February 7, 2011
A course freshmen can dig into
Two dozen Johns Hopkins freshmen will get their hands dirty next fall, scratching in the soil of the Homewood campus in search of undiscovered organisms as part of an innovative one-year course offered through the Howard Hughes Medical Institute’s Science Education Alliance.
Johns Hopkins recently became one of only 12 colleges and universities nationwide in the newest cohort selected by the Chevy Chase, Md.–based HHMI to offer this National Genomics Research Initiative course, which lasts one academic year and gives students the opportunity to perform hands on research that includes extracting phages—viruses that infect bacteria—from soil samples and using sophisticated bioinformatics tools to analyze them. The program will be offered for three years.
“We’re very excited about being chosen to offer this course, which introduces students to laboratory research,” said Joel Schildbach, professor and director of undergraduate studies for the Krieger School of Arts and Sciences’ Department of Biology. Schildbach and Emily Fisher, an instructor in the Biology Department, will direct the SEA program. “Students in this course will experience the excitement that comes with discovering things for themselves,” Schildbach said.
Other institutions recently selected include Brown University, The Ohio State University and the University of Florida.
Since 2008, almost 1,700 students have spent a year gathering these dirt-dwelling organisms from the soil of 40 different colleges and universities nationwide. In the process, these young scientists have collectively isolated 1,400
different strains of phages and analyzed dozens of their DNA sequences. These phage genomes have been submitted to the National GenBank database, produced and maintained by the National Center for Biotechnology Information. The genomes then become available to anyone who wishes to study them.
At Johns Hopkins, the new course will count toward students’ general biology laboratory, research or distribution requirements and will be open to freshmen regardless of intended major, according to Schildbach.
“Naturally, I would expect students interested in the biological sciences to be attracted to this course, but I am hoping it will also bring in students who are planning to major in Writing Seminars or art history or sociology or international relations,” he said. “Students in this lab course will be spending a lot of time together and learning as much from each other as they will from their instructors and teaching assistants. A diverse group will make it that much more interesting.”
During the fall semester, the students will collect soil samples from wooded and leafy areas around campus and then, in the laboratory, isolate “significant amounts” of the phages and purify their DNA. The class will then select one of the phages to have its genome sequenced, Schildbach said.
During winter break, scientists at one of several research centers across the country will do the sequencing work. According to Schildbach, the fact that there are innumerable strains of phages greatly increases the odds that the students will each discover a previously unknown phage. If they do, the students will be allowed to name them.
In the spring semester, participants will use modern bioinformatics tools to analyze and annotate the phage’s genome before comparing it against the larger phage database.
“Our goal with this course is to get students into a lab setting so that they can learn basic lab skills, learn how to manage their time and complete a long-term project and learn to read and analyze primary literature,” Schildbach said. “They will also have to regularly present their findings to their peers. In short, we want to introduce them to one way that science is done.”
In addition, the course allows Johns Hopkins students to join a community that includes students at the other colleges offering the SEA program. These students will interact electronically, and each year one student from each college will be selected to travel to an annual symposium held in June to present the results of his or her group.
“Though there is a possibility that all students who are in this course will become enthralled by biological research and end up in graduate biology programs, that certainly isn’t our goal,” Schildbach said. “The hope is that the students will be intellectually engaged, gain some skills and take control of their education, whatever their chosen fields.”