This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).
This project aims to elucidate the roles of small genes in bacteria. In particular, the project focuses on two classes of elusive genes, namely small noncoding RNA genes and small protein coding genes in bacteria. While the bioinformatics methods developed in this project will be assessed in Escherichia coli or Shewanella oneidensis, they will be applicable to bacteria more broadly. Specific aims include the following: (1) Bioinformatics methods for systematic identification of small, noncoding RNA genes and their regulatory targets will be developed and evolved. (2) Using a combination of computational and experimental approaches, small noncoding RNA genes will be investigated in Shewanella oneidensis. In particular, the role of noncoding RNAs in metal reduction will be studied. (3) A bioinformatics tool will be developed for characterizing short open reading frames in bacterial genomes. The bioinformatics tool will be based on a framework that incorporates primary sequence data with comparative genomics information and genome-tiling microarray measurements for the purpose of predicting short genes encoding new small proteins.
The belief that excellent teaching is integrally coupled with active scholarship is a cornerstone of this project. Aspects of the research project will be incorporated into existing undergraduate courses as well as new courses under development. Undergraduate students will be integrally involved in all aspects of the research program. Wellesley College's productive record in the education of women scientists, coupled with the increased participation of talented young women in the bioinformatics research community, bodes well for the sustained and broad impact of this project on research training and learning in bioinformatics. Also, a broader community will be reached by making the bioinformatics tools developed from this work available through user-friendly web interfaces, and results will be disseminated via peer-reviewed publications and by active participation of students and faculty at professional meetings.
