Posts Tagged ‘RNA’

26 Hours on the Marsh — November edition

November 6, 2014

Associate Professor Aron Stubbins led a 26 hour sampling program on the marsh. The team, including Thais Bittar, Robert Spencer, Zachary Tait, Megan Thompson, Alison Buchan, and Drew Steen, spent the day and night monitoring a day in the life of the microbes, gases and organic carbon molecules that form the biogeochemical milieu of the marsh. This work is part of two National Science Foundation projects involving professors and students from Skidaway Institute of Oceanography, University of Tennessee – Knoxville, and Florida State University.

Cutting edge techniques are being employed to watch the marsh creek in real time over 18 months. The sampling event shown in the time lapse video is the fall rendition of four seasonal sampling events that are recording the daily life of the creek. Manual sampling is required so that we can collect live bacteria and gas (such as carbon dioxide) samples that need to be processed by hand, immediately upon collection. The bacteria collected are being genetically characterized, so we know who was in the creek at different times of day (DNA). Then we will also determine which genes were active (RNA). This tells us what the bacteria present in the marsh were doing throughout the day.

We also record the changes in dissolved organic carbon throughout the day. Dissolved organic carbon is a major part of the global carbon cycle and so understanding its cycling is important with respect to understanding how natural carbon cycling responds to and plays a role in climate change. For the microbes in the creek, the dissolved organic carbon (DOC) is food. So by looking at which bacteria are there (DNA), what they are doing (RNA), and what types of food is present (DOC), we hope to gain a more complete understanding of the miniature world within every drop of creek water. The daily routines of these tiny bacteria and dissolved organic molecules shape the marsh ecosystem and play important roles in determining the current and future climate of our planet.

UGA Skidaway Institute researchers complete ‘26 Hours on the Marsh’

July 30, 2014

Pitching a tent in the woods and fighting off mosquitos may not sound like logistics of a typical oceanography experiment, but that is how researchers at the University of Georgia Skidaway Institute of Oceanography completed an intensive, round-the-clock sampling regimen this month. The project, dubbed “26 Hours on the Marsh” was designed to investigate how salt marshes function and interact with their surrounding environment—specifically how bacteria consume and process carbon in the marsh.

The team set up a sampling station and an outdoor laboratory on a bluff overlooking the Groves Creek salt marsh on the UGA Skidaway Institute campus. The scientists collected and processed water samples from the salt marsh every two hours, beginning at 11 a.m. on July 16 and running through 1 p.m. July 17. By conducting the tests for a continuous 26 hours, the team can compare the samples collected during the day with those collected at night, as well as through two full tidal cycles.

The UGA Skidaway Institute team processes water samples at their outdoor laboratory. (l-r) Megan Thompson, John DeRosa (UGA Intern), Zachary Tait and Dylan Munn (UGA Intern.)

The UGA Skidaway Institute team processes water samples at their outdoor laboratory. (l-r) Megan Thompson, John DeRosa (UGA Intern), Zachary Tait and Dylan Munn (UGA Intern.)

“We wanted to be able to compare not only what is happening to the carbon throughout the tidal cycle, but also what the microbes are doing at high and low tides and also during the day and night,” said Zachary Tait, a UGA Skidaway Institute research technician. “So we had to have two high tides and two low tides and a day and night for each. That works out to about 26 hours.”

The research team ran more than 30 different tests on each sample. The samples will provide data to several ongoing research projects. A research team from the University of Tennessee also participated in the sampling program. Their primary focus was to identify the bacterial population using DNA and RNA analysis.

This sampling project is one of many the researchers conduct during the year. They use an automatic sampling system for most of the other activities. The automatic system collects a liter of water every two hours, and holds it to be collected and processed at the end of the 26-hour cycle. The team could not use the auto sampler this time for several reasons; the scientists needed to collect much more water in each sample than the auto sampler could handle and the auto sampler tends to produce bubbles in the water, so it is not effective for measuring dissolved gasses.

Megan Thompson supervises Dan Barrett (l) and John DeRosa, both UGA interns, as they process samples in a UGA Skidaway Institute laboratory.

Megan Thompson supervises Dan Barrett (l) and John DeRosa, both UGA interns, as they process samples in a UGA Skidaway Institute laboratory.

“The UT scientists wanted to conduct enzyme analysis as well as RNA and DNA tests on the samples, and for those, the samples must be very fresh,” said Megan Thompson, a UGA Skidaway Institute research technician. “You can’t just go out and pick them up the next day.”

About a dozen scientists and students were involved in the project, including Thompson, Tait, a group of undergraduate students completing summer internships at UGA’s Skidaway Institute and a similar group from UT. They split their time between the tent and outdoor laboratory on a bluff overlooking Groves Creek, and the UGA Skidaway Institute laboratories a mile away.

“It was an interesting experience, and I think it went very well,” said Thompson. “However, when we wrapped it up, we were all ready to just go home and sleep.”

“26 Hours on the Marsh” is supported by two grants from the National Science Foundation, totaling $1.7 million that represent larger, three-year, multi-institutional and multi-disciplinary research projects into salt marsh activity. These projects bring together faculty, students and staff from UGA’s Skidaway Institute, UT and Woods Hole Research Center. UGA Skidaway Institute scientists include principal investigator Jay Brandes; chemical oceanographers Aron Stubbins and Bill Savidge; physical oceanographers Dana Savidge, Catherine Edwards and Jack Blanton; and geologist Clark Alexander. Additional investigators include microbial ecologist Alison Buchan and chemical oceanographer Drew Steen, both from UT; as well as geochemist Robert Spencer from WHRC.

Barrow — Jan 16

January 19, 2012

16 Jan 2012

Ice conditions are still unstable.  Our UMIAQ support team spent the morning doing reconnaissance of our intended sampling sites. After yesterday’s efforts they suggested that since it might be dangerous, it wasn’t a good idea for anyone on the science team to accompany them. Because the ice is still forming and the ocean is a powerful force, the ice can break-up pretty quickly. The team first scouted out our near shore site, but it was inaccessible due to a major crack between it and our ice trail. We use a trail cut through the ice to guide us on a safe snow machine run over it. They continued on to our second site located further out into the ocean and to the north. The ice in that area seems to be more stable. They liked what they saw and decided that it would be safe for us to set up camp there.

Brower Frantz, UMIAQ logistics leader proudly stands by the ice camp.

After making this decision the team came back, loaded up the camp gear (tents, generators, heaters, ice augers, etc) and went back out. This time Steven Baer from the Bronk group went with them to help orient the tents and make some basic measurements. Before starting we need to know the ice thickness, water depth, and usually how far light penetrates. In this case there basically isn’t any light but hey, we’re scientists. Measuring zero’s (or close to zero) can be just as important. Its data!

Meanwhile, back on the NARL campus where our labs are, there was a flurry of activity as we all checked and prepped our gear. Finally, around 3pm the camp was set-up and we were ready to go. I was pretty worried about how late it was getting, but because we have such a short time up here and the ice was deemed safe now we needed to push a little bit. Who knows if we’ll even get another chance given the dynamic condition of the ice.

The ride out was relatively uneventful. The ice was remarkably smooth compared to our previous trips.  As was explained to me, when the ice first forms it is relatively flat and it only gets jumbled up later as storms, wind, currents, and tides push it around. Flat ice generally means that it is new ice.  That is what was worrying everybody. We know the ice is still forming and moving a lot. Hopefully it won’t move while we’re on it! After about 30 min of driving we made it to our camp. Having well established sampling routines by now, this is our 6th expedition, we all got to work unloading our gear and starting to sample. The Yager group occupies their own tent (the smaller one) while the Frischer and Bronk group occupy the larger one.

Ice Camp 16 January 2012

In the Frischer tent I got started right away making measurements of the water column. We are using a new instrument that lets us measure depth, temperature, salinity, oxygen, chlorophyll, pH, and turbidity. It’s a pretty nice instrument but a bit delicate and the computer software is not straightforward. We transported it as if it was a delicate infant wrapped in blankets with warm water bottles and hand warmers to make sure it didn’t freeze on the way out. I think we overdid it! When I unwrapped it in the tent it was positively hot. The instrument worked well and we got a good look at the water conditions. As expected the water temperatures was -1.8 deg C, salinity was around 33 PSU (normal for the Arctic coastal ocean), there was almost no chlorophyll in the water (no light no algae in the water). Most importantly the water column was well mixed which means that we could sample at one depth and be reasonably assured that it would be representative of the whole water column. We decided to sample at 2 meters below the bottom of the ice.

Graph of water data from the MANTA, Eureka Environmental

After I was finished measuring the water the Bronk group got rolling. They rinse and fill what seem like a million small bottles to which they add a very small amount of nutrients enriched in their stable isotope concentrations. Stable isotopes are non-radioactive form of elements (atoms) that are slightly heavier than the normal form. For example, the normal atomic weight of Carbon is 12 (meaning it has 12 protons) while the stable isotopic form has a weight of 13. We refer to it as 13C.  Because 13C  is slightly heavier than 12C, it can be measured on a mass spectrometer. By measuring how much of it goes into cells during an incubation, the rate of uptake can be calculated. The Bronk group is making some of the first ever measurements of nutrient uptake rates by microbes in this region of the Arctic coastal ocean.

The process went pretty smoothly but since it was so cold, even in the tent, the pipettes which they were using to inject the stable isotope into the samples were freezing and slowing the process.

Dr. Debbie Bronk injects stable isotope labeled nutrients into seawater.

Meanwhile in the other tent the Yager group were having even more problems with freezing. They are collecting water samples to make measurements of the carbon chemistry and general activity of the microbes, so it is especially important that their samples do not freeze and are not exposed to the atmosphere which can contaminate the dissolved gas content of the seawater. Unfortunately, their samples were freezing.  However, after getting them off the ice floor of the tent and placing them into a seawater bath (a cooler filled with seawater) they seem to have solved the problem and were able to collect most of the samples they needed.

Dr Tish Yager and Colin Willams collecting water.

When the Bronk group was finished it was our turn.  Our sampling is probably the most straightforward, but we need to collect a lot of water.  We’re collecting enough water so that we can extract DNA and RNA from the bacteria in it.  We collect about 140 liters (about 40 gal or 310 lbs). Using a specially designed submersible pump we collected water in seven 20 liter carboys wrapped in neoprene and then place them in a cooler of snow. Believe it or not, the snow actually keeps the water from freezing. But, as simple as it sounds, we had our problems too. The generator that was running our pump ran out of gas.  Actually, the generator had a gas leak so it’s lucky it just ran out of gas and didn’t explode. But, because of excellent planning on the part of the UMIAQ team we had two generators on site. However, that meant the Yager group was without lights in their tent. We solved that problem by moving two snow machines so they pointed at the tent and the headlights provided enough light.

Finally we were all done and got all our gear and samples loaded back onto the sleds.  It was unbelievably cold and windy and we were all tired and ready to get back. The trip started off smoothly until I managed to get my sled stuck. It’s really tricky pulling a very heavily loaded sled. I had to slow down over a series of small ridges because the person in front of me slowed, and that was all it took for the snow machine to sink a little too much into some soft snow and lose traction. With all of us helping we disconnected the sled and managed to lift the back end of the snow machine out of snow, enough to get it moving. Then we were able to push the sled back to some more level ice and reconnect it to the snow machine. It was exhausting! But the fun wasn’t quite over. As we started moving again Debbie, in an effort to make it over the hole I had dug with the snow machine, went a little too fast over the area and bumped into Rachel and Jenna who were on the snow machine in front of them. No real harm though. Jenna fell off the snow machine but it was into soft snow and she wasn’t hurt. The brand new snow machine Deb was driving suffered a cosmetic crack in its fairing. Without further incident we all made it back safely to campus and quickly rushed our samples to our respective labs for processing.

Victoria and I spent the next 5 hours in our cold room filtering all that water we had collected. We had hoped to start another humic addition bioassay that is a component of Zac Tait’s thesis research, but it was just too late so we decided we’d do that first thing in the morning. After all the filtering was done, our samples put away safely, and all our gear cleaned-up it was time for some well deserved rest. I felt weary and frozen to the bone but pleased with the progress we had made.

Even though the sun won’t shine, tomorrow is a new day.

Sunday 1 May 2011 – Last Lab Day

May 4, 2011

Today was our last full lab day and the beginning of the end for this trip.

After breakfast in the cafeteria, Zac and I began to purify bacterial messenger RNA (mRNA) from the water we had filtered yesterday. mRNA is the molecule that acts as the intermediate between DNA and proteins. All the information necessary to code for complex macromolecules like proteins are stored in DNA, but in order to use those instructions a cell must transcribe its DNA information into RNA that can then be translated by another complex molecule called a ribosome into proteins.

Truly life is amazing and it boggles the mind how complex and elegant it is. From the very smallest scale of atoms and molecules to the grandest scales of the universe, everything is connected. Anyway, I digress.

Our goal today was to purify RNA from the bacteria that we had captured on our filters so that we can determine which genes are turned on and how active those genes are. We are particularly interested in those genes that bacteria use to assimilate inorganic nitrogen because we suspect that the addition of new carbon in the form of the humics released from the melting permafrost will require bacteria to use more inorganic nitrogen. If this is true we should see an increase in the genetic expression of the genes involved in inorganic nitrogen assimilation.  Anyway, that’s why we need the RNA.

The initial step of our purification procedure requires two sets of hands and that was my job this morning.  Once we had safely gotten our filters containing all those bacteria into the first extraction reagent which stabilizes the RNA I was free to start packing-up our labs while Zac completed the RNA extractions.

Zac purifying RNA

I started with the cold room where we had filtered all the water.  Although it took us many hours to set-up the lab and to make sure that we had everything in exactly the right place, it only took me about half an hour to dismantle it.

Cold room during use and after being cleaned-up.

It’s kind of sad to tear down a lab that was so functional, but we know we’ll be back in the summer to do it again. Just for grins we left one little piece of orange tape on the floor to see if anyone else uses the space before we get back.

Once Zac finished the purifications we really got busy rinsing and cleaning all our gear and getting everything ready to be packed away.  At around 3pm we stopped to sample Zac’s ongoing experiment; there’s only one more time point to go in that study. Then we went to help Lollie pack her bags and get checked in for her flight home.

Because the airport here is so small but still requires the TSA agents to screen all bags, travelers are encouraged to check in early. This greatly reduces the check in wait times and relieves congestion in the very small arrival/departure area.  After Lollie checked in she went back home and finished preparing a fabulous Mexican dinner for the whole team.

Alas all good things must come to an end and finally it was time for Lollie, Adriane, and Debbie to head back to the airport to start their long journeys home.  We miss them already.

Friday April 29, 2011 – Moving Ice Camp

May 2, 2011

Today was another lab day, and although our special pipettes still hadn’t arrived we felt we had to go ahead and process our RNA samples.  During our first trip to Barrow last spring we had experimented with holding these samples until we got home before processing them. The results were not good, and so we decided that we had to process the samples as soon as possible after they were collected. We felt it was risky to even holding the samples a single extra day so we moved ahead using our back-up pipettes. But can you believe?! Exactly as Zac was finishing-up with the extractions the pipettes were delivered. The only saving grace was that both Zac and I had both missed lunch and when we unpacked the box and found the Twizzlers and peanut m&m’s that Victoria had used as packing material we were thrilled.  Thanks Vic!

While Zac was hard at work in the lab purifying RNA, I spent the morning and most of the afternoon out on the ice helping to move our ice camp. During our last trip in January we were unable to reach our primary sampling site about 1.5 miles offshore due to ice conditions and the lack of a suitable ice trail, so we had to settle for a location closer in. The water there was quite a bit shallower. Although all our measurements indicated that we still were in oceanic and well-mixed water, we can’t be certain that we can directly compare the data from that site to all the rest of the data that we are generating. So during the planning for the current trip we had decided that if we managed to get two samples from our primary site and we still had time during this trip, that we would move our camp and sample from the more inshore location.

Sampling both locations at essentially the same time will allow us to directly compare results from both the near shore and offshore locations. We’re hoping they are similar!

All has gone well, so today we began to implement our decision and moved our ice camp inshore.  With Rachel Siple, myself, and the UMIAQ crew, we headed out on the ice. Reaching our destination we drilled an exploratory hole in the ice and measured the water depth and ice thickness. We’re really looking for 10 meters of water, but our minimum is 8.  Unfortunately at the first hole we drilled we only had 7M of water so we were a bit disappointed.  From experience we knew that the bathymetry in this area is highly variable so we moved about 30 meters from the first hole and drilled another.  At this location we measured the water depth to be a little over 8 meters. Although marginal, it met our criteria.  We are still hoping to find a better site. We got back on our snow machines and moved to the other side of a very large ice ridge and drilled a third exploratory hole. Alas, the depth was even less there so we decided to go ahead and set-up camp at the second place we looked.

Setting up an ice camp.

Setting-up camp involves removing the snow from the area (lots of shoveling); positioning holes for the pump inlet and outlet (for the big tent) and a large hole to accommodate the Niskin bottle in the small tent; and documenting water depth, ice thickness, water temperature, salinity, and light attenuation.  It’s especially important that we know light attenuation since we need this information in order to set-up our incubations back in the lab and to decide at what depth to sample.

All this was pretty hard, manual labor and, to my surprise, I found myself sweating and discarding some of my layers of clothes despite the cold temperatures.

Drilling a hole in the ice.

Drilling all those holes was especially hard work and made me appreciate more than ever the support we are receiving from our UMIAQ logistics team.

While drilling one of the holes we had a visitor from a ctenophore. I sent this picture to a colleague Jenny Purcell and she identified it as Bolinopsis infundibuluma common Arctic species of ctenophore.

The Arctic ctenophore Bolinopsis infundibulum.

Jenny is a world renowned jellyfish authority from Western Washington University. Ctenophores, commonly known as comb jellies are almost all predators that feed on small zooplankton. Their most distinctive features are their “combs” which consist of cilia that they use for swimming. Interestingly, ctenophores are the largest animals that swim by means of cilia. Bolinopsis is commonly found throughout the Arctic Ocean in the upper 500 meters and subsists on small zooplankton species like copeopods. Undoubtedly this individual was enjoying eating all the organisms growing at the bottom of the ice pack and we must have disturbed his/her lunch when we drilled our hole. I say his/her because Bolinopsis is a hermaphrodite.

By about 2pm we were finished and headed back and I arrived just in time to watch Zac finish his lab work and eat Twizzlers.

For dinner Steven Baer (a Ph.D. student with Debbie Bronk) and I had planned a Shabbat dinner for everyone. We are Jewish and enjoy the ritual of Shabbat that marks the end of the week and gives us all a moment to stop and reflect on the many blessings of our lives. Steven prepared an awesome dinner of pasta primavera and hosted us all to dinner. Steven had also brought candles from home and I managed to bring a bottle of wine. Because we can’t buy wine (or any alcohol) in Barrow (at least not legally) I had to smuggle it in. In the local grocery store we found a loaf of bread that resembled a Challah. Challah is a type of bread traditionally served at festive Jewish meals.

Barrow Shabbat table.

So, with everyone in attendance we took a moment to pause our work, say a few prayers, and enjoy a fantastic meal together. It didn’t last long though since most of us had to run off to finish something or other, and to get ready for tomorrow’s sampling expedition.  But at least it was a moment.

Wed 27 April 2011 – Lab Day

May 2, 2011

After yesterday’s first day on the ice, today was supposed to have been spent processing all the samples we collected.  However, we forgot our special set of RNA-only pipettes and are still waiting for the set that Victoria sent by Fed-X. We have a back-up set available, but we are concerned that sometime in their past they may have been used with the preservative formalin, something we really don’t want to contaminate our precious RNA samples with.  So we decided to postpone our RNA purifications in the hope that the new pipettes will be here tomorrow.

The thing about shipping stuff up here by Fed-X is that Fed-X doesn’t actually ship to Barrow, they ship to Anchorage and then transfer them to a company called Northern Air Cargo (NAC). Although NAC does get it up here, like all things in Barrow, they are not necessarily punctual. We checked at their warehouse today if the pipettes had arrived but they hadn’t.

We also tried to confirm that it was going to be ok to ship our dry liquid nitrogen containers home this time.

Liquid Nitrogen Dry Shipper. For the record it is not a shipping hazard.

It turns out that for some reason NAC lost their license to ship HAZMAT (Hazardous Materials); we don’t know why. Dry liquid nitrogen containers are not considered hazardous since the liquid nitrogen is trapped in Styrofoam and therefore cannot spill, even if the container is tipped over or even breaks. However, they do look a little suspicious and we just wanted to confirm with NAC that they could be shipped. It would be a disaster if we couldn’t get our samples home.  We need to keep our samples super cold otherwise they will be ruined.  The temperature of liquid nitrogen is -196°C (-321°F) which definitely classifies it as “super cold”.  However, the one person we needed to talk to wasn’t available so we’ll have to wait for that too.

Even though we weren’t working that hard in the lab the other groups were. The Bronk group (Debbie, Quinn, Rachel, and Steven) were in full swing and, as Deb likes to say, were “filtering like the wind.”

“Filtering Like the Wind”. Bronk group hard at work..

The basic design of their primary experiment is to incubate the water samples we retrieve from under the ice in the presence of various nutrients that have been “labeled” with a slightly heavier version of that nutrient (either nitrogen or carbon) so that that uptake or release of the nutrient can be measured on an instrument called a mass spectrometer. After a defined period of incubation, in this case 24 hours, the sample is passed through a filter and all the cells that incorporated the labeled compound of interest are captured on the filter and then can be analyzed.

Incubating water samples at ambient temperature and light conditions (Bronk lab).

From these experiments we derive uptake and release rates of various nutrients by the microorganisms we are studying. Watching the Bronk group filter is like watching a well choreographed ballet.

Meanwhile, back in our lab, after postponing our RNA purifications and fruitlessly trying to retrieve our pipettes and make sure we can send our samples home, we did manage to sample Zac’s ongoing experiment. As promised Zac wrote a few words about his project:

Hello blog readers, this is Zachary Tait. I am a masters student at Savannah State University and have been working on this Arctic project with Dr. Frischer at the Skidaway Institute of Oceanography since the beginning of 2010 when I moved to Savannah from North Carolina.

Zac setting-up his experiment.

In the last year, Dr. Frischer and I have been planning my masters project and this is the first trip that it has been implemented. The focus of my experiment is to measure the effects that the melting of permafrost will have on the microbial community in the coastal Arctic Ocean. As permafrost melts in the Arctic, the organic materials locked in the soil will flow into the Arctic Ocean, possibly changing the dynamics of nutrient uptake in the food web. I have set up 8 incubations to test what effect  permafrost material has on bacterial growth and nutrient use, and am very excited to report that the experiment is going well. This last year of planning has paid off.

We are taking a total of 40 samples per day, most of which have to be filtered through a syringe filter that is wearing our hands out much more than expected. We will have extra firm handshakes when we return!

Zac filtering.

The experiment is going to run through Monday then the samples will be sent to the Virginia Institute of Marine Science, University of Georgia and back to our lab on Skidaway Island. It is going to be a group effort getting all of the samples processed.  Luckily, we have generous partners willing to help.

This experiment will be repeated two more times in the summer then the winter of 2012.  Hopefully, I will be able to post some results on the blog this summer.

Extra extra, this just in on the radio, the first whale of the season has been landed.  A 29 foot Bowhead!

Packing Up – January 31, 2011

February 2, 2011

With all our samples collected today was spent processing samples and starting the long process of packing up the labs.

First, the two male students (Steve and Zac) hosted a pancake breakfast at their hut.

A welcome meal!

They earned major brownie points is all I can say. Besides it being an excellent meal, it was nice to be all together to savor a bit the final days of this trip and to inspire us to begin the tedious job of cleaning and packing everything up.

It’s so much effort to get ready for the trip; to set-up all our gear; and to collect samples — that it seems almost a shame to be putting everything away. But we got what we came for and now its time to think about getting back to the lab where the real science begins.

The sun was above the horizon for a little shy of 4 hours today.

Midday January 31, 2011

As I’ve mentioned before, a remarkable difference given that the sun made its first appearance of the year last week, and then for only a hour.  Today, as I was heading east to the BARC lab where we did our RNA extractions and which has served as home base for Zac and me, I almost needed to put on sunglasses. Wow!

Not too much else to report right now.  The day was spent gathering all our stuff which was spread across the relatively large NARL (Naval Arctic Research Lab) campus and washing it all. Tomorrow, when it is all warm and defrosted, we’ll carefully pack it up and put it back into storage until we need it again in the spring.

marc

Happy Birthday Lollie – January 27, 2011

January 28, 2011

Dr. Marc Frischer continues his blog postings on his current research expedition to Barrow, Alaska.

Day 6 into our trip, just past the mid-point. After spending most of the day in the lab, the first set of RNA samples have been processed and are awaiting shipment back to Skidaway.

One of the primary goals of our work is to understand the underlying mechanisms that allow bacteria to adapt and respond to a changing environment, particularly to changes in the nutrients available to them. To do this one of the things we’re looking at is the genetic expression of important genes involved in nutrient assimilation.  To get at those questions we need to look at their messenger RNA (mRNA), but because mRNA is typically very unstable, this is not an easy task.

To put some perspective on the problem, a typical mRNA molecule, if left alone, will degrade in seconds.  Much of the challenge for us during these studies is to get the bacterial mRNA stabilized so that we can analyze it.  Basically, that is what we were doing in the lab today, extracting, purifying, and stabilizing the mRNA from the bacteria we collected on our filters.

Zac purifying RNA

Besides working in the lab and getting ready for another sampling trip on the ice tomorrow, we did manage to enjoy the relatively relaxed day.  First off, I started by oversleeping, something I haven’t been able to do for it seems months.  Even though I missed breakfast, I think the sleep did me a lot more good than breakfast would have.  Finally, I seem to be kicking the cold I’ve been struggling with for the past couple of weeks.

Later in the day we enjoyed another beautiful sunrise.  The sun rose today at 12:27pm, 43 minutes earlier than on January 24th when the sun first rose.  The sun was visible for 1hr and 8 minutes today.

Marc watching sunrise

What’s really remarkable is how much it changes from day to day this time of year.  On the day we leave next week the sun will rise at 11:23 am.

This evening we were invited to a dinner hosted by Peggy Cowan.

Dinner at Superintendent Cowan’s home (Peggy is at the head of the table in the blue shirt)

Peggy is the superintendent of the North Slope Borough School District Board of Education and a friend of Savannah’s Joyce Murlless.  Peggy started her career in Savannah as a teacher at Oatland Island Wildlife Center. Joyce made the introduction for me and we jumped at the opportunity.  Peggy invited several local science teachers, other educators and planners, and Deb, Tish and myself for dinner at her home.  We had an absolutely lovely evening eating pizza and getting to know each other. We’re hoping that this will lead to some long term collaborations whereby we can contribute back to the local community.  Thanks for the hook-up Joyce!

Upon returning we celebrated Lollie’s 61st birthday.

Happy Birthday, Lollie!

The rest of the team had baked a cake and decorated the hut.  Lollie blew out the candles.  Happy Birthday Lollie!

marc

Notes from the Arctic – The end is near. August 30th, 2010

August 31, 2010

Hi All,

For a brief moment this morning the sun graced us with its presence and it was glorious.

Arctic summer splendor.

Today was our last day of sampling at our standard station and we made the best of it. Captain Quuniq and Nelson again took us out to our standard station and we quickly sampled and came back in to process our samples in the lab.

Sampling complete!

Compared to conditions yesterday afternoon, the ocean was a bathtub today. And, with all the kinks worked out of our equipment and protocols, we made record time processing the samples. Victoria was even able to complete our RNA purifications by dinner time.

Molecular biology on the go.

All the samples are now safely stored in liquid nitrogen and in shipping containers ready to be shipped out in the morning.

Shipping containers ready to go.

With all the sampling complete and after a quick and not very satisfying dinner of Ramen noodles, it was time to think about starting the process of cleaning and packing-up. Since our stuff is scattered all over the campus its quite a daunting task gathering everything, cleaning all of our salty equipment and packing it so that it will be organized and ready for next January.

Its nearly 2 am now and I’ve been at it since 7 so I think I have to cut this one short. Tomorrow promises to be a busy day of cleaning and packing, but the end is near and we’re all looking forward to heading home.

Marc