I am in Montreal for 10 days during the Christmas holidays, so I'm back in the snow again after escaping Antarctica. HaHa. Luckily though, I won't be sleeping in a tent this time.
Wednesday, December 23, 2009
Santa bring his gifts early...
The initial batch of samples have arrived back at LSU. The majority of our ice samples come back on a ship, and won't be here until April, but a lucky few of our sample filters got to come home early for Christmas by airplane. Unfortunately, it is very expensive to ship samples home by air, and the majority of our samples must come home on the boat. Nevertheless, I am confident that the these initial filtered samples will provide some great results during the mean time.
I am in Montreal for 10 days during the Christmas holidays, so I'm back in the snow again after escaping Antarctica. HaHa. Luckily though, I won't be sleeping in a tent this time.
I am in Montreal for 10 days during the Christmas holidays, so I'm back in the snow again after escaping Antarctica. HaHa. Luckily though, I won't be sleeping in a tent this time.
Thursday, November 19, 2009
Experimentation Complete
Filtering has finally been completed. In total we filtered ~91 liters of sample! Our next primary objective was to extract RNA from one of the filters and quickly convert it to cDNA to prevent degradation. We can then ship the cDNA back to LSU to sequence.
While challenging, the information we will learn from this type of analysis will be very valuable. Sequencing the 16s rRNA fragment directly allows us to determine which species of microbes have remained viable when trapped inside Taylor Glacier. The normal method of just sequencing the 16s rRNA gene (which is located on DNA, not RNA) only tells us which microbes were present in the glacier at one point in time. Any microbes which died in the glacier thousands of years ago would no longer be viable, but may have have left there DNA behind. In other words, with DNA alone, it is difficult to tell which sequences came from viable cells as opposed to those sequences which came from dead cells.
Our extraction turned out to be a success as we managed to extract ~25ng of RNA from one filter!!! From this RNA we reverse-transcribed the 16s rRNA molecules to cDNA which is now on it's way to LSU to be sequenced!
Additionally, we measured the amount of ATP in our samples with the luminometer (as described last month on the blog). This experiment was successful as well, indicating about 10,000 cells/mL. This reinforces some direct microscopic cell counts we did earlier which yield roughly the same amount.
While challenging, the information we will learn from this type of analysis will be very valuable. Sequencing the 16s rRNA fragment directly allows us to determine which species of microbes have remained viable when trapped inside Taylor Glacier. The normal method of just sequencing the 16s rRNA gene (which is located on DNA, not RNA) only tells us which microbes were present in the glacier at one point in time. Any microbes which died in the glacier thousands of years ago would no longer be viable, but may have have left there DNA behind. In other words, with DNA alone, it is difficult to tell which sequences came from viable cells as opposed to those sequences which came from dead cells.
Our extraction turned out to be a success as we managed to extract ~25ng of RNA from one filter!!! From this RNA we reverse-transcribed the 16s rRNA molecules to cDNA which is now on it's way to LSU to be sequenced!
Additionally, we measured the amount of ATP in our samples with the luminometer (as described last month on the blog). This experiment was successful as well, indicating about 10,000 cells/mL. This reinforces some direct microscopic cell counts we did earlier which yield roughly the same amount.
Sunday, November 8, 2009
Filter, filter, filter...
After some initial difficulties with filters clogging Amanda and I have finally gotten into a good rhythm of cleaning ice, melting ice, pre-filtering melt water, centrifuging sediment, and filtering. We are managing to put about 10 liters of melt through each filter!
Wednesday, November 4, 2009
Analysis Begins...
Hey Guys! I'm back in McMurdo and back in the lab ready to go. Its nice to be back and enjoy the comforts of being inside, out of the wind. Here's an overview of what I am doing in the lab:
I want to concentrate about 150kg of our sample ice down onto filters for further experimentation. Several tests such as DNA or RNA analysis rely on relatively large amounts of cells to work efficiently. Our ice samples only have a few thousand microbial cells per mililiter. This may sound like a lot, but it's actually quite low. For example, one gram of soil commonly contains several million cells per mililiter. By filtering several gallons of melted sample onto a filter, I can thus concentrate the microbes to levels which will result in a reliable signal.
First, I will need to decontaminate the outer surfaces of our samples. The ice has been handled extensively during collection and it's imperitive we remove any foreign chemicals or microorganisms we inadvertantly added.
Here is what happens when you don't decontaminate samples. These are microscope images of filtered ice. The samples have been stained with a dye which glows bright green when it binds to DNA. As you can see on the left, the sample that was not decontaminated has lots of foreign material. The sample on the right was cleaned prior to filtering.
To decontaimnant the ice, we melt the outer surfaces away from the ice using sterilized water. This is the apparatus I setup to sterilize the water. Normally, we would just autoclave large carboys of water but unfortunately, McMurdo does not have any autoclaves large enough to do so on station. As a result, I must sterilize the water by filtration as shown above. On the far left is the carboy of water to be sterilized, followed to the right by a large parastolic pump. The wooden box in the middle is a portable laminar flow hood which is simply a fan which pushes air through a HEPA filter. This is to help prevent contamination from any microbes normally floating around in the lab. Finally, on the far right, is my collection bottle in which the filtered water is collected.
A variety of glassware which has been washed and autoclaved. As you can see, one cannot take contaimination lightly in a microbiology lab.
This is the ice cleaning station we created. We set samples on the grill right next to the laminar flow hood and pour the clean water all over the sample to melt away the outer contaimination.
Amanda uses forceps to manipulate and position the ice sample on the cleaning station.
A close-up of one of our samples. It looks pretty awesome once you clean them off.
This is the leftover sediment which was washed off the outside of our samples.
A dear, dear, friend of mine which I haven't seen since I left Louisiana. I was very happy to find a six-pack in the station store.
I want to concentrate about 150kg of our sample ice down onto filters for further experimentation. Several tests such as DNA or RNA analysis rely on relatively large amounts of cells to work efficiently. Our ice samples only have a few thousand microbial cells per mililiter. This may sound like a lot, but it's actually quite low. For example, one gram of soil commonly contains several million cells per mililiter. By filtering several gallons of melted sample onto a filter, I can thus concentrate the microbes to levels which will result in a reliable signal.
First, I will need to decontaminate the outer surfaces of our samples. The ice has been handled extensively during collection and it's imperitive we remove any foreign chemicals or microorganisms we inadvertantly added.
Here is what happens when you don't decontaminate samples. These are microscope images of filtered ice. The samples have been stained with a dye which glows bright green when it binds to DNA. As you can see on the left, the sample that was not decontaminated has lots of foreign material. The sample on the right was cleaned prior to filtering.
To decontaimnant the ice, we melt the outer surfaces away from the ice using sterilized water. This is the apparatus I setup to sterilize the water. Normally, we would just autoclave large carboys of water but unfortunately, McMurdo does not have any autoclaves large enough to do so on station. As a result, I must sterilize the water by filtration as shown above. On the far left is the carboy of water to be sterilized, followed to the right by a large parastolic pump. The wooden box in the middle is a portable laminar flow hood which is simply a fan which pushes air through a HEPA filter. This is to help prevent contamination from any microbes normally floating around in the lab. Finally, on the far right, is my collection bottle in which the filtered water is collected.
A variety of glassware which has been washed and autoclaved. As you can see, one cannot take contaimination lightly in a microbiology lab.
This is the ice cleaning station we created. We set samples on the grill right next to the laminar flow hood and pour the clean water all over the sample to melt away the outer contaimination.
Amanda uses forceps to manipulate and position the ice sample on the cleaning station.
A close-up of one of our samples. It looks pretty awesome once you clean them off.
This is the leftover sediment which was washed off the outside of our samples.
A dear, dear, friend of mine which I haven't seen since I left Louisiana. I was very happy to find a six-pack in the station store.
Monday, November 2, 2009
A brief update..
We have completed sampling and I will be heading back to McMurdo tomorrow to begin analysis.
My main goals will be to concentrate a large volume of sample onto filters. More details and pictures to come once I return to McMurdo.
My main goals will be to concentrate a large volume of sample onto filters. More details and pictures to come once I return to McMurdo.
Sunday, November 1, 2009
Friday, October 30, 2009
New and improved with dual chainsaw action!!!
After completion of the tunnel and sampling room, we must construct a small "freezer" to store our samples inside the tunnel until they can be flown out by helicopter. Otherwise, any samples stored outside the tunnel would be subject to direct 24-hour sunshine.
To construct this "freezer", Tim and I use the same technique we used to build the tunnel last week: Cut a tic-tac-toe pattern into a wall, and then smash the ice out with a demolition hammer. Because of the increased space of the sampling room (4x3 meters), were able to hook up two chainsaws to speed up the process (we also both possess Totin' Chips)!
To construct this "freezer", Tim and I use the same technique we used to build the tunnel last week: Cut a tic-tac-toe pattern into a wall, and then smash the ice out with a demolition hammer. Because of the increased space of the sampling room (4x3 meters), were able to hook up two chainsaws to speed up the process (we also both possess Totin' Chips)!
Wednesday, October 28, 2009
Tuesday, October 27, 2009
Nearing the end of the tunnel
Sorry for the late update. The repeater which allowed us to have internet at our field site was offline for a few days after a storm.
Lindsay Knippenberg hikes back up the glacial apron pulling the "ice removal" sled behind her. Notice the large pile of ice we have created in the construction of the tunnel. Last season we removed over 55 metric tons of ice during the tunnel excavation. We might be close to beating that record this season.
Lindsay and Tim inspect the "sampling room's" rear wall as it nears completion. The large dark band in the middle is a layer of sediment entrapped in the glacier. Currently, it is not fully understood how these layers form.
A look from the inside of the tunnel out.
Myself inside the tunnel.
Pretty cool photo of an A-Star which just dropped off some more supplies at camp via sling load (cargo net carried underneath the chopper).
P.S. Anyone is able to post comments or questions in the comments section below each post. It is not reserved for only the SHS students.
Lindsay Knippenberg hikes back up the glacial apron pulling the "ice removal" sled behind her. Notice the large pile of ice we have created in the construction of the tunnel. Last season we removed over 55 metric tons of ice during the tunnel excavation. We might be close to beating that record this season.
Lindsay and Tim inspect the "sampling room's" rear wall as it nears completion. The large dark band in the middle is a layer of sediment entrapped in the glacier. Currently, it is not fully understood how these layers form.
A look from the inside of the tunnel out.
Myself inside the tunnel.
Pretty cool photo of an A-Star which just dropped off some more supplies at camp via sling load (cargo net carried underneath the chopper).P.S. Anyone is able to post comments or questions in the comments section below each post. It is not reserved for only the SHS students.
Sunday, October 25, 2009
Into the glacier we go...
We have completed our first three days of tunneling and have already reached 6.0 meters! A few more meters inwards and we will being to dig downwards and prep for sampling. The idea is that once we tunnel far enough inside the glacier we will reach an area where the glacial ice is not highly deformed from margin effects. The margins, the edges of a glacier, are often deformed due to events such as calving (breaking off of a large mass of ice from the glacier) or melting.
Once we feel we are sufficiently inside the glacier, we will dig a pit down to sample the sediment-laden striated ice underneath. It is in these sediment layers we have detected high levels of CO2 paired with low levels of O2, indicating a possibility of microbial aerobic respiration! Additionally, we have found increased areas of methane, another possible signal of microbial activity in ice.
Once we feel we are sufficiently inside the glacier, we will dig a pit down to sample the sediment-laden striated ice underneath. It is in these sediment layers we have detected high levels of CO2 paired with low levels of O2, indicating a possibility of microbial aerobic respiration! Additionally, we have found increased areas of methane, another possible signal of microbial activity in ice.
Friday, October 23, 2009
Some photos from Antarctica!!!
This is a view of the Ferrar glacier on the way to Taylor Glacier.
We land at camp and unload all our gear from the Bell 212 Helicopter. Our camp is now officially in the field and goes by the call sign "Bravo Two Three Six - Blood Falls" over radios comms.
Working as a group to set up a Scott tent at camp. This tent serves as our bathroom.
A few of our personal tents in which we sleep.
Here's a few from Lake Bonney towards our main camp. The red polar haven is our kitchen/food tent where we cook and eat our meals. The blue polar haven serves as a heated storage tent for storing items which can't freeze (i.e. canned goods, cokes, etc...).
A close up of the main polar haven.
We all have our laptops out checking our emails. Most of us had dozens of unread messages to check due to the internet downtime this past week.
Melting glacial ice from Taylor for drinking water.
Amanda Achberger cutting stairs into the glacial apron leading up to our tunnel with the gas-powered chainsaw.
Amanda and Brent work on the very beginning of our tunnel into Taylor Glacier. At this point we have moved to using electric chainsaws. The gas powered chainsaws release too much exhaust to use safely in the tunnel.
Saturday, October 17, 2009
Possible Internet Outage
I have been assured that we will have internet at the field camp this season, but it may take a few day to be setup correctly.
Just a heads up back to you guys in the states that I might be unable to post for a few days.
Regardless, I'll have lots of great close-up pictures of camping in Antarctica and the construction of our new tunnel coming soon.
If you have any requests for images of anything in particular, don't hesitate to let me know!
-Shawn
Just a heads up back to you guys in the states that I might be unable to post for a few days.
Regardless, I'll have lots of great close-up pictures of camping in Antarctica and the construction of our new tunnel coming soon.
If you have any requests for images of anything in particular, don't hesitate to let me know!
-Shawn
Delayed!!!
Our helicopter flight out to the field camp was delayed until after the weekend. Before we are allowed to deploy, McMurdo sends out carpenters to build the Polar Havens. These are large, durable tents which we use for our kitchen and storage. Because of weather delays earlier in the week, they weren't able to build them in time for us to deploy on the weekend.
This isn't our polar haven, but it is very similar to what ours will look like.
This isn't our polar haven, but it is very similar to what ours will look like.
Wednesday, October 14, 2009
Q+A with SHS Students
What are the buffers and reagents your making for your analysis?
Great Question! I am making Tris-Acetate and Tris-HCL buffers. These are commonly used buffers in biochemical assays that help keep the pH of a solution stable. In my specific application, I am using them in the "firefly" assay. This technique is used to measure the amount of ATP in a sample. The assay derives its nickname from the use of luciferase and luciferin, an enzyme and pigment found in a fireflies. Luciferase catalyzes the oxidation of luciferin when ATP is present, producing light.
We use a special instrument called a Luminometer for this measurement. I can place a sample inside and shut the door to block out all ambient light. The luminometer then injects a mixture of Luciferase and Luciferin into the sample and measures how much light is produced using a super-sensitive light detector called a photomultiplier tube. Based on this measurement, we can then calculate how much ATP was in the sample!
What are some of the foods that you take on your trip, do you use any freeze dried food?
Surprisingly, we eat pretty well in the field. Breakfast almost always consists of bagels or English muffins with juice or coffee. During lunch, we are usually up at the tunnel site working on excavating the tunnel or sampling ice blocks. As a result, we usually just chow down on granola bars, trail mix, and lots of chocolate to keep our energy up. For dinner, We cook lots of canned veggies and pasta mixes, but we also have frozen chicken, pork, and beef as well. Each camp member takes a turn cooking dinner each evening, and some of us are very good cooks: Roast pork tenderloin with mashed potatoes and brown gravy... yum!!
We do have freeze dried meals in our survival bags in case of emergencies. Last season in 2007, I had to eat a few during snow survival training. They don't taste amazing but in a survival situation comfort is not a priority.
P.S. Whats with the metal icecream cone in the background in the New Zealand picture?
The big ice cream cone is actually a sculpture called the Chalice. It was built in the square in 2000 to commemorate the new millennium.
Great Question! I am making Tris-Acetate and Tris-HCL buffers. These are commonly used buffers in biochemical assays that help keep the pH of a solution stable. In my specific application, I am using them in the "firefly" assay. This technique is used to measure the amount of ATP in a sample. The assay derives its nickname from the use of luciferase and luciferin, an enzyme and pigment found in a fireflies. Luciferase catalyzes the oxidation of luciferin when ATP is present, producing light.
We use a special instrument called a Luminometer for this measurement. I can place a sample inside and shut the door to block out all ambient light. The luminometer then injects a mixture of Luciferase and Luciferin into the sample and measures how much light is produced using a super-sensitive light detector called a photomultiplier tube. Based on this measurement, we can then calculate how much ATP was in the sample!
What are some of the foods that you take on your trip, do you use any freeze dried food?
Surprisingly, we eat pretty well in the field. Breakfast almost always consists of bagels or English muffins with juice or coffee. During lunch, we are usually up at the tunnel site working on excavating the tunnel or sampling ice blocks. As a result, we usually just chow down on granola bars, trail mix, and lots of chocolate to keep our energy up. For dinner, We cook lots of canned veggies and pasta mixes, but we also have frozen chicken, pork, and beef as well. Each camp member takes a turn cooking dinner each evening, and some of us are very good cooks: Roast pork tenderloin with mashed potatoes and brown gravy... yum!!
We do have freeze dried meals in our survival bags in case of emergencies. Last season in 2007, I had to eat a few during snow survival training. They don't taste amazing but in a survival situation comfort is not a priority.
P.S. Whats with the metal icecream cone in the background in the New Zealand picture?
The big ice cream cone is actually a sculpture called the Chalice. It was built in the square in 2000 to commemorate the new millennium.
Monday, October 12, 2009
Life in McMurdo
Hey guys!
I hope all is going well back in the States. The last few days have been focused mainly on adjusting to McMurdo life and preparation for our field deployment to the Dry Valleys. We've had briefings on everything from sorting trash and protecting the environment to operating Vietnam-era HF radios. I'll give you a quick tour of some of our activities.
As you can see here, all trash at McMurdo is sorted so that as much as possible can be recycled. Because of how remote it is, we have to conserve as much as we can while minimizing waste at the same time. Shipping in fuel, food, and supplies is very expensive and can only happen a few months out of the year. Also, all garbage eventually has to be shipped back to the States to be processed. As a result, McMurdo is one of the most effcient towns in the world: sixty-five percent of all trash in McMurdo is recycled!!
The next few weeks, our team will be in the field chainsawwing more ice samples from the glacier. Beforehand, I need to prepare some buffers and reagents that we will use during our upcoming analyses.
This is a time lapse video created by Tim Brox. He is another undergradute on our team majoring in Physics at Montana State University. The food pull is where we select and package the food we will eat while in the field. This includes everything from breakfast, lunch, dinner and snacks. The only thing we don't bring to the field is water, which we "make" in the field by melting pieces of the glacier.
Myself at the edge of town looking across the sound to Antarctica! Keep in mind, McMurdo is located on Ross Island in the Ross Sea. Technically, one could say that McMurdo is not actually on the Antarctica continent. The temperature tells me otherwise.
Finally, I leave you with a picture of myself and the two P.I.'s (Primary investigators) of the project. On the left is Mark Skidmore, in the center is myself, and on the right is my PhD advisor during graduate school, Brent Christner.
I hope all is going well back in the States. The last few days have been focused mainly on adjusting to McMurdo life and preparation for our field deployment to the Dry Valleys. We've had briefings on everything from sorting trash and protecting the environment to operating Vietnam-era HF radios. I'll give you a quick tour of some of our activities.
As you can see here, all trash at McMurdo is sorted so that as much as possible can be recycled. Because of how remote it is, we have to conserve as much as we can while minimizing waste at the same time. Shipping in fuel, food, and supplies is very expensive and can only happen a few months out of the year. Also, all garbage eventually has to be shipped back to the States to be processed. As a result, McMurdo is one of the most effcient towns in the world: sixty-five percent of all trash in McMurdo is recycled!!
The next few weeks, our team will be in the field chainsawwing more ice samples from the glacier. Beforehand, I need to prepare some buffers and reagents that we will use during our upcoming analyses.
This is a time lapse video created by Tim Brox. He is another undergradute on our team majoring in Physics at Montana State University. The food pull is where we select and package the food we will eat while in the field. This includes everything from breakfast, lunch, dinner and snacks. The only thing we don't bring to the field is water, which we "make" in the field by melting pieces of the glacier.
Myself at the edge of town looking across the sound to Antarctica! Keep in mind, McMurdo is located on Ross Island in the Ross Sea. Technically, one could say that McMurdo is not actually on the Antarctica continent. The temperature tells me otherwise.
Finally, I leave you with a picture of myself and the two P.I.'s (Primary investigators) of the project. On the left is Mark Skidmore, in the center is myself, and on the right is my PhD advisor during graduate school, Brent Christner.
Friday, October 9, 2009
Antarctica!!!
Sorry for the delay on the update, it's been a long couple of days since flying down from New Zealand. Thursday afternoon, I gathered all of my issued ECW gear (parka, gloves, polar fleece, etc..) and the next morning at 6am we began our 5 hour flight to McMurdo.
Inside the C-17 shortly before take-off. I was actually one of the first boarding, so all those seats in the background actually filled up before we left.
Here is Amanda Achberger and myself on the Pegasus airfield just outside McMurdo shortly after we landed. Amanda is an undergraduate research assistant in our lab majoring in microbiology. The temperature was about -33°C (-27.4° F). It's still quite cold down here in Antarctica as the southern hemisphere's summer hasn't quite started yet.
The next couple of days in Antarctica will be spent in various briefings and trainings to help adjust us to life in McMurdo as well as prepare us for our field deployment in about 6-8 days. More pictures of McMurdo to come...
Wednesday, October 7, 2009
New Zealand at Last!!!
Well, after a long 27 hours of travel, we arrived in Christchurch, NZ. The flights went relatively well this time, but almost everyone on our team were missing their luggage!!! Luckily, after much discussion with the airilines, we found that our luggage was left behind in Sydney, Austrailia.
This afternoon, we will head to the CDC (Clothing Distribution Center) where we will recieve all our ECW (extreme cold weather gear). This consists of things like our parka (aka BIG RED) gloves, pants, etc. Also, we will find out when our deployment flight to McMurdo will be. We are currently scheduled to leave Friday morning (which is actually Thursday night for you guys back in LA), but because of some weather delays, we might get bumped to Saturday.
I'll keep you guys updated on the luggage story and when our official deployment is.
P.S. Here's a picture of me in the central square of Christchurch. It's still late spring here down in the southern hemisphere, so the cool weather (~50°F) is a welcome change from the Louisiana heat.
Monday, September 28, 2009
Subscribe to:
Comments (Atom)
