Phagehunter Lab Has Undergraduates Searching for Tuberculosis Cure

Field of bacteriophage plaques. A bacteriophage, or phage, is a virus that infects a bacterium and reproduces inside it killing the bacterium, then infecting those around it. Ultimately such infections spread to give clear areas in a lawn of bacteria

I've learned that in the research process there are no right or wrong answers. Things happen during the lab that make us question our methods, our knowledge, and ourselves. Out of those surprises come some blessings and some tragic failures, but through all of it, we are learning more about the process of “doing science.” –Brittany Truscott, sophomore, biology major

This is a unique lab course. While other labs are sometimes controlled and scripted, in this lab we view ourselves as real scientists doing real research. You have to put in a lot of extra work and effort to succeed, but it’s also fun and rewarding. I'm looking forward to continuing my research and learning more. –Andre Johnson, sophomore, biology major

The results you expect are not necessarily the results you get. Several times throughout the semester, we got results that were completely unexpected. We never knew exactly what would happen next—we were venturing into uncharted waters. No one at Penn State has done what we started. –Elisabet Bjanes, sophomore, double major in immunology & infectious diseases and toxicology

These undergraduate students are participating in a new biology lab course, BIO 220W: Biology Populations and Communities, which gives them the opportunity to do pioneering, real-world research. The course, funded by a grant from Howard Hughes Medical Institute (HHMI), is part of a multi-university effort (more than 60 universities are involved) to bring true research into the undergraduate classroom. Graham Thomas, associate professor of biology and of biochemistry and molecular biology, organized and taught the lab this past spring, and the lab will continue for the fall 2011 semester. Nicknamed the Phagehunter Lab, its focus is to search for an alternative therapy for multidrug-resistant tuberculosis.

Tuberculosis, or TB, is an infectious bacterial disease caused by Mycobacterium tuberculosis, which most commonly affects the lungs. According to the World Health Organization and the Centers for Disease Control, about two billion people worldwide carry the latent form of TB, nine million are symptomatic each year, and two million die annually from TB. Although the disease is treatable with antibiotics, multi-drug resistant strains of M. tuberculosis continue to crop up.

As an alternative to antibiotics, researchers have been exploring the use of viruses called bacteriophage to infect and kill bacteria. Bacteriophage were discovered around 1915, and they were developed for therapeutic use until antibiotics came along and displaced them. Since bacteriophage work differently than antibiotics to kill bacteria, scientists believe they have potential for treating multidrug-resistant strains of TB. 
 
“Bacteriophage are the most common life form on the planet,” explains Thomas. “There are a billion-trillion times as many bacteriophage as there are people. So the first thing we did was to send the students out to collect soil and water samples, and since bacteriophage are everywhere, the students were guaranteed to find some.”

Electron micrograph imaged by Audra Kelly who participated in the Phagehunter lab this year. The scale bar indicates a distance of 200 nanometers (a billionth of a meter).

From their samples, collected throughout campus and surrounding areas, the students isolated bacteriophage that infects Mycobacterium smegmatis, a non-pathogenic bacterium that is closely related to M. tuberculosis. Bacteriophage often infects multiple strains of bacteria, Thomas explains, “and we hope the ones that infect the smegmatis strain can also infect the TB strain. Using a non-pathogenic strain is a safety issue, and in any case, to work with the actual tuberculosis pathogen we’d need all sorts of elaborate containment and safety procedures that are not possible in an undergraduate lab. It’s also a practical issue because the TB strain grows very slowly, and we need to get results on a weekly basis. With the smegmatis strain we can get results in two or three days, whereas the TB strain takes a couple of weeks to produce results.”

Once the students isolated the bacteriophage, they examined it using electron microscopy, then purified its DNA. These procedures allowed students to “type” the bacteriophage. Students also used a wiki site created by HHMI’s Science Education Alliance (SEA), where they posted pictures of their phage and discussed problems and successes.

Some students were surprised at the time commitment required. “About halfway through the semester, many of us started coming into the lab on extra days, just so we could keep on schedule with the purification processes,” says Elisabet Bjanes. “But it’s all been worth it. I feel a strong sense of accomplishment and purpose because I know my work is important and could make a difference in the treatment of tuberculosis.”

Over the summer, the genome of each phage is being sequenced on campus, and when students return in the fall they’ll further characterize various aspects of their strains and annotate the genomes. On the SEA wiki site, they’ll use custom software to analyze and compare their genome sequences with those of others across the country.

“It was really exciting to use the electron microscope and having our own phage to isolate and name,” says Brittany Truscott. “I’m looking to seeing my phage's own unique DNA sequence.”

“It was really exciting to use the electron microscope and having our own phage to isolate and name,” says Brittany Truscott. “I’m looking to seeing my phage's own unique DNA sequence.”

Courses like the Phagehunter Lab are designed to convey to students the nature of real research. “We’re concerned that too many undergraduate labs are ‘cookie cutter’ models,” Thomas says. “They are formulaic and constrained, and we can predict the outcomes. In real-world research, you start with a hypothesis and you use techniques and protocols to answer the question you’ve proposed. Along the way, a lot happens. Things can go wrong, you get distracted by some interesting results that turn out to be irrelevant, questions lead to more questions, and sometimes the way you planned to do it just doesn’t work. It takes persistence and self-motivation, and it requires an understanding that you might have to put some ideas aside and get back to them.”

Thomas and his colleagues want to introduce real-world research into more science core courses, and they hope courses such as the Phagehunter Lab will serve as a model for the future of science education. “Even though many of these students won’t become research biologists, they will be reading science stories in the news, and they’re going to have a greater understanding of the research process and its challenges,” Thomas says. “And a better appreciation of the research process improves the scientific literacy of the general population.”

Additional credits:

The original concept for the Phagehunter Lab was developed at the University of Pittsburgh by Graham Hatfull, an investigator for Howard Hughes Medical Institute (HHMI), and has been promulgated by the Science Education Alliance at HHMI (hhmi.org/grants/sea/)

Richard Cyr, professor of biology and head of the Biology Department’s undergraduate curriculum, was the recipient of the HHMI grant.

Carl Sillman, senior lecturer in biochemistry and molecular biology, and Beth Shapiro, assistant professor of biology, will help teach the Phagehunter Lab during the fall 2011 semester.

CONTACTS

Krista Weidner: 814-234-8839, krista@kristaweidner.com

Graham Thomas: 814-863-0716, gxt5@psu.edu

Tara Carson: 814-867-3388, tlc26@psu.edu