Theoretical and experimental approaches in synthetic biology

该提案描述了合成生物学的一个项目，这是一个基于人为设计目的修改活细胞的领域。我们的长期目标是探索系统生物系统设计的方法，包括数学和计算方法来设计新的生物控制器，以及在细菌和酵母细胞中实验实施这些系统，以测试和验证理论的努力。我们也致力于让我们的蜂窝系统发挥作用，将它们应用于解决现实世界的问题。这项研究工作本质上是跨学科的，利用了物理/生物化学、分子生物学、生物物理学、非线性动力学和工程学的知识。******1。合成生物学设计方法的发展和验证***我们将实验测试最近开发的设计稳态控制系统的理论方法，该系统可以在扰动下保持生物状态。建立多节点遗传控制系统的变体库将允许我们探索由数学建议的参数空间区域，并测试系统对扰动的响应。******超越我们以前开发的方法，我们将探索频率响应方法在合成生物学中的潜力。细胞可以受到不同频率的周期性输入的干扰，把许多这样的测量放在一起可以让我们建立一个频率响应剖面。工程师使用这些来系统地设计新的控制器，我们将创建和表征我们的控制器变体库的频率响应特性，以提供响应概况的工具箱，并为合成生物学中基于频率的设计方法奠定基础。******2。研究细胞解决现实问题的可行性和实用性***廉价生长的细胞有可能为现实问题提供廉价的解决方案。我们将研究使用酵母细胞检测抗体的系统的潜在现实影响，从而作为一种廉价的诊断/监测工具。通过在细胞表面设计带有抗原和抗体结合域的细胞，我们可以让它们产生简单的视觉信号（“点”或“无点”输出），每次测试的成本很低，而且不需要专门的设备或培训。（在最好的情况下，甚至不需要电！）我们将把显示成功检测到恰加斯病抗体的初步结果扩展到新的疾病目标（疟疾和登革热），同时对优化系统功能的确切条件及其视觉输出机制进行系统研究。

The proposal describes a program in synthetic biology, a field based on modifying living cells for human-designed purposes. Our long-term objectives are to explore methods of systematic biological system design, including mathematical and computational approaches to design new biological controllers, as well as implementing these systems experimentally in bacteria and yeast cells, to test and validate the theoretical efforts. We also aim to put our cellular systems to work, applying them to the solution of real-world problems. This research effort is interdisciplinary in nature, drawing on knowledge from physical/biological chemistry, molecular biology, biological physics, nonlinear dynamics, and engineering.******1. Development and validation of synthetic biology design methods***We will experimentally test recently-developed theoretical methods for designing homeostatic control systems that maintain a biological state despite perturbations. Building libraries of variants of a multi-node genetic control system will allow us to explore a region of parameter space suggested by the mathematics, and test the system responses to perturbations.******Moving beyond our previously-developed methods, we will explore the potential of frequency-response approaches in synthetic biology. Cells can be perturbed with periodic inputs of different frequencies, and putting many such measurements together allows us to build up a frequency-response profile. Engineers use these to systematically design new controllers, and we will create and characterize the frequency-response characteristics of our library of controller variants, to provide a toolbox of response profiles and lay the foundation for frequency-based design methods in synthetic biology.******2. Investigations of the feasibility and utility of cellular solutions for real-world problems***Cheaply-grown cells have the potential to offer inexpensive solutions to real-world problems. We will investigate the potential real-world impact of a system that uses yeast cells to detect antibodies, thus acting as an inexpensive diagnostic/surveillance tool. By engineering cells with antigens and antibody-binding domains on their surfaces, we can potentially arrange for them to produce a simple visual signal (a “dot” or “no dot” output), at a low cost-per-test and without requirements for specialized equipment or training. (And in the best case, without even the need for electricity!) We will extend our preliminary results that show successful detection of Chagas disease antibodies to new disease targets (malaria and dengue fever), while making a systematic study of the exact conditions that optimize the system's functionality and the mechanisms underlying its visual output.