To Michael D.P. Boyle, it’s an ideal arrangement: A group of professors who teach genetics at liberal-arts colleges band together and bundle genome-sequencing requests to fit into one or two runs on a nearby university’s pricey, up-to-the-minute equipment. They find someone else to pick up the tab—$20,000, which is about half what it would cost to run all of their requests individually, but still beyond what most of their institutions could afford. Then they take the resulting data back to their classrooms and use it to get undergraduates excited about learning biology.
Mr. Boyle, a professor of biomedical sciences at Juniata College here, says the point of his pilot project—which the National Science Foundation is supporting with $49,449 this year—is that undergraduates are far more likely to be engaged by real-life research problems than by canned exercises, which he refers to as busywork. The professors he’s collected for the genome-sequencing project include a Hood College faculty member hoping to sort out different populations of cownose rays that migrate into the Chesapeake Bay every summer, and a Susquehanna University biology professor investigating whether a coal-mine fire that’s been burning under Centralia, Pa., since 1962 has created species of bacteria that might have properties useful in making drugs. All of the professors will work with undergraduates on the data they get back—a requirement for joining the project.
“We anticipate that we will get published papers out of this, but our goal is to translate the passion for research to the next generation,” Mr. Boyle says. “We wanted to make data from next-generation sequencing available so undergraduates can play with it like the big-time folks.”
If all goes smoothly, Mr. Boyle envisions that groups of faculty members around the country could pool sequencing requests and send them to the nearest university genome facility—which they might also be able to visit with their students. Federal agencies that finance the genome facilities, he adds, might even require them to do one free run a year to benefit undergraduate education.
The project here is one of two closely related efforts to put the latest genomics technology into the hands of students at liberal-arts colleges. The other project, which is less costly and is already a year old, is creating a catalog of standardized DNA components available to faculty members working to assemble new biological systems.
Both projects, says Deborah E. Allen, the NSF grant manager who worked with them, aim to “capture authentic research experiences within biology courses” at the undergraduate level.
In recent years, Ms. Allen says, the science foundation has been more and more impressed by the value of undergraduates’ getting involved in faculty members’ research and having professors as mentors. But only a limited number of students can actually work alongside their professors at any given time. The hope is that a project like Mr. Boyle’s can bring some of the same benefits to a larger number of students.
Mr. Boyle may be exaggerating slightly when he says that a single genome-sequencing run can provide enough raw data for several faculty members to work on for a decade, but the amount of information the researchers get back is prodigious—"megs and megs of data,” says the Susquehanna professor, Tammy C. Tobin, whose sequencing request was selected for a recent test run at the Genomics Core Facility at Pennsylvania State University’s main campus, about half an hour north of Juniata.
“My research students will immediately start playing with this data this fall,” she says. She’ll also use the information in her introductory genetics course, in which students will sort through data she would never have enough time to look at by herself.
Communal Benefit
Mr. Boyle’s project is a direct descendant of a project that a Davidson College biology professor, A. Malcolm Campbell, has been running for a decade. In Mr. Campbell’s project, called the Genome Consortium for Active Teaching, or GCAT, faculty members who teach undergraduates request chips for genome sequencing, prepare them with the DNA to be studied, and send them to one of five colleges for scanning. The data are posted online, at a cost to the faculty members of less than $100 per scan.
The GCAT program—the initials are the same as those of the four bases in DNA—has been supported by the science foundation and the Howard Hughes Medical Institute, among others. It has benefited about 400 faculty members and 24,000 undergraduates, Mr. Campbell says.
Besides making data available for undergraduates’ use at a low cost, the program has united professors who teach genetics through its e-mail list and its conferences. “There’s a benefit of working in a community,” Mr. Campbell says. In many cases, “you’re the only one doing this on your campus, and it’s always so much easier to have a network of people so that when you get in a jam you can send out an e-mail.”
“Because of GCAT, there are undergrads who are co-authors on real scientific peer-reviewed papers,” he adds. “Undergraduates can do more than people give them credit for. They’re keen to do something challenging.” Many students who have worked with GCAT data have gone on to graduate school, he says.
But now the chip-based microarrays that the original GCAT program uses have become outmoded, and manufacturers have stopped producing the chips. Mr. Campbell is still taking requests for the limited assortment of chips that are still available—some faculty members are requesting two- and three-year supplies—but he’s moving on to synthetic biology—essentially, assembling DNA for specific purposes out of standardized parts.
He created GCAT-SynBio as a home base for the synthetic-biology project, in which participating faculty members contribute vials of frozen DNA building blocks, each with particular attributes, to common stockpiles from which others can draw as needed to build whatever they’re working on.
Mr. Campbell also welcomed Mr. Boyle’s effort, dubbed GCAT-SEEK, to carrying genome sequencing for undergraduates to a new technological level. Besides Hood, Juniata, and Susquehanna, the pilot project involves Gettysburg, Lycoming, and Mount Aloysius Colleges, Ramapo College of New Jersey, and Bucknell, Duquesne, Hampton, Lock Haven, and Morgan State Universities.
The savings from bundling sequencing work are significant. Deborah Grove, director of genetic analysis at the genomics facility at Penn State, says the nine requests selected for the pilot program would have cost $4,000 to $5,000 each—about $40,000 total. By combining them into three sequencing runs, she can do the work for $20,000.
“Normally I couldn’t afford to get the genome of a new bacteria sequenced,” says Ms. Tobin, of Susquehanna. “That data can go straight into the classroom.” Her interest in the bacteria near the underground fire, she says, stems from the changes it has brought to soils nearby, which have been heated and suffused with gases containing dissolved chemicals.
“Bacteria make antibiotics to kill off competition,” she says. “Theoretically these bacteria should be making antibiotics that aren’t sensitive to the heat.”
The goal, she says, is to find out whether the bacteria have come up with tricks that could be used to make antibiotics that don’t need refrigeration—a big benefit to doctors in developing countries. “Students can be looking for information that could make a real difference,” she says.