DNA capture progress by Mayeesha (June 1st)

Update for Monday, June 1, 2015

Last week, we ran our first capture, which is the process by which we made our modern beaver DNA baits bind to the ancient DNA in our samples, so that non-target materials could be removed. So, on Monday, we wanted to amplify the target DNA that we (hopefully) captured. In order to do that, we had to run a quantitative PCR (qPCR) to find out the optimum number of cycles each of our samples had to go through during amplification. After finding out the required number of cycles for each sample, we amplified our captured libraries using PCR. By now we were very curious to find out how much ancient DNA we were able to capture and amplify so we did a High Sensitivity Qubit and ran a Tapestation. The results showed we had DNA in our samples (whew, looks like there’s still hope!).

Hey check it out, we’re listed on the University of Potsdam website as guests of the Biology and Biochemistry department. This feels so official!

website

And now you know how to say guest in German.

On Tuesday, we started a second capture and we left it in the thermocycler called Clive. All the thermocyclers in the lab have names instead of numbers and their names are: Juan, Stu, Lee, Ford and Clive which I found pretty funny because they kind of sound like one, two, three, four, five. Since we don’t have any lab work to do while we wait for our capture to be completed, we decided to use our time to make a list of all the reagents and lab materials we used so we could pay the department back. This was a long process because we had to go through all the protocols to figure out how many times we did each protocol and how much stuff we used. After an afternoon of calculations, we got the wonderful opportunity to meet with Dr Michael Hofreiter. Michi took some time off his extremely busy schedule to have a conversation with us and we were super excited to be able to chat with the great scientist whose lab we were working in!

On Wednesday, we decided to arrive at the university at 10am, which is an hour later than usual. Jacob and Heather go to campus on their bikes, while I take the bus (I developed a phobia of bikes after a pretty bad fall last year). Usually when I take the 8:40am bus, the bus is mostly empty and I get to have two seats to myself which is really nice. However, when I took the 9:40 bus that day, it was so crowded that people had to get off at each stop to allow new passengers to get on. But no one got off to leave; they got back on with the new passengers so the bus kept getting more and more crowded. I had to stand on the whole way and kept trying my best not to lose balance and fall on the other passengers every time the bus made a turn. When we finally arrived at the university, everyone got off and the bus was totally empty! I made a mental note to never take the 9:40 bus with all the university students again. Nope.

When we got to the lab, we decided to keep our capture running for 48 hours instead of 24. So we didn’t really have to do any lab work that day and being the awesome person that Heather is, she let us have the rest of the day off! So I took the bus back to Brandenburger Straße (ß is the equivalent of ss in pronunciation) and explored the shops on either side of the street. They have some cute souvenir stores, some handicrafts stores, and amazing restaurants! I found a really nice restaurant where I had a delicious crepe with banana and nutella and went on to exploring all the nearby streets and discovered some shortcuts to our hotel from there. I really enjoyed walking around the pretty streets by myself and discovering new places that I liked! It was wonderful to get a day off to relax in the middle of the week!

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