Cesium Chloride Density Gradients

By: Sarah Turner

I last spoke about our BrdU project here. Once we have incubated the Antarctic fungi DNA with BrdU, we then must seperate out the unlabelled DNA from the BrdU labelled DNA. We accomplish this by ultracentrifugation in a solution of cesium chloride. Ultracentrifugation is like normal centrifugation, only it's much faster and for a lot longer. We usually spin our CsCl density gradients for 48 hours at 48,000 x gravity.

Due to the density differences of BrdU labelled DNA (BrdU labelled DNA is more dense than non-labelled DNA) the two seperate and form two bands, similarly to this:

Source

After 48 hours of ultracentrifugation, we are then able to fraction off the gradient in order to determine where the bands have developed in the tube. Fractionating separates the two bands into new tubes.

After fractionating, we precipitate the DNA out of the CsCl solution so we now have pure BrdU labelled DNA.

Here's a great video that helps to explain a similar application of CsCl density gradients, fractionating, and precipitating.

JoVE: DNA Stable-Isotope Probing (DNA-SIP)

Also, check out this video for more information on the chemistry of cesium chloride density gradients:

15 November 2012: Off to Mount Erebus!

 By: Dr. Laurie Connell

15 November 2012

Off to Mount Erebus!

We have been getting things ready here in McMurdo for quite some time.  Our team is assembled and we have been working with our mountaineer to hone our mountain skills.  Now it’s finally time to begin our trip up. 

First we need to weigh all the gear and get it to the helo hanger.  Accurate weights are important so the pilots know how much fuel needs to be on board.  With six people and our gear we will need several flights just to get to the acclimation camp at Fang Glacier.

We only bring what we need to rest and get used to the altitude.  Fang Camp is on a glacier at about 9000 ft.   We will be staying in Scott tents, a kind of tent that has been shown to be very good in the kinds of conditions we can expect.  

But if we get the chance to walk around we should do some light exercise so we acclimate better.  Below is a photo of the rock formation that gave Fang Glacier it’s name- I guess it looks a bit like a fang.   After two nights at Fang, we will move up again to Lower Erebus hut, we call it LEH for short.  I won’t be using email from Mount Erebus so we will post some photos and reports from back home at the lab.

Cheerio!

13 November 2012: Discovery Hut

13 November 2012

Discovery Hut

The history of this part of the world is pretty recent compared to most places, but quite interesting.  In the McMurdo area there are several historic huts remaining from the historic era of Antarctic exploration.  These huts are now maintained by the Antarctic Historic trust and there is an ongoing effort to archive the contents- in fact for some of the huts artifacts are now being returned by people who had taken souvenirs in the 1950’s before the huts were protected.

You can find a more complete list of Antarctic huts and ruins at http://www.polarheritage.com/index.cfm/anthutlist.

The hut that is closest to McMurdo station is called Discovery Hut.  Captain Robert Falcon Scott built it for the British Antarctic expedition of 1901-1904.  It is the smallest of the three huts.  Captain Scott decided that the members of the party would live aboard the ship after it was frozen in for it’s two-year stay and the hut was primarily used as a science observation hut, storehouse, a work room and even a theater.    This was partly because the hut was difficult to keep warm with the limited amount of available coal and there had been some difficulty in digging into the permafrost for a foundation.  The hut was used by a number of other groups over the next decade. 

Originally there were a number of smaller huts used as research labs for magnetic and seismographic work.   One of the most interesting parts left in the Discovery Hut is the pit that had been used by Louis Bernacchi and Reginald Skelton for the pendulum apparatus used for gravity measurements.  This was constructed in November 1902 when the seismograph was moved to the main hut.

For more details and some great old photographs please check the Antarctic Historic trust website

http://www.nzaht.org/AHT/HutPointP1/

9 November 2012: Getting food!

 By: Dr. Laurie Connell

9 November 2012

Getting food!

As we prepare for our trips out into the field one of our tasks is doing a “Food Pull”.  We make a calculation of how many days we will be out and how many people will be on the trip.  We also have to take into consideration how we will be able to cook.  In some places, such as Fang Glacier, we will make hot water only so the food will consist of dehydrated meals, dry soups and tea.  When we are at a fixed field camp with a building then we have a stove and more room so we can have more regular meals.  Either way we have to collect, pack and weigh all the food so it can be transported with us out to our location. 

We did our dry food pull for our Mount Erebus trip yesterday and will do the frozen foods (meat and cheese) on Saturday.  Just the dry part of the pull took us well over 3 ½ hours to collect and pack. 

               So, What is the food room like?  It’s kind of like a small grocery store and the food manager, Peggy, has the inventory all bar coded so she can keep track of how much goes out to each field party.

9 November 2012: Our First Samples Are Up!

By: Dr. Laurie Connell

9 November 2012

Our first samples are up!

Most of our job while in Antarctica is to collect samples and bring them back home for analysis but as we retrieve our samples they need to be processed for the archive and travel home.

The first step is to open up the container.  In this case the sample was from a dive site at Cape Evan’s Wall.

The charge after opening.

The inside of the container had some small starfish and crabs as well as the usual fouling organisms.   The star fish were released into the McMurdo aquarium touch tank.

The remainder of the sample was split into parts that were fixed for microscopy and some that were stored for DNA extraction or for culturing.  We have a variety of rock types as well as slides to determine how the microbes alter the glass surface.

8 November 2012: Getting down to science

By: Dr. Laurie Connell

This project is focused on determining what the microbial community is that colonizes rocks from volcanoes- basaltic rocks.  These rocks are high in iron (Fe) and manganese (Mn).  There are some microbes that can get their energy directly from rocks and some that can get their carbon from the air as either carbon dioxide (CO₂) or carbon monoxide (CO).  Our part of the project is interested in the fungi in these microbial communities.

Four years ago we made microbe traps.  They were tubes and sachets with bits of rock with various amounts of Fe or Mn in them.  We then put them in several different habitats that have a natural basaltic substrate nearby. 

The first one we placed out is near a basaltic wall that is under seawater- called Cape Evan’s Wall.  Hubert and the divers will be recovering that trap later today.

Next we put traps at various depths in a permantly ice covered lake in the McMurdo Dry Valleys- Lake Fryxell.  The ice is quite thick on the lake and although light does penetrate the ice never goes off the surface.

Two other sets of traps were put in seasonal streams from Hughes Glacier and from Walcott glacier.  These streams are usually frozen but flow a few weeks a year when the glacier is actively melting.   The last set of traps was put on the active volcano, Mount Erebus. We are getting packed now to begin our Mount Erebus ascent next week.  More about Mount Erebus  and what we are doing up there in later posts. 

 Right now it is getting warmer as spring progresses but it is still very cold in the wind with a -41^oF windchill temperature.  That makes for a cold skidoo ride out to Cape Evan’s Wall to pick up our samples today!

Photo of the Day: Crevasse Training

Submitted by: Dr. Laurie Connell

Here I am all set for crevasse training.  We need to be in climbing harnesses so get into and out of the fumarole caves on Mount Erebus so practice is important.

30 October 2012: Driving to the South Pole

 By: Dr. Laurie Connell

30 October 2012

Driving to the South Pole

Yes, there actually is a pole at the South Pole, in fact there are several!

There is the geographic South Pole that is put in each year by the USGS and the ceremonial South Pole- that’s were people go to get their photos taken.  Here is a photo of one of our friends at the geographic South Pole a few years ago. 

But did you know that there is also a Road to the South Pole?  It is the ULTIMATE Ice Road and is a bit over 1600km (that is nearly 1000 miles) long from McMurdo Station to The Amundsen-Scott South Pole Station.  It took several years to build by filling in crevasses in the steep glacier section.   The McMurdo Ice Shelf and the Polar Plateau are relatively stable so required much less work to develop a road but the section between that climbs the Leverett glacier and is a mass of crevasses.  This is what is called the shear zone- where two ice sheets collide.  This highway to the South Pole was first used in 2007.  The South Pole Traverse, as it is known, is a convoy of vehicles that carry fuel and other supplies up the glacier and onward to the pole.  It takes about 40 days to get there but faster on the way back since they carry less weight.

 

Map From Wikipedia

It takes big vehicles to pull all that weight and equipment up the traverse route.  Here is one of the Case tractors that have been fitted with treads that they use.  They pull housing modules (also pictured) and well as fuel bladders.   The first of two trips will leave McMurdo in a few days and the second will leave a week or two later.  They can transport enough fuel to reduce the need for LC130 flights significantly.  The LC130s burn 2 gallons of fuel for each gallon they deliver but the traverse burns only 1 gallon for each gallon they deliver- a significant savings on a precious commodity.

Photo of the Day: 1 Nov 2012: Say Cheese

Photo by Hubert Staudigel
Emperor penguin on the Sea Ice near the Barnes Glacier, Ross Island, Antarctica.

The people in the photo are (Left to right)  Anthony Rigoni, Laurie Connell and Forrest McCarthy