On Tuesday morning, we set off to go to the University of Potsdam where we are going to work with a team of researchers working under Prof Dr Michael Hofreiter. We are really excited to be given this opportunity to work in his ancient DNA lab because the DNA extraction method we will be using here is fairly new and is the best-suited method for our research. Matthias Meyer was one of Dr Hofreiter’s graduate students at the Max Planck Institute for Evolutionary Anthropology in Leipzig, and his group developed a new DNA extraction method in 2013 that is specific for short fragment DNA. This method has been used to sequence DNA that is ~300,000 years old (before this method was developed, the oldest DNA that could be extracted was ~120,000 years old!). That’s so cool! We spent the rest of the day ordering primers for generating mitochondrial genomes and chalking out a timeline for our experiments. Since we handled modern samples that day, we could not go into the ancient lab.
Today (Wednesday), we showered and put on clean clothes right before coming to the university. This is important because we are going to be working in the ancient lab so we have to be as clean as possible, so that we can reduce contamination in the ancient DNA lab. Before entering the ancient lab, we put on hairnets, masks and blue suits (hooded onesies!), clean clogs and double gloves. The sign on the lab door had the perfect description of what we looked like:
(For a more realistic photo, check out Jacob’s post!)
In the lab, we cleaned the work surfaces and prepared our samples by crushing with a mortar and pestle. We added 1mL of extraction buffer to our samples, vortexed them and left them in and incubator at 37°C to be digested overnight. We then prepared the buffers that we will use tomorrow to finish our DNA extraction. We also got to use the Tape Station to measure the lengths of the DNA fragments we extracted from modern beaver tissue and now we know that our fragments are long enough to be used as baits in our hybridization capture method.
George showing us how to use the TapeStation (above)
Jacob and I are happy to see that our modern beaver samples have long enough DNA fragments (above)
I am looking forward to extracting DNA from our samples. Ideally, we should have sampled from the petrous bone as it is known to contain best-preserved DNA but this bone was missing in all of our giant beaver specimens. So, as our next best alternative, we brought mostly samples from dentin in teeth of the giant beaver fossils. This may or may not work; we won’t know until we do our extraction. For now, I am going to keep my fingers crossed and hope that we are able to sequence at least some giant beaver DNA from our ancient samples.