T minus Beamtime and Bye-Bye Liam.

Phew what a hell of a week. It’s amazing to think that I’ve already been here san-shu (three weeks). I guess I’ve just been too busy to get home sick. So the science has finally stepped up a gear as we have moved things onto the beamline to finally try and do some imaging. Suffice to say I am now far more familiar with the innards of Josie than I ever planned to be, but more on that later.

First things first something a bit more exciting. On Getsuyoubi no yoru (Monday night) myself Cheung and Liam were taken out for a meal by an old friend of Cheungs, Yaki-san, to a local izakaya. Izakaya’s are a little akin to british gastropubs, in that you order drinks and eat food, but are probably a lot less rubbish.

Needless to say there were plenty of Kanpai’s shouted (cheers), as the beer, sake and other Japanese alcohols were drunk. I even tried out some sake myself, though since I A) hadn’t eaten before I started drinking and B) arima nomimasen (hardly ever drink) it went a little to my head. An interesting taste though.

The food was excellent anyway. Yaki-san ordered for us. The first starter was raw, that's right raw, chicken. An interesting texture and it was in a very nice spicy sauce. This was followed by pork and beansprouts, grilled chicken with rock salt, some really nice fish (species unknown) deep fried octopus, tofu soup, yaki gyuuniku, thinly sliced beef that came with it’s own grill for cooking. The whole thing was finished off with a mound of ice cream, sadly I couldn’t eat it but I did have some of the sweet yam chips that came on top tasty.

Anyway twas a fun night and a really fun way to experience food however totemo takkai (very expensive). The final bill came out at 16,000 yen. As I missed about 3 course and didn’t drink too much I got away without paying to much and we agreed to cover Yaki-sans bill for hosting us.

Anyway back to the lab, back to reality. As I’ve stated earlier this week, anything + Jimi Hendrix = cool so:

 

Protein haze all in my brain,

DIT just ain’t running the same,

Actin funny and I don’t know why,

Oh josie why do you make me cry.

As I’m sure you’ve gathered the Beta5 has not been behaving this week. Our troubles started on Tuesday. Buoyed by the good results on Monday we decided to move onto our trickiest sample, Thyroglobulin. This beast of a protein is about 5 times larger than any of the others we’ve trialed in the machine.

It originates in the thyroid gland of all humans and is the precursor protein of many hormones secreted by the thyroid. It is also the body’s main store of the element Iodine. This is actually the reason the release of radioactive Iodine during nuclear power station leaks and explosions is so dangerous.

The thyroglobulin will take up the radioactive iodine that enters the body and concentrate it at the thyroid, leading to large doses of radiation in one tissue, and ultimately cancer. The issue of iodine tablets is actually an effort to saturate the bodies thyroglobulin with iodine so none of the radioactive iodine can bind.

Interesting though that is our main reason for using it is because it is huge. In fact it may well be one of the largest proteins that exists as a single strand. Proteins are made up of chains of individual molecules called amino acids. The sequence of these amino acids is important in determining the overall shape and function of a protein. Most large proteins exist as complexes of various, separate chains, kind of like an adders nest. Thyroglobulin on the other hand would be the mother of all anacondas.

The practical upshot of this for us is that due to it’s larger mass we should see more scattering when it interacts with x-rays, the more dense an atom or molecule, the stronger it will scatter. Or at least in theory, previous attempts have not shown much.

The reason having a single chain is good is because of the nature of our experiments. During the process of ionizing samples into a gas, a complex would simply fall apart as most of the interactions that hold it together are electrostatic, similar to the forces that hold a negative and positive magnet together. With a long chain this isn’t a problem.

Sadly the system has not been designed to withstand the high concentrations we use and so the bulky thyroglobulin has a tendency to unfold, clump together and block the DIT’s plumbing. So we spent Tuesday and Wednesday dismantling the thing and trying, in vain, to remove the blockage. No joy though sadly but in a moment of inspiration Liam managed to jerry rig a new probe tip, the part that was blocked, out of a few suage locks and some old syringe tips. Sugoi.

Onto Thursday then. It was time to move the, semi, working DIT onto the beamline itself. This was no small feat as it is a major piece of metal. Through the use of a crane and some major elbow greasefrom Takaaki-san, Sako-san and the rest of us we got Josie into her new home. Next job was to set up the pipeline.

The kind of experiments we are performing are known as SAXS (small angle x-ray scattering). Possibly one of sciences more awesome acronyms. Back to x-rays. When x-rays interact with matter they scatter, as I keep banging on about but it's a pretty central idea. These scattered x-rays fire off at all angles and depending on the angle different pieces of information can be inferred.

Small angle scattering tends to be weaker than high angle and holds more information on the shape of an object. To detect small angle scattering you must position your detector a long way from the sample. The distance allows the scattered rays to extend further away from the direct beam. Too close and the small angles will be indistinguishable from the central beam as it will just saturate the detector. How is this achieved I hear you cry? Why with a stupidly long vacuum tunnel that we call a ‘camera’.

Here at BL45XU we use a camera length of about 2m. It is actually this camera that caused us our second major headache. Keeping the pipe under vacuum is critical, without it the x-ray beam will diminish through interactions with air molecules. Sadly we had a leak. This resulted in a long night of hard work from Takaaki, in fact he ended up working till 6am the following morning.

So onto Friday and thankfully our luck was changing. Takaaki after pulling one hell of an all nighter had set up the optics for the experiment. This consists of a few different pieces. Firstly there is the monochromator. This is essentially a set of mirrors that ‘tune’ the x-ray beams released from the synchrotrons to a given wavelength. Next are a series of pinholes and slits, these are to restrict the size and focus the beam onto your sample.

All of this must be aligned perfectly and the use of lasers and photographic film is required since x-rays are invisible. It was a pretty long process. In the meantime some spare parts we’d ordered for the DIT finally arrived meaning we could fix the dodgy probe. All that was left now was to zap some proteins.

So after 7 months of hard work, and 3, 65 hour working weeks in Japan, I finally got to go into the experimental hutch. It’s a pretty cool feeling, if you are a massive geek like myself. The hutch is a large metal chamber full of all kinds of electrical connections, gas valves, pipes and so on. To actually use it there are loads of failsafe mechanisms that must be triggered before the beam comes on, lots of big buttons to push.

Last night, at about 10pm we ran our first sample, Cytochrome C. No joy sadly but that was to be expected, it's a pretty small protein, about a 30^th of the size of thyroglobulin. Hopefully all the hard work will pay off.

To move away from science a bit, today also saw the departure of Liam from Japan. He is one of the two people who came out here to help me with Josie and an electronics expert. That aside though he’s also been great craic and I’m sad to see him leave.

Yoshi-san, Yoshitaka-san to give him his full name, whom we met early last night offered to take us out for lunch and also take Liam to the station. This guy is a great character and I can see me having some fun times with him in the future. He’s a little manic, always busy and full of stories about the various places he’s lived and worked.

 

After blitzing our way through the mountains on the expressway we trawled through Himeji in search of somewhere to go. In the end Yoshi-san settled on a cheap sushi-ya just outside of the city center. He said it wouldn’t be proper sushi but it was reasonable and fun.

This place was like the stereotypical sushi places, loads of plates on a massive conveyor belt. Yo sushi springs to mind but this place was about half the price and three times as tasty. Yoshi san had us trying all kinds of delicious things, plenty of raw fish of course, also cuttlefish, eel (Unagi) and a weird omlette thing made with dashi. Also we tried Uni (sea urchin) at my request. I’ll be honest it was an acquired taste, it tastes like New Brighton front smells I’ll not lie, but it had to be tried.

The sushi-ya was awesome fun and Yoshi-san refused to let us pay. I have to sya I’m loving the communal attitude to food out here it makes all mealtimes a pleasure and it’s always a giggle. Anyway it was a lovely way to send off Liam and I hope he gets back home safely.

Dewa, shigoto ni modoru (well, back to work). Also here are some pics of my second cooking attempt. This one was more successful, home made okonomiyaki yum yum.