Capturing: Blog Post 1/6/151
Mid-week, we met with George and Johanna, the two scientists working with us, to discuss our plan. We wanted to capture ASAP, but the capturing process takes 24-48 hours, so we had to figure out how to best time it. Heather suggested coming in on the weekend, but Mayeesha and I selflessly pointed out what a burden that would be on the lab staff. We decided our best bet was to start Thursday and finish Friday.
Capturing is the process of getting our baits, segments made from modern beavers, to bind to the ancient DNA. This allows us to clean our samples, removing contaminants and non-target beaver DNA. We are analyzing the mitochondrial genome, so we are also removing the nuclear beaver DNA. It’s a labor intensive and unexciting process, and involves a lot of waiting around and some pipetting. We used a magnet to separate out our DNA, which was pretty cool. When combined, the ancient segments H-bond to the baits, since the ancient beaver and modern beaver have very similar DNA. On one end of the bait is a segment that binds to magnetic beads. We add the beads, let the solution sit, and then use a magnet to pull the beads to the side. Theoretically, all our target DNA (from ancient beavers) is sticking to the bait sticking to the beads, so the liquid (the supernatant) can be removed and replaced, cleaning and purifying our samples.
The most exciting turn of events was when I forgot to label a tube, unleashing an afternoon of horror. I placed our entire collection of baits into a tube, and then put it in our rack. Mayeesha thought it was empty, and pipetted in a different solution, and then wrote the name of the new solution on the tube. Someone then noticed we didn’t have a bait library, and a multi-hour frantic search ensued. I dug through every trashcan in the lab, sorting out the old tubes and checking if any could be our baits. Luckily, Mayeesha finally realized what had happened, and we were able to save our project. For a while though, I thought I had ruined our entire project, which was very traumatic.
Friday morning we helped clean the lab. We worked in the modern lab. I mostly mopped. After lab clean, we had journal club. Johanna emailed around a paper describing a new phylogeny of Darwin’s finches created using genetic sequencing. We met in the conference room, and we (or more accurately they) discussed and critiqued the article and the methods the researchers used. It was really interesting to see how these geneticists deconstructed the article and came up with ideas for future projects based off of others’ work.
Friday evening, we kicked off the weekend going out to celebrate with our coworkers. Saturday we switched hotels, moving into this tiny house in downtown Potsdam. It has one room, one bed, and no shower, but it is much closer to the lab and to the food, and it has bikes. Heather and I are planning to bike to the lab next week instead of taking the bus. Sunday, Mayeesha and I went into Berlin. Mayeesha insisted we not pay for train tickets, and we almost got caught by the train police. Luckily, we escaped unarrested, and got to enjoy some of the sites. We went to the Reichstag, the Brandenburg Gate, the Holocaust memorial, and the zoo.
The zoo was fun, except we couldn’t find the entrance, and spent 45 minutes wandering around the outside of the zoo. I got incredibly frustrated, but we finally got inside and got to look at the animals, and the elephants and penguins made it all worth it.
Stay tuned for next week’s blog, where I talk about pippetting colorless liquids, eating spargle (asparagus, apparently the favorite food of all Germans), and getting woken up by the three hundred alarms Mayeesha sets every morning.
1 Check out the European date!