UC San Diego

The rapid growth of synthetic and systems biology has resulted in engineered microbes with impactful applications in industries such as environmental biosensing and fermentation. The coupling of these fields with microfluidic technology has enabled the imaging of microbial colonies under continuous growth conditions with precise environmental control to better understand the dynamics involved in complex molecular networks. The emergence of genome-scale microfluidic devices has bridged the gap between the multiplexing of -omics technology and the dynamics of microfluidics; however, existing high-throughput microfluidic devices are cumbersome and often unable to be applied outside of a laboratory. Towards this end, we have developed an elegantly simple microfluidic platform capable of monitoring the temporal gene expression of 2,176 unique microbes with both research and industrial application. In Chapter 1, I introduce the role of microfluidics in synthetic and systems biology. In Chapter 2, I describe the high-throughput microfluidic platform we have engineered and the protocol for building these devices. In Chapter 3, I show the platform's application as an environmental biosensor where the dynamics of 1,807 E. coli GFP-promoter strains coupled with machine learning algorithms are used to detect the presence of six heavy metals in real-time in both laboratory and real-world settings. Finally in Chapter 4, I show the device's application as a fermentation process monitoring system where the dynamics of 4,156 S. cerevisiae strains of a GFP-fusion library show the gene expression profile of a batch culture undergoing a diauxic shift, in real-time, depicting when the batch culture enters different growth states and changes its metabolic profile.