Over the summer I worked on a project which aims to understand how fragmentation and other changing environmental conditions impact disease resistance in Brook Trout (Salvelinus fontinalis). For this project disease resistance will be characterized by looking at the functional diversity of the organism. More specifically we will characterize variation in the Major Histocompatibility Complex (MHC) genes, specifically the MHC IIß exon 2 region. We used Brook trout fin clip samples from 5 different river systems in Western Massachusetts. Four of these river systems contain some type of barrier leading the river system to be fragmented. In order to characterize the MHC diversity DNA must be extracted from the fin clips. Once the DNA is extracted the samples will undergo a 2-step polymerase chain reaction (PCR) in order to target the desired MHC region and prepare the samples for Illumina sequencing. Once the samples are sequenced they will undergo bioinformatic analysis to quantify the allelic diversity within and among the various locations.
Prior to this summer I completed the DNA extraction step of the project. During the summer I completed the first step of the two step PCR reaction. Prior to completing the PCR1 reaction there were a series of tests I completed in order to ensure proper amplification of the desired MHC IIß exon 2 region. Once all the first step PCR reactions were completed I organized my data and began testing the second step of the PCR reactions. Throughout the summer I began enhancing my understanding of coding in R in order to complete the R analysis later in this project. During this summer I got the opportunity to develop my laboratory skills as well as improve my data management skills. I also got the opportunity to collaborate with other lab members on various projects and learn new skills and techniques along the way.