Perfecting PCRs

4/16/12
Today Dr. Kirchman and I got to do some lab work (luckily, I had even remembered to bring along a pair of closed-toe shoes to replace my flip-flops). Dr. Kirchman is also working on a project with spruce grouse so today I helped him run a gel. A previous PCR on the gel hadn't turned out so well so Dr. Kirchman decided to try and run a longer strand of the mitochondrial gene of the spruce grouse. To do this, we first needed to collect a bunch of primers so that they would be able to sequence the strip all the way from one section to the next. After going on a primer search through the freezers in the lab, we finally had enough and I started to make a gel. There were a lot of leftover gels from previous uses so I carefully (no explosions this time) melted down the gels in the microwave and then added the mutagen. Since we had 16 different DNA samples, I used two different combs for the same gel so that we would have enough slots to run all 16 samples at once. After the gel turned opaque and congealed, I was able to mix the ultraviolet sensitive dye with all 16 samples and squirt them into the gel with no mistakes and no desperate cry for assistance. I believe I am now worthy of the title of pipet master-in-training. When Dr. Kirchman and I went to run the gel however, there were some difficulties. The machine did not seem to want to send any electricity through the gel! However, after some fiddling around, we finally added more buffer which did the trick and the machine began to conduct electricity through the gel.
Since it takes 40 minutes for a gel to be successfully run, Dr. Kirchman and I went to the prep lab and after giving Joe a quick hello, I started cleaning my skeletons and putting them into boxes. Fist we put the skeletons on a metal container with holes in the bottom that let the ammonia fall through, but keep the bones from going down the drain of the sink. Next we put the bones on blotting paper and let them dry, sorting through the bones and extracting any remaining tissue or tendons from the skeleton. Once the skeleton was dry, it was put in a box corresponding with its size and then properly labeled with its scientific name, where it was found, when it was found, and other important details of the like.

Hello Joe!

When Dr. Kirchman and I went back to the lab to check on our PCR, it worked very well to our surprise. Every single one of our DNA samples was showing up and all of our negative controls were not showing anything. After marveling at our perfect PCR for a couple seconds, my time was up and Dr. Kirchman and I had to clean up. All over all it was a pretty good day in the lab with a minimum of technical difficulties and an abundance of success.