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!

The Porta-Lyser (TM) And Other Wins

by Emmett Smith on 2021-06-02 with No Comments

Today Charlie and I had a few wins – seems like the 4th trip to Iceland is the charm. We’ve been continually working to streamline our DNA extraction procedures so they can be done reliably in a makeshift lab at Skalanes. Today we took another step toward creating that reality.

One of the major steps of extracting DNA from soils is to physically separate the DNA strands from soil particles. This is not as easy as it might seem. Many soils strongly attract DNA, and the specific soil type we are working with in Iceland, a Brown Andisol, is one of these strong DNA attractors. In order to separate the DNA from soil, we need to mix a bit of soil with specially-made beads. We also add a bit of powdered skim milk to help keep the DNA from re-binding to the soil particles once it unbinds. However, the mixing step, or “bead-beating,” is critical. It needs to be done using a special vortex adapter for 10-20 minutes. We have a small vortex in the lab at Skalanes, but we’re not sure if the adapter will fit it, or if it goes as fast as we need. Therefore, Charlie rigged up what we are calling the “Porta-Lyser.” Here is a video if it in action – looks like it works a treat.

Other wins for today – we were able to reduce our checked baggage quota by one; we have almost all of our gear ready to pack into the van (which means we get a late start tomorrow morning!); and we were able to score some great NatGeo t-shirts to wear while working in Iceland!

Tonight we will gather for some Gulzars and watch an Icelandic documentary at my house. Tomorrow we will finalize our checklists, print and laminate them so they are ready for the field, and pack up the van that will take us to Chicago early Friday morning for the first leg of our journey.

Sunday Funday

by Emmett Smith on 2019-06-16 with No Comments

Hello faithful blog readers. Today was pretty foggy, so we were unable to fly any drones due to condensation on the electronics. However, folks got other projects to work on like analyzing the data we had already collected and working on monitoring the flow of one of the rivers, to assess its potential for hydropower. The fjord is beautiful in the fog, though, and many of us appreciated it by taking hikes, both long and small.

An exciting test pit was dug – over 1 meter of soil was removed from a square meter of land in a known previously habitated site at Skálanes. Óli and Rannveig worked hard to excavate the area, and then we took 13 samples – one for every 10 centimeters. We hope to measure the amount of sheep DNA in each layer – we assume that settlers brought sheep with them, and so sheep DNA should be present in habitated layers and not present in layers that are not habitated. We’re also working to identify the tephra layers (soil horizons which were layed down by volcanic eruptions). It’s not clear out here which layer is which.

Tomorrow is Icelandic Independence Day! We will continue to collect soil samples and drone imagery in the morning, since it is supposed to begin to rain in the afternoon.

In which we take a scenic drive

by Emmett Smith on 2019-06-09 with No Comments

Hello dear readers! We awoke to another day of beautiful weather and warm sunshine, which was enjoyed by the small herd of napping horses along the river. Charlie and I can’t figure out what we’ve done right to have 9 straight days of sun but the students are starting to doubt they need all that rain gear we emphasized so strongly …

Today we drove from Kirkjubæjuarklauster to Stöðvarfjördur with many stops in between. This drive took us from the south coast of Iceland to about half way up the east coast. Our first destination was to another glacier coming from the Vatnajökull ice cap (the largest in Europe) called Kviárjökull. We are scouting this glacier to see if it’s a good candidate for additional sampling in the future, so we can compare data from Sólheimajökull with another Icelandic glacier.

Note the mounds leading up to the glacier (moraines) – these mark places the front of the glacier has been in past years.

Our second stop is the lovely “Glacier Lagoon,” or Jökulsárion, where the Norðlingalægðarjökull glacier calves into the sea. This is the only glacier that calves directly into the sea in all of Iceland. We saw seals swimming in the lagoon along with eider ducks, gulls, Arctic terns and a few foolish/brave humans in kayaks!

The round black dots are indeed seal heads – 4 in total!

Stunning. I’ve never seen Iceland skies this clear.

After driving past 3 other outlet glaciers, we took a brief detour to the fishing town Höfn, where we were treated to a fabulous view of Vatnajökull and its outlet glaciers.

The day was getting more cloudy (finally!) as we drove another stretch of Route 1 to the small village of Djúpivogur for a bathroom break and important re-caffination. Yours truly also acquired a traditional Icelandic doughnut. Yum! The town is quite old and has a number of buildings dating from the late 1800s and early 1900s. They are also, apparently, quite proud of their toilets.

After journeying along a few more fjords and twisty roads, passing a number of camping vans along the way, we arrived at our destination – a schoolhouse in the small village of Stöðvarfjördur, a 5 minute drive away from the archaeological site we’ll be working at Monday and Tuesday. This site is significant for a number of reasons, which you can read about here and here. Tomorrow we will work with the drones, flying over the site and gathering information such as Near Infrared, which can point us to locations that were previously populated by humans. On Tuesday we’ll use that information to collect soil samples and test differences between microbial populations in soils that have been previously inhabited versus those that have not. But perhaps most importantly, the school has a washing machine, which has allowed us to finally get some clean clothes.

Good thing tomorrow is a holiday and school is not in session!

Wish us luck on all our work in the next few days. Signing off, your friendly neighborhood molecular biologist!

I Participated in IFS2018 and all I got was “Hooked on a Feeling” Stuck in my Head

by Emmett Smith on 2018-06-23 with No Comments

Sing it with us now … (https://www.youtube.com/watch?v=NrI-UBIB8Jk)

Ooga-chaka Ooga-Ooga
Ooga-chaka Ooga-Ooga
Ooga-chaka Ooga-Ooga
Ooga-chaka Ooga-Ooga

I can’t stop this feeling
Deep inside of me
Iceland, you just don’t realize
What you do to me

So much day-light
There is never night
Hiked a glacier
Everything’s all right

I’m hooked on a feeling
I’m high on believing
The beauty of this place

Terns aren’t sweet as candy

They dive-bomb all the time
Chicks got weighed and measured
Getting pooped on is just fine

We got bugs on stickers
But we don’t need no cure
Just keep flying Kia
We’ll get data for sure

Let’s play Euchre

Or some Carcassonne
Oh-oh, Iceland
Yeah, you turn me on

I’m hooked on a feeling
I’m high on believing
The beauty of this place

Did some camping
Spent some time alone
Oh-oh, Iceland
Yeah, you turn me on

I’m hooked on a feeling
I’m high on believing
The beauty of this place

I’m hooked on a feeling
And I’m high on believin’
The beauty of this place

I said I’m hooked on a feeling
And I’m high on believin’
The beauty of this place

Icelandic Field Studies 2018 is officially in the books. It was a great trip. It’s hard to believe we have been in country for 3 full weeks – things have gone by so fast. There were many firsts on this trip – it was the first trip to collect soil for aDNA extraction from an archaeological dig. The first measurement of tern eggs and hatchling weight in lupine vs. non-lupine environments. The first Earlham study of insect populations in lupine vs. non-lupine environments. The first structure-for-motion attempts from our drones. The first camping trips into the Skálanes hills. The first hikes in the Klauster hills. The first viewing of Iceland in the World Cup!

We had lots of similarities from previous years. We toured the Golden Circle to see historical and natural sites of interest. We hiked the volcanoes on Heimaey to test our elevation platforms. We spent quality time at Sólheimajökull, using our elevation platforms and drone to approximate the volume of its nose, as well as collecting soil for bacterial DNA extraction and measurement. We enjoyed our stay at Skálanes – what a beautiful and soul-filling place. We played many a game of Euchre, Carcassonne and Settlers of Catan.

To everyone following along on this blog, thanks. We’ve had a really great time. We got to know each other better, and at one point or another we all had “Hooked on a Feeling” stuck in our heads (thanks, Dre!). We hope we’ve been able to share some of this experience with you – though you can’t fully experience Iceland without being here. The stark beauty and power of the landscape has a unique pull on the soul. If you are able to visit, please do so – and get off the beaten path for a day or two. Give yourself the gift of Icelandic solitude.

Signing off till next year,

Emi Smith (and the whole IFS crew)

Go East, EC

by Emmett Smith on 2018-06-04 with No Comments

Today was a combination of exploring, testing and traveling. This morning we briefed the group on what will take place the next few days that we spend working at the glacier Sólheimajökull. Then we packed up and checked out of the B&B Guesthouse after a lovely stay. A subset of us worked on the drones and elevation platforms, while others of us were took one last hike on the island. After boarding the ferry, we drove east on route 1 to Vik, our destination for the next few days.

I was able to hike a very fun steep path up to a cliff top where we got a fantastic view of the island. We had to use a rope to climb a steep slope of scree, but the views were worth it!

A great view of the lava flow from Eldfell in the 1970s eruption.

Intrepid scree hikers – Faith, Emi and Neil

Here you can see the ferry coming into the island. The white “cloud” is actually the icecap Mýrdalsjökull on the mainland.

After hiking, we all got on the ferry to head back to Iceland.

Goodbye Vestmannaeyjar (Vestmann Islands)!

We drove past Sólheimajökull on our way to Vik. This is the first major science stop. In the next few days, we will be hiking on the glacier itself to measure its elevation and calculate the volume of its snout. We will also be collecting soil samples from a variety of locations surrounding the glacier. DNA will be extracted from the soil and we will sequence it to determine what types of bacteria are living in each sample. This will tell us how Icelandic soils recover from glacial coverage over the years. I’m excited to begin!

Birds of Iceland

by Emmett Smith on 2017-06-29 with No Comments

Like any good amateur birder, I kept a list of all the birds we saw on our trip. Special shout out to Neil who made many sightings, as well as to Sage, Cait, Nic and Kellan for contributing to the list. Total count: 27 species!

Bird Date Location

Common Snipe 24 May Thingveller

Pink-footed Goose

Mallard Duck

Black-headed Gull

Pied Wagtail

Redwing

Oystercatcher 25 May Selfoss

Whooper Swan Geysir

Arctic Skua 26 May Solheimajokull

Arctic Tern 28 May Klauster

Eider Duck Jokulsarlon

Snow Bunting

Whimbrel or Dunlin

Pidgeon Elgisstadir

Canada Geese

Fullmar 29 May Skalanes

Puffin

Kittiwake

Ringed Plover 30 May

Grey Phalarope 31 May

Robin

Gyrfalcon

Greylag Goose

Harlequin Duck 2 June

Black-tailed Godwit

Whimbrel

Raven 4 June

Next year I want to see the gyrfalcon!!!! It was spotted by Nic and Kellan while flying the drone.

No one has died of dysentery …

by Emmett Smith on 2017-06-01 with 1 Comment

… but we did ford some rivers! I have no photographic evidence of our journey (because I was worried about dying) so use your imagination as I walk you through the day.

Goal: Drive to Egilsstaðir to get to the airport to pick up a rental car so Dan, Neil and I can visit an archaeological dig on Friday (excitement!!) and do some shopping since the food delivery to Skalanes was delayed.

Problem: It’s been raining here pretty solidly for the last few days. The three (3) rivers that one must cross to get to civilization are rising … and rising … and rising …

Oli (the owner and manager of Skalanes) arrives in his big 4×4 truck circa 9 am. Charlie and I hop in ASAP, since Oli says the rivers are nearing the point of unfordability. We approach the first river. The water is rushing madly down to the sea. It is easily 3x higher than yesterday. Oli puts the differential lock on so the rear wheels will have more power. We charge through the river. It’s pretty intense but we clear it. We zoom down the road to the second ford and cross it, with similar trepidation (and a larger drop off downstream). Then we approach the third and final ford, which is the largest and most dangerous. The waters are roaring down the mountain. Oli angles the truck well upstream of our exit point, throws on the differential lock and moves forward into the current. I feel the truck being pushed downstream – the water level is almost up to the windows! Charlie is ready with his window-breaking tool, and I’m planning how I will roll down the window and climb out as soon as the river thrusts us against the rocks we are quickly approaching. Can I grab my pack (which contains all my cash, ID, credit card and passport)? Nope, better not risk it … the truck is groaning and lurching and then, inches away from the rocks at the end of the ford, the nose of the truck rises out of the torrent onto the road and we’re safe. Water has made it into the floor of the truck but we escape the mad dash to the sea.

You may think that the rest of the day will be tame compared to this adventure. Incorrect. After picking up our car and getting some serendipitous shopping completed, Charlie and I head back toward Skalanes with myself at the wheel. I head into the mountain pass of route 93 from Egilsstaðir to Seyðisfjörður. The wind is gusting at 20 knots and the rain turns into snow as we crest the pass. We drive through intense pea-soup fog patches as we pass by snowpack, and it’s a good thing that all cars in Iceland are required to have their lights on 24 hours a day so we don’t strike each other in the fog. We finally descend into the valley, and drive past waterfalls which are being blown backwards and upwards by the strong winds. As we approach Skalanes, we know there is no way we can drive our SUV past the rivers (indeed, Oli hung the “Closed” chain over the road as we left). We now face a 4.5 km trek from the road to the house. We call in reinforcements and Dan, Neil and Jacob answer the call. We trudge into the east wind with our groceries. Where there was a road, there is now a series of deep, large puddles and quickly forming new rivers. In one location, the land immediately next to the trail has disappeared (even since Dan, Neil and Jacob walked out to the car) and is quickly being eroded away. The cold wind is blowing the rain directly into our faces. After about 45 minutes, we reach the house. We drag our soaking carcasses into the warm, dry lodge and jump into showers to warm up.

The rest of the day really pales into comparison – mostly because I was exhausted and just sat around by the fire. Shout out to my Marmot water-proof pants and North Face GorTex jacket – they kept me mostly dry!

Tomorrow I take Dan and Neil and drive to the dig site in Stöðvarfjörður. We’re hopeful that we can offer them our services to aid their excavation! http://icelandreview.com/news/2016/09/15/major-archaeological-find-iceland

P.S. Sage’s code is working!!!!!

Signing off for now,

Emi

I’m leaving on a jet plane

by Emmett Smith on 2017-05-22 with No Comments

All my bags are packed, I’m ready to go!

We’re just about ready for departure. Three of us leave this afternoon for flights out of Chicago, and the rest of the crew departs early tomorrow morning: Earlham –> IND/DAY –> JFK (7 hour layover) –> KEF –> Reykjavik!

It’s been a very busy 1.5 weeks, but, ready or not, we will all be in Iceland in less than 48 hours. We can anticipate cloudy weather in the 40s and 50s. We’re looking forward to experiencing another place, expanding our horizons (culturally, scientifically, emotionally), eating fermented shark, implementing our algorithms and devices, going back to Skalanes, to run in Iceland, seeing birds (especially Puffins), geocaching, standing on a glacier (and possibly sledding down it), climbing a volcano or two, lounging in a hot spring, and trying to learn some of the language.

Our gear is packed.

Our daily plans have been formulated.

Our devices are primed and charged.

Our sense of adventure is fully present.

Our Spotify playlist has been populated. What more do we need?

See you in Iceland!

The next generation of next generation sequencers has arrived!

by Emmett Smith on 2017-05-11 with No Comments

We have received, from Oxford Nanopore, the MinION. (Min-ION, not one-eyed yellow minions, get it straight.) This device promises whole-genome sequencing of microbes, viruses and archaea from soil samples we will collect at the Solheimajokull glacier. This device is extremely small and portable, and one sequencing run can be done on a laptop in 6-8 hours. One flow cell can run up to 12 samples at a time, and while the samples are being sequenced, internet access will allow simultaneous queries of a database that will determine what species were in our sample. Thus, in REAL TIME, we can identify the composition of the soil microbiome. This is a drastic improvement over prior methods, which involved sending 16s rRNA samples to a company and waiting for 2-3 weeks for results.

What kind of science are we doing with this device?

We will be collecting soil samples at the Solheimajokull glacier (near the town of Vik in Iceland). We want to obtain samples that have been “out of the freezer” i.e. not covered by the glacier for a specific number of years – 10, 20, 50, 75, 100, 150, 200, etc. We will compare the microbial populations present in these different soil samples and look at the type of soil and flora growing in these different locations. This will teach us how the land “recovers” once it is freed from a glacier.

This device will help us do this analysis on site and give us the data almost immediately. It’s really new, cool and exciting. We’re looking forward to learning about soil succession with the use of this device!

Blogger: Emi (Biology Professor and MinION hand modeler)