After 8 weeks of annotating our dear little Manatee’s genome and working incessantly on our computers we finally get to welcome back our beloved wet lab! Don’t get me wrong, I thought annotating the genome was an amazing experience and something few of us are lucky enough to get the chance to do, and I have learned so much more than I ever thought I would in this class. But I feel like I can speak for most of my fellow “phage lab mates” that what we all really love is the practical, hands-on work that our lab provides with the countless experiments we can do.
And this time it gets even better… we get to design our own experiment! It was hard to choose at first, but I knew one thing: that I wanted to once again work on my very own phage from last semester, Bwunder. It’s not everyday we get to name something, much less a virus, so I want to find out as much as I can about mine. In the end I decided to work alongside John, and we’re going to try to find out which phage cluster our little phages belong to.
Phages are grouped with those that are most closely related to each other, and these are called clusters (some even have sub-clusters). What we plan on doing is discovering which specific one our phages belong to. There are 16 different cluster primers available, and what we will be doing in the next couple of weeks is using the PCR (Polymerase Chain Reaction – which makes a huge number of copies of a gene) and “replicate” our phages DNA with each different primer – more specifically, one should work. We will then run them with gel electrophoresis and hope to get 15 failed reactions and one positive – which will be our cluster! Obviously there are chances of this not working, as they could belong to a different cluster or subcluster entirely or our DNA is not good enough, but hopefully we won’t have to worry about that.
We will also take it one step further. My phage came from an enrichment, and my lab partner Ben’s phage, AverageJoe, came from that very same one. John has a similar case, as his phage, BugSlayer, came from Peter’s enrichment, which also yielded his phage, Boss. We will therefore carry out the same procedure on their phages so as to determine if our enrichments isolated two genetically similar phages (if both phages belong to the same clusters) or two phages that are totally different. We will then re-do the experiments to verify our results.
Hopefully all will go well with our experiments, but regardless I am happy to be back in the lab and excited to find out more about our phages. Everybody is now working on their own experiments, and it will be very interesting to see all the different results and new things we discover. And as for me, I hope to end this semester knowing exactly what cluster my little phage belongs to!