We have two free events this September!

Building with Biology


Learn about the emerging field of synthetic biology and its connections to society. Talk with real scientists and other interested people!

These events are part of a nationwide festival designed to introduce guests to synthetic biology content. They aim to promote informal, two-way conversations between the scientists and visitors about how synthetic biology is interconnected with our society. Free admission to the public!

Should We Bioengineer the Mosquito: A Public Discussion

Thursday September 22, 7-9pm

Center for Science and Technology at Earlham College, Room 300

Register here, space is limited to 60 participants: Registration Form

This is a special opportunity for scientists and the public to interact and learn from each other, and share ideas and opinions about how we want to see these new technologies developed and adopted.


Building with Biology Activity Day

Saturday September 24, 1-5pm

Joseph Moore Museum

Enjoy fun, hands-on activities facilitated by Earlham College science students. You can:

  • Design a “Super Organism” to solve a problem
  • Extract DNA from wheat germ
  • Discuss which future technologies you’d support


The Building with Biology project is funded by the National Science Foundation and led by the Museum of Science, Boston. Building with Biology kits are developed and distributed nationwide in collaboration with the American Association for the Advancement of Science (AAAS)BioBuilder Educational Foundation, the National Informal STEM Education Network, Science Museum of Minnesota, Sciencenter, and Synthetic Biology Engineering Research Center (Synberc). Events are taking place at over 150 museums and institutions throughout the country from June through September, 2016.

Categories: Uncategorized | Leave a comment

Debriefing: Notable Quotes

Overheard in the lab:

“Science isn’t all serious.”

“Maybe there was a giant beaver war”–suggestion as to why giant beavers became extinct

“For people who enjoy beavers, this is a sad time.”

“Tiny baby beaver teeth”

“We may be able to use the force, but we can’t keep the lights on”–when the lights in the modern lab kept automatically going off even when we were using the centrifuge

“My fingers are indeed dirty. I will get new fingers.”–said when new gloves were needed

Tare Puns:

“That’s terrible,” “Only a terrorist would do that,” “You’re tearing up our hearts,” “I’m going to tear myself away,” and many more.

2016-05-11 14.40.48

Heather wearing a beaver


Categories: Uncategorized | Leave a comment

qPCR, Strawberries, and Kids

Heather came in on Saturday to check on our DNA library that we had left on the heat block overnight. She discovered that the liquid at the bottom of the tubes was brown. It seemed like some of the liquid had evaporated. This was not good, so she vortexed them and hoped for the best.

We spent Tuesday morning washing our beads. The beads are magnetic and can attach to the DNA. Using magnetic beads is great for ancient DNA because they prevent tiny DNA fragments from escaping. Washing the beads was very visually pleasing because they were brown as opposed to clear. Moreover, we got to use the magnetic rack, which has magnets that pull the beads to one side of the tube. We would start by adding a wash buffer to the tube with the magnets and the solution would be brown. We would then place the tube on the magnetic rack and watch the solution gradually become transparent (video) with a small ball of beads huddling by the magnet.

2016-05-31 10.52.00

Emily showing of the magnetic rack. The black circles are the magnets.

In the afternoon we made a qPCR to see if our DNA library was successful. Unfortunately it was not. The samples started amplifying at around 25-28 cycles and looked no different than the qPCR blank. Last year the samples started amplifying at 20 cycles. It is possible something went wrong with the qPCR machine, but we guessed that the library didn’t work because of Saturday’s discovery of the brown liquid and evaporation. Luckily, a heated lid for the heat block would prevent evaporation and the formation of brown liquid. We are ordering one now.

On Wednesday afternoon we did a DNA demonstration with Miller Farm’s kids’ camp. We showed 7 kids ages 5-8 strawberry DNA and let them help us mash the strawberries. We added dish soap and Gatorade to break down the strawberry cells and then pineapple juice, which has enzymes that break down proteins. Finally we added cold alcohol to separate out the DNA. After letting the test tube sit, we could see a layer of white, goopy stuff that was the DNA.

2016-06-01 15.05.08

The white layer is strawberry DNA

2016-06-01 14.02.29

Using transfer pipettes for pineapple juice

2016-06-01 13.54.56

Extracting DNA from cheek cells

We then let the kids see their own DNA. After swishing Gatorade in their mouths for two minutes, they spit into test tubes. We added dish soap and cold alcohol and showed the kids how to use a transfer pipettes to add the pineapple juice. The kids loved using the transfer pipettes. While waiting for the DNA to separate out, we had the kids make DNA bracelets. They got to choose a DNA sequence from options such as human, butterfly, cobra, flesh-eating microbe, and cockroach DNA. They had to read the sequence and put colored beads corresponding to A,T,C, and G on one string and then figure out the corresponding base pairs to put on the other string. After they finished the bracelets their DNA had separated from the Gatorade and soap. We put the DNA in a little test tube and attached the test tube to a string to make a necklace. It was a nice change of pace to be outside with the kids, and the kids seemed to enjoy learning about DNA.

2016-06-01 14.29.02

DNA bracelets

2016-06-01 14.31.28

Emily helping with bracelets

Categories: Uncategorized | Leave a comment

Shear Joy

On Tuesday the 24th, we tried to shear our modern beaver DNA into pieces about 150-200 base pairs long so that we could continue making our baits. Shearing DNA involves putting the sample into a machine called a sonicator that uses ultrasonic waves to break up the DNA. Think of an ultrasonic jewelry cleaner, but much more powerful. The sonication machine was brand new, so we didn’t know for sure how long to run it for or what intensity to use. Our first try was a conservative 3 minutes at 30% intensity, which worked nicely; the DNA got down to about 900 base pairs. After this, we ran into trouble. We sheared the DNA again to get it down to the size we wanted it, but it seemed like no matter how long or on what intensity we ran the sonicator, we couldn’t get the DNA below about 300 base pairs. We ran the sonicator five times on Tuesday, and after calling the company for troubleshooting on Wednesday morning, we ran it three more times. Finally we got the DNA down to about 200 base pairs. On Thursday, we used the sheared DNA to finish creating the baits. We used the Nanodrop machine to see how many baits were present, and the result was incredibly high. So high, in fact, that we were very suspicious about how true that was. We plan to run a more accurate test later to see how successful we actually were.

2016-05-24 12.56.30

The sonicator  makes an ear-splitting noise

2016-05-24 13.03.45

Up close and personal with the sonicator. We had to maintain the water level exactly at the level of the samples in the tubes. If it got to high, the samples would jump up the sides of the tube and escape shearing. 

2016-05-25 12.21.24

Shearing is a three-person job

Categories: Uncategorized | Leave a comment

Cats and Korlević

Doing research involves a lot more than just lab work. We also read a lot of papers from people who have done foundational research that we’re building from. Two such papers are “Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA” by Gansauge and Meyer (2013), and “Reducing microbial and human contamination in DNA extractions from ancient bones and teeth” by Korlević et al. (2015).

Gansauge and Meyer introduce and test a new method for improving the recovery of ancient DNA for DNA sequencing. In this method we take ancient DNA and add little bits of known DNA sequence to them that we can use later to copy the ancient DNA and sequence it. Many copies of the ancient DNA (with attached known sequences) are called a DNA library. In ancient DNA, many strands of DNA are often damaged and broken. DNA is present as two attached copies. Previous methods required both strands to be present and intact, but if they’re broken they get lost during processing. The thing that differs in this method versus others before it is that this method uses single-stranded DNA instead of double-stranded, so much more of the DNA is sequenceable. Another cool thing about this method is that they bind the DNA to magnetic beads so that they can be sure they aren’t losing any of it.

Korlević et al. talk about the contamination present in ancient DNA and how to decrease it. We don’t often think about it, but literally everything is covered with bacteria, and bacteria all have their own DNA. This means that any sample will be contaminated with bacterial DNA, and often with human DNA from handling. Korlevic et al. test three different methods of getting rid of the extra DNA: (1) using bleach on the samples, (2) incubating the samples in a phosphate buffer, and (3) re-extracting the DNA from the sample multiple times. Bleach was the best at getting rid of the contaminating DNA, but it also got rid of a lot of the target DNA, so it isn’t a good method for rare or precious samples. The phosphate treatment turned out to be the safest, since it preserved all of the target DNA, but it also didn’t get rid of as much contaminating DNA. The re-extraction method didn’t help significantly, and even made the contamination worse in some cases.

Reading papers like these is important for understanding the work that came before ours, and putting our own work into context. The papers can be difficult to read and understand, but reading them is an essential part of the research process. It’s also not too bad when you get to pet kitties while reading!



Maren and me at Heather’s house reading papers with her cat, Legolas.

Categories: Uncategorized | Leave a comment

Playing with fun machines


On Wednesday Chris Smith kindly showed us how to use fluorescence to determine how much mitochondrial DNA we amplified last week. This is done on a Quantitative PCR (qPCR) machine using picogreen.

When we ran our reaction, both long products and unintended smaller pieces amplified. We needed to separate the unwanted smaller products out from the longer ones. To run all nine samples using four primer pairs, we had to run two gels. Gels use charge to push DNA through the gel. DNA is negatively charged, so applying a negative charge forces the DNA to move through the gel. Bigger pieces of DNA will get stopped in the gel earlier and smaller pieces will travel further, so when looking at the gel after it is finished running, we can determine which bands are bigger pieces of DNA.

I enjoy making and running gels because we can finally see what we are dealing with. We mixed 1 g of Agarose in TAE, and then heated the mixture up in a microwave. Apparently Agarose is quite viscous and will burn you and refuse to come off if it touches your skin, so Heather kindly didn’t let us handle it while it’s heating. After the Agarose dissolved we poured the gels and learned the hard way to not assume that they’re set before trying to yank them up.

Unlike yesterday, we ran the gels at the recommended 60 mV so that our bigger chunks of DNA wouldn’t be pushed through the gel too quickly or get heated up and damaged. After an hour we read the gels under UV light and they both showed DNA, which was a good sign.

However, we still needed to get the DNA out of the gels. The Gel-Doc has a UV light underneath the tray that the gel sits on, so the DNA bands are illuminated. We cut the brightest bands (the DNA) out with a razor and put them in a tube. This was dicey because we had to wear sunglasses and a scratched or damaged UV shield so that the UV light didn’t burn us up. This made spatial reasoning more difficult. The bands were completely surrounded by the gel, so we had to cut the gel away from all six sides of the band while moving quickly enough so that the DNA wouldn’t be damaged by the UV light. While one person cut out a band, another would tare a labeled tube and then hold it out for the cutting person to put the band in, then weigh and record the tube, and finally return for another band and repeat the process. We had an exchange of tare puns with Peter’s group. There were some terrible ones and we finally had to tear ourselves away.

2016-05-18 15.20.51

Cutting out the bigger bands from the gel using the guidance of the Gel-Doc’s inner UV light. 

After we got the bands in the tubes with nobody burned from the UV light, we added a Guanidium buffer (more Guanidium! Yay!) to each tube and centrifuged the tubes. We ended the day by eluting the DNA cut from the gels and loading the qPCR machine. Unfortunately, we failed to retrieve the data but the next morning Chris saved the day and exported our data. Luckily the data was there; we had just messed up getting it off the computer. Unfortunately, the data wasn’t great: some of the samples that should have had similar values were drastically different and our standard curve was not a nice line. We figured that our pipettes were off and got permission to use Chris’s pipettes for the next time. We re-ran the picogreen assay and got improved results: our standard curve had an r^2 of 0.89 and the values were more similar across primers. Primers A-D had reasonable amounts of DNA but Primers E-H had extremely low amounts.

2016-05-18 17.23.45

Plastic knuckles for ensuring that the caps on the tubes are secure for the picogreen assay! 

Categories: Uncategorized | Leave a comment

In which we calculate Molarity and get our First Results

The past few days have gone by quickly! Apparently, we did six days of work in our first five-day week, which was satisfying to learn. By the end of last week we had made our binding buffers, added them to our samples, and centrifuged them, and set up our Long Range PCRs.

However, Friday was the 13th, so some mishaps were to be expected. The Binding Buffer called for 39.8 g of Guanidine, a solid that looks like sugar that’s been sitting in someone’s china cabinet for 10 years. Guanidine becomes Guanidium in water, although it is notoriously hard to dissolve. Even still, 39.8 g seemed like too much, so we ran around and did math until we figured out that it was supposed to be 23.8825 g. Today, Heather found out that the protocol we had been using had miscalculations, and that we were correct to use 32.8825 g of Guanidine. That was a relief!

We have a vortex in the Ancient lab, but it strangely didn’t come with a plug. The cord just ended in a series of wires. Heather bought a plug and we wired it ourselves to no avail. In the end, we used our inner human vortexes and it was fine. At the same time, our pH meter didn’t want to calibrate, so Emily spent a long time fiddling with it. We needed to get the pH of the sodium acetate to 5.2. Eventually, we got close enough.

On Monday, we had a shorter day. In the morning, we made several Wash Buffers in the Ancient lab. Everything went smoothly. The only hiccup was when we discovered our SDS was 10% instead of 20%, so we compensated by using twice as much and adjusting the amount of water added to the solution. After lunch, we went up to the modern lab and made a gel to run the Long Range PCRs on. Previously, I had only used pre-cast gels, so it was satisfying to make the gel ourselves. We pipetted our DNA into the wells as quickly as possible so that the DNA couldn’t leak out. After the gel was finished running, we looked it on an imager. The gel (below) showed excellent amplification of partial mitochondrial genomes for the modern beaver!

LR PCR Gel 16 May 2016

Gel of Beaver Mitochondrial DNA: There are two rows. The two long smears on each end of the top row and in the second to last lane of the bottom row show a DNA ladder with known (short!) sizes of DNA fragment. The other bands on the top row are ~11,500 bps of DNA, while the bottom row has ~6,000bp fragments of DNA. 

Now we can go forward turning those sequences into baits to fish out ancient DNA.

Categories: Uncategorized | Leave a comment

A Beaver Up Your Sleeve, or What Happened on Wednesday

On Wednesday, we went into the Joseph Moore Museum research collections and decided on three museum specimens to sample for sequencing.

The first was a male Castor canadensis, the North American beaver. It was collected in 1965 from Beaver Creek in Alaska. Initially, we wanted to sample from one of its toe pads, but it turns out whoever prepped its skin turned its feet inside out so the pads were unreachable. Heather tried really hard to get to them, though!

2016-05-11 14.40.48

A beaver up your sleeve? Heather tries to reach the beaver’s toe pads.


We ended up taking a molar from its skull instead.

2016-05-11 14.42.11

Maren extracts a molar from the beaver specimen.


The second specimen was a male Geomys bursarius, the plains pocket gopher. It was collected in 2001 from Gimlet Lake in Nebraska. Pocket gophers are pretty small, and therefore don’t have very large toe pads, so we elected to sample teeth from this specimen as well.


Plains Pocket Gopher (Geomys bursarius)


The final specimen was a Dipodomys ordii, the Ord’s kangaroo rat. It was also collected from Gimlet Lake in Nebraska, in 2010. The sex of this specimen was unknown because the tag was marked with an ambiguous gender symbol. This specimen had no skull associated with it, so we were sampled a toe pad. However, its entire right front paw was barely hanging on. We decided to help it along the rest of the way, and took the entire paw.


Ord’s Kangaroo Rat (Dipodomys ordii)

In addition to sampling museum specimens, we also took time on Wednesday to clean the ancient lab. It had been a while since anyone had used it extensively, so it needed a deep clean. Everything, and I mean everything, had to be wiped down with bleach to get rid of any potential contaminating DNA. Benchtops, equipment, bags of tubes, and boxes of gloves, all bleached thoroughly. We swept the floors and organized everything as well, all while wearing full body suits and masks to prevent our own DNA from contaminating the lab. It was hard work, but everything looked great once we were done.

2016-05-11 16.45.26.jpg

All suited up for the ancient DNA lab (Left to right: Heather Lerner, Emily Buttrum, Maren Schroeder)

Categories: Uncategorized | Leave a comment

Emily’s Introduction

Hi guys! My name is Emily Buttrum, and I’m Heather’s other research assistant for this summer. I’m a senior biology major from Indianapolis, and I have an intense love for all critters, giant and otherwise.

On Tuesday, we finished our extraction of the modern beaver DNA while practicing our pipetting skills. Micropipettes are surprisingly sophisticated and delicate tools used to transfer extremely precise volumes of liquids. Knowing how to use them properly is key to getting good results. Thankfully, good results are exactly what we got. A quick analysis of our extract with the Nanodrop system showed that it contained tons of useable modern DNA (more than 60 ng/ul!). We stored the DNA in the refrigerator until we get some of the materials necessary for the next step in the process: DNA amplification via PCR.

2016-05-10 13.52.23

Maren (left) and me, Emily (right), finishing the extraction of modern beaver DNA.

In the afternoon, we read a paper about the mitochondrial genome of the modern beaver and how slowly that DNA changes. In short, the study asserts that because beavers have such long lifespans (for rodents), their mitochondrial DNA changes very slowly. We think that this slow evolution could be a contributing factor to why every other past beaver species (38 in all!) have all become extinct.

In the process of reading the paper and filling out a “message box” on it, we also discovered that modern beavers might be most closely related to a family of rodents called Geomyoidea, which includes pocket gophers and kangaroo mice, but that has not been tested with mitochondrial genome data.

We want to sequence a genome from a specimen or two of Geomyoidea, to test this hypothesis.


The Plains Pocket Gopher  (Geomys bursarius) is a member of the Geoymoidea.


Categories: Uncategorized | Leave a comment

Ancient DNA Summer Research Intro

My name is Maren Schroeder, and I’m a junior at Earlham. I’m lucky enough to be one of Heather’s research assistants this summer. I’m a neuroscience and comparative languages and linguistics double major. In my spare time, I enjoy horseback riding, wandering around outside, petting the barn cats, eating peppers, and thinking. I’m excited to work with ancient Giant Beaver DNA because I’ve never done anything like it before and I love learning about DNA. No matter how this project turns out, I’ll learn something and that’ll be cool.

As for the actual project, our science-y goal is to extract DNA from an ancient Giant Beaver (Castoroides ohioensis). If you’ve been to the Joseph Moore Museum or follow our blog, you probably already know that Giant Beavers are an extinct species of beavers that lived during the Pleistocene era. We aim to see how genetically similar the Giant Beaver is to the modern beaver.

Since we may or may not be successful in extracting Ancient Beaver DNA, we made some other goals. Our other goals are to do science for ourselves and not for our grades, improve our lab skills, understand the nuances of working with ancient DNA, maybe publish something, and have fun. If we fail to get a single base pair of ancient DNA, that failure will be purely a learning experience and not a GPA-tarnishing humiliation. We’ll all learn something and it will be fine.

On our first day, we did a mishmash of everything, from meeting each other, going over our goals, writing a schedule that was erased and rewritten multiple times, ordering oligonucleotides (short DNA sequences that will be attached to the ancient DNA), finding some modern beaver tissue to get DNA from, digesting the tissue, and leaving it in a tube to float in some hot water overnight.

As it turns out, it is very unlikely to successfully extract and analyze ancient DNA. DNA degrades and makes errors over time. Living organisms have cellular mechanisms to catch errors in DNA replication, which is why we’re still alive. However, dead things do not have this ability, so their DNA basically sits and messes itself up for thousands of years before we come along and try to analyze it. The DNA may be mixed with bacterial DNA from the outside environment, various proteins may chop the DNA up, there might be a T base pair where there was originally a C base pair, heat may degrade the DNA, and the list goes on. Therefore, any ancient DNA strands we get will be very short, likely less than 100bp. Depending on the environment, DNA that is 100,000-1,000,000 may be preserved. DNA will be better preserved in cold, dry environments.

After going over all of that, we got to work. We found some modern beaver tissue in a freezer, weighed it (about 21 mg), chopped it up into tiny pieces and put the pieces into a tube, added some enzymes, and left the tube to sit in a hot water bath overnight.

2016-05-09 16.03.12

Emily weighing out modern beaver tissue.

2016-05-09 16.03.21

Getting tiny bits of chopped up beaver tissue in a tube.

We read a paper about the evolution of swimming and tree-exploitation behavior in beavers, which found that swimming and woodcutting evolved in beavers only once, and had implications for how beavers might evolve/react to climate change in the future. The paper noted that beavers survive winter by creating food caches underwater from trees that they cut down themselves. The chemical defenses in Poplar trees probably evolved as defenses against beavers. If the earth becomes warmer and beavers stop creating caches, there could be secondary effects on the species that interact with beavers, including animals that live in the lakes created by beavers and the trees beavers predate.


That’s all for now! Thanks for reading!



Categories: Uncategorized | Leave a comment

Blog at WordPress.com.

%d bloggers like this: