by Andrea Carrassi
It is my first semester in Phage Hunting, and I am already loving the challenges that we are faced with as a group. I have become fluent in terms such as HHPred, coding potential, BlastHits, Glimmer, Genemark, Shine-Dalgarno sequences and more, and as John said, I pretty much sound like I know the meaning to life when I speak to other people that have no idea what any of that means. But what it comes down to is the most frustrating of all: choices. When do you know a gene is active, or a huge gap in a genome is not a gene? Or how do you know that all of the other people who have declared one gene are actually correct? There are thousands of things that one can know from one phage; it is impressive how an infinitely small bacteriophage can be used in so many ways. Now that we have finished determining whether Manatee’s genes are acceptable, then comes determining what each one does, or of they are active in the phage, etc. You can only know so much by decoding a genome, because, first, there is a lot of guessing and listening to your “gut” when it comes to analyzing that sequence, and second, you need countless numbers of tests to know only one trait out of hundreds that a phage could have.
Many students are looking into further categorizing and understanding Manatee, and others have chosen to work with their isolated phage. The monotony of going over Manatee’s gene sequence is over for me, and these next five weeks I will attempt to isolate my own phage. Due to his/her unexpected personality, and potential to make my life very difficult, it will be called Marcus Junius Brutus, or, Brutus. It is chasing and catching up to my classmates’ work, and with their help, Dr. Schildbach, Dr. Fisher, and our wonderful TAs expertise and advise, I will manage to complete this semester-long project in just five weeks. I have decided to expedite this process by only doing strategic, quick, and efficient steps of the procedure. Also, I will need the force on my side in getting positive plaques, due to the fact that I have been limited to only testing three soil samples. With hope, no infection will get in the way of my project being completed on time. One of my samples smelled particularly weird, and I hope phages inside my samples take a liking to M. smegmatis when I come back to continue the experiment this Monday after their incubation.
I have many worries in doing this kind of project, but I am equally excited. Skyler has also chosen to isolate an original phage, and I am happy to not be the only one doing it. The kind of work that we do in this lab is going to be lasting, and leave a tiny dent in the world of science – my ambition is at is highest and hopefully not knocked down by unforeseen struggles.