My immediate career objective is to continue my training as a research scientist who is able to use both bioinformatic and molecular biology-based approaches to answer fundamental questions in microbial biology and pathogenesis. My long-term goal is to become an independent investigator and faculty member heading a truly interdisciplinary research group at a leading academic institution. Dr. Waldor's laboratory will afford me an excellent environment in which to both complete my postdoctoral training and establish a productive research project that will ensure my successful transition to independence. The research described in this proposal focuses on the identification and characterization of sRNAs, small, non-coding transcripts that regulate diverse cellular processes in numerous bacterial species. In my previous postdoctoral research, I developed and used two bioinformatic programs to predict nearly 3000 previously unannotated sRNA-encoding genes in 12 diverse species of bacterial pathogens. Experimental testing of some of these predictions resulted in the discovery of 22 new sRNAs, the biological activities of several of which are currently being investigated. The fundamental objective of the proposed research is to develop and utilize both computational and experimental approaches to identify and characterize sRNAs in diverse bacterial species.
Aim I is to characterize the biological activities of several recently discovered sRNAs.
Aim II is to develop a high throughput computational approaches using automated workflow management and distributed computing that will enable genome-wide prediction and annotations for sRNA-encoding genes to be efficiently conducted in all sequenced bacterial genomes.
Aims III and IV are to improve upon current predictive algorithms by determining consensus motifs for the binding sites of several transcription factors and of the RNA chaperone Hfq and utilizing these motifs in the prediction and ? annotation of previously predicted sRNAs and in the search for novel sRNA-encoding genes. Finally, Aim V is to develop a high throughput hybridization assay to experimentally test large numbers of predicted sRNAs. Recent studies have implicated a role for sRNAs in mediating the virulence of a number of bacterial pathogens. Thus, identifying and characterizing novel sRNAs in a wider variety of species, in addition to providing insight into basic biological processes, will likely lead to a better understanding of microbial pathogenesis that may ultimately aid in the prevention and treatment of infectious diseases. ? ? ?
