There is a long list of learning objectives for the phage genomics course in which first-year undergraduates conduct hands-on research.
They learn how to purify and isolate novel bacteriophages — viruses that infect bacterial hosts — from soil samples.
The students learn how to characterize their individual phages — which are around 65 nanometers in diameter and can only be viewed using an electron microscope. The undergrads learn essential laboratory techniques, including microscopy, aseptic methods and comparative genomic analysis.
They learn how to analyze data and design unique experiments. And they learn to read and think like scientists.
But most importantly, the first-year UMaine students learn how to learn. Because without that knowledge, the rest is moot.
“It is not a sink-or-swim situation,” says Sally Molloy, assistant professor of genomics and co-instructor of the course. “We teach students how to learn so they can function in any learning situation in the future, whether that is in STEM fields or the humanities.”
The yearlong course is sponsored by the Howard Hughes Medical Institute (HHMI) and is part of a nationwide program called the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (PHAGES) research course.
The national program that started in 2008 now involves 70 campuses and 4,800 undergraduate researchers. To date, Molloy says nearly 100 UMaine students have completed the program.
UMaine’s course, BMB/HON 150/155, is a joint effort of the Honors College and the Department of Molecular and Biomedical Sciences. It is now required for all incoming and transfer students in the molecular and cellular biology program.
In the classroom, students try to figure out how their isolated virus is related to many of the others that have been isolated across the United States through HHMI’s program.
The procedures students learn to analyze phages closely resemble those used to understand more complex genomes, such as the human genome. By comparing their phage with others that infect the same host, students develop an understanding of the evolution of genomes.
Keith Hutchison, professor emeritus in the UMaine Department of Molecular and Biomedical Sciences, has been teaching the course since its inception five years ago.
“Before we had our first students, I went to a national meeting and I was listening to these students who had just completed their first year presenting their work. I remember thinking, ‘I wish my graduate students could talk this well,’” he says.
Hutchison is now amazed when he listens to the first-year students in his own classroom.
UMaine has pushed me to strive for excellence and has allowed me to pursue research that I never expected I would have the opportunity to do as a first-year student.”
“Many institutions don’t even have laboratories, let alone a laboratory like this. Often, before the students even get a job, they have to go on to get a master’s or a job working in a lab in order to get into graduate school,” Hutchison says. “Our students are prepared for that by the time they walk out of the classroom at the end of their first year.”
The microscopic phages the students isolate resemble tiny lunar landers that attack bacterial hosts of the species Mycobacterium smegmatis — nonpathogenic organisms found in soil, water and plants. Bacteriophages are consi-dered the most numerous biological entity on Earth. For every bacterium in the world, scientists estimate there are at least 10 phages that can attack it. This makes the phase an incredibly effective educational tool because the amount of scientific discovery available to students is seemingly endless, Molloy says.
Every phage that is isolated is unique.
“Incorporating fundamental research in the classroom is one way to motivate students to become more autonomous learners,” says Molloy. “Students cultivate an intrinsic curiosity that promotes independent learning and a desire for more research opportunities outside of the classroom.”
In addition, training on a transmission electron microscope (TEM) during a student’s first year is almost unheard of, says Kelly Edwards, lab technician for the Electron Microscopy Laboratory.
“The students may have some kind of picture in their mind of what this thing looks like. But when you put it in the TEM, you actually see the creature that you have isolated and grown up and purified. It’s really exciting for the students,” Edwards says.
The information that students gather helps them classify what type of virus they have isolated, which goes into HHMI’s national database.
“It’s a big deal,” she says.
At the end of the first semester, UMaine students select one DNA sample from the isolated phages to get sequenced, which provides the precise order of nucleotides in a DNA molecule. Only one sample is chosen because the process costs around $1,500, which is covered by HHMI.
When students return for the spring semester, they conduct independent research projects using computer-based analyses to understand the biology of their individual phages and the structure of its genome.
At the end of the year, students make a similar decision about who will represent the class at the national meeting at HHMI headquarters in Virginia.
Ethan Thibault, an honors student from Colchester, Vermont who is double majoring in microbiology, and molecular and cellular biology, was one of two students selected in spring 2015 to present at the national phage conference.
“Not only did we get to perform research beyond most freshmen experiences, we gained practice writing manuscripts, and reading and analyzing scientific journal articles,” says Thibault, who plans to pursue graduate studies after he graduates in 2018.
“I learned how to be a researcher and skills that will help me for the rest of my scientific career,” he says.
Because of those skills, Thibault was accepted to a National Science Foundation Research Experience for Undergraduates, which included a paid internship at South Dakota State University, working with salinity tolerance of prairie cordgrass.
“UMaine has pushed me to strive for excellence and has allowed me to pursue research that I never expected I would have the opportunity to do as a first-year student,” says Thibault.
Max Dorman of Keene, New Hampshire, a molecular and cellular biology major in the Honors College, also presented his research at HHMI’s national meeting in 2015, alongside Thibault.
“To me, the phage course was what every course should be like,” Dorman says. “There was full-group discussion; there was debate; there was learning; there were experiments.”
A life-changing skill that Dorman learned in the course was how to develop a growth mind-set. In order to do that, he says, you must “embrace failure as a part of the learning process.”
It’s a skill that Molloy hopes all her students take from her class because, in science, the answer is not always apparent.
“That’s the biggest part of this course — teaching students how to learn, how to apply information to new problems, and to tackle things that would at first seem impossible,” she says.Back to top