Puppets, Pot Noodle Pilgrimage and Progress

A weekend off at last. I feel as though I’m saying that more and more of late but well I knew what I was signing up for right? Well either way it’s always good to get some downtime and some rest. So naturally I spent the whole weekend travelling about.

The reason was actually because a friend from university is actually over in Japan right now on her honeymoon. During the trip she had a few days planned in Kyoto and asked if I’d like to meet up somewhere in Hyogo. We decided on Osaka and I set off bright and early on Saturday.

After the classic moment of phoning someone then realizing you were staring right at them we set off on the underground for Namba. I didn’t have so many plans for what to do really as I wasn’t sure what they’d be interested in. Also the weather was not on our side so anywhere indoors would likely be best.

Our first stop was Dotombori for some lunch. It was time to introduce my friends to Okonomiyaki. Definitely one of my favorite foods and as my friend is both vegetarian and allergic to milk a pretty safe bet. This time I actually ended up ordering Monjayaki by mistake. It’s very similar but the batter is much more watery meaning it has a gooey texture similar to melted cheddar. Still tasty though.

Following our meal we walked a little ways away to check out Amerika mura, home of many imported clothing and other items. It wasn’t quite as exciting as I expected, I think it really comes to life at night. Still there was a burger king, something I hadn’t seen before in Japan, and also a shop that had it’s own DJ. Also all of the streetlights in the area had this kind of iRobot design that was simultaneously creepy and awesome. I kind of hoped they moved but sadly not.

Next we headed off to the national Bunraku theatre just a short walk away. This is somewhere I’d been meaning to go to for a while and was happy to have some people with me to share the experience.  Arriving at the theatre it seemed fairly full, with a more or less even split between Japanese and overseas patrons.

Bunraku is a type of traditional Japanese theatre using highly intricate puppets to tell the story that originated in Osaka. These puppets are incredible, usually about 2 to 3 feet in height and controlled by more multiple puppeteers dressed all in black. Accompanying the puppets are people playing the Shamisen and also a chanter known as a “Tayu”.

We decided to opt out of the English headset and just try and pick up as much as we could. I made the error of trying to read the subtitles above the stage rather than just siting back and being absorbed in the action and impressive movements of the puppets. I could understand more than I expected but still not much. Thankfully we were given a pamphlet with an explanation of the different acts.

We only stayed for the first act since the whole thing takes 4 hours, although I was up for watching the whole thing so maybe I’ll go another time. We were quite fortunate really as the Bunraku season only runs for 20 days in November and actually finished on Sunday.

Cultured out my friends kindly headed back with me to Umeda so I could check into my hotel. Sadly it was back to the capsule hotel since I hadn’t managed to book into a hostel. On the way we stopped by a supermarket that was selling the autumn flavor range  of my favorite (never thought I’d say that) Soy milk brand. Well I had to buy a couple to try out, purin and chestnut yum.

Checked in it was sadly time to say good buy although not before introducing my friends to the wonders of でっぱちっか or department store food. The quality always amazes me considering the price. I spent the rest of the evening in a mangakisa since I couldn’t face the thought of hanging around a bunch of seedy old men in the capsule hotel. Plus free manga and anime what’s not to like.

The following day I set off bright and early for Ikeda, a district just outside of central Osaka. This was somewhat of a pilgrimage for me as it is the birthplace of instant ramen. It’s no secret that I’m a fan of instant noodles, I think I’ve been eating them consistently since the age of 3 so it shouldn’t be too much of a shock.

Before arriving however I sat down on the train and an old man sat next to me. Nothing strange about that but he started talking to me and obviously, it'd be rude not to, I responded. Suddenly we were having a conversation. I learned about his travels. His son in San-Francisco. His love of climbing mountains and plans to visit Yosemite next spring. He also told me about the time he'd spent in Italy and how he'd really like to visit England one day. All of course in Japanese. I think I might be getting somewhere finally and my responses were a little more than just 'hmm' and 'I see' for a change. Truly a light bulb moment.

Leaving the station and following noodle dori (no joke that's the name of the street) I soon came across my destination, the Momofuke Ando Istant Ramen museum. A.k.a noodle heaven. Greeting me at the entrance was a Christmas tree covered in little plushies of chicken ramen’s (the worlds first instant noodle brand) mascot. No prize for guessing what it is.

The museum was two things. Firstly very cool and informative, you’d be amazed at how much thought actually went into the pot noodle, seriously. Secondly it was jam-packed with people. The Japanese it would seem love instant noodles even more than myself.

The exhibits were well laid out, there was a reconstruction of Momofuke Ando’s shed where the instant noodle was invented and an entire wall displaying a timeline of potnoodle releases in japan. Sadly there were no English explanations but it was fairly simple, this place is actually aimed at school kids I think, so I got the gist. It’ amazing to think that the instant noodle has been around since th 50’s and that pot noodles are over 40 years old.

Anyway the highlight for me, and the hundreds of other people, was the my cup noodle factory. You got to make your own pot noodle, design the cup and choose the filling. Yeah ok I’m sad but I enjoyed it. Actually the cup I made will be a gift for someone else, maybe I’ll go again sometime to make my own.

That's all for this weekend but I'll leave you with a few extra piccies from the museum cause I'm that cool..

Mata ne Minna-san

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.