基于优化的真核生物遗传电路设计（EuGeneCiD）和建模（EuGeneCiM）工具：合成生物学的计算方法。
Optimization-based Eukaryotic Genetic Circuit Design (EuGeneCiD) and modeling (EuGeneCiM) tools: Computational approach to synthetic biology.
作者信息
Schroeder Wheaton L, Baber Anna S, Saha Rajib
机构信息
Department of Chemical and Biomolecular Engineering, University of Nebraska - Lincoln, Lincoln, NE 68588, USA.
Center for Root and Rhizobiome Innovation, University of Nebraska - Lincoln, Lincoln, NE 68588, USA.
出版信息
iScience. 2021 Sep 6;24(9):103000. doi: 10.1016/j.isci.2021.103000. eCollection 2021 Sep 24.
Synthetic biology has the potential to revolutionize the biotech industry and our everyday lives and is already making an impact. Developing synthetic biology applications requires several steps including design and modeling efforts which may be performed by tools. In this work, we have developed two such tools, Eukaryotic Genetic Circuit Design (EuGeneCiD) and Modeling (EuGeneCiM), which use optimization concepts and bioparts including promotors, transcripts, and terminators in designing and modeling genetic circuits. EuGeneCiD and EuGeneCiM preclude problematic designs leading to future synthetic biology application development pipelines. EuGeneCiD and EuGeneCiM are applied to developing 30 basic logic gates as genetic circuit conceptualizations which respond to heavy metal ions pairs as input signals for . For each conceptualization, hundreds of potential solutions were designed and modeled. Demonstrating its time-dependence and the importance of including enzyme and transcript degradation in modeling, EuGeneCiM is used to model a repressilator circuit.
合成生物学有潜力彻底改变生物技术产业和我们的日常生活，并且已经在产生影响。开发合成生物学应用需要几个步骤，包括设计和建模工作，这些工作可以通过工具来完成。在这项工作中，我们开发了两个这样的工具，即真核生物遗传电路设计（EuGeneCiD）和建模（EuGeneCiM），它们在设计和建模遗传电路时使用优化概念以及包括启动子、转录本和终止子在内的生物部件。EuGeneCiD和EuGeneCiM排除了导致未来合成生物学应用开发流程出现问题的设计。EuGeneCiD和EuGeneCiM被应用于开发30种基本逻辑门作为遗传电路概念化，这些逻辑门对重金属离子对作为输入信号做出响应。对于每种概念化，设计并建模了数百种潜在解决方案。EuGeneCiM用于对一个抑制振荡电路进行建模，展示了其时间依赖性以及在建模中纳入酶和转录本降解的重要性。
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