Being a dry lab person has benefits.
Rather than spending hours a day moving around volumes of liquid or waiting for microbes to grow, I’m able to assemble accurate genomes of 300 bacterial isolates in one day. But the learning curve for the coding skills to do dry lab is steep. Before I can even get to a meaningful biological result, I need to concern myself with more mundane questions like “How do I move this file?” And “Is the computer running?”
Contemporary microbiology research projects are considered either “wet” lab (experimental laboratory science) with tubes and liquids and petri dishes, or “dry” lab — meaning computer work.
In the last lab I worked in, there was a divide between dry lab people and wet lab people. They didn’t understand each other. They poked fun at the silliness of how the others spent their time. “I haven’t pipetted in years and I never will!” a dry lab person would shout, unprompted, after someone walked by, gloves holding the laboratory tool.
“The computational projects look pretty but don’t show a single causal relationship,” the wet-lab person would whisper after a PowerPoint presentation with colorful diagrams and gigantic heat maps with unlabeled axes, or worse, no axes at all and a bunch of circles with lines connecting them.
The bacterial species I study is called Gardnerella vaginalis. Gardnerella vaginalis is the cause of bacterial vaginosis (known colloquially as BV). At its best, it is annoying and smelly and resolves itself; at its worst it causes preterm birth and an increased susceptibility to HIV. It is really hard to get rid of because antibiotics don’t always kill it; this is because it grows in a film called a biofilm.
Biofilms are colonies of bacteria that adhere to each other and a surface, forming a slime. Like dental plaque. A biofilm, like a tiny city, offers a community and structural protection for the bacteria.
BV causes a lot of vaginal discomfort and an unpleasant odor. Part of what we’re studying is that there is a common intermediate phase between having and not having BV. Another thing we are studying is that Black and Latinx people get BV at a much higher rate than white people, and we don’t know why.
There are two types of people I talk to about my research. The first has no idea what bacterial vaginosis is or thinks it’s a yeast infection. The second has had bacterial vaginosis once or twice or ten times and is completely traumatized. “What you’re doing is so important!” they tell me, with desperation in their voices. “Please let me know if you find out anything. Please!”
Bacterial vaginosis is not well studied, and the cause and mechanism of infection is pretty much unknown aside from some guesses. The genome of Gardnerella vaginalis is complete, but we don’t know the function of over half of its genes. Yet, it is the most common vaginal infection. I have to wonder if it is understudied because it is an infection of the vagina, because it causes a smelly vagina, something our culture is terrified of, shames, jokes about, and ignores. We don’t want to think about it, much less devote our life to studying it.
Day to day, I worry and stress about running the right lines of code and putting forth the next experiment to my advisor. As a scientist I’m trying to put together a complex puzzle, but in the moment, I’m focused on the outline of one piece. Is it one of those little knobs jutting out? Is it part of the edge or the middle? Does this knob fit in that hollow?
What does this result mean? Where do I go from here?
I’m not simply wrestling with Gardnerella vaginalis’ unruly genome, banging my head against the wall for clicking in the wrong way two months ago, or coming to my advisor, tail between my legs, with half-analyzed data on a piece of paper written in a language I can’t read. I am trying, working, a little at a time to solve a problem that will really make people’s lives better.
After I do get BV (statistically speaking) maybe the treatment won’t be a pitying look and a pat on the shoulder any longer, fingers crossed that the antibiotics take. Or a last-ditch recommendation to sit in a tub of vinegar (it worked).
I’m going to figure out what makes BV so hard to get rid of by figuring out how Gardnerella’s genetics enable it to make a biofilm. Then, we can go forth with better and more informed treatments. It seems obvious, but it isn’t always obvious; the work of a Ph.D. is work on a gigantic problem zoomed in 100X.
You squint, you think you’re looking at a squiggly line but really you’re looking at the edge of the lost piece that fits perfectly in the puzzle that’s been sitting out for decades.
Or maybe you realize the puzzle was not put together correctly at all. What you thought was the sky is really a large lake. Once you turn it upside down, your piece fits and it all, finally, becomes clear.
Madeline Topf is a second-year graduate student getting a Ph.D. in microbiology from UW-Madison.
If you are interested in submitting an essay to Isthmus, please query lindaf@isthmus.com.
