North Texas Daily

Freshman biology program identifies dozens of new viruses

Freshman biology program identifies dozens of new viruses

Freshman biology program identifies dozens of new viruses
March 26
01:19 2014

Joshua Knopp // Senior Staff Writer

Many entry-level biology classes are so focused on incoming students that the curriculum starts with the basics, like how to use a microscope.

Now, a year-long, in-depth program called SEA-PHAGES gives 32 students fresh out of high school the chance to discover and name their own strain of virus, whose data will be recorded in a national database.

Some of the viruses have their DNA sequenced and end up on GenBank, an international collection of all publicly available DNA sequences, with the students as authors.

“They basically have something to point to,” program co-director Lee Hughes said.

Hughes has worked at UNT since 2002, and said the program has made entry-level biology more rewarding.

“Before PHAGES, it would be extremely rare for anyone in our department to be involved in research before being a junior,” he said.

In the course, students isolate and identify a bacteriophage, or bacteria-eating virus, for study. At the beginning of the class, students take a soil sample from somewhere on campus. They spend much of the fall purifying their sample, isolating a single virus strain and destroying other genetic material, Hughes said.

A couple of viruses are selected to have their DNA sequenced over the winter, and in the spring semester, students study and understand the genome sequence of those viruses.

Two students are selected to present the school’s findings at the SEA-PHAGES symposium in June. Once the students collect it, published data is available for everyone.

“Once this data is out there, it becomes the subject of other scientific research,” Hughes said. “People could request a sample from the archives. Anything could happen at this point.”

Currently, the students are looking at individual genes that were identified last winter from the two viruses that were sequenced. Biology sophomore Melody Vo said this year’s sample includes an arthrobacter phage, a virus specializing in a different bacteria genus.

Though the program has remained mostly focused on mycobacteria phages, viruses that infect mycobacteria, Vo said this is exciting because research into arthrobacter phages is just starting out. This means she’s doing cutting-edge research early in her college career.

“Instead of doing a regular freshman class where I’m looking through a microscope, I’m actually doing field research,” she said. “This is a growing field, and what we’re researching has a lot of applications.”

Since 2009, UNT has participated in the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science program, sponsored by the Howard Hughes Medical Institute in Maryland.

Hughes said because of the vast genetic diversity among viruses, it is very rare for a virus to have already been discovered. Of the 654 phages the national SEA-PHAGES program has identified, UNT is responsible for 111.

UNT was one of the first 12 schools to participate in the national program, which was developed by Graham Hatfull, who teaches biology at the University of Pittsburgh.

Hatfull has worked for years studying mycobacteria, the genus of bacteria from which tuberculosis and leprosy originate. He received support from the Howard Hughes Medical Institute in 2002, and developed the PHIRE program – Phage Hunters Integrating Research and Education – in which high school students researched mycobacteria phages. SEA-PHAGES is a nationalization of that program.

“The motivations for developing this were both scientific and educational,” Hatfull said.

“The scientific rational is we wanted to understand the diversity and the evolution of viruses. When the SEA-PHAGES program started, we had 40 or 50 phages that we had characterized, and because of the SEA-PHAGES program, we now have more than 650.”

Hatfull said the sequenced phages have yielded thousands of individual genes, most of which scientists don’t know what they’re for. He said students are not only discovering new bacteriophages, but new genes and possibly new functions of genes. The research will also help scientists understand the processes by which viruses evolve and share information.

EXTRA

Here’s a link to the SEA PHAGES database where they have all the data for the phages-

From the main site, you can go to the “Phages” tab and hit filter, and you get to a page where you can filter it out so you’re only looking at UNT students’ work. Clicking on the name of each virus that was sequenced (each virus with a “Date finished”) takes you to a page that has a link to the virus’ GenBank entry

Feature photo: Biology sophomores Quynh Vo, Melody Vo and Morgan Silva and biology freshman Dominic Obando work on identifying what sequenced genes are used for. Quynh Vo will represent UNT at the SEA-PHAGES symposium in June. Photo by Joshua Knopp / Senior Staff Writer  

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