First years conduct research on bacteriophages

First-years interested in research have it rather easy now: They no longer need to go through the frustrating process of first figuring out which faculty member they want to work with, then trying to contact the faculty member, and after weeks of anticipation, receiving a response saying that upperclassmen have already filled all the undergraduate lab positions. Now, all that first-years need to do is sign up for 03-115, Phage Genomics Research, and they automatically get a chance to work on a nationwide research project with some of the brightest minds in the country.

The course is part of a project started by the Howard Hughes Medical Institute’s (HHMI) Science Education Alliance (SEA). According to a Carnegie Mellon press release, HHMI chose Carnegie Mellon’s department of biological sciences to be a part of the 12-member team of different universities that will be a part of this initiative.
The course has the students collect bacteriophages, which are typical viruses that attack bacteria, and analyze their structure and genome. The exciting part is that the students will also have the chance to be co-authors of a research paper if their findings are published in journals.

The popularity of the course is evident from the overwhelming response received from students currently enrolled. “I wanted to be involved in research or a lab somehow as a freshman, and this course seemed like the perfect way to do it,” said Lianne Cohen, a first-year in the Science and Humanities Scholars program.

For the students, being involved in a lab course during their first year is a great advantage, but this course is even more special as it is not like a typical biology lab course. As Antonio-Javier Lopez, an associate professor in the biological sciences department and also one of the instructors for the course, explained, unlike typical lab courses, the experiments in this course do not have any fixed results.

“There is a high expectation that we are going to find something really interesting, but we don’t know exactly what that is ahead of time,” Lopez said. The students will also have the chance to take decisions on what steps to perform next. “It’s really doing real science,” Lopez added.

Jonathan Jarvik, an associate professor in the biology department and an instructor for the course, said that one of the greatest advantages of this course is that it is not as hectic and intensive as the laboratory courses that students take in their junior year. “The intensity level in this course is much lower, [so] they have time to think about very basic aspects of biology. And that’s very good,” Jarvik said.

In the course, students isolate bacteriophages from soil samples, clone the DNA from these phages, and send the DNA samples for sequencing. This portion of the project was to be completed this semester. The students, however, are way ahead of schedule. “[Our goal this semester] was isolating 50 micrograms of DNA to send off for sequencing. We actually exceeded this goal by isolating approximately 300 micrograms,” said Stephanie Guerra, a first-year in the Science and Humanities Scholars program. Guerra also explained that the extra time and extra DNA that was isolated will now be used by the students for carrying out experiments of their own.

The project will continue next semester when the sequences of the DNA are sent back to the students. The students will then assemble these sequences and use bioinformatics techniques to analyze the sequences. The data that will be collected will be compared to the data collected by other participating institutions.

One of the goals of the course was to make a significant impact on phage research. “[The goal is] to learn about the biology, the ecology, and the evolution of bacteriophages and also to identify novel bacteriophages that infect mycobacteria,” Lopez said. He explained that this project was very important as diseases like tuberculosis were caused by mycobacteria. Finding phages that could destroy mycobacteria would thus provide a way to find cures for these diseases.

The second, and more important, goal was to encourage the students to get involved in research. From the feedback received, it seems that this goal, at least, has been achieved. “I didn’t really have much research experience before Carnegie Mellon, so being in this phage genomics course has helped introduce me to scientific research and has shown me how much I enjoy it,” Guerra said.

While the course has been enjoyable for the students, the faculty, too, have been having a great experience teaching the course. “[The best part is teaching] smart engaged students with a broad range of personalities,” Jarvik added.

HHMI has funded Carnegie Mellon for a period of three years. The project can be continued beyond this time frame as the number of phages that can be isolated is enormous. Lopez explained that Carnegie Mellon would probably continue the project after the three-year period to continue promoting research among undergraduate students.