Archive for June, 2009

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Learning the Molecular Alphabet: DNA/RNA analysis at Pavilion Lake

Posted on June 29th, 2009 by Zena Cardman

I am an undergraduate at the University of North Carolina, and this year I’ll be collecting microbialite samples, to figure out how the microscopic species living on the microbialites vary throughout the lake. Currently I’m working in a lab in the Department of Marine Science at UNC with Andreas Teske and Jen Biddle, where I study the genetic diversity of microbes living around a deep-sea hydrothermal vent site near Guaymas, Mexico. Even though Pavilion Lake is a very different environment, I’ll be using many of the same techniques to study the microbial life in Pavilion Lake as I do to study the microbes living in mud almost 3,000 meters below the surface of the ocean.

My background is in molecular biology, so to study the diversity of the microbialites’ microbes, Jen and I will extract their DNA and RNA, and then determine the sequences of particular genes that they code for. If you need a quick crash course in molecular biology: DNA is a molecule made up of four different types of subunits (called A, T, G and C for short), which are repeated and reordered to form a long chain. The particular order of these subunits stores the genetic information for all life forms, much like different combinations of letters spell out different words. Genes that are “switched on” write the words that code for RNA, a molecule which in turn gets translated into proteins. By looking at the differences between these sequences, we can gain some insight into what types of organisms they are, and how closely related they are. It would be very cool if we find differences in the microbes associated with different types of microbialites!

The DNA and RNA of a biological sample degrade quickly, so you have to preserve it if you want to be able to study it back home in your lab. Often samples are frozen at –80 degrees, or in liquid Nitrogen, in order to preserve their genetic information for future analysis. But it can be difficult to freeze samples like this, and safely ship them back to your lab when you are out doing field research. Instead, I’ll be using a salty solution to preserve the RNA in the microbialite samples I take. Field work is a fun challenge, because you have to be so prepared ahead of time! Everyone with the Pavilion Lake Research Project has been working hard for months already to make sure we’re ready for anything at the lake.

While there is barely a week left I leave for Pavilion Lake, I’m currently attending a course on astrobiology in Spain. The students are all young (mostly in graduate school, or recent PhDs), and it’s wonderful to witness the beginnings of collaborations between young scientists. I think astrobiology is especially conducive to collaboration, because it’s so interdisciplinary, and field projects like PLRP are no exception.

I can’t wait to see everyone at Pavilion Lake!

~Zena

Zena behind a mammoth-sized stack of clone libraries

Zena behind a mammoth-sized stack of clone libraries

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UBC-Gavia: The (Un)Common Loon in the Lake

Posted on June 25th, 2009 by Andrew Hamilton

Behold the Common Loon. The Great Northern Diver. Scientific name Gavia immer. The bird that lent its image and name to the one dollar coin, the “loonie”.

The Common Loon, Gavia immer

The Common Loon, Gavia immer

Well, there’s a new loon in town, and this one is not very common. UBC-Gavia, the autonomous underwater vehicle (AUV) named after the Common Loon, is the robot that will be diving beneath the surface of Pavilion Lake this summer. As one of only a handful of Gavia-class AUVs in the world, and one of only two in Canada, seeing this uncommon loon is a rare and special sight in Canadian lakes.

This year we are particularly excited to have Dr. Art Trembanis joining the project who will be bringing some very high-tech toys with him from the University of Delaware. Dr. Trembanis may have an uncommon name (apparently he is one of only 6 Trembanis’ in the world – the other 5 being his immediate family) but he’s certainly no loon. Art is the happy owner of another Gavia AUV that is equipped with an inertial navigation system (INS), the navigation instrument found on commercial airliners. This allows his Gavia to fly with unprecedented location accuracy and precision underwater. Due to the interchangeable modules on the Gavia AUVs, this also means he can bring the INS module with him to attach to UBC-Gavia for the Pavilion Lake project to collect high-resolution spatially referenced data. It is also an excellent idea when there are multiple submersibles flying around the lake at the same time (UBC-Gavia and the Deepworkers) to know precisely where each one is. Avoiding an unplanned underwater encounter is priority one!

Four uncommon loons. Doug Miller, Andrew Hamilton and Art Trembanis with the University of Delaware's Gavia AUV

Four uncommon loons. Doug Miller, Andrew Hamilton and Art Trembanis with the University of Delaware's Gavia AUV

One of the goals of Gavia at Pavilion is to help us track the flow of groundwater inputs into the lake. There are several springs that flow into the lake underwater and depending on the chemistry of this groundwater these springs may play a role in microbialite formation. We expect the groundwater may be more saline and dense than the lake water and so will creep along the bottom from its sources to the deepest part of the lake. Flying UBC-Gavia in precise bottom tracking mode, equipped with the INS, will help us focus in on the path of the groundwater and allow us to send the Deepworkers in for a closer inspection.

Another exciting first for this field season is that we hope to test a water sampler prototype designed by three undergraduate engineering students at UBC. Gabriel Hamilton, Jadon Harrison and Mark Mosher, designed and built an independent bottle system that attaches to the the outside of UBC-Gavia. This will allow us to collect small water samples at depth during the mission and return them to the surface for analysis. The team has successfully tested the sampling system independently, now we want to put it through its paces in the field on UBC-Gavia. A robust and functional water sampler attached to the AUV would permit the collection of samples from locations that may otherwise be inaccessible and expand UBC-Gavia’s capabilities for biological analysis (as a molecular oceanographer this is very exciting to me!). The team of undergrads will be giving us a demonstration of their water sampler this evening, so we’re looking forward to seeing it in action.

So if you happen to be at Pavilion Lake during the first two weeks of July, watch for the rare uncommon loon diving under the water. It will be followed closely at the surface by a more common loonie (yours truly) in a zodiac (although I think it’ll be a while before my image makes it onto a coin!).

Cheers,

Andrew

An uncommon loon on the beach. Art's Gavia AUV staying cool in Delaware

An uncommon loon on the beach. Art's Gavia AUV staying cool in Delaware

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Piloting DeepWorker: not your everyday commute!

Posted on June 24th, 2009 by Allyson Brady

As the field season draws closer, I think about how lucky I am to be part of the Pavilion Lake project and of all the amazing people and activities that are part of my research. This year will be my second time driving the submersibles at Pavilion and I can’t wait! It’s hard to believe that already a year has gone by since the last field season. We’ve been so busy prepping for the science and how we’re going to use the subs this year that I feel the need to stop and remember what a unique opportunity this is and how much fun it is to actually drive the DeepWorkers! Everything from launch, to navigating our flights plans, and to recovery is done with the support of an amazing team of people that allows the pilots to focus on the science and of course, on our driving!

Driving the submersible is in some ways similar to driving a car, but we usually describe how the subs move through the water as ‘flying’, because you are moving in three dimensions like the pilot of an aircraft. Most of the power and control over speed comes from your feet and foot pedals that let you move forward and back, but they also allow you to move up and down at the same time. Of course, learning to steer with your feet rather than a steering wheel is a different story. One little twist of the foot is all it takes to start heading in a new direction. That is, unless you have small feet like me and then it’s a big twist of the foot before you go anywhere! Fortunately I have comfy slippers that help fill the foot pedals and keep my feet toasty warm in chilly depths of the lake. It can definitely get cold down at the bottom of the lake (about 4 ºC) so wearing several layers of warm clothing is a must if you want to stay comfortable. Unfortunately, sweatshirts are not too much fun when you’re waiting on deck in the middle of hot July day but they’re definitely worth it once you’re in the water. I’d also recommend a hearty breakfast before launch as it’s hard to find good snacks at 200 ft. Our missions tend to run around 2 hours and despite the fact that it may sound like a long time, it’s amazing how quickly time flies. In addition to keeping our eyes open for interesting microbialites or other intriguing finds, we also have to keep track of our navigation, video recording, life support and maintain a narration of the environment around us. But it’s very easy to simply get caught up in the wonder of being surrounded by fields of microbialites.

We really are lucky to have the opportunity to explore such a unique and interesting environment. There are so many exciting things to see that I’m always disappointed when the dive is over and it’s time to return to the surface. So with only two more weeks to go, my slippers are packed and I’m ready to fly!

~ Allyson

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Focusing on the details: 2009 DeepWorker Science Goals

Posted on June 22nd, 2009 by Margarita Marinova
Submersible tracks from the 2008 field season. Satellite image from Google Earth.

Submersible tracks from the 2008 field season. Satellite image from Google Earth.

As the field season nears, and everyone is busy finishing up all those details necessary to make our time in the field run smoothly, it’s important to refocus on our science goals for this year.

To quickly recap last year’s field season : our science pilots managed to explore most of the lake, giving a wealth of video footage and personal observations for the entire science team to analyze during the past year. You can see just how much of the lake we covered last year from all the submarine tracks! For the 2009 field season we have two main goals: to finish exploring some of the areas that we didn’t reach last year (you never know what’s hiding in the dark!); and to explore in detail the areas that we found to be particularly fascinating from our analysis of the 2008 data.

Following-up on the extensive exploration from last year, we are turning our attention to understanding some of the already identified features and trends, and using these to answer some big questions. In the lake we find microbialite structures that vary in shape and size. Some lake bottom areas are covered with the microbialites, while others have just sediment, or algae, or rocks from landslides. So why is there such a variation in what we find in the lake? How do the microbialites form? What sets their shape, their size, their distribution? And what can they tell us about the preservation of biosignatures – the fossils of microorganisms? These are hard questions that geobiologists have been trying to answer for decades, and we think that studying Pavilion Lake will contribute to the understanding of microbialites throughout Earth’s history. To tackle these questions, this field season we will be using the DeepWorkers to get detailed imaging and data at previously identified areas of interest.

Microbialite structures among the chara (algae). Are the microbialites using the chara as a base to grow on?

Microbialite structures among the chara (algae). Are the microbialites using the chara as a base to grow on?

Analysis of last year’s DeepWorker observations gave some surprising results, but also showed some possible trends that need to be investigated further. Last year we were surprised that the macro-morphology – the large-scale shape of the microbialite structures – was not strictly correlated with depth, like we thought it would be. So this year we hope that detailed observations needed to answer some smaller questions will ultimately help us answer our big questions. Some smaller questions we’re asking are: what are the microbialites growing on? Do they need a rock as a growing base, or algae, or do they just sit in the sediment? And does the growing medium have an effect on the shape or size of the microbialite? What about the small-scale structure (micro-morphology)? Microbialites with similar macro-morphologies can still be composed of differently shaped and sized components. The answers from all of these smaller questions will hopefully shed light on the bigger questions.

Every year we get some answers, and come up with even more questions. But that’s why this project is fascinating: Pavilion Lake is such a complex system! Little by little – by asking the right questions – the answers are coming together and we are starting to understand Pavilion Lake.

~Mars

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Rebreathers and Robots

Posted on June 18th, 2009 by Alex Forrest

Robert A. Heinlein once wrote a book called ‘Have Space Suit – Will Travel’ but I would argue that the same thing could be said for underwater robots. During the past several weeks of preparation for this summer’s Deepworker deployment I have been doing some extensive travel with some of the other AUV (Autonomous Underwater Vehicle) projects in which I am involved. Two of the more interesting places have been Aberdeen, Scotland and Chesapeake Bay, Maryland.

The helicopter underwater escape training simulator

The helicopter underwater escape training simulator

The first of these was to do the Basic Offshore Safety Induction and Training course (BOSIET). This is the training necessary to prepare for potential rescue scenarios for transport to offshore oil rigs, and is required for an upcoming AUV project. One of the more intimidating parts of the training was an inverted exit of a flooded helicopter simulator. The simulator shown on the right is lowered into the water while you breathe through a rebreather (where air is temporarily stored in your life jacket). This allows you to breathe underwater for about 30 seconds and allows you enough time to release from the harness and push out the window and exit. This was a definitely a unique experience that puts a new perspective on working in and around the water, at Pavilion Lake and elsewhere over open water in the Caspian Sea and over sea-ice in the Canadian High Arctic.

Adam Skarke from the University of Delaware getting ready to deploy the Gavia vehicle

Adam Skarke from the University of Delaware getting ready to deploy the Gavia vehicle

On my return from Aberdeen, I stopped over in Chesapeake Bay to attend an event informally known as AUVFest 2009 where four AUV groups from around the United States met to perform a demonstration of their technologies, and to work with educators on how to transfer knowledge from the practice to the classroom. This was a fantastic workshop that really emphasized how every vehicle, with their varied sensor setups, fills a different niche for underwater exploration. For me, this really hit home as an important concept at Pavilion Lake, where we have a wide array of tools and vehicles that must be optimized in order to get the best scientific returns. Sharing the varied and extensive experience at this workshop showed that Heinlein was right with a slight variation: “Have AUV – Will Travel”.

~Alex Forrest

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Communicating Science: Education and Public Outreach

Posted on June 15th, 2009 by Ben Cowie

Arguably, the most important part of doing science is telling people about your discoveries. It is only when you share your results that your experiments can be verified, and others can learn from your successes (and yes, mistakes)! However, a different type of communication is called Education and Public Outreach, or EPO. Education and Public Outreach covers a broad range of activities, from those as simple as arranging visits to schools from our scientists or developing this blog, to more complicated programs like podcasts and website design. These types of activities make science both accessible and exciting!

This year the PLRP is engaged in several EPO activities with teachers, students and Pavilion Lake community members so we can share our excitement about the lake with others. For example, on the evening of July 11 we will host our annual Community Day and Open House, where the local community is encouraged to come to the Lake, meet our team, and discuss our science and exploration activities. Our science team has benefitted greatly in the past on Community Day from hearing stories from the local community about the lake and its history. As always we are looking forward to seeing familiar faces, and meeting new people who are interested in our project at Pavilion Lake.

Ben speaking about Pavilion Lake at Alexander Hamilton Elementary School in Richmond, BC with teacher Leanne Shortridge

Ben Cowie (right) speaking about Pavilion Lake at Alexander Hamilton Elementary School in Richmond, BC with teacher Leanne Shortridge (left)

A second project we are developing is a field science integration program for elementary and high school teachers. This year the PLRP will host several teachers at Pavilion Lake for a few days during field operations. During their time in the field, they will have the opportunity to work alongside our science team, receiving hands-on experience doing real field science.  Our aim is to provide these teachers with the materials and experience to train the next generation of young scientists.

Another unique opportunity we have developed this year is a partnership with Shad Valley – UBC Campus. Shad Valley (www.shad.ca) is a summer camp for talented high school students interested in science and engineering. In the field, we will touch base regularly with the Shad students via videoconference, simulating a discussion between an active science operation in space and Mission Control on Earth. This program will give the students insight into a large-scale science operation, develop their interest in space, robotics and analogue research, and help them develop inquiry skills by developing scientific questions for the scientists at the Lake. I am excited to work with some young and very bright people at Shad Valley. Welcome, Shads!

With all the amazing science happening at Pavilion Lake, our team thinks it’s important to share with the community around us, and around the world. By developing effective EPO, we hope to make our science accessible, exciting and engaging for everyone.

Cheers,

Ben Cowie
EPO Project Lead, PLRP

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