M.Sc. candidate, Biomedical & Molecular Sciences
Making The Transition From Undergrad To Grad
by Sharday Mosurinjohn, July 2014
Tyler Vance shoots X-rays at protein crystals. To be more precise, what Vance is doing as a Master’s student in Dr. Peter Davies’ biochemistry lab is studying the proteins within biofilms—that is, 3D clusters of bacteria that are highly ordered, and hard to get rid of, “like plaque on your teeth, build-ups in waterways, and even the material that can collect on medical implants.” To do so, Vance has to determine a protein’s structure (or “tertiary fold”) based on how it diffracts X-rays. This is called “X-ray crystallography.”
Proteins are notoriously difficult to image due to their complexity and flexibility. (For more on this problem, see fellow grad student Hazem Ahmed’s research on protein folding and swarm intelligence. Vance coaxes proteins into stable configurations—into protein crystals—with specially tailored solutions and then, essentially, analyzes the shadows cast by the X-rays hitting the crystals. If that wasn’t cool enough, Vance mentions that scientists are now doing studies like his in outer space, in order to glean insights into protein structure and function, without the interference of gravity.
However, Vance's work keeps his feet firmly planted on the grounds of Queen's campus, instead of rocketing through the stars. Heading into the second year of his MSc, Vance says that his project has stayed true to what he originally proposed, but “branched.” “I’ve now got four or five projects on the go. It’s like Jenga,” he laughs, ”You pull at blocks in one area till you can’t any more, then you switch track, make a few more changes, switch, and on and on.” The main thrust of Vance’s work with protein structure is trying to determine the molecular interactions that allow biofilms to form. There are three major “glues” that do the job of allowing bacteria to bond into biofilms. These are “giant polysaccharides [big sugars), external DNA from lysed [burst] cells, and protein interactions.” Vance is looking at the last of the three, specifically at something called “RTX proteins,” which are important for adhesion to surfaces but also cell-to-cell interactions.
RTX proteins have two ends with properties that allow them to stick. “You could think about it like this,” says Vance, “One end, the C terminus, is like a hand, and the other terminus is like a shoulder attaching the protein to the bacteria's body. In the middle, there's a long repetitive segment called the extender domain, which is like an arm. It allows the hand to stretch away from the body, in order to grab something and stick to it." The length of the arm is fixed, but elements in the environment can change its flexibility, making the arm rigid at some times and bendy at others.
Vance and his colleagues were recently able to solve the structure of a portion of the extender domain from an Antarctic bacterial RTX protein, which uses calcium ions to rigidify the arm. They published these positive results just a few weeks ago. Now Vance is turning his attention to a bacterium called Marinobacter hydrocarbonoclasticus, which forms biofilms at the interface of water and oil, making the oil more bioavailable so the bacteria can eat it. “The fact that the bacteria can break oil down could be important in bioremediation,” explains Vance. The issue of biofilms is of wider interest, too. “It was originally thought that biofilms only formed with some bacteria, but now it’s thought that most (maybe all) species of bacteria may be capable of forming them.”
Vance stayed to work at the Davies lab after doing his 4th year honours project there. “I enjoyed Dr. Davies as a supervisor, and thought the lab well prepped and full of smart people. It was a wonderful environment where experienced students were willing to help new people. It made the transition from undergrad to grad school smooth.” Vance smiles, and invokes a kind of realism that’s hard to argue with: “I could have taken my chances elsewhere but why risk it?”
Nonetheless, that transition was a bit odd, reflects Vance. “At Queen’s, the first year of undergraduate studies is very much about school spirit but grad school isn’t quite like that. Now I notice people tend to think about themselves in terms of their field, which is much more specific than school identity.” Chuckling, he quips that sometimes it makes “the rest of campus seem superfluous.” This isn’t to say that he doesn’t feel part of a community. Over this summer, Vance, the social convenor of the Davies lab, is organizing a number of trips—including canoeing, visiting an amusement park, and wine tasting—for his fifteen lab mates.
In his professional development at Queen’s, Vance’s favourite experience so far has been the teaching component of being a TA. “It was more rewarding than I would have given it credit for. It helped with my presentation skills but also with my sense of what needs to be said, as a teacher, in order to key in that understanding for students.” The transition from undergrad to grad studies now seems to be a complete and a happy one, because, in closing, Vance says that, in many ways, his ideal future would be to just keep doing what he’s doing.