Queens University student discovers a virus strain

Sydney Dishman collected a soil sample at this sign; the sample led to her discovery of Rex16 – a bacteriophage species now part of a worldwide database for scientists.
Sydney Dishman collected a soil sample at this sign; the sample led to her discovery of Rex16 – a bacteriophage species now part of a worldwide database for scientists. Queens University of Charlotte

Sydney Dishman’s new pet isn’t cute and certainly isn’t something you’d want to cuddle with. But she feels good just thinking about it.

Her “pet” is named Rex16, after the Queens University of Charlotte mascot and her year of graduation. Rex16 is a bacteriophage species she discovered while completing her honors research thesis, investigating bacteriophages in local soil samples.

A bacteriophage, often just called a phage (rhymes with “stage”), is a virus that specifically infects bacteria.

“It’s incredibly exciting,” said the 21-year-old senior, who took her soil sample from under the Queens sign in front of the university last spring. She’s grateful for the widespread help and support she got on the project, especially from Queens biology professors Joanna Mantis Katsanos and Jennifer Easterwood and Hampden-Sydney College in Farmville, Va.

Not only did her discovery become a permanent part of a worldwide database, it may help scientists learn more about fighting bacterial infections. Bacteriophages were discovered about 100 years ago and immediately used to fight bacterial infections in animals, and eventually for treating bacterial diseases in humans in the Soviet Union. The emergence of antibiotics in the 1950s pushed phage therapy into the background; now phage technology is growing due to its key advantages over antibiotics.

Phages are target-specific and go deeper into the affected area than do antibiotics. “We have these organisms that can attack bacteria and not attack the human body, and can be used as a tool as a way to get rid of that bacteria,” Dishman said.

“Although over 300 bacteria species fall within the Bacillus thuringiensis genus (category), Rex16 is one of only 32 bacteriophages that have been found to specifically infect and eventually kill off Bacillus bacteria. The genus of Bacillus includes anthrax.

“There are a bunch of difficulties in using phages to infect bacteria in a medical sense. It’s hard to get the virus specifically to the location of the bacteria in the body.”

Katsanos, who was Dishman’s primary adviser, said the project could have all kinds of implications. “Discovering new species opens new doors,” she said. “You never know what this new species can be used for.”

Easterwood said that phage species “have a ways to go in the human health aspect, but discoveries can help us get there eventually. There are a few publications out there about using phages in agricultural settings.”

Isolating the bacteria-killing virus

To fully explain Dishman’s methodology would be the stuff of research papers or articles in scientific journals. The basics: Because each soil sample may have thousands of phage individuals and hundreds of phage species, she had to isolate one strain of the virus. Utilizing an approach that uses a specific Bacillus bacteria, “I found a single phage population that all have the same DNA that infects that type of bacteria. That was the more tedious lab part of it.”

Using a transmission electron microscope, she had high-resolution pictures taken of the virus in a little drop of water, where she was excited to see the phages. From those phages, she extracted the DNA and had the entire genome sequenced. This involves determining the length and base pair sequence of the phage’s unique DNA code (a base pair is each letter in a long chain of letters that make up the DNA molecule’s code). The genome of Rex16 is 162,605 base pairs long!

The next step, genome annotation, verified the uniqueness of Rex16. Dishman divided Rex16’s genome into shorter segments called genes or “open-reading frames.” Each gene is coded for a different protein.

When Dishman used the online database GenBank to compare the gene segments and their protein products to every gene and protein or every organism recorded to date, she found that the vast majority of Rex16’s 299 proteins aren’t related to anything previously recorded.

Her discovery was no accident. The project was part of SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science), a national cooperative initiative among more than 100 colleges to discover new bacteriophage species. “SEA-PHAGES encourages undergraduate students to isolate these phages and get the genomic sequence started,” Dishman said. “Now upper-level researchers are able to use this data for the first time.”

Her senior year has been a whirlwind since learning last fall that Rex16 would be added to GenBank. A couple weeks ago she presented the research to the Association of Southeastern Biologists, the first time for the general public.

“I almost think of (Rex16) as a pet,” said Dishman, now in the final stages of applying for medical school. “My parents almost think of it as their first grandchild. …

“I remember the first time I saw an electron micrograph of Rex 16. I was actually doing a clinical internship in Peru over the summer and had access to WiFi for a small while. I got an email from my adviser with the photographs attached. I believe I responded with something like, ‘That’s the most beautiful thing I’ve ever seen.’