In March 2020, while the world shuttered its doors to control a pandemic, the international scientific community threw open theirs to create global collaborations unlike any in recorded history. With a laser-focused urgency, researchers united to focus on one single topic, COVID-19. Walsh University was one of them.
Through an ongoing collaboration with the Michigan State University Grand Rapids Research Center, Walsh’s team of faculty and undergraduate students were able to help analyze hundreds of viral genome sequences. The team produced new information that was combined into an openly accessible database for use by both the scientific community and the public to research and learn more about SARS CoV2, the virus that causes COVID-19.
Walsh Professor of Biology Adam Underwood, Ph.D., was packing up his lab and classroom materials for the mandatory shut-down of campus in mid-March, when he was contacted by longtime research partner Jeremy W. Prokop, Ph.D., Assistant Professor of Pharmacology and Toxicology at Michigan State University.
“Everybody was locked out of their labs simultaneously across the country. When we got the call we literally grabbed our laptops from the Bioinformatics lab and sent the students home with what they needed to do research virtual,” said Dr. Underwood. “Within days, we met with a team of researchers across the country via Zoom and laid the framework and our goals, which was to establish a new database as quickly as possible to provide researchers from around the world with pertinent information about the biological attributes of SARS CoV2 that could be used to help find a treatment.”
Bioinformatics is a scientific field that combines biology and chemistry with math and computer science. By using bioinformatics, scientists can store, retrieve, analyze and interpret data from biological research within a computerized system. Medical professionals and biological scientists use bioinformatics to transform massive amounts of raw data into an insightful understanding of the functions of genes, proteins and cells. These insights lead to new developments in the diagnosis and treatment of disease, pharmaceutical breakthroughs and improved quality of life.
Given the undergraduate research training in bioinformatics and genomics, Walsh students were poised to quickly contribute to the large multi-institutional research endeavor, coordinated by Dr. Prokop, focused on elucidating the structural attributes and evolutionary genomics of SARS-CoV2.
Walsh’s Professor of Biology Tom Freeland, Ph.D., and seniors Olivia Sirpilla ’20, Xavier Soehnlen ’20 and Michelle Cugino ’20 helped to lead the Walsh team of researchers in their modeling contributions to the Viral Integrated Structural Evolution Dynamic Database. Their work resulted in published research papers in two separate national publications, the Journal of Biochemistry and Journal of Proteome Research.
“Multiple Walsh students were part of a summer research internship in 2019 at MSU, where we elucidated several mechanisms for viral genetics,” states Dr. Prokop of MSU. “When COVID-19 hit, we needed scientists and students who could do research at a speed we have never attempted. I knew I could rely on these Walsh students and faculty to aid in a rapid research program to get to a functional database within such a short time window.”
The database compiled contributions from multiple universities and healthcare centers from around the country and included the work of individuals from a wide range of expertise in different fields. Through Walsh’s Bioinformatics program, faculty and students were able to seamlessly shift from the lab to working at home while still making a meaningful contribution.
“The image we have all come to associate with COVID-19 is actually a very generalized photo. In reality, the models look quite different. Through modeling, this team created a visual shape of how each viral protein contributes to function. So, once we have a model, we can now look at that shape and equate to it certain functional features like interactions with other viral proteins or host proteins. From this new knowledge, work to create novel therapies for the virus may be possible.”
Walsh’s state-of-the-art Bioinformatics laboratory opened for hands-on learning experiences in 2004, and to date, the University remains one of the select few colleges in Ohio to offer a Bioinformatics degree. Walsh’s program consistently produces students who are in high demand in the field of exploratory molecular science.
“Looking back, It is almost ridiculous to think how much information this team of researchers assembled in such a short amount of time, especially given the computing power necessary to complete it,” said Dr. Underwood. “For those of us in academic research, our focus went beyond research experience for our students or professional recognition for published research. Every institution and researcher involved were unified on one goal: to help end a global pandemic.”
To access the database, visit VIStEDD at prokoplab.com/vistedd.
