This week we took some of our first year Animal Behaviour and Conservation Biology students to watch a Dartmoor Pony (Equus ferus Boddaert) dissection at Dartmoor Zoo, which is a relatively short drive from the University and is just on the south tip of Dartmoor, surrounded by beautiful countryside. Dartmoor ponies are an essential part of the moor’s ecosystem and are semi-feral at present. In order to conserve the moor’s ecosystem, it is vital that the ponies are preserved in a viable and healthy state. Because of the small gene pool getting even smaller, there is a scheme under way to cull individual female ponies that consistently deliver deformed or ill foals. This sounds quite an extreme means to deal with the problem but it’s really the only way.

To ensure this is a waste-free process, once the animals have been slaughtered, the zoo butchers the meat for use as feed for zoo animals such as tigers and lions. They also enjoy the occasional horse’s head but the public tends not to like to have to see that, so it’s kept to an occasional treat! The skin is used for leather or to make toys for the big cats to train with - as are the tails. The bones and offal are sent to be rendered into tallow and gelatine for non-human use, such as in laboratories.

In this photo, the underside of the horse has been opened and the digestive tract is spilling out. The bright yellow matter is adipose (fat) tissue under the skin of the pony. The large structure hanging to the floor is the cecum - in humans this is a small pouch at the junction of the small and large intestines, but in some animals like this pony that eat a lot of cellulose (in plant material), the cecum is much larger. This is because it is the location in which hind-gut fermentation takes place, where anaerobic Bacteria ferment cellulose to enable it to be digested. 

Simply put, without its cecal Bacteria, this horse would not be able to survive on its diet of grass and plant matter since it would not be able to digest the cellulose present at all. 

Who Do You Mink You Are?

I’ve just been discussing water aminals with one of my favourite Twitter scientists (and fellow King’s College London alumnus, though he started there after I’d left) @jayneale and he mentioned mink, which reminded me of fieldwork story so I said I’d blog it for him to read, and here it is, for everyone to read!

In the early summer of 2006, I spent some time working at the University of Bergen in their Marine Biological Station as per this map (you can streetview it), at the end of Espelandsvegen. The floating pontoon thingy out in the fjord is where our work was done - we had giant bags containing thousands of litres of fjordwater, into which plankton blooms were induced by adding nutrients. The overall aim was to look at how increased carbon dioxide levels would effect a planktonic bloom event - my work concentrated on sulfur gases released when these blooms die.

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There were about 20 of us there at any point in time and we were mostly scientists from the UK and Germany but we did have intermittent visits from IT people (to learn more about how scientists work so they can develop better software for us) and spouses/family members. As field campaigns go, it wasn’t managed that well though scientifically, it was a pleasant experience and the bonding of most of the team there was really nice. 

The Station comprises a boat house and dock and two main buildings, built fairly recently. The first contains the laboratories, a seminar room and office space and the second contains 20 bedrooms with bunk beds and en suite bathrooms, a massive kitchen suitable for catering, a living area and, of course, a sauna. We had a lot of fun borrowing the boats after each day of work and going out to explore the various islands, in the manner of Swallows and Amazons, renaming Veste Synsthoimen as “Goat Island”, as it was being used to graze goats at the time - cute little chaps they were too - very inquisitive and tiny! Søre Egdholmen became “Slug Island” as that was just about the only distinguishing feature and, once, we made it all the way over to Tyssøy, which was “Crab Island” for the number of broken shells we found on the rocky shore.

We seldom left the Station other than to buy food at the Supermarket, in bulk. Foot in Norway costs a fortune but with 20 of us, it worked out about £15 each per day. As a special treat, we could just about afford (from our own pockets, not the budget!) a couple of bottles of beer each day. During the National Day Parade on 17th May, we were not only allowed into Bergen itself but we actually took part in the Parade! Long story…

Whilst the Station is quite modern, a facility had been there for many years as there was an old, derelict Station behind it (now demolished). It was a huge old building with peeling paint, holes in the floors, creepy old bits of furniture and decor left here and there - a great place to go and take pictures. One evening, after a few beers, a few of us thought it would be a fun time to go and explore the Old Station and off they went. Myself and the only other person who stayed behind in the Station on the pretext of “being tired” both had the intention of sneaking into the building to scare them, so up we got and ran around the other side of the small hill next to the Station to get behind the Old Station without them seeing us. Once we could hear them moving about inside, we started throwing bits of gravel through the broken windows to scare them. Giggling and trying to be quiet whilst stumbling about a bit pissed, suddenly we heard the most blood-curdling, sickening noise I have ever heard in my life. It sounded like a baby being strangled to death, it was just terrifying. We screamed. They all screamed inside the building and ran outside. We then, as a big group, for safety in numbers, decided to track the noise down. 

We discovered that the culpret wasn’t the enormous beast fresh from Hell that our minds had conjured but a tiny juvenile European mink (Mustela lutreola L.), absolutely terrified out of his wits having been woken up by a gaggle of scientists. The poor little thing soon settled as we walked away and left him alone. We saw him a few times (or could’ve been a different one) around the Station in the coming weeks, exploring and trying to find out who all of these people wandering about by his home were. Very elegant creatures and SO fast! The only downside is that sickening scream that they have. I tried to find an example on YouTube to share but the noise is probably so evil that it’s banned from being recorded!

"Go west! Life is peaceful there!"

Some readers will know this already but, now that I have the contract signed and the resignation letter written, I can finally announce that I am leaving the University of Warwick in early 2012 to take up as post as Lecturer in Ecology and Environmental Biology at Plymouth University. 

It is a time of great excitement and opportunity and the last month has been a complete whirlwind - I cannot wait to get started on my next adventure early next year! It will be very sad to leave behind some frankly amazing friends here in Coventry but quite simply, I would’ve been a complete idiot to say no!

The Blackleg Miner - Part 2

In yesterday’s post about biomining, I mentioned I was involved in a second type of mining and that’s the subject of today’s post: genome mining.

Last week I submitted a manuscript that I had written to a journal for consideration for publication concerning the genome sequence of a strain of Methylomonas methanica. The manuscript has 27 authors based at 8 institutions in 5 different countries and is the biggest project in terms of number of authors that I have been involved in and, of those 27 authors, I’m at the front, because I pulled most of it together in the end, though I started out about 5th and gradually moved forwards, particularly as I ended up writing the manuscript itself - that wasn’t planned originally but that’s how it ended up. This is the second genome sequence that I have worked on - the first being that of Methylophaga thiooxydans, which I published earlier this year with a much smaller team. 

Both of these organisms are Bacteria found in the marine environment and, since they both have “Methylo-” generic names, they evidently have a lot in common. Members of the genus Methylomonas are methanotrophic, which means that they can grow on methane as a source of carbon. There is an apparent peculiarity amongst a lot of Bacteria that can grow on methane in that they seem to depend upon it - they’ve lost the ability to grow on pretty much anything else. Personally, I don’t think this makes evolutionary sense and I’m sure they can use other things though refuse to do so in the lab. Members of the genus Methylophaga are still fussy eaters but far less so - they can’t grow on methane but they can grow on methanol, methylated amines, dimethylsulfide and a lot of other “one-carbon” or “C1” compounds, in addition to fructose and a few other multicarbon compounds - they are methylotrophic. These C1 compounds are prevalent in seawater (yes, even methane) and it makes sense, therefore, that there is something out there eating them. After decades of C1 research around the world, we now know which enzymes and genes are responsible for the metabolism of a lot of these compounds but we’re still struggling with some of the details - which is why the genome sequences are so useful.

The Blackleg Miner - Part 1

Ok - this has nothing to do with the NACODS during the NUM strike or 19th century folk songs - no, this is about a different kind of mining.

Father and son, we’re both miners. My Father mined coal until the mid-1980s but me? I’m a different kind of miner - in fact, I’m TWO different kinds of miner, thinking about it. Firstly, I’m a biominer - I worked for a while mining copper using Bacteria. You might think that a bit far-fetched but, would you believe that gold, copper and uranium are often mined in this way? Amazing though it may seem, over 25% of all the copper mined in the world is mined by Bacteria (well, Archaea too but but let’s keep it simple!). It’s not even a new process either - the Romans discovered it around 2,000 years ago!