Faculty Profiles - KURATA Hiroyuki

Papers - KURATA Hiroyuki

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BIOCAD Project for Synthesis and Analysis of Gene Regulatory Networks Reviewed

Kurata Hiroyuki, Sumida Yoshiyuki, Tanaka Shin, Masaki Kouichi, Tanaka Takayuki, Urago Yuki, Ohashi Ken

Genome Informatics 13 467 - 468 2002.01

Building Common Patterns for Transcription Factor Binding Sites of <I>Escherichia coli</I> Reviewed

Li Weijiang, Kurata Hiroyuki

Genome Informatics 13 301 - 302 2002.01

Robustness analysis of the heat shock response in E. coli Reviewed

El-Samad H., Khammash M., Kurata H., Doyle J.

Proceedings of the American Control Conference 3 1742 - 1747 2002.01

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

The bacterial heat shock response refers to the mechanism by which bacteria react to a sudden increase in the ambient temperature of growth. The consequences of such an unmediated temperature increase at the cellular level is the unfolding, misfolding, or aggregation of cell proteins, which threatens the life of the cell. Cells respond to the heat stress by initiating the production of heat-shock proteins whose function is to refold denatured proteins into their native states. The heat shock response, through the elevated synthesis of molecular chaperones and proteases, enables the repair of protein damage and the degradation of aggregated proteins. In a previous work [1], we have devised a dynamic model for the heat shock response in E. coli. In the present paper, we provide a thorough discussion of the dynamical nature of this model. We use sensitivity analysis and simulation tools to illustrate the remarkable efficiency, robustness, and stability of the heat shock response system.

DOI： 10.1109/ACC.2002.1023817

Scopus

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BIOCAD project for constructing a biological system in silico

T.Adachi,N. Matoba,H. Kurata

Genome Informatics Series 12 284 - 285 2001.12

Simulation and system analysis of gene regulatory networks using the two-phase partition method

H. Kurata,T. Inoue,Y. Sumida,S. Tanaka,T. Ohashi

Genome Informatics Series 286 - 287 2001.12

Feedback regulation of the heat shock response in E. coli Reviewed

H. Kurata,H. El-Samad,T.-M. Yi,M. Khammash,J. C. Doyle

Proceedings of the 40th IEEE Conference on Decision and Control 837 - 842 2001.12

A simple and rapid system for the quantitation of RNA interference in plant cultured cells Reviewed

Akashi H,Miyagishi M,Kurata H,Nagata T,Taira K.

Nucleic Acids Res. Suppl. ( 1 ) 235 - 236 2001.01

BIOCAD Project for Constructing a Biological System <I>in Silico</I> Reviewed

Adachi Tadashi, Matoba Nana, Kurata Hiroyuki

Genome Informatics 12 284 - 285 2001.01

A simple and rapid system for the quantitation of RNA interference in plant cultured cells. Reviewed

Akashi H., Miyagishi M., Kurata H., Nagata T., Taira K.

Nucleic acids research. Supplement (2001) ( 1 ) 235 - 236 2001.01

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

The phenomenon known as RNA interference (RNAi) by double-stranded RNA (dsRNA) that was reported recently in the nematode Caenorhabditis elegans has been shown to operate by a mechanism that is widely conserved among species including plant cells. No quantitative analysis of the effects of RNAi on the expression of specific genes in plant cultured cells has been reported. An RNAi effect was observed 24 h after the introduction of dsRNA expression plasmids into tobacco BY-2 cells by electroporation. The simple system for suppression of specific genes in plant cells should be useful in attempts to elucidate the roles of individual genes in plant cells.

DOI： 10.1093/nass/1.1.235

Scopus

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Glucocorticoid-induced expression of a foreign gene by the GVG system in transformed tobacco BY-2 cells Reviewed

Nara Y., Kurata H., Seki M., Taira K.

Biochemical Engineering Journal 6 ( 3 ) 185 - 191 2000.12

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

A glucocorticoid-induced target gene expression system was used to control the expression of the uidA gene, whose product was β-glucuronidase (GUS), in tobacco BY-2 cell suspension culture. This targeting system showed quick, sensitive, and reversible response to dexamethazone (DEX), an artificial glucocorticoid hormone. Addition of DEX greatly and quickly enhanced uidA gene expression, whose level was as high as that under the control of the CaMV 35S promoter whereas in the absence of DEX, the GUS specific activity was suppressed to be as low as that of nontransformed BY-2 cells. The dilution of DEX decreased GUS specific activity showing that the concentration of DEX plays a major role in controlling the expression level of the target. The use of the glucocorticoid-induced system in plant cell suspension culture was demonstrated to precisely control target gene expression. (C) 2000 Elsevier Science S.A.

DOI： 10.1016/S1369-703X(00)00087-5

Scopus

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MAXIZYMEs: Allosterically controllable ribozymes with biosensor functions Reviewed

Kurata H., Miyagishi M., Kuwabara T., Warashina M., Taira K.

Journal of Biochemistry and Molecular Biology 33 ( 5 ) 359 - 365 2000.09

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

Ribozymes are catalytic RNAs that can cleave RNAs at specific sites, thus they have been employed to degrade a target mRNA in vivo. Development of allosterically controllable ribozymes is of great current interest, but it remained difficult to furnish such functions to ribozymes in cultured cells or in animals. Recently, we designed allosterically controllable ribozymes termed maxizymes, which have sensor arms that recognize target mRNA sequences and, in the presence of such target sequences only, they form a cavity that can capture catalytically indispensable Mg2+ ions, cleaving the target The maxizyme was applied to therapy for chronic myelogenous leukemia (CML). It cleaved specifically the chimeric BCR-ABL mRNA, which caused CML, without damaging the normal ABL or BCR mRNA in mammalian cells and also in mice, providing the first successful example for allosteric control of the activity of artificial ribozymes in vivo.

Scopus

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Intermittent light irradiation with second- or hour-scale periods controls anthocyanin production by strawberry cells Reviewed

Kurata H., Mochizuki A., Okuda N., Seki M., Furusaki S.

Enzyme and Microbial Technology 26 ( 8 ) 621 - 629 2000.05

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

Anthocyanin production by strawberry cells depends not only on light intensity but also on the light/dark cycle operation with hour- or second- scale periods. These findings are useful for designing and operating photobioreactors for enhanced anthocyanin production. Intermittent illumination with a second-scale period produces the same amount of anthocyanin as continuous light, suggesting that the light intensity distribution within a photobioreactor does not cause suppressed production. In the hour-scale cycle, continuous light operation enhanced anthocyanin production more than the light/dark cycle process. (C) 2000 Elsevier Science Inc.

DOI： 10.1016/S0141-0229(00)00143-5

Scopus

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Intermittent light irradiation with second- or hour- scale periods controls anthocyanin production by strawberry cells Reviewed

Kurata H.,Mochizuki A.,Okuda N.,Seki M.,Furusaki S.

Enzyme Microb. Technol. 26 ( # ) 621 - 629 2000.04

Grucocorticoid-induced expression of a foreign gene by the GVG system in transformed tobacco BY-2 Reviewed

Nara Y.,Kurata H.,Seki M,Taira K.

Biochem. Eng. J. 6 ( # ) 185 - 191 2000.04

Two-phase partition method for simulating a biological system at an extremely high speed Reviewed

Kurata H.,Taira K.

Genome Informatics 11 ( # ) 185195 - 185195 2000.04

Complexity in Regulation Generates Robustness in Bacterial Molecular Networks

Kurata H.,Taira K.

Proceedings of the First International Conference on Systems Biology 1 ( # ) 167 - 172 2000.04

Evolution of Ammonia Assimilation System in E. coli. ,17-24.

Kurata H.,Taira K.

Technical Report of IEICE AI2000-12 ( # ) 17 - 24 2000.04

Two-Phase Partition Method for Simulating a Biological System at an Extremely High Speed Reviewed

Kurata Hiroyuki, Taira Kazunari

Genome Informatics 11 185 - 195 2000.01

Two-phase partition method for simulating a biological system at an extremely high speed. Reviewed

Kurata H., Taira K.

Genome informatics. Workshop on Genome Informatics 11 185 - 195 2000.01

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

To accelerate the calculation speed for simulating a biological system, we proposed a novel simulation method, the two-phase partition method, which calculated molecular processes at a higher speed than any other proposed method. This method divides a biological system, which can be described by chemical reaction equations, into two-phases: the binding and reaction phases. We demonstrated the capability of the two-phase partition method to simulate a complex biological system at an extremely high speed and clarified the accuracy of the simulation. The two-phase partition method is very useful for simulating complex interactions among proteins and DNAs.

Scopus

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Mathematical model analyzes light-controlled expression of the CHS promoter in BY-2 cells Reviewed

Kurata H., Kaizuka Y., Seki M., Furusaki S.

Biochemical Engineering Journal 4 ( 1 ) 65 - 72 1999.09

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

The β-glucuronidase (GUS) reporter gene was fused to the 2.0-kb upstream region of Arabidopsis thaliana chalcone synthase (CHS) gene and transferred into BY-2 cells. CHS promoter expression showed a quick response to light/darkness and its expression level was more than that by the Cauliflower Mosaic Virus (CaMV) 35S promoter [1]. In this study, a kinetic model was developed for describing light-enhanced expression of the CHS promoter by tobacco BY-2 cells. This model simulates the behavior of CHS promoter expression by two factors: the specific light absorption rate (light intensity) and the illumination time. The dependency of GUS synthesis on light intensity is well characterized by using the Monod equation. The dependency on the illumination time is calculated by using a saturation time constant of illumination. The mathematical model demonstrated that the conditioned medium or past illumination changed the kinetics of CHS promoter expression.

DOI： 10.1016/S1369-703X(99)00034-0

Scopus

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Papers - KURATA Hiroyuki