The Final Week in Germany by Jacob

The last week was here was much more relaxed. With our libraries prepared for sequencing, we were basically finished. We couldn’t run our samples in the sequencer until Wednesday, so we had planned to work in the Ancient Lab, reextracting several samples, mostly to get more practice working in the clean lab. Unfortunately, the lab was booked all day Monday, so we did some quick practice in one of the modern labs, reviewing technique and basic lab habits. Although that sounds easy, it’s actually very difficult to consistently follow George’s protocols. There’s a million little steps that have to be done in a specific and not necessarily obvious order. For example, you have to remember to open the tubes before you put the tip on the pipette, even though I would have thought the reverse to minimize contamination of the buffers and samples!

Tuesday, we went into the ancient lab and began new extractions. We used two samples that didn’t work the first time, as well as three new ones. Using the mortar and pestle to grind the specimens made a nice break from pipetting. Before work Tuesday, Mayeesha and I went to a German breakfast buffet, which was awesome. Germans have excellent breakfasts, mostly bread, croissants, and different types of meat, although there are also eggs, yogurt, and cereals.

Wednesday, we finished our work in the ancient lab, getting to a stable stopping point with our libraries. That afternoon, when Johanna and Carolina, who were also putting samples on the sequencer, were ready, we began prepping our samples for sequencing. This took a long time, as there are a lot of calculations necessary to ensure the samples are placed on the sequencer in the right concentrations. George explained to us how the sequencer works, which is actually very cool. It measures flashes of light to tell the order of nucleotides.

Because the sequencer takes about 24 hours, and we didn’t start running it until 7pm Wednesday, there wasn’t anything for us to do Thursday, so we took the day off. I used it to explore more of Potsdam. I’ve been trying to run in different directions, and I found a new park complex which is pretty cool.

Friday, our last day in the lab, we finally saw our sequencing results! But, we’re not going to tell you what they show just yet…stay tuned for a bigger announcement!

We are leaving on Sunday! Mayeesha has friends from high school coming to visit this weekend, and I am going to continue exploring Potsdam and Berlin. Working in the lab has been so fun, but I’m looking forward to coming home and continuing with my summer.

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The story of how four scientists met the challenge of sequencing the Giant Beaver by Heather Lerner

In a country far, far away, four scientists set forth to capture DNA from an extinct Giant Beaver. George, Heather, Jacob and Mayeesha met in Potsdam, Germany to begin their mission in June 2015. Five fossils of giant beaver teeth were their best hope. They ground the bones to a fine powder, digested them in solution overnight and returned the next morning to finish extracting the DNA. But, no separation column existed that could handle the massive amount of digested Beaver samples. Undaunted, our fearless scientists crammed together pieces from two different kits to make the perfect column system. Early signs were good: four of the extracted bones showed evidence of ancient DNA. That is, short fragments of ~100-200 nucleotides in length.

There was no way to know if that DNA belonged to a Giant Beaver unless they sequenced it. Our scientists knew they would need a lot more copies of each DNA fragment in the samples to be able to sequence them. But this copying process would be risky. At any step, a simple mistake could mean that all of the DNA was lost. Over three days, they attached strings of known DNA (barcodes and adaptors) to the ancient DNA in each tube. Using those known strings as “primers” and a DNA copying enzyme (polymerase), they attempted to copy the ancient DNA. Signs were again good, four of the remaining samples still showed evidence of ancient DNA! An ice cream celebration ensued with much joy.

Our intrepid scientists faced another challenge: DNA sequencing is too expensive to waste time and money on sequences that aren’t Giant Beaver. They would have to somehow pull out only sequences that were likely to be Giant Beaver. “What else might be in that tube?” you might ask. The most likely contaminants are bacteria, any humans who had handled the samples, and any DNA that might have been floating around the lab or in the chemicals they used. They called on another scientist, Johanna, to help them solve this problem. She proposed capturing Giant Beaver DNA with a trap made of modern beaver DNA. Using a similar copying process as before (i.e. PCR), the scientists essentially made a net of modern beaver DNA to capture the Giant Beaver DNA.  When the two types of DNA were mixed, strands of DNA that were similar would be attracted to each other. As the strands paired up, one strand would be made from modern beaver DNA and the other from extinct Giant Beaver.

They faced yet another challenge: to separate the captured beaver DNA from contaminating DNA. Brilliantly, they had modified their original modern beaver DNA by attaching a molecule that sticks to special enhanced magnetic beads (i.e. biotin). By applying a magnet to each tube, they could pull the hybridized strands to the side and pipette everything else away!

One final challenge remained: How would they get their ancient DNA away from the modern DNA, (which would be too expensive to sequence)? Luckily, it is easy to get DNA strands to separate by just heating them up. Again, that magnetic bead came in handy: after heating the tubes, they used the same magnet and pipetted off the ancient DNA that had once been trapped by the modern beaver DNA. It was time to check again to see if they had been successful. This was an important moment after three arduous weeks of challenges, including several mishaps in which they all believed the project had been lost. This time, three of the samples showed evidence of short strands of ancient DNA!

One final step remains in our heroes’ saga: sequence the potential three ancient Giant Beaver samples. And that is where we will leave you…until we hear from our heroes again, we will wonder and dream about if they have recovered the first ever Giant Beaver DNA sequence…

 

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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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Capturing, by Jacob

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.

Jacob at the Reichstag, the German capital in Berlin

Jacob at the Reichstag, the German capital in Berlin

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.

 

Rhino at the Berlin Zoological Garden

Rhino at the Berlin Zoological Garden

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!

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Gels and Beads by Mayeesha

Gels and Beads

After a 3-day weekend, on Tuesday we were all well-rested and ready to come back to the lab! We continued working with our ancient DNA extractions. We had already added a short DNA sequence to one end of the DNA fragments (i.e. an adaptor) that we can use later to amplify the DNA (that’s stage 3 of the single-stranded library prep–see previous post). On Tuesday we continued from Stage 4 all the way to Stage 7 (listed below and explained in the figure).

Diagram of Capture Process

Diagram of Capture Process

Stage 4: Attaching DNA to magnetic beads (using the adaptor we aded on Friday)

Stage 5: Copying the DNA (new copy shown in red below, making it double-stranded again)

Stage 6: Cutting the strands to be the same length

Stage 7: Attaching a second adaptor to both strands and separating the new copy (in red below) to use later—this is our ancient DNA library!

 

We then ran a quantitative PCR (qPCR) to find out how much DNA we had to be able to optimize the next reactions.

In the modern lab, we learned how to do gel clean-ups of the Long-Range PCR we had done on Friday.

This was a long day of lab work and by the end of it we were all tired and ravenous. So on the way we went to our favorite Turkish fast food restaurant to get doners and it felt like the best meal ever because the food came quickly and it was very yummy and filling.

Delicious Chicken Doner

Delicious Chicken Doner

On Wednesday morning, we were anxious to see our qPCR results because that would tell us if our library preparation was a success or not. It was!

We then proceeded with our library prep from Stage 8 where we amplified our library. After amplification, we purified the amplified libraries using MinElute and determined the fragment size distributions and concentrations of the libraries using Bioanalyzer with the DNA 100 chip. Next, we quantified the concentrations of our library using a Qubit and we were done for the day.

(P.S. When you read Jacob’s post, I did not insist we don’t buy tickets for the train to Berlin! Jacob just won’t admit that he couldn’t figure out how to use the ticket machine…)

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Friday’s lab work a success! by Mayeesha

So far, things look great: from using the TapeStation on our DNA extracts, we know that there are small fragments of DNA (likely ancient DNA, or aDNA) preserved in the samples that we brought from our C.ohioensis specimens at JMM– Heather treated us to ice cream to celebrate! We do not yet know for sure whether the ancient DNA is endogenous giant beaver DNA (which is what we want) or whether it’s environmental DNA (we don’t want that). Ancient DNA is difficult to find in specimens that are so old, for various reasons including DNA damage due to poor preservation. At least, now we know that our samples probably contain aDNA and for now, that’s reason enough to celebrate!

For our next step on Thursday, we started a long-range PCR with the modern beaver DNA. (Just a heads up, from here onwards this post is going to have a lot of scientific details, so you can skip to the last paragraph if you’re not into all the details). The whole mitochondrial DNA of a modern beaver is about 16,000 base pairs (bp) long. So, we ordered primers that would amplify the entire mitochondrion in two large overlapping pieces that are 6,000 bp and 11,000bp. We ran a long range PCR to amplify those fragments. We were a little nervous whether the long range PCR would work at the first attempt, because Heather told us that they fail more often than not. We left the products in the thermocycler overnight because it takes ~6 hours to run a PCR that can amplify such long fragments!

Every day, we plan our work in such a way that we finish all our ancient DNA lab work first, before moving on to the modern lab, in order to reduce contamination from modern DNA and PCR products. So, the next morning (Friday), we couldn’t go in to look at our long range PCR results until after we finished any work we wanted to do in the ancient DNA lab. So, first we suited up in our smurf suits and started working on our single-stranded DNA library prep. This method has been optimized to retain very small DNA fragments, which is important for working with the small fragments of aDNA. Since the library prep is a long process, we decided to break up our work over 3 days and on Friday, we did the first three steps:

  1. Ancient DNA is often damaged by the Cytosine base being deaminated and converted into Uracil, artificially changing the DNA sequence from a Cytosine to a Thymine. Since we want accurate DNA sequences, we cut the damaged DNA at any Uracil site.
  2. We then dephosphorylated and denatured the DNA using heat to separate the two DNA strands from each other so we could work with single stranded DNA.
  3. We then added a short DNA sequence, called an adaptor, to each DNA strand. This adaptor has a biotin molecule on it, which will make it easier to use in later steps, which we will explain in future posts!

This is a good stopping point because ligation products can be stored for several days at 20°C.

After finishing up our work in the aDNA lab for the day, we went back to our long range PCR. Heather was very nervous about how the PCR would turn out because we had limited time on hand before she has to return to the U.S. and so we really needed the first trial to work out. I, on the other hand, was (way too) excited about the pretty purple gloves they had in the modern lab!

Luckily, our PCR did work on the first try (see the photo below)! The 6kb piece was amplified very nicely (right side of the photo on top and bottom left) but the 11kb needs to be cleaned by running a second gel because some other smaller pieces of DNA were also amplified (top left). After cleaning, we will chop the DNA to ~500bp fragments which will be used to make baits for hybridization capture (more details on this later).

long range PCR success

This photo shows the PCR products and a DNA ladder run out on a gel to visualize the results of our long range PCR. It worked!!!

Since our long range PCR worked, it was time for another celebration! We know that we are still many steps away from getting our final results which means there are many steps where things could go wrong and we could end up with no results. So far, nothing had gone wrong, and that’s what we were going to celebrate!

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Holiday Weekend in Germany by Jacob

Mayeesha and I have decided to write about different things this time, so make sure to read both posts! She is going to discuss our lab work and provide updates on our research. I’m going to talk about our weekend.

After work on Friday, we went out with some of the other scientists. We went to a nearby restaurant and got flammkuchen (direct translation: flame cakes), these weird, flat German cream-cheese pizzas. While we ate, I got a chance to talk to some of the scientists I hadn’t met before. I really like the staff here. They’re all so funny. Afterwards, we went to a cafe in downtown Potsdam to get dessert.

We slept in late Saturday morning. I went on a run through some of the parks in the city. Potsdam is thirty percent parks and forests and thirty percent lakes and rivers, so the running trails are beautiful and plentiful. In the afternoon, we went to Sanssouci Park, the summer palace of Frederick the Great. It was very touristy, but very fun. We explored the gardens, which are incredibly elaborate and pretty. I love that in Germany most people keep their dogs off leash, so there are always dogs running around with which you can play. We also went grocery shopping. Most places are closed Sundays and holidays, so we had to make sure we bought enough food for the rest of the weekend.

Fitting in with the statues at Sanssouci Park

Fitting in with the statues at Sanssouci Park

Neues Palais in Sanssouci, built from 1763-1769 was a place to receive royal guests for Frederick the Great.

Neues Palais in Sanssouci, built from 1763-1769 was a place to receive royal guests for Frederick the Great.

Sunday, we went into Berlin to see a parade for the karneval der kulturen. The floats were pretty cool, with music and dancing and some crazy costumes. Interestingly, each float had a long rope around it held up by a group of people that walked with the float.

Note the people holding up a rope around the upcoming float!

Note the people holding up a rope around the upcoming float!

It was a long and slow parade though, so I explored the neighborhood after a while. I bought some bratwurst, which was delicious and the most German food I’ve had so far. After we all tired of the parade and the 1.3 million people attending it (!), we walked through a large park (Volkspark Hasenheide) south of the parade for a while. It was very busy and had a full carnival with rides and lots of sugary food. Then, Heather and Mayeesha went back to Potsdam, while I stayed and wandered around the city a little more. I wasn’t able to find any of the sites I wanted though, so I’m going to go back next weekend with a better plan. I especially want to see the Reichstag and the Holocaust Memorial.

My trip back to Potsdam was uneventful until I had to use the bathroom. The only bathroom in the train station cost one euro, which is ridiculous. I wasn’t about to pay to use a bathroom, so I jumped the turnstile. That set off an alarm, so I ran and hid in a stall. A security guard came in and tromped up and down in his heavy boots, looking for me, while I crouched on top of the toilet seat, so he couldn’t see my feet under the door. It was pretty scary. Luckily, my hiding place was too good and I was able to escape, without spending my hard-earned euro.

We had Monday off for some unknown German holiday. Heather and Mayeesha had work to do, so they mostly hung around the hotel. I went on a long run in the morning, leaving Potsdam and running through the farms in the surrounding countryside. I ran probably around 15 miles, so I was pretty tired and spent the rest of the day eating and napping. Heather was working on a paper, which she finished, so we celebrated by eating nachos. We feel rested and recharged, and are excited to continue our project and our adventure!

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Hallo! from Jacob

Hallo from Deutschland! Yesterday we began our research at the University of Potsdam. Our first day at the lab we met the scientists and made a schedule. This is a large lab group of ~25 people, all here working on different projects. Everyone is incredibly nice and friendly. Our work is facilitated by George Xenikoudakis, a PhD student. In the next two weeks, we’re aiming to work through half our samples with Heather taking point, and then the following two weeks Mayeesha and I will work with George to process the other half.

There are multiple sections of the facility, with different rooms for different procedures. It’s really important not to contaminate the labs, so if you go into the PCR room or modern lab, you can’t go back into the ancient lab until you’ve changed and showered.

Today, we donned our protective suits (and gloves and mask and hairnet and crocs and more gloves) and began the DNA extraction process, working in the ancient lab. We ground our samples into powder and added buffers to begin digestion, and left them heating in an incubator overnight. Tomorrow we’re going to finish the aDNA extraction, and test to see whether we have any DNA in our samples.

Jacob Harris in his ancient DNA smurf suit

My cool suit

We worked a little with our modern specimens as well, running them through the TapeStation machine, which through a gel electrophoresis-type process created a distribution showing the frequencies of different size DNA fragments. Longer fragments work better later in the process, and luckily our samples look like they have plenty of those. We’ve ordered the primers we need to start the PCR, and hopefully they’ll arrive soon.

I’m still a little jetlagged, so I didn’t say much and kept bumping into things. I think I’ve made an excellent first impression.

Potsdam is a beautiful city. I’ve been running every morning, and the trails and paths are awesome. I’ll be running on a forested dirt trail, and suddenly find myself in the ruins of a Prussian castle. There are walking and bike paths everywhere, so it’s really easy to run and explore. The food is great too. The bread is especially delicious, and I get these excellent sandwiches for lunch from the school cafe.

I’ve been learning so much. Being immersed in a lab environment is a great experience, and our work is clarifying a lot of what I’ve been studying, both last week and in CGI. I’m really looking forward to continuing our research, and hopefully not knocking anything else over.

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Arriving in Germany (by Mayeesha)

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:

IMG_0135

(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.

IMG_0142

George showing us how to use the TapeStation (above)

IMG_0144

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.

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Off to Germany!

My name is Jacob Harris, and I just finished my freshman year here at Earlham. I’m so excited to be part of this research. Mayeesha, the museum director Heather, and I are studying DNA from C. ohioensis, the ancient giant beaver. Because the DNA is so old, it’s incredibly unstable and difficult to sequence and study. We’re sampling some of the specimens in the Joseph Moore Museum, and then we’re going to Germany to work in a specialized aDNA (ancient DNA) lab!

The first two days of the project, we focused on learning background information about ancient beavers. We reviewed beaver phylogenies, and read current studies. Scientists are debating whether beaver populations in the Midwest and Southeast were the same species. These articles focus on the morphological differences, mainly altered bone structures in the skull and different dental patterns. Ancient beavers in Florida tend to have more smushed-shape skulls and broken lines on their molars, whereas beavers in the Midwest, the traditional C. ohioensis, have an elongated skull and jaw. John Iverson came by and gave us an anatomy lesson, which really helpful.

We hope that by sequencing the DNA we can add a genetic element to the discussion. Unfortunately, it’s very difficult to get DNA from ancient specimens. What little DNA is left is likely heavily contaminated with bacterial and human DNA, even with extensive precautions. Temperature changes and UV radiation fragment and destroy DNA as well, and so ancient DNA can be seriously damaged. Specimens in places with more stable temperatures tend to preserve DNA more effectively, and so we’re looking for specimens found underwater. One thing we hope to prove with this project is that we can get DNA from common specimens, which would set us up for further research. In this project, our methods are just as important as our findings.

Today we started the DNA extraction process. We took samples from areas of our specimens more likely to contain DNA, primarily dentine from the interior of molars and incisors, where odontoblasts grew new teeth cells. Between each sampling we cleaned our equipment with bleach and changed gloves, so hopefully we avoided contamination. We asked to borrow specimens from other museums, and they’re being shipped. We’ll take samples from them as well. I’m excited to find out if we managed to sample any DNA, and I can’t wait to go to Germany!

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