(6cb) Next Generation Approaches to Biomolecular Engineering: Synthetic Biology Meets Directed Evolution

Rapidly advancing technologies like multiplex oligonucleotide synthesis and next-generation high-throughput sequencing have opened the door to tremendous progress in synthetic biology. My experience in both protein engineering and strain engineering puts me in an excellent position to forge the next generation of synthetic biology tools for biomolecular engineering.

Background

My research career started as an undergraduate at Johns Hopkins University under Prof. Marc Ostermeier, where I helped engineer allosteric molecular switches via directed evolution. For my M.S.E. research I created several modifications of chimeras of maltose binding protein and β-lactamase (BLA), the enzymatic activity of which could be allosterically regulated by the addition of maltose (published in PNAS). During my PhD with Prof. Matthew DeLisa (Cornell), I developed a suite of tools for examining protein folding, protein-protein interactions, and post- translational modifications in E. coli. I developed a protein folding reporter for the bacterial periplasm using a BLA-based selection. I showed that we could not only probe intrinsic protein folding, but factors in the cellular environment (e.g., chaperones, redox state) that affect protein folding (published in Protein Science). Later, I refactored the protein folding reporter to function as a detector for N-linked glycosylation in bacteria as a pipeline for engineering post-translational modifications (published in Biotechnology Journal).

Current Research
The postdoctoral work I am pursuing with Prof. Ryan Gill at CU-Boulder has provided me a broader view of both metabolic engineering and the design of directed evolution experiments. I am currently involved in three projects: (1) Performing selections on genome-scale libraries to discover genomic factors underlying bacterial antibiotic resistance. (2) Combining multiplex oligonucleotide synthesis and recombineering, I developed a platform for directed evolution of orthogonal repressors for cellular circuits on both the DNA and RNA level. (3) Regulator engineering for ethanol tolerance in E. coli. This work has given me a unique perspective on constructing targeted libraries on the genome scale, generating programmed diversity to complement my expertise in selection design. Specifically, leveraging the fast-developing technologies of multiplex oligo synthesis and next-generation sequencing will be key to my research as a principal investigator.

Future Research Directions
My lab will apply the latest synthetic biology technologies to tackling protein expression in bacteria with applications fpr human health, biofuel production, and synthetic circuit design. Targeted libraries of expression elements coupled with selections for protein folding will allow optimization of expression in difficult-to-produce proteins (e.g., membrane, heterologous proteins). Genome mining of heterologous proteins leverages the tremendous and ever-increasing amount of metagenomic data to inform and improve selection of enzyme activity. Sub-genome scale libraries of various families of proteins will provide in-depth exploration of cellular factors (and combinations thereof) that contribute to protein production. Finally, expanding into Gram-positive bacteria with genome-scale libraries on lactic acid bacteria will provide insight into protein folding and secretion in these clinically-relevant but understudied organisms.

Teaching
Beyond my research accomplishments, I have been fortunate to gain valuable teaching experience. In graduate school I served as a teaching assistant for four different courses, with topics ranging from process control and reaction kinetics (ChemE) to understanding wine and beer (Enology and Viticulture). Throughout my teaching pursuits I strove to implement active and cooperative learning techniques to keep students engaged and reinforce concepts learned in lecture. TA evaluations I have received consistently mention my enthusiasm for the material and creative approaches to teaching and exam review. I was also employed by Cornell Engineering Learning Initiatives, where I constructed and facilitated Engineering TA Development workshops in Assessment, Academic Integrity, Active and Cooperative Learning, Public Speaking, and Microteaching.

Inspiring students to pursue biomolecular engineering, whether in the classroom or the laboratory, is highly valuable. After all, Niels Bohr once supposedly said: "Biology is too important to be left to the biologists."