got milk?

by Emmett Smith on 2021-06-14 with 1 Comment

We woke up to snow-covered mountains surrounding the fjord. Iceland is beautiful because of its contrasts, and the starkness of white snow on black rock is no exception. After marveling at the view through the window, it was time to get down to business.

Me in the Skalanes Lab Area, working on DNA extraction. Photo by Yuejong Lee.

Yesterday, Faith Jackobs ’18 joined us from Houston, TX to work with us for a week while we’re camped out here at Skalanes. Faith has been on a previous EPIC Advantage Iceland trip, and joined us in 2019 to help with our ancient DNA project. Today we tackled DNA Extraction from Icelandic Soils, a protocol that has been in development since 2017. We have never had much success getting the DNA out of the soils of Iceland, because the type of soils we collect (brown andisols) are very good at binding DNA, and not very good at releasing it! I spent a lot of time in the fall of 2019 attempting to improve the DNA extraction protocol, and stumbled across a winning recipe. The secret? Skim Milk!

In 2005, Hoshino and Matsumoto published the following paper: “Skim Milk Drastically Improves the Efficacy of DNA Extraction from Andisol, a Volcanic Ash Soil.” In this paper, skim milk was added to a DNA extraction protocol during the first, important bead-beading step. This step is where the DNA is removed from the soil, and removed from any organisms living in the soil. It typically involves 10 or more minutes of intense vibrations in a small tube containing specialty beads and a buffer that protects the DNA from any enzymes/cellular debris present in the sample. I decided to incorporate the skim milk into our method. Back at EC, I meticulously added 10 mg of powdered skim milk to all of the bead-beating tubes in our kit to prepare them for the protocol.

The other piece of the puzzle that fell into place was creating enough of a vibration that the bead-beating step could properly do its job. Charlie and I created a device we’re calling the “Porta-lyzer” – see my previous post for a video. It seems that, in combination, this device and the addition of the skim milk worked like a charm. We’ve gotten the best DNA extraction results ever here at Skalanes.

Need proof?

	2017	2018	2019	2021
Average:	4.2	27.2	52.7	66.83
StDev:	2.67	14.82	42.15	47.04
StErr:	1.20	4.28	12.17	10.79

Table of DNA Extraction Performances for the past 4 trips to Iceland. Note that 2019 samples were processed at Earlham, with all the best lab equipment, not here at Skalanes.

Needless to say, I’m thrilled. We even collected DNA from the elusive Solo era A – which has only been out of the ice for ~20 years, and is always an era that gives us lots of trouble.

Now it’s time for a celebratory adult beverage and a walk out to see the puffins. Cheers!

To see a condensed video of Faith and I working on the extraction protocol, click here!

Finally, in Skálanes

by Davit Kvartskhava on 2021-06-09 with No Comments

Writing’s not really my forte, so I’ve been postponing writing a blogpost for quite a while now. I guess it’s the right time to introduce myself, the work I’m doing in Iceland, and some highlights from the past couple of days.

My name is Davit. I recently graduated from Earlham with a degree in Computer Science. I’ve been involved in Icelandic field science research since my junior year. Our plan to go to Iceland in 2020 failed miserably because of the global pandemic. We all waited patiently (or not) for one full year, and then a week ago we drove to Chicago, flew to New York and then to Keflavík. In reality, the trip was way more complicated and tiresome than I just made it sound; but arriving at Skálanes flushed away all the annoying details of getting here.

*Me and Craig, working side by side. Photo by Yujeong Lee.*

Wet, exhausted and frozen, we made the final 2 km hike on foot. As we walked, our path took us through a permanent tern colony, which is an important part of the preserve. At Skálanes we were greeted by our host – Olí who had already prepared a hot meal for us. He told us that the next day would be sunny – an Icelandic luxury that we had to take advantage of. Next morning, we got up early and started working on using our drones to survey areas of archeological interest.

A few details about how I’m involved in this research:

Most of the work that I did on campus involved refining the workflow of surveying to ensure that everything would go smoothly in Iceland. This included familiarizing myself with the drones and practicing flying them manually. I also built a web interface for the visualization of the near-infrared (NIR) images taken by the drones. I have been a sysadmin at Earlham for almost 3 years, so I was also helping in plumbing up different software and tools that the research depends on.

The last two days the clear weather has allowed us to fly the drones. We have tried to make the most out of it! After Charlie picked the first spot for us, Craig, Tamara and I went to the surveying site. We have been using a Phantom P4 drone with PixD4 software to make automated flights. By taking a good amount of photos from 50 meters of elevation we will be able to build 2D and 3D models of the terrain.

*Waiting for the drone to finish the flight mission. Photo by Yujeong Lee.*

Unfortunately, we had a bit of bad news too. Our only drone with NIR lenses is a bit jet lagged and is stubbornly refusing to calibrate its gimbal. Once it starts raining again (it won’t be long!) we will be forced to work inside. Then, we’ll have the chance to focus and solve the NIR issue. Meanwhile, we are using the ordinary lenses to harvest as much data as we can.

Today, we flew the drones at a spot where the terns are nesting. They’re beautiful birds, but they were not at all happy to see us doing science nearby. They made continual short ranged attacks by pecking us, and also engaged in long ranged bombing efforts as they dropped their biological weapons on our heads.