News - Six Weeks In Parasites: Student Researchers Take On Tropical Foe

Six Weeks In Parasites: Student Researchers Take On Tropical Foe

By Carla Morris

How does learning by conducting research differ from learning in the classroom? “There is no answer key,” says Ethan Clements ’20. “You venture into new territory and have to figure it out yourself.” 

Mosquito-1“Six weeks focusing on one topic and being able to contribute to the scientific community—[that] could never really be done in a classroom,” adds Gabriella Pflederer ’22.  

Nor could a classroom facilitate the level of creativity Ethan and Gabriella demonstrated over the summer as they studied a common parasite that causes malaria. 

“Our goal was to find out why some cases of malaria are more serious than others,”says Gabriella. 

It sounded simple, but the process proved challenging. Here’s a snapshot of hurdles Gabriella and Ethan encountered, and solutions they devised to keep their genomics exploration—part of GU’s donor-funded Summer Research Experience—moving forward. 

Problem: Overwhelming options
Solution: Let’s do this together

The students’ research supervisor, Biology Instructor Lindsey Mao, gave them full autonomy in choosing their subjects of study. Initial plans called for two separate projects, one for Gabriella, and one for Ethan; but they found the scope of options overwhelming. “[We] decided to work together on the same topic,” said Gabriella, who generally prefers working alone: “I realized that it was essential to have someone to bounce ideas off of and to use each other’s strengths.”

BigDataProblem: Immense data, limited computing power
Solution: Free online resources

Ethan and Gabriella accessed an existing online dataset of about 50 patients in Indonesia who experienced either severe or non-severe cases of malaria. The dataset contained millions of RNA sequences for each patient. The prospect of sorting, comparing, and matching the sequences to specific criteria demanded computing power that eclipsed GU’s capacity. The team turned to a free online resource for biomedical research called Galaxy. “[This] allowed us to do the trimming and filtering,” said Ethan.

Problem: The bottleneck of free resources
Solution: Work during low traffic hours

It’s no surprise that “free” means a crowd of users queueing up for Galaxy’s services. Wait times during business hours tended to be extraordinarily long. The students began working on weekends and at nights to speed up the process.

Problem: Nothing less than perfection
Solution: Trial, error, and help from an expert

“Each program has very specific requirements for its inputs,” said Ethan. “The file formatting and contents must be tightly controlled, and any small detail can cause an error.” He and Gabriella spent days steeped in trial and error, trying to nail the needed precision for file conversion. They also tapped the expertise of GU’s Eric Nord, department chair and professor of biology. Nord is well-versed in the statistical software Gabriella and Ethan used for computations.

Problem: Effectively telling their story
Solution: Multiple drafts, even when it’s painful

Mao recalls that the students “hit a wall” while attempting to capture their work in writing. “As their mentor, I chose to play a light hand in the writing process and a heavy hand in the editing. This meant that even after the first, second, third drafts of their writings, I would still request full rewrites of entire sections . . . This not easy on the students emotionally and mentally, but I can definitely say that as of now, in September—two months after the official end of summer research—their scientific writing skills have improved about five-fold.” 

What’s NextGabriella

Ethan (below right) and Gabriella (right) continue to fine tune their writing. Eventually, they will submit their work for publication. The prospects excite them because their research fills an existing gap in what we already know about malaria. 

“The original paper under which the dataset was published focused on computational clustering of the gene expression data,” explains Mao. “It was also written by a student focused on statistical and mathematical questions. These students further developed this research by applying a more metabolic and molecular lens to the same dataset.”

Maximizing Existing DataEthan

In the process, Gabriella and Ethan also demonstrated that many questions can be
asked and answered by analyzing pre-existing datasets. “In a way, a lot of the answers are already out there,” says Mao, “We just need the researchers to keep asking the questions.”  

Ethan and Gabriella will present their research in a poster format during Homecoming weekend, October 17-20. GU Financial Champions who support scholarships and/or The Catalyst Fund won’t want to miss seeing the fruits of their investments and the work of all GU’s student researchers. 

Learn More

Benefits of Undergraduate Research Reach Far Beyond Campus
Research Team to Publish in Stanford U. Scientific Journal
Undergraduate Research: A High-Impact Learning Experience for Princeton-Bound Chappel
Corrosion and Copper: Local Business Teams Up With GU Students to Solve the Geo-thermal Piping Puzzle

Undergraduate research at GU equips students with skills that graduate schools and employers value. Help a student today with a gift to The Greenville University Fund, a primary source of scholarships, or GU’s Catalyst Fund that makes summer research possible. Thank you for giving.

This story was published on September 26, 2019




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