(6iz) Single-Cell Analysis for Advancing Synthetic Biology

The aim of synthetic biology is to design and build novel biological functions and systems. The promise of synthetic biology relies on the successful integration of engineering principles and biological systems. Single-cell heterogeneity, as a fundamental aspect in all biological systems, holds the key for further advancing synthetic biology. However, the impact of it on synthetic biology has not been extensively explored. Analyzing, understanding and utilizing single-cell heterogeneity will promote our ability of creating and altering the heterologous cellular community, which is the key for many applications in synthetic biology (e.g. bioproduction, microbiome engineering and immunotherapy etc.). My research will focus on (1) supplying novel parts and tools for synthetic biology through single-cell analysis and (2) advancing the understanding and engineering of heterogeneous cellular community through single-cell system biology. The synergistic effects of these two research directions will ultimately allow engineering heterologous cellular community with high precision and efficiency. In my future research, I plan to fully utilize the power of microfluidics, synthetic biology, metabolic engineering and bioinformatics to push the boundaries of bioengineering. In the short-term, I will expand our current synthetic biology toolbox through single-cell droplet microfluidic bioprospecting and bioengineering. In the long-term, my research will focus on advancing our ability to engineer complex cellular community using synthetic parts and design principles acquired through single-cell analysis. This research program will enhance our understanding of single-cell biology, enable the exploration of biological “dark matter” and advance our ability to design and build biological functions and systems to address the major challenges in the future.

Research experience:

My graduate research with Dr. Hal Alper at UT Austin focused on applying synthetic biology and metabolic engineering strategies to engineer nonconventional yeast Yarrowia lipolyticafor high lipid production. Successfully rewiring the oleaginous yeast Y. lipolytica’s innate lipogenic capacity is critical for transforming it into a production platform for numerous fatty acids based value-added chemicals such as biofuels and nutrients. To achieve this goal, I first expanded Y. lipolytica’s genetic toolbox by developing hybrid promoters and centromere regulated plasmids to allow efficient manipulation of gene expression. Powered by these tools, I further employed combinatorial and evolutionary engineering strategies to increase the lipid production titer to over 40 g/L. I also performed comparative sequencing analysis to identify genomic and transcriptomic changes associated with the high lipogenic phenotype. These work demonstrated the synergistic effects of synthetic biology, genome scale analysis and metabolic engineering for reprograming the metabolic wiring of cells.

My postdoc work with Dr. Adam Abate at UCSF focused on droplet microfluidics based single-cell analysis. As a platform method for single-cell analysis, droplet microfluidic analysis offers an opportunity to exam the cellular heterogeneity and diversity in an unprecedented level of throughput and sensitivity. During my postdoc training, I have worked on the interface of droplet microfluidics and single-cell analysis: I showcased the power of droplet based in vitro compartmentalization for engineering secretion phenotype by isolating Y. lipolytica strains with high riboflavin production; I applied single-cell RNA-seq (Drop-seq) to map cellular heterogeneity in lung fibrosis induced by bleomycin injury in mice and identified a profibrotic macrophage niche after tissue injury; I developed a novel workflow for highly parallel genome wide expression analysis of yeast colonies by combining microgel cultivation and Drop-seq. These work demonstrated the advantages of throughput, sensitivity and modularity of droplet microfluidics. It also showcased the needs for further developing and applying droplet based single cell analysis in bioengineering and biomedical researches.

Teaching Interests:

Teaching is more than just passing on information. It is also a process of nurturing critical, creative and divergent thinking, as well as acquiring ability to execute effectively and to work as a team collaboratively. I plan to use the proven system of lectures in combination of problem sets and group discussion for teaching technical expertise. I believe that granting research opportunities to undergraduates is a powerful tool for education, mentorship, and career development. As for the graduate level, I will focus on refining and deepening technical expertise, teaching technical writing, providing access to equipment and funding, and fostering career development. I will supply the overall picture and the access of new concepts and methods of the research field. I will also be available for discussing and exploring the potential focus of the research field in the future.

Serving as teaching assistant at UT Austin, I have taught biochemistry laboratory and general microbiology course. I have also successfully mentored several undergraduate and junior graduate students, who have either gone on to contribute to industry or received NSF GRFP awards. Based on my academia background and training, 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, single-cell analysis and microfluidics.

Selected publications:

1. Liu L, Dalal C, Heineike H, Abate A. “High throughput gene expression profiling of yeast colonies with microgel-culture Drop-seq.” In preparation.
2. Aran D*, Looney A*, Liu L*, (equal contribution) Hsu A, Fong V, Sheppard D, Abate A, Butte A, Bhattacharya M. “Reference-based annotation of single-cell transcriptomes identifies a profibrotic macrophage niche after tissue injury.” bioRxiv. 284604 (Nature Immunology, in revision).
3. Wagner J*, Liu L*, (equal contribution) Yuan S, Venkataraman M, Abate A, Alper H. “High-throughput screening of secretory phenotypes with double emulsion.” Metabolic Engineering. 2018, 47, 346-356.
4. Liu L, Markham K, Blazeck J, Zhou N, Leon D, Otoupal P, Alper H. “Surveying the lipogenesis landscape in Yarrowia lipolytica through understanding the function of a Mga2p regulatory protein mutant.” Metabolic Engineering. 2015, 31, 102-111.
5. Liu L, Pan A, Spofford C, Zhou N, Alper H. “An evolutionary metabolic engineering approach for enhancing lipogenesis in Yarrowia lipolytica.” Metabolic Engineering. 2015, 29, 36-45.
6. Liu L, Otoupal P, Pan A, Alper H. “Increasing expression level and copy number of a Yarrowia lipolyticaplasmid through regulated centromere function.” FEMS Yeast Research. 2014, 14 (7), 1124-1127
7. Blazeck J*, Hill A*, Liu L*, (equal contribution) Knight R, Miller J, Pan A, Otoupal P, Alper H. “Harnessing Yarrowia lipolyticalipogenesis to create a platform for lipid and biofuel production.” Nature Communication. 2014, 5:3131.
8. Blazeck J*, Liu L*, (equal contribution) Redden H, Alper H. “Tuning gene expression in Yarrowia lipolytica using a hybrid promoter approach.” Applied and Environmental Microbiology. 2011, 77(42), 7905-7914.