UAB's Phage Genomics Explorations Program Gives Students a Head Start

By Caperton Gillett

Thanks to an intrepid band of UAB freshmen and sophomores, the world now knows of the existence of OSmaximus and BengaliBalla92. The students discovered and named the two bacteriophages—viruses that infect bacteria—in their first college biology class. Unlike most introductory undergraduate biology courses, which use lectures to begin teaching about research, the new UAB Phage Explorations Program puts students in the lab on day one. There they learn scientific protocols and techniques as they experience the thrill of discovery.

fall2011_student1Sherwin ThomasPerforming research so early offers “a really great opportunity to gain skills working in a lab setting, use the different instruments, and get a feel for the atmosphere,” says junior biology major Sherwin Thomas, who took the course in fall 2010. The program also offered a unique opportunity to explore the field of phage genomics, which uses gene sequencing to study bacteriophages.

The UAB Phage Explorations Program was established in 2010 with the support of a Howard Hughes Medical Institute (HHMI) Science Education Alliance grant. At UAB, the Phage Explorations research team is led by Denise Monti, Ph.D., M.P.H., an instructor in the Department of Biology. Sixteen UAB students—eight freshmen and eight sophomores—were selected to participate in the research-intensive course.

Naming Rights

fall2011_student5Olamide AlakijaThe yearlong program begins with one semester in the lab. Students start by collecting samples from soil or dirty water—junior Olamide Alakija, then a sophomore, collected the water that would yield OSmaximus from a storm drain on campus—and isolating individual bacteriophages from them. With a staggering number of unique bacteriophages throughout the world—10^31, according to sophomore Amiya Ahmed—chances were good that each student would find a bacteriophage of his or her own. After naming the newly discovered bacteriophages and examining them under an electron microscope, the students selected one phage to be sent to Virginia Commonwealth University for full-genome sequencing.

In the lab, the students worked independently under the eyes of their mentors. “When you’re in a lab-based class, you have protocols set out for you. You’re told what to do,” says Ahmed, who identified and named BengaliBalla92. He had prior research experience from high school, he says, but appreciated the opportunity to go straight into the lab on the first day of his freshman year. “This is more like an experimental lab. It’s more spontaneous, because anything can happen. You might have to make your own protocol when certain things arise in the experiment.”

fall2011_student4Courtney DunkerleyAnd things frequently arose. Junior Courtney Dunkerley, then a sophomore, says she was surprised by the number of “bumps in the road” during the course of the research. Experiments occasionally resulted in unexpected findings, and protocols had to be changed on the fly or even scrapped entirely. “I guess I thought research went smoothly,” Dunkerley says. “I definitely found out what it was really all about. I don’t think you get that in any other biology course.”

“It’s not just following protocol. Things don’t always go right,” Alakija says. He says his experiences working with phage genomics prepared him for his current work in the lab of Louis Dell’Italia, M.D., a UAB professor of medicine and cardiovascular disease researcher. “That’s how it is in a real research lab. Things don’t go right. You can’t waste the day—you have to just keep going and figure things out.”

Computer Science

The students don’t spend all of their time toiling over an electron microscope. They also toiled over their computers, learning to write research papers and grant proposals. Students even presented research proposals before a mock review board, Thomas says. “We get a holistic view of everything that goes on in the world of research. We do everything you think of when you think about research—working with plates, using pipettes. But then we go through the process of asking, ‘How do you actually get funding for a research project like this?’”

fall2011_student2Amiya AhmedThe second semester of the Phage Explorations Program introduces the students to bioinformatics—the branch of computer science focusing on biological systems and processes. They learn to download the gene sequence of their bacteriophage, analyze the different genes and structures, and compare them to other phages in the National Center for Biotechnology Information’s worldwide database. Students presented their findings at conferences ranging from UAB’s own research expo to an HHMI-sponsored symposium; Thomas was selected to present his work as UAB’s representative at that national symposium.

Thomas hopes to continue researching throughout his college career and then go to medical school, and Dunkerley intends to do the same until she becomes an occupational therapist.

As for Ahmed and Alakija, both students plan to study basic science and clinical science for an M.D./Ph.D. or M.D./M.P.H. and careers in translational medicine. “It definitely solidified my research background and cemented my plans for the future, wherever I go,” Ahmed says. “If I ever submit a paper to be published, I’ll know how to write it at a level that could be accepted by scientific journals, and I know that medical schools look highly on research and endeavors in academics.”

Alakija, who wants to conduct further research with Dell’Italia, says that merely being selected for the program was enough to motivate him and excite him about his chosen career. “I thought, ‘I must be doing pretty well. They must see something in me.’ It gave me the confidence to talk to mentors, use my skills, and get right into it.”

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