Effective Biophysical Modeling of Cell Free Transcription and Translation Processes.
Effective Biophysical Modeling of Cell Free Transcription and Translation Processes.
复制标题
DOI：
10.3389/fbioe.2020.539081
复制
发表时间：
2020
影响因子：
5.7
通讯作者：
Varner JD
中科院分区：
文献类型：
--
作者：
Adhikari A;Vilkhovoy M;Vadhin S;Lim HE;Varner JD
转录和翻译是新陈代谢和信号转导的核心。在这项研究中，我们开发了一种有效的生物物理建模方法来模拟转录和翻译过程。该模型由耦合常微分方程组成，通过比较两个细胞自由合成电路与本研究中产生的实验测量值的模拟进行了测试。首先，我们考虑一个简单的电路，其中sigma因子70诱导绿色荧光蛋白的表达。这个相对简单的例子之后是一个更复杂的负反馈回路，其中两个控制基因与第三个报告基因绿色荧光蛋白的表达偶联。许多模型参数是从文献中以前的生物物理研究中估计的，而每个电路的其余未知模型参数是通过最小化模型模拟与本研究中产生的信使RNA（mRNA）和蛋白质测量之间的差异来估计的。特别是，要么直接使用已发表研究的参数估计值，要么使用文献中发现的特征值来建立参数估计问题的可行范围。为了详细分析各个模型参数对每个电路的表达动态的影响，使用了全局灵敏度分析。总之，有效的生物物理建模方法捕获了两种合成无细胞回路的表达动态，包括转录动态。虽然，我们在这里只考虑了两个电路，但这种方法可能会扩展到模拟无细胞和全细胞生物分子应用中的其他遗传电路，因为管理调节控制功能的方程是模块化的，易于修改。模型代码、参数和分析脚本可在MIT软件许可下从Varnerlab GitHub存储库下载。
Transcription and translation are at the heart of metabolism and signal transduction. In this study, we developed an effective biophysical modeling approach to simulate transcription and translation processes. The model, composed of coupled ordinary differential equations, was tested by comparing simulations of two cell free synthetic circuits with experimental measurements generated in this study. First, we considered a simple circuit in which sigma factor 70 induced the expression of green fluorescent protein. This relatively simple case was then followed by a more complex negative feedback circuit in which two control genes were coupled to the expression of a third reporter gene, green fluorescent protein. Many of the model parameters were estimated from previous biophysical studies in the literature, while the remaining unknown model parameters for each circuit were estimated by minimizing the difference between model simulations and messenger RNA (mRNA) and protein measurements generated in this study. In particular, either parameter estimates from published studies were used directly, or characteristic values found in the literature were used to establish feasible ranges for the parameter estimation problem. In order to perform a detailed analysis of the influence of individual model parameters on the expression dynamics of each circuit, global sensitivity analysis was used. Taken together, the effective biophysical modeling approach captured the expression dynamics, including the transcription dynamics, for the two synthetic cell free circuits. While, we considered only two circuits here, this approach could potentially be extended to simulate other genetic circuits in both cell free and whole cell biomolecular applications as the equations governing the regulatory control functions are modular and easily modifiable. The model code, parameters, and analysis scripts are available for download under an MIT software license from the Varnerlab GitHub repository.
登录
查看更多内容
影响因子：
4.3
作者：
Brewster RC;Jones DL;Phillips R
通讯作者：
Phillips R
影响因子：
16
作者：
Flynn, JM;Neher, SB;Baker, TA
通讯作者：
Baker, TA
DOI：
10.1007/978-1-4939-7795-6_4
发表时间：
2018-01-01
期刊：
SYNTHETIC BIOLOGY: METHODS AND PROTOCOLS
影响因子：
--
作者：
Marshall, Ryan;Noireaux, Vincent
通讯作者：
Noireaux, Vincent
影响因子：
3.8
作者：
LEE, SB;BAILEY, JE
通讯作者：
BAILEY, JE
影响因子：
2
作者：
GLASS, L;KAUFFMAN, SA
通讯作者：
KAUFFMAN, SA