Under the Microscope: A look into Tarleton’s scientific research

SEA-PHAGE Discovery is a research program that focuses on the discovery, identification and publication of bacteriophages. 

Bacteriophages are viruses that target only bacteria. There are thousands of phages, and new ones are being discovered all the time. This program is designed to do just that. 

The SEA-PHAGE Discovery Program is a national initiative through the Howard Hughes Medical Institute (HHMI) that was started by Bacteriophage Biologist, Dr. Graham Hatful at the University of Pittsburgh about 14 years ago. 

“This initiative was designed so that students that normally would not be involved in research could have an opportunity to see research first hand and understand the world around them,” SEA-PHAGE and SEA-GENES advisor, Dr. Dustin Edwards said.

Dr. Edwards is an Associate Professor for the Department of Biological Sciences. 

“Science and information is constantly changing, so you have to readjust how you are thinking about things, and this is one way to teach people how that works,” Dr. Edwards said. 

There are around 120 universities involved with this program, and Tarleton joined that list six years ago when Dr. Edwards attended a regional conference of the American Society of Microbiology and saw presentations from other universities regarding the program.

“I was absolutely blown away by how much they were able to accomplish and the value of the work they were doing, and I wanted to get in on it,” Dr. Edwards said. 

Soon after, Dr. Edwards put in an application for Tarleton and got accepted. 

The students involved in SEA-PHAGE will collect samples from things like soil and water, bring it back to the lab and isolate a phage if it is present. If they find a phage, they amplify it and extract the DNA to identify it. 

“The interesting thing is they only infect bacteria,” SEA-PHAGE and SEA-GENES intern Selina Alvarado said.

Alvarado is a Biomedical Sciences major with a minor in Chemistry and is in charge of preparing labs, collecting reagents, collecting data and helping other students in the lab.

“By amplifying a phage and looking at its genome, we can see what each gene does and [that] can potentially help us combat bacterial infections,” Alvarado said.

All of the research from SEA-PHAGE gets sent to the University of Pittsburgh and the HHMI where it will be put into an online database. This database will include pictures and information about each phage that is discovered. The samples collected of these phages will also be sent there, where it will be sequenced and kept frozen

For SEA-GENES, the samples will be sent to Baltimore to be sequenced and kept frozen as well.

For both programs, all the data gets published in scientific academic journals.

“This semester we are going more in depth with the genetic sequencing of the phage,” Ounsinegad said.

Ounsinegad is a Mathematics major with a minor in Biology. 

“Right now, we know there are 26 genes on the phage that we have, which is common for the family it’s in. We want to focus on sequencing the genome of this phage,” Ounsinegad said.

The SEA-GENES program goes hand-in-hand with SEA-PHAGES, but is more advanced and specific. SEA-GENES focuses solely on the genome of one of the phages to see what each gene does. Tarleton has been involved with this program for two years.

“This semester we are working with a phage called Pixie. The phage has 100 genes, which is weird [for a phage], but it’s a nice even number to work with,” SEA-GENES student Aeron Pennington said. 

Pennington is a Biology major with a concentration in Molecular Chemistry. 

“We are taking those genes and putting them into a plasmid, which is a self-replicating circular part of DNA inside of a bacterium. By inserting the genes into the plasmid, we can have that bacterium express that specific protein that we can use [for future] work or testing. This is to see which genes are cytotoxic, or capable of killing host cells,” Pennington said. 

“The cool thing about this is that you can see it,” Alvarado said. “You spot positive and negative controls on the plasmid, give it a few days and we will be able to see whether it affected the bacteria or not.” 

The unique aspect of these programs is that there are set class meetings but it is independent research.

“One of the most fun parts about these programs is that students get to work more independently,” Alvarado said. “I’ve been in multiple other labs, but it doesn’t compare to what we do in here because it’s more independent and you learn so much more on your own.”

While the advisors and interns are there to help, most of the sample collection and experiments are done by the students independently.

“What’s so great about the class that I really enjoy is that Dr. Edwards trusts you to know what you’re doing and lets you do what the instructions say, but is also there to help you or answer any questions,” Ounsinegad said. “You really learn what it means to be independent but also still have help when you need it.“

These programs have not only helped students gain knowledge, experience and independence in the lab, but also confidence.

“[This program] definitely boosted my lab confidence,” Pennington said. “Everyone starts off nervous, but [the students and advisors] are helpful and guide you through it and that boosts your confidence in the lab.” 

The research done in these programs can possibly help fight antibiotic resistance in bacteria.

“Part of the reason for SEA-GENES is to find out which gene of the phage is toxic to the bacteria and use it as a treatment for bacterial infections that are resistant to antibiotics,” Alvarado said.

There have been a handful of cases where phage therapy, which is the use of phages as treatment for bacterial infections, was successful and even saved lives. 

“Phages evolve, adapt and change so a practical outcome of that would be the treatment of antibiotic resistant infections,” Dr. Edwards said. “But since we do not know what all the genes [of the phages] do, there are some downsides.”

“The primary reason why this research is important is trying to think about using phages for medicinal and therapeutic reasons,” Dr. Harold Rathburn, Associate Professor for the Biological Sciences Department, said. “One of the things we’re trying to do with these is look for genes in these phages that can be used in this way.”

The SEA-PHAGE program is called “Viral Isolation” in DuckTrax. It requires no prerequisites and can be registered by any student. The SEA-GENES program requires a prerequisite of Biochemistry.

More information about these programs can be found at https://www.tarleton.edu/biology/index.html or https://seaphages.org/ or by contacting Dr. Edwards and Dr. Rathburn.