ in their biochemical, cellular, and physiological functions. Both enzymes may be useful as therapeutic targets for diseases. Here we review the current knowledge of DGAT enzymes, focusing on new advances since the cloning of their genes, including possible roles in human health and diseases. PMID:18757836

  12. de novo computational enzyme design.

    Science.gov (United States)

    Zanghellini, Alexandre

    2014-10-01

    Recent advances in systems and synthetic biology as well as metabolic engineering are poised to transform industrial biotechnology by allowing us to design cell factories for the sustainable production of valuable fuels and chemicals. To deliver on their promises, such cell factories, as much as their brick-and-mortar counterparts, will require appropriate catalysts, especially for classes of reactions that are not known to be catalyzed by enzymes in natural organisms. A recently developed methodology, de novo computational enzyme design can be used to create enzymes catalyzing novel reactions. Here we review the different classes of chemical reactions for which active protein catalysts have been designed as well as the results of detailed biochemical and structural characterization studies. We also discuss how combining de novo computational enzyme design with more traditional protein engineering techniques can alleviate the shortcomings of state-of-the-art computational design techniques and create novel enzymes with catalytic proficiencies on par with natural enzymes. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. Measurement of enzyme activity.

    Science.gov (United States)

    Harris, T K; Keshwani, M M

    2009-01-01

    To study and understand the nature of living cells, scientists have continually employed traditional biochemical techniques aimed to fractionate and characterize a designated network of macromolecular components required to carry out a particular cellular function. At the most rudimentary level, cellular functions ultimately entail rapid chemical transformations that otherwise would not occur in the physiological environment of the cell. The term enzyme is used to singularly designate a macromolecular gene product that specifically and greatly enhances the rate of a chemical transformation. Purification and characterization of individual and collective groups of enzymes has been and will remain essential toward advancement of the molecular biological sciences; and developing and utilizing enzyme reaction assays is central to this mission. First, basic kinetic principles are described for understanding chemical reaction rates and the catalytic effects of enzymes on such rates. Then, a number of methods are described for measuring enzyme-catalyzed reaction rates, which mainly differ with regard to techniques used to detect and quantify concentration changes of given reactants or products. Finally, short commentary is given toward formulation of reaction mixtures used to measure enzyme activity. Whereas a comprehensive treatment of enzymatic reaction assays is not within the scope of this chapter, the very core principles that are presented should enable new researchers to better understand the logic and utility of any given enzymatic assay that becomes of interest.

  14. Screening of Enzyme Biomarker for Nanotoxicity of Zinc Oxide in OREOCHROMIS MOSSAMBICUS

    Science.gov (United States)

    Subramanian, Periasamy; Bupesh, Giridharan

    2011-06-01

    Experiments were conducted to determine the effects of Zinc oxide (ZnO) nanoparticles (NPs) on fish models. Oreochromis mossambicus was orally administered with ZnO NPs (50-100 nm) once and its effects at five different concentrations (60 ppm-100 ppm) were observed for 12 days. Enzymatic assays were performed at every three days interval in the vital tissues of liver, gill, muscle and kidney. The defense enzymes, ethoxyresorufin O-deethylase (EROD) and glutathione S transferase (GST) exerted a dose dependent elevation up to 6 days. This hike then declines in higher concentrations and extended duration. Whereas the tissue damaging enzymes, glutamate oxaloacetic transaminase (GOT), glutamate pyruvic transaminase (GPT) and alkaline phosphatase (ALP) as well as the antioxidant enzymes superoxide dismutase (SOD), catalase (CAT) exhibited a dose and duration dependent increase until the end of the experiment. Among these enzymes, the antioxidant enzymes response to ZnO NP toxicity on fish showed notable continuous induction. This study demonstrates that antioxidant enzymes responses in O. mossambicus could be used as a biomarker for the early detection of nanotoxicity.

  15. Preparation and features of polycaprolactone vascular grafts with the incorporated vascular endothelial growth factor

    Energy Technology Data Exchange (ETDEWEB)

    Sevostyanova, V. V., E-mail: sevostyanova.victoria@gmail.com; Khodyrevskaya, Y. I.; Glushkova, T. V.; Antonova, L. V.; Kudryavtseva, Y. A.; Barbarash, O. L.; Barbarash, L. S. [Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo (Russian Federation)

    2015-10-27

    The development of tissue-engineered small-diameter vascular grafts is an urgent issue in cardiovascular surgery. In this study, we assessed how the incorporation of the vascular endothelial growth factor (VEGF) affects morphological and mechanical properties of polycaprolactone (PCL) vascular grafts along with its release kinetics. Vascular grafts were prepared using two-phase electrospinning. In pursuing our aims, we performed scanning electron microscopy, mechanical testing, and enzyme-linked immunosorbent assay. Our results demonstrated the preservation of a highly porous structure and improvement of PCL/VEGF scaffold mechanical properties as compared to PCL grafts. A prolonged VEGF release testifies the use of this construct as a scaffold for tissue-engineered vascular grafts.

  16. Analysis of residuals from enzyme kinetic and protein folding experiments in the presence of correlated experimental noise.

    Science.gov (United States)

    Kuzmic, Petr; Lorenz, Thorsten; Reinstein, Jochen

    2009-12-01

    Experimental data from continuous enzyme assays or protein folding experiments often contain hundreds, or even thousands, of densely spaced data points. When the sampling interval is extremely short, the experimental data points might not be statistically independent. The resulting neighborhood correlation invalidates important theoretical assumptions of nonlinear regression analysis. As a consequence, certain goodness-of-fit criteria, such as the runs-of-signs test and the autocorrelation function, might indicate a systematic lack of fit even if the experiment does agree very well with the underlying theoretical model. A solution to this problem is to analyze only a subset of the residuals of fit, such that any excessive neighborhood correlation is eliminated. Substrate kinetics of the HIV protease and the unfolding kinetics of UMP/CMP kinase, a globular protein from Dictyostelium discoideum, serve as two illustrative examples. A suitable data-reduction algorithm has been incorporated into software DYNAFIT [P. Kuzmic, Anal. Biochem. 237 (1996) 260-273], freely available to all academic researchers from http://www.biokin.com.

  17. Regulatory proteins (inhibitors or activators) affect estimates of Msub(r) of enzymes and receptors by radiation inactivation

    International Nuclear Information System (INIS)

    Potier, M.; Giroux, S.

    1985-01-01

    The radiation-inactivation method allows the determination of the Msub(r) of enzymes and receptors by monitoring the decay of biological activity as a function of absorbed dose. The presence of regulatory or effector proteins (inhibitors or activators) associated with an enzyme or receptor, or released in the preparation after tissue homogenization, may affect the decay of biological activity. How the activity is affected, however, will depend on the type of inhibition (competitive or non-competitive), the inhibitor or activator concentration, the dissociation constant of the enzyme-effector system, and the effector Msub(r) relative to that of the enzyme. Since little is known on how effector proteins influence radiation inactivation of enzymes and receptors, we have considered a theoretical model in an effort to provide a framework for the interpretation of experimentally obtained data. Our model predicts that competitive and non-competitive inhibitors of enzymes could be distinguished by analysing irradiated samples with various substrate concentrations. Inhibitors will decrease whereas activators will increase the apparent target size of enzymes or receptors. (author)

  18. An etiologic prediction model incorporating biomarkers to predict the bladder cancer risk associated with occupational exposure to aromatic amines: a pilot study

    OpenAIRE

    Mastrangelo, Giuseppe; Carta, Angela; Arici, Cecilia; Pavanello, Sofia; Porru, Stefano

    2017-01-01

    Background No etiological prediction model incorporating biomarkers is available to predict bladder cancer risk associated with occupational exposure to aromatic amines. Methods Cases were 199 bladder cancer patients. Clinical, laboratory and genetic data were predictors in logistic regression models (full and short) in which the dependent variable was 1 for 15 patients with aromatic amines related bladder cancer and 0 otherwise. The receiver operating characteristics approach was adopted; th...

  19. Thermodynamics of Enzyme-Catalyzed Reactions Database

    Science.gov (United States)

    SRD 74 Thermodynamics of Enzyme-Catalyzed Reactions Database (Web, free access)   The Thermodynamics of Enzyme-Catalyzed Reactions Database contains thermodynamic data on enzyme-catalyzed reactions that have been recently published in the Journal of Physical and Chemical Reference Data (JPCRD). For each reaction the following information is provided: the reference for the data, the reaction studied, the name of the enzyme used and its Enzyme Commission number, the method of measurement, the data and an evaluation thereof.

  20. Reconstitution of a thermostable xylan-degrading enzyme mixture from the bacterium Caldicellulosiruptor bescii.

    Science.gov (United States)

    Su, Xiaoyun; Han, Yejun; Dodd, Dylan; Moon, Young Hwan; Yoshida, Shosuke; Mackie, Roderick I; Cann, Isaac K O

    2013-03-01

    Xylose, the major constituent of xylans, as well as the side chain sugars, such as arabinose, can be metabolized by engineered yeasts into ethanol. Therefore, xylan-degrading enzymes that efficiently hydrolyze xylans will add value to cellulases used in hydrolysis of plant cell wall polysaccharides for conversion to biofuels. Heterogeneous xylan is a complex substrate, and it requires multiple enzymes to release its constituent sugars. However, the components of xylan-degrading enzymes are often individually characterized, leading to a dearth of research that analyzes synergistic actions of the components of xylan-degrading enzymes. In the present report, six genes predicted to encode components of the xylan-degrading enzymes of the thermophilic bacterium Caldicellulosiruptor bescii were expressed in Escherichia coli, and the recombinant proteins were investigated as individual enzymes and also as a xylan-degrading enzyme cocktail. Most of the component enzymes of the xylan-degrading enzyme mixture had similar optimal pH (5.5 to ∼6.5) and temperature (75 to ∼90°C), and this facilitated their investigation as an enzyme cocktail for deconstruction of xylans. The core enzymes (two endoxylanases and a β-xylosidase) exhibited high turnover numbers during catalysis, with the two endoxylanases yielding estimated k(cat) values of ∼8,000 and ∼4,500 s(-1), respectively, on soluble wheat arabinoxylan. Addition of side chain-cleaving enzymes to the core enzymes increased depolymerization of a more complex model substrate, oat spelt xylan. The C. bescii xylan-degrading enzyme mixture effectively hydrolyzes xylan at 65 to 80°C and can serve as a basal mixture for deconstruction of xylans in bioenergy feedstock at high temperatures.