A Computational Method for Automated Characterization of Genetic Components
A Computational Method for Automated Characterization of Genetic Components
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DOI：
10.1021/sb400152n
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发表时间：
2014-08-01
影响因子：
4.7
通讯作者：
Phillips, Andrew
中科院分区：
文献类型：
--
作者：
Yordanov, Boyan;Dalchau, Neil;Phillips, Andrew
设计和构建具有可预测行为的合成生物系统的能力可能会在医疗、农业可持续性和生物能源生产方面带来重大进展。然而，要达到能够从生物组件可靠地设计此类系统的阶段，就需要有能够对组件进行稳健表征的综合实验和计算技术。在本文中，我们提出了一种用于基因组件自动表征的计算方法。我们的方法利用了最近开发的多通道实验方案，并整合了细菌生长建模、贝叶斯参数估计和模型选择，以及适合自动化的数据处理步骤。我们在细胞基因工程建模和设计环境中实施了该方法，这使得表征和设计能够在一个通用的软件框架内集成。为了演示该方法的应用，我们在一系列实验条件下对一种对3 - 氧代己酰基 - 高丝氨酸内酯信号有反应的合成接收装置进行了定量表征。
The ability to design and construct synthetic biological systems with predictable behavior could enable significant advances in medical treatment, agricultural sustainability, and bioenergy production. However, to reach a stage where such systems can be reliably designed from biological components, integrated experimental and computational techniques that enable robust component characterization are needed. In this paper we present a computational method for the automated characterization of genetic components. Our method exploits a recently developed multichannel experimental protocol and integrates bacterial growth modeling, Bayesian parameter estimation, and model selection, together with data processing steps that are amenable to automation. We implement the method within the Genetic Engineering of Cells modeling and design environment, which enables both characterization and design to be integrated within a common software framework. To demonstrate the application of the method, we quantitatively characterize a synthetic receiver device that responds to the 3-oxohexanoyl-homoserine lactone signal, across a range of experimental conditions.