It’s all just endless pipetting, all day every day.

My intention was to keep this blog updated with everything I’ve done in the past few months of photosynthesis research. I’ve been so busy that I’ve neglected my writing. There have been plenty funny stories of lab antics to tell y’all, as well as scientific intrigues.

To summarise: I’ve been working on some genetic manipulation of biosynthesis pathways, but after Christmas I get to do some structural work. I am a chemist in a biologist’s world.

Here’s a list of some of my favourite things I’ve done so far:

• Making up solutions. If I have to make up a 10mM solution of EDTA, well I am the most content chicken in the world. My lab has no volumetric flasks though. It’s all measuring cylinders. What’s up with that?
• Loading PCR samples onto an agarose gel. It’s SO FUN filling those wells. The smaller the wells the funnerer it gets.
• 1.5 ml Eppendorfs. What a brilliant name for fantastically useful little tubes. Ditto “bijoux”, which are another type of tube. How dainty.
• I’ve just started some protein purification for some membrane protein crystallization trials, I am SO excited.
• Analyzing data. Maths is so clean compared to smelly Rhodobacter flying around the room.
• Creating sucrose density gradients. The theory that the less dense layers should chillax at the top and the densest layer mulches around at the bottom actually works in practice.  Isn’t that fun?
• Snap freezing cells in liquid nitrogen. Makes me cackle with sinister glee.
• Coming out of working in the green room and seeing everything as pink for a while.

I’m sure I’ll add more in future.

Whilst sitting around in a classroom the other day, one of my fellow students, mused “Candida albicans sounds like it could be the name of a football team”.

The discussion turned into a conversation about the practicalities of getting yeast to play football (soccer to any Americans in the room). However, I pointed out that C. albicans do not have legs, so it could never be called “football”. A bright spark pointed out that the game could still work if they played with hyphae.

As for the ball, someone cleverly suggested using a buckyball. We all found this too amusing to quibble about the size problems (a buckyball is about 10 Angstroms – something like 10,000 times smaller than an average-large yeast cell).

As for getting the yeast to play along, it was suggested some sort of chemoattractant was applied to the buckyball. However, fears were raised that the yeast may try and eat the ball as opposed to scoring a goal with it.

Of course, if Candida albicans were to play professionally, they would simply immobilize their opponents by causing acute candidiasis, thus placing them at the top of the League.

I apologise to any of my fellow students who stumble across this and feel RAGE

that they are not credited using proper scientific referencing convention.

However, I felt it prudent not to identify anyone by name!

This entry is pitched at the level of people who have no idea what “science” is

but love me enough to be interested in what I am doing.

From September, when I start the masters year of my degree, I will be ferrietting around in a lab working on photosynthesis research. As a result, all I will be babbling about from now until Easter are “light harvesting complexes”.

In a nutshell, plants use sun light, water and carbon dioxide to make energy. The only “waste” product is oxygen.

We’ve all had enough drummed in to us about being green to realise that coming up with a way to produce energy without polluting the world with noxious substances is, like, the Holy Grail. Plants have been doing this for 3,500 million years AND they do it way more efficently than we’ve managed even with all our exhaust-spewing machinery.

The plant does this using a bafflingly complex array of molecular machinery, posssibly a bit of quantum physics and, most likely, magic.
If we can find out exactly how plants manage to do this remarkable feat, it’s a step towards the possibility of being able to power our world in a truly green and eco-friendly way.

So, I will have my little part to play in all this and it’s all rather exciting.

I finished my third year of university over two months ago. In the time since then I’ve been to Chicago (USA, obviously), France, Belgium, Luxembourg, Switzerland and Italy. “Ooh you lucky chicken” you may be thinking. However, I tend to get rather fidgety if I have no work to do.

My brain is constantly flitting around solving problems, defining objects by their chemical properties and mentally mixing bicarb and vinegar, but sometimes I want something a bit more meaty (like a test tube full of bovine heart extract from which I shall isolate mitochondrial enzymes).

Whilst sitting in a chalet up the side of a mountain somewhere in the Alps, my eyes happened to cast upon a bottle of Evian mineral water. I noticed that the label included a mineral analysis of the mg/l concentrations of various ions in the water. I then did something horribly, shamefully, nerdy – I converted all the values in to molar concentrations to see if it could tell me anything interesting.

I learned two useful things from this exercise:

1. In this case, averaged values completely ruin data sets – the concentrations of different ions just weren’t comparable to a sensible degree of sanity. The data I got back looked like a camel had dribbled on a newspaper. Truly a case of garbage in, garbage out.

2. I need to go back to work and do something useful with my brain. Urgently.

Postscript: when In Chicago I was staying very near Fermilab, and in The Alps, CERN. I visited neither. Poor show.

I have an exam tomorrow morning, which means that I am frantically reading all the scientific literature I can get my mandibles on.

I’ve just read a paper that declares it was published in July 2010.

DOES IT KNOW SOMETHING I DON’T?

Or is it in fact July and have I completely missed my exam? If so, there is further cause for alarm; ARGH what am I still doing in *undisclosed Northern-England city*? I’m meant to be in *undisclosed Northern American city* right now!

I think I’m going loopy. I’m not feeling all that confident about tomorrow and am therefore hitting myself over the head with my pizza in angst.

On the plus side, if I do cite this paper in the exam, I guess it’ll give me the edge over my peers – not only am I up to date on my knowledge, I see the future.

In other news, I had a Molecular Immunology exam yesterday, but I don’t have anything particular to comment on it.

The full reference for the paper is Visual integration of quantitative proteomic data, 

pathways, and protein interactions.  Jianu, Radu; Yu, Kebing; Cao, Lulu, et al. 

IEEE Trans Vis Comput Graph   Volume: 16   Issue: 4   Pages: 609-20   

Published: 2010 Jul-Aug.

What sort of sadist makes poor 3rd year students take an exam at 9am on a Saturday? The Molecular Biology department at my university, that’s who.

The exam was “assembly of supramolecular structures” – how big massive complicated protein complexes assemble.
I was pretty nervous about this one, during revision I just felt that no specific details were sticking to my brain. There were only a couple of topics from the module I felt confident about.

I wanted to write about ferritin. Ferritin is basically a hollow protein shell that sucks up iron into its innards. It has incredibly high affinity for iron – if you put it in an iron test tube, it would actually slurp the metal out of the tube. If you don’t find that utterly thrilling then there is evidently something wrong with your brain’s thrill receptors.

I even made a model of it, look, it’s cute:

I didn’t get asked about ferritin. Instead I wrote about the tobacco mosaic virus (TMV), and the formation of amyloid proteins. I was very lucky with the questions I was given to choose from, thank llama.

The TMV essay asked me to explain the experimental evidence that indicated how the long rod-shaped virus assembles. I was able to explain how they found out that the rod is built up from disk shapes stacking on top of each other, but when it came to explaining how the genetic material gets inside the protein coat I was stumped. I know how it happens, I just couldn’t remember the experiments that were done to prove it. EEK. So what I did was made up experiments that I would do it show how it’s done. I hope they’ll let me get away with that.

This is TMV:

Amyloids occur when protein folds up all wrong. Sort of. It’s actually more like “oh no this protein has folded itself in to a knot – so to stop it going renegade and causing havoc, I’ll fold it in to a nice stable amyloid form that’ll just hang around not doing much”. Unfortunately, over time amyloid can build up and melt yer brain.
Diseases like CJD are caused by prions, which is a sort of amyloid protein. I’ve always been pretty interested in this topic so I had plenty to ramble on about.

Three more exams to go now. I hope my hand doesn’t fall off from all the writing. Holding a pen is already painful because I slammed my finger in a door the other day, oops-a-daisy.

Disclaimer: I’m only taking my lecturer’s word for it that ferritin slurps iron out of a text tube.

I would just like to say, with misty eyes, that Douglas Adams’ writing has had a huge impact on my life. I have read the entire Hitch Hiker’s Guide “trilogy” at least 30 times in the past 13 years.

So yeah, this hoopy frood knows where her towel is

Well towelS. I have two useful ones.

Joy to the world. Doom and gloom upon my face.
Third year exams are in the format of 4 essay questions, of which you have to pick two. I did four modules this semester, so I have five exams. The fifth exam is a 2 hour synoptic essay.
To gain good marks, you’re expected to show evidence of extra reading – for example in the form of a critical analysis of techniques or the use of specific examples.

My modules this semester are:
– Macromolecular machines – experimental methods to find out how these work. E.g ribosomes.
– Protein assembly – how proteins fold up, virus assembly and such gubbins. Epically interesting.
– Immunology
– Human disease

The exam I had today, my first one, was all about human disease, specifically when inflammation goes haywire, as well as autoimmune disease. I only really chose this module for interest. My main focus is biophysics – protein folding and such gubbins, but I thought I’d better chose some “lighter” modules to stop myself getting bogged down in all the maths. Besides, my main drive in life is to find out how and why everything works – including why the body goes “wrong” sometimes.

Scanning down the list of questions, deciding which essay to attack first, almost caused me to jump up and do a little dance on my table. “Compare and contrast the cells and molecules involved in atherosclerosis and asthma” was exactly the question I wanted to answer. I had done insane buckets of extra reading on these topics, so i could insert all sorts of smug references to literature. At once point I even had a crisis of nausea when I realised how exceedingly pompous my tone sounded. As I completed my answer with a flourish I knew that, unless I had made some horrendous glaring error, that essay would grab me a good mark.

The second essay was another barrel of eels entirely. I had to pick one question from the remaining three, all of which resembled soup of doom, or some odd alien substance you might find on the bottom of your shoe after a long drunken night out.

Question one was all about apoptosis – fair enough if it wasn’t necessary for me to remember the names of the infinite number of molecules involved and how they all hook up to form a tangled spaghetti network. Apoptosis presumably works by confusing the cell to death.

Candidate two was the process of diabetic kidney nephropathy. This made me irrationally angry and I nearly tore the paper up in rage. If they had asked me to describe mechanisms by which the kidney fails and the stages of this process – well that would be the essay of my dreams. I could have drawn examples from the many mechanisms that may cause kidneys to fail, including diabetes. The problem was this question was just about diabetes and I simply could not remember enough specifics about it to be able to do an entire essay on it. The question left no scope for interpretation or diversity. Frankly, question number two was irresponsible and unimaginative and pure laziness on the part of the dude who comes up with the questions.

So that just left question three. This one was all about immune tolerance – how the immune system goes about attacking foreign gubbins, but does not attack your own cells. The question was in two parts, firstly I had to write about how the immune system “creates” tolerance and how these mechanisms can go wrong. I couldn’t remember being taught much about that in this module. Fortunately, my immunology module came in handy, I just wrote everything I could remember from that. After burbling for a bit, I was faced with a predicament – this was meant to be half the essay and yet I had only been writing for ten minutes. Then TV saved the day. I KNEW watching episodes of House in between revision sessions was a brilliant idea – I was able to smatter “for example” all over my essay giving the impression I had done copious amounts of extra reading. I happily scrawled “paraneoplastic syndrome” in cancer as an example of how the immune system can accidentally attack itself. “LUPUS!” I joyfully thought with glee – in House it’s never lupus, but oh yes in this case it was definitely lupus.

Things started to go spazzmoid with the second part of the question. It commanded me to “pick one example of an organ-specific autoimmune disease, and describe its clinical characteristics”. My mind went blank and instead got fixated on semantics. I just could not think of an example that involved the mechanisms I had described above that was also organ-specific. “Rheumatoid arthritis,” I thought, “are joints on organ?” The odd thing was that this second part of the question didn’t seem very clear – did I have to relate it to the mechanisms of a breakdown in tolerance? In the end I figured anything autoimmune must be related to tolerance going silly bananas so I just picked autoimmune thyroid disease. My answer was along the lines of “errr, so an agonist binds the TSH receptor, meaning the thyroid is always switched on, errr. Yah.”

Then I mumbled something about weight loss, lethargy and goitre and got the hell out of the exam hall.

I’m revising for some exams right now, and I keep coming across “witty” comments I’ve left myself in my lecture notes. They reveal vital and important insights in my attitudes towards the importance of various topics (my “molecular biology of disease” notes are littered with inane comments, my biophysics notes are largely untouched). Presumably at the time I thought it would cause me some amusement when it came to doing my revision. While most of them did cause me to chuckle vaguely, they backfired by causing me to procrastinate by compiling some of them here:

Injection of CD25 depleted T cells into nude mice led to a range of autoimmune conditions (nude mice are defective in genes for clothes).

Inhalers prevent bronchospasm and other stuff that i don’t know because my brain switched off momentarily because I found a cat hair on my jumper and I don’t even own a cat WTF.

Comparison of the NMR spectra reveals that the intermediate state is very similar to the native American Indian state of America with teepees and stuff.

Apparently the activation loop that goes up and down on kinases looks like a nose. It doesn’t look like a nose. Noses don’t go up and down. It looks like a penis.

Cytotoxic juvenile delinquents should be sent to the thymus to mature.

The pathology and cellular mechanisms of atherosclerosis – I just know this lecture is going to make me die of squeamishness, better leave now.

The association rate constant is a 2nd order rate constant and ENZYME KINETICS ARE HAWT <3

Dr Ford is about to give us a lecture on the assembly of the tobacco mosaic virus. To get us excited and enthused, he starts with telling us that the lecture will be just like he’s telling us a fairy story – but with actual experimental evidence.

kapp=k1[ribosome] + k-1, where k1 is the gradient and – OMG THAT’S THE y= mx + c equation that I learned in GCSE algebra! OMG OMG SKOOL CAME IN USEFUL.

The Phi X174 phage proteins contain a jelly-roll motif (like a Swiss roll to us English). Who knew Delia Smith would pop up in a lecture about bacteriophage Phi X174…

..so they developed this really clever idea to measure distances by fluorescence energy transfer… but then it turned out the distances were too big and/or too close to measure. So it told us nothing. What rotten luck.

If you get a snake bite/whatever and get passive immunization afterwards – if you get exposed to the venom a second time you go URK as you will mount a response to it and go in to shock and POP GOES YOUR FACE. Lesson: DON’T GET BITTEN TWICE, NUMBSKULL.