by Luke Jenusaitis
Not three months ago we were hands on in a lab, getting elbow deep in plaques, and DNA material. This semester is a very different type of lab. During class now we are surfing the web non-stop. My colleagues aren’t trolling on Facebook or Stumbleupon; we are looking for answers to Manatee’s Genome. Manatee was the bacteriophage that was chosen to have its genome decoded. Annotating the genome is an extremely tiresome process, but is definitely rewarding. Every gene goes through a process of recording the BLAST hit, the Shine Dalgarno (a short stretch of nucleotides that are upstream of the start codon), the HHpred (homology detection and structure prediction) and the coding potential. Other factors include the number of base pairs that overlap between genes and the input from our class. Everyone has an opinion on a gene, whether the gene is expressed or not, giving various reasons for and against. The entire ordeal is very democratic and the strongest argument usually wins. We have gained two new phage hunters that have been very active, one particularly in my group. Andrea completely jumped into this topic after missing last semester and she has contributed exponentially to our conversations.
This semester subsequently requires more prep work at home. This particularly has been challenging for me because many of the clubs and organizations have started to come to fruition in the spring. For instance my involvement in Spring Fair has me working on decoding the genome while in my office hour. Every free moment I try to get on the computer attempting to solve one or more questions that arise from the genome. The decoding of the genome is slowly coming to a close however, and next we will start our own special projects. I think for my special project I am going to be finding the clusters for each of the phages. Phages are grouped into clusters with similar genetic characteristics. I will be working mostly in the wet lab for this using my personal phage, Landshark and some of the other phages. This will be done through several tests like the PCR Test and Lysogenic Test. The PCR test is more commonly known as the polymerase chain reaction test, which involves testing the DNA of the phage.
That’s all for now, we will keep you updated! As always we enjoy the fact that we are succeeding in our research or as I like to say WINNING.