研究者詳細 - 倉田　博之

論文 - 倉田　博之

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Metabolic analysis of antibody producing Chinese hamster ovary cell culture under different stresses conditions 査読有り

Badsha M., Kurata H., Onitsuka M., Oga T., Omasa T.

Journal of Bioscience and Bioengineering 122 ( 1 ) 117 - 124 2016年07月

担当区分：責任著者記述言語：英語掲載種別：研究論文（学術雑誌）

© 2015 The Society for Biotechnology, Japan. Chinese hamster ovary (CHO) cells are commonly used as the host cell lines concerning their ability to produce therapeutic proteins with complex post-translational modifications. In this study, we have investigated the time course extra- and intracellular metabolome data of the CHO-K1 cell line, under a control and stress conditions. The addition of NaCl and trehalose greatly suppressed cell growth, where the maximum viable cell density of NaCl and trehalose cultures were 2.2-fold and 2.8-fold less than that of a control culture. Contrariwise, the antibody production of both the NaCl and trehalose cultures was sustained for a longer time to surpass that of the control culture. The NaCl and trehalose cultures showed relatively similar dynamics of cell growth, antibody production, and substrate/product concentrations, while they indicated different dynamics from the control culture. The principal component analysis of extra- and intracellular metabolome dynamics indicated that their dynamic behaviors were consistent with biological functions. The qualitative pattern matching classification and hierarchical clustering analyses for the intracellular metabolome identified the metabolite clusters whose dynamic behaviors depend on NaCl and trehalose. The volcano plot revealed several reporter metabolites whose dynamics greatly change between in the NaCl and trehalose cultures. The elastic net identified some critical, intracellular metabolites that are distinct between the NaCl and trehalose. While a relatively small number of intracellular metabolites related to the cell growth, glucose, glutamine, lactate and ammonium ion concentrations, the mechanism of antibody production was suggested to be very complicated or not to be explained by elastic net regression analysis.

DOI： 10.1016/j.jbiosc.2015.12.013

Scopus

その他リンク： https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85027930962&origin=inward

Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli 査読有り国際誌

Jahan N., Maeda K., Matsuoka Y., Sugimoto Y., Kurata H.

Microbial Cell Factories 15 ( 1 ) 2016年06月

担当区分：責任著者記述言語：英語掲載種別：研究論文（学術雑誌）

© 2016 The Author(s).Background: A kinetic model provides insights into the dynamic response of biological systems and predicts how their complex metabolic and gene regulatory networks generate particular functions. Of many biological systems, Escherichia coli metabolic pathways have been modeled extensively at the enzymatic and genetic levels, but existing models cannot accurately reproduce experimental behaviors in a batch culture, due to the inadequate estimation of a specific cell growth rate and a large number of unmeasured parameters. Results: In this study, we developed a detailed kinetic model for the central carbon metabolism of E. coli in a batch culture, which includes the glycolytic pathway, tricarboxylic acid cycle, pentose phosphate pathway, Entner-Doudoroff pathway, anaplerotic pathway, glyoxylate shunt, oxidative phosphorylation, phosphotransferase system (Pts), non-Pts and metabolic gene regulations by four protein transcription factors: cAMP receptor, catabolite repressor/activator, pyruvate dehydrogenase complex repressor and isocitrate lyase regulator. The kinetic parameters were estimated by a constrained optimization method on a supercomputer. The model estimated a specific growth rate based on reaction kinetics and accurately reproduced the dynamics of wild-type E. coli and multiple genetic mutants in a batch culture. Conclusions: This model overcame the intrinsic limitations of existing kinetic models in a batch culture, predicted the effects of multilayer regulations (allosteric effectors and gene expression) on central carbon metabolism and proposed rationally designed fast-growing cells based on understandings of molecular processes.

DOI： 10.1186/s12934-016-0511-x

Scopus

その他リンク： https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84975299249&origin=inward

Web application for genetic modification flux with database to estimate metabolic fluxes of genetic mutants. 査読有り国際誌

Noorlin Mohd Ali, Ryo Tsuboi, Yuta Matsumoto, Daisuke Koishi, Kazuhiro Maeda, Hiroyuki Kurata

Journal of Bioscience and Bioengineering 2016年03月

S-system-based Analysis of the Robust Properties Common to Many Biochemical Network Models 査読有り

Yu Matsuoka, Nusrat Jahan, Hiroyuki Kurata

Bioprocess and Biosystems Engineering 2016年03月

Metabolic analysis of antibody producing CHO cell culture under different stresses conditions 査読有り

Md. Bahadur Badsha, Hiroyuki Kurata, Masayoshi Onitsuka, Takushi Oga, Takeshi Omasa

Journal of Bioscience and Bioengineering 2016年03月

Developing a kinetic model of the E. coli ammonium assimilation network 国際誌

Kazuhiro Maeda, Fred C. Boogerd, Hans V. Westerhoff, Hiroyuki Kurata

Proceedings of the 16th International Conference on Systems Biology 2015年11月

Effect of NaCl and Trehalose Condition on Antibody Producing CHO Cell Culture 査読有り国際誌

Md. Bahadur Badsha, Hiroyuki Kurata, Masayoshi Onitsuka, Takushi Oga, Takeshi Omasa

Proceedings of Asian Congress on Biotechnology 2015 (ACB2015) 2015年11月

A detailed kinetic model of E. coli central metabolism in a batch culture 査読有り国際誌

Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto, Hiroyuki Kurata,

Proceedings of Asian Congress on Biotechnology 2015 (ACB2015) 2015年11月

Synthesis and decomposition approach for rational design of a biochemical network 国際誌

Hiroyuki Kurata

Proceedings of the Third BMIRC International Symposium for Virtual Physiological Human 2015年03月

Toward a quantitative in silico model for the E. coli ammonium assimilation system

Kazuhiro Maeda, Fred C. Boogerd, Frank J. Bruggeman, Hans V. Westerhoff, Hiroyuki Kurata

Proceedings of the Third BMIRC International Symposium for Virtual Physiological Human 2015年03月

Analytical study of robustness of a negative feedback oscillator by multiparameter sensitivity 査読有り国際誌

Kazuhiro Maeda, Hiroyuki Kurata

BMC Syst. Biol. 8 ( Suppl 5 ) S1 - S12 2014年12月

Analytical study of robustness of a negative feedback oscillator by multiparameter sensitivity 査読有り

Kazuhiro Maeda, Hiroyuki Kurata

GIW/ISCB-Asia 2014 2014年12月

Complementary elementary modes for fast and efficient analysis of metabolic networks 査読有り

Md. Bahadur Badsha, Hiroyuki Kurata

Biochem Eng J. 90 121 - 130 2014年06月

Integration of omics into metabolic flux distribution by complementary elementary mode analysis for large-scale metabolic networks 査読有り

Md Bahadur Badsha, Hiroyuki Kurata

3rd International Conference and Exhibition on Metabolomics & Systems Biology 2014年03月

CADLIVE toolbox for MATLAB: automatic dynamic modeling of biochemical networks with comprehensive system analysis, 査読有り

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

Bioproc. Biosys. Eng. 2014年03月

S-systemを用いた代謝反応モデルの感度解析査読有り

松岡結 , NusratJahan , 倉田博之

情報処理学会研究報告. BIO, バイオ情報学 ( 一般社団法人情報処理学会 ) 2014 ( 1 ) 1 - 2 2014年02月

担当区分：責任著者記述言語：英語掲載種別：研究論文（学術雑誌）

細胞は,様々な環境の変化に絶えず直面しており,そのような摂動に対するシステムの感度を理解することは重要である.本研究では,感度解析や安定性解析によって,代謝反応システムの特性をロバストネスの観点から明らかにしようとした.その結果、システム全体のロバストネスを評価するマルチパラメータ感度は、シングルパラメータ感度の最大値と相関した。一方、代謝反応のネットワークサイズはシステム全体のロバストネスと相関がないことが示唆された.

CiNii Article

その他リンク： https://ci.nii.ac.jp/naid/110009675848

Aim and scope of the BMIRC at Kyutech

Hiroyuki Kurata

Proceedings of the Second BMIRC International Symposium on Advances in Bioinformatics and Medical Engineering 2014年02月

Dynamic modeling of metabolic and gene regulatory systems toward developing virtual microbes 査読有り

Hiroyuki Kurata, Kazuhiro Maeda, Yu Matsuoka

Journal of Chemical Engineering of Japan 47 1 - 9 2014年01月

バイオテクノロジー査読有り

神谷典穂, 田中孝明, 宮坂武寛, 倉田博之, 近藤昭彦, 市川創作

化学工学 = Chemical engineering 77 ( 10 ) 719 - 724 2013年10月

大腸菌アンモニア同化制御機構のダイナミックモデルの構築査読有り

前田和勲 , FredC.Boogerd , FrankJ.Bruggeman , HansV.Westerhoff , 倉田博之

情報処理学会研究報告. BIO, バイオ情報学 ( 一般社団法人情報処理学会 ) 2013 ( 7 ) 1 - 6 2013年09月

担当区分：責任著者記述言語：英語掲載種別：研究論文（学術雑誌）

アンモニアは大腸菌にとって最適な窒素源である.大腸菌は,TCA 回路の中間代謝物である α-ケトグルタル酸にアンモニアを付加し,グルタミン酸とグルタミンを合成する.細胞内の窒素のほとんどはこの 2 つの代謝物に由来するものである.このような理由から,大腸菌がどのようにアンモニアを同化し,グルタミン酸とグルタミンの合成を制御しているのか明らかにすることは重要である.我々は,大腸菌アンモニア同化システムの新しいダイナミックモデルを構築した.動力学パラメータ推定では,推定値と測定値の差が最小になるように遺伝的アルゴリズムにペナルティ戦略を組み合わせた.我々のモデルは,近年発表されたメタボロームデータを定量的に再現できる.最近,グルタミン酸合成酵素に対するアスパラギン酸の競争阻害の重要性が指摘されたが,本稿ではその検証も行う.また GOGAT 欠損株と GOGAT 欠損サプレッサー変異株の解析も行う.アンモニアが豊富な条件では,グルタミン酸の過剰な蓄積によってサプレッサー変異株は野生株よりも増殖が遅いことが予測された.

CiNii Article

その他リンク： https://ci.nii.ac.jp/naid/110009605329

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