Saturday, 7 December 2013

Day 4 of IR beamtime - more sample analysis action

So now we have some data. After 5 hours of analysis this is what you tend to end up with.

A screen shot from the FTIR software showing a series of point analysis.
During our sample preparation we were hoping to get nice round slices cut through granules. As mentioned previously what happened was that the granules crumbled as they cut and we just got material stuck around the edge. We've told the machine to do point analyses around the edge and in the middle screen in the image above you can see the points we analysed. Along the bottom you can just about see some typical spectra from those points. The really sharp eyed will notice the calcite peaks towards the right hand edge. What we need to do now (this will take some time) is process the data to see whether we get any variation in the ratio of amorphous calcium carbonate to crystalline material.

In order to maximise our time, Liane had brought her portable FTIR machine along as well.

Liane's portable FTIR machine in action
In many ways this works in the same way as the Synchrotron FTIR that we're using (it's all FTIR!). We used it to analyse a few samples from Emma Versteegh's project on the isotopic composition of granules. Emma's results suggest some sort of isotope fractionation from the initial secretion of the milky fluid in the calciferous glands to the secretion of the granules into the soil. This is most likely related to crystalisation of the amorphous calcium carbonate and we just needed to confirm that our samples start off amorphous and then crystalise - we have done, job done.

So all told, not a bad session - there is data to analyse that approximates to what we were after in the first place, we have done a few samples for another (related) project in our spare time and we have a good plan for what to do on the next visit in February.

Many thanks to Mark Frogley and Katia Webhe for their help and to Steffi Lutz and Liane Benning for putting up with me.

And the food wasn't as bad as last time either.....

Day 3 of IR beamtime - some success

Plan C sort of worked and Plan D didn't.

Plan C was to try the cryomicrotoming again. The granules still crumbled as we sliced them but we did get a rim of granule material around a hole.

Here you can see the outlines of two granules left on a cryomicrotomed section. Granule material is just left around the rims. We took this image using the FTIR microscope (in visible light) and then told the machine to collect FTIR spectra around the rims. Field of view is about 3 mm.
We are producing maps from these sections (actually a whole host of individual point analyses) to see what we shall see. We need to process the spectra to remove any signal from the glue used in the cryomicrotoming (a pva adhesive) and then look at the ratio of a few peaks to determine the amorphous calcium carbonate content in each spectrum.

A FTIR spectrum of calcite taken off line (i.e. we've done this on a normal machine as a reference material) with an ATR (attenuated reflectance) set up. The 3 big peaks on the right (at about 1400, 870 and 710 cm-1) are characteristic of crystalline calcium carbonate. If the 710 cm-1 peak is missing it's amorphous calcium carbonate.

Plan D was to simply squash a granule on to a slide but it didn't work. You can do IR in a number of ways. For the thin slices produced by microtoming we look at the light going through the sample - a transmission measurement - and that seems to work for our slices. For the crushed granule the sample is to thick for transmission so we look at the IR light reflected from the surface - a reflectance measurement. However, the crushed samples didn't give good spectra in reflectance - they may not have been smooth enough.

When we return in February we're still going to try the slices produced using "normal" methods - embed the granule in resin, polish it down with a Diamond polishing nap to get a thin section. However we will try (another) FTIR measurement technique - ATR (attenuated reflection). In this technique we actually have contact between a diamond lens and the sample. This is how "classical" FTIR works and should be fine giving spectra like the one above.

Meanwhile we were visited on the beamline by Brian Clegg, a science writer, who is doing an article for the Observer. The article will be about Diamond and the science we do here and should appear in January.
Brian Clegg (science writer) and Sarah Bucknall from the Diamond Communications team.

Wednesday, 4 December 2013

Day 1 on Beamline B22 Sample prep nightmares

Another 5.15 am start to get to Diamond for 10 am. This time I'm here for 5 days to try and do some infrared mapping to locate amorphous calcium carbonate in the granules. Liane and Steffi arrived on Monday and have been working to optimise the system for the calcite and also their snow algae. We've hit a few problems. There are problems with the samples we cryomicrotomed last time we were here. The samples are stored at - 80 C but when they are transferred to the sample holders for the beamline water in the atmosphere sticks to the samples and freezes producing ice crystals. This makes the samples no good for analysis.

Plan B was to use the samples I prepared in York and Liane prepared in Leeds - these are simply balls of calcite embedded in araldite. We tried microtoming these and the samples just crumbled. It looks like the balls are too fragile to slice into 10 micron thicknesses.

Plan C is to have a final go with basic granules and the cryomicrotome tomorrow but the feeling is that it's a long shot. Plan D is to simply crush the granules and look for amorphous calcium carbonate in the powder - we'll try that tomorrow or possibly Friday depending on how things go tomorrow.

For our next beamtime in February we'll prepare some "classic" thin sections which should definitely work.

Steffi (left) and Liane (right) setting up a sample map.

In the meantime we are running some of Steffi and Liane's snow algae samples that have simply been smeared onto slides.

Liane is now off to bed (11 pm). Steffi and I will stay up until 2 am to put on another sample then we'll reconvene at 9 am tomorrow.

Oh the joys of beamtime