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Phage Hunters Handbook: Make the Most of the SEA-PHAGES Program

Biology professor Steven Caruso, PhD, has turned a bacteriophage ID program into something that can be the highlight of a student’s college career.

Educator

Steven Caruso, PhD

Senior Lecturer of Biology, University of Maryland,Baltimore County, in Baltimore

PhD in Biology, BS in Biologyand Psychology

When it comes to student engagement, “go big or go home” may seem like a good approach. But for Steven Caruso, PhD, a senior lecturer of biology at the University of Maryland, Baltimore County, the exact opposite was true. By having students hunt for and analyze microscopic organisms, he has seen their interest in his microbiology course go viral.

The program that Caruso uses is called SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science). Founded in 2008 by the Howard Hughes Medical Institute, SEA-PHAGES is a two-semester, discovery-based course that involves immersion in authentic, valuable research. Simply put, students take a soil sample and hunt through it for viruses that infect bacteria, which they learn are called bacteriophages, or phages for short. Because phages are among the most common and diverse entities in the entire biosphere, they are easy to find, and some students will actually discover (and get to name) a new phage.

At UMBC, students who participate in the SEA-PHAGES program are known as “Phage Hunters.” “What we do in Phage Hunters is treat students like researchers instead of like students,” Caruso says. “If something doesn’t work in their experiment, they have to do it again. And if there’s something wrong in the protocol, then we have to adjust the protocol to make it work.”

Caruso has been involved in the SEA-PHAGES program since its inception. (UMBC was one of first 12 schools to participate.) Below, he shares how he has adapted the program for use in his lab, maximizing the benefit to his students.

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Context

“In Phage Hunters, students participate in an experiment that is genuinely theirs, and [their discoveries] are submitted to databases used by real scientists around the world. They’ll be authors on these entries. [Some of them] get to name the phage and everything. It’s amazing.”

— Steven Caruso, PhD

Course: BIOL 302L: Molecular and General Genetics Laboratory

Course description: A laboratory course designed to illustrate fundamental genetic principles by experimentation. Such principles include the nature of genetic material, transfer of genetic information in prokaryotic and eukaryotic systems, organization and regulation of gene expression, Mendel’s rules of heredity, linkage and crossing over, and genetic variation. Students will be expected to work independently, spending periods of time outside the scheduled lab period collecting data.

Caruso’s tips for turning students into Phage Hunters

To date, UMBC Phage Hunters have isolated, characterized, and archived nearly 199 Actinobacteriophages and 315 Bacillus phages. In addition, undergraduate researchers have sequenced 62 phages, 38 of which have been annotated and submitted to GenBank—the genetic sequence database overseen by the National Institutes of Health—with UMBC Phage Hunters listed as authors.

The work with SEA-PHAGES always starts the same way: Caruso’s students collect soil samples from wherever they can and want to—their back yard, another state, or even another country. Then they follow the protocols outlined by the SEA-PHAGES founders, which include isolating the phage, isolating its DNA, and characterizing the virus. “Students chop the DNA into pieces, and they can run different pieces of DNA on gels, like they do on television crime dramas,” says Caruso. “They can even take a picture of the phage with a transmission electron microscope.” Then they select a subset of the phages to be sequenced—another integral part of biological research.

In the second semester, students analyze their phages’ sequences, explore open databases on the web—such as GenBank—and use bioinformatics tools to further investigate the phages. They annotate the genes on the phage sequences; compare the phages to other, previously sequenced, phages to further characterize them; and ultimately prepare them for submission to GenBank.

Below, Caruso shares some tips on how he has adapted the approach over the years, adding valuable skills such as teamwork, project management, and public speaking.

Weave teamwork throughout the project—including the writing

“People who aren’t in science think of it as the lonely scientist in the lab. But in reality, science is very collaborative,” says Caruso. So, for the Phage Hunters project, he has students work in pairs on the experiment—as well as the writing. “I have them collaborate on their formal lab report, formatted as a science paper,” he explains. “That’s the way papers are written in real life. You don’t write them individually; you write them together. And in the end, you end up with better writing.”

Foster project management skills in face-to-face meetings

To encourage students to ask questions and engage in active discussions, Caruso holds weekly lab meetings, rotating through the student teams. “Each group presents where they are in the experiment and what trouble they’ve run into,” Caruso says. “It’s common for them to run into technical challenges. And ideally, it turns into a discussion.” To further increase participation, these meetings count for a portion of their grade.

Encourage decision-making (and feelings of ownership)

At the conclusion of the first semester, when it is time to decide which phages to sequence, Caruso does not select the ones he wants; he invites his students to choose by voting. This encourages even more of a sense of ownership in the entire process.

“First, the phages have to qualify materially,” Caruso explains. “They need [to have] enough DNA [to sequence].” From the eligible phages, students choose six, and Caruso sends them off to be sequenced. Caruso says the Pittsburgh Bacteriophage Institute will work with the Howard Hughes Medical Institute to sequence several for free; if he and his students want result for more, they sometimes send them elsewhere, such as to NCSU (which charges about $300 per phage genome). Caruso generally sends the phages in November and receives the results in January, for use during the second semester.

Develop presentation skills with a poster session

To give his students experience in presenting their work, Caruso schedules a poster session during the last lab period of both semesters. Each team of students presents their work simultaneously in the form of a poster, which they stand with and answer questions about to anyone who asks questions. Caruso invites a diverse group of people—other students, faculty, graduate students, and “anyone he can get to show up.”

“Some of the people—like faculty— will be very knowledgeable, and some will be people who are just walking by, who have no idea what a bacteriophage is,” he says. “The exercise of having to scale the presentation up or down depending on audience is a key skill for students to develop.”

Finally, help students get published—and celebrate it!

Caruso feels strongly that one of the most important factors to the success of his program is that students have the chance for their work to be published. “That’s something we work hard to do,” he says.

“At the end of the year, not only are they going to be published in GenBank and other databases that real scientists around the world use, but they will, hopefully, also be published in short abstract announcements, such as Microbiology Resource Announcements,” he says. “The idea of a class that results in students having genuine, peer-reviewed publications of actual science is phenomenal. It really blows my mind.”

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