Phage biology is enjoying a renaissance due to the recent realization of their role in bacterial pathogenicity, bacterial population dynamics and potential as therapeutic and diagnostic agents. Phage are remarkably genetically diverse however the amount of phage complete genome sequence in the data bases is less then that from an average bacterial genome. These entries are biased towards lambdoid phage with host specificity from either classic coliform bacteria or bacteria involved in industrial fermentation. Many dsDNA tailed phage have genomes of less then 100 kb. Current genome methodologies generated by the eukaryotic and bacterial genome mapping and sequencing projects have rendered sequence analysis of DNA fragments of this size routine. We are taking advantage of this standardized technology to introduce undergraduates in a classroom/lab situation to real data acquisition and genome analysis through the sequencing of novel phage genomes. We are focusing on new phage isolated from high organic content soil samples that infect plant- and animal- pathogenic genomovars of Burkholderia cepacia. With a 48 kb genome (our typical size), a 4 student team provides hypothetical 8 fold genome coverage. Students are instructed how to predict genes, utilize genomic and proteomic analysis tools and finally to determine the overall genome organization of their phage. The annotated sequences are submitted with the students listed as authors to the NCBI data base.
Here are some reasons for this:
We have had several projects run by talented undergraduate students based on this genomic sequence. Some of these are focused on analysis of the phage growth cycle and others are efforts to demonstrate experimentally the function of some of the phage genes.
Look for updates to this web site to see results of other experiments the students are undertaking.
Last modified: December 16 2005 18:50:13.