This past weekend, the museum held a Homecoming Alumni Open House from 10 a.m. until 2 p.m. The event was a smashing success, with over 150 visitors stopping by the museum, some of whom increased our Memory Jar collection, leaving behind memories of their time here at the Joseph Moore Museum. Visitors also got to enjoy a sneak peak at our new exhibit on climate change. Alumni, current students, and faculty roamed the entire museum, commenting on the changes that have taken place, the climate change sneak preview, and enjoying refreshments in the lobby while chatting and sharing memories. Having the chance to talk with past museum staff members provided our current staff members with new tips and tricks and connected past generations to current members.
Associate Professor Julia Nelson-Hawkins’s talk on Friday, October 9th, went very well. Listeners were arriving early to the presentation, until every seat was taken and students, faculty, and other listeners began to stand around the perimeters of the room. Professor Nelson-Hawkins talked about how the ancient methods of medicine practiced by the Greeks have influenced today’s medical field and the new classes that are being created to delve into the intricacies of how ancient medicine and modern medicine are connected. Professor Nelson-Hawkins discussed how the ancients viewed diseases and the emphasis that was placed on the connections with the divine and the natural world.
The reception afterwards went swimmingly, as well. Students were asking questions and were engaging in the discussions. Overall, the presentation given by Associate Professor Julia Nelson-Hawkins gave students and faculty new understanding about how ancient medicine is affecting today’s medical field.
We’d like to give a warm welcome to Erika Nelson, who has joined us to work as the museum’s Community Engagement Director. Her work managing tours, outreach, and events makes it possible for the museum to connect and interact with the community. She was gracious enough to sit down for an interview with me, and I was able to learn more about her background and interests, as well as find out her goals for the future.
Mia: Where are you from?
Erika: I’m from Oxford Indiana, around 40 minutes away. My parents came 53 years ago and thought they’d stay for only one year.
M: What’s your job like at the museum?
E: At this job, I get to be very creative. I’m passionate about connecting people to each other, nature, and science. The museum can be a way for people to access these things. My goal is to be that. Have after school programs, and get kids in here to ask questions or touch something as a way of learning.
M: How did you find out about the museum? What brought you here?
E: I’m an educator. I teach at Miami University. I was looking for additional jobs and saw “community engagement”, and I thought, “That’s what I do!”.
M: What kind of background do you have with museums? With community engagement?
E: I’ve always worked in volunteer development and education development. I’ve worked with volunteers, and you need to have good relationships, listen to people, and be an advocate for them. As an anthropologist it’s been a natural thing for me to be responsive to other people’s needs and help people engage.
M: What’s your favorite part of the museum?
E: I love the mummy. It’s so fascinating to think that that was a real human being that people touched and knew. But I love elephants, so I also love the Mastodon because I lived in Africa.
M: What are you looking forward to this upcoming year? Do you have any long term goals?
E: I want to increase people’s access to the museum, have more students coming in, and multigenerational programs. I’d like to have inside and outside activities because kids get enough time inside.
M: If you had an unlimited budget for the museum, what would you do?
E: Where to begin right? Brand new building, new space, and space for things to be preserved properly. Expand the interactive learning centers and be closer to the woods and road.
M: What’s your favorite animal?
E: My totem animal is the slug. They are patient and slow moving, probably characteristics I need to develop. I am a very forward thinking and driven person.
A big thank you to Erika for participating in this interview. The museum is super excited to have you, for you are a great addition to this community. We are looking forward to seeing where your skills and ambition takes us!
It’s been a few weeks since the first day of classes, and the fall semester is in full swing. Each semester always brings change to the museum: students graduate, or leave campus to study abroad, and new team members are greeted with open arms. This semester’s change is particularly poignant, as we bade farewell to nine graduating students (a third of the staff!) Alongside the departure of many other staff members for study abroad programs, the effect was stark.
Yet with our first meeting of the school year, we were able to welcome back staff members who had studied abroad last semester, as well as many excited new faces. Each staff meeting is bustling with people, and everyone is energetically working towards completing their goals each week, from replacing collections trays to preparing for tours. We also welcomed a new non-student staff member this semester, our new community engagement director Erika Nelson. (Stay tuned into the blog in the next couple weeks to learn more about Erika and her work with the museum!)
The new semester promises exciting new events, and other changes to the museum beyond staff demographics. We are all eagerly looking forward to the introduction of a new exhibit on climate change in November, and are hard at work planning for the myriad other events set to make this semester great! We are also very excited to begin work on redesigning our existing exhibits, and we have wonderful guidance in the process.
Things are different, as they always are at the start of a new semester. Perhaps it’s a little more different this semester than last. But it’s good to be back, and the rest of 2015 promises to be even better.
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.
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…
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!
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!
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!
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).
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.
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…)
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:
- 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.
- 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.
- 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).
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!