Fragment 2.

Wednesday 17th August 2011:

Wednesday was also an amazing day.

On Tuesday night in Akihabara, Saito-san asked me what I would spend my last day doing, and when he heard I was going to spend it on my own, offered (along with Kaki) to come with me!

So on Wednesday morning, I woke up really early with the intention of going to Tsukiji market (finally) with the guys. However, I then found out that it was closed for Obon. We decided to still go to Tsukiji for some fish for breakfast, but just not to the market proper. So I spent the early morning packing and cleaning ready for my check-out inspection, and met up with Kaki at Suitengumae station at about 10am.

He told me Saito was running late and would meet us there. So we took the train to Tsukiji together.

When we arrived, we had a look around the shops and restaurants, but a lot of them were also closed for the festival. We found one place that was offering free samples of Korean food, and because that was his favourite he asked me to try some. It was really good actually – not as spicey as I’d been led to believe, but good!

Saito met us about half an hour later, and we tried to decide on a place to eat. His favourite place was one of the ones that wasn’t open, so instead we aggreed on going to a carousel sushi place because that way I could pick what I wanted rather than having to struggle with a Japanese menu.

The fish was beautiful. So so so good! Possibly the best sushi I’ve had since I arrived in Japan (and I know that I say that a lot! But it’s true!) I had maybe 6 plates, and I tried a lot of different types that Saito recommended. Kaki kept trying to get me to take more plates, but it was really filling so I couldn’t do it! I drank a hell of a lot of green tea too. Mmmm.

Afterwards, Saito said that we should go get some Japanese sweets. He was adamant that we go to a specific place for it in Ginza, so we started walking there. When we arrived though, it was also closed. We finally found somewhere else to go in a shopping mall, but he told me that it wasn’t as good. I had matcha kakigori with a sweet bean sauce. It was pretty damn good, but I was still full from the fish. Saito treated me to both the sushi and the kakigori, which was kind.

We strolled around Ginza for a bit, looking in some shops and stalls. We went to a bookshop and Kaki pointed out his favourite book to me. He found a copy that had been translated into English, and then bought me a copy as a gift. It was really sweet, and usually I suck at accepting gifts and free meals etc, but it’s impossible not to in Japan because it’s really culturally offensive to turn down an offer. So I accepted it, and really appreciated it. 😀

Then, Saito went back to work as he was really busy with an experiment. Kaki decided to spend the day with me instead of going back to the lab. I was a bit worried about him getting told off because he was also late on Tuesday from oversleeping, but he told me it’d be fine.

We then took the train to Shibuya. I really like Shibuya because it’s so vibrant and interesting. Instead of going to the big shops this time, he took me to some of the quieter areas and we looked at the little boutiques and stuff. On the way back into the main town, we stopped for a Frappuccino and chatted. He’s pretty shy, so I think it was the most I’d heard him speak since I arrived! We then went to the Disney store (because I’m a massive kid) and Tower records. He showed me some of his favourite Japanese bands and I showed him some Western ones. I was really shocked to hear he’d never heard a Nirvana record. That’s just crazy by English standards! Haha.

We were going to go to Asakusa for a while to look for souvenirs, but it was getting late and I had to be back at the apartment for my check out inspection. It started at 5.45 and I hadn’t hoovered or anything. Woops. So instead we went back on the train.

I mentioned that I’d got no plans for dinner, so we agreed to meet for Korean food in the evening. I was really looking forward to it because the Korean in the morning was so good!

So I got home, cleaned, packed, yadayadayada, and then had the inspection. It went well, and they said everything was fine. So afterwards I had a quick shower and headed back onto campus to meet for dinner. I got to the lab about 5 minutes late. Not that that detail is important, but just weirdly it bothered me. I hate being late. haha.

It was a pretty good turn out. 7 of us went for the meal: Me, Kaki, Watanabe, Akimoto, Yugi, Toyoshima, and Uda. (-san. etc.) Unfortunately, the Korean restaurant was closed (Grrr) so we went for Japanese food instead. I had a rice dish cooked with soy sauce, with eel on top. It was really delicious – It’s just a shame we couldn’t have the Korean. Everyone was really chatty which was nice. Even Akimoto who I’ve sat next to for the past 6 weeks but have barely said 2 words to. I was really glad to get to know them better, even if it was so close to the end! I’m really going to miss everyone!

We went back to the lab briefly after the meal and I said goodbye to a few more people. Then, Kaki and I went down to the  main campus to meet up with Kyle for a drink. We walked into the area around Hongo-sanchome, and went to a bar Kaki recommended. We all had beer. I like Japanese beer.

We left at about 11 and went to the station. Kaki walked us there and we said goodbye by the ticket gates. I know I keep saying it, but I’m really really going to miss my labmates. Urgh.

When I got in, I packed my final bits and bobs, had a bit of a cry about leaving (I was exhausted, emotional, a little tipsy, and didn’t want to go home).

Then I slept.

Thursday 18th August 2011:

Thursday. Hometime. Depressing.

I woke up at 4.30am after nowhere near enough sleep. I set both phones’ alarms because I was paranoid about oversleeping, and was so glad I did when I realised my iPhone is buggared and didn’t ring at all.

I got to TCAT really early (and thankfully had some help with my massive suitcases) and took the 6.15 bus to Narita. I was thinking too much on the way. Always dangerous. It got me all upset again.

I was at the airport much to0 early, and check-in didn’t even open for another hour. On the bright side, that meant that when it did open, I was nearly the first to check-in and so didn’t have to stand in a queue. I also got offered a seat upgrade because they hadn’t sold out the World Traveller Plus seats. I didn’t want to pay 3000 yen though (perhaps a stupid decision) considering I needed to pay for an extra suitcase in check-in, so I turned it down.

I spent the next few hours regretting that decision while walking around the airport. 12 hour flight. Insanely cheap considering. Stupid Sophie.

I had some waffles in a cafe in the airport, and had a brief moment where I felt like I’d never seen a knife and fork before in my life. How awkward. I definitely prefer chopsticks.

When I got on the plane, I had a really shitty seat. I was next to an elderly Japanese couple who smelled like mold and greasy hair. The man also spent 3/4 of his time farting. Definitely regretting not accepting the seat upgrade.

I then found my telly didn’t work. It was a long flight, and so I was a bit miffed, so I asked one of the air hostesses if there were any free seats I could change to.

I got moved. To an exit seat. To EPIC LEGROOM!

Best.Thing.Ever! (And much more legroom than I would have had if I’d taken the upgrade.) SUCH A GOOD MOVE.

The flight was boring, so I won’t write more other than that I watched 4 movies (“Thor” – Epic; “Terminator” – AMAZINGLY EPIC; “Red Riding Hood” – shit; and “Sucker Punch” – Epic.) and spent a lot of the flight thinking back on my time in Japan and reminiscing.

I am so sad to now be home.

I miss Japan already. A lot.

And that concludes my Japanese adventure!* 😦

* Excluding randomness which I will blog about over the next few days. Afterthoughts etc.

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It’s Friday, Friday, gotta get down on Friday…

… And so we did.

But first, what happened during the day time?

 

Friday 5th August 2011:

I woke up after the worst night’s sleep ever (as ranted about on my blog at the time), and then went onto campus. The presentations were due to begin at 10.30am, so I arrived for around 10.05. I went through what I was going to say at my desk again, and then we were called over.

Davis went first. His presentation was on the application of his area of work to structural biology, and how that ties in with systems biology. I personally didn’t like his presentation very much as areas of it were somewhat condescending (for example, a beginner’s introduction to glycolysis, complete with a few glaring inaccuracies) and the whole thing overran massively. He spoke for approximately half an hour, and despite being asked by Kuroda-sensee at one point how many slides he had left, he continued to proceed at a similar pace. I found this quite disrespectful to the schedules of the other lab members, and completely unnecessary since as it was his idea to do the presentations in the first place, he had had plenty of time to prepare it better so as it wouldn’t overrun. He later blamed it on his fluency in English, although the problem was much more to do with content than expression.

But never mind. After that, I did my presentation. I worry that it was very boring, as (as I mentioned before) I haven’t done any research of my own and so I just had to run through my brief background and mention my future dissertation plan. Because we were short on time after Davis’ presentation, I ran through mine much faster than I had prepared, and cut our several large chunks of content. I finished the presentation in around 6 minutes, I think. Perhaps this made me look rushed and unorganised (I hope not!), but my priority became ‘don’t hold up your labmates’ rather than ‘make yourself look good’. I was rather uncomfortable, but I think I got through it okay.

After the presentations were finished, it was time for lunch. I went to the second refectory and met up with some UTRIPpers for a little while. It was Rachel’s last lunch on campus, and so we were all talking about how fast it’s gone and how none of us really feel ready for it to end. It was a lot of fun, and it was nice to catch up with people. I feel like I haven’t seen them a much as I’d have liked recently because everyone is so tied down with work.

I went back to the lab to start the afternoon practical work. At 1pm, we began. I was both excited and nervous, because the experiment was now differing from the initial, and my own protocol was becoming important. It was the first time that I’d been able to plan my own project from scratch and work it through without the strict guidance and regulations of the University of York staff. Fun stuff!

First I had to prepare the clean bench – I’ve started really enjoying this step because it’s a little bit OCD and very me. I then make my EGF dilutions. I followed my calculations precisely, and had the samples lined up in my ice bucket within no time. Then the exciting bit happened – performing the stimulations.

I had my timing protocol attached to the cabinet above my head so that I could check it easily as I went along. I had planned it so that there would be at least 2 minute intervals between each step. A good move, I believe, as it meant that the procedure was much less stressful than it could have been.

Good timing was essential, and the repetitive mechanical processes started to seem like a well orchestrated, well synchronised dance. Science dance. Wow… I’m such a geek.

The stimulation was separated into two parts, which I inventively named “Experiment 1” and “Experiment 2”. After I had finished Experiment 1, which took exactly 61 minutes, I took a short 5 minute break before proceeding to the next one. It was weirdly relaxing and the time flew so fast.

I refrigerated all of my samples, and then went to buy a Mountain Dew. Davis had another 35 minutes to complete, and so I enjoyed a rest before the next step. I also took my antihistamine tablets and slathered my legs in steroid cream, because I’d got more new bites. Ouch!

The next step involved retrieving the proteins from the freshly-lysed cell samples. The best way of doing this was to simply extract all of the liquid from the plates. Easier said than done when the mixture is rather viscous. We were shown the best way of extracting it, by strong mixing, addition of further buffer, and subsequent pipetting. This step took much longer than it did in our initial experiments because of the added washing step, but hopefully our data will benefit as a result of it.

The final step of the day was making the gel for the Western blot. The ratio of ‘ingredients’ differed somewhat from the first time because it was too solid to add the samples effectively. I was a bit concerned about it solidifying because of this, but I think it worked out okay.

I poured my gel, cleaned the bench, and then left the lab by around half 6. Not bad, considering we’d been told it would be a late one!

I really enjoyed the day in the lab – it felt like the most successful and productive day so far, despite the awkwardness of the self-centred presentation. Haha.

When I got to the lounge, I was told by Kubota-sensee that the office would be closed on Monday and Tuesday and so I needed an electronic key card to get into the building. Kaki was asked to show me how it worked, so he walked me to the entrance and showed me. It was pretty obvious actually, and I felt a bit sorry for him having to stop work to come show the silly white girl how keys work. Haha. He told me that he finished today and so wanted to know if I fancied going sightseeing on Saturday. I said yes, but completely forgot that I was meant to be going to Odaiba with Maria, and for numerous other reasons it wouldn’t really have been possible, so I had to email later and cancel again. I felt really bad for altering his plans and then cancelling, but it just couldn’t be done.

Then I headed home.

In the Evening…

This deserves its own subheading as it was pretty amazing.

As it was some people’s last weekend in Tokyo, we’d decided to go clubbing to celebrate. I met Stas in the Hakozaki lobby and we started to walk to the river. Anet had asked me to buy some Sake, and I hadn’t had dinner yet, so we went via the 7-11 to get some grub (I had sushi and a waffle, as per).

When we got to the river at about 9.15pm, we couldn’t see anybody from the program. At all. We started to get a bit concerned that we’d come to the wrong place (neither of us had met them there before, hence why we decided to go together) so we walked around half a mile down the river each way. Eventually we gave up, sat down on the steps, and started eating without them. It was only then that Anet turned up and we were told we were in the right place after all!

Shortly after, Anna came, and then Till, and then Mark and his girlfriend Kumi. We had some sake, enjoyed some good company, and the mosquitoes enjoyed eating my legs. Mark and Kumi left after a little while so she could change her shoes, and they told us they’d meet us in Shibuya. We left the river and headed to Suitengumae to get the last train into town.

Kyle met us at the station, but we couldn’t find Mark and Kumi anywhere, even after we’d arrived in Shibuya. We posed for some terrible photos (see above! haha) and made our way towards the clubs. We were planning on going to a specific one, but when we arrived the doorman was demanding something crazy like 4,000 yen per person for entry alone, when the website said 1,200! Obviously that wasn’t going to happen!

We walked around for a little while and met some other Westerners who were in a similar situation. They had a Japanese friend (I can’t remember her name right now, which makes me feel bad because she was really nice!) who told me that she’s only been to England once, and only visited York while there which was amazingly weird!

We never met up with Mark again. When I got home I had an email from him saying that Kumi wasn’t feeling well so they went home. It’s a shame, and I hope she’s feeling better now!

We found a club in the end which was free entry, and apparantly a good place to go. It was called Gas Panic and was in a basement. I’m going to be completely honest – I was disappointed by the venue. If that was somewhere I’d been in England, I wouldn’t have stayed. It was effectively a glorified bar with no dancefloor, pretty terrible music, and  extortionate drink prices! The company made it a great night though! Everyone was really fun (albiet Stas was very drunk and as such became a bit of a pest) and we had a great time. We all danced and sang and it was awesome. After what felt like maybe 30 minutes, Till told me he was feeling a bit funny from the music and heat, so we went outside. It was only when we got out that I saw the time on my phone and realised how long we’d been there! It was about 4.10am by this point. Mental.

We sat outside and chatted for a while, as my ears got used to the silence and Till started to feel a bit better. Kyle, Anet and Stas joined us soon after and we went to get some junk food. Anet had been saying she wanted a burger for weeks, and so we found a Burger King and she bought two! It was getting light now, so we sat in Shibuya as the sun rose, and then made our way to the station in time for the first train.

The journey was so bad. It was just one train, and it didn’t take long, but I just really wanted to get some sleep. It was impossible though with the movement of the carriage.

I got back to my room at an obscene time in the morning and went straight on Skype to Matt. I have never stayed up all night in my life, and so felt absolutely rotton. I wasn’t particularly drunk at this point, but exhausted! Matt either found it funny or pathetic. I can’t really work out which 😛

I managed to go to bed at around 6am, and slept until about 9. After a bath and a few glasses of water, I was ready to start the day!

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This, my good friends, is what we call ‘Lazy Blogging’.

Firstly, apologies for yet again not blogging for a few days solid. I have been exhausted.

To be honest, it makes little difference this time though. The last few days have very much blurred together. Since Monday, I’ve essentially been doing different stages of the same thing. And so rather than separating out the days, I’ll just blog them together.

So what have I been doing? This week, I have been programming. Amongst other things.

Monday morning began with the weekly cleaning of the office, followed by the briefing (which this week, was in Japanese). Following that, we had a presentation by Iwaki-san about his work on sampled max-sum algorithms. It was really interesting actually, and I enjoyed it.

After that, I went for lunch on my own (because I’m a cool kid, right?), and then began work on the programming. Yugi-san and Uda-san were training us on the program Matlab and how to use it to model biological reactions and processes. To start with, I was following the instructions pretty well, and understood the logic behind why we were doing it. However, around 3 hours in I started to get quite lost. The instructions I felt were written for people who had some prior knowledge of how to program, and why the codes were used. Shortly after beginning, Davis announced that he was bored and wanted to train himself instead. He went off on his own, and Yugi-san was able to help me a little more one-on-one. That helped a bit.

What I found most confusing was not so much the coding itself, but following the instructions provided on the handout. There was a lot of ‘swapping between windows’  without cues for when and where, and so it was easy to take a wrong turn and get into a big tangle. Yugi-san was very helpful, but I felt that just a few days was an unrealistic time to learn and appreciate all the codes that we were using.

After about 5 hours, however, I had successfully created my first program! We were modelling the effects of EGF signalling on various downstream signalling molecules, taking into account the data produced from our first wet experiment. The program needed to run overnight to account for all variables and produce a result, and so I left the lab at around 6.30pm.

That evening, I didn’t do a lot really. I skyped mum and Matt, and then went to bed. Oh… and there was a big earthquake while I was in the bath! Which I briefly ranted about in my blog.

The next day followed a somewhat similar pattern. I went onto campus, began programming at around 1pm with Yugi-san and Uda-san, and then left the lab in the evening. Slightly later this time, at around 7.30pm. This time, we actually incorporated the data from the practical, and also the data from Sasagawa’s paper (which greatly influenced our research topic) as a control for the somewhat sketchy results we obtained in our own experiments.

I was able to produce some graphs based on the data, which will later be used to aid my predictions and planning for the final project. We also simulated a ramp stimulation process to assess the effect of slowly increasing concentrations of EGF of the cell. However, because it is incredibly difficult to implement ramp-stimulation in vitro we also needed to make a step-stimulation simulation. Due to timing constraints, that had to wait until this afternoon.

So after a hard, and somewhat frustrating day programming, I finally left the lab!

I came home, and ran into Till on the way back. I hadn’t spoken to him in a few days, so that was nice. He’ll be leaving soon – I’m a bit sad about it actually cause I get on with him well. Hopefully we’ll keep in contact after the program.

When I got back, I skyped home briefly, had a bath, and then had an early night.

Sorry for utterly skimming the last few days. But literally, all I’ve really done is sleep, eat, and program, and I don’t wanna become the kind of blogger that just talks about food all.the.goddamn.time. And the details of the programming aren’t blogworthy either. Plus I’m tired.

So that brings me up to today. I accidentally overslept a bit again today. I don’t trust the alarm on my new phone.

I headed onto campus and began programming from 1pm again. As usual, Davis was late, and spent most of the day complaining that he was bored and wanted to do independent research. I actually got into quite a heated debate with him about his appreciation for the program and other lab members’ schedules. But it just went straight over his head so eventually I gave up trying and just went back to my work.

We finally finished programming today. After making some graphs showing the results of a step-stimulation simulation I began to plan my final experiment. It was pretty fun actually, and I am happy to be moving away from the theoretical and back into the practical hands-on parts of the placement. Part of this is because having the programs for it installed on my computer is causing it to lag massively, and crash at least 5 times a day. That’s frustrating, when it is my main source of communication and cheap entertainment here!

Yugi-san helped me to interpret my data, and then I proceeded to use it as a starting point for my design. I found that during the step stimulation, if I used 3 subsequent stimulae, the resulting curves differed depending on the ratio of concentrations used. I.e. if the first and second stimulation concentrations were relatively low with regards to the third, then 3 peaks were observed. However, if there was less difference between the concentrations of the stimulae, then the third peak was no longer observed, and the system appeared to have been blunted. This could potentially be due to ubiquitinylation and degradation (a known result of the pathway itself), receptor saturation, or even inhibition. I was pretty excited when I worked out the implications and am now really looking forward to the practical itself.

At around 5.30pm, Kaki came up to me and asked if Davis and I wanted to go to dinner with some of the lab. I hadn’t realised how much time had passed, and because I was running late that day hadn’t actually had any lunch, so decided to go along. Davis didn’t come, as per, and so in the end it was me, Yugi-san and Kaki. We went to a restaurant by the Akamon down a small side street. The owner didn’t speak any English, and so Kaki helped me to order. I had sashimi, rice, japanese pickles, tamago with vegetables, and miso soup. It sounds like a lot, but it was one of the set menus again. The food was really good, and I enjoyed it a lot. I also had about 5 cups of tea because it tasted awesome.

Yugi-san and Kaki were telling me about themselves which was nice. I enjoy learning about my labmates and they’re really friendly.

After dinner, I went back to the lab with them and carried on preparing my project. I worked out the stimulation schedule based on what I wanted to achieve and how long I planned on stimulating each plate with the EGF. It was really confusing trying to prevent an overlap in the stimulation, but eventually I worked out a solid plan, and finished writing up my research proposal. I went to speak to Kubota-sensee who read through it and gave it the go-ahead. He could see what I was trying to show with my experiment, and said that the science behind it was sound.

That was a big relief, and so after a short while fine-tuning the proposal, I left the lab at about 8.15pm and went home. Even though I’d had dinner, I really fancied something salty and so planned on going to McDonalds again on the way back, but it was closed. Massive disappointment when you’ve got a craving!

I got home quite late (maybe 9.10pm) and began blogging. That leads me to here.

I’m sorry I haven’t had a lot to say really. Sometimes I have so much that I can’t fit it all on the page!… but for the last few days life has been pretty ‘samey’ so it makes no sense to write it all in excruciating detail.

Now, a few random notes:

Tomorrow I might be going to Tsukiji fish market before work with Anet if I can get up early enough! (We are due to meet at 5.30am for the tuna auction… it might be pushing it a little!) If not, it will be another day in the lab!

I’ve missed a few social things with UTRIP this week because of work and tiredness. I feel a bit rubbish about it because people are starting to go home now, and I’ll never see them again! But work needs to come first right now.

On Friday morning, I have to give a presentation on myself. I’m really starting to panic about this, because I feel like I haven’t got enough to say! 😦 Wish me luck!

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