The Attractin Gene

This week was very successful and productive. I completed the steps necessary to sequence intron four in all specimen from the panel that I am utilizing. I then returned to intron 17, preparing the remaining samples from the backcross (a cross of individuals with individuals genetically identical to the parents) for sequencing in order to further determine the relation between variation in intron 17 of the attractin gene and variation in coat color. The data I have collected for the back cross so far reveals a direct relation between coat color variation and variation in this intron, as is found in the agouti gene. However, if one sample shows imperfect association between variation in the attractin gene and variation in coat color, than the agouti gene has a stronger association and linkage disequilibrium (the non-random association of a version of alleles [versions of a gene] at two or more loci) has begun to break down. After submitting forty-one samples for sequencing, I will have a large volume of sequences to clean and analyze in the coming weeks.

At the laboratory meeting this week, a graduate student discussed his research involving the genetic basis of the coat color of three species of bats. Based on his calculations comparing the Mc1r gene (a gene highly involved in the coat color pathway) in chimpanzees and humans, there is an expected divergence of 10% within this single exon (coding region) gene in bats; however, his sequences reveal no difference in the gene among these species. Thus, the lab meeting consisted of working backwards through his experimental process in search of the cause of this result. The first consideration was that the results may be accurate; however, this is unlikely, as, based on probability calculations, there are sixteen expected differences among the Mc1r genes in these bat species. The conversion then turned to a search for sources of error, which are very useful for all researchers in the laboratory to consider, as research consists of a majority of problem solving prior to receiving actual data. Suspected sources of error included contaminated DNA samples, contaminated PCR reactions, accidental extraction of the same DNA three consecutive times, mislabeled DNA extractions, mislabeled tissue from the museum that delivered the bat tissue or mislabeled specimen at the museum, or a mistake during the sequencing process at the sequencing center. In a search for valid results, the graduate student will continue his experiment by first repeating the PCR reaction and attempting to use new primers if the mitochondrial DNA sent for sequencing does show differences in the nucleotide base pairs. If the mitochondrial DNA sequences among the bat species are identical, he will extract new samples of DNA from new museum specimen in order to create accurate primers for continued work on non-contaminated samples. The graduate student then concluded his allotted presentation time by discussing his rotation in a laboratory studying the genetic makeup of a toxic algae and the extent of expression of the toxin in various environments. Each laboratory meeting has concluded with an important moral to remember when performing research: for each step of progress in one’s research, there is always some setback; however, collaboration with one’s colleagues will lead to progress in one’s research.