A Hands-on Bioinformatics Class Lets Students Get Practical Experience While Keeping It Experimental

There are just 35 Certified Living Buildings in the world, and two of them — the R.W. Kern Center and the Hitchcock Center for the Environment — are on the Hampshire College campus. Living Buildings use greywater systems to achieve net-zero water use.

“Greywater is used water from sinks, showers, and washing machines,” explains Kit Abatecola F24 (above left), a Div II studying botany, toxicology, and ecology. “It’s not sewage but it does have soap and dead skin cells and that sort of stuff in it, which changes the microbiome. [A microbiome is a collective community of microorganisms, such as fungi, viruses, and bacteria, that exist in a specific environment.] We’re looking into how reusing that greywater to water plants might affect the plants and the soil they live in, especially in regard to their microbiome.” Using greywater on plants is one way to reduce reliance on potable freshwater, which is particularly important in areas experiencing water scarcity or drought.

Abatecola and Amelia Roberts F25 (second from left) began the greywater experiment last fall, and the current analysis work is part of Assistant Professor of Environmental Microbiology and Bioremediation Julie Johnston’s spring class Bioinformatics: Community Analysis. The class hopes to publish the final results in a peer-reviewed journal, as have other classes taught by Johnston as well as by Assistant Professor of Ecology and Global Change Jenny VanWyk.

Roberts is a Div II student studying plant and soil sciences. She planned to study agriculture, inspired by a love of plants, but realized she also liked lab work, and expanded her studies to encompass both applied and research sciences.

“Hampshire is my third college,” says Roberts. “I started by studying engineering at a standard university and then went to a community college and shifted to ecology. Initially, it was Hampshire’s Farm that caught my eye, but what drew me in was the promise of something different and more substantial than what I’d already tried. I feel that I’ve gotten just that; Hampshire has given me experiences and opportunities I was unable to find at other schools.” Roberts is also developing labs for two intertwined courses that will premiere next year, Plant Chemical Ecology, to be taught by VanWyk, and Bioremediation, which Johnston will teach.

Rio Villarreal-Mentz F23 (second from right) is working with Zoe Littlefield F23 (above right) to sort the experimental greywater data and identify and flag any hazardous bacteria and viruses, especially ones that would be detrimental to humans. “Zoe and I will eventually produce a sound metagenomic analysis [examining the genetic material] of any harmful organisms within the soil samples,” Villarreal-Mentz says. “We’ll also be able to better determine the differing impacts on plant life.” Littlefield notes, "Rio and I are trying to find a way to make the data other folks were able to generate from the soil samples into comprehensible visual representations and to analyze what all this computer stuff means."

Villarreal-Mentz is a second year Div II student and plans to study public health and epidemiology postgraduation, but says she also “really enjoys learning about physiology, pathology, and bioinformatics.” She originally planned to study physics, but, she says, was “very inspired by Jenny VanWyk’s Disease Ecology course, which sparked my passion for disease research.” 

Littlefield is in the last semester of their Div II and studies clinical neuroscience and microbiology. "I came to Hampshire thinking I wanted to be a psychology major, and then that completely changed as soon as I started taking STEM classes and finding my niche. Small class sizes and written evaluations are what originally attracted me to Hampshire, and now that I have had the chance to check out classes from all Five Colleges, I can say that those qualities create a unique classroom environment at Hampshire. Professors here build close relationships with students who are willing to reach out and put in the work. That also means that there are more opportunities to work directly with professors on research projects and independent studies that allow us to get actual hands-on lab experience." 

Says Johnston, “Both students excel in lab-based science and are currently learning metagenomic data analysis on the greywater independent study.”

“Dr. VanWyk and Dr. Johnston are two of the driving forces behind my success here,” says Roberts. “Dr. VanWyk consistently teaches courses that foster immense engagement and student-led learning in the fields of agriculture and ecology, which have transformed my way of thinking about college. I can focus on my genuine curiosity and a desire to chase what I want to know instead of just seeing college as a means to an end. And Dr. Johnston is one of the most inspiring people I’ve ever met. As a transfeminine person, getting to see someone like myself in STEM, working in a position I hope one day to achieve, really makes me feel that my dreams are possible, even in the hostile world we live in today.”

“Jenny’s classes are consistently interesting, and she ties in useful skills very well,” says Abatecola. “And the same goes for Julie, who has also been a great advisor and shown me lots of useful opportunities.”