Joe came by this afternoon to test the quality and concentration of the bifax
PCR work he did last week using just a single primer in the reactions. It came out at much higher concentrations, with better ratios and spectrophotometric properties, than what we'd been doing before for which I'm happy. Next week he'll move on and PCR these amplified samples using the other primer, and if they look good we'll have those six samples sequenced to see how well they turn out. And if that works then we'll attack the remaining 32 or so samples. I keep thinking this should be easy but at least for me it hasn't been, in a future life maybe I'll be a for-real gene jockey.
We hope to go out this Sunday to Sipsey Fork on the last day of my collecting permit and snag another group of silverstripe shiners for brain examination. Four of us are going, which will be good for dealing with cold, fairly high water. But this time the temperature shouldn't be worse than the low 40's, almost balmy compared to our last trip.
Kris came by to talk about his thesis with the mummichog DNA. It's just about done for once and all, and next week he should be able to give full review copies to all members of the committee. We're aiming for his defense on Feb. 24. It's a concise, short thesis as part of our new campaign to cut out extraneous verbiage from theses. Basically, we reinforce previous work on mummichogs showing a north/south population split, and identify 16 SNPs in the cytochrome b
gene that are informative for defining haplotypes. In the south population there's a subdivide between Virginia populations and South Carolina/Georgia populations, with the Virginia populations showing SNPs that change the first codons of three amino acids, two of them for a different amino acid. Given that this protein is a key part of the mitochondrial electron transport chain this is interesting stuff. We don't know exactly what function(s) may change, that's beyond the scope of this work, but it would be good to follow up with crystallographic studies. I hope that we can get this work published, maybe in Northeastern Naturalist.