Friday, October 9, 2009

At Last

I've been working on a project at work that was one of those that was supposed to be pretty straightforward, but wasn't. The data mostly told the story we were hoping they would tell, with one exception. The most isolated population was supposed to show signs of that and have a measurable amount of inbreeding. Instead, the other 5 populations showed it, and this one didn't.

This led to several weeks of trying to figure out a biological answer to explain these results. In the end there wasn't one. It was more or less user error (i.e. my error). When we amplify fragments of DNA, the process, called PCR, cycles the temperature of the reactions up close to boiling, and back down to 50-60 degrees C, over and over again. I was using a cycling program that was recommended by the company that makes the machine that we visualize the PCR fragments on. Turns out the program was too hot, and some fragments must have dropped out to give me these results.

I figured this out by rerunning some of the samples at a lower temperature, and lo and behold, no inbreeding. Just like that. So now I'm trying to get the rest of the 300 or so samples processed as fast as I can, so we can get the manuscript out. My boss and another investigator discovered a new population of this certain form of mosquito and I've been holding up the show as far as what their population genetics look like.

This is one aspect of my job that I would change if I could. The part of the CDC I work for doesn't generally look at population genetics, so if I run into a problem, I have to go outside to get help. Since I'm still living where I went to school, this isn't too big of a deal, it's just that there's no one to bounce ideas off of in house. I think things run slower sometimes because I have to figure them out on my own.

I feel like there's something I should do to "make up for" the fact that this took so long. I'll have to think about that.

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Hi, sorry to make the humans do an extra step.