Analyze This

by John Cotoia

I always feel so amazing when I tell people I analyzed the genetic material of a bacteriophage. Most of the time people stare back in bewildered wonder before I begin my litany of explanations, but of course this only leaves them with more questions and confusion – they say “That’s interesting,” or “Cool,” and the conversation changes. Regardless of others’ reactions, I definitely feel satisfaction in accomplishing a scientific feat never imagined in my most productive day dreams – geneticist is a dashing title.

We recently completed annotating Manatee’s 51040 bp (base pair) DNA sequence, a process riddled with questions and debate: Do our programs agree, is it long enough, which direction is it going, where does the gene start/end, does it overlap with other genes, does this start have an acceptable ribosome bonding site, does this start/end include all the genetic potential (is there any genetic potential) compared to several different bacterium, does this genetic potential code for anything useful, do other phage within its cluster have this gene (how aligned and identical are they) … ? This system of questions was used 92 (and then some) times independently, then rehashed in small groups, and finalized in a class setting. With our collaborative efforts, we will be checking, re-checking, debating and amending our decisions before we decide upon one genome to present to HHMI.

Alongside Manatee, we will be finishing the semester with individual projects. We will be presenting our putative project this week to our peers in a mock scientific colloquium. Our projects will range from investigating aspects of Manatee’s gene sequence to characteristics of our own individually isolated phage that interest or demand further exploration and investigation. Several students, including myself, will be using PCR (polymerase chain reaction) to identify what cluster our phage belong to. Provided with primers for all 16 bacteriophage, if one primer properly aligns and binds with my phage DNA, PCR will exponentially replicate the DNA. When run through a gel electrophoresis, I will then determine the cluster.

Extremely excited, I hope to find the family of my phage – I am an awesome father, but everyone needs friends.

About johncotoia

Me: Bacteriophage Hunter, then a Johns Hopkins Undergraduate, followed by the various aspects that constitute my life ...
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