Description:

The Chemical and Biological Engineering Department is pleased to present student seminars by Sam Gowland and Kevin Shebek as part of our ChBE Seminar Series.

Sam Gowland will present a seminar titled "Design and Optimization of a Genome-Engineering Platform for Systems-Level Optimization of Synthetic Translation Systems.”

Cellular translation is responsible for the synthesis of proteins, a highly diverse class of macromolecules that form the basis of biological function. In Escherichia coli, harnessing and engineering of the biomolecular components of translation, such as ribosomes, transfer RNAs (tRNAs) and aminoacyl-tRNA synthetases, has led to both biotechnology products (i.e., amylases, insulin) and an expanded genetic code. However, the engineering potential of molecular translation is hampered by the limited capabilities for rapidly sampling the large genomic space necessary to evolve well-coordinated synthetic translation networks inside cells. To address this limitation, I developed a genome engineering method inspired by the action of mobile genetic elements termed mobilization. Mobilization utilizes the stochastic action of the recombinase flippase (FLP) to generate up to ~400 million genomic insertions, deletions, or rearrangements at short flippase recognition target (FRT) sites per mL culture per OD in living E. coli cells. As a model, I applied this approach to evolve faster-growing E. coli strains living exclusively off genomically expressed tethered ribosomes. In an iterative “pulse-passaging scheme,” I generated genomic libraries of cells via induction of FLP recombinase (pulse) followed by passaging the population without induction of FLP to enrich the resulting population for cells with higher fitness. I observed large structural genomic diversity across these cells, with the fastest growing strains exhibiting a 71% increase in growth rate compared to the ancestral strain. I anticipate both these strains, and the mobilization method will be useful tools for synthetic biology efforts to engineer translation systems. 

Kevin Shebek will present a seminar titled "Computational design and production of novel polymers from biological feedstocks.”

The environmental impact of materials and chemicals production from non-renewable petrochemical feedstocks has necessitated a transition to more sustainable practices, such as biological processes. Advances in synthetic biology have opened the door to synthesize novel compounds through engineered bioplatforms. However, the identification of attractive materials and pathways is complicated by the immense design space. In this work, we developed computational tools for both the generation and discovery of novel polymers from existing biological databases, as well as the design of pathways to produce them. Pickaxe, a software utilizing enzyme promiscuity and chemical catalysis to generate novel reactions and compounds, was used to identify novel monomers from the biological database KEGG. We then applied a machine learning model (PolyID) to screen the candidate monomers based on the thermal and mechanical properties. Finally, Pickaxe was used to identify promising pathways to produce the top monomer candidates. To highlight this workflow, we identified candidates for the replacement of poly(ethylene terephthalate) from novel poly(hydroxyalkanoates) generated from KEGG.

Bagels and coffee will be provided. Plan to arrive a few minutes early to grab a bagel and mingle!

*Please note that there will be no Zoom option for seminars this year.