Engineering systems with emergent patterns in synthetic biofilms

该项目将开发计算方法来指导空间模式合成生物学基因电路的工程。在发育生物学中，空间模式和结构的自组织是一个基本问题，它有望支撑我们未来在组织工程和再生医学方面的努力。计算系统生物学家和合成生物学家可以通过构建工作原型系统，共同提供从理论到实际应用的桥梁。在我们的团队中，我们已经利用细胞构建了简单的合成模式，并正在朝着我们的梦想努力，即随意设计自组织组织和器官。尽管在经典发育生物学中已经提出了几种模式机制，但图灵模式机制在自我纠正和设计经济性方面是独一无二的，并且从未使用定义的生物成分从头开始构建规则模式。因此，这是一个诱人的工程和建模目标，我们选择在细菌“草坪”或生物膜中设计这些系统。在Endres小组的这个理论项目中，我们将为这种生长的生物膜实现一个生物物理反应-平流扩散模型，考虑基因表达，以及流体和细胞力学方面。理论预测将在附近的Isalan实验室进行测试。

The project will develop computational approaches to guide engineering of synthetic biology gene circuits for spatial pattering.The self-organisation of spatial patterns and structures in developmental biology is a fundamental problem that promises to underpin our future efforts in tissue engineering and regenerative medicine. Computational Systems Biologists and Synthetic Biologists can together provide a bridge from theory towards practical applications, by building working prototype systems.In our groups, we have already built simple synthetic patterns using cells, and are working towards our dream of engineering self-organising tissues and organs at will. Although several patterning mechanisms have been proposed in classical developmental biology, the Turing pattern mechanism is unique in terms of self-correction, and economy of design, and regular patterns have never been constructed ab initio using defined biological components. It is therefore a tantalising engineering and modelling target, and we have chosen to engineer these systems in bacterial 'lawns' or biofilms. In this theory project in the Endres group, we will implement a biophysical reaction-advection diffusion model for such a growing biofilm, considering gene expression, as well as fluid- and cell-mechanical aspects. Theoretical predictions will be tested in the nearby Isalan lab.