Rachel Tullsen's blog

It's hard to believe that this is the final week of my internship. On Monday, I cleaned up the DNA for sequencing and on Tuesday Rick took it to the Primate Center to be sequenced. Unfortunately, we won't get any of the sequencing results back until next week. I would like to have a look at the final results, so I will probably work for a couple of days next week. After doing all that work, it would be a pity if I didn't analyze some of the results!

Last week I continued to try to figure out why the barcoded samples weren't working. I tried different annealing temperatures, different amounts of DNA, different DNA samples and different reagents to help it work... And the DNA still wouldn't amplify with the barcoded primers. Finally, I did a PCR where I diluted the barcoded primers. After so many disappointments, I wasn't expecting it to work, but to my surprise, it did.

Everything is becoming so busy now. The summer started off at an easy pace and now the stress is beginning to set in. Most days I find myself so busy with things that I don't realize how late it is. The new barcoded primers came in earlier than expected. So, this week Rick and I have been trying to determine the best method of barcoding the samples. So far, things haven't been working too well. I did a PCR with the barcoded primers today and they didn't amplify the DNA.

Each week I've been looking forward to completing the qPCR of the cave samples, but each week, it has been delayed for one reason or another. Last week, I was finally able to do it. The qPCR is a way to amplify DNA samples and figure out how many copies of DNA were in the tube before the amplification began. It's fun to use, because it creates real-time graphs showing the amount of DNA present after each cycle. The lines on the graph start off horizontal as the PCR begins and the amplification is slow. Then, they begin to rise sharply in a curve and, finally, level off.

Most of this week was spent working with primers. Firstly, I had to optimize the new primer sets. I used the qPCR machine, so that I could do the samples at different temperatures all at one time. This was the biggest PCR I'd ever done: 44 tubes. I can't imagine filling up an entire 96-well plate. After that, I ran all of the PCR results on gels. The results weren't as clear as I had hoped.

One of my main objectives this week was to figure out if the new primers work. There are three new sets of primers - one for bacteria, one for archaea, and one for fungus. It was easy to test the bacteria primers, because there are plenty of bacterial DNA samples in the lab. Unfortunately, however, that was not the case for the fungus and achaea primers. I tried using a couple of samples that might contain fungal or archael DNA, but I got strange results, which were difficult to interpret without definite positive controls.

The highlight of this week was preparing a presentation to give on Wednesday to the other interns and their mentors. The biggest challenge was designing a presentation that I could get through in less than 5 minutes. Despite my doubts, I actually had a lot of fun designing my presentation, which went through several drafts as I got a better idea of what I should say.

This week's work was cut short by the 4th of July, but it feels like I got a lot done. The majority of my time this week was spent on extracting DNA from 9 more soil samples. It took me a little longer than necessary to complete the extractions, because I didn't want to work with too many of the samples at once, so I did it in two batches. I wasn't too familar with the technique yet, so I wanted go more slowly and make sure I didn't make any mistakes.

This week was very exciting, because I started studying the Antartica bacteria. I also learned a lot more about the context for my project and projects that other people in Tebo's lab are working on. It was interesting to learn about the diverse work that everyone in the lab is doing and yet it all ties together.

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.