The Attractin Gene

This week, I spent a majority of my time analyzing DNA sequences. I further learned about numerous statistical tests to apply to my data. In addition, I attended the laboratory meeting on Tuesday. This laboratory meeting focused on the research being conducted by the laboratory technician who is sequencing genes surrounding the agouti gene in search of a break-down of linkage disequilibrium (the non-random association of alleles at two or more loci [regions of the gene]) around agouti; if found, this would indicate that variation in agouti is the probable source of coat color variation. Upstream of agouti and even within agouti on that region of the chromosome, linkage disequilibrium decays. The laboratory technician is now sequencing genes downstream of agouti in order to study linkage disequilibrium. In her effort to sequence additional genes, she has applied the twelve buffer system, a new addition to the laboratory; this system is meant to optimize PCR by utilizing twelve buffers of varying MgCl2 and KCl concentration and pH to identify the optimum conditions for the amplification reactions of the DNA fragments. This system will be very useful in future attempts to sequence a region of any gene with new primers and will hopefully make the sequencing process more rapid to allow for greater accumulation of data. Furthermore, as many of her PCR reactions have resulted in numerous nonspecific DNA fragments of undesired length, we discussed further options at her stage in the research for troubleshooting such results. For instance, she may consider nested primers, which are primers designed to splice the DNA within the initial sequence obtained from the first set of primers. She may also consider applying a gel stab, in which she extracts the distinct possible bands of desired DNA sequence from the gel and cleans them for sequencing; she would then align these sequences to her primers to determine the accurate sequence. Once again, the most important aspect of the laboratory meetings is the amount of applicable knowledge one obtains from cooperation and communication.