Rationale: 

The purpose of today’s lab was to come up with 4 testable scientific questions that could be tested for our independent projects.

Tools:

• Canvas Module with phage genomics research topics
• Laptop

Procedure:

• Group met up and began discussing several project ideas and different research possibilities.
• Asked research mentor for thoughts on different project ideas, and which would possibly offer the best research.
• Ranked each question 1-4, 1 being the best question, 4 being the least preferred question.

Results:

Research Questions:

• NapoleonB has both a holin and an endolysin gene, but other phages in the AM cluster do not have this (or people simply did not call it). Bioinformatic tools could be used to compare holin protein structure and the mechanism behind the interactions with the bacterial cell walls.
• Random Reverse gene (no coding potential, was called)
  • Is gene 2 an actual gene even if it has no coding potential? If so, why?
  • Are there other random reverse genes in other phage genomes that were called and break the guiding principles of gene annotation? (maybe phylogenetic tree to suggest any relationships?)
• Why does NapoleonB have multiple tail proteins? How does that compare to other phages?

Conclusions:

It was chosen to rank the question regarding the holin and endolysin proteins, mostly due to the fact that it was a question that posed both a level of difficulty that would challenge the group and it was different from the rest of the class. It also presented an opportunity to do a more in depth analysis of the essential functions of a lytic bacteriophage.

Next Steps:

The next steps for this project are to begin with researching the literature behind this question.