By Sahini Pothireddy
Despite the fact that the focus of my first blog has been mostly on the practical aspects of this course (getting accustomed to research and understanding how important it is, practicing with the scientific instruments, and learning about the nature of bacteriophages), part of the appeal of this class also has to do with the actual phage hunting and identifying the phage that we found from a community garden.
There was a slight adrenaline rush every time I came to the lab, and it only became more intense when we started prepping the DNA . First time around, the phage’s, Hoodwinker’s, DNA was prepped, it was a little bit of a failure. The concentration of the DNA, which was measured using the Nanodrop, was way too low; it was 19 ng/uL, whereas the average was expected to be in the 100 – 200ng/uL range. However, when the DNA was prepped again, the concentration was 195.3ng/uL! But both DNA samples were run on the QC gel, and the gel did not have any smearing and only showed one clear band proving that the DNA was pure and was prepped accurately.
After that, I was ecstatic – everything was almost done; all I had left was running the digest gel. I finally was able to catch up with everyone and reach all the benchmarks. But that was presumptuous. The gel that Hoodwinker’s reaction samples were put in had slight disturbances; including the ladder, none of the solution in the wells formed clear, distinct bands. As such, unfortunately, the pattern that Hoodwinker’s DNA made could not be identified, and consequently, could not be compared to other patterns to determine the type of mycobacteriophage that Hoodwinker is. Although, on the bright side, due to the pictures taken by the electron microscopy, I was able to identify Hoodwinker as a myoviridae. Even though, this is common type of phage, Hoodwinker was a little bit unique in the fact that its tails were relatively short – they were on average 200 nm in length – compared to its heads.