Friday, 18 July 2008

SXR376: Summer school Day 7

The last day dawns - and there are now labs. There is only the presentation to do, and it has been worked on hard, and is foremost in our minds!
We finish up the writing and last minute adjustments in the lab, and it is a work of art I have to say. Dave has put a lot of work into the formatting, but we're all a little nervous.

The fats people go first, and there is a usual mix. Some people are good, so people not so good - and some just go on too long! Then the plants people did there bit, and overan a little so there were no questions as we needed lunch. Mark remarks over lunch that he was wondering if his presentation was too short, but then decided there is no such thing as a too short presentation at this sort of event - and that is very true!

After lunch it was our turn. Again we had some good and bad bits, but the presentation did look good. By the time it got to my bit we were running behind schedule, so I spead through my slides mentioning only a few salient points.

We wrapped up, and the week was done. We got our attendance slips, collected our luggage, said our goodbyes and left. Suddenly we were back in the real world - how weird!

Thursday, 17 July 2008

SXR376: Summer school day 6

Its the last but one day, and the last day that we can complete our experiments.
We start by getting the tray out of the fridge and washing off antibodies, before adding more. Its quite a time consuming job to go through the procedure to get everything stuck to everything else - although of course we can't see any of this happening and are just hoping its going to come out well when we look at it under the microscope!

Anyway, when it is finally washed and incubated in all the different solutions, we have to extract the cell coated cover slips from the wells we've been using. This is no mean feat, with them being almost invisible and fearsomely difficult to get out of these wells.

Then they are mounted on the slide and we take them over to the microscope to see what we've got. Has the two days spent washing and dousing these cells with various chemicals been worth while or not. At least there is a clear brown hue on the ones we want - the positive controls and the ones dosed with the ligand. They look rather similar though by eye!
Time to have a look.

Positive control, negative control, and experimental data.
Its difficult to say if the experiment worked, and it takes a while with the tutors to understand what we are actually seeing. Anyway, we have some data for the presentation at least.

The rest of the afternoon we spend on the presentation and doing some practising in the lecture theatre. The time for tea, and no tutorials tonight. there is a disco, but I decide with a few others to give it a miss, and we have a good time in the bar going over the weeks events! Now its just the final presentation to finish and then present and we're done!

Wednesday, 16 July 2008

SXR376: Summer school day 5

Well - as today dawns we start a new set of stuff. We've now finished all the core activities, and we need to go on and look at the further experiment set. In this there are a number of topics which you can pick, although they want all areas to be cover by someone. We elect to do an experiment involving immuno-cytochemistry. This is basically about attaching antibodies to the surface of cells using some amplification to get them to show up.

There are quite a few steps, but each of them after the first few take an hour or more to wait for the incubations. So by lunch time we discover that we didn't have enough time in the rest of the day to finish the procedure, so the tray was put in the fridge and left while we did some graphs and stuff. We also took a few other readings and prepared some slides for the upcoming talk.

There was a tutorial after tea on presenting a talk, and then on dividing up the talk. After that we went to a tutorial on the ECA itself, so we'd know what to write up.

Tuesday, 15 July 2008

SXR376: Summer school day 4

Day 4 dawns, and it looks initially like a bit of a rest day. We are to run PCR machines and then look at DNA tracks in gels. These are apparently much easier than the SDS-PAGE gels to get right, and the initial stuff goes well. There is some really tricky diluting, we have to pipette one micro-litre of DNA - which is almost impossible to see if you have anything at all in the pipette!

While the mixture we make up is in the PCR machine, we poured out the agarose gels to let them set. These are quite easy to do, the liquid is at 60C and you pour it smoothly, move any bubbles that appear to the side out of the way, and then leave it to set. As it has a flourescing agent in it - it has to set in the dark so it doesn't bleach.

After lunch, we came back and loaded up the gels with DNA to see what we'd got. After running them for a while, we took a look at them in the UV viewer, and we had only very faint bands. In fact they were practically useless. So we decided to rerun the procedure and see what we could do. We ran out of time, but luckily the demonstrater was able to finish it off and the results were good this time - very clear.

After tea - another tutorial. We swapped partners and had to prepare a quick talk on a given topic to do with the procedures we had used. We did a quick poster on paper and then had to present it to the group. This was clearly practice for the main symposium on Friday. After that there was a quick chat about the ECA we will have to do, and then a review of the data we had collected, followed by the further experiments.

Monday, 14 July 2008

SXR376: Summer school day 3

Its day three already, and we continue on with the gel stuff. SDS-PAGE is harder than it seems to do the first time - but luckily enough has been salvaged from the first day to make progress.

The gels were run and blotted overnight by the tutors after our small disaster and we actually got some reasonable results. We managed to get all the stuff off the gel, and then stained it for what was left and despite it tearing a little, we actually got something recogniseable.

Then we set to work on the blotted paper to see if we could use antibodies to pick up CCR5 and CD4 on them, and after a while we got that too! It takes a lot of washes and other stuff to get there but we could see bands in it.

What's more they almost make sense.

At the same time as all this was going on, we made up an ELISA dish with a number of standard protein concentrations and also put in our three cell lines at different dilutions and then after adding all the reagents, popped it into a machine which produced a set of results, in seconds!

After this, there was much plotting of graphs and interpolation to try and find out what we had got. Then it stopped for tea.
After tea we had two more tutorials, one on HIV infection methods and its life cycle, and the 2nd on how to read a science paper - which went rather quickly as we were all too tired to do much with the material we were suppose to be interacting with.
And so to the bar...

Sunday, 13 July 2008

SXR376: Summer school day 2

Day two - and the first real lab day. We are going to be doing some western blotting and protein analysis from some sample T cells. We're going to be looking for CD4 receptors as a control, and CCR5 receptors to see if different cell lines have different amounts of that receptor.

We started by getting our samples out of deep frozen state into a form we could work with. This involved some washing and centrifuging, and then some extraction buffers to break down the cells to get at the proteins.

After that we had to make up a polyacrylamide gel to do the runs on. In this we had a bit of a disaster, as we made our first gel up OK, but the stacking gel on top vanished when we pulled the comb out. So we had to start again which put us a couple of hours behind everyone else. We managed to get the second gel to work, and start to run, but then we had to leave the lab, and hope that the tutors could do the transfer and other stuff that we didn't have time to do.

After tea, it was time for a tutorial. The first was on HIV and the genetic susceptibility of various groups and associated issues, given by our tutor Chris. The second was by the course directory on presentation techniques for the final presentation.

Retire to the bar to discuss the day and drown our sorrows!

Saturday, 12 July 2008

SXR376: Summer school day 1

Day 1 at the summer school on "The molecular basis for human disease".

After turning up with the family (its only 10 mins from our house) and registering for the course, we walked around the campus a bit to find the lab and other things. We found the biology building and even wandered around it a bit looking at the set of various animal skeletons they had. Also found the lab I'll be calling home for the next few days.

At 4:10 we all went into the lecture theatre to learn about general things about the week. Then we split up into the three different courses (SXR374 and SXR375 are in the same building) and met up with our tutors and assistants. We went off to our lab and had briefings and lab manuals handed out and picked up lab coats and stuff like that. Then we did a bit of practice pipetting with the automatic pipettes wearing gloves and safety goggles. You can set these up to deliver various sizes and we tried dispensing droplets of water of the appropriate amounts.

Then, back to the hall for a spot of tea, and some time to ourselves until a lecture on GM crops.
This was very interesting and very well presented and we all enjoyed it with a number of question and answers going on. Then to the bar, where I got to meet a number of the people involved in the residential school informally as well as meeting up with some old, and new friends.

Thursday, 10 July 2008

S282: TMA-3

It can't be put off any longer - another TMA to submit.

Question 1 (25%) looks at stellar evolution and reactions - and its in three parts.
Part a) gives you 6 nuclear reactions and then asks a number of true/false type questions. However the joke in the pack is that if you think it is false, you have to give a reason why it is false. So this means getting your reasons in order.
Part b) is similar, in that you are given 8 statements, and told to pick out two that are false, and then explain why they are false. All the questions concern binary star systems in one way or another.
Part c) is another list of 8 statements about stellar evolution, and again pick out the true ones, and explain why the false ones are incorrect.

Question 2 (20%) is split into a-c with subparts for each.
Part a) looks at the stability of stars and you need to draw a diagram showing the forces in balance in a star, then to consider what forces are important in various sized stars.
Part b), with 4 subparts, looks at the collapse of a stellar remnant to a white dwarf and a neutron star and what conditions each are formed in.
Part c) takes the part b) further and introduces black holes into the mix and you have to do some calculations on back hole radii.

Question 3 (18%) looks at supernovae, and its just 4 subparts. Its based around a given table and you need to consider what type or supernova each represents, what they can be used for, and what would happen to the remnant left over.

Question 4 (22%) is a little different in that you are given a spreadsheet of cepheid data from M81 and you have to calculate various equations and end up with a value for its distance. There are a few formulas to rearrange and some averaging to be done, and then some general questions about the results.

Question 5 (20%) is again different in that you have to read one of three recent articles published on the website and then write a short account of its significance

Its not too bad as there is a bit of variety in amongst it, although I found the first question dragged on a bit as I trawled through various pages looking for clear refutation of this point or that.

Tuesday, 8 July 2008

S282: Book2 - Chapter 3 & 4

Book 3 continues with some more chapters about galaxies. In chapter 3 we are considering active galaxies. This looks at all sorts of the more weird end of the galactic spectrum. It considers galaxies that have active cores - these include Seyfert galaxies, quasars and blazars - and whether they are the same thing viewed from different angles. Active galaxies appear to be associated with early galactic structure, at least in some cases. I found it all a bit dull to be honest after the first few pages. Maybe galaxies aren't my thing - or I'm missing the point!

Then chapter 4 looks at the distribution of galaxies. The fact that the milky way is just one of a local group of galaxies that includes a number of others. Then our local group is part of a supergroup of groups grouped together. Beyond that there doesn't seem to be any further discernible structure to the universe.

Wednesday, 2 July 2008

S320: TMA-2

Another TMA comes around. There are only 3 in the course, but the 3rd counts double. Anyway, time to tackle this one.

Question 1 (14%) is about immunology. We have to draw a diagram with Interferon-γ in the middle of it, and around it all the things it affects and produce it. IFNγ is used a lot for signalling, and has over 20 interactions, but luckily the book doesn't list most of those, and I confine myself to those given in the book.

Question 2 (18%) we have to do a search of the literature to find a couple of papers that look at HLA haplotypes and their effect on tuberculosis.

Question 3 (8%) is about pathogen identification and asks you the steps you would take to identify a bacterial pathogen. Its rather a general question as the steps depend quite heavily on what you suspect it might be.

Question 4 (10%) is like in the last TMA where you are given two statements one true, and one that might be true, might be explained by the first, or might not. 5 sub-questions, related to worm infections, sterilisation, bacteriology, antibodies and PCR.

Question 5 (50%) you have to read a published article about dengue disease and:
(a) Comment on the general style of the article.
(b) Define a number of terms (with references) used in the article.
(c) Draw a diagram of the life cycle and intervention points of the disease.
(d) Write a 200 word summary of the article.

Its still hard to spot the marks in these TMAs and to ensure you have written enough points for the number of marks on offer, but I did ok on this one.

S320: Book 6 - Modelling epidemics

This book looks at how epidemics happen, and what can be done to stop them.
It starts by looking at some very basic maths. It revolves around a number called R0, which is the average number of people who will be infected by a infective individual.
If the R0 is less than 1, then the infection will die out, if its greater it will survive.

It also looks at the affect of Herd Immunity. This has a big effect on diseases. Its brought on either by lots of the population having caught the disease and so being immune, or else through vaccination. The key thing here is that it is related to R0, if enough of the population is immune, then the R0 will drop below 1. This is because obviously most people an infected individual meets will be immune so will not be infected themselves. So with something like smallpox, you only need to get more than 85% of the population immune, and the disease will die out. This doesn't work so well with zoonotic diseases, as there is a reservoir of infections.

On the other hand, partial herd immunity can sometimes be a bad thing. If only a fraction of the population are immune, then the disease still thrives, but not as well. However the age at which one becomes infected tends to move up. This can be a problem, as some diseases caught in childhood (mumps for instance) can have much more severe consequences in adulthood.

Its a balance, and not always obvious what is going to be good in the long run!
An interesting book - and at only 70 odd pages, not too difficult to digest.