Spring Phage Lab: From Annotating to Experimenting

By Jessica Bauer

I can honestly say that this semester of Phage lab was not what I expected. Coming back from winter break, I was excited to start looking at the genome and doing whatever “annotating” entailed. I was not sure exactly what we would be doing, but I assumed it would be just as interesting and fun as being in lab was last semester. I may have been slightly disappointed. Don’t get me wrong, I liked debating start codons and staring at coding potentials just as much as everyone else, but it got boring after the 5oth or so gene. Finding SD scores, ORFs, and blast hits got really repetitive and did not have the same excitement that being in a lab and waiting for a surprising turn of events to happen gave me. Thankfully, all this annotating is mostly done though and we can finally get back to lab! Yay! I will say though that one thing I liked about annotating was how smart it made me feel to explain to someone else not in the class what I was doing. Just throwing around words like Shine Delgarno scores, ORFs, coding potential, and BLAST hits left so many of my friends with blank stares on their faces and made me feel like some mad scientific genius who does cool things like annotate a genome. Luckily they didn’t figure out how little I actually knew about what I was talking about.

Annotating is done, though, and finally we can all return to our lab benches, put on our favorite white coats, and start doing whatever we want to our phages. One thing about this semester that I am starting to really enjoy is all the different projects people are doing. We are no longer all streaking and plating and diluting, we have a wide array of topics and experiments to do. I personally have decided to do experiments testing how my phage responds to changes in pH. I figured being from Ohio, my phage is used to changing environments since weather in my town can move from spring to fall to winter to summer all in the same week. Going into lab last week I was a little worried since I was not sure on all the details of my project, but I just dove right into it and so far it has been successful. My little phage even grew in it’s titer count. This was a big surprise seeing as I was a little disappointed in him/her (it feels too impersonal to call my phage “it”) for not making it to phage olympics because of too little DNA. This growth in titer is a big accomplishment. The latest thing that I have done for my experiment up to today was make different phage buffers with an array of pH values. Word to the wise, although the name of the stuff is “phage buffer” it does not have a great buffer itself. I added just a little bit of concentrated hydrochloric acid to it and it’s pH dropped from 7.6 to almost 1.  A lot of diluting had to be done to fix that accident seeing as although I have faith that my phage will be able to survive changing pH, I don’t thing he/she would survive in that acidic of an environment. I’m excited to see where my experiment will take me in the next few days. Although surprises can be bad during an experiment, I’m kind of hoping for maybe a few harmless ones just to make things more interesting.

Although Phage Lab this semester did not start off how I thought it would, it has definitely made a turn for the better. It will be interesting  to hear about the results of everyone’s experiments and what they deduced from them. I’m not too thrilled about having to go back to finishing the annotation, but I know that it is something that we have to do so I’m fine with it. I’m also not too thrilled about it though because it will mean that Phage Lab is actually over which is a very depressing idea, probably for everyone.

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