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CBE Dissertation Defense: Brian Mendoza

Title: "The Democratization of Genome Engineering: Tools and Techniques for Manipulating Microorganisms with CRISPR-Cas."

The discovery of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) family of genome sequences in bacteria and archaea has led to expansive application of the system as a means of interrogating and modifying genetic material across all kingdoms of life. This dissertation has developed algorithms and accompanying software, collectively named CASPER (CRISPR Associated Software for Pathway Engineering and Research), to identify promising sequences for effectively utilizing CRISPR associated (Cas) proteins in any species or community/metagenome of interest. The on- and off-target activity scoring algorithms improve upon previous work, first by utilizing an evolutionary algorithm and then by employing protein simulation to identify the contribution of sequence stability and mismatches to overall activity. Two algorithms, multitargeting and population analysis, employ searches across multiple genomes for deploying both degenerate and specific guides across multiple genomes with immediate application in microbiome manipulation and CRISPR-Cas enabled rapid sequence detection assays. Finally, the CASPERpam algorithm was written to rapidly identify potential protospacer adjacent motifs (PAM) that are required for initial binding by Cas proteins/complexes. CASPERpam successfully re-identified 12 experimental PAM sequences and further identified putative PAM sequences for another 1,037 species.

The application of CRISPR-Cas as an antimicrobial is of immediate interest due to rising prevalence of antibiotic resistance and the associated costs of development. Using the aforementioned algorithms for sequence design, this dissertation identified key barriers and opportunities for development of novel CRISPR-Cas antimicrobials that are both highly specific and highly tunable. Specifically, the identification of kinetic limitations to the transient introduction and expression of CRISPR-Cas machinery is a key mechanism of cell persistence. Studies in both model yeast (Saccharomyces cerevisiae) and multiple species of bacteria highlight the benefits of co-targeting defensive genes with high turnover rate Cas enzymes as a means of mitigating such kinetic barriers. These design principles are inherently generalizable to multiple pathogenic species, and benefit from the inherent specificity of CRISPR-Cas sequences to lay the foundation for a powerful new class of antimicrobials.

Brian Mendoza is a PhD candidate at UT in the lab of Cong Trinh, Ferguson Faculty Fellow. His research focuses on the development of CRISPR-Cas tools for manipulating microorganisms in both antimicrobial and microbiome engineering contexts. His work on antimicrobials is funded by a DARPA YFA (Young Faculty Award) and Director’s Fellowship. Prior to his doctoral studies he spent two years working on new market strategies for grid-level energy storage solutions. He graduated from Stanford University in 2012 with a BS in Chemistry and a BA in Classics.

Wednesday, March 11 at 3:00pm to 4:00pm

Min H. Kao Electrical Engineering and Computer Science, 435
1520 Middle Drive, Knoxville, TN 37996

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Lectures & Presentations




Current Students, Faculty & Staff


CBE Dissertation Defense

Chemical and Biomolecular Engineering
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