WEKO3
アイテム
Ranking network mechanisms by how they fit diverse experiments and deciding on E. coli's ammonium transport and assimilation network
http://hdl.handle.net/10228/00007537
http://hdl.handle.net/10228/00007537abcbcb08-37f4-4986-bd88-8d0c4f4bc4dd
| 名前 / ファイル | ライセンス | アクション |
|---|---|---|
s41540-019-0091-6.pdf (1.1 MB)
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| Item type | 学術雑誌論文 = Journal Article(1) | |||||||||||||||||||||
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| 公開日 | 2020-01-16 | |||||||||||||||||||||
| 資源タイプ | ||||||||||||||||||||||
| 資源タイプ識別子 | http://purl.org/coar/resource_type/c_6501 | |||||||||||||||||||||
| 資源タイプ | journal article | |||||||||||||||||||||
| タイトル | ||||||||||||||||||||||
| タイトル | Ranking network mechanisms by how they fit diverse experiments and deciding on E. coli's ammonium transport and assimilation network | |||||||||||||||||||||
| 言語 | ||||||||||||||||||||||
| 言語 | eng | |||||||||||||||||||||
| 著者 |
前田, 和勲
× 前田, 和勲
WEKO
16743
× Westerhoff, Hans V.× 倉田, 博之
WEKO
2130
× Boogerd, Fred C. |
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| 抄録 | ||||||||||||||||||||||
| 内容記述タイプ | Abstract | |||||||||||||||||||||
| 内容記述 | The complex ammonium transport and assimilation network of E. coli involves the ammonium transporter AmtB, the regulatory proteins GlnK and GlnB, and the central N-assimilating enzymes together with their highly complex interactions. The engineering and modelling of such a complex network seem impossible because functioning depends critically on a gamut of data known at patchy accuracy. We developed a way out of this predicament, which employs: (i) a constrained optimization-based technology for the simultaneous fitting of models to heterogeneous experimental data sets gathered through diverse experimental set-ups, (ii) a ‘rubber band method’ to deal with different degrees of uncertainty, both in experimentally determined or estimated parameter values and in measured transient or steady-state variables (training data sets), (iii) integration of human expertise to decide on accuracies of both parameters and variables, (iv) massive computation employing a fast algorithm and a supercomputer, (v) an objective way of quantifying the plausibility of models, which makes it possible to decide which model is the best and how much better that model is than the others. We applied the new technology to the ammonium transport and assimilation network, integrating recent and older data of various accuracies, from different expert laboratories. The kinetic model objectively ranked best, has E. coli's AmtB as an active transporter of ammonia to be assimilated with GlnK minimizing the futile cycling that is an inevitable consequence of intracellular ammonium accumulation. It is 130 times better than a model with facilitated passive transport of ammonia. | |||||||||||||||||||||
| 書誌情報 |
npj Systems Biology and Applications 巻 5, p. 14-1-14-11, 発行日 2019-04-12 |
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| 出版社 | ||||||||||||||||||||||
| 出版者 | Nature Research | |||||||||||||||||||||
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| 関連タイプ | isIdenticalTo | |||||||||||||||||||||
| 識別子タイプ | DOI | |||||||||||||||||||||
| 関連識別子 | info:doi/10.1038/s41540-019-0091-6 | |||||||||||||||||||||
| ISSN | ||||||||||||||||||||||
| 収録物識別子タイプ | ISSN | |||||||||||||||||||||
| 収録物識別子 | 2056-7189 | |||||||||||||||||||||
| 著作権関連情報 | ||||||||||||||||||||||
| 権利情報 | Copyright (c) The Author(s) 2019 | |||||||||||||||||||||
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| 権利情報 | Creative Commons Attribution 4.0 International License | |||||||||||||||||||||
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| 権利情報 | http://creativecommons.org/licenses/by/4.0/ | |||||||||||||||||||||
| キーワード | ||||||||||||||||||||||
| 主題Scheme | Other | |||||||||||||||||||||
| 主題 | Computer modelling | |||||||||||||||||||||
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| 主題Scheme | Other | |||||||||||||||||||||
| 主題 | Differential equations | |||||||||||||||||||||
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| 主題Scheme | Other | |||||||||||||||||||||
| 主題 | Numerical simulations | |||||||||||||||||||||
| 出版タイプ | ||||||||||||||||||||||
| 出版タイプ | VoR | |||||||||||||||||||||
| 出版タイプResource | http://purl.org/coar/version/c_970fb48d4fbd8a85 | |||||||||||||||||||||
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| 値 | yes | |||||||||||||||||||||
| 研究者情報 | ||||||||||||||||||||||
| URL | https://hyokadb02.jimu.kyutech.ac.jp/html/265_ja.html | |||||||||||||||||||||
| 論文ID（連携） | ||||||||||||||||||||||
| 値 | 10346186 | |||||||||||||||||||||
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| 値 | 8044 | |||||||||||||||||||||
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| 識別子タイプ | DOI | |||||||||||||||||||||
| 関連識別子 | https://doi.org/10.1038/s41540-019-0091-6 | |||||||||||||||||||||
| 関連名称 | https://doi.org/10.1038/s41540-019-0091-6 | |||||||||||||||||||||
