USA Biology Undergraduates Co-Author Paper in Important Journal

Posted on February 16, 2016 by

Shivam Amin

Biology Class Describes 58 New Salmonella Genes:
18 Undergrads Coauthor Article in Highly Renowned Journal

In a clear demonstration of the potential of incorporating undergraduate training into cutting edge research, 18 undergraduates (along with 3 Biology graduate students and 3 Professors) recently carried out an innovative project resulting in the identification of 58 entirely novel genes in Salmonella enterica. Salmonella enterica serovars are rod-shaped bacterium implicated in food-borne diarrheal and systemic disease, causing thousands of human deaths worldwide each year. As they represent a major source of human infection, these bacteria have been intensely studied for many years, and it was widely believed (until very recently) that essentially all of Salmonella enterica’s genes had been defined. As such, the article describing this group’s findings represents one of only a handful of reports identifying a new class of genes in bacterial genomes critical for genomic regulation and was therefore recently accepted for publication in the highly prestigious research journal RNA Biology (Impact Factor 5.0).

Amin, Shivam et al. Novel Small RNA (sRNA) Landscape of the Starvation-Stress Response Transcriptome of Salmonella enterica Typhimurium. RNA Biology. 2016. 

Of note, this project originally began as a UCUR summer research project carried out by the lead author of the study, Shivam Amin, a biology major in the Borchert Laboratory. In collaboration with the Spector Laboratory in Basic Medical Sciences, Shivam successfully experimentally identified over 60 potential new gene sequences in Salmonella enterica. In depth characterization of these genes was next passed to a newly developed computational genetics class offered by Dr. Borchert (Bly445) the following semester during which Shivam’s findings were fully analyzed by the undergraduates enrolled in the course as a collaborative term project. Of note, the success of this “informatics for non-programmers” course has been particularly striking. Utilizing a project-based learning strategy, this computational genomics course equips students with a novel informatics toolset and teaches them how to work both independently and in small groups in order to complete a class-wide research analysis. Remarkably, in its first few semesters, this course has now generated 63 undergraduate authorships in peer-reviewed journals.

In summary, the collaborative effort represented by this work is significant for two principle reasons: (1) The scientific findings described by this analysis are innovative and exciting and have wide reaching implications and collectively confirm that these results are of physiological relevance and could have pathophysiological relevance for virulence of Salmonella and perhaps many other bacterial species. And (2) this work demonstrates the largely untapped value of actively integrating undergraduate education into legitimate research efforts.

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