The Attractin Gene

This week, I have been continuing my work from the previous week of analyzing data and running PCRs to amplify various regions of the attractin gene. Analyzing the data is very exciting because I have the opportunity to actually see the progress I am making in discovering more about the association of the attractin gene to coat color variation in rock pocket mice. The new DNA sequences I collected last week included two regions of the attractin gene, introns (unexpressed regions of the gene) 27 and 4. The sequence for intron 27 was low quality, as I could not determine which bases were present in each region from the condensed and overlapping chromatogram, which is a graph showing the presence of each base with peaks of various colors. Thus, I ordered internal primers and will perform nested PCR on this region by diluting the product of my original PCR and running a new PCR with the internal primers to obtain more specific sequences. I will also attempt varying the conditions of the PCR to obtain better results, such as using supplies meant for long sequences. I did, however, obtain a successful sequence for intron 4 in one specimen, which contained two regions of heterozygosity (the presence of different versions of the same gene). I will continue to sequence this region in additional specimen in order to determine if there is any association of this variation (if it is present in more than one individual) to variation in coat color in any of the populations of rock pocket mice. In order to try to amplify additional regions of the attractin gene that have not successfully amplified with the previously ordered primers, I ordered internal primers for introns 23 and 13, as well.

I have also continued running PCR reactions and performing gel electrophoresis (to test whether the PCR was successful by separating bands of DNA in a gel that allows DNA to move from the negative to positive end of the container) this week. I am currently working with exon 1 (an expressed region of the attractin gene), altering the conditions of the reaction in order to obtain a clean fragment of DNA. This process has become very familiar to me, as I have currently run 157 PCR tubes in the month I have been working here (after the second trimester), and I am now able to complete the process very rapidly and locate the DNA stocks in the crowded freezer and refrigerator when I need to dilute the DNA to an appropriate concentration for the reaction.

I also had the opportunity to speak to Professor Nachman for an extended period of time this week. He explained the research currently being conducted concerning the mechanism for regulating the X chromosome in various animals, as females have two X chromosomes and males only have one. It is very interesting how different types of organisms have dealt with this dilemma in differing ways; for instance, the male fly upregulates the X chromosome to produce the effect of having two of each gene on that chromosome, while many female mammals turn off one X chromosome to produce the effect of having only one of each gene on the chromosome. However, while many ideas for this occurrence have been proposed, there is still no definite explanation of the mechanism responsible for this incidence. Professor Nachman further described the reasons for why he chose to study coat color (a trait essential for survival) and what brought his focus to the agouti gene (a gene shown in mice bred in the laboratory to have mutations prior to Professor Nachman’s research of this gene in wild mice populations). Additionally, Professor Nachman explained a very interesting connection between dentistry and evolution, as various mammals have developed tooth number and growth patterns independently of one another. Speaking to Professor Nachman is always a wonderful experience, as I learn so much in a brief period of time and become even more enthused by scientific discovery.

I look forward to completing this week by amplifying additional regions of the attractin gene and again nearing the number of samples necessary to prepare a plate of DNA for sequencing.