Students hunt for viruses in soil samples

In Lehigh's SEA-PHAGES lab, students hunt for viruses in soil samples and program to complex genome annotation and analysis.

What Happened to the Genomes—and the Fruit Flies?

Labs began reopening in June to graduate students and research staff, as the state’s stay-at-home orders were eased.

Story by

Mary Ellen Alu

Photography by

Christa Neu

When word came that Lehigh was moving to remote learning for the remainder of the spring semester, the students conducting biomedical research on soil samples in Lehigh’s SEA-PHAGES lab, like the rest of Lehigh’s students, were on spring break. 

SEA-PHAGES stands for Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science. The program is sponsored by the Howard Hughes Medical Institute (HMMI), a philanthropy headquartered in Chevy Chase, Md., that aims to advance biomedical research and science education for the good of humanity. 

The course began with students digging in soil in their backyards or elsewhere, then bringing the samples to Lehigh to hunt for viruses in the soil and progress to complex genome annotation and bioinformatic analyses. Later, they would share findings in a public database.

“Everyone in the lab had isolated a virus,” recalled Vassie Ware, professor of molecular biology and co-director of Lehigh’s HHMI program. “They were at the point where most of them, if not all of them, had gotten constant high concentrations of the virus, and they were now isolating the genomes from the virus, which are double-stranded DNA genomes. They were in the process of cutting their genomes with enzymes, so that they could determine some aspects of the characteristics of a genome.” 

Initially, graduate students were going to be able to continue with their research. Ware said she, her colleague Meg Kenna and graduate student Hamidu Mohammed figured they would take two weeks to do “the last little bits” of experimental work in the lab for the undergraduate students not able to return to campus, then send them the data to analyze and assess.

“That was the plan until we were told that all the labs were going to shut down,” said Mohammed. (With Pennsylvania Gov. Tom Wolf eventually ordering the statewide closure of all non-life-sustaining businesses in the COVID-19 fight, Lehigh announced that all on-campus research would shut down by March 20.) 

“At that time, Dr. Ware thought everything was kind of derailed, that there was no way we were going to get those results within some two, three-days window,” Mohammed said. 

Unhappy about that prospect, he said, “I decided to see what I could do to be able to salvage the rest of the semester. I had to go in two nights. I worked throughout the night [each night from around 7 p.m. to 7 a.m. the next morning] to be able to get the DNAs that were lacking and to set up their restriction enzymes for some of them.” Kenna also helped complete the experiments.

Professor Vassie Ware works with a student in SEA-PHAGES lab

Professor Vassie Ware, right, is co-director of Lehigh's Howard Hughes Medical Institute (HMMI) program.

In addition to having students analyze and assess the data, Ware said, other elements of the course transferred well to online: the composition and critique of students’ “elevator” speeches in which they have to explain their work to someone, students’ self-reflections on their progression as researchers, and data entries to the Howard Hughes Medical Institute on their discoveries in the SEA-PHAGES lab. 

Some of Ware’s students were also in the midst of a writing-intensive course, and Ware provided one-on-one feedback. Zoom sessions allowed for student interactions. The projects related to obtaining an understanding of what happens when a phage infects a bacterium.

Ware told the students who expressed disappointment in not being able to return to campus, “Wherever we are is where we will pick up. So don't sweat it. It's going to be okay, because that's the way research is. You just keep plugging at it. There's no deadline, per se, to solve the problem. You want to solve it as quickly as you can, but things come up that may prevent you from being able to do certain things, and that's one of these things now.”

Similar scenarios had played out in labs across Lehigh’s campuses. 

In his lab in Mountaintop’s Iacocca Hall, neuroscientist Daniel Babcock and his graduate and undergraduate students were conducting research on fruit flies to pave the way to treatments for Parkinson’s and other diseases. There, dissections and behavioral testing were put on hold, Babcock said. But he and others were alternately allowed to go back into the lab about every three weeks to feed and maintain the fruit flies for when the research could continue.

Fruit flies for research

Tiny fruit flies share about 70 percent of the same genes as humans, making them model organisms for the study of disease.

“Whenever we get back in, it's not as simple as just resuming right where you left off,” he said during the shutdown. “You're going to have to restart the entire process.”  

With the lab closed, the students focused on analyzing data from previous experiments, conducted literature searches and wrote their manuscripts. Seniors worked on their theses.  Unfortunately for the graduating seniors, Babcock said, the shutdown changed the end for them. “Whereas, the students who are going to be coming back next year, it interrupts things, but we'll be able to get back in the swing of things, hopefully without too much delay.”

Babcock said he tried to help students keep matters in perspective. “I'm letting them know that despite our frustrations, things could be so much worse, that we're actually really fortunate,” he said during the shutdown. “I frame it in a way of, there are people going through a lot worse than we are right now, and reinforce that we have so much going in our favor and that we're committed to getting things back on track as soon as it’s safely possible.”

Editor’s Note: Labs began reopening in June to graduate students and research staff, as the state’s stay-at-home orders were eased. The SEA-PHAGES team packaged up DNAs and sent them to the University of Pittsburgh, where they will be sequenced then sent back to Lehigh for the fall semester for further research.

Story by

Mary Ellen Alu

Photography by

Christa Neu

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