Tag Archives: antarctica

Hut Point Calibration

This morning we woke up to snow! It made for some beautiful views, and the mountains looked especially pretty with the dusting of snow. Sadly, this also meant unsafe conditions for flight, and so our first day in the field was delayed – i.e. cancelled. I’m glad that Helo Ops (helicopter operations) made that call as the wind and snow picked up later in the day.

Not to worry – we find plenty to keep ourselves busy with, testing our lab equipment with DNA standards to make sure everything’s working properly and ready for samples as soon as we are able to collect and extract them. For our work into testing mechanisms of long-term cell survival, we are planning to do some sequencing in the field. That’s right, sequencing out in the Dry Valleys in real time. The sequencer we’d use for this is Oxford Nanopore’s MinION that we are running offline with our laptop. To make sure that the laptop and sequencer wouldn’t complain too much about the cold when we’re at our sample sites, we needed to verify the setup in the cold. What better day for this than today? Angela and I packed up the laptop and MinION (that we’ve yet to name) and hiked out to Hut Point. It doesn’t get better than combining science and recreation!

DSCN1487 editedFigure 1. A misty view of our dorms and the energy powerhouses of McMurdo in the snow. 

DSCN1516 editedFigure 2. Elena with Dasse the penguin, our lab manager.

Hut Point is a narrow peninsula on Ross Island where McMurdo Station is located. Less than half a kilometer from the Station is the Discovery Hut built by Robert Falcon Scott in 1902 during the Discovery Expedition. The hut has been designated as a Historic Site, so we couldn’t go in, but it was great to see this amazing witness to exploration.

Once there, we marveled at the beauty around us, thanked our lucky stars, saw a Weddell seal, and then got down to business testing our sequencer setup. We connected the MinION to the laptop, launched the MinKNOW software, and ran a test using the configuration test cell. We were impressed at how quickly and smoothly it ran. We got a warning that it could not “ping”, but the software continued running as we were running it locally (not using the online server). The test completed successfully within a few minutes, so now we know it is doable in the extreme cold. Can’t wait to run some ancient microbial DNA on a Nanopore flow cell!

DSCN1518 editedFigure 3. Configuring the minION sequencer

DSCN1522 editedFigure 4. It works! 

 

Quirky McMurdo

Our field season falls near the height of the austral summer. As we are far below the Antarctic Circle, we get 24 hours of sunlight per day. Not only do the ~900 summer residents of McMurdo have to adjust to the remoteness of the location, they must also reconcile with the strangeness of passing time under perpetual sunlight. Those who are crazy enough to plant themselves in such a place take pride in their weirdness and go above and beyond to make this ecosystem thrive.

It’s immediately evident that McMurdoans have a quirky sense of humor, and they’re not afraid to show it. Hidden among announcements of upcoming helo schedules and base-wide maintenance events are little gems of humor that never fail to bring a smile to my face.

IMG_0524smFigure 1. Make sure you stay safe. 

IMG_3591smFigure 2. We don’t want to spook them! 

IMG_3709Figure 3. Your daily dose of poetic desperation. 

IMG_3731Figure 4. Specializing in Cool Ranch flavor

A serendipitous conversation with Dave, a military Chaplain deployed here for the season, revealed how truly wonderful this community is. Because it is so difficult to obtain employment here, people who do get to work here radiate extraordinary passion and vibrancy. Not only do they express their colors without fear, they strive to create a warm place that encourages everyone here to do the same. Just a couple days here, and I’m already in love with this place!

Agilent magic

After a long journey from Singapore, through Auckland and Christchurch New Zealand, the Agilent Bioanalyzer 2100 has also arrived at McMurdo Station, Antarctica and has been successfully installed into the Crary lab space assigned to team G062M. The instrument was generously donated to us from Agilent (thanks Agilent!) and will be a critical instrument for our mission of sequencing DNA and RNA isolated from the field samples we will collect in the coming days from the McMurdo Dry Valleys.

The Agilent Bioanalyzer is the gold standard for sizing and analysis of DNA and RNA isolated from biological samples, and is a critical component for quality assessment of DNA libraries for next-generation sequencing. The instrument is a unique analysis tool which uses a DNA “chip” comprised of wells to load microliter volumes of DNA or RNA samples, along with a sieving polymer matrix and an external “ladder” control. Micro-channels are fabricated in glass to create interconnected networks among these wells.

To prepare the chip, the micro-channels are first filled with the sieving polymer and fluorescence dye. Then, the experimental samples and ladder with marker are loaded in each well. Once the wells and channels are filled, the chip becomes an integrated electrical circuit. The chip then contacts a 16-pin electrode array arranged to fit into the wells of the chip, and a power supply passes a current through the electrodes to create a voltage gradient. As DNA and RNA are electrically charged, the molecules migrate through the gel matrix, electrophoretically driven by the voltage gradient, similar to slab gel electrophoresis. Because of a constant mass-to-charge ratio and the presence of the sieving polymer, the molecules are separated by size, with smaller fragments migrating faster than larger ones. During migration the dye molecules intercalate into the DNA or RNA strands and these complexes are detected by laser-induced fluorescence. The software automatically compares the unknown samples to the ladder fragments and the results are translated into gel-like images (bands) and electropherograms (peaks) that contain data such as fragment length and the concentration of the DNA or RNA samples.

We really couldn’t do our work down here without this instrument, and for that we thank the generosity of Agilent, Inc.

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Figure 1: An Agilent High Sensitivity DNA Chip.

Take nothing, leave nothing

Our second day of training and safety and protocol lectures. But only three today. Whew! The first was an Environmental Field brief. Antarctica is a pristine continent with many unique sites. Treating our sampling sites with respect and practicing good environmental stewardship is a must in Antarctica. That means packing everything that brought to a sampling site, and bringing it all back. Everything. There’s nowhere in Antarctica that you can pee on the ground, they reminded us, and while it’s gross to wash a pee bottle, it’s even grosser to wash someone else’s.

IMG_3603Figure 1. The golden rule: clean your own pee bottles. 

Since we will be working in the Dry Valleys, we were given some additional information specifically for working within the McMurdo Dry Valleys ASMA, which contains five ASPAs. ASPAs are Antarctic Specially Protected Areas, and an ASMA is an Antarctic Specially Managed Area. Science (and other) activities in these areas are managed and coordinated to minimize human impacts to protect the ecological, environmental, and aesthetic qualities.

Our third and final safety talk was the Outdoor Safety Lecture, which is necessary for any recreation that involves being outside. We immediately put this training to good use. We went to see marine life thriving under the ice in McMurdo Sound (McMurdo Station is on the Southern tip of Ross Island). How can you do that without donning dive gear? The “Ob Tube” (observation tube)! The tube is narrow, and about 20 feet long, with windows all around at the bottom. There, you can sit and enjoy the marvels of the sea – the schools of silvery fish, jellies, a sponge and some crustaceans. We could hear seals and were hoping to see them, but sound can travel far distances under water so they may have been nowhere near us. I guess we’ll just have to hike around this beautiful landscape to catch a glimpse of the seals.

20161203_130610_069Figure 2. Whoa Dave, where’d ya come from?!

 

It’s all about the buddy system

The theme of the day was training, training and more training! In comparison to our last few mornings, we had the luxury of sleeping in today, with our first class at the late hour of 7:30 am. We started off with briefing and then went on to Core Training, which consisted of Light Vehicle (F350 “light” not Civic “light”), Fire Safety, Waste Management, and Health training. Most of what was covered involved cold weather considerations, and proper water and waste management associated with remote locations. Some topics were less obvious or expected, although they make perfect sense. For example, always park facing the wind since an open door is essentially a large sail when the wind is behind it. Also, writing or creating art with a finger on a muddy car, is literally etching musings into the side of the vehicle for years to come (the mud is made of sharp volcanic rock). Wonder if there’s a book of the “best” efforts somewhere…

After a break for lunch, we were in for a few hours of Field Safety and Training, which was a lot of fun! We got to start a fire, put up a tent and practice our knots. These would all be helpful should we ever have to dip into our emergency kits filled with survival equipment.

The day can be summarized in two statements that inevitably go hand in hand:

  • Safety is the priority
  • Communication is key

The importance of communication and safety planning, both within the team and with support staff, before hitting the field, while out in the field and a debrief after are the best ways to ensure that science is done successfully and safely (injured scientist = no science). Most injuries are found by other team members rather than the affected person, so it is important not only to pay attention to your own body (am I dehydrated? unfocused? cranky?) but the moods and well-being of others as well. Much like any other activity where even momentary inattention can have severe consequences, the buddy system is key.

McMurdo Station functions like a small town – a special and wonderful small town dedicated to understanding the world around us. It’s everyone’s job to make sure everyone is safe and happy. Looking forward to what the coming days will bring!

 

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Figure 1. Angela can save us from dehydration and cold!

A “warm” welcome from Provost Groves

We arrived at McMurdo (finally) after the longest day, which started at 4:00 AM and included 8-hour flight followed by a 1-hour drive. We got the most amazing welcome from Provost Groves.  He’s so personable, funny, and genuinely curious!  He was inspecting McMurdo and Amundsen-Scott as a member of the National Science Board. In the interests of this responsibility, he visited scientists of all stripes at both stations, and he even took a Georgetown banner to the South Pole! I was moved by the probing and insightful questions he asked us and all the scientists here. It’s clear that he cares deeply about scientific endeavors both at Georgetown and in the world at large, and that he does not dismiss these visits as merely duties but as the opportunity to have meaningful conversations about scientific progress and potential. I’m thankful for Provost Groves as well as the other NSB members for their unceasing support of the work that we do!

DSC_1356Figure 1: With Provost Groves (and Rear Admiral Byrd)!

We’re here!

The amazing journey from the Antarctica Research Center in Christchurch, New Zealand to “The Ice” started with a 8 hour flight in a C130 Hercules airplane (aka The Herc). After a 24 hour delay (because of weather in McMurdo) we finally got clearance to depart and start our journey. We headed through a NZ military security screening gate area and boarded the shuttle to the C130 boarding area… and then…BANG…it hit me; all of a sudden my lifelong dream of going to this remote continent was becoming real. No turning back now! Talk is cheap, but when you’re looking at that C130, it really sinks in. This was really happening and that’s when then butterflies and anxiousness began. Sarah’s been to Antarctica before, but it was all new and all unknown for a first timer like me.

When we boarded the C130 (SAFAIR of South Africa), we were handed a brown bag lunch.  We all piled in and found a seat. The plane was truly a military style C130 and had 45 standard comair style seating along with a ton of cargo. The flight crew were all military personal and gave us a safety briefing, some water, and ear plugs. Ear plugs were definitely required because it was noisy. Very noisy. Elena was the smart one in our group. She brought a set of Bose noise cancelling head phones- a true asset for this flight! After takeoff, the flight was smooth and it didn’t take long for the butterflies to go anyway.

During the flight, the pilots allowed us to spend some time in the cockpit. It was amazing… Awesome sights as we approached Antarctica. Much to my surprise, they used both Celestial navigation (by tracking the position of the sun) and GPS because we were too close to the magnetic south pole for traditional NAVs. Pretty cool. They even took time out to teach me how to use sight reduction tables. Not just an overview, but calculators and reference books! I guess you could call it the beginning of my Antarctica endless training program.

As we approached the continent, everyone was excited- looking out the windows, talking, chattering, laughing, a lot of oohh’s and Aahh’s … The excitement was electrifying. We were almost there.

We landed on the ice runway called Pegasus Field (NZPG). It was breathtaking! We scrambled to get on our ECW gear and get out of the plane so we could finally step foot on Antarctica. This was definitely a moment to behold forever! White everywhere! Snow and Ice and very unusual shuttle vehicles. We finally made it!

20161201_175652Figure 1. Our ride onto Continent. 

20161201_175704Figure 2. Our ride into town! 

Christchurch

Altogether, accounting for both flying time and layovers, we’ve already been on the move for

2 + 6 + 2 + 13 + 3 + 1.5 = 27.5 hours

from Washington, D.C. to Christchurch, New Zealand. Flights and airports disorient all senses of space and time; we become more anonymous while we traverse time zones and distorted political borders. It’s an apt preview of the transcendence of our destination. Under the Antarctic Treaty, Antarctica does not belong to any single political entity. The continent spans all 24 time zones, yet it can be continuously illuminated or dark for months at a time. Facing nature in its rawest form, we will indeed be reminded of our anonymity as we coexist with the cornucopia of flora, fauna, and microbiota on Earth.

Christchurch is a beautiful city located on South Island in New Zealand. We stopped here to regroup, rest, and get our government issued Extreme Cold Weather (ECW) clothing. We were delayed for 24 hours so we had some extra time to catch up on sleep and get to know a vibrantly hip and deeply resilient locale.

IMG_3307 editedsmFigure 1. All the gear we need to survive in Antarctica! Far left: Big Red, the canonical parka for all US Antarctic Program grantees and personnel.

 

IMG_3280 editedsmFigure 2. A little garden across from the Canterbury Museum, which documents Māori history and British colonization of New Zealand. 

 

IMG_3381 editedsmFigure 3. Re:START, the mall built from upcycled shipping containers. 

 

IMG_3459 editedsmFigure 4. On exhibit at the Christchurch Art Gallery; it’s built from 0.5 mm pencil lead! 

Updates from Antarctica

Welcome to our Antarctic blog! We thought it would be fun to post some updates from the field for students and colleagues, and friends and family. The National Science Foundation and the US Antarctic Program are supporting our lab’s research into long-term cell survival in the Dry Valleys, so over the coming weeks, our team of five will be collecting samples from our planet’s coldest, driest desert. We’ll be analyzing many of them in real time with a variety of advanced sequencing technologies. We’ll have updates as the science unfolds!

Oy, but we have to get there first. We’re 3/4th of the way to Antarctica, but our cargo plane to the ice was delayed, then scrubbed, then rescheduled, and now it’s delayed again. We’ve spent a few nights in Christchurch now, and we’re just waiting for the weather to improve at our destination, McMurdo Station. It’s nearly eight hours away over the empty waters of the vast Southern Ocean. The C-130 Hercules we’re flying down on doesn’t carry enough fuel to get all the way to Antarctica and then back to New Zealand if weather conditions prevent a landing, so the pilots are pretty conservative. A couple times this season, flights have “boomeranged” at the last point of safe return, meaning ten hours of flying just to end up where they started and have to do it all again the next day. Fingers crossed that won’t be us!

IMG_3356 sm
Figure 1. Ready to go.