Wednesday, April 3, 2013
If not for viruses, Joanna Kettlewell might still be folding towels in a nursing home. That’s what she was doing for a part-time job in the fall of 2010, when she stumbled on the class that changed the course of her college career and transformed her into a scientist.
Allison Johnson, Ph.D., the instructor of a class on phages, or bacterial viruses, at Virginia Commonwealth University, inspired Kettlewell, a sophomore at the time, to focus her undergraduate research on one virus. That virus, the focus of Johnson’s current work, represents one of the world’s greatest public health crises: human immunodeficiency virus (HIV), which kills about 2 million people per year.
Thanks to a summer fellowship through the VCU Undergraduate Research Opportunities Program (UROP), Kettlewell, a biology major and chemistry minor in the College of Humanities and Sciences, has explored what it means to be a scientist by studying one of the enzymes that gives HIV its bite. Her efforts represent one of many student research success stories at VCU, which celebrates its Third Annual Research Week from April 19 to April 27. (A complete list of Research Week events can be found here.)
Kettlewell and her mentors, Johnson, assistant professor and assistant director of the Center for the Study of Biological Complexity in VCU Life Sciences, and Vamsi Yadavali, Ph.D., assistant professor of chemical and life sciences engineering in the VCU School of Engineering, hope their work ultimately may help scientists better understand how current HIV medications work so that they can design better drugs to fight the epidemic.
VCU Hosts Student
Virginia Commonwealth University this month will host its Third Annual Student Research Week, a series of events that bring together undergraduate and graduate students from across disciplines to celebrate research and creative and scholarly projects.
Events will take place from April 19 to April 27. A schedule of events can be found here.
Undergraduate and graduate students will present overviews of their projects, theses or dissertations during the week of activities. These projects span many academic disciplines, including the College of Humanities & Sciences and the schools of Allied Health Professions, Arts, Business, Education, Engineering, Medicine, Nursing, Pharmacy, Social Work and Interdisciplinary Studies. Students will be available to demonstrate and discuss their projects.
Finding her place
As a volunteer emergency medical technician (EMT) in Goochland County, Kettlewell knew she was interested in science and medicine, but had no particular focus.
“Freshman year I bumbled around not knowing what I wanted to do,” Kettlewell said.
Then during her sophomore year, her biology instructor, Anneke Padolina, Ph.D., advertised for a course called Phage Discovery Lab, which was being offered for the first time.
“I saw a picture of a virus and I thought, ‘I might as well try that!’” she said. “I didn’t know what I was getting myself into.”
In the class, undergraduates learn about viruses – specifically, bacterial viruses called bacteriophages, or phages – through hands-on research. They are able to isolate their own phages from soil samples, name them, visualize them under a microscope and sequence their genomes.
The Phage Discovery Lab at VCU was Kettlewell’s first taste of scientific research and discovery. It left a strong impression.
Bridging biology and engineering
Now in her senior year, Kettlewell isn’t folding towels anymore. Instead, she’s busy working with Johnson and Yadavalli to understand an enzyme that allows HIV to do its dirty work: HIV-1 integrase.
According to Johnson, HIV-1 integrase is the enzyme that inserts the virus’ genome into human chromosomes, hijacking human cell’s replication processes to harbor the virus. This cascade leads to persistent HIV infection, undermining the immune system of the infected person. Kettlewell and her mentors are merging cutting-edge molecular imaging technology with modern biochemistry to examine the mechanism of this deadly enzyme.
“Vamsi (Yadavalli) has two very cool machines,” Johnson explained. The first is called an Atomic Force Microscope (AFM), which the researchers use “to make a topographic map of a protein.” This microscope is, in Kettlewell’s words, “like a phonographic needle tapping over a source. We can use this to tell the shape of a molecule.”
Yadavalli’s second cool machine, the Quartz Crystal Microbalance, is “like a very tiny scale,” said Johnson. “A super finicky one!” Kettlewell added, explaining that it has taken her a year just to get the devices calibrated and to gather preliminary results.
Collaboration is key to the project: Johnson is a biochemist, Yadavalli an engineer. “I think you get the best data from interdisciplinary approaches,” Johnson said. “You can approach the problem with two different sets of eyes, two different perspectives. He knows more about the machinery; I know more about the protein and how it works.” Since both her mentors bridge life science and engineering, Kettlewell has seen the link between the disciplines. “I see them talk, and I can see how collaboration happens,” Kettlewell said. “Taking our results, and applying math.”
Using the two machines, the team hopes to isolate a single molecule of integrase and a single molecule of viral DNA, to combine them and then measure how much force is required to pull them apart. This will help visualize exactly how integrase changes the shape of viral DNA to help it invade human chromosomes.
Attacking the virus
This is how HIV kills. To date, at least 60 million people worldwide have been infected by HIV, according to recent estimates, and 25 million people have died of HIV-related causes, according to USAIDS data. The number of deaths attributable to HIV peaked in 2004, but has declined since, to less than 2 million in 2010, thanks to the use of antiretroviral therapy, including a cocktail of drugs. Different drugs target different steps of the HIV infection pathway, from virus entry into cells to viral replication.
“You have to attack the virus from multiple directions, because it mutates,” Johnson said. “The goal is to prevent further infection — to keep viral load low.”
One kind of current HIV treatment, called an “HIV integrase inhibitor,” works by blocking the enzyme that allows HIV to inject its DNA into immune cells (the drug Raltegavir is an example). The first integrase inhibitor to treat AIDS was approved by the FDA in October 2007 after 15 years of research. But scientists still don't know exactly how the enzyme interacts with viral DNA, changing its shape to invade the human immune cell’s genome.
“I think there’s a step after the enzyme binds (to HIV) – where binding gets tighter – that has not been documented yet,” said Johnson. Integrase inhibitors, she said, may act by interfering with this tightening of enzyme and virus.
If the enzyme can’t hug tightly enough onto the virus’ DNA, it can’t twist HIV into the shape required to insert itself into an immune cell’s genome. If scientists can understand how this shape-shifting works, they can understand current HIV drugs and design improvements of them.
Birth of a scientific career
The lab is currently testing how well integrase binds to viral sequences of DNA as opposed to random sequences — a precursor to visualizing the virus-enzyme bond. The project is still in its early stages, but Kettlewell is proud to have contributed her part.
Kettlewell is not finished with science, she said. Now in her senior spring at VCU, she is looking for research jobs in science and health care. She plans to apply to medical school in 2014 and to pursue a career as a doctor and a medical researcher.
“I wouldn’t be here today if it weren’t for Dr. Johnson,” Kettlewell said.
“I never thought going to a big school like VCU that I would get close to my professors – people (who) care about where you go (in your career)… I really lucked out.”
“I asked Joanna to work on this project because she didn’t give up in my phage class,” Johnson said, emphasizing how important persistence is in science. Persistence and patience.
“Patience, I admit, isn’t my forte,” Kettlewell said. “Science has definitely taught me patience. I don’t have a lot of patience, but I don’t like to give up. I’m always going to want to find answers. And on the way, you find more questions. You can’t get out (of science) once they pull you in, like in ‘The Godfather.’”
She is grateful to VCU and her mentors Johnson and Yadavalli for leading her to her calling.
“That’s what’s so great about science,” Kettlewell said. “There are always more questions. That’s why it’s a career, and not a job.”
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