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Rapid, inexpensive, and sensitive nucleic acid detection may aid point-of-care pathogen detection, genotyping, and disease monitoring. The RNA-guided, RNA-targeting clustered regularly interspaced short palindromic repeats (CRISPR) effector Cas13a (previously known as C2c2) exhibits a "collateral effect" of promiscuous ribonuclease activity upon target recognition. We combine the collateral effect of Cas13a with isothermal amplification to establish a CRISPR-based diagnostic (CRISPR-Dx), providing rapid DNA or RNA detection with attomolar sensitivity and single-base mismatch specificity. We use this Cas13a-based molecular detection platform, termed Specific High-Sensitivity Enzymatic Reporter UnLOCKing (SHERLOCK), to detect specific strains of Zika and Dengue virus, distinguish pathogenic bacteria, genotype human DNA, and identify mutations in cell-free tumor DNA. Furthermore, SHERLOCK reaction reagents can be lyophilized for cold-chain independence and long-term storage and be readily reconstituted on paper for field applications., United States. Air Force Office of Scientific Research (Grant FA9550-14-1-0060), Defense Threat Reduction Agency (DTRA) (Grant HDTRA1-14-1-0006), National Institute of Mental Health (U.S.) (Grant 5DP1-MH100706), National Institutes of Health (U.S.) (Grant 1R01-MH110049)

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2015., Cataloged from PDF version of thesis., Includes bibliographical references (pages 105-118)., Pathogen genomes, especially those of viruses, often change rapidly. Changes in pathogen genomes may have important functional implications, for example by altering adaptation to the host or conferring drug resistance. Accumulated genomic changes, many of which are functionally neutral, also serve as markers that can elucidate transmission dynamics or reveal how long a pathogen has been present in a given environment. Moreover, systematically probing portions of the pathogen genome that are changing more or less rapidly than expected can provide important clues about the function of these regions. In this thesis, I (1) examine changes in the Vibrio cholerae genome shortly after the introduction of the pathogen to Hispaniola to gain insight into genomic change and functional evolution during an epidemic. I then (2) use changes in the Lassa genome to estimate the time that the pathogen has been circulating in Nigeria and in Sierra Leone, and to pinpoint sites that have recurrent, independent mutations that may be markers for lineage-specific selection. I (3) develop a method to identify regions of overlapping function in viral genomes, and apply the approach to a wide range of viral genomes. Finally, I (4) use changes in the genome of Ebola virus to elucidate the virus' origin, evolution, and transmission dynamics at the start of the outbreak in Sierra Leone., by Rachel Sealfon., Ph. D.