VCU news

By Sathya Achia Abraham

A class of 18 energetic, aspiring biologists at Virginia Commonwealth University kicked off the new semester getting reacquainted with several old friends — Shi-Lan, Turbido, Cornelius, SmurfKing, Theia, Trixie, Zeus, Wile and Charlie.

Those creative names belong to a unique set of organisms — bacterial viruses called bacteriophage, or phage — collected and identified by the freshman class from soil samples found in Richmond, Northern Virginia and Chesapeake during the fall semester.

Given the diversity of phage — each one is almost certain to be distinctive — the students had the opportunity to name their newly identified life form. They wrapped up the fall term purifying and characterizing their phage and extracting its DNA.

For the majority of these students, the experience is their first glimpse into scientific discovery, and a chance to be involved with a scientific investigation — creating hypotheses, carrying out experimental procedures and techniques, documenting their observations and eventually, reporting their findings.

The students in the class are contributing to a nationwide genomics research study sponsored by the Howard Hughes Medical Institute Science Education Alliance. The exploratory lab experience allows the VCU group, along with students at 40 institutions across the country, the opportunity to engage in hands-on research.

The project, known as the National Genomics Research Initiative, is a two-part, yearlong research course designed to enable students to contribute to research and to help prepare them for careers in science.

“Throughout the Phage Discovery Lab we were challenged to think like scientists while learning the process of doing science. Just like real scientists, we had a budget to keep and deadlines to meet,” explained Ross Campbell, a sophomore majoring in chemistry, of the first semester wet lab.

“We experienced setbacks and had to make challenging decisions to deal with them. We read and discussed challenging publications and learned invaluable laboratory techniques,” he said. “Throughout this course, we were presented with challenges and opportunities unavailable in a typical freshman biology lab.”

This semester, as Campbell and his classmates move through the second half of the Phage Discovery Lab, they will get to know their viruses from the inside out – literally. By unraveling its DNA and using a series of computer-based analysis — something like a science video game – they’ll look at the phage’s genome and determine what its genes do to further understand its biology.

“The goal here is to have our students be like scientists — think like scientists. Phage lab is a research-based teaching lab with the goal of giving students a realistic experience of being a scientist,” said Allison Johnson, Ph.D., an assistant professor and assistant director of the VCU Center for the Study of Biological Complexity. She is co-instructor for the program. VCU Life Sciences and the Department of Biology jointly supported the implementation of this course at VCU.

“The students learn science through discovery and characterization of a novel bacteriophage,” she said. “The discovery aspect is motivating and engaging to students - they take real ownership of the project. It is also a lot more fun for us to teach.”

According to Johnson, between the fall and spring terms, the purified DNA of nine VCU phages and 16 phages from other schools participating in the program were sequenced using high-throughput genomic technology at the VCU Nucleic Acids Research Facility. The next-generation sequencing equipment available at the center reduces the amount of time it takes to sequence a genome.

The students this week received files containing their phage’s DNA sequence.

“Just like all researchers, our students will take the data they’ve worked so hard to collect over the last four months and analyze their results,” said Anneke Padolina, Ph.D., an instructor in the VCU Department of Biology who has been co-teaching the program with Johnson.

“Hopefully, they will be able to make connections between the phage’s physical characteristics that they saw in the lab and the phage’s genes. We’ve already seen that some of our phage genomes are very unique in comparison to anything that is currently published,” she said.

During the course of the semester the students will complete an electronic notebook based on their lab experience, write a report and give a presentation on their phage. The students also will participate in the VCU Undergraduate Research Festival to be held at the end of April. One VCU student will be selected to present what the class has accomplished to HHMI at the end of the term.

For Sarah Williamson, a pre-nursing major, her introduction to Phage Lab was a welcome experience — a class she considered fun among the list in her course load.

“Being involved with real research was exciting and informative. In the class we were able to form our own hypotheses and encouraged to test and present the hypotheses to the class,” she said. “I loved the independence the class provided, yet the teachers were there in case we had questions or needed help.”