Foreign Perspectives

On to SDS-PAGE today. That’s another gel but a polyacrimide one this time which means a bit of fume cupboard work. It’s more complicated to assemble this gel as it’s run vertically so there’s a bit of assembly work to be done then you’ve to use two gels, one to actually run the analysis and the other to make sure that all the samples start off at the same time.

Things went rather well and we’d a relatively early finish to the lab work this afternoon. The downside of today is that we finished with nothing actually visible.

The gel was processed in a sandwich to move some of the proteins onto a nitrocellulose membrane with the encouragement of a little electricity yet again. With that done, processing of the gel and the membrane separates with the gel going into a coomassie blue bath to visualise the proteins whilst the membrane is cut in two so that the CD4 and CCR5 sections can be processed separately tomorrow. For today, the gel is washed in the coomassie whilst the membrane is washed in western blot blocking buffer.

The evening lecture on the biology of HIV was fascinating though it would have been better to have it earlier in the day as there was an awful lot to take in at that time of night. The optional lecture on how to write the research plan was useful and fairly short too. Those that didn’t go to it will regret that when the marks come out.

The morning went in preparing our samples for the PCR machine. Lots of pipetting samples in minuscule amounts, ice buckets and taking a of care to make sure our own DNA didn’t contaminate the samples. Quite a busy morning which finished with us assembling the gel for our agarose gel electrophoresis in the afternoon as it takes quite a while to set. Actually, the one consistent theme for this week seems to be that business of waiting around for something to set or be mixed and the like.

What the PCR setup sequence does is to slice out the bit of DNA that we were interested in ie CCR5-delta-32. That’s an interesting sequence as people that don’t have it are essentially immune to HIV, hence the focus on it through this summer school. Anyway, the PCR takes that bit out and produces millions of copies of it, increasing the concentration of the gene segment enough that it can be detected by the gel we used in the afternoon.

The gel process separates out the various proteins in the post-PCR mixes depending on the size of the fragments (their original shape doesn’t matter as the PCR process chops up the DNA or rather amplifies just the fragments that you want to look at). After half an hour or so it’s finished but you can’t see anything until the gel is placed under UV illumination as the dye used is UV sensitive which is a shame as you can’t see the proteins moving along the gel.

The various gaps in the day were filled in by the theory behind it all though, mainly, running behind the practical bits.

We’d our first SXR376-exclusive lecture this evening on genetic variation (the one last night on transposons was shared with SXR375) followed by the optional one on giving a research presentation.

With the change to FlyBE this year, it was well after 12 before I reached the Nottingham campus. There’s only the level 3 summer schools running this year so it was quiet the whole day.

Surprisingly the taxi was the same price as the last two years (Lenton on 0115 9 781 781 do the airport pickups for £19.50, just over half the price of the airport taxis; it’s best to arrange for them to collect you at the petrol station just outside the airport parking area as otherwise they charge for the airport parking.

Registration runs on ’til after 3pm with the introductory lecture in the biology building just after 4pm so I took the time to stock up on a few nibbles at the hospital shops (the campus shops are closed over the weekend).

It was a blue dot this year signifying that I’m in SXR376 rather than the green dot of the SXR375 people.

The introductory spiel from the admin people, learning advisor, OUSA and the course director was a joint one for both SXR375 and SXR376 kicking off just after 4pm and running on to almost 5pm. That was immediately followed by the course specific stuff in our respective laboratories. Just one lab for the course again this year as there are only about 30 of us but we’ve been split up into two groups to do the experiments over the next two days, which we’ll be doing in groups of three. For a change, we actually did some lab work this evening to get us back into the swing of pipetting.

In the room is a phone (free internal calls), wired internet connection (you need a cable for this which you can get (free) in the Cripps security office; the wifi varies from poor to non-existent in the rooms), desk, tea/coffee tray with kettle, sink, wardrobe, towels (with soap & shampoos) and a single bed. The shower-room and toilet is shared  by about half a dozen rooms. No Internet worth talking about this year as there’s some network problem that can’t be fixed until the computer people return on Monday.

Thanks to the excellent pre-exam briefings by the course team, this was one exam that didn’t seem to cause people anything like the level of anxiety that others have been known to do.

As noted in the earlier post, the chemistry exam follows a very similar pattern from one year to the next. Almost to the point of being identical in many respects. Thus, question 1 is always a box diagram question and, as the course team commented, just about everyone gets full marks for it. In fact, the majority of the short questions are very similar from one year to the next and, because they follow the order of the books, you can pretty much bank on, say, question 7 being on whatever question 7 was on last year. That’s not to say that they’re all doable as it’s a massive course and few people revise everything but it does mean that selective revision is quite effective.

That follows through largely for the longer questions too although as the years have gone on, there seems to be more of a tendency to have one question covering parts of one or two other related areas ie if you’re doing selective revision then you’ll not be on totally firm ground all of the time. Moreover, the second and third longer sections are less easy use focused revision with than in the first section (which I think is always a choice between kinetics, orbitals and retrosynthetic analysis). Or perhaps it’s just that I’m less keen on the section C  and Dquestions?

What I did find pleasantly surprising was that even on my pessimistic in-exam estimate, I was well clear of 40%. That’s not so much because the exam was easy but that the whole exam is broken up into what’s effectively a very long list of short questions, albeit with several grouped into topics (ie the long questions).

That’s the problem with the euro situation at the moment: it really is placing a bet on it surviving.

Spain is being given another 100 billion to bet on it’s banking system surviving the crisis. Greece, unless they elect a far left or right government, will probably be given a similar amount to bet on it’s banking system and not too long from now Italy and Portugal will follow with equally large bets.

All this is just fine if the bets win. If they don’t that money will need replaced and the amount remaining in the kitty will be rather low at that point. Moreover, if the bets don’t win there’ll be a whole bunch of real-world things needing financing at the same time that the bets are written off which is a nightmare scenario for everyone in Europe and none too good for anyone anywhere else for that matter.

Either way, it would appear that we’re in for an interesting second half of 2012.