WorldWideScience

Sample records for near-monotone biochemical networks

  1. Risk-Sensitive Control with Near Monotone Cost

    International Nuclear Information System (INIS)

    Biswas, Anup; Borkar, V. S.; Suresh Kumar, K.

    2010-01-01

    The infinite horizon risk-sensitive control problem for non-degenerate controlled diffusions is analyzed under a 'near monotonicity' condition on the running cost that penalizes large excursions of the process.

  2. Risk-Sensitive Control of Pure Jump Process on Countable Space with Near Monotone Cost

    International Nuclear Information System (INIS)

    Suresh Kumar, K.; Pal, Chandan

    2013-01-01

    In this article, we study risk-sensitive control problem with controlled continuous time pure jump process on a countable space as state dynamics. We prove multiplicative dynamic programming principle, elliptic and parabolic Harnack’s inequalities. Using the multiplicative dynamic programing principle and the Harnack’s inequalities, we prove the existence and a characterization of optimal risk-sensitive control under the near monotone condition

  3. RMBNToolbox: random models for biochemical networks

    Directory of Open Access Journals (Sweden)

    Niemi Jari

    2007-05-01

    Full Text Available Abstract Background There is an increasing interest to model biochemical and cell biological networks, as well as to the computational analysis of these models. The development of analysis methodologies and related software is rapid in the field. However, the number of available models is still relatively small and the model sizes remain limited. The lack of kinetic information is usually the limiting factor for the construction of detailed simulation models. Results We present a computational toolbox for generating random biochemical network models which mimic real biochemical networks. The toolbox is called Random Models for Biochemical Networks. The toolbox works in the Matlab environment, and it makes it possible to generate various network structures, stoichiometries, kinetic laws for reactions, and parameters therein. The generation can be based on statistical rules and distributions, and more detailed information of real biochemical networks can be used in situations where it is known. The toolbox can be easily extended. The resulting network models can be exported in the format of Systems Biology Markup Language. Conclusion While more information is accumulating on biochemical networks, random networks can be used as an intermediate step towards their better understanding. Random networks make it possible to study the effects of various network characteristics to the overall behavior of the network. Moreover, the construction of artificial network models provides the ground truth data needed in the validation of various computational methods in the fields of parameter estimation and data analysis.

  4. Characterizing multistationarity regimes in biochemical reaction networks.

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    Irene Otero-Muras

    Full Text Available Switch like responses appear as common strategies in the regulation of cellular systems. Here we present a method to characterize bistable regimes in biochemical reaction networks that can be of use to both direct and reverse engineering of biological switches. In the design of a synthetic biological switch, it is important to study the capability for bistability of the underlying biochemical network structure. Chemical Reaction Network Theory (CRNT may help at this level to decide whether a given network has the capacity for multiple positive equilibria, based on their structural properties. However, in order to build a working switch, we also need to ensure that the bistability property is robust, by studying the conditions leading to the existence of two different steady states. In the reverse engineering of biological switches, knowledge collected about the bistable regimes of the underlying potential model structures can contribute at the model identification stage to a drastic reduction of the feasible region in the parameter space of search. In this work, we make use and extend previous results of the CRNT, aiming not only to discriminate whether a biochemical reaction network can exhibit multiple steady states, but also to determine the regions within the whole space of parameters capable of producing multistationarity. To that purpose we present and justify a condition on the parameters of biochemical networks for the appearance of multistationarity, and propose an efficient and reliable computational method to check its satisfaction through the parameter space.

  5. Optimal Information Processing in Biochemical Networks

    Science.gov (United States)

    Wiggins, Chris

    2012-02-01

    A variety of experimental results over the past decades provide examples of near-optimal information processing in biological networks, including in biochemical and transcriptional regulatory networks. Computing information-theoretic quantities requires first choosing or computing the joint probability distribution describing multiple nodes in such a network --- for example, representing the probability distribution of finding an integer copy number of each of two interacting reactants or gene products while respecting the `intrinsic' small copy number noise constraining information transmission at the scale of the cell. I'll given an overview of some recent analytic and numerical work facilitating calculation of such joint distributions and the associated information, which in turn makes possible numerical optimization of information flow in models of noisy regulatory and biochemical networks. Illustrating cases include quantification of form-function relations, ideal design of regulatory cascades, and response to oscillatory driving.

  6. Conservation Laws in Biochemical Reaction Networks

    DEFF Research Database (Denmark)

    Mahdi, Adam; Ferragut, Antoni; Valls, Claudia

    2017-01-01

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

  7. Biochemical Network Stochastic Simulator (BioNetS: software for stochastic modeling of biochemical networks

    Directory of Open Access Journals (Sweden)

    Elston Timothy C

    2004-03-01

    Full Text Available Abstract Background Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true for pathways that involve transcriptional regulation, where generally there are two copies of each gene and the number of messenger RNA (mRNA molecules can be small. Therefore, there is a need for computational tools for developing and investigating stochastic models of biochemical networks. Results We have developed the software package Biochemical Network Stochastic Simulator (BioNetS for efficientlyand accurately simulating stochastic models of biochemical networks. BioNetS has a graphical user interface that allows models to be entered in a straightforward manner, and allows the user to specify the type of random variable (discrete or continuous for each chemical species in the network. The discrete variables are simulated using an efficient implementation of the Gillespie algorithm. For the continuous random variables, BioNetS constructs and numerically solvesthe appropriate chemical Langevin equations. The software package has been developed to scale efficiently with network size, thereby allowing large systems to be studied. BioNetS runs as a BioSpice agent and can be downloaded from http://www.biospice.org. BioNetS also can be run as a stand alone package. All the required files are accessible from http://x.amath.unc.edu/BioNetS. Conclusions We have developed BioNetS to be a reliable tool for studying the stochastic dynamics of large biochemical networks. Important features of BioNetS are its ability to handle hybrid models that consist of both continuous and discrete random variables and its ability to model cell growth and division. We have verified the accuracy and efficiency of the numerical methods by considering several test systems.

  8. On the Adaptive Design Rules of Biochemical Networks in Evolution

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    Bor-Sen Chen

    2007-01-01

    Full Text Available Biochemical networks are the backbones of physiological systems of organisms. Therefore, a biochemical network should be sufficiently robust (not sensitive to tolerate genetic mutations and environmental changes in the evolutionary process. In this study, based on the robustness and sensitivity criteria of biochemical networks, the adaptive design rules are developed for natural selection in the evolutionary process. This will provide insights into the robust adaptive mechanism of biochemical networks in the evolutionary process. We find that if a mutated biochemical network satisfies the robustness and sensitivity criteria of natural selection, there is a high probability for the biochemical network to prevail during natural selection in the evolutionary process. Since there are various mutated biochemical networks that can satisfy these criteria but have some differences in phenotype, the biochemical networks increase their diversities in the evolutionary process. The robustness of a biochemical network enables co-option so that new phenotypes can be generated in evolution. The proposed robust adaptive design rules of natural selection gain much insight into the evolutionary mechanism and provide a systematic robust biochemical circuit design method of biochemical networks for biotechnological and therapeutic purposes in the future.

  9. BioNessie - a grid enabled biochemical networks simulation environment

    OpenAIRE

    Liu, X.; Jiang, J.; Ajayi, O.; Gu, X.; Gilbert, D.; Sinnott, R.O.

    2008-01-01

    The simulation of biochemical networks provides insight and understanding about the underlying biochemical processes and pathways used by cells and organisms. BioNessie is a biochemical network simulator which has been developed at the University of Glasgow. This paper describes the simulator and focuses in particular on how it has been extended to benefit from a wide variety of high performance compute resources across the UK through Grid technologies to support larger scale simulations.

  10. Mean field interaction in biochemical reaction networks

    KAUST Repository

    Tembine, Hamidou; Tempone, Raul; Vilanova, Pedro

    2011-01-01

    In this paper we establish a relationship between chemical dynamics and mean field game dynamics. We show that chemical reaction networks can be studied using noisy mean field limits. We provide deterministic, noisy and switching mean field limits

  11. Mean field interaction in biochemical reaction networks

    KAUST Repository

    Tembine, Hamidou

    2011-09-01

    In this paper we establish a relationship between chemical dynamics and mean field game dynamics. We show that chemical reaction networks can be studied using noisy mean field limits. We provide deterministic, noisy and switching mean field limits and illustrate them with numerical examples. © 2011 IEEE.

  12. Autocatalytic sets in a partitioned biochemical network.

    Science.gov (United States)

    Smith, Joshua I; Steel, Mike; Hordijk, Wim

    2014-01-01

    In previous work, RAF theory has been developed as a tool for making theoretical progress on the origin of life question, providing insight into the structure and occurrence of self-sustaining and collectively autocatalytic sets within catalytic polymer networks. We present here an extension in which there are two "independent" polymer sets, where catalysis occurs within and between the sets, but there are no reactions combining polymers from both sets. Such an extension reflects the interaction between nucleic acids and peptides observed in modern cells and proposed forms of early life. We present theoretical work and simulations which suggest that the occurrence of autocatalytic sets is robust to the partitioned structure of the network. We also show that autocatalytic sets remain likely even when the molecules in the system are not polymers, and a low level of inhibition is present. Finally, we present a kinetic extension which assigns a rate to each reaction in the system, and show that identifying autocatalytic sets within such a system is an NP-complete problem. Recent experimental work has challenged the necessity of an RNA world by suggesting that peptide-nucleic acid interactions occurred early in chemical evolution. The present work indicates that such a peptide-RNA world could support the spontaneous development of autocatalytic sets and is thus a feasible alternative worthy of investigation.

  13. Modeling stochasticity in biochemical reaction networks

    International Nuclear Information System (INIS)

    Constantino, P H; Vlysidis, M; Smadbeck, P; Kaznessis, Y N

    2016-01-01

    Small biomolecular systems are inherently stochastic. Indeed, fluctuations of molecular species are substantial in living organisms and may result in significant variation in cellular phenotypes. The chemical master equation (CME) is the most detailed mathematical model that can describe stochastic behaviors. However, because of its complexity the CME has been solved for only few, very small reaction networks. As a result, the contribution of CME-based approaches to biology has been very limited. In this review we discuss the approach of solving CME by a set of differential equations of probability moments, called moment equations. We present different approaches to produce and to solve these equations, emphasizing the use of factorial moments and the zero information entropy closure scheme. We also provide information on the stability analysis of stochastic systems. Finally, we speculate on the utility of CME-based modeling formalisms, especially in the context of synthetic biology efforts. (topical review)

  14. Propagating semantic information in biochemical network models

    Directory of Open Access Journals (Sweden)

    Schulz Marvin

    2012-01-01

    Full Text Available Abstract Background To enable automatic searches, alignments, and model combination, the elements of systems biology models need to be compared and matched across models. Elements can be identified by machine-readable biological annotations, but assigning such annotations and matching non-annotated elements is tedious work and calls for automation. Results A new method called "semantic propagation" allows the comparison of model elements based not only on their own annotations, but also on annotations of surrounding elements in the network. One may either propagate feature vectors, describing the annotations of individual elements, or quantitative similarities between elements from different models. Based on semantic propagation, we align partially annotated models and find annotations for non-annotated model elements. Conclusions Semantic propagation and model alignment are included in the open-source library semanticSBML, available on sourceforge. Online services for model alignment and for annotation prediction can be used at http://www.semanticsbml.org.

  15. Computing with competition in biochemical networks.

    Science.gov (United States)

    Genot, Anthony J; Fujii, Teruo; Rondelez, Yannick

    2012-11-16

    Cells rely on limited resources such as enzymes or transcription factors to process signals and make decisions. However, independent cellular pathways often compete for a common molecular resource. Competition is difficult to analyze because of its nonlinear global nature, and its role remains unclear. Here we show how decision pathways such as transcription networks may exploit competition to process information. Competition for one resource leads to the recognition of convex sets of patterns, whereas competition for several resources (overlapping or cascaded regulons) allows even more general pattern recognition. Competition also generates surprising couplings, such as correlating species that share no resource but a common competitor. The mechanism we propose relies on three primitives that are ubiquitous in cells: multiinput motifs, competition for a resource, and positive feedback loops.

  16. Hierarchical thinking in network biology: the unbiased modularization of biochemical networks.

    Science.gov (United States)

    Papin, Jason A; Reed, Jennifer L; Palsson, Bernhard O

    2004-12-01

    As reconstructed biochemical reaction networks continue to grow in size and scope, there is a growing need to describe the functional modules within them. Such modules facilitate the study of biological processes by deconstructing complex biological networks into conceptually simple entities. The definition of network modules is often based on intuitive reasoning. As an alternative, methods are being developed for defining biochemical network modules in an unbiased fashion. These unbiased network modules are mathematically derived from the structure of the whole network under consideration.

  17. Structuring evolution: biochemical networks and metabolic diversification in birds.

    Science.gov (United States)

    Morrison, Erin S; Badyaev, Alexander V

    2016-08-25

    Recurrence and predictability of evolution are thought to reflect the correspondence between genomic and phenotypic dimensions of organisms, and the connectivity in deterministic networks within these dimensions. Direct examination of the correspondence between opportunities for diversification imbedded in such networks and realized diversity is illuminating, but is empirically challenging because both the deterministic networks and phenotypic diversity are modified in the course of evolution. Here we overcome this problem by directly comparing the structure of a "global" carotenoid network - comprising of all known enzymatic reactions among naturally occurring carotenoids - with the patterns of evolutionary diversification in carotenoid-producing metabolic networks utilized by birds. We found that phenotypic diversification in carotenoid networks across 250 species was closely associated with enzymatic connectivity of the underlying biochemical network - compounds with greater connectivity occurred the most frequently across species and were the hotspots of metabolic pathway diversification. In contrast, we found no evidence for diversification along the metabolic pathways, corroborating findings that the utilization of the global carotenoid network was not strongly influenced by history in avian evolution. The finding that the diversification in species-specific carotenoid networks is qualitatively predictable from the connectivity of the underlying enzymatic network points to significant structural determinism in phenotypic evolution.

  18. Biophysical constraints on the computational capacity of biochemical signaling networks

    Science.gov (United States)

    Wang, Ching-Hao; Mehta, Pankaj

    Biophysics fundamentally constrains the computations that cells can carry out. Here, we derive fundamental bounds on the computational capacity of biochemical signaling networks that utilize post-translational modifications (e.g. phosphorylation). To do so, we combine ideas from the statistical physics of disordered systems and the observation by Tony Pawson and others that the biochemistry underlying protein-protein interaction networks is combinatorial and modular. Our results indicate that the computational capacity of signaling networks is severely limited by the energetics of binding and the need to achieve specificity. We relate our results to one of the theoretical pillars of statistical learning theory, Cover's theorem, which places bounds on the computational capacity of perceptrons. PM and CHW were supported by a Simons Investigator in the Mathematical Modeling of Living Systems Grant, and NIH Grant No. 1R35GM119461 (both to PM).

  19. Efficient Parallel Statistical Model Checking of Biochemical Networks

    Directory of Open Access Journals (Sweden)

    Paolo Ballarini

    2009-12-01

    Full Text Available We consider the problem of verifying stochastic models of biochemical networks against behavioral properties expressed in temporal logic terms. Exact probabilistic verification approaches such as, for example, CSL/PCTL model checking, are undermined by a huge computational demand which rule them out for most real case studies. Less demanding approaches, such as statistical model checking, estimate the likelihood that a property is satisfied by sampling executions out of the stochastic model. We propose a methodology for efficiently estimating the likelihood that a LTL property P holds of a stochastic model of a biochemical network. As with other statistical verification techniques, the methodology we propose uses a stochastic simulation algorithm for generating execution samples, however there are three key aspects that improve the efficiency: first, the sample generation is driven by on-the-fly verification of P which results in optimal overall simulation time. Second, the confidence interval estimation for the probability of P to hold is based on an efficient variant of the Wilson method which ensures a faster convergence. Third, the whole methodology is designed according to a parallel fashion and a prototype software tool has been implemented that performs the sampling/verification process in parallel over an HPC architecture.

  20. Coarse-graining stochastic biochemical networks: adiabaticity and fast simulations

    Energy Technology Data Exchange (ETDEWEB)

    Nemenman, Ilya [Los Alamos National Laboratory; Sinitsyn, Nikolai [Los Alamos National Laboratory; Hengartner, Nick [Los Alamos National Laboratory

    2008-01-01

    We propose a universal approach for analysis and fast simulations of stiff stochastic biochemical kinetics networks, which rests on elimination of fast chemical species without a loss of information about mesoscoplc, non-Poissonian fluctuations of the slow ones. Our approach, which is similar to the Born-Oppenhelmer approximation in quantum mechanics, follows from the stochastic path Integral representation of the cumulant generating function of reaction events. In applications with a small number of chemIcal reactions, It produces analytical expressions for cumulants of chemical fluxes between the slow variables. This allows for a low-dimensional, Interpretable representation and can be used for coarse-grained numerical simulation schemes with a small computational complexity and yet high accuracy. As an example, we derive the coarse-grained description for a chain of biochemical reactions, and show that the coarse-grained and the microscopic simulations are in an agreement, but the coarse-gralned simulations are three orders of magnitude faster.

  1. HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks

    Directory of Open Access Journals (Sweden)

    Luca Marchetti

    2017-01-01

    Full Text Available HSimulator is a multithread simulator for mass-action biochemical reaction systems placed in a well-mixed environment. HSimulator provides optimized implementation of a set of widespread state-of-the-art stochastic, deterministic, and hybrid simulation strategies including the first publicly available implementation of the Hybrid Rejection-based Stochastic Simulation Algorithm (HRSSA. HRSSA, the fastest hybrid algorithm to date, allows for an efficient simulation of the models while ensuring the exact simulation of a subset of the reaction network modeling slow reactions. Benchmarks show that HSimulator is often considerably faster than the other considered simulators. The software, running on Java v6.0 or higher, offers a simulation GUI for modeling and visually exploring biological processes and a Javadoc-documented Java library to support the development of custom applications. HSimulator is released under the COSBI Shared Source license agreement (COSBI-SSLA.

  2. 'BioNessie(G) - a grid enabled biochemical networks simulation environment

    OpenAIRE

    Liu, X; Jiang, J; Ajayi, O; Gu, X; Gilbert, D; Sinnott, R

    2008-01-01

    The simulation of biochemical networks provides insight and understanding about the underlying biochemical processes and pathways used by cells and organisms. BioNessie is a biochemical network simulator which has been developed at the University of Glasgow. This paper describes the simulator and focuses in particular on how it has been extended to benefit from a wide variety of high performance compute resources across the UK through Grid technologies to support larger scal...

  3. The alterations in biochemical signaling of hippocampal network activity in the autism brain The alterations in biochemical signaling of hippocampal network activity in the autism brain The alterations in biochemical signaling of hippocampal network activity in the autism brain

    Institute of Scientific and Technical Information of China (English)

    田允; 黄继云; 王锐; 陶蓉蓉; 卢应梅; 廖美华; 陆楠楠; 李静; 芦博; 韩峰

    2012-01-01

    Autism is a highly heritable neurodevelopmental condition characterized by impaired social interaction and communication. However, the role of synaptic dysfunction during development of autism remains unclear. In the present study, we address the alterations of biochemical signaling in hippocampal network following induction of the autism in experimental animals. Here, the an- imal disease model and DNA array being used to investigate the differences in transcriptome or- ganization between autistic and normal brain by gene co--expression network analysis.

  4. A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks.

    Science.gov (United States)

    Fleming, R M T; Maes, C M; Saunders, M A; Ye, Y; Palsson, B Ø

    2012-01-07

    We derive a convex optimization problem on a steady-state nonequilibrium network of biochemical reactions, with the property that energy conservation and the second law of thermodynamics both hold at the problem solution. This suggests a new variational principle for biochemical networks that can be implemented in a computationally tractable manner. We derive the Lagrange dual of the optimization problem and use strong duality to demonstrate that a biochemical analogue of Tellegen's theorem holds at optimality. Each optimal flux is dependent on a free parameter that we relate to an elementary kinetic parameter when mass action kinetics is assumed. Copyright © 2011 Elsevier Ltd. All rights reserved.

  5. A probabilistic approach to identify putative drug targets in biochemical networks.

    NARCIS (Netherlands)

    Murabito, E.; Smalbone, K.; Swinton, J.; Westerhoff, H.V.; Steuer, R.

    2011-01-01

    Network-based drug design holds great promise in clinical research as a way to overcome the limitations of traditional approaches in the development of drugs with high efficacy and low toxicity. This novel strategy aims to study how a biochemical network as a whole, rather than its individual

  6. Hidden long evolutionary memory in a model biochemical network

    Science.gov (United States)

    Ali, Md. Zulfikar; Wingreen, Ned S.; Mukhopadhyay, Ranjan

    2018-04-01

    We introduce a minimal model for the evolution of functional protein-interaction networks using a sequence-based mutational algorithm, and apply the model to study neutral drift in networks that yield oscillatory dynamics. Starting with a functional core module, random evolutionary drift increases network complexity even in the absence of specific selective pressures. Surprisingly, we uncover a hidden order in sequence space that gives rise to long-term evolutionary memory, implying strong constraints on network evolution due to the topology of accessible sequence space.

  7. Validation of artificial neural network models for predicting biochemical markers associated with male infertility.

    Science.gov (United States)

    Vickram, A S; Kamini, A Rao; Das, Raja; Pathy, M Ramesh; Parameswari, R; Archana, K; Sridharan, T B

    2016-08-01

    Seminal fluid is the secretion from many glands comprised of several organic and inorganic compounds including free amino acids, proteins, fructose, glucosidase, zinc, and other scavenging elements like Mg(2+), Ca(2+), K(+), and Na(+). Therefore, in the view of development of novel approaches and proper diagnosis to male infertility, overall understanding of the biochemical and molecular composition and its role in regulation of sperm quality is highly desirable. Perhaps this can be achieved through artificial intelligence. This study was aimed to elucidate and predict various biochemical markers present in human seminal plasma with three different neural network models. A total of 177 semen samples were collected for this research (both fertile and infertile samples) and immediately processed to prepare a semen analysis report, based on the protocol of the World Health Organization (WHO [2010]). The semen samples were then categorized into oligoasthenospermia (n=35), asthenospermia (n=35), azoospermia (n=22), normospermia (n=34), oligospermia (n=34), and control (n=17). The major biochemical parameters like total protein content, fructose, glucosidase, and zinc content were elucidated by standard protocols. All the biochemical markers were predicted by using three different artificial neural network (ANN) models with semen parameters as inputs. Of the three models, the back propagation neural network model (BPNN) yielded the best results with mean absolute error 0.025, -0.080, 0.166, and -0.057 for protein, fructose, glucosidase, and zinc, respectively. This suggests that BPNN can be used to predict biochemical parameters for the proper diagnosis of male infertility in assisted reproductive technology (ART) centres. AAS: absorption spectroscopy; AI: artificial intelligence; ANN: artificial neural networks; ART: assisted reproductive technology; BPNN: back propagation neural network model; DT: decision tress; MLP: multilayer perceptron; PESA: percutaneous

  8. Identification of neutral biochemical network models from time series data

    Directory of Open Access Journals (Sweden)

    Maia Marco

    2009-05-01

    Full Text Available Abstract Background The major difficulty in modeling biological systems from multivariate time series is the identification of parameter sets that endow a model with dynamical behaviors sufficiently similar to the experimental data. Directly related to this parameter estimation issue is the task of identifying the structure and regulation of ill-characterized systems. Both tasks are simplified if the mathematical model is canonical, i.e., if it is constructed according to strict guidelines. Results In this report, we propose a method for the identification of admissible parameter sets of canonical S-systems from biological time series. The method is based on a Monte Carlo process that is combined with an improved version of our previous parameter optimization algorithm. The method maps the parameter space into the network space, which characterizes the connectivity among components, by creating an ensemble of decoupled S-system models that imitate the dynamical behavior of the time series with sufficient accuracy. The concept of sloppiness is revisited in the context of these S-system models with an exploration not only of different parameter sets that produce similar dynamical behaviors but also different network topologies that yield dynamical similarity. Conclusion The proposed parameter estimation methodology was applied to actual time series data from the glycolytic pathway of the bacterium Lactococcus lactis and led to ensembles of models with different network topologies. In parallel, the parameter optimization algorithm was applied to the same dynamical data upon imposing a pre-specified network topology derived from prior biological knowledge, and the results from both strategies were compared. The results suggest that the proposed method may serve as a powerful exploration tool for testing hypotheses and the design of new experiments.

  9. Identification of neutral biochemical network models from time series data.

    Science.gov (United States)

    Vilela, Marco; Vinga, Susana; Maia, Marco A Grivet Mattoso; Voit, Eberhard O; Almeida, Jonas S

    2009-05-05

    The major difficulty in modeling biological systems from multivariate time series is the identification of parameter sets that endow a model with dynamical behaviors sufficiently similar to the experimental data. Directly related to this parameter estimation issue is the task of identifying the structure and regulation of ill-characterized systems. Both tasks are simplified if the mathematical model is canonical, i.e., if it is constructed according to strict guidelines. In this report, we propose a method for the identification of admissible parameter sets of canonical S-systems from biological time series. The method is based on a Monte Carlo process that is combined with an improved version of our previous parameter optimization algorithm. The method maps the parameter space into the network space, which characterizes the connectivity among components, by creating an ensemble of decoupled S-system models that imitate the dynamical behavior of the time series with sufficient accuracy. The concept of sloppiness is revisited in the context of these S-system models with an exploration not only of different parameter sets that produce similar dynamical behaviors but also different network topologies that yield dynamical similarity. The proposed parameter estimation methodology was applied to actual time series data from the glycolytic pathway of the bacterium Lactococcus lactis and led to ensembles of models with different network topologies. In parallel, the parameter optimization algorithm was applied to the same dynamical data upon imposing a pre-specified network topology derived from prior biological knowledge, and the results from both strategies were compared. The results suggest that the proposed method may serve as a powerful exploration tool for testing hypotheses and the design of new experiments.

  10. Thermodynamically based constraints for rate coefficients of large biochemical networks.

    Science.gov (United States)

    Vlad, Marcel O; Ross, John

    2009-01-01

    Wegscheider cyclicity conditions are relationships among the rate coefficients of a complex reaction network, which ensure the compatibility of kinetic equations with the conditions for thermodynamic equilibrium. The detailed balance at equilibrium, that is the equilibration of forward and backward rates for each elementary reaction, leads to compatibility between the conditions of kinetic and thermodynamic equilibrium. Therefore, Wegscheider cyclicity conditions can be derived by eliminating the equilibrium concentrations from the conditions of detailed balance. We develop matrix algebra tools needed to carry out this elimination, reexamine an old derivation of the general form of Wegscheider cyclicity condition, and develop new derivations which lead to more compact and easier-to-use formulas. We derive scaling laws for the nonequilibrium rates of a complex reaction network, which include Wegscheider conditions as a particular case. The scaling laws for the rates are used for clarifying the kinetic and thermodynamic meaning of Wegscheider cyclicity conditions. Finally, we discuss different ways of using Wegscheider cyclicity conditions for kinetic computations in systems biology.

  11. Efficient Characterization of Parametric Uncertainty of Complex (Biochemical Networks.

    Directory of Open Access Journals (Sweden)

    Claudia Schillings

    2015-08-01

    Full Text Available Parametric uncertainty is a particularly challenging and relevant aspect of systems analysis in domains such as systems biology where, both for inference and for assessing prediction uncertainties, it is essential to characterize the system behavior globally in the parameter space. However, current methods based on local approximations or on Monte-Carlo sampling cope only insufficiently with high-dimensional parameter spaces associated with complex network models. Here, we propose an alternative deterministic methodology that relies on sparse polynomial approximations. We propose a deterministic computational interpolation scheme which identifies most significant expansion coefficients adaptively. We present its performance in kinetic model equations from computational systems biology with several hundred parameters and state variables, leading to numerical approximations of the parametric solution on the entire parameter space. The scheme is based on adaptive Smolyak interpolation of the parametric solution at judiciously and adaptively chosen points in parameter space. As Monte-Carlo sampling, it is "non-intrusive" and well-suited for massively parallel implementation, but affords higher convergence rates. This opens up new avenues for large-scale dynamic network analysis by enabling scaling for many applications, including parameter estimation, uncertainty quantification, and systems design.

  12. Automated analysis of information processing, kinetic independence and modular architecture in biochemical networks using MIDIA.

    Science.gov (United States)

    Bowsher, Clive G

    2011-02-15

    Understanding the encoding and propagation of information by biochemical reaction networks and the relationship of such information processing properties to modular network structure is of fundamental importance in the study of cell signalling and regulation. However, a rigorous, automated approach for general biochemical networks has not been available, and high-throughput analysis has therefore been out of reach. Modularization Identification by Dynamic Independence Algorithms (MIDIA) is a user-friendly, extensible R package that performs automated analysis of how information is processed by biochemical networks. An important component is the algorithm's ability to identify exact network decompositions based on both the mass action kinetics and informational properties of the network. These modularizations are visualized using a tree structure from which important dynamic conditional independence properties can be directly read. Only partial stoichiometric information needs to be used as input to MIDIA, and neither simulations nor knowledge of rate parameters are required. When applied to a signalling network, for example, the method identifies the routes and species involved in the sequential propagation of information between its multiple inputs and outputs. These routes correspond to the relevant paths in the tree structure and may be further visualized using the Input-Output Path Matrix tool. MIDIA remains computationally feasible for the largest network reconstructions currently available and is straightforward to use with models written in Systems Biology Markup Language (SBML). The package is distributed under the GNU General Public License and is available, together with a link to browsable Supplementary Material, at http://code.google.com/p/midia. Further information is at www.maths.bris.ac.uk/~macgb/Software.html.

  13. CADLIVE toolbox for MATLAB: automatic dynamic modeling of biochemical networks with comprehensive system analysis.

    Science.gov (United States)

    Inoue, Kentaro; Maeda, Kazuhiro; Miyabe, Takaaki; Matsuoka, Yu; Kurata, Hiroyuki

    2014-09-01

    Mathematical modeling has become a standard technique to understand the dynamics of complex biochemical systems. To promote the modeling, we had developed the CADLIVE dynamic simulator that automatically converted a biochemical map into its associated mathematical model, simulated its dynamic behaviors and analyzed its robustness. To enhance the feasibility by CADLIVE and extend its functions, we propose the CADLIVE toolbox available for MATLAB, which implements not only the existing functions of the CADLIVE dynamic simulator, but also the latest tools including global parameter search methods with robustness analysis. The seamless, bottom-up processes consisting of biochemical network construction, automatic construction of its dynamic model, simulation, optimization, and S-system analysis greatly facilitate dynamic modeling, contributing to the research of systems biology and synthetic biology. This application can be freely downloaded from http://www.cadlive.jp/CADLIVE_MATLAB/ together with an instruction.

  14. Emergence of switch-like behavior in a large family of simple biochemical networks.

    Directory of Open Access Journals (Sweden)

    Dan Siegal-Gaskins

    2011-05-01

    Full Text Available Bistability plays a central role in the gene regulatory networks (GRNs controlling many essential biological functions, including cellular differentiation and cell cycle control. However, establishing the network topologies that can exhibit bistability remains a challenge, in part due to the exceedingly large variety of GRNs that exist for even a small number of components. We begin to address this problem by employing chemical reaction network theory in a comprehensive in silico survey to determine the capacity for bistability of more than 40,000 simple networks that can be formed by two transcription factor-coding genes and their associated proteins (assuming only the most elementary biochemical processes. We find that there exist reaction rate constants leading to bistability in ∼90% of these GRN models, including several circuits that do not contain any of the TF cooperativity commonly associated with bistable systems, and the majority of which could only be identified as bistable through an original subnetwork-based analysis. A topological sorting of the two-gene family of networks based on the presence or absence of biochemical reactions reveals eleven minimal bistable networks (i.e., bistable networks that do not contain within them a smaller bistable subnetwork. The large number of previously unknown bistable network topologies suggests that the capacity for switch-like behavior in GRNs arises with relative ease and is not easily lost through network evolution. To highlight the relevance of the systematic application of CRNT to bistable network identification in real biological systems, we integrated publicly available protein-protein interaction, protein-DNA interaction, and gene expression data from Saccharomyces cerevisiae, and identified several GRNs predicted to behave in a bistable fashion.

  15. Least-squares methods for identifying biochemical regulatory networks from noisy measurements

    Directory of Open Access Journals (Sweden)

    Heslop-Harrison Pat

    2007-01-01

    Full Text Available Abstract Background We consider the problem of identifying the dynamic interactions in biochemical networks from noisy experimental data. Typically, approaches for solving this problem make use of an estimation algorithm such as the well-known linear Least-Squares (LS estimation technique. We demonstrate that when time-series measurements are corrupted by white noise and/or drift noise, more accurate and reliable identification of network interactions can be achieved by employing an estimation algorithm known as Constrained Total Least Squares (CTLS. The Total Least Squares (TLS technique is a generalised least squares method to solve an overdetermined set of equations whose coefficients are noisy. The CTLS is a natural extension of TLS to the case where the noise components of the coefficients are correlated, as is usually the case with time-series measurements of concentrations and expression profiles in gene networks. Results The superior performance of the CTLS method in identifying network interactions is demonstrated on three examples: a genetic network containing four genes, a network describing p53 activity and mdm2 messenger RNA interactions, and a recently proposed kinetic model for interleukin (IL-6 and (IL-12b messenger RNA expression as a function of ATF3 and NF-κB promoter binding. For the first example, the CTLS significantly reduces the errors in the estimation of the Jacobian for the gene network. For the second, the CTLS reduces the errors from the measurements that are corrupted by white noise and the effect of neglected kinetics. For the third, it allows the correct identification, from noisy data, of the negative regulation of (IL-6 and (IL-12b by ATF3. Conclusion The significant improvements in performance demonstrated by the CTLS method under the wide range of conditions tested here, including different levels and types of measurement noise and different numbers of data points, suggests that its application will enable

  16. Modelling biochemical networks with intrinsic time delays: a hybrid semi-parametric approach

    Directory of Open Access Journals (Sweden)

    Oliveira Rui

    2010-09-01

    Full Text Available Abstract Background This paper presents a method for modelling dynamical biochemical networks with intrinsic time delays. Since the fundamental mechanisms leading to such delays are many times unknown, non conventional modelling approaches become necessary. Herein, a hybrid semi-parametric identification methodology is proposed in which discrete time series are incorporated into fundamental material balance models. This integration results in hybrid delay differential equations which can be applied to identify unknown cellular dynamics. Results The proposed hybrid modelling methodology was evaluated using two case studies. The first of these deals with dynamic modelling of transcriptional factor A in mammalian cells. The protein transport from the cytosol to the nucleus introduced a delay that was accounted for by discrete time series formulation. The second case study focused on a simple network with distributed time delays that demonstrated that the discrete time delay formalism has broad applicability to both discrete and distributed delay problems. Conclusions Significantly better prediction qualities of the novel hybrid model were obtained when compared to dynamical structures without time delays, being the more distinctive the more significant the underlying system delay is. The identification of the system delays by studies of different discrete modelling delays was enabled by the proposed structure. Further, it was shown that the hybrid discrete delay methodology is not limited to discrete delay systems. The proposed method is a powerful tool to identify time delays in ill-defined biochemical networks.

  17. Scalable rule-based modelling of allosteric proteins and biochemical networks.

    Directory of Open Access Journals (Sweden)

    Julien F Ollivier

    2010-11-01

    Full Text Available Much of the complexity of biochemical networks comes from the information-processing abilities of allosteric proteins, be they receptors, ion-channels, signalling molecules or transcription factors. An allosteric protein can be uniquely regulated by each combination of input molecules that it binds. This "regulatory complexity" causes a combinatorial increase in the number of parameters required to fit experimental data as the number of protein interactions increases. It therefore challenges the creation, updating, and re-use of biochemical models. Here, we propose a rule-based modelling framework that exploits the intrinsic modularity of protein structure to address regulatory complexity. Rather than treating proteins as "black boxes", we model their hierarchical structure and, as conformational changes, internal dynamics. By modelling the regulation of allosteric proteins through these conformational changes, we often decrease the number of parameters required to fit data, and so reduce over-fitting and improve the predictive power of a model. Our method is thermodynamically grounded, imposes detailed balance, and also includes molecular cross-talk and the background activity of enzymes. We use our Allosteric Network Compiler to examine how allostery can facilitate macromolecular assembly and how competitive ligands can change the observed cooperativity of an allosteric protein. We also develop a parsimonious model of G protein-coupled receptors that explains functional selectivity and can predict the rank order of potency of agonists acting through a receptor. Our methodology should provide a basis for scalable, modular and executable modelling of biochemical networks in systems and synthetic biology.

  18. Shape, size, and robustness: feasible regions in the parameter space of biochemical networks.

    Directory of Open Access Journals (Sweden)

    Adel Dayarian

    2009-01-01

    Full Text Available The concept of robustness of regulatory networks has received much attention in the last decade. One measure of robustness has been associated with the volume of the feasible region, namely, the region in the parameter space in which the system is functional. In this paper, we show that, in addition to volume, the geometry of this region has important consequences for the robustness and the fragility of a network. We develop an approximation within which we could algebraically specify the feasible region. We analyze the segment polarity gene network to illustrate our approach. The study of random walks in the parameter space and how they exit the feasible region provide us with a rich perspective on the different modes of failure of this network model. In particular, we found that, between two alternative ways of activating Wingless, one is more robust than the other. Our method provides a more complete measure of robustness to parameter variation. As a general modeling strategy, our approach is an interesting alternative to Boolean representation of biochemical networks.

  19. A moment-convergence method for stochastic analysis of biochemical reaction networks.

    Science.gov (United States)

    Zhang, Jiajun; Nie, Qing; Zhou, Tianshou

    2016-05-21

    Traditional moment-closure methods need to assume that high-order cumulants of a probability distribution approximate to zero. However, this strong assumption is not satisfied for many biochemical reaction networks. Here, we introduce convergent moments (defined in mathematics as the coefficients in the Taylor expansion of the probability-generating function at some point) to overcome this drawback of the moment-closure methods. As such, we develop a new analysis method for stochastic chemical kinetics. This method provides an accurate approximation for the master probability equation (MPE). In particular, the connection between low-order convergent moments and rate constants can be more easily derived in terms of explicit and analytical forms, allowing insights that would be difficult to obtain through direct simulation or manipulation of the MPE. In addition, it provides an accurate and efficient way to compute steady-state or transient probability distribution, avoiding the algorithmic difficulty associated with stiffness of the MPE due to large differences in sizes of rate constants. Applications of the method to several systems reveal nontrivial stochastic mechanisms of gene expression dynamics, e.g., intrinsic fluctuations can induce transient bimodality and amplify transient signals, and slow switching between promoter states can increase fluctuations in spatially heterogeneous signals. The overall approach has broad applications in modeling, analysis, and computation of complex biochemical networks with intrinsic noise.

  20. A moment-convergence method for stochastic analysis of biochemical reaction networks

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Jiajun [School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275 (China); Nie, Qing [Department of Mathematics, University of California at Irvine, Irvine, California 92697 (United States); Zhou, Tianshou, E-mail: mcszhtsh@mail.sysu.edu.cn [School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275 (China); Guangdong Province Key Laboratory of Computational Science and School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275 (China)

    2016-05-21

    Traditional moment-closure methods need to assume that high-order cumulants of a probability distribution approximate to zero. However, this strong assumption is not satisfied for many biochemical reaction networks. Here, we introduce convergent moments (defined in mathematics as the coefficients in the Taylor expansion of the probability-generating function at some point) to overcome this drawback of the moment-closure methods. As such, we develop a new analysis method for stochastic chemical kinetics. This method provides an accurate approximation for the master probability equation (MPE). In particular, the connection between low-order convergent moments and rate constants can be more easily derived in terms of explicit and analytical forms, allowing insights that would be difficult to obtain through direct simulation or manipulation of the MPE. In addition, it provides an accurate and efficient way to compute steady-state or transient probability distribution, avoiding the algorithmic difficulty associated with stiffness of the MPE due to large differences in sizes of rate constants. Applications of the method to several systems reveal nontrivial stochastic mechanisms of gene expression dynamics, e.g., intrinsic fluctuations can induce transient bimodality and amplify transient signals, and slow switching between promoter states can increase fluctuations in spatially heterogeneous signals. The overall approach has broad applications in modeling, analysis, and computation of complex biochemical networks with intrinsic noise.

  1. Modularization of biochemical networks based on classification of Petri net t-invariants.

    Science.gov (United States)

    Grafahrend-Belau, Eva; Schreiber, Falk; Heiner, Monika; Sackmann, Andrea; Junker, Björn H; Grunwald, Stefanie; Speer, Astrid; Winder, Katja; Koch, Ina

    2008-02-08

    Structural analysis of biochemical networks is a growing field in bioinformatics and systems biology. The availability of an increasing amount of biological data from molecular biological networks promises a deeper understanding but confronts researchers with the problem of combinatorial explosion. The amount of qualitative network data is growing much faster than the amount of quantitative data, such as enzyme kinetics. In many cases it is even impossible to measure quantitative data because of limitations of experimental methods, or for ethical reasons. Thus, a huge amount of qualitative data, such as interaction data, is available, but it was not sufficiently used for modeling purposes, until now. New approaches have been developed, but the complexity of data often limits the application of many of the methods. Biochemical Petri nets make it possible to explore static and dynamic qualitative system properties. One Petri net approach is model validation based on the computation of the system's invariant properties, focusing on t-invariants. T-invariants correspond to subnetworks, which describe the basic system behavior.With increasing system complexity, the basic behavior can only be expressed by a huge number of t-invariants. According to our validation criteria for biochemical Petri nets, the necessary verification of the biological meaning, by interpreting each subnetwork (t-invariant) manually, is not possible anymore. Thus, an automated, biologically meaningful classification would be helpful in analyzing t-invariants, and supporting the understanding of the basic behavior of the considered biological system. Here, we introduce a new approach to automatically classify t-invariants to cope with network complexity. We apply clustering techniques such as UPGMA, Complete Linkage, Single Linkage, and Neighbor Joining in combination with different distance measures to get biologically meaningful clusters (t-clusters), which can be interpreted as modules. To find

  2. Modularization of biochemical networks based on classification of Petri net t-invariants

    Directory of Open Access Journals (Sweden)

    Grunwald Stefanie

    2008-02-01

    Full Text Available Abstract Background Structural analysis of biochemical networks is a growing field in bioinformatics and systems biology. The availability of an increasing amount of biological data from molecular biological networks promises a deeper understanding but confronts researchers with the problem of combinatorial explosion. The amount of qualitative network data is growing much faster than the amount of quantitative data, such as enzyme kinetics. In many cases it is even impossible to measure quantitative data because of limitations of experimental methods, or for ethical reasons. Thus, a huge amount of qualitative data, such as interaction data, is available, but it was not sufficiently used for modeling purposes, until now. New approaches have been developed, but the complexity of data often limits the application of many of the methods. Biochemical Petri nets make it possible to explore static and dynamic qualitative system properties. One Petri net approach is model validation based on the computation of the system's invariant properties, focusing on t-invariants. T-invariants correspond to subnetworks, which describe the basic system behavior. With increasing system complexity, the basic behavior can only be expressed by a huge number of t-invariants. According to our validation criteria for biochemical Petri nets, the necessary verification of the biological meaning, by interpreting each subnetwork (t-invariant manually, is not possible anymore. Thus, an automated, biologically meaningful classification would be helpful in analyzing t-invariants, and supporting the understanding of the basic behavior of the considered biological system. Methods Here, we introduce a new approach to automatically classify t-invariants to cope with network complexity. We apply clustering techniques such as UPGMA, Complete Linkage, Single Linkage, and Neighbor Joining in combination with different distance measures to get biologically meaningful clusters (t

  3. Parametric sensitivity analysis for biochemical reaction networks based on pathwise information theory.

    Science.gov (United States)

    Pantazis, Yannis; Katsoulakis, Markos A; Vlachos, Dionisios G

    2013-10-22

    Stochastic modeling and simulation provide powerful predictive methods for the intrinsic understanding of fundamental mechanisms in complex biochemical networks. Typically, such mathematical models involve networks of coupled jump stochastic processes with a large number of parameters that need to be suitably calibrated against experimental data. In this direction, the parameter sensitivity analysis of reaction networks is an essential mathematical and computational tool, yielding information regarding the robustness and the identifiability of model parameters. However, existing sensitivity analysis approaches such as variants of the finite difference method can have an overwhelming computational cost in models with a high-dimensional parameter space. We develop a sensitivity analysis methodology suitable for complex stochastic reaction networks with a large number of parameters. The proposed approach is based on Information Theory methods and relies on the quantification of information loss due to parameter perturbations between time-series distributions. For this reason, we need to work on path-space, i.e., the set consisting of all stochastic trajectories, hence the proposed approach is referred to as "pathwise". The pathwise sensitivity analysis method is realized by employing the rigorously-derived Relative Entropy Rate, which is directly computable from the propensity functions. A key aspect of the method is that an associated pathwise Fisher Information Matrix (FIM) is defined, which in turn constitutes a gradient-free approach to quantifying parameter sensitivities. The structure of the FIM turns out to be block-diagonal, revealing hidden parameter dependencies and sensitivities in reaction networks. As a gradient-free method, the proposed sensitivity analysis provides a significant advantage when dealing with complex stochastic systems with a large number of parameters. In addition, the knowledge of the structure of the FIM can allow to efficiently address

  4. An efficient algorithm for computing fixed length attractors based on bounded model checking in synchronous Boolean networks with biochemical applications.

    Science.gov (United States)

    Li, X Y; Yang, G W; Zheng, D S; Guo, W S; Hung, W N N

    2015-04-28

    Genetic regulatory networks are the key to understanding biochemical systems. One condition of the genetic regulatory network under different living environments can be modeled as a synchronous Boolean network. The attractors of these Boolean networks will help biologists to identify determinant and stable factors. Existing methods identify attractors based on a random initial state or the entire state simultaneously. They cannot identify the fixed length attractors directly. The complexity of including time increases exponentially with respect to the attractor number and length of attractors. This study used the bounded model checking to quickly locate fixed length attractors. Based on the SAT solver, we propose a new algorithm for efficiently computing the fixed length attractors, which is more suitable for large Boolean networks and numerous attractors' networks. After comparison using the tool BooleNet, empirical experiments involving biochemical systems demonstrated the feasibility and efficiency of our approach.

  5. Linear analysis near a steady-state of biochemical networks: control analysis, correlation metrics and circuit theory

    Directory of Open Access Journals (Sweden)

    Qian Hong

    2008-05-01

    Full Text Available Abstract Background: Several approaches, including metabolic control analysis (MCA, flux balance analysis (FBA, correlation metric construction (CMC, and biochemical circuit theory (BCT, have been developed for the quantitative analysis of complex biochemical networks. Here, we present a comprehensive theory of linear analysis for nonequilibrium steady-state (NESS biochemical reaction networks that unites these disparate approaches in a common mathematical framework and thermodynamic basis. Results: In this theory a number of relationships between key matrices are introduced: the matrix A obtained in the standard, linear-dynamic-stability analysis of the steady-state can be decomposed as A = SRT where R and S are directly related to the elasticity-coefficient matrix for the fluxes and chemical potentials in MCA, respectively; the control-coefficients for the fluxes and chemical potentials can be written in terms of RT BS and ST BS respectively where matrix B is the inverse of A; the matrix S is precisely the stoichiometric matrix in FBA; and the matrix eAt plays a central role in CMC. Conclusion: One key finding that emerges from this analysis is that the well-known summation theorems in MCA take different forms depending on whether metabolic steady-state is maintained by flux injection or concentration clamping. We demonstrate that if rate-limiting steps exist in a biochemical pathway, they are the steps with smallest biochemical conductances and largest flux control-coefficients. We hypothesize that biochemical networks for cellular signaling have a different strategy for minimizing energy waste and being efficient than do biochemical networks for biosynthesis. We also discuss the intimate relationship between MCA and biochemical systems analysis (BSA.

  6. Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs

    LENUS (Irish Health Repository)

    Casey, Fergal

    2011-08-22

    Abstract Background Gene and protein interactions are commonly represented as networks, with the genes or proteins comprising the nodes and the relationship between them as edges. Motifs, or small local configurations of edges and nodes that arise repeatedly, can be used to simplify the interpretation of networks. Results We examined triplet motifs in a network of quantitative epistatic genetic relationships, and found a non-random distribution of particular motif classes. Individual motif classes were found to be associated with different functional properties, suggestive of an underlying biological significance. These associations were apparent not only for motif classes, but for individual positions within the motifs. As expected, NNN (all negative) motifs were strongly associated with previously reported genetic (i.e. synthetic lethal) interactions, while PPP (all positive) motifs were associated with protein complexes. The two other motif classes (NNP: a positive interaction spanned by two negative interactions, and NPP: a negative spanned by two positives) showed very distinct functional associations, with physical interactions dominating for the former but alternative enrichments, typical of biochemical pathways, dominating for the latter. Conclusion We present a model showing how NNP motifs can be used to recognize supportive relationships between protein complexes, while NPP motifs often identify opposing or regulatory behaviour between a gene and an associated pathway. The ability to use motifs to point toward underlying biological organizational themes is likely to be increasingly important as more extensive epistasis mapping projects in higher organisms begin.

  7. HRSSA – Efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks

    International Nuclear Information System (INIS)

    Marchetti, Luca; Priami, Corrado; Thanh, Vo Hong

    2016-01-01

    This paper introduces HRSSA (Hybrid Rejection-based Stochastic Simulation Algorithm), a new efficient hybrid stochastic simulation algorithm for spatially homogeneous biochemical reaction networks. HRSSA is built on top of RSSA, an exact stochastic simulation algorithm which relies on propensity bounds to select next reaction firings and to reduce the average number of reaction propensity updates needed during the simulation. HRSSA exploits the computational advantage of propensity bounds to manage time-varying transition propensities and to apply dynamic partitioning of reactions, which constitute the two most significant bottlenecks of hybrid simulation. A comprehensive set of simulation benchmarks is provided for evaluating performance and accuracy of HRSSA against other state of the art algorithms.

  8. HRSSA – Efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks

    Energy Technology Data Exchange (ETDEWEB)

    Marchetti, Luca, E-mail: marchetti@cosbi.eu [The Microsoft Research – University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, 1, 38068 Rovereto (Italy); Priami, Corrado, E-mail: priami@cosbi.eu [The Microsoft Research – University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, 1, 38068 Rovereto (Italy); University of Trento, Department of Mathematics (Italy); Thanh, Vo Hong, E-mail: vo@cosbi.eu [The Microsoft Research – University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, 1, 38068 Rovereto (Italy)

    2016-07-15

    This paper introduces HRSSA (Hybrid Rejection-based Stochastic Simulation Algorithm), a new efficient hybrid stochastic simulation algorithm for spatially homogeneous biochemical reaction networks. HRSSA is built on top of RSSA, an exact stochastic simulation algorithm which relies on propensity bounds to select next reaction firings and to reduce the average number of reaction propensity updates needed during the simulation. HRSSA exploits the computational advantage of propensity bounds to manage time-varying transition propensities and to apply dynamic partitioning of reactions, which constitute the two most significant bottlenecks of hybrid simulation. A comprehensive set of simulation benchmarks is provided for evaluating performance and accuracy of HRSSA against other state of the art algorithms.

  9. Dynamic Modeling of Cell-Free Biochemical Networks Using Effective Kinetic Models

    Directory of Open Access Journals (Sweden)

    Joseph A. Wayman

    2015-03-01

    Full Text Available Cell-free systems offer many advantages for the study, manipulation and modeling of metabolism compared to in vivo processes. Many of the challenges confronting genome-scale kinetic modeling can potentially be overcome in a cell-free system. For example, there is no complex transcriptional regulation to consider, transient metabolic measurements are easier to obtain, and we no longer have to consider cell growth. Thus, cell-free operation holds several significant advantages for model development, identification and validation. Theoretically, genome-scale cell-free kinetic models may be possible for industrially important organisms, such as E. coli, if a simple, tractable framework for integrating allosteric regulation with enzyme kinetics can be formulated. Toward this unmet need, we present an effective biochemical network modeling framework for building dynamic cell-free metabolic models. The key innovation of our approach is the integration of simple effective rules encoding complex allosteric regulation with traditional kinetic pathway modeling. We tested our approach by modeling the time evolution of several hypothetical cell-free metabolic networks. We found that simple effective rules, when integrated with traditional enzyme kinetic expressions, captured complex allosteric patterns such as ultrasensitivity or non-competitive inhibition in the absence of mechanistic information. Second, when integrated into network models, these rules captured classic regulatory patterns such as product-induced feedback inhibition. Lastly, we showed, at least for the network architectures considered here, that we could simultaneously estimate kinetic parameters and allosteric connectivity from synthetic data starting from an unbiased collection of possible allosteric structures using particle swarm optimization. However, when starting with an initial population that was heavily enriched with incorrect structures, our particle swarm approach could converge

  10. Application of approximate pattern matching in two dimensional spaces to grid layout for biochemical network maps.

    Science.gov (United States)

    Inoue, Kentaro; Shimozono, Shinichi; Yoshida, Hideaki; Kurata, Hiroyuki

    2012-01-01

    For visualizing large-scale biochemical network maps, it is important to calculate the coordinates of molecular nodes quickly and to enhance the understanding or traceability of them. The grid layout is effective in drawing compact, orderly, balanced network maps with node label spaces, but existing grid layout algorithms often require a high computational cost because they have to consider complicated positional constraints through the entire optimization process. We propose a hybrid grid layout algorithm that consists of a non-grid, fast layout (preprocessor) algorithm and an approximate pattern matching algorithm that distributes the resultant preprocessed nodes on square grid points. To demonstrate the feasibility of the hybrid layout algorithm, it is characterized in terms of the calculation time, numbers of edge-edge and node-edge crossings, relative edge lengths, and F-measures. The proposed algorithm achieves outstanding performances compared with other existing grid layouts. Use of an approximate pattern matching algorithm quickly redistributes the laid-out nodes by fast, non-grid algorithms on the square grid points, while preserving the topological relationships among the nodes. The proposed algorithm is a novel use of the pattern matching, thereby providing a breakthrough for grid layout. This application program can be freely downloaded from http://www.cadlive.jp/hybridlayout/hybridlayout.html.

  11. Application of approximate pattern matching in two dimensional spaces to grid layout for biochemical network maps.

    Directory of Open Access Journals (Sweden)

    Kentaro Inoue

    Full Text Available BACKGROUND: For visualizing large-scale biochemical network maps, it is important to calculate the coordinates of molecular nodes quickly and to enhance the understanding or traceability of them. The grid layout is effective in drawing compact, orderly, balanced network maps with node label spaces, but existing grid layout algorithms often require a high computational cost because they have to consider complicated positional constraints through the entire optimization process. RESULTS: We propose a hybrid grid layout algorithm that consists of a non-grid, fast layout (preprocessor algorithm and an approximate pattern matching algorithm that distributes the resultant preprocessed nodes on square grid points. To demonstrate the feasibility of the hybrid layout algorithm, it is characterized in terms of the calculation time, numbers of edge-edge and node-edge crossings, relative edge lengths, and F-measures. The proposed algorithm achieves outstanding performances compared with other existing grid layouts. CONCLUSIONS: Use of an approximate pattern matching algorithm quickly redistributes the laid-out nodes by fast, non-grid algorithms on the square grid points, while preserving the topological relationships among the nodes. The proposed algorithm is a novel use of the pattern matching, thereby providing a breakthrough for grid layout. This application program can be freely downloaded from http://www.cadlive.jp/hybridlayout/hybridlayout.html.

  12. Patterns of Stochastic Behavior in Dynamically Unstable High-Dimensional Biochemical Networks

    Directory of Open Access Journals (Sweden)

    Simon Rosenfeld

    2009-01-01

    Full Text Available The question of dynamical stability and stochastic behavior of large biochemical networks is discussed. It is argued that stringent conditions of asymptotic stability have very little chance to materialize in a multidimensional system described by the differential equations of chemical kinetics. The reason is that the criteria of asymptotic stability (Routh- Hurwitz, Lyapunov criteria, Feinberg’s Deficiency Zero theorem would impose the limitations of very high algebraic order on the kinetic rates and stoichiometric coefficients, and there are no natural laws that would guarantee their unconditional validity. Highly nonlinear, dynamically unstable systems, however, are not necessarily doomed to collapse, as a simple Jacobian analysis would suggest. It is possible that their dynamics may assume the form of pseudo-random fluctuations quite similar to a shot noise, and, therefore, their behavior may be described in terms of Langevin and Fokker-Plank equations. We have shown by simulation that the resulting pseudo-stochastic processes obey the heavy-tailed Generalized Pareto Distribution with temporal sequence of pulses forming the set of constituent-specific Poisson processes. Being applied to intracellular dynamics, these properties are naturally associated with burstiness, a well documented phenomenon in the biology of gene expression.

  13. Set-base dynamical parameter estimation and model invalidation for biochemical reaction networks.

    Science.gov (United States)

    Rumschinski, Philipp; Borchers, Steffen; Bosio, Sandro; Weismantel, Robert; Findeisen, Rolf

    2010-05-25

    Mathematical modeling and analysis have become, for the study of biological and cellular processes, an important complement to experimental research. However, the structural and quantitative knowledge available for such processes is frequently limited, and measurements are often subject to inherent and possibly large uncertainties. This results in competing model hypotheses, whose kinetic parameters may not be experimentally determinable. Discriminating among these alternatives and estimating their kinetic parameters is crucial to improve the understanding of the considered process, and to benefit from the analytical tools at hand. In this work we present a set-based framework that allows to discriminate between competing model hypotheses and to provide guaranteed outer estimates on the model parameters that are consistent with the (possibly sparse and uncertain) experimental measurements. This is obtained by means of exact proofs of model invalidity that exploit the polynomial/rational structure of biochemical reaction networks, and by making use of an efficient strategy to balance solution accuracy and computational effort. The practicability of our approach is illustrated with two case studies. The first study shows that our approach allows to conclusively rule out wrong model hypotheses. The second study focuses on parameter estimation, and shows that the proposed method allows to evaluate the global influence of measurement sparsity, uncertainty, and prior knowledge on the parameter estimates. This can help in designing further experiments leading to improved parameter estimates.

  14. Reduced linear noise approximation for biochemical reaction networks with time-scale separation: The stochastic tQSSA+

    Science.gov (United States)

    Herath, Narmada; Del Vecchio, Domitilla

    2018-03-01

    Biochemical reaction networks often involve reactions that take place on different time scales, giving rise to "slow" and "fast" system variables. This property is widely used in the analysis of systems to obtain dynamical models with reduced dimensions. In this paper, we consider stochastic dynamics of biochemical reaction networks modeled using the Linear Noise Approximation (LNA). Under time-scale separation conditions, we obtain a reduced-order LNA that approximates both the slow and fast variables in the system. We mathematically prove that the first and second moments of this reduced-order model converge to those of the full system as the time-scale separation becomes large. These mathematical results, in particular, provide a rigorous justification to the accuracy of LNA models derived using the stochastic total quasi-steady state approximation (tQSSA). Since, in contrast to the stochastic tQSSA, our reduced-order model also provides approximations for the fast variable stochastic properties, we term our method the "stochastic tQSSA+". Finally, we demonstrate the application of our approach on two biochemical network motifs found in gene-regulatory and signal transduction networks.

  15. Identification of alterations in the Jacobian of biochemical reaction networks from steady state covariance data at two conditions.

    Science.gov (United States)

    Kügler, Philipp; Yang, Wei

    2014-06-01

    Model building of biochemical reaction networks typically involves experiments in which changes in the behavior due to natural or experimental perturbations are observed. Computational models of reaction networks are also used in a systems biology approach to study how transitions from a healthy to a diseased state result from changes in genetic or environmental conditions. In this paper we consider the nonlinear inverse problem of inferring information about the Jacobian of a Langevin type network model from covariance data of steady state concentrations associated to two different experimental conditions. Under idealized assumptions on the Langevin fluctuation matrices we prove that relative alterations in the network Jacobian can be uniquely identified when comparing the two data sets. Based on this result and the premise that alteration is locally confined to separable parts due to network modularity we suggest a computational approach using hybrid stochastic-deterministic optimization for the detection of perturbations in the network Jacobian using the sparsity promoting effect of [Formula: see text]-penalization. Our approach is illustrated by means of published metabolomic and signaling reaction networks.

  16. Dynamic Modeling of Cell-Free Biochemical Networks Using Effective Kinetic Models

    Science.gov (United States)

    2015-03-03

    based whole-cell models of E. coli [6]. Conversely , highly abstracted kinetic frameworks, such as the cybernetic framework, represented a paradigm shift...metabolic objective function has been the optimization of biomass formation [18], although other metabolic objectives have also been estimated [19...experimental data. Toward these questions, we explored five hypothetical cell-free networks. Each network shared the same enzymatic connectivity, but

  17. Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks.

    Science.gov (United States)

    Schillings, Claudia; Sunnåker, Mikael; Stelling, Jörg; Schwab, Christoph

    2015-08-01

    Parametric uncertainty is a particularly challenging and relevant aspect of systems analysis in domains such as systems biology where, both for inference and for assessing prediction uncertainties, it is essential to characterize the system behavior globally in the parameter space. However, current methods based on local approximations or on Monte-Carlo sampling cope only insufficiently with high-dimensional parameter spaces associated with complex network models. Here, we propose an alternative deterministic methodology that relies on sparse polynomial approximations. We propose a deterministic computational interpolation scheme which identifies most significant expansion coefficients adaptively. We present its performance in kinetic model equations from computational systems biology with several hundred parameters and state variables, leading to numerical approximations of the parametric solution on the entire parameter space. The scheme is based on adaptive Smolyak interpolation of the parametric solution at judiciously and adaptively chosen points in parameter space. As Monte-Carlo sampling, it is "non-intrusive" and well-suited for massively parallel implementation, but affords higher convergence rates. This opens up new avenues for large-scale dynamic network analysis by enabling scaling for many applications, including parameter estimation, uncertainty quantification, and systems design.

  18. Noise transmission and delay-induced stochasticoscillations in biochemical network motifs

    Institute of Scientific and Technical Information of China (English)

    Liu Sheng-Jun; Wang Qi; Liu Bo; Yan Shi-Wei; Fumihiko Sakata

    2011-01-01

    With the aid of stochastic delayed-feedback differential equations,we derive an analytic expression for the power spectra of reacting molecules included in a generic biological network motif that is incorporated with a feedback mechanism and time delays in gene regulation.We systematically analyse the effects of time delays,the feedback mechanism,and biological stochasticity on the power spectra.It has been clarified that the time delays together with the feedback mechanism can induce stochastic oscillations at the molecular level and invalidate the noise addition rule for a modular description of the noise propagator.Delay-induced stochastic resonance can be expected,which is related to the stability loss of the reaction systems and Hopf bifurcation occurring for solutions of the corresponding deterministic reaction equations.Through the analysis of the power spectrum,a new approach is proposed to estimate the oscillation period.

  19. Noise transmission and delay-induced stochastic oscillations in biochemical network motifs

    International Nuclear Information System (INIS)

    Liu Sheng-Jun; Wang Qi; Liu Bo; Yan Shi-Wei; Sakata Fumihiko

    2011-01-01

    With the aid of stochastic delayed-feedback differential equations, we derive an analytic expression for the power spectra of reacting molecules included in a generic biological network motif that is incorporated with a feedback mechanism and time delays in gene regulation. We systematically analyse the effects of time delays, the feedback mechanism, and biological stochasticity on the power spectra. It has been clarified that the time delays together with the feedback mechanism can induce stochastic oscillations at the molecular level and invalidate the noise addition rule for a modular description of the noise propagator. Delay-induced stochastic resonance can be expected, which is related to the stability loss of the reaction systems and Hopf bifurcation occurring for solutions of the corresponding deterministic reaction equations. Through the analysis of the power spectrum, a new approach is proposed to estimate the oscillation period. (interdisciplinary physics and related areas of science and technology)

  20. Biochemical alterations in inflammatory reactive chondrocytes: evidence for intercellular network communication

    Directory of Open Access Journals (Sweden)

    Eva Skiöldebrand

    2018-01-01

    Full Text Available Chondrocytes are effectively involved in the pathophysiological processes of inflammation in joints. They form cellular processes in the superficial layer of the articular cartilage and form gap junction coupled syncytium to facilitate cell-to-cell communication. However, very little is known about their physiological cellular identity and communication. The aim with the present work is to evaluate the physiological behavior after stimulation with the inflammatory inducers interleukin-1β and lipopolysaccharide. The cytoskeleton integrity and intracellular Ca2+ release were assessed as indicators of inflammatory state. Cytoskeleton integrity was analyzed through cartilage oligomeric matrix protein and actin labeling with an Alexa 488-conjugated phalloidin probe. Ca2+ responses were assessed through the Ca2+ sensitive fluorophore Fura-2/AM. Western blot analyses of several inflammatory markers were performed. The results show reorganization of the actin filaments. Glutamate, 5-hydoxytryptamine, and ATP evoked intracellular Ca2+ release changed from single peaks to oscillations after inflammatory induction in the chondrocytes. The expression of toll-like receptor 4, the glutamate transporters GLAST and GLT-1, and the matrix metalloproteinase-13 increased. This work demonstrates that chondrocytes are a key part in conditions that lead to inflammation in the cartilage. The inflammatory inducers modulate the cytoskeleton, the Ca2+ signaling, and several inflammatory parameters. In conclusion, our data show that the cellular responses to inflammatory insults from healthy and inflammatory chondrocytes resemble those previously observed in astrocyte and cardiac fibroblasts networks.

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

    Directory of Open Access Journals (Sweden)

    St Laurent Georges

    2010-03-01

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

  2. Gene network inference and biochemical assessment delineates GPCR pathways and CREB targets in small intestinal neuroendocrine neoplasia.

    Directory of Open Access Journals (Sweden)

    Ignat Drozdov

    Full Text Available Small intestinal (SI neuroendocrine tumors (NET are increasing in incidence, however little is known about their biology. High throughput techniques such as inference of gene regulatory networks from microarray experiments can objectively define signaling machinery in this disease. Genome-wide co-expression analysis was used to infer gene relevance network in SI-NETs. The network was confirmed to be non-random, scale-free, and highly modular. Functional analysis of gene co-expression modules revealed processes including 'Nervous system development', 'Immune response', and 'Cell-cycle'. Importantly, gene network topology and differential expression analysis identified over-expression of the GPCR signaling regulators, the cAMP synthetase, ADCY2, and the protein kinase A, PRKAR1A. Seven CREB response element (CRE transcripts associated with proliferation and secretion: BEX1, BICD1, CHGB, CPE, GABRB3, SCG2 and SCG3 as well as ADCY2 and PRKAR1A were measured in an independent SI dataset (n = 10 NETs; n = 8 normal preparations. All were up-regulated (p<0.035 with the exception of SCG3 which was not differently expressed. Forskolin (a direct cAMP activator, 10(-5 M significantly stimulated transcription of pCREB and 3/7 CREB targets, isoproterenol (a selective ß-adrenergic receptor agonist and cAMP activator, 10(-5 M stimulated pCREB and 4/7 targets while BIM-53061 (a dopamine D(2 and Serotonin [5-HT(2] receptor agonist, 10(-6 M stimulated 100% of targets as well as pCREB; CRE transcription correlated with the levels of cAMP accumulation and PKA activity; BIM-53061 stimulated the highest levels of cAMP and PKA (2.8-fold and 2.5-fold vs. 1.8-2-fold for isoproterenol and forskolin. Gene network inference and graph topology analysis in SI NETs suggests that SI NETs express neural GPCRs that activate different CRE targets associated with proliferation and secretion. In vitro studies, in a model NET cell system, confirmed that transcriptional

  3. Real-time relationship between PKA biochemical signal network dynamics and increased action potential firing rate in heart pacemaker cells

    Science.gov (United States)

    Yaniv, Yael; Ganesan, Ambhighainath; Yang, Dongmei; Ziman, Bruce D.; Lyashkov, Alexey E.; Levchenko, Andre; Zhang, Jin; Lakatta, Edward G.

    2015-01-01

    cAMP-PKA protein kinase is a key nodal signaling pathway that regulates a wide range of heart pacemaker cell functions. These functions are predicted to be involved in regulation of spontaneous action potential (AP) generation of these cells. Here we investigate if the kinetics and stoichiometry of increase in PKA activity match the increase in AP firing rate in response to β-adrenergic receptor (β-AR) stimulation or phosphodiesterase (PDE) inhibition, that alter the AP firing rate of heart sinoatrial pacemaker cells. In cultured adult rabbit pacemaker cells infected with an adenovirous expressing the FRET sensor AKAR3, the EC50 in response to graded increases in the intensity of β-AR stimulation (by Isoproterenol) the magnitude of the increases in PKA activity and the spontaneous AP firing rate were similar (0.4±0.1nM vs. 0.6±0.15nM, respectively). Moreover, the kinetics (t1/2) of the increases in PKA activity and spontaneous AP firing rate in response to β-AR stimulation or PDE inhibition were tightly linked. We characterized the system rate-limiting biochemical reactions by integrating these experimentally derived data into mechanistic-computational model. Model simulations predicted that phospholamban phosphorylation is a potent target of the increase in PKA activity that links to increase in spontaneous AP firing rate. In summary, the kinetics and stoichiometry of increases in PKA activity in response to a physiological (β-AR stimulation) or pharmacological (PDE inhibitor) stimuli match those of changes in the AP firing rate. Thus Ca2+-cAMP/PKA-dependent phosphorylation limits the rate and magnitude of increase in spontaneous AP firing rate. PMID:26241846

  4. Network of vascular diseases, death and biochemical characteristics in a set of 4,197 patients with type 1 diabetes (The FinnDiane Study

    Directory of Open Access Journals (Sweden)

    Wadén Johan

    2009-10-01

    Full Text Available Background Cardiovascular disease is the main cause of premature death in patients with type 1 diabetes. Patients with diabetic kidney disease have an increased risk of heart attack or stroke. Accurate knowledge of the complex inter-dependencies between the risk factors is critical for pinpointing the best targets for research and treatment. Therefore, the aim of this study was to describe the association patterns between clinical and biochemical features of diabetic complications. Methods Medical records and serum and urine samples of 4,197 patients with type 1 diabetes were collected from health care centers in Finland. At baseline, the mean diabetes duration was 22 years, 52% were male, 23% had kidney disease (urine albumin excretion over 300 mg/24 h or end-stage renal disease and 8% had a history of macrovascular events. All-cause mortality was evaluated after an average of 6.5 years of follow-up (25,714 patient years. The dataset comprised 28 clinical and 25 biochemical variables that were regarded as the nodes of a network to assess their mutual relationships. Results The networks contained cliques that were densely inter-connected (r > 0.6, including cliques for high-density lipoprotein (HDL markers, for triglycerides and cholesterol, for urinary excretion and for indices of body mass. The links between the cliques showed biologically relevant interactions: an inverse relationship between HDL cholesterol and the triglyceride clique (r P -16, a connection between triglycerides and body mass via C-reactive protein (r > 0.3, P -16 and intermediate-density cholesterol as the connector between lipoprotein metabolism and albuminuria (r > 0.3, P -16. Aging and macrovascular disease were linked to death via working ability and retinopathy. Diabetic kidney disease, serum creatinine and potassium, retinopathy and blood pressure were inter-connected. Blood pressure correlations indicated accelerated vascular aging in individuals with kidney disease

  5. Systems biology and the origins of life? part II. Are biochemical networks possible ancestors of living systems? networks of catalysed chemical reactions: non-equilibrium, self-organization and evolution.

    Science.gov (United States)

    Ricard, Jacques

    2010-01-01

    The present article discusses the possibility that catalysed chemical networks can evolve. Even simple enzyme-catalysed chemical reactions can display this property. The example studied is that of a two-substrate proteinoid, or enzyme, reaction displaying random binding of its substrates A and B. The fundamental property of such a system is to display either emergence or integration depending on the respective values of the probabilities that the enzyme has bound one of its substrate regardless it has bound the other substrate, or, specifically, after it has bound the other substrate. There is emergence of information if p(A)>p(AB) and p(B)>p(BA). Conversely, if p(A)equilibrium. Moreover, in such systems, emergence results in an increase of the energy level of the ternary EAB complex that becomes closer to the transition state of the reaction, thus leading to the enhancement of catalysis. Hence a drift from quasi-equilibrium is, to a large extent, responsible for the production of information and enhancement of catalysis. Non-equilibrium of these simple systems must be an important aspect that leads to both self-organization and evolutionary processes. These conclusions can be extended to networks of catalysed chemical reactions. Such networks are, in fact, networks of networks, viz. meta-networks. In this formal representation, nodes are chemical reactions catalysed by poorly specific proteinoids, and links can be identified to the transport of metabolites from proteinoid to proteinoid. The concepts of integration and emergence can be applied to such situations and can be used to define the identity of these networks and therefore their evolution. Defined as open non-equilibrium structures, such biochemical networks possess two remarkable properties: (1) the probability of occurrence of their nodes is dependant upon the input and output of matter in, and from, the system and (2) the probability of occurrence of the nodes is strictly linked to their degree of

  6. BISEN: Biochemical simulation environment

    NARCIS (Netherlands)

    Vanlier, J.; Wu, F.; Qi, F.; Vinnakota, K.C.; Han, Y.; Dash, R.K.; Yang, F.; Beard, D.A.

    2009-01-01

    The Biochemical Simulation Environment (BISEN) is a suite of tools for generating equations and associated computer programs for simulating biochemical systems in the MATLAB® computing environment. This is the first package that can generate appropriate systems of differential equations for

  7. Real-time relationship between PKA biochemical signal network dynamics and increased action potential firing rate in heart pacemaker cells: Kinetics of PKA activation in heart pacemaker cells.

    Science.gov (United States)

    Yaniv, Yael; Ganesan, Ambhighainath; Yang, Dongmei; Ziman, Bruce D; Lyashkov, Alexey E; Levchenko, Andre; Zhang, Jin; Lakatta, Edward G

    2015-09-01

    cAMP-PKA protein kinase is a key nodal signaling pathway that regulates a wide range of heart pacemaker cell functions. These functions are predicted to be involved in regulation of spontaneous action potential (AP) generation of these cells. Here we investigate if the kinetics and stoichiometry of increase in PKA activity match the increase in AP firing rate in response to β-adrenergic receptor (β-AR) stimulation or phosphodiesterase (PDE) inhibition, that alters the AP firing rate of heart sinoatrial pacemaker cells. In cultured adult rabbit pacemaker cells infected with an adenovirus expressing the FRET sensor AKAR3, the EC50 in response to graded increases in the intensity of β-AR stimulation (by Isoproterenol) the magnitude of the increases in PKA activity and the spontaneous AP firing rate were similar (0.4±0.1nM vs. 0.6±0.15nM, respectively). Moreover, the kinetics (t1/2) of the increases in PKA activity and spontaneous AP firing rate in response to β-AR stimulation or PDE inhibition were tightly linked. We characterized the system rate-limiting biochemical reactions by integrating these experimentally derived data into a mechanistic-computational model. Model simulations predicted that phospholamban phosphorylation is a potent target of the increase in PKA activity that links to increase in spontaneous AP firing rate. In summary, the kinetics and stoichiometry of increases in PKA activity in response to a physiological (β-AR stimulation) or pharmacological (PDE inhibitor) stimuli match those of changes in the AP firing rate. Thus Ca(2+)-cAMP/PKA-dependent phosphorylation limits the rate and magnitude of increase in spontaneous AP firing rate. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. A Simple Approach to Study Designs in Complex Biochemical ...

    Indian Academy of Sciences (India)

    Somdatta Sinha

    Protein sequences. • Biochemical & Genetic information. REVERSE ENGINEERING. LARGE NETWORKS. FORWARD ENGINEERING. All designs that are not physically forbidden are realizable, but not all realizable designs are functionally effective. (in relation to context and constraints of the system and environment).

  9. Measures of Biochemical Sociology

    Science.gov (United States)

    Snell, Joel; Marsh, Mitchell

    2008-01-01

    In a previous article, the authors introduced a new sub field in sociology that we labeled "biochemical sociology." We introduced the definition of a sociology that encompasses sociological measures, psychological measures, and biological indicators Snell & Marsh (2003). In this article, we want to demonstrate a research strategy that would assess…

  10. Multidimensional biochemical information processing of dynamical patterns.

    Science.gov (United States)

    Hasegawa, Yoshihiko

    2018-02-01

    Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multidimensional information from dynamical concentration patterns of signaling molecules. We herein study how biochemical systems can process multidimensional information embedded in dynamical patterns. We model the decoding networks by linear response functions, and optimize the functions with the calculus of variations to maximize the mutual information between patterns and output. We find that, when the noise intensity is lower, decoders with different linear response functions, i.e., distinct decoders, can extract much information. However, when the noise intensity is higher, distinct decoders do not provide the maximum amount of information. This indicates that, when transmitting information by dynamical patterns, embedding information in multiple patterns is not optimal when the noise intensity is very large. Furthermore, we explore the biochemical implementations of these decoders using control theory and demonstrate that these decoders can be implemented biochemically through the modification of cascade-type networks, which are prevalent in actual signaling pathways.

  11. Networking

    OpenAIRE

    Rauno Lindholm, Daniel; Boisen Devantier, Lykke; Nyborg, Karoline Lykke; Høgsbro, Andreas; Fries, de; Skovlund, Louise

    2016-01-01

    The purpose of this project was to examine what influencing factor that has had an impact on the presumed increasement of the use of networking among academics on the labour market and how it is expressed. On the basis of the influence from globalization on the labour market it can be concluded that the globalization has transformed the labour market into a market based on the organization of networks. In this new organization there is a greater emphasis on employees having social qualificati...

  12. Simulation studies in biochemical signaling and enzyme reactions

    Science.gov (United States)

    Nelatury, Sudarshan R.; Vagula, Mary C.

    2014-06-01

    Biochemical pathways characterize various biochemical reaction schemes that involve a set of species and the manner in which they are connected. Determination of schematics that represent these pathways is an important task in understanding metabolism and signal transduction. Examples of these Pathways are: DNA and protein synthesis, and production of several macro-molecules essential for cell survival. A sustained feedback mechanism arises in gene expression and production of mRNA that lead to protein synthesis if the protein so synthesized serves as a transcription factor and becomes a repressor of the gene expression. The cellular regulations are carried out through biochemical networks consisting of reactions and regulatory proteins. Systems biology is a relatively new area that attempts to describe the biochemical pathways analytically and develop reliable mathematical models for the pathways. A complete understanding of chemical reaction kinetics is prohibitively hard thanks to the nonlinear and highly complex mechanisms that regulate protein formation, but attempting to numerically solve some of the governing differential equations seems to offer significant insight about their biochemical picture. To validate these models, one can perform simple experiments in the lab. This paper introduces fundamental ideas in biochemical signaling and attempts to take first steps into the understanding of biochemical oscillations. Initially, the two-pool model of calcium is used to describe the dynamics behind the oscillations. Later we present some elementary results showing biochemical oscillations arising from solving differential equations of Elowitz and Leibler using MATLAB software.

  13. Biochemical Hypermedia: Galactose Metabolism.

    Directory of Open Access Journals (Sweden)

    J.K. Sugai

    2013-05-01

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

  14. Implantable biochemical fuel cell

    Energy Technology Data Exchange (ETDEWEB)

    Richter, G; Rao, J R

    1978-01-05

    Implantable biochemical fuel cells for the operation of heart pacemakers or artificial hearts convert oxidisable body substances such as glucose on the anode side and reduce the oxygen contained in body fluids at the cathode. The anode and cathode are separated by membranes which are impermeable to albumen and blood corpuscles in body fluids. A chemical shortcircuit cannot occur in practice if, according to the invention, one or more selective oxygen electrodes with carbon as catalyst are arranged so that the mixture which diffuses into the cell from body fluids during operation reaches the fuel cell electrode through the porous oxygen electrode. The membranes used must be permeable to water. Cellulose, polymerised polyvinyl alcohol or an ion exchanger with a buffering capacity between pH5 and 8 act as permeable materials.

  15. Ouroboros - Playing A Biochemical

    Directory of Open Access Journals (Sweden)

    D. T. Rodrigues

    2014-08-01

    Full Text Available Ouroboros: Playing A Biochemical RODRIGUES,D.T.1,2;GAYER, M.C.1,2; ESCOTO, D.F.1; DENARDIN, E.L.G.2, ROEHRS, R.1,2 1Interdisciplinary Research Group on Teaching Practice, Graduate Program in Biochemistry, Unipampa, RS, Brazil 2Laboratory of Physicochemical Studies and Natural Products, Post Graduate Program in Biochemistry, Unipampa, RS, Brazil Introduction: Currently, teachers seek different alternatives to enhance the teaching-learning process. Innovative teaching methodologies are increasingly common tools in educational routine. The use of games, electronic or conventional, is an effective tool to assist in learning and also to raise the social interaction between students. Objective: In this sense our work aims to evaluate the card game and "Ouroboros" board as a teaching and learning tool in biochemistry for a graduating class in Natural Sciences. Materials and methods: The class gathered 22 students of BSc in Natural Sciences. Each letter contained a question across the board that was drawn to a group to answer within the allotted time. The questions related concepts of metabolism, organic and inorganic chemical reactions, bioenergetics, etc.. Before the game application, students underwent a pre-test with four issues involving the content that was being developed. Soon after, the game was applied. Then again questions were asked. Data analysis was performed from the ratio of the number of correct pre-test and post-test answers. Results and discussion: In the pre-test 18.1% of the students knew all issues, 18.1% got 3 correct answers, 40.9% answered only 2 questions correctly and 22.7% did not hit any. In post-test 45.4% answered all the questions right, 31.8% got 3 questions and 22.7% got 2 correct answers. The results show a significant improvement of the students about the field of content taught through the game. Conclusion: Generally, traditional approaches of chemistry and biochemistry are abstract and complex. Thus, through games

  16. Enzyme and biochemical producing fungi

    DEFF Research Database (Denmark)

    Lübeck, Peter Stephensen; Lübeck, Mette; Nilsson, Lena

    2010-01-01

    factories for sustainable production of important molecules. For developing fungi into efficient cell factories, the project includes identification of important factors that control the flux through the pathways using metabolic flux analysis and metabolic engineering of biochemical pathways....

  17. Biochemical reactions of the organism

    International Nuclear Information System (INIS)

    Fedorova, A.V.

    1984-01-01

    Effects of mercury, strontium chloride, GMDA, trichlorfon as well as some radionuclides ( 89 Sr, 137 Cs, 203 Hg) were studied on rats. Changes in biochemical parameters (histamine content, activity of cholinesterase and histaminase) are noted. Most noticeable changes were observed in enzymatic activity. Distortion of enzymatic systems and accumulation of intermediate exchange and decay products of tissues in excess quantities affecting other systems can be the reason for changes in the organism. The observed changes in biochemical parameters should be necessarily taken into account at hygienic regulations of harmful effects of enviroment

  18. Complexity of generic biochemical circuits: topology versus strength of interactions

    Science.gov (United States)

    Tikhonov, Mikhail; Bialek, William

    2016-12-01

    The historical focus on network topology as a determinant of biological function is still largely maintained today, illustrated by the rise of structure-only approaches to network analysis. However, biochemical circuits and genetic regulatory networks are defined both by their topology and by a multitude of continuously adjustable parameters, such as the strength of interactions between nodes, also recognized as important. Here we present a class of simple perceptron-based Boolean models within which comparing the relative importance of topology versus interaction strengths becomes a quantitatively well-posed problem. We quantify the intuition that for generic networks, optimization of interaction strengths is a crucial ingredient of achieving high complexity, defined here as the number of fixed points the network can accommodate. We propose a new methodology for characterizing the relative role of parameter optimization for topologies of a given class.

  19. Modeling of uncertainties in biochemical reactions.

    Science.gov (United States)

    Mišković, Ljubiša; Hatzimanikatis, Vassily

    2011-02-01

    Mathematical modeling is an indispensable tool for research and development in biotechnology and bioengineering. The formulation of kinetic models of biochemical networks depends on knowledge of the kinetic properties of the enzymes of the individual reactions. However, kinetic data acquired from experimental observations bring along uncertainties due to various experimental conditions and measurement methods. In this contribution, we propose a novel way to model the uncertainty in the enzyme kinetics and to predict quantitatively the responses of metabolic reactions to the changes in enzyme activities under uncertainty. The proposed methodology accounts explicitly for mechanistic properties of enzymes and physico-chemical and thermodynamic constraints, and is based on formalism from systems theory and metabolic control analysis. We achieve this by observing that kinetic responses of metabolic reactions depend: (i) on the distribution of the enzymes among their free form and all reactive states; (ii) on the equilibrium displacements of the overall reaction and that of the individual enzymatic steps; and (iii) on the net fluxes through the enzyme. Relying on this observation, we develop a novel, efficient Monte Carlo sampling procedure to generate all states within a metabolic reaction that satisfy imposed constrains. Thus, we derive the statistics of the expected responses of the metabolic reactions to changes in enzyme levels and activities, in the levels of metabolites, and in the values of the kinetic parameters. We present aspects of the proposed framework through an example of the fundamental three-step reversible enzymatic reaction mechanism. We demonstrate that the equilibrium displacements of the individual enzymatic steps have an important influence on kinetic responses of the enzyme. Furthermore, we derive the conditions that must be satisfied by a reversible three-step enzymatic reaction operating far away from the equilibrium in order to respond to

  20. Circadian Clocks: Unexpected Biochemical Cogs.

    Science.gov (United States)

    Mori, Tetsuya; Mchaourab, Hassane; Johnson, Carl Hirschie

    2015-10-05

    A circadian oscillation can be reconstituted in vitro from three proteins that cycles with a period of ∼ 24 h. Two recent studies provide surprising biochemical answers to why this remarkable oscillator has such a long time constant and how it can switch effortlessly between alternating enzymatic modes. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Circadian Clocks: Unexpected Biochemical Cogs

    OpenAIRE

    Mori, Tetsuya; Mchaourab, Hassane; Johnson, Carl Hirschie

    2015-01-01

    A circadian oscillation can be reconstituted in vitro from three proteins that cycles with a period of ~24 h. Two recent studies provide surprising biochemical answers to why this remarkable oscillator has such a long time constant and how it can switch effortlessly between alternating enzymatic modes.

  2. Biochemical Process Development and Integration | Bioenergy | NREL

    Science.gov (United States)

    Biochemical Process Development and Integration Biochemical Process Development and Integration Our conversion and separation processes to pilot-scale integrated process development and scale up. We also Publications Accounting for all sugar produced during integrated production of ethanol from lignocellulosic

  3. Biochemical markers of bone turnover

    International Nuclear Information System (INIS)

    Kim, Deog Yoon

    1999-01-01

    Biochemical markers of bone turnover has received increasing attention over the past few years, because of the need for sensitivity and specific tool in the clinical investigation of osteoporosis. Bone markers should be unique to bone, reflect changes of bone less, and should be correlated with radiocalcium kinetics, histomorphometry, or changes in bone mass. The markers also should be useful in monitoring treatment efficacy. Although no bone marker has been established to meet all these criteria, currently osteocalcin and pyridinium crosslinks are the most efficient markers to assess the level of bone turnover in the menopausal and senile osteoporosis. Recently, N-terminal telopeptide (NTX), C-terminal telopeptide (CTX) and bone specific alkaline phosphatase are considered as new valid markers of bone turnover. Recent data suggest that CTX and free deoxypyridinoline could predict the subsequent risk of hip fracture of elderly women. Treatment of postmenopausal women with estrogen, calcitonin and bisphosphonates demonstrated rapid decrease of the levels of bone markers that correlated with the long-term increase of bone mass. Factors such as circadian rhythms, diet, age, sex, bone mass and renal function affect the results of biochemical markers and should be appropriately adjusted whenever possible. Each biochemical markers of bone turnover may have its own specific advantages and limitations. Recent advances in research will provide more sensitive and specific assays

  4. Biochemical toxicology of environmental agents

    International Nuclear Information System (INIS)

    Bruin, A. de

    1976-01-01

    A thorough and up-to-date account of the molecular-biological aspects of harmful agents - both chemical and physical - is given. This current treatise is principally intended to serve as an informative reference work for researchers in various areas of the field. In the pursuit of this aim, a devision of the entire field into 42 chapters has been made. Each chapter starts with a short introductory account dealing with the biochemical essentials of the particular subject. Radiation effects are discussed briefly at the end of each treatise. In order to make the treatise useful as a source book, a substantial collection of pertinent literature references is provided which are numbered in order of citation in the text. Initial chapters are devoted to the metabolic fate of the major classes of xenobiotic compounds. Peripheral topics, closely related to metabolism and dealing with modification of xenobiotic-metabolizing ability, as well as interaction phenomena follow (chs. 5-8). Subjects that draw heavily on the practical field of occupational hygiene are dealt with in chapters 9 and 10. The systematic treatment of how chemical and physical agents interact with the various biochemical and enzymatic systems they encounter during their passage through the organism occupies quantitatively the main part of the book (chs. 11-36). Finally, radiation biochemistry is discussed from the viewpoint of its high degree of scientific advancement, and secondly because the type of biochemical changes produced in vivo by X-rays closely parallel those evoked by chemical agents

  5. SABIO-RK: A data warehouse for biochemical reactions and their kinetics

    Directory of Open Access Journals (Sweden)

    Krebs Olga

    2007-03-01

    Full Text Available Systems biology is an emerging field that aims at obtaining a system-level understanding of biological processes. The modelling and simulation of networks of biochemical reactions have great and promising application potential but require reliable kinetic data. In order to support the systems biology community with such data we have developed SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics, a curated database with information about biochemical reactions and their kinetic properties, which allows researchers to obtain and compare kinetic data and to integrate them into models of biochemical networks. SABIO-RK is freely available for academic use at http://sabio.villa-bosch.de/SABIORK/.

  6. Biochemical Abnormalities in Batten's Syndrome

    DEFF Research Database (Denmark)

    Clausen, Jytte Lene; Nielsen, Gunnar Gissel; Jensen, Gunde Egeskov

    1978-01-01

    The present data indicate that a group of ten patients with Batten's syndrome showed reduced activity of erythrocyte glutathione (GSH) peroxidase (Px) (glutathione: H2O2 oxidoreductase, EC 1.1.1.9.) using H2O2 as peroxide donor. Assay of erythrocyte GSHPx using H2O2, cumene hydroperoxide and t......-butyl hydroperoxide as donors also makes it possible biochemically to divide Batten's syndrome into two types: (1) one type with decreased values when H2O2 and cumene hydroperoxide are used, and (2) one type with increased values when t-butyl hydroperoxide is used. Furthermore an increased content of palmitic, oleic...

  7. Slot-waveguide biochemical sensor.

    Science.gov (United States)

    Barrios, Carlos A; Gylfason, Kristinn B; Sánchez, Benito; Griol, Amadeu; Sohlström, H; Holgado, M; Casquel, R

    2007-11-01

    We report an experimental demonstration of an integrated biochemical sensor based on a slot-waveguide microring resonator. The microresonator is fabricated on a Si3N4-SiO2 platform and operates at a wavelength of 1.3 microm. The transmission spectrum of the sensor is measured with different ambient refractive indices ranging from n=1.33 to 1.42. A linear shift of the resonant wavelength with increasing ambient refractive index of 212 nm/refractive index units (RIU) is observed. The sensor detects a minimal refractive index variation of 2x10(-4) RIU.

  8. Thermodynamic analysis of biochemical systems

    International Nuclear Information System (INIS)

    Yuan, Y.; Fan, L.T.; Shieh, J.H.

    1989-01-01

    Introduction of the concepts of the availability (or exergy), datum level materials, and the dead state has been regarded as some of the most significant recent developments in classical thermodynamics. Not only the available energy balance but also the material and energy balances of a biological system may be established in reference to the datum level materials in the dead state or environment. In this paper these concepts are illustrated with two examples of fermentation and are shown to be useful in identifying sources of thermodynamic inefficiency, thereby leading naturally to the rational definition of thermodynamic efficiency of a biochemical process

  9. Biochemical nature of Russell Bodies.

    Science.gov (United States)

    Mossuto, Maria Francesca; Ami, Diletta; Anelli, Tiziana; Fagioli, Claudio; Doglia, Silvia Maria; Sitia, Roberto

    2015-07-30

    Professional secretory cells produce and release abundant proteins. Particularly in case of mutations and/or insufficient chaperoning, these can aggregate and become toxic within or amongst cells. Immunoglobulins (Ig) are no exception. In the extracellular space, certain Ig-L chains form fibrils causing systemic amyloidosis. On the other hand, Ig variants lacking the first constant domain condense in dilated cisternae of the early secretory compartment, called Russell Bodies (RB), frequently observed in plasma cell dyscrasias, autoimmune diseases and chronic infections. RB biogenesis can be recapitulated in lymphoid and non-lymphoid cells by expressing mutant Ig-μ, providing powerful models to investigate the pathophysiology of endoplasmic reticulum storage disorders. Here we analyze the aggregation propensity and the biochemical features of the intra- and extra-cellular Ig deposits in human cells, revealing β-aggregated features for RB.

  10. Biochemical Markers in Neurocritical Care

    Directory of Open Access Journals (Sweden)

    Omidvar Rezae

    2016-07-01

    Full Text Available During the past two decades, a variety of serum or cerebrospinal fluid (CSF biochemical markers in daily clinical practice have been recommended to diagnose and monitor diverse diseases or pathologic situations. It will be essential to develop a panel of biomarkers, to be suitable for evaluation of treatment efficacy, representing distinct phases of injury and recovery and consider the temporal profile of those. Among the possible and different biochemical markers, S100b appeared to fulfill many of optimized criteria of an ideal marker. S100b, a cytosolic low molecular weight dimeric calciumbinding protein from chromosome 21, synthesized in glial cells throughout the CNS, an homodimeric diffusible, belongs to a family of closely related protein, predominantly expressed by astrocytes and Schwann cells and a classic immunohistochemical marker for these cells, is implicated in brain development and neurophysiology. Of the 3 isoforms of S-100, the BB subunit (S100B is present in high concentrations in central and peripheral glial and Schwann cells, Langerhans and anterior pituitary cells, fat, muscle, and bone marrow tissues. The biomarker has shown to be a sensitive marker of clinical and subclinical cerebral damage, such as stroke, traumatic brain injury, and spinal cord injury. Increasing evidence suggests that the biomarker plays a double function as an intracellular regulator and an extracellular signal of the CNS. S100b is found in the cytoplasm in a soluble form and also is associated with intracellular membranes, centrosomes, microtubules, and type III intermediate filaments. Their genomic organization now is known, and many of their target proteins have been identified, although the mechanisms of regulating S100b secretion are not completely understood and appear to be related to many factors, such as the proinflammatory cytokines, tumor necrosis factor alpha (TNF-a, interleukin (IL-1b, and metabolic stress. 

  11. A case study of evolutionary computation of biochemical adaptation

    International Nuclear Information System (INIS)

    François, Paul; Siggia, Eric D

    2008-01-01

    Simulations of evolution have a long history, but their relation to biology is questioned because of the perceived contingency of evolution. Here we provide an example of a biological process, adaptation, where simulations are argued to approach closer to biology. Adaptation is a common feature of sensory systems, and a plausible component of other biochemical networks because it rescales upstream signals to facilitate downstream processing. We create random gene networks numerically, by linking genes with interactions that model transcription, phosphorylation and protein–protein association. We define a fitness function for adaptation in terms of two functional metrics, and show that any reasonable combination of them will yield the same adaptive networks after repeated rounds of mutation and selection. Convergence to these networks is driven by positive selection and thus fast. There is always a path in parameter space of continuously improving fitness that leads to perfect adaptation, implying that the actual mutation rates we use in the simulation do not bias the results. Our results imply a kinetic view of evolution, i.e., it favors gene networks that can be learned quickly from the random examples supplied by mutation. This formulation allows for deductive predictions of the networks realized in nature

  12. Bistable responses in bacterial genetic networks: Designs and dynamical consequences

    Science.gov (United States)

    Tiwari, Abhinav; Ray, J. Christian J.; Narula, Jatin; Igoshin, Oleg A.

    2011-01-01

    A key property of living cells is their ability to react to stimuli with specific biochemical responses. These responses can be understood through the dynamics of underlying biochemical and genetic networks. Evolutionary design principles have been well studied in networks that display graded responses, with a continuous relationship between input signal and system output. Alternatively, biochemical networks can exhibit bistable responses so that over a range of signals the network possesses two stable steady states. In this review, we discuss several conceptual examples illustrating network designs that can result in a bistable response of the biochemical network. Next, we examine manifestations of these designs in bacterial master-regulatory genetic circuits. In particular, we discuss mechanisms and dynamic consequences of bistability in three circuits: two-component systems, sigma-factor networks, and a multistep phosphorelay. Analyzing these examples allows us to expand our knowledge of evolutionary design principles for networks with bistable responses. PMID:21385588

  13. Prevalence of biochemical and immunological abnormalities in ...

    African Journals Online (AJOL)

    Tile prevalence of biochemical and immunological abnormalities was studied in a group of 256 patients with rheumatoid arthritis (104 coloureds, 100 whites and 52 blacks). The most common biochemical abnormalities detected were a reduction in the serum creatinine value (43,4%), raised globulins (39,7%), raised serum ...

  14. Organic and biochemical synthesis group

    International Nuclear Information System (INIS)

    Anon.

    1976-01-01

    Stable isotopes, because of their unique properties and non-radioactive nature, have great potential for many fields of science and technology. In particular, isotopes of carbon, nitrogen, oxygen, and sulfur (the basic building blocks of all biological molecules) would be widely used in biomedical and environmental research if they were economically available in sufficient quantities and in the required chemical forms. The major objective of our program continues to be stimulation of the widespread utilization of stable isotopes and commercial involvement through development and demonstration of applications which have potential requirements for large quantities of isotopes. Thus, demand will be created which is necessary for large-scale production of stable isotopes and labeled compounds and concomitant low unit costs. The program continues to produce a variety of labeled materials needed for clinical, biomedical, chemical, and environmental applications which serve as effective demonstrations of unique and advantageous utilization of stable isotopes. Future commercial involvement should benefit, and is a consideration in our research and development, from the technology transfer that can readily be made as a result of our organic and biochemical syntheses and also of various techniques involved in applications

  15. Deterministic modelling and stochastic simulation of biochemical pathways using MATLAB.

    Science.gov (United States)

    Ullah, M; Schmidt, H; Cho, K H; Wolkenhauer, O

    2006-03-01

    The analysis of complex biochemical networks is conducted in two popular conceptual frameworks for modelling. The deterministic approach requires the solution of ordinary differential equations (ODEs, reaction rate equations) with concentrations as continuous state variables. The stochastic approach involves the simulation of differential-difference equations (chemical master equations, CMEs) with probabilities as variables. This is to generate counts of molecules for chemical species as realisations of random variables drawn from the probability distribution described by the CMEs. Although there are numerous tools available, many of them free, the modelling and simulation environment MATLAB is widely used in the physical and engineering sciences. We describe a collection of MATLAB functions to construct and solve ODEs for deterministic simulation and to implement realisations of CMEs for stochastic simulation using advanced MATLAB coding (Release 14). The program was successfully applied to pathway models from the literature for both cases. The results were compared to implementations using alternative tools for dynamic modelling and simulation of biochemical networks. The aim is to provide a concise set of MATLAB functions that encourage the experimentation with systems biology models. All the script files are available from www.sbi.uni-rostock.de/ publications_matlab-paper.html.

  16. Biochemical thermodynamics: applications of Mathematica.

    Science.gov (United States)

    Alberty, Robert A

    2006-01-01

    reactants. Thus loading this package makes available 774 mathematical functions for these properties. These functions can be added and subtracted to obtain changes in these properties in biochemical reactions and apparent equilibrium constants.

  17. Morphological, physiological and biochemical studies on Pyricularia ...

    African Journals Online (AJOL)

    SARAH

    2014-02-28

    Feb 28, 2014 ... compounds seem to reflect inherent biochemical and physiological differences among P. grisea isolates .... solutions for imaging and microscopy, soft image system .... characteristics among 12 P. grisea isolates from rice were.

  18. Biochemical changes in blood caused by radioisotopes

    International Nuclear Information System (INIS)

    Zapol'skaya, N.A.; Fedorova, A.V.

    1975-01-01

    The changes were studied occurring in some biochemical indicators in blood at chronic peroral administration of strontium-90, cesium-137 and iodine-131 in amounts resulting in accumulation of commensurable doses in critical organs corresponding to each isotope

  19. Biochemical and kinetic characterization of geranylgeraniol 18 ...

    African Journals Online (AJOL)

    Suchart

    2015-07-22

    Jul 22, 2015 ... biochemical characterization of GGOH 18-hydroxylase activity in the microsomal fraction from C. .... method as previously described (Chanama et al., 2009). Briefly, 30 g of frozen ..... Catalytic properties of the plant cytochrome.

  20. Short Report Biochemical derangements prior to emergency ...

    African Journals Online (AJOL)

    MMJ VOL 29 (1): March 2017. Biochemical derangements prior to emergency laparotomy at QECH 55. Malawi Medical Journal 29 (1): March 2017 ... Venepuncture was performed preoperatively for urgent cases, defined as those requiring.

  1. A Program on Biochemical and Biomedical Engineering.

    Science.gov (United States)

    San, Ka-Yiu; McIntire, Larry V.

    1989-01-01

    Presents an introduction to the Biochemical and Biomedical Engineering program at Rice University. Describes the development of the academic and enhancement programs, including organizational structure and research project titles. (YP)

  2. Raman spectroscopic biochemical mapping of tissues

    Science.gov (United States)

    Stone, Nicholas; Hart Prieto, Maria C.; Kendall, Catherine A.; Shetty, Geeta; Barr, Hugh

    2006-02-01

    Advances in technologies have brought us closer to routine spectroscopic diagnosis of early malignant disease. However, there is still a poor understanding of the carcinogenesis process. For example it is not known whether many cancers follow a logical sequence from dysplasia, to carcinoma in situ, to invasion. Biochemical tissue changes, triggered by genetic mutations, precede morphological and structural changes. These can be probed using Raman or FTIR microspectroscopy and the spectra analysed for biochemical constituents. Local microscopic distribution of various constituents can then be visualised. Raman mapping has been performed on a number of tissues including oesophagus, breast, bladder and prostate. The biochemical constituents have been calculated at each point using basis spectra and least squares analysis. The residual of the least squares fit indicates any unfit spectral components. The biochemical distribution will be compared with the defined histopathological boundaries. The distribution of nucleic acids, glycogen, actin, collagen I, III, IV, lipids and others appear to follow expected patterns.

  3. [Biochemical diagnostics of fatal opium intoxication].

    Science.gov (United States)

    Papyshev, I P; Astashkina, O G; Tuchik, E S; Nikolaev, B S; Cherniaev, A L

    2013-01-01

    Biochemical diagnostics of fatal opium intoxication remains a topical problem in forensic medical science and practice. We investigated materials obtained in the course of forensic medical expertise of the cases of fatal opium intoxication. The study revealed significant differences between myoglobin levels in blood, urine, myocardium, and skeletal muscles. The proposed approach to biochemical diagnostics of fatal opium intoxication enhances the accuracy and the level of evidence of expert conclusions.

  4. Improving Marine Ecosystem Models with Biochemical Tracers

    Science.gov (United States)

    Pethybridge, Heidi R.; Choy, C. Anela; Polovina, Jeffrey J.; Fulton, Elizabeth A.

    2018-01-01

    Empirical data on food web dynamics and predator-prey interactions underpin ecosystem models, which are increasingly used to support strategic management of marine resources. These data have traditionally derived from stomach content analysis, but new and complementary forms of ecological data are increasingly available from biochemical tracer techniques. Extensive opportunities exist to improve the empirical robustness of ecosystem models through the incorporation of biochemical tracer data and derived indices, an area that is rapidly expanding because of advances in analytical developments and sophisticated statistical techniques. Here, we explore the trophic information required by ecosystem model frameworks (species, individual, and size based) and match them to the most commonly used biochemical tracers (bulk tissue and compound-specific stable isotopes, fatty acids, and trace elements). Key quantitative parameters derived from biochemical tracers include estimates of diet composition, niche width, and trophic position. Biochemical tracers also provide powerful insight into the spatial and temporal variability of food web structure and the characterization of dominant basal and microbial food web groups. A major challenge in incorporating biochemical tracer data into ecosystem models is scale and data type mismatches, which can be overcome with greater knowledge exchange and numerical approaches that transform, integrate, and visualize data.

  5. Computing molecular fluctuations in biochemical reaction systems based on a mechanistic, statistical theory of irreversible processes.

    Science.gov (United States)

    Kulasiri, Don

    2011-01-01

    We discuss the quantification of molecular fluctuations in the biochemical reaction systems within the context of intracellular processes associated with gene expression. We take the molecular reactions pertaining to circadian rhythms to develop models of molecular fluctuations in this chapter. There are a significant number of studies on stochastic fluctuations in intracellular genetic regulatory networks based on single cell-level experiments. In order to understand the fluctuations associated with the gene expression in circadian rhythm networks, it is important to model the interactions of transcriptional factors with the E-boxes in the promoter regions of some of the genes. The pertinent aspects of a near-equilibrium theory that would integrate the thermodynamical and particle dynamic characteristics of intracellular molecular fluctuations would be discussed, and the theory is extended by using the theory of stochastic differential equations. We then model the fluctuations associated with the promoter regions using general mathematical settings. We implemented ubiquitous Gillespie's algorithms, which are used to simulate stochasticity in biochemical networks, for each of the motifs. Both the theory and the Gillespie's algorithms gave the same results in terms of the time evolution of means and variances of molecular numbers. As biochemical reactions occur far away from equilibrium-hence the use of the Gillespie algorithm-these results suggest that the near-equilibrium theory should be a good approximation for some of the biochemical reactions. © 2011 Elsevier Inc. All rights reserved.

  6. Stochastic analysis of biochemical systems

    CERN Document Server

    Anderson, David F

    2015-01-01

    This book focuses on counting processes and continuous-time Markov chains motivated by examples and applications drawn from chemical networks in systems biology.  The book should serve well as a supplement for courses in probability and stochastic processes.  While the material is presented in a manner most suitable for students who have studied stochastic processes up to and including martingales in continuous time, much of the necessary background material is summarized in the Appendix. Students and Researchers with a solid understanding of calculus, differential equations, and elementary probability and who are well-motivated by the applications will find this book of interest.    David F. Anderson is Associate Professor in the Department of Mathematics at the University of Wisconsin and Thomas G. Kurtz is Emeritus Professor in the Departments of Mathematics and Statistics at that university. Their research is focused on probability and stochastic processes with applications in biology and other ar...

  7. Improved methods for the mathematically controlled comparison of biochemical systems

    Directory of Open Access Journals (Sweden)

    Schwacke John H

    2004-06-01

    Full Text Available Abstract The method of mathematically controlled comparison provides a structured approach for the comparison of alternative biochemical pathways with respect to selected functional effectiveness measures. Under this approach, alternative implementations of a biochemical pathway are modeled mathematically, forced to be equivalent through the application of selected constraints, and compared with respect to selected functional effectiveness measures. While the method has been applied successfully in a variety of studies, we offer recommendations for improvements to the method that (1 relax requirements for definition of constraints sufficient to remove all degrees of freedom in forming the equivalent alternative, (2 facilitate generalization of the results thus avoiding the need to condition those findings on the selected constraints, and (3 provide additional insights into the effect of selected constraints on the functional effectiveness measures. We present improvements to the method and related statistical models, apply the method to a previously conducted comparison of network regulation in the immune system, and compare our results to those previously reported.

  8. Biochemical Removal of HAP Precursors From Coal

    International Nuclear Information System (INIS)

    Olson, G.; Tucker, L.; Richards, J.

    1997-07-01

    This project addresses DOE's interest in advanced concepts for controlling emissions of air toxics from coal-fired utility boilers. We are determining the feasibility of developing a biochemical process for the precombustion removal of substantial percentages of 13 inorganic hazardous air pollutant (HAP) precursors from coal. These HAP precursors are Sb, As, Be, Cd, Cr, Cl, Co, F, Pb, Hg, Mn, Ni, and Se. Although rapid physical coal cleaning is done routinely in preparation plants, biochemical processes for removal of HAP precursors from coal potentially offer advantages of deeper cleaning, more specificity, and less coal loss. Compared to chemical processes for coal cleaning, biochemical processes potentially offer lower costs and milder process conditions. Pyrite oxidizing bacteria, most notably Thiobacillusferrooxidans, are being evaluated in this project for their ability to remove HAP precursors from U.S. coals

  9. Biochemical Removal of HAP Precursors From Coal

    Energy Technology Data Exchange (ETDEWEB)

    Olson, G.; Tucker, L.; Richards, J.

    1997-07-01

    This project addresses DOE`s interest in advanced concepts for controlling emissions of air toxics from coal-fired utility boilers. We are determining the feasibility of developing a biochemical process for the precombustion removal of substantial percentages of 13 inorganic hazardous air pollutant (HAP) precursors from coal. These HAP precursors are Sb, As, Be, Cd, Cr, Cl, Co, F, Pb, Hg, Mn, Ni, and Se. Although rapid physical coal cleaning is done routinely in preparation plants, biochemical processes for removal of HAP precursors from coal potentially offer advantages of deeper cleaning, more specificity, and less coal loss. Compared to chemical processes for coal cleaning, biochemical processes potentially offer lower costs and milder process conditions. Pyrite oxidizing bacteria, most notably Thiobacillusferrooxidans, are being evaluated in this project for their ability to remove HAP precursors from U.S. coals.

  10. eQuilibrator--the biochemical thermodynamics calculator.

    Science.gov (United States)

    Flamholz, Avi; Noor, Elad; Bar-Even, Arren; Milo, Ron

    2012-01-01

    The laws of thermodynamics constrain the action of biochemical systems. However, thermodynamic data on biochemical compounds can be difficult to find and is cumbersome to perform calculations with manually. Even simple thermodynamic questions like 'how much Gibbs energy is released by ATP hydrolysis at pH 5?' are complicated excessively by the search for accurate data. To address this problem, eQuilibrator couples a comprehensive and accurate database of thermodynamic properties of biochemical compounds and reactions with a simple and powerful online search and calculation interface. The web interface to eQuilibrator (http://equilibrator.weizmann.ac.il) enables easy calculation of Gibbs energies of compounds and reactions given arbitrary pH, ionic strength and metabolite concentrations. The eQuilibrator code is open-source and all thermodynamic source data are freely downloadable in standard formats. Here we describe the database characteristics and implementation and demonstrate its use.

  11. eQuilibrator—the biochemical thermodynamics calculator

    Science.gov (United States)

    Flamholz, Avi; Noor, Elad; Bar-Even, Arren; Milo, Ron

    2012-01-01

    The laws of thermodynamics constrain the action of biochemical systems. However, thermodynamic data on biochemical compounds can be difficult to find and is cumbersome to perform calculations with manually. Even simple thermodynamic questions like ‘how much Gibbs energy is released by ATP hydrolysis at pH 5?’ are complicated excessively by the search for accurate data. To address this problem, eQuilibrator couples a comprehensive and accurate database of thermodynamic properties of biochemical compounds and reactions with a simple and powerful online search and calculation interface. The web interface to eQuilibrator (http://equilibrator.weizmann.ac.il) enables easy calculation of Gibbs energies of compounds and reactions given arbitrary pH, ionic strength and metabolite concentrations. The eQuilibrator code is open-source and all thermodynamic source data are freely downloadable in standard formats. Here we describe the database characteristics and implementation and demonstrate its use. PMID:22064852

  12. Biochemical activity of fullerenes and related derivatives

    International Nuclear Information System (INIS)

    Huczko, A.; Lange, H.; Calko, E.

    1999-01-01

    An astonishing scientific interest, embodied in over 15000 research articles so far, has been encountered since 1985 when fullerenes were discovered. From new superconductors to a rich electrochemistry and reaction chemistry, fullerene nanostructures continue to excite the scientific world, and new findings continue at record pace. This review presents many examples of the biochemical activities of fullerenes and derivatives, e. g. cytotoxic activity, selective DNA cleavage and antiviral activity against HIV. We also present some results of our testing which show that, despite its chemical and biochemical activity, fullerene matter does not present any health hazard directly related to skin irritation and allergic risks. (author)

  13. Autonomous bio-chemical decontaminator (ABCD) against weapons of mass destruction

    Science.gov (United States)

    Hyacinthe, Berg P.

    2006-05-01

    The proliferation of weapons of mass destruction (WMD) and the use of such elements pose an eminent asymmetric threat with disastrous consequences to the national security of any nation. In particular, the use of biochemical warfare agents against civilians and unprotected troops in international conflicts or by terrorists against civilians is considered as a very peculiar threat. Accordingly, taking a quarantine-before-inhalation approach to biochemical warfare, the author introduces the notion of autonomous biochemical decontamination against WMD. In the unfortunate event of a biochemical attack, the apparatus proposed herein is intended to automatically detect, identify, and more importantly neutralize a biochemical threat. Along with warnings concerning a cyber-WMD nexus, various sections cover discussions on human senses and computer sensors, corroborating evidence related to detection and neutralization of chemical toxins, and cyber-assisted olfaction in stand alone, peer-to-peer, and network settings. In essence, the apparatus can be used in aviation and mass transit security to initiate mass decontamination by dispersing a decontaminant aerosol or to protect the public water supply against a potential bioterrorist attack. Future effort may involve a system-on-chip (SoC) embodiment of this apparatus that allows a safer environment for the emerging phenomenon of cyber-assisted olfaction and morph cell phones into ubiquitous sensors/decontaminators. Although this paper covers mechanisms and protocols to avail a neutralizing substance, further research will need to explore the substance's various pharmacological profiles and potential side effects.

  14. Biochemical component identification by plasmonic improved whispering gallery mode optical resonance based sensor

    Science.gov (United States)

    Saetchnikov, Vladimir A.; Tcherniavskaia, Elina A.; Saetchnikov, Anton V.; Schweiger, Gustav; Ostendorf, Andreas

    2014-05-01

    Experimental data on detection and identification of variety of biochemical agents, such as proteins, microelements, antibiotic of different generation etc. in both single and multi component solutions under varied in wide range concentration analyzed on the light scattering parameters of whispering gallery mode optical resonance based sensor are represented. Multiplexing on parameters and components has been realized using developed fluidic sensor cell with fixed in adhesive layer dielectric microspheres and data processing. Biochemical component identification has been performed by developed network analysis techniques. Developed approach is demonstrated to be applicable both for single agent and for multi component biochemical analysis. Novel technique based on optical resonance on microring structures, plasmon resonance and identification tools has been developed. To improve a sensitivity of microring structures microspheres fixed by adhesive had been treated previously by gold nanoparticle solution. Another technique used thin film gold layers deposited on the substrate below adhesive. Both biomolecule and nanoparticle injections caused considerable changes of optical resonance spectra. Plasmonic gold layers under optimized thickness also improve parameters of optical resonance spectra. Biochemical component identification has been also performed by developed network analysis techniques both for single and for multi component solution. So advantages of plasmon enhancing optical microcavity resonance with multiparameter identification tools is used for development of a new platform for ultra sensitive label-free biomedical sensor.

  15. Biochemical characterization of Tunisian grapevine varieties

    Directory of Open Access Journals (Sweden)

    Ferjani Ben Abdallah

    1998-03-01

    The study of GPI, PGM, AAT and peroxydase isozyme banding patterns in combination with berry colour has led to establish a classification of the 61 autochton varieties into 37 groups including 26 varieties definitely differentiated through the results of this biochemical study.

  16. Survey of Biochemical Education in Japanese Universities.

    Science.gov (United States)

    Kagawa, Yasuo

    1995-01-01

    Reports findings of questionnaires sent to faculty in charge of biochemical education in medical schools and other programs from dentistry to agriculture. Total class hours have declined since 1984. New trends include bioethics and computer-assisted learning. Tables show trends in lecture hours, lecture content, laboratory hours, core subject…

  17. Haematological and biochemical responses of starter broiler ...

    African Journals Online (AJOL)

    A study was conducted to investigate the haematological and biochemical responses of starter broiler chickens fed copper and probiotics supplemented diets. A total of 180-day old Marshal broiler chicks were randomly allotted to six treatment groups of 30 birds each. The treatments were divided into three replicates of ten ...

  18. Probabilistic sensitivity analysis of biochemical reaction systems.

    Science.gov (United States)

    Zhang, Hong-Xuan; Dempsey, William P; Goutsias, John

    2009-09-07

    Sensitivity analysis is an indispensable tool for studying the robustness and fragility properties of biochemical reaction systems as well as for designing optimal approaches for selective perturbation and intervention. Deterministic sensitivity analysis techniques, using derivatives of the system response, have been extensively used in the literature. However, these techniques suffer from several drawbacks, which must be carefully considered before using them in problems of systems biology. We develop here a probabilistic approach to sensitivity analysis of biochemical reaction systems. The proposed technique employs a biophysically derived model for parameter fluctuations and, by using a recently suggested variance-based approach to sensitivity analysis [Saltelli et al., Chem. Rev. (Washington, D.C.) 105, 2811 (2005)], it leads to a powerful sensitivity analysis methodology for biochemical reaction systems. The approach presented in this paper addresses many problems associated with derivative-based sensitivity analysis techniques. Most importantly, it produces thermodynamically consistent sensitivity analysis results, can easily accommodate appreciable parameter variations, and allows for systematic investigation of high-order interaction effects. By employing a computational model of the mitogen-activated protein kinase signaling cascade, we demonstrate that our approach is well suited for sensitivity analysis of biochemical reaction systems and can produce a wealth of information about the sensitivity properties of such systems. The price to be paid, however, is a substantial increase in computational complexity over derivative-based techniques, which must be effectively addressed in order to make the proposed approach to sensitivity analysis more practical.

  19. Biochemical applications of FT-IR spectroscopy

    NARCIS (Netherlands)

    Pistorius, A.M.A.

    1996-01-01

    This thesis describes the use of (FT-)IR spectroscopy in general biochemical research. In chapter 3, IR spectroscopy is used in the quantitation of residual detergent after reconstitution of an integral membrane protein in a pre-defined lipid matrix. This chapter discusses the choice of the

  20. Some hematological and biochemical parameters in smokeless ...

    African Journals Online (AJOL)

    AJB SERVER

    2007-01-04

    Jan 4, 2007 ... The effect of Jharda powder (smokeless tobacco) on some hematological and biochemical parameters in consumers was investigated. Hematological parameters including hemoglobin content and white blood cell and leukocyte counts were higher in jharda powder consumers, while monocytes and.

  1. 2009 Biochemical Conversion Platform Review Report

    Energy Technology Data Exchange (ETDEWEB)

    Ferrell, John [Office of Energy Efficiency and Renewable Energy (EERE), Washington, DC (United States)

    2009-12-01

    This document summarizes the recommendations and evaluations provided by an independent external panel of experts at the U.S. Department of Energy Biomass Program’s Biochemical Conversion platform review meeting, held on April 14-16, 2009, at the Sheraton Denver Downtown, Denver, Colorado.

  2. Some hematological and biochemical parameters in smokeless ...

    African Journals Online (AJOL)

    The effect of Jharda powder (smokeless tobacco) on some hematological and biochemical parameters in consumers was investigated. Hematological parameters including hemoglobin content and white blood cell and leukocyte counts were higher in jharda powder consumers, while monocytes and basophiles counts were ...

  3. Haematological And Biochemical Effects Of Sulphadimidine In ...

    African Journals Online (AJOL)

    Haematological and biochemical efects of sulphadmidine were studied in Nigerian mongrel dogs. Five Nigerian mongrel dogs of either sex weighing between 7 and 12 kg were used for the study. The pretreatment blood and serum samples were collected and the weight of animals taken before the administraton of 100 ...

  4. Biochemical and secondary metabolites changes under moisture ...

    African Journals Online (AJOL)

    The study showed the importance of carbohydrate and nitrogen cycle related metabolites in mediating tolerance in cassava by affecting their phenotypic expression in the plant. Keywords: Hydrothermal stress, bio-chemicals, pigments, secondary metabolites, cassava. African Journal of Biotechnology, Vol 13(31) 3173-3186 ...

  5. Biochemical and serological characterization of Escherichia coli ...

    African Journals Online (AJOL)

    This study was designed to determine the isolation rate, serotypes and biochemical profiles of E. coli from colibacillosis and dead-in-shell embryos in Zaria, Northern-Nigeria. The isolation rate of E. coli from hatcheries studied were 4.67% and 7.50% from farms of Simtu Agricultural Company and National Animal Production ...

  6. Biochemical and Kinetic Characterization of Geranylgeraniol 18 ...

    African Journals Online (AJOL)

    This enzyme and its gene are an attractive target for development of plaunotol production and its detailed biochemical properties need to be understood. Recently, even though the gene (CYP97C27) coding for GGOH 18-hydroxylase has been identified, cloned, and expressed in Escherichia coli system, the enzyme activity ...

  7. Evaluation of Haematological and Biochemical Parameters of ...

    African Journals Online (AJOL)

    ADOWIE PERE

    Evaluation of Haematological and Biochemical Parameters of Juvenile Oreochromis niloticus after Exposure to Water Soluble Fractions of ... niloticus were evaluated. After a preliminary determination of the 96 h-LC50 of ... evaporation, dissolution, emulsion, photolysis and biodegradation which generate a water soluble.

  8. Metabonomics and medicine: the Biochemical Oracle.

    Science.gov (United States)

    Mitchell, Steve; Holmes, Elaine; Carmichael, Paul

    2002-10-01

    Occasionally, a new idea emerges that has the potential to revolutionize an entire field of scientific endeavour. It is now within our grasp to be able to detect subtle perturbations within the phenomenally complex biochemical matrix of living organisms. The discipline of metabonomics promises an all-encompassing approach to understanding total, yet fundamental, changes occurring in disease processes, drug toxicity and cell function.

  9. Discordant results between biochemical and molecular transthyretin

    Indian Academy of Sciences (India)

    Discordant results between biochemical and molecular transthyretin assays: lessons learned from a unique testing algorithm at the Mayo Clinic. Honey V. Reddi Brittany C. Thomas Kurt S. Willkomm Matthew J. Ferber Kandelaria M. Rumilla Kimiyo M. Raymond John F. O'Brien W. Edward Highsmith. Research Note Volume ...

  10. Biochemical and microstructural characteristics of meat samples ...

    African Journals Online (AJOL)

    This study was conducted to compare the efficiency of different plant proteases for changing biochemical and microstructural characteristics in muscle foods. The meat samples from chicken, giant catfish, pork and beef were treated with four types of proteolytic enzymes: Calotropis procera latex proteases, papaya latex ...

  11. Kombucha tea fermentation: Microbial and biochemical dynamics.

    Science.gov (United States)

    Chakravorty, Somnath; Bhattacharya, Semantee; Chatzinotas, Antonis; Chakraborty, Writachit; Bhattacharya, Debanjana; Gachhui, Ratan

    2016-03-02

    Kombucha tea, a non-alcoholic beverage, is acquiring significant interest due to its claimed beneficial properties. The microbial community of Kombucha tea consists of bacteria and yeast which thrive in two mutually non-exclusive compartments: the soup or the beverage and the biofilm floating on it. The microbial community and the biochemical properties of the beverage have so far mostly been described in separate studies. This, however, may prevent understanding the causal links between the microbial communities and the beneficial properties of Kombucha tea. Moreover, an extensive study into the microbial and biochemical dynamics has also been missing. In this study, we thus explored the structure and dynamics of the microbial community along with the biochemical properties of Kombucha tea at different time points up to 21 days of fermentation. We hypothesized that several biochemical properties will change during the course of fermentation along with the shifts in the yeast and bacterial communities. The yeast community of the biofilm did not show much variation over time and was dominated by Candida sp. (73.5-83%). The soup however, showed a significant shift in dominance from Candida sp. to Lachancea sp. on the 7th day of fermentation. This is the first report showing Candida as the most dominating yeast genus during Kombucha fermentation. Komagateibacter was identified as the single largest bacterial genus present in both the biofilm and the soup (~50%). The bacterial diversity was higher in the soup than in the biofilm with a peak on the seventh day of fermentation. The biochemical properties changed with the progression of the fermentation, i.e., beneficial properties of the beverage such as the radical scavenging ability increased significantly with a maximum increase at day 7. We further observed a significantly higher D-saccharic acid-1,4-lactone content and caffeine degradation property compared to previously described Kombucha tea fermentations. Our

  12. Statistical physics approaches to subnetwork dynamics in biochemical systems

    Science.gov (United States)

    Bravi, B.; Sollich, P.

    2017-08-01

    We apply a Gaussian variational approximation to model reduction in large biochemical networks of unary and binary reactions. We focus on a small subset of variables (subnetwork) of interest, e.g. because they are accessible experimentally, embedded in a larger network (bulk). The key goal is to write dynamical equations reduced to the subnetwork but still retaining the effects of the bulk. As a result, the subnetwork-reduced dynamics contains a memory term and an extrinsic noise term with non-trivial temporal correlations. We first derive expressions for this memory and noise in the linearized (Gaussian) dynamics and then use a perturbative power expansion to obtain first order nonlinear corrections. For the case of vanishing intrinsic noise, our description is explicitly shown to be equivalent to projection methods up to quadratic terms, but it is applicable also in the presence of stochastic fluctuations in the original dynamics. An example from the epidermal growth factor receptor signalling pathway is provided to probe the increased prediction accuracy and computational efficiency of our method.

  13. LeishCyc: a biochemical pathways database for Leishmania major

    Directory of Open Access Journals (Sweden)

    Doyle Maria A

    2009-06-01

    Full Text Available Abstract Background Leishmania spp. are sandfly transmitted protozoan parasites that cause a spectrum of diseases in more than 12 million people worldwide. Much research is now focusing on how these parasites adapt to the distinct nutrient environments they encounter in the digestive tract of the sandfly vector and the phagolysosome compartment of mammalian macrophages. While data mining and annotation of the genomes of three Leishmania species has provided an initial inventory of predicted metabolic components and associated pathways, resources for integrating this information into metabolic networks and incorporating data from transcript, protein, and metabolite profiling studies is currently lacking. The development of a reliable, expertly curated, and widely available model of Leishmania metabolic networks is required to facilitate systems analysis, as well as discovery and prioritization of new drug targets for this important human pathogen. Description The LeishCyc database was initially built from the genome sequence of Leishmania major (v5.2, based on the annotation published by the Wellcome Trust Sanger Institute. LeishCyc was manually curated to remove errors, correct automated predictions, and add information from the literature. The ongoing curation is based on public sources, literature searches, and our own experimental and bioinformatics studies. In a number of instances we have improved on the original genome annotation, and, in some ambiguous cases, collected relevant information from the literature in order to help clarify gene or protein annotation in the future. All genes in LeishCyc are linked to the corresponding entry in GeneDB (Wellcome Trust Sanger Institute. Conclusion The LeishCyc database describes Leishmania major genes, gene products, metabolites, their relationships and biochemical organization into metabolic pathways. LeishCyc provides a systematic approach to organizing the evolving information about Leishmania

  14. Biochemical and toxicological studies of aqueous extract of ...

    African Journals Online (AJOL)

    Biochemical and toxicological studies of aqueous extract of Syzigium ... tract diseases and also used as food spices), on some biochemical indices, such as ... liver functions and blood parameters were studied in adult albino rats of both sexes.

  15. Biochemical changes during aging of soybean seed

    Directory of Open Access Journals (Sweden)

    Balešević-Tubić Svetlana

    2009-01-01

    Full Text Available Biochemical changes that occur in the seed as a result of ageing are very significant for seed quality and longevity. Because of its characteristic composition, processes occurring in the seed of oil crops during storage will be typical as well. Six soybean varieties developed in Institute of field and vegetable crops Novi Sad, submitted to accelerated and natural aging, under controlled and conventional storage conditions were used in these trials. The content of malondialdehyde, superoxide dismutase and peroxidase activities were studied. The biochemical processes i.e. lipid peroxidation, as well as the decrease in supeoxide dismutase and peroxidase activities (especially pronounced by applied accelerated aging were caused by both type of aging. The degree of seed damage and the ability of seed to resist the negative consequences of aging were influenced, beside duration of aging period, by type of storage and characteristics of soybean varieties. .

  16. Reconstructing biochemical pathways from time course data.

    Science.gov (United States)

    Srividhya, Jeyaraman; Crampin, Edmund J; McSharry, Patrick E; Schnell, Santiago

    2007-03-01

    Time series data on biochemical reactions reveal transient behavior, away from chemical equilibrium, and contain information on the dynamic interactions among reacting components. However, this information can be difficult to extract using conventional analysis techniques. We present a new method to infer biochemical pathway mechanisms from time course data using a global nonlinear modeling technique to identify the elementary reaction steps which constitute the pathway. The method involves the generation of a complete dictionary of polynomial basis functions based on the law of mass action. Using these basis functions, there are two approaches to model construction, namely the general to specific and the specific to general approach. We demonstrate that our new methodology reconstructs the chemical reaction steps and connectivity of the glycolytic pathway of Lactococcus lactis from time course experimental data.

  17. Optical Slot-Waveguide Based Biochemical Sensors

    Directory of Open Access Journals (Sweden)

    Carlos Angulo Barrios

    2009-06-01

    Full Text Available Slot-waveguides allow light to be guided and strongly confined inside a nanometer-scale region of low refractive index. Thus stronger light-analyte interaction can be obtained as compared to that achievable by a conventional waveguide, in which the propagating beam is confined to the high-refractive-index core of the waveguide. In addition, slot-waveguides can be fabricated by employing CMOS compatible materials and technology, enabling miniaturization, integration with electronic, photonic and fluidic components in a chip, and mass production. These advantages have made the use of slot-waveguides for highly sensitive biochemical optical integrated sensors an emerging field. In this paper, recent achievements in slot-waveguide based biochemical sensing will be reviewed. These include slot-waveguide ring resonator based refractometric label-free biosensors, label-based optical sensing, and nano-opto-mechanical sensors.

  18. Some biochemical studies on thyroid immunity

    International Nuclear Information System (INIS)

    Shoush, M.A.M.

    1980-01-01

    The present study was carried out to investigate the effect of induced immunological environment on: a - Carbohydrate metabolism as reflected by immunoreactive insulin and blood sugar levels. b - Biochemical parameters, namely total protein, albumin, globulin, alkaline phosphatase and transaminases, reflecting liver function. c - Radioimmunological tests reflecting thyroid function. The study comprised 36 male rabbits, boscate strain of six months age assigned randomly to : control, albumin immunized and thyroglobulin immunized groups

  19. Biochemical composition and methane production correlations

    OpenAIRE

    Charnier, Cyrille; Latrille, Eric; Moscoviz, Roman; Miroux, Jérémie; Steyer, Jean-Philippe

    2016-01-01

    Substrates for anaerobic digestion are composed of heterogeneous and complex organic matter. General parameters of the organic matter can be used to describe its composition such as sugar, protein and lipid contents, Chemical Oxygen Demand (COD), Biochemical Methane Potential (BMP) and kinetic of methane production. These parameters are required for the monitoring of digesters but their characterization are time consuming and expensive; thus, these parameters are rarely assessed all together....

  20. Biochemical characterization of cholesterol-reducing Eubacterium.

    OpenAIRE

    Mott, G E; Brinkley, A W; Mersinger, C L

    1980-01-01

    We characterized two isolates of cholesterol-reducing Eubacterium by conducting conventional biochemical tests and by testing various sterols and glycerolipids as potential growth factors. In media containing cholesterol and plasmenylethanolamine, the tests for nitrate reduction, indole production, and gelatin and starch hydrolyses were negative, and no acid was produced from any of 22 carbohydrates. Both isolates hydrolyzed esculin to esculetin, indicating beta-glycosidase activity. In addit...

  1. Biochemical changes in ginger after gamma irradiation

    International Nuclear Information System (INIS)

    Kausar, T.; Salahuddin; Pervaiz, K.; Niazi, A.H.K.

    2001-01-01

    Ginger (Zingiber officinate) was irradiated with gamma rays (0.1Kgy, 1.0Kgy). Biochemical changes during storage at room temperature (23-28 degree centigrade), in sand (23-28 degree centigrade) and at cold (8 degree centigrade) temperature were observed. Changes in starch, soluble protein, fixed oil and volatile oil contents showed that treatment of ginger at 0.1Kgy radiation level was most appropriate for storage upto 45 days

  2. Estimation of parameter sensitivities for stochastic reaction networks

    KAUST Repository

    Gupta, Ankit

    2016-01-01

    Quantification of the effects of parameter uncertainty is an important and challenging problem in Systems Biology. We consider this problem in the context of stochastic models of biochemical reaction networks where the dynamics is described as a

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

    DEFF Research Database (Denmark)

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

    2003-01-01

    The metabolic network in the yeast Saccharomyces cerevisiae was reconstructed using currently available genomic, biochemical, and physiological information. The metabolic reactions were compartmentalized between the cytosol and the mitochondria, and transport steps between the compartments...

  4. Biochemical Factors Modulating Cellular Neurotoxicity of Methylmercury

    Directory of Open Access Journals (Sweden)

    Parvinder Kaur

    2011-01-01

    Full Text Available Methylmercury (MeHg, an environmental toxicant primarily found in fish and seafood, poses a dilemma to both consumers and regulatory authorities, given the nutritional benefits of fish consumption versus the possible adverse neurological damage. Several studies have shown that MeHg toxicity is influenced by a number of biochemical factors, such as glutathione (GSH, fatty acids, vitamins, and essential elements, but the cellular mechanisms underlying these complex interactions have not yet been fully elucidated. The objective of this paper is to outline the cellular response to dietary nutrients, as well as to describe the neurotoxic exposures to MeHg. In order to determine the cellular mechanism(s of toxicity, the effect of pretreatment with biochemical factors (e.g., N-acetyl cysteine, (NAC; diethyl maleate, (DEM; docosahexaenoic acid, (DHA; selenomethionine, SeM; Trolox and MeHg treatment on intercellular antioxidant status, MeHg content, and other endpoints was evaluated. This paper emphasizes that the protection against oxidative stress offered by these biochemical factors is among one of the major mechanisms responsible for conferring neuroprotection. It is therefore critical to ascertain the cellular mechanisms associated with various dietary nutrients as well as to determine the potential effects of neurotoxic exposures for accurately assessing the risks and benefits associated with fish consumption.

  5. Explorations into Chemical Reactions and Biochemical Pathways.

    Science.gov (United States)

    Gasteiger, Johann

    2016-12-01

    A brief overview of the work in the research group of the present author on extracting knowledge from chemical reaction data is presented. Methods have been developed to calculate physicochemical effects at the reaction site. It is shown that these physicochemical effects can quite favourably be used to derive equations for the calculation of data on gas phase reactions and on reactions in solution such as aqueous acidity of alcohols or carboxylic acids or the hydrolysis of amides. Furthermore, it is shown that these physicochemical effects are quite effective for assigning reactions into reaction classes that correspond to chemical knowledge. Biochemical reactions constitute a particularly interesting and challenging task for increasing our understanding of living species. The BioPath.Database is a rich source of information on biochemical reactions and has been used for a variety of applications of chemical, biological, or medicinal interests. Thus, it was shown that biochemical reactions can be assigned by the physicochemical effects into classes that correspond to the classification of enzymes by the EC numbers. Furthermore, 3D models of reaction intermediates can be used for searching for novel enzyme inhibitors. It was shown in a combined application of chemoinformatics and bioinformatics that essential pathways of diseases can be uncovered. Furthermore, a study showed that bacterial flavor-forming pathways can be discovered. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Learning Networks, Networked Learning

    NARCIS (Netherlands)

    Sloep, Peter; Berlanga, Adriana

    2010-01-01

    Sloep, P. B., & Berlanga, A. J. (2011). Learning Networks, Networked Learning [Redes de Aprendizaje, Aprendizaje en Red]. Comunicar, XIX(37), 55-63. Retrieved from http://dx.doi.org/10.3916/C37-2011-02-05

  7. Estimation of biochemical variables using quantumbehaved particle ...

    African Journals Online (AJOL)

    To generate a more efficient neural network estimator, we employed the previously proposed quantum-behaved particle swarm optimization (QPSO) algorithm for neural network training. The experiment results of L-glutamic acid fermentation process showed that our established estimator could predict variables such as the ...

  8. Estimating Biochemical Parameters of Tea (camellia Sinensis (L.)) Using Hyperspectral Techniques

    Science.gov (United States)

    Bian, M.; Skidmore, A. K.; Schlerf, M.; Liu, Y.; Wang, T.

    2012-07-01

    Tea (Camellia Sinensis (L.)) is an important economic crop and the market price of tea depends largely on its quality. This research aims to explore the potential of hyperspectral remote sensing on predicting the concentration of biochemical components, namely total tea polyphenols, as indicators of tea quality at canopy scale. Experiments were carried out for tea plants growing in the field and greenhouse. Partial least squares regression (PLSR), which has proven to be the one of the most successful empirical approach, was performed to establish the relationship between reflectance and biochemical concentration across six tea varieties in the field. Moreover, a novel integrated approach involving successive projections algorithms as band selection method and neural networks was developed and applied to detect the concentration of total tea polyphenols for one tea variety, in order to explore and model complex nonlinearity relationships between independent (wavebands) and dependent (biochemicals) variables. The good prediction accuracies (r2 > 0.8 and relative RMSEP < 10 %) achieved for tea plants using both linear (partial lease squares regress) and nonlinear (artificial neural networks) modelling approaches in this study demonstrates the feasibility of using airborne and spaceborne sensors to cover wide areas of tea plantation for in situ monitoring of tea quality cheaply and rapidly.

  9. Biochemical Markers for Assessing Aquatic Contamination

    Directory of Open Access Journals (Sweden)

    Zdeňka Svobodová

    2007-11-01

    Full Text Available Biochemical markers, specifically enzymes of the first phase of xenobiotic transformation - cytochrome P450 and ethoxyresorufin-O-deethylase (EROD - were used to determine the quantities of persistent organic pollutants (POPs in fish muscle (PCB, HCB, HCH, OCS, DDT. Eight rivers were monitored (Orlice, Chrudimka, Cidlina, Jizera, Vltava, Ohře and Bílina; and the River Blanice was used as a control. The indicator species selected was the chub (Leuciscus cephalus L.. There were no significant differences in cytochrome P450 content between the locations monitored. The highest concentration of cytochrome P450 in fish liver was in the Vltava (0.241 nmol mg-1 protein, and the lowest was in the Orlice (0.120 nmol mg-1 protein. Analysis of EROD activity showed a significant difference between the Blanice and the Vltava (P< 0.05, and also between the Orlice and the Vltava (P< 0.01, the Orlice and the Bílina (P< 0.01, and the Orlice and the Ohře (P< 0.05. The highest EROD activity in fish liver was in the Vltava (576.4 pmol min-1 mg-1 protein, and the lowest was in the Orlice (63.05 pmol min-1 mg-1 protein. In individual locations, results of chemical monitoring and values of biochemical markers were compared. A significant correlation (P< 0.05 was found between biochemical markers and OCS, and PCB. Among the tributaries studied those that contaminated the Elbe most were the Vltava and the Bílina. These tributaries should not be considered the main sources of industrial contamination of the River Elbe, because the most important contamination sources were along the river Elbe itself.

  10. Biochemical Disincentives to Fertilizing Cellulosic Ethanol Crops

    Science.gov (United States)

    Gallagher, M. E.; Hockaday, W. C.; Snapp, S.; McSwiney, C.; Baldock, J.

    2010-12-01

    Corn grain biofuel crops produce the highest yields when the cropping ecosystem is not nitrogen (N)-limited, achieved by application of fertilizer. There are environmental consequences for excessive fertilizer application to crops, including greenhouse gas emissions, hypoxic “dead zones,” and health problems from N runoff into groundwater. The increase in corn acreage in response to demand for alternative fuels (i.e. ethanol) could exacerbate these problems, and divert food supplies to fuel production. A potential substitute for grain ethanol that could reduce some of these impacts is cellulosic ethanol. Cellulosic ethanol feedstocks include grasses (switchgrass), hardwoods, and crop residues (e.g. corn stover, wheat straw). It has been assumed that these feedstocks will require similar N fertilization rates to grain biofuel crops to maximize yields, but carbohydrate yield versus N application has not previously been monitored. We report the biochemical stocks (carbohydrate, protein, and lignin in Mg ha-1) of a corn ecosystem grown under varying N levels. We measured biochemical yield in Mg ha-1 within the grain, leaf and stem, and reproductive parts of corn plants grown at seven N fertilization rates (0-202 kg N ha-1), to evaluate the quantity and quality of these feedstocks across a N fertilization gradient. The N fertilization rate study was performed at the Kellogg Biological Station-Long Term Ecological Research Site (KBS-LTER) in Michigan. Biochemical stocks were measured using 13C nuclear magnetic resonance spectroscopy (NMR), combined with a molecular mixing model (Baldock et al. 2004). Carbohydrate and lignin are the main biochemicals of interest in ethanol production since carbohydrate is the ethanol feedstock, and lignin hinders the carbohydrate to ethanol conversion process. We show that corn residue carbohydrate yields respond only weakly to N fertilization compared to grain. Grain carbohydrate yields plateau in response to fertilization at

  11. The biochemical womb of schizophrenia: A review.

    Science.gov (United States)

    Gaur, N; Gautam, S; Gaur, M; Sharma, P; Dadheech, G; Mishra, S

    2008-10-01

    The conclusive identification of specific etiological factors or pathogenic processes in the illness of schizophrenia has remained elusive despite great technological progress. The convergence of state-of-art scientific studies in molecular genetics, molecular neuropathophysiology, in vivo brain imaging and psychopharmacology, however, indicates that we may be coming much closer to understanding the genesis of schizophrenia. In near future, the diagnosis and assessment of schizophrenia using biochemical markers may become a "dream come true" for the medical community as well as for the general population. An understanding of the biochemistry/ visa vis pathophysiology of schizophrenia is essential to the discovery of preventive measures and therapeutic intervention.

  12. Lipoprotein (a) and biochemical parameters in elderly

    OpenAIRE

    Yuttana Sudjaroen

    2016-01-01

    Background: Lipoprotein (a) [Lp(a)] is an low-density lipoprotein like particle and is an important independent risk factor for coronary artery diseases (CAD). Few studies on Lp(a) level in Thai elderly to screening risk of CAD may concerned. Aims: To study the relation of Lp(a) level and routine biochemical parameters including lipid profiles and fasting blood glucose in elderly and to determine risk of subclinical symptoms by using Lp(a) levels as early risk predictor. Settings and Design: ...

  13. Radiation treatment of drugs, biochemicals and vaccines

    International Nuclear Information System (INIS)

    Nordheim, W.; Braeuniger, S.; Kirsch, B.; Kotowski, H.; Teupel, D.

    1984-12-01

    The concise and tabulated review reports experimental results on the effects of radiation treatment on drugs, vaccines, biochemicals and adjuvants including enzymes as well. Irradiation was mostly performed by γ-radiation using 60 Co and to a lesser extent by 137 Cs, 182 Ta, X-rays and accelerators. Ionizing radiation proved to be a useful tool for sterilization and inactivation in producing drugs, vaccines, and bioactive agents and will contribute to realize procedures difficultly solvable as to engineering and economy, respectively. 124 refs

  14. [Biochemical principles of early saturnism recognition].

    Science.gov (United States)

    Tsimakuridze, M P; Mansuradze, E A; Zurashvili, D G; Tsimakuridze, M P

    2009-03-01

    The aim of the work is to determine the major sensitive criteria of biochemical indicators that allow timely discovery of negative influence of lead on organism and assist in early diagnosis of primary stages of saturnism. The workers of Georgian typographies, performing technological processes of letterpress printing were observed. Professional groups having contact with lead aerosols (main group of 66 people) and the workers of the same typography not being in touch with the poison (control group of 24 people) were studied. It was distinguished that, protracted professional contact with lead causes moderate increase of lead, coproporphyrin and DALA in daily urine in most cases; it is more clearly evidenced in the professional groups of lead smelters and lino operators and less clearly among typesetter and printers. Upon the checkup of people, having a direct contact with lead, biochemical analysis of urine should be given a preference, especially the determination of quantitative content of lead and coproporphyrin in urine with the aim of revealing the lead carrier, which is one of the first signals for occupational lookout and medical monitoring of the similar contingent.

  15. Identifying optimal models to represent biochemical systems.

    Directory of Open Access Journals (Sweden)

    Mochamad Apri

    Full Text Available Biochemical systems involving a high number of components with intricate interactions often lead to complex models containing a large number of parameters. Although a large model could describe in detail the mechanisms that underlie the system, its very large size may hinder us in understanding the key elements of the system. Also in terms of parameter identification, large models are often problematic. Therefore, a reduced model may be preferred to represent the system. Yet, in order to efficaciously replace the large model, the reduced model should have the same ability as the large model to produce reliable predictions for a broad set of testable experimental conditions. We present a novel method to extract an "optimal" reduced model from a large model to represent biochemical systems by combining a reduction method and a model discrimination method. The former assures that the reduced model contains only those components that are important to produce the dynamics observed in given experiments, whereas the latter ensures that the reduced model gives a good prediction for any feasible experimental conditions that are relevant to answer questions at hand. These two techniques are applied iteratively. The method reveals the biological core of a model mathematically, indicating the processes that are likely to be responsible for certain behavior. We demonstrate the algorithm on two realistic model examples. We show that in both cases the core is substantially smaller than the full model.

  16. Biochemical Manifestation of HIV Lipodystrophy Syndrome.

    Science.gov (United States)

    Ihenetu, Kenneth; Mason, Darius

    2012-01-01

    Highly active anti-retroviral therapy (HAART), including protease inhibitors (PI) have led to dramatic improvements in the quality and quantity of life in patients with acquired immunodeficiency syndrome (AIDS). However, a significant number of AIDS patients on HAART develop characteristic changes in body fat redistribution referred to as lipodystrophy syndrome (LDS). Features of LDS include hypertrophy in the neck fat pad (buffalo hump), increased fat in the abdominal region (protease paunch), gynecomastia and loss of fat in the mid-face and extremities. The aim of this paper is to review the current knowledge regarding this syndrome. This article reviews the published investigations on biochemical manifestation of HIV lipodystrophy syndrome. It is estimated that approximately 64% of patients treated with PI will experience this syndrome. Biochemically, these patients have increased triglycerides (Trig), total cholesterol (TC), low-density lipoprotein-cholesterol (LDL-C) and extremely low high-density lipoprotein-cholesterol (HDL-C). It is hoped that awareness of this syndrome would aid in early diagnosis and better patient management, possibly leading to a lower incidence of cardiovascular complications among these patients.

  17. Biochemical research elucidating metabolic pathways in Pneumocystis*

    Directory of Open Access Journals (Sweden)

    Kaneshiro E.S.

    2010-12-01

    Full Text Available Advances in sequencing the Pneumocystis carinii genome have helped identify potential metabolic pathways operative in the organism. Also, data from characterizing the biochemical and physiological nature of these organisms now allow elucidation of metabolic pathways as well as pose new challenges and questions that require additional experiments. These experiments are being performed despite the difficulty in doing experiments directly on this pathogen that has yet to be subcultured indefinitely and produce mass numbers of cells in vitro. This article reviews biochemical approaches that have provided insights into several Pneumocystis metabolic pathways. It focuses on 1 S-adenosyl-L-methionine (AdoMet; SAM, which is a ubiquitous participant in numerous cellular reactions; 2 sterols: focusing on oxidosqualene cyclase that forms lanosterol in P. carinii; SAM:sterol C-24 methyltransferase that adds methyl groups at the C-24 position of the sterol side chain; and sterol 14α-demethylase that removes a methyl group at the C-14 position of the sterol nucleus; and 3 synthesis of ubiquinone homologs, which play a pivotal role in mitochondrial inner membrane and other cellular membrane electron transport.

  18. Pheochromocytoma-paraganglioma: Biochemical and genetic diagnosis.

    Science.gov (United States)

    Cano Megías, Marta; Rodriguez Puyol, Diego; Fernández Rodríguez, Loreto; Sención Martinez, Gloria Lisette; Martínez Miguel, Patricia

    Pheochromocytomas and paragangliomas are tumours derived from neural crest cells, which can be diagnosed by biochemical measurement of metanephrine and methoxytyramine. Advances in genetic research have identified many genes involved in the pathogenesis of these tumours, suggesting that up to 35-45% may have an underlying germline mutation. These genes have a singular transcriptional signature and can be grouped into 2 clusters (or groups): cluster 1 (VHL and SHDx), involved in angiogenesis and hypoxia pathways; and cluster 2 (MEN2 and NF1), linked to the kinase signalling pathway. In turn, these genes are associated with a characteristic biochemical phenotype (noradrenergic and adrenergic), and clinical features (location, biological behaviour, age of presentation, etc.) in a large number of cases. Early diagnosis of these tumours, accompanied by a correct genetic diagnosis, should eventually become a priority to enable better treatment, early detection of complications, proper screening of family members and related tumours, as well as an improvement in the overall prognosis of these patients. Copyright © 2016 Sociedad Española de Nefrología. Published by Elsevier España, S.L.U. All rights reserved.

  19. Biochemical Control With Radiotherapy Improves Overall Survival in Intermediate and High-Risk Prostate Cancer Patients Who Have an Estimated 10-Year Overall Survival of >90%

    International Nuclear Information System (INIS)

    Herbert, Christopher; Liu, Mitchell; Tyldesley, Scott; Morris, W. James; Joffres, Michel; Khaira, Mandip; Kwan, Winkle; Moiseenko, Vitali; Pickles, Thomas

    2012-01-01

    Purpose: To identify subgroups of patients with carcinoma of the prostate treated with radical radiotherapy that have improved overall survival when disease is biochemically controlled. Methods and Materials: A cohort of 1,060 prostate cancer patients treated with radical radiotherapy was divided into nine subgroups based on National Comprehensive Cancer Network risk category and estimated 10-year overall survival (eOS 10y) derived from the age adjusted Charlson Comorbidity Index. Patients with and without biochemical control were compared with respect to overall survival. Actuarial estimates of overall survival were calculated using the Kaplan-Meier method. Univariate and multivariate Cox proportional hazards models were used for analysis of overall survival. Results: Median follow-up was 125 months (range, 51–176 months). Only the subgroups with high or intermediate risk disease and an eOS 10y of >90% had a statistically significantly improved overall survival when prostate cancer was biochemically controlled. In all other groups, biochemical control made no significant difference to overall survival. In the subgroup with high-risk disease and eOS 10y >90%, actuarial overall survival was 86.3% (95% confidence interval [CI] 78.5%–94.1%) and 62.1% (95% CI 52.9%–71.3%) for patients with biochemical control and biochemical relapse respectively (p = 0.002). In the intermediate risk group with eOS >90%, actuarial overall survival was 95.3% (95% CI 89.0%–100%) and 79.8% (95% CI 68.0%–91.6%) for biochemically controlled and biochemically relapsed patients (p = 0.033). On multivariate analysis, National Comprehensive Cancer Network risk group (p = 0.005), biochemical control (p = 0.033) and eOS 10y (p 90%.

  20. Possibilities and methods for biochemical assessment of radiation injury

    Energy Technology Data Exchange (ETDEWEB)

    Minkova, M [Meditsinska Akademiya, Sofia (Bulgaria). Nauchen Inst. po Rentgenologiya i Radiobiologiya

    1986-01-01

    An extensitive review (77 references) is made of the application of biochemical diagnostic methods for assessment of radiation diseases. A brief characteristics of several biochemical indicators is given: deoxycytidine, thymidine, rho-aminoisocarboxylic acid, DNA-ase, nucleic acids. Influence of such factors as age, sex, season etc. is studied by means of functional biochemical indicators as: creatine, triptophanic metabolites, 5-hydroxy-indolacetic acid, biogenic amines, serum proteins, enzymes, etc.

  1. Prions: the danger of biochemical weapons

    Directory of Open Access Journals (Sweden)

    Eric Almeida Xavier

    2014-09-01

    Full Text Available The knowledge of biotechnology increases the risk of using biochemical weapons for mass destruction. Prions are unprecedented infectious pathogens that cause a group of fatal neurodegenerative diseases by a novel mechanism. They are transmissible particles that are devoid of nucleic acid. Due to their singular characteristics, Prions emerge as potential danger since they can be used in the development of such weapons. Prions cause fatal infectious diseases, and to date there is no therapeutic or prophylactic approach against these diseases. Furthermore, Prions are resistant to food-preparation treatments such as high heat and can find their way from the digestive system into the nervous system; recombinant Prions are infectious either bound to soil particles or in aerosols. Therefore, lethal Prions can be developed by malicious researchers who could use it to attack political enemies since such weapons cause diseases that could be above suspicion.

  2. Biochemical Basis of Sestrin Physiological Activities

    Energy Technology Data Exchange (ETDEWEB)

    Ho, Allison; Cho, Chun-Seok; Namkoong, Sim; Cho, Uhn-Soo; Lee, Jun Hee (Michigan)

    2016-05-10

    Excessive accumulation of reactive oxygen species (ROS) and chronic activation of mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) are well-characterized promoters of aging and age-associated degenerative pathologies. Sestrins, a family of highly conserved stress-inducible proteins, are important negative regulators of both ROS and mTORC1 signaling pathways; however, the mechanistic basis of how Sestrins suppress these pathways remains elusive. In the past couple of years, breakthrough discoveries about Sestrin signaling and its molecular nature have markedly increased our biochemical understanding of Sestrin function. These discoveries have also uncovered new potential therapeutic strategies that may eventually enable us to attenuate aging and age-associated diseases.

  3. Simplifying biochemical models with intermediate species

    DEFF Research Database (Denmark)

    Feliu, Elisenda; Wiuf, Carsten

    2013-01-01

    techniques, we study systematically the effects of intermediate, or transient, species in biochemical systems and provide a simple, yet rigorous mathematical classification of all models obtained from a core model by including intermediates. Main examples include enzymatic and post-translational modification...... systems, where intermediates often are considered insignificant and neglected in a model, or they are not included because we are unaware of their existence. All possible models obtained from the core model are classified into a finite number of classes. Each class is defined by a mathematically simple...... canonical model that characterizes crucial dynamical properties, such as mono- and multistationarity and stability of steady states, of all models in the class. We show that if the core model does not have conservation laws, then the introduction of intermediates does not change the steady...

  4. Biochemical and genetic improvement of Zymomonas mobilis

    Energy Technology Data Exchange (ETDEWEB)

    Ingram, L O; Carey, V C; Dombek, K M; Holt, A S; Holt, W A; Osman, Y A; Walia, S K

    1984-01-01

    Zymomonas mobilis offers many advantages for alcohol production including three- to five-fold higher rates of substrate conversion. Current progress and approaches are discussed for the biochemical and genetic improvement of this organism. These include the isolation of salt-resistant mutants and low pH-tolerant mutants. Gene banks of Lactobacillus heterohiochi are being screened for genes encoding alcohol resistance which can be subsequently introduced into Zymomonas mobilis. In addition, an enteric lactose operon has been inserted into Zymomonas mobilis and is expressed. These new strains are being further modified to increase the substrate range of Zymomonas mobilis to include lactose. This lactose operon serves as a model system to investigate the expression of foreign genes in Zymomonas mobilis. 25 references.

  5. Implantable biochemical fuel cell. [German patent

    Energy Technology Data Exchange (ETDEWEB)

    Richter, G; Rao, J R

    1978-09-14

    Implantable biochemical fuel cells for the operation of heart pacemakers or artificial hearts convert oxidisable body substances such as glucose on the anode side and reduce the oxygen contained in body fluids at the cathode. The anode and cathode are separated by membranes which are impermeable to albumen and blood corpuscles in body fluids. A chemical shortcircuit cannot occur in practice if, according to the invention, one or more selective oxygen electrodes with carbon as catalyst are arranged so that the mixture which diffuses into the cell from body fluids during operation reaches the fuel cell electrode through the porous oxygen electrode. The membranes used must be permeable to water. Cellulose, polymerised polyvinyl alcohol or an ion exchanger with a buffering capacity between pH5 and 8 act as permeable materials.

  6. The biochemical anatomy of cortical inhibitory synapses.

    Directory of Open Access Journals (Sweden)

    Elizabeth A Heller

    Full Text Available Classical electron microscopic studies of the mammalian brain revealed two major classes of synapses, distinguished by the presence of a large postsynaptic density (PSD exclusively at type 1, excitatory synapses. Biochemical studies of the PSD have established the paradigm of the synapse as a complex signal-processing machine that controls synaptic plasticity. We report here the results of a proteomic analysis of type 2, inhibitory synaptic complexes isolated by affinity purification from the cerebral cortex. We show that these synaptic complexes contain a variety of neurotransmitter receptors, neural cell-scaffolding and adhesion molecules, but that they are entirely lacking in cell signaling proteins. This fundamental distinction between the functions of type 1 and type 2 synapses in the nervous system has far reaching implications for models of synaptic plasticity, rapid adaptations in neural circuits, and homeostatic mechanisms controlling the balance of excitation and inhibition in the mature brain.

  7. Highly valuable microalgae: biochemical and topological aspects.

    Science.gov (United States)

    Pignolet, Olivier; Jubeau, Sébastien; Vaca-Garcia, Carlos; Michaud, Philippe

    2013-08-01

    The past decade has seen a surge in the interest in microalgae culture for biodiesel production and other applications as renewable biofuels as an alternative to petroleum transport fuels. The development of new technologies for the culture of these photosynthetic microorganisms and improved knowledge of their biochemical composition has spurred innovation in the field of high-value biomolecules. These developments are only economically viable if all the microalgae fractions are valorized in a biorefinery strategy. Achieving this objective requires an understanding of microalgae content and the cellular localization of the main biomolecular families in order to develop efficient harvest and sequential recovery technologies. This review summarizes the state of the art in microalgae compositions and topologies using some examples of the main industrially farmed microalgae.

  8. Hemoglobin Variants: Biochemical Properties and Clinical Correlates

    Science.gov (United States)

    Thom, Christopher S.; Dickson, Claire F.; Gell, David A.; Weiss, Mitchell J.

    2013-01-01

    Diseases affecting hemoglobin synthesis and function are extremely common worldwide. More than 1000 naturally occurring human hemoglobin variants with single amino acid substitutions throughout the molecule have been discovered, mainly through their clinical and/or laboratory manifestations. These variants alter hemoglobin structure and biochemical properties with physiological effects ranging from insignificant to severe. Studies of these mutations in patients and in the laboratory have produced a wealth of information on hemoglobin biochemistry and biology with significant implications for hematology practice. More generally, landmark studies of hemoglobin performed over the past 60 years have established important paradigms for the disciplines of structural biology, genetics, biochemistry, and medicine. Here we review the major classes of hemoglobin variants, emphasizing general concepts and illustrative examples. PMID:23388674

  9. Biochemically enhanced methane production from coal

    Science.gov (United States)

    Opara, Aleksandra

    For many years, biogas was connected mostly with the organic matter decomposition in shallow sediments (e.g., wetlands, landfill gas, etc.). Recently, it has been realized that biogenic methane production is ongoing in many hydrocarbon reservoirs. This research examined microbial methane and carbon dioxide generation from coal. As original contributions methane production from various coal materials was examined in classical and electro-biochemical bench-scale reactors using unique, developed facultative microbial consortia that generate methane under anaerobic conditions. Facultative methanogenic populations are important as all known methanogens are strict anaerobes and their application outside laboratory would be problematic. Additional testing examined the influence of environmental conditions, such as pH, salinity, and nutrient amendments on methane and carbon dioxide generation. In 44-day ex-situ bench-scale batch bioreactor tests, up to 300,000 and 250,000 ppm methane was generated from bituminous coal and bituminous coal waste respectively, a significant improvement over 20-40 ppm methane generated from control samples. Chemical degradation of complex hydrocarbons using environmentally benign reagents, prior to microbial biodegradation and methanogenesis, resulted in dissolution of up to 5% bituminous coal and bituminous coal waste and up to 25% lignite in samples tested. Research results confirm that coal waste may be a significant underutilized resource that could be converted to useful fuel. Rapid acidification of lignite samples resulted in low pH (below 4.0), regardless of chemical pretreatment applied, and did not generate significant methane amounts. These results confirmed the importance of monitoring and adjusting in situ and ex situ environmental conditions during methane production. A patented Electro-Biochemical Reactor technology was used to supply electrons and electron acceptor environments, but appeared to influence methane generation in a

  10. Biochemical parameters in chronic renal failure.

    Science.gov (United States)

    Hakim, R M; Lazarus, J M

    1988-03-01

    We analyzed biochemical data derived from 911 patients with renal insufficiency observed at our institution for periods up to 7 years. During early renal failure (RF) (creatinine less than 5 mg/dL), the rate of change of hematocrit, total CO2 (tCO2) and urea per unit change of creatinine was significantly higher than during moderate (creatinine between 5 and 10 mg/dL) or advanced (creatinine greater than 10 mg/dL) RF. For example, the rate of change of hematocrit (%, volume/volume [v/v]) was (mean +/- SEM) -2.15 +/- 0.15% for each 1 mg/dL increase in creatinine in the range of creatinine less than 5 mg/dL, whereas for the range of creatinine greater than 10 mg/dL, the rate of change was only -0.48 +/- 0.06% (P less than 0.001). Similarly, the rate of change of tCO2 was -1.68 +/- 0.09 mEq/L for each 1 mg/dL increment in creatinine concentration during early RF, and -0.19 +/- 0.09 mEq/L per unit increase in creatinine during advanced RF (P less than 0.001). Chloride concentration initially increased as a function of creatinine in early RF, but decreased in advanced RF, whereas the anion gap increased throughout the course of RF. Mean serum phosphate concentration also increased steadily, but remained below the upper range of normal (4.7 mg/dL) during early RF without the use of phosphate binders. These data suggest that different biochemical parameters change at different rates as a function of the severity of renal dysfunction, and that although phosphate retention may occur, hyperphosphatemia is not a hallmark of early RF.

  11. Soya bean Gα proteins with distinct biochemical properties exhibit differential ability to complement Saccharomyces cerevisiae gpa1 mutant.

    Science.gov (United States)

    Roy Choudhury, Swarup; Wang, Yuqi; Pandey, Sona

    2014-07-01

    Signalling pathways mediated by heterotrimeric G-proteins are common to all eukaryotes. Plants have a limited number of each of the G-protein subunits, with the most elaborate G-protein network discovered so far in soya bean (Glycine max, also known as soybean) which has four Gα, four Gβ and ten Gγ proteins. Biochemical characterization of Gα proteins from plants suggests significant variation in their properties compared with the well-characterized non-plant proteins. Furthermore, the four soya bean Gα (GmGα) proteins exhibit distinct biochemical activities among themselves, but the extent to which such biochemical differences contribute to their in vivo function is also not known. We used the yeast gpa1 mutant which displays constitutive signalling and growth arrest in the pheromone-response pathway as an in vivo model to evaluate the effect of distinct biochemical activities of GmGα proteins. We showed that specific GmGα proteins can be activated during pheromone-dependent receptor-mediated signalling in yeast and they display different strengths towards complementation of yeast gpa1 phenotypes. We also identified amino acids that are responsible for differential complementation abilities of specific Gα proteins. These data establish that specific plant Gα proteins are functional in the receptor-mediated pheromone-response pathway in yeast and that the subtle biochemical differences in their activity are physiologically relevant.

  12. Exploring biological network structure with clustered random networks

    Directory of Open Access Journals (Sweden)

    Bansal Shweta

    2009-12-01

    Full Text Available Abstract Background Complex biological systems are often modeled as networks of interacting units. Networks of biochemical interactions among proteins, epidemiological contacts among hosts, and trophic interactions in ecosystems, to name a few, have provided useful insights into the dynamical processes that shape and traverse these systems. The degrees of nodes (numbers of interactions and the extent of clustering (the tendency for a set of three nodes to be interconnected are two of many well-studied network properties that can fundamentally shape a system. Disentangling the interdependent effects of the various network properties, however, can be difficult. Simple network models can help us quantify the structure of empirical networked systems and understand the impact of various topological properties on dynamics. Results Here we develop and implement a new Markov chain simulation algorithm to generate simple, connected random graphs that have a specified degree sequence and level of clustering, but are random in all other respects. The implementation of the algorithm (ClustRNet: Clustered Random Networks provides the generation of random graphs optimized according to a local or global, and relative or absolute measure of clustering. We compare our algorithm to other similar methods and show that ours more successfully produces desired network characteristics. Finding appropriate null models is crucial in bioinformatics research, and is often difficult, particularly for biological networks. As we demonstrate, the networks generated by ClustRNet can serve as random controls when investigating the impacts of complex network features beyond the byproduct of degree and clustering in empirical networks. Conclusion ClustRNet generates ensembles of graphs of specified edge structure and clustering. These graphs allow for systematic study of the impacts of connectivity and redundancies on network function and dynamics. This process is a key step in

  13. Exploring basic biochemical constituents in the body tissues of ...

    African Journals Online (AJOL)

    Feeding regime did not influence susceptibility to mass loss during export. Animal age influenced the biochemical composition and export performance of abalone. Keywords: abalone; aquaculture; feeds; Haliotis midae; live export; mass loss; tissue biochemical constituents. African Journal of Marine Science 2010, 32(1): ...

  14. Haematological and blood biochemical indices of West African ...

    African Journals Online (AJOL)

    Haematological and blood biochemical indices of West African dwarf goats vaccinated against Pestes des petit ruminants (PPR) ... blood biochemical indices of forty randomly selected West African dwarf (WAD) goats were studied. Packed cell volume ... neutrophil/lymphocyte ratio and white blood cells (WBC) than females.

  15. An improved solution of first order kinetics for biochemical oxygen ...

    African Journals Online (AJOL)

    This paper evaluated selected Biochemical Oxygen Demand first order kinetics methods. Domesticinstitutional wastewaters were collected twice in a month for three months from the Obafemi Awolowo University, Ile-Ife waste stabilization ponds. Biochemical Oxygen Demand concentrations at different days were determined ...

  16. Local biochemical and morphological differences in human Achilles tendinopathy

    DEFF Research Database (Denmark)

    Pingel, Jessica; Fredberg, U.; Qvortrup, Klaus

    2012-01-01

    The incidence of Achilles tendinopathy is high and underlying etiology as well as biochemical and morphological pathology associated with the disease is largely unknown. The aim of the present study was to describe biochemical and morphological differences in chronic Achilles tendinopathy....... The expressions of growth factors, inflammatory mediators and tendon morphology were determined in both chronically diseased and healthy tendon parts....

  17. Possible Biochemical Markers in Protein-Energy Malnutrition and ...

    African Journals Online (AJOL)

    This study was carried out to determine possible biochemical markers in children suffering from Plasmodium falciparum malaria and Protein-Energy Malnutrition in a Hospital setting in Western Kenya. Spectrophotometric assays of selected biochemical parameters namely, albumin, total proteins, glucose, glutamate ...

  18. Biochemical evaluation of phenylketonuria (PKU: from diagnosis to treatment

    Directory of Open Access Journals (Sweden)

    Leticia Belmont-Martínez

    2014-07-01

    Besides periodical Phe and Tyr testing, biochemical follow-up includes the measurement of necessary elements that guarantee normal physical and intellectual development such as selenium, zinc, B12 vitamin, folates, iron and long chain fatty acids. Clinical context is as important as biochemical status so periodic evaluation of nutritional, medical, social and psychological aspects should be included.

  19. Developments in commercially produced microbials at Biochem Products

    Science.gov (United States)

    John Lublinkhof; Douglas H. Ross

    1985-01-01

    Biochem Products is part of a large industrial and scientific family - the Solvay Group. Solvay, headquartered in Brussels, Belgium is a multinational company with 46,000 employees worldwide. In the U.S., our working partners include a large polymer manufacturer, a peroxygen producer and a leading poultry and animal health products company. Biochem Products is a...

  20. Efficient simulation of intrinsic, extrinsic and external noise in biochemical systems

    Science.gov (United States)

    Pischel, Dennis; Sundmacher, Kai; Flassig, Robert J.

    2017-01-01

    Abstract Motivation: Biological cells operate in a noisy regime influenced by intrinsic, extrinsic and external noise, which leads to large differences of individual cell states. Stochastic effects must be taken into account to characterize biochemical kinetics accurately. Since the exact solution of the chemical master equation, which governs the underlying stochastic process, cannot be derived for most biochemical systems, approximate methods are used to obtain a solution. Results: In this study, a method to efficiently simulate the various sources of noise simultaneously is proposed and benchmarked on several examples. The method relies on the combination of the sigma point approach to describe extrinsic and external variability and the τ-leaping algorithm to account for the stochasticity due to probabilistic reactions. The comparison of our method to extensive Monte Carlo calculations demonstrates an immense computational advantage while losing an acceptable amount of accuracy. Additionally, the application to parameter optimization problems in stochastic biochemical reaction networks is shown, which is rarely applied due to its huge computational burden. To give further insight, a MATLAB script is provided including the proposed method applied to a simple toy example of gene expression. Availability and implementation: MATLAB code is available at Bioinformatics online. Contact: flassig@mpi-magdeburg.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28881987

  1. Declarative Networking

    CERN Document Server

    Loo, Boon Thau

    2012-01-01

    Declarative Networking is a programming methodology that enables developers to concisely specify network protocols and services, which are directly compiled to a dataflow framework that executes the specifications. Declarative networking proposes the use of a declarative query language for specifying and implementing network protocols, and employs a dataflow framework at runtime for communication and maintenance of network state. The primary goal of declarative networking is to greatly simplify the process of specifying, implementing, deploying and evolving a network design. In addition, decla

  2. Definitions of biochemical failure in prostate cancer following radiation therapy

    International Nuclear Information System (INIS)

    Taylor, Jeremy M.G.; Griffith, Kent A.; Sandler, Howard M.

    2001-01-01

    Purpose: The American Society for Therapeutic Radiology and Oncology (ASTRO) published a consensus panel definition of biochemical failure following radiation therapy for prostate cancer. In this paper, we develop a series of alternative definitions of biochemical failure. Using data from 688 patients, we evaluated the sensitivity and specificity of the various definitions, with respect to a defined 'clinically meaningful' outcome. Methods and Materials: The ASTRO definition of biochemical failure requires 3 consecutive rises in prostate-specific antigen (PSA). We considered several modifications to the standard definition: to require PSA rises of a certain magnitude, to consider 2 instead of 3 rises, to require the final PSA value to be greater than a fixed cutoff level, and to define biochemical failure based on the slope of PSA over 1, 1.5, or 2 years. A clinically meaningful failure is defined as local recurrence, distant metastases, initiation of unplanned hormonal therapy, unplanned radical prostatectomy, or a PSA>25 later than 6 months after radiation. Results: Requiring the final PSA in a series of consecutive rises to be larger than 1.5 ng/mL increased the specificity of biochemical failure. For a fixed specificity, defining biochemical failure based on 2 consecutive rises, or the slope over the last year, could increase the sensitivity by up to approximately 20%, compared to the ASTRO definition. Using a rule based on the slope over the previous year or 2 rises leads to a slightly earlier detection of biochemical failure than does the ASTRO definition. Even with the best rule, only approximately 20% of true failures are biochemically detected more than 1 year before the clinically meaningful event time. Conclusion: There is potential for improvement in the ASTRO consensus definition of biochemical failure. Further research is needed, in studies with long follow-up times, to evaluate the relationship between various definitions of biochemical failure and

  3. Applied spectrophotometry: analysis of a biochemical mixture.

    Science.gov (United States)

    Trumbo, Toni A; Schultz, Emeric; Borland, Michael G; Pugh, Michael Eugene

    2013-01-01

    Spectrophotometric analysis is essential for determining biomolecule concentration of a solution and is employed ubiquitously in biochemistry and molecular biology. The application of the Beer-Lambert-Bouguer Lawis routinely used to determine the concentration of DNA, RNA or protein. There is however a significant difference in determining the concentration of a given species (RNA, DNA, protein) in isolation (a contrived circumstance) as opposed to determining that concentration in the presence of other species (a more realistic situation). To present the student with a more realistic laboratory experience and also to fill a hole that we believe exists in student experience prior to reaching a biochemistry course, we have devised a three week laboratory experience designed so that students learn to: connect laboratory practice with theory, apply the Beer-Lambert-Bougert Law to biochemical analyses, demonstrate the utility and limitations of example quantitative colorimetric assays, demonstrate the utility and limitations of UV analyses for biomolecules, develop strategies for analysis of a solution of unknown biomolecular composition, use digital micropipettors to make accurate and precise measurements, and apply graphing software. Copyright © 2013 Wiley Periodicals, Inc.

  4. Interactions of Cannabinoids With Biochemical Substrates

    Directory of Open Access Journals (Sweden)

    Brian F Thomas

    2017-05-01

    Full Text Available Recent decades have seen much progress in the identification and characterization of cannabinoid receptors and the elucidation of the mechanisms by which derivatives of the Cannabis sativa plant bind to receptors and produce their physiological and psychological effects. The information generated in this process has enabled better understanding of the fundamental physiological and psychological processes controlled by the central and peripheral nervous systems and has fostered the development of natural and synthetic cannabinoids as therapeutic agents. A negative aspect of this decades-long effort is the proliferation of clandestinely synthesized analogs as recreational street drugs with dangerous effects. Currently, the interactions of cannabinoids with their biochemical substrates are extensively but inadequately understood, and the clinical application of derived and synthetic receptor ligands remains quite limited. The wide anatomical distribution and functional complexity of the cannabinoid system continue to indicate potential for both therapeutic and side effects, which offers challenges and opportunities for medicinal chemists involved in drug discovery and development.

  5. BALL - biochemical algorithms library 1.3

    Directory of Open Access Journals (Sweden)

    Stöckel Daniel

    2010-10-01

    Full Text Available Abstract Background The Biochemical Algorithms Library (BALL is a comprehensive rapid application development framework for structural bioinformatics. It provides an extensive C++ class library of data structures and algorithms for molecular modeling and structural bioinformatics. Using BALL as a programming toolbox does not only allow to greatly reduce application development times but also helps in ensuring stability and correctness by avoiding the error-prone reimplementation of complex algorithms and replacing them with calls into the library that has been well-tested by a large number of developers. In the ten years since its original publication, BALL has seen a substantial increase in functionality and numerous other improvements. Results Here, we discuss BALL's current functionality and highlight the key additions and improvements: support for additional file formats, molecular edit-functionality, new molecular mechanics force fields, novel energy minimization techniques, docking algorithms, and support for cheminformatics. Conclusions BALL is available for all major operating systems, including Linux, Windows, and MacOS X. It is available free of charge under the Lesser GNU Public License (LPGL. Parts of the code are distributed under the GNU Public License (GPL. BALL is available as source code and binary packages from the project web site at http://www.ball-project.org. Recently, it has been accepted into the debian project; integration into further distributions is currently pursued.

  6. PHA bioplastics, biochemicals, and energy from crops.

    Science.gov (United States)

    Somleva, Maria N; Peoples, Oliver P; Snell, Kristi D

    2013-02-01

    Large scale production of polyhydroxyalkanoates (PHAs) in plants can provide a sustainable supply of bioplastics, biochemicals, and energy from sunlight and atmospheric CO(2). PHAs are a class of polymers with various chain lengths that are naturally produced by some microorganisms as storage materials. The properties of these polyesters make them functionally equivalent to many of the petroleum-based plastics that are currently in the market place. However, unlike most petroleum-derived plastics, PHAs can be produced from renewable feedstocks and easily degrade in most biologically active environments. This review highlights research efforts over the last 20 years to engineer the production of PHAs in plants with a focus on polyhydroxybutryrate (PHB) production in bioenergy crops with C(4) photosynthesis. PHB has the potential to be a high volume commercial product with uses not only in the plastics and materials markets, but also in renewable chemicals and feed. The major challenges of improving product yield and plant fitness in high biomass yielding C(4) crops are discussed in detail. Plant Biotechnology Journal © 2013 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd.

  7. Skin biochemical composition analysis by Raman spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, Patricia Karen; Tosato, Maira Gaspar; Alves, Rani de Souza; Martin, Airton Abrahao; Favero, Priscila Pereira; Raniero, Leandro, E-mail: amartin@univap.br [Laboratorio de Espectroscopia Vibracional Biomedica, Instituto de Pesquisa e Desenvolvimento - IP e D, Universidade do Vale do Paraiba - UniVap, Sao Jose dos Campos, SP (Brazil)

    2012-09-15

    Skin aging is characterized by cellular and molecular alterations. In this context, Confocal Raman spectroscopy was used in vivo to measure these biochemical changes as function of the skin depth. In this study we have tried to correlate spectra from pure amino acids to in vivo spectra from volunteers with different ages. This study was performed on 32 volunteers: 11 from Group A (20-23 years), 11 from Group B (39-42 years) and 10 from Group C (59-62 years). For each group, the Raman spectra were measured on the surface (0 mm), 30 +- 3 mm and 60 +- 3 {mu}m below the surface. The results from intergroup comparisons showed that the oldest group had a prevalence of the tyrosine band, but it also presented a decrease in the band centered at 875 cm{sup -1} of pyrrolidone acid. The amide I band centered at 1637 cm{sup -1} that is attributed to collagen, as well as other proteins and lipid, showed a smaller amount of these biomolecules for Group C, which can be explained by the decrease in collagen concentration as a function of age. (author)

  8. Biochemical characterization of cholesterol-reducing Eubacterium.

    Science.gov (United States)

    Mott, G E; Brinkley, A W; Mersinger, C L

    1980-12-01

    We characterized two isolates of cholesterol-reducing Eubacterium by conducting conventional biochemical tests and by testing various sterols and glycerolipids as potential growth factors. In media containing cholesterol and plasmenylethanolamine, the tests for nitrate reduction, indole production, and gelatin and starch hydrolyses were negative, and no acid was produced from any of 22 carbohydrates. Both isolates hydrolyzed esculin to esculetin, indicating beta-glycosidase activity. In addition to plasmenylethanolamine, five other lipids which contain an alkenyl ether residue supported growth of Eubacterium strain 403 in a lecithin-cholesterol base medium. Of six steroids tested, cholesterol, cholest-4-en-3-one, cholest-4-en-3 beta-ol (allocholesterol), and androst-5-en-3 beta-ol-17-one supported growth of Eubacterium strain 403. All four steroids were reduced to the 3 beta-ol, 5 beta-H products. The delta 5 steroids cholest-5-en-3 alpha-ol (epicholesterol) and 22,23-bisnor-5-cholenic acid-3-beta-ol were not reduced and did not support growth of the Eubacterium strain.

  9. Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator.

    Science.gov (United States)

    Weitz, Maximilian; Kim, Jongmin; Kapsner, Korbinian; Winfree, Erik; Franco, Elisa; Simmel, Friedrich C

    2014-04-01

    In vitro compartmentalization of biochemical reaction networks is a crucial step towards engineering artificial cell-scale devices and systems. At this scale the dynamics of molecular systems becomes stochastic, which introduces several engineering challenges and opportunities. Here we study a programmable transcriptional oscillator system that is compartmentalized into microemulsion droplets with volumes between 33 fl and 16 pl. Simultaneous measurement of large populations of droplets reveals major variations in the amplitude, frequency and damping of the oscillations. Variability increases for smaller droplets and depends on the operating point of the oscillator. Rather than reflecting the stochastic kinetics of the chemical reaction network itself, the variability can be attributed to the statistical variation of reactant concentrations created during their partitioning into droplets. We anticipate that robustness to partitioning variability will be a critical challenge for engineering cell-scale systems, and that highly parallel time-series acquisition from microemulsion droplets will become a key tool for characterization of stochastic circuit function.

  10. The Biochemical Prognostic Factors of Subclinical Hypothyroidism

    Directory of Open Access Journals (Sweden)

    Myung Won Lee

    2014-06-01

    Full Text Available BackgroundPatients with subclinical hypothyroidism (SHT are common in clinical practice. However, the clinical significance of SHT, including prognosis, has not been established. Further clarifying SHT will be critical in devising a management plan and treatment guidelines for SHT patients. Thus, the aim of this study was to investigate the prognostic factors of SHT.MethodsWe reviewed the medical records of Korean patients who visited the endocrinology outpatient clinic of Severance Hospital from January 2008 to September 2012. Newly-diagnosed patients with SHT were selected and reviewed retrospectively. We compared two groups: the SHT maintenance group and the spontaneous improvement group.ResultsThe SHT maintenance group and the spontaneous improvement group had initial thyroid-stimulating hormone (TSH levels that were significantly different (P=0.035. In subanalysis for subjects with TSH levels between 5 to 10 µIU/mL, the spontaneous improvement group showed significantly lower antithyroid peroxidase antibody (anti-TPO-Ab titer than the SHT maintenance group (P=0.039. Regarding lipid profiles, only triglyceride level, unlike total cholesterol and low density lipoprotein cholesterol, was related to TSH level, which is correlated with the severity of SHT. Diffuse thyroiditis on ultrasonography only contributed to the severity of SHT, not to the prognosis. High sensitivity C-reactive protein and urine iodine excretion, generally regarded as possible prognostic factors, did not show any significant relation with the prognosis and severity of SHT.ConclusionOnly initial TSH level was a definite prognostic factor of SHT. TPO-Ab titer was also a helpful prognostic factor for SHT in cases with mildly elevated TSH. Other than TSH and TPO-Ab, we were unable to validate biochemical prognostic factors in this retrospective study for Korean SHT patients.

  11. A flood-based information flow analysis and network minimization method for gene regulatory networks.

    Science.gov (United States)

    Pavlogiannis, Andreas; Mozhayskiy, Vadim; Tagkopoulos, Ilias

    2013-04-24

    Biological networks tend to have high interconnectivity, complex topologies and multiple types of interactions. This renders difficult the identification of sub-networks that are involved in condition- specific responses. In addition, we generally lack scalable methods that can reveal the information flow in gene regulatory and biochemical pathways. Doing so will help us to identify key participants and paths under specific environmental and cellular context. This paper introduces the theory of network flooding, which aims to address the problem of network minimization and regulatory information flow in gene regulatory networks. Given a regulatory biological network, a set of source (input) nodes and optionally a set of sink (output) nodes, our task is to find (a) the minimal sub-network that encodes the regulatory program involving all input and output nodes and (b) the information flow from the source to the sink nodes of the network. Here, we describe a novel, scalable, network traversal algorithm and we assess its potential to achieve significant network size reduction in both synthetic and E. coli networks. Scalability and sensitivity analysis show that the proposed method scales well with the size of the network, and is robust to noise and missing data. The method of network flooding proves to be a useful, practical approach towards information flow analysis in gene regulatory networks. Further extension of the proposed theory has the potential to lead in a unifying framework for the simultaneous network minimization and information flow analysis across various "omics" levels.

  12. Simulation and Statistical Inference of Stochastic Reaction Networks with Applications to Epidemic Models

    KAUST Repository

    Moraes, Alvaro

    2015-01-01

    Networks (SRNs), that are intended to describe the time evolution of interacting particle systems where one particle interacts with the others through a finite set of reaction channels. SRNs have been mainly developed to model biochemical reactions

  13. Network cohesion

    OpenAIRE

    Cavalcanti, Tiago Vanderlei; Giannitsarou, Chrysi; Johnson, CR

    2017-01-01

    We define a measure of network cohesion and show how it arises naturally in a broad class of dynamic models of endogenous perpetual growth with network externalities. Via a standard growth model, we show why network cohesion is crucial for conditional convergence and explain that as cohesion increases, convergence is faster. We prove properties of network cohesion and define a network aggregator that preserves network cohesion.

  14. The network researchers' network

    DEFF Research Database (Denmark)

    Henneberg, Stephan C.; Jiang, Zhizhong; Naudé, Peter

    2009-01-01

    The Industrial Marketing and Purchasing (IMP) Group is a network of academic researchers working in the area of business-to-business marketing. The group meets every year to discuss and exchange ideas, with a conference having been held every year since 1984 (there was no meeting in 1987). In thi......The Industrial Marketing and Purchasing (IMP) Group is a network of academic researchers working in the area of business-to-business marketing. The group meets every year to discuss and exchange ideas, with a conference having been held every year since 1984 (there was no meeting in 1987......). In this paper, based upon the papers presented at the 22 conferences held to date, we undertake a Social Network Analysis in order to examine the degree of co-publishing that has taken place between this group of researchers. We identify the different components in this database, and examine the large main...

  15. Network cosmology.

    Science.gov (United States)

    Krioukov, Dmitri; Kitsak, Maksim; Sinkovits, Robert S; Rideout, David; Meyer, David; Boguñá, Marián

    2012-01-01

    Prediction and control of the dynamics of complex networks is a central problem in network science. Structural and dynamical similarities of different real networks suggest that some universal laws might accurately describe the dynamics of these networks, albeit the nature and common origin of such laws remain elusive. Here we show that the causal network representing the large-scale structure of spacetime in our accelerating universe is a power-law graph with strong clustering, similar to many complex networks such as the Internet, social, or biological networks. We prove that this structural similarity is a consequence of the asymptotic equivalence between the large-scale growth dynamics of complex networks and causal networks. This equivalence suggests that unexpectedly similar laws govern the dynamics of complex networks and spacetime in the universe, with implications to network science and cosmology.

  16. Biochemical investigation of cypermethrin toxicity in rabbits.

    Science.gov (United States)

    Dahamna, S; Harzallah, D; Guemache, A; Sekfali, N

    2009-01-01

    cypermethrin on the erythropoiesis. An increase of plasma enzyme activities in GOT, GPT and CPK were recorded, explain a high energy-generating product. An increase, in the plasma enzyme activity in Alkaline phosphatase, related to their role in the cell permeability. The histopathological results showed lesions and morphological changes of hepato-cellular, fibrosis and appearance of inflammatory infiltrate, confirmed disturbances of the biochemical parameters. These changes were much underlines during the animal toxicity.

  17. Biochemical profile of cuttings used for in vitro organogenesis of ...

    African Journals Online (AJOL)

    Biochemical profile of cuttings used for in vitro organogenesis of Prunus africana: An endangered species in Cameroon. JG Nzweundji, N Niemenak, O Oumar, JJ Tsafack, K Konan, L Nyochembeng, C Noumi, DT Nehemie, DO Ndoumou ...

  18. Biochemical constituents of seaweeds along the Maharashtra coast

    Digital Repository Service at National Institute of Oceanography (India)

    Dhargalkar, V.K.; Jagtap, T.G.; Untawale, A.G.

    Protein, carbohydrate and organic carbon were estimated in 43 marine algal species from different stations along the Maharashtra Coast in India These species showed variation in their biochemical contents Protein varied from 10 to 33% Chlorophyceae...

  19. Seasonal changes in biochemical composition of Holothuria leucospilota (Echinodermata)

    Digital Repository Service at National Institute of Oceanography (India)

    Jayasree, V.; Parulekar, A.H.; Wahidullah, S.; Kamat, S.Y.

    Biochemical composition of body wall and gonads of Holothuria leucospilota was analysed for protein, carbohydrate, lipid, ash, dry weight and calorific values and was discussed in relation to its spawning activities. Lipids constituted the major...

  20. Modulation of key biochemical markers relevant to stroke by Antiaris ...

    African Journals Online (AJOL)

    Modulation of key biochemical markers relevant to stroke by Antiaris africana leaf extract following cerebral ischemia/reperfusion injury. Omotayo B. Ilesanmi, Afolabi C. Akinmoladun, Olanrewaju Sam Olayeriju, Ibrahim Olabayode Saliu, M. Tolulope Olaleye, Afolabi A. Akindahunsi ...

  1. Biochemical and Histological effects of Aqueous extract of Cyperus ...

    African Journals Online (AJOL)

    ADOWIE PERE

    Biochemical and Histological effects of Triton Wr-1339 and Aqueous extract. 674. INNIH, SO; UBHENIN, AE; ... fatty liver, chronic hepatitis, and cirrhosis is not giving much ..... Alcoholic Fatty Liver Disease in Southern Iran: A Population Based ...

  2. haematological parameters and serum biochemical indices of pre

    African Journals Online (AJOL)

    mrmrsolayiwola

    2012-05-01

    BWSFM) on haematological and serum biochemical parameters in rabbit were studied. Thirty-two (32) cross-bred. (New Zealand-white X Chinchilla) male weaner rabbits aged between 6 and 9 weeks were randomly.

  3. Biochemical composition of muscle tissue of penaeid prawns

    Digital Repository Service at National Institute of Oceanography (India)

    Achuthankutty, C.T.; Parulekar, A.H.

    Biochemical composition of muscle tissue of females belonging to four species of penaeid prawns, viz. Metapenaeus affinis, M. dobsoni, Penaeus merguiensis and Parapenaeopsis stylifera, inhabiting the coastal waters of Goa, India, was estimated...

  4. A Review of the Biochemical and Haematological Effects of Caffeine ...

    African Journals Online (AJOL)

    A Review of the Biochemical and Haematological Effects of Caffeine. ... be found in different food and drinks which includes; coffee, tea, chocolate, beverages, ... when taken in excess over a period of time can result in adverse health hazards.

  5. Appraisal of biochemical and genetic diversity of mango cultivars ...

    African Journals Online (AJOL)

    Appraisal of biochemical and genetic diversity of mango cultivars using molecular markers. ... Mango (Mangifera indica L.) is one of the oldest fruit crops and is broadly cultivated worldwide. To determine the level of ... HOW TO USE AJOL.

  6. Evaluation of biochemical changes in unstimulated salivary, calcium ...

    African Journals Online (AJOL)

    TORNADO

    2012-01-26

    Jan 26, 2012 ... salivary, calcium, phosphorous and total protein during ... teins in saliva are important components and any chan- ... Sialochemical analysis .... quantities of protein utilizing the principal of protein-dye binding. Anal biochem.

  7. Diagnostic utility of clinical and biochemical parameters in ...

    African Journals Online (AJOL)

    Diagnostic utility of clinical and biochemical parameters in pancreatic head malignancy ... Department of Surgery, Sir Run Run Shaw Hospital College of Medicine, Zhejiang University, ..... technical review on the epidemiology, diagnosis, and.

  8. Anthropometric and biochemical profiles of black south african women

    African Journals Online (AJOL)

    ... with the urban diet composed of more refined carbohydrates and fatty food. ... A significant association was found between insulin sensitivity and BMI and ... anthropometric indicators, biochemical parameters, obesity, type 2 diabetes mellitus ...

  9. Haematological and serum biochemical profiles of broiler chickens ...

    African Journals Online (AJOL)

    MOLM) on the haematological and serum biochemical profile of broiler chickens. Fresh Moringa leaves (FML) were shade-dried for four days and milled into meal. A total of two hundred broilers unsexed chickens (Anak strain) were randomly ...

  10. Effect of Probiotics on Serum Biochemical and Blood Constituents in ...

    African Journals Online (AJOL)

    Department of Animal Production, College of Food and Agriculture Sciences, King ... enzyme activities, and hematological and biochemical indices of broiler chickens challenged with ..... Brancaster and Enteritidis from humans and broiler.

  11. Growth and Biochemical performance of Cassava-Manihot ...

    African Journals Online (AJOL)

    MICHAEL HORSFALL

    the crude oil polluted soil improved the growth and biochemical performance of cassava. For the qualitative .... delay in the rate of soil recovery and a decrease in crop yield ... enhances biodegradation of polluted soil presumably by removing ...

  12. Anthropometric and Biochemical Profiles of Black South African ...

    African Journals Online (AJOL)

    Rev Dr Olaleye

    Anthropometric and biochemical profiles were determined according to standard methods. From the ... Email: bejufemi@yahoo.co.uk ... 995 plots, Pahameng 1 711, Joe Slovo 1 359, and. Botchabela 2 ...... York: John Wiley & Sons, Inc. Steyn K ...

  13. Decoupling of Growth from Production of Biochemicals and Proteins

    DEFF Research Database (Denmark)

    Li, Songyuan

    With increasing awareness of sustainability in our current society, alternative approaches to produce fuels and petro-derived chemicals are required. Biofuels and biochemicals produced from microbial cell factories provide an alternative to current fossil based chemicals. Meanwhile, microbial cell...

  14. 2011 Biomass Program Platform Peer Review: Biochemical Conversion

    Energy Technology Data Exchange (ETDEWEB)

    Pezzullo, Leslie [Office of Energy Efficiency and Renewable Energy (EERE), Washington, DC (United States)

    2012-02-01

    This document summarizes the recommendations and evaluations provided by an independent external panel of experts at the 2011 U.S. Department of Energy Biomass Program’s Biochemical Conversion Platform Review meeting.

  15. Biochemical and Haematological Indices of Weanly Albino Rats Fed ...

    African Journals Online (AJOL)

    acer

    ABSTRACT: Malnutrition is a public health problem in Nigeria accounting for more than 50% of ... weanly albino rats using nutritional, biochemical ... groundnut (16%), soy beans (16%), crayfish ... consumption was observed in rats on PC and.

  16. Biochemical evaluation of Gmelina arborea fruit meal as a swine ...

    African Journals Online (AJOL)

    Dr. J. T. Ekanem

    Division of Nutritional Biochemistry, Department of Animal Production,. University of Ilorin ... certain biochemical parameters including blood enzyme profile of wean pigs. 16-piglets ..... 1992) who reported similar results in guinea fowls fed test ...

  17. Biochemical methane potential (BMP) of solid organic materials

    DEFF Research Database (Denmark)

    Raposo, Francisco; Fernández-Cegrí, V.; De la Rubia, M.A.

    2010-01-01

    This paper describes the results obtained for different participating research groups in an interlaboratory study related to the biochemical methane potential (BMP). In this research work, the full experimental conditions influencing the test such as inoculum, substrate characteristics and experi...

  18. Psoriatic arthritis: An assessment of clinical, biochemical and ...

    African Journals Online (AJOL)

    , epidemiological, clinical and radiological studies of South African (SA) patients are scarce. Objectives. To assess clinical, biochemical and radiological features in a single-centre SA cohort. Methods. We conducted a prospective assessment ...

  19. an improved solution of first order kinetics for biochemical oxygen ...

    African Journals Online (AJOL)

    DELL

    Accuracies of these methods were evaluated using relative error, Akaike ... Keywords: Wastewater, Environmental Engineering, Biochemical Oxygen Demand Kinetic Parameters,. Statistical ... evaluating organic pollution level and quality of wastewaters. ... compounds ...... method can be applied on electronic devices, and.

  20. Biochem-Env, a plateform of environmental biochemistry for research

    OpenAIRE

    GRONDIN, VIRGINIE; Nelieu, Sylvie; Crouzet, Olivier; Hedde, Mickaël; Mougin, Christian

    2016-01-01

    As a service of the research infrastructure AnaEE-France (http://www.anaee-france.fr/fr/), the platform Biochem-Env (http://www.biochemenv.fr) offers skills and innovative analytical tools for biochemical characterizations of soils, sediments, and micro-macro-organisms living in terrestrial and aquatic ecosystems. The platform provides methods validated according to Quality Guidelines, i.e. to measure global soil enzymatic activities. Our robot-supported protocols allow great number of enzyme...

  1. Biochemical basis for the action of radioprotective drugs

    International Nuclear Information System (INIS)

    Romantsev, E.F.; Blokhina, V.D.; Zhulanova, Z.I.; Koshcheenko, N.N.; Filippovich, I.V.

    1977-01-01

    The hypothesis of complex biochemical mechanism of action of radioprotective drugs is described. Shortly after injection of radioprotective aminothiols into animals the inhibition of radiosensitive biochemical processes: DNA and RNA synthesis, protein synthesis and oxidative phosphorylation has been observed. The molecular mechanism of these phenomena consists of radioprotectors ability to form adsorption, thioester, amide, and disulphide bonds with appropriate enzymes. The curve reflecting the formation and breakdown of mixed disulphides between radioprotectors and proteins coincides well with that reflecting the radioprotective effect dependence on time. The radiobiological significance of molecular interactions observed may be interpreted as the diminution in ''spoiled'' molecules formation (inhibition of replication) and elevation in repartion rate. The inhibition of biochemical processes has the reversible nature and last for short time. The drugs acting according to so-called oxygen effect protect also by means of biochemical mechanisms. The molecular mechanism is mediated through their ability to bind to receptors, and biologically important molecules and macromolecules. As a result the inhibition of radiosensitive processes occurs, the ''spoiled'' molecules number is diminished and reparation takes place more easily. The idea on the complex biochemical mechanism of action of radioprotectors correlates with the proposal on complex biochemical mechanism responsible for interphase death occured after irradiation

  2. A comparison of approximation techniques for variance-based sensitivity analysis of biochemical reaction systems

    Directory of Open Access Journals (Sweden)

    Goutsias John

    2010-05-01

    Full Text Available Abstract Background Sensitivity analysis is an indispensable tool for the analysis of complex systems. In a recent paper, we have introduced a thermodynamically consistent variance-based sensitivity analysis approach for studying the robustness and fragility properties of biochemical reaction systems under uncertainty in the standard chemical potentials of the activated complexes of the reactions and the standard chemical potentials of the molecular species. In that approach, key sensitivity indices were estimated by Monte Carlo sampling, which is computationally very demanding and impractical for large biochemical reaction systems. Computationally efficient algorithms are needed to make variance-based sensitivity analysis applicable to realistic cellular networks, modeled by biochemical reaction systems that consist of a large number of reactions and molecular species. Results We present four techniques, derivative approximation (DA, polynomial approximation (PA, Gauss-Hermite integration (GHI, and orthonormal Hermite approximation (OHA, for analytically approximating the variance-based sensitivity indices associated with a biochemical reaction system. By using a well-known model of the mitogen-activated protein kinase signaling cascade as a case study, we numerically compare the approximation quality of these techniques against traditional Monte Carlo sampling. Our results indicate that, although DA is computationally the most attractive technique, special care should be exercised when using it for sensitivity analysis, since it may only be accurate at low levels of uncertainty. On the other hand, PA, GHI, and OHA are computationally more demanding than DA but can work well at high levels of uncertainty. GHI results in a slightly better accuracy than PA, but it is more difficult to implement. OHA produces the most accurate approximation results and can be implemented in a straightforward manner. It turns out that the computational cost of the

  3. Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli.

    Directory of Open Access Journals (Sweden)

    Melody K Morris

    2011-03-01

    Full Text Available Predictive understanding of cell signaling network operation based on general prior knowledge but consistent with empirical data in a specific environmental context is a current challenge in computational biology. Recent work has demonstrated that Boolean logic can be used to create context-specific network models by training proteomic pathway maps to dedicated biochemical data; however, the Boolean formalism is restricted to characterizing protein species as either fully active or inactive. To advance beyond this limitation, we propose a novel form of fuzzy logic sufficiently flexible to model quantitative data but also sufficiently simple to efficiently construct models by training pathway maps on dedicated experimental measurements. Our new approach, termed constrained fuzzy logic (cFL, converts a prior knowledge network (obtained from literature or interactome databases into a computable model that describes graded values of protein activation across multiple pathways. We train a cFL-converted network to experimental data describing hepatocytic protein activation by inflammatory cytokines and demonstrate the application of the resultant trained models for three important purposes: (a generating experimentally testable biological hypotheses concerning pathway crosstalk, (b establishing capability for quantitative prediction of protein activity, and (c prediction and understanding of the cytokine release phenotypic response. Our methodology systematically and quantitatively trains a protein pathway map summarizing curated literature to context-specific biochemical data. This process generates a computable model yielding successful prediction of new test data and offering biological insight into complex datasets that are difficult to fully analyze by intuition alone.

  4. Multistate Model Builder (MSMB): a flexible editor for compact biochemical models.

    Science.gov (United States)

    Palmisano, Alida; Hoops, Stefan; Watson, Layne T; Jones, Thomas C; Tyson, John J; Shaffer, Clifford A

    2014-04-04

    Building models of molecular regulatory networks is challenging not just because of the intrinsic difficulty of describing complex biological processes. Writing a model is a creative effort that calls for more flexibility and interactive support than offered by many of today's biochemical model editors. Our model editor MSMB - Multistate Model Builder - supports multistate models created using different modeling styles. MSMB provides two separate advances on existing network model editors. (1) A simple but powerful syntax is used to describe multistate species. This reduces the number of reactions needed to represent certain molecular systems, thereby reducing the complexity of model creation. (2) Extensive feedback is given during all stages of the model creation process on the existing state of the model. Users may activate error notifications of varying stringency on the fly, and use these messages as a guide toward a consistent, syntactically correct model. MSMB default values and behavior during model manipulation (e.g., when renaming or deleting an element) can be adapted to suit the modeler, thus supporting creativity rather than interfering with it. MSMB's internal model representation allows saving a model with errors and inconsistencies (e.g., an undefined function argument; a syntactically malformed reaction). A consistent model can be exported to SBML or COPASI formats. We show the effectiveness of MSMB's multistate syntax through models of the cell cycle and mRNA transcription. Using multistate reactions reduces the number of reactions need to encode many biochemical network models. This reduces the cognitive load for a given model, thereby making it easier for modelers to build more complex models. The many interactive editing support features provided by MSMB make it easier for modelers to create syntactically valid models, thus speeding model creation. Complete information and the installation package can be found at http

  5. Telecommunication networks

    CERN Document Server

    Iannone, Eugenio

    2011-01-01

    Many argue that telecommunications network infrastructure is the most impressive and important technology ever developed. Analyzing the telecom market's constantly evolving trends, research directions, infrastructure, and vital needs, Telecommunication Networks responds with revolutionized engineering strategies to optimize network construction. Omnipresent in society, telecom networks integrate a wide range of technologies. These include quantum field theory for the study of optical amplifiers, software architectures for network control, abstract algebra required to design error correction co

  6. Activating and inhibiting connections in biological network dynamics

    Directory of Open Access Journals (Sweden)

    Knight Rob

    2008-12-01

    Full Text Available Abstract Background Many studies of biochemical networks have analyzed network topology. Such work has suggested that specific types of network wiring may increase network robustness and therefore confer a selective advantage. However, knowledge of network topology does not allow one to predict network dynamical behavior – for example, whether deleting a protein from a signaling network would maintain the network's dynamical behavior, or induce oscillations or chaos. Results Here we report that the balance between activating and inhibiting connections is important in determining whether network dynamics reach steady state or oscillate. We use a simple dynamical model of a network of interacting genes or proteins. Using the model, we study random networks, networks selected for robust dynamics, and examples of biological network topologies. The fraction of activating connections influences whether the network dynamics reach steady state or oscillate. Conclusion The activating fraction may predispose a network to oscillate or reach steady state, and neutral evolution or selection of this parameter may affect the behavior of biological networks. This principle may unify the dynamics of a wide range of cellular networks. Reviewers Reviewed by Sergei Maslov, Eugene Koonin, and Yu (Brandon Xia (nominated by Mark Gerstein. For the full reviews, please go to the Reviewers' comments section.

  7. Biochemical failure after radical external beam radiotherapy for prostate cancer

    International Nuclear Information System (INIS)

    Nomoto, Satoshi; Imada, Hajime; Kato, Fumio; Yahara, Katsuya; Morioka, Tomoaki; Ohguri, Takayuki; Nakano, Keita; Korogi, Yukunori

    2005-01-01

    The purpose of this study was to evaluate biochemical failures after radical external beam radiotherapy for prostate cancer. A total of 143 patients with prostate cancer (5 cases in stage A2, 95 in stage B and 43 in stage C; 18 in low risk group, 37 in intermediate risk group, 67 in high risk group and 21 in unknown group) were included in this study. Patients of stage A2 and B underwent external irradiation of 46 Gy to the prostate gland and seminal vesicle and additional 20 Gy to the prostate gland, while patients of stage C underwent external irradiation of 66 Gy to the prostate gland and seminal vesicle including 46 Gy to the pelvis. Neoadjuvant hormonal therapy was done in 66 cases, and long-term hormonal therapy in 75 cases; two cases were treated with radiation therapy alone. The 3-year relapse free survival rates by stage A2, B and C were 100%, 96.7% and 88.1%, respectively. The 3-year relapse free survival rates by low, intermediate and high risk groups were 100%, 92.3% and 89.7%, respectively. Biochemical failure was noted in nine cases during the average observation term of 32.2 months; in this group the median of prostate specific antigen (PSA) value was 2.6 ng/ml, the doubling time was 8.6 months, and the term of biochemical failure was 33.2 months. Six of eight cases with biochemical failure were the neoadjuvant hormonal therapy group, but biochemical no evidence of disease (bNED) curve showed no significant difference between neoadjuvant and long-term hormonal groups. It is supposed that unnecessary hormonal therapies were performed based on the nonspecific diagnosis of biochemical failure after radical radiotherapy in our group of patients. A precise criterion of biochemical failure after radical radiotherapy for prostate cancer is necessary. (author)

  8. Temporal networks

    CERN Document Server

    Saramäki, Jari

    2013-01-01

    The concept of temporal networks is an extension of complex networks as a modeling framework to include information on when interactions between nodes happen. Many studies of the last decade examine how the static network structure affect dynamic systems on the network. In this traditional approach  the temporal aspects are pre-encoded in the dynamic system model. Temporal-network methods, on the other hand, lift the temporal information from the level of system dynamics to the mathematical representation of the contact network itself. This framework becomes particularly useful for cases where there is a lot of structure and heterogeneity both in the timings of interaction events and the network topology. The advantage compared to common static network approaches is the ability to design more accurate models in order to explain and predict large-scale dynamic phenomena (such as, e.g., epidemic outbreaks and other spreading phenomena). On the other hand, temporal network methods are mathematically and concept...

  9. Interconnected networks

    CERN Document Server

    2016-01-01

    This volume provides an introduction to and overview of the emerging field of interconnected networks which include multi layer or multiplex networks, as well as networks of networks. Such networks present structural and dynamical features quite different from those observed in isolated networks. The presence of links between different networks or layers of a network typically alters the way such interconnected networks behave – understanding the role of interconnecting links is therefore a crucial step towards a more accurate description of real-world systems. While examples of such dissimilar properties are becoming more abundant – for example regarding diffusion, robustness and competition – the root of such differences remains to be elucidated. Each chapter in this topical collection is self-contained and can be read on its own, thus making it also suitable as reference for experienced researchers wishing to focus on a particular topic.

  10. Network maintenance

    CERN Multimedia

    GS Department

    2009-01-01

    A site-wide network maintenance operation has been scheduled for Saturday 28 February. Most of the network devices of the general purpose network will be upgraded to a newer software version, in order to improve our network monitoring capabilities. This will result in a series of short (2-5 minutes) random interruptions everywhere on the CERN sites throughout the day. This upgrade will not affect the Computer Centre itself, Building 613, the Technical Network and the LHC experiments, dedicated networks at the pits. For further details of this intervention, please contact Netops by phone 74927 or e-mail mailto:Netops@cern.ch. IT/CS Group

  11. Network maintenance

    CERN Multimedia

    IT Department

    2009-01-01

    A site wide network maintenance has been scheduled for Saturday 28 February. Most of the network devices of the General Purpose network will be upgraded to a newer software version, in order to improve our network monitoring capabilities. This will result in a series of short (2-5 minutes) random interruptions everywhere on the CERN sites along this day. This upgrade will not affect: the Computer centre itself, building 613, the Technical Network and the LHC experiments dedicated networks at the pits. Should you need more details on this intervention, please contact Netops by phone 74927 or email mailto:Netops@cern.ch. IT/CS Group

  12. Evolving phenotypic networks in silico.

    Science.gov (United States)

    François, Paul

    2014-11-01

    Evolved gene networks are constrained by natural selection. Their structures and functions are consequently far from being random, as exemplified by the multiple instances of parallel/convergent evolution. One can thus ask if features of actual gene networks can be recovered from evolutionary first principles. I review a method for in silico evolution of small models of gene networks aiming at performing predefined biological functions. I summarize the current implementation of the algorithm, insisting on the construction of a proper "fitness" function. I illustrate the approach on three examples: biochemical adaptation, ligand discrimination and vertebrate segmentation (somitogenesis). While the structure of the evolved networks is variable, dynamics of our evolved networks are usually constrained and present many similar features to actual gene networks, including properties that were not explicitly selected for. In silico evolution can thus be used to predict biological behaviours without a detailed knowledge of the mapping between genotype and phenotype. Copyright © 2014 The Author. Published by Elsevier Ltd.. All rights reserved.

  13. Sublethal microcystin exposure and biochemical outcomes among hemodialysis patients.

    Directory of Open Access Journals (Sweden)

    Elizabeth D Hilborn

    Full Text Available Cyanobacteria are commonly-occurring contaminants of surface waters worldwide. Microcystins, potent hepatotoxins, are among the best characterized cyanotoxins. During November, 2001, a group of 44 hemodialysis patients were exposed to microcystins via contaminated dialysate. Serum microcystin concentrations were quantified with enzyme-linked immunosorbent assay which measures free serum microcystin LR equivalents (ME. We describe serum ME concentrations and biochemical outcomes among a subset of patients during 8 weeks following exposure. Thirteen patients were included; 6 were males, patients' median age was 45 years (range 16-80, one was seropositive for hepatitis B surface antigen. The median serum ME concentration was 0.33 ng/mL (range: <0.16-0.96. One hundred thirty nine blood samples were collected following exposure. Patients' biochemical outcomes varied, but overall indicated a mixed liver injury. Linear regression evaluated each patient's weekly mean biochemical outcome with their maximum serum ME concentration; a measure of the extrinsic pathway of clotting function, prothrombin time, was negatively and significantly associated with serum ME concentrations. This group of exposed patients' biochemical outcomes display evidence of a mixed liver injury temporally associated with microcystin exposure. Interpretation of biochemical outcomes are complicated by the study population's underlying chronic disease status. It is clear that dialysis patients are a distinct 'at risk' group for cyanotoxin exposures due to direct intravenous exposure to dialysate prepared from surface drinking water supplies. Careful monitoring and treatment of water supplies used to prepare dialysate is required to prevent future cyanotoxin exposure events.

  14. Network Ambivalence

    Directory of Open Access Journals (Sweden)

    Patrick Jagoda

    2015-08-01

    Full Text Available The language of networks now describes everything from the Internet to the economy to terrorist organizations. In distinction to a common view of networks as a universal, originary, or necessary form that promises to explain everything from neural structures to online traffic, this essay emphasizes the contingency of the network imaginary. Network form, in its role as our current cultural dominant, makes scarcely imaginable the possibility of an alternative or an outside uninflected by networks. If so many things and relationships are figured as networks, however, then what is not a network? If a network points towards particular logics and qualities of relation in our historical present, what others might we envision in the future? In  many ways, these questions are unanswerable from within the contemporary moment. Instead of seeking an avant-garde approach (to move beyond networks or opting out of networks (in some cases, to recover elements of pre-networked existence, this essay proposes a third orientation: one of ambivalence that operates as a mode of extreme presence. I propose the concept of "network aesthetics," which can be tracked across artistic media and cultural forms, as a model, style, and pedagogy for approaching interconnection in the twenty-first century. The following essay is excerpted from Network Ambivalence (Forthcoming from University of Chicago Press. 

  15. Near-infrared Raman spectroscopy for estimating biochemical changes associated with different pathological conditions of cervix

    Science.gov (United States)

    Daniel, Amuthachelvi; Prakasarao, Aruna; Ganesan, Singaravelu

    2018-02-01

    The molecular level changes associated with oncogenesis precede the morphological changes in cells and tissues. Hence molecular level diagnosis would promote early diagnosis of the disease. Raman spectroscopy is capable of providing specific spectral signature of various biomolecules present in the cells and tissues under various pathological conditions. The aim of this work is to develop a non-linear multi-class statistical methodology for discrimination of normal, neoplastic and malignant cells/tissues. The tissues were classified as normal, pre-malignant and malignant by employing Principal Component Analysis followed by Artificial Neural Network (PC-ANN). The overall accuracy achieved was 99%. Further, to get an insight into the quantitative biochemical composition of the normal, neoplastic and malignant tissues, a linear combination of the major biochemicals by non-negative least squares technique was fit to the measured Raman spectra of the tissues. This technique confirms the changes in the major biomolecules such as lipids, nucleic acids, actin, glycogen and collagen associated with the different pathological conditions. To study the efficacy of this technique in comparison with histopathology, we have utilized Principal Component followed by Linear Discriminant Analysis (PC-LDA) to discriminate the well differentiated, moderately differentiated and poorly differentiated squamous cell carcinoma with an accuracy of 94.0%. And the results demonstrated that Raman spectroscopy has the potential to complement the good old technique of histopathology.

  16. Network workshop

    DEFF Research Database (Denmark)

    Bruun, Jesper; Evans, Robert Harry

    2014-01-01

    This paper describes the background for, realisation of and author reflections on a network workshop held at ESERA2013. As a new research area in science education, networks offer a unique opportunity to visualise and find patterns and relationships in complicated social or academic network data....... These include student relations and interactions and epistemic and linguistic networks of words, concepts and actions. Network methodology has already found use in science education research. However, while networks hold the potential for new insights, they have not yet found wide use in the science education...... research community. With this workshop, participants were offered a way into network science based on authentic educational research data. The workshop was constructed as an inquiry lesson with emphasis on user autonomy. Learning activities had participants choose to work with one of two cases of networks...

  17. Network Convergence

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. Network Convergence. User is interested in application and content - not technical means of distribution. Boundaries between distribution channels fade out. Network convergence leads to seamless application and content solutions.

  18. Industrial Networks

    DEFF Research Database (Denmark)

    Karlsson, Christer

    2015-01-01

    Companies organize in a way that involves many activities that are external to the traditional organizational boundaries. This presents challenges to operations management and managing operations involves many issues and actions dealing with external networks. Taking a network perspective changes...

  19. Network Science

    National Research Council Canada - National Science Library

    Leland, Will

    2006-01-01

    OVERVIEW: (1) A committee of technical experts, military officers and R&D managers was assembled by the National Research Council to reach consensus on the nature of networks and network research. (2...

  20. Changes in Biochemical Properties of the Blood in Winter Swimmers.

    Science.gov (United States)

    Teleglow, Aneta; Marchewka, Jakub; Marchewka, Anna; Kulpa, Jan

    The aim of the study was to investigate the effects of winter swimming on biochemical indicators of the blood. The subjects - winter swimmers - belonged to the Krakow Walrus Club "Kaloryfer" - "The Heater". The study group consisted of 11 men, aged 30-50 years, 'walrusing' throughout the whole season from November to March. Statistically significant changes throughout the 'walrusing' season were observed for the following biochemical parameters: a decrease in sodium (mmol/1), chloride (mmol/1), alpha-2 globulin(g/1), gamma globulin (g/1), IgG (g/1), and an increase in albumin (g/1), indicator A/G, IgA (g/l ), Herpes simplex virus IgM. Seasonal effort of winter swimmers has a positive influence on biochemical blood parameters.

  1. Designing Epigenome Editors: Considerations of Biochemical and Locus Specificities.

    Science.gov (United States)

    Sen, Dilara; Keung, Albert J

    2018-01-01

    The advent of locus-specific protein recruitment technologies has enabled a new class of studies in chromatin biology. Epigenome editors enable biochemical modifications of chromatin at almost any specific endogenous locus. Their locus specificity unlocks unique information including the functional roles of distinct modifications at specific genomic loci. Given the growing interest in using these tools for biological and translational studies, there are many specific design considerations depending on the scientific question or clinical need. Here we present and discuss important design considerations and challenges regarding the biochemical and locus specificities of epigenome editors. These include how to account for the complex biochemical diversity of chromatin; control for potential interdependency of epigenome editors and their resultant modifications; avoid sequestration effects; quantify the locus specificity of epigenome editors; and improve locus specificity by considering concentration, affinity, avidity, and sequestration effects.

  2. Network Coded Software Defined Networking

    DEFF Research Database (Denmark)

    Krigslund, Jeppe; Hansen, Jonas; Roetter, Daniel Enrique Lucani

    2015-01-01

    Software Defined Networking (SDN) and Network Coding (NC) are two key concepts in networking that have garnered a large attention in recent years. On the one hand, SDN's potential to virtualize services in the Internet allows a large flexibility not only for routing data, but also to manage....... This paper advocates for the use of SDN to bring about future Internet and 5G network services by incorporating network coding (NC) functionalities. The inherent flexibility of both SDN and NC provides a fertile ground to envision more efficient, robust, and secure networking designs, that may also...

  3. Network Simulation

    CERN Document Server

    Fujimoto, Richard

    2006-01-01

    "Network Simulation" presents a detailed introduction to the design, implementation, and use of network simulation tools. Discussion topics include the requirements and issues faced for simulator design and use in wired networks, wireless networks, distributed simulation environments, and fluid model abstractions. Several existing simulations are given as examples, with details regarding design decisions and why those decisions were made. Issues regarding performance and scalability are discussed in detail, describing how one can utilize distributed simulation methods to increase the

  4. Accessible methods for the dynamic time-scale decomposition of biochemical systems.

    Science.gov (United States)

    Surovtsova, Irina; Simus, Natalia; Lorenz, Thomas; König, Artjom; Sahle, Sven; Kummer, Ursula

    2009-11-01

    The growing complexity of biochemical models asks for means to rationally dissect the networks into meaningful and rather independent subnetworks. Such foregoing should ensure an understanding of the system without any heuristics employed. Important for the success of such an approach is its accessibility and the clarity of the presentation of the results. In order to achieve this goal, we developed a method which is a modification of the classical approach of time-scale separation. This modified method as well as the more classical approach have been implemented for time-dependent application within the widely used software COPASI. The implementation includes different possibilities for the representation of the results including 3D-visualization. The methods are included in COPASI which is free for academic use and available at www.copasi.org. irina.surovtsova@bioquant.uni-heidelberg.de Supplementary data are available at Bioinformatics online.

  5. Biochemical System Analysis of Lutein Production by Heterotrophic Chlorella pyrenoidosa in a Fermentor

    Directory of Open Access Journals (Sweden)

    Zheng-Yun Wu

    2009-01-01

    Full Text Available Chlorella is a promising alternative source of lutein, as it can be cultivated heterotrophically with high efficiency. In this study, the carotenoids in Chlorella pyrenoidosa heterotrophically cultivated in a 19-litre fermentor have been analyzed and determined by using HPLC and HPLC-MS. A biochemical system theory (BST model was developed for understanding the regulatory features of carotenoid metabolism during the batch cultivation. Factors that influence lutein production by C. pyrenoidosa were discussed based on the model. It shows that low flux for lycopene formation is the major bottleneck for lutein production, while by-product syntheses and inhibitions affect the cellular lutein content much less. However, with further increase of the cellular lutein content, the inhibition on lycopene formation by lutein may become a limiting factor. Although speculative, these results may provide useful information for further elucidation of the regulatory mechanisms of carotenoid biosynthesis in Chlorella and modifying its metabolic network to enhance lutein production.

  6. Simulation of biochemical reactions with time-dependent rates by the rejection-based algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Thanh, Vo Hong, E-mail: vo@cosbi.eu [The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, Rovereto 38068 (Italy); Priami, Corrado, E-mail: priami@cosbi.eu [The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, Rovereto 38068 (Italy); Department of Mathematics, University of Trento, Trento (Italy)

    2015-08-07

    We address the problem of simulating biochemical reaction networks with time-dependent rates and propose a new algorithm based on our rejection-based stochastic simulation algorithm (RSSA) [Thanh et al., J. Chem. Phys. 141(13), 134116 (2014)]. The computation for selecting next reaction firings by our time-dependent RSSA (tRSSA) is computationally efficient. Furthermore, the generated trajectory is exact by exploiting the rejection-based mechanism. We benchmark tRSSA on different biological systems with varying forms of reaction rates to demonstrate its applicability and efficiency. We reveal that for nontrivial cases, the selection of reaction firings in existing algorithms introduces approximations because the integration of reaction rates is very computationally demanding and simplifying assumptions are introduced. The selection of the next reaction firing by our approach is easier while preserving the exactness.

  7. Soft Measurement Modeling Based on Chaos Theory for Biochemical Oxygen Demand (BOD

    Directory of Open Access Journals (Sweden)

    Junfei Qiao

    2016-12-01

    Full Text Available The precision of soft measurement for biochemical oxygen demand (BOD is always restricted due to various factors in the wastewater treatment plant (WWTP. To solve this problem, a new soft measurement modeling method based on chaos theory is proposed and is applied to BOD measurement in this paper. Phase space reconstruction (PSR based on Takens embedding theorem is used to extract more information from the limited datasets of the chaotic system. The WWTP is first testified as a chaotic system by the correlation dimension (D, the largest Lyapunov exponents (λ1, the Kolmogorov entropy (K of the BOD and other water quality parameters time series. Multivariate chaotic time series modeling method with principal component analysis (PCA and artificial neural network (ANN is then adopted to estimate the value of the effluent BOD. Simulation results show that the proposed approach has higher accuracy and better prediction ability than the corresponding modeling approaches not based on chaos theory.

  8. Lignin plays a negative role in the biochemical process for producing lignocellulosic biofuels.

    Science.gov (United States)

    Zeng, Yining; Zhao, Shuai; Yang, Shihui; Ding, Shi-You

    2014-06-01

    A biochemical platform holds the most promising route toward lignocellulosic biofuels, in which polysaccharides are hydrolyzed by cellulase enzymes into simple sugars and fermented to ethanol by microbes. However, these polysaccharides are cross-linked in the plant cell walls with the hydrophobic network of lignin that physically impedes enzymatic deconstruction. A thermochemical pretreatment process is often required to remove or delocalize lignin, which may also generate inhibitors that hamper enzymatic hydrolysis and fermentation. Here we review recent advances in understanding lignin structure in the plant cell walls and the negative roles of lignin in the processes of converting biomass to biofuels. Perspectives and future directions to improve the biomass conversion process are also discussed. Copyright © 2013. Published by Elsevier Ltd.

  9. From chemical or biochemical microsensors to fast detection systems

    International Nuclear Information System (INIS)

    Pistre, J.; Dejous, C.; Rebiere, D.

    2011-01-01

    The market of chemical and biochemical sensors is increasing and represents a large opportunity. The problem of chemical and biochemicaldetection involves the use of one/several transducing layer/interface. Several types of detection exist. Among them, acoustic wave devices present many advantages. The paper deals with surface acoustic waves devices and their implementation. The role and properties of the sensing layer are discussed for chemical sensors and biochemical sensors as well. Examples of realizations are presented taking into account the microfluidic approach.

  10. Diagnosis Of Inherited Neurometabolic Disorders : A Biochemical Approach

    Directory of Open Access Journals (Sweden)

    Christopher R

    1999-01-01

    Full Text Available The past two decades have witnessed a rapid increase in the knowledge of the inherited neurometabolic disorders. The precise diagnosis of these disorders which is a challenge to the physician can be best accomplished by biochemical methods. Screening of clinically selected patients with simple chemical urine tests and routine blood chemistry investigations followed by measurement of specific metabolites and assay of the relevant enzymes confirms the diagnosis in most cases. Biochemical diagnosis of inherited neurometabolic disorders although expensive is rapid and confirmatory and therefore aids in treatment and further prevention of these rare disorders.

  11. Physiological and molecular biochemical mechanisms of bile formation

    Science.gov (United States)

    Reshetnyak, Vasiliy Ivanovich

    2013-01-01

    This review considers the physiological and molecular biochemical mechanisms of bile formation. The composition of bile and structure of a bile canaliculus, biosynthesis and conjugation of bile acids, bile phospholipids, formation of bile micellar structures, and enterohepatic circulation of bile acids are described. In general, the review focuses on the molecular physiology of the transporting systems of the hepatocyte sinusoidal and apical membranes. Knowledge of physiological and biochemical basis of bile formation has implications for understanding the mechanisms of development of pathological processes, associated with diseases of the liver and biliary tract. PMID:24259965

  12. Teaching Biochemical Pathways Using Concept Maps

    Directory of Open Access Journals (Sweden)

    Simon Brown

    2013-08-01

    Full Text Available The interesting paper by Dinarvand and Vaisi-Raygan (1 makes valuable points about a particularly challenging aspect of biochemistry learning and teaching. Their work prompts me to ask two questions and make a comment. First, what do the authors mean by a concept map (CM? A pathway map could be considered a CM, but a CM could cover modes of regulation and kinetics in relation to particular reactions or pathways and there are many other possibilities. Irrespective of this, a CM can get extremely complex if more than a few concepts are involved (2, as can be seen in examples given by Novak (3. This is the fundamental problem of teaching and learning biochemistry (4, which combines the network of pathways, compartmentation, macromol¬ecular structure, regulation, kinetics and some fairly sophisticated chemical concepts.Second, how did the students go about preparing CMs? My experience is that students prefer to use a computer for most tasks, but standard CM software (5 may not be suitable. For example, they often struggle unnec¬essarily to use software to prepare a graphical summary of the structural features of a protein, its precursors and the gene encoding it. This distracts them from the material. My suggestions that pencil and paper might be sufficient are usually met with amazement. Third, as Dinarvand and Vaisi-Raygan (1 make clear, a coherent summary of the metabolism considered in a course in metabolic biochemistry is crucial if students are to appreciate the pathways and their interconn-ection and regulation. For many years I have used an approach in which students collaborate in tutorials to achieve this. The sessions are usually initiated by me drawing the plasma membrane and the mitochondrial membranes on a large board and inviting the students to fill in the blanks (I provide large sheets of paper so that students can make copies. With coaxing, someone volunteers and I explain that the volunteer is not alone because everyone is

  13. Technical Network

    CERN Multimedia

    2007-01-01

    In order to optimise the management of the Technical Network (TN), to facilitate understanding of the purpose of devices connected to the TN and to improve security incident handling, the Technical Network Administrators and the CNIC WG have asked IT/CS to verify the "description" and "tag" fields of devices connected to the TN. Therefore, persons responsible for systems connected to the TN will receive e-mails from IT/CS asking them to add the corresponding information in the network database at "network-cern-ch". Thank you very much for your cooperation. The Technical Network Administrators & the CNIC WG

  14. Spatial networks

    Science.gov (United States)

    Barthélemy, Marc

    2011-02-01

    Complex systems are very often organized under the form of networks where nodes and edges are embedded in space. Transportation and mobility networks, Internet, mobile phone networks, power grids, social and contact networks, and neural networks, are all examples where space is relevant and where topology alone does not contain all the information. Characterizing and understanding the structure and the evolution of spatial networks is thus crucial for many different fields, ranging from urbanism to epidemiology. An important consequence of space on networks is that there is a cost associated with the length of edges which in turn has dramatic effects on the topological structure of these networks. We will thoroughly explain the current state of our understanding of how the spatial constraints affect the structure and properties of these networks. We will review the most recent empirical observations and the most important models of spatial networks. We will also discuss various processes which take place on these spatial networks, such as phase transitions, random walks, synchronization, navigation, resilience, and disease spread.

  15. Network science

    CERN Document Server

    Barabasi, Albert-Laszlo

    2016-01-01

    Networks are everywhere, from the Internet, to social networks, and the genetic networks that determine our biological existence. Illustrated throughout in full colour, this pioneering textbook, spanning a wide range of topics from physics to computer science, engineering, economics and the social sciences, introduces network science to an interdisciplinary audience. From the origins of the six degrees of separation to explaining why networks are robust to random failures, the author explores how viruses like Ebola and H1N1 spread, and why it is that our friends have more friends than we do. Using numerous real-world examples, this innovatively designed text includes clear delineation between undergraduate and graduate level material. The mathematical formulas and derivations are included within Advanced Topics sections, enabling use at a range of levels. Extensive online resources, including films and software for network analysis, make this a multifaceted companion for anyone with an interest in network sci...

  16. Vulnerability of network of networks

    Science.gov (United States)

    Havlin, S.; Kenett, D. Y.; Bashan, A.; Gao, J.; Stanley, H. E.

    2014-10-01

    Our dependence on networks - be they infrastructure, economic, social or others - leaves us prone to crises caused by the vulnerabilities of these networks. There is a great need to develop new methods to protect infrastructure networks and prevent cascade of failures (especially in cases of coupled networks). Terrorist attacks on transportation networks have traumatized modern societies. With a single blast, it has become possible to paralyze airline traffic, electric power supply, ground transportation or Internet communication. How, and at which cost can one restructure the network such that it will become more robust against malicious attacks? The gradual increase in attacks on the networks society depends on - Internet, mobile phone, transportation, air travel, banking, etc. - emphasize the need to develop new strategies to protect and defend these crucial networks of communication and infrastructure networks. One example is the threat of liquid explosives a few years ago, which completely shut down air travel for days, and has created extreme changes in regulations. Such threats and dangers warrant the need for new tools and strategies to defend critical infrastructure. In this paper we review recent advances in the theoretical understanding of the vulnerabilities of interdependent networks with and without spatial embedding, attack strategies and their affect on such networks of networks as well as recently developed strategies to optimize and repair failures caused by such attacks.

  17. biochemical and haematological findings in alcohol consumers in Ile

    African Journals Online (AJOL)

    Administrator

    Effect of drinking patterns on biochemical and haematological parameters was conducted on ... disease depends on a variety of factors, including genetic ... by cirrhosis, cancer and violent deaths. .... (1985) stated that the marked influence of alcohol ... The relationship between alcohol consumption, health indicators and.

  18. Effect of Probiotics on Serum Biochemical and Blood Constituents in ...

    African Journals Online (AJOL)

    Purpose: To examine the effects of two commercial probiotics (Toyocerin and CloSTAT) on serum enzyme activities, and hematological and biochemical indices of broiler chickens challenged with Salmonella enterica serovars Typhimurium (ST). Methods: The chicks received one of the following treatments at 0 day of age: ...

  19. Effect of genotype on haematology and biochemical parameters of ...

    African Journals Online (AJOL)

    Frizzle n = 33, Naked neck, n= 33 and Normal n = 33) were generated from 36 matured local chickens and used for the study to determine the effect of genotype on hematological and biochemical parameters of local chicken in the humid ...

  20. Serum biochemical indices of Finisher Broiler Chickens fed diets ...

    African Journals Online (AJOL)

    A 4 week feeding trial was conducted using 180 five-week old Hubbard broiler chickens to determine the effect of feeding variously processed roselle(Hibiscus sabdariffa) seeds on serum biochemical indices with a view to determining the potential of roselle seed as an alternative to soybeans. Five broiler finisher diets were ...

  1. Some Biochemical and Haematological Studies on the Prevalence ...

    African Journals Online (AJOL)

    Dr J. T. Ekanem

    Printed in Nigeria. Some Biochemical and Haematological Studies on the Prevalence of Congenital Malaria in. Ilorin, Nigeria. Olatunji M. KOLAWOLE. 1 ... appropriate information filled such as maternal age, parity, past clinical history of malaria, anti malaria drug (such as chloroquine, amodiaquine in combination with.

  2. Development of a new first-aid biochemical detector

    Science.gov (United States)

    Hu, Jingfei; Liao, Haiyang; Su, Shilin; Ding, Hao; Liu, Suquan

    2016-10-01

    The traditional biochemical detector exhibits poor adaptability, inconvenient carrying and slow detection, which can't meet the needs of first-aid under field condition like natural or man-made disasters etc. Therefore a scheme of first-aid biochemical detector based on MOMES Micro Spectrometer, UV LED and Photodiode was proposed. An optical detection structure combined continuous spectrum sweep with fixed wavelength measurement was designed, which adopted mobile detection optical path consisting of Micro Spectrometer and Halogen Lamp to detect Chloride (Cl-), Creatinine (Cre), Glucose (Glu), Hemoglobin (Hb). The UV LED and Photodiode were designed to detect Potassium (K-), Carbon dioxide (CO2), Sodium (Na+). According to the field diagnosis and treatment requirements, we designed the embedded control hardware circuit and software system, the prototype of first-aid biochemical detector was developed and the clinical trials were conducted. Experimental results show that the sample's absorbance repeatability is less than 2%, the max coefficient of variation (CV) in the batch repeatability test of all 7 biochemical parameters in blood samples is 4.68%, less than the clinical requirements 10%, the correlation coefficient (R2) in the clinical contrast test with AU5800 is almost greater than 0.97. To sum up, the prototype meets the requirements of clinical application.

  3. Biochemical and genetic diagnosis of Smith-Lemli- Opitz syndrome ...

    African Journals Online (AJOL)

    The clinical spectrum of manifestations is broad, ... delay as well as selfinjurious behaviour and autism are reported. ... recessive disorder that is more common than other defects in cholesterol biosynthesis. ... To perform biochemical and genetic workups in four South African families of European ancestry with suspected ...

  4. Study on color difference estimation method of medicine biochemical analysis

    Science.gov (United States)

    Wang, Chunhong; Zhou, Yue; Zhao, Hongxia; Sun, Jiashi; Zhou, Fengkun

    2006-01-01

    The biochemical analysis in medicine is an important inspection and diagnosis method in hospital clinic. The biochemical analysis of urine is one important item. The Urine test paper shows corresponding color with different detection project or different illness degree. The color difference between the standard threshold and the test paper color of urine can be used to judge the illness degree, so that further analysis and diagnosis to urine is gotten. The color is a three-dimensional physical variable concerning psychology, while reflectance is one-dimensional variable; therefore, the estimation method of color difference in urine test can have better precision and facility than the conventional test method with one-dimensional reflectance, it can make an accurate diagnose. The digital camera is easy to take an image of urine test paper and is used to carry out the urine biochemical analysis conveniently. On the experiment, the color image of urine test paper is taken by popular color digital camera and saved in the computer which installs a simple color space conversion (RGB -> XYZ -> L *a *b *)and the calculation software. Test sample is graded according to intelligent detection of quantitative color. The images taken every time were saved in computer, and the whole illness process will be monitored. This method can also use in other medicine biochemical analyses that have relation with color. Experiment result shows that this test method is quick and accurate; it can be used in hospital, calibrating organization and family, so its application prospect is extensive.

  5. Biochemical correlates in an animal model of depression

    International Nuclear Information System (INIS)

    Johnson, J.O.

    1986-01-01

    A valid animal model of depression was used to explore specific adrenergic receptor differences between rats exhibiting aberrant behavior and control groups. Preliminary experiments revealed a distinct upregulation of hippocampal beta-receptors (as compared to other brain regions) in those animals acquiring a response deficit as a result of exposure to inescapable footshock. Concurrent studies using standard receptor binding techniques showed no large changes in the density of alpha-adrenergic, serotonergic, or dopaminergic receptor densities. This led to the hypothesis that the hippocampal beta-receptor in responses deficient animals could be correlated with the behavioral changes seen after exposure to the aversive stimulus. Normalization of the behavior through the administration of antidepressants could be expected to reverse the biochemical changes if these are related to the mechanism of action of antidepressant drugs. This study makes three important points: (1) there is a relevant biochemical change in the hippocampus of response deficient rats which occurs in parallel to a well-defined behavior, (2) the biochemical and behavioral changes are normalized by antidepressant treatments exhibiting both serotonergic and adrenergic mechanisms of action, and (3) the mode of action of antidepressants in this model is probably a combination of serotonergic and adrenergic influences modulating the hippocampal beta-receptor. These results are discussed in relation to anatomical and biochemical aspects of antidepressant action

  6. Biochemical changes induced by five pathogenic fungi on seeds of ...

    African Journals Online (AJOL)

    Different biochemical analysis were carried out to determine the changes induced by some fungi inoculated on Hibiscus sabdariffa linn seed for 14days. The inoculated fungi are Aspergillus niger Van Tieghem, Aspergillus flavus Link Ex fr, Fusarium oxysporum Schlecht, Penicillium chrysogenum Thom and Penicillium ...

  7. Biochemical markers predictive for bone marrow involvement in systemic mastocytosis

    NARCIS (Netherlands)

    Donker, Marjolein L.; van Doormaal, Jasper J.; van Doormaal, Frederiek F.; Kluin, Philip M.; van der Veer, Eveline; de Monchy, Jan G. R.; Kema, Ido P.; Kluin-Nelemans, Hanneke C.

    Systemic mastocytosis is characterized by bone marrow involvement, which requires a bone marrow biopsy for diagnostic work-up. We questioned whether bone marrow involvement could be predicted using biochemical markers. We selected patients with various symptoms suggestive of indolent systemic

  8. Egg quality parameters and blood biochemical profile of six strains ...

    African Journals Online (AJOL)

    Six different poultry strains (Indigenous chicken, Broiler, Turkey, Geese, Duck and Guinea fowl) were studied under extensive system of management to investigate the effect of rearing system on their egg quality and the blood biochemical profile, respectively. Birds used for the study were obtained from four different ...

  9. Haematological and serum biochemical parameters of West African ...

    African Journals Online (AJOL)

    The study was conducted to evaluate the haematological and serum biochemical parameters of West African dwarf goats fed ensiled cassava leaves with molasses and caged layer waste. Eighteen West African dwarf goats were randomly assigned to three experimental diets consisting of cassava leaves ensiled alone ...

  10. Erythrocyte indices and serum biochemical constituents of broiler ...

    African Journals Online (AJOL)

    One hundred and twenty (120) four weeks old Ross breed broiler finisher birds were used to study the effect of feeding maggot meal as a replacement for fish meal on erythrocyte indices and serum biochemical constituents. The birds were divided into 5 treatment groups identified as T1, T2, T3 , T4 and T5 with 24 birds per ...

  11. Effect Of Chromium- Picolinat On Biochemical And Histopathological ...

    African Journals Online (AJOL)

    Chromium III tris (picolinate) [Cr(pic)3]is a popular nutritional supplement; however its safety has been questioned, especially with regard to its ability to act as a clastogen. The aim of the present work was to evaluate the biochemical and morphological changes in the liver following oral administration of Cr-picolinate and ...

  12. Haematological and Serum Bio-Chemical Parameters of West ...

    African Journals Online (AJOL)

    Haematological and Serum Bio-Chemical Parameters of West African Dwarf and Kalahari Red Goats in the Humid Tropics. ... Haematological results showed that white blood cell count, haemoglobin concentration, haematocrit, mean corpuscular volume, mean corpuscular haemoglobin and mean corpuscular haemoglobin ...

  13. Complement Levels and Haemate-Biochemical Parameters as ...

    African Journals Online (AJOL)

    Complement levels and haemato-biochemical parameters in West African Dwarf (WAD) and Borno White (BW) goats experimentally infected with Trypanosoma congolense were investigated. Parasitaemia was established in both breeds of goats by day 7 post-infection. Peak parasitaemia of 7.5 x 103/µL for WAD goats was ...

  14. Insulin-mimetic activity of stevioside on diabetic rats: biochemical ...

    African Journals Online (AJOL)

    Biochemical, molecular and histopathological studies have been done to evaluate the therapeutic effect of stevioside on minimizing levels of glucose and its ... For mRNA expression, stevioside up-regulated the expressions of PK and IRS-1 genes, which are down-regulated in diabetic rats, and was very effective in the ...

  15. Clinico-haematological and serum biochemical alterations in ...

    African Journals Online (AJOL)

    An increase in serum CRE and BUN values were recorded in all cases of pyometra which reduced to lower levels during both treatments in follow-ups. All the haemato-biochemical parameters were comparable to their respective reference values after either medicinal treatment or ovariohysterectomy of dogs. Thus the dogs ...

  16. Pattern Of Biochemical Derangements Seen In Chronic Renal ...

    African Journals Online (AJOL)

    Objective: To study the pattern of biochemical derangements in advanced renal failure patients. Subjects and Methods: Ninety adult patients [54 males and 36 females] were recruited from the renal clinic of the University of Nigeria Teaching Hospital (UNTH) Enugu over a period of one year. History and physical ...

  17. Biochemical and histological evidences for the antitumor potential of ...

    African Journals Online (AJOL)

    Biochemical and histological evidences for the antitumor potential of Teucrium Oliverianum and Rhazya stricta in chemically-induced hepatocellular carcinoma. ... Photomicrograph of liver tissue sections of rats in HCC revealed hepatic parenchyma with foci of anaplastic hepatocellular carcinoma as well as other foci of ...

  18. Haemato-biochemical and endocrine profiling of north western ...

    African Journals Online (AJOL)

    The study was aimed to provide baseline data regarding haemato-biochemical and endocrine profiling of Gaddi sheep found in north western Himalayan region of Himachal Pradesh, India. Each random sample was collected from 45 Gaddi sheep reared in government sheep breeding farm Tal, Hamirpur, India, during ...

  19. Article Neurotransmitters – A biochemical view | Shalayel | Sudan ...

    African Journals Online (AJOL)

    The neurotransmission at most if not all synapses is chemical and is of great biochemical, physiological and pharmacological importance. Neurons communicate with each other at synapses by a process called synaptic transmission in which the release of small quantities of chemical messengers, called neurotransmitters ...

  20. Vitamin b 12 supplementation: effects on some biochemical and ...

    African Journals Online (AJOL)

    Phenytoin is known to have some toxicological implications. Vitamin B12 supplementation during phenytoin administration was investigated to assess the benefits and risks of single vitamin supplementation. This study evaluated the biochemical and haematological effects of vitamin B12 on phenytoin toxicity. Twenty-four ...

  1. Effect of natural growth promoters on immunity, and biochemical and ...

    African Journals Online (AJOL)

    biochemical and haematological parameters of broiler chickens. Syed Muddassar ... acids, phytobiotics, and their combinations) as feed additives in poultry feed. Methods: Different feed ... by nutrition, season, climate change, age, sex, type of birds and ... glucose, cholesterol, triglyceride, high density lipoprotein (HDL), low ...

  2. Biochemical response of ouda sheep to water contaminated with ...

    African Journals Online (AJOL)

    Also, biochemical examinations of fasting blood glucose(FBGL), total serum protein(TSP), serum albumin(S.ALB), blood urea nitrogen(BUN), serum creatinine(S.CREAT.), serum phosphate(S.PO4), aspartate ... hours of the experiment following standard procedures. The result showed that all the parameters measured were ...

  3. Biochemical evaluation of Gmelina arborea fruit meal as a swine ...

    African Journals Online (AJOL)

    An experiment was conducted to evaluate the influence of Gmelina arborea fruits (GAF) meal on haematology and certain biochemical parameters including blood ... regards to blood urea nitrogen, creatinine in blood and urine and uric acids) though not significantly as the dietary inclusion level of raw GAF meal increased.

  4. studies on blood and plasma biochemical characteristics of the ...

    African Journals Online (AJOL)

    User

    A study to determine the blood parameters and plasma biochemical values of ... highest in animals at the 4th month state (9.75g/dl) and lowest at the 12th ... study is indicative of satisfactory physiological, nutritional and pathological ... domestication and integration into the micro-livestock farming system is ..... Principles and.

  5. Biochemical and pathological studies in rats following dietary ...

    African Journals Online (AJOL)

    Biochemical and pathological studies in rats following dietary supplementation with high levels of polyunsaturated fatty acids and vitamin E. ... Furthermore, high dietary supplementation of vitamin E showed no deleterious effects on rats and no pathological changes in the liver, kidney and heart tissues were observed in the ...

  6. Serum Biochemical Changes Associated With The Digestibility Of ...

    African Journals Online (AJOL)

    Serum Biochemical Changes Associated With The Digestibility Of Raw And Heat Processed Cajanus cajan Seeds In Rats. ... The level of anti-nutritive food toxicants in exotic breed of Cajanus cajan L. (pigeon pea) was evaluated in this study using an animal model experiment in which animals were fed with raw and heat ...

  7. Evaluation of biogas production rate and biochemical changes in ...

    African Journals Online (AJOL)

    The rate of biogas generation and biochemical changes in pig dung used in a simple mobile biogas digester designed and constructed at the Department of Environmental Technology, Federal University of Technology Owerri, Nigeria were evaluated. Measurable gas production started 4 days after feeding the digester with ...

  8. Haematological and Serum Biochemical Variables in rats Treated ...

    African Journals Online (AJOL)

    The haematology and serum biochemical effects of oral administration of the ethanolic extract of the root of Moringa oleifera at 50, 100 and 150 mg/kg were investigated in 30 mated female Wistar rats. The rats were assigned into five groups of six rats each. Group A was given 50mg/kg of the extract; group B, 100mg/kg; ...

  9. Biological and biochemical evaluation of some prepared high ...

    African Journals Online (AJOL)

    Biological and biochemical evaluation of some prepared high antioxidant fruit beverages as functional foods. W A El-Malky ... The beverage which contain mango, red grape, carrot and tomato was the best prepared beverages according to the sensory evaluation, chemical composition and antioxidant activity. The high ...

  10. An evaluation of solutions to moment method of biochemical oxygen ...

    African Journals Online (AJOL)

    This paper evaluated selected solutions of moment method in respect to Biochemical Oxygen Demand (BOD) kinetics with the aim of ascertain error free solution. Domestic - institutional wastewaters were collected two - weekly for three months from waste - stabilization ponds in Obafemi Awolowo University, Ile - Ife.

  11. Laying performance, haematology and serum biochemical profile of ...

    African Journals Online (AJOL)

    The study was carried out to compare the effects of unfermented and fermented African locust bean on laying performance, haematology and serum biochemical profile of hens in a twelve week feeding trial. The unfermented African locust bean (UALB) contained seeds that were dehulled and boiled in water, without going ...

  12. Haematological and biochemical values of 10 green iguanas (Iguana iguana).

    Science.gov (United States)

    Divers, S J; Redmayne, G; Aves, E K

    1996-03-02

    Ten clinically healthy green iguanas (Iguana iguana) imported from South America were examined, and haematological and biochemical measurements were made on samples of blood. This paper describes the methods of blood sampling, handling and laboratory analysis, and presents the results as a set of normal blood ranges for the green iguana.

  13. Fragrance analysis using molecular and biochemical methods in ...

    African Journals Online (AJOL)

    admin

    Biochemical analysis of aroma was performed with the 1.7% KOH solution and molecular analysis of aroma was carried out with microsatellite markers present on chromosome 8 (BAD2, BADEX7-5, SCUSSR1) to determine the extent of association between trait, marker and chromosome 8. Among these markers, BAD2 ...

  14. Serum biochemical and liver enzymes changes in dogs with single ...

    African Journals Online (AJOL)

    The serum biochemical changes that occur in dogs with single and conjunct experimental infections of Trypanosoma brucei and Ancylostoma caninum were studied. Four groups (GPI, GPII, GPIII and GPIV) of five dogs each were used for this study. GPI was the uninfected control while GPII, GPIII and GPIV were infected ...

  15. Dynamic changes in biochemical markers of renal function with ...

    African Journals Online (AJOL)

    Thyroid dysfunction is known to cause significant changes in glomerular filtration rate. The present cross-sectional study was performed to evaluate the changes in biochemical markers of renal function in hypothyroid subjects before and after treatment. Thyroid function tests (T3, T4 and TSH levels) were assayed in 385 ...

  16. Toxicological Effects of Cigarette Smoke on Some Biochemical ...

    African Journals Online (AJOL)

    It is believed that while normal people may suffer complications of active and passive cigarette smoking, diabetes patients may suffer more. This study therefore aimed at investigating the toxicological effects of cigarette smoke on some biochemical parameters of alloxan-induced diabetic rats. Adult male Wistar rats (n ...

  17. Biochemical and hematological profile of different breeds of goat ...

    African Journals Online (AJOL)

    shthomas

    index of transportation stress (Ambore et al., 2009). The biochemical ... conditions were typical of the Arabian desert, temperature was high. (up to 52°C) ..... Int. J. Food Agric. Vet. Sci. .... Statistical Package for the Social Sciences, release 10.0.

  18. Effects of phospholipids in the diet on biochemical factors of ...

    African Journals Online (AJOL)

    A study was carried out to determine the influence of dietary phospholipids biochemical factors parameters of beluga sturgeon (Huso huso) juveniles. Juveniles were fed formulated diet with four varying dietary levels of PL, that is, 0 (D1), 2 (D2), 4 (D3) and 6% (D4). At the end of the experimental period (56 days), there were ...

  19. Biochemical response of normal albino rats to the addition of ...

    African Journals Online (AJOL)

    Experiments were conducted to determine the biochemical effect of Hibiscus cannabinus and Murraya koenigii extracts on normal albino rats using standard methods. Analyses carried out indicated that the aqueous leaf extract of H. cannabinus and M. koenigii exhibited significant hypolipideamic activity in normal rats.

  20. on the biochemical indicators of lead poisoning in

    African Journals Online (AJOL)

    N. Sadi

    1 sept. 2017 ... ABSTRACT. This study is conducted to examine the effect of the oral administration of pectin of dates on perturbation of the biochemical parameters induced by lead. Male rats were exposed to lead acetate at 350mg/Kg for one month, after this period, rats treated during one month with the pectin of date at ...

  1. Physicochemical and biochemical characterization of biosurfactants released by Lactobacillus strains

    NARCIS (Netherlands)

    Velraeds, MMC; vanderMei, HC; Reid, G; Busscher, HJ

    1996-01-01

    Biosurfactants from Lactobacillus casei subsp. rhamnosus 36 and ATCC 7469, Lactobacillus fermentum B54 and Lactobacillus acidophilus RC14 were isolated from bacteria in their mid-exponential (4-5 h) and stationary growth phases (18 h) and physicochemical and biochemical properties of the

  2. Altered biochemical specificity of G-quadruplexes with mutated tetrads

    Czech Academy of Sciences Publication Activity Database

    Švehlová, Kateřina; Lawrence, M. S.; Bednárová, Lucie; Curtis, Edward A.

    2016-01-01

    Roč. 44, č. 22 (2016), s. 10789-10803 ISSN 0305-1048 Institutional support: RVO:61388963 Keywords : G-quadruplex * G motif GTP aptamer * peroxidase deoxyribozyme Subject RIV: CE - Biochemistry Impact factor: 10.162, year: 2016 https://academic.oup.com/nar/article/44/22/10789/2333933/Altered-biochemical-specificity-of-G-quadruplexes

  3. Xanthine, hypoxanthine and muscle pain. Histochemical and biochemical observations

    Energy Technology Data Exchange (ETDEWEB)

    Isaacs, H; Badenhorst, M; Pickering, A [University of the Witwatersrand, Johannesburg (South Africa). Department of Physiology; Heffron, J J.A. [University of the Witwatersrand, Johannesburg (South Africa). Department of Physiological Chemistry; Berman, L

    1975-06-21

    A suspected case of xanthine oxidase deficiency has been further investigated. The patient complained of arthralgia and myalgia. Further studies included histochemical and ultramicroscopic analysis of muscle sarcoplasmic recticulum, and biochemical studies. High levels of xanthine and hypoxanthine were found, while uric acid was absent in the muscle extracts.

  4. Studies on blood and plasma biochemical characteristics of the ...

    African Journals Online (AJOL)

    The rats were fed on commercial grower mash and water provided ad libitum. Two separate blood samples were collected from the jugular veins of eight rats at 4th, 8th and 12th month stages of the experiment. One group of the samples was used for haematological studies and the other for biochemical tests. Data collected

  5. Differential response of biochemical parameters to EMS and MMS ...

    African Journals Online (AJOL)

    (1964) and biochemical estimations from the liver was done by the method of Sinha (1972) for catalase, Van der Vies (1954) for glycogen and Uchiyama and Mihara (1978) for MDA. Results: The study has revealed that EMS and MMS induced a dose dependent increase in chromosomal aberrations of chromatid type in the ...

  6. Effects of Pineal Proteins on Biochemical, Enzyme Profile and Non ...

    African Journals Online (AJOL)

    Effects of Pineal Proteins on Biochemical, Enzyme Profile and Non-Specific Immune Response of Indian Goats under Thermal Stress. ... Total precipitated pineal proteins successfully and significantly relieved the animals from adverse effects of heat stress and metyrapone treatment. There is evidence that most of the ...

  7. Iodine-125 safety procedures in a biochemical laboratory

    International Nuclear Information System (INIS)

    1989-01-01

    Radioactive isotopes of iodine are of considerable importance in biochemical research and this 14 minute videotape is designed to give workers an introduction to the radiation safety aspects of their use. It deals with I-125, which is now generally used in preference to I-131, but the principles of safe working practice are the same for both isotopes. (author)

  8. Impact of parathion exposure on some biochemical parameters in ...

    African Journals Online (AJOL)

    Nagat Aly

    2014-09-16

    Sep 16, 2014 ... developing field aims to reveal environmental threats before obvious toxic effects such as ... followed by the Student–Newman–Keuls test to determine sig- nificance between ..... open-field activity in chicks. Toxicol Lett 2007 ... ical and serum biochemical changes in mice and protective effect · of vitamin C. J ...

  9. A MULTILAYER BIOCHEMICAL DRY DEPOSITION MODEL 1. MODEL FORMULATION

    Science.gov (United States)

    A multilayer biochemical dry deposition model has been developed based on the NOAA Multilayer Model (MLM) to study gaseous exchanges between the soil, plants, and the atmosphere. Most of the parameterizations and submodels have been updated or replaced. The numerical integration ...

  10. A MULTILAYER BIOCHEMICAL DRY DEPOSITION MODEL 2. MODEL EVALUATION

    Science.gov (United States)

    The multilayer biochemical dry deposition model (MLBC) described in the accompanying paper was tested against half-hourly eddy correlation data from six field sites under a wide range of climate conditions with various plant types. Modeled CO2, O3, SO2<...

  11. Hybrid Nanogenerator for Concurrently Harvesting Biomechanical and Biochemical Energy

    KAUST Repository

    Hansen, Benjamin J.; Liu, Ying; Yang, Rusen; Wang, Zhong Lin

    2010-01-01

    the beat of a heart, and a flexible enzymatic biofuel cell for harvesting the biochemical (glucose/O2) energy in biofluid, which are two types of energy available in vivo. The two energy harvesting approaches can work simultaneously or individually, thereby

  12. Study on the alteration of bubaline blood biochemical composition ...

    African Journals Online (AJOL)

    Bubaline blood biochemistry as affected by slaughter was the agenda for this work. Blood samples were collected from 30 buffaloes from abattoirs before and at slaughter. After biochemical and statistical analysis (mean was compared with t-test), it was observed that the albumin, lactate dehydrogenase and creatine kinase ...

  13. Biochemical characterization of blood plasma of coronary artery ...

    Indian Academy of Sciences (India)

    This study aimed to investigate the biochemical profile of blood plasma of patients with coronary artery disease (CAD) and angiographically normal subjects (controls) to determine biomarkers for their differentiation. In this double blind study, 5 mL venous blood was drawn before angiography from CAD patients (n=60) and ...

  14. Opium and heroin alter biochemical parameters of human's serum.

    Science.gov (United States)

    Kouros, Divsalar; Tahereh, Haghpanah; Mohammadreza, Afarinesh; Minoo, Mahmoudi Zarandi

    2010-05-01

    Iran is a significant consumer of opium, and, generally, of opioids, in the world. Addiction is one of the important issues of the 21st century and is an imperative issue in Iran. Long-term consumption of opioids affects homeostasis. To determine the effects of opium and heroin consumption on serum biochemical parameters. In a cross-sectional study, subjects who had consumed heroin (n = 35) or opium (n = 42) for more than two years and 35 nonaddict volunteers as the control group were compared in regard to various biochemical parameters such as fasting blood sugar (FBS), Na(+), K(+), Ca(2+), blood urea nitrogen (BUN), uric acid (UA), triglyceride (TG), cholesterol, creatinine, and total protein. Chromatography was used to confirm opioid consumption, and the concentration of biochemical parameters was determined by laboratory diagnostic tests on serum. No significant differences were found in Na(+), Ca(2+), BUN, UA, TG, creatinine, and total protein concentrations among the three groups. FBS, K(+), and UA levels were significantly lower in opium addicts compared to the control group. Serum Ca(2+) concentration of heroin addicts showed a significant decrease compared to that of the control group. Both addict groups showed a significant decrease in serum cholesterol levels. Chronic use of opium and heroin can change serum FBS, K(+), Ca(2+), UA, and cholesterol. This study, one of few on the effects of opium on serum biochemical parameters in human subjects, has the potential to contribute to the investigation of new approaches for further basic studies.

  15. Evaluation of haematological and plasma biochemical effects of ...

    African Journals Online (AJOL)

    TAYO AJIBADE

    2012-11-01

    Nov 1, 2012 ... African Journal of Biotechnology Vol. 11(88), pp. ... biochemical values revealed significant increase in total protein, albumin and aspartate amino transferase. However ... functions and damages to cellular membrane normally leads to the .... way analysis of variance (ANOVA) for statistical significance was.

  16. Haematological profile and serum biochemical indices of weaned ...

    African Journals Online (AJOL)

    This study was carried out to determine the haematological profile and serum biochemical indices of rabbits fed pawpaw (Carica papaya) leaves as feed supplement to a corn – soybean mealbasal diet. The study involved thirty six (36) cross bred (New Zealand White X Chinchilla) mixed sex weaned rabbits of five - six ...

  17. Effect of Modifying Factors on Radiosensitive Biochemical Reactions

    Energy Technology Data Exchange (ETDEWEB)

    Romantsev, E. F.; Filippovich, I. V.; Zhulanova, Z. I.; Blokhina, V. D.; Trebenok, Z. A.; Kolesnikov, E. E.; Sheremetyevskaya, T. N.; Nikolsky, A. V.; Zymaleva, O. G. [Institute of Biophysics, USSR Ministry of Health, Moscow, USSR (Russian Federation)

    1971-03-15

    Some of the radioprotective aminothiols are now routine pharmacopoeial drugs and are used in clinics to decrease the radiation reaction which appears as a side effect during the radiotherapy of cancer. The action of effective modifying agents on radiosensitive biochemical reactions in the organisms of mammals, in principle, cannot be different from the same effects of the protectors on biochemical systems of the human organism. The effect of modifying agents is mediated by biochemical systems. The administration of radioprotective doses of MEA to rats before irradiation results in a significant normalization of the excretion in urine of degradation products of nucleic acids (so-called Dische-positive compounds), the excretion of which sharply rises after irradiation. The curve of the radioprotective effect of MEA (survival rate after administration of radioprotectors at different intervals of time) completely corresponds to curves of the accumulation of MEA which is bound (by mixed disulphide links) to the proteins of liver mitochondria, to proteins of the nuclear-sap, to the hyaloplasm of rat thymus and to the nuclear ribosomes of the spleen. After MEA administration the curve of the biosynthesis of deoxycytidine represents a mirror reflection of the curve of MEA bound to proteins of the thymus hyaloplasm by means of mixed disulphide links. The mechanism of action of such modifying factors as MEA in experiments on mammals is mediated to a great degree through the temporary formation of mixed disulphide links between the aminothiol and the protein component of enzymes in different biochemical systems. (author)

  18. Silicon mediated biochemical changes in wheat under salinized and ...

    African Journals Online (AJOL)

    Silicon (Si) can alleviate salinity damage, a major threat to agriculture that causes instability in wheat production. We report on the effects of silicon (150 mg L-1) on the morphological, physiological and biochemical traits in wheat (Triticum aestivum L.) cultivars (salt sensitive; Auqab-2000 and salt tolerant; SARC-5) differing ...

  19. A coupled mechano-biochemical model for bone adaptation

    Czech Academy of Sciences Publication Activity Database

    Klika, Václav; Pérez, M. A.; García-Aznar, J. M.; Maršík, F.; Doblaré, M.

    2014-01-01

    Roč. 69, 6-7 (2014), s. 1383-1429 ISSN 0303-6812 Institutional support: RVO:61388998 Keywords : mechano-biochemical model * bone remodelling * BMU Subject RIV: BJ - Thermodynamics Impact factor: 1.846, year: 2014 http://link.springer.com/article/10.1007%2Fs00285-013-0736-9

  20. Molecular and biochemical diagnosis of Salmonella in wastewater ...

    African Journals Online (AJOL)

    This study aimed to employ biochemical and molecular assays to detect and diagnose Salmonella in wastewater. For this reason, two water samples were collected from Alexandria wastewater treatment plant (S1) and septic tank of a hospital at Alexandria governorate (S2). Selective culture media specific for Salmonella ...

  1. Biochemical and cytological analysis of five cultivars of Cicer ...

    African Journals Online (AJOL)

    SAM

    2014-03-12

    Mar 12, 2014 ... variability and relatedness, seed storage protein analysis represents a valid alternative to ... Indian Institute of Pulse Research, Kanpur (U.P.) India. During the present study, five accessions were used for biochemical and cytological analysis. The details of five ... using pestle and mortar. 500 ml of protein ...

  2. MATLAB-Based Teaching Modules in Biochemical Engineering

    Science.gov (United States)

    Lee, Kilho; Comolli, Noelle K.; Kelly, William J.; Huang, Zuyi

    2015-01-01

    Mathematical models play an important role in biochemical engineering. For example, the models developed in the field of systems biology have been used to identify drug targets to treat pathogens such as Pseudomonas aeruginosa in biofilms. In addition, competitive binding models for chromatography processes have been developed to predict expanded…

  3. 40 CFR 798.5195 - Mouse biochemical specific locus test.

    Science.gov (United States)

    2010-07-01

    ...-induced variants are bred to determine the genetic nature of the change. (f) Data and reports—(1... SUBSTANCES CONTROL ACT (CONTINUED) HEALTH EFFECTS TESTING GUIDELINES Genetic Toxicity § 798.5195 Mouse...) A biochemical specific locus mutation is a genetic change resulting from a DNA lesion causing...

  4. Plasma Atrial Natriuretic Peptide as a non-invasive biochemical ...

    African Journals Online (AJOL)

    Plasma Atrial Natriuretic Peptide as a non-invasive biochemical marker of dyspnoea in congestive heart failure patients. ... University of Mauritius Research Journal ... score assessed by a 10 graded visual analogue scale in the control group (mean score = 1) and an increased from 1.6 to 6.4 in the heart failure patients.

  5. Molecular and biochemical studies of some yeast strains

    African Journals Online (AJOL)

    user

    2011-02-21

    Feb 21, 2011 ... Kluyveromyces lactis (Y.9) and Pichia jadinii (Y.10) contained almost double the amount of total amino ... Differences between ... biochemical analysis (total protein profile and total amino acids) were used as tools to select the best yeast strains in Saudi Arabia and Egypt as a rich source of animal protein.

  6. Haematological and biochemical evaluation of the n -hexane extract ...

    African Journals Online (AJOL)

    The study undertook to evaluate the sub-chronic toxicological profile of the seed of Ricinus communis var. minor (RICOM-1013-J), widely used as anticonceptive agent among Bassa people of Plateau State, Nigeria, on haematological and biochemical parameters in adult rats. Thirty-six (36) adult female rats were divided ...

  7. Genetic and biochemical evidences reveal novel insights into the ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Biosciences; Volume 41; Issue 4. Genetic and biochemical evidences reveal novel insights into the mechanism underlying Saccharomyces cerevisiae Sae2-mediated abrogation of DNA replication stress. INDRAJEET GHODKE K MUNIYAPPA. ARTICLE Volume 41 Issue 4 December 2016 pp ...

  8. Seasonal variation in the biochemical composition of red seaweed

    Indian Academy of Sciences (India)

    Abstract. The biochemical composition of red seaweeds,Catenella repens was investigated in this present study along with subsequent analysis of relevant physico-chemical variables.In this study, the relationship between the nutritive components of this species and the ambient environmental parameters was established.

  9. Blood biochemical of nile crocodile ( Crocodylus niloticus ) in Kano ...

    African Journals Online (AJOL)

    This study investigates serum biochemistry of Nile crocodile from Kano Zoological Garden, Kano, Nigeria. Six (6) adult Nile crocodile (Crocodylus niloticus) were captured from crocodile pond. Blood was collected from post occipital sinus of the physically restrain crocodile and used for serum biochemical parameters.

  10. Biochemical and Heamatological Indices of Broiler Chickens fed ...

    African Journals Online (AJOL)

    SH

    investigate the implications of feeding broiler chickens with mucuna bean processed by simple domestic methods on performance, haematological and biochemical parameters. Materials and Methods. Sample preparation: The raw Mucuna pruriens beans used in this study were purchased from International Institute of.

  11. haematological parameters and serum biochemical indices of pre

    African Journals Online (AJOL)

    mrmrsolayiwola

    2012-05-01

    May 1, 2012 ... pubertal male rabbits fed with graded level of blood- ... The effects of feeding graded levels of blood wild sunflower forage meal ... and serum biochemical parameters in rabbit were studied. ... (Cheeke et al., 1986), high in protein, low in cholesterol ..... assay of nutritional anaemia (dietary deficiency of iron,.

  12. Physiological and biochemical responses to low temperature stress ...

    African Journals Online (AJOL)

    Cuttings of three hybrid clones of P. ussuriensis × P. deltoides were exposed to different low temperatures (cold and freezing) for 24 h, or consecutive low temperatures (5°C, 0 to 120 h), to determine physiological and biochemical responses to cold stress in these woody plants. Soluble sugar and protein contents increased ...

  13. Fragrance analysis using molecular and biochemical methods in ...

    African Journals Online (AJOL)

    For molecular and biochemical analysis of aroma, a mapping population comprising 208 recombinant inbred lines (RILs) derived from a diverse cross between CSR10 and Taraori Basmati through Single seed descent (SSD) method was used. RILs are among the best mapping populations, which provide a novel material ...

  14. Polycystic ovaries and associated clinical and biochemical features ...

    African Journals Online (AJOL)

    The aim of this study was to determine prevalence of polycystic ovaries (PCO) and associated clinical and biochemical features among women with infertility attending gynaecological outpatient department (GOPD) at Muhimbili National Hospital (MNH) in Dar es Salaam, Tanzania. All women with infertility attending the ...

  15. Diagnostic utility of clinical and biochemical parameters in ...

    African Journals Online (AJOL)

    Diagnostic utility of clinical and biochemical parameters in pancreatic head malignancy patients with normal carbohydrate antigen 19-9 levels. Xiaoli Jin1, Yulian Wu2. 1. Department of Surgery, Sir Run Run Shaw Hospital College of Medicine, Zhejiang University, 3 Qingchun. Road East, Hangzhou, Zhejiang Province ...

  16. The biochemical, physiological and therapeutic roles of ascorbic acid

    African Journals Online (AJOL)

    Ascorbic acid is an important micronutrient necessary for a significant number of metabolic reactions in humans and other primates. It is a strong reducing agent involved in reduction reaction and it is structurally related to glucose. Experimental and epidemiological studies have documented the biochemical, physiological ...

  17. Association of Biochemical Markers, Hepatitis C Virus and Diabetes ...

    African Journals Online (AJOL)

    Purpose: To investigate the association between Hepatitis C Virus (HCV) infection and diabetes mellitus (DM), and the effects of these pathological conditions on some biochemical markers in Pakistanis. Methods: A total number of 4717 chronic HCV patients were enrolled in this study out of which 4250 were positive with ...

  18. Sex Hormones And Biochemical Profiles Of Male Gossypol Users In ...

    African Journals Online (AJOL)

    The present study was designed to evaluate the effects of gossypol administration on sex hormones and biochemical parameters of male subjects. Twelve male subjects receiving 20mg daily gossypol at the family planning clinic of University College Hospital, Ibadan were studied. Blood samples collected from the subjects ...

  19. Dactylifera L) on the biochemical indicators of lead poisoning in ...

    African Journals Online (AJOL)

    This study is conducted to examine the effect of the oral administration of pectin of dates on perturbation of the biochemical parameters induced by lead. Male rats were exposed to lead acetate at 350mg/Kg for one month, after this period, rats treated during one month with the pectin of date at 3%. Rats were sacrificed, the ...

  20. Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems

    Directory of Open Access Journals (Sweden)

    Goutsias John

    2010-11-01

    Full Text Available Abstract Background Estimating the rate constants of a biochemical reaction system with known stoichiometry from noisy time series measurements of molecular concentrations is an important step for building predictive models of cellular function. Inference techniques currently available in the literature may produce rate constant values that defy necessary constraints imposed by the fundamental laws of thermodynamics. As a result, these techniques may lead to biochemical reaction systems whose concentration dynamics could not possibly occur in nature. Therefore, development of a thermodynamically consistent approach for estimating the rate constants of a biochemical reaction system is highly desirable. Results We introduce a Bayesian analysis approach for computing thermodynamically consistent estimates of the rate constants of a closed biochemical reaction system with known stoichiometry given experimental data. Our method employs an appropriately designed prior probability density function that effectively integrates fundamental biophysical and thermodynamic knowledge into the inference problem. Moreover, it takes into account experimental strategies for collecting informative observations of molecular concentrations through perturbations. The proposed method employs a maximization-expectation-maximization algorithm that provides thermodynamically feasible estimates of the rate constant values and computes appropriate measures of estimation accuracy. We demonstrate various aspects of the proposed method on synthetic data obtained by simulating a subset of a well-known model of the EGF/ERK signaling pathway, and examine its robustness under conditions that violate key assumptions. Software, coded in MATLAB®, which implements all Bayesian analysis techniques discussed in this paper, is available free of charge at http://www.cis.jhu.edu/~goutsias/CSS%20lab/software.html. Conclusions Our approach provides an attractive statistical methodology for

  1. Network Coded Software Defined Networking

    DEFF Research Database (Denmark)

    Hansen, Jonas; Roetter, Daniel Enrique Lucani; Krigslund, Jeppe

    2015-01-01

    Software defined networking has garnered large attention due to its potential to virtualize services in the Internet, introducing flexibility in the buffering, scheduling, processing, and routing of data in network routers. SDN breaks the deadlock that has kept Internet network protocols stagnant...... for decades, while applications and physical links have evolved. This article advocates for the use of SDN to bring about 5G network services by incorporating network coding (NC) functionalities. The latter constitutes a major leap forward compared to the state-of-the- art store and forward Internet paradigm...

  2. INVESTIGATIONS ON BIOCHEMICAL PURIFICATION OF GROUND WATER FROM HYDROGEN SULFIDE

    Directory of Open Access Journals (Sweden)

    Yu. P. Sedlukho

    2015-01-01

    Full Text Available The paper considers problems and features of biochemical removal of hydrogen sulfide from ground water. The analysis of existing methods for purification of ground water from hydrogen sulfide has been given in the paper. The paper has established shortcomings of physical and chemical purification of ground water. While using aeration methods for removal of hydrogen sulfide formation of colloidal sulfur that gives muddiness and opalescence to water occurs due to partial chemical air oxidation. In addition to this violation of sulfide-carbonate equilibrium taking place in the process of aeration due to desorption of H2S and CO2, often leads to clogging of degasifier nozzles with formed CaCO3 that causes serious operational problems. Chemical methods require relatively large flow of complex reagent facilities, storage facilities and transportation costs.In terms of hydrogen sulfide ground water purification the greatest interest is given to the biochemical method. Factors deterring widespread application of the biochemical method is its insufficient previous investigation and necessity to execute special research in order to determine optimal process parameters while purifying groundwater of a particular water supply source. Biochemical methods for oxidation of sulfur compounds are based on natural biological processes that ensure natural sulfur cycle. S. Vinogradsky has established a two-stage mechanism for oxidation of hydrogen sulfide with sulfur bacteria (Beggiatoa. The first stage presupposes oxidation of hydrogen sulphide to elemental sulfur which is accumulating in the cytoplasm in the form of globules. During the second stage sulfur bacteria begin to oxidize intracellular sulfur to sulfuric acid due to shortage of hydrogen sulfide.The paper provides the results of technological tests of large-scale pilot plants for biochemical purification of groundwater from hydrogen sulfide in semi-industrial conditions. Dependences of water quality

  3. Family history and biochemical diagnosis in 1948 kidney stone formers

    Directory of Open Access Journals (Sweden)

    Francisco R. Spivacow

    2016-12-01

    Full Text Available Introduction: The presence of family history of nephrolithiasis is associated with an increased risk of renal lithiasis. Different epidemiological studies have shown a family component in the incidence of it, which is independent of dietary and environmental factors. The role of heredity is evident in monogenic diseases such as cystinuria, Dent’s disease or primary hyperoxaluria, while a polygenic inheritance has been proposed to explain the tendency to form calcium oxalate stones. Objective: Our objective was to evaluate the family history of patients with renal lithiasis and the correlation of family history with its corresponding biochemical alteration, considering only those with a single metabolic alteration. Methods: a prospective and retrospective observational and analytical study that included 1948 adults over 17 years of age and a normal control group of 165 individuals, all evaluated according to an ambulatory protocol to obtain a biochemical diagnosis. They were asked about their family history of nephrolithiasis and classified into five groups according to the degree of kinship and the number of people affected in the family. Results: a positive family history of nephrolithiasis was found in 27.4% of renal stone formers, predominantly in women, compared to 15.2% of normal controls. The family history of nephrolithiasis was observed especially in 31.4% of patients with hypomagnesuria and in 29.6% of hypercalciuric patients. The rest of the biochemical alterations had a positive family history between 28.6% in hyperoxaluria and 21.9% in hypocitraturia. The highest percentage of family history of nephrolithiasis was found in cystinuria (75% although there were few patients with this diagnosis. Conclusions: the inheritance has a clear impact on urolithiasis independently of the present biochemical alteration. Family history of nephrolithiasis of the first and second degree was observed between 21 and 32% of patients with renal

  4. Accurate atom-mapping computation for biochemical reactions.

    Science.gov (United States)

    Latendresse, Mario; Malerich, Jeremiah P; Travers, Mike; Karp, Peter D

    2012-11-26

    The complete atom mapping of a chemical reaction is a bijection of the reactant atoms to the product atoms that specifies the terminus of each reactant atom. Atom mapping of biochemical reactions is useful for many applications of systems biology, in particular for metabolic engineering where synthesizing new biochemical pathways has to take into account for the number of carbon atoms from a source compound that are conserved in the synthesis of a target compound. Rapid, accurate computation of the atom mapping(s) of a biochemical reaction remains elusive despite significant work on this topic. In particular, past researchers did not validate the accuracy of mapping algorithms. We introduce a new method for computing atom mappings called the minimum weighted edit-distance (MWED) metric. The metric is based on bond propensity to react and computes biochemically valid atom mappings for a large percentage of biochemical reactions. MWED models can be formulated efficiently as Mixed-Integer Linear Programs (MILPs). We have demonstrated this approach on 7501 reactions of the MetaCyc database for which 87% of the models could be solved in less than 10 s. For 2.1% of the reactions, we found multiple optimal atom mappings. We show that the error rate is 0.9% (22 reactions) by comparing these atom mappings to 2446 atom mappings of the manually curated Kyoto Encyclopedia of Genes and Genomes (KEGG) RPAIR database. To our knowledge, our computational atom-mapping approach is the most accurate and among the fastest published to date. The atom-mapping data will be available in the MetaCyc database later in 2012; the atom-mapping software will be available within the Pathway Tools software later in 2012.

  5. Aspects on the Physiological and Biochemical Foundations of Neurocritical Care

    Directory of Open Access Journals (Sweden)

    Carl-Henrik Nordström

    2017-06-01

    Full Text Available Neurocritical care (NCC is a branch of intensive care medicine characterized by specific physiological and biochemical monitoring techniques necessary for identifying cerebral adverse events and for evaluating specific therapies. Information is primarily obtained from physiological variables related to intracranial pressure (ICP and cerebral blood flow (CBF and from physiological and biochemical variables related to cerebral energy metabolism. Non-surgical therapies developed for treating increased ICP are based on knowledge regarding transport of water across the intact and injured blood–brain barrier (BBB and the regulation of CBF. Brain volume is strictly controlled as the BBB permeability to crystalloids is very low restricting net transport of water across the capillary wall. Cerebral pressure autoregulation prevents changes in intracranial blood volume and intracapillary hydrostatic pressure at variations in arterial blood pressure. Information regarding cerebral oxidative metabolism is obtained from measurements of brain tissue oxygen tension (PbtO2 and biochemical data obtained from intracerebral microdialysis. As interstitial lactate/pyruvate (LP ratio instantaneously reflects shifts in intracellular cytoplasmatic redox state, it is an important indicator of compromised cerebral oxidative metabolism. The combined information obtained from PbtO2, LP ratio, and the pattern of biochemical variables reveals whether impaired oxidative metabolism is due to insufficient perfusion (ischemia or mitochondrial dysfunction. Intracerebral microdialysis and PbtO2 give information from a very small volume of tissue. Accordingly, clinical interpretation of the data must be based on information of the probe location in relation to focal brain damage. Attempts to evaluate global cerebral energy state from microdialysis of intraventricular fluid and from the LP ratio of the draining venous blood have recently been presented. To be of clinical relevance

  6. Networked Identities

    DEFF Research Database (Denmark)

    Ryberg, Thomas; Larsen, Malene Charlotte

    2008-01-01

    of CoPs we shall argue that the metaphor or theory of networked learning is itself confronted with some central tensions and challenges that need to be addressed. We then explore these theoretical and analytic challenges to the network metaphor, through an analysis of a Danish social networking site. We......In this article we take up a critique of the concept of Communities of Practice (CoP) voiced by several authors, who suggest that networks may provide a better metaphor to understand social forms of organisation and learning. Through a discussion of the notion of networked learning and the critique...... argue that understanding meaning-making and ‘networked identities’ may be relevant analytic entry points in navigating the challenges....

  7. Rational design of functional and tunable oscillating enzymatic networks

    Science.gov (United States)

    Semenov, Sergey N.; Wong, Albert S. Y.; van der Made, R. Martijn; Postma, Sjoerd G. J.; Groen, Joost; van Roekel, Hendrik W. H.; de Greef, Tom F. A.; Huck, Wilhelm T. S.

    2015-02-01

    Life is sustained by complex systems operating far from equilibrium and consisting of a multitude of enzymatic reaction networks. The operating principles of biology's regulatory networks are known, but the in vitro assembly of out-of-equilibrium enzymatic reaction networks has proved challenging, limiting the development of synthetic systems showing autonomous behaviour. Here, we present a strategy for the rational design of programmable functional reaction networks that exhibit dynamic behaviour. We demonstrate that a network built around autoactivation and delayed negative feedback of the enzyme trypsin is capable of producing sustained oscillating concentrations of active trypsin for over 65 h. Other functions, such as amplification, analog-to-digital conversion and periodic control over equilibrium systems, are obtained by linking multiple network modules in microfluidic flow reactors. The methodology developed here provides a general framework to construct dissipative, tunable and robust (bio)chemical reaction networks.

  8. Temporal motifs in time-dependent networks

    International Nuclear Information System (INIS)

    Kovanen, Lauri; Karsai, Márton; Kaski, Kimmo; Kertész, János; Saramäki, Jari

    2011-01-01

    Temporal networks are commonly used to represent systems where connections between elements are active only for restricted periods of time, such as telecommunication, neural signal processing, biochemical reaction and human social interaction networks. We introduce the framework of temporal motifs to study the mesoscale topological–temporal structure of temporal networks in which the events of nodes do not overlap in time. Temporal motifs are classes of similar event sequences, where the similarity refers not only to topology but also to the temporal order of the events. We provide a mapping from event sequences to coloured directed graphs that enables an efficient algorithm for identifying temporal motifs. We discuss some aspects of temporal motifs, including causality and null models, and present basic statistics of temporal motifs in a large mobile call network

  9. Network security

    CERN Document Server

    Perez, André

    2014-01-01

    This book introduces the security mechanisms deployed in Ethernet, Wireless-Fidelity (Wi-Fi), Internet Protocol (IP) and MultiProtocol Label Switching (MPLS) networks. These mechanisms are grouped throughout the book according to the following four functions: data protection, access control, network isolation, and data monitoring. Data protection is supplied by data confidentiality and integrity control services. Access control is provided by a third-party authentication service. Network isolation is supplied by the Virtual Private Network (VPN) service. Data monitoring consists of applying

  10. Network cohesion

    OpenAIRE

    Cavalcanti, Tiago V. V.; Giannitsarou, Chryssi; Johnson, Charles R.

    2016-01-01

    This is the final version of the article. It first appeared from Springer via http://dx.doi.org/10.1007/s00199-016-0992-1 We define a measure of network cohesion and show how it arises naturally in a broad class of dynamic models of endogenous perpetual growth with network externalities. Via a standard growth model, we show why network cohesion is crucial for conditional convergence and explain that as cohesion increases, convergence is faster. We prove properties of network cohesion and d...

  11. Technical Network

    CERN Multimedia

    2007-01-01

    In order to optimize the management of the Technical Network (TN), to ease the understanding and purpose of devices connected to the TN, and to improve security incident handling, the Technical Network Administrators and the CNIC WG have asked IT/CS to verify the "description" and "tag" fields of devices connected to the TN. Therefore, persons responsible for systems connected to the TN will receive email notifications from IT/CS asking them to add the corresponding information in the network database. Thank you very much for your cooperation. The Technical Network Administrators & the CNIC WG

  12. Communication: Limitations of the stochastic quasi-steady-state approximation in open biochemical reaction networks

    Science.gov (United States)

    Thomas, Philipp; Straube, Arthur V.; Grima, Ramon

    2011-11-01

    It is commonly believed that, whenever timescale separation holds, the predictions of reduced chemical master equations obtained using the stochastic quasi-steady-state approximation are in very good agreement with the predictions of the full master equations. We use the linear noise approximation to obtain a simple formula for the relative error between the predictions of the two master equations for the Michaelis-Menten reaction with substrate input. The reduced approach is predicted to overestimate the variance of the substrate concentration fluctuations by as much as 30%. The theoretical results are validated by stochastic simulations using experimental parameter values for enzymes involved in proteolysis, gluconeogenesis, and fermentation.

  13. Identifying the molecular functions of electron transport proteins using radial basis function networks and biochemical properties.

    Science.gov (United States)

    Le, Nguyen-Quoc-Khanh; Nguyen, Trinh-Trung-Duong; Ou, Yu-Yen

    2017-05-01

    The electron transport proteins have an important role in storing and transferring electrons in cellular respiration, which is the most proficient process through which cells gather energy from consumed food. According to the molecular functions, the electron transport chain components could be formed with five complexes with several different electron carriers and functions. Therefore, identifying the molecular functions in the electron transport chain is vital for helping biologists understand the electron transport chain process and energy production in cells. This work includes two phases for discriminating electron transport proteins from transport proteins and classifying categories of five complexes in electron transport proteins. In the first phase, the performances from PSSM with AAIndex feature set were successful in identifying electron transport proteins in transport proteins with achieved sensitivity of 73.2%, specificity of 94.1%, and accuracy of 91.3%, with MCC of 0.64 for independent data set. With the second phase, our method can approach a precise model for identifying of five complexes with different molecular functions in electron transport proteins. The PSSM with AAIndex properties in five complexes achieved MCC of 0.51, 0.47, 0.42, 0.74, and 1.00 for independent data set, respectively. We suggest that our study could be a power model for determining new proteins that belongs into which molecular function of electron transport proteins. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Dynamic Modeling of Cell-Free Biochemical Networks Using Effective Kinetic Models

    Science.gov (United States)

    2015-03-16

    sensitivity value was the maximum uncertainty in that value estimated by the Sobol method. 2.4. Global Sensitivity Analysis of the Reduced Order Coagulation...sensitivity analysis, using the variance-based method of Sobol , to estimate which parameters controlled the performance of the reduced order model [69]. We...Environment. Comput. Sci. Eng. 2007, 9, 90–95. 69. Sobol , I. Global sensitivity indices for nonlinear mathematical models and their Monte Carlo estimates

  15. Overlay networks toward information networking

    CERN Document Server

    Tarkoma, Sasu

    2010-01-01

    With their ability to solve problems in massive information distribution and processing, while keeping scaling costs low, overlay systems represent a rapidly growing area of R&D with important implications for the evolution of Internet architecture. Inspired by the author's articles on content based routing, Overlay Networks: Toward Information Networking provides a complete introduction to overlay networks. Examining what they are and what kind of structures they require, the text covers the key structures, protocols, and algorithms used in overlay networks. It reviews the current state of th

  16. Probabilistic Networks

    DEFF Research Database (Denmark)

    Jensen, Finn Verner; Lauritzen, Steffen Lilholt

    2001-01-01

    This article describes the basic ideas and algorithms behind specification and inference in probabilistic networks based on directed acyclic graphs, undirected graphs, and chain graphs.......This article describes the basic ideas and algorithms behind specification and inference in probabilistic networks based on directed acyclic graphs, undirected graphs, and chain graphs....

  17. Bipartite Networks

    NARCIS (Netherlands)

    Agneessens, F.; Moser, C.; Barnett, G.A.

    2011-01-01

    Bipartite networks refer to a specific kind of network in which the nodes (or actors) can be partitioned into two subsets based on the fact that no links exist between actors within each subset, but only between the two subsets. Due to the partition of actors in two sets and the absence of relations

  18. Biochemical studies on some zooplankton off the west coast of India

    Digital Repository Service at National Institute of Oceanography (India)

    Goswami, S.C.; Rao, T.S.S.; Matondkar, S.G.P.

    Proximate biochemical analyses on twelve zooplankton species showed that protein was the predominant biochemical component followed by lipid. Carbohydrate content was very low especially in species with high water content or calcareous shell...

  19. Seasonal changes in meat weight and biochemical composition in the Black Clam Villorita cyprinoides (Grey)

    Digital Repository Service at National Institute of Oceanography (India)

    Ansari, Z.A.; Parulekar, A.H.; Matondkar, S.G.P.

    Seasonal changes in meat weight and biochemical composition are associated with reproduction, storage and utilization of reserves. The main period of increase in biochemical constituents corresponds to gametogenesis and maturation of gonads just...

  20. Homocystein: A new biochemical marker in livestock sector

    Directory of Open Access Journals (Sweden)

    Suleyman Kozat

    2017-12-01

    Full Text Available The livestock sector is making great contributions to the world economy. Many different diseases, such as cardiovascular diseases, kidney and mineral substance insufficiency, cause huge losses in yield and production in the livestock sector. Early diagnosis is essential to combat these diseases. Today, homocysteine levels are used as biochemical markers in the diagnosis of the functions and diseases of many different organs in human medicine. Homocysteine is an amino acid that occurs in the process of methionine metabolism and does not enter the primary structure of proteins. Homocysteine is a biochemical marker used in the assessment of cardiovascular and renal diseases as well as other organ functions. In this review, homocysteine determination methods and detailed information about which organ and system diseases can be used in livestock sector will be given. [J Adv Vet Anim Res 2017; 4(4.000: 319-332

  1. BIOCHEMICAL PROCESSES IN CHERNOZEM SOIL UNDER DIFFERENT FERTILIZATION SYSTEMS

    Directory of Open Access Journals (Sweden)

    Ecaterina Emnova

    2012-06-01

    Full Text Available The paper deals with the evaluation of the intensity of certain soil biochemical processes (e.g. soil organic C mineralization at Organic and mixed Mineral+Organic fertilization of typical chernozem in crop rotation dynamics (for 6 years by use of eco-physiological indicators of biological soil quality: microbial biomass carbon, basal soil respiration, as well as, microbial and metabolic quotients. Soil sampling was performed from a long-term field crop experiment, which has been established in 1971 at the Balti steppe (Northern Moldova. The crop types had a more considerable impact on the soil microbial biomass accumulation and community biochemical activity compared to long-term Organic or mixed Mineral + Organic fertilizers amendments. The Org fertilization system doesn’t make it possible to avoid the loss of organic C in arable typical chernozem. The organic fertilizer (cattle manure is able to mitigate the negative consequences of long-term mineral fertilization.

  2. Elevation of PSA after prostate radiotherapy: Rebound or biochemical recurrence?

    International Nuclear Information System (INIS)

    Toledano, A.; Kanoui, A.; Chiche, R.; Lamallem, H.; Beley, S.; Thibault, F.; Sebe, P.

    2008-01-01

    The fact that external beam radiotherapy and brachytherapy are now considered to be curative techniques has led to major review of the modalities of follow-up after radiotherapy for prostate cancer. The problem concerns both the diagnosis of recurrence, rapidly announced by elevation of prostatic-specific antigen (PSA), usually at a subclinical stage, and the validity of criteria of biochemical recurrence to allow comparison of various study. Physicians involved in follow-up should be aware of the potential of bounce in PSA follow-up after external beam radiotherapy or brachytherapy. The PSA bounce phenomenon was defined by a rise of PSA values (+ 0.1 -0.8 ng/ml) with a subsequent fall. Biochemical failure after external beam radiotherapy or brachytherapy (with or without hormonotherapy) was defined by Phoenix criteria by a rise of 2 ng/ml above an initial PSA nadir. This definition was more correlated to PSA bounce phenomenon. (authors)

  3. Biomphalaria prona (Gastropoda: Planorbidae: a morphological and biochemical study

    Directory of Open Access Journals (Sweden)

    W. Lobato Paraense

    1992-06-01

    Full Text Available Two samples of Biomphalaria prona (Martens, 1873 from Lake Valencia (type locality and seven from other Venezuelan localities were studied morphologically (shell and reproductive system and biochemically (allozyme electrophoresis. In spite of marked differences in shell characters, all of them proved indistinguishable under the anatomic and biochemical criteria. So far B. prona has been considered an endemic species, restricted to Lake Valencia. It is now demonstrated that the extralacustrine populations refered to Biomphalaria havanensis (Pfeiffer, 1839 by several authors correspond in shell characters to an extreme variant of B. prona from the Lake and really belong to the last*mentioned species. They may be regarded as the result of a process of directional selection favoring a shell phenotype other than those making up the modal class in the Lake.

  4. Temporal networks

    Science.gov (United States)

    Holme, Petter; Saramäki, Jari

    2012-10-01

    A great variety of systems in nature, society and technology-from the web of sexual contacts to the Internet, from the nervous system to power grids-can be modeled as graphs of vertices coupled by edges. The network structure, describing how the graph is wired, helps us understand, predict and optimize the behavior of dynamical systems. In many cases, however, the edges are not continuously active. As an example, in networks of communication via e-mail, text messages, or phone calls, edges represent sequences of instantaneous or practically instantaneous contacts. In some cases, edges are active for non-negligible periods of time: e.g., the proximity patterns of inpatients at hospitals can be represented by a graph where an edge between two individuals is on throughout the time they are at the same ward. Like network topology, the temporal structure of edge activations can affect dynamics of systems interacting through the network, from disease contagion on the network of patients to information diffusion over an e-mail network. In this review, we present the emergent field of temporal networks, and discuss methods for analyzing topological and temporal structure and models for elucidating their relation to the behavior of dynamical systems. In the light of traditional network theory, one can see this framework as moving the information of when things happen from the dynamical system on the network, to the network itself. Since fundamental properties, such as the transitivity of edges, do not necessarily hold in temporal networks, many of these methods need to be quite different from those for static networks. The study of temporal networks is very interdisciplinary in nature. Reflecting this, even the object of study has many names-temporal graphs, evolving graphs, time-varying graphs, time-aggregated graphs, time-stamped graphs, dynamic networks, dynamic graphs, dynamical graphs, and so on. This review covers different fields where temporal graphs are considered

  5. Network Affordances

    DEFF Research Database (Denmark)

    Samson, Audrey; Soon, Winnie

    2015-01-01

    This paper examines the notion of network affordance within the context of network art. Building on Gibson's theory (Gibson, 1979) we understand affordance as the perceived and actual parameters of a thing. We expand on Gaver's affordance of predictability (Gaver, 1996) to include ecological...... and computational parameters of unpredictability. We illustrate the notion of unpredictability by considering four specific works that were included in a network art exhibiton, SPEED SHOW [2.0] Hong Kong. The paper discusses how the artworks are contingent upon the parameteric relations (Parisi, 2013......), of the network. We introduce network affordance as a dynamic framework that could articulate the experienced tension arising from the (visible) symbolic representation of computational processes and its hidden occurrences. We base our proposal on the experience of both organising the SPEED SHOW and participating...

  6. Network chemistry, network toxicology, network informatics, and network behavioristics: A scientific outline

    OpenAIRE

    WenJun Zhang

    2016-01-01

    In present study, I proposed some new sciences: network chemistry, network toxicology, network informatics, and network behavioristics. The aims, scope and scientific foundation of these sciences are outlined.

  7. Accelerated maximum likelihood parameter estimation for stochastic biochemical systems

    Directory of Open Access Journals (Sweden)

    Daigle Bernie J

    2012-05-01

    Full Text Available Abstract Background A prerequisite for the mechanistic simulation of a biochemical system is detailed knowledge of its kinetic parameters. Despite recent experimental advances, the estimation of unknown parameter values from observed data is still a bottleneck for obtaining accurate simulation results. Many methods exist for parameter estimation in deterministic biochemical systems; methods for discrete stochastic systems are less well developed. Given the probabilistic nature of stochastic biochemical models, a natural approach is to choose parameter values that maximize the probability of the observed data with respect to the unknown parameters, a.k.a. the maximum likelihood parameter estimates (MLEs. MLE computation for all but the simplest models requires the simulation of many system trajectories that are consistent with experimental data. For models with unknown parameters, this presents a computational challenge, as the generation of consistent trajectories can be an extremely rare occurrence. Results We have developed Monte Carlo Expectation-Maximization with Modified Cross-Entropy Method (MCEM2: an accelerated method for calculating MLEs that combines advances in rare event simulation with a computationally efficient version of the Monte Carlo expectation-maximization (MCEM algorithm. Our method requires no prior knowledge regarding parameter values, and it automatically provides a multivariate parameter uncertainty estimate. We applied the method to five stochastic systems of increasing complexity, progressing from an analytically tractable pure-birth model to a computationally demanding model of yeast-polarization. Our results demonstrate that MCEM2 substantially accelerates MLE computation on all tested models when compared to a stand-alone version of MCEM. Additionally, we show how our method identifies parameter values for certain classes of models more accurately than two recently proposed computationally efficient methods

  8. The emergence of mass spectrometry in biochemical research

    OpenAIRE

    1995-01-01

    The initial steps toward routinely applying mass spectrometry in the biochemical laboratory have been achieved. In the past, mass spectrometry was confined to the realm of small, relatively stable molecules; large or thermally labile molecules did not survive the desorption and ionization processes intact. Electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry allow for the analysis of both small and large biomolecules through "mild" desorption...

  9. Advances in Metabolic Engineering of Cyanobacteria for Photosynthetic Biochemical Production

    OpenAIRE

    Lai, Martin C.; Lan, Ethan I.

    2015-01-01

    Engineering cyanobacteria into photosynthetic microbial cell factories for the production of biochemicals and biofuels is a promising approach toward sustainability. Cyanobacteria naturally grow on light and carbon dioxide, bypassing the need of fermentable plant biomass and arable land. By tapping into the central metabolism and rerouting carbon flux towards desirable compound production, cyanobacteria are engineered to directly convert CO2 into various chemicals. This review discusses the d...

  10. Biochemical genetics in marine fisheries management and conservation

    Digital Repository Service at National Institute of Oceanography (India)

    Menezes, M.R.

    - 403004 NBDBlDBTSponsored Training on Taxonomy, GOIdia turd Gme Bturking o/Coastal and Marine Bloresources, CIFE, Mumbal BIOCHEMICAL GENETICS IN MARINE FISHERIES MANAGEMENT AND CONSERVATION Maria R. Menezes Introduction . Species of fish, like most... population structure may have evolved and been maintained in species of fish ofeconomic interest has led to the concept of 'stock'. The stock concept dominates much of marine fisheries management, theory and practice because the identification of discrete...

  11. Biochemical mechanisms determine the functional compatibility of heterologous genes

    DEFF Research Database (Denmark)

    Porse, Andreas; Schou, Thea S.; Munck, Christian

    2018-01-01

    -gene libraries have suggested that sequence composition is a strong barrier for the successful integration of heterologous genes. Here we sample 200 diverse genes, representing >80% of sequenced antibiotic resistance genes, to interrogate the factors governing genetic compatibility in new hosts. In contrast...... factors governing the functionality and fitness of antibiotic resistance genes. These findings emphasize the importance of biochemical mechanism for heterologous gene compatibility, and suggest physiological constraints as a pivotal feature orienting the evolution of antibiotic resistance....

  12. Valuation of Biochemical and Microbiological Indicators in Soil Quality Assessment

    OpenAIRE

    Peruzzi, Elisabetta

    2017-01-01

    This thesis research aimed at valuating the suitability of biochemical and microbiological indicators in soil quality and soil health assessment, applying an interdisciplinary approach by means of different methodologies. As the concept of soil quality encompasses both functionality and biological diversity, two cases of study are proposed and each of them aimed at the description of this two aspects. The first case study examined the degree of interference of high soil copper contamination w...

  13. Intermittency route to chaos in a biochemical system.

    Science.gov (United States)

    De la Fuente, I M; Martinez, L; Veguillas, J

    1996-01-01

    The numerical analysis of a glycolytic model performed through the construction of a system of three differential-delay equations reveals a phenomenon of intermittency route to chaos. In our biochemical system, the consideration of delay time variations under constant input flux as well as frequency variations of the periodic substrate input flux allows us, in both cases, to observe a type of transition to chaos different from the 'Feigenbaum route'.

  14. Biochemical changes in diabetic retinopathy triggered by hyperglycaemia: A review

    Directory of Open Access Journals (Sweden)

    Solani D. Mathebula

    2018-04-01

    Full Text Available Background: Diabetes mellitus (DM is now a global health problem which will lead to increasing incidence of macrovascular and microvascular complications that contribute to morbidity, mortality and premature deaths. Diabetic retinopathy (DR is a serious complication of DM, and its prevalence is increasing worldwide. Diabetes mellitus is one of the fastest growing causes of visual impairment and blindness in the working-age population. Aim: The aim of this paper was to introduce the multiple interconnecting biochemical pathways that have been proposed and tested as key contributors in how the diabetic eye loses vision. Method: An extensive literature search was performed using the Medline database from 1970 to present. The search subjects included diabetes and eye, diabetic retinopathy and diabetic complications in the eye. The search was limited to the literature pertaining to humans and to English language. Preference was given to recent published papers. Results: Results were limited to human participants with publications in English. References of all included papers were also scrutinized to identify additional studies. Studies were selected for inclusion in the review if they met the following criteria: subjects with diabetes, pathophysiology of diabetic retinopathy. Conclusion: Although the biochemical pathways involved in DR have been researched, to date the exact mechanism involved in the onset and progression of the disease is uncertain, which makes therapeutic interventions challenging. The aim of this review is to discuss the possible biochemical pathways and clinical and anatomical changes that occur during the onset and progression of DR that link hyperglycaemia with retinal tissue damage. An understanding of the biochemical and molecular changes may lead to health care practitioners advising patients with DR on events that lead to possible complications of the diseases.

  15. Biochemical and biomechanical characterisation of equine cervical facet joint cartilage.

    Science.gov (United States)

    O'Leary, S A; White, J L; Hu, J C; Athanasiou, K A

    2018-04-15

    The equine cervical facet joint is a site of significant pathology. Located bilaterally on the dorsal spine, these diarthrodial joints work in conjunction with the intervertebral disc to facilitate appropriate spinal motion. Despite the high prevalence of pathology in this joint, the facet joint is understudied and thus lacking in viable treatment options. The goal of this study was to characterise equine facet joint cartilage and provide a comprehensive database describing the morphological, histological, biochemical and biomechanical properties of this tissue. Descriptive cadaver studies. A total of 132 facet joint surfaces were harvested from the cervical spines of six skeletally mature horses (11 surfaces per animal) for compiling biomechanical and biochemical properties of hyaline cartilage of the equine cervical facet joints. Gross morphometric measurements and histological staining were performed on facet joint cartilage. Creep indentation and uniaxial strain-to-failure testing were used to determine the biomechanical compressive and tensile properties. Biochemical assays included quantification of total collagen, sulfated glycosaminoglycan and DNA content. The facet joint surfaces were ovoid in shape with a flat articular surface. Histological analyses highlighted structures akin to articular cartilage of other synovial joints. In general, biomechanical and biochemical properties did not differ significantly between the inferior and superior joint surfaces as well as among spinal levels. Interestingly, compressive and tensile properties of cervical facet articular cartilage were lower than those of articular cartilage from other previously characterised equine joints. Removal of the superficial zone reduced the tissue's tensile strength, suggesting that this zone is important for the tensile integrity of the tissue. Facet surfaces were sampled at a single, central location and do not capture the potential topographic variation in cartilage properties. This

  16. Gluconeogenesis: An ancient biochemical pathway with a new twist

    OpenAIRE

    Miyamoto, Tetsuya; Amrein, Hubert

    2017-01-01

    Synthesis of sugars from simple carbon sources is critical for survival of animals under limited nutrient availability. Thus, sugar-synthesizing enzymes should be present across the entire metazoan spectrum. Here, we explore the evolution of glucose and trehalose synthesis using a phylogenetic analysis of enzymes specific for the two pathways. Our analysis reveals that the production of trehalose is the more ancestral biochemical process, found in single cell organisms and primitive metazoans...

  17. Pretreatment Endorectal Coil Magnetic Resonance Imaging Findings Predict Biochemical Tumor Control in Prostate Cancer Patients Treated With Combination Brachytherapy and External-Beam Radiotherapy

    International Nuclear Information System (INIS)

    Riaz, Nadeem; Afaq, Asim; Akin, Oguz; Pei Xin; Kollmeier, Marisa A.; Cox, Brett; Hricak, Hedvig; Zelefsky, Michael J.

    2012-01-01

    Purpose: To investigate the utility of endorectal coil magenetic resonance imaging (eMRI) in predicting biochemical relapse in prostate cancer patients treated with combination brachytherapy and external-beam radiotherapy. Methods and Materials: Between 2000 and 2008, 279 men with intermediate- or high-risk prostate cancer underwent eMRI of their prostate before receiving brachytherapy and supplemental intensity-modulated radiotherapy. Endorectal coil MRI was performed before treatment and retrospectively reviewed by two radiologists experienced in genitourinary MRI. Image-based variables, including tumor diameter, location, number of sextants involved, and the presence of extracapsular extension (ECE), were incorporated with other established clinical variables to predict biochemical control outcomes. The median follow-up was 49 months (range, 1–13 years). Results: The 5-year biochemical relapse-free survival for the cohort was 92%. Clinical findings predicting recurrence on univariate analysis included Gleason score (hazard ratio [HR] 3.6, p = 0.001), PSA (HR 1.04, p = 0.005), and National Comprehensive Cancer Network risk group (HR 4.1, p = 0.002). Clinical T stage and the use of androgen deprivation therapy were not correlated with biochemical failure. Imaging findings on univariate analysis associated with relapse included ECE on MRI (HR 3.79, p = 0.003), tumor size (HR 2.58, p = 0.04), and T stage (HR 1.71, p = 0.004). On multivariate analysis incorporating both clinical and imaging findings, only ECE on MRI and Gleason score were independent predictors of recurrence. Conclusions: Pretreatment eMRI findings predict for biochemical recurrence in intermediate- and high-risk prostate cancer patients treated with combination brachytherapy and external-beam radiotherapy. Gleason score and the presence of ECE on MRI were the only significant predictors of biochemical relapse in this group of patients.

  18. Relationship between obesity and biochemical markers in Brazilian adolescents

    Directory of Open Access Journals (Sweden)

    Alexandre Romero

    2014-03-01

    The aim of this study was to describe the prevalence of biochemical markers and associate with obesity in Brazilian adolescents enrolled in public schools in a rural area. The sample consisted of 199 adolescents between 10 to 14 years old from Piracicaba, Brazil. The obesity was measured by body mass index (BMI and according to the World Health Organization curves. We collected blood for biochemical markers analysis (total cholesterol, high density lipoprotein, low density lipoprotein, triacylglycerol, insulin and glycemia. Mann Whitney test was used to compare continuous variables between sexes. Chi-square test was used to compare proportions. To investigate the association between the independent variables and biochemical markers a multiple logistic regression model was performed. Among 199 adolescents, 23.1% was obese and 65.8% were insufficiently active. A high prevalence of dyslipidemia (71.4% was observed, whereas the low levels of high density lipoprotein (40.7% were the most prevalent. An association between obesity and undesirable values for high density lipoprotein, triacylglycerol and insulin resistance was found. Obese adolescents were less likely to present a desirable value for high density lipoprotein. It is understood that obesity is detrimental to metabolic profile and should be prevented and treated even in adolescence.

  19. Considerations on the biochemical composition of some freshwater zooplankton species.

    Directory of Open Access Journals (Sweden)

    Nicoletta RICCARDI

    1999-02-01

    Full Text Available The mean elemental (C, H, N and biochemical composition (lipids, carbohydrates and proteins of some abundant crustacean zooplankton species of Italian insubric lakes has been estimated by the analysis of samples collected at different seasons from various environments (Lake Maggiore, Lake Varese, Lake Comabbio, Lake Monate. From each sample an adequate number of specimens of each abundant species was sorted and analyzed by a CHN elemental analyzer. The percentage of lipids, carbohydrates and proteins and the calorific content were calculated from the elemental composition according to Gnaiger & Bitterlich (1984. Inter- and intraspecific variability of biochemical composition was quite high, while elemental composition and calorific content were less variable. An estimate of the mean elemental and biochemical composition of each species was obtained by pooling the data. These mean values have been used to estimate the pools of elements and compounds in the crustacean zooplankton of Lake Comabbio to provide an example of the importance of a multiple approach in zooplankton studies.

  20. Identification of biochemical features of defective Coffea arabica L. beans.

    Science.gov (United States)

    Casas, María I; Vaughan, Michael J; Bonello, Pierluigi; McSpadden Gardener, Brian; Grotewold, Erich; Alonso, Ana P

    2017-05-01

    Coffee organoleptic properties are based in part on the quality and chemical composition of coffee beans. The presence of defective beans during processing and roasting contribute to off flavors and reduce overall cup quality. A multipronged approach was undertaken to identify specific biochemical markers for defective beans. To this end, beans were split into defective and non-defective fractions and biochemically profiled in both green and roasted states. A set of 17 compounds in green beans, including organic acids, amino acids and reducing sugars; and 35 compounds in roasted beans, dominated by volatile compounds, organic acids, sugars and sugar alcohols, were sufficient to separate the defective and non-defective fractions. Unsorted coffee was examined for the presence of the biochemical markers to test their utility in detecting defective beans. Although the green coffee marker compounds were found in all fractions, three of the roasted coffee marker compounds (1-methylpyrrole, 5-methyl- 2-furfurylfuran, and 2-methylfuran) were uniquely present in defective fractions. Published by Elsevier Ltd.

  1. Improved biochemical preservation of heart slices during cold storage.

    Science.gov (United States)

    Bull, D A; Reid, B B; Connors, R C; Albanil, A; Stringham, J C; Karwande, S V

    2000-01-01

    Development of myocardial preservation solutions requires the use of whole organ models which are animal and labor intensive. These models rely on physiologic rather than biochemical endpoints, making accurate comparison of the relative efficacy of individual solution components difficult. We hypothesized that myocardial slices could be used to assess preservation of biochemical function during cold storage. Whole rat hearts were precision cut into slices with a thickness of 200 microm and preserved at 4 degrees C in one of the following solutions: Columbia University (CU), University of Wisconsin (UW), D5 0.2% normal saline with 20 meq/l KCL (QNS), normal saline (NS), or a novel cardiac preservation solution (NPS) developed using this model. Myocardial biochemical function was assessed by ATP content (etamoles ATP/mg wet weight) and capacity for protein synthesis (counts per minute (cpm)/mg protein) immediately following slicing (0 hours), and at 6, 12, 18, and 24 hours of cold storage. Six slices were assayed at each time point for each solution. The data were analyzed using analysis of variance and are presented as the mean +/- standard deviation. ATP content was higher in the heart slices stored in the NPS compared to all other solutions at 6, 12, 18 and 24 hours of cold storage (p cold storage (p cold storage.

  2. Improved biochemical preservation of lung slices during cold storage.

    Science.gov (United States)

    Bull, D A; Connors, R C; Reid, B B; Albanil, A; Stringham, J C; Karwande, S V

    2000-05-15

    Development of lung preservation solutions typically requires whole-organ models which are animal and labor intensive. These models rely on physiologic rather than biochemical endpoints, making accurate comparison of the relative efficacy of individual solution components difficult. We hypothesized that lung slices could be used to assess preservation of biochemical function during cold storage. Whole rat lungs were precision cut into slices with a thickness of 500 microm and preserved at 4 degrees C in the following solutions: University of Wisconsin (UW), Euro-Collins (EC), low-potassium-dextran (LPD), Kyoto (K), normal saline (NS), or a novel lung preservation solution (NPS) developed using this model. Lung biochemical function was assessed by ATP content (etamol ATP/mg wet wt) and capacity for protein synthesis (cpm/mg protein) immediately following slicing (0 h) and at 6, 12, 18, and 24 h of cold storage. Six slices were assayed at each time point for each solution. The data were analyzed using analysis of variance and are presented as means +/- SD. ATP content was significantly higher in the lung slices stored in NPS compared with all other solutions at each time point (P cold storage. Copyright 2000 Academic Press.

  3. Biochemical recurrence after radical prostatectomy: what does it mean?

    Science.gov (United States)

    Tourinho-Barbosa, Rafael; Srougi, Victor; Nunes-Silva, Igor; Baghdadi, Mohammed; Rembeyo, Gregory; Eiffel, Sophie S.; Barret, Eric; Rozet, Francois; Galiano, Marc; Cathelineau, Xavier; Sanchez-Salas, Rafael

    2018-01-01

    ABSTRACT Background Radical prostatectomy (RP) has been used as the main primary treatment for prostate cancer (PCa) for many years with excellent oncologic results. However, approximately 20-40% of those patients has failed to RP and presented biochemical recurrence (BCR). Prostatic specific antigen (PSA) has been the pivotal tool for recurrence diagnosis, but there is no consensus about the best PSA threshold to define BCR until this moment. The natural history of BCR after surgical procedure is highly variable, but it is important to distinguish biochemical and clinical recurrence and to find the correct timing to start multimodal treatment strategy. Also, it is important to understand the role of each clinical and pathological feature of prostate cancer in BCR, progression to metastatic disease and cancer specific mortality (CSM). Review design A simple review was made in Medline for articles written in English language about biochemical recurrence after radical prostatectomy. Objective To provide an updated assessment of BCR definition, its meaning, PCa natural history after BCR and the weight of each clinical/pathological feature and risk group classifications in BCR, metastatic disease and CSM. PMID:29039897

  4. PHYSIOLOGICAL AND BIOCHEMICAL MARKERS OF SALINITY TOLERANCE IN PLANTS

    Directory of Open Access Journals (Sweden)

    Mustafa YILDIZ

    2011-02-01

    Full Text Available Salt stress limits plant productivity in arid and semi arid regions. Salt stress causes decrease in plant growth by adversely affecting physiological processes, especially photosynthesis. Salinity tolerance is defined as the ability of plant to maintain normal rowth and development under salt conditions. Salt stress results in accumulation of low molecular weight compounds, termed compatible solutes, which do not interfere with the normal biochemical reactions. These compatible solutes such as carbohydrates, polyols, amino acids and amides, quaternary ammonium compounds, polyamines andsoluble proteins may play a crucial role in osmotic adjustment, protection of macromolecules, maintenance of cellular pH and detoxification of free radicals. On the other hand, plants subjected to environmental stresses such as salinity produce reactive oxygen species (ROS and these ROS are efficiently eliminated by antioxidant enzyme systems. In plant breeding studies, the use of some physiological and biochemical markers for improving the salt tolerance in plants is crucial. In this review, the possibility of using some physiological and biochemical markers as selection criteria for salt tolerance is discussed.

  5. Biochemical and biomedical applications of multifunctional magnetic nanoparticles: a review

    International Nuclear Information System (INIS)

    Huang, Shih-Hung; Juang, Ruey-Shin

    2011-01-01

    Nanotechnology offers tremendous potential for future medical diagnosis and therapy. Various types of nanoparticles have been extensively studied for numerous biochemical and biomedical applications. Magnetic nanoparticles are well-established nanomaterials that offer controlled size, ability to be manipulated by an external magnetic field, and enhancement of contrast in magnetic resonance imaging. As a result, these nanoparticles could have many applications including bacterial detection, protein purification, enzyme immobilization, contamination decorporation, drug delivery, hyperthermia, etc. All these biochemical and biomedical applications require that these nanoparticles should satisfy some prerequisites including high magnetization, good stability, biocompatibility, and biodegradability. Because of the potential benefits of multimodal functionality in biomedical applications, in this account highlights some general strategies to generate magnetic nanoparticle-based multifunctional nanostructures. After these magnetic nanoparticles are conjugated with proper ligands (e.g., nitrilotriacetate), polymers (e.g., polyacrylic acid, chitosan, temperature- and pH-sensitive polymers), antibodies, enzymes, and inorganic metals (e.g., gold), such biofunctional magnetic nanoparticles exhibit many advantages in biomedical applications. In addition, the multifunctional magnetic nanoparticles have been widely applied in biochemical fields including enzyme immobilization and protein purification.

  6. Polyphenol Oxidase as a Biochemical Seed Defense Mechanism

    Directory of Open Access Journals (Sweden)

    E. Patrick Fuerst

    2014-12-01

    Full Text Available Seed dormancy and resistance to decay are fundamental survival strategies, which allow a population of seeds to germinate over long periods of time. Seeds have physical, chemical, and biological defense mechanisms that protect their food reserves from decay-inducing organisms and herbivores. Here, we hypothesize that seeds also possess enzyme-based biochemical defenses, based on induction of the plant defense enzyme, polyphenol oxidase (PPO, when wild oat (Avena fatua L. caryopses and seeds were challenged with seed-decaying Fusarium fungi. These studies suggest that dormant seeds are capable of mounting a defense response to pathogens. The pathogen-induced PPO activity from wild oat was attributed to a soluble isoform of the enzyme that appeared to result, at least in part, from proteolytic activation of a latent PPO isoform. PPO activity was also induced in wild oat hulls (lemma and palea, non-living tissues that cover and protect the caryopsis. These results are consistent with the hypothesis that seeds possess inducible enzyme-based biochemical defenses arrayed on the exterior of seeds and these defenses represent a fundamental mechanism of seed survival and longevity in the soil. Enzyme-based biochemical defenses may have broader implications since they may apply to other defense enzymes as well as to a diversity of plant species and ecosystems.

  7. Modelling biochemical reaction systems by stochastic differential equations with reflection.

    Science.gov (United States)

    Niu, Yuanling; Burrage, Kevin; Chen, Luonan

    2016-05-07

    In this paper, we gave a new framework for modelling and simulating biochemical reaction systems by stochastic differential equations with reflection not in a heuristic way but in a mathematical way. The model is computationally efficient compared with the discrete-state Markov chain approach, and it ensures that both analytic and numerical solutions remain in a biologically plausible region. Specifically, our model mathematically ensures that species numbers lie in the domain D, which is a physical constraint for biochemical reactions, in contrast to the previous models. The domain D is actually obtained according to the structure of the corresponding chemical Langevin equations, i.e., the boundary is inherent in the biochemical reaction system. A variant of projection method was employed to solve the reflected stochastic differential equation model, and it includes three simple steps, i.e., Euler-Maruyama method was applied to the equations first, and then check whether or not the point lies within the domain D, and if not perform an orthogonal projection. It is found that the projection onto the closure D¯ is the solution to a convex quadratic programming problem. Thus, existing methods for the convex quadratic programming problem can be employed for the orthogonal projection map. Numerical tests on several important problems in biological systems confirmed the efficiency and accuracy of this approach. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Studies on some biochemical parameters in viral hepatitis patients

    International Nuclear Information System (INIS)

    El-Sherbiny, E.M.

    2002-01-01

    The present investigation deals with studying liver amino transferases (ALT. AST). Cholesterol and triglycerides. As well as testosterone and protection hormones in blood of Egyptian men infected with hepatitis C virus.hepatitis B virus and mixed B and C viruses. These biochemical parameters were evaluated to be used in diagnosis and prognosis of viral hepatitis. Which considered the most important health problem in Egypt and developing countries. Biochemical analysis were performed using spectrophotometric and radioimmunoassay techniques. All data will be subjected to statistical analysis in order to detect the most suitable biochemical analysis that can be used as specific tests for early diagnosis of viral hepatitis and to detect the parameters that show abnormalities among the different groups of infected patients. The data revealed that AST and ALT levels were increased in all patient groups. Concerning the level of triglycerides, it was increased only in the group of mixed viral hepatitis B and C, while cholesterol showed non-significant changes in all viral hepatitis groups. The sex hormone testosterone was decreased in all infected patients while the prolactin level was increased only in case of patients infected with mixed B and C viruses. However, these abnormal values in such sex hormones play a serious role in male sterility

  9. BIOCHEMICAL NUTRITIONAL PROFILE OF LIVER CIRRHOSIS PATIENTS WITH HEPATOCELLULAR CARCINOMA

    Directory of Open Access Journals (Sweden)

    Gabriela Zanatta PORT

    2014-03-01

    Full Text Available Context Liver cirrhosis patients with hepatocellular carcinoma present nutritional alterations and metabolic disorders that negatively impact the prognosis. Objective The objective is to identify alterations in the metabolism of macro and micronutrients among liver cirrhosis patients with and without hepatocellular carcinoma and their relation to the Child-Turcote-Pugh score and Barcelona Clinic Liver Cancer staging. Methods Analytical transversal study, with 31 hepatocellular carcinoma patients and 48 liver cirrhosis patients. Laboratorial exams were carried out. The existence of an association between the biochemical parameters and the disease severity as well as the presence of hepatocellular carcinoma was assessed. Results The metabolic-nutritional profile of liver cirrhosis patients caused by the hepatitis C virus and hepatocellular carcinoma showed alterations, specifically the lipid (total cholesterol, HDL and triglycerides, protein (albumin, creatinine and uric acid, iron (transferrin, iron and ferritin saturation, hematocrit and hemoglobin, zinc and B12 vitamin profiles. There is a relation between nutritional biochemical markers and the Child-Turcote-Pugh, as well as Barcelona Clinic Liver Cancer staging. Conclusions Considering the existence of alterations in the metabolism of nutrients in liver cirrhosis patients with and without hepatocellular carcinoma, and also that conventional nutritional assessment methods present limitations for this population, the biochemical laboratorial exams are valid to complement the diagnosis of the nutritional state in a quick and practical manner.

  10. Biochemical comparison of osteoarthritic knees with and without effusion

    Science.gov (United States)

    2011-01-01

    Background Several symptom-relieving interventions have been shown to be efficacious among osteoarthritis (OA) patients with knee effusion; however, not every symptomatic knee OA patient has clinical effusion. Results may be over-generalized since it is unclear if effused knees represent a unique pathological condition or subset compared to knees without effusion. The primary purpose of this study was to determine if biochemical differences existed between OA knees with and without effusion. Methods The present cross-sectional study consisted of 22 volunteers (11 with knee effusion, 11 without knee effusion) with confirmed late-stage radiographic knee OA (Kellgren-Lawrence score ≥ 3). Synovial fluid samples were collected and analyzed using a custom multiplex enzyme-linked immunosorbent assay to determine eight specific biomarker concentrations (e.g., catabolic, anabolic). Results Matrix metalloproteinase (MMP)-3, tissue inhibitor of MMPs (TIMP)-1, TIMP-2, and interleukin-10 were significantly higher in the knees with effusion than in the knees without effusion. Conclusions The biochemical differences that existed between knees with and without effusion provide support that OA subsets may exist, characterized by distinct biochemical characteristics and clinical findings (e.g., effusion). PMID:22122951

  11. Discovering Reliable Sources of Biochemical Thermodynamic Data to Aid Students' Understanding

    Science.gov (United States)

    Me´ndez, Eduardo; Cerda´, María F.

    2016-01-01

    Students of physical chemistry in biochemical disciplines need biochemical examples to capture the need, not always understood, of a difficult area in their studies. The use of thermodynamic data in the chemical reference state may lead to incorrect interpretations in the analysis of biochemical examples when the analysis does not include relevant…

  12. 40 CFR 158.2080 - Experimental use permit data requirements-biochemical pesticides.

    Science.gov (United States)

    2010-07-01

    ... requirements-biochemical pesticides. 158.2080 Section 158.2080 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2080 Experimental use permit data requirements—biochemical pesticides. (a) Sections 158.2081...

  13. Reconstructed Ancestral Enzymes Impose a Fitness Cost upon Modern Bacteria Despite Exhibiting Favourable Biochemical Properties.

    Science.gov (United States)

    Hobbs, Joanne K; Prentice, Erica J; Groussin, Mathieu; Arcus, Vickery L

    2015-10-01

    Ancestral sequence reconstruction has been widely used to study historical enzyme evolution, both from biochemical and cellular perspectives. Two properties of reconstructed ancestral proteins/enzymes are commonly reported--high thermostability and high catalytic activity--compared with their contemporaries. Increased protein stability is associated with lower aggregation rates, higher soluble protein abundance and a greater capacity to evolve, and therefore, these proteins could be considered "superior" to their contemporary counterparts. In this study, we investigate the relationship between the favourable in vitro biochemical properties of reconstructed ancestral enzymes and the organismal fitness they confer in vivo. We have previously reconstructed several ancestors of the enzyme LeuB, which is essential for leucine biosynthesis. Our initial fitness experiments revealed that overexpression of ANC4, a reconstructed LeuB that exhibits high stability and activity, was only able to partially rescue the growth of a ΔleuB strain, and that a strain complemented with this enzyme was outcompeted by strains carrying one of its descendants. When we expanded our study to include five reconstructed LeuBs and one contemporary, we found that neither in vitro protein stability nor the catalytic rate was correlated with fitness. Instead, fitness showed a strong, negative correlation with estimated evolutionary age (based on phylogenetic relationships). Our findings suggest that, for reconstructed ancestral enzymes, superior in vitro properties do not translate into organismal fitness in vivo. The molecular basis of the relationship between fitness and the inferred age of ancestral LeuB enzymes is unknown, but may be related to the reconstruction process. We also hypothesise that the ancestral enzymes may be incompatible with the other, contemporary enzymes of the metabolic network.

  14. On the Interplay between the Evolvability and Network Robustness in an Evolutionary Biological Network: A Systems Biology Approach

    Science.gov (United States)

    Chen, Bor-Sen; Lin, Ying-Po

    2011-01-01

    In the evolutionary process, the random transmission and mutation of genes provide biological diversities for natural selection. In order to preserve functional phenotypes between generations, gene networks need to evolve robustly under the influence of random perturbations. Therefore, the robustness of the phenotype, in the evolutionary process, exerts a selection force on gene networks to keep network functions. However, gene networks need to adjust, by variations in genetic content, to generate phenotypes for new challenges in the network’s evolution, ie, the evolvability. Hence, there should be some interplay between the evolvability and network robustness in evolutionary gene networks. In this study, the interplay between the evolvability and network robustness of a gene network and a biochemical network is discussed from a nonlinear stochastic system point of view. It was found that if the genetic robustness plus environmental robustness is less than the network robustness, the phenotype of the biological network is robust in evolution. The tradeoff between the genetic robustness and environmental robustness in evolution is discussed from the stochastic stability robustness and sensitivity of the nonlinear stochastic biological network, which may be relevant to the statistical tradeoff between bias and variance, the so-called bias/variance dilemma. Further, the tradeoff could be considered as an antagonistic pleiotropic action of a gene network and discussed from the systems biology perspective. PMID:22084563

  15. Accelerating networks

    International Nuclear Information System (INIS)

    Smith, David M D; Onnela, Jukka-Pekka; Johnson, Neil F

    2007-01-01

    Evolving out-of-equilibrium networks have been under intense scrutiny recently. In many real-world settings the number of links added per new node is not constant but depends on the time at which the node is introduced in the system. This simple idea gives rise to the concept of accelerating networks, for which we review an existing definition and-after finding it somewhat constrictive-offer a new definition. The new definition provided here views network acceleration as a time dependent property of a given system as opposed to being a property of the specific algorithm applied to grow the network. The definition also covers both unweighted and weighted networks. As time-stamped network data becomes increasingly available, the proposed measures may be easily applied to such empirical datasets. As a simple case study we apply the concepts to study the evolution of three different instances of Wikipedia, namely, those in English, German, and Japanese, and find that the networks undergo different acceleration regimes in their evolution

  16. Social networks

    CERN Document Server

    Etaner-Uyar, A Sima

    2014-01-01

    The present volume provides a comprehensive resource for practitioners and researchers alike-both those new to the field as well as those who already have some experience. The work covers Social Network Analysis theory and methods with a focus on current applications and case studies applied in various domains such as mobile networks, security, machine learning and health. With the increasing popularity of Web 2.0, social media has become a widely used communication platform. Parallel to this development, Social Network Analysis gained in importance as a research field, while opening up many

  17. Network Warrior

    CERN Document Server

    Donahue, Gary

    2011-01-01

    Pick up where certification exams leave off. With this practical, in-depth guide to the entire network infrastructure, you'll learn how to deal with real Cisco networks, rather than the hypothetical situations presented on exams like the CCNA. Network Warrior takes you step by step through the world of routers, switches, firewalls, and other technologies based on the author's extensive field experience. You'll find new content for MPLS, IPv6, VoIP, and wireless in this completely revised second edition, along with examples of Cisco Nexus 5000 and 7000 switches throughout. Topics include: An

  18. Heterodox networks

    DEFF Research Database (Denmark)

    Lala, Purnima; Kumar, Ambuj

    2016-01-01

    It is imperative for the service providers to bring innovation in the network design to meet the exponential growth of mobile subscribers for multi-technology future wireless networks. As a matter of research, studies on providing services to moving subscriber groups aka ‘Place Time Capacity (PTC......)’ have not been considered much in the literature. In this article we present Heterodox networks as an innovative and alternate approach to handle the PTC congestion. We describe two different approaches to combat the PTC congestion where the traditional terrestrial infrastructure fails to provide......-Configurable Intelligent Distributed Antenna System (SCIDAS)’ that overlays intelligence over the conventional DAS architecture and latter is in the form of a swarm of intelligent hovering base stations working in a team to cooperatively resolve the PTC congestion at the Area of Event (AoE). A suitable network...

  19. Networking Japan

    DEFF Research Database (Denmark)

    Hansen, Annette Skovsted

    Human Resource Development was the first and remains an important pillar in Japanese foreign aid. I will argue that Japan has access to a global network of alumni who will co-define Japanese foreign aid in the future, because Japan has encouraged alumni societies and networking since 1965. A total...... of more than a million people in more than 100 countries have attended courses in Japan funded fully or partly by Japanese ODA since the inception of the technical assistance programs in 1954 through the Colombo Plan and since 1959 through the Association of Overseas Technical Scholarships (AOTS from 2009...... HIDA). Many of these alumni have and will in the future exchange ideas and keep contact not only to Japan, but also to fellow alumni around the globe and, thereby, practice south-south exchanges, which are made possible and traceable by their established alumni network and the World Network of Friends...

  20. Sentinel Network

    Science.gov (United States)

    The Sentinel Network is an integrated, electronic, national medical product safety initiative that compiles information about the safe and effective use of medical products accessible to patients and healthcare practitioners.

  1. Exchange Network

    Science.gov (United States)

    The Environmental Information Exchange Network (EN) is an Internet-based system used by state, tribal and territorial partners to securely share environmental and health information with one another and EPA.

  2. Diversity Networks

    Science.gov (United States)

    and professional growth of women through networking, mentoring and training. We strive to ensure that will be used. National Processing Center Seniors Leader: Jo Anne Hankins Champion: Eric Milliner NO

  3. Nepal Networking

    DEFF Research Database (Denmark)

    Hansen, Annette Skovsted

    , as a Danida fellow. Today, the older sister works in Nepal and the younger in Seattle, where they still make use of their personal networks including connections to their fellow alumni of technical assistance courses. Inspired by work on social remittances in combination with network theory , I argue......Technical Assistance courses have many functions apart from disseminating knowledge and information, one such function is to engender networks. During the course period, participants meet and establish contact and some of these contacts remain connections between alumni for many years after...... the courses are finished. The alumni networks depend on the uses they are put to by the individual alumni and the support they get from alumni and host countries. The United Nations initiated technical assistance courses in the late 1940s in order to train nationals from developing countries as a means...

  4. computer networks

    Directory of Open Access Journals (Sweden)

    N. U. Ahmed

    2002-01-01

    Full Text Available In this paper, we construct a new dynamic model for the Token Bucket (TB algorithm used in computer networks and use systems approach for its analysis. This model is then augmented by adding a dynamic model for a multiplexor at an access node where the TB exercises a policing function. In the model, traffic policing, multiplexing and network utilization are formally defined. Based on the model, we study such issues as (quality of service QoS, traffic sizing and network dimensioning. Also we propose an algorithm using feedback control to improve QoS and network utilization. Applying MPEG video traces as the input traffic to the model, we verify the usefulness and effectiveness of our model.

  5. Neural networks

    International Nuclear Information System (INIS)

    Denby, Bruce; Lindsey, Clark; Lyons, Louis

    1992-01-01

    The 1980s saw a tremendous renewal of interest in 'neural' information processing systems, or 'artificial neural networks', among computer scientists and computational biologists studying cognition. Since then, the growth of interest in neural networks in high energy physics, fueled by the need for new information processing technologies for the next generation of high energy proton colliders, can only be described as explosive

  6. Pintadas network

    OpenAIRE

    Cruz, Maria do Carmo Meirelles T.

    2006-01-01

    The Pintadas Network has been organized in Pintadas, a small municipality (11.254 inhabitants) in Bahia, located in the semi-arid region. It has been composed by civil society organizacions (social, productive, cultural and religious organizations and a credit cooperative), with support from the local town hall and from national and international institutions. The Network is a space for articulation, which intends to formulate, execute, follow-up, inspect and evaluate the municipal public pol...

  7. Organizational Networks

    DEFF Research Database (Denmark)

    Grande, Bård; Sørensen, Ole Henning

    1998-01-01

    The paper focuses on the concept of organizational networks. Four different uses of the concept of organizational network are identified and critically discussed. Special focus is placed on how information and communication technologies as communication mediators and cognitive pictures influence...... the organizational forms discussed in the paper. It is asserted that the underlying organizational phenomena are not changing but that the manifestations and representations are shifting due to technological developments....

  8. Complex Networks

    CERN Document Server

    Evsukoff, Alexandre; González, Marta

    2013-01-01

    In the last decade we have seen the emergence of a new inter-disciplinary field focusing on the understanding of networks which are dynamic, large, open, and have a structure sometimes called random-biased. The field of Complex Networks is helping us better understand many complex phenomena such as the spread of  deseases, protein interactions, social relationships, to name but a few. Studies in Complex Networks are gaining attention due to some major scientific breakthroughs proposed by network scientists helping us understand and model interactions contained in large datasets. In fact, if we could point to one event leading to the widespread use of complex network analysis is the availability of online databases. Theories of Random Graphs from Erdös and Rényi from the late 1950s led us to believe that most networks had random characteristics. The work on large online datasets told us otherwise. Starting with the work of Barabási and Albert as well as Watts and Strogatz in the late 1990s, we now know th...

  9. GKIN: a tool for drawing genetic networks

    Directory of Open Access Journals (Sweden)

    Jonathan Arnold

    2012-03-01

    Full Text Available We present GKIN, a simulator and a comprehensive graphical interface where one can draw the model specification of reactions between hypothesized molecular participants in a gene regulatory and biochemical reaction network (or genetic network for short. The solver is written in C++ in a nearly platform independentmanner to simulate large ensembles of models, which can run on PCs, Macintoshes, and UNIX machines, and its graphical user interface is written in Java which can run as a standalone or WebStart application. The drawing capability for rendering a network significantly enhances the ease of use of other reaction network simulators, such as KINSOLVER (Aleman-Meza et al., 2009 and enforces a correct semantic specification of the network. In a usability study with novice users, drawing the network with GKIN was preferred and faster in comparison with entry with a dialog-box guided interface in COPASI (Hoops, et al., 2006 with no difference in error rates between GKIN and COPASI in specifying the network. GKIN is freely available at http://faculty.cs.wit.edu/~ldeligia/PROJECTS/GKIN/.

  10. Markovian dynamics on complex reaction networks

    Energy Technology Data Exchange (ETDEWEB)

    Goutsias, J., E-mail: goutsias@jhu.edu; Jenkinson, G., E-mail: jenkinson@jhu.edu

    2013-08-10

    Complex networks, comprised of individual elements that interact with each other through reaction channels, are ubiquitous across many scientific and engineering disciplines. Examples include biochemical, pharmacokinetic, epidemiological, ecological, social, neural, and multi-agent networks. A common approach to modeling such networks is by a master equation that governs the dynamic evolution of the joint probability mass function of the underlying population process and naturally leads to Markovian dynamics for such process. Due however to the nonlinear nature of most reactions and the large size of the underlying state-spaces, computation and analysis of the resulting stochastic population dynamics is a difficult task. This review article provides a coherent and comprehensive coverage of recently developed approaches and methods to tackle this problem. After reviewing a general framework for modeling Markovian reaction networks and giving specific examples, the authors present numerical and computational techniques capable of evaluating or approximating the solution of the master equation, discuss a recently developed approach for studying the stationary behavior of Markovian reaction networks using a potential energy landscape perspective, and provide an introduction to the emerging theory of thermodynamic analysis of such networks. Three representative problems of opinion formation, transcription regulation, and neural network dynamics are used as illustrative examples.

  11. Markovian dynamics on complex reaction networks

    International Nuclear Information System (INIS)

    Goutsias, J.; Jenkinson, G.

    2013-01-01

    Complex networks, comprised of individual elements that interact with each other through reaction channels, are ubiquitous across many scientific and engineering disciplines. Examples include biochemical, pharmacokinetic, epidemiological, ecological, social, neural, and multi-agent networks. A common approach to modeling such networks is by a master equation that governs the dynamic evolution of the joint probability mass function of the underlying population process and naturally leads to Markovian dynamics for such process. Due however to the nonlinear nature of most reactions and the large size of the underlying state-spaces, computation and analysis of the resulting stochastic population dynamics is a difficult task. This review article provides a coherent and comprehensive coverage of recently developed approaches and methods to tackle this problem. After reviewing a general framework for modeling Markovian reaction networks and giving specific examples, the authors present numerical and computational techniques capable of evaluating or approximating the solution of the master equation, discuss a recently developed approach for studying the stationary behavior of Markovian reaction networks using a potential energy landscape perspective, and provide an introduction to the emerging theory of thermodynamic analysis of such networks. Three representative problems of opinion formation, transcription regulation, and neural network dynamics are used as illustrative examples

  12. Biochemical Post-Irradiation Changes and Radiation Indicators: A Review

    Energy Technology Data Exchange (ETDEWEB)

    Streffer, G. [Radiologisches Institut, University of Freiburg, Freiburg im Breisgau, Federal Republic of Germany (Germany)

    1971-03-15

    In a number of mammalian tissues a breakdown of the biological macromolecules, as nucleic acids and proteins, is observed after irradiation. This degradation appears in lymphatic tissues even after a radiation exposure less than 100 R and proceeds with increasing exposure to about 600 R. On the other hand, other biochemical effects are found after the whole-body irradiation of mammals which seem to have some relation to the functional status of the organs and the organisms. It appears therefore useful to classify the biochemical effects of radiation into two groups: (1) Observations which are a consequence of the degradation processes; (2) observations which are a consequence of functional changes. Most investigations in the field of biochemical indicators after irradiation have been concerned with the first class of reactions. The excretion of deoxycytidine, thymidine and pseudouridine have been extensively investigated in animals during recent years. However, in humans the normal deoxycytidine excretion is very low, as this substance is metabolized to a higher degree in humans than in other species. {beta}-aminoisobutyric acid (BAIBA), a metabolite of thymine, was also investigated in this connection. Besides nucleic acids, proteins are broken down in these radiosensitive organs. This leads to an increased content of amino acids for instance in the lymphatic tissues and to an increase in urinary excretion of amino acids. There are two amino acids which play a special role for this discussion: cysteine and tryptophan. Taurine, a metabolite of cysteine, is excreted in the urine to an increased extent after the irradiation of mice, rats and man. Again the enhancement is proportional to the radiation exposure between 100 and 300 R. Another substance which has been extensively studied is creatine. It has been shown that there is a good relationship between radiation exposure (up to about 600 R) and the increased excretion of creatine/creatinine in the urine of rats

  13. Self-organizing ontology of biochemically relevant small molecules.

    Science.gov (United States)

    Chepelev, Leonid L; Hastings, Janna; Ennis, Marcus; Steinbeck, Christoph; Dumontier, Michel

    2012-01-06

    The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while providing new challenges, the biggest being the curation, annotation, and classification of this information to facilitate useful biochemical pattern analysis. Unfortunately, the human resources currently employed by the organizations supporting these efforts (e.g. ChEBI) are expanding linearly, while new useful scientific information is being released in a seemingly exponential fashion. Compounding this, currently existing chemical classification and annotation systems are not amenable to automated classification, formal and transparent chemical class definition axiomatization, facile class redefinition, or novel class integration, thus further limiting chemical ontology growth by necessitating human involvement in curation. Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest. To address this, we present a formal framework based on Semantic Web technologies for the automatic design of chemical ontology which can be used for automated classification of novel entities. We demonstrate the automatic self-assembly of a structure-based chemical ontology based on 60 MeSH and 40 ChEBI chemical classes. This ontology is then used to classify 200 compounds with an accuracy of 92.7%. We extend these structure-based classes with molecular feature information and demonstrate the utility of our framework for classification of functionally relevant chemicals. Finally, we discuss an iterative approach that we envision for future biochemical ontology development. We conclude that the proposed methodology can ease the burden of chemical data annotators and

  14. Self-organizing ontology of biochemically relevant small molecules

    Science.gov (United States)

    2012-01-01

    Background The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while providing new challenges, the biggest being the curation, annotation, and classification of this information to facilitate useful biochemical pattern analysis. Unfortunately, the human resources currently employed by the organizations supporting these efforts (e.g. ChEBI) are expanding linearly, while new useful scientific information is being released in a seemingly exponential fashion. Compounding this, currently existing chemical classification and annotation systems are not amenable to automated classification, formal and transparent chemical class definition axiomatization, facile class redefinition, or novel class integration, thus further limiting chemical ontology growth by necessitating human involvement in curation. Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest. Results To address this, we present a formal framework based on Semantic Web technologies for the automatic design of chemical ontology which can be used for automated classification of novel entities. We demonstrate the automatic self-assembly of a structure-based chemical ontology based on 60 MeSH and 40 ChEBI chemical classes. This ontology is then used to classify 200 compounds with an accuracy of 92.7%. We extend these structure-based classes with molecular feature information and demonstrate the utility of our framework for classification of functionally relevant chemicals. Finally, we discuss an iterative approach that we envision for future biochemical ontology development. Conclusions We conclude that the proposed methodology can ease the burden of

  15. Self-organizing ontology of biochemically relevant small molecules

    Directory of Open Access Journals (Sweden)

    Chepelev Leonid L

    2012-01-01

    Full Text Available Abstract Background The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while providing new challenges, the biggest being the curation, annotation, and classification of this information to facilitate useful biochemical pattern analysis. Unfortunately, the human resources currently employed by the organizations supporting these efforts (e.g. ChEBI are expanding linearly, while new useful scientific information is being released in a seemingly exponential fashion. Compounding this, currently existing chemical classification and annotation systems are not amenable to automated classification, formal and transparent chemical class definition axiomatization, facile class redefinition, or novel class integration, thus further limiting chemical ontology growth by necessitating human involvement in curation. Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest. Results To address this, we present a formal framework based on Semantic Web technologies for the automatic design of chemical ontology which can be used for automated classification of novel entities. We demonstrate the automatic self-assembly of a structure-based chemical ontology based on 60 MeSH and 40 ChEBI chemical classes. This ontology is then used to classify 200 compounds with an accuracy of 92.7%. We extend these structure-based classes with molecular feature information and demonstrate the utility of our framework for classification of functionally relevant chemicals. Finally, we discuss an iterative approach that we envision for future biochemical ontology development. Conclusions We conclude that the proposed methodology

  16. Clinico-hemato-biochemical profile of dogs with liver cirrhosis

    Directory of Open Access Journals (Sweden)

    M. A. Elhiblu

    2015-04-01

    Full Text Available Aim: The aim of this study was to determine the relevant tools in the diagnosis of liver cirrhosis in dogs. Material and Methods: A total of 140 dogs presented at Veterinary Teaching Hospital, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, showing clinical signs of hepatic insufficiency were subjected to clinico-hemato biochemical, urological, ultrasonographic (USG, and USG guided fine-needle biopsy examinations by standard methods. On the basis of these results, 6 dogs out of 140 dogs were found to be suffering from liver cirrhosis. Six clinically healthy dogs constituted the control group. Results: The dogs suffering from liver cirrhosis manifested inappetence, halitosis, abdominal distension, weight loss, melena, icterus, anemia, and neutrophilic leukocytosis with the left shift. Levels of hemoglobin, lymphocytes, packed cell volume, mean corpuscular volume, mean corpuscular Hb (MCH, and platelet count were significantly lower in liver cirrhosis group than control group while total leukocyte count, neutrophils, and MCH concentration were significantly higher. Glucose, total protein, albumin, A/G ratio, and fibrinogen were significantly lower, and creatinine, alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, prothrombin time, and APTT were significantly higher than the control values. Ultrasound revealed diffuse increase in echogenicity with rounded and irregular liver margins. Cytological examination of the ascitic fluid and fine-needle aspiration biopsy of liver was not fruitful in the diagnosis of liver cirrhosis. Conclusions: Liver cirrhosis causes clinical and hemo-biochemical alterations, which require special consideration when treating diseased animals. USG, diffuse increase in echogenicity of liver, rounding and irregularity of liver margins and microhepatica were the consistent findings. It is suggested that USG along with hemo-biochemical alterations may be used as a diagnostic tool for

  17. DMPD: Toll-like receptor (TLR)-based networks regulate neutrophilic inflammation inrespiratory disease. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 18031251 Toll-like receptor (TLR)-based networks regulate neutrophilic inflammation inrespiratory...l) (.csml) Show Toll-like receptor (TLR)-based networks regulate neutrophilic inflammation inrespiratory dis...utrophilic inflammation inrespiratory disease. Authors Sabroe I, Whyte MK. Publication Biochem Soc Trans. 20

  18. Stoichiometric estimates of the biochemical conversion efficiencies in tsetse metabolism

    Directory of Open Access Journals (Sweden)

    Custer Adrian V

    2005-08-01

    Full Text Available Abstract Background The time varying flows of biomass and energy in tsetse (Glossina can be examined through the construction of a dynamic mass-energy budget specific to these flies but such a budget depends on efficiencies of metabolic conversion which are unknown. These efficiencies of conversion determine the overall yields when food or storage tissue is converted into body tissue or into metabolic energy. A biochemical approach to the estimation of these efficiencies uses stoichiometry and a simplified description of tsetse metabolism to derive estimates of the yields, for a given amount of each substrate, of conversion product, by-products, and exchanged gases. This biochemical approach improves on estimates obtained through calorimetry because the stoichiometric calculations explicitly include the inefficiencies and costs of the reactions of conversion. However, the biochemical approach still overestimates the actual conversion efficiency because the approach ignores all the biological inefficiencies and costs such as the inefficiencies of leaky membranes and the costs of molecular transport, enzyme production, and cell growth. Results This paper presents estimates of the net amounts of ATP, fat, or protein obtained by tsetse from a starting milligram of blood, and provides estimates of the net amounts of ATP formed from the catabolism of a milligram of fat along two separate pathways, one used for resting metabolism and one for flight. These estimates are derived from stoichiometric calculations constructed based on a detailed quantification of the composition of food and body tissue and on a description of the major metabolic pathways in tsetse simplified to single reaction sequences between substrates and products. The estimates include the expected amounts of uric acid formed, oxygen required, and carbon dioxide released during each conversion. The calculated estimates of uric acid egestion and of oxygen use compare favorably to

  19. Biochemical and ultrasonographic predictors of outcome in threatened abortion

    Directory of Open Access Journals (Sweden)

    Ahmed M. Maged

    2013-09-01

    Conclusion: CA125, β HCG and progesterone are good biochemical markers and FHR and CRL are good ultrasonographic markers for the prediction of outcome in women with threatened abortion. FHR at 110 bpm gives the best predictivity followed by serum P at 25 ng/ml, β HCG at 19887 mIU/ml, CA 125 at 80 IU/ml and CRL at 21 mm with the least predictive accuracy among studied markers. Adding serum progesterone to FHR gave a sensitivity and specificity of 100%.

  20. A neurological and biochemical study of early lead poisoning

    Energy Technology Data Exchange (ETDEWEB)

    Ashby, J A.S.

    1980-05-01

    Motor nerve conduction velocities in 194 workers exposed to lead in a battery factory were compared with those of 94 age-matched controls. Changes in nerve conduction velocities of the 94 lead workers were found to have occurred. All mean maximum motor nerve conducting velocities measured were significantly lower in the lead-exposed group than in the control group. There was no statistically significant correlation to indicate that progressive slowing of nerve conduction was associated with increasing exposure to lead or with the commonly measured biochemical changes associated with disturbed haemopoiesis in lead exposure. Results suggest that the onset of nerve conduction changes occurs within two years.

  1. Lignin biodegradation: experimental evidence, molecular, biochemical and physiological mechanisms

    Energy Technology Data Exchange (ETDEWEB)

    Monties, B

    1985-01-01

    A critical review is presented of English, French and some German language literature, mainly from 1983 onwards. It examines experimental evidence on the behaviour as barriers to biodegradation of lignins and phenolic polymers such as tannins and suberins. The different molecular mechanisms of lignolysis by fungi (mainly), actinomycetes and bacteria are examined. A new biochemical approach to the physiological mechanism of regulation of lignolytic activities is suggested based on the discoveries of ligniolytic enzymes: effects of nitrogen, oxygen and substrate are discussed. It is concluded that a better knowledge of the structure and reactivity of phenolic barriers is needed in order to control the process of lignolysis.

  2. Fibre optic system for biochemical and microbiological sensing

    International Nuclear Information System (INIS)

    Penwill, L A; Slater, J H; Hayes, N W; Tremlett, C J

    2007-01-01

    This poster will discuss state-of-the-art fibre optic sensors based on evanescent wave technology emphasising chemophotonic sensors for biochemical reactions and microbe detection. Devices based on antibody specificity and unique DNA sequences will be described. The development of simple sensor devices with disposable single use sensor probes will be illustrated with a view to providing cost effective field based or point of care analysis of major themes such as hospital acquired infections or bioterrorism events. This presentation will discuss the nature and detection thresholds required, the optical detection techniques investigated, results of sensor trials and the potential for wider commercial application

  3. Biochemical composition of the biomass of some yeasts

    Energy Technology Data Exchange (ETDEWEB)

    Filippova, T.V.; Tyurina, Z.P.

    1981-01-01

    The biochemical composition of Rhodotorula gracilis was dependent on the culture medium. Cultivation of the yeast on molasses, starch, and plant hydrolyzates gave a high biomass yield with high protein and carbohydrate contents and relatively low nucleic acid contents. Similar results were obtained with fodder yeasts: Candida tropicalis, C. scotti, and Sporobolomyces pararoseus. There were 17 amino acids in yeast biomass. The amino acid content of R. gracilis and C. scotti was 29-30 percent and 39 percent respectively. Both species were deficient in methionine.

  4. Biochemical disease-free survival following I-125 prostate implantation

    Energy Technology Data Exchange (ETDEWEB)

    Beyer, David C; Priestley, Joseph B

    1995-07-01

    Purpose/Objective: To assess the five-year clinical and biochemical results of ultrasound-guided permanent I-125 brachytherapy in early prostate cancer. Biochemical disease-free survival (BDFS) is reported, using PSA follow-up and is compared to the surgical and radiation therapy literature. Materials and Methods: From 12/88 through 12/93, ultrasound-guided brachytherapy was preplanned with I-125 and delivered 16,000 cGy as the sole treatment in 499 patients. All were clinically staged as T1 or T2 - N0M0 adenocarcinoma of the prostate. Within the first year, 19 patients were lost to follow-up and have been excluded from further study. The remaining 480 patients form the basis of this report. Clinical status and PSA values were systematically recorded before and after treatment. Results: With a median follow-up of 35 months (3-70) the actuarial clinical local control is 83%. Both stage and grade are shown to predict for this endpoint. Actuarial BDFS is also correlated with stage, grade, and PSA at presentation. Biochemical disease-free survival at five years is 94% for T1, 70% for unilateral T2, and 34% for T2c tumors. Grade is also predictive, ranging from 85% in low-grade tumors to 30% in high-grade tumors. In a multivariate analysis, the pretreatment PSA is most highly correlated (p < 0.0001). Patients with a normal pretreatment PSA enjoyed 93% BDFS, while those presenting with PSA > 10 had a BDFS of 40%. Complications have been few, with severe urinary urgency or dysuria in 4% and both incontinence and proctitis seen in 1%. Conclusion: While biochemical disease-free survival reports in the literature are immature and have short follow-up, our data compares favorably with studies following radical prostatectomy or radiation therapy. Further follow-up of this cohort is required. The complication rate is low and patient acceptance excellent. Permanent implantation of I-125 as the sole treatment for early prostate cancer is a viable alternative for patients with

  5. Analytical interference by contrast agents in biochemical assays

    DEFF Research Database (Denmark)

    Otnes, Sigrid; Fogh-Andersen, Niels; Rømsing, Janne

    2017-01-01

    Objective. To provide a clinically relevant overview of the analytical interference by contrast agents (CA) in laboratory blood test measurements. Materials and Methods. The effects of five CAs, gadobutrol, gadoterate meglumine, gadoxetate disodium, iodixanol, and iomeprol, were studied on the 29...... most frequently performed biochemical assays. One-day-old plasma, serum, and whole blood were spiked with doses of each agent such that the gadolinium agents and the iodine agents reached concentrations of 0.5mMand 12mg iodine/mL, respectively. Subsequently, 12 assays were reexamined using 1/2 and 1...

  6. Integrating Carbon Nanotubes into Microfluidic Chip for Separating Biochemical Compounds

    DEFF Research Database (Denmark)

    Chen, Miaoxiang Max; Mogensen, Klaus Bo; Bøggild, Peter

    2012-01-01

    We present a new type of device to separate biochemical compounds wherein carbon nanotubes (CNTs) are integrated as chromatographic stationary phase. The CNTs were directly grown on the bottom of microfluidic channels on Si/SiO2 substrates by chemical vapor deposition (CVD). Acetylene was used...... as carbon source and Ni was employed as catalyst. For electrokinetic separations, higher electrical field strength is usually required; therefore, the CNTs were constructed in pillar-array-form by patterning the catalyst layer. Electrical field strength of 2.0 kV/cm has been realized, which is more than one...

  7. Use of laminar flow patterning for miniaturised biochemical assays

    DEFF Research Database (Denmark)

    Regenberg, Birgitte; Krühne, Ulrich; Beyer, M.

    2004-01-01

    Laminar flow in microfluidic chambers was used to construct low (one dimensional) density arrays suitable for miniaturized biochemical assays. By varying the ratio of flows of two guiding streams flanking a sample stream, precise focusing and positioning of the latter was achieved, and reactive s...... species carried in the sample stream were deposited on functionalized chip surfaces as discrete 50 mm wide lanes. Using different model systems we have confirmed the method's suitability for qualitative screening and quantification tasks in receptor-ligand assays, recording biotin...

  8. Biochemical disease-free survival following I-125 prostate implantation

    International Nuclear Information System (INIS)

    Beyer, David C.; Priestley, Joseph B.

    1995-01-01

    Purpose/Objective: To assess the five-year clinical and biochemical results of ultrasound-guided permanent I-125 brachytherapy in early prostate cancer. Biochemical disease-free survival (BDFS) is reported, using PSA follow-up and is compared to the surgical and radiation therapy literature. Materials and Methods: From 12/88 through 12/93, ultrasound-guided brachytherapy was preplanned with I-125 and delivered 16,000 cGy as the sole treatment in 499 patients. All were clinically staged as T1 or T2 - N0M0 adenocarcinoma of the prostate. Within the first year, 19 patients were lost to follow-up and have been excluded from further study. The remaining 480 patients form the basis of this report. Clinical status and PSA values were systematically recorded before and after treatment. Results: With a median follow-up of 35 months (3-70) the actuarial clinical local control is 83%. Both stage and grade are shown to predict for this endpoint. Actuarial BDFS is also correlated with stage, grade, and PSA at presentation. Biochemical disease-free survival at five years is 94% for T1, 70% for unilateral T2, and 34% for T2c tumors. Grade is also predictive, ranging from 85% in low-grade tumors to 30% in high-grade tumors. In a multivariate analysis, the pretreatment PSA is most highly correlated (p 10 had a BDFS of 40%. Complications have been few, with severe urinary urgency or dysuria in 4% and both incontinence and proctitis seen in 1%. Conclusion: While biochemical disease-free survival reports in the literature are immature and have short follow-up, our data compares favorably with studies following radical prostatectomy or radiation therapy. Further follow-up of this cohort is required. The complication rate is low and patient acceptance excellent. Permanent implantation of I-125 as the sole treatment for early prostate cancer is a viable alternative for patients with early stage and low- to moderate-grade cancers. The PSA provides significant prognostic information and

  9. Laser induced fluorescence of biochemical for UV LIDAR application.

    Science.gov (United States)

    Gupta, L; Sharma, R C; Razdan, A K; Maini, A K

    2014-05-01

    Laser induced fluorescence spectroscopy in the ultraviolet regime has been used for the detection of biochemical through a fiber coupled CCD detector from a distance of 2 m. The effect of concentration and laser excitation energy on the fluorescence spectra of nicotinamide adenine dinucleotide (NADH) has been investigated. The signature fluorescence peak of NADH was centred about 460 nm. At lower concentration Raman peak centred at 405 nm was also observed. The origin of this peak has been discussed. Detection limit with the proposed set up is found to be 1 ppm.

  10. Ultraviolet transparent silicon oxynitride waveguides for biochemical microsystems

    DEFF Research Database (Denmark)

    Mogensen, Klaus Bo; Friis, Peter; Hübner, Jörg

    2001-01-01

    The UV wavelength region is of great interest in absorption spectroscopy, which is employed for chemical analysis, since many organic compounds absorb in only this region. Germanium-doped silica, which is often preferred as the waveguide core material in optical devices for telecommunication....... The applicability of these waveguides was demonstrated in a biochemical microsystem consisting of multimode buried-channel SiOxNy waveguides that were monolithically integrated with microfluidic channels. Absorption measurements of a beta -blocking agent, propranolol, at 212-215 nm were performed. The detection...

  11. Neural Networks

    International Nuclear Information System (INIS)

    Smith, Patrick I.

    2003-01-01

    Physicists use large detectors to measure particles created in high-energy collisions at particle accelerators. These detectors typically produce signals indicating either where ionization occurs along the path of the particle, or where energy is deposited by the particle. The data produced by these signals is fed into pattern recognition programs to try to identify what particles were produced, and to measure the energy and direction of these particles. Ideally, there are many techniques used in this pattern recognition software. One technique, neural networks, is particularly suitable for identifying what type of particle caused by a set of energy deposits. Neural networks can derive meaning from complicated or imprecise data, extract patterns, and detect trends that are too complex to be noticed by either humans or other computer related processes. To assist in the advancement of this technology, Physicists use a tool kit to experiment with several neural network techniques. The goal of this research is interface a neural network tool kit into Java Analysis Studio (JAS3), an application that allows data to be analyzed from any experiment. As the final result, a physicist will have the ability to train, test, and implement a neural network with the desired output while using JAS3 to analyze the results or output. Before an implementation of a neural network can take place, a firm understanding of what a neural network is and how it works is beneficial. A neural network is an artificial representation of the human brain that tries to simulate the learning process [5]. It is also important to think of the word artificial in that definition as computer programs that use calculations during the learning process. In short, a neural network learns by representative examples. Perhaps the easiest way to describe the way neural networks learn is to explain how the human brain functions. The human brain contains billions of neural cells that are responsible for processing

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

    Science.gov (United States)

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

    2016-01-01

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

  13. Vulnerability of complex networks

    Science.gov (United States)

    Mishkovski, Igor; Biey, Mario; Kocarev, Ljupco

    2011-01-01

    We consider normalized average edge betweenness of a network as a metric of network vulnerability. We suggest that normalized average edge betweenness together with is relative difference when certain number of nodes and/or edges are removed from the network is a measure of network vulnerability, called vulnerability index. Vulnerability index is calculated for four synthetic networks: Erdős-Rényi (ER) random networks, Barabási-Albert (BA) model of scale-free networks, Watts-Strogatz (WS) model of small-world networks, and geometric random networks. Real-world networks for which vulnerability index is calculated include: two human brain networks, three urban networks, one collaboration network, and two power grid networks. We find that WS model of small-world networks and biological networks (human brain networks) are the most robust networks among all networks studied in the paper.

  14. NEXCADE: perturbation analysis for complex networks.

    Directory of Open Access Journals (Sweden)

    Gitanjali Yadav

    Full Text Available Recent advances in network theory have led to considerable progress in our understanding of complex real world systems and their behavior in response to external threats or fluctuations. Much of this research has been invigorated by demonstration of the 'robust, yet fragile' nature of cellular and large-scale systems transcending biology, sociology, and ecology, through application of the network theory to diverse interactions observed in nature such as plant-pollinator, seed-dispersal agent and host-parasite relationships. In this work, we report the development of NEXCADE, an automated and interactive program for inducing disturbances into complex systems defined by networks, focusing on the changes in global network topology and connectivity as a function of the perturbation. NEXCADE uses a graph theoretical approach to simulate perturbations in a user-defined manner, singly, in clusters, or sequentially. To demonstrate the promise it holds for broader adoption by the research community, we provide pre-simulated examples from diverse real-world networks including eukaryotic protein-protein interaction networks, fungal biochemical networks, a variety of ecological food webs in nature as well as social networks. NEXCADE not only enables network visualization at every step of the targeted attacks, but also allows risk assessment, i.e. identification of nodes critical for the robustness of the system of interest, in order to devise and implement context-based strategies for restructuring a network, or to achieve resilience against link or node failures. Source code and license for the software, designed to work on a Linux-based operating system (OS can be downloaded at http://www.nipgr.res.in/nexcade_download.html. In addition, we have developed NEXCADE as an OS-independent online web server freely available to the scientific community without any login requirement at http://www.nipgr.res.in/nexcade.html.

  15. Combination of biochemical and mechanical cues for tendon tissue engineering.

    Science.gov (United States)

    Testa, Stefano; Costantini, Marco; Fornetti, Ersilia; Bernardini, Sergio; Trombetta, Marcella; Seliktar, Dror; Cannata, Stefano; Rainer, Alberto; Gargioli, Cesare

    2017-11-01

    Tendinopathies negatively affect the life quality of millions of people in occupational and athletic settings, as well as the general population. Tendon healing is a slow process, often with insufficient results to restore complete endurance and functionality of the tissue. Tissue engineering, using tendon progenitors, artificial matrices and bioreactors for mechanical stimulation, could be an important approach for treating rips, fraying and tissue rupture. In our work, C3H10T1/2 murine fibroblast cell line was exposed to a combination of stimuli: a biochemical stimulus provided by Transforming Growth Factor Beta (TGF-β) and Ascorbic Acid (AA); a three-dimensional environment represented by PEGylated-Fibrinogen (PEG-Fibrinogen) biomimetic matrix; and a mechanical induction exploiting a custom bioreactor applying uniaxial stretching. In vitro analyses by immunofluorescence and mechanical testing revealed that the proposed combined approach favours the organization of a three-dimensional tissue-like structure promoting a remarkable arrangement of the cells and the neo-extracellular matrix, reflecting into enhanced mechanical strength. The proposed method represents a novel approach for tendon tissue engineering, demonstrating how the combined effect of biochemical and mechanical stimuli ameliorates biological and mechanical properties of the artificial tissue compared to those obtained with single inducement. © 2017 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

  16. Dust Fertilization of the Western Atlantic Biota: a Biochemical Model

    Science.gov (United States)

    Holmes, C. W.

    2017-12-01

    Every year an estimated 50 million tons of African dust reaches the Western Atlantic. This dust is composed of quartz sand, clay, and a mixture of quartz and clay particles agglutinated with micronutrient enriched ferruginous cement. However, whether it is friend or foe to biochemical systems is a matter of conjecture. Corals are ideal recorders of changing conditions as the layers can be dated so that the record of chemical changes is easily assessed. There is extensive shallow-and deep water coral development bordering the Florida Straits. The changes in trace element chemistry within these corals show a positive relationship with the African dust record. Recently, it has been demonstrated that many of the metals contained within the dust are necessary micronutrients in the fertilization of plankton. Using the results of these studies, a biochemical model has been constructed. This model suggests a path from inorganic dust through microbial transformation to micronutrient enzymes (i.e. Cd-enriched carbonic anahydrase) and carbonate precipitation on the Bahamian Banks. It is estimated that more than ten million metric tons of this fine, metal-rich sediment is formed each year. However, for much of this sediment, its deposition is temporary, as it is transported into the Florida Straits yearly by tropical cyclones. This metal-enriched fine carbonate becomes nutrients for phytoplankton, providing food for the corals, both shallow and deep.

  17. Physiological and biochemical performances of menthol-induced aposymbiotic corals.

    Directory of Open Access Journals (Sweden)

    Jih-Terng Wang

    Full Text Available The unique mutualism between corals and their photosynthetic zooxanthellae (Symbiodinium spp. is the driving force behind functional assemblages of coral reefs. However, the respective roles of hosts and Symbiodinium in this endosymbiotic association, particularly in response to environmental challenges (e.g., high sea surface temperatures, remain unsettled. One of the key obstacles is to produce and maintain aposymbiotic coral hosts for experimental purposes. In this study, a simple and gentle protocol to generate aposymbiotic coral hosts (Isopora palifera and Stylophora pistillata was developed using repeated incubation in menthol/artificial seawater (ASW medium under light and in ASW in darkness, which depleted more than 99% of Symbiodinium from the host within 4∼8 days. As indicated by the respiration rate, energy metabolism (by malate dehydrogenase activity, and nitrogen metabolism (by glutamate dehydrogenase activity and profiles of free amino acids, the physiological and biochemical performances of the menthol-induced aposymbiotic corals were comparable to their symbiotic counterparts without nutrient supplementation (e.g., for Stylophora or with a nutrient supplement containing glycerol, vitamins, and a host mimic of free amino acid mixture (e.g., for Isopora. Differences in biochemical responses to menthol-induced bleaching between Stylophora and Isopora were attributed to the former digesting Symbiodinium rather than expelling the algae live as found in the latter species. Our studies showed that menthol could successfully bleach corals and provided aposymbiotic corals for further exploration of coral-alga symbioses.

  18. The clinical presentation and biochemical diagnosis of acromegaly and gigantism.

    Science.gov (United States)

    Jialal, I; Nathoo, B C; Joubert, S; Asmal, A C; Pillay, N L

    1982-04-24

    Over a 5-year period 14 patients with acromegaly and gigantism were seen at the endocrine clinic of King Edward VIII Hospital: 9 were Blacks and 5 Indians; 8 of the patients were women. The mean age of the patients was 46 years. Surprisingly, only 2 patients complained of acral overgrowth. Symptomatology was varied and not characteristic of the condition. On examination all patients had unequivocal signs of soft-tissue and bony overgrowth, 64% had visual abnormalities and 50% hypertension. Radiologically, 88% showed an enlarged pituitary fossa. On biochemical investigation, the fasting levels of growth hormone (GH) were increased in 12 patients and during oral glucose tolerance tests, the GH levels in these 12 patients were not suppressed. One patient in whom the fasting GH level was not increased had progressed to the stage of panhypopituitarism, in the remaining patient challenge with thyrotrophin-releasing hormone (TRH) led to increased GH levels and L-dopa challenge resulted in a paradoxical decrease in GH levels. Seven patients with increased GH levels who were challenged with L-dopa showed the typical decrease in GH levels found in this condition; in 5 of these patients, challenged with TRH, GH levels increased. The findings emphasize that despite the ease of clinical diagnosis, appropriate biochemical investigations are necessary to confirm the exact status of the disease, which is rare in the population studied.

  19. Biochemical and immunological responses to low doses of ionizing radiation

    International Nuclear Information System (INIS)

    Shabon, M.H.; Sayed, Z.S.; Mahdy, E.M.; El-Gawish, M.A.; Shosha, W.

    2006-01-01

    Malondialdehyde, lactate dehydrogenase, iron concentration, IL-6 and IL-1b concentration, hemoglobin content, red cells, white cells and platelet counts were determined in seventy-two male albino rats divided into two main groups. The first one was subdivided into 7 subgroups; control and 6 irradiated subgroups with 0.1, 0.2, 0.3, 0.5, 0.7 and 1 Gy single dose of gamma radiation. The other was subdivided into 4 subgroups irradiated with fractionated doses of gamma radiation; three groups were irradiated with 0.3, 0.7 and 1 Gy (0.1 Gy/day) and the last subgroup with 1 Gy (0.2 Gy/day). All animals were sacrificed after three days of the last irradiation dose. The results revealed that all biochemical parameters were increased in rats exposed to fractionated doses more than the single doses. Hematological parameters were decreased in rats exposed to single doses more than the fractionated ones. In conclusion, the data of this study highlights the stimulatory effect of low ionizing radiation doses (= 1 Gy), whether single or fractionated, on some biochemical and immunological parameters

  20. Biochemical and Molecular Characterization of Plant-Parasitic Nematodes

    Directory of Open Access Journals (Sweden)

    I.M. de O. Abrantes

    2004-08-01

    Full Text Available Nematologists need correct species identification to carry out research, teaching, extension and other activities. Therefore, nematode taxonomy must be pursued diligently at all levels. The identification of plant-parasitic nematodes is not always easy and that of some species is especially difficult. Most of the information that nematologists use when characterizing and identifying specimens is based on morphological and morphometrical characters. Although these characters are of primary importance, in the last three decades they have been supplemented by biochemical/ molecular characters. Biochemical approaches include the separation of proteins (general proteins and isozymes by one-dimensional gel electrophoresis, isoelectric focusing, two-dimensional gel electrophoresis, and sodium dodecyl sulphate-capillary gel electrophoresis. Serology has also been found effective in the identification and quantification of nematodes, monoclonal antibodies being a more useful immunological tool than polyclonal antibodies. Identification based on the direct examination of DNA is potentially a more powerful method to characterize inter- and intra-specific variability. The development of techniques such as the polymerase chain reaction, restriction fragment length polymorphism, randomly amplified polymorphic DNA, and amplified fragment length polymorphism has increased the accuracy and speed of nematode characterization/identification. Progress continues to be made and more and more nematologists are using molecular techniques for diagnostic purposes and to assess genetic variation.

  1. The human sunburn reaction: histologic and biochemical studies

    International Nuclear Information System (INIS)

    Gilchrest, B.A.; Soter, N.A.; Stoff, J.S.; Mihm, M.C. Jr.

    1981-01-01

    The ultraviolet-induced erythema reaction was investigated histologically and biochemically in four subjects, utilizing suction blister aspirates, analyzed for histamine and prostaglandin E2 (PGE2), and Epon-embedded 1-mu skin biopsy sections from control skin and from irradiated skin at intervals for 72 hours after exposure to a Hanovia lamp. Major histologic alterations in the epidermis included dyskeratotic and vacuolated keratinocytes (sunburn cells), and disappearance of Langerhans cells. In the dermis the major changes were vascular, involving both the superficial and deep venular plexuses. Endothelial cell enlargement was first apparent within 30 minutes of irradiation, peaked at 24 hours, and persisted throughout the 72-hour study period. Mast cell degranulation and associated perivenular edema were first apparent at 1 hour and striking at the onset of erythema, 3 to 4 hours postirradiation; edema was absent and mast cells were again normal in number and granule content at 24 hours. Histamine levels rose approximately fourfold above control values immediately after the onset of erythema and returned to baseline within 24 hours. PGE2 levels were statistically elevated even before the onset of erythema and reached approximately 150% of the control value at 24 hours. These data provide the first evidence that histamine may mediate the early phase of the human sunburn reaction and increase our understanding of its complex histologic and biochemical sequelae

  2. Estimating rare events in biochemical systems using conditional sampling

    Science.gov (United States)

    Sundar, V. S.

    2017-01-01

    The paper focuses on development of variance reduction strategies to estimate rare events in biochemical systems. Obtaining this probability using brute force Monte Carlo simulations in conjunction with the stochastic simulation algorithm (Gillespie's method) is computationally prohibitive. To circumvent this, important sampling tools such as the weighted stochastic simulation algorithm and the doubly weighted stochastic simulation algorithm have been proposed. However, these strategies require an additional step of determining the important region to sample from, which is not straightforward for most of the problems. In this paper, we apply the subset simulation method, developed as a variance reduction tool in the context of structural engineering, to the problem of rare event estimation in biochemical systems. The main idea is that the rare event probability is expressed as a product of more frequent conditional probabilities. These conditional probabilities are estimated with high accuracy using Monte Carlo simulations, specifically the Markov chain Monte Carlo method with the modified Metropolis-Hastings algorithm. Generating sample realizations of the state vector using the stochastic simulation algorithm is viewed as mapping the discrete-state continuous-time random process to the standard normal random variable vector. This viewpoint opens up the possibility of applying more sophisticated and efficient sampling schemes developed elsewhere to problems in stochastic chemical kinetics. The results obtained using the subset simulation method are compared with existing variance reduction strategies for a few benchmark problems, and a satisfactory improvement in computational time is demonstrated.

  3. Energy analysis of biochemical conversion processes of biomass to bioethanol

    Energy Technology Data Exchange (ETDEWEB)

    Bakari, M.; Ngadi, M.; Bergthorson, T. [McGill Univ., Ste-Anne-de-Bellevue, PQ (Canada). Dept. of Bioresource Engineering

    2010-07-01

    Bioethanol is among the most promising of biofuels that can be produced from different biomass such as agricultural products, waste and byproducts. This paper reported on a study that examined the energy conversion of different groups of biomass to bioethanol, including lignocelluloses, starches and sugar. Biochemical conversion generally involves the breakdown of biomass to simple sugars using different pretreatment methods. The energy needed for the conversion steps was calculated in order to obtain mass and energy efficiencies for the conversions. Mass conversion ratios of corn, molasses and rice straw were calculated as 0.3396, 0.2300 and 0.2296 kg of bioethanol per kg of biomass, respectively. The energy efficiency of biochemical conversion of corn, molasses and rice straw was calculated as 28.57, 28.21 and 31.33 per cent, respectively. The results demonstrated that lignocelluloses can be efficiently converted with specific microorganisms such as Mucor indicus, Rhizopus oryzae using the Simultaneous Saccharification and Fermentation (SSF) methods.

  4. Biochemical markers for the assessment of aquatic environment contamination

    Science.gov (United States)

    Havelková, Marcela; Randák, Tomáš; Blahová, Jana; Slatinská, Iveta; Svobodová, Zdeňka

    2008-01-01

    The need for assessment of aquatic ecosystem contamination and of its impact on water dwelling organisms was developed in response to rising aquatic environmental pollution. In this field study, liver enzymes of phase I and phase II of xenobiotic transformation, namely cytochrome P450, ethoxyresorufin-O-deethylase, glutathione-S-transferase and tripeptide glutathione were used to assess the contamination of the aquatic environment at different rivers in the Czech Republic. The indicator species selected was the male chub (Leuciscus cephalus L.) and male brown trout (Salmo trutta fario). Chemical analyses included also the assessment of the most important inductors of previously mentioned biochemical markers. The major inductors of monitored biomarkers are industrial contaminants which belong to a large group of organic pollutants (PCB, PAH, PCDD/F, DDT, HCH, HCB and OCS), persistent in the environment. Four different groups of river basins were assessed: the River Tichá Orlice and its tributary the Kralický brook; important tributaries of the River Elbe (the rivers Orlice, Chrudimka, Cidlina, Jizera, Vltava, Ohře and Bílina); major rivers in the Czech Republic (the rivers Lužnice, Otava, Sázava, Berounka, Vltava, Labe, Ohře, Svratka, Dyje, Morava and Odra) and the River Vltava. The use of the biochemical markers together with chemical analyses seems to be an effective way to monitor the quality of aquatic environment. PMID:21218108

  5. Biochemical and cytological effects of sulphur dioxide on plant metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Malhotra, S S; Hocking, D

    1976-01-01

    Biochemical effects of sulfur dioxide arise from its unique ability to act as an oxidizing or a reducing agent. Among some of the important metabolic effects are direct interference with photosynthetic CO/sub 2/ fixation (competitive inhibiton of ribulose diphosphate carbosylase by SO/sub 3/) and with energy metabolism (inhibition of mitochondrial ATP production by SO/sub 3//sup =/). Many indirect effects result from formation of sulfites and organic sulfonates with other cell constituents. These compounds can cause inhibition of a variety of metabolic enzyme systems. All these factors are probably instrumental in the gross disruption of chloroplast and mitochondrial ultrastructure. Injurious effects result when sulfur dioxide is taken up in excess of the capacity of the tissue to incorporate sulfur into the normal metabolic activities. The ubiquitous presence of small amounts of SO/sub 2/ and the subtle and varied nature of its biochemical effects suggest that crop losses to SO/sub 2/ pollution may be more widespread and serious than is generally suspected.

  6. [INVITED] Tilted fiber grating mechanical and biochemical sensors

    Science.gov (United States)

    Guo, Tuan; Liu, Fu; Guan, Bai-Ou; Albert, Jacques

    2016-04-01

    The tilted fiber Bragg grating (TFBG) is a new kind of fiber-optic sensor that possesses all the advantages of well-established Bragg grating technology in addition to being able to excite cladding modes resonantly. This device opens up a multitude of opportunities for single-point sensing in hard-to-reach spaces with very controllable cross-sensitivities, absolute and relative measurements of various parameters, and an extreme sensitivity to materials external to the fiber without requiring the fiber to be etched or tapered. Over the past five years, our research group has been developing multimodal fiber-optic sensors based on TFBG in various shapes and forms, always keeping the device itself simple to fabricate and compatible with low-cost manufacturing. This paper presents a brief review of the principle, fabrication, characterization, and implementation of TFBGs, followed by our progress in TFBG sensors for mechanical and biochemical applications, including one-dimensional TFBG vibroscopes, accelerometers and micro-displacement sensors; two-dimensional TFBG vector vibroscopes and vector rotation sensors; reflective TFBG refractometers with in-fiber and fiber-to-fiber configurations; polarimetric and plasmonic TFBG biochemical sensors for in-situ detection of cell, protein and glucose.

  7. Clinical and Biochemical Characteristics of Children with Juvenile Idiopathic Arthritis

    International Nuclear Information System (INIS)

    Ahmed, S.; Ali, S. R.; Ishaque, S.

    2014-01-01

    Objective: To determine the clinical and biochemical characteristics of children with Juvenile Idiopathic Arthritis (JIA) at a tertiary care centre in Karachi, Pakistan. Study Design: A descriptive study. Place and Duration of Study: Paediatric Rheumatology Clinic of The Aga Khan University Hospital (AKUH), Karachi, from January 2008 to December 2011. Methodology: Clinical and laboratory profile and outcome of children less than 15 years of age attending the Paediatric Rheumatology Clinic of the Aga Khan University, Karachi with the diagnosis of Juvenile Idiopathic Arthritis according to International League against Rheumatism were studied. These children were classified into different types of JIA; their clinical and laboratory characteristics, response to therapy and outcome was evaluated. Results: Sixty eight patients satisfying the criteria of International League against Rheumatism (ILAR) for Juvenile Idiopathic Arthritis were enrolled during the study period of four consecutive years, their age ranged from 9 months to 15 years. Mean age at onset was 6.45 +- 4.03 years while mean age at diagnosis was 7.60 +- 3.93 years. Polyarticular was the most predominant subtype with 37 (54%) patients, out of these, 9 (24%) were rheumatoid factor positive. An almost equal gender predisposition was observed. Fever and arthritis were the most common presenting symptoms, with only 2 patients presenting with uveitis. Conclusion: The clinico-biochemical characteristics of JIA at the study centre showed a pattern distinct with early onset of disease, high frequency of polyarticular type and a higher rheumatoid factor (QRA) and ANA positivity in girls. (author)

  8. A biochemical basis for induction of retina regeneration by antioxidants.

    Science.gov (United States)

    Echeverri-Ruiz, Nancy; Haynes, Tracy; Landers, Joseph; Woods, Justin; Gemma, Michael J; Hughes, Michael; Del Rio-Tsonis, Katia

    2018-01-15

    The use of antioxidants in tissue regeneration has been studied, but their mechanism of action is not well understood. Here, we analyze the role of the antioxidant N-acetylcysteine (NAC) in retina regeneration. Embryonic chicks are able to regenerate their retina after its complete removal from retinal stem/progenitor cells present in the ciliary margin (CM) of the eye only if a source of exogenous factors, such as FGF2, is present. This study shows that NAC modifies the redox status of the CM, initiates self-renewal of the stem/progenitor cells, and induces regeneration in the absence of FGF2. NAC works as an antioxidant by scavenging free radicals either independently or through the synthesis of glutathione (GSH), and/or by reducing oxidized proteins through a thiol disulfide exchange activity. We dissected the mechanism used by NAC to induce regeneration through the use of inhibitors of GSH synthesis and the use of other antioxidants with different biochemical structures and modes of action, and found that NAC induces regeneration through its thiol disulfide exchange activity. Thus, our results provide, for the first time, a biochemical basis for induction of retina regeneration. Furthermore, NAC induction was independent of FGF receptor signaling, but dependent on the MAPK (pErk1/2) pathway. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  9. Chemical networks with inflows and outflows: a positive linear differential inclusions approach.

    Science.gov (United States)

    Angeli, David; De Leenheer, Patrick; Sontag, Eduardo D

    2009-01-01

    Certain mass-action kinetics models of biochemical reaction networks, although described by nonlinear differential equations, may be partially viewed as state-dependent linear time-varying systems, which in turn may be modeled by convex compact valued positive linear differential inclusions. A result is provided on asymptotic stability of such inclusions, and applied to a ubiquitous biochemical reaction network with inflows and outflows, known as the futile cycle. We also provide a characterization of exponential stability of general homogeneous switched systems which is not only of interest in itself, but also plays a role in the analysis of the futile cycle. 2009 American Institute of Chemical Engineers

  10. Network Survivability

    DEFF Research Database (Denmark)

    Marzo, José L.; Stidsen, Thomas Riis; Ruepp, Sarah Renée

    2010-01-01

    – are vital to modern services such as mobile telephony, online banking and VoIP. This book examines communication networking from a mathematical viewpoint. The contributing authors took part in the European COST action 293 – a four-year program of multidisciplinary research on this subject. In this book...... they offer introductory overviews and state-of-the-art assessments of current and future research in the fields of broadband, optical, wireless and ad hoc networks. Particular topics of interest are design, optimization, robustness and energy consumption. The book will be of interest to graduate students......, researchers and practitioners in the areas of networking, theoretical computer science, operations research, distributed computing and mathematics....

  11. Nuclear networking.

    Science.gov (United States)

    Xie, Wei; Burke, Brian

    2017-07-04

    Nuclear lamins are intermediate filament proteins that represent important structural components of metazoan nuclear envelopes (NEs). By combining proteomics and superresolution microscopy, we recently reported that both A- and B-type nuclear lamins form spatially distinct filament networks at the nuclear periphery of mouse fibroblasts. In particular, A-type lamins exhibit differential association with nuclear pore complexes (NPCs). Our studies reveal that the nuclear lamina network in mammalian somatic cells is less ordered and more complex than that of amphibian oocytes, the only other system in which the lamina has been visualized at high resolution. In addition, the NPC component Tpr likely links NPCs to the A-type lamin network, an association that appears to be regulated by C-terminal modification of various A-type lamin isoforms. Many questions remain, however, concerning the structure and assembly of lamin filaments, as well as with their mode of association with other nuclear components such as peripheral chromatin.

  12. Telecommunication Networks

    DEFF Research Database (Denmark)

    Olsen, Rasmus Løvenstein; Balachandran, Kartheepan; Hald, Sara Ligaard

    2014-01-01

    In this chapter, we look into the role of telecommunication networks and their capability of supporting critical infrastructure systems and applications. The focus is on smart grids as the key driving example, bearing in mind that other such systems do exist, e.g., water management, traffic control......, etc. First, the role of basic communication is examined with a focus on critical infrastructures. We look at heterogenic networks and standards for smart grids, to give some insight into what has been done to ensure inter-operability in this direction. We then go to the physical network, and look...... threats to the critical infrastructure. Finally, before our conclusions and outlook, we give a brief overview of some key activities in the field and what research directions are currently investigated....

  13. Network interruptions

    CERN Multimedia

    2005-01-01

    On Sunday 12 June 2005, a site-wide security software upgrade will be performed on all CERN network equipment. This maintenance operation will cause at least 2 short network interruptions of 2 minutes on each equipment item. There are hundreds of such items across the CERN site (Meyrin, Prévessin and all SPS and LHC pits), and it will thus take the whole day to treat them all. All network users and services will be affected. Central batch computing services will be interrupted during this period, expected to last from 8 a.m. until late evening. Job submission will still be possible but no jobs will actually be run. It is hoped to complete the computer centre upgrades in the morning so that stable access can be restored to lxplus, afs and nice services as soon as possible; this cannot be guaranteed, however. The opportunity will be used to interrupt and perform upgrades on the CERN Document Servers.

  14. Managing Networks

    DEFF Research Database (Denmark)

    Jørgensen, Heidi; Vintergaard, Christian

    Logically it seems that companies pursuing different business strategies wouldalso manage their relationships with other firms accordingly. Nevertheless, due tothe lack of research in the field of network strategies, this link still remainsinadequately examined. Based on the well-known framework...... isprovided, that the relation between a company's strategy, structure and processesin fact have a considerable influence on its pattern of network behaviour. Threecase studies from the Danish biotech industry exemplify and illustrate how acompany's strategy is directly correlated with how it manages its...... of networkbehaviour, knowing how to manage this relation becomes essential, especiallyduring the development of new strategies....

  15. Structural and biochemical characterization of the cell fate determining nucleotidyltransferase fold protein MAB21L1.

    Science.gov (United States)

    de Oliveira Mann, Carina C; Kiefersauer, Reiner; Witte, Gregor; Hopfner, Karl-Peter

    2016-06-08

    The exceptionally conserved metazoan MAB21 proteins are implicated in cell fate decisions and share considerable sequence homology with the cyclic GMP-AMP synthase. cGAS is the major innate immune sensor for cytosolic DNA and produces the second messenger 2'-5', 3'-5' cyclic GMP-AMP. Little is known about the structure and biochemical function of other proteins of the cGAS-MAB21 subfamily, such as MAB21L1, MAB21L2 and MAB21L3. We have determined the crystal structure of human full-length MAB21L1. Our analysis reveals high structural conservation between MAB21L1 and cGAS but also uncovers important differences. Although monomeric in solution, MAB21L1 forms a highly symmetric double-pentameric oligomer in the crystal, raising the possibility that oligomerization could be a feature of MAB21L1. In the crystal, MAB21L1 is in an inactive conformation requiring a conformational change - similar to cGAS - to develop any nucleotidyltransferase activity. Co-crystallization with NTP identified a putative ligand binding site of MAB21 proteins that corresponds to the DNA binding site of cGAS. Finally, we offer a structure-based explanation for the effects of MAB21L2 mutations in patients with eye malformations. The underlying residues participate in fold-stabilizing interaction networks and mutations destabilize the protein. In summary, we provide a first structural framework for MAB21 proteins.

  16. Accelerating rejection-based simulation of biochemical reactions with bounded acceptance probability

    Energy Technology Data Exchange (ETDEWEB)

    Thanh, Vo Hong, E-mail: vo@cosbi.eu [The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, Rovereto 38068 (Italy); Priami, Corrado, E-mail: priami@cosbi.eu [The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, Rovereto 38068 (Italy); Department of Mathematics, University of Trento, Trento (Italy); Zunino, Roberto, E-mail: roberto.zunino@unitn.it [Department of Mathematics, University of Trento, Trento (Italy)

    2016-06-14

    Stochastic simulation of large biochemical reaction networks is often computationally expensive due to the disparate reaction rates and high variability of population of chemical species. An approach to accelerate the simulation is to allow multiple reaction firings before performing update by assuming that reaction propensities are changing of a negligible amount during a time interval. Species with small population in the firings of fast reactions significantly affect both performance and accuracy of this simulation approach. It is even worse when these small population species are involved in a large number of reactions. We present in this paper a new approximate algorithm to cope with this problem. It is based on bounding the acceptance probability of a reaction selected by the exact rejection-based simulation algorithm, which employs propensity bounds of reactions and the rejection-based mechanism to select next reaction firings. The reaction is ensured to be selected to fire with an acceptance rate greater than a predefined probability in which the selection becomes exact if the probability is set to one. Our new algorithm improves the computational cost for selecting the next reaction firing and reduces the updating the propensities of reactions.

  17. Hybrid modeling of the crosstalk between signaling and transcriptional networks using ordinary differential equations and multi-valued logic.

    Science.gov (United States)

    Khan, Faiz M; Schmitz, Ulf; Nikolov, Svetoslav; Engelmann, David; Pützer, Brigitte M; Wolkenhauer, Olaf; Vera, Julio

    2014-01-01

    A decade of successful results indicates that systems biology is the appropriate approach to investigate the regulation of complex biochemical networks involving transcriptional and post-transcriptional regulations. It becomes mandatory when dealing with highly interconnected biochemical networks, composed of hundreds of compounds, or when networks are enriched in non-linear motifs like feedback and feedforward loops. An emerging dilemma is to conciliate models of massive networks and the adequate description of non-linear dynamics in a suitable modeling framework. Boolean networks are an ideal representation of massive networks that are humble in terms of computational complexity and data demand. However, they are inappropriate when dealing with nested feedback/feedforward loops, structural motifs common in biochemical networks. On the other hand, models of ordinary differential equations (ODEs) cope well with these loops, but they require enormous amounts of quantitative data for a full characterization of the model. Here we propose hybrid models, composed of ODE and logical sub-modules, as a strategy to handle large scale, non-linear biochemical networks that include transcriptional and post-transcriptional regulations. We illustrate the construction of this kind of models using as example a regulatory network centered on E2F1, a transcription factor involved in cancer. The hybrid modeling approach proposed is a good compromise between quantitative/qualitative accuracy and scalability when considering large biochemical networks with a small highly interconnected core, and module of transcriptionally regulated genes that are not part of critical regulatory loops. This article is part of a Special Issue entitled: Computational Proteomics, Systems Biology & Clinical Implications. Guest Editor: Yudong Cai. Copyright © 2013 Elsevier B.V. All rights reserved.

  18. Multiple network alignment on quantum computers

    Science.gov (United States)

    Daskin, Anmer; Grama, Ananth; Kais, Sabre

    2014-12-01

    Comparative analyses of graph-structured datasets underly diverse problems. Examples of these problems include identification of conserved functional components (biochemical interactions) across species, structural similarity of large biomolecules, and recurring patterns of interactions in social networks. A large class of such analyses methods quantify the topological similarity of nodes across networks. The resulting correspondence of nodes across networks, also called node alignment, can be used to identify invariant subgraphs across the input graphs. Given graphs as input, alignment algorithms use topological information to assign a similarity score to each -tuple of nodes, with elements (nodes) drawn from each of the input graphs. Nodes are considered similar if their neighbors are also similar. An alternate, equivalent view of these network alignment algorithms is to consider the Kronecker product of the input graphs and to identify high-ranked nodes in the Kronecker product graph. Conventional methods such as PageRank and HITS (Hypertext-Induced Topic Selection) can be used for this purpose. These methods typically require computation of the principal eigenvector of a suitably modified Kronecker product matrix of the input graphs. We adopt this alternate view of the problem to address the problem of multiple network alignment. Using the phase estimation algorithm, we show that the multiple network alignment problem can be efficiently solved on quantum computers. We characterize the accuracy and performance of our method and show that it can deliver exponential speedups over conventional (non-quantum) methods.

  19. Percolation of interdependent network of networks

    International Nuclear Information System (INIS)

    Havlin, Shlomo; Stanley, H. Eugene; Bashan, Amir; Gao, Jianxi; Kenett, Dror Y.

    2015-01-01

    Complex networks appear in almost every aspect of science and technology. Previous work in network theory has focused primarily on analyzing single networks that do not interact with other networks, despite the fact that many real-world networks interact with and depend on each other. Very recently an analytical framework for studying the percolation properties of interacting networks has been introduced. Here we review the analytical framework and the results for percolation laws for a Network Of Networks (NONs) formed by n interdependent random networks. The percolation properties of a network of networks differ greatly from those of single isolated networks. In particular, because the constituent networks of a NON are connected by node dependencies, a NON is subject to cascading failure. When there is strong interdependent coupling between networks, the percolation transition is discontinuous (first-order) phase transition, unlike the well-known continuous second-order transition in single isolated networks. Moreover, although networks with broader degree distributions, e.g., scale-free networks, are more robust when analyzed as single networks, they become more vulnerable in a NON. We also review the effect of space embedding on network vulnerability. It is shown that for spatially embedded networks any finite fraction of dependency nodes will lead to abrupt transition

  20. Dynamics in steady state in vitro acto-myosin networks

    International Nuclear Information System (INIS)

    Sonn-Segev, Adar; Roichman, Yael; Bernheim-Groswasser, Anne

    2017-01-01

    It is well known that many biochemical processes in the cell such as gene regulation, growth signals and activation of ion channels, rely on mechanical stimuli. However, the mechanism by which mechanical signals propagate through cells is not as well understood. In this review we focus on stress propagation in a minimal model for cell elasticity, actomyosin networks, which are comprised of a sub-family of cytoskeleton proteins. After giving an overview of th actomyosin network components, structure and evolution we review stress propagation in these materials as measured through the correlated motion of tracer beads. We also discuss the possibility to extract structural features of these networks from the same experiments. We show that stress transmission through these networks has two pathways, a quickly dissipative one through the bulk, and a long ranged weakly dissipative one through the pre-stressed actin network. (topical review)

  1. Quantifying the dynamics of coupled networks of switches and oscillators.

    Directory of Open Access Journals (Sweden)

    Matthew R Francis

    Full Text Available Complex network dynamics have been analyzed with models of systems of coupled switches or systems of coupled oscillators. However, many complex systems are composed of components with diverse dynamics whose interactions drive the system's evolution. We, therefore, introduce a new modeling framework that describes the dynamics of networks composed of both oscillators and switches. Both oscillator synchronization and switch stability are preserved in these heterogeneous, coupled networks. Furthermore, this model recapitulates the qualitative dynamics for the yeast cell cycle consistent with the hypothesized dynamics resulting from decomposition of the regulatory network into dynamic motifs. Introducing feedback into the cell-cycle network induces qualitative dynamics analogous to limitless replicative potential that is a hallmark of cancer. As a result, the proposed model of switch and oscillator coupling provides the ability to incorporate mechanisms that underlie the synchronized stimulus response ubiquitous in biochemical systems.

  2. Network Society

    DEFF Research Database (Denmark)

    Clausen, Lars; Tække, Jesper

    2017-01-01

    the five strands of theory on the network society. Each theoretical position has its specific implications for acting toward strategic goals. In its entirety, the five perspectives give a thorough understanding of the conditions for successful strategic communication in the 21st century....

  3. Network Society

    DEFF Research Database (Denmark)

    Clausen, Lars; Tække, Jesper

    2018-01-01

    the five strands of theory on the network society. Each theoretical position has its specific implications for acting toward strategic goals. In its entirety, the five perspectives give a thorough understanding of the conditions for successful strategic communication in the 21st century....

  4. Network Views

    Science.gov (United States)

    Alexander, Louis

    2010-01-01

    The world changed in 2008. The financial crisis brought with it a deepening sense of insecurity, and the desire to be connected to a network increased. Throughout the summer and fall of 2008, events were unfolding with alarming rapidity. The Massachusetts Institute of Technology (MIT) Alumni Association wanted to respond to this change in the…

  5. Network Coding

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 15; Issue 7. Network Coding. K V Rashmi Nihar B Shah P Vijay Kumar. General Article Volume 15 Issue 7 July 2010 pp 604-621. Fulltext. Click here to view fulltext PDF. Permanent link: https://www.ias.ac.in/article/fulltext/reso/015/07/0604-0621 ...

  6. Global Networking.

    Science.gov (United States)

    Lynch, Clifford

    1997-01-01

    Discusses the state of the Internet. Highlights include the magnitude of the infrastructure, costs, its increasing pace, constraints in international links, provision of network capacity to homes and small businesses, cable television modems, political and cultural problems, the digital library concept, search engines, the failure of personal…

  7. Initial biochemical and functional characterization of a 5'-nucleotidase from Xylella fastidiosa related to the human cytosolic 5'-nucleotidase I.

    Science.gov (United States)

    Santos, Clelton A; Saraiva, Antonio M; Toledo, Marcelo A S; Beloti, Lilian L; Crucello, Aline; Favaro, Marianna T P; Horta, Maria A C; Santiago, André S; Mendes, Juliano S; Souza, Alessandra A; Souza, Anete P

    2013-01-01

    The 5'-nucleotidases constitute a ubiquitous family of enzymes that catalyze either the hydrolysis or the transfer of esterified phosphate at the 5' position of nucleoside monophosphates. These enzymes are responsible for the regulation of nucleotide and nucleoside levels in the cell and can interfere with the phosphorylation-dependent activation of nucleoside analogs used in therapies targeting solid tumors and viral infections. In the present study, we report the initial biochemical and functional characterization of a 5'-nucleotidase from Xylella fastidiosa that is related to the human cytosolic 5'-nucleotidase I. X. fastidiosa is a plant pathogenic bacterium that is responsible for numerous economically important crop diseases. Biochemical assays confirmed the phosphatase activity of the recombinant purified enzyme and revealed metal ion dependence for full enzyme activity. In addition, we investigated the involvement of Xf5'-Nt in the formation of X. fastidiosa biofilms, which are structures that occlude the xylem vessels of susceptible plants and are strictly associated with bacterial pathogenesis. Using polyclonal antibodies against Xf5'-Nt, we observed an overexpression of Xf5'-Nt during the initial phases of X. fastidiosa biofilm formation that was not observed during X. fastidiosa planktonic growth. Our results demonstrate that the de/phosphorylation network catalyzed by 5'-nucleotidases may play an important role in bacterial biofilm formation, thereby contributing novel insights into bacterial nucleotide metabolism and pathogenicity. Copyright © 2013 Elsevier Ltd. All rights reserved.

  8. Efficacy of topical honey therapy against silver sulphadiazine treatment in burns: A biochemical study

    OpenAIRE

    Nagane, N. S.; Ganu, J. V.; Bhagwat, V. R.; Subramanium, M.

    2004-01-01

    Thermal injury is associated with biochemical changes. The present study was undertaken to investigate relation of oxidative free radical generation and related biochemical parameters in burn trauma. The specific aim was to compare the levels of serum lipid peroxide, Ceruloplasmin and Uric Acid in burn patients during treatment with Silver Sulfadiazine Cream and honey therapy. It is a single blind prospective controlled study involving comparison of biochemical changes after treatment with si...

  9. The Evolution of Biochemical Indices After Basal Cell Epithelioma Removal - Case Report

    Directory of Open Access Journals (Sweden)

    Gurgas L.

    2017-05-01

    Full Text Available The paper proposes new exposure data on etiopathogenesis basal cell epithelioma and present a clinical case investigated dermatoscopic, biochemically, treated surgically and guided to avoid relapses. The case presented is part of typical cases of pigmented basal cell carcinoma. Biochemical and haematological investigations performed one day before the excisional intervention (results 1 and 30 days (results 2 after the intervention: It is recommended to monitor biochemical investigations in which alterations were found, and ways for raising the immunological status.

  10. From dirt to industrial applications: Pseudomonas putida as a Synthetic Biology chassis for hosting harsh biochemical reactions.

    Science.gov (United States)

    Nikel, Pablo I; Chavarría, Max; Danchin, Antoine; de Lorenzo, Víctor

    2016-10-01

    The soil bacterium Pseudomonas putida is endowed with a central carbon metabolic network capable of fulfilling high demands of reducing power. This situation arises from a unique metabolic architecture that encompasses the partial recycling of triose phosphates to hexose phosphates-the so-called EDEMP cycle. In this article, the value of P. putida as a bacterial chassis of choice for contemporary, industrially-oriented metabolic engineering is addressed. The biochemical properties that make this bacterium adequate for hosting biotransformations involving redox reactions as well as toxic compounds and intermediates are discussed. Finally, novel developments and open questions in the continuous quest for an optimal microbial cell factory are presented at the light of current and future needs in the area of biocatalysis. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Haematological and biochemical effects of polyphenolics in animal models.

    Science.gov (United States)

    Gnanamani, Arumugam; Sudha, Munusamy; Deepa, G; Sudha, M; Deivanai, K; Sadulla, S

    2008-07-01

    Polyphenols of natural and synthetic origin are exploited in tanning sector to convert putrescible skin/hide to non-putrescible leather. However, only 30-40% of the inputs have been taken up for processing, the remaining is released as unspent. The existing conventional wastewater treatment systems are inefficient in removing or degrading these unspent polyphenols and thus detrimental to ecosystem. The present study demonstrates the evaluation of impact of both synthetic and natural polyphenols on biochemical and haematological properties of blood and serum in animal models. The results reveal that concentrations of polyphenols play a major role. At higher concentrations, irrespective of their nature, there was a marked change in the lipid profile (81% reduction), followed by insignificant change in glucose levels, RBC and WBC counts and other haematological parameters. At lower concentrations, no significant changes in the above said properties were observed.

  12. Polyphenol Oxidases in Crops: Biochemical, Physiological and Genetic Aspects

    Directory of Open Access Journals (Sweden)

    Francesca Taranto

    2017-02-01

    Full Text Available Enzymatic browning is a colour reaction occurring in plants, including cereals, fruit and horticultural crops, due to oxidation during postharvest processing and storage. This has a negative impact on the colour, flavour, nutritional properties and shelf life of food products. Browning is usually caused by polyphenol oxidases (PPOs, following cell damage caused by senescence, wounding and the attack of pests and pathogens. Several studies indicated that PPOs play a role in plant immunity, and emerging evidence suggested that PPOs might also be involved in other physiological processes. Genomic investigations ultimately led to the isolation of PPO homologs in several crops, which will be possibly characterized at the functional level in the near future. Here, focusing on the botanic families of Poaceae and Solanaceae, we provide an overview on available scientific literature on PPOs, resulting in useful information on biochemical, physiological and genetic aspects.

  13. Dynamics of biochemical parameters of blood serum in kidney injuries

    Directory of Open Access Journals (Sweden)

    Y. L. Podgainiy

    2014-12-01

    Full Text Available Aim. Annually injuries of varying severity are registered in more than 4,5 million people (up to 10% of the population in Ukraine; renal injury in polytrauma is detected in 26,4% of cases and takes 2 – 3 place of injury of the abdominal cavity and retroperitoneal space. In order to study the kidney function and other vital organs systems 108 patients were examined. Methods and results. Laboratory methods (clinical and biochemical parameters of blood and urine tests, ultrasound and CT scans of the kidneys and abdominal organs were used. Conclusion. It was established that polytrauma often occurs in males (73,5% of middle-age. 42% of patients presented renal function violation - nitrogen excretion and 84% of patients had activated blood coagulation in the first 7 – 10 days of injury.

  14. Optical bio-chemical sensors on SNOW ring resonators

    Science.gov (United States)

    Khorasaninejad, Mohammadreza; Clarke, Nigel; Anantram, M. P.; Singh Saini, Simarjeet

    2011-08-01

    In this paper, we propose and analyze novel ring resonator based bio-chemical sensors on silicon nanowire optical waveguide (SNOW) and show that the sensitivity of the sensors can be increased by an order of magnitude as compared to silicon-on-insulator based ring resonators while maintaining high index contrast and compact devices. The core of the waveguide is hollow and allows for introduction of biomaterial in the center of the mode, thereby increasing the sensitivity of detection. A sensitivity of 243 nm/refractive index unit (RIU) is achieved for a change in bulk refractive index. For surface attachment, the sensor is able to detect monolayer attachments as small as 1 Å on the surface of the silicon nanowires.

  15. Biochemical paths in humans and cells: Frontiers of AMS bioanalysis

    International Nuclear Information System (INIS)

    Vogel, J.S.; Palmblad, N.M.; Ognibene, T.; Kabir, M.M.; Buchholz, B.A.; Bench, G.

    2007-01-01

    The publication rate of 3 H and 14 C use in biomedical research decreased by a factor of three since 1990 when the first applications of AMS in biomedicine were published. Against this decrease, the high sensitivity of AMS for these isotopes in small isolated samples has made significant contributions. New smaller spectrometers and increased commercial availability of AMS have solved some of the issues surrounding availability and cost, but improved quantitation in non-isotopic methods now compete with some early uses of AMS. We review the strength of AMS for quantifying rare biochemical events and chemical passages through individual people or cells and consider these as the frontiers of quantitation leading to profitable science unavailable to other techniques

  16. In vitro biochemical characterization of all barley endosperm starch synthases

    DEFF Research Database (Denmark)

    Cuesta-Seijo, Jose A.; Nielsen, Morten M.; Ruzanski, Christian

    2016-01-01

    Starch is the main storage polysaccharide in cereals and the major source of calories in the human diet. It is synthesized by a panel of enzymes including five classes of starch synthases (SSs). While the overall starch synthase (SS) reaction is known, the functional differences between the five SS....... Here we provide a detailed biochemical study of the activity of all five classes of SSs in barley endosperm. Each enzyme was produced recombinantly in E. coli and the properties and modes of action in vitro were studied in isolation from other SSs and other substrate modifying activities. Our results...... define the mode of action of each SS class in unprecedented detail; we analyze their substrate selection, temperature dependence and stability, substrate affinity and temporal abundance during barley development. Our results are at variance with some generally accepted ideas about starch biosynthesis...

  17. Biochemical methane potential (BMP) of artichoke waste: the inoculum effect.

    Science.gov (United States)

    Fabbri, Andrea; Serranti, Silvia; Bonifazi, Giuseppe

    2014-03-01

    The aim of this work was to investigate anaerobic digestibility of artichoke waste resulting from industrial transformation. A series of batch anaerobic digestion tests was performed in order to evaluate the biochemical methane potential of the matrix in respect of the process. A comparison of the different performances of the laboratory-scale reactors operating in mesophilic conditions and utilizing three different values of the inoculum/substrate ratio was carried out. The best performance was achieved with an inoculum/substrate ratio of 2. Artichoke-processing byproducts showed a classical organic waste decomposition behaviour: a fast start-up phase, an acclimation stage, and a final stabilization phase. Following this approach, artichoke waste reached chemical oxygen demand removal of about 90% in 40 days. The high methane yield (average 408.62 mL CH4 gvs (-1) voltatile solids), makes artichoke waste a good product to be utilized in anaerobic digestion plants for biogas production.

  18. Gluconeogenesis: An ancient biochemical pathway with a new twist.

    Science.gov (United States)

    Miyamoto, Tetsuya; Amrein, Hubert

    2017-07-03

    Synthesis of sugars from simple carbon sources is critical for survival of animals under limited nutrient availability. Thus, sugar-synthesizing enzymes should be present across the entire metazoan spectrum. Here, we explore the evolution of glucose and trehalose synthesis using a phylogenetic analysis of enzymes specific for the two pathways. Our analysis reveals that the production of trehalose is the more ancestral biochemical process, found in single cell organisms and primitive metazoans, but also in insects. The gluconeogenic-specific enzyme glucose-6-phosphatase (G6Pase) first appears in Cnidaria, but is also present in Echinodermata, Mollusca and Vertebrata. Intriguingly, some species of nematodes and arthropods possess the genes for both pathways. Moreover, expression data from Drosophila suggests that G6Pase and, hence, gluconeogenesis, initially had a neuronal function. We speculate that in insects-and possibly in some vertebrates-gluconeogenesis may be used as a means of neuronal signaling.

  19. Recommended Nordic paediatric reference intervals for 21 common biochemical properties

    DEFF Research Database (Denmark)

    Hilsted, Linda; Rustad, Pål; Aksglæde, Lise

    2013-01-01

    healthy Danish children were collected for establishing reference intervals for 21 common biochemical properties (Alanine transaminase, Albumin, Alkaline phosphatase, Aspartate transaminase, Bilirubin, Calcium, Cholesterol, Creatinine, Creatine kinase, HDL-Cholesterol, Iron, Lactate dehydrogenase, LDL...... values of X for the properties and statistical calculations carried out as performed in the NORIP study. Thus commutable (regarding analytical method) reference intervals for 20 properties were established and for LDL-Cholesterol reference intervals were reported for the specific analytical method...... employed. The data were compared to previous studies and to those obtained from the youngest age group in the NORIP study. Marked age differences were observed for most of the properties. Several properties also showed gender-related differences, mainly at the onset of puberty. Data are presented...

  20. [Cardiorenal syndrome: the role of new biochemical markers].

    Science.gov (United States)

    Vernuccio, Federica; Grutta, Giuseppe; Ferrara, Filippo; Novo, Giuseppina; Novo, Salvatore

    2012-12-01

    Cardiorenal syndrome is a pathophysiological heart and kidney disorder, in which acute or chronic dysfunction of one organ induces a damage in the other. It's a syndrome more and more often encountered in clinical practice and this implies the need to recognize the syndrome through biochemical markers with a good sensitivity and specificity, since its earliest stages in order to optimize therapy. In addition to widely validated biomarkers, such as BNP, pro BNP, creatinine, GFR and cystatin C, other promising molecules are available, like NGAL (neutrophil gelatinase-associated lipocalin, KIM-1 (kidney injury molecule-1), MCP-1 (monocyte chemotactic peptide), Netrin-1, interleuchin 18 and NAG (N-acetyl-β-glucosa-minidase). The role of these emerging biomarkers is still not completely clarified: hence the need of new clinical trials.

  1. Biochemical markers for prediction of preclampsia: review of the literature.

    Science.gov (United States)

    Monte, Santo

    2011-07-01

    Preeclampsia (PE) is one of the most common diseases worldwide, complicating ~5% of all pregnancies.Although no major progress has been achieved in the treatment of PE, our ability to identify women at highrisk has increased considerably during the past decade.The early identification of patients with an increased risk for preeclampsia is therefore one of the most important goals in obstetrics. Today, several markers may offer the potential to be used, most likely in a combinatory analysis, as predictors or diagnostic tools. We present here the current knowledge on the biology of preeclampsia and review several biochemical markers which may be used to monitor preeclampsia in a future, that, we hope, is not to distant from today.

  2. Biochemical effects of gamma irradiation on banana fruits

    International Nuclear Information System (INIS)

    El-Motaium, R.A.

    1980-01-01

    It is of important to study the extension of shelf-life at ambient temperature. This study would be of significant in the case of non- refrigerated transport, practices within the country and transhipment to distant countries. studies have therefore extended to assess the shelf-life of irradiated banana stored under-room temperature. Extension of shelf -life have been achieved by many methods, the most modern one is using gamma irradiation as a promising technology for developing nations. the aim of this investigation is to study the biochemical effects of gamma irradiation on G ros Michel m ature green banana fruits and also to determine the optimum dose level and the optimum storage conditions which resulted in, keeping the organoleptic qualities as it is and maximum extension in shelf-life

  3. Biochemical characteristics of four marine fish skins in Korea.

    Science.gov (United States)

    Cho, Jae-Kwon; Jin, Young-Guk; Rha, Sung-Ju; Kim, Seon-Jae; Hwang, Jae-Ho

    2014-09-15

    In this study, we investigated the biochemical characteristics of the fish skins of four industrial species: olive flounder (Paralichthys olivaceus), black rockfish (Sebastes schlegeli), sea bass (Lateolabrax maculatus) and red sea bream (Pagrus major). There is high domestic demand in Korea for farming of these fish for human consumption. Crude protein contents in the skin of these fish ranged from 73% to 94% by dry weight; this was in part due to a high content of the structural protein, collagen. Among the four species, olive flounder had the thickest dermal and epidermal layers in the dorsal skin. This species was also associated with the highest extraction ratio of acid-soluble collagen. We also examined whether fish skin could be a cost-effective alternative to current fish meal sources. Our analysis indicates that, when supplemented with additional fish oils and essential amino acids, fish skin is a viable alternative for fish meal formulations. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. Biochemical fundamentals of rational radurization technology of cooled meat

    International Nuclear Information System (INIS)

    Gel'fand, S.Yu.; Anisimov, B.N.

    1974-01-01

    A series of experiments has been conducted in the last few years to explore the possibility of prolonging the storage life of meat in a cooled state. These experiments have shown that a clearly promising approach is to use relatively low doses of ionizing radiation (300-600 Krad). Irradiation of meat and fowl with such doses strongly reduced microbial contamination while increasing 3- to 5-fold the storage life of the products at low above-zero C temperatures. An important consideration is that the organoleptic and nutritive properties remain largely unchanged. The present communication reports the main results of biochemical studies necessary before an irradiation scheme for semifinished meat products can be developed. (E.T.)

  5. Clinical and Biochemical Pitfalls in the Diagnosis of Peroxisomal Disorders.

    Science.gov (United States)

    Klouwer, Femke C C; Huffnagel, Irene C; Ferdinandusse, Sacha; Waterham, Hans R; Wanders, Ronald J A; Engelen, Marc; Poll-The, Bwee Tien

    2016-08-01

    Peroxisomal disorders are a heterogeneous group of genetic metabolic disorders, caused by a defect in peroxisome biogenesis or a deficiency of a single peroxisomal enzyme. The peroxisomal disorders include the Zellweger spectrum disorders, the rhizomelic chondrodysplasia punctata spectrum disorders, X-linked adrenoleukodystrophy, and multiple single enzyme deficiencies. There are several core phenotypes caused by peroxisomal dysfunction that clinicians can recognize. The diagnosis is suggested by biochemical testing in blood and urine and confirmed by functional assays in cultured skin fibroblasts, followed by mutation analysis. This review describes the phenotype of the main peroxisomal disorders and possible pitfalls in (laboratory) diagnosis to aid clinicians in the recognition of this group of diseases. Georg Thieme Verlag KG Stuttgart · New York.

  6. Hybrid Nanogenerator for Concurrently Harvesting Biomechanical and Biochemical Energy

    KAUST Repository

    Hansen, Benjamin J.

    2010-07-27

    Harvesting energy from multiple sources available in our personal and daily environments is highly desirable, not only for powering personal electronics, but also for future implantable sensor-transmitter devices for biomedical and healthcare applications. Here we present a hybrid energy scavenging device for potential in vivo applications. The hybrid device consists of a piezoelectric poly(vinylidene fluoride) nanofiber nanogenerator for harvesting mechanical energy, such as from breathing or from the beat of a heart, and a flexible enzymatic biofuel cell for harvesting the biochemical (glucose/O2) energy in biofluid, which are two types of energy available in vivo. The two energy harvesting approaches can work simultaneously or individually, thereby boosting output and lifetime. Using the hybrid device, we demonstrate a "self-powered" nanosystem by powering a ZnO nanowire UV light sensor. © 2010 American Chemical Society.

  7. Biochemical Importance of Glycosylation of Plasminogen Activator Inhibitor-1

    DEFF Research Database (Denmark)

    Gils, Ann; Pedersen, Katrine Egelund; Skottrup, Peter

    2003-01-01

    The serpin plasminogen activator inhibitor-1 (PAI-1) is a potential target for anti-thrombotic and anti-cancer therapy. PAI-1 has 3 potential sites for N-linked glycosylation. We demonstrate here that PAI-1 expressed recombinantly or naturally by human cell lines display a heterogeneous glycosyla......The serpin plasminogen activator inhibitor-1 (PAI-1) is a potential target for anti-thrombotic and anti-cancer therapy. PAI-1 has 3 potential sites for N-linked glycosylation. We demonstrate here that PAI-1 expressed recombinantly or naturally by human cell lines display a heterogeneous...... with the glycosylation sites could be excluded as explanation for the differential reactivity. The latency transition of non-glycosylated, but not of glycosylated PAI-1, was strongly accelerated by a non-ionic detergent. The different biochemical properties of glycosylated and non-glycosylated PAI-1 depended...

  8. Biochemical Markers for Osteoarthritis: Is There any Promising Candidate?

    Directory of Open Access Journals (Sweden)

    Elif Aydın

    2016-04-01

    Full Text Available Osteoarthritis (OA is the most common degenerative joint disease. OA affects millions of individuals each year and becoming the most important cause of pain in geriatric population. Progressive destruction of articular cartilage is one of the prominent features of the disease. The diagnosis of OA is generally based on clinical and radiographical findings, which are insufficient to determine early-stage OA and predict disease course. There is a need for biomarkers that help clinicians early diagnose, assess disease activity, predict prognosis and monitor response to therapy. There are a growing number of publications regarding candidate markers in this field. The aim of this paper was to review recent studies on biochemical markers that reflect cartilage, synovial and bone turnover and their clinical use in patients with OA.

  9. [The biochemical carcinogenesis of selected heavy metals in bladder cancer].

    Science.gov (United States)

    Rorbach-Dolata, Anna; Marchewka, Zofia; Piwowar, Agnieszka

    2015-01-01

    Bladder cancer takes the second place in the classification of morbidity of urinary system cancers. Many chemical factors take part in cancerogenesis. It is suggested that exposure to heavy metals such as arsenic, chromium, nickel and cadmium as well as its metabolites may trigger the bladder cancer through inducing excessive reactive oxygen species production and oxidative stress formation which are responsible for DNA damage. In patients with bladder cancer is observed the disorder of processes regulated by p-53, including apoptosis. There are many patients with bladder cancer with confirmed absence of retinoblastoma protein, which is responsible of holding on the process of coming up the cells with mutation into synthesis, where the replication process undergoes. It is mentioned that excessive expression of proto-oncogenes may also cause the bladder cancer. The article concerns biochemical effects of exposure to chosen heavy metals and their potential role in bladder cancer progression.

  10. γ-Glutamyltranspeptidases: sequence, structure, biochemical properties, and biotechnological applications.

    Science.gov (United States)

    Castellano, Immacolata; Merlino, Antonello

    2012-10-01

    γ-Glutamyltranspeptidases (γ-GTs) are ubiquitous enzymes that catalyze the hydrolysis of γ-glutamyl bonds in glutathione and glutamine and the transfer of the released γ-glutamyl group to amino acids or short peptides. These enzymes are involved in glutathione metabolism and play critical roles in antioxidant defense, detoxification, and inflammation processes. Moreover, γ-GTs have been recently found to be involved in many physiological disorders, such as Parkinson's disease and diabetes. In this review, the main biochemical and structural properties of γ-GTs isolated from different sources, as well as their conformational stability and mechanism of catalysis, are described and examined with the aim of contributing to the discussion on their structure-function relationships. Possible applications of γ-glutamyltranspeptidases in different fields of biotechnology and medicine are also discussed.

  11. Prediction of the preeclampsia: a view of biochemical markers

    Directory of Open Access Journals (Sweden)

    Mehmet Sühha Bostancı

    2013-10-01

    Full Text Available Preeclampsia is a diverse, multiorgan group of related disease processes that occurs in up to 5%-8% of pregnancies after 20 weeks’ gestation and it is one of the leading causes of maternal and fetal morbidity and mortality. Many molecular mechanisms are contributed to the pathogenesis of preeclampsia. Although it is unknown whether the mechanisms act independently or have synergistic effects. This review describes review of primary papers investigating blood based biomarker such as PAP-A, Inhibin A, sFlt1, and PP13 in general and first trimester biochemical markers and combinations of them specifically for preeclampsia.http://dx.doi.org/10.7175/rhc.v4i4.699

  12. Biochemical adaptation of camelids during periods where feed is withheld

    Directory of Open Access Journals (Sweden)

    J. Wensvoort

    2001-03-01

    Full Text Available Biochemical changes during fasting or the withholding of feed for 5 day were studied in serum of camelids (dromedary camel, llama and ruminants (sheep, steers. Camels maintained low levels of 13-hydroxybutyrate (BHB and high levels of glucose but showed some increased levels of non-esterified fatty acid (NEFA and urea when fasting. Sheep and steers showed a rise in serum BHB and much higher increases of NEFA than camels and llamas. Sheep showed decreased serum glucose. The llama showed some increase in BHB but NEFA was lower than the other three species. The results indicate that camelids have a unique ability to control lipolytic and gluconeogenic activity to prevent or postpone the state of ketosis. Understanding and manipulation of these metabolic mechanisms in cattle and sheep could have great benefit to the livestock industry.

  13. Structural and Biochemical Studies of LysM Proteins

    DEFF Research Database (Denmark)

    Wong, Mei Mei Jaslyn Elizabeth

    2017-01-01

    . Most of the signalling components in the Nod factor signalling pathway have been identified through genetic approaches. The current symbiosis signalling model, however, lacks components that could link Nod factor perception at the plasma membrane to downstream responses, such as calcium influx and perinuclear calcium...... involved in peptidoglycan hydrolysis; the Cell Wall Lytic enzyme associated with cell Separation (CwlS) from Bacillus subtilis, and P60_Tth from Thermus thermopiles. Biochemical studies conducted on purified CwlS showed that multiple LysM modules function cooperatively to bind N-acetylglucosamine (NAG......-induced intermolecular dimerization was observed in the co-crystal structure of P60_2LysM and NAG6. Until today, this is the only structural evidence illustrating intermolecular dimerization of LysM proteins. Intermolecular dimerization of plant LysM receptor kinases (RK) has been proposed as a mechanism...

  14. Biochemical markers and neuropsychological functioning in distal urea cycle disorders.

    Science.gov (United States)

    Waisbren, Susan E; Cuthbertson, David; Burgard, Peter; Holbert, Amy; McCarter, Robert; Cederbaum, Stephen

    2018-02-08

    Urea cycle disorders often present as devastating metabolic conditions, resulting in high mortality and significant neuropsychological damage, despite treatment. The Urea Cycle Disorders Longitudinal Study is a natural history study that collects data from regular clinical follow-up and neuropsychological testing. This report examines links between biochemical markers (ammonia, glutamine, arginine, citrulline) and primary neuropsychological endpoints in three distal disorders, argininosuccinic acid synthetase deficiency (ASD or citrullinemia type I), argininosuccinic acid lyase deficiency (ASA or ALD), and arginase deficiency (ARGD). Laboratory results and test scores from neuropsychological evaluations were assessed in 145 study participants, ages 3 years and older, with ASD (n = 64), ASA (n = 65) and ARGD (n = 16). Mean full scale IQ was below the population mean of 100 ± 15 for all groups: (ASD = 79 ± 24; ASA = 71 ± 21; ARGD = 65 ± 19). The greatest deficits were noted in visual performance and motor skills for all groups. While ammonia levels remain prominent as prognostic biomarkers, other biomarkers may be equally valuable as correlates of neuropsychological functioning. Cumulative exposure to the biomarkers included in the study proved to be highly sensitive indicators of neuropsychological outcomes, even when below the cut-off levels generally considered toxic. Blood levels of biomarkers obtained on the day of neuropsychological evaluations were not correlated with measures of functioning for any disorder in any domain. The importance of cumulative exposure supports early identification and confirms the need for well-controlled management of all biochemical abnormalities (and not just ammonia) that occur in urea cycle disorders.

  15. Simulation methods with extended stability for stiff biochemical Kinetics

    Directory of Open Access Journals (Sweden)

    Rué Pau

    2010-08-01

    Full Text Available Abstract Background With increasing computer power, simulating the dynamics of complex systems in chemistry and biology is becoming increasingly routine. The modelling of individual reactions in (biochemical systems involves a large number of random events that can be simulated by the stochastic simulation algorithm (SSA. The key quantity is the step size, or waiting time, τ, whose value inversely depends on the size of the propensities of the different channel reactions and which needs to be re-evaluated after every firing event. Such a discrete event simulation may be extremely expensive, in particular for stiff systems where τ can be very short due to the fast kinetics of some of the channel reactions. Several alternative methods have been put forward to increase the integration step size. The so-called τ-leap approach takes a larger step size by allowing all the reactions to fire, from a Poisson or Binomial distribution, within that step. Although the expected value for the different species in the reactive system is maintained with respect to more precise methods, the variance at steady state can suffer from large errors as τ grows. Results In this paper we extend Poisson τ-leap methods to a general class of Runge-Kutta (RK τ-leap methods. We show that with the proper selection of the coefficients, the variance of the extended τ-leap can be well-behaved, leading to significantly larger step sizes. Conclusions The benefit of adapting the extended method to the use of RK frameworks is clear in terms of speed of calculation, as the number of evaluations of the Poisson distribution is still one set per time step, as in the original τ-leap method. The approach paves the way to explore new multiscale methods to simulate (biochemical systems.

  16. Antimony-Induced Neurobehavioral and Biochemical Perturbations in Mice.

    Science.gov (United States)

    Tanu, Tanzina; Anjum, Adiba; Jahan, Momotaj; Nikkon, Farjana; Hoque, Mominul; Roy, Apurba Kumar; Haque, Azizul; Himeno, Seiichiro; Hossain, Khaled; Saud, Zahangir Alam

    2018-03-08

    Groundwater used for drinking has been contaminated with naturally occurring inorganic arsenic and other metals, and metal-contaminated drinking water is the biggest threat to public health in Bangladesh. Toxic metals present in the drinking water have a strong relationship with chronic diseases in humans. Antimony (Sb), a naturally occurring metal, has been reported to be present in the drinking water along with other heavy metals in Bangladesh. Although Sb is present in the environment, very little attention has been given to the toxic effects of Sb. The present study was designed to investigate the in vivo effects of Sb on neurobehavioral changes like anxiety, learning and memory impairment, and blood indices related to organ dysfunction. Mice exposed to antimony potassium-tartrate hydrate (Sb) (10 mg/kg body weight) significantly (p < 0.05) decreased the time spent in open arms while increased the time spent in closed arms compared to the control mice in elevated plus maze. The mean latency time of control group to find the platform decreased (p < 0.05) significantly during 7 days learning as compared to Sb-treated group in Morris water maze test, and Sb-exposed group spent significantly (p < 0.05) less time in the desired quadrant as compared to the control group in probe trial. Sb treatment also significantly altered blood indices related to liver and kidney dysfunction. Additionally, Sb-induced biochemical alterations were associated with significant perturbations in histological architecture of liver and kidney of Sb-exposed mice. These data suggest that Sb has a toxic effect on neurobehavioral and biochemical changes in mice.

  17. Association between sugar consumption, sociodemographic, anthropometric and biochemical profiles

    Directory of Open Access Journals (Sweden)

    Zorada Hattingh

    2013-11-01

    Full Text Available Background: The increase in prevalence of coronary heart disease, type 2 diabetes, obesity and abnormal blood lipid levels has raised the question of a possible relationship between these conditions and the consumption of sugar. Objectives: This study investigated the sugar consumption of financially-restricted Black women in Mangaung, South Africa. Method: Five hundred women were selected randomly and divided into younger (25–34 years and older (35–44 years groups. Dietary intake, sociodemographic status, anthropometry and biochemical data were obtained. Total sugar (TS and added sugar (AS consumption were compared between older and younger women as well as sociodemographic, anthropometric and biochemical categories. Results: AS intake contributed 12% and 13% of total energy intake in younger and older women, respectively. AS consumption was higher in younger women living in brick houses and those who possessed a microwave oven. In older women, it was higher in husband-headed households. Underweight women with the lowest body mass index had higher sugar consumption than overweight and/or obese women. Women with a lower body fat percentage had a higher AS consumption than women with a high body fat percentage. Sugar consumption was significantly lower in younger women with elevated serum lymphocytecounts. TS and AS consumption was higher in younger women with elevated serum glucose levels. Older women with elevated serum insulin had a significantly higher TS consumption compared to those with normal insulin concentrations. Conclusion: The amounts of TS and AS consumed by women in this observational study were unlikely to contribute to overweight and/or obesity.

  18. Association between sugar consumption, sociodemographic, anthropometric and biochemical profiles

    Directory of Open Access Journals (Sweden)

    Zorada Hattingh

    2013-11-01

    Full Text Available Background: The increase in prevalence of coronary heart disease, type 2 diabetes, obesity and abnormal blood lipid levels has raised the question of a possible relationship between these conditions and the consumption of sugar.Objectives: This study investigated the sugar consumption of financially-restricted Black women in Mangaung, South Africa.Method: Five hundred women were selected randomly and divided into younger (25–34 yearsand older (35–44 years groups. Dietary intake, sociodemographic status, anthropometry and biochemical data were obtained. Total sugar (TS and added sugar (AS consumption were compared between older and younger women as well as sociodemographic, anthropometric and biochemical categories.Results: AS intake contributed 12% and 13% of total energy intake in younger and older women, respectively. AS consumption was higher in younger women living in brick houses and those who possessed a microwave oven. In older women, it was higher in husbandheaded households. Underweight women with the lowest body mass index had highersugar consumption than overweight and/or obese women. Women with a lower body fat percentage had a higher AS consumption than women with a high body fat percentage. Sugar consumption was significantly lower in younger women with elevated serum lymphocyte counts. TS and AS consumption was higher in younger women with elevated serum glucoselevels. Older women with elevated serum insulin had a significantly higher TS consumption compared to those with normal insulin concentrations.Conclusion: The amounts of TS and AS consumed by women in this observational study were unlikely to contribute to overweight and/or obesity.

  19. POTENTIALITIES AND RISKS OF BIOCHEMICAL EDUCATIONAL RESEARCH VIA INTERNET

    Directory of Open Access Journals (Sweden)

    M.C. Gomes

    2004-05-01

    Full Text Available The internet is more and more present in worldwide education. There are innumerable projects thatstimulate its usage for aiding the teaching-learning process. This new trend modies the reality of thewhole school. However, many copies of identical information are found in several sites: graphs, gures,texts, links and even errors. The aim of this work is to analyse the biochemical issues photosynthesisand cellular respiration available in web pages, taking into account contents quality, trustworthinessand eectiveness. Firstly, 6th secondary level students were inquired by a questionnaire on their use ofinternet resources. More than 80 percent of them were regular users. The result conrms the alreadyknown potential of internet in education. Fourteen sites were analysed regarding to contents, presenceof bibliographical references, authorship, titles of responsibles and adequacy to the target public. Inrelation to contents, presence of conceptual errors, illustrations and other stimulant elements wereanalysed. None of the sites presented biblioghraphic references; less than half divulged responsiblenames and their graduation. The great majority do not mention intended public target. In general,the sites did not contained grave conceptual errors, except for two that mention estoma insteadestroma, cilica/acilica phosphorylation (for cyclic and acyclic, grama (for grana and place oxygenas essential for anaerobic respiration. However, one of these sites was the only one that mentionedenzymes and regulation steps of cellular respiration. Half of the sites presented identical texts andgures. None used livened up resources. The majority showed contents as virtual versions of printedbooks. Illustrations did not present necessary legends. None of the analysed sites, thus, was consideredexcellent. Trustworthiness is also questionable as much of the contents arte clearly copies of otherpages, recurrent even on the errors. Our data strengthen the need for

  20. Trace element deficiency and its diagnosis by biochemical criteria

    International Nuclear Information System (INIS)

    Kirchgessner, M.; Grassmann, E.; Roth, H.P.; Spoerl, R.; Schnegg, A.

    1976-01-01

    The effect of trace element deficiency on growth of rats and dairy cows is demonstrated using zinc and nickel. The effect of copper deficiency on reproductive performance is shown to be associated with increased death rates of pregnant animals and their foetuses. For the diagnosis of suboptimum states of trace element supply, biochemical criteria are needed. The mere analysis of the trace element content of various body tissues may lead to falase diagnoses because of the often slow response to varying intake and because of interactions with other dietary ingredients affecting absorption and metabolic efficiency of utilization. Thus copper deficiency is associated with a decrease in the serum level of both copper and iron, despite adequate iron intake, and simultaneously with an accumulation of iron in the liver of the animal. Enzymes and hormones containing the essential trace element as an integral constituent may serve as biochemical criteria. A sensitive response to zinc intake is exhibited by the activity of the alkaline phosphatase of serum or bones, and by the activity of the pancreatic carboxypeptidase A, all of which show a significant reaction to deficient intake within two to four days, and perhaps by the biopotency of insulin. Ceruloplasmin responds to the supply of copper. Its biosynthesis in the liver is possible only from copper available for this purpose. Thus, the determination of ceruloplasmin may take account of at least part of the copper available to the body for metabolic functions. Among various criteria, the catalase activity in blood may provide additional information on the state of iron supply. Malate dehydrogenase and glucose-6-phosphate dehydrogenase respond to nickel-deficient intake. Nickel deficiency also involves anaemia due to disorders in iron absorption