Microfluidics for automating and integrating synthetic biology

合成生物学已被用于设计治疗、生物能源和生物材料等领域的复杂生物系统。然而，这受到两个挑战的限制：可伸缩性和合成生物学设计-构建-测试-学习工作流程的集成自动化。目前的研究实验室配备了旨在加速合成生物学并提供高通量解决方案的机器人；然而，它们需要更多的精力来指导机器人执行一项新任务，而不是节省研究人员执行任务的时间。此外，它们非常昂贵--远远超出了许多科学实验室的预算范围，而且占用的空间很大，使得系统集成变得困难。因此，需要创建新的自动化技术来加快合成生物学工作流程，其优点是降低成本和时间，同时增加所创建的生物系统的复杂性。 为了应对这一挑战，拟议的研究计划是为合成生物学开发微流控自动化平台。这一新工具将由数字微流体(DMF)驱动，这是一种流体处理技术，可以在图案化的电极阵列上并行操作~NL体积。为了促进高通量应用，我们将DMF与通道中液滴集成在一起，这是一个两相系统，它使用不相容的相来创建单分散液滴的乳状液，这些乳状液可以用作包含单个电池或混合化学试剂的微反应器。为了促进自动化，这两种微流控范例将一起用于创建包含DNA文库的液滴，这些液滴将转化为细菌或酵母，并将在定向进化筛选的基础上评估这些变体的功能。这项研究计划跨越两个流程：(1)开发微流控自动化和表征站(M.A.C.S)，以及(2)合成生物循环的微流控集成。 拟议的研究计划将使新的自动化技术能够减少成本、时间和人工干预；此外，自动化系统将是廉价的，将没有移动部件和较小的实验室占地面积。同时，在开发用于合成生物学的微流体的同时，M.A.C.S将能够(A)自动将试剂输送到微流体，(B)液滴运动的自动化，(C)用于快速分析的在线检测系统。该系统的特点将是实施合成生物学，以发现用于生物燃料生产的新工程微生物。如果成功，这种方法可能会改变自动化和合成生物学领域，并使基础科学家和应用科学家能够解决可能改变加拿大(乃至世界)制造业、食品生产和医疗保健等其他领域的问题。

Synthetic biology has been used to engineer complex biological systems in areas such as therapeutics, bioenergy, and biological materials. However, this has been limited by two challenges: scalability and integrating automation of the synthetic biology Design-Build-Test-Learn workflow. Current research laboratories are equipped with robots that are aimed to accelerate synthetic biology and provide high-throughput solutions; however, they require more effort to instruct a robot to perform a new task than saving the researcher time in performing the task. Furthermore, they are expensive -- well outside of the budgetary reach of many scientific laboratories and have large footprints making it difficult for systems integration. Therefore, there is a need to create new automation technologies to expedite the synthetic biology workflow with the advantages of reducing costs and time while increasing the complexity of the biological systems that are created. In response to this challenge, the proposed research program is to develop microfluidic automation platforms for synthetic biology. This new tool will be powered by digital microfluidics (DMF), a fluid handling technique in which ~nL volumes can be manipulated in parallel on a patterned array of electrodes. To facilitate high-throughput applications, we will integrate DMF with droplet-in-channels a two-phase system where it uses immiscible phases to create emulsions of monodisperse droplets that can act as microreactors containing a single cell or a cocktail of chemical reagents. To facilitate automation, these two microfluidic paradigms will be used together to create droplets containing DNA libraries that are transformed into bacteria or yeast and the functionality of these variants will be evaluated on the basis of directed evolution screening. This research program spans two streams: (1) development of a Microfluidic Automation and Characterization Station (M.A.C.S), and (2) microfluidic integration of the synthetic biology cycle. The proposed research program will enable new automation technologies with reduced costs, time, and manual intervention; in addition, the automation system will be inexpensive, will have no moving parts and a small laboratory footprint. In parallel, with developing microfluidics for synthetic biology, a M.A.C.S will enable (a) automatic reagent delivery to the microfluidics, (b) automation of droplet movement, (c) in-line detection system for rapid analysis. This system will be characterized by implementing synthetic biology to discover newly engineered microbes for biofuel production. If successful, this method could transform the field of automation and synthetic biology, and making it accessible for basic and applied scientists to solve problems that could transform other areas such as manufacturing, food production, and healthcare in Canada (and world-wide).