Learning About PCR and Gel Electrophoresis (Week 1)

This week I did a series of PCRs and gel electrophoresis experiments. Again and again and again. I learned that science is about repeating things again and again and again. I also learned that it's very frustrating when your experiment doesn't go as planned, which happens all the time, I'm told.

My lab work started on Tuesday, when Rick showed me how to run a PCR and a gel. I had never done a PCR or a gel electrophoresis before, so I learned a lot that day. Because it was my first time, Rick had me use DNA from an unknown bacteria he had been culturing, instead of starting me with the bacteria from the Antartica caves that I will be studying. Unfortunately, when I took a picture of the gel, I saw that there was DNA in the negative control.

After that, the rest of the week was a series of experiments to determine where the contamination was coming from. First, I ran the experiment exactly the same way with the same reagents, hoping the contamination was merely the result of some cross-contamination during the experiment. It wasn't. So, then Rick replaced some of the reagents with new, clean ones. But those reagents weren't the problem either. By Friday, we had figured out that the contamination was either in the BSA or the primers. So, we ran two PCRs, one without BSA and one with new primers. As a result of this, we discovered that the contamination was in the BSA.

During this process, I learned a few important things about running gels. Firstly, you have to mix in a fluoreescent dye in with the gel in order to see the DNA. This created some confusion when Rick and I were looking at the gel and couldn't see anything on it. Oops! Also, I learned that if you don't measure out the amount of gel, you can create a gel that is so thick that the TAE solution won't cover it. And this also makes it difficult to run the gel electrophoresis. Despite these mishaps (or perhaps because of them) I now feel very confident with PCR and gel techniques.

I did a lot of things outside the lab, too. On Monday, Vanessa gave us new interns an orientation. On Wednesday, I went to blog training and safety training. On Friday, I attended a very interesting lecture on ethics in research. Also, I read some papers related to my work, including Brad Tebo's proposal for funding for the Antartica research. That sums up my week.