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How does antimycin inhibit the bc₁ complex? A part-time twin

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010年第12期1797卷 1849-1857页

作者： Ransac, Stephane Mazat, Jean-Pierre Univ Bordeaux 2 INSERM U688 F-33076 Bordeaux France INSERM U688 Mitochondrial Physiopathol Lab Bordeaux France

Using a stochastic simulation without any other hypotheses we recently demonstrated the natural emergence of the modified Mitchell Q-cycle in the functioning of the bc(1) complex with few short-circuits and a very low residence time of the reactive semiquinone species in the Q(o) site However this simple model fails to explain both the inhibition by antimycin of the bc(1) complex and the accompanying increase in ROS production To obtain inhibition we show that it is necessary to block the return of the electron from the reduced haem b(L) to Q(o). With this added hypothesis we obtain a rigmoid inhibition curve due to the fact that when only one antimycin is bound per bc(1) dimer the electron of the inhibited monomer systematically crosses the dimer interface from b(L) to b(L) to reduce a quinone or semiquinone species in the other (free) Q(i) site Because this step is not limiting the activity is unchanged (ompared to the activity of the free dimer) Interestingly this b(L)-b(L) pathway is almost exclusively taken in this half-bound antimycin dimer In the free dimer the natural faster pathway is b(L)-b(H) on the same monome The addition of the assumption of half-of-the-sites reactivity to the previous hypothesis leads to a transient activation in the antimycin titration curve preceding a quasi-complete inhibition at antimycin saturation (C) 2010 Elsevier B V All rights reserved

关键词： gillespie algorithm bc(1) complex Antimycin A Stochastic modelling

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A strategic model for epidemic control in aquaculture

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PREVENTIVE VETERINARY MEDICINE 2010年第1-2期94卷 119-127页

作者： Green, Darren M. Univ Stirling Inst Aquaculture Stirling FK9 4LA Scotland

A stochastic metapopulation model of infectious disease was developed to model the spread of disease within and between sites of a region of an aquaculture industry. The study was a theoretical one examining the effect of transmission parameters through a sensitivity analysis. Production was modelled as either dispersed over many sites, or concentrated into small areas to provide 'firebreaks' between such areas as a disease control strategy. The effectiveness of such a control strategy could then be examined for different industry and disease parameters (for example, overall production, and rates of within- and between-site infection). At the within-site level, contact was modelled as either frequency or density dependent, either of these extreme formulations being potentially appropriate for different diseases. Under density dependence, the effect of high host density of increasing the basic reproduction number R(0) dominates, in contrast to the frequency-dependent model. However, for both model types, concentration of production into separate areas successfully slows the spread of simulated disease, particularly where long-distance transmission of the pathogen is weak due to fast attenuation of infectious agent over distance and time. (C) 2010 Elsevier B.V. All rights reserved.

关键词： Aquaculture Monte Carlo R(0) gillespie algorithm

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Amount of Escape Estimation Based on Bayesian and MCMC Approaches for RNA Interference

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MOLECULAR THERAPY-NUCLEIC ACIDS 2019年 18卷 893-902页

作者： Liu, Tian Pei, Yongzhen Li, Changguo Ye, Ming Tiangong Univ Sch Comp Sci & Technol Tianjin 300387 Peoples R China Tiangong Univ Sch Math Sci Binshui West Rd Tianjin 300387 Peoples R China Army Mil Transportat Univ Dept Basic Sci Tianjin 300387 Peoples R China Florida State Univ Dept Sci Comp Tallahassee FL 32306 USA

The amount of short interfering RNA (siRNA) escaping from the endosome has a significant impact on the efficiency of RNAi. In general, the initial injected amount of siRNAs during the experiment is known, and also the amount of siRNAs after the experiment can be revealed by the level of mRNA measured. However, it is impossible to measure the amount of siRNAs that escape from the endosome and really take part in the chemical reaction of RNAi by detecting the biological organism and its tissues. Inspired by the bottleneck effect in the virus, we introduce the Bayesian approach to infer the amount of escape based on a single type and multiple types of siRNA, respectively. With the consideration of the large calculation quantity of the accurate posterior distribution and the unavailable analytic expression of the likelihood function, our article proposes to take samples by the improved Markov chain Monte Carlo (MCMC) method. The article takes the silencing gene of the synthesis of chitin and the interfering multiple target oncogene as numerical examples to show that our improved MCMC method has higher operation efficiency compared to the Bayesian approach. Our research models siRNA endosome escape using statistical methods for the first time. It perhaps provides a theoretical basis to decrease the cost of a biotic experiment for the future and the standardized statistical approaches for the amount of escape estimation.

关键词： Bayesian inference gillespie algorithm MCMC method RNA interference amount of escape

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An efficient method for stochastic simulation of biological populations in continuous time

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BIOSYSTEMS 2009年第1期98卷 37-42页

作者： Allen, George Edward Dytham, Calvin Univ York Dept Biol Area 4 York YO10 5YW N Yorkshire England

We present an efficient algorithm for individual-based, stochastic simulation of biological populations in continuous time. A simple method for its implementation is given and it is compared to gillespie's commonly used Direct Method. These two methods are proven to be exactly equivalent and, using a basic evolutionary model, it is demonstrated that the new algorithm can run thousands of times faster. Furthermore, while computational cost per event increases linearly with population size under the Direct Method, this cost is independent of population size under the new algorithm. We argue that this gain in efficiency opens up the possibility to explore a new class of models in population biology. (C) 2009 Elsevier Ireland Ltd. All rights reserved.

关键词： Individual-based model Continuous-time model Efficient simulation gillespie algorithm Biological modelling Population ecology

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The flitting of electrons in complex I: A stochastic approach

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BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010年第6-7期1797卷 641-648页

作者： Ransac, Stephane Arnarez, Clement Mazat, Jean-Pierre Univ Bordeaux 2 INSERM U688 F-33076 Bordeaux France INSERM Mitochondrial Physiopathol Lab U688 Bordeaux France CBMN UMR 5248 F-33600 Pessac France

A stochastic approach based on the gillespie algorithm is particularly well adapted to describe the time course of the redox reactions that occur inside the respiratory chain complexes because they involve the motion of single electrons between the individual unique redox centres of a given complex. We use this approach to describe the molecular functioning of the peripheral arm of complex I based on its known crystallographic structure and the rate constants of electron tunnelling derived from the Moser and Dutton phenomenological equations. There are several possible electrons pathways but we show that most of them take the route defined by the successive sites and redox centres: NADH(+) site - FMN - N3 - N1b - N4 - N5 - N6a - N6b - N2 - Q site. However, the electrons do not go directly from NADH towards the ubiquinone molecule. They frequently jump back and forth between neighbouring redox centres with the result that the net flux of electrons through complex I (i.e. net number of electrons reducing a ubiquinone) is far smaller than the number of redox reactions which actually occur. While most of the redox centres are reduced in our simulations the degree of reduction can vary according to the individual midpoint potentials. The high turnover number observed in our simulation seems to indicate that, in the whole complex I. one or several slower step(s) follow(s) the redox reactions involved in the peripheral arm. It also appears that the residence time of FMNH center dot and SQ center dot (possible producers of ROS) is low (around 4% and between 1.6% and 5% respectively according to the values of the midpoint potentials). We did not find any evidence for a role of N7 which remains mainly reduced in our simulations. The role of N1a is complex and depends upon its midpoint potential. In all cases its presence slightly decreases the life time of the flavosemiquinone species. These simulations demonstrate the interest of this type of model which links the molecular

关键词： gillespie algorithm Complex I Stochastic modelling

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Chromatin computation: Epigenetic inheritance as a pattern reconstruction problem

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JOURNAL OF THEORETICAL BIOLOGY 2013年 336卷 61-74页

作者： Arnold, Christian Stadler, Peter F. Prohaska, Sonja J. Univ Leipzig Dept Comp Sci Computat EvoDevo Grp D-04107 Leipzig Germany Univ Leipzig Interdisciplinary Ctr Bioinformat D-04107 Leipzig Germany Univ Leipzig Dept Comp Sci Bioinformat Grp D-04107 Leipzig Germany Harvard Univ Dept Human Evolutionary Biol Cambridge MA 02138 USA Max Planck Inst Math Sci D-04103 Leipzig Germany Fraunhofer Inst Zelltherapie & Immunol D-04103 Leipzig Germany Univ Vienna Dept Theoret Chem A-1090 Vienna Austria Santa Fe Inst Santa Fe NM 87501 USA

Eukaryotic histones carry a diverse set of specific chemical modifications that accumulate over the life-time of a cell and have a crucial impact on the cell state in general and the transcriptional program in particular. Replication constitutes a dramatic disruption of the chromatin states that effectively amounts to partial erasure of stored information. To preserve its epigenetic state the cell reconstructs (at least part of) the histone modifications by means of processes that are still very poorly understood. A plausible hypothesis is that the different combinations of reader and writer domains in histone-modifying enzymes implement local rewriting rules that are capable of "recomputing" the desired parental modification patterns on the basis of the partial information contained in that half of the nucleosomes that predate replication. To test whether such a mechanism is theoretically feasible, we have developed a flexible stochastic simulation system (available at http://***/Software/StoChDyn) for studying the dynamics of histone modification states. The implementation is based on gillespie's approach, i.e., it models the master equation of a detailed chemical model. It is efficient enough to use an evolutionary algorithm to find patterns across multiple cell divisions with high accuracy. We found that it is easy to evolve a system of enzymes that can maintain a particular chromatin state roughly stable, even without explicit boundary elements separating differentially modified chromatin domains. However, the success of this task depends on several previously unanticipated factors, such as the length of the initial state, the specific pattern that should be maintained, the time between replications, and chemical parameters such as enzymatic binding and dissociation rates. All these factors also influence the accumulation of errors in the wake of cell divisions. (C) 2013 Elsevier Ltd. All rights reserved.

关键词： Chromatin complexity gillespie algorithm Evolutionary algorithm Epigenetic inheritance Histone modifications Chromatin computation

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Demographic stochasticity reduces the synchronizing effect of dispersal in predator-prey metapopulations

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ECOLOGY 2012年第7期93卷 1517-1524页

作者： Simonis, Joseph L. Cornell Univ Dept Ecol & Evolutionary Biol Ithaca NY 14853 USA

Dispersal may affect predator-prey metapopulations by rescuing local sink populations from extinction or by synchronizing population dynamics across the metapopulation, increasing the risk of regional extinction. Dispersal is likely influenced by demographic stochasticity, however, particularly because dispersal rates are often very low in metapopulations. Yet the effects of demographic stochasticity on predator-prey metapopulations are not well known. To that end, I constructed three models of a two-patch predator-prey system. The models constitute a hierarchy of complexity, allowing direct comparisons. Two models included demographic stochasticity (pure jump process [PJP] and stochastic differential equations [SDE]), and the third was deterministic (ordinary differential equations [ODE]). One stochastic model (PJP) treated population sizes as discrete, while the other (SDE) allowed population sizes to change continuously. Both stochastic models only produced synchronized predator-prey dynamics when dispersal was high for both trophic levels. Frequent dispersal by only predators or prey in the PJP and SDE spatially decoupled the trophic interaction, reducing synchrony of the non-dispersive species. Conversely, the ODE generated synchronized predator-prey dynamics across all dispersal rates, except when initial conditions produced anti-phase transients. These results indicate that demographic stochasticity strongly reduces the synchronizing effect of dispersal, which is ironic because demographic stochasticity is often invoked post hoc as a driver of extinctions in synchronized metapopulations.

关键词： demographic stochasticity dispersal gillespie algorithm metapopulation Rosenzweig-MacArthur stochastic differential equation trophic interactions

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How the extrinsic noise in gene expression can be controlled?

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IFAC-PapersOnLine 2017年第1期50卷 15092-15096页

作者： Vázquez-Jiménez, Aarón Santillán, Moisés Rodríguez-González, Jesús Center for Research and Advanced Studies of the National Polytechnic Institute Unit Monterrey Apodaca66600 Mexico

Gene regulation is crucial for adaptation and biological signals processing. It is known that the process of gene expression involves the unavoidable interaction with the molecular noise. Which is particularized by two sources: extrinsic and intrinsic. To know the impact of each source, we implemented an in silico plasmid with two identical copies of a gene. Quantifying the noise components through statistical differences of the time series solved through gillespie algorithm. The model predicted that the degradations rates are crucial to control the extrinsic noise perception in constitutive gene expression. © 2017

关键词： Gene expression Biological systems Signal processing Stochastic control systems Stochastic systems Biological signals Cellular model gillespie algorithm Molecular noise Noise components Noise perception Statistical differences Two sources

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The loneliness of the electrons in the bc₁ complex

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BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008年第7-8期1777卷 1053-1059页

作者： Ransac, Stephane Parisey, Nicolas Mazat, Jean-Pierre Univ Bordeaux 2 INSERM U668 Mitochondrial Physiopathol Lab F-33076 Bordeaux France LABRI Cours Liberat F-33405 Talence France

A stochastic approach based on gillespie algorithm is particularly well adapted to describe the time course of the redox reactions that occur inside the respiratory chain complexes because they involve the motion of single electrons between individual unique redox centres of a given complex and not populations of electrons and redox centres as usually considered in ordinary differential equations. In this way we approach the molecular functioning of the bc(1) complex based on its known crystallographic structure and the rate constants of electron tunnelling derived from the Moser and Dutton phenomenological equation. The main features of our simulations are the dominant and robust emergence of a Q-cycle mechanism and the near absence of short-circuits in the normal functioning of the bc(1) complex. Thus, in our paper, the Mitchell Q-cycle no longer appears as an a prior! hypothesis but arises out of the bc(1) complex structure and of the kinetic laws of redox reactions. (C) 2008 Elsevier B.V. All rights reserved.

关键词： gillespie algorithm bc(1) complex stochastic modelling Q-cycle short-circuit

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Stochastic modelling of the eukaryotic heat shock response

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JOURNAL OF THEORETICAL BIOLOGY 2010年第3期265卷 455-466页

作者： Mizera, Andrzej Gambin, Barbara Abo Akad Univ Dept Informat Technol FIN-20520 Turku Finland Turku Ctr Comp Sci FIN-20520 Turku Finland Polish Acad Sci Inst Fundamental Technol Res PL-02106 Warsaw Poland

The heat shock response (HSR) is a highly evolutionarily conserved defence mechanism allowing the cell to promptly react to elevated temperature conditions and other forms of stress. It has been subject to intense research for at least two main reasons. First, it is considered a promising candidate for deciphering the engineering principles underlying regulatory networks. Second, heat shock proteins (main actors of the HSR) play crucial role in many fundamental cellular processes. Therefore, profound understanding of the heat shock response would have far-reaching ramifications for the cell biology. Recently, a new deterministic model of the eukaryotic heat shock response has been proposed in the literature. It is very attractive since it consists of only the minimum number of components required by any functional regulatory network, while yet being capable of biological validation. However, it admits small molecule populations of some of the considered metabolites. In this paper a stochastic model corresponding to the deterministic one is constructed and the outcomes of these two models are confronted. The aim with this comparison is to show that, in the case of the heat shock response, the approximation of a discrete system with a continuous model is a reasonable approach. This is not always the truth, especially when the numbers of molecules of the considered species are small. By making the effort of performing and analysing 1000 stochastic simulations, we investigate the range of behaviour the stochastic model is likely to exhibit. We demonstrate that the obtained results agree well with the dynamics displayed by the continuous model, which strengthens the trust in the deterministic description. A proof of the existence and uniqueness of the stationary distribution of the Markov chain underlying the stochastic model is given. Moreover, the obtained view of the stochastic dynamics and the performed comparison to the outcome of the continuous formulation provide

关键词： Stochastic model Computer simulations Markov chain gillespie algorithm Stationary distribution

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