Specification and Simulation of Synthetic Multicelled Behaviors
Specification and Simulation of Synthetic Multicelled Behaviors
复制标题
DOI：
10.1021/sb300034m
复制
发表时间：
2012-08-01
影响因子：
4.7
通讯作者：
Klavins, Eric
中科院分区：
文献类型：
--
作者：
Jang, Seunghee S.;Oishi, Kevin T.;Klavins, Eric
本文综述了近年来在大肠杆菌人工合成多细胞系统的设计与构建方面的研究进展。coli和革兰氏阳性菌S. Cerevisiae提出，用这些相对简单生物体来实现复杂的分布式算法是可能的。然而，现有的合成生物学设计框架没有考虑生长小菌落的独特形态、基因回路与分子信号空间扩散的相互作用、或多细胞系统与并行算法之间的关系。在这里，我们介绍了一个用于多细胞行为的规范和模拟的框架，该框架将小菌落生长和分子信号的简单模拟与一种新的规范语言gro相结合。该框架允许研究者探索由单个细胞行为的高水平描述所诱导的集体行为。我们描述了先前发表的系统的示例规范，并介绍了两个新的规范：小菌落边缘检测和程序化小菌落形态发生。最后，我们通过例子说明了如何对用gro编写的规范进行细化，以包括有关其双分子实现的更多细节。
Recent advances in the design and construction of synthetic multicelled systems in E. coli and S. cerevisiae suggest that it may be possible to implement sophisticated distributed algorithms with these relatively simple organisms. However, existing design frameworks for synthetic biology do not account for the unique morphologies of growing microcolonies, the interaction of gene circuits with the spatial diffusion of molecular signals, or the relationship between multicelled systems and parallel algorithms. Here, we introduce a framework for the specification and simulation of multicelled behaviors that combines a simple simulation of microcolony growth and molecular signaling with a new specification language called gro. The framework allows the researcher to explore the collective behaviors induced by high level descriptions of individual cell behaviors. We describe example specifications of previously published systems and introduce two novel specifications: microcolony edge detection and programmed microcolony morphogenesis. Finally, we illustrate through example how specifications written in gro can be refined to include increasing levels of detail about their bimolecular implementations.