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Evolutionary Approaches for Strain Optimization Using Dynamic Models under a Metabolic Engineering Perspective

机译:代谢工程视角下使用动态模型的应变优化进化方法

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摘要

One of the purposes of Systems Biology is the quantitative modeling of biochemical networks. In this effort, the use of dynamical mathematical models provides for powerful tools in the prediction of the phenotypical behavior of microorganisms under distinct environmental conditions or subject to genetic modifications.rnThe purpose of the present study is to explore a computational environment where dynamical models are used to support simulation and optimization tasks. These will be used to study the effects of two distinct types of modifications over metabolic models: deleting a few reactions (knockouts) and changing the values of reaction kinetic parameters. In the former case, we aim to reach an optimal knockout set, under a defined objective function. In the latter, the same objective function is used, but the aim is to optimize the values of certain enzymatic kinetic coefficients. In both cases, we seek for the best model modifications that might lead to a desired impact on the concentration of chemical species in a metabolic pathway. This concept was tested by trying to maximize the production of dihydroxyacetone phosphate, using Evolutionary Computation approaches. As a case study, the central carbon metabolism of Escherichia coli is considered. A dynamical model based on ordinary differential equations is used to perform the simulations. The results validate the main features of the approach.
机译:系统生物学的目的之一是生化网络的定量建模。在这项工作中,动力学数学模型的使用提供了强大的工具,可以预测在不同的环境条件下或经过遗传修饰的微生物的表型行为。本研究的目的是探索使用动力学模型的计算环境。支持模拟和优化任务。这些将用于研究两种不同类型的修饰对代谢模型的影响:删除一些反应(敲除)和更改反应动力学参数的值。在前一种情况下,我们的目标是在定义的目标函数下达到最佳的淘汰集。在后者中,使用了相同的目标函数,但目的是优化某些酶动力学系数的值。在这两种情况下,我们都寻求最佳的模型修改,以对代谢途径中的化学物质浓度产生预期的影响。通过尝试使用进化计算方法最大程度地生产磷酸二羟基丙酮,对这一概念进行了测试。作为案例研究,考虑了大肠杆菌的中央碳代谢。基于常微分方程的动力学模型用于执行仿真。结果验证了该方法的主要特征。

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  • 来源
  • 会议地点 Tubingen(DE);Tubingen(DE)
  • 作者单位

    Departament of Informatics / CCTC - University of Minho Campus de Gualtar, 4710-057 Braga - Portugal IBB - Institute for Biotechnology and Bioengineering Center of Biological Engineering - University of Minho Campus de Gualtar, 4710-057 Braga - Portugal;

    rnIBB - Institute for Biotechnology and Bioengineering Center of Biological Engineering - University of Minho Campus de Gualtar, 4710-057 Braga - Portugal;

    rnIBB - Institute for Biotechnology and Bioengineering Center of Biological Engineering - University of Minho Campus de Gualtar, 4710-057 Braga - Portugal;

    rnDepartament of Informatics / CCTC - University of Minho Campus de Gualtar, 4710-057 Braga - Portugal;

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  • 正文语种 eng
  • 中图分类 程序设计、软件工程;
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