Knight Campus assistant professor Calin Plesa delivered his midterm tenure review seminar on Monday, March 6 at 11 a.m. in the Beetham Family Seminar Room. The talk, "Exploring Biological Sequence Space at Scale," detailed the Plesa Lab's tools and methods to explore protein function at large scales, which rely on a combination of DropSynth gene synthesis, DNA barcode-enabled functional assays, and NGS sequencing to achieve high-scale measurements.

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About the Talk:

"Exploring Biological Sequence Space at Scale" — The ability to explore protein functional space is crucial for protein engineering applications and could have an enormous impact on medicine, biotechnology, and basic life sciences research. This problem is complicated by the vast combinatorial size of sequence space which is intractable to experimental approaches. The Plesa Lab designs tools and methods to explore protein function at large scales. The key to achieving high-scale measurements is the combination of DropSynth gene synthesis, DNA barcode-enabled functional assays, and NGS sequencing. We describe recent efforts to improve the length, scale, and percentage of perfect gene assemblies. First, we outline a multiplexed approach to carry out targeted enrichment of genes from large libraries using CRISPR Cas9.

We then apply these technologies to measure and engineer two protein families: dihydrofolate reductases and fluorescent proteins. The latter data is used to train machine learning methods that find underlying patterns in sequence data, help guide limited experimental resources to the most promising sequences, and even generate completely novel sequences distant from any input and potentially inaccessible by evolutionary processes. Finally, we describe efforts to move beyond fluorescence and growth-based measurements by characterizing thousands of receptor histidine kinase biosensors. Overall these technologies enable efficient exploration of functional sequence space at scales far larger than previously possible.  

About Calin Plesa:

A synthetic biologist whose research interests lie at the intersection of biochemistry, protein engineering, microbiology, synthetic biology, genetics and technology, Calin Plesa is improving and lowering the cost of gene synthesis, which is used in nearly all areas of life sciences research including studies on how mutations influence disease development and the development of new therapeutics. Plesa developed a method called DropSynth, which allows the generation of large libraries of thousands of genes and functional testing of all possible mutations at relatively low cost. This opens many new avenues of research and potential applications previously deemed too expensive. Before joining the Knight Campus in 2019, he was a postdoctoral fellow at UCLA. He earned his doctorate in bio-nanoscience in 2015 from Delft University of Technology. He received master’s degrees in nanoscience and nanotechnology from Delft in 2009 and Chalmers University of Technology in 2010. He received a bachelor’s of applied science, engineering physics in 2007 from Simon Fraser University.