(7h) Single Cell Analysis Using Droplet Microfluidics

The complexity of biological systems suggests the existence of a whole new universe of novel catalysts, functions and mechanisms. Dissection and analysis of this complexity at single cell level will lead to the study of these novel catalysts, functions and mechanisms, hence, largely enhance our understanding of biological systems and drastically expand the capacity of bioengineering. Droplet microfluidics emerged as a versatile tool for single cell screening and analysis in recent years. In this poster, I will highlight several of recent efforts to demonstrate the promise of droplet based single cell analysis for bioengineering and biomedical research.

My graduate research focused on applying synthetic biology and metabolic engineering strategies to engineer nonconventional yeast Yarrowia lipolytica for high lipid production. Y. lipolytica, as an oleaginous yeast, possesses intrinsic capacity of accumulating large amount of lipid, which can be converted into numerous value-added chemicals including biofuels and nutrients. To expand its genetic toolbox, I first developed a set of hybrid promoters and centromere regulated plasmids to allow efficient manipulation of gene expression in this yeast. I then employed combinatorial, evolutionary and inverse metabolic engineering strategies to drastically increase the lipid production titer. Finally, to gain insights over the lipogenic phenotype, I also performed comparative genomic analysis to identify beneficial genomic and transcriptomic changes in high lipogenic strains. With these works, I applied synthetic biology concepts and genome scale analysis to achieve the success of engineering for value-added chemical production and to gain insights of mechanism of lipogenesis.

While I was engineering Y. lipolytica for high lipid production, I started to appreciate the existence of cellular heterogeneity. Characterization at population level, rather than single cell level, greatly limited our ability to understand and engineer biology. During my postdoc, I applied droplet microfluidics to develop novel bioengineering methods and to gain better understanding of biological systems. First, I applied droplet microfluidic workflows for effective screening of secretory phenotype. I applied flow cytometric sorting of double emulsion for improving riboflavin production in Y. lipolytica. I also worked on developing RAPID (RNA aptamers in droplets) by taking advantage of the quantification function of RNA aptamers and droplet sorting ability to improve tyrosine and streptavidin production in S. cerevisiae. Second, I developed a novel workflow for high throughput yeast colony RNA-seq by combining yeast colony formation in hydrogel microdroplets and Drop-seq (barcoded single cell RNA-seq). I further applied this method to study the white-opaque transition in C. albicans. Third, I employed Drop-seq to collect and analyze single cell genome wide expression data from dissociated mouse lung tissues and revealed an important subgroup of macrophage with mouse model of pulmonary fibrosis. We also started to look into the relation between gut microbiome to pulmonary fibrosis in mouse using single cell RNA-seq. In addition, I have also gained experience with droplet microfluidic techniques such as PACS (PCR-activated cell sorting), In-Drop single cell RNA-seq and droplet MDA for single cell genomic sequencing.

Looking ahead, the expertise and experience I gained through my training will enable my future lab to fully utilize the power of droplet microfluidic based single cell analysis to accelerate the engineering and discovery of biology. I will start by using droplet microfluidic platform to screen for novel industrial relevant enzymes and strains from environmental samples through in situ cultivation method and cultivation free method. I will then apply my expertise in synthetic biology to conduct protein engineering and strain development with promising candidates. In the meantime, I am also looking for establishing fruitful collaborations in the field of single cell sequencing, such as characterization of gut microbiome (single cell genome sequencing) and host response (single cell transcriptome sequencing).

Teaching Interests:

I have served as teaching assistant for biochemistry laboratory course and general microbiology course. Through the process, I gained valuable experiences such as interacting with students from different backgrounds and leading discussion and review section. I have also mentored several undergraduate students teaching them basic lab techniques, experimental design and critical thinking. Based on my academic background, I am willing to teach undergraduate lecture courses such as Introduction of Chemical and Biomolecular engineering and Biochemical Engineering. I also plan to develop course focusing on introducing core concepts and methods in the fields of metabolic engineering, synthetic biology and microfluidics.