Monday, 13 July 2015

Food at Diamond improves?

It's 0715 on our final morning. The beam goes off at 0900 and a new set of victims / scientists arrive for their beamtime. Over the last two days we've taken lots of element maps and measured the form of calciumj and strontium in four earthworm species - Amynthus and Pontescolex as initially planned and, thanks to John and Stephen's hero run to Cardiff, Eisenia fetida, Lumbricus rubellus and Lumbricus terrestris. So two Azorean earthworms then a compost worm and two good old fashioned worms from  UK soils. We've checked out the calcium and strontium in the skin (epidermis), liver like tissues (chloragog) and the calciferous gland (Amynthus doesn't have one, E. fetida's is rather different from that of Pontescolex, L. rubellus and L. terrestris). We've got some lovely images and there is possibly a story emerging about how calcium is stored in earthworm tissues but I think that will need to be digested a bit before something emerges.
A calcium map of a L. rubellus calciferous gland - you can even see the structure in the gland - the vertical stripes. The image reminds us of a fish.

The food has been instructive! Last visit I drew the conclusion that most food served in the staff canteen was beige and not great. I may be forced to reassess. Because of the open day on Saturday food on Friday and Saturday was served in the accommodation block, Ridgeway house. These guys are set up for breakfasts but have a small kitchen. I'm sure that they did their best but lunches and dinners were less than inspiring.

Standard lunch and dinner choices at Ridgeway house - the ubiquitous baked potato, beans, sausages and soft veg.

On Sunday the staff canteen was open and it shone in comparison to Ridgeway house. So perhaps I take all those food reviews back!
Stephen, John, Dave and Pete (clockwise from left) enjoying dinner on Monday evening.

All told we've got quite a lot done, working in shifts. Five people seems to have been a good number to run things, get enough sleep and have time to get to Cardiff and back for more specimens.

John and Dave on the beamline.

Pete either catching up on some sleep or deeply pondering our data.

Stephen organising files.

Saturday, 11 July 2015

Beamtime fun at Diamond

I don't think I've been on this beamline since 2012 and the famous "which chocolate bar floats the best" experiment. On that visit we were looking at the calcium carbonate secreted by earthworms and it's pretty much the same system we're looking at on this visit, but in more exotic earthworms.

The reason we're at Diamond again is (or was) to investigate how earthworms deal with carbon dioxide. Specifically we're looking at earthworms from the Azores that live on the sides of mountains with high levels of carbon dioxide flowing through the soil that they live in. Normally these high levels would be sufficient to suffocate the earthworms but not in this case. There are two types of earthworm that we're looking at, Pontoscolex and Amynthus. Pontoscolex has a calciferous gland and so perhaps locks up the carbon dioxide by precipitating it as calcium carbonate whereas Amynthus doesn't have a calciferous gland. There is an enzyme, carbonic anhydrase, that moves carbonate around and contains zinc. Luis de Cunha, a postdoc. from Cardiff, has shown that zinc is concentrated in the skin of Amynthus, so we thought that perhaps that is where the carbonic anhydrase is as well and maybe Amynthus copes with the carbon dioxide by precipitating calcium carbonate in its skin. Two days in and we can say that this isn't the case which isn't particularly exciting but there you go.

The way this beamline works - i18, microfocus spectroscopy - is that first you section your sample which is a skill in itself, done on this occasion by John Morgan in Cardiff.
Thin section, about 6 cm x 3 cm. The faint white patches are slices through earthworms.

You then place these in the beamline and zap the section with X-rays to produce an XRF plot - this shows you the distribution of the elements you're interested in, e.g. calcium for us.

The top screen shows a close-up optical microscope image of our sample. The lower screen shows the XRF map. You can see a bright white diagonal line that indicates high calcium. From the optical image we can see this is associated with the earthworms chloragog - a liver like organ.

Once you have the map you can identify individual points that look like they have an interesting concentration of the element and do something called XANES (or EXAFS depending on precisely what you want to know). XANES is a fingerprinting technique - different forms of the element have different patterns and this allows you to work out what form your element is in.
Here, the lower screen shows a wiggle - this is a XANES spectrum, characteristic of the form that the calcium is present in the chloragog. By comparing with standards we can see that it looks like the calcium is present as a calcium phosphate. 

The controls look rather intimidating but as long as everything works there are relatively few buttons to press and we have had excellent instruction from the beamline scientist Tina Geraki.
Tina Geraki on the beamline.

i18 control screens
So we've shown that our hypothesis was incorrect - there isn't calcium carbonate concentrated in the Amnythus earthworm skin. We now have two more days beamtime so John Morgan and Stephen Short have high tailed it back to Cardiff to get some more samples so we can do a fuller comparison of calcium in calciferous glands.

Today has been a little odd as there is an Open day across the entire Harwell campus. True to the promises they made there were dinosaurs and volcanoes. Everyone seems to have had fun.
A dinosaur overlooks members of the public. Scientists use the synchrotron to investigate chemical traces in fossils.

and a model volcano - not sure what that was all about

Thursday, 9 July 2015

Strikes and travel

It dawned on me today that my last work-related trip also had the spectre of strike action hovering over it. That trip was to Nanjing whereas this one has been to the slightly less exotic Didcot. Nonetheless strike action can be waring if you're travelling; there is currently a tube strike in London and the Great Western trains that go between London and Didcot are also experiencing industrial action. There have been TV shots of massive queues for buses in London which looked at bit mad but I wasn't that bothered about that as I enjoy walking through London. On the otherhand I was a little concerned about the Great Western industrial action that could potentially mess up getting from Paddington to Didcot. In the end there were no problems and I arrived nicely on time at the Premier Inn in Didcot. Tomorrow the science starts.

No wild mobs queuing for the bus

A closed tube station

Destinations end - the Didcot South Premier Inn
No traffic jams

Odd things scientists do

Over the last two weeks I have cut up 5 plastic carrier bags into teeny tiny pieces. I've done this in Cafes whilst waiting for children's birthday parties to finish or during swimming lessons as well as at work and in the evenings. It is very dull. There is a good reason for cutting up the plastic but what is possibly more interesting is the reaction of the public when I do this in front of people.
A bag in the process of being cut up
Several bags now cut up. I am pleased to say that one of my sons spotted the colour differences and suggested that if I was going to use the material in an experiment I'd need to mix it all up so that it was the same and therefore could be used in "a fair test". Excellent observation.
I spent an hour in a Costa and only one person, a tourist from Norway, asked what I was doing. In contrast, whilst at the swimming pool I was surrounded by four or five young(ish) children, probably aged 6 or 7, asking me what I was doing. As soon as I said that it was for a science project I was regaled for about 20 minutes about how they had enjoyed science week a few weeks ago at school and the fun things that they had done. It was possibly my most interactive bit of outreach for some time and did leave me wondering why science often becomes perceived as dull and boring at some point in a child's school career.

We also hosted the Earthworm Society of Britain last weekend for one of their periodic earthworm collection and identification sessions.
My ex-PhD student Dan Carpenter, now Biodiversity Officer with Bracknell Forest council and a leading light in the Earthworm Society of Britain, looks on as people identify the earthworms that they collected earlier in the day.
The building, semi-unwrapped
Not sure about that orange paint colour
Finally, our new building continues to progress. I looked around the inside about two weeks ago and things are coming on. Gas lines are in the labs and some walls have been painted. Not sure about the orange colour some people have chosen but each to their own. Up to now the building has been wrapped in polythene, rather like one of those modern art installations but now the plastic is slowly coming of as the building gradually and seductively unveils itself.
Next up is another trip to Diamond. This could be a trying visit. I have to get across London during todays tube strike and then take a Great Western train to Didcot which is also subject to industrial action. Then, rather than staying on site I have to stay two nights in Didcot travel lodge before moving to the onsite accommodation on Saturday whilst a massive open day (c. 10000 people expected) is happening all across site - mind you they are promising dinosaurs and volcanoes so it could be good!