Bin Team
Assistant Professor Bin Xu (right) and undergraduates Robert Burnham and Rebekah Watkins study biochemical and molecular structure-function relationships of proteins. Their work offers insight for human health conditions, like diabetes and cardiovascular diseases.

Hands-on training prepares two undergraduates for careers in life science research

Two years ago, Robert Burnham and Rebekah Watkins joined the lab of Bin Xu, an assistant professor of biochemistry in the College of Agriculture and Life Sciences and a Fralin Life Science Institute affiliate.

During that time, they learned the ins and outs of studying microscopic cell parts and their roles in human diseases like diabetes, obesity, and infection, said Xu, who is also a faculty member in the Virginia Tech Center for Drug Discovery and the Fralin Translational Obesity Research Center.    

Here’s a glimpse of what they have learned and where they are headed.

robert
Robert Burnham is on a mission to understand how small parts like proteins fit into greater wholes, like the human body's immune system.

How a virus steals the show

Robert Burnham respects a virus for its ability to take over a host’s immune system.

“We can learn a lot about how our immune system works by studying how a virus evades it,” Burnham said. “A lot of what we know about the immune system has come from how pathogens like viruses evade, subvert, or hide from it.”

Viruses like herpes take over the body’s immune system by mimicking host proteins. Though researchers aren’t exactly sure how, often viruses make their own version of a host’s protein by using bits of DNA. Sometimes viruses get lucky and find specific proteins, called interferons, that are sent out by infected host cells to warn neighbors of the infection.

Burnham looks at large, double-stranded viruses that offer a lot to work with, he said. They allow him to study the structure and function of important proteins within host-pathogen interactions using highly efficient computational methods.

“The functionality of proteins is relevant because it teaches us the functionality of the virus,” said Burnham. “Once we see functions, we get clues as to where the protein came from and how it was captured.”

Doing what’s called protein refolding, Burnham attempts to make recombinant viral proteins to find further clues about how a virus fits within the immune system.

“I like the simplicity of viruses,” he said. “They only have a couple of dozen proteins, but at the same time they interact with extremely complex host systems that they are completely dependent on. For example, despite that fact that influenza only has 11 proteins and we have several thousand, the virus still works brilliantly at the host-immune response. All of our body’s complexity falls apart in the face of something so simple.”

Burnham recently graduated from Virginia Tech with a bachelor’s degree in biochemistry and a minor in Interdisciplinary Engineering and Science, which is part of the university’s Scieneering Program, bringing together science, engineering, and law.

He also jointly presented and won a poster award at the 2013 Virginia Tech Center for Drug Discovery symposium for a project related to his research in the Scieneering program.

In 2014, he received the Ann L. and John L. Hess travel award to attend the American Association of Immunologists conference in Pittsburg, PA and was selected as an outstanding senior in the Department of Biochemistry in Virginia Tech’s College of Science.

In the fall, Burnham will begin his Ph.D. in molecular genetics and microbiology at Duke University.

rebekah
Watch out, proteins. Rebekah Watkins has a plan for you.

Little bits may go a long way 

Rebekah Watkins’ experience taught her that sometimes it’s important to sweat the small stuff. In this case, that small stuff is irisin, a newly discovered hormone secreted by muscle tissue during exercise. Little is known about how, but it – as well as other proteins – may be key to fighting obesity and diabetes.

Working with Xu lab members Dr. Ling Wu, a research scientist, and Lu Zhai, a Ph.D. student, Watkins engineers different versions of irisin to figure out the important parts of its structure, and how altering it might change its function.

Another protein she works with is amylin, a small peptide hormone naturally released in the body along with insulin.

“Because more insulin is released in Type 2 diabetes, more amylin will be released as well,” said Watkins. “In the process, amylin forms toxic plaques in the pancreas, so it will actually start killing off cells. As a result, less insulin is produced, which may cause diabetics to need even more insulin.”

Watkins also works with Ph.D. student Paul Velander in an effort to inhibit amylin’s growth, as well as perfect techniques to study and produce it in the lab.

“Amylin is difficult to study because it is extremely small and misbehaves in solution,” Watkins said. “It tends to clump together and slide off the gel.”

Watkins is also writing a review paper on nanoparticles and natural compounds – matter produced by our bodies and other living organisms. Small particles, referred to as nanoparticles, that carry natural compounds into the body could be used to treat conditions like cancer, infectious diseases, and diabetes.  

“We’ve known that certain natural products have potential anti-cancer, anti-diabetes, and anti-inflammation abilities, but many of them are not soluble in water and would require us consume a lot each day,” said Watkins. “We’re hoping that getting these compounds into nanoparticles will increase the available amount in the body, which will mean consuming less for the same effect.” 

Watkins received the 2015 James Lewis Howe award from the Virginia Tech Biochemistry Blue Ridge Chapter of the American Chemical Society. In the fall, she will be a Ph.D. student in the Biological and Biomedical Sciences program at the University of North Carolina at Chapel Hill.

 

Bin Team 2
Xu and his team work closely to find the latest molecular knowledge. Great work, team Xu!

Posted June 19, 2015

By Cassandra Hockman, communications coordinator at Fralin

Q&A: Meet Robert

Hometown: 

South Riding, Virginia

Academic year, major: 

B.S. in Biochemistry

Fralin Advisor: 

Bin Xu

What attracts you to biochemistry?

I enjoy biochemistry because it provides a means by which to understand how life operates on a mechanistic level.  Gene expression screens or cell death assays are valuable sources of evidence, but nothing quite as satisfying as seeing the structure of an interesting protein bound to a key receptor and catching it in the act.

What interests you most about infectious disease, virology, or the structure and function of proteins?

I enjoy trying to understand how pathogens, despite their relative simplicity, manage to outwit a system that is vastly larger and more complex.  By understanding the structure and function of viral proteins and how they interact with the host proteome, the mechanisms of this subversion can be revealed, better described, or even counteracted through the development of therapeutics.

What is one of the most important skills you have learned by working in the Xu lab?

I have learned how to transform E. coli, recombinantly express, refold, purify, and crystalize protein, use computational prediction algorithms, and write and review papers and proposals.    

How has this research experience contributed to your undergraduate degree?

This research provided context for what I was learning in my major and helped me gain experience that is relevant for my future graduate studies.

Knowing what you do about applying to graduate school, what advice would you give to other undergraduates considering undergraduate research and/or graduate school?

I would recommend choosing undergraduate research projects or graduate program based on the skillset you want to learn.  While it is important to be a part of a research project you are interested in, the experimental techniques and procedures that you learn over the course of a project are ultimately what carry over to your next experience, be it graduate school or a career.

What do you do for fun outside of school?

I have rowed for the Virginia Tech crew team for the past four years.  I also enjoy hiking and weekly board game nights.

What will you miss about Blacksburg or Virginia Tech?

I’ll miss the excitement of home football games and being in the mountains.

 

Meet Rebekah

Hometown: 

Phoenix, AZ

Academic year, major: 

B.S. in Biochemistry and Nanoscience

Current research focus: 

protein chemistry, integration to nanoscience

Fralin Advisor: 

Bin Xu

What attracts you to biochemistry?

I enjoy biochemistry because the complexity of proteins fascinates me. The fact that 20 amino acids can come together and make up all the proteins and enzymes that allow something as complex as a human to live is amazing. I enjoy being able to study proteins because it helps me better understanding how to treat living organisms.

What interests you most about studying diabetes, drug synthesis, or the structure and function of proteins?

What interests me most about these areas is about how they all come together. In order to synthesis a drug, say for diabetes, a researcher needs to know the details of the disease, such as what proteins are affected and what could be a possible drug target. The researcher then needs to know what compounds can bind to what proteins and how that binding occurs. This depends on the structure of the protein

What is one of the most important skills you have learned by working in the Xu lab?

I think the most important skill I’ve learned is it’s okay to fail. As I have talked with graduate students, I have realized that research involves failing. My time doing research has had its ups and downs and Dr. Xu has taught me that the failures are just as important as the successes. I think this will be a beneficial lesson as I start graduate school.

How has this research experience contributed to your undergraduate degree?

I believe that research is something every undergraduate in science should do because it has allowed me to apply what I learned in the classroom. It is one thing to read a book, but to actually do the research and realize how hard it is and how much time it takes to get something simple to work. Research has given me an appreciation and understanding I could not get in the classroom.

Knowing what you do about applying to graduate school, what advice would you give to other undergraduates considering undergraduate research and/or graduate school?

I would say to start working on your statement of purpose early. Ask your research advisors/professors to edit your statement because they know what the admissions board expects to see. Finally choose a school that has options. You don’t know who has funding and what could change so its better to have too many options then not enough.

What do you do for fun outside of school?

I am an avid VT football and Philadelphia Flyers fan. I have attended every VT football game since my sophomore year, when I could get season tickets, and truly miss the game day atmosphere when spring comes around. I also enjoy watching movies on the weekend, some of my favorites being marvel movies.

What will you miss about Blacksburg or Virginia Tech?

I am going to miss being able to attend VT football games in the fall and the amazing professors at Virginia Tech. I am also going to miss the Virginia Tech atmosphere. The campus is beautiful and the Hokie stone buildings are unlike anything else.