This past year, a new undergraduate course was successfully introduced at Virginia Tech: Phage Hunters, BIOL 1135 and 1136.
Housed in the department of biological sciences in the College of Science, the two-semester course, offered beginning each fall, gives students the chance to undertake a genomics project from start to finish, while gaining experience beyond the typical coursework in introductory laboratory classes.
During the fall semester, students were tasked with finding bacteriophage, or viruses that infect bacteria, using wet lab isolation techniques.
Bacteriophage, or phage for short, are often studied in clinical research settings for their ability to target bacteria. While in the class, the students cultured the phage using Mycobacterium smegmatis, which is similar (though non-pathogenic) to the strain of bacteria that causes tuberculosis.
After the phage were isolated, they were sent for genomic sequencing at the University of Pittsburgh, which works in tandem with the Howard Hughes Medical Institute’s Science Education division to administer the SEA-PHAGES program, in which Virginia Tech is now a part.
Once in Pittsburgh, the genomes of the phages were sequenced and then sent back to Virginia Tech to be annotated – or in layman’s terms, thoroughly described – during the spring semester.
From there, the students had to describe each genome, and argue for each gene’s location based on outside research. Finally, they had to present the function of each gene as they understood it based on their research of gene functioning in other phages, as well as what they had learned with their instructor, Stephanie Voshell, and in other biology courses.
“The annotating was incredibly difficult to grasp at first,” said Tetyana Senchyshyn, an undergraduate majoring in biological sciences who took the second semester of the course first.
“Once you get the hang of the software and the annotating, it’s not as hard as I thought it might be. It’s actually a lot of fun. Every gene is a new puzzle piece you’re trying to fit into the genome and the entire phage as a whole.”
Initially, the students got a feel for the techniques used to annotate genes. They then spent the rest of the semester working in teams to annotate the genomes of the three sequenced phages, with each having 89-112 genes.
Using computer software designed at the University of Pittsburgh, they began identifying the genes in order to identify their location on the phage genome and, ultimately, each gene’s function.
“The students had to look at each site where the computer thought a gene was, and use logic to reason through and take all the pieces of evidence into consideration to decide if that was the correct call,” said Voshell, an instructor of biological sciences who teaches the two-semester sequence along with Kristi DeCourcy, a research associate at the Fralin Life Science Institute, in the fall.
“You want to find the genes so you can determine the amino acid sequence, because if you don’t know what the specific start and stop sites are, you can’t study the translations to learn about their structure and function,” said Voshell.
By the end of the semester, the students fine-tuned their descriptions for every single gene for each of these three genomes. Their work culminated in a final report that will be published in the Actinobacteriophage database, which is run and maintained by the Pittsburgh Bacteriophage Institute at the University of Pittsburgh, and GenBank, a genetic sequence database at the National Institutes of Health. Both include annotated sequences from other participating students and scientists so others can reference them in future research. This includes when scientists are studying bacteria that cause disease.
“Because their work builds on what others have done, the students always had to be thinking, is this logical or could someone have perpetuated a mistake?” said Voshell. “They really had to think about what’s happening in the phage, what it’s doing in the host when it’s replicating itself, and use that knowledge to decide what functions these genes might have.”
In addition to Voshell and DeCourcy, Kyle Szwetkowski, a master’s student in biological sciences who studies mycobacteria, and Holly Packard, a graduate student also in biological sciences, joined the students. Both served as the course’s graduate teaching assistants, with Packard helping guide the students in the fall, and Szwetkowski helping throughout the entire yearlong process.