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Sunday, 25 July 2010

S366: TMA-3

The third TMA in this course. Three questions to answer - more conventional than TMA-2.

The first question has parts (a) - (h) and covers things from basic definitions of evolution, to matching up statements and definitions, interpreting graphs in evolutionary terms. designing experiments, working out FST numbers, molecular clocks and mutation effects. Phew! 40%

Question 2 is all about Hardy-Weinberger equilibriums and is just (a) - (f). It looks at a sample of mice in the wild and how closely it matches theoretical H-W models. 20%

Question 3 involves quite a lot of rather tedious measuring on a virtual experiment. It looks at the size of house sparrow bib markings and if they might give an advantage. (a) - (d) - some of them involving calculations, others speculating on how these markings might enhance or diminish an individuals prospects. It also looks at a variety of habitats and how this also changes the dynamics. 40%.

Friday, 23 July 2010

SXR270 Tutor - Day 7

Day 7 and the last breakfast. Some combination of the last few days...

Anyway - off to the final lab. Students doing things to bits of rat tissue. We have a few failures with oxygen electrodes, and I get the chance to see one being rebuilt. Who would have thought cigarette papers had such a use in research!

Lots of mixed results, the end of the week is in site, but the students battle on to get results.

Then lunch - chicken kiev and some more chocolate.

Final summing up lecture, I had out the written assignment to my group - then home! Mixed feelings. It was a great week, but it will be nice to be back to normality in some ways.

SXR270 Tutor - Day 6

Day 6, and breakfast starts again - 2 sausage and two types of egg. I think that's all the variations tried now.

To the lab - theme 2, energy. We start with the Manduca caterpillar. I'm in charge of the microscope section - having to brief on those. Not too bad - I know how to use a microscope more or less, but then so do the students by this time of the week. I also help with the ion transport experiment as things come back to me.

It goes not too badly, we get some results - which is about par for this experiment.
video

Lunch then - I settle for sandwich and a big slice of walnut cake.

In the afternoon its the oxygen electrode again! I had a run in with this during plants week. Luckily they are almost the same as I am asked to show the students how to calibrate them. I surprise myself by remembering most of the steps. They can be tricky, but I manage to get through it without too many hitches. Then its into the experiment. There are one or two people waving cyanide filled micro-pipettes around which makes me slightly nervous. However its all pretty successful, despite one or two machines breaking down.

Then - leaving the students to think about an experiment to do tomorrow, we go back for tea (salmon and lemon meringue) and I dash down the hill for a lecture on black holes, although I struggle to stay away all the way through.

Now back to the room, and a shower. Then some vague attempt at initial packing.

Now then, bar then disco? Probably.

So - yes - I went to the disco, yes I danced like someone undergoing electro shock treatment, yes there will probably be an inquiry, and yes there is evidence.... unless I pay

Thursday, 22 July 2010

SXR270 Tutor - Day 5

Day 5 - and the sausages and bacon go with the mushroom - although only 3 of them.

Then off to the lab to do some cardiovascular work.
This involved using various heart rate monitors, blood pressure meters and stethoscopes.
The students planned a lot of their own experiments, from the effect of exercise on BP & pulse, to caffeine intake, to mental stress. Some clever ideas came out of the session.

Lunch was cauliflower and potato bake, and more chocolate stashed.

After lunch, they were given 2 hours to construct a scientific poster, and some very good ones were made.

It was a bit of a panic at the end. Then after they were all finished, I had to go and mark my groups, which was a bit of a responsibility. It took quite a time to read them all and examine.They all passed, and I wrote comments for them.

Then a mad dash back for tea (chicken and chocolate pudding), in rather muggy weather. A shower was needed before I went back to the room to give feedback and forms to the students.

Then back up the hill once more, and to the bar. I bought a disco ticket, and decided to leave earlier as tomorrow could be a late night.

Tuesday, 20 July 2010

SXR270 Tutor - Day 4

Breakfast, two sausages, eggs and tomato.

Then off to the lab once more. Today a new theme, which starts with a glucose assay. However two students had forgotten lab coats so I had to run around and find them ones to borrow to start with. All part of the service. The students have to make up 42 different tubes of assay samples - so there is a lot of pipetting going on. The glucose turns a shade of pink - depending on how much there is present.


The group gets some very accurate graphs - not down to my influence I hasten to add. Then its a break for lunch, and a chance to stock up on chocolate. I had the steak, and got 3 bars of chocolate.

After lunch we went on to metabolic rates, where you have to analyse expired air collected in a huge bag thing - called a Douglas bag.


There is a chance to design your own experiments here, and some tried the effect of different exercises, others the effect of hot and cold. Seeing them wrapped in blankets with only noses poking out, or sitting in front of 5 fans was amusing to say the least.

Then to tea - the korma again for me, though it could have been anything I think. The apple pie was nice though. Not that I really need any more food at this point.

Now another set of tutorials to sort out, before the evening finishes, and a "blue parrot soiree" invite for tutors. Slightly nervous!
Well the tutorials went ok I think, I'll have to see. Then some cokes, yes I said cokes, in the bar, as I think I hit the wall on this marathon.

Then to the blue parrot thing - which turned out to be a VERY blue cocktail, looking rather too much like anti-freeze for my tastes, and with a fearsome reputation. Anyway - chatted with a few of the tutors, nibbled some cheese, and then eventually retired.

S377: Book 4 (The Interactive Cell)

Book 4 - the final book in the course.

It starts with a short chapter (15) on cellular interaction. Just a few pages long and a sort of introduction.

Then onto chapter 16 about Cell Migration and Adhesion. Looks at the various cell adhesion molecules, cell movement, chemotaxis and control. Also disintegrins and a few other bits and pieces.

Chapter 17 is about differentiation, how a single cell can grow into a multicellular organism. What different ways growth and differentiation is controlled, and how nerve systems and other organs develop.

Chapter 18 is the other end of the cycle so to speak. It looks at cell death, ageing and damage. It looks at a number of ways ageing may occur, and concludes it is probably multi-faceted.

Chapter 19 is the last part, and looks at tumorigenesis. This sort of brings lots of things together, becase for tumours to come about a number of the pathways and mechanisms have to fail. So some of the pathways get stuck in the on position. Some of the checks get switched off. Cells migrate away from their location spreading the tumour. They have to avoid the apoptotic signals that would otherwise kill them, become immortal and grow without limit whiles maintaining blood supply. So a lot of things have to happen to get to the final part.

So - I suppose its a good round up, but not always the sort of thing you want to read about.

SXR270 Tutor - Day 3

Day 3 starts - and I choose the scrambled egg - not very memorable.

Then off to the lab. On the way we have to wander into a copse of trees to grab a sample of lime leaves - some shaded, some in bright sunlight. It's one of the rituals apparently. It's also one of the experiments the students will be doing later.

Getting to the lab, its the leaf disc experiment, and it all goes pretty well - if you exclude the results. They have to subject leaf discs of various plants to radioactive carbon-14 to see how much is taken up by different surfaces and colours of plants.

About 5 different plants were tested including the huge maize plant.
Note the cameo role of the air conditioner next to it - which probably isn't doing it a great deal of good. There is a lot of radioactive marker tape around, and we have to take extra precautions. Special lab coats so as not to spread contamination, gloves and goggles, and a special fume cupboard with lots of admin sheets to account for all the radioactive material.

Most of the results were the exact opposite of what they should have been, oh well - that's science - something I had to say more than once today.

The afternoon brings the presentation skills, and the students have an hour and a half to put together presentations to present to the rest of the group. Then its off to a very large lecture theatre where they get to present them to the group (only 18 people). All very successful. Then a tutor debrief as we prepared to hand over to the next theme.

Then back for tea (pork and various veg, bread and butter pudding).
Then to be with my group as they get introduced to the next theme, and to help out with the poster design workshop.

Then, I think I see the bar in my near future! Oh karaoke.... hum. Its OK - but you can't hear people talk or hold a conversation. Just the one tonight then.

Monday, 19 July 2010

SXR270 Tutor - Day 2

The first full day in the lab. In truth I'd forgotten a lot of the first experiment, but it all came flooding back once it had been demo'd. Managed to remember most of the details, and by listening carefully to the theme tutor I picked up some useful details to pass on. I felt quite confident at points, then I was put in charge of the cronky old 1970's era centrifuge, and it took a while to get that to go. However it all came out ok, the students got their chloroplast suspensions, and were able to proceed with the experiment.

I got lost finding the coffee bar first time, and nearly led a large group of students to the wrong exit to the cafe. However we got there in the end, a good Sunday lunch of roast beef and Yorkshire puddings. and I'm up two mars bars on the day!

This afternoon both tutor groups combined to do one bigger experiment on stomatal openings. It went pretty well to, although the actual results were pretty marginal.

Then back for tea (chickeny thing in mushroom sauce & apple pie) after picking up the materials I'll need for tonight's talk.  Then I got talked into a quiz - actually it didn't take much talking. And then after we didn't win, we went back to the bar just in time for last orders, and sat drinking in the garden until late.

Saturday, 17 July 2010

SXR270 Tutor - Day 1

First day as an SXR 270 tutor. Well, no ones run off screaming yet anyway!

So - what was my day like? Well 12:00 a briefing on the course with the other tutors, and a chance to meet all the team.  I knew at least a couple of the other tutors, so that was good. No real surprises at the meeting.
Then off to the labs to go through the equipment - that was OK too. Most of it came back to me eventually. Some of it more quickly than others.

Then off to hear the course directors introduction talk, followed by taking the group up to the lab for introductions. We split the group into two, and I had my 10 students. I then had to do some ice breaking, and a quick talk on keeping a lab book. It all seemed to go OK, although I wasn't sure.

After that its time for tea after the walk back from the medical school - they are building AGAIN! Tea - was a repeat of last Saturdays menu - I turned down the mushroom rice thingy I had last week (risotto I think), and went for the chicken instead.

After that, I had to give a talk on the scientific method and formulating a hypothesis. I seemed to go through the material quite quickly, even though I'd brought along some of my own slides.

Then to the bar - to have some drinks with my group, and a few other friends I knew from previous courses. I decided on an early night at about 10:30 as tiredness is a real possibility, and other nights might not be so easy to sneak away.

Next SXR270tutor

Friday, 16 July 2010

SXR375 - Day 7

The last day :-(
Today no labs - we just have to give presentations. Breakfast - and wonder of wonders - you're allowed 5 items today!!! I only had 4, as I could hardly believe it!

Then we had an hour to tinker with our presentations. Ours was all finished, but I did have one addition. The only person who had published a paper on our plant, I'd sent an email to the previous day, asking him what pigments he'd found. He lives in New Zealand, but even so I thought it worth a shot. He replied in time for me to include his answer in the presentation. So I quickly inserted a slide in to show his thoughts on it. He hadn't found specific pigments, so we were one better than him. Of course he'd found other details that we referenced, so it was a good trade.

Anyway - then me being the computer geek, I took over the lecture theatre computer and got every ones presentations loaded up, in order and ready to go. I also had my handy dandy laser pointer which everyone used for advancing the slides and pointing things out.

The presentations went very well, and we finished in just over two hours. No one really had a problem, despite most people being full of nerves, and it was a really good session.

Then we had a quick last talk in the lab about the ECA and what was required, then back for our last lunch (fish and chips).
Then it was a few good byes and the whole thing was over. Slowly real life starts to fade back in. I went back to my room, because I'm in the same place next week - being a tutor on a different course. I made a start on the ECA (well just the headings - so a good 15 words from the 2500 required!) - hey its a start.
Then - pickup time for a nights sleep in a proper bed, then a similar thing to do next week!

SXR375 - Day 6

Last day in the labs today. Breakfast first - the usual mix.

Then down to the labs, to complete our last few bits and pieces. We had a go at the full pigment spectroscopy, but with mixed results. We tried a couple of times, really grinding the leaves up hard with abrasive sand, but it always came out as a green colour and the spectroscopy showed a classic chlorophyll curve.



The the tutor gave us another idea, to mix in acid to try and release the attached molecules, and suddenly we got our nearly flat black spectrum that we wanted - hooray! 


Now we had the full story. So we finished off and went up to start work on the presentation.
We broke for lunch with about half of it done (sweet and sour chicken).

Back down to the lab for a quick briefing on what happens next, and we then worked some more on our presentation. Soon had it finished and then we went to try it in the big lecture theatre. 
A few more tweaks, then printed out the slides and went back to write some notes for the talk around the slides.
Tea coming up (lasagne and lemon meringue with ice cream - no soup), then - to disco or not to disco - that is the question?

Well in the end, we sat in the bar, drank and laughed a lot about presentation skills. It was a release I think from the weeks work.

Wednesday, 14 July 2010

SXR375 - Day 5

Day five - project start day. We get to do our own thing a bit more now.
Breakfast, and at last the mushrooms make an appearance.

Then down to the lab - and to decide on the project. Our team of three want to investigate the black leaved flowers and see what they contain. We started off with an ambitious three pronged attack, wanting to measure photosynthetic activity of green v. black leaves, the pigments in the black leaves, and whether the flowers had any insect attractants. After a few false starts with the oxygen electrode we decided to leave that bit. It looks a bit fiddly, and our initial tests were a bit difficult to understand.

We go and fetch some fresh leaves and flowers and set to work. We do chlorophyll extraction first, to see if there are extra pigments there. However nothing unusual shows up.

Then we set to work extracting the other pigments. Anthrocyanins and flavinoids.

The pinky one is from the flowers, and the darker red from the leaves. We leave them evaporating and go and get some lunch (chicken fajitas - pretty good i have to say).

The afternoon brings mixed results. We get very poor TLC plates for the pigments - although the flavones come through. We rerun them a number of time but a smear is the best you could describe them as.
We attempt to use the UV spectrophotometer, but it appears to be a cranky old beast and ignores our best attempts. Then we notice that the visible light spectrophotometers dip into the UV a bit, and they are far easier to use in comparison. So we do a few runs of that, and get something we can talk about I think.
In the end - it looks like we have the data to talk a story, but there is one more thing that would help, and I ask Andy about full spectrum of the pigments.
He told us how it can be done, so that's one more thing for tomorrow.
Tea time (mushroom soup - good,  beef steak - ermmm passs, chocolate sponge - not the best ever). Then another two tutorials. One on our upcoming presentation to the group, and then another on our final piece of written work, and where the marks will be.

We were all a little tired now, and trudged back up the hill. The bar called, and most of us answered.

Tuesday, 13 July 2010

SXR375 - Day 4

Another day. Another breakfast - much the same as all the others. This 3 items thing does make the plate look a little empty. Anyway - onwards. Its raining again on the walk down to the lab.

We start the lab by doing assays of chlorophyll and protein in the chlamydamonas that we used yesterday. This will help us plot our curves - although really we need a miracle for any curve to come out of ours!

We head for lunch (baked potato with cheese and ham) and then all meet up to go off to a garden, to look at some plants - with the ulterior motive of selecting species to do our projects on. I find some of my black leaved plants in there, which I'm considering doing a pigment analysis on.




After that - its back to the labs for some to finish up assays - collect data and do graphs and things. We do extensive surgery on our graphs - they still look awful, its a very noisy circuit we have so very difficult to pick out data.

Tea - crunchy minestrone soup (interesting idea - not sure it will catch on), chicken korma with rice and nan, and a rather good rhubarb and ginger fool (no not me).
The back to the lab in the pouring rain to discuss the last three days work, and see what data we have for the end of course assessment write up.
Then to the bar, for a light evening avoiding an impromptu quiz.

Monday, 12 July 2010

SXR375 - Day 3

Day three. Another breakfast (fried egg, bacon and veggy thingy), and its started to rain.

The morning brings experiments on single celled green algae (Chlamydomonas reinhardtii). We want to get some of them, shine light through them and see how much oxygen they make at different light intensities, including none at all.

Well its a bit of a disaster really, and we're trying to recover some data. First the water bath wasn't switched on, so we had to wait for that to come up to temperature. Then something went wrong with our calibration of the oxygen electrode, so we had to wash it all out and redo that, about 15 mins gone. We then eventually got results, but the electrode gave very spikey traces, and the results were not really what anyone was expecting, except in general terms.

So lunch, and then we'll try and get some useful data out of the noise (pasta of some sort)

After lunch things were no better - our graph looked like a roller coaster.
Everyone elses graphs were perfect.

Oh well - there is always the bar to drown our sorrows... oh after tea (something vaguely porcine) a tutorial or two...
Now done, and some sorrows drowned. Tomorrow is another day.

Sunday, 11 July 2010

SXR375 - Day 2

Day two. A patchy breakfast, fried egg or scrambled, sausage and tomatoes. I was reliably informed by others on the table that they doubted anything organic went into the scrambled egg, so my choice of fried seemed good. Still cereal and toast is ok, and coffee was welcome.

Off to the lab, and our first task was to grind up some leaves. We chose petunia leaves, other groups did tobacco, pak choi, coleus and others. We then extracted the pigments in acetone and diethyl ether. Then we did some thin layer chromatography, try to separate out the pigments such as chlorophylls, lutein, violaxanthin and neoxanthin. Some nice bands separated.
We then tried to take some of the bands - and analyse them in spectrophotometer. FIrst time it didn't work - we had the tube the wrong way round. Second time looked better, but one of the peaks was in the wrong place.

Then just time to put some flowers in to stew in HCl before a break for lunch.
After lunch, we came back and did similar procedures with the extract from flowers. We were looking for flavones and anthocyanins, using similar techniques. We had a hitch when we put our first TLC papers in the solvent, which turned out to have too much acid in, and they all dissolved into mush! Anyway - after coffee break we redid things, and they worked much better.
More chromatography, and some absorption spectra helped us isolate pigments from the various plants we'd looked at. We collated the data - wrote it all down and then went to tea (roast beef and yorkshire pudding).

After that I attended a tutorial on photosynthesis and plant pigments, and another on giving presentations.

Then - to the bar!

Saturday, 10 July 2010

SXR375 - Day 1

Its a hot day. with the help of the family I've got registered, found my room, and unpacked just a little.
The family were with me, and they helped me label by books and name tag.
The room has a fridge in it, a desk and a bed. A few other things like a kettle and so on.
Still - I won't be in it a lot. Lots of time in labs, tutorials, eating, or in the bar.

We had a walk around the campus to locate the biology building.

Then the family left, and I sorted out my things. The course started with an introductory talk which covered various administrative things, and then we went down to the labs. We were introduced to the courses tutors and formed up into small teams. I found two others who thought I would at least not cripple their efforts. We then had a look at the range of plants they had on offer, which tomorrow we will be extracting chlorophyll and other pigments from.
After that - back to the hall for lunch and a coffee to keep things going.

Next there is a guest lecture on pesticides, so I'm off to that.

This was good - with a good discussion of issues involved in feeding the world, GM crops, organic produce and so on. We then retired to the bar, where I started a table that grew to about 8-9 people discussing a variety of topics. It was a good evening - hope the alcohol intake doesn't disrupt tomorrows labs!

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Wednesday, 7 July 2010

SXR375: Plants and Pigments - CMA

There is a CMA that has to be done before attending the school. You have to score 35% or more on this, to stand a chance of passing the course. Sneakily, although you can see why, you don't get the results until after the residential school.

Its 20 questions, all multi choice. However some are "choose the correct answer", some are "select up to 3 true statements", some are "find the two false statements" and some require work to be done, graphs to be plotted to get the answer. A few of them are based on research papers which we have a copy of, that we have to dig the results out of.

All in all, its not too bad. I think some of the questions are a little ambiguous, but I think I'll pass OK. One question that insults my sense of logic is "Select three correct answers" and we have A-F to choose from... except F's answer is "All of A-E are true". So if you choose this, doesn't that invalidate choosing 3?

I have a slightly freaky moment, when on the last 4 questions, I realise I've been using last years question paper rather than this years! Ooops - good job I spotted that.

Anyway - its gone now! Time to pack now - and remember to take my new white (well it is currently) lab coat!

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S377: TMA-2

So TMA-2 of the course. Five questions.

The first one is about mitosis, and the anaphase part. You have to draw a diagram of a cell on the verge of splitting its chromosomes. Then talk about the proteins involved in the separation and the conditions required to bring about the separatation. Then a bit to answer on what happens if any of the mechanisms fail.


The next question is about DNA replication and how it happens, what speed it goes at and how it differs between eukaryotes and prokaryotes. Also a classic experiment on the process is investigated to explain how it works.

Question 3 is about transcription. It considers the TATA box, and how transcription factors are involved. Then the epigenetic DNA modifications and how they are preserved.

Question 4 you have to investigate a zinc finger transcription factor and look into the structure of it. How the metal ions are held, and how it interacts with the DNA molecule. Finally you have to show part of the model with some parts highlighted in colour and labelled.

Question 5 you have a paper about a membrane bound protein, and there are a whole load of questions on it. Some is stuff from the course, other is data from the paper. There are a lot of questions, and I found it easy to get out of step answering a little too much in a) and then not including some of the data in b) so losing marks.

Tuesday, 6 July 2010

S377: Book 3 - The Dynamic Cell (Vol 2)

Book 3 which is confusingly entitled The Dynamic Cell - Volume 2 carries on from the previous book.
There are just three chapters in this, although some of them are pretty big.

Cpater 12 Transport and Compartmentalization: It starts with a chapter on transport and compartmentalisation. This covers how the cell moves stuff around, how signal in the code are recognised as labels to send the packages to the correct destination. It also looks at hte transport network, which moves these vesicles around. It covers endocytosis (bringing stuff into the cell) and exocytosis - the opposite. 64 pages in this chapter!

Chapter 13 Signal Transduction: The next chapter is about signal transduction. How signal are recognised on the cell surface and how they trigger cascades. Also some words on the different receptors and ligands that are in common usage.

Chapter 14 Cell Death: The final chapter is on the subject of cell death. All cells have the ability to commit suicide, either on command or if they detect things are going wrong. So this chapter covers some of the mechanisms that trigger these events.

So 180 pages or so in this book.  Some of it is pretty heavy going, but interesting.

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