La Sierra freshmen discover new viruses through national research program

Jang discovered a soil bacterium-infecting virus, called a bacteriophage, during a new hands-on biology class at La Sierra this school year which engages freshmen in scientific research at a level traditionally reserved for graduate students and professors. The class, which is part of a national program called SEA-PHAGES, consisted of two quarters of study, which began this winter quarter culminating in a presentation this month at a national symposium.

At the initiative of La Sierra University Assistant Professor of Biology Arturo Diaz, the university’s biology department was accepted last year into SEA-PHAGES, a science education alliance of about 117 colleges and universities and jointly administered by the Howard Hughes Medical Institute and the lab of Graham F. Hatfull, professor of biological sciences at the University of Pittsburgh. The initiative aims to spur undergraduate interest in the biological sciences and provides research and publication opportunities for younger students.

The SEA-PHAGES program replaces La Sierra’s standard introductory biology lab courses for high-performing freshmen. Students in the new program spent more than four months isolating, naming, sequencing, and analyzing newly-discovered bacterial viruses better known in the scientific world as bacteriophages, or phages for short.

Overall, 14 of the 16 students in the SEA-PHAGES course at La Sierra were able to isolate a phage from soil samples collected around campus. The students performed isolation and characterization processes that included electron microscopy and DNA restriction analysis to discover previously unknown bacteriophages.

To conduct these analyses, the class traveled on March 1 to nearby University of California, Riverside to use an electron microscope and observe the shapes of the viruses discovered by the students’ research. Based on the electron microscopy results, the genomes of the phages isolated by Jang and her classmates Shaquille Fyfe and Brian Hwang were sequenced at the University of Pittsburgh. Comparing the genomes isolated at La Sierra to those found in the public databases led to the conclusion that the students had found new viruses.

Jang named the virus she found JangDynasty to pass along her father’s last name, and because this was the nickname applied to her and her two sisters when they played sports together, she said. “I was fortunate to have found a phage in the first place, and then of course it was amazing that it happened to be one that hadn't been discovered yet,” said Jang.

“The involvement of undergraduates in scientific research is common, but has often been constrained to apprentice-like experiences in research labs, and as such typically constrained to universities and colleges that have a robust research infrastructure,” said University of Pittsburgh’s Hatfull. “There has been strong movement towards the development of course-based research experiences that can engage greater numbers of students, although most are locally implemented. SEA-PHAGES is an example of a different type of a model …that encompasses multiple institutions and includes students from all backgrounds without biased pre-selection.

“Nationally, only about 40 percent of students starting a degree in STEM disciplines go on to get a STEM degree,” he added. “Much of the problem is a lack of persistence past the first year. All too often we put students in large lecture classes and ask them to do lab classes that bore them to tears. The ‘secret sauce’ of the SEA-PHAGES program is the development of an authentic research question that can be addressed by students without extensive prior content, concept or technical skills or knowledge.”

The first week of June, Jang and freshman Nancy Kalaj presented a poster of their class’s work during the national SEA-PHAGES symposium at the Howard Hughes Medical Institute research campus in Ashburn, Va. For Kalaj, the experience with SEA-PHAGES proved pivotal in her decision to pursue a scientific career. “I've always been extremely fascinated by the world of research and I've always been dreaming to get the chance to experience what doing research is really like,” she said in an email a couple of days after returning from the symposium in Virginia. “Having this opportunity during my freshman year exposed me to this world and to the scientific community out there, making me realize how much I truly love science and the best way in which I can invest my potential as a scientist.”

“One of our goals is to stimulate students’ interest in science, positively influence academic achievement, develop their critical thinking skills, and enhance persistence in STEM disciplines,” said Diaz who co-teaches the course along with biology professors Nate Sutter, Arun Muthiah and Natasha Dean. “Another perk for those who are part of the program is that the results could be published in scientific journals with the students listed as co-authors,” he said. As a result of the work done in class, students wrote a short paper describing the phage JangDynasty that will be submitted to the journal Genome Announcements in the upcoming weeks.

“Research on phages that infect the soil bacterium Mycobacterium smegmatis can lay the groundwork for the therapeutic use of phages, especially in light of the emergence of antibiotic resistance among bacterial pathogens,” Diaz said. “The large collection of sequenced mycobacteriophage genomes provides insights into viral diversity and new approaches to understand and combat Mycobacterium tuberculosis and Mycobacterium leprae, which cause tuberculosis and leprosy in humans, respectively.”

In evaluations of the SEA-PHAGES class, students praised its open structure as well the scientific opportunities presented.

“Instead of emulating experiments with known results set forth by standard biology lab manuals, we were creating our own science at our own pace without the pressure of doing things ‘wrong’ or getting the ‘wrong’ results,” wrote Hwang, a film major and biology minor.

“This is the one science class that I've taken that I have liked,” said Jang. “I didn't have to focus on studying and turning in lab reports so I could pass. Instead, I was able to focus on what I was really doing in the lab and learn. It wasn't just words and definitions I had to memorize. The class made me want to work.”

“Our goal is to implement the SEA-PHAGES model into all of our General Biology labs in the near future as we want to offer all students the chance to gain research experience during their freshman year,” Diaz said.