Variations on a Gene
- By Amanda Kenyon Waite
Scientists around the world who study malaria and the parasites that cause it will breathe a collective sigh of relief this month when they read UVM senior Katie St. Denis' research paper. It goes a long way toward substantiating a commonly held -- yet unproven -- belief about how to distinguish malaria parasite species.
Researchers have been operating on an assumption that one gene in the DNA of these parasites can be used as a marker for species identification; that is, if the gene, cytochrome b, varies from one parasite to another, you're looking at two different species of parasites. While some research has generated data for parasites that infect humans with malaria, no comparative data existed on parasites that infect non-human hosts.
St. Denis' paper documenting her results, co-authored with biology professor and adviser Joseph Schall, is now in press with the Journal of Parasitology, one of the field's three journals of record.
The supposition about how to determine species in malaria parasites began in Schall's lab more than a decade ago. "Ten to 15 years ago, we found a gene that evolves very slowly in parasites (the cytochrome b gene)," explains Schall, "so people have said a tiny change, a tiny difference in that gene means that you have a different species of malaria parasite." This idea has led to the categorization of many thousands of bird malaria parasite species -- all based on variations in the cytochrome b gene. Although some scientists have built careers on this common sense understanding about species identification, no one had yet done the legwork in the lab to test its veracity for non-human malaria parasites.
Enter St. Denis.
She'd made herself known as a bit of a trouble-maker in Schall's spring semester 2009 class, by sitting in the front row and relentlessly asking impertinent, difficult questions. When it was time to choose an adviser for her McNair Scholars Program summer research project, she was hesitant to approach Schall, not knowing what he really thought of her. What she didn't know was that Schall saw her curiosity as one of the necessary ingredients of an excellent scientist and found her an ideal candidate to work on this very problem: is cytochrome b a useful marker of species differentiation? Throughout that summer, she'd prove that she also possesses the other two ingredients of Schall's recipe: academic honesty, or a willingness to "let nature tell you what it's going to tell you," and a strong work ethic.
St. Denis spent 40-hour work weeks in the lab, extracting and isolating the DNA of plasmodium mexicanum, a malaria parasite that infects the western fence lizard. On her second attempt, St. Denis designed a successful primer to amplify the cytochrome b gene, a feat that Schall says takes a certain level of artistry. The samples were sent to a Cornell laboratory for sequencing, and St. Denis moved from the lab bench to the computer to use a program to analyze the results. "She's learning all the standard techniques that any lab in the world doing molecular genetics uses," Schall says.
What, exactly, did she find? "We found that there is absolutely no variation, not even variation that would indicate silent mutation," St. Denis explains. "We would have expected to see a few nucleotide changes in an area where there may have been a silent mutation because that doesn't make any difference to the function of the gene, but we didn't even see any of those for all 200 samples, both segments of the gene."
For now, cytochrome b holds onto its species differentiating characteristic for malaria parasites. "I don't think this has necessarily solved the issue," St. Denis says, showing off that academic honesty Schall describes, "but I do think that it's putting another piece of the puzzle together, helping us understand whether or not this is a useful way to determine a species of malaria parasite and how it co-evolves with its host."
"Every person who works with malaria parasites will want to know this information," Schall says. "No matter where they are in the world, no matter what species they work with, they'll want to know how much variation has been found in one species. It's only the third species it's been done for. The other two were in humans. It's a really nice result for a one-summer project from somebody who was a beginner when she started."
Although this project is concluded and its paper is in press, St. Denis isn't finished with her research in Schall's lab. Having secured an APLE (Academic Programs for Learning and Engagement) award, St. Denis continues her work with plasmodium mexicanum, this time analyzing data that spans 32 years, asking how rapidly evolutionary change happens in a non-human malaria parasite population that is free from drug treatments. See the above video to learn more.