Friends from Afar

Don’t you love those moments when things just seem to come together. Anyone who has been following me for a bit will no doubt have noticed that things haven’t exactly been going my way of late. Well that has changed in the past couple of days. Suddenly my proteins expressing exceptionally well. I fixed the piece of equipment I broke and whilst writing my 2^nd year report (a daunter at 25 pages) I’ve had a bit of an epiphany regarding my PhD direction. 

It’s remembering days like this that get me through all of the other rubbish. It’s easy to get into a spiral when things go wrong. They say that bad things always come in 3s, or 4s in oriental culture as that's the number associated with bad luck. I think I’ve had a bit more than three but my luck has turned, maybe it’s thanks to the Korean shaman treatment from one of my colleagues (link). I have been working stupid hours again recently but when things are going well it’s easy to throw yourself at it.

Capitalizing on my uplift I tried to make the most of the past weekend before my free time evaporates once more. First stop was into my local city, Himeji, for the Yukata matsuri (浴衣祭り). Now from an outsiders point of view this may seem like an excuse for pretty girls to dress up in pretty outfits and wander the streets gorging on food from the various yatai’s dotted about the place but in fact...nah that’d be a lie that's exactly what it’s about.

Many of Japan’s numerous festivals are deeply rooted in history and intertwined with the Shinto religion. This is not one of them. Well sort of. The festival commemorates the moving of the Osakabe shrine from within the castle grounds to downtown Himeji. This made the shrine available for all the people to worship at.

The movement was commemorated with a festival. Normally people would have to wear their formal (and expensive) kimono’s to such an event, however due to the suddenness of the ceremony many did not have the time or money to make such items of clothing. The feudal lord at the time permitted them to wear their less formal Yukata and it has remained that way for the past 260 years. Of course this isn’t well known and what most people think of is the abundant street vendors, I think it has the most out of every festival in the Kansai area.

Well it was certainly interesting. Besides the usual Japanese festival fare there were many other foods and games on offer, some I’d not heard of before. Sadly I had other plans later on that day so I had to rush off. I doubt I’ll get to it next year but to be honest it was ridonkulesly crowded and there wasn’t much going on besides the street vendors.

In Osaka I met up with some of the friends I’d made surfing. They own a bar out that way and since I had plans to be in Kyoto the following day it was a good excuse to make the journey. It was tiny though so we spent most of the night on the stairs outside. Whenever I’m in Osaka I feel like my Japanese comprehension has gotten worse, or maybe it has just gotten worse who knows?

I hadn’t really thought about where I was staying that night so I headed back to Umeda to scout out somewhere. I remembered being here last time and seeing a very cheap night deal at one of the mangakisa’s (internet café’s) that seemed as good a place as any, though not before netting my first ever win on a UFO catcher.

 

Internet café’s in Japan are something else. Besides renting sitting space and a computer you also get access to a library of comics, movies and all you can drink soft drinks and coffee. They are almost always open 24hrs and I think they do the most business between the hours of 3am to 8am. A night pack gets you a reclining chair and a blanket to get some shut-eye for about 1100yen. Or you could just be like me and stay up all night watching films and dossing around on the Internet.

The following day I set off for Kyoto. I’ve said it many times before. I love this place. It has none of the hustle and bustle of Tokyo, nor the Concrete Jungle feel of Osaka. Well it is massively steeped in history with a ridiculous number of world heritage sites so not so surprising.

My friends are currently on a yearlong tour of southern asia from their honeymoon and they were looking incredible. It was so nice to see them looking so happy and healthy. I basically had no plans for the day as I figured they had plenty of things they wanted to do. I was right fortunately.

First on the list was to try our hand at 弓道、Japanese archery. The “shooting range” was absolutely tiny, a dinky little shop tucked away behind the bushes in northern Gion with only three targets. It was very interesting however, considerably different to western archery.

For a start the bows (called yumi) are like 2 metres tall, it was bigger than me at any rate. Secondly the grip is about two thirds of the way down the shaft, compared to being in the middle in the west. This makes holding the bow a little clumsy at first as the weighting takes a bit of getting used to. Finally the method for drawing is very different. The string is drawn with the thumb whilst the arrow rests on the index finger.

We were ushered inside by a wonderful Ojisan who seemed very happy to have oversees customers. Small though the place was he spoke exceptionally good (albeit very specific to his purpose) English so I’m guessing he gets a fair few people passing through. After a quick demo and some patchwork instruction we were sat down on the cushions and firing away. It was pretty reasonable, 10 arrows for 800yen and hopefully I’ll go back given the chance. I even managed to hit the target with my final shot.

Finished up we did a bit of temple hopping before lunch. I can’t remember which ones, there are like 1000 in Kyoto, but I do remember the gardens of the second being particularily amazing. There were also some incredible trees, old and oddly shaped, inside. It got us talking about how amazing it is that in Japan even in this day and age they have a reverence for nature. In the UK we’d just level it, here they work around it, even in the major cities.

 

For lunch we hit a famous Okonomiyaki place in central Gion. The front of the store has a statue depicting a little boy having his trousers yanked down. That is nothing however compared to the menu. Each table has a large European style menu book and when opened it reveals...a giant picture of an okonomiyaki.

Having only one thing on the menu is pretty amusing when the name of the food translates literally as “your grilled preference.” Tasty all the same and very different again to Osakan and Hiroshima style. I do love all the quirky little regional differences in dishes around Japan.

We had a great chat over lunch about our travels so far. It is amazing how much just seeing a little bit of the world changes your out look on life. I could see the changes in my friends and it helped me see the changes in myself. Sometimes I don’t realise it and I think it’ll really hit home when I get back.　

One thing I think it has done for me is made me more mindful of all the little things around me. When everything is so different, when everything is outside of you comfort zone, it all stands out. I’d like to take that back with me. All three of us agreed that spending so much time away from home has made us realise how little of our own country we’ve really seen. I think travelling is any time spent outside of the known. Any little venture into the unknown is a journey and we take them everyday.

I’ve not been sleeping much again recently but insomnia does make for wonderful introspective time and so I’ve been doing a fair bit. I need to travel more, that much is true. Even though my course has less than a year left I’m not sure if I’m ready to come back home just yet. I miss my friends and family sure, but how will life feel when everyday is just that bit more normal. Perhaps normal is just a perception; time is just what we make it maybe? Who knows but I think there are more places left for me to look to really find out the answer.

長いだけど、継続的な関心をしていただきありがとうございます

Mata nee.

ぼちぼちでなあ

I decided I didn’t want to tackle a new post until I’d had a decent amount of sleep. It’s been a busy week in Science and life this week and I think the title (meaning little by little) sums up my progress well.

With the great help of my collegues from Liverpool I had Josie working better than ever. Whilst this shoul of been fantastic news Josie is merely a platform for my research, not the project itself. The goal is to use Josie as a means to hold samples in the path of  focussed X-ray beam to produce images.

Sadly although I only slept about 7 hours between Tuesday and Friday trying to get this working, 何も見えなかった、I couldn’t see anything. Or at least maybe we saw something sadly we only had a small amount of sample and one result (whilst still a result) is not a significant one.

So of course after that I deserve a break right? Nah I’ve been stuck in front of a microscope all weekend preparing stuff for more experiments next week. This at least has gone fairly well. I managed to track down some bits and pieces of equipment, a pimping microscope, and my labeling work has borne fruit. It’s left me a little more confident for next weeks experiments.

What I’ve been trying to do is label the individual molecules that make up fibrous structures within living cells called microtubules. Each one is made up of many strands of 2 types of a protein called tubulin. These molecules arranged head to tail to form strands, which then coil together to form the tubules. I’ve been targeting particular amino-acids, the chemicals that make up the tubulin molecules, and labeling them with either a fluorescent residue or gold to help me see them.

Of course work isn’t everything and I’ve been a busy bee in other respects to. I’ve been working hard writing away recently. I’ve once again regained my passion for short fiction and have been furiously writing away and sending stuff out to see if I can get anywhere with it.

Having never been any good at art words were always my thing growing up and, whilst trying as best as I can to not sound conceited, I think I’ve got a bit of a flair for them. Either way this has actually culminated in something. About 3 months ago I entered a competition put out by the Diamond Light source, a synchrotron in Oxford. I managed to place in the top 15 (admittedly out of 65) but it’s a start.

All in all I’m pleased with the way things are going and it actually got me thinking about an odd quirk of the Japanese language. In Japanese you don’t really wish someone good luck. Instead you say “がんばってください“meaning please try your best.

It’s not that they don’t have a word for luck (“運”　for the record), I think it’s more a belief that one can achieve anything with perseverance and grit. I think it’s a mentality shared by us Brits and particularly northerners and I like it as an idea.

Grit is definitely what counts in science, and to be honest anything really. It is far easier to fail that it is to succeed; there are always more ways to fail right? But also no failure is complete, there is always something that can be taken from it.

Right that's all from me, busy busy. Here is a link to my story on light reading.

http://light-reading.org/LightReading/HiglyCommended.html

Ja ne.

Ample sample but...no results.

Imagine for a moment the worst all-nighter you’ve ever pulled. Now times it by nine. Factor into that the fact that during this all-nighter you have to focus at 100% (or as close to it as is possible), you have to operate and move complex equipment, performing basic algebra and figuring out geometrical problems in reflective space. Congratulations you’ve just completed your first slot of CDI beamtime.

So science is tough. I knew this to begin with, however I didn’t realize just how tough. This week has nearly finished me off with a massive build up of stress, fatigue and disappointment. It’s a good job I’ve hardened myself to the rollercoaster of emotions through years of Ultimate tournaments.

Sadly things did not go our way this time, try as we might. It’s hard to stumble through those last few nights fuelled only by caffeine and pot noodles knowing you are unlikely to get results. We thought we’d prepared well but life always likes to throw us a curve ball from time to time.

 

I was actually really excited about this beamtime. Not only was I getting to play around with the equipment a lot more but we would be analyzing my sample this time. Or so I thought. Due to some unexpected equipment errors we spent about five days aligning, re-aligning, and then aligning some more. A bit rubbish really. Looks like my date with data was cancelled.

That means it’s back to the drawing board, and I do so love drawing. Or at least I love the scientific process, I’ve usually got a million and one ideas running through my mind and what is great about working here is no one tells you no. The research we are doing is very much frontier work so how can it go wrong when no one knows what is right.

Still planning doesn’t make for exciting blogging unfortunately so instead I’ve decided to dish up two exciting pieces of research from the world of Malaria. One of these has featured in the news quite prominently, and the other is pretty groundbreaking as well.

The first paper relates to the interactions between proteins at the surface of both Plasmodium falciparum merozoite, the parasite responsible for malaria, and red blood cells. These proteins are involved in the invasion of  blood cells by this parasite, the subsequent destruction of red blood cells by P. falciparum is what leads to the symptoms of malaria. As this disease kills millions worldwide year on year it is no surprise that falciparum is so intensively studied.

People have been trying for years to create a new vaccine for malaria however it has been a struggle. One of the big problems is that these proteins at the cell surface show a high degree of redundancy. A protein that is essential for one strain of the parasite to enter a cell will not be for another. This makes it difficult to make one vaccine that is effective for all P. falciparum strains and block malarial infection.

Enter the cell surface signaling lab at the Wellcome trust Sanger institute. This group have developed a very robust and effective technology for screening extracellular interactions. Here they express simply the external ‘stump’ of these proteins, the bit that sticks outside the parasite cell, as part of a more stable fusion protein. They then probe these with similar constructs of blood cell proteins. By linking this to a protein that can cause a colour change they could discern what binds to what.

What they found was a novel reaction between two proteins, PtRH5 on the parasite, and Basigin on the erythrocyte. This interaction proved critical in invasion, deleting PtRH5 from the parasites genome or blocking Basigin with an antibody almost completely stopped blood cell invasion.

 

So what’s the most exciting part? Well they tested this on not just one but all the strains of P. falciparum they had available and found the same result. This means produce a vaccine to provide resistance blocking this interaction could provide a reliable preventative treatment for malaria. It’s still early days yet but it is a truly fantastic result.

I am a bit biased of course. I actually worked with the group whom did the main body of the work during my year in industry. I actually remember the main author setting up the screens just before I finished. Interestingly they only worked 9-5 generally as they have a family, proof that it is definitely quality of work not quantity that pays of.

Ok next paper. This is one is also intriguing although I’d say it doesn’t yet have quite the human impact that the previous study does, probably why that one was published in Nature and this was not. This one concerned two topics particularly close to my heart. The cytoskeleton, something I’ve always been interested in, and Sickle cell anemia, because of my African heritage.

Sickle cell anemia is so named because of the odd elongated shape that red blood cells take when they become de-oxygenated. It  is a particularly nasty inherited disorder and leads to anemia as well as acute pain due to the bursting of blood capillaries that become blocked by these oddly shaped blood cells.

The cause of this is a mutation in the protein heamogloblin, the red molecule responsible for binding oxygen in blood cells. The single change in its sequence causes the hemoglobin proteins to clump together making the blood cell much more rigid. Whilst this is a debilitating disease it is recessive, meaning you need a copy of the faulty gene from both your mother and father, to express the symptoms.

So how does malaria tie into this? Well if in fact you only have one copy of the gene you do in fact show partial symptoms, not as severe but still somewhat uncomfortable. The upshot however is the added rigidity seems to convey some protection to malarial infection.

 

Up until now although there are plenty of theories dancing about no one was really sure exactly what the cause of this protection was. That is until a German group looked at the effects of this mutation on the actin cytoskeleton. Actin is one of the proteins that make up a network of fibrous molecules that contribute to the internal structure of cells.

When a red blood cell is invaded by the malaria parasite it’s actin cytoskeleton is reorganized to aid the delivery of a pathogen protein called adhesin to the cells surface. These proteins are, unsurprisingly given their name, responsible for sticking cells to surfaces. The over expression of this protein helps to prevent the destruction of the infected cells by preventing their entry into the spleen.

Through a powerful microscopy technique known as Electron microscopy these researchers discovered that the critical reorganization of actin in cells expressing the Sickle cell heamoglobin was blocked. This lead to a depletion of adhesion at the red blood cells surface and so they could enter the spleen to be cleared.

Whilst this does not have as obvious practical application as the first paper it is an excellent insight into the complex interplay of various cellular components, It’s quite amazing really that even 50 years after the protective phenotype of sickle cell anemia was discovered, only now are we gaining insight into how it works.

Makes me feel better about my lack of results anyway.

Ja, mata ne.

Coming to an understanding

So can you tell who the odd one out is? That's right it’s me, I’m the only one without glasses right. Ok this wonderful picture of my lab group aside I do stick out like a sore thumb in this country. This has been hardest thing to adjust to for me being from such a cultural melting pot as Britain I really don’t like sticking out so much, being in the minority when I travel about, the staring took a little getting used to.

I don’t want to make it sound negative, it’s not malicious or anything but I do feel my neck burning often. It’s something many people talk about, the ‘gaijin’ bubble. You never truly accepted out here no matter what your current status, language skill level, or who your friends are and after talking to a few it’s something that just doesn’t change.

It’s a little bit sad in a way, it makes it very difficult to meet locals as most don’t want to know or are afraid of looking foolish, as they can’t speak English so well. Most of the people I do meet are exceptional for wanting to associate with foreigners. It doesn't make them bad people, far from it, but it does give a rather skewed impression of the Japanese people as a whole. I’m sure this would change once I grasp the language a little better but after 8 months of being here I still feel like I’m watching Japan from inside a glass box.

This post is mainly stemming from the fact I’ve had little time to travel of late and therefore plenty of time for reflection. Sadly work has taken the forefront again, lots to do. Josie is still out of action and as yet I don’t know how to fix her. Also after a hectic week we have now started another slot of beamtime, 9 days our longest yet. It’s scary and tiring but exciting. My new samples are looking good and I really think we can take some good images.

 

So back to being an outsider, it’s not that bleak I guess, though sometimes the gawping from the school kids (particularly teenage boys) gets to me. It’s not a nice feeling for anyone and I don’t like being looked at like I'm an alien. Still I’m making some sort of headway. Sam and myself were actually approached by some of the staff at our local climbing gym the other day whilst struggling with a problem. So our conversation was pretty rudimentary but it was something. Slowly getting there I guess, just need to work harder, grow some balls and speak more.

Also I really do feel as though I’m starting to bond with my colleagues. I’m not sure if Koreans are just a bit more open, if it’s because my  boss spent some time in the states, or if it’s my continued hard work that's impressed them, but I definitely feel more included. I’ve also recently started learning the Korean language (the alphabet is awesome its like lego) so that may factor into it a bit more also. I think showing appreciation and interest in anyone's home culture will always endear you to people.

I’m not sure if these feelings will last, maybe I’m just on a low ebb right now. Over tired, over stressed and over worked. I’m not in bad shape or anything just fed up of being in the middle of nowhere. Perhaps things would be different if I lived near a city? I don’t really know and I guess I won’t anytime soon. At any rate for every bad experience I’ve had there are plenty of good ones to outweigh them. For the time being I’m still fairly happy with where I am. I mean look how pretty it is.

Right tant over I’ll talk a bit more bout what I’ve been up to recently. So as some of you may already know I’ve been trying to take my writing to new levels, particularily in the field close to my heart, trashy sci-fi. At the moment I’m working on a story for a writing contest put forward by a synchrotron in the UK called Diamond. As well as this I’ve submitted a story to nature, I’m pretty excited that the editor actually accepted it. Whilst that's by no means a publication at least it will get read.

I also tried my hand at a bit of scientific writing for the Medical Research Centre in London. They plan to put out a picture of scientific importance everyday of the year and they needed writers to pen the caption. Suffice to say I didn’t make the cut but I was thrilled at the opportunity to try and even got some helpful feedback.

Hopefully I’ll get to put some of this practice to good use soon as if this beamtime goes well I should have some data of my own to analyze and potentially publish. This time I’m hoping to look at one of my own samples, rather than one supplied by a collaborator.

My sample of choice is a preparation of microtubules, one of the three filamentous structures that contribute to the internal structure of our cells known as the cytoskeleton. Microtubules are large biological structures consisting of two proteins, alpha and beta tubulin, arranged head to tail in a cylindrical fashion. They are involved in all aspects of cellular activity, movement, replication, transport of materials and overall shape.

What is particularly interesting about them is a property known as dynamic instability. These complexes structures can rapidly assemble and disassemble within our cells in a very organized fashion. This is particularly important in events such as cellular migration, replication and differentiation which rely on the rapid movement of components within a cell at a much faster rate than can be achieved by diffusion alone..

The forces involved in these complex processes, from the linking of individual tubulins, organisation into single fibres and then the packing of fibres into bundles, are of great interest to many scientists, however there are a few problems. Firstly the process is call Dynamic INSTABILITY for a reason. The structures formed are very transient and so to image them you have to be either really fast or fix them in some way. Of course once fixed you lose a lot of important information about the process. Still the process of fixation itself isn't so well understood so there could be something interesting to investigate there also

The second is that whilst fairly long these things are also very thin. This makes it difficult to see any of the minor details of their arrangement particularly tricky. We are hoping that we can use the technologies we’ve been developing over the past few years to get a closer look at these stupendous strands. I’m not sure what the data will look like but I think we might be able to find something interesting out. Right back to work, all aboard the chirpy bus of wonder.

がんばるやん。

Ja mata Minna-san.

My future extends brightly forward.

Ee. Konshu wa sugku itsogashi desu ne! What a week its been. Sadly I can’t report that I’ve been up to any exciting adventures, not of the physical variety anyway but I have been delving in to the depths of frontier x-ray imaging science. Ok so perhaps I’m bigging myself up a bit there but there really have been some exciting things going on out here.

First things first my supervisor from Liverpool swung by, I love how casual I make flying 6000 miles sound there, to check on the progress of my experiments. Luckily for us Josie chose that day to behave and we could show off the wonderful spectra of trapped Cytochrome C molecules. Yatta.

There was also another purpose for his visit, namely to sort out what I’ll be doing here over the next few years. This meant a day full of meetings, introduction and discussion. I met a lot of new people on Monday and I’d be lying if I said I could remember all their names. One I do remember of course is Song-san, or Changyung Song. He is a scientist from Korea and head of a group here known as the Song initiative, and also my new supervisor (The guy with glasses whom I'm standing next to).

I’ve finally been placed in a team at Spring-8 so I’m feeling a little more like a proper member of Riken, plus I have my badge and dosimeter, making everything feel more official.

Now the interesting stuff. So I’ve actually been following Song-san’s research for a couple of months as, although not entirely the same, it is somewhat related to my own.

His field of expertise is in X-ray diffraction microscopy, or lens-less diffractive imaging. A lot of scary words there for a non-specialist but allow me to break it down. This technique is used as a new method for imaging biological samples on the micron scale, such as cells and their internal structures, known as organelles, about an order of magnitude large than the proteins I’m interested in.

To achieve this samples are first fixated as gently as possible, usually in a dilute fixing solution the composition of which isn’t very important for the theory, onto thin film of silicon nitride. The sample holders look like 1cm, see through time capsules, I was actually shocked at the small scale of the device when I saw it in person. Anyway this set up is very unlike what you’d consider a microscope in the traditional sense.

Once samples are fixated they are mounted in a sample holder and exposed to a hard x-ray, or UV free electron laser beamline. At the other end of the set up is a powerful photon detector. This reads two things. First it will measure the absorbance of the light photons, i.e. compares the intensity of photons that pass through the sample to those of the direct uninterrupted beam. This works similar to a standard medical x-ray. From this absorption you can get an impression of the surface structure as well as the areas of relative density from a sample, the more dense the sample the more absorption will occur.

Right that's the microscopy bit out the way now onto the diffraction part. So this set up is similar to those I’ve mentioned before. Here the detector will be measuring discrete packets of photons that are diffracted by the sample.. The detector needs to be a fair distance away for this as the photons are only weakly diffracted and so need a large distance for the small angles to extend far enough away from the direct beam. The diffraction pattern, essentially a circular arrangement of spots of various sizes, can be used to determine the position of internal structures within your sample.

By combining the diffraction data with the absorption data you can simultaneously get a picture of the internal and external configuration of, for example, and individual cell. Amazing.  Normally to do this very thin slices of cells need to be taken, stained and then imaged and put back together. Wilst the resolution is higher the process is very destructive and it is not possible to know how the images you capture compare to nature. This new method is a lot less invasive.

So where do I come in? Well the Song initiative consists primarily of physicists and Material scientists. Their knowledge of biology is limited. So I’ll be looking at the best ways of preparing samples, what samples to selected, whether readouts are in fact accurate to nature and so on. Also this group plans to be using the XFEL when it comes online so it would make sense for me to be involved in their work.

That brings me on to the next point. The XFEL. It’s coming on line in just under 2 months. That means the first round of experiments will be starting in mid June. The nerd in me is very excited. I’m going to be around at the point when some truly groundbreaking experiments are carried out. Plus I can’t wait to have a look inside the experimental hall.

So this week although I’ve been suck in the lab with Josie quite a bit, some good results have been obtained. We’ve managed to successfully 2 out of the 5 samples that we want to run when we move the beta5 to the beamline next Thursday. This has of course been the product of a week of 9am-10pm working days ugh. It should be worth it in the long run though.

I have also been able to meet some new people, something I was concerned about not doing due to all the lab work. The members of the Song initiative are all really nice, Kim-san has not long joined so he’s experiencing all the problems I’m having sorting accommodation and Nam-san is a PhD student like myself and lives pretty close by. We’ve also met some other gaijins. Two French guys named Ignace and Arneaud who also seem pretty interesting. 

There is so much incredible science going on around here that I can’t help but remain fascinated by everyone I meet. I’m, as I’ve mentioned on numerous occasions, very keen on my writing. So when I found out about the welcome trust writing competition I leapt at the chance. This has been occupying my time between DIT runs. I’m still drafting my entry so if anyone fancies a read let me know.

Anyway you’ll notice there are not many pictures of food. The canteen is starting to rotate its meals haha so nothing really exciting, except baby squid for breakfast yum.

Anyway kon shumatsu holds a trip to Himeji so expect some interesting snaps of locations from the last samurai, a film I’m still yet to watch, and hopefully I’ll have some gear for my rather barren new flat hurrah.

Right off to my First Sprng8 no Nihongo no ressun. Dewa matta mina-san