Biology research compares local sediment for pollution levels

While Naomi Fernandes ’23 vetted her own topic for her unique Independent Study at The College of Wooster, with faculty mentor Rebecca Williams, assistant professor of biology, she and her three classmates had the opportunity to answer a larger question. The group worked together to compare the level of Polycyclic Aromatic Hydrocarbon (PAH) pollutants in Wooster-area water sources. Fernandes’ study specifically examined sediment and the level of pollutants that cause altered gene expression in brown bullhead fish (Ameiurus nebulosus). The Environmental Protection Agency defined 16 of these PAHs as high priority pollutants because they are detrimental to environmental and human health, so studying gene expression (the process where an organism’s cells respond to its environment like an on/off switch that affects protein production) could reveal how the pollutants are affecting living creatures.

“I thought this topic was something unique, and it would contribute most to the group,” said Fernandes, a biochemistry and molecular biology major. “Previous seniors have compared gene expression changes in so-called clean and polluted areas, but no one had analyzed the sediment before. They only estimated pollution based on the fact that the ‘polluted site’ was near a wastewater treatment plant.”

The student team planned to use wild-caught fish for their studies, but they didn’t have much luck on a group fishing trip. Ultimately, they purchased and exposed lab fish to the compound instead. “Collecting sediment was easy so it was nice to complete that portion without any issue, unlike fishing,” said Fernandes.

The collection process required holding a plastic centrifuge tube and scooping off the surface of sediment into the tube. She’d wait for sediment to settle, pour out water that rose to the top, and cap it to take back to the lab. She poured additional water out and let the uncapped sediment tubes dry for a few months. After the lengthy waiting process, Fernandes performed Gas Chromatography coupled with Mass Spectrometry (GC/MS) analysis to detect compounds in the sediment samples based on mass.

“I thought this topic was something unique and it would contribute most to the group. Previous seniors have compared gene expression changes in so-called clean and polluted areas, but no one had actually analyzed the sediment before.” -Naomi Fernandes ’23, I.S. title: Polycyclic Aromatic Hydrocarbon (PAH) Pollution Analysis and Ameiurus Nebulosus Gene Expression Can Predict Environmental Health

Surprisingly, there were a few outlier compounds with higher concentrations at the clean site, including Benzo[k]fluoranthene, Benzo[ghi]perylene, and Indeno[1,2,3-cd]pyrene. But overall, Fernandes found more compounds at the polluted site as she expected. “The gene expression we were looking for is a tumor suppressor and another liver enzyme that helps metabolize these compounds,” explained Fernandes. “My colleague did find increased liver enzymes in the fish, which often happens when they’re exposed to more pollution, but because this wasn’t wild-caught fish, it’s hard to know exactly how this correlates.”

Fernandes said the next generation of her group’s study could use GC/MS and chemical tests on fish tissues, not just sediments, to give the most direct correlation between the levels of compounds in the tissues and the gene expression changes.

While she did face some hurdles during the research process, Fernandes said she felt prepared for this work having learned time management and scientific writing skills since her first year at Wooster. She also gained valuable experience creating and presenting a poster with her mentor at the Midwest Ecology and Evolution Conference (MEEC) March 31 to April 2 in Kentucky. “People seemed genuinely interested in what I did and asked a lot of cool questions I wouldn’t have thought of, so it was a good way to prepare for the I.S. Symposium and I.S. Oral Exam,” said Fernandes.

Posted in Independent Study on June 26, 2023.