Archive for the ‘Bonnie Laverock’ Category

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There’s no business like snow business

May 22, 2009

One of the best things about coming to a place like Ny-Alesund is that it’s not just for marine biologists – there are all sorts of other scientists here, from glaciologists to meteorologists. This means that we get the chance to talk to people who are doing totally different things to ourselves, and to learn a bit about what they study. On Wednesday evening, we jumped at the chance to do some field work with a snow scientist … and not just because it meant we had to drive skidoos!

We set off for the field site after dinner. It was only about 10 minutes’ drive away by snow scooter, but even at that short distance, it felt really good to be outside in the open after a couple of weeks on base. Our first job when we arrived was to pack away the equipment that Wiley the friendly snow scientist had set up earlier in the day. This consisted of a rig-up holding three different irradiance meters; one which measures the amount of light coming from above, and two which measure the light being reflected back again by the snow. Wiley is studying the reflective properties (“albedo”) of snow, which can affect the world’s climate because light-coloured objects tend to reflect rather than absorb heat. Wiley and his colleagues are particularly interested in how soot pollution from the atmosphere affects the reflectivity of the snow once it becomes trapped between the ice crystals, and they also use small aircraft to take measures of irradiance from the air, which they can compare with their field measurements.

Wiley and Helen start to dismantle the equipment used for measuring sky- and snow- irradiance. Photo: Bonnie Laverock

Wiley and Helen start to dismantle the equipment used for measuring sky- and snow- irradiance. Photo: Bonnie Laverock

Once the equipment had been packed away, it was time to dig some snow pits! Wiley had previously marked out three squares in the snow, and we dug a pit next to each of these so that we could look at a vertical section of snow going down the side of the pit. Basically, Wiley sits inside the pit and studies the layers that make up this section, particularly to look at the size and shape of the ice crystals in each layer.

A layered section of snow with fingertip for scale. Photo: Bonnie Laverock

A layered section of snow with fingertip for scale. Photo: Bonnie Laverock

The size and shape of the ice crystals within the snow layers affects the reflective properties of the snow as a whole. For instance, round grains of ice might reflect light in all directions, whereas more angular grains would reflect light less predictably, some of which might bounce back up, and some of which might get absorbed by deeper snow layers. The individual layers of snow are often separated by ice lenses, which absorb more light rather than reflecting it back at the sky. Wiley made a note of the type of ice crystal present at each layer, measuring the size of the crystals with a magnifying lens called a loupe, while we took notes in his field notebook. We were surprised by how many different types of snow there were!

Studying the size of ice crystals using a loupe and a millimetre-square meausuring card. Photo: Bonnie Laverock

Studying the size of ice crystals using a loupe and a millimetre-square meausuring card. Photo: Bonnie Laverock

While we were doing all of this digging and measuring, Hannah was set to work to collect the pristine snow from the three squares that Wiley had drawn earlier. The top 5 cm of snow was collected to be taken back to the laboratory for analysis of carbon content – this gives an idea for how much carbon soot is in the snow, and therefore how polluted the air was when the snow fell. It was important to be very clean when collecting this, because the carbon is present in such low amounts that it can easily be contaminated – so Wiley had marked three particularly clean areas of snow, which Hannah carefully bagged up and labelled.

Hannah carefully collects clean snow while Wiley studies the deeper layers in his snow pit. Photo: Bonnie Laverock

Hannah carefully collects clean snow while Wiley studies the deeper layers in his snow pit. Photo: Bonnie Laverock

Finally, when everything was measured and collected, we filled in the snow pits, packed everything onto a sledge, and attached it to a snow scooter to be towed back to base. We had one final rest with some chocolate – a reward for 3 hours’ hard work as snow science field assistants – and then it was back to base for a well-earned dip in the hot tub before resuming our lives as marine biologists!

Photo: Bonnie Laverock

Photo: Bonnie Laverock

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Mud, mud, glorious mud!

May 14, 2009

I’ve been looking forward to being able to write a “sediment blog” – because it means things are progressing with the sediment experiments!

On Monday, the divers collected 10 large sediment cores for the ocean acidification experiments. These cores have come from the sediment around the pier, which is right in front of the marine lab, and we now have 20 cores which are spread over the 5 pH treatments being used for the other studies. Fred and Pieter will be performing incubations throughout the experiment, to look at the oxygen consumption and nutrient fluxes. This gives us information about the biological processes that are going on within the sediment (such as respiration and growth). Measurements of temperature, total alkalinity, pH and dissolved inorganic carbon will also be taken from the overlying water to monitor the environmental conditions in the cores.

The divers returning from a sampling trip. Photo: Bonnie Laverock

The divers returning from a sampling trip. Photo: Bonnie Laverock

At the end of the experiment, samples will be taken for analysis of nitrification and denitrification. These processes are carried out by bacteria, and are important processes in marine sediment because they allow nutrients to be cycled back into the water column in a form that other organisms can feed on. We’re interested in how ocean acidification might affect this nitrogen cycle in the sediment. Therefore, Karen and I will also be looking at the bacteria that are present in the sediment. We’ll be looking at how the overall diversity of bacteria is affected by ocean acidification, and also whether the genes responsible for nitrogen cycling are affected.

Pieter and I have already taken some sediment samples so that we can have a look at diversity in normal sediment – this will give us a good baseline so that we can tell whether the communities have changed at the end of the experiment. We’ve got two lots of sediment so far: some really smelly, muddy sediment from the pier in front of the marine lab, and some sandy sediment from a site further downstream, called Brandal. As you can see, they are quite different, so it will be interesting to compare the bacteria in there!

Muddy sediment from the pier (left) and sandy sediment from Brandal (right). The interface between the oxic layer (light-coloured) and the anoxic layer (dark-coloured) is an important site for nitrification-denitrification reactions.

Muddy sediment from the pier (left) and sandy sediment from Brandal (right). The interface between the oxic layer (light-coloured) and the anoxic layer (dark-coloured) is an important site for nitrification-denitrification reactions. Photos: Bonnie Laverock

So how do we look at the bacteria in the sediment??

Most bacteria cannot be grown in the laboratory, so we have to use molecular methods to look at their internal molecules, such as proteins, DNA, or RNA. To look at diversity (what organisms are there and how many), we look at the differences between the DNA, just as we might look at a human’s DNA to investigate that person’s ancestry. To look at genes which control a specific function, such as nitrogen cycling, we can look at RNA – this is similar to DNA, but it tells us which genes are being made into proteins – so we’re looking at the genes that are actually being used in the environment. We can use “fingerprinting” techniques to look at the structure of a bacterial community, and how it changes.

Extracting DNA – a classroom experiment

You can extract DNA in your classroom from a piece of fruit or vegetable – peas, onions and bananas usually work pretty well. Follow the instructions below … the way in which scientists extract bacterial DNA is slightly different, but it uses the same principles (cell wall disruption, salty environment, protein breakdown and alcohol precipitation) …

Banana DNA (left) and bacterial DNA from a sediment sample (right). Both have been beaten to release DNA from cells, prepared in a salty environment, had their proteins removed, and have been precipitated in alcohol. Photos: Bonnie Laverock.

Banana DNA (left) and bacterial DNA from a sediment sample (right). Both have been beaten to release DNA from cells, prepared in a salty environment, had their proteins removed, and have been precipitated in alcohol. Photos: Bonnie Laverock.

Step 1: Dissolve 3 grams of salt in about 100 millilitres of warm water (distilled water is best if you have access to a lab).
Why? The salt provides a “good environment” for the DNA so that it is more likely that the DNA will come out of the cells and into solution (DNA is negatively charged, and salt is positively charged)

Step 2: Add a mashed up banana to a food blender, pour the salty water over the top, and blend for 5 to 10 seconds. Pour through a sieve into a glass.
Why? The blender helps to break open the cells which contain the DNA.
 
Step 3: Add 2 to 3 teaspoons of normal washing-up liquid and stir gently (we don’t want bubbles!).
Why? Washing-up liquid works by breaking up the fat and grease stuck to our dishes. We have fatty molecules in our body – they are called lipids, and they hold cells together. The washing-up liquid helps to break open cells by attacking these lipids – this releases the DNA from the cells.
Optional extra step: If you want, you can also add pineapple juice to your mixture!
Why? The pineapple juice contains a compound called bromelain, which is an enzyme that breaks down proteins. Adding this to the mix prevents your DNA from being contaminated by cell proteins.
 
Step 4: Use “rubbing alcohol” (or ethanol if you’re in a lab) and pour it very slowly down the side of the glass so that you can see it floating on top of the soapy mixture. Let it sit for a few minutes and watch what happens. The stringy whitish stuff you can see rising upwards is the banana’s DNA!
Why? DNA dissolves in water, so you cannot see it when it is in the soapy mixture. When you add the alcohol, the DNA rises upwards because it is less dense than water, soap, and the other cell goo. The reason you can see it now is that DNA does not dissolve in alcohol, so it becomes a gloopy solid as it leaves the watery layer.
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Ny-Alesund from a newbie’s point-of-view!

May 8, 2009

Well, after 2 days of travelling I arrived in Ny-Alesund yesterday, via Oslo and Longyearbyen. I’ve been looking forward to arriving here for a long time now, especially after reading the blog for the last couple of weeks – so as you can imagine I was very excited to finally get here! (So excited that I tried to run before I could walk, and before I’d got my ice-legs working, as you can see in the video!)

When you’ve built something up in your head for so long, it’s a bit surreal to experience it at last, so I’m struggling to describe what it feels like to be up here. The most striking thing to a new-person-on-base is how much like a normal town it is. Apart from the precautions you have to take, like dressing for the cold and not straying beyond the boundaries in case of polar bears, it feels pretty much like walking around any other base or university, and sometimes sitting at my desk I have to catch myself, look out of the window at the gleaming white mountains over the fjord, and think “yeah – I really am in the Arctic!”

The other really striking thing is the 24-hour sunlight. It gives the day a weirdly timeless quality, so hours can pass and it feels like you’ve just been sitting there for 20 minutes. I think my favourite thing to photograph at the moment is the midnight sun peeping over the edge of a hut or mountain – although the sun doesn’t set, the light changes at nighttime and gives the sky a beautiful golden hue. Below is a photograph I took in Longyearbyen, of people walking around the town at 2 o’clock in the morning.

Longyearbyen at 2am. Photo: Bonnie Laverock

Longyearbyen at 2am. Photo: Bonnie Laverock

My job while I’m here is to work with the sediment, which is what I do back at Plymouth Marine Laboratory. Unfortunately, the fjord has frozen over so much this year that it’s proving a difficult task for the divers to collect the sediment. However, when we do have some, I’ll be sampling it and extracting the bacterial DNA so that we can see what bacteria are there, what they’re doing (e.g. nitrogen cycling) and how ocean acidification changes this. I’ll also be helping out on the nutrient and bioturbation studies. As well as the sediment work, I’ll be helping to look after the sea urchins, and yesterday Helen and I took the first set of measurements for pH, salinity, temperature and TCO2. We’ll be measuring these parameters twice a week for the duration of the experiment, to monitor the environmental conditions in each of the tubs the urchins are living in. We only had one escapee yesterday, so we’re doing well …

I’ll leave you with a picture of me standing on the sea ice in front of our marine laboratory – the ice breaker has cleared the fjord up to the pier in the background, but here it’s still thick enough to stand on, and if you’re really quiet you can hear it creaking as it moves slightly beneath you …

Standing on the sea ice. Photo: Bonnie Laverock

Standing on the sea ice. Photo: Bonnie Laverock