Graduate Advisor: Samuel Cartinhour
My long-term research interest is to study biological system in a holistic sense using computational and experimental tools. Living things are composed of many interconnected components that cannot be understood completely by studying each component separately. Computational tools may play many roles to support biologists from giving predictions, analyzing results to modeling the whole system. Moreover with the rapid advance of high-throughput sequencing and other molecular techniques, the amount of data is exceeding the level we can handle without help from computational tools.
My current project is to understand how Pseudomonas syringae pv. tomato DC3000 regulates its Type III secretion system (T3SS) to defeat multiple layers of plant defense. HrpL, an alternative sigma factor, is the direct regulator of the T3SS. ChIPseq, RNAseq results and HrpL motif search reveal that HrpL binds at several interesting and unexpected sites, suggesting that the scope of HrpL-regulation is, in fact, not exhaustively known. These binding sites potentially implicate genes that were thought to be unrelated to pathogenesis or which were not even annotated as genes when the P. syringae genome was fully sequenced. Monitoring the effect on in planta growth and hypersensitive response of new members of the hrpL regulon may provide insight into the interaction of the bacterium and its host.
Research and training:
Filiatrault MJ, Stodghill PV, Myers CR, Bronstein PA, Butcher BG, Lam H, Grills G, Schweitzer P, Wang W, Schneider DJ, Cartinhour SW. Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000. PLoS One. 2011;6(12):e29335.