A&S Undergraduate Research Award Winner
Posted on October 23, 2015 by
Shivam Amin is a double major in Philosophy and Biology and a part of the University Honors Program. He is currently a senior on track to finish his Honors thesis and graduate by the end of Fall semester. For the past 10 months, he has been working with Dr. Borchert in the Department of Biology. Research in the Borchert Lab focuses on the regulation of gene expression by small RNAs. Part of what the lab does is characterize novel small RNAs in prokaryotic and eukaryotic species.
This past summer, Shivam participated in the UCUR program, which serves to promote and fund undergraduate research at South Alabama. He recently won the award for the best poster presentation at the UCUR symposium. The purpose of his project was to identify novel small RNAs in Salmonella enterica. He was successful in this endeavor, and the Borchert Lab (in collaboration with the Spector Lab in BMD) has discovered 65 unique, previously undescribed sequences they believe to function as small RNAs (sRNAs) in Salmonella enterica. Small RNAs are short sequences (~50-200 bps) of RNA that act as bacterial regulators in a host of microbial organisms, usually by modifying levels of messenger RNA (mRNA) translation.
Like most species of bacteria, a common stress Salmonella face is the starvation of an essential nutrient—such as carbon, phosphate, or nitrogen. In particular, Salmonella starved of a carbon-energy source (C) experience a host of genetic and physiological changes broadly referred to as the starvation-stress response (SSR). The Spector Lab grew log-phase, 5-hour C-starved, and 24-hour C-starved cultures of the mouse virulent Salmonella enterica subsp. Typhimurium strain SL1344 (S. Typhimurium). The total RNA from the three cultures was then isolated by the Borchert Lab and submitted to Otogenetics for commercial Illumina miseq (small RNA) sequencing. Sequencing results were analyzed using various bioinformatic techniques, and 65 distinct sequences were identified as potential novel sRNAs.
In their analysis, the Borchert Lab focused exclusively on sequences that mapped to unannotated regions of the Salmonella genome. 24 of their 65 sRNA candidates bore high similarity to functional sRNAs in other bacterial species or other RNA elements. Others overlapped with the 5’ or 3’ untranslated regions (UTRs) of annotated Salmonella genes, which are known to commonly house sRNAs in bacteria. In the future, the lab will experimentally validate many of their remaining sRNA candidates and possibly explore their potential as novel targets for therapeutic care.
Presently, Shivam is writing a manuscript to submit his findings to a relevant scholarly journal. After graduation, he plans to attend medical school.