Microfluidics for synthetic biology

合成生物学描述了改造细胞以获得新的或改进的功能的过程。近年来，合成生物学工具的使用迅速增加，使科学家能够创造尚未呈现自然界的生物实体。例子包括几个具有里程碑意义的基因组项目，它们带来了基本的合成生物学工具，例如“下一代”测序的革命，以及CRISPR-Cas9的发现，这被认为是合成生物学领域最重要的贡献之一，并开创了快速基因编辑的新时代。尽管新生物系统和技术如潮水般涌来，但开发这些新生物系统的过程极其劳动密集，成本高昂，而且不太确定。在许多情况下，必须进行高通量实验，以提供系统参数如何相互作用的高分辨率图像，同时还要在尽可能短的时间内交付。为了对工作的不同阶段进行分类，合成生物学采用了工程学的设计-构建-测试-学习周期。正是通过这种循环的多次循环，研究人员才能设计出一个生物系统。即使在工业制造基本自动化的今天，合成生物学研究的大部分工作仍然是通过频繁的移液和将样品从一个平台转移到另一个平台来手工完成的。因此，技术是通过试错来学习的，而文档化的协议则需要解释。微流体技术的出现为合成生物学中的“闭环”提供了解决方案，用于自动化循环的多个方面以及与合成生物学相关的许多不同应用。这些平台是合成生物学中处理液体样品的理想选择，考虑到昂贵的试剂，繁琐的液体处理工作流程，占地面积小，这些平台的可移植性使它们特别适合自动化这一过程。在这个提案中，我概述了我的研究计划，以微流体自动化合成生物学为主题。该计划跨越两个流：(1)我描述了我们如何自动化构建周期的一部分，描述了大型构建物的合成、组装和交付的自动化，以及高保真度的按需基因编辑细胞。(2)我描述了我们如何将微流体集成到几个合成生物学测试应用中，以及我们如何学习推导新的（重新）设计。例如，我们将描述我们在酶的定向进化，光遗传学控制基因表达的代谢工程，设计新的生物传感器检测食物腐败和病毒疾病方面的创新努力。总体而言，该计划将对生物技术领域的突破性进展产生重大影响，为加拿大和世界其他国家的人类健康和生物能源等领域带来巨大的长期利益。

Synthetic biology describes the process of engineering a cell for new or improved functionality. In recent years, there has been a rapid surge in the use of synthetic biology tools to enable scientists to create biological entities not yet present natural world. Examples include several landmark genomic projects that have brought-forth essential synthetic biology tools, such as the revolution of `next-generation' sequencing, and the discovery of CRISPR-Cas9, regarded  as one of the most important contribution to the field of synthetic biology and has ushered in a new era of rapid gene editing. Despite this flood of new biological systems and technologies, the process of developing these new biological systems is extremely labour-intensive, expensive and less-than deterministic. In many cases, high-throughput experimentation must be carried-out to provide a high-resolution picture of how a system's parameters interact while also delivering in the shortest possible timeframe. To categorize different stages of work, synthetic biology has adopted the design-build-test-learn cycle of engineering. It is through many rounds of this cycle that researchers can engineer a biological system. Even today where industrial manufacturing is largely automated, much of the work in synthetic biology research is done by hand through frequent pipetting and transferring samples from one platform to another. As a result, technique is learned by trial-and-error, while documented protocols are subject to interpretation. Microfluidics have emerged to provide solutions to "close-the-loop" in synthetic biology lending platforms for automating multiple aspects of the cycle and many different applications related to synthetic biology. These platforms are ideal for processing liquid samples in synthetic biology considering the expensive reagents, the tedious liquid processing workflows, the small footprint, and portability of these platforms makes them especially suitable for automating this process. In this proposal, I outline my research program unified by the theme of automating synthetic biology using microfluidics. The program spans two streams:  (1) I describe how we automate the build-part of the cycle, describing automation of synthesis, assembly, and delivery of large constructs and to gene edit cells on-demand with high-fidelity. (2) I describe how we integrate microfluidics for several synthetic biology test applications and how we can learn to derive new (re)designs. For instance, we will describe our innovative efforts in directed evolution of enzymes, optogenetics to control gene expression for metabolic engineering, and design new biosensors for detecting food spoilage and viral-based diseases. Overall, this program is poised to have significant impact leading to groundbreaking advances in the biotechnology sector with enormous long-term benefits for areas like human health and bio-energy in Canada and other countries worldwide.