In Vitro Diagnostics for Tracking Microbes and Viruses

I work to create new diagnostics using synthetic biology tools that enable detection of bacteria, like those present in the gut microbiome, and common viruses like human papillomavirus (HPV) that cause cervical cancer.

Our ability to better engineer biological parts can have a major impact on our ability to detect biomolecules of interest. Right now my focus is on using cell-free system to cheaply express genetically encoded sensors. By freeze-drying the sensors + cell-free on paper we get diagnostics that are portable at room temperature. By choosing enzymes that work at a single temperature and color changes as outputs, we can reduce the hardware costs for performing the diagnostic tests.

Scheme for detecting DNA using isothermal amplification and cell-free expression.

Relevant publications:

M. K. Takahashi*, X. Tan*, A. J. Dy*, D. Braff, R. T Akana, Y. Furuta, N. Donghia, A. Ananthakrishnan, J. J. Collins “A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers.” Nature Communications 9, no. 1 (2018): 3347.

J. S. Gootenberg*, O. O. Abudayyeh*, J. W. Lee, P. Essletzbichler, A. J. Dy , J. Joung, V. Verdine, N. Donghia, N. M. Daringer, C. A. Freije, C. Myhrvold, R. P. Bhattacharyya, J. Livny, A. Regev, E. V. Koonin, D. T. Hung, P. C. Sabeti, J. J. Collins, and F. Zhang. “Nucleic acid detection with CRISPR-Cas13a/C2c2.” Science 356.6336 (2017) 438-442. (pdf)