Faculty Profiles - KURATA Hiroyuki

Papers - KURATA Hiroyuki

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CADLIVE for Construction and Dynamic Simulation of Biochemical Networks Reviewed

Kazuhiro Maeda,Hiroyuki Kurata

Proceedings of Asia Pacific Biochemical Engineering Conference ( J0013 ) 2007.11

Systems Biology of the Nitrogen Assimilation System in E.coli Reviewed

Koichi Masaki,Hiroyuki Kurata

Proceedings of Asia Pacific Biochemical Engineering Conference J0108 - J0108 2007.11

Extended CADLIVE: A novel graphical notation for design of biochemical network maps and computational pathway analysis Reviewed

Kurata H., Inoue K., Maeda K., Masaki K., Shimokawa Y., Zhao Q.

Nucleic Acids Research 35 ( 20 ) 2007.11

Authorship：Corresponding author Publishing type：Research paper (scientific journal)

Biochemical network maps are helpful for understanding the mechanism of how a collection of biochemical reactions generate particular functions within a cell. We developed a new and computationally feasible notation that enables drawing a wide resolution map from the domain-level reactions to phenomenological events and implemented it as the extended GUI network constructor of CADLIVE (Computer-Aided Design of LIVing systEms). The new notation presents 'Domain expansion' for proteins and RNAs, 'Virtual reaction and nodes' that are responsible for illustrating domain-based interaction and 'InnerLink' that links real complex nodes to virtual nodes to illustrate the exact components of the real complex. A modular box is also presented that packs related reactions as a module or a subnetwork, which gives CADLIVE a capability to draw biochemical maps in a hierarchical modular architecture. Furthermore, we developed a pathway search module for virtual knockout mutants as a built-in application of CADLIVE. This module analyzes gene function in the same way as molecular genetics, which simulates a change in mutant phenotypes or confirms the validity of the network map. The extended CADLIVE with the newly proposed notation is demonstrated to be feasible for computational simulation and analysis. © 2007 The Author(s).

DOI： 10.1093/nar/gkm769

Scopus

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Mathematical identification of critical reactions in the interlocked feedback model Reviewed

Kurata H., Tanaka T., Ohnishi F.

PLoS ONE 2 ( 10 ) 2007.10

Authorship：Corresponding author Publishing type：Research paper (scientific journal)

Dynamic simulations are necessary for understanding the mechanism of how biochemical network generate robust properties to environmental stresses or genetic changes. Sensitivity analysis allows the linking of robustness to network structure. However, it yields only local properties regarding a particular choice of plausible parameter values, because it is hard to know the exact parameter values in vivo. Global and firm results are needed that do not depend on particular parameter values. We propose mathematical analysis for robustness (MAR) that consists of the novel evolutionary search that explores all possible solution vectors of kinetic parameters satisfying the target dynamics and robustness analysis. New criteria, parameter spectrum width and the variability of solution vectors for parameters, are introduced to determine whether the search is exhaustive. In robustness analysis, in addition to single parameter sensitivity analysis, robustness to multiple parameter perturbation is defined. Combining the sensitivity analysis and the robustness analysis to multiple parameter perturbation enables identifying critical reactions. Use of MAR clearly identified the critical reactions responsible for determining the circadian cycle in the Drosophila interlocked circadian clock model. In highly robust models, while the parameter vectors are greatly varied, the critical reactions with a high sensitivity are uniquely determined. Interestingly, not only the per-timloop but also the dclk-cyc loop strongly affect the period of PER, although the dclk-cyc loop hardly changes its amplitude and it is not potentially influential. In conclusion, MAR is a powerful method to explore wide parameter space without human-biases and to link a robust property to network architectures without knowing the exact parameter values. MARS identifies the reactions critically responsible for determining the period and amplitude in the interlocked feedback model and suggests that the circadian clock intensively evolves or designs the kinetic parameters so that it creates a highly robust cycle. © 2007 Kurata et al.

DOI： 10.1371/journal.pone.0001103

Scopus

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生物情報 Reviewed

倉田博之

化学工学 = CHEMICAL ENGINEERING OF JAPAN 71 ( 10 ) 682 - 683 2007.10

A Stochastic Simulation of Diffusion Reaction Model in Embryo Development Reviewed

NAKANO Katsutoshi, IWASAKI Rei, KURATA Hiroyuki

IPSJ SIG Notes ( Information Processing Society of Japan (IPSJ) ) 66 95 - 98 2007.09

Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal)

The deterministic simulation that uses ordinary differential equations to clarify dynamic behaviors of life-giving molecular networks is actively implemented now. However, gene expressions in cells happen stochastically and materials diffusion. In the deterministic simulation, time variations of molecular concentrations are decided when parameters are decided. Therefore, we propose the new method of spatiotemporal Monte Carlo simulation for achieving the simulation applied to gene expression and diffusion of materials in space and time.

CiNii Article

Other Link： https://ci.nii.ac.jp/naid/110006403660

Global Optimization of Large-scale Dynamic Biomolecular Network Model Reviewed

MAEDA KAZUHIRO, YOSHIDA KEISUKE, KURATA HIROYUKI

IPSJ SIG Notes ( Information Processing Society of Japan (IPSJ) ) 66 91 - 94 2007.09

Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal)

Dynamic simulation is a way to analyze dynamics of biomolecular networks consisting of proteins, metabolites and genes. In order to simulate their intrinsic dynamics, it is necessary to optimize the values of many kinetic parameters by reverse-engineering. We developed a new optimization method, DIS (Decomposition and Integration with Statistical analysis) combining decomposition and integration method with statistical analysis. By using DIS and genetic algorithm (GA), we optimized the parameters of large-scale biomolecular network which conventional GA cannot optimize. In this article, we also show that this method can obtain global solutions.

CiNii Article

Other Link： https://ci.nii.ac.jp/naid/110006403659

Effective and fast optimization for a dynamic model of the Drosophila circadian oscillator Reviewed

Tanaka S., Kurata H., Ohashi T.

Conference Proceedings - IEEE International Conference on Systems, Man and Cybernetics 5 3596 - 3601 2007.08

Authorship：Corresponding author Publishing type：Research paper (international conference proceedings)

In the field of systems biology, biochemical networks are being reconstructed in computer to understand their dynamic features. In this study, we focused on the estimation problem for a dynamic model of the Drosophila circadian oscillator, which is defined by two evaluation functions that represent oscillatory features. However, since the search space is multimodal and logarithmically large, it is quite difficult for ordinary GAs to optimize this evaluation problem. Therefore, we had used two-step optimizing, a random search with GA. It successfully optimized the circadian oscillator, but required a long calculation time, causing a local search. On the other hand, to optimize two evaluation functions simultaneously, we proposed the survival ratio GA, where genes have lifetimes and a population holds search histories. By alternating two evaluation functions every generation, the population holds previously evaluated genes and children inherit each and mixed properties. The survival ratio GA exhibited wider space search and higher success ratio, thus we applied the one-step optimizing with the survival ratio GA to the circadian estimation problem, which shortens the total calculation times and finds out more local optimums than the previous two-step optimizing method. © 2006 IEEE.

DOI： 10.1109/ICSMC.2006.384687

Scopus

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Integration of enzyme activities into metabolic flux distributions by elementary mode analysis Reviewed

Kurata H., Zhao Q., Okuda R., Shimizu K.

BMC Systems Biology 1 2007.07

Authorship：Corresponding author Publishing type：Research paper (scientific journal)

Background: In systems biology, network-based pathway analysis facilitates understanding or designing metabolic systems and enables prediction of metabolic flux distributions. Network-based flux analysis requires considering not only pathway architectures but also the proteome or transcriptome to predict flux distributions, because recombinant microbes significantly change the distribution of gene expressions. The current problem is how to integrate such heterogeneous data to build a network-based model. Results: To link enzyme activity data to flux distributions of metabolic networks, we have proposed Enzyme Control Flux (ECF), a novel model that integrates enzyme activity into elementary mode analysis (EMA). ECF presents the power-law formula describing how changes in enzyme activities between wild-type and a mutant are related to changes in the elementary mode coefficients (EMCs). To validate the feasibility of ECF, we integrated enzyme activity data into the EMCs of Escherichia coli and Bacillus subtilis wild-type. The ECF model effectively uses an enzyme activity profile to estimate the flux distribution of the mutants and the increase in the number of incorporated enzyme activities decreases the model error of ECF. Conclusion: The ECF model is a non-mechanistic and static model to link an enzyme activity profile to a metabolic flux distribution by introducing the power-law formula into EMA, suggesting that the change in an enzyme profile rather reflects the change in the flux distribution. The ECF model is highly applicable to the central metabolism in knockout mutants of E. coli and B. subtilis. © 2007 Kurata et al; licensee BioMed Central Ltd.

DOI： 10.1186/1752-0509-1-31

Scopus

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Integration of enzyme activities into metabolic flux distributions by elementary mode analysis Reviewed

Hiroyuki Kurata,Quanyu Zhao,Ryuichi Okuda,Kazuyuki Shimizu

BMC Systems Biology 1 31 - 31 2007.04

Mathematical identification of critical reactions in the interlocked feedback model Reviewed

H. Kurata,T. Tanaka,F. Ohnishi

PLoS One 2 e1103 - e1103 2007.04

Extended CADLIVE: a novel graphical notation for designing a biochemical network map that enables computational pathway analysis Reviewed

Hiroyuki Kurata,Kentaro Inoue,Kazuhiro Maeda,Koichi Masaki,Yuki Shimokawa,Quanyu Zhao

Nucleic Acids Res 35 e134 - e134 2007.04

大腸菌窒素同化システムのポジティブフィードバック制御のシンプルモデル Reviewed

真崎浩一，倉田博之

情報処理学会論文誌数理モデル化と応用 48 104 - 109 2007.04

大規模な動的生命分子ネットワークモデルのグローバルな最適化

前田和勲，吉田圭介，倉田博之

情報処理学会研究報告 MPS-66 91 - 94 2007.04

胚発生における拡散反応モデルの確率的シミュレーション

中野克俊，岩崎麗，倉田博之

情報処理学会研究報告 MPS-66 95 - 98 2007.04

A Simple Model of Positive Feedback of the Nitrogen Assimilation System in E. coli Reviewed

MASAKI KOICHI, KURATA HIROYUKI

情報処理学会論文誌数理モデル化と応用(TOM) ( Information Processing Society of Japan (IPSJ) ) 48 ( 6 ) 104 - 109 2007.03

Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal)

Computer simulation predicted that the nitrogen assimilation system in the GlnK knockout mutant of E. coli shows hysteresis with respect to changes in the extracellular ammonia concentration. To theoretically elucidate the mechanism of how hysteresis is generated, we reduced the dynamic model to a simple model with third-order equations. Theoretical analysis of the simple model shows that a positive feedback control is responsible for hysteresis. The system has two steady-state solutions within a specific range of ammonia concentrations. The range that provides two solutions expands when the positive feedback becomes strong, while the system has only one solution when the positive feedback is weakened.

CiNii Article

Other Link： https://ci.nii.ac.jp/naid/110006242974

Bioinformatics Reviewed

倉田博之

化学工学 = CHEMICAL ENGINEERING OF JAPAN 70 ( 10 ) 2006.10

Systems Biology and Design of Biological Systems Reviewed

KURATA Hiroyuki

Seibutsu Butsuri ( The Biophysical Society of Japan General Incorporated Association ) 46 ( 5 ) 244 - 250 2006.09

Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal)

Advances in the postgenomic technology produce huge data regarding molecular interactions. Systems biology requires a model-based analysis to understand the molecular architecture of biological systems. Systems biology consists of four stages: network identification, system analysis, system control, and system design. First, a large-scale biochemical network model is reconstructed in computer by elucidating gene functions or by inferring gene regulation networks from postgenomic data. Second, we analyze the network architectures that generate robust properties to various types of perturbations and explore some design principles underlying molecular architectures. Third, dynamic behaviors are controlled at the molecular level. Finally, we develop new technologies to rationally design a biochemical system at the molecular levels.<br>

DOI： 10.2142/biophys.46.244

CiNii Article

Other Link： https://ci.nii.ac.jp/naid/110004810269

CADLIVE : Computer-Aided Design of biological systems and its application Reviewed

KURATA Hiroyuki

Bioscience & industry 64 ( 9 ) 508 - 511 2006.09

Module-based analysis of robustness tradeoffs in the heat shock response system Reviewed

Kurata H., El-Samad H., Iwasaki R., Ohtake H., Doyle J., Grigorova I., Gross C., Khammash M.

PLoS Computational Biology 2 ( 7 ) 0663 - 0675 2006.08

Authorship：Corresponding author Publishing type：Research paper (scientific journal)

Biological systems have evolved complex regulatory mechanisms, even in situations where much simpler designs seem to be sufficient for generating nominal functionality. Using module-based analysis coupled with rigorous mathematical comparisons, we propose that in analogy to control engineering architectures, the complexity of cellular systems and the presence of hierarchical modular structures can be attributed to the necessity of achieving robustness. We employ the Escherichia coli heat shock response system, a strongly conserved cellular mechanism, as an example to explore the design principles of such modular architectures. In the heat shock response system, the sigma-factor σ32 is a central regulator that integrates multiple feedforward and feedback modules. Each of these modules provides a different type of robustness with its inherent tradeoffs in terms of transient response and efficiency. We demonstrate how the overall architecture of the system balances such tradeoffs. An extensive mathematical exploration nevertheless points to the existence of an array of alternative strategies for the existing heat shock response that could exhibit similar behavior. We therefore deduce that the evolutionary constraints facing the system might have steered its architecture toward one of many robustly functional solutions. © 2006 Kurata et al.

DOI： 10.1371/journal.pcbi.0020059

Scopus

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Papers - KURATA Hiroyuki