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The Course
The genomics course selected as the prototype will be run at the University of Pittsburgh under the direction of Graham Hatfull, HHMI professor and originator of the Phage Hunters, a successful undergraduate research program from which a high school outreach program has been developed. The course that represents SEA's initiative is truly a research experience: hands-on discovery where the scientists, who are novice undergraduates, literally learn by doing. The result will be minimal lecture time and enhanced critical-thinking and communication skills.
The course will run for two consecutive semesters. In the fall semester, students will isolate bacteriophages from local soil samples, purify them, perform electron microscopy, and isolate the viruses' DNA. During winter break, DNA samples will be sent to the Joint Genome Institute in Walnut Creek, California, to be sequenced. In the spring semester, students will download their sequence information from the Internet, annotate their selected phage genome (that is, identify the genes and other structures present), and compare their genome to other phage genomes. All participants will share their discoveries, ideas, and challenges via an Internet-based communication network.
“We hope the students will get a sense of how in today's world, science is a true collaborative effort,” says Tuajuanda Jordan, director of SEA. “When the students get their tubes of soil, it may mean nothing initially.” Eventually, they will see plaques of phages growing on bacteria and the shape of the phage by electron microscopy, and get to name the new discovery. “They will truly be contributing to the scientific knowledge about this phage, more and more questions will arise in their minds, and hopefully it will capture their scientific curiosity enough that they will want to pursue research as soon as they leave this class,” she says.
Fall Semester
In the fall semester, students will learn the concepts and procedures for:
- extracting bacteriophages from a local soil sample;
- purifying bacteriophages by plating and growing on a lawn of bacteria;
- further purifying a single bacteriophage by picking plaques and making a concentrated stock;
- isolating the bacteriophage DNA;
- preparing the bacteriophage DNA for sequencing and learning how sequencing is done;
- digesting a sample of bacteriophage DNA with restriction enzymes and analyzing the fragments by electrophoresis and comparing fragment pattern to other samples;
- preparing a bacteriophage sample for electron microscopy;
- characterizing the bacteriophage type/structure from electron micrographs.
Winter Break
The samples will be mailed to the Joint Genome Institute in Walnut Creek, California, for sequencing. JGI will post data onto the SEA server.
Spring Semester
In the spring semester, students will learn the concepts and procedures for:
- annotating segments of the genome to identify open reading frames, genes, and regulatory sequences;
- comparing this bacteriophage genome to other sequenced bacteriophage genomes;
- comparing and analyzing the amino acid sequence to reveal relationships between species;
- using Web-based tools and software programs for these activities;
- following up any unusual features that emerge, such as genes transferred from the host bacterial genome to the phage genome;
- writing and presenting scientific results.
Online Networking
While the course is running, all students, faculty, and SEA staff will be connected via the Internet so that data can be shared and compared, troubleshooting questions can be asked, advice can be given, and discussions can occur in near real-time.
Final Report
Each class will write a final report that will include the methods and protocols used, results, and discussion of what the results mean. The final report will also include the finished sequence information, which will be proofed by the professor and an outside expert. This sequence information will eventually be deposited into GenBank. All final reports will be sent to the lead scientist for this particular initiative, Graham Hatfull at the University of Pittsburgh, who, with help from other SEA faculty, will develop the appropriate manuscript(s) of SEA's bacteriophage genome findings.
Annual Symposium
During the last half of the spring semester, HHMI will host a research symposium for SEA participants. Faculty members and one student from each class will attend to present their class results to the SEA community. The symposium will also feature prominent researchers speaking about the latest genomic breakthroughs.
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