Students see dividends in phage hunting

Students see dividends in phage hunting

Electron microscopic photos of phages Darionha, Salz and ThreeRngTarjay.

Alex Jackman and Andrea Sandoval say their undergraduate careers were completely reshaped by SEA-PHAGES.

SEA-PHAGES sparked Laila Sareini’s passion for science and research, and showed Amber Abram she belonged in the scientific community despite her disadvantaged background.

SEA-PHAGES, which stands for Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science, is profoundly impacting University of Detroit Mercy students because it’s designed to excite students about scientific research.

The yearlong freshman laboratory course — part of the ReBUILDetroit first-year research curriculum and supported by the Howard Hughes Medical Institute’s SEA-PHAGES program — allows Detroit Mercy students to discover, isolate and analyze bacterial-killing viruses known as bacteriophage, or phage for short.

Over the last year, students like Jackman, Sandoval, Sareini and Abram worked to produce a paper detailing three phages they had discovered in soil samples on Detroit Mercy’s McNichols Campus and analyzed in the class from 2016-18.

The genomes of phages, named Darionha, Salz and ThreeRngTarjay, were characterized in the piece, which was recently published by Microbiology Resource Announcements.

Thirty-one undergraduate students and three faculty members co-authored the paper for the online-peer reviewed journal. Of those 31 students, 22 were from ReBUILDetroit, a National Institutes of Health program.

“Understanding how these genomes are organized helps us to better understand evolution, viral-host interactions and how gene sequence relates to function,” said Jacob Kagey, an associate professor of Biology at Detroit Mercy.

Kagey teaches the winter portion of the SEA-PHAGES course — Fundamentals of Bioinformatics — where students annotate the genomes of phages that were unearthed and genetically sequenced in the fall. He knows how performing scientific research can affect a young college student because it’s what sparked his passion of research 20 years ago and led him to a career in higher education.

“This experience is transformative for our students. There are numerous studies that show early research experiences increase retention, persistence in STEM and sense of belonging,” Kagey said. “These students are also getting the opportunity to become published authors as undergraduates, which is typically not something that scientists accomplish until they are in graduate school.”

Laila Sareini, left, and her lab partner, Zahraa Alhabib, perform research in the SEA-PHAGES course.Sandoval, a fourth-year Biology student, was the lead author of the paper, something she never could have imagined when signing up for the SEA-PHAGES course. She knew these types of research experiences are rare for undergraduate students and is thankful for its lessons.

“My whole major changed because of this class,” Sandoval said. “I was able to realize and gain a new passion.”

The three phages characterized in the paper were discovered by five students.

Jackman, a fourth-year Biology student, and Nour El Yaman discovered ThreeRngTarjay in the fall of 2016. Its genome was annotated, meaning students used computer programs to identify all of the phage’s genes, in the winter of 2017.

Sareini , a fourth-year Biochemistry major on the pre-med track, and Zahraaa Alhabib unearthed Salz. And Darionha was collected by Abram, a rising fourth-year Biology student.

Both Salz and Darionha were found in the fall of 2018 and annotated the following winter.

Phages are named by the students who made the discovery, and while the origins of the names vary, they must follow a specific set of guidelines.

Jackman said ThreeRngTarjay’s name was inspired by the target and ring shape of its plaques, while Abram named Darionha to honor her older sister, who passed away in 2016.

“My sister is the reason why I strive to reach my full potential in science, so I wanted to honor her name by naming my first scientific discovery after her,” Abram said.

“It was mind-blowing that through this class I was able to actually discover and name a novel bacteriophage and complete research on its genome and possible protein construction, all in my first year of college,” added Jackman, who plans on becoming a professor because of SEA-PHAGES.

After participating in the SEA-PHAGES program, Sareini was prepared to do the several research experiences required for ReBUILDetroit scholars. She says it gave her a solid foundation, and the skills garnered through phage research smoothed the transition.

“My experience in SEA-PHAGES laid the foundation for my future career in medicine and science by providing me with the opportunity to learn, fail and succeed at something which I put great effort toward,” Sareini said.

While SEA-PHAGES provides valuable research opportunities for students across the world, the discoveries can be instrumental for medicine.

Recently, phages discovered in the program were used to help an English teenager combat a life-threatening bacterial infection. Fred313, a phage discovered by Detroit Mercy in 2015, is currently being used in the treatment of another patient with an antibiotic-resistant infection.

“While we had initial discoveries in this paper that help us to better understand genome organization, phage biology and other aspects of these phage, these phage are also kept in a freezer, and if the antibiotic-resistant bacterial infection of a patient ever matches with one of these phage, they could be used therapeutically,” Kagey said.

Learn more about Detroit Mercy’s SEA-PHAGES program online.

— Original story by Ricky Lindsay. Follow Detroit Mercy on FacebookTwitter and Instagram. Have a story idea? Let us know by submitting your idea.