Tweet led student to a project untangling the genomes of large viruses
Alaina Weinheimer, an ICTAS Doctoral Scholar, loved coding and working with marine microbes. She found a way to combine them.
Alaina Weinheimer came to Virginia Tech after finishing a master’s degree at the Max Planck Institute for Marine Microbiology in Germany. She works in the lab of Frank Aylward, an assistant professor of biology, where she uses coding techniques to study the genomes of large viruses called jumbo phages that affect the complex microbial communities across the globe. Her work is supported in part by the Doctoral Scholars program of the Institute for Critical Technology and Applied Science.
Interview has been condensed and edited for clarity.
What’s the problem you’re trying to solve?
My work focuses on jumbo phages — viruses with relatively large genomes that infect bacteria. I’m trying to understand how prevalent these big viruses are, what bacteria they’re infecting, and how they might be affecting the microbiome and the nutrient cycles in the ocean. Most environmental virus studies have tended to overlook these phages because techniques in the lab tend to favor smaller phages, and filtration of ocean samples often excludes them from microscopy and genetic sequencing analysis.
I’m also working to understand why some phages get so big. What are they gaining when they get bigger genomes? I’ve never considered myself an evolution person — I’ve always thought of myself as an ecologist, but I’m slowly realizing that all of my questions and curiosities are rooted in evolution, or can be explained by evolution.
What led you to Virginia Tech?
While I was doing my master’s I was thinking about the next steps, and I wasn’t sure if I wanted to do the Ph.D. I knew I liked coding and I liked working with marine microbes, so I was looking for an opportunity that would let me combine them. I saw an advertisement on Twitter from Frank’s lab that said he was working on projects using metagenomic sequence data to study microbes in the ocean, and I thought it would be a perfect opportunity to explore. And since it was a new lab, I also thought it would be exciting to be a part of that.
How did you get into coding?
I never thought I would like coding. I knew it was important to learn because the size of biological data is starting to require intense computational analysis, so I thought, “okay, I’ll learn it, but I’ll still try to SCUBA dive as much as I can.” And I discovered I liked the thinking that goes into it. I’ve always loved languages. Learning a few new words and then trying to use them in a sentence — that’s kind of how I see coding. I learn a few new tools and then apply them, and it’s fun for me.
What do you think is a common misconception about the microbes you study?
Not all microbes are bad — disease gets a lot of press, but there are good guys and they’re doing a lot for many animals, plants, and ecosystems. I’m drawn to how microbes can help us, rather than hurt us. I just wonder how many other things are going on that we don’t know about, because we can’t see it. People sometimes refer to microbes as a ‘black box.’ I’m hoping to understand some of what’s going on in that black box.
The ICTAS Doctoral Scholars program helps attract exceptional students to Virginia Tech and increase the educational and experiential diversity of research by offering a competitive graduate fellowship and professional development opportunities to top students pursuing transdisciplinary research. The program is led by ICTAS and supported by significant contributions from the Graduate School and each scholar’s college and department. Faculty members interested in nominating an incoming graduate student for the program should contact their college’s associate dean or graduate director; more information is available on the ICTAS website.