Phage Genomics for Undergraduates (PGU) is a signature pedagogical effort of the Center for Phage Technology. The key experience is simple in concept: an undergraduate student gets to do real creative research by doing the complete annotation of a novel phage genome and publishing this research in a real academic journal. This is done in the context of an upper-level 3 credit course, BICH464 Phage Genomics, where lectures give the student an intensive introduction into phage biology as well as in the bioinformatic techniques required for the de novo annotation and laboratory periods give hands-on experience with isolation, propagation, characterization and electron-microscopic imaging of phages from the environment. In addition, the PGU features an assortment of “491” research experiences available in the laboratories of the faculty of the Center for Phage Technology, where the BICH464 experience can be leveraged as a basis for further independent projects, both basic and applied.
History of the PGU
The PGU dates back to the 1999-2000 academic year, with a pilot group of undergraduates, fondly designated as the “G-nomes”. At the time, the total amount of known phage genomic sequence was much less than that of a single bacterial genome, despite the already-known preponderance of genome diversity resident in the biosphere’s phages. We were initially led into phage genomics because of our long-standing interest in phage lysis genes (refs), where we discovered that phage “lysis casssettes”, or clusters of lysis genes, were highly mosaic. That is, although each cassette had to provide the same four or five functions to accomplish host lysis, each particular function could be fulfilled by multiple unrelated genes. Because these genes were small (typically 50 – 200 codons), and phages and phage DNA were relatively straightforward to isolate, we thought that sequencing phages might be a great inspirational activity for senior undergraduates who were considering graduate school. Because our university requires biochemistry, genetics and molecular biology majors to do real laboratory research (designated as “491” research), we had a large pool of students with a solid background in basic science who could be drawn on for phage sequencing projects. The pilot program, which we called Practical Genomics, assigned one phage to each team of 3-4 students and was structured as a lecture/lab course with one lecture a week focused on basic phage biology and sequencing technology, and then 2-3 laboratory sessions where a library of the phage DNA was prepared, processed by “Big Dye” sequencing reactions and sent off for analysis on an ABI DNA sequencer. At the end of the semester, besides taking exams on the elements of phage biology and the biochemistry and elementary bioinformatics of DNA sequencing, the students assembled the raw sequence data manually, using Sequencher, and then attempted to at least partically annotate the genome during the last week.
Besides technical development, the pilot program revealed that the concept of “owning” a complete, novel phage genome, as opposed to a tiny fraction of a bacterial or eukaryotic genome, was a powerful motivator for the subject undergraduates. Frankly, the structure of the original program was much more oriented to the basics of phage biology and the technical issues of cloning and dideoxy sequencing, which made the genome processing at the end of the semester more like a last-minute lab report, corresponding to only a fraction of the course grade. Nevertheless, we discovered that the G-nomes were absolutely captivated by this last step, as they watched “their” phage genome gradually assemble and get populated with the genes that they had been hearing about during lecture. It was not unusual to find that the students had been huddled around the computer all night, despite the fact that they were facing final exams in other courses.
Between 2000 and the present, the phage genomics program has been supported by three National Science Foundation grants, which provided the resources for undertaking several thematic and organizational changes. The course evolved out of its BICH489 Special Topics classification, where all new undergraduate course offerings start, and became an official numbered offering of the Biochemistry program in 2008. The biggest substantive change, derived from the impact of “Next Generation Sequencing”, is that now the actual sequencing has been completely removed from the student experience, as it has in real world science where genome sequencing is entirely commercial. The BICH464 student now performs all of the steps, including taking samples from the environment, identifying phages by plaque formation on a designated host, purification of phage particles and DNA, testing the DNA by restriction enzyme analysis, EM imaging, plus analysis and annotation of a complete genome. You can take a closer look at BICH464 here.
It is important to note that our PGU program antedates the very successful HHMI PHAGES program, which was launched in 2008. We were contacted by the HHMI development staff in 2007 and participated in meetings that prefigured the PHAGES program. However, the PHAGES system is focused on participation of freshman-level students, giving them their first exposure to science. In contrast, we have deliberately pitched our Phage Genomics for Undergraduates to junior and senior students who have had basic molecular biology and microbiology and are in a phase where they are deciding whether or not to pursue a career that would involve graduate school. We deliberately make the academic segment on the essentials of phage biology a very intense experience that would be completely inappropriate for early year underclass students. During recruitment and during the first week of class, the students are advised that, although the course is officially only 3 hours, the volume and sophistication of the information plus the demands for systematic thinking in annotation of the genome will consume the majority of their time, serving in a sense as a simulation of an immersive graduate school experience.