Lab Work

Hello! So, although photos of pretty castles and things are more exciting, I should probably explain what I'm doing here in Copenhagen! I summed it up in my intro post, but I'm working at the Centre for Geogenetics, a large genetics group at the University of Copenhagen, with a special focus on ancient DNA. I'm specifically collaborating with Tom Gilbert, who focuses on human evolutionary history and domestication - he heads the Evogenetics group. His students/postdocs work on everything from grape domestication to human disease resistance to the introduction of sheep to Denmark. It's all really cool research, and I love hearing about what other people study here!

Ancient DNA doesn't actually have to be that old to qualify as "ancient" - DNA from something that has only been dead a few weeks is considered ancient, too! When DNA is no longer protected by cells (ie through decay, for example), it's very vulnerable to damage. This can cause breaks in the strand, or even changes in the base pairs (for example, it's common for Cs to end up as As thanks to chemical reactions!) Sunlight, water, and heat can be bad for DNA strands. Over time, the strands break down into smaller and smaller fragments, to the point where they're too short to tell you anything useful. So, when you're working with remains of some kind, remains from dark, dry and cold environments (or from permafrost) are much more likely to have DNA that is still long enough to be sequenced.

This is why, when you're working with ancient DNA, it helps to have a protective environment for it. Mostly, we're protecting our samples from ourselves. DNA from a skin cell or a strand of hair is in much better shape than DNA from ancient remains, and it's easy to "contaminate" our samples with our own DNA. This is a much bigger problem in human research, but can be problematic when you work with other animals, too. When working with ancient DNA, people often wear full body-suits, multiple layers of gloves, face masks, hair nets, and more. Here's how we generally look in our ancient lab at Illinois - it's a little hard to identify people sometimes!

Our lab setup at Illinois is pretty nice - we have an anteroom where we store our suits and get changed, and another room devoted to working with ancient DNA. It has special air filters to keep the air clean, and there are separate spaces for the three main tasks - drilling bone (to powder it up), extracting DNA (to get rid of all the other junk in the bone powder), and amplifying (to make more copies of the DNA). Here you can see all three of the stations (Thanks to Amanda, my labmate and skilled photographer!).

The labs here in Copenhagen are on another level completely. First, they have separate labs for human and animal/plant DNA. Second, the labs are not just one room but several - the door into the lab opens onto this hallway, with a long row of freezers. From there, depending on what stage of the process you're in, you go to different rooms. There's a room for drilling, as well as two separate rooms each for extractions and amplifications. Each room is outfitted with all the equipment you need, so you can work in your own space without worrying about getting in someone else's way. The room at the end of the hallway above is an amplification prep room, and the next picture is of the drilling room.

The white walls and obsessive focus on cleanliness (we bleach everything we use and there are UV lights that are turned on at night to help reduce contamination risks) makes it a little hard to work long hours in the lab. I think I'd go a little crazy without the radio - there's one in each room. I've found Europop to be a great motivator! But also, there are some nice places to hang out in right by the lab. When I have to wait for something to finish, it's nice to walk around in the Botanical Garden right by the lab or in the King's Garden across the street. Between the beautiful weather and the pretty greenery, it's a nice break from the ancient lab.

And my favorite foodie market, Torvehallerne, is only 5 minutes away! I think it's going to be hard to *not* get lunch from that pizza place every day, especially when it's so close. Luckily, there are lots of other foodie goodies to distract me. :) Next time, I hope to have some more sightseeing photos for you!

Adventures in Copenhagen

Hello! Although this blog originally began as a travel journal of sorts for my semester abroad in Japan, I thought I'd expand it to include my month-long research trip to Copenhagen. Here's a bit of background!

The Centre for Geogenetics is a world-renowned ancient DNA facility, and a ton of high-profile research papers dealing with ancient samples have come out of the lab. Here's an example, with a quote from the head of CGG, Eske Willerslev. CGG is home to multiple "research groups", each with a different focus. Thanks to my advisor's collaborations with Eske, I've gotten the opportunity to work with some ancient Siberian dogs, as well as learn some new techniques and get to see another ancient lab. I arrived on July 12th (ie yesterday), and will be living here until August 12th. In that time, I have a lot of research to do, but I hope to balance it with plenty of sightseeing. :)

My arrival was pretty uneventful - I flew to Copenhagen via Chicago and London. The total trip took about 17 hours, including a few long layovers. I did see something neat at the Chicago airport, though - pictures from IGB! The Institute for Genomic Biology is where the ancient lab is at the University of Illinois. There are a lot of really powerful microscopes at IGB, and so they made a gallery of some of the cool images that come out of the microscopy labs.

Saturday I mostly spent settling in - after finding my hotel, it was already 4 pm. It's an extended stay hotel, and they serve breakfast 7 days a week and dinner on weeknights. As much as I'd like to cook, it's so expensive to live in Copenhagen I figured that letting someone else handle my meals wouldn't be a bad idea. It's a little older, but really not bad. I have wi-fi, a hot shower and big windows, so I can't complain! My window overlooks a large courtyard with a lot of other apartments and hotel rooms - it feels like I'm an observer of a lot of other peoples' lives, which is an interesting feeling. There's no air conditioning, but that's really common in Denmark. So far, the temperature hasn't been above the mid-seventies, and it's supposed to stay that way through August! I never thought I'd say this, but I'm almost missing the Texas heat. Almost.

On Sunday I jump-started my trip by being trained in the ancient lab! I met Nathan, a post-doc in the lab group I'm working with, at 9:30, and we spent the rest of the day training. It's not quite as bad as it sounds - he took a very leisurely approach, so we spent probably less than half the time in lab. He and Randi, a graduate student at CGG, took me to lunch at a really cool foodie market at Norreport Station, which is one of the larger stations in Copenhagen. There, we had some amazing pizza (see above!). So far the food has been pretty good here, though I'm not sure I've had any authentic Danish meals yet.

Today, I'm meeting with Tom Gilbert, the head of the lab group and the owner of the Siberian dog samples, to figure out the plan for my stay. I think a lot of different people are involved, since the summer is a popular time to go on vacation! I've heard that when it's sunny, everyone just takes time off from work and goes on vacation because the sun comes out so rarely.

Hopefully I'll have some more sightseeing photos for you in the next few days. This last picture is of the park I cut through on my way to the lab - the Danish really believe in green spaces everywhere! :) Take care!
-Kelsey